Identification for a bird in the middle of the tree

Identification for a bird in the middle of the tree

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In the central city of Dobrich Bulgaria, I was following a Great spotted woodpecker in a tree and suddenly I found this other bird on the same tree.

The context of the picture is:

  • Country: Bulgaria
  • City: Dobrich, Center urban area
  • Period: mid August (2016)

I think this is a specimen ofSilvia Curruca, can anybody confirm this?

Yes, Lesser whitethroat indeed. Grey head with contrasting white throat and brown body, small bill (the similar Orphean warbler has a much bigger bill).

Using Tree Anatomy and Physiology for Identification

Trees are among the earth's most useful and beautiful products of nature. Trees have been crucial to mankind's survival. The oxygen we breath is released by trees and other plants trees prevent erosion trees provide food, shelter, and material for animals and man.

Worldwide, the number of tree species may exceed 50,000. With this said, I would like to point you in a direction that will help you identify and name the 100 most common of 700 tree species that are native to North America. A bit ambitious, maybe, but this is one small step toward using the Internet to learn about trees and their names.

Oh, and you just might want to consider making a leaf collection as you study this identification guide. A leaf collection will become a permanent field guide to trees you have identified. Learn How To Make a Tree Leaf Collection and use it as your personal reference for future identifications.

What is a tree?

Let's start with the definition of a tree. A tree is a woody plant with a single erect perennial trunk at least 3 inches in diameter at breast height (DBH). Most trees have definitely formed crowns of foliage and attains heights in excess of 13 feet. In contrast, a shrub is a small, low growing woody plant with multiple stems. A vine is a woody plant that depends on an erect substrate to grow on.

Just knowing a plant is a tree, as opposed to a vine or a shrub, is the first step in it's identification.

Identification is really quite simple if you use these next three "helps":

Tips: Collecting a branch and/or leaf and/or fruit will help you in the next discussions. If you are really industrious, you need to make a collection of wax paper leaf pressings. Here is How to Make a Wax Paper Leaf Pressing.

If you have a common leaf but don't know the tree - use this Tree Finder!

If you have a common leaf with an average silhouette - use this Leaf Silhouette Image Gallery!

If you don't have a leaf and don't know the tree - use this dormant Winter Tree Finder!

Using Tree Parts and Natural Ranges for Species Identification

Help #1 - Find out what your tree and its parts look like.

Tree botanical parts like leaves , flowers , bark , twigs , shape , and fruit are all used to identify tree species. These "markers" are unique - and in combination - can make quick work of identifying a tree. Colors, textures, smells, and even taste will also help in finding the name of a particular tree. You will find reference to all of these identification markers in the links I have provided. You might also want to use my Tree ID Glossary for terms used to describe the markers.

Help #2 - Find out if your tree will or won't grow in a particular area.

Tree species are not distributed at random but are associated with unique habitats. This is another way to help you discern a tree's name. You can possibly (but not always) eliminate trees that don't normally live wild in the forest where your tree lives. There are unique timber types located throughout North America.

The northern coniferous forests of spruces and firs extend across Canada and into the northeastern United States and down the Appalachian Mountains. You will find unique hardwood species in the eastern deciduous forests , pine in the forests of the South, Tamarack in the bogs of Canada, the Jack pine in the Great Lakes region , the Doug Fir of the Pacific Northwest , the Ponderosa Pine forests of the southern Rockies.

Many sources of identification use a key. A dichotomous key is a tool that allows the user to determine the identity of items in the natural world, such as trees, wildflowers, mammals, reptiles, rocks, and fish. Keys consist of a series of choices that lead the user to the correct name of a given item. "Dichotomous" means "divided into two parts". Therefore, dichotomous keys always give two choices in each step.
My Tree Finder is a leaf key. Find yourself a tree, collect or photograph a leaf or needle and use this simple "key" style finder to identify the tree. This tree finder is designed to help you identify most common North American trees at least to the genus level. I am confident you can also select the exact species with the links provided and a little research.

Here is another great tree key you can use from Virginia Tech: A Twig Key - used during tree dormancy when leaves are not available.

Online Tree Identification

You now have real information to help identify and name nearly any tree in North America. The problem is finding a specific source describing a specific tree.

The good news is that I have found sites that help in identifying specific trees. Review these sites for more information on tree identification. If you have a particular tree that needs a name, start right here:

A Tree Leaf Key
An identification field guide that helps you quickly and easily identify 50 major conifers and hardwoods using their leaves.

Top 100 North American Trees
A heavily linked guide to conifers and hardwoods.

