Birds To Dinosaur: Genetic Similarity Between Birds and Crocodiles

Genetic Similarity Between Birds and Crocodiles

I found the article (click) on birds and crocodiles and the 93% similarity between alligator and crocodiles. Very interesting research. What is the approximate percentage of similarity between bird and crocodile genome?

This burning question is answered by the persons who actually did whole genome alignments between the crocodilians and several birds. Explanations which include Benedict Paten, David Ray and Joel Armstrong, which goes a little deeper than the whole genome alignments on the alligator and crocodile.

On to estimating just how similar any given bird vs. a crocodilian might be... what is the average percent identity for crocs vs. birds?

BENEDICT: The math answer is to take the neutral rate tree from the ancient repeats (it's in the paper), sum the branch lengths along the path between the two genomes of interest and reverse the multiple substitutions per site correction calculation. You should get close to the genome wide % identity between your chosen pair of genomes.
Alternatively, you could directly count from the genome alignment, which is available (see the supplementary materials). The alignment is in HAL format, and I believe you can calculate this using the HAL stats command (see (click)).

JOEL: We did a count of the genome-wide % ID of all genomes to the crocodile genome using our alignment a while ago.
The rate varies somewhat between birds, but for example, chicken has 61.7% identity with crocodile according to our alignment. This is a bit higher than what you would expect given the distance in the 4d site tree: the crocodile-chicken distance is 0.688, which if my math is right, works out to about 55% expected identity. The difference is due to the 4d rate being a neutral rate, while a significant portion of the aligned bases between chicken and crocodile are conserved.

Thanks. I'm going to safely assume then, that chickens actually do bear a closer relationship with crocodiles (61.7%) than T-Rex (58%).
Thank you for answering that question. There is absolutely nothing substantial on the web about the actual percentage of DNA similarity between Chickens and Crocodiles.

"...About 60 percent of chicken genes correspond to a similar human gene. However, researchers uncovered more small sequence differences between corresponding pairs of chicken and human genes, which are 75 percent identical on average, than between rodent and human gene pairs, which are 88 percent identical on average. Differences between human and chicken genes were not uniform across the board, however. Chicken genes involved in the cell's basic structure and function showed more sequence similarity with human genes than did those implicated in reproduction, immune response and adaptation to the environment."
(click) and (click)

So, in some places chickens are closer in their genetic relation with humans than either t. rex or even crocodiles.

Based on genetic evidence, it really is difficult to make such a drastic conclusion that "chickens definitively evolved from T. Rex".

"...About 60 percent of chicken genes correspond to a similar human gene."

"...chicken has 61.7% identity with crocodile according to our alignment."

"...many pieces of the protein (t. rex) they came up with a number of 58% sequence identity (with chicken)..."

And some conclude the chicken is more related to the T. Rex, than the crocodile or the mammal. In what alternative mathematical reality?

All that fuss about "life began on Mars," well that explains the dinosaur extinction too. They went home.

They're barely related to anything known on this earth. The genetic evidence clinches it.

Not kidding.

Don't say I didn't tell you so.

Now, you know.

There is a lot of misleading information out there. Notice the emphasis on the word, "closest living relative," as if something extinct, were even closer.

That's why I contacted the dudes who sequenced the crocodile genomes. They had the Alligator vs. Crocodiles genome sequencing (determining 93% similarity) so what was the similarity between Crocodiles and Birds?!

Crocodilia
"They appeared 83.5 million years ago in the Late Cretaceous period (Campanian stage) and are the closest living relatives of birds..."
(click)

Are they implying dinosaurs were even closer than crocodiles?

The crocodile is the "closest living AND EXTINCT relative of birds."
(Considering the fact that Crocodile DNA has changed very little over the past 100 million years.)

EXTINCT dinosaur: 58% genetic similarity to a chicken.
EXTINCT AND EXTANT crocodile : 61.7% genetic similarity to a chicken.

Hmmm and I bet if you compared ancient Crocodile DNA with the chicken genome that % of similarity would be quite possibly higher than that of modern crocodiles!

The proper wording should be "Crocodilia are the closest known relative of birds."
PERIOD.

REACTION FROM DR. ALAN FEDUCCIA:

"Interesting, but we do not know anything about the T. rex genome, just size, and even that is somewhat speculative."
Best, alan

That isn't what the "Orthodox" crowd are saying.

See attachment culled from one book I came across on Google Books.
They swear by the "conclusive" DNA evidence.

^{"conclusive" (in quotes) denotes sarcasm.}

58%

Dr. Alan Feduccia:

Yes, but our "T. rex skeptics group" has seriously questioned that study by Schweitzer; see chapter one in my book Riddle. And even if true (which I seriously doubt) it is just a small snippet of collagen. . . .

No comments:

Interesting Related Links

A Marine Shorebird (Archosaurian Descendant) that behaved like some lizards who ran over water to escape predation.
Hollow bones helped high-flying reptiles stay aloft
"...Similar design features exist in modern birds, which evolved them independently, say the scientists."
Swimming led to flying physicists say
"...Fruit flies 'swim' through air, using the same physics as fish, study shows
Fruit flies and other flyers also use drag to "swim" through the air, the scientists say. Their discovery lends support to the evolutionary theory that flight in insects emerged from swimming.

Flying snakes... flying squirrels... flying reptiles and flying birds?

Early bird makes a splash
"...although many people think of ducks, geese and other waterfowl as specialized animals, they are quite primitive in comparison to highly evolved species such as songbirds... almost every bird group alive today has representatives that live in or around water, Chiappe says, suggesting that a watery lifestyle may be an ancient tradition that has persisted in many lineages... Chiappe admits that the aquatic-origins theory could be cast into doubt if somebody finds a fossilized land bird of the same vintage as Gansus.
Bird-from-dinosaur theory of evolution challenged: Was it the other way around?
"...A new study provides yet more evidence that birds did not descend from ground-dwelling theropod dinosaurs, experts say, and continues to challenge decades of accepted theories about the evolution of flight."

