Fwd: Late Cretaceous concurrent rise of modern birds and flowering plants (free pdf)
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Ben Creisler
Jul 10, 2024, 3:36:41 PMJul 10
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Comment and response:
Free pdfs:
Mark S. Springer and John Gatesy (2024)
A new phylogeny for Aves is compromised by pervasive misalignment and homology problems
Proceedings of the National Academy of Sciences 121(29): e2406494121
doi: https://doi.org/10.1073/pnas.2406494121
https://www.pnas.org/doi/10.1073/pnas.2406494121
Free pdf:
https://www.pnas.org/doi/epdf/10.1073/pnas.2406494121
*****
Shaoyuan Wu, Frank E Rheindt, Jin Zhang, Jiajia Wang, Lei Zhang, Cheng Quan, Zhiheng Li, Min Wang, Feixiang Wu, Yanhua Qu, Scott V Edwards, Zhonghe Zhou & Liang Liu (2024)
Reply to Springer and Gatesy: The impact of long branches and misalignments on phylogenetic analysis is minimal.
Proceedings of the National Academy of Sciences 121(29): e2409344121
doi: https://doi.org/10.1073/pnas.2409344121
https://www.pnas.org/doi/10.1073/pnas.2409344121
Free pdf:
https://www.pnas.org/doi/epdf/10.1073/pnas.2409344121
---------- Forwarded message ---------
From: Ben Creisler <bcre...@gmail.com>
Date: Mon, Feb 12, 2024 at 12:58 PM
Subject: Late Cretaceous concurrent rise of modern birds and flowering plants (free pdf)
To: <dinos...@usc.edu>
From: Ben Creisler <bcre...@gmail.com>
Date: Mon, Feb 12, 2024 at 12:58 PM
Subject: Late Cretaceous concurrent rise of modern birds and flowering plants (free pdf)
To: <dinos...@usc.edu>
Ben Creisler
A new paper:
Shaoyuan Wu, Frank E. Rheindt, Jin Zhang, Jiajia Wang, Lei Zhang, Cheng Quan, Zhiheng Li, Min Wang, Feixiang Wu, Yanhua Qu, Scott V. Edwards, Zhonghe Zhou, and Liang Liu (2024)
Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous
Proceedings of the National Academy of Sciences 121(8): e231969612
doi: 10.1073/pnas.2319696121
https://www.pnas.org/doi/10.1073/pnas.2319696121
Despite modern DNA advances, scientists still know little about how and when early bird groups evolved. Using new approaches to mine genomic information among 124 species covering most of modern bird diversity, we found that the main lineages of birds first divided into two groups: one mostly land-based and the other containing water-associated species. We demonstrate that modern birds date back further than previously assumed, much earlier than the dinosaurian extinction event, which seems to have had a limited impact on birds’ evolution. Instead, a warming event around ~55 Mya appears to have triggered the diversification of modern seabirds. Our study indicates that the radiation of modern birds was in remarkable lockstep with that of flowering plants and other organisms.
Abstract
The phylogeny and divergence timing of the Neoavian radiation remain controversial despite recent progress. We analyzed the genomes of 124 species across all Neoavian orders, using data from 25,460 loci spanning four DNA classes, including 5,756 coding sequences, 12,449 conserved nonexonic elements, 4,871 introns, and 2,384 intergenic segments. We conducted a comprehensive sensitivity analysis to account for the heterogeneity across different DNA classes, leading to an optimal tree of Neoaves with high resolution. This phylogeny features a novel Neoavian dichotomy comprising two monophyletic clades: a previously recognized Telluraves (land birds) and a newly circumscribed Aquaterraves (waterbirds and relatives). Molecular dating analyses with 20 fossil calibrations indicate that the diversification of modern birds began in the Late Cretaceous and underwent a constant and steady radiation across the KPg boundary, concurrent with the rise of angiosperms as well as other major Cenozoic animal groups including placental and multituberculate mammals. The KPg catastrophe had a limited impact on avian evolution compared to the Paleocene–Eocene Thermal Maximum, which triggered a rapid diversification of seabirds. Our findings suggest that the evolution of modern birds followed a slow process of gradualism rather than a rapid process of punctuated equilibrium, with limited interruption by the KPg catastrophe. This study places bird evolution into a new context within vertebrates, with ramifications for the evolution of the Earth’s biota.