Biologists Find Evidence of Migration Gene in Birds

Millions of migratory birds occupy seasonally favorable breeding grounds in the Arctic, but scientists know little about the formation, maintenance and future of the migration routes of Arctic birds and the genetic determinants of migratory distance. In new research, a multinational team of researchers established a continental-scale migration system that used satellite tracking to follow 56 peregrine falcons (Falco peregrinus) from six populations that breed in the Eurasian Arctic, and sequenced the genomes of 35 birds from four of these populations. They found that a gene called ADCY8 is associated with population-level differences in migratory distance.

Tagged peregrine falcon (Falco peregrinus). Image credit: Andrew Dixon.

“Previous studies have identified several candidate genomic regions that may regulate migration — but our work is the strongest demonstration of a specific gene associated with migratory behavior yet identified,” said co-author Professor Mike Bruford, a molecular ecologist in the School of Biosciences at Cardiff University.

For the study, Professor Bruford and colleagues tagged 56 Arctic peregrine falcons and tracked their journeys by satellite, following their annual flight distances and directions in detail.

“Peregrines initiated their autumn migration mainly in September, traveled 2,280-11,002 km in about 27 days and arrived at their wintering areas mainly in October,” they said.

“Peregrines migrate solitarily birds that depart from different breeding grounds use different routes, and winter at widely distributed sites across four distinct regions.”

“Individual birds that were tracked for more than one year exhibited strong path repeatability during migration, complete fidelity to wintering locations and limited breeding dispersal (5.37 km on average).”

“All populations demonstrated a high degree of migratory connectivity, which suggests strong selection for long-term memory.”

Five migration routes for 56 peregrine falcons tracked by satellite. Image credit: Gu et al., doi: 10.1038/s41586-021-03265-0.

The scientists found that the birds used five migration routes across Eurasia, probably established between the last Ice Age 22,000 years ago and the middle-Holocene 6,000 years ago.

They used whole genome sequencing and found a gene — ADCY8, which is known to be involved in long-term memory in other animals — associated with differences in migratory distance.

They found ADCY8 had a variant at high frequency in long-distance (eastern) migrant populations of peregrines, indicating this variant is being preferentially selected because it may increase powers of long-term memory thought to be essential for long-distance migration.

“Our work is the first to begin to understand the way ecological and evolutionary factors may interact in migratory birds,” said senior author Professor Xiangjiang Zhan, a researcher in the Institute of Zoology at the Chinese Academy of Sciences.

“We hope it will serve as a cornerstone to help conserve migratory species in the world.”

The authors looked at simulations of likely future migration behavior to predict the impact of global warming.

If the climate warms at the same rate it has in recent decades, they predict peregrine populations in western Eurasia have the highest probability of population decline and may stop migrating altogether.

“In this study, we were able to combine animal movement and genomic data to identify that climate change has a major role in the formation and maintenance of migration patterns of peregrines,” Professor Bruford said.

The results were published in the journal Nature.

Z. Gu et al. Climate-driven flyway changes and memory-based long-distance migration. Nature, published online March 3, 2021 doi: 10.1038/s41586-021-03265-0

Is it unusual to see American Robins in the middle of winter?

We do get a lot of questions from people surprised by seeing American Robins in winter. But although some American Robins do migrate, many remain in the same place year-round. Over the past 10 years, robins have been reported in January in every U.S. state, except Hawaii, (see map) and in all of the southern provinces of Canada.

As with many birds, the wintering range of American Robins is affected by weather and natural food supply, but as long as food is available, these birds are able to do well for themselves by staying up north.

One reason why they seem to disappear every winter is that their behavior changes. In winter robins form nomadic flocks, which can consist of hundreds to thousands of birds. Usually these flocks appear where there are plentiful fruits on trees and shrubs, such as crabapples, hawthorns, holly, juniper, and others.

When spring rolls around, these flocks split up. Suddenly we start seeing American Robins yanking worms out of our yards again, and it’s easy to assume they’ve “returned” from migration. But what we’re seeing is the switch from being nonterritorial in the winter time to aggressively defending a territory in advance of courting and raising chicks. This behavioral switch is quite common in birds.

You can report your robin sightings (and any other birds you see) at eBird. Read more about American Robins in our All About Birds Species guide.

Which Bird Made That Nest?

The diversity of behavior among bird species is nowhere so dramatic as in their nest construction. Each species builds a specifically precise nest that differs in functional ways from those of almost all others. The variations are as endlessly diverse as the color patterns on a feather. Chimney swifts use their saliva to glue dry twigs onto vertical walls in a chimney cavity or hollow tree. A masked weaver bird&rsquos nest is a finely woven bag with a long, vertical entrance tunnel that is hung from the tip of a thin branch, whereas a sociable weaver builds a communal structure that may weigh a ton. An eagle&rsquos massive structure of branches can support a large man, while a plover merely scratches a few pebbles together on a sandbar. Owls never build anything at all but use others&rsquo nests or nest holes. A murre lays its single egg on a sea ledge, and a fairy tern &ldquonest&rdquo is a bare fork on a tree limb.

