Another paper dating diversification of birds. I include it here because of the above discussion.
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Phylogeny of birds (2 Viewers)
- Thread starter Peter Kovalik
- Start date
Martin Stervander
Birder, senior curator, evolutionary biologist
Massive family-level global bird tree based on whole-genome analyses
BOOM! Today, our new bird phylogeny was published in Nature (soon also at https://doi.org/10.1038/s41586-024-07323-1). Or, well, an ugly preview version that should soon be prettified was made available. This is the main result of the family phase of the Bird 10,000 Genomes Project (B10K), and thus is “the new Jarvis et al. (2014) tree”. The work has been incredibly intensive and demanding, and the 52-headed crew of co-authors has been led by Josefin Stiller (University of Copenhagen), Siavash Mirarab (UCSD) and Guojie Zhang (Zhejiang University). I should stress already here that my contributions have been rather minor, but I’m probably the only one on BirdForum, so I figured it falls on me to report our study here.
This is the most detailed, highly resolved, and precise phylogeny of birds to date. It is based on 363 species, representing 92% of all bird families (as per Howard & Moore 4; the last 8% representing taxa we have so far been unable to get usable samples from), whose whole genomes have been sequenced, assembled, and annotated. They have then put into a whole-genome alignment and, in total, these analyses cover nearly 100 BILLION basepairs. With quite some margin, this makes up the most extensive phylogenetic analyses of birds to date. There’s long been a debate about whether increased taxon sampling is better to increase precision and reliability or increased genetic sequencing (more loci; more base pairs). Here, we’ve been able to test this. More about that below, but first some of the taxonomic news. Let’s start with something that makes some intuitive sense.
Strigformes and Accipitriformes are sister orders (but it’s complicated…)
In the main two previous genome-scale phylogenies by Jarvis et al. 2014 (based on 48 taxa and 48,000,000 bp of genes and ultra-conserved elements (UCEs)) and Prum et al. 2015 (based on 198 species and 395,000 bp from protein-coding genes), Strigiformes (owls) have been recovered as a sister lineage to a clade within Afroaves comprising Coliiformes, Leptosomatiformes, Trogoniformes, Bucerotiformes, Coraciiformes, and Piciformes, i.e. the bulk of clade Afroaves. Accipitriformes, however, was recovered as having branched off earlier from that clade (Jarvis et al. 2014) or even earlier, from the branch leading to the ancestor of Afroaves and the Australaves orders Cariamiformes, Falconiformes, Psittaciformes, and Passeriformes (Prum et al. 2015).
In our main tree, which was produced with coalescent-based analyses of a 63,430,000-bp matrix of spaced intergenic sequence (63,430 loci of 1,000 bp each), diurnal birds of prey and their nocturnal counterparts come out as sister lineages, placed basally within Afroaves. Having said that, these orders are particularly problematic to place and ancient hybridization may have played a role. More details in the paper. Now for a newly recovered grouping that none of you would have seen coming!
Elementaves is an exceedingly diverse neoavian clade of surprising relatives
As expected, at the base of our tree sits infraclass Palaeognathae (ratites), sister to all other extant birds, which sort under infraclass Neognathae. Neognathae diverges into parvclasses Galloanseres (fowl and ducks) and Neoaves, the latter comprising all remaining birds. The arrangement within parvclass Neoaves has been subject to many changes, since the very rapid diversification at its base has been near-impossible to sort out with any confidence. Our analyses recover four basal clades within Neoaves. The first one to branch out is Mirandornithes (Phoenicopteriformes, Podicipediformes); next comes Columbaves (Mesitornithiformes, Pterocliformes, Columbiformes, Musophagiformes, Otidiformes, Cuculiformes)—although there is a whole interesting story about Columbaves, that shows that Columbimorphae may in fact be sister to Mirandornthes instead, forming Columbea (see separate paper by Mirarab et al. released today in PNAS). Left is a two-way split between Telluraves, which comprises Afroaves and Australaves as above, and our novel cool gang/unruly bunch.
