12.9: Putting It Together- Plant Reproduction - Biology

12.9: Putting It Together- Plant Reproduction - Biology

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As we discussed at the beginning of this module, pollen in the air can cause problems for a lot of people (over 50 million Americans per year, in fact). However, without pollen, a large number of plants wouldn’t be able to reproduce.

For allergy sufferers, the best treatment is to avoid the offending allergens altogether. This may be possible if the allergen is a specific food, like peanuts, which can be cut out of the diet, but not when the very air we breathe is loaded with allergens, such as ragweed pollen. Air purifiers, filters, humidifiers, and conditioners provide varying degrees of relief, but none is 100 percent effective. Various over-the-counter or prescription medications offer relief, too.

  • Antihistamines counter the effects of histamine, the substance that makes eyes water and noses itch and causes sneezing during allergic reactions. Sleepiness was a problem with the first generation of antihistamines, but the newest drugs do not cause such a problem.
  • Nasal steroids are give as anti-inflammatory sprays. They help decrease inflammation, swelling, and mucus production. They work well in combination with antihistamines and, in low doses for brief periods of time, are relatively free of side effects.
  • A nasal spray, cromolyn sodium can help stop hay fever, perhaps by blocking release of histamine and other symptom-producing chemicals. It has few side effects.
  • Available in capsule and spray form, decongestants thin nasal secretions and can reduce swelling and sinus discomfort. Intended for short-term use, they are usually used in combination with antihistamines. Long-term usage of spray decongestants can actually make symptoms worse, while decongestant pills do not have this problem.
  • Immunotherapy (allergy shots) might provide relief for patients who don’t find relief with antihistamines or nasal steroids. They alter the body’s immune response to allergens, thereby helping to prevent allergic reactions. Current immunotherapy treatments are limited because of potential side effects.

Many complementary health approaches have been studied for seasonal allergies. There’s some evidence that a few may be helpful.

  • A 2007 evaluation of six studies of the herb butterbur for seasonal allergies, involving a total of 720 participants, indicated that butterbur may be helpful.
  • Researchers have been investigating probiotics (live microorganisms that may have health benefits) for diseases of the immune system, including allergies. Although some studies have had promising results, the overall evidence on probiotics and seasonal allergies is inconsistent. It’s possible that some types of probiotics might be helpful but that others are not.
  • It’s been thought that eating honey might help to relieve pollen allergies because honey contains small amounts of pollen and might help people build up a tolerance to it. Another possibility is that honey could act as an antihistamine or anti-inflammatory agent. Only a few studies have examined the effects of honey in people with seasonal allergies, and their results have been inconsistent.

Many other natural products have been studied for seasonal allergies, including astragalus, capsaicin, grape seed extract, omega-3 fatty acids, Pycnogenol (French maritime pine bark extract), quercetin, spirulina, stinging nettle, and an herb used in Ayurvedic medicine called tinospora or guduchi. In all instances, the evidence is either inconsistent or too limited to show whether these products are helpful.

Skeletal muscle regeneration in Xenopus tadpoles and zebrafish larvae

Mammals are not able to restore lost appendages, while many amphibians are. One important question about epimorphic regeneration is related to the origin of the new tissues and whether they come from mature cells via dedifferentiation and/or from stem cells. Several studies in urodele amphibians (salamanders) indicate that, after limb or tail amputation, the multinucleated muscle fibres do dedifferentiate by fragmentation and proliferation, thereby contributing to the regenerate. In Xenopus laevis tadpoles, however, it was shown that muscle fibres do not contribute directly to the tail regenerate. We set out to study whether dedifferentiation was present during muscle regeneration of the tadpole limb and zebrafish larval tail, mainly by cell tracing and histological observations.


Cell tracing and histological observations indicate that zebrafish tail muscle do not dedifferentiate during regeneration. Technical limitations did not allow us to trace tadpole limb cells, nevertheless we observed no signs of dedifferentiation histologically. However, ultrastructural and gene expression analysis of regenerating muscle in tadpole tail revealed an unexpected dedifferentiation phenotype. Further histological studies showed that dedifferentiating tail fibres did not enter the cell cycle and in vivo cell tracing revealed no evidences of muscle fibre fragmentation. In addition, our results indicate that this incomplete dedifferentiation was initiated by the retraction of muscle fibres.


Our results show that complete skeletal muscle dedifferentiation is less common than expected in lower vertebrates. In addition, the discovery of incomplete dedifferentiation in muscle fibres of the tadpole tail stresses the importance of coupling histological studies with in vivo cell tracing experiments to better understand the regenerative mechanisms.

Early Edit

While evidence suggests human occupation as far back as 500 BC, the first maps of the area date to 1542, when it was labeled "Las Islas Sabines" by a Spanish cartographer. [ citation needed ] An archaeological dig at Shell Mound, 9 miles (14 km) north of Cedar Key, found artifacts dating back to 500 BC in the top 10 feet (3.0 m) of the 28-foot-tall (8.5 m) mound. The only ancient burial found in Cedar Key was a 2,000-year-old skeleton found in 1999. [7] Arrow heads and spear points dating from the Paleo period (12,000 years old) were collected by Cedar Key historian St. Clair Whitman and are displayed at the Cedar Key Museum State Park.

Followers of William Augustus Bowles, self-declared "Director General of the State of Muskogee", built a watchtower in the vicinity of Cedar Key in 1801. The tower was destroyed by a Spanish force in 1802. [8] In the period leading up to the First Seminole War, the British subjects Alexander Arbuthnot and Robert Ambrister used the Cedar Keys to deliver supplies to the Seminoles. [9] The Cedar Keys may have been a refuge for escaped slaves in the early 1820s, and an entry point for the illegal slave trade later that decade. [10]

Indian War Edit

During the Second Seminole War, the United States Army established Fort No. 4 on the mainland adjacent to the Cedar Keys. (The name "No. 4" was later applied to a boat channel next to the fort, and then to a railroad trestle and a highway bridge over that channel.) In 1840, General Zachary Taylor requested the Cedar Keys be reserved for military use for the duration of the war, and that Seahorse Key be permanently reserved for a lighthouse. [11] In 1840, General Walker Keith Armistead, who had succeeded Zachary Taylor as commander of United States troops in the war, ordered construction of a hospital on what had become known as Depot Key. [12] (The island's name may reflect the establishment of a depot there by Florida militia general Leigh Read. The primary depot for the U.S. Army in Florida at the time was at Palatka, Florida.) [13] [12] Depot Key was the headquarters for the Army in Florida, but Fishburne states headquarters was not in a fixed place, but wherever the commander was. [14]

Cantonment Morgan was established on nearby Seahorse Key by 1841 and used as a troop deployment station and as a holding station for Seminoles who had been captured or who had surrendered until they could be sent to the West. A hurricane with a 27-foot (8.2 m) storm surge struck the Cedar Keys on October 4, 1842, destroying Cantonment Morgan and causing much damage on Depot Key. Some Seminole leaders had been meeting with Army officers at Depot Key to negotiate their surrender or a retreat to a reservation in the Everglades. After the hurricane, the Seminoles refused to return to the area. Colonel William J. Worth had declared the war to be over in August 1842, and Depot Key was abandoned by the Army after the hurricane. [15] [16]

Pre-Civil War Edit

In 1842, the United States Congress had enacted the Armed Occupation Act, a precursor of the Homestead Act, to increase white settlement in Florida as a way to force the Seminoles to leave the territory. With the abandonment of the Army base on Depot Key, the Cedar Keys became available for settlement under the act. Under the terms of the act, several people received permits for settlement on Depot Key, Way Key, and Scale Key. Augustus Steele, US Customs House Officer for Hillsborough County, Florida, and postmaster for Tampa Bay, received the permit for Depot Key, which he renamed Atsena Otie Key. In 1843, he bought the buildings on the island, and built some cottages for wealthy guests. In 1844, he became the Collector of Customs for the port of Cedar Key, as well as for Tampa, Florida. A post office named "Cedar Key" was established on Atsena Otie Key in 1845. The Florida legislature chartered the "City of Atseena Otie" in 1859. [17]

Cedar Key became an important port, shipping lumber and naval stores harvested on the mainland. By 1860, two mills on Atsena Otie Key were producing "cedar" slats for shipment to northern pencil factories. As a result of the growth, the US Congress appropriated funds for a lighthouse on Seahorse Key in 1850. The Cedar Key Light was completed in 1854. The lighthouse lantern is 28 feet (8.5 m) above the ground, but the lighthouse sits on a 47-foot-high (14 m) hill, putting the light 75 feet (23 m) above sea level. The light was visible for 16 miles (26 km). Wood-frame residences were added to each side of the lighthouse several years later. [18] [19]

In 1860, Cedar Key became the western terminus of the Florida Railroad, connecting it to Fernandina Beach, Florida on the east coast of Florida. [20] David Levy Yulee, U.S. senator and president of the Florida Railroad, had acquired most of Way Key to house the railroad's terminal facilities. A town was platted on Way Key in 1859, and Parsons and Hale's General Store, which is now the Island Hotel, was built there in the same year. [21] On March 1, 1861, the first train arrived in Cedar Key, just weeks before the Civil War began.

Civil War and the Gilded Age Edit

With the advent of the American Civil War in 1861, Confederate agents extinguished the light at Seahorse Key and removed its supply of sperm oil. The defense of Cedar Key was assigned to the Columbia and New River Rifles, two companies of the 4th Florida Infantry Regiment, under the command of Lt. Colonel M. Whit Smith. [22] On July 3, 1861, four Federal war prize schooners appeared off Cedar Key. The schooners, originally captured by the USS Massachusetts off New Orleans, were under the command of U. S. Navy Lieutenant George L. Selden, nephew of former Treasurer of the United States William Selden, and manned by nineteen sailors. [23] Col. Smith led his two rifle companies along with one six-pounder cannon twenty miles offshore on the steamer Madison and captured the schooners after firing two warning shots. With the recovery, Col. Smith and his men liberated fifteen Confederate sailors, recovered the vessels’ valuable cargo of railroad iron and turpentine and effected the first capture of a U. S. Naval officer at sea during the war. [24]

The USS Hatteras raided Cedar Key in January 1862, burning several ships loaded with cotton and turpentine and destroying the railroad's rolling stock and buildings on Way Key. Most of the Confederate troops guarding Cedar Key had been sent to Fernandina in anticipation of a Federal attack there. Cedar Key was an important source of salt for the Confederacy during the early part of the war. In October 1862 a Union raid destroyed sixty kettles on Salt Key capable of producing 150 bushels of salt a day. The Union occupied the Cedar Keys in early 1864, staying for the remainder of the war. [25] [26]

In 1865, the Eberhard Faber mill was built on Atsena Otie Key. The Eagle Pencil Company mill was built on Way Key, and Way Key, with its railroad terminal, surpassed Atsena Otie Key in population. Repairs to the Florida Railroad were completed in 1868, and freight and passenger traffic again flowed into Cedar Key. The Town of Cedar Keys was incorporated in 1869, and had a population of 400 in 1870. [27]

Early in his career as a naturalist, John Muir walked 1,000 miles (1,600 km) from Louisville, Kentucky to Cedar Key in just two months in 1867. Muir contracted malaria while working in a sawmill in Cedar Key, and recovered in the house of the mill's superintendent. Muir recovered enough to sail from Cedar Key to Cuba in January 1868. He recorded his impressions of Cedar Key in his memoir A Thousand-Mile Walk to the Gulf, published in 1916, after his death. [28]

Decline and restoration of wildlife Edit

When Henry Plant's railroad to Tampa began service in 1886, Tampa took shipping away from Cedar Key, causing an economic decline in the area. Earlier, growth in population had led to the Cedar Key town limits being expanded in 1881 and again in 1884. But with the decline in the local economy, the town limits were contracted in 1890. [29] Also in 1890 the island town was affected by the reign of terror of Cedar Keys mayor William Cottrell, who took advantage of his Florida state legislature connections and the restricted one-way road access to impose his will and conduct acts of violence. He was deposed from power only after the island was invaded by a naval (U.S. Coast Guard) boat manned with a squad of U.S. Marshals, who were sent there after Custom House officers and other federal government workers requested federal aid due to being unable to discharge their duties on the islands. [30] [31]

The 1896 Cedar Keys hurricane was the final blow. Around 4 am on September 29, 1896, a 10-foot (3.0 m) storm surge swept over the town, killing more than 100 people. Winds north of town were estimated at 125 miles per hour (201 km/h), which would classify it as a category 3. [32] The hurricane wiped out the juniper trees still standing and destroyed all the mills. A fire on December 2, 1896, further damaged the town. In following years, structures were rebuilt on Way Key, a more protected island inland, but the damage was done. Today, only a few reminders of the original town on Atsena Otie Key remain, including stone water cisterns, and a graveyard whose headstones conspicuously date prior to 1896. Also, many of the eastern red cedar trees that originally attracted the pencil company, and for which the community was named, are gone.

At the start of the 20th century, fishing, sponge hooking, and oystering had become the major industries, but around 1909, the oyster beds were exhausted. President Herbert Hoover established the Cedar Keys National Wildlife Refuge in 1929 by naming three of the islands as a breeding ground for colonial birds. The lighthouse was abandoned in 1952, just as the tourism industry began to grow as a result of interest in the historic community, but it remains in use as a marine biology research center by the University of Florida in Gainesville. [33]

Present Edit

The old-fashioned fishing village is now a tourist center with several regionally famous seafood restaurants. The village holds two festivals a year, the Spring Sidewalk Art Festival and the Fall Seafood Festival, that each attract thousands of visitors to the area.

In 1950, Hurricane Easy, a category-3 storm with 125-mile-per-hour (201 km/h) winds, looped around Cedar Key three times before finally making landfall, dumping 38 inches (970 mm) of rain and destroying two-thirds of the homes. The storm came ashore at low tide, so the surge was only 5 feet (1.5 m). [32]

Hurricane Elena followed a similar path in 1985, but did not make landfall. Packing 115-mile-per-hour (185 km/h) winds, the storm churned for two days in the Gulf, 50 miles (80 km) to the west, battering the waterfront. All the businesses and restaurants on Dock Street were either damaged or destroyed, and a section of the seawall collapsed. [32]

After a statewide ban on large-scale net fishing went into effect July 1, 1995, a government retraining program helped many local fishermen begin farming clams in the muddy waters. Today, Cedar Key's clam-based aquaculture is a multimillion-dollar industry.

A local museum exhibit displays a reproduction of one of the first air conditioning installations. The system, with compressor and fans, was used in Cedar Key to ease the lot of malaria patients.

Cedar Key is home to the George T. Lewis Airport (CDK).

Hurricane Eta made one of its two landfalls in Florida at about 4 a.m. Thursday, November 10, 2020 near Cedar Key, as a tropical storm. [34]

Cedar Key's importance in Florida's history, which began as far back as 1000 BC with pre-Columbian habitation of the region, was recognized on October 3, 1989, by the federal government. At that time, 8,000 acres (32 km 2 ) in and around the town were added to the National Register of Historic Places under the title of the Cedar Keys Historic and Archaeological District.

The Cedar Key Museum State Park depicts the town's 19th century history and displays sea shells and Indian artifacts from the collection of Saint Clair Whitman. Tours of Whitman's restored 1920s house are available during museum hours. As the museum photo indicates, the building was constructed to withstand the hurricane conditions that the town is subjected to periodically. [36]

The naturalist John Muir visited Cedar Key in 1867 on his historic walk from Kentucky to Florida. He wrote:

For nineteen years my vision was bounded by forests, but today, emerging from a multitude of tropical plants, I beheld the Gulf of Mexico stretching away unbounded, except by the sky. What dreams and speculative matter for thought arose as I stood on the strand, gazing out on the burnished, treeless plain! [37]

The John Muir historic marker was placed on the museum grounds in 1983, commemorating his visit. [37]

According to the United States Census Bureau, the city has a total area of 2.1 square miles (5.5 km 2 ), of which 0.97 square miles (2.5 km 2 ) is land and 1.2 square miles (3.0 km 2 ), or 54.28%, is water. [5]

Cedar Key has a humid subtropical climate (Köppen Cfa) with hot, humid summers and mild winters.

Climate data for Cedar Key 1 WSW, Florida, 1907-1976 normals and extremes
Month Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Year
Record high °F (°C) 84
Average high °F (°C) 66.6
Daily mean °F (°C) 57.6
Average low °F (°C) 48.8
Record low °F (°C) 8
Average precipitation inches (mm) 2.70
Average precipitation days (≥ 0.01 in) 5 5 5 3 4 7 10 10 7 4 3 5 69
Source: WRCC [39]
Historical population
Census Pop.
1910864 16.9%
1920695 −19.6%
19301,066 53.4%
1940988 −7.3%
1950900 −8.9%
1960668 −25.8%
1970714 6.9%
1980700 −2.0%
1990668 −4.6%
2000790 18.3%
2010702 −11.1%
2019 (est.)720 [2] 2.6%
U.S. Decennial Census [40]

As of the census [3] of 2000, there were 790 people, 411 households, and 244 families residing in the city. The population density was 864.7 inhabitants per square mile (335.2/km 2 ). There were 686 housing units at an average density of 750.9 per square mile (291.1/km 2 ). The racial makeup of the city was 97.47% White, 0.13% African American, 0.63% Native American, 0.25% Asian, 0.51% from other races, and 1.01% from two or more races. Hispanic or Latino of any race were 1.52% of the population.

There were 411 households, out of which 14.4% had children under the age of 18 living with them, 48.7% were married couples living together, 8.3% had a female householder with no husband present, and 40.4% were non-families. 34.8% of all households were made up of individuals, and 14.8% had someone living alone who was 65 years of age or older. The average household size was 1.92 and the average family size was 2.42.

In the city the population was spread out, with 13.2% under the age of 18, 4.8% from 18 to 24, 15.6% from 25 to 44, 40.1% from 45 to 64, and 26.3% who were 65 years of age or older. The median age was 54 years. For every 100 females, there were 91.7 males. For every 100 females age 18 and over, there were 92.2 males.

The median income for a household in the city was $32,232, and the median income for a family was $41,190. Males had a median income of $27,375 versus $31,806 for females. The per capita income for the city was $22,568. About 6.6% of families and 11.1% of the population were below the poverty line, including 10.5% of those under age 18 and 9.9% of those age 65 or over.