While some northern woodland birds build their nests on the ground, many nest in trees. One of the pleasures to be had in the winter months is seeing these nests that had been hidden by summer foliage. When leaves drop, nests are revealed full of snow, they seem to glow against stark tree limbs. The nest owners are no longer around, making positive identification difficult, but many of these nests can be identified if you match them to geographical area, habitat, and other aspects of nest location.

Below are descriptions of some of the more common nests likely to be found and identified in the winter woods. You may not find them all in one winter, but this &ldquofield guide&rdquo should provide you with the basis for a continuing adventure.

Robin, Turdus migratorius: A robin&rsquos nest is both universally familiar and frequently misidentified. Nests are built at any height but generally in a protected place, such as inside a barn or where a thick limb forks. The giveaway clue is a mud cup about 3 inches across that in the summer is lined with a thin layer of fine grass. The exterior of the nest is a rough jumble of twigs, leaves, and pieces of bark. Nests exposed to the weather will usually dissolve and collapse by spring nests under cover can persist for years.

Red-eyed vireo, Vireo olivaceus: Red-eyed vireos build their nests at any height, but always in a deciduous tree. Their nests can be found in both forest and edge habitat. The nest is always a hanging cup suspended along its edges from a thin, horizontal, forked branch. It is a neat, tidy, compact structure that will have bits of birch bark, and usually also wasp paper, decorating the outside. The inside cup diameter of a vireo nest is 2 inches.

Baltimore oriole, Icterus galbula: Oriole nests are baglike nests woven out of fibers, most commonly those stripped from old, decaying milkweed plants. Nests are almost always high in deciduous trees and at the tips of branches, not in deep forest.

Chectnut-sided warbler, Dendroica pensylvanica: Chestnut-sided warblers nest in open, edge habitat and also close to the ground, in small shrubs and bushes. This nest, with its very light and flimsy appearance, is made almost entirely of very fine grasses.

Cedar waxwing, Bombycilla cedrorum:Cedar waxwings nest in small evergreens or deciduous trees in edge habitat. The nest cup is untidy on the outside like a robin&rsquos and of similar size, but it lacks the mud cup and is typically garnished on the outside with lichens and/or moss.

American goldfinch, Carduelis tristis: American goldfinches make solid and tidy cup nests out of plant fibers and line them with thistle down. Nests are usually found out on a branch of a deciduous tree in fairly open habitat, such as a bog, edge of field, or suburban area. The nest is built with its base on the branch, not suspended like that of the vireo. Droppings are a dead giveaway (although they may be washed off by late winter), since goldfinches are the only local open-nesting songbird that allows feces to accumulate on the nest edge.

Least flycatcher, Empidonax minimus: A narrow (1.5 inches across) but deep nest cup placed into a thick, vertical fork so as to be almost hidden by it. Nests are found in deep edge habitat.

Red-winged blackbird, Agelaius phoeniceus: Red-winged blackbird nests could be confused with catbird nests, except that they&rsquore found in relatively open marshland. Nests are often built into a tuft of grass, or in a bush, or in cattails within a foot of the ground or water. Common grackles may nest in the same sites (but also in many others). Grackle nests can be distinguished from those of red-winged blackbirds by their larger (inside diameter about 3.5 inches), more compacted nest cup.

Scarlet tanager, Piranga olivacea: Unlike the other nests in this story, scarlet tanager nests are composed almost entirely of twigs. Nests have an interior nest cup 3 inches across and feature a thin lining of rootlets. They are almost see-through in the winter. They can be distinguished from the similar-looking nest of the rose-breasted grosbeak by their location: tanagers nest high in forest trees, whereas grosbeaks tend to nest in young bushy trees. Mourning dove nests have a similarly flimsy structure but no visible cup. Most mourning dove nests are blown away before winter arrives.

Red-breasted nuthatch, Sitta canadensis: Chickadees, nuthatches, and woodpeckers nest in holes in trees, and the nests of these species can be differentiated, to some extent, by the size of the hole. A pileated woodpecker nest hole is 4 inches in diameter, a hairy woodpecker&rsquos is 2 inches, a sapsucker&rsquos is 1.5 inches, a chickadee&rsquos is 1 inch (in those cases where it makes its own nest hole), and a red-breasted nuthatch&rsquos, like the one pictured here, is also 1 inch. The holes are almost perfectly round.

Red-breasted nuthatches build substantial nests of moss, down, and fibers in their nest cavities, whereas woodpeckers never put in any nest material. When abandoned, tree-hole nests can be recycled by any of a variety of birds or by other tenants. Note the diagnostic globs of pitch brought to the nest to plaster at and below the entrance to the hole this pitch probably functions to restrict predator access. The tree in this photograph is a dead red maple.