Free pdf:
Shaoyuan Wu, Frank E. Rheindt, Jin Zhang, Jiajia Wang, Lei Zhang, Cheng Quan, Zhiheng Li, Min Wang, Feixiang Wu, Yanhua Qu, Scott V. Edwards, Zhonghe Zhou, and Liang Liu (2024)
Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous
Proceedings of the National Academy of Sciences 121(8): e231969612
doi: 10.1073/pnas.2319696121
https://www.pnas.org/doi/10.1073/pnas.2319696121
Despite modern DNA advances, scientists still know little about how and when early bird groups evolved. Using new approaches to mine genomic information among 124 species covering most of modern bird diversity, we found that the main lineages of birds first divided into two groups: one mostly land-based and the other containing water-associated species. We demonstrate that modern birds date back further than previously assumed, much earlier than the dinosaurian extinction event, which seems to have had a limited impact on birds’ evolution. Instead, a warming event around ~55 Mya appears to have triggered the diversification of modern seabirds. Our study indicates that the radiation of modern birds was in remarkable lockstep with that of flowering plants and other organisms.
Abstract
The phylogeny and divergence timing of the Neoavian radiation remain controversial despite recent progress. We analyzed the genomes of 124 species across all Neoavian orders, using data from 25,460 loci spanning four DNA classes, including 5,756 coding sequences, 12,449 conserved nonexonic elements, 4,871 introns, and 2,384 intergenic segments. We conducted a comprehensive sensitivity analysis to account for the heterogeneity across different DNA classes, leading to an optimal tree of Neoaves with high resolution. This phylogeny features a novel Neoavian dichotomy comprising two monophyletic clades: a previously recognized Telluraves (land birds) and a newly circumscribed Aquaterraves (waterbirds and relatives). Molecular dating analyses with 20 fossil calibrations indicate that the diversification of modern birds began in the Late Cretaceous and underwent a constant and steady radiation across the KPg boundary, concurrent with the rise of angiosperms as well as other major Cenozoic animal groups including placental and multituberculate mammals. The KPg catastrophe had a limited impact on avian evolution compared to the Paleocene–Eocene Thermal Maximum, which triggered a rapid diversification of seabirds. Our findings suggest that the evolution of modern birds followed a slow process of gradualism rather than a rapid process of punctuated equilibrium, with limited interruption by the KPg catastrophe. This study places bird evolution into a new context within vertebrates, with ramifications for the evolution of the Earth’s biota.
====
Ben Creisler
Sep 17, 2024, 2:41:05 PMSep 17
to DinosaurMa...@googlegroups.com
Another response:
Santiago Claramunt, Edward L. Braun, Joel Cracraft, Jon Fjeldså, Simon Y. W. Ho, Peter Houde, Jacqueline M. T. Nguyen, and Josefin Stiller (2024)
Calibrating the genomic clock of modern birds using fossils
Proceedings of the National Academy of Sciences 121(39): e2405887121
doi: https://doi.org/10.1073/pnas.240588712
https://www.pnas.org/doi/10.1073/pnas.2405887121
Free pdf:
https://www.pnas.org/doi/epub/10.1073/pnas.2405887121
Wu et al. (1) 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.
Free pdf:
Santiago Claramunt, Edward L. Braun, Joel Cracraft, Jon Fjeldså, Simon Y. W. Ho, Peter Houde, Jacqueline M. T. Nguyen, and Josefin Stiller (2024)
Calibrating the genomic clock of modern birds using fossils
Proceedings of the National Academy of Sciences 121(39): e2405887121
doi: https://doi.org/10.1073/pnas.240588712
https://www.pnas.org/doi/10.1073/pnas.2405887121
Free pdf:
https://www.pnas.org/doi/epub/10.1073/pnas.2405887121
Wu et al. (1) 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.
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