Population genetics began as a reconciliation of Mendelian inheritance and biostatistics models. Natural selection will only cause evolution if there is enough genetic variation in a population. Before the discovery of Mendelian genetics, one common hypothesis was blending inheritance. But with blending inheritance, genetic variance would be rapidly lost, making evolution by natural or sexual selection implausible. The Hardy–Weinberg principle provides the solution to how variation is maintained in a population with Mendelian inheritance. According to this principle, the frequencies of alleles (variations in a gene) will remain constant in the absence of selection, mutation, migration and genetic drift. [3]

The next key step was the work of the British biologist and statistician Ronald Fisher. In a series of papers starting in 1918 and culminating in his 1930 book The Genetical Theory of Natural Selection, Fisher showed that the continuous variation measured by the biometricians could be produced by the combined action of many discrete genes, and that natural selection could change allele frequencies in a population, resulting in evolution. In a series of papers beginning in 1924, another British geneticist, J. B. S. Haldane, worked out the mathematics of allele frequency change at a single gene locus under a broad range of conditions. Haldane also applied statistical analysis to real-world examples of natural selection, such as peppered moth evolution and industrial melanism, and showed that selection coefficients could be larger than Fisher assumed, leading to more rapid adaptive evolution as a camouflage strategy following increased pollution. [4] [5]

The American biologist Sewall Wright, who had a background in animal breeding experiments, focused on combinations of interacting genes, and the effects of inbreeding on small, relatively isolated populations that exhibited genetic drift. In 1932 Wright introduced the concept of an adaptive landscape and argued that genetic drift and inbreeding could drive a small, isolated sub-population away from an adaptive peak, allowing natural selection to drive it towards different adaptive peaks. [ citation needed ]

The work of Fisher, Haldane and Wright founded the discipline of population genetics. This integrated natural selection with Mendelian genetics, which was the critical first step in developing a unified theory of how evolution worked. [4] [5] John Maynard Smith was Haldane's pupil, whilst W. D. Hamilton was influenced by the writings of Fisher. The American George R. Price worked with both Hamilton and Maynard Smith. American Richard Lewontin and Japanese Motoo Kimura were influenced by Wright and Haldane. [ citation needed ]

Gertrude Hauser and Heidi Danker–Hopfe have suggested that Hubert Walter also contributed to the creation of the subdiscipline population genetics. [6]

Modern synthesis Edit

The mathematics of population genetics were originally developed as the beginning of the modern synthesis. Authors such as Beatty [7] have asserted that population genetics defines the core of the modern synthesis. For the first few decades of the 20th century, most field naturalists continued to believe that Lamarckism and orthogenesis provided the best explanation for the complexity they observed in the living world. [8] During the modern synthesis, these ideas were purged, and only evolutionary causes that could be expressed in the mathematical framework of population genetics were retained. [9] Consensus was reached as to which evolutionary factors might influence evolution, but not as to the relative importance of the various factors. [9]

Theodosius Dobzhansky, a postdoctoral worker in T. H. Morgan's lab, had been influenced by the work on genetic diversity by Russian geneticists such as Sergei Chetverikov. He helped to bridge the divide between the foundations of microevolution developed by the population geneticists and the patterns of macroevolution observed by field biologists, with his 1937 book Genetics and the Origin of Species. Dobzhansky examined the genetic diversity of wild populations and showed that, contrary to the assumptions of the population geneticists, these populations had large amounts of genetic diversity, with marked differences between sub-populations. The book also took the highly mathematical work of the population geneticists and put it into a more accessible form. Many more biologists were influenced by population genetics via Dobzhansky than were able to read the highly mathematical works in the original. [10]

In Great Britain E. B. Ford, the pioneer of ecological genetics, [11] continued throughout the 1930s and 1940s to empirically demonstrate the power of selection due to ecological factors including the ability to maintain genetic diversity through genetic polymorphisms such as human blood types. Ford's work, in collaboration with Fisher, contributed to a shift in emphasis during the modern synthesis towards natural selection as the dominant force. [4] [5] [12] [13]

Neutral theory and origin-fixation dynamics Edit

The original, modern synthesis view of population genetics assumes that mutations provide ample raw material, and focuses only on the change in frequency of alleles within populations. [14] The main processes influencing allele frequencies are natural selection, genetic drift, gene flow and recurrent mutation. Fisher and Wright had some fundamental disagreements about the relative roles of selection and drift. [15] The availability of molecular data on all genetic differences led to the neutral theory of molecular evolution. In this view, many mutations are deleterious and so never observed, and most of the remainder are neutral, i.e. are not under selection. With the fate of each neutral mutation left to chance (genetic drift), the direction of evolutionary change is driven by which mutations occur, and so cannot be captured by models of change in the frequency of (existing) alleles alone. [14] [16]

The origin-fixation view of population genetics generalizes this approach beyond strictly neutral mutations, and sees the rate at which a particular change happens as the product of the mutation rate and the fixation probability. [14]

Selection Edit

Natural selection, which includes sexual selection, is the fact that some traits make it more likely for an organism to survive and reproduce. Population genetics describes natural selection by defining fitness as a propensity or probability of survival and reproduction in a particular environment. The fitness is normally given by the symbol w=1-s where s is the selection coefficient. Natural selection acts on phenotypes, so population genetic models assume relatively simple relationships to predict the phenotype and hence fitness from the allele at one or a small number of loci. In this way, natural selection converts differences in the fitness of individuals with different phenotypes into changes in allele frequency in a population over successive generations. [ citation needed ]

Before the advent of population genetics, many biologists doubted that small differences in fitness were sufficient to make a large difference to evolution. [10] Population geneticists addressed this concern in part by comparing selection to genetic drift. Selection can overcome genetic drift when s is greater than 1 divided by the effective population size. When this criterion is met, the probability that a new advantageous mutant becomes fixed is approximately equal to 2s. [17] [18] The time until fixation of such an allele depends little on genetic drift, and is approximately proportional to log(sN)/s. [19]

Dominance Edit

Dominance means that the phenotypic and/or fitness effect of one allele at a locus depends on which allele is present in the second copy for that locus. Consider three genotypes at one locus, with the following fitness values [20]

Genotype: A1A1 A1A2 A2A2
Relative fitness: 1 1-hs 1-s

s is the selection coefficient and h is the dominance coefficient. The value of h yields the following information:

h=0 A1 dominant, A2 recessive
h=1 A2 dominant, A1 recessive
0<h<1 incomplete dominance
h<0 overdominance
h>1 Underdominance

Epistasis Edit

Epistasis means that the phenotypic and/or fitness effect of an allele at one locus depends on which alleles are present at other loci. Selection does not act on a single locus, but on a phenotype that arises through development from a complete genotype. [21] However, many population genetics models of sexual species are "single locus" models, where the fitness of an individual is calculated as the product of the contributions from each of its loci—effectively assuming no epistasis.

In fact, the genotype to fitness landscape is more complex. Population genetics must either model this complexity in detail, or capture it by some simpler average rule. Empirically, beneficial mutations tend to have a smaller fitness benefit when added to a genetic background that already has high fitness: this is known as diminishing returns epistasis. [22] When deleterious mutations also have a smaller fitness effect on high fitness backgrounds, this is known as "synergistic epistasis". However, the effect of deleterious mutations tends on average to be very close to multiplicative, or can even show the opposite pattern, known as "antagonistic epistasis". [23]

Synergistic epistasis is central to some theories of the purging of mutation load [24] and to the evolution of sexual reproduction.

Mutation Edit

Mutation is the ultimate source of genetic variation in the form of new alleles. In addition, mutation may influence the direction of evolution when there is mutation bias, i.e. different probabilities for different mutations to occur. For example, recurrent mutation that tends to be in the opposite direction to selection can lead to mutation–selection balance. At the molecular level, if mutation from G to A happens more often than mutation from A to G, then genotypes with A will tend to evolve. [25] Different insertion vs. deletion mutation biases in different taxa can lead to the evolution of different genome sizes. [26] [27] Developmental or mutational biases have also been observed in morphological evolution. [28] [29] For example, according to the phenotype-first theory of evolution, mutations can eventually cause the genetic assimilation of traits that were previously induced by the environment. [30] [31]

Mutation bias effects are superimposed on other processes. If selection would favor either one out of two mutations, but there is no extra advantage to having both, then the mutation that occurs the most frequently is the one that is most likely to become fixed in a population. [32] [33]

Mutation can have no effect, alter the product of a gene, or prevent the gene from functioning. Studies in the fly Drosophila melanogaster suggest that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70 percent of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial. [34] Most loss of function mutations are selected against. But when selection is weak, mutation bias towards loss of function can affect evolution. [35] For example, pigments are no longer useful when animals live in the darkness of caves, and tend to be lost. [36] This kind of loss of function can occur because of mutation bias, and/or because the function had a cost, and once the benefit of the function disappeared, natural selection leads to the loss. Loss of sporulation ability in a bacterium during laboratory evolution appears to have been caused by mutation bias, rather than natural selection against the cost of maintaining sporulation ability. [37] When there is no selection for loss of function, the speed at which loss evolves depends more on the mutation rate than it does on the effective population size, [38] indicating that it is driven more by mutation bias than by genetic drift.

Mutations can involve large sections of DNA becoming duplicated, usually through genetic recombination. [39] This leads to copy-number variation within a population. Duplications are a major source of raw material for evolving new genes. [40] Other types of mutation occasionally create new genes from previously noncoding DNA. [41] [42]

Genetic drift Edit

Genetic drift is a change in allele frequencies caused by random sampling. [43] That is, the alleles in the offspring are a random sample of those in the parents. [44] Genetic drift may cause gene variants to disappear completely, and thereby reduce genetic variability. In contrast to natural selection, which makes gene variants more common or less common depending on their reproductive success, [45] the changes due to genetic drift are not driven by environmental or adaptive pressures, and are equally likely to make an allele more common as less common.

The effect of genetic drift is larger for alleles present in few copies than when an allele is present in many copies. The population genetics of genetic drift are described using either branching processes or a diffusion equation describing changes in allele frequency. [46] These approaches are usually applied to the Wright-Fisher and Moran models of population genetics. Assuming genetic drift is the only evolutionary force acting on an allele, after t generations in many replicated populations, starting with allele frequencies of p and q, the variance in allele frequency across those populations is

Ronald Fisher held the view that genetic drift plays at the most a minor role in evolution, and this remained the dominant view for several decades. No population genetics perspective have ever given genetic drift a central role by itself, but some have made genetic drift important in combination with another non-selective force. The shifting balance theory of Sewall Wright held that the combination of population structure and genetic drift was important. Motoo Kimura's neutral theory of molecular evolution claims that most genetic differences within and between populations are caused by the combination of neutral mutations and genetic drift. [48]

The role of genetic drift by means of sampling error in evolution has been criticized by John H Gillespie [49] and Will Provine, [50] who argue that selection on linked sites is a more important stochastic force, doing the work traditionally ascribed to genetic drift by means of sampling error. The mathematical properties of genetic draft are different from those of genetic drift. [51] The direction of the random change in allele frequency is autocorrelated across generations. [43]

Gene flow Edit

Because of physical barriers to migration, along with the limited tendency for individuals to move or spread (vagility), and tendency to remain or come back to natal place (philopatry), natural populations rarely all interbreed as may be assumed in theoretical random models (panmixy). [52] There is usually a geographic range within which individuals are more closely related to one another than those randomly selected from the general population. This is described as the extent to which a population is genetically structured. [53]

Genetic structuring can be caused by migration due to historical climate change, species range expansion or current availability of habitat. Gene flow is hindered by mountain ranges, oceans and deserts or even man-made structures such as the Great Wall of China, which has hindered the flow of plant genes. [54]

Gene flow is the exchange of genes between populations or species, breaking down the structure. Examples of gene flow within a species include the migration and then breeding of organisms, or the exchange of pollen. Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer. Population genetic models can be used to identify which populations show significant genetic isolation from one another, and to reconstruct their history. [55]

Subjecting a population to isolation leads to inbreeding depression. Migration into a population can introduce new genetic variants, [56] potentially contributing to evolutionary rescue. If a significant proportion of individuals or gametes migrate, it can also change allele frequencies, e.g. giving rise to migration load. [57]

In the presence of gene flow, other barriers to hybridization between two diverging populations of an outcrossing species are required for the populations to become new species.

Horizontal gene transfer Edit

Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring this is most common among prokaryotes. [58] In medicine, this contributes to the spread of antibiotic resistance, as when one bacteria acquires resistance genes it can rapidly transfer them to other species. [59] Horizontal transfer of genes from bacteria to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean beetle Callosobruchus chinensis may also have occurred. [60] [61] An example of larger-scale transfers are the eukaryotic bdelloid rotifers, which appear to have received a range of genes from bacteria, fungi, and plants. [62] Viruses can also carry DNA between organisms, allowing transfer of genes even across biological domains. [63] Large-scale gene transfer has also occurred between the ancestors of eukaryotic cells and prokaryotes, during the acquisition of chloroplasts and mitochondria. [64]

If all genes are in linkage equilibrium, the effect of an allele at one locus can be averaged across the gene pool at other loci. In reality, one allele is frequently found in linkage disequilibrium with genes at other loci, especially with genes located nearby on the same chromosome. Recombination breaks up this linkage disequilibrium too slowly to avoid genetic hitchhiking, where an allele at one locus rises to high frequency because it is linked to an allele under selection at a nearby locus. Linkage also slows down the rate of adaptation, even in sexual populations. [65] [66] [67] The effect of linkage disequilibrium in slowing down the rate of adaptive evolution arises from a combination of the Hill–Robertson effect (delays in bringing beneficial mutations together) and background selection (delays in separating beneficial mutations from deleterious hitchhikers).

Linkage is a problem for population genetic models that treat one gene locus at a time. It can, however, be exploited as a method for detecting the action of natural selection via selective sweeps.

In the extreme case of an asexual population, linkage is complete, and population genetic equations can be derived and solved in terms of a travelling wave of genotype frequencies along a simple fitness landscape. [68] Most microbes, such as bacteria, are asexual. The population genetics of their adaptation have two contrasting regimes. When the product of the beneficial mutation rate and population size is small, asexual populations follow a "successional regime" of origin-fixation dynamics, with adaptation rate strongly dependent on this product. When the product is much larger, asexual populations follow a "concurrent mutations" regime with adaptation rate less dependent on the product, characterized by clonal interference and the appearance of a new beneficial mutation before the last one has fixed.

Explaining levels of genetic variation Edit

Neutral theory predicts that the level of nucleotide diversity in a population will be proportional to the product of the population size and the neutral mutation rate. The fact that levels of genetic diversity vary much less than population sizes do is known as the "paradox of variation". [69] While high levels of genetic diversity were one of the original arguments in favor of neutral theory, the paradox of variation has been one of the strongest arguments against neutral theory.

It is clear that levels of genetic diversity vary greatly within a species as a function of local recombination rate, due to both genetic hitchhiking and background selection. Most current solutions to the paradox of variation invoke some level of selection at linked sites. [70] For example, one analysis suggests that larger populations have more selective sweeps, which remove more neutral genetic diversity. [71] A negative correlation between mutation rate and population size may also contribute. [72]

Life history affects genetic diversity more than population history does, e.g. r-strategists have more genetic diversity. [70]

Detecting selection Edit

Population genetics models are used to infer which genes are undergoing selection. One common approach is to look for regions of high linkage disequilibrium and low genetic variance along the chromosome, to detect recent selective sweeps.

A second common approach is the McDonald–Kreitman test. The McDonald–Kreitman test compares the amount of variation within a species (polymorphism) to the divergence between species (substitutions) at two types of sites, one assumed to be neutral. Typically, synonymous sites are assumed to be neutral. [73] Genes undergoing positive selection have an excess of divergent sites relative to polymorphic sites. The test can also be used to obtain a genome-wide estimate of the proportion of substitutions that are fixed by positive selection, α. [74] [75] According to the neutral theory of molecular evolution, this number should be near zero. High numbers have therefore been interpreted as a genome-wide falsification of neutral theory. [76]

Demographic inference Edit

The simplest test for population structure in a sexually reproducing, diploid species, is to see whether genotype frequencies follow Hardy-Weinberg proportions as a function of allele frequencies. For example, in the simplest case of a single locus with two alleles denoted A and a at frequencies p and q, random mating predicts freq(AA) = p 2 for the AA homozygotes, freq(aa) = q 2 for the aa homozygotes, and freq(Aa) = 2pq for the heterozygotes. In the absence of population structure, Hardy-Weinberg proportions are reached within 1-2 generations of random mating. More typically, there is an excess of homozygotes, indicative of population structure. The extent of this excess can be quantified as the inbreeding coefficient, F.

Individuals can be clustered into K subpopulations. [77] [78] The degree of population structure can then be calculated using FST, which is a measure of the proportion of genetic variance that can be explained by population structure. Genetic population structure can then be related to geographic structure, and genetic admixture can be detected.

Coalescent theory relates genetic diversity in a sample to demographic history of the population from which it was taken. It normally assumes neutrality, and so sequences from more neutrally-evolving portions of genomes are therefore selected for such analyses. It can be used to infer the relationships between species (phylogenetics), as well as the population structure, demographic history (e.g. population bottlenecks, population growth), biological dispersal, source–sink dynamics [79] and introgression within a species.

Another approach to demographic inference relies on the allele frequency spectrum. [80]

Evolution of genetic systems Edit

By assuming that there are loci that control the genetic system itself, population genetic models are created to describe the evolution of dominance and other forms of robustness, the evolution of sexual reproduction and recombination rates, the evolution of mutation rates, the evolution of evolutionary capacitors, the evolution of costly signalling traits, the evolution of ageing, and the evolution of co-operation. For example, most mutations are deleterious, so the optimal mutation rate for a species may be a trade-off between the damage from a high deleterious mutation rate and the metabolic costs of maintaining systems to reduce the mutation rate, such as DNA repair enzymes. [81]

12.9: Putting It Together- Plant Reproduction - Biology

1. Find your seats.
2. Planner handed out.
3. The Hunt is On Activity
4. Motivation Wheel

Period 5, 6
Bell Ringer: Setting up Bell Ringers (see me or a classmate) .

1. #1-3 on your Notes Packet
2. Read through your notes packet.

Period 5, 6
Bell Ringer : Using the characteristics of life we talked about last week, explain why fire is living or non-living?

1. Drops on a Penny Lab
2. Scientific Method Notes Packet

Resources :
Day 5 Scientific Method

1. #1-3 on your Notes Packet
2. Read through your notes packet.
Period 1
Bell Ringer:
1. Based on the Penny Lab we did, what are some other questions you have and want to investigate?
a. Ex: Would the temperature of the water affect the amount of water droplets onto the penny?