Winter wren, Troglodytes troglodytes: All wren nests are domed, with a small entrance hole at the side. Those of the winter wren are most commonly garnished on the outside with green moss and small spruce or fir twigs. Although the wrens may place their nest under a stream bank, in hanging moss close to the ground, or in a small, densely branched tree, they are most commonly found in root tip-ups of wind-blown trees.

Ruby-throated hummingbird, Archilochus colubris: Ruby-throated hummingbirds garnish their walnut-sized nests with lichens to &ldquomimic&rdquo bumps on limbs. Nests are lined with soft white plant down. The only nest that is similar in habitat, placement, and appearance, though it is substantially larger, is that of the wood peewee.

Bernd Heinrich is professor emeritus of biology at the University of Vermont. His book Nesting Season is scheduled for publication in March 2010.

Bird Nest Photos & Illustrations Photo Gallery

© 2009 by the author this article may not be copied or reproduced without the author's consent.


This is a very well thought-out article. I’m doing some research on birds for a Cub Scout project. I found some info in here that will help as I work up an outdoor adventure for the boys! :-)

Thanks, and good luck with your book.

When cleaning out my Purple Martin gourds I found a straw nest that was completely round with an opening in one side. What bird makes a nest like this?

I found a nest like a robin’s, however it was mud lined. What bird makes such a nest?

I saw a couple of huge nests here in upstate NY and would love to know what kind of bird built them. They were on top of a powerline and they look to be about 3 feet wide. One of the nests had babies in it, that were not really babies at all, cause they were huge. The bird looks to be mostly black, or dark in color, with a white breast. Can anyone help me identify these amazing birds.

I believe you saw an osprey’s nest. Osprey often nest on powerline platforms. They are large, fish-eating raptors, so their nests are usually not too far from water (sometimes they build their large nests on piers or bridges in/over water)—and they have large babies! See this site for more information on osprey, and photos of their powerline nesting sites:

Thanks for writing!

Yesterday in Lindsborg, KS I saw a shallow-cupped nest. The whole nest was on the flattish side. It was made entirely of cedar bark and was underneath a large red cedar. Any ideas on the bird who made that nest?

We have lived in our house for 10 years. This year (in April) we noticed a very large nest about half way up a tall pine tree. It appears to be about three feet across, and made out of sticks. We don’t have any large body of water in the immediate area. We do feed birds, but the biggest one we’ve seen is an occasional crow. We do live out of town, in a semi-rural setting. What type of bird would build such a large nest? Someone suggested it may be a squirrel’s nest, but it is not made of leaves.

I have two small birds that came last year and are back this year. I have a hanging bird house on my porch and they took up in it last year. They are small and really make a loud sound, like they are calling or talking to each other. They make their out of sticks. Any idea what kind of bird this is

Do blackbirds nest in cedar trees?

My birdhouse is filled with small dead twigs about 4” to 6” long. Does anyone know who would have put them in? A chickadee nested in it first and most of her nest was taken out and all these sticks put in.

I’ve noticed a small triangle/beehive looking bird nest in several places around DC. The nest is gray in color, appears to be made of paper/mud about the size of a melon with a small opening on the side. It hangs from a single branch with the pointy end toward the ground. Any ideals? I thought it was a wasp nest or beehive, but there are so many of them and I haven’t seen any insects flying around.

My birdhouse is filled with small dead twigs about 4” to 6” long. Does anyone know who would have put them in? We see swallows around the area, these birdhouses are specific for blue birds.

Evelyn, that sounds like a house sparrow nest. These non-native invasives are vicious predators that kill native birds like bluebirds. They pecked a phoebe to death in one of my boxes. They will sometimes create dummy nests of sticks to keep other birds from using nest boxes that they themselves are not using.

In our yard beneath a small maple I found a small nest (less than 4” across, shallow, less than 2” from top to bottom) made entirely of thistle down. What made this nest?

I found a fairly good sized nest under the hood of my propane tank with 5 blue eggs in it today. The nest is made of straw and feathers. Do you have any idea what it might be?

A nest the size of a regular orange with the hole the size of nickel in the side. There is a bird flying in and out but too small to see. The pictures here are too big . This nest is all enclosed. Thank you

I saw a few nests on a mango tree in Bhopal India.The leaves of a branch were almost moulded together with cobwebs & they were big & oblong.Which birds nest could that be?

The 3 foot nest is probably Osprey. I’ve seen them nesting in Colorado. My question is what bird lays white speckled eggs smaller than a dime in an enclosed nest shaped like a football with no hole. I found one dropped at a park with 5 eggs.

Anyone know what bird uses cedar bark to build a nest other then the Golden-cheeked warbler? I found an old bird nest in my yard made of cedar bark.

