Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
This is why I do not take them into account and we must wait for a more complete study on them.
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Phylogeny of birds (1 Viewer)
- Thread starter Peter Kovalik
- Start date
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Is there Netta erythrophthalma?
Mysticete
Well-known member
I would assume so but I don't remember
albertonykus
Well-known member
Springer, M.S. and J. Gatesy (2024)
A new phylogeny for Aves is compromised by pervasive misalignment and homology problems
PNAS 121: e2406494121
doi: 10.1073/pnas.2406494121
First paragraph reproduced below:
The phylogeny of birds has been extensively studied, but basal relationships within Neoaves remain contentious. Wu et al. constructed a species tree for 124 bird species based on a phylogenomic dataset (13,011 loci) that included protein-coding sequences (CDS), introns, and intergenic segments. These authors recovered a novel split at the base of Neoaves between the previously recognized clade Telluraves (land birds) and the newly recognized clade Aquaterraves (waterbirds and relatives). Outlier gene trees were removed to improve fit to the multispecies-coalescent model, and analysis of this cleaned dataset (9,108 gene trees) yielded an “optimum tree” (their figure 2) that increased bootstrap support for Aquaterraves from 78 to 100%. Wu et al.’s coalescence method (NJst) is less accurate in simulations than the coalescence method ASTRAL, so we reanalyzed their cleaned dataset with ASTRAL-III. The inferred species tree conflicted at >10% of nodes, and Aquaterraves were not supported, contradicting their main systematic conclusion.
Wu, S., F.E. Rheindt, J. Zhang, J. Wang, L. Zhang, C. Quan, Z. Li, M. Wang, F. Wu, Y. Qu, S.V. Edwards, Z. Zhou, and L. Liu (2024)
Reply to Springer and Gatesy: the impact of long branches and misalignments on phylogenetic analysis is minimal
PNAS 121: e2409344121
doi: 10.1073/pnas.2409344121
First paragraph reproduced below:
Springer and Gatesy suggested that our avian species tree, constructed using NJst, may be inaccurate due to observed disparities with the ASTRAL tree and potential misalignments. However, akin to their critiques of our other work, their criticisms stem from subjective opinions and misconceptions of phylogenetic analysis, rendering their arguments unfounded.
A new phylogeny for Aves is compromised by pervasive misalignment and homology problems
PNAS 121: e2406494121
doi: 10.1073/pnas.2406494121
First paragraph reproduced below:
The phylogeny of birds has been extensively studied, but basal relationships within Neoaves remain contentious. Wu et al. constructed a species tree for 124 bird species based on a phylogenomic dataset (13,011 loci) that included protein-coding sequences (CDS), introns, and intergenic segments. These authors recovered a novel split at the base of Neoaves between the previously recognized clade Telluraves (land birds) and the newly recognized clade Aquaterraves (waterbirds and relatives). Outlier gene trees were removed to improve fit to the multispecies-coalescent model, and analysis of this cleaned dataset (9,108 gene trees) yielded an “optimum tree” (their figure 2) that increased bootstrap support for Aquaterraves from 78 to 100%. Wu et al.’s coalescence method (NJst) is less accurate in simulations than the coalescence method ASTRAL, so we reanalyzed their cleaned dataset with ASTRAL-III. The inferred species tree conflicted at >10% of nodes, and Aquaterraves were not supported, contradicting their main systematic conclusion.
Wu, S., F.E. Rheindt, J. Zhang, J. Wang, L. Zhang, C. Quan, Z. Li, M. Wang, F. Wu, Y. Qu, S.V. Edwards, Z. Zhou, and L. Liu (2024)
Reply to Springer and Gatesy: the impact of long branches and misalignments on phylogenetic analysis is minimal
PNAS 121: e2409344121
doi: 10.1073/pnas.2409344121
First paragraph reproduced below:
Springer and Gatesy suggested that our avian species tree, constructed using NJst, may be inaccurate due to observed disparities with the ASTRAL tree and potential misalignments. However, akin to their critiques of our other work, their criticisms stem from subjective opinions and misconceptions of phylogenetic analysis, rendering their arguments unfounded.
Perhaps the most important part of the Wu et al rebuttal is this:
The ASTRAL tree of Springer & Gatesey doesn't recover Aquaterraves, but only Columbiformes is absent from their "Aquaterraves". The internal topology is very different, though. While I think the basal split between Telluraves and Aquaterraves is too different from the other genomic studies to be the real relationship, the NJst analysis in Wu et al does recovered the groups that are widely recovered in other studies (i.e. Columbaves, Guimorphae, Phaethoquornithes). The ASTRAL reanalysis is even more unusual than the original Wu et al one.