1. Finish Scientific Method Notes Packet
2. Independent Investigation (Scroll down to Pg. 2)

1. Carry out your investigation
2. Writing a Conclusion
3. Starting your Final Draft
4. Binder Organization

1. Test on Characteristics of Life and Scientific Method
2. Binder Check #1
3. Intro to Ecology Notes
4. Abiotic vs Biotic Factor Walkthrough

Intro to Ecology Slides

Period 5, 6
Bell Ringer:
List the 7 Characteristics of Life.

1. Test on Characteristics of Life and Scientific Method
2. Binder Check #1
3. Intro to Ecology Notes
4. Abiotic vs Biotic Factor Walkthrough

Intro to Ecology Slides

1. Level of Organization
2. Species Interactions
3. Species Interaction Activity (M&M's Activity)

- Intro to Ecology Slides (scroll down)
- Species Interactions Slides

1. Finish Level of Organization Foldables!
2. Species Interaction Activity (Read Part A, DO Part C)
3. Workbook Pgs 12-13 (due Friday 9/11)

Period 1
Bell Ringer:
Explain the following relationships:
a. Rabbit + Foxes
b. Rabbit + Grass
c. Rabbit + Deer

1. Test Return &
Test Correction Resource Handout
2. Species Interaction Activity (M&M's Activity)

Species Interactions Slides (scroll down)

1. Finish Workbook Pgs. 12-14
2. Finish Species Interactions Post-Activity Questions
3. Test Corrections due 9/16 Wednesday

Period 1
Bell Ringer:
List the following levels into smallest-->largest organization
a. Ecosystem b. Community
c. Organism d. Biome
e. Population f. Biosphere

1. Species Interaction Review
2. Quiz on Levels of Organization, Biotic/Abiotic, and Species Interactions via Plickers.
3. Energy Flow Note-Taking
4. Energy Pyramid 3-D
5. Food Web Practice

Energy Flow in Ecosystems

1. Finish Energy Pyramid 3-D due Monday
2. Workbook Pgs. 15-17 (due next Friday 9/16)
3. Food Web Practice due next Wednesday

Period 5, 6
Bell Ringer:
List the following levels into smallest-->largest organization
a. Ecosystem b. Community
c. Organism d. Biome
e. Population f. Biosphere

1. Species Interaction Review
2. Quiz on Levels of Organization, Biotic/Abiotic, and Species Interactions via Plickers.
3. Energy Flow Note-Taking
4. Energy Pyramid 3-D
5. Food Web Practice

Energy Flow in Ecosystems

1. Finish Food Web Practice
2. Finish Workbook Pgs 15-17.
3. Finish Test Corrections

Period 5, 6
Bell Ringer:
1. What are the 3 types of -trophs (based on ways that organisms get their energy)? 2. What are the 4 different categories of heterotroph?
1. Diet Coke Activity
2. Food Chain & Food Web labeling

Using the above food chain, what happens to the population of Grass and Fox if we add another herbivore (deer)?

Using the above food chain, what happens to the population of Grass and Fox if we add another herbivore (deer)?

1. Complicated Relationships Web Activity!

1. Organize your binder!
2. Make up any late/missing work!

1. Read Pgs. 28-44 in the Textbook
2. Write question and answer in complete sentences the following:
a. Section 2.1 Assessment Questions (Pg 40)
b. Section 2.2 Assessment Questions (Pg 44)
c. Chapter 2 Assessment #1-25 (Pg. 53)


Mouse and grasshoppers eat grains (plant)

Owls consume mouse and grasshopper

Interactive Web Activity Slides (last few slides)

1. Finish Questions
2. Finish Reflection Paper
3. Complete and turn in any late/missing work.
4. Textbook Pgs 40, 44, and 53

Keystone Species & Activity

1. Finish Reflection Paper

Period 1
Bell Ringer:
1. What is a Foundation Species?
2. What is a Keystone Species?
3. Is the Tiger Shark a foundation species or a keystone species?

1. Finish Keystone Species Activity
a. Walkthrough
b. Questions
c. Wrap-Up

Keystone Species & Activity

1. Finish Keystone Species Group Activity Discussion
2. Introduce Biogeochemical Cycles Notes
Note-taking Guide
3. Cycles Vocabulary
4. What adds/subtracts?

Biogeochemical Cycles Slides

1. Workbook Pgs 19-20 due Wed.
2. Vocabulary Cycles Notes

Period 1
Bell Ringer:
1. We currently have a drought in CA. How come we don't have enough water/rain when the water cycle is continuous?
2. How do YOU contribute to the Carbon Cycle?

1. What's Carbon? Anticipatory Set
Carbon, Life, and Health Handout
2. Paired Reading with Post-Reading Questions Carbon, Life, and Health Reading (first two pages)

1. Finish Post-Reading Questions .

1. Caron - Harmful/Helpful?
2. Wraping up Carbon, Life, and Health
3. Carbon Moves! Activity - Start

Carbon, Life, and Health Slides

1. Finish Carbon Moves Round 1 Map
2. Quiz next week!

Carbon, Life, and Health Slides

1. Finish Traveling Nitrogen Passport Activity

Period 1
Bell Ringer:
1. What did you noticed about your Carbon Map from Round 1?
2. What do you know about Nitrogen?

1. Finish up Carbon Moves!
2. Traveling Nitrogen Passport Activity (see me for handout)

Carbon, Life, and Health Slides
(Scroll down)

1. Finish Carbon Moves Activity!
2. Finish Traveling Nitrogen Passport Activity
3. Study for Quiz

Period 5, 6
Bell Ringer:
1. What did you noticed about your Carbon Map from Round 1?
2. What do you know about Nitrogen?

1. Finish up Carbon Moves!
2. Traveling Nitrogen Passport Activity (see me for handout)

Carbon, Life, and Health Slides
(Scroll down)

Population Slides

1. Finish Workbook Pgs. 31-34
2. Quiz Corrections
3. Finish Definitions (#22b)

Period 1
Bell Ringer:
1. Can you guess what the current world population is?
2. Which country do you think has the most human population?
3. Which state do you think has the most human population?

1. Complete Human Population Growth Web Activity (#23)

1. Complete Human Population Growth Web Activity (#23)

Period 1
Bell Ringer:
1. What is the world's population when you were born?
2. If I asked you to graph your age against world's population, what would go on the x-axis and what would go on the y-axis?

1. Finished Human Population Web Activity
2. Graphing & Math Review
3. Ecological Footprint Web Activity

Human Population

1. Finish #23 Human Population Growth Web Activity
2. Finish #23a (Front Side) Ecological Footprint Web Activity
3. Quiz Corrections
4. E.C.: Workbook Pgs. 35-37

1. Finish #23 Human Population Growth Web Activity
2. Finish #23a (Front Side) Ecological Footprint Web Activity
3. Quiz Corrections
4. E.C.: Workbook Pgs. 35-37

Period 1
Bell Ringer:
1. What is an ecological footprint?
2. Did you think that you would used up that many earths?

1. Biodiversity & Human Impact
2. Update Binder
3. Biodiversity Questions

1. Binder Organization
2. Study Guide
3. Class Review

Human Population

1. Finish Study Guide
2. Organize Binder Pgs. 15-24

Materials and Methods

General methods

Research was conducted under permission of the Government of French Polynesia. We studied sensitive plants near UC Berkeley Gump South Pacific Research Station (17°32′S, 149°50′W) in Mo’orea, French Polynesia between 20 January and 11 February 2016. For our purposes, an individual is defined as a single plant with one root system and at least ten leaves. These plants must have been far enough from other conspecifics to be distinguishable as individuals. The study was conducted at the edge of a wooded area next to a clearing. We assigned numbers to all individuals and elevated stems using metal stakes and twist ties. Plants were allowed to return to their original, expanded positions and acclimate for 48 h before further experimentation. In the following experiments, we touched leaves to induce hiding and measured individual differences in leaf hiding time. Prior to experimentation, all three experimenters standardized the intensity and manner with which they touched the leaf. Trials were conducted between 0700 h and 1600 h. Previous studies have shown that taller plants have increased access to light (Falster & Westoby, 2003). Specific leaf area is also positively correlated with photosynthetic rate (Reich, Ellsworth & Walters, 1998). Thus, we measured plant height (cm), number of leaves per plant, and length of tested leaf (mm) as covariates that we assumed would be associated with plant condition. Plant height (cm) was measured from base of plant, where it joined the ground, to the top of the tallest stem of the plant using a transect tape. Leaf length (mm) was measured using electronic callipers from the base of the leaf where leaflets began to the furthest leaflet tip. Number of leaves was log10 transformed to fit a normal distribution.

To explain variation in hiding time in our experiments, we fitted linear mixed effect models using the package lme4 (Bates et al., 2015) on R 3.2.3 (R Core Team, 2015). The parameters used in analysis throughout the study were plant height, leaf number, and leaf length.

For each experiment, we began by fitting a general linear null model with no fixed or random effects. An individual effects only model, one with only individual plant as a random effect, was fitted next. We followed this by fitting a full model, with random and fixed effects. In the experiments with multiple observations of hiding time, we also fitted, a full model where we also estimated random slopes. This model permitted us to estimate the degree to which these individuals differed in their slopes or, in other words, their behavioral response to a repeated stimulus (Dingemanse & Dochtermann, 2013). We compared these models using AIC values to see which best explained the data. When two models were not significantly different, we parsimoniously interpreted the simpler one. We then compared the best model, the one with the lowest AIC, to the null model using a likelihood ratio test. For models with no significant random effects, we then calculated the intra-class correlation coefficient (ICC) as the ratio of variation explained by the individual to total variation. For models with significant random effects, we also calculated adjusted repeatability (Nakagawa & Schielzeth, 2010). Hiding time was log10 transformed to fit a normal distribution and we examined residuals with qq plots and plotted residuals against fitted values to evaluate model fit and distributional assumptions.

Experiment 1: is there individual variation in hiding time among sensitive plants?


We aimed to understand the extent to which sensitive plants were individually specific in their induced hiding response, if individuality explained the majority of inter-individual differences in hiding time, and if those differences were significant. We examined variation in hiding time by measuring the hiding times of ten leaves in 14 different individual plants. The environments of these 14 individuals differed somewhat in light exposure and level of disturbance by humans, but we did not formally quantify these microclimatic differences that could explain some differences between individuals but not consistency within individuals. The mean height of the individuals in this experiment was 39.5 cm (±12.4 cm SD, range 22–60.1 cm). The mean number of leaves per plant was 76.3 (±41.4 SD, range 20–157). The mean leaf length was 36.8 mm (±12.9 mm SD, range 4.7–85.5 mm).


Plants varied in their hiding times (Fig. 1, Table 1). We found that the model only with the random effect of individual plant better explained variation in hiding time than either a null model (p < 2.2e −16 ), or a full model with both fixed and random effects. Thus, plants differed in their average hiding time and the intraclass correlation coefficient revealed that 44% of this variation was explained by individual plant. We found that when models included any of the fixed effects, other than leaf length, their ability to predict individual hiding was not improved and these models were therefore excluded from Table 1. The estimate for the effect of leaf length on hiding time was −0.00109 (±0.0009 SEM, t-value = − 1.272).

Figure 1: Hiding time (s) as a function of the individual plant.
Description Model AIC
Null model Hiding time ∼ 1 −154
Null model with random effect only Hiding time ∼1∣ID −203 a
Full model Hiding time ∼ Leaf length + (1∣ID) −204

Experiment 2: do individuals vary their hiding time over time?


To assess repeatability under short-term and longer-term time intervals, we measured hiding times in the same leaf of each individual. In experiment 2a, we marked the stem of one leaf on 18 individuals with flagging tape and recorded the hiding time. We then stimulated each leaf again immediately upon fully reopening and did so a total of 4 times. Of 18 individuals, 11 were partially exposed to the sun, seven were fully exposed to the sun, four were on areas that had a history of trimming (not during the duration of this experiment), and 14 were on areas that were not trimmed. In experiment 2b, we marked one leaf on 13 individuals with flagging tape and recorded the hiding time. Each leaf was stimulated every other day at the same time of day as its original trial for a total of four trials. Of 13 individuals, nine were partially exposed to the sun and four were fully exposed to the sun, five were on areas that had a history of trimming (not during this experiment) and eight were on areas that were not trimmed.

In experiments 2a and 2b, we calculated the adjusted repeatability to control for fixed effects in our model (Nakagawa & Schielzeth, 2010). Number of leaves was log10 transformed to fit a normal distribution. Again, residuals were plotted to confirm normality.

Experiment 2a occurred on average over a period of 24.5 min (±5.46 min SD, range 12.1–33.2 min). The mean height of the individuals in experiment 2a was 42.8 cm (±18.0 cm SD, range 8–73 cm). The mean number of leaves per plant was 74.5 (±52.6 SD, range 11–225). The mean leaf length was 42.5 mm (±14.1 mm SD, range 20.5–62.2 mm). In experiment 2b, the mean inter-trial time was 3 h 58 min (±26.3 SD min, range 2 h 55 min–4 h 48 min). The mean height of the individuals in experiment 2b was 40.3 cm (±11.8 cm SD, range 19.5–60.1 cm). The mean number of leaves per plant was 84.3 (±36.4 SD, range 22–157). The mean leaf length was 40.1 mm (±9.8 mm SD, range 28–61.1 mm).

Figure 2: Hiding time (s) as a function of trial number, grouped by individual.


Plants varied in their average hiding time (Fig. 2). In experiment 2a, we found that the full model including the fixed effects of log10(number of leaves), leaf length, and trial as parameters best explained variation in hiding time (Table 2). The full model with the above fixed effects was significantly better than either a null model (p < 2.2e −16 ), or a null model only with random effects of individual plant (p = 0.0001442). It was not significantly different from a full model that included estimates of the random slope with (p = 0.64). The full model showed that plants differed in their mean hiding time and the adjusted repeatability revealed that 75% of this variation was explained by the individual plant. The intraclass correlation coefficient (ICC) was 78.3%. Hiding time increased by 5.05 s (± 1.40 SEM) for each 1 mm increase in leaf length (t-value = 3.597). Hiding time also increased with the log10 number of leaves per plant (27.1 ± 43.5 SEM, t-value = 0.623). Hiding time increased with trial as well (13.6 ± 3.98 SEM, t-value = 3.42).

Description Model AIC
Null model Hiding time ∼ 1 856
Null model with random effect only Hiding time ∼1∣ID 797
Full model Hiding time ∼ Leaf length + log10 Number of leaves + Trial + (1∣ID) 782 a
Full model with random slope Hiding time ∼ Leaf length + log10 Number of leaves + Trial + (1 + Trial∣ID) 785

In experiment 2b, we found that the null model with the random effect of ID best explained variation in hiding time (Table 3). The random effects only model was significantly better fitting than a null model (p < 2.2e −16 ). It was not significantly better than a full model (p = 0.132), or a full model that included estimates of the random slope (p = 0.084). The null model with random effects only showed that plants differed in their average hiding time and the adjusted repeatability revealed that 65% of this variation was explained by individual plant. The ICC for this experiment was 63%.

Description Model AIC
Null model Hiding time ∼ 1 608
Null model with random effect only Hiding time ∼1∣ID 584 a
Full model Hiding time ∼ Leaf length + Trial + (1∣ID) 584
Full model with random slope Hiding time ∼ Leaf length + Trial + (1 + Trial∣ID) 583

Experiment 3: is variation in hiding time condition-dependent?


Experiment 2 showed that the percent of variation explained by individual declined as time increased. Conditions change more over a 48 h period than they do over a 24 min period. To examine the effect of condition on an individual’s behavior, we manipulated sunlight exposure and tested hiding time before and after treatment.

To determine how light availability affects sensitive plant hiding time, we exposed individual plants to one of three light treatments. We aimed to treat all individuals for 6 h, but the actual average treatment duration was 5.9 h (±0.33 h SD, range 5.17–7.82 h). These treatments were designed to deprive the plants of light and to control for any physical disturbance that may induce leaf closure. Prior to any manipulation, we measured the hiding time of a single leaf on each individual. Leaves were then marked with flagging tape for measurement post-treatment. After treatment, we waited 5–7 min for the plant to reopen, then re-measured the hiding time of the same marked leaf. We then deprived 20 sensitive plants of light by placing black, plastic HDX garbage bags (Atlanta, GA) over them (two plants died after this treatment and were thus eliminated from subsequent analysis). To control for the effect of disturbance caused by placing the bags on the plants, we also placed clear, plastic HDX garbage (Atlanta, GA) bags on 19 plants (one plant died after this treatment and was thus eliminated from subsequent analysis). The clear bags controlled for any disturbance caused by putting a bag on the plant, while allowing light to pass through. We acknowledge that the bags may have also manipulated the temperature and the humidity. However, this increase is likely to be similar between black and clear bags, which means the resulting effect is largely due to differences in sunlight availability. Our third treatment was a control treatment in which we recorded the hiding time of a leaf, marked it, and measured the hiding time again after the same interval (around 6 h) that we used for the two experimental manipulations. We performed this treatment on 20 individuals. In this experiment, the sample size was 56 individuals. Plants were randomly assigned to different treatments. To compare the effects of treatment, the model formally compares the slopes of individuals between trials, across treatments. The mean height of the individuals in experiment 3 was 40.0 cm (±21.5 cm SD, range 5.5–108.5 cm). The mean number of leaves per plant was 77.4 (±52.3 SD, range 16–279). The mean leaf length was 43.2 mm (±11.4 mm SD, range 18.9–63.3 mm).


In experiment 3, we found that the full model that included the fixed effects of treatment and trial along with the interaction between treatment and trial best explained variation in hiding time (Table 4). The full model with random slope and the above fixed effects was significantly better than either a full model that included measurement as a parameter (p = 0.004), or a null random model (p = 0.00003).

Description Model AIC
Null model Hiding time ∼ 1 1,331
Null model with random effect only Hiding time ∼1∣ID 1,330
Full model Hiding time ∼ Measurement +1∣ID 1,315
Full model with random slope Hiding time ∼ Measurement a Treatment + (1 + trial∣ID) 1,308 a

There was a significant effect of treatment on hiding time (Fig. 3). Plants deprived of photosynthesis with the black-bag treatments had significantly shorter hiding times post-treatment than did control (p = 0.002) or clear-bag treatments (p = 0.018), which were not significantly different from each other (p = 0.097). The adjusted repeatability showed that 41% of this variation can be attributed to individual plant and the ICC was 58.8%.

Figure 3: Difference in hiding time (s) as a function of total plant treatment (black plastic bag, clear plastic bag, no bag).

Experiment 4: are consistent responses at the level of the whole plant or at the level of the individual leaf?