I don’t know a lot about birds, but I found a lovely straw cup shaped nest in a thorny bush 4 or 5 feet up. It had 5 blue speckled/mottled eggs in it. I was pruning the bush back, and I got to one or two feet from the nest before I saw it. A bird nearby had been squawking away, and stopped as soon as I left. Am I a home wrecker? Will the mama bird go back?

This is a very informative article. Makes it simpler to find out the bird from its nest. Check out these amazing bird nests made in the strangest places.

Is there a bird other than a Robin that makes a rounded nest with blue eggs? A bird nearby resembled a lark.

I put pieces of yarn out last spring, and was not sure if it had been used in any bird nests, but this spring when pruning my gardenia shrub, I found a nest made of coir strands (probably pulled out from my hanging baskets), with pieces of the yarn interwoven, and some of it actually “glued” on. What species of bird builds a nest like this?

We have a bird house that something has made a mud nest inside with only a small passage to get in or out unless it can sweeze in under the bird house eves. Any ideas what this is?

I see a mud nest about six inches high near a creek water flow area near a grass field in country type setting. Is that a red winged blackbird nest or robin or walking type bird nest? Or is it for snakes because it is dug in ground about 1 1/2 inches wide?

My friend found a neatly made nest of fine roots in a blue bird box. It is not a bluebird nest, nor a chickadee or titmouse. Any ideas who would make a nest of roots in a bird box?

January 2017, I have a nest about the size of a small soccer ball, but the shape of a hot air balloon, high in a tree at the at the tip end of a thin branch. Our home is on a lake in a forested area. The outside seems somewhat smooth, no sticks poking out. I have not seen a bird near it yet.

Kerri that birdhouse with the mud and small opening is probably bees or wasps. I had one two years ago on my porch and I couldn’t paint my porch because they kept chasing me away. So be careful. They got me more than once.

This nest was beautifully constructed in the middle of a hanging flower arrangement outside of our porch. The nest is tight. I swear if it fell in a pond it would float for days. The eggs (6) are a half inch in length, colour is light to medium shade of blue with a few tiny black spots on the ends. Nobody has seen the mother yet though she scared me one night after dark when I went to water the plant. This was before I knew the nest was there. Anyway the chicks are beginning to hatch this morning I’d like to know what species of bird we are raising.

I have found a tree with three or four nesting cavities only 3 or 4 feet off the ground. They are similar in size it pileated woodpecker cavities. Would the make cavities so close to the ground?

Remember not to take nests from the wild it is always best to leave them where they are, even if you think they re not being used.

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These results have implications for patterns of species diversification and the interpretation of timetrees. If adaptation is largely decoupled from speciation, we should not expect it to be a driver of speciation as is frequently assumed. Also, we should not expect to see major diversification rate increases following mass extinction events, even though large adaptive changes took place at those times. That expectation is realized in our analyses ( fig. 4) where we see constant splitting through time across the two major Phanerozoic extinction events (251 and 66 Ma). Likewise, our diversification analyses of smaller groups, such as birds and mammals ( supplementary fig. S4 , Supplementary Material online), and past studies of those groups ( Bininda-Emonds et al. 2007 Meredith et al. 2011 Jetz et al. 2012) have not found rate increases immediately following the end-Cretaceous mass extinction event (66 Ma). Rate decreases from the extinction events themselves are not expected because of the inability to detect, in trees, a large proportion of species extinctions that occurred ( Nee and May 1997).

The consistency in TTS among groups found here suggests that the time-based acquisition of GIs, and not adaptive change, is driving reproductive isolation, almost in a neutral process. By implication, geographically isolated populations, even if morphologically different and diagnosable, are not expected to be species until they have reached the point of no return. This is because some differentiation and adaptive change should occur in isolation, and many isolates will be ephemeral ( Rosenblum et al. 2012), merging with other isolates or disappearing and never becoming species that enter the tree of life. More population data are needed before it is possible to identify the point of no return with precision. Nonetheless, these data suggest that, in most cases, described species separated by only tens of thousands of years are not real species. The Linnaean rank of subspecies, which has declined in use for decades, might be appropriate for such diagnosable isolates that have not yet reached the point of no return. Oversplitting of species by taxonomists may explain the sharp peak in diversification (hyper-expansion) in the last 10 My of eukaryote history ( fig. 4b). On the other hand, it could also result from statistical (small sample) artifacts that were published in many different studies (summarized in the TTOL). Therefore, further analysis of that unusual rate spike is warranted.