After excluding 991 CDS and 180 intergenic gene trees, we reconstructed NJst and ASTRAL trees. The resulting NJst tree remained identical to the tree including all gene trees (Fig. 2A), whereas the ASTRAL tree changed to support Aquaterraves (Fig. 2B). These results underscore NJst's robustness to data heterogeneity, contrasting sharply with ASTRAL's evident sensitivity.
The ASTRAL tree of Springer & Gatesey doesn't recover Aquaterraves, but only Columbiformes is absent from their "Aquaterraves". The internal topology is very different, though. While I think the basal split between Telluraves and Aquaterraves is too different from the other genomic studies to be the real relationship, the NJst analysis in Wu et al does recovered the groups that are widely recovered in other studies (i.e. Columbaves, Guimorphae, Phaethoquornithes). The ASTRAL reanalysis is even more unusual than the original Wu et al one.
albertonykus
Well-known member
Claramunt, S., E.L. Braun, J. Cracraft, J. Fjeldså, S.Y.W. Ho, P. Houde, J.M.T. Nguyen, and J. Stiller (2024)
Calibrating the genomic clock of modern birds using fossils
PNAS 121: e2405887121
doi: 10.1073/pnas.2405887121
First paragraph reproduced below:
Wu et al. conducted a phylogenomic analysis resulting in a new time frame for the diversification of modern birds, concluding that the rapid radiation of Neoaves occurred well before the Cretaceous–Paleogene (K–Pg) extinction event and that this catastrophic event did not affect their diversification dynamics. Here, we show that the divergence times obtained by Wu et al. were compromised by problems with their choices of fossils and calibration strategy.
Wu, S., F.E. Rheindt, J. Zhang, J. Wang, L. Zhang, C. Quan, Z. Li, M. Wang, F. Wu, Y. Qu, S.V. Edwards, Z. Zhou, and L. Liu (2024)
Reply to Claramunt et al.: Robustness of the Cretaceous radiation of crown aves
PNAS 121: e2412448121
doi: 10.1073/pnas.2412448121
First paragraph reproduced below:
Claramunt et al. suggested our dating results for a Cretaceous radiation of crown Aves may be inaccurate due to the inappropriate use of fossil calibrations. However, their criticisms stem from misinterpretations of fossil evidence and misconceptions of clock methodology, rendering their arguments baseless.
Calibrating the genomic clock of modern birds using fossils
PNAS 121: e2405887121
doi: 10.1073/pnas.2405887121
First paragraph reproduced below:
Wu et al. conducted a phylogenomic analysis resulting in a new time frame for the diversification of modern birds, concluding that the rapid radiation of Neoaves occurred well before the Cretaceous–Paleogene (K–Pg) extinction event and that this catastrophic event did not affect their diversification dynamics. Here, we show that the divergence times obtained by Wu et al. were compromised by problems with their choices of fossils and calibration strategy.
Wu, S., F.E. Rheindt, J. Zhang, J. Wang, L. Zhang, C. Quan, Z. Li, M. Wang, F. Wu, Y. Qu, S.V. Edwards, Z. Zhou, and L. Liu (2024)
Reply to Claramunt et al.: Robustness of the Cretaceous radiation of crown aves
PNAS 121: e2412448121
doi: 10.1073/pnas.2412448121
First paragraph reproduced below:
Claramunt et al. suggested our dating results for a Cretaceous radiation of crown Aves may be inaccurate due to the inappropriate use of fossil calibrations. However, their criticisms stem from misinterpretations of fossil evidence and misconceptions of clock methodology, rendering their arguments baseless.
Peter Kovalik
Well-known member
McTavish, Emily Jane, Jeff A. Gerbracht, Mark T. Holder, Marshall J. Iliff, Denis Lepage, Pam Rasmussen, Benjamin Redelings, Luna Luisa Sanchez Reyes, and Eliot T. Miller. (2024) A complete and dynamic tree of birds. bioRxiv 2024.05.20.595017
A complete and dynamic tree of birds
Abstract
We present a complete, time-scaled, evolutionary tree of the world's bird species. This tree unites phylogenetic estimates for 9,239 species from 262 studies published between 1990 and 2024, using the Open Tree synthesis algorithm. The remaining species are placed in the tree based on curated taxonomic information. The tips of this complete tree are aligned to the species in the Clements Taxonomy used by eBird and other resources, and cross-mapped to other taxonomic systems including the Open Tree of Life (Open Tree), National Center for Biotechnology Information (NCBI), and Global Biodiversity Information Facility (GBIF). The total number of named bird species varies between 10,824 and 11,017 across the taxonomy versions we applied (v2021, v2022 and v2023). We share complete trees for each taxonomy version. The procedure, software and data-stores we used to generate this tree are public and reproducible. The tree presented here is Aves v1.2 and can be easily updated with new phylogenetic information as new estimates are published. We demonstrate the types of large scale analyses this data resource enables by linking geographic data with the phylogeny to calculate the regional phylogenetic diversity of birds across the world. We will release updated versions of the phylogenetic synthesis and taxonomic translation tables annually. The procedure we describe here can be applied to developing complete phylogenetic estimates for any taxonomic group of interest.