To determine if light effects are localized or systemic across the entire plant, we covered half of a plant’s leaves to prevent photosynthesis in the covered half and tested hiding time before and after treatment. Prior to treatment, we measured the hiding time of one leaf on two sides of the plant and designated a treatment and non-treatment side for each plant. These leaves were marked with flagging tape around their woody stem for future measurement. We partially covered 17 sensitive plants by wrapping the leaves on the treatment side with aluminium foil. To control for effects of disturbance, we wrapped leaves on the treatment side of 17 sensitive plants in clear plastic (Saran™, Oakland, CA, USA) so that light could still pass through. We had an additional control group in which 19 plants were not subject to any treatment on either side. Again, we acknowledge that there may be the possibility of temperature and humidity effects. However, this increase is likely to be similar between foil wrapped and saran wrapped leaves, which means the resulting effect is largely due to differences in sunlight availability. We removed these treatments after an average of 5.8 h (±0.43 h SD, range 4.18–6.65 h). After the leaves reopened, we re-measured the hiding time of the same marked leaf. In this experiment, the sample size was 53 leaves from 51 different plants that were randomly assigned to different treatments. As with experiment 3, to compare the effects of treatment, the model formally compares the slopes of individuals between trials, across treatments. The mean height of the individuals on experiment 4 was 37.1 cm (±16.9 cm SD, range 5.5–79.5 cm). The mean number of leaves was 62.8 (±44.7 SD, range 10–223). The mean leaf length was 40.7 mm (±11.8 mm SD, range 11.5–70.4 mm).


In experiment 4, we found that the full model including the fixed effect of measurement, best explained variation in hiding time (Table 5). The full model with the above fixed effect was significantly better than either a null model (p < 2.2e −16 ), null random model (p = 0.0035) or a full model with random slope that included the fixed effects of measurement, treatment, and control or treatment (p = 0.0165).

Description Model AIC
Null model Hiding time ∼ 1 2,570
Null model with random effect only Hiding time ∼1∣ID 2,446
Full model Hiding time ∼ measurement +1∣ID 2,439 a
Full model with random slope Hiding time ∼ measurement a Treatment a ControlorTreat + (1 + trial∣ID) 2,438

There was no significant effect of treatment on hiding time of the treated leaf. There was no significant effect of the foil treatment with final and initial hiding time and with control or treatment type (p = 0.2413) when compared to the base model, which included clear plastic wrap treatment. Furthermore, there was no significant effect of the control treatment with final and initial hiding time and control or treatment type (p = 0.9236) when compared to the base model. The adjusted repeatability showed that 71% of this variation in hiding time can be attributed to individual plant and the ICC for this experiment was 70.8%. The estimate for the effect of measurement on hiding time was 23.019 (±7.772 SEM, t-value = − 2.962).

Biology Final exam question

An enzyme within the ribosome structure catalyzes the formation of the polypeptide bond.

Elongation continues until a special 'stop codon' (UAA, UAG, or UGA) causes termination of the process. The finished
polypeptide is released, and the ribosome splits into its two subunits.

Translation can be divided into 4 steps, all of which occur in the cytoplasm.

Insertions are mutations in which extra base pairs are inserted into a new place in the DNA. -2.

Deletions are mutations in which a section of DNA is lost, or deleted.

2) viral disease can spread from a small, isolated population to become a widespread epidemic
- AIDS went unnamed and virtually unnoticed for decades before spreading around the world
- technological and social factors, including affordable international travel, blood transfusion technology, sexual promiscuity, and the abuse of intravenous drugs, allowed a previously rare disease to become a global scourge

transduction=the process of transferring genetic material from one cell to another by a plasmid or bacteriophage

When miRNA forms a complex with protein, it can bind to any mRNA to degrade it or block its translation.

A difference is that most eukaryotic genes have individual promoters and other control sequences and are not clustered together as operons.

cDNA molecules (from the mRNA transcribed from genes in a particular type of cell) bind to the DNA fragments in the microarray. The cDNA attached to the DNA produces a glow, which enables researchers to determine which genes were being transcribed in the starting cells.

The binding activates the first in a series of relay proteins within the target cell, each of which activates the next.

Mutations to proto-oncogenes create the cancer-causing oncogenes that often stimulate cell division by coding for growth factors. When the mutation occurs, normal gene expression is changed, and the cell is stimulated to divide excessively.

Tumor-suppressor genes have products that inhibit cell division the proteins they encode help prevent uncontrolled cell growth.

The other principle is that it depends on the environment.

A population is a group of individuals of the same species that live in the same area and interbreed.

Gene flow occurs when a population loses or gains alleles when fertile individuals move in/out of a population or when gametes (plant pollen) is transferred between populations - reduces differences between populations.

Disruptive selection occurs when environmental changes force the environment favors either extreme, not the intermediate phenotype → two contrasting phenotypes of a population.

Overprescribing antibiotics, putting it in animal feed, taking antibiotics and then stopping because you feel better, all contribute to antibiotic resistance, bacteria mutates and could lead to full-blown antibiotic resistance.

Antibiotic resistance is high in hospitals where antibiotic use is high, and we continually have to keep developing new antibiotics.

Heterozygote advantage is when heterozygous individuals have greater reproductive success than homozygotes, results in recessive genes being preserved (heterozygous sickle cell carriers in malaria ridden areas escape most severe malaria symptoms).

Morphological: classifies organisms based on observable physical traits.

Ecological: defines a species by its ecological niche and focuses on unique adaptations to particular roles in a biological community.

Studies of flies from different food sources (starch and maltose), were allowed to mate, and the flies mated more frequently with same food source flies (not necessarily same population), this is an example of a prezygotic barrier that formed through environmental differentiation.

Hybrid zones are regions in which members of different species meet and mate, producing at least some hybrid offspring. It starts with ancestral species, 3 populations connected by gene flow, then a barrier to gene flow separates one population, over time the population diverges from the other two, creating a separate species, then gene flow is reestablished in the hybrid zone, creating hybrid offspring.

Reinforcement is when stronger barriers are formed after unfit hybrids are born in order to stop the production of unfit hybrids . An example is when flycatcher bird species are sympatric and their hybrids are unfit, a change in appearance was wise so the females don't make mistakes in mating.

Fusion is when species come into contact in a hybrid zone and so much gene flow occurs between the species that speciation reverses and the 2 species become 1, an example is when Cichlid fish species fused into 1 due to increase in hybridization due to murky water.

Divided into three eras - Paleozoic, Mesozoic, and Cenozoic.

Paleozoic begins with the appearance of most major animal lineages and ends with the obliteration of almost all multicellular life-forms at the end of the Permian period (last period of the Paleozoic era). The Paleozoic era includes the origin and initial diversification of the animals, land plants and fungi, as well as the appearance of land animals.Began 544 million years ago and is the period in which many vertebrates and invertebrates lived.
Phanerozoic Eon:

Mesozoic begins with the end-Permian extinction events and ends with the extinction of the dinosaurs (except birds) and other groups at the boundary between the Cretaceous period (last period of mesozoic) and the Paleogene period (first period of cenozoic). In terrestrial environments of the Mesozoic, gymnosperms were the most dominant plants and dinosaurs were the most dominant vertebrates. middle life (245-144 million years ago) rise of mammals and dinosaurs the rise of birds extinction of dinosaurs, rise of flowering plants
Phanerozoic Eon:

Cenozoic is divided into the Paleocene, Neogene, and Quaternary periods. On land, angiosperms were the most dominant plants and mammals were the largest vertebrates. the latest of the four eras into which geologic time is subdivided 65 million years ago to the present: sometimes called the age of the mammels.

Homo sapiens appeared int he Quaternary period

Archaean eon oldest fossils of cells (prokaryotes) appear origin of Earth

Biology and functional ecology of Equisetum with emphasis on the giant horsetails.

Equisetum is the only remaining representative of the once abundant and diverse subdivision Sphenophytina. The 15 living species of the genus comprise the plants commonly known as horsetails. The antiquity an uniqueness of the genus has inspired sustained interest in the botanical community and a rich literature (Reed, 1971). The genus name is derived from the Latin equis, meaning horse and seta, meaning bristle, in reference to the coarse black roots of Equisetum fluviatile which resemble a horse's tail (Hauke, 1993). The horsetails range in size from the diminutive E. scripoides (stems averaging 12.9 cm tall and 0.5-1.0 mm diameter) (Hauke, 1963) to the giant horsetails, E. giganteum and E. myriochaetum, reaching heights of 8 or more meters (Hauke, 1963) and stem diameters of ca. 4 cm. Equisetum species are vascular plants which reproduce sexually by means of spores that are borne on cones. Hence, together with the other spore-bearing vascular plants, the Lycophytes (club mosses), Psilophytes (whisk ferns) and Pterophytes (true ferns), Equisetum species are classified as pteridophytes. However, recent molecular phylogenetic studies suggest that Equisetum should be classified within the monilophytes (Karol et al., 2010 Pryer et al., 2001 Qiu et al., 2007). In fact, Equisetum, ferns and Psilophytes appear to be closer to seed plants (to which they form a sister group) than they are to Lycophytes, making the traditional classification of "pteridophyte" one of convenience only (Kranz and Huss, 1996 Qiu et al., 2007). The placement of Equisetum within the monilophytes remains unclear, with certain markers providing weak support linking the genus with the Marattiaceae (Pryer et al., 2001 Qiu et al., 2007) and a large number of plastome genes providing moderate support for a sister relationship with Psilotum (Karol et al., 2010). Like both of these families, horsetails are eusporangiate. Interestingly, affinity between the gametophytes of Equisetum and those of eusporangiate ferns was recognized as early as the 1920's (Campbell, 1927).

However, enigmas remain in the placement of Equisetum within vascular plants, because inclusion of fossil taxa in the phylogeny creates a different picture, but with Equisetum still allied more closely to ferns than with Lycophytes (Rothwell and Nixon, 2006). Furthermore, Equisetum cell walls have recently been shown to contain a hemicellulose, (1 [right arrow] 3,1 [right arrow] 4)-[beta]-D-glucan, thought to be unique to the Poales that is not shared by eusporangiate ferns (Equisetum's closest relatives according to molecular data), Psilotum, or Lycophytes (Fry et al., 2008b Sorensen et al., 2008 Knox, 2008). This hemicellulose may be linked to silica accumulation and deposition (Fry et al., 2008b). In addition, Equisetum contains a cell wall remodeling enzyme that it appears to share only with Charophytic algae, not with other pteridophytes (even the the most basal pteridophytes, the Lycophyes) (Fry et al., 2008a). Further evidence of the uniqueness of the genus is provided by two introns that the genus shares with the liverwort Marchantia, but that are not round in other vascular plants, including lycophytes (Begu & Araya, 2009). Bower (1908) noted that the early embryonic assertion of the stem axis in Equisetum and only significantly later and secondary formation of the first leaf sheath, would be expected in ancestral vascular plants. In contrast, cotyledons assert early in the embryo development of Lycopodium (Bower, 1908). These observations are intriguing evidence of the extreme isolation of the genus Equisetum and its retention of ancient features. Remarkably, the modern genus Equisetum has a history stretching back to the Jurassic (Channing et al., 2011) and possibly as far back as the Triassic (Hauke, 1978). As a result, Equisetum may perhaps be the oldest living genus of vascular plants (Hauke, 1963).

All Equisetum species are herbaceous perennials. The plant consists of upright aerial stems that arise from a very extensive underground rhizome system (Hauke, 1963). Morphologically, the genus Equisetum is characterized by jointed aerial stems and jointed rhizomes. The stems of horsetails are "anatomically [. ] unique among plants" (Niklas, 1997) (Fig. 1a) although they have an external appearance somewhat reminiscent of bamboo. The upright aerial stems exhibit a monopodial branching pattern, having one main axis of growth. This is the pattern which is also round in most gymnosperms and angiosperms (Scagel et al., 1984). Equisetum species also have small microphyllous leaves that are arranged in true whorls (Rutishauser, 1999) and the leaves of each whorl are fused together to form a cylindrical sheath around each node (Hauke, 1993) (Fig. 1d). Some, but hOt all, species form whorls of lateral branches at the nodes of the aerial stems (Hauke, 1993). The aerial stems, but not the rhizomes, of some species die back seasonally, whereas other species are evergreen. Rhizomes have the same general morphology as upright stems (Fig. 1b), although rhizomes bear adventitious roots (i.e. roots arising from the stem rather than from other roots) at their joints in addition to leaf sheaths and branches (Fig. 1c). Aerial stems range in height from the 8 m high tropical species, E. myriochaetum, to the 4-5 cm tall temperate species, E. scirpoides (Hauke, 1963).

Stem lengthening is produced by intercalary meristems above each node and this growth pattern produces a relatively rapid extension (Stewart & Rothwell, 1993). This is a process similar to that which occurs in bamboo, which also have stems that lengthen primarily via intercalary meristem growth (Judziewicz et al., 1999). The nature of stem elongation in Equisetum is easy to observe. In developing stems, the region of the internode close above a node is noticeably lighter green than the internode further away from the node. This is because the internode tissue nearer the node is more recently generated by the intercalary meristem and is therefore less mature than tissue farther away. Two types of elongation meristems are found in Equisetum rhizomes. French (1984) found that the three subgenus Equisetum species he studied had uninterrupted meristems "charactersized by acropetal internode maturation". In contrast, the four species of subgenus Hippochaete that he studied had intercalary meristems in their rhizomes.

Beyond typical Equisetum morphology, several interesting aberrations have been observerd (Schaffner, 1933). These include a spiraling entire leaf sheath along the length of the stem, as opposed to the normal separation of each sheath and lack of any spiraling (Schaffner, 1927, 1933 Tschudy, 1939 Bierhorst, 1971). Other peculiar teratologies include flexuous stems, extremely short internodes, dichotomous branching of shoots, cones that continue vegetative growth, and cones borne on the lateral branches of species that normally only have a cone at the apex of the central stem (Page, 1968 Schaffner 1924, 1933 Tschudy, 1939 Westwood, 1989). In general, the appearance of Equisetum shoots can be remarkably plastic in response to the environment (Hauke, 1963 Schaffner, 1928). These abnormalities and plasticities may provide clues to understanding the development of the unique architecture and ecology of Equisetum. They may also provide clues as to the origins and ontogeny of vegetative and reproductive structures within extinct Sphenophyta.

Unique Characteristics of the Genus Equisetum Among Vascular Plants

Unlike all other vascular plants which produce branches exogenously (and most in the axils of leaves), the branches of Equisetum are produced endogenously (Hofmeister, 1851 Stutzel & Jadicke, 2000) and, furthermore, the leaves of Equisetum alternate with branches at each node (Scagel et al., 1984) (Fig. 1d). In other plants with lateral (as distinguished from terminal) branching, branches originate in leaf axils (i.e. in the vertex of the upper angle between a leaf and the stem from which it arises)

Dayanandan (1977) observed that Equisetum species "possess perhaps the most structurally complex stomata in the entire plant kingdom" (p. 175). The stomata of equisetum are so unique that "a single well-preserved stomatal apparatus is all that is needed to identify the genus Equisetum (even the two subgenera) from among all other living plants" (Dayanandan, 1977). The uniqueness of Equisetum stomata is the result of two characteristics (Dayanandan, 1977):

1.) The two subsidiary cells overlie the guard cells completely, whereas in other plants the guard cells are the superficial cells.

2.) "The inner tangential wall of each subsidiary cell develops 7 to 24 ridge-like thickenings, a feature not found in any other genus." (Dayanandan, 1977)

Each Equisetum spore has four strap-like structures called elaters attached to the spore surface at a common point (Hauke, 1963).

Among terrestrial plants, only the horsetails have been definitively shown to require Silicon as an essential, not simply beneficial, mineral nutrient (Epstein, 1999). The requirement for silicon has been shown for Equisetum arvense (Chen & Lewin, 1969) and for E. hyemale (Hoffman and Hillson, 1979), so this requirement appears to hold for members of both subgenera within Equisetum.

Golub and Whetmore (1948) excavated the rhizome system of a colony of Equisetum arvense to a depth of 2 m and found five successive horizontal layers of rhizomes connected by vertical rhizomes. This rhizome system extended below 2 m, but the investigators did not excavate further. This "tiered" rhizome architecture may be unique in the plant kingdom. Indeed, other rhizomatous plants generally have but a single horizontal rhizome system layer (Bell & Tomlinson, 1980).

Equisetum is an ancient genus and comprises the sole surviving representatives of the class Sphenopsida (the only class of the subdivision Sphenophytina) (Scagel et al., 1984). Sphenopsids first appeared in the fossil record of the late Devonian. The earliest unequivocal sphenopsid that has been discovered is Pseudobornia ursina, a monopodial arborescent clonal plant of the upper Devonian which grew up to 20 m tall with stems up to 60 cm in diameter (Scagel et al., 1984 Stewart and Rothwell, 1993). Pseudobornia dominated clastic streamside habitats during this time (Behrensmeyer et al. 1992). Later, during the early Carboniferous, a greater diversity of distinctly sphenopsid plants became prominent. These Carboniferous sphenopsids are currently classified into two orders, the Sphenophyllales and the Equisetales (Stewart and Rothwell, 1993). The Sphenophyllales, consisting of a single genus, Sphenophyllum, were herbaceous plants with whorls of wedge-shaped leaves on a jointed stem. Sphenophyllum species increased in abundance until the Upper Carboniferous, but vanished by the end of the Permian. The Equisetales include the major families Archaeocalamitaceae, Calamitaceae, and Equisetacae. The Archaeocalamitaceae were arborescent sphenopsids which persisted from the Upper Devonian through the Lower Permian and were similar to the much more numerous Calamitaceae (Stewart & Rothwell, 1993). The Calamitaceae, which has a single genus, Calamites, encompasses the now extinct arborescent woody sphenopsids, some of which attained heights of up to 30 m and diameters of up to 1 m (Cleal & Thomas, 1999 Scagel et al., 1984, Spatz et al., 1998b). Finally, the family Equisetaceae consists of the living genus Equisetum as well as other extinct herbaceous sphenopsids resembling Equisetum. Interestingly, the Calamitaceae closely resembled the Equisetaceae in having rhizomatous growth, fused leaf sheaths at the nodes, and in many other respects. The chief differences between the two families lie in cone morphology and in the lack of secondary (woody) growth in the Equisetaceae in contrast to the presence of secondary growth in the Calamitaceae (Stewart & Rothwell, 1993).