Included here is a clade with Opisthocomiformes as probable sister to the sister pair Gruiformes and Charadriiformes; another clade where Caprimulgiformes (sensu lato, i.e. = Strisores) likely sits at the base as sister to a clade which bifurcates into Phaetontimorphae (Eurypygiformes, Phaetontiformes) and Aequornithes (Gaviformes, Pelecaniformes, Procellariformes, Sphenisciformes). This means that our very smallest (hummers) and largest (one way to measure at least; albatrosses) are part of the same clade. I see lots of shaking heads and furrowed brows right now, and expect several of you to think that “this just cannot be right”. While no phylogeny can claim to be the truth, I will say, however, that this is not a random grouping that has just been accepted without challenge (and loads of additional analyses). It does nicely illustrate, however, how the amount of data affects both support and topology – and that different methods of analyses recover different topologies. There’s lots more to read about this in the paper.
As for the name, we name it Elementaves because the clade’s lineages have diversified into terrestrial, aquatic, and aerial niches (holding several of our most impressive specialists like penguins, albatrosses, and swifts), corresponding to the classical elements of earth, water, and air. So, what about fire? Well, several species within Phaethontimorphae have names derived from the sun, a big ball of fire.
What are the differences in topology and which tree should you believe in?
We argue overall that our extensive taxon sampling combined with extensive genomic sampling (i.e. not taxa vs loci, but preferably both) of regions that are not under direct or indirect selection (unlike previous trees), analysed in a coalescence-based framework, produces a stronger and more reliable bird phylogeny. There’s lots more to read about this in the paper. But what are the differences from the two previous main panavian phylogenies, Jarvis et al. (2014) and Prum et al. (2015)? This is made easy to assess as it is summarised in this figure:
View attachment EDF5annot_high.jpg
Should you trust this new tree over Jarvis or Prum? We argue yes, but we also offer a fun analyses that lends some support to this claim. If one explores the phylogenetic signal (based on the tree) in how morphological trait (co-)vary, it turns out that in morphometric variables (bill measurements, body mass, tail length, wing length and shape, and tarsus length), the distribution of measurements across species “make more sense” with the new tree. That is, there is less sudden variation (evolutionary shifts) along the tree branching toward the present with our new topology, than compared with the tree of Prum et al. (2015) [too few species in Jarvis et al. 2014].
Precision of age estimation and timing relative the
The final cool thing I’d like to bring up about this new phylogeny is that the precision is vastly higher for node age estimation than has ever been achieved before (including Jarvis et al. 2014 and Prum et al. 2015). This has much to do with the extensive work to classify avian fossils and empirically generate ‘calibration densities’ for no less than 34 nodes. Many node age estimates differ from previous studies, but most fall within the latter’s large 95% confidence intervals. Our new dating offers much narrower confidence intervals (and some surprises in terms of actual age, like very much older Tinamidae, older Apodidae, younger Pipridae and Accipitridae). This offers more insight to the timing around the Cretaceous–Paleogene boundary, which coincides with the rapid and extensive diversification of Neoaves. Some folks have proposed a scenario in which the main lineages of Neoaves would have evolved prior to the asteroid impact and survived through it. More favoured and more well-supported by fossils, though so far not supported with any precision by molecular data, is the ‘big bang’ scenario. This means that the main diversification of Neoaves would have happened after the asteroid impact, as a response to the vacation of whole ecological niches previously occupied by non-avian dinosaurs and other animals. Our tree lends support to this scenario.
That’s over and out from me at this point, but I promise you that there is much more to be gleaned from Stiller et al. (2024)! Not least, a lot of additional goodies are hiding in the supplemental extended data figures, so don’t miss out on them.
The links are not working for me.
This seems a report on two papers, but the links to the Nature and PNAS papers are not working there either.
www.sci.news
This seems a report on two papers, but the links to the Nature and PNAS papers are not working there either.
Scientists Create Largest and Most Detailed Bird Family Tree to Date | Sci.News
The updated family tree reveals patterns in the evolutionary history of birds following the cataclysmic mass extinction event that wiped out the dinosaurs 66 million years ago.
www.sci.news
Xenospiza
Distracted
You probably were a bit too early!