Significance statement
Birds are charismatic - well loved, and highly studied. Many new phylogenies elucidating avian birds evolutionary relationships are published every year. We have united phylogenetic estimates from hundreds of studies to create a complete evolutionary tree of all birds. While a variety of resources aggregate huge collections of trait, behavior and location data for birds, previously the barriers to linking data between these data resources and bird evolutionary history have limited the opportunities to do exciting large scale analyses. We have bridged that gap, and developed a system that allows us to easily update our understanding of bird evolution as new estimates are generated. We share a workflow and the software needed to create a complete evolutionary tree for any group.
A complete and dynamic tree of birds
Abstract
We present a complete, time-scaled, evolutionary tree of the world's bird species. This tree unites phylogenetic estimates for 9,239 species from 262 studies published between 1990 and 2024, using the Open Tree synthesis algorithm. The remaining species are placed in the tree based on curated taxonomic information. The tips of this complete tree are aligned to the species in the Clements Taxonomy used by eBird and other resources, and cross-mapped to other taxonomic systems including the Open Tree of Life (Open Tree), National Center for Biotechnology Information (NCBI), and Global Biodiversity Information Facility (GBIF). The total number of named bird species varies between 10,824 and 11,017 across the taxonomy versions we applied (v2021, v2022 and v2023). We share complete trees for each taxonomy version. The procedure, software and data-stores we used to generate this tree are public and reproducible. The tree presented here is Aves v1.2 and can be easily updated with new phylogenetic information as new estimates are published. We demonstrate the types of large scale analyses this data resource enables by linking geographic data with the phylogeny to calculate the regional phylogenetic diversity of birds across the world. We will release updated versions of the phylogenetic synthesis and taxonomic translation tables annually. The procedure we describe here can be applied to developing complete phylogenetic estimates for any taxonomic group of interest.
Significance statement
Birds are charismatic - well loved, and highly studied. Many new phylogenies elucidating avian birds evolutionary relationships are published every year. We have united phylogenetic estimates from hundreds of studies to create a complete evolutionary tree of all birds. While a variety of resources aggregate huge collections of trait, behavior and location data for birds, previously the barriers to linking data between these data resources and bird evolutionary history have limited the opportunities to do exciting large scale analyses. We have bridged that gap, and developed a system that allows us to easily update our understanding of bird evolution as new estimates are generated. We share a workflow and the software needed to create a complete evolutionary tree for any group.
Very interesting! Maybe I'm daft, but where's the actual readable tree they say they present?
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Nowhere
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Jacana
Will Jones
The above pre-print has now found a home in PNAS:
E.J. McTavish, J.A. Gerbracht, M.T. Holder, M.J. Iliff, D. Lepage, P.C. Rasmussen, B.D. Redelings, L.L. Sánchez Reyes, & E.T. Miller, A complete and dynamic tree of birds, Proc. Natl. Acad. Sci. U.S.A. 122 (18) e2409658122, https://doi.org/10.1073/pnas.2409658122 (2025).
E.J. McTavish, J.A. Gerbracht, M.T. Holder, M.J. Iliff, D. Lepage, P.C. Rasmussen, B.D. Redelings, L.L. Sánchez Reyes, & E.T. Miller, A complete and dynamic tree of birds, Proc. Natl. Acad. Sci. U.S.A. 122 (18) e2409658122, https://doi.org/10.1073/pnas.2409658122 (2025).
Snapdragyn
Well-known member
OK, I've reached that age where I need someone younger to explain tech stuff to me.
Where do I get the actual tree to look at? I've followed the GitHub link, and (as I often find on GitHub) cannot locate an actual FILE link. Where is this thing hidden, please? >/
Where do I get the actual tree to look at? I've followed the GitHub link, and (as I often find on GitHub) cannot locate an actual FILE link. Where is this thing hidden, please? >/
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Frankly, if there is a PDF with the phylogeny of 9000 species, I'll take it. The most interesting phylogenies are never shown.
Mysticete
Well-known member
You can look at the phylogeny here through there webpage interface, although I am not sure how easy it will be to parse or navigate. Since it was a preprint I don't think this page was online accessible yet, but is now.
These won't be new issues because they'll all have been raised by one or other of the studies that were fed into this, but that's going to keep the taxonomists busy for a while.
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