The Carboniferous represented the peak of pteridophyte diversity and abundance (Rothwell, 1996). It was also during this period that about 75 % of the world's coal was formed. Hence, there is rich fossil evidence for the ecology and biogeography of this period. The great Carboniferous coal swamps were warm and humid and occupied the wet tropical low-lying areas (Pearson, 1995). These swamps were dominated by giant arborescent Lycopods in genera such as Lepidodenderon (Stewart & Rothwell, 1993). Sphenopsids, especially in the genera Calamites and Sphenophyllum were common members of the flora during the Carboniferous. The Pennsylvanian plant assemblages are probably the best known plant assemblages of the Paleozoic, and possibly the entire pre-Cretaceous. From palynological and coal-ball analyses of Pennsylvanian floras, it is possible to gain insight into the ecology of Carboniferous sphenopsids. Sphenophyllum species were ground-cover plants which occurred in nearly all lowland habitats (Behrensmeyer et al., 1992). Calamites were hydrophytes, like Equisetum, and grew on loosely consolidated substrates such as sand bars, lake and stream margins, and other unstable moist substrates (Tiffney, 1985). Therefore, it is probable that Calamites were centered outside the comparatively stable coal swamps. Calamites were the only Carboniferous lowland arborescent plants that had the capability for extensive vegetative propagation (Tiffney, 1985). The rhizomatous growth of Calamites, like that of modern Equisetum, allowed them to form extensive colonies on disturbed wetland areas. However, Calamites and Sphenophyllum were relatively minor components of the vegetation in terms of overall biomass contribution (Behrensmeyer et al., 1992 Tiffney, 1985). The aerial stems of Calamites were of determinate growth, like those of modern horsetails, despite their capacity for secondary xylem formation (Eggert, 1962).

During the Carboniferous, Laurasia and Gondwana collided and thus began the formation of the supercontinent Pangea. In the Late Carboniferous, there was widespread peat formation in the moist equatorial region coal forests in what is now Europe and central and eastern North America. However, climate changes in the late Pennsylvanian and early Permian began to herald the demise of the great coal swamps. During this time, the equatorial regions of Pangea became drier and rainfall became more seasonal (Parrish, 1993). The climate also became cooler with extensive glaciation in the southern hemisphere. This trend continued through the Triassic when arid to semiarid climates prevailed (Stewart and Rothwell, 1993). This led to a worldwide change from hydric conditions to mesic conditions which are less favorable to sphenopsid growth. In addition, the inability of sphenopsids to grow in the increasingly dry sites probably reduced their ability to compete with the increasingly successful ferns, cycads, and conifers (Koske et al., 1985). These changes probably led to the extinction of Calamites during the Lower Permian and the extinction of the Sphenphyllales by the end of the Permian. These extinctions left the remaining members of the Equisetales as the only representatives of the Sphenophytina (Stewart and Rothwell, 1993).

By the Mesozoic, all sphenopsids had the same basic structure as present day Equisetum (Behrensmeyer et al., 1992). The remaining Equisetales included the widespread Schizoneura, an upright herbaceous genus, with stems up to 2 meters tall and 2 cm wide (Behrensmeyer et al., 1992), which first appeared in the Carboniferous and continued into the Jurassic (Stewart and Rothwell, 1993). Schizoneura's large fiat unfused leaves were a distinctive feature of this genus not commonly found in the Equisetales (Scagel et al., 1984). Another herbaceous sphenopsid which survived from the Carboniferous to the Lower Cretaceous was the genus Phyllotheca (Stewart and Rothwell, 1993). In addition, the genus Neocalamites first appeared in the Upper Permian and survived until the Lower Jurassic. Neocalamites resembled a small Calamites in gross morphology (Stewart and Rothwell, 1993) with stems 10 to 30 cm thick and possibly 10 m high (Behrensmeyer et al., 1992). It was widely distributed during the latter Triassic (Seward, 1959). Equisetites, a genus which first appeared in the Carboniferous, was the other major surviving genus of sphenopsids. Equisetites were very similar to present day Equisetum and there is some controversy as to whether they may actually have been congeneric with present day Equisetum. If Equisetites actually were Equisetum, then Equisetum has existed since the Paleozoic and may indeed be the oldest extant vascular plant genus (Hauke, 1963). However, some Triassic and Jurassic Equisetites were significantly larger than present day Equisetum, reaching 8 to 14 cm in diameter (Stewart and Rothwell, 1993). Perhaps the largest Equisetites species, E. arenaceus, lived during the Upper Triassic period (Kelber & van Konijnenburg-van Cittert, 1998). This remarkable species had stems that averaged 25 cm in diameter and may have reached 10 m in height. Stewart and Rothwell (1993) hypothesized that large Equisetites may have had secondary growth due to their size, but mention that there is no direct evidence for this. Seward (1898) mentioned interesting indirect evidence that E. areanceus had secondary growth. Some bamboos have stems approaching the diameter of E. arenaceus, yet lack secondary growth (Judziewicz et al., 1999). Bamboo stems are supported by extensive lignification (Judziewicz et al., 1999) and it seems possible that the large Equisetites likewise had lignified support tissues. Spatz et al. (1998a) did not find lignification in the supporting tissues of giant Equisetum stems. Gierlinger et al. (2008) found E. hyemale stems to be free of lignin, but Speck et al. (1998) reported slight lignification in supporting tissues of the latter species. Yamanaka et al. (2012) found that lignin is present in E. hyemale vascular bundles, but not the outer siliceous layers, and that lignin plays no mechanical role.

The distribution and anatomy of Mesozoic sphenopsids was consistent with primary colonization of open or disturbed moist habitats. The sphenopsids as a whole became less diverse and increasingly limited to herbaceous forms during the Triassic (Behrensmeyer et al., 1992). This trend was probably due to increasingly arid conditions during the Triassic. However, the surviving order Equisetales was widely distributed and diverse during the Mesozoic. During the Jurassic, the large Equisetites were present in nearly all parts of the world. From the Jurassic onwards, however, Equisetales become smaller and less numerous (Schaffner, 1930). The Jurassic has also yielded the earliest definitive fossil species of Equisetum (Channing et al., 2011). By the beginning of the Cenozoic, relatively small species of Equisetum are all that appear (Stewart and Rothwell, 1993). This decrease in size and abundance during the Cretaceous was probably also related to the rapid rise of angiosperms to dominance and the resulting general decline in the prominence of pteridophytes and conifers (Schaffner, 1930). However, despite this decline, during the Quatemary Equisetum species were found to be widely distributed in the temperate zone (Seward, 1959).

Present day Distribution and Species Relationships

Present day Equisetum species are naturally distributed throughout much of the world, although they are notably absent from Australia and New Zealand (Scagel et al., 1984) and from the islands of the central Pacific, Indian, and South Atlantic oceans (Schaffner, 1930). The diversity of species increases from the equator to the temperate zone in the northern hemisphere, whereas there are only four species in the Southern Hemisphere (Hauke, 1963, 1978).

The present day species of the genus Equisetum has traditionally been divided into two distinct subgenera: subgenus Equisetum, with eight species and subgenus Hippochaete, with seven species. However, recent molecular phylogenetics studies have caused a reconsideration of the placement of E. bogotense, once thought to be a member of subgenus Equisetum and even a specialized member of that subgenus (Hauke, 1968, 1969a), but now thought to be either basal to the genus as a whole (Des Marais et al., 2003 Guillon, 2004), or sister to Hippochaete (Guillon, 2007). Due to the ongoing uncertainty about the placement of E. bogotense, the traditional subgeneric names will be retained in this review, with the understanding that intrageneric groupings will likely need to be revised pending further evidence on the placement of this species and pending more comprehensive molecular studies. The placement of E. bogotense aside, the other 14 species make up two sister monophyletic groups in agreement their traditional subgeneric placement. Another surprising finding of molecular phylogenies of Equisetum is the nesting of E. giganteum well within the Hippochaete (Des Marais et al., 2003 Guillon, 2004, 2007), whereas this species had long been considered the basal member of the whole genus based on several macromorphological similarities with fossil taxa such as Equisetites (Hauke, 1963) and bolstered by the apparently unique sexual expression (typically bisexual) of the gametophytes of this species (Hauke, 1969a, 1985), although this character was questioned by Duckett and Pang (1984) based on misidentified experimental plants (Hauke, 1985). Browne (1920) did not find any clear evidence that E. giganteum exhibits any vascular characters that would ally it with Equisetites, but Browne (1922) did find some vascular features she considered basal within the genus, although this interpretation was not clearcut. However, study of the rhizome anatomy did not reveal clear differences with other members of the genus (Browne, 1925). Likewise, recent studies of strobilus structure and ontogeny in E. giganteum suggest no substantial differences with other Equisetum (Rincon et al., 2011).

There are several primary differences between the two subgenera. Species in subgenus Equisetum have stomata that are flush with the epidermal surface, whereas members of the subgenus Hippochaete have stomata that are sunken below the epidermal surface. Stems of subgenus Equisetum are short-lived, relatively sot, and tend to be regularly branched, whereas stems of the subgenus Hippochaete, with few exceptions, tend to be long-lived, hard, fibrous, and unbranched or irregularly branched (Hauke, 1963, 1969b). In addition, four of the species of subgenus Equisetum demonstrate stem dimorphism between non-photosynthetic, unbranched, coniferous stems and photosynthetic, branched, vegetative stems (Hauke, 1978). No such dimorphism occurs in the subgenus Hippochaete (Hauke, 1963). Although the chromosome number (n= 108) is the same for all Equisetum species, the subgenus Hippochaete has larger chromosomes than those of subgenus Equisetum (Hauke, 1978).

The subgenus Hippochaete includes the Equisetum species often called "scouring rushes" (although also known generally as horsetails) due to their rough, silica-impregnated epidermis. The rough siliceous stems of plants of this subgenus were used by American pioneer settlers for scouring dirty cookware and polishing wood (Scagel et al., 1984). The seven species in this group are E. giganteum, E. myriochaetum, E. ramosissimum, E. laevigatum, E. hyemale, E. variegatum and E. scirpoides. This group contains the two largest Equisetum species, E. giganteum and E. myriochaetum. With the exception of E. laevigatum, and some varieties of E. ramosissimum, all of the species in this subgenus have evergreen stems (Hauke, 1963). This group is very widespread with species distributed over large areas of every continent, except for Australia and New Zealand. The Old World species E. ramosissimum, which ranges from 60[degrees] North latitude to 30[degrees] South latitude, has the widest latitudinal range of any Equisetum species (Schaffner, 1930). The subgenus Hippochaete, as a whole, ranges as far north as Ellesmere Island (greater than 80[degrees] North latitude) and as far south as Argentina (approximately 40[degrees] South latitude) (Hauke, 1963).

The subgenus Equisetum contains the species commonly known as "horsetails." The eight species of this group are E. arvense, E. pratense, E. sylvaticum, E. fluviatile, E. palustre, E. diffusum, and E. telmateia. The species in this group tend to be regularly branched. Members of this subgenus are found from 80[degrees] North latitude to 40[degrees] South latitude. No species in this subgenus extends into the Southern Hemisphere. The other seven species of this group are found in the Northern Hemisphere (Hauke, 1963). Most species of subgenus Equisetum are temperate, with a few extending their ranges into the subtropics and only E. bogotense ranging into the tropics. The aerial stems of all of these species, except for E. bogotense and E. diffusum, (the species from the warmest climates), are annual (Hauke, 1978).

Equisetum species grow in wet places such as moist woods, ditches, wetlands, and in road fill where sufficient groundwater is available. Rhizomatous clonal growth is a universal feature of the genus and is very important in its ecology and its ability to utilize ground water. A single rhizome system may cover hundreds of square feet (Hauke, 1963). The rhizomes can penetrate to soil depths of four meters in some circumstances (Page, 1997). This deep rhizome growth gives the plants the ability to survive environmental disturbances such as plowing, burial, fire and drought. The extensive rhizome system also allows the Equisetum plants to supply themselves with water and mineral nutrients from deep underground and hence allows them to grow in habitats, such as road fill, which appear dry on the surface (Hauke, 1963).

As in other pteridophytes, sexual dispersal in Equisetum occurs by means of spores. Equisetum spores are green, spherical, and have thin spore walls (Hauke, 1963). Each Equisetum spore has four unique strap-like structures called elaters attached to the spore surface at a common point. These elaters are hygroscopic (i.e. they expand and contract with changes in humidity) and probably function to help disperse the spores (Hauke, 1963). Equisetum spores are short-lived and can germinate within 24 h of release from the cone. After 5-17 days, depending on humidity, they are no longer capable of germination (Hauke, 1963), although very cold storage temperatures can extend viability to 2 years or more (Ballesteros et al., 2011). In non-tropical species (the majority of Equisetum), the spores are produced over a short period of time during the growing season (Duckett, 1985). Equisetum gametophytes appear to require a substrate of recently exposed bare mud in order to become established (Duckett & Duckett, 1980). The two subgenera tend to have consistent differences in their gametophytes, with those of the Hippochaete being considerably larger and having more embryos than those of subgenus Equisetum (Campbell, 1928), sometimes reaching 3.5 cm in diameter (Mesler & Lu, 1977). However, form and sexuality can be plastic in response to environmental differences (Walker, 1931 Buchtein, 1887 Mesler & Lu, 1977). Like pioneer species, they rapidly attain sexual maturity and are adversely affected by competition from bryophytes and vascular plants (Duckett & Duckett, 1980 Duckett, 1985). The resulting inefficiency of spore germination and gametophyte reproduction in non-pioneer situations probably limits gene flow and leads the high degree of genetic divergence found between Equisetum populations (Korpelainen & Kolkkala, 1996). Therefore, sexual reproduction in Equisetum is limited to rather narrow ecological conditions and this limits the establishment of Equisetum via spores.

The uniform chromosome number throughout the genus (n= 108) facilitates hybridization between Equisetum species (Scagel et al., 1984). Hybridization is also favored by the relatively narrow ecological requirements of gametophytes which encourages the formation of mixed populations of gametophytes on suitable sites (Hauke, 1978). These mixed populations increase the probability of cross fertilization between gametophytes of different, but compatible, species. In areas where environmental conditions are especially conducive to spore germination and gametophyte establishment, Equisetum hybrids are particularly frequent and widespread. In Britain and Ireland, for example, Equisetum hybrids are particularly successful (Page, 1985). This success appears to be due primarily to the moist temperate oceanic climate and relatively low competition from other plants, conditions which favor both gametophyte and sporophyte generations of Equisetum (Page, 1985). Equisetum hybridization is especially frequent within the subgenus Hippochaete where five common hybrids are known. Within the subgenus Equisetum, there is only one common hybrid (Hauke, 1978) and the most common species involved in hybridization is E. arvense (Lubienski, 2010). There are many more known hybrids within each subgenus, but these hybrids tend to be much less common (Hauke, 1978). No hybrids between the two subgenera have yet been reported and this adds further evidence that the two subgenera are naturally distinct (Krahulec et al., 1996). Furthermore, there are no known hybrids of the enigmatic Equisetum bogotense, though this may be partly due to its lack of distributional overlap with any species besides the giant horsetails. Use of ISSR fingerprinting has facilitated identification and verification of hybrids (Brune et al., 2008).

Several triploid taxa have been discovered in subgenus Hippochaetae, either the result of introgression within hybrids or of crossing of a gametophyte from an unreduced spore of one species and a normal gamete from another species (Bennert et al., 2005 Lubienski et al., 2010). Tetraploids are unknown (Bennert et al., 2005).

Equisetum species have a remarkable ability to reproduce vegetatively. This mode of reproduction predominates in some species (e.g. E. arvense), whereas others reproduce sexually with greater frequency (e.g. E. telmateia) (Brune et al., 2008). Vegetative reproduction helps to compensate for the inefficiency of spore reproduction. An extensive rhizome system allows Equisetum species to rapidly colonize disturbed areas (Hauke, 1963). This ability gives Equisetum a distinct advantage over species requiring seed establishment or which have slow-growing rhizomes (Hauke, 1969b). For instance, the widespread creation of roadside ditches in America has created significant new habitat for some Equisetum species. This is because the soil in ditch habitats tends to be moist and the rhizomatous growth of Equisetum species allows them to survive and thrive under the conditions of sediment accumulation that are characteristic of ditches (Rutz and Farrar, 1984). The ability of Equisetum to survive and spread in areas of heavy sediment accumulation was dramatically demonstrated after the 1912 eruption of Katmai Volcano in Alaska. In studies of vegetational recovery from the volcanic tephra (ash and silt) deposited by this eruption, E. arvense was found to be the most successful herb. It was able to penetrate as much as one meter of tephra, more than any other herbaceous species, and colonize large areas via rapid rhizomatous growth (Bilderback, 1987). The remarkable ability of Equisetum to prosper under disturbed conditions was also demonstrated after the eruption of Mount St. Helens in 1980 when Equisetum formed almost monotypic stands in the newly deposited tephra (Siegel & Siegel, 1982 Rothwell, 1996). The deep rhizome system of Equisetum also allows these plants to survive fire and rapidly recolonize burned-over sites (Beasleigh & Yarranton, 1974). It is probable that the vigorous and extensive rhizomatous habit of Equisetum has been very important to the long term survival and spread of the genus (Hauke, 1969b).

Fragmentation of rhizomes and stems allows Equisetum to disperse readily in suitable habitats where there is sufficient moisture. Even the aerial stem fragments can sprout and form new colonies (Praeger, 1934 Schaffner, 1931 Wagner & Hammitt, 1970). Some members of the subgenus Equisetum (e.g. E. arvense and E. palustre) also reproduce vegetatively via tubers produced on the rhizomes (Hauke, 1978). These tubers can contribute substantially to vegetative spread through soil disturbance (Marshall, 1986 Sakamaki and Ino, 2006). Hence, vegetative reproduction allows Equisetum clones to persist and spread even in the absence of sexual reproduction (Hauke, 1963).

Vegetative reproduction probably accounts for the widespread occurrence and persistence of common Equisetum hybrids even where one or both of the parents are absent. This is because hybrids are generally sterile and hence are without means of sexual reproduction. The rhizome system of a vigorous hybrid clone theoretically has the ability to maintain dense colonies within limited areas for long periods. Fragmentation and transport of rhizomes and stems then has the potential to disperse the clone from the site of the original hybridization. This would account for the abundance of Equisetum hybrids even if hybridization is a relatively uncommon occurrence (Hauke, 1963).

Spatz et al. (1998a) studied the biomechanics of a giant horsetail, Equisetum giganteum. The investigators found that E. giganteum has a turgor-based support structure that is distinct from the lignification-based support found in hollow-stemmed grasses. The results of the study demonstrated stems taller than

2.0-2.5 m were not mechanically stable (i.e. they buckle without external support). Taller stems required support of neighboring stems (facilitated by intertwined side branches) to remain upright. The stems of the clone they studied were relatively thin, only reaching

1 cm at the widest. Husby (2009) studied the biomechanical properties of E. giganteum stems in the field in southern South America. The bulk tissue modulus of elasticity values measured on wild-grown stems were much higher than those measured by Spatz et al. (1998a). This finding, along with larger maximum diameters (

3.9 cm) of field grown plants explains the significantly taller (5+ m) stems found in the wild.

