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Sat Aug 8, 2020, 08:38 AM

The Genome of the Last Surviving Member of an Order from which Dinosaurs, Birds, Mammals...

...and modern reptiles evolved has been sequenced.

The paper to which I'll refer is this one: The tuatara genome reveals ancient features of amniote evolution (Gemmel et al., Nature, https://doi.org/10.1038/s41586-020-2561-9).

An amniote is an animal whose embryonic development takes place in an amiotic fluid surrounded by a membrane called a chorion. This class of animals includes all reptiles, birds, and mammals.

The paper is open sourced, anyone can read it. It describes the last member of a class of animals which once dominated the Earth before branching out to evolve as dinosaurs, birds, modern reptiles, and mammals including that somewhat destructive animal the human being.

An excerpt from the abstract:

The tuatara (Sphenodon punctatus)—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2—is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which—at approximately 5 Gb—is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago.


From the introduction:

The tuatara (Sphenodon punctatus)—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2—is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which—at approximately 5 Gb—is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago.

It is also a species of importance in other contexts. First, the tuatara is a taonga (special treasure) for Māori, who hold that tuatara are the guardians of special places2. Second, the tuatara is internationally recognized as a critically important species that is vulnerable to extinction owing to habitat loss, predation, disease, global warming and other factors2. Third, the tuatara displays a variety of morphological and physiological innovations that have puzzled scientists since its first description2. These include a unique combination of features that are shared variously with lizards, turtles and birds, which left its taxonomic position in doubt for many decades2. This taxonomic conundrum has largely been addressed using molecular approaches4, but the timing of the split of the tuatara from the lineage that forms the modern squamates (lizards and snakes), the rate of evolution of tuatara and the number of species of tuatara remain contentious2. Finally, there are aspects of tuatara biology that are unique within, or atypical of, reptiles. These include a unique form of temperature-dependent sex determination (which sees females produced below, and males above, 22 °C), extremely low basal metabolic rates and considerable longevity2.


A graphic from the paper:



The caption:

a, The tuatara, (S. punctatus) is the sole survivor of the order Rhynchocephalia. b, c, The rhynchocephalians appear to have originated in the early Mesozoic period (about 250–240 million years ago (Ma)) and were common, speciose and globally distributed for much of that era. The geographical range of the rhynchocephalians progressively contracted after the Early Jurassic epoch (about 200–175 Ma); the most recent fossil record outside of New Zealand is from Argentina in the Late Cretaceous epoch (about 70 Ma). c, The last bastions of the rhynchocephalians are 32 islands off the coast of New Zealand, which have recently been augmented by the establishment of about 10 new island or mainland sanctuary populations using translocations. The current global population is estimated to be around 100,000 individuals. Rhynchocephalian and tuatara fossil localities are redrawn and adapted from ref. 1 with permission, and incorporate data from ref. 2. In the global distribution map (c, top); triangle = Triassic; square = Jurassic; circle = Cretaceous; and diamond = Palaeocene. In the map of the New Zealand distribution (c, bottom); asterisk = Miocene; cross = Pleistocene; circle = Holocene; blue triangle = extant population; and orange triangle = population investigated in this study. Scale bar, 200 km. Photograph credit, F. Lanting.


It's well worth a look, and again, open sourced. It's well worth a look.

If interested, enjoy...

I wish you a safe, healthy and pleasant weekend.

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Reply The Genome of the Last Surviving Member of an Order from which Dinosaurs, Birds, Mammals... (Original post)
NNadir Aug 8 OP
tblue37 Aug 8 #1
wendyb-NC Aug 8 #2
abqtommy Aug 8 #3
eppur_se_muova Aug 8 #4
NNadir Aug 8 #7
eppur_se_muova Aug 8 #8
NNadir Aug 8 #9
eppur_se_muova Aug 9 #10
muriel_volestrangler Aug 9 #11
eppur_se_muova Aug 9 #12
niyad Aug 8 #5
burrowowl Aug 8 #6

Response to NNadir (Original post)

Sat Aug 8, 2020, 08:42 AM

1. K&R and thanks! nt

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Response to NNadir (Original post)

Sat Aug 8, 2020, 08:49 AM

2. Thank you, that's a fascinating article.

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Response to NNadir (Original post)

Sat Aug 8, 2020, 09:17 AM

3. Thanks. Had to bookmark it...

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Response to NNadir (Original post)

Sat Aug 8, 2020, 09:27 AM

4. No Archosaurs in their chart ?!?

Last edited Sat Aug 8, 2020, 11:27 AM - Edit history (4)

Is the bird/dinosaur branch point too hotly debated for them to stake a position ?