Stiller et al, 2024: Complexity of avian evolution revealed by family-level genomes: Complexity of avian evolution revealed by family-level genomes - Nature
Mirarab et al., 2024, A region of suppressed recombination misleads neoavian phylogenomics: https://www.pnas.org/doi/10.1073/pnas.2319506121
Stiller et al, 2024: Complexity of avian evolution revealed by family-level genomes: Complexity of avian evolution revealed by family-level genomes - Nature
Mirarab et al., 2024, A region of suppressed recombination misleads neoavian phylogenomics: https://www.pnas.org/doi/10.1073/pnas.2319506121
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Jacana
Will Jones
Click on the "Nature" link instead of the DOI link, then you'll get it.The links are not working for me.
This seems a report on two papers, but the links to the Nature and PNAS papers are not working there either.
Scientists Create Largest and Most Detailed Bird Family Tree to Date | Sci.News
The updated family tree reveals patterns in the evolutionary history of birds following the cataclysmic mass extinction event that wiped out the dinosaurs 66 million years ago.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Resolutely, none of these studies will agree on the position of certain lineages
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Martin Stervander
Birder, senior curator, evolutionary biologist
Hi @jts1882, I'm sorry about the link faff. The DOI has for whatever reason not been activated as it should. Thanks to @Xenospiza and @Jacana for providing links and clarifications. Importantly, though, my post really only covers (some of!) Stiller et al. (2024) Nature paper, which I have been involved in, and only winks at the Mirarab et al. (2024) PNAS paper.
Martin Stervander
Birder, senior curator, evolutionary biologist
Bonsoir,
Who is "he" in this context? Moi? If so, I certainly should not be given as much cred for this paper, where I played a rather small role. (Though I did come up with the name Elementaves, which I pride myself for.) This work was led by Josefin Stiller, Siavash Mirarab, and Guojie Zhang.
Happy to discuss the actual positions of the certain lineages—or other aspects—nonetheless.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Oops, Google translate is not always reliable in its translations 😋
The Extended Data Fig 3 has the Passeriformes families labelled and has a timescale.
Martin Stervander
Birder, senior curator, evolutionary biologist
Exactly. @Mysticete, on pages 48–49 there is what used to be Extended Data Figure 2a and 2b, but which now looks like they've been renumbered as EDF 2–3. Might be able to post non-watermarked versions here later.
Fig 2 needs that "Passeriformes (see Extended Data Fig. 2)" terminal changed to Fig 3.
I note in Fig 3 you have Tichodroma in Sittidae rather than Tichodromidae, making Sittidae paraphyletic. Similarly for Chloropsis in Irenidae. I assume this is because you are using H&M4 families, but this is confusing. Wouldn't it be better to update them?
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
In which paper?
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
I do not find anything
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
I no longer have a computer, I can no longer download zip files. Could someone send me pdfs by email?
Mysticete
Well-known member
Can someone send me the direct link? The extended data page I found for the paper has captions but no actual figures. There is no extended data link in the supplementary material as far as I can see, and I don't have access, at least at home, to more than the abstract. So if there is a link in the paper itself I can't get to it?
Martin Stervander
Birder, senior curator, evolutionary biologist
It is page 48-49 of the pdf that contains the main article, which also contains all figures and extended data figures. It will all be easier to navigate once Nature have done their bit and typeset it all. Nevertheless, I am happy to send pdf(s), please just send me your email address in a direct message! This goes for you too, @Jim LeNomenclatoriste, and anyone else who cannot access the file.
Cheers!
Martin Stervander
Birder, senior curator, evolutionary biologist
Thanks for pointing this out! I've made sure this should get fixed for the final version. As for Tichodroma, it's in Sittidae because we follow H&M4 in the paper, so you're absolutely right. Sadly I don't think it's less confusing to update them, because what do we update and what do we not? Suddenly we will either be following IOC or a complete mix in between. (There is, however, a strange inconsistency in that Caprimulgiformes in its wide sense, which is the definition in H&M4, has generally been labeled as Strisores (which is used as a higher-clade name when Caprimulgiformes is split in several orders, like in the more modern taxonomic references). Sadly, this has spilled over to some tip labeling as well. It will be updated in EDF2, but that's it.
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