Speck et al. (1998) found that another member of the subgenus Hippochaete, E. hyemale, had some biomechanical properties quite distinct from those of the E. giganteum that Spatz et al. (1998a) studied. In E. hyemale, stem stability is not turgor dependent, but is primarily attained through the arrangement of two endodermis layers and a hypodermal sterome. Equisetum hyemale is primarily a cold-climate species (Hauke, 1963), and stems remain evergreen and functional for multiple seasons (Niklas, 1989a). During subfreezing temperatures, E. hyemale has the ability to dehydrate its tissues via extracellular freezing to avoid ice crystal damage to tissue (Niklas, 1989a). The non-turgor-dependent structure of E. hyemale thus permits the stems of this species to avoid buckling even when turgor pressure is decreased during winter. The nodal septa of E. hyemale shoots contributed 17 to 32 % of the flexural rigidity of the axes (Niklas, 1989b). Furthermore Niklas (1989c) found that the stems of E. hyemale are primarily designed for mechanical stability, rather than economy of tissue allocation.

Spatz et al. (1998b) combined the mechanical properties of extant Equisetum with insights from the arborescent Paleozoic genus Calamites which has a very similar stelar structure to Equisetum (Verdoorn, 1938) to model the biomechanical properties of the latter. The maximum heights of Calamites stems in exposed areas were likely limited by wind stresses. In addition, like E. hyemale, but in contrast to E. giganteum, Calamites appears to have had a non-turgor-dependent reinforcing structure.

Treitel (1943) carried out experiments on the rhizome hiomechanics of several Equisetum species from both subgenus Hippochaete and subgenus Equisetum. He investigated rhizome elasticity, breaking stress, and breaking strain. The results of the study indicated that different Equisetum species often had markedly different stress-strain curves. The investigator attributed these differences to differences in amount of strengthening elements in rhizomes (e.g. suberization and schlerenchyma cells) that are in turn due to differences in soil environment (wetter vs. drier soil) and to rhizome maturity. The two species for which Treitel calculated the modulus of elasticity had very different values of this parameter, with E. fluviatile (subgenus Equisetum) having much more elastic rhizomes than E. scirpoides (subgenus Hippochaete). He attributed E. fluviatile's greater elastiscity to its much wetter habitat and hence its lesser need for strengthening tissues to reinforce its rhizomes against soil pressure.

David et al. (1990) observed a marked water potential depression in Equisetum telmateia around noon even when vapor pressure deficit was relatively mild, despite the presence of a high surface water table. This suggests that either water transport or root absorption, or both, were unable to keep up with evaporative demand during those periods. Also, Husby (2009) observed low maximum stomatal conductance in Equisetum giganteum. Since hydraulic conductivity is generally closely correlated with stomatal conductance (Franks & Brodribb, 2005), it appears likely that there exist hydraulic "bottlenecks" at the nodes in Equisetum stems that limit water transport sufficiently to reduce stomatal conductance. The carinal canals are not continuous through the nodes (Gifford & Foster, 1989), which likely increases resistance to water flow. These observations suggest that hydraulic conductivity is a limiting factor for modern horsetails, even thought their evaporative surface area is decreased by the absence of exposed leafly lamina.

The hydraulic architecture of Equisetum stems has yet to be elucidated, although the carinal canals in each internode appear to provide low resistance pathways through internodes, analogous to the role played by vessels in angiosperms (Leroux et al., 2011 Xia et al., 1993 Bierhorst, 1958). Such a function would have particular importance during internode elongation when xylem pathways are not yet functional (Leroux et al., 2011). Furthermore, Leroux et al. (2011) discovered a distinctive cell wall matrix lining the carinal canals, which may function to facilitate water transport. Husby (2009) observed that young stems guttate much more readily and show less sensitivity of stomatal conductance to environmental factors than do mature stems, which may be indicative of differences in water transport physiology. There is also evidence that some species of Equisetum transpire much more than others, with the most hydrophilic species, E. fluviatile, showing the highest transpiration rates (Dosdall, 1919). Investigation of water transport physiology for a variety of ecologically distinct Equisetum species would likely yield interesting insights.

Equisetum species, like many other plants, have hydathodes (Johnson, 1936). In Equisetum, these are structures that are associated with veins on the leaf and/or sheath (Johnson, 1936) and serve as exit routes for xylem water when there is positive hydrostatic pressure (called root pressure) in the xylem (Nobel, 1999). The exit of this xylem water, termed guttation, results in the formation of small droplets in the vicinity of the hydathodes. Guttation occurs when transpiration is nil, such as under very high relative humidity conditions or at night (Nobel, 1999) (Fig. 1e). This phenomenon may serve to prevent flooding of mesophyll tissue in leaves (Johnson, 1936). Johnson (1936) studied the anatomy of hydathodes in many Equisetum species and noted that the hydathodes of E. giganteum are "confined to the leaf and sheath bases."

Soil and Root Interactions

Adventitious Rooting as an Adaptation to Disturbance

All equiseta have pre-formed bud and root primordia at each node of both the aerial stems and underground rhizomes (Gifford & Foster, 1989). This allows Equisetum stems to quickly put forth new roots and shoots on aerial stems when the stems are partly or wholly buried in sediment. Hence, even if the deeper parts of a stem or rhizome become crushed or smothered by sediment, the upper parts may be able to survive and reestablish the clone (Gastaldo, 1992). This ability is clearly advantageous for enhancing survival of Equisetum species in the wake of disturbance events in riparian and other wetland habitats. The pre-formed primordia can also facilitate vegetative propagation and dispersal via stem pieces (Wagner & Hammitt, 1970 Hauke, 1963). Schaffner (1931) and Praeger (1934) utilized the adventitious rooting capabilities of Equisetum stems to successfully propagate many species from aerial stem cuttings.

Gastaldo (1992) gives evidence for similar stem regeneration abilities in the large extinct Equisetum relative Calamites and discusses the ecological importance of these abilities. Similarly, Kelber & van Konijnenburg-van Cittert (1998) found that the extinct close relative of extant horsetails, Equisetites arenaceus, could propagate vegetatively via the adventitious rooting of shed branches.

Adaptations to Waterlogged Soil

Like nearly all organisms, plants require oxygen ([O.sub.2]) for efficient cellular respiration. Plants that grow in water-saturated soil often have to cope with anoxic conditions around their underground organs (Blom and Voesenek, 1995). This is because [O.sub.2] diffuses 10,000 times more slowly through liquid water than through air (Grable, 1966). Under waterlogged conditions, cellular respiration by plant roots and soil microorganisms often quickly depletes the available [O.sub.2], leading to anoxic soil conditions (Drew & Lynch, 1980 Kludze & DeLaune, 1995). These conditions lead to a large decrease in plant nutrient availability (Ernst, 1990) and to buildup of phytotoxins produced by anaerbic soil mierobes or by anaerobie respiration in plant roots (Koch & Mendellsohn, 1989).

To deal with anoxic conditions, wetland plants have several morphological and physiological adaptations to maintain aerobic respiration by facilitating transport of [O.sub.2] from the atmosphere to underground and underwater organs (Allen, 1997). In many wetland plants, gas spaces (lacunae) in specialized tissue (called aerenchyma) provide pathways for [O.sub.2] and carbon dioxide (C[O.sub.2]) to move from one part of the plant to another much more quickly than would be possible through tissue without lacunae (Allen, 1977). Rhizomes and stems of wetland Equisetum species have large canals that are thought to function like aerenchyma tissue in facilitating [O.sub.2] transport (Hauke, 1963 Hyvonen et al., 1998). Oxygen movement through aerenchyma occurs either by diffusion alone or by diffusion combined with convection (Allen, 1997). These mechanisms and their relative effectiveness have many important implications both for wetland ecology and for the growth and productivity of crop plants, such as rice (Oryza sativa L.), that typically grow in waterlogged soils (Allen, 1997 Wassmann & Aulakh, 2000). The most efficient known mechanism for oxygen transport to submerged plant parts is via pressurized convection (Allen, 1997).

Until very recently, studies of pressurized [O.sub.2] transport in wetland plants have focused exclusively on angiosperms, with the exception of one study that investigated the gymnosperm Taxodium distichum L. (Grosse et al., 1992). However, the rhizomes of Equisetum species often concentrate more deeply than the roots and rhizomes of accompanying vegetation (Borg, 1971). Marsh et al. (2000) found that, in an Alaska wetland Equisetum rhizomes were concentrated in the deeper C soil horizon whereas the roots and rhizomes of other species were concentrated in the surface O horizon. The especially deep penetration of waterlogged sediments by Equisetum rhizomes suggests the existence of efficient mechanisms for rhizome aeration, Page (2002) mentioned that Equisetum species in the British Isles vary in their tolerance of anaerobic soil water conditions. Equisetum fluviatile appears able to tolerate the greatest degree hypoxia in soil water whereas E. telmateia is least tolerant of anaerobic soil water and occupies sites with continually flowing groundwater.

The first studies of gas transport in Equisetum dealt with E. fluviatile, a species that frequently grows as an emergent aquatic plant (Hauke, 1978) and one of the most anaerobiosis tolerant Equisetum species (Page, 2002). An early study by Barber (1961) found a diffusion gradient from high concentrations of [O.sub.2] and low concentrations of C[O.sub.2] in aerial stems to the inverse condition in submerged rhizomes. In addition, Barber (1961) found that diffusion along excised aerial stems was relatively efficient. However, this study did not provide information that would indicate whether or not a pressurized ventilation mechanism might be active in E. fluviatile. A study by Hyvonen et al. (1998) of methane release from an E. fluviatile stand suggested that this species does not have a pressurized ventilation flow system because there was not a discernable diurnal pattern of methane efflux. Similarly, Strand (2002) found that E. fluviatile had a "low or non-detectable" air flow rate in its stems, yet was found in "unexpectedly deep water".

Two recent studies have found surprisingly high rates of pressurized ventilation in some Equisetum species. Armstrong and Armstrong (2009) found the first clear case of substantial pressurized ventilation in a nonflowering plant, Equisetum telmateia. In fact, the ventilation rates discovered in this plant were higher than any rates recorded in angiosperms, including the giant water lily, Victoria amazonica. The relevant features of Calamites stem structure (e.g. stomatal structure and stem anatomy) are similar to those of E. telmateia, suggesting that this ancient genus may also have tolerated waterlogged soils via pressurized ventilation.

However, not all Equisetum species exhibit pressurized ventilation. Only species with cortical araenchyma that is interconnected among the branches, aerial shoots and rhizomes exhibited convection (Armstrong and Armstrong, 2010). Nine horsetail species were studied, but only four exhibited pressurized convection, including species from both subgenera. Stomatal behavior also played a role in the differences. Whether the gas flow channels within Equisetum shoots and rhizomes allow for refixation of C[O.sub.2] respired underground remains to be investigated (Raven, 2009).

Soil Preferences and Nutrient Cycling

Alvarez de Zayas (1982) observed that in Cuba Equisetum giganteum is associated with mineral rich, acidic, alluvial soils. Correspondingly, recent experience with Equisetum in cultivation suggests that they have a high requirement for some micronutrients (C. Husby, unpublished observation). However, some species are capable of tolerating and even dominating nutrient poor environments (Sarvala et al., 1982)

Equisetum tissue is frequently observed to be rich in the minerals P, K, Ca, magnesium (Mg), and silicon (Si) (Auclair, 1979 Marsh et al., 2000 Pulliainen & Tunkkari, 1991 Saint Paul, 1979 Thomas & Prevett, 1982). Andersson (1999a, b) showed experimentally that E. arvense has a high K demand under high light conditions and was able to tolerate lower N levels (although its inability to respond much to increased N availability renders it vulernable to being out-competed by faster growing plants). Furthermore, certain Equisetum species have been shown to be highly nutritious for wildlife. For example, young stems of E. fluviatile can contain more than 20 % protein along with sufficiently high levels of P, K, Ca and Mg to meet the mineral needs of breeding geese and their young (Thomas and Prevett, 1982). In some areas, Equisetum species are an important part of the diet of black bears (Machutchon, 1989), voles (Holisova, 1976 Jean & Bergeron, 1986), rock ptarmigan (Emison & White, 1988), young trumpeter swans (Grant et al., 1994) and fish (Brabrand, 1985). Hauke (1969b) observed that cattle in Costa Rica appear to relish giant horsetails and one rancher believed that his cattle benefited from eating it.

Members of the genus Equisetum have the ability to extend their rhizomes deeply into saturated soil (Borg, 1971 Marsh et al., 2000). The rhizome system has generally been found to comprise most of the plant's biomass (Borg, 1971 Marshall, 1986). The ability of Equisetum rhizomes to penetrate deeply into wetland soils plays an important part in their recently discovered role as nutrient pumps. In an Alaskan shrub wetland, Marsh et al. (2000) found that Equisetum species can acquire and accumulate substantial amounts of phosphorus (P), potassium (K), and calcium (Ca) from lower soil layers and transport these nutrients to the surface where they are available to other plants. Remarkably, these investigators found that, although Equisetum species made up only 5 % of the total biomass of the wetland community, the Equisetum tissues had 16 % of the total phosphorus and 24 % of the total potassium (Marsh et al., 2000). Furthermore, Equisetum species contributed disproportionately to soil nutrient inputs in the shrub wetland. During the two year study period, Equisetum litter provided 75 % of the calcium, 55 % of the phosphorus, and 41% of the K input to the soil (Marsh et al., 2000). The nutrient pumping of Equisetum species in the shrub wetland probably contributed to the unusually high primary productivity of the ecosystem (Marsh et al., 2000). This nutrient pumping function of the shrub wetland Equisetum species appears to be at least partly due to the ability of Equisetum rhizomes and roots to penetrate more deeply into the soil than roots and rhizomes of other wetland plants. While Equisetum roots and rhizomes were concentrated in the deeper C horizon of the soil, roots and rhizomes of other wetland plants concentrated in the surface O horizon (Marsh et al., 2000).

A remarkable characteristic of Equisetum species is their ability to take up and accumulate silicon in their tissues. The resulting silicon concentrations in Equisetum stems are the highest among vascular plants, but lower than liverworts (Hodson et al., 2005). Silica accumulates on the epidermis of the plants (Parsons & Cuthbertson, 1992 Sapei et al., 2007). It is also incorporated into the cell walls, perhaps crosslinking wall polymers and increasing their rigidity and stability (Currie & Perry, 2009). Research on the protective value of silica seems to indicate that silica solutions when applied to plants can provide effective protection from fungal diseases and from insect attack (Epstein, 1999). This would explain why gardeners have long used horsetail extract to protect plants against pathogens and predators (Quarles, 1995). The outer layer of silica on Equisetum stems may help explain why horsetails appear to be little bothered by insect feeding or fungal diseases (Hauke, 1969b Kaufman et al., 1971). This outer layer may also help reduce water loss through the epidermis (Kaufman et al., 1971).

Timell (1964 found that silicic acid content of E. palustre could reach 25.3 % of dry weight. An important function of cell wall silica in Equisetum is in maintenance of shoot erectness (Kaufman et al., 1971) as an alternative to lignin (Siegel, 1968 Yamanaka et al., 2012). Furthermore, silica content of stems appears to be directly associated with stem longevity (Srinivasan et al., 1979). Horsetails incorporate much silicon into their stem tissues and external ridges, knobs, and rosettes of silicon give the stems of many species their rough and abrasive character (Gifford & Foster, 1989 Hauke, 1963). People have taken advantage of this abrasive quality by using Equisetum stems to wash dishes (hence the common names 'scouring rush' and 'limpiaplata'), polish woodwind reeds, and polish silver (whence the name 'yerba del platero' in Argentina).

Mycorrhizae and Root Hairs

Until recently, there has been little convincing evidence of mycotrophy in Equisetum species (either in the gametophyte or the sporophyte stage) and most studies have found essentially no mycorrhizal colonization of horsetails (Read et al., 2000). Although Koske et al. (1985) found fungal structures in roots of Equisetum species growing in a sand dune habitat, the close association of the Equisetum roots with roots of characteristically mycotrophic plants raised the possibility that the observed fungal structures represented "simply the penetration [of Equisetum roots by] a 'non-host" (Read et al., 2000). Hence, the role of mycorrhizae in Equisetum ecology remains controversial. Overall, however, Equisetum species clearly appear to do quite well in many situations without mycorrhizal associations (Read et al., 2000). For example, Marsh et al. (2000) found no mycorrhizal colonization of Equisetum roots in the Alaskan shrub wetland they studied. Although enhanced phosphorus acquisition is often a major contribution of mycorrhizal associations to plant nutrition (Orcutt and Nilsen, 2000), the mycorrhizae-free Equisetum species studied by Marsh et al. (2000) absorbed soil nutrients, including phosphorus, very effectively. A recent study of Equisetum bogotense in Argentinian Patagonia produced evidence of falcultative mycotrophy (some individuals were mycorrhizal and others were not) (Fernandez et al., 2008). By contrast, relatively high rates of colonization were found for plants growing at the northern extreme of the genus' distribution on Ellesmere Island (82[degrees]N) in the Canadian Arctic, although non-mycorrhizal plants were also found, indicating once again that the relationship is facultative (Hodson et al., 2009). The authors of this study suggest that previous negative findings may have been primarily due to the lack of adequately sensitive equipment that allows detection of very fine mycorrhizae that accounted for most of the endophyte abundance in the arctic samples.

Schaffner (1938) and Page (2002) have observed that Equisetum species have exceptionally long root hairs and Page (2002) has noted that these hairs are "unusually persistent", at least in water culture. Page (2002) hypothesized that these root hairs may function to enhance the absorptive capacity of Equisetum roots in a manner similar to mycorrhizae. Marsh et al. (2000) noted the presence of root hairs on Equisetum roots in the O horizon but not on roots in the C horizon of the Alaskan shrub wetland they studied. The investigators hypothesized that nutrient concentrations were lower in the O horizon, necessitating greater roots surface area for absorption, whereas nutrient concentrations were high enough in the C horizon to inhibit formation of root hairs. However, this phenomenon may also have been due to lower oxygen availability suppressing root hair formation deeper in the soil.

Uchino et al. (1984) found evidence for high rates of nitrogen fixation activity (attributed to several strains of Enterobacteriaceae) in association with rhizomes and roots of several temperate Equisetum species (two from each subgenus). This was based on measurements of acetylene reduction activity. These investigators hypothesized that association of Equisetum species with nitrogen-fixing bacteria may help horsetails survive in the nitrogen-limited habitats where they frequently grow.