In summary, the diversification of life as a whole is expanding at a constant rate and only in some small clades (<500 species) is there evidence of decline or saturation in diversification rate. We believe these results can be explained as many different groups of organisms undergoing expansion and contraction through time, with those patterns captured in different stages (expanding, slowing, or in equilibrium). If true, the predominant pattern of expansion in large clades is expected from the law of large numbers, where such smaller, random events would average to a constant rate. Constant expansion also follows from random environmental changes leading to isolation and speciation. Rate constancy is consistent with the fossil record ( Benton 2009) and does not deny the importance of biotic factors in evolution ( Ricklefs 2007), but it suggests an uncoupling of speciation and adaptation. Cases where the phenotype has changed little (e.g., cryptic species) or greatly during the TTS are interpreted here as evidence of uncoupling. The lineage splitting seen in trees probably reflects, in most instances, random environmental events leading to isolation of populations, and potentially many in a short time. However, the relatively long TTS (∼2 My), a process resulting from random genetic events, will limit the number of isolates that eventually become species. Under this model, diversification is the product of those two random processes, abiotic and genetic, and rate increases (bursts of speciation) are more likely to be associated with long-term changes in the physical environment (e.g., climate, sea level) causing extended isolation rather than with short-term ecological interactions. However, reductions in extinction rate could also explain increases in diversification rate. Adaptive change that characterizes the phenotypic diversity of life would appear to be a separate process from speciation. Although a full understanding of these processes remains a challenge, determining how speciation and adaptation are temporally related would be an important “next step.”

Departed Birds as Spirit Guides

You might see in a dream or vision an image of a bird with which you've shared a bond but has since flown out of your life. God could be delivering a message to you through the bird as a spirit guide.

Arin Murphy-Hiscock writes in "Birds: A Spiritual Field Guide" that relationships with birds can be rewarding in connecting you to the natural world and helping you gain insights into your soul.

People who were close to you before they died may send you comforting messages through bird spirit guides, writes Andrea Wansbury in "Birds: Divine Messengers," "People in spirit use many means to let us know they are fine, and sending the message via the bird kingdom is just one way."

Familiar Cavity-Nesting Birds

Many birds will easily nest in cavities, and many bird families have at least a few members who are cavity nesters. Familiar examples include many woodpeckers, chickadees, parrots, nuthatches, trogons, flycatchers, wrens and bluebirds. Some ducks, such as the mandarin duck and wood duck, nest in cavities, as do some of the smaller raptors and owls. The American kestrel, barn owl, purple martin, great tit, and European robin are all common cavity-nesters.


Phylogenetic results

Our phylogenomic dataset provides strong support for the phylogenetic position of turtles as a sister group to Archosauria within Amniota based on concatenation analyses (Figure 1). All of our Bayesian and ML analyses of the concatenated amino-acid dataset recovered this topology with maximal ML bootstrap support (BP) and Bayesian posterior probabilities (PP) irrespective of the model used (BPML = 100 BPPARTG = 100 PPBAY = 1.0 PPCAT = 1.0) (Figure 1a Table 1). The same result was obtained from analyses of the complete nucleotide dataset with ML and Bayesian analyses when a mixed model partitioned by codon was applied (BPPARTC = 100 PPPARTC = 1.0), and in Bayesian analyses conducted under the site-heterogeneous CAT-GTR + G4 mixture model (PPCAT = 1.0) (Figure 1b Table 1). Conversely, ML and Bayesian phylogenetic reconstructions from the complete nucleotide dataset using a single site-homogeneous GTR + G model for the whole concatenation (BPML = 76 PPBAY = 1.0), and a mixed model partitioned by gene (BPPARTG = 54) tended to support an alternative topology grouping turtles with crocodilians (Table 1).

Phylogenetic relationships of amniotes as inferred from analyses of the 248-gene dataset. (a) Bayesian consensus topology obtained from analyses of the amino-acid dataset (62,342 sites) under the CAT-GTR + G4 mixture model. (b) Bayesian consensus topology obtained from analyses of the complete nucleotide dataset (187,026 sites) under the CAT-GTR + G4 mixture model. The nodal values indicate the clade Bayesian posterior probability (PP). Statistical support values obtained with different methods, models and data partitions detailed in Table 1 are reported in boxes for turtles plus archosaurs. Note the relative incongruence between the two trees concerning the position of Python. All pictures are from Wikimedia Commons, except for Chelonoidis from Y. Chiari. Please note also that the taxonomy of Galapagos turtles being currently revised, the appropriate species name for the Chelonoidis specimen included here might be Chelonoidis sp.

Likelihood-based comparisons of partitioned models based on the Akaike information criterion (AIC) showed that partitioning by codon position using the GTR + G model was by far the best partition scheme (AICCONCAT = 2,109,010 AICByGene = 2,082,688 AICByCodon = 2,008,142). The fact that only the suboptimal and poorly fitting models supported a turtles + crocodilians relationship suggests that this topology is a phylogenetic reconstruction artefact, most likely the result of the inability of these models to account efficiently for site-specific heterogeneities in the substitution process. The better fit offered by the codon position partition scheme over the gene partition scheme indicates that the main source of heterogeneity lies in the codon positions, most probably because of multiple substitutions accumulating at third codon positions.