ETA: Thanks for posting this. The tuatara has been my favorite "living fossil" for a long time, even though it's hardly ever mentioned.

I even felt compelled to look up the book where I first read about the tuatara (and either my first or second book on dinos):

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Response to eppur_se_muova (Reply #4)

Sat Aug 8, 2020, 12:45 PM

7. I didn't notice that. The authors are obviously...

...cowards.

I had no idea the tuatara existed until coming across this paper.

I believe my parents bought me dinosaur books, but then again, my father believed the world was 6,000 years old although my mother didn't let him push the issue. He only pushed after she died, and by that time I was, um, educated, and not at Liberty University.

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Response to NNadir (Reply #7)

Sat Aug 8, 2020, 01:09 PM

8. Ouch. Glad I didn't have to deal with that.

My father didn't do a lot of things right, but that was one of them. And he was the son of a church organist.

He also grew up with a really racist father (seriously, a Southern version of Archie Bunker who knew ethnic slurs for ethnic groups I didn't know existed) and didn't pass that on.

Sometimes it's good not to be influenced too much by your parents. Of course, my kids will find me perfect ... but then they only exist in my imagination.

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Response to eppur_se_muova (Reply #8)

Sat Aug 8, 2020, 01:50 PM

9. I loved my father very much, and miss him still. He quit school in the 8th grade...

...to support his mother after his alcoholic and violent father abandoned her for the umpteenth time. He witnessed drunken beatings, and the last time he saw his father alive he threw him down down the stairs and told him never to set foot in the house again, because my grandfather was threatening to burn my grandmother's face off with a hot iron.

The next time he saw his father, it was to identify the body after my grandfather had been murdered in a bar fight and thrown into the East River. The cops didn't even bother to look for the killer, and frankly, nobody gave a damn, except the British Army that buried him.

My father was sunk in the North Atlantic; shot at in the Pacific by Japanese aircraft.

He met my mother and until the day she died, he treated her with profound respect and love. I never saw anyone show as much love to a dying woman as he showed to her; he was literally willing to die for her. I will never forget what he did and what he endured.

As a father, my father made absolutely sure to be everything his father wasn't, because he was a father. As a father myself, I try my damnedest to be as good a father as he was. There are many ways I work to be different than him, but as a father, well, he was the best and I'm just a pale imitation.

We fought; we argued; but we loved one another very much.

Although he had no formal education, he taught me that one could teach oneself anything. He worked long hours in physical labor to see there was a roof over my head, food on the table, and took on extra jobs to buy my brother and I what I now understand to be trinkets. He read a great deal, talked about the world, thought about the world, and tried to be decent as he understood it.

It was not how I understood decency; but nevertheless having a vision of decency mattered.

He was, in many ways, a right winged bastard, but he was very proud of the fact that I had my own mind and forgave it was not his mind, reveled in our differences.

He was uneducated, but very bright.

He's dead now for decades, and still, after all these years, I can still weep that he's not here.

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Response to NNadir (Reply #9)

Sun Aug 9, 2020, 10:41 AM

10. Well, everyone has their flaws ... your Dad sounds like one of the good guys ...

... with a flaw that would have annoyed me, but it could have been a lot worse, I guess.

When I think of the positive attributes I associate with my own father, they are all things he *didn't* do -- he wasn't an alcoholic, or a wife-beater, or a fundamentalist, or a racist, or a right-wing nut job. But he just didn't like people, and made no exceptions for his own family, whether by blood or marriage. He died recently, and it took no more than a few words for his survivors to agree there would be no funeral and no remembrance. It is sad that he was able to live in such a way that he is not missed by anyone.

"... made absolutely sure to be everything his father wasn't" is not that far from how I've tried to do things.

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Response to eppur_se_muova (Reply #4)

Sun Aug 9, 2020, 10:58 AM

11. They've only shown living genera in the chart

The dinosaur/bird relation is implied, however, since birds are grouped as being closer to crocodiles than to turtles. Crocodiles are archosaurs.

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Response to muriel_volestrangler (Reply #11)

Sun Aug 9, 2020, 11:56 AM

12. Aha! I did note the crocodiles, and thought that made it doubly odd, but if it's only living genera

then all's well, I suppose.

I had to think about that a bit -- fossil genera are so important to any discussion of evolution -- why leave them out ? Why, lack of DNA, of course, and this is a DNA study, after all. Clarity has been achieved.

Thanks for pointing that out.

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Response to NNadir (Original post)

Sat Aug 8, 2020, 09:57 AM

5. KNR and bookmarking

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Response to NNadir (Original post)

Sat Aug 8, 2020, 10:38 AM

6. Kick

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