Salinity and Heavy Metal Tolerance

Horsetails are known to tolerate stressful soil environments and this ability appears to extend all the way back to the Jurassic, where Equisetum thermale inhabited a geothermal environment likely characterized by high levels of mercury, arsenic and other elements that tend to be phytotoxic (Channing et al., 2011). Modern Equisetum are also tolerant of heavy metal uptake (Hozhina et al., 2001 Siegel et al., 1985) and have even been used for gold bioprospecting (Brooks et al., 1981).

In some areas Equisetum species grow in saline wetlands. They are sometimes found in association with saline lakes (Williams, 1991) coastal dune slacks (Van der Hagen et al., 2008) and saline boreal wetlands (Purdy et al., 2005).

Page (1997) discussed isolated colonies of the hybrid horsetail, Equisetum x moorei, on the southeast coast of Ireland. These colonies, which are the only known populations of this hybrid in the British Isles, are on dunes and grow quite near to the high tide line, suggesting considerable exposure to saline soil water and salt spray. Interestingly, only one parent, E. hyemale, of this hybrid is present in the British Isles. However, both the other parent, E. ramossisimum, and other populations of E. x moorei are present on the European mainland. These facts lead naturally to the hypothesis that sterile E. x moorei arrived in Ireland via vegetative propagules, such as stem pieces or rhizomes, that may have floated to Ireland from the mainland. Page (1997) noted an experiment (unpublished) with this hybrid wherein cut stem pieces were floated in seawater for various lengths of time and their ability to re-sprout was evaluated. Remarkably, immersion for up to 10 days in seawater did not reduce the ability of stems to sprout roots and form new plants.

Husby et al. (2011) documented a substantial degree of salinity tolerance in E. giganteum populations growing in river valleys in the Atacama Desert in northern Chile. Some of the populations in this area grow close to the ocean where the groundwater they access is up to 50 % of ocean water salinity. Like many other salt tolerant plants, E. giganteum exhibits an ability to exclude sodium and preferentially accumulate potassium under high salinity conditions.

Equisetum species, like many angiosperms, appear to exhibit allelopathy. Milton and Duckett (1985) found that sporophytes of E. sylvaticum inhibit gametophyte development of that species. Furthermore, the same investigators round that water extracts from several Equisetum species reduced the germination of grass seedlings. Two of the three species studied were members of the subgenus Equisetum (E. arvense and E. palustre) and one was a member of the subgenus Hippochaete (E. variegatum). The inibitory effects of the members of the subgenus Equisetum were greater than that of E. variegatum. This suggests that members of the subgenus Hippochaete, and hence the giant equiseta, may be less allelopathic than members of the subgenus Equisetum.

The giant horsetails are of special interest within the genus Equisetum because they give the closest approximation among living plants to the large stature once attained by primeval Sphenopsids (Fig. 1f). Furthermore, because the giant horsetails inhabit the tropics, they provide insights into how Equisetum has adapted to the challenges of living in tropical ecosystems, in contrast to the majority of species which are temperate. As for all equiseta, the giant horsetails spread vegetatively via extensive rhizome systems, often forming large clones. The rhizomes give rise to erect, determinate, aerial stems that produce regular whorls of lateral branches, giving the stems a remarkably precise radial symmetry. Colonies of such stems have a remarkably ancient appearance, as the 19th century botanist Richard Spruce (1908) remarked upon seeing a grove of giant horsetails for the first time:

"But the most remarkable plant in the forest of Canelos is a gigantic Equisetum, 20 ft high, and the stem nearly as thick as the wrist! . It extends for a distance of a mile on a plain bordering the Pastasa, but elevated some 200 ft above it, where at every few steps one sinks over the knees in black, white, and red mud. A wood of young larches may give you an idea of its appearance. I have never seen anything which so much astonished me. I could almost fancy myself in some primeval forest of Calamites, and if some gigantic Saurian had suddenly appeared, crushing its way among the succulent stems, my surprise could hardly have been increased. I could find no fruit, so that whether it be terminal, as in E. giganteum, or radical, as in E. fluviatile, is still doubtful, and for this reason I took no specimens at the time, though I shall make a point of gathering it in any state" (Spruce, 1908)

Giant horsetails inhabit elevations between 150 and 3000 m and their distributions tend to follow mountain ranges in the tropics (but not at the southern end of the range of E. giganteum, which reaches temperate southern latitudes). Like other Equisetum species, giant horsetails grow in areas with ample groundwater supply, often along rivers and in wetlands (Hauke, 1963, 1969b). Equisetum giganteum in particular exhibits several morphological features that appear to tie it with its fossil progenitors such as Equisetites: cones borne on lateral branches (Fig. 1g), large size, and sheath teeth (Hauke, 1963).

Although giant horsetails are of considerable botanical interest, relatively little is known about these remarkable plants beyond their taxonomy and anatomy. Indeed, most papers that have dealt specifically with giant horsetail ecology were limited to some qualitative (but intriguing) observations on their natural history (Alvarez de Zayas, 1982 Hauke, 1969b). Although a recent study dealt with quantitative aspects of ecophysiology of E. giganteum (Husby et al., 2011). Two studies have investigated the biomechanics of aerial stems in E. giganteum (Spatz et al., 1998a Husby et al., in review).

The most extensively studied aspects of the giant horsetails has been their medicinal properties. The medicinal use of giant horsetails has a history that reaches back to the Inca of Peru (Tryon, 1959) and the plants are currently used in medicine (often as diuretics, but also for many other medicinal purposes) throughout Latin America (Gorzalczany et al., 1999 Hauke, 1967 Morton, 1981 Murillo, 1983). Investigators using animal models have found that giant horsetail extracts have diuretic (Gutierrez et al., 1985) and hypoglycemic (Cetto et al., 2000) effects and have "nerve growth factor (NGF)-potentiating activity" (Li et al., 1999). Furthermore, a controlled study by Revilla (2002) showed that traditionally prepared Equisetum myriochaetum extract had significant hypoglycemic effect (not resulting from increased insulin secretion) in type 2 diabetics.

The taxonomy of the giant horsetails gives a good example of the typical means of distinguishing species and hybrids within Equisetum. Taxonomists currently recognize two species of giant horsetail and a hybrid between them: Equisetum giganteum L., E. myriochaetum Schlecht. and Cham., and E. x schaffneri Milde (E. giganteum x E. myriochaetum) (Hauke, 1963). Prior to Hauke's (1963) work, taxonomists recognized a relatively large number of species and varieties of giant horsetails. For example, Milde, in his 1867 monograph of Equisetum, recognized seven species of giant horsetails.

The giant horsetails are some of the least known of the 15 species in the genus Equisetum. All of the giant horsetails are members of the subgenus Hippochaete within the genus Equisetum. Most of the seven members of the subgenus Hippochaete, including the giant horsetails and the familiar temperate "scouring rush", E. hyemale, have tough evergreen stems. However, the giant horsetails are the only Equisetum species that have stems that are both evergreen and regularly (i.e. radially symmetrically) branched. Furthermore, the regular branching habit of the giant horsetails is unique in the subgenus Hippochaete (Hauke, 1963, 1978).

Because the three giant horsetails appear similar in overall habit, and because Equisetum species exhibit considerable morphological plasticity (Hauke, 1963 Schaffner, 1928) (Fig. 1h), more stable anatomical characters are used to distinguish the species (Table 1). The most important diagnostic characters (branch ridge patterns, stomatal patterns, and endodermal patterns) can only be observed under high magnification and many of characters of E. x schaffneri overlap with its parent species (Hauke, 1963). Therefore, accurate identification of giant horsetails can be problematic. As a result, both dried specimens in herbaria (Stolze, 1983 Husby, personal observation) and living specimens in botanical gardens (Moyroud, 1991 Husby, personal observation) are often misidentified.

Giant horsetails are pioneer (early-successional) obligate wetland plants and are poor competitors (Hauke, 1969b). Abundance of groundwater supply and lack of competition are key habitat requirements of these plants. Hence, they are often associated with rivers and alluvial soils (Hauke, 1969b Alvarez de Zayas, 1982). The limitation of giant horsetails to higher altitudes in the tropics is probably due to their poor competitive abilities and their inability to tolerate shade. Hauke (1969b) observed that the giant horsetails stop producing cones when shaded by other vegetation and are subsequently displaced by other plants. Hence, giant horsetails do not tend to persist in a given site unless the disturbance regime or other factor prevents shading-out of colonies. The lower competitive pressure in the cooler high altitudes combined with increased light intensity may allow the horsetails to "hold their own" against other vegetation (Hauke, 1969b). This would explain why the genus is absent from the lowland Amazon basin where temperatures are warm and plant competition is especially intense. However, E. giganteum grows down to nearly sea level in northern and central Chile where competition is much less (C. Husby, personal observation) and there is even a report of giant horsetails growing near sea level along streams in western Ecuador (Haught, 1944). Hauke (1969b) described several cases wherein giant horsetail colonies in Costa Rica had disappeared, presumably due to the process of succession at once-suitable sites. Dr. Benjamin Ollgaard (2000, personal communication) has observed that giant horsetails are frequent pioneers on land and mud slides in the valleys of the Rio Pilaton and Rio Pastaza in Ecuador. Ollgaard suspects that these pioneer stands can probably persist until sufficient forest regeneration occurs to shade out the horsetails (after

The giant horsetails, like other Equisetum species, develop extensive underground rhizome systems. Unfortunately, there has been no study of the rhizome architecture of the giant horsetails. However, it is known that the rhizomes of E. telmateia (the largest member of the subgenus Equisetum) can extend more than 4 m deep into wet clay soil (Page, 1997). Anthony Huxley reported in the book "Plant and Planet" (1975, p. 243) that "field bindweed is recorded at a depth of 7 m and horsetails in light soil two or three times as deep again". This report suggests that Equisetum rhizomes may penetrate to the extraordinary depth of 21 m in certain situations! Unfortunately, Huxley did not mention his source for this report or the species and location involved, so it would be proper to remain skeptical of this claim.

Rhizome segments that are exposed by erosion and broken-off can be carried downstream to establish new clones (Hauke, 1969b). Equisetum species generally invest a large proportion of resources in rhizome growth. Borg (1971) found that E. palustre may produce more than 100 times more rhizome biomass than aerial stem biomass. Equisetum arvense also allocates the larger proportion of its dry matter to rhizomes and tubers, thought not to such an extreme extent as E. palustre (Marshall, 1986). The large pool of resources stored in Equsietum rhizomes facilitates aerial shoot regeneration if a distrubance destroys the aboveground stems. Hence, this growth strategy is adaptive for the types of disturbance-prone habitats favored by many equiseta, including giant equiseta. There have been no studies of the ratio of aboveground to belowground biomass allocation in giant horsetails. It would also be interesting to know whether the two subgenera of the genus Equisetum differ overall in their biomass allocation patterns.

The distribution and ecology of the giant Equisetum species of the American tropics, E. giganteum, E. myriochaetum and E. x schaffneri provide a striking example the importance of vegetative persistence of hybrids in the genus. These three species are largely confined to upper elevations between 150 and 3000 m. Equisetum giganteum is a giant species which grows up to 5 m in height. It is the most widespread horsetail in Latin America, ranging from Guatemala to Brazil, Argentina and Chile as well as on Hispaniola, Jamaica and Cuba (Hauke, 1963 1969b). Equisetum myriochaetum is also a giant species and is known to grow to 8 m in height. Equisetum myriochaetum bas a more limited range and is distributed from southern Mexico to Peru (Hauke, 1963). There is also a widespread hybrid, E. x schaffneri, between these two giant horsetails which ranges from Mexico to Peru (Hauke, 1963). Although E. x schaffneri is sterile, it persists via vegetative reproduction and may form large colonies (Hauke, 1967). This hybrid is found throughout the region of overlap between its parent species, but it is also found in Mexico, where E. giganteum is not known to occur, and in Venezuela, where E. myriochaetum is not known to occur. This unexpectedly extensive distribution may be due to vegetative dispersal or to the production of an occasional, rare, viable spore (Hauke, 1963). Viable spores have been observed for other Equisetum subgenus Hippochaete hybrids (Krahulec et al., 1996), so this hypothesis appears plausible. Equisetum x schaffneri demonstrates the remarkable frequency and persistence of Equisetum hybrids.

Equisetum is a surprising case of an ancient and morphologically conservative plant genus, with many unusual characteristics and adaptations, that bas persevered across geological time and geographical and ecological space. These observations make a strong case for considering Equisetum "the most successful living genus of vascular plants" (Stanich et al., 2009 Rothwell, 1996 Bierhorst, 1971).

Acknowledgments I would like to thank the late Dr. Warren H. Wagner, Jr. for his encouragement to pursue studies of Equisetum. I also thank Dr. Jack Fisher for suggesting the development of this manuscript.

Published online: 15 January 2013

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-- 2002. Ecological strategies in fern evolution: a neopteridological overview. Review of Palaeobotany and Palynology 119:1-33.

Parrish, J. T. 1993. Climate of the supercontinent Pangea. The Journal of Geology. 101:215-233.

Pearson, L. C. 1995. The Diversity and Evolution of Plants. CRC Press. Boca Raton, Florida.

Parsons, W. T. & E. G. Cuthbertson. 1992. Noxious Weeds of Australia. Inkata Press, Melbourne, Australia.

Praeger, R. L. 1934. Propagation from aerial shoots in Equisetum. Journal of Botany, British and Foreign. 72:175-176.

Proctor, G. R. 1985. Ferns of Jamaica: a guide to the Pteridophytes. British Museuam of Natural History, London.

Pryer, K. M., H. Schneider, A. R. Smith, R. Cranfill, P. G. Wolf, J. S. Hunt & S. D. Sipes. 2001. Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 409:618-622.

Pulliainen, E. & S. Tunkkari. 1991. Responses by the capercaillie Tetrao urugallus, and the willow grouse Lagopus lagopus, to the green matter available in early spring. Holarctic Ecology 14:156-160.

Purdy, B. G., S. E. MacDonald & V. J. Lieffers. 2005. Naturally saline boreal communities as models for reclamation of saline oil sand tailings. Restoration Ecology 13: 667-677.

Qiu, Y. L., L. B. Li, B. Wang, Z. D. Chen, O. Dombrovska, J. Lee, L. Kent, R. Q. Li, R. W. Jobson, T. A. Hendry, D. W. Taylor, C. M. Testa & M. Ambros. 2007. A nonflowering land plant phylogeny inferred from nucleotide sequences of seven chloroplast, mitochondrial, and nuclear genes. International Journal of Plant Sciences. 168:691-708.

Quarles, W. 1995. The truth about horsetails or natural plant disease protection from silica. Common Sense Pest Control 11:18.

Raven, J. A. 2009. Horsetails get the wind up. New Phytologist 18: 6-9.

Read, D. J., J. G. Duckett, R. Francis, R. Ligrone & A. Russell. 2000. Symbiotic fungal associations in 'lower' land plants. Philosophical Transactions of the Royal Society of London B 355:815-831.

Reed, C. E 1971. Index to Equisetophyta: 2, Extantes, Index Equisetorum. Reed Herbarium, Baltimore, MD.

Revilla, C. R. 2002. Hypoglycemic effect of Equisetum myriochaetum aerial parts on type 2 diabetic patients. Journal of Ethnopharmacology 81 : 117-120.

Rincon, E. J., H. G. Forero, L. V. Gelvez, G. A. Torres & C. H. Rolleri. 2011. Ontogenia de lost estrobilos, desarrollo de los esporangios y esporogenesis de Equisetum giganteum (Equisetaceae) en los Andes de Colombia. Revista de Biologia Tropical 59: 1845-1858.

Rothwell, G. W. 1996. Pteridophytic evolution: an often underappreciated phytological success story. Review of Paleobotany and Palynology. 90: 209-222.

-- & K. C. Nixon. 2006. How does the inclusion of fossil data change our conclusions about the phylogenetic history of euphyllophytes? International Journal of Plant Sciences 167: 737-749.

Rutishauser, R. 1999. Polymerous leaf whorls in vascular plants: Developmental morphology and fuzziness of organ identities. International Journal of Plant Sciences 160(6 Suppl.): S81-S103.

Rutz, L. M. & D. R. Farrar. 1984. The habitat characteristics and abundance of Equisetum xferrissii and its parent species, Equisetum hyemale and Equisetum laevigatum, in Iowa. American Fern Journal. 74: 65-76.

Saint Paul, A. 1979. Seasonal variations in the contents of some mineral elements of Equisetum telmateia. Plantes Medicinales et Phytotherapie 13: 268-277.

Sakamaki, Y. & Y. Ino. 2006. Tubers and rhizome fragments as propagules: competence for vegetative reproduction in Equisetum arvense. Journal of Plant Research 119: 677-683.

Sapei, L., G. Notburga, J. Hartmann, R. Noske, P. Strauch & O. Paris. 2007. Structural and analytical studies of silica accumulations in Equisetum hyemale. Analytical and Bioanalytical Chemistry. 389: 1249-1257.

Sarvala, J. T., T. Kairesalo, I. Koskimies, A. Lehtovaara, J. Ruuhijarvi & I. Vaha-Piikkio. 1982. Carbon, phosphorus and nitrogen budgets of the littoral Equisetum belt in an oligotrophic lake. Hydrobiologia 86:41-53.

Scagel, R. F., R. J. Bondini, J. R. Maze, G. E. Rouse, W. B. Schofield & J. R. Stein. 1984. Plants, An Evolutionary Survey. Wadsworth Publishing Company, Belmont, CA.

Schaffner, J. H. 1924. Dichotomous branching in Equisetum. American Fera Journal 14: 56-57.

-- 1927. Spiral shoots of Equisetum. American Fern Journal 17: 43-46.

-- 1928. Fluctuation in Equisetum. American Fera Journal. 18:69-79.

-- 1930. Geographic distribution of the species of Equisetum in relation to their phylogeny. American Fera Journal. 20: 89-106.

--- 1931. Propagation of Equisetum from sterile aerial shoots. Bulletin of the Torrey Botanical Club 58: 531-535.

-- 1933. Six interesting characters of sporadic occurrence in Equisetum. American Fera Journal 23: 83-90.

-- 1938. Root hairs of Equisetum praealtum Raf. American Fera Journal 28: 122.

Seward, A. C. 1898. Fossil Plants: for Students of Botany and Geology. Cambridge University Press, Cambridge, UK.

Seward, A. C. 1959. Plant Life through the Ages, a Geological and Botanical Retrospect. Hafner, New York.