Comparisons of ML-based saturation plots [34] between the amino-acid and the complete nucleotide datasets (Figure 2a) did not reveal clear evidence for global substitutional saturation of the complete nucleotide dataset relative to the amino-acid dataset, despite a slightly lower slope (0.36 versus 0.50, respectively). However, as expected in protein-coding genes conserved at this level of divergence, substitutional saturation was particularly pronounced at the third codon positions (Figure 2b). In cases in which the substitutional saturation of third codon positions was particularly high, excluding this third codon position partition from the dataset would be expected to result in less biased phylogenetic reconstructions. In agreement with this prediction, all ML and Bayesian reconstructions performed on the nucleotide dataset after exclusion of third codon positions provide unambiguous support (BPML = 100 PPBAY = 1.0 PPCAT = 1.0) for regrouping turtles and archosaurs (Table 1). Conversely, ML and Bayesian analyses of concatenated third codon positions using a single GTR + G model returned maximal support (BPML = 100 PPBAY = 1.0) for the topology clustering turtles with crocodilians (Table 1). Only the CAT-GTR + G4 mixture model seemed to be able to deal efficiently with the saturated third codon positions dataset by strongly supporting the turtles + archosaurs clade (PPCAT = 1.0). These analyses indicate that substitutional saturation at third codon positions is so strong in this phylogenomic dataset that it is able to impede phylogenetic reconstruction when inappropriate models of sequence evolution are used.

Analyses of substitution saturation at each codon position. Maximum likelihood saturation plots [34] were compared (a) between the complete amino-acid and nucleotide datasets, and (b) between the codon positions of the complete nucleotide dataset. The observed pairwise distances between the 16 taxa were directly computed from sequence alignments, and the corresponding inferred pairwise tree distances calculated from branch lengths of the ML topology. The Y = × line marks the theoretical limit where the number of observed substitutions equals the number of inferred substitutions. The slope of the linear regression indicates the amount of substitution saturation the smaller the slope, the greater the number of inferred multiple substitutions.

Statistical tests between competing topologies confirmed the above results (Table 2). The approximately unbiased (AU) likelihood-based test showed that all proposed alternative hypotheses to the sister group relationship of turtles with archosaurs were rejected based on the amino-acid dataset, irrespective of the model used. In concordance with the results of saturation analyses, the complete nucleotide dataset did not distinguish statistically between the competing alternatives of turtles plus archosaurs and turtles plus crocodilians. These more equivocal and method-dependent results, when nucleotide sequences were used, are suggestive of conflicting phylogenetic signals between codon positions. However, the alternative topologies proposing turtles as the sister group to other reptiles (including birds), and grouping turtles with squamates (lizards and snakes) received no support from our data.

Finally, given the fact that the internal branch lengths connecting the main reptiles lineages seemed to be relatively short in trees obtained from concatenated analyses (Figure 1), we also explored the potential influence of the underlying gene-tree heterogeneity created by deep coalescence events, which might lead to statistical inconsistency of concatenation-based methods in the anomaly zone [35, 36]. The results obtained using the maximum pseudo-likelihood for estimating species trees (MP-EST) approach showed high consistency with the results of our concatenation-based analyses (Figure 3). Indeed, the species tree reconstructed from the amino-acid ML gene trees unambiguously supported (BP = 100) the grouping of turtles and archosaurs (Figure 3a), whereas the species tree based on nucleotide ML gene trees supported (BP = 87) a conflicting turtles plus crocodilians clade (Figure 3b), as previously shown in concatenation-based analyses using suboptimal models of sequence evolution. In fact, only six amino-acid and three nucleotide ML gene trees were fully compatible with their corresponding species trees. These figures illustrate the large extent of gene-tree heterogeneity in this dataset, which probably reflects the large effect of stochastic error on individual gene-tree inference. We interpret these congruent results between concatenation and species tree inference as good evidence that the source of the statistical inconsistency resulting in the grouping of turtles with crocodiles does not come from potential discordances between gene trees and the species tree, but rather from the influence of substitutional saturation of third codon positions in individual gene-tree inference.

Species trees inferred from the 248 individual maximum likelihood (ML) gene trees using a pseudo-ML approach. Maximum pseudo-likelihood for estimating species trees (MP-EST) bootstrap consensus species tree obtained for (a) the amino-acid and (b) the nucleotide dataset. (a) This consensus tree was computed from the species trees estimated by the MP-EST method for 100 bootstrap datasets of the 248 ML gene trees inferred under the LG + G8 model. (b) This consensus tree was computed from the species trees estimated by the MP-EST method for 100 bootstrap datasets of the 248 ML gene trees inferred under the GTR + G8 model. Values at nodes indicate bootstrap percentages obtained with 100 replicates. Note the strong incongruence between the two species trees concerning the position of turtles.