Look at these wonderful visceral arches hinting at the aquatic ancestry for birds!

Bright Red Feathers on T. Rex?!

Ancient origins and multiple appearances of carotenoid-pigmented feathers in birds
"...The broad palette of feather colours displayed by birds serves diverse biological functions, including communication and camouflage. Fossil feathers provide evidence that some avian colours, like black and brown melanins, have existed for at least 160 million years (Myr), but no traces of bright carotenoid pigments in ancient feathers have been reported."
Leading Ornithologist, "Arguments for ancient bird feather color 'Pure Mythology'"
Synchrotron-based chemical imaging reveals plumage patterns in a 150 million year old early bird
"...Studies on the elucidation of colour in fossil feathers have suggested that the presence of melanosomes within fossil feathers may be used to tentatively reconstruct feather colours by tracking variations in melanosome shape. [...] This structural approach has some shortcomings, primarily that there is known diversity in melanin granule morphology among different species, and melanosome preservation may not be uniform. Therefore, serious questions may be raised about colour interpretation based solely on fossilised melanosome morphology and distribution. Additionally, these studies did not account for other known contributors to colour in feathers, such as the possible presence of other pigments (e.g. carotenoids) or other physical structures."
Winter cardinals don their brightest red feathers
"...Cardinals get the pigments responsible for red feathers from their food. Cardinals, tanagers and goldfinches can't synthesize carotenoids - the pigments responsible for red, orange and yellow feathers. If the birds don't eat enough carotenoid-rich fruits and insects, feathers that grow in during the next molt will be less colorful. Dogwood, rose and Japanese honeysuckle berries are locally abundant sources of carotenoid pigments."

"Frugivore Raptor" and "Vegan Rex" may have confidence in the Dinosaur-Bird myth but any person with a reasonably adequate understanding of the fossil record and how legitimate paleontology functions, can not.
Disciples of Dino-Bird Mythology may choose to believe T. Rex was a conscientious "vegetarian which dined upon an abundant supply of berries."
However, they are not alone. One other well-known group of people who make claim T. Rex was a Vegetarian: CREATIONISTS. They too claim there were no carnivorous diets (death) "before the fall".
And that's all I can say of such silly mythology vs. legitimate science!

Molecular evidence for the origin of birds (backup)
Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles
Exploring the biofluiddynamics of swimming and flight
Researchers Compare Chicken, Human Genomes: Analysis Of First Avian Genome Uncovers Differences Between Birds And Mammals (click) and (click)
Brush Your Beak: 10 Amazing Birds With Teeth
Do birds have teeth? Ask any biologist and the answer will be “absolutely not!”, but “absolute” is a relative term and when one stretches the definitions of what makes a bird or a tooth, birds with teeth aren’t absolutely impossible anymore.

For the Anti-Creationism Darwinist Among Us

My Other Blog:
Genesis in the Ancient World
"The Jews integrated into Greek culture around 300 BC. Notably, much of the modern Biblical literature is actually Greek. Enlightened Greek thought becomes apparent in the opening of Genesis. "One of the first evolutionary theories was proposed by Thales of Miletus (640–546 BC) in the province of Ionia on the coast near Greece followed by Anaximander (550 B.C.) who speculated that life evolved from the water; lower forms of life, in a very primitive precursor to evolutionary theory."

Namely this *ouch!*

Evolution and Paleontology in the Ancient World
"...For Anaximander, the world had arisen from an undifferentiated, indeterminate substance, the apeiron. The Earth, which had coalesced out of the apeiron, had been covered in water at one stage, with plants and animals arising from mud. Humans were not present at the earliest stages; they arose from fish. This poem was quite influential on later thinkers, including Aristotle.
Had Anaximander looked at fossils? Did he study comparative fish and human anatomy? Unfortunately, we have no way of knowing what evidence Anaximander used to support his ideas. His theory bears some resemblance to evolutionary theory, but also seems to have been derived from various Greek myths, such as the story of Deucalion and Pyrrha, in which peoples or tribes are born from the Earth or from stones. His concept of the apeiron seems similar to the Tao of Chinese philosophy and religion, and to the "formless and void" Earth of the Hebrew creation account and other creation myths. However, even though Anaximander's ideas drew on the religious and mythical ideas of his time, he was still one of the first to attempt an explanation of the origin and evolution of the cosmos based on natural laws."
(Source, ucmp.berkeley.edu History)

[Sadly, what the site fails to mention is that the oldest known biblical manuscripts date no earlier than around 300 B.C., therefore, Anaximander (610-545 B.C.) could not have based any of his concepts on Biblical Hebrew. However it can be deduced, the Hebrew Genesis account was borrowed from mainstream Greek philosophy.] [The analysis by Harvard and several other University sources are quite impressive: (Scala Naturae of the Bible, Charles Darwin and Ancient Greek Philosophy)]

Genetic similarity between chicken and t. rex: 58% (click)
Genetic similarity between human and chicken: 60-75% (click)
Genetic similarity between chicken and crocodilians 61.7% (click)
NOW who's your daddy?!

In Memoriam

Sorry T. Rex. You did not evolve into chickens. You went extinct like 99% of the species on this planet who ever lived and, your similarities with birds were due to a shared Archosaurian ancestor or, merely a result of convergent evolution.
(And here is the genetic evidence.)

"Superficially bird-like dinosaurs occurred some 25 million to 80 million years after the earliest known bird, which is 150 million years old.” See (here).

..."denying the fossil record" isn't for just Creationists anymore! ...