Siegel, S. M. 1968. Biochemistry of the plant cell wall. Pp. 1-51 in Comprehensive Biochemistry, Volume 26, M. Florkin & E. H. Stotz (eds.). Elsevier, Amsterdam.

Siegel, B. Z. & S. M. Siegel. 1982. Mercury content of Equisetum plants around Mount St. Helens one year after the major emption. Science 216: 292-293.

Siegel, S. M., B. Z. Siegel, C. Lipp, A. Kruckbeberg, G. H. N. Towers & H. Warren. 1985. Indicator plan--soil mercury patterns in a mercury-rich mining area of British Columbia. Water, Air, and Soil Pollution 25: 73-85.

Sorensen, I., F. A. Pettolino, S. M. Wilson, M. S. Doblin, B. Johansen, A. Bacic & W. G. T. Willats. 2008. Mixed-linkage (1 [right arrow] 3), (1 [right arrow] 4)-[beta]-D-glucan is hot unique to to Poales and is an abundant component of Equisetum arvense cell walls. The Plant Journal 54:510-521.

Spatz, H.-C., L. Kohler & T. Speck. 1998a. Biomechanics and functional anatomy of hollow-stemmed sphenopsids. I. Equisetum giganteum (Equisetaceae). American Journal of Botany 85:305-314.

--, N. Rowe, T. Speck & V. Daviero. 1998b. Biomechanics of hollow stemmed sphenopsids: II. Calamites: to have or hot to have secondary xylem. Review of Palaeobotany and Palynology 102: 63-77.

Speck, T., O. Speck, A. Emanns & H.-C. Spatz. 1998. Biomechanics and functional anatomy of hollow-stemmed sphenopsids: III. Equisetum hyemale. Botanica Acta 111 : 366-376.

Spruce, R. 1908. Notes of a Botanist on the Amazon & Andes. A. R. Wallace, editor. St. Martin's Press, London.

Srinivasan, J., P. Dayananandan & P. B. Kaufman. 1979. Silica distribution in Equisetum hyemale var affine in relation to the negative geotropic response. New Phytologist 83: 623-626.

Stanich, N. A., G. W. Rothweil & R. A. Stockey. 2009. Phylogenetic diversification of Equisetum (Equisetales) as inferred from Lower Cretaceous species of British Columbia, Canada. American Journal of Botany 96: 1289-1299.

Stewart, W. N. & G. W. Rothwell. 1993. Paleobotany and the evolution of plants. Cambridge University Press, Cambridge, England.

Stolze, R. G. 1983. Equisetaceae. Pages 16-20 in Feras and Fera Allies of Guatemala, Part III: Marsileaceae, Salviniaceae, and the Fern Allies. Field Museum of Natural History, Chicago.

Strand, V. V. 2002. The influence of ventilation systems on water depth penetration of emergent macrophytes. Freshwater Biology 47:1097-1105.

Stutzel, T. & A. Jadicke. 2000. Verzweigung bei Schachtelhalmen. Feddes Repertorium 111: 15-22.

Thomas, V. G. & J. P. Prevett. 1982. The role of horsetails (Equisetaceae) in the nutrition of northern-breeding geese. Oecologia 53: 359-363.

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Timell, T. E. 1964. Studies on some ancient plants. Svensk Papperstidning 67: 356-363.

Treitel, O. 1943. The elasticity, breaking stress, and breaking strain of the horizontal rhizomes of species of Equisetum. Transactions of the Kansas Academy of Science 46:122-132.

Tryon, A. F. 1959. Ferns of the Incas. American Fern Journal 49: 10-24.

Tryon, R. M. & A. F. Tryon. 1982. Feras and allied plants, with special reference to Tropical America. Springer Veflag, New York.

Tschudy, R. H. 1939. The significance of certain abnormalities in Equisetum. American Journal of Botany 26: 744-749.

Uchino, F., T. Hiyoshi & M. Yatazawa. 1984. Nitrogen-fixing activities associated with rhizomes and roots of Equisetum species. Soil Biology and Biochemistry 16:663-667.

Van der Hagen, H. G. J. M., L. H. W. T. Geelen & C. N. De Vries. 2008. Dune slack restoration in Dutch mainland coastal dunes. Journal for Nature Conservation 16:1-11.

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Wagner, W. H. & E. W. Hammitt. 1970. Natural proliferation of floating stems of scouring-rush, Equisetum hyemale. The Michigan Botanist 9:166-174.

Walker, E. R. 1931. The gametophytes of three species of Equisetum. Botanical Gazette 92:1-22.

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Calf-Fed Holstein Initiative


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Cattle Euthanasia

Grazing 101: Sustainable Pasture Management for Livestock

Online Courses

Beef Production and Management

Online Courses

Curriculum Links

We strive to make sure that all of our links are intact. If you find anything that seems to be missing or out of place, please let us know.

Grade 1

Language Arts

Lesson 31: phonics & reading activities
Phonics lesson plans at teAchnology
Word games at PBS Kids

Social Studies

Lesson 15: state maps
Blank outline state maps at
State maps and data at
Printable maps and state quizzes at

Lesson 36: appreciating diversity
“Helping Children Understand Other Cultures” at Ohio State University
“Appreciating Diversity” at A Place of Our Own


Lesson 5: animal tracking sites
Mammal Tracks at
Princeton University’s Outdoor Action Guide to Animal Tracking

Lesson 20: diurnal and nocturnal animals
Night vision page at Nova Online

Lesson 30: sounds in nature
Animal sounds at
Birdsong recordings at the Audubon Society
“Listening to Nature” at the California Library of Natural Sounds

Lesson 31: birds’ nests
Bird houses at
Bird Nests from Backyard Nature


Grade 2

Language Arts

Lesson 8: phonics & word study
Favorite Phonics Games, Apps, and Websites from Common Sense Education
Word games at Word Central

Social Studies


Lesson 30: the desert biome
Deserts at Blue Planet
The Desert Biome at the University of California, Berkeley
Biomes: Desert

Lesson 32: reptiles
Reptiles Magazine
Animals at the San Diego Zoo


Grade 3

Language Arts

Social Studies

Lesson 12: maps of the ancient world
Phoenician Time Map
Ancient World Maps
Historical Maps at the Perry-Castañeda Library Map Collection

Lesson 33: basis of government
“Join the Signers” at the National Archives
U.S. Electoral College


Lesson 23: ecological conservation
Ecology for Kids

Lesson 33: the freshwater biome
Freshwater Wetlands at the World Wildlife Fund
Aquatic Biomes

Lesson 35: classifying plants
Mosses at Backyard Nature

Lesson 36: extinct & endangered animals & plants
Endangered Species at the World Wildlife Fund


Grade 4

Language Arts

Social Studies

Lesson 1: Local topography very old tree
What is topography?

Lesson 11: Model of a traditional Native American village
Dwellings of Native Americans


Lesson 4: Similarities between forms in nature
Finding Geometry in Nature

Lesson 7: Chart experiment data compare seed growth
Types of Graphs

Music & Art

Lesson 4: Drawing from a close-up viewpoint
Drawing from near and far

Lesson 10: Foreshortened circles shading
Foreshortened circle

Lesson 13: Still life surface lines law of perspective
Observational drawing for kids

Grade 5


U.S. History


Lesson 4: Magnification as a scientific tool
Animal Cells
Plant Cells

Grade 6


Lesson 6: Direct and indirect quotations
Using Speech Marks

Ancient Civilizations


Grade 7 - English


Grade 7 - Science


Lesson 23: Winds and Atmospheric Pressure
Video: Bill Nye the Science Guy on Wind
Video: What Is Wind?
Video: Hot and Cold Water Science Experiment (imagine this happening to air—high pressure and low pressure systems—instead of water)
Video: Crush a Bottle with Air

Lesson 31: Human Population Growth
U.S. and World Population Clock
World Population Interactive Map (use the slider at the bottom to see population increases over time)
Video: Human Population Through Time

Grade 7 - World History

World History

Unit I: Age of Empires

Unit II: Renaissance and Enlightenment

Unit III: Revolution and Independence

Unit IV: Worldwide Change

Unit V: Global Conflict and Resolution

Unit VI: Modern Developments

Grade 8 - English


Grade 8 - Civics


Grade 8 - Physical Science

Physical Science

Lesson 1: Measurements and Quantitative Data
Scientific Argument

Lesson 2: Controlled Experiments and the Scientific Method
Video: Controlled Experiments
Video: Correlation and Causality

High School Courses

Advanced Mathematics

Oak Meadow Lesson 1 (Textbook Lessons 1 – 4)

Oak Meadow Lesson 2 (Textbook Lessons 5 – 8)

Oak Meadow Lesson 3 (Textbook Lessons 9-12)

Oak Meadow Lesson 4 (Textbook Lessons 13-16)

Oak Meadow Lesson 5 (Textbook Lessons 17-20)

Oak Meadow Lesson 6 (Textbook Lessons 21-24)

Oak Meadow Lesson 7 (Textbook Lessons 25-28)

Oak Meadow Lesson 8 (Textbook Lessons 29-32)

Oak Meadow Lesson 9 (Textbook Lesson 33-36)

Oak Meadow Lesson 10 (Textbook Lessons 37-40)

Oak Meadow Lesson 11 (Textbook Lessons 41-44)

Oak Meadow Lesson 12 (Textbook Lessons 45-48)

Oak Meadow Lesson 13 (Textbook Lessons 49-52)

50: Trigonometric Equations
Instructional Video: Solving Trig Equations *Ignore the +2n part of the solution for now

Oak Meadow Lesson 14 (Textbook Lessons 53-56)

Oak Meadow Lesson 15 (Textbook Lessons 57-60)

60: Factorable Trigonometric Equations, Loss of Solutions Caused by Division
Instructional Video: Factoring Trig Equations GCF

Oak Meadow Lesson 16 (Textbook Lessons 61-64)

Oak Meadow Lesson 17 (Textbook Lessons 65-68)

Oak Meadow Lesson 18 (Textbook Lessons 69-72)

Oak Meadow Lesson 19 (Textbook Lessons 73-76)

Oak Meadow Lesson 20 (Textbook Lessons 77-80)

Oak Meadow Lesson 21 (Textbook Lessons 81-84)

Oak Meadow Lesson 22 (Textbook Lessons 85-88)

Oak Meadow Lesson 23 (Textbook Lessons 89-92)

Oak Meadow Lesson 24 (Textbook Lessons 93-96)

96: More Double Angle Identities, Triangle Area Formula, Proof of the Law of Sines, Equal Angles Imply Proportional Sides
Instructional Video: Area of a Triangle Using Sine
Instructional Video: Proof of the Law of Sines

Oak Meadow Lesson 25 (Textbook Lessons 97-100)

Oak Meadow Lesson 26 (Textbook Lessons 101-104)

Oak Meadow Lesson 27 (Textbook Lessons 105-108)

Oak Meadow Lesson 28 (Textbook Lessons 109-112)

111: Logarithmic Inequalities: Base Greater Than 1, Logarithmic Inequalities: Base Less Than 1
Instructional Video: Log Inequalities Base Greater Than 1

Oak Meadow Lesson 29 (Textbook Lessons 113-116)

Oak Meadow Lesson 30 (Textbook Lessons 117-120)

Oak Meadow Lesson 31 (Textbook Lessons 121-125)


This weekly two-minute podcast from Science Underground has cool science facts.

Lesson 8
Short video: DNA structure and function. It’s a good overview of the big picture behind several lessons, including protein synthesis, mutations, and natural selection.
Video: Hershey and Chase’s work, including actual photos of viruses and bacteria. This is also applicable to lesson 19.

Lesson 10
New findings about the DNA of ancient humans in Europe. It answers some questions about human evolution, linking genetic research to evolution and nutrition.

Lesson 12
NPR News report: Challenging the assumption that life evolved in the ocean and then moved to land when the ozone layer formed, protecting land from UV radiation. It’s another example of how science keeps changing with every new discovery!
Possibility of life originating on Mars! When reading these articles, always check out the comments by readers, as some of them share intelligent thoughts. It is the seemingly outlandish research such as this that eventually builds up to a credible scientific case.
New species of ancient human, Homo naledi, discovered in South Africa, just announced to the world in September, 2015.

Lesson 26
Animal eye shape as related to their lifestyle. They even connect it to designing fictitious animals used in Hollywood movies!

Chemistry Matters

Foodways: Sustainable Food Systems

Forensic Science


Oak Meadow Lesson 1 (Textbook Lessons 1 – 10)

Oak Meadow Lesson 2 (Textbook Lessons 11-20)

Oak Meadow Lesson 3 (Textbook Lessons 21-30)

Oak Meadow Lesson 4 (Textbook Lessons 31-40)

Oak Meadow Lesson 5 (Textbook Lessons 41-50)

Oak Meadow Lesson 6 (Textbook Lessons 51-60)

Oak Meadow Lesson 7 (Textbook Lessons 61-70)

Oak Meadow Lesson 8 (Textbook Lessons 71-80)

Oak Meadow Lesson 9 (Textbook Lesson 81-90)

Oak Meadow Lesson 10 (Textbook Lessons 91-100)

Human Anatomy and Physiology

Math Connections

Lesson 1: Problem Solving and Critical Thinking

For help and extra practice with the concepts in this chapter:

For fun and deeper exploration:

How to Solve It by George Polya

Logic puzzles and riddles

Real problem-solving in the news

For help and extra practice with the concepts in this chapter:

For fun and deeper exploration:

Games involving set theory:

SET, a fun and educational card game, is also available online and as an app

Lesson 3: Number Theory and the Real Number System

For help and extra practice with the concepts in this chapter:

For additional inspiration for the Fibonacci Inspiration activity, check out these videos:
Vi Hart’s Spirals, Fibonacci and being a plant video series (3 parts)
Arthur Benjamin’s TED Talk

For fun and deeper exploration:

Prime and composite numbers game
Learn how Eratosthenes calculated the circumference of the Earth in Khan Academy’s article
Learn more about that famous number, pi: To see what a million digits of pi really looks like, check out Numberphile’s “A Mile of Pi” video
To hear a tonal representation of the digits of pi, check out Numberphile’s “Sounds of Pi” video
To see artistic data visualizations of the digits of pi, check out Numberphile’s “Pi is Beautiful” video

Lesson 4: Algebra: Equations and Inequalities

For help and extra practice with the concepts in this chapter:

For fun and deeper exploration:

For additional discussion to help you explore whether you believe mathematics was invented or discovered, check out PBS Idea Channel’s “Is Math a Feature of the Universe or a Feature of Human Creation?”

Lesson 5: Algebra: Graphs, Functions, Linear Functions, and Linear Systems

Line of Best Fit tool on the NCTM Illuminations website

For help and extra practice with the concepts in this chapter:

For fun and deeper exploration:

Now that you know a bit about correlation, it’s important to understand that correlation does not imply causation. In other words, just because two variables are related does not mean that one of the variables caused the other. This is a common logical fallacy that leads to invalid conclusions. Check out this Los Angeles Times article that makes the point that correlation does not imply causation . Then to drive the point home, visit the site that inspired the article, Spurious Correlations, to view a variety of amusing graphs showing two completely unrelated variables that just happen to be closely correlated.

Lesson 6: Polynomials, Quadratic Equations, and Quadratic Functions

For help and extra practice with the concepts in this chapter:

For fun and deeper exploration:

More on the legend of Newton and the falling apple
Additional Vi Hart videos (part 2 and part 3 of the “Doodling” series)

Lesson 7: Personal Finance: Taxes and Interest

For help and extra practice with the concepts in this chapter:

For fun and deeper exploration:

Lesson 8: Personal Finance: Saving, Investing, and Spending

For help and extra practice with the concepts in this chapter:

For fun and deeper exploration:

For fun and deeper exploration:

Math is Fun Reflectional Symmetry page
Math is Fun Rotational Symmetry page
Dr. James Tanton’s “Generating Pythagorean Triples” video
Escher Gallery
Tessellation Creator tool at the National Council of Teachers of Mathematics’ Illuminations site
Platonic Solids tool from the National Council of Teachers of Mathematics’ Illuminations site
Platonic Solids Models from Math is Fun

For help and extra practice with the concepts in this chapter:

For fun and deeper exploration:

If you enjoyed the Platonic Solids activity, explore the duals of the Platonic Solids with these videos
For more on tessellations, visit here, or try this app

Lesson 11: Counting Methods and Probability Theory

For help and extra practice with the concepts in this chapter:

Watch video explanations and try practice problems with the Khan Academy Probability and Combinatorics lessons
Practice figuring out which counting method to use and try your hand at some problems with the Counting Methods Review and Self-Test

For fun and deeper exploration:

Try challenging counting methods problems at
Try challenging probability problems at
Play some probability games here and here
Learn about the origins of Probability as discovered by Blaise Pascal and Pierre de Fermat in solving the Problem of Points

For help and extra practice with the concepts in this chapter:

Videos on descriptive statistics, including the mean, median, mode, range, quartiles, and standard deviation
Explanations of the Normal Distribution and z-scores

For fun and deeper exploration:

Hans Rosling about world statistics, watch his 2014 TED talk, “How Not to Be Ignorant About the World.”
“Improving Human Welfare in 2013 International Year of Statistics,” presented by

For help and extra practice with the concepts in this chapter:

Math Goodies has a list of articles explaining various topics in symbolic logic from this chapter
Truth tables video explanation by ProfessorSerna
Activity A help: Additional worked example of a Lewis Carroll logic puzzle, as well as more challenging puzzles
Activity B help: Khan Academy logic videos and exercises. The validity and fallacy videos, in particular, may be helpful.

For fun and deeper exploration:

Lewis Carroll’s Paradox
Lewis Carroll’s book, Symbolic Logic (full text available online through Project Gutenberg)
The books The Mathematical Recreations of Lewis Carroll: Pillow Problems and a Tangled Tale by Lewis Carroll and C. L. Dodgson and Lewis Carroll’s Games and Puzzles by Lewis Carroll and Edward WakelingBrain teasers and puzzles has several fantastic pages with brain teasers and logic puzzles. The river crossing puzzles tend to be a student favorite. Try this and this to start, but be sure to explore some of the other pages. Answers are hidden until you click them. Don’t peek until you are sure you are ready to know the answer!
Challenge puzzles and problems: has a section with questions for all levels of logic. Quiz yourself on topics ranging from symbolic logic to games of strategy.

Grid-based logic puzzles:
Solve grid-based logic puzzles online or on an app
Learn about Euler’s Konigsberg Bridges Problem
An interview with Andrew Wiles, the mathematician who finally solved Fermat’s Last Theorem in 1993.

Watch the video: Εισαγωγή στην (February 2023).