Molecular dating results

Detailed results from the molecular dating analyses performed under auto-correlated models of molecular clock relaxation are presented in Table 3. Divergence date estimates varied depending on the methods and datasets used, but were nevertheless consistent between the two programs we used (MCMCTree and PhyloBayes). We generally found more consistency with published estimates for the results obtained with PhyloBayes under the CAT-GTR + G site-heterogeneous mixture model (Table 3) than for the results obtained with the site-homogeneous LG + G / WAG + G and GTR + G models. Our analyses based on the CAT-GTR + G model placed the divergence between turtles and archosaurs around the Permian-Triassic boundary at a mean of 255 Mya (range 274 to 233 Mya), the separation of crocodilians and birds in the Upper Triassic with a mean of 219 Mya (249 to 186 Mya), and the most recent common ancestor (MRCA) of living turtles (corresponding to the separation between Pleurodira and Cryptodira) in the Upper Jurassic with a mean of 157 Mya (207 to 104 Mya) depending on whether amino acids or nucleotides are considered (Table 3). The chronogram obtained from the analysis of the nucleotide dataset using the CAT-GTR + G model is shown in Figure 4.

Bayesian relaxed molecular clock time scale. Chronogram obtained from the analysis of the nucleotide dataset using the CAT-GTR + G mixture model. Numbers in circles at nodes refer to lines of Table 3, and squared boxes represent 95% credibility intervals. Numbers between brackets represent the six calibration constraints implemented as soft bounds. Absolute ages of the geological periods follow Gradstein and Hogg [91].

Strikingly different results were obtained when using uncorrelated models of clock relaxation (see Additional file 1). Again, dating estimates were fairly consistent between the different program implementations (BEAST, MCMCTree, and PhyloBayes), but using uncorrelated rate models generally led to much smaller age estimates than the ones obtained under auto-correlated rate models. For example, using uncorrelated models, the MRCA of living turtles was estimated to be half the age of that found with auto-correlated models, with mean estimates ranging from 81 to 64 Mya versus 167 to 107 Mya, respectively. Other estimates, such as the caiman/alligator divergence, were reduced by two-thirds, resulting in unreasonably recent estimations relative to the TimeTree values (see Additional file 1).

How to identify 20 winter backyard birds at your feeders: Aerial View (photos)

CLEVELAND, Ohio -- Birding is the country's second-most popular outdoor pastime (after gardening), and the majority of birders pursue their hobby by watching bird feeders from the comfort of their home.

Nearly two dozen species can be seen during winter in Northeast Ohio, depending on whether you live in a city, a suburb or the rural countryside. The following slideshow will help you identify the most common birds to be found this winter around Northeast Ohio feeders.

What you feed the birds also plays a large part in the variety of species you attract. For Northern cardinals, blue jays, tufted titmice, black-capped chickadees, and white-breasted nuthatches offer black oil sunflower seed. Scatter millet on the ground for sparrows, mourning doves and juncos.

Insect-eaters such as woodpeckers and Carolina wrens will appreciate a block of suet or a peanut butter concoction. And finches such as American goldfinch, common redpolls and pine siskins prefer thistle seed, also known as nyger.

A bird-friendly habitat also will improve your chances of seeing more birds. The National Audubon Society suggests planting a border of native berry producing trees and shrubs, allowing your wildflowers to go to seed, providing fresh water in a plastic heated bird bath, making a brush pile in a corner of your yard, and raking leaves under your trees and shrubs to provide a mulch bed where scratching birds such as sparrows, towhees, blackbirds and thrush can find insects and seed.

For nine steps to winterize your yard go here.

To predict what Arctic and boreal species you might hope to see in your yard go here.

Story by Jim McCarty, The Plain Dealer

(Tufted titmice are common year-round residents of Northeast Ohio, and frequent visitors to backyard feeders during winter.)

Dave Lewis/Special to The Plain Dealer

Black-capped chickadee

Black-capped chickadees will occasionally eat seed out of your hand, especially at the Brecksville and North Chagrin Reservations.

Kenn & Kim Kaufman/Special to The Plain Dealer

Dark-eyed juncos are reliable visitors from the north during winter at Northeast Ohio feeders.

Jim Roetzel/Special to The Plain Dealer

Blue jays are beautiful bullies at backyard feeders.

Jerry Talkington/Special to The Plain Dealer

Snow buntings arrive in large flocks from the north during the late fall/early winter, and occasionally visit feeders in rural Northeast Ohio.

Watch the video: Guess the Animal Sound Game. 12 Nocturnal Animal Sounds Quiz (November 2022).