Complexity of avian evolution revealed by family-level genomes

Nature, Journal Year: 2024, Volume and Issue: 629(8013), P. 851 - 860

Published: April 1, 2024

Abstract Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and choice genomic regions 1–3 . Here we address these issues by analysing genomes 363 bird 4 (218 taxonomic families, 92% total). Using intergenic coalescent methods, present well-supported tree but also marked degree discordance. The confirms that Neoaves experienced rapid radiation at or near Cretaceous–Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective resolving difficult nodes. Remaining recalcitrant nodes involve are challenge model due either extreme DNA composition, variable substitution rates, incomplete lineage sorting complex evolutionary events such as ancient hybridization. Assessment effects different partitions showed high heterogeneity across genome. We discovered sharp increases population size, rates relative brain size following extinction event, supporting hypothesis emerging ecological opportunities catalysed diversification modern birds. resulting estimate offers fresh insights into birds provides taxon-rich backbone for future comparative studies.

Language: Английский

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Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(8)

Published: Feb. 12, 2024

The phylogeny and divergence timing of the Neoavian radiation remain controversial despite recent progress. We analyzed genomes 124 species across all orders, using data from 25,460 loci spanning four DNA classes, including 5,756 coding sequences, 12,449 conserved nonexonic elements, 4,871 introns, 2,384 intergenic segments. conducted a comprehensive sensitivity analysis to account for heterogeneity different leading an optimal tree Neoaves with high resolution. This features novel dichotomy comprising two monophyletic clades: previously recognized Telluraves (land birds) newly circumscribed Aquaterraves (waterbirds relatives). Molecular dating analyses 20 fossil calibrations indicate that diversification modern birds began in Late Cretaceous underwent constant steady KPg boundary, concurrent rise angiosperms as well other major Cenozoic animal groups placental multituberculate mammals. catastrophe had limited impact on avian evolution compared Paleocene–Eocene Thermal Maximum, which triggered rapid seabirds. Our findings suggest followed slow process gradualism rather than punctuated equilibrium, interruption by catastrophe. study places bird into new context within vertebrates, ramifications Earth’s biota.

Language: Английский

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A complete and dynamic tree of birds

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 22, 2024

Abstract We present a complete, time-scaled, evolutionary tree of the world’s bird species. This unites phylogenetic estimates for 9,239 species from 262 studies published between 1990 and 2024, using Open Tree synthesis algorithm. The remaining are placed in based on curated taxonomic information. tips this complete aligned to Clements Taxonomy used by eBird other resources, cross-mapped systems including Life (Open Tree), National Center Biotechnology Information (NCBI), Global Biodiversity Facility (GBIF). total number named varies 10,824 11,017 across taxonomy versions we applied (v2021, v2022 v2023). share trees each version. procedure, software data-stores generate public reproducible. presented here is Aves v1.2 can be easily updated with new information as published. demonstrate types large scale analyses data resource enables linking geographic phylogeny calculate regional diversity birds world. will release translation tables annually. procedure describe developing any group interest. Significance statement Birds charismatic - well loved, highly studied. Many phylogenies elucidating avian relationships every year. have united hundreds create all birds. While variety resources aggregate huge collections trait, behavior location birds, previously barriers these history limited opportunities do exciting analyses. bridged that gap, developed system allows us update our understanding evolution generated. workflow needed group.

Language: Английский

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A comparative developmental study of the avian syrinx: Insights into the homology of the sound‐producing muscles in birds

Journal of Anatomy, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 17, 2025

Abstract The anatomical innovation of sound‐producing organs, which gives rise to a wide variety sound signals, is one the most fundamental factors leading explosive speciation modern birds. Despite being key clue resolving homology sound‐controlling muscles among birds, only few studies have explored embryonic development syringeal muscles. Using serial histological sections and immunohistochemistry, we described three‐dimensional anatomy cartilage, muscle, innervation pattern tracheobronchi in three avian species: domestic fowls, cockatiels, zebra finches. Crucially, muscle primordia tracheobronchial develop from caudal end lateral tracheal cockatiels Furthermore, finches are subsequently split during development. Based on our findings identity hypoglossal nerve between finches, suggest that component traditionally documented as superficial parrots homologous ventral These facts not orchestrate terminological discrepancies previous studies, but also were acquired by common ancestor passerines, further compartmentalized perhaps song repertoire for acoustic communication.

Language: Английский

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Exceptionally Weak Continental Weathering During the Early Cretaceous Hyperthermal Crisis: Rain Shadow Effect by a High-Altitude Mountain Range in East China

Published: Jan. 1, 2025

Language: Английский

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A complete and dynamic tree of birds

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(18)

Published: April 29, 2025

We present a complete, time-scaled, evolutionary tree of the world’s bird species. This unites phylogenetic estimates for 9,239 species from 262 studies published between 1990 and 2024, using Open Tree synthesis algorithm. The remaining are placed in based on curated taxonomic information. tips this complete aligned to Clements Taxonomy used by eBird other resources, cross-mapped systems including Life (Open Tree), National Center Biotechnology Information, Global Biodiversity Information Facility. total number named varies 10,824 11,017 across taxonomy versions we applied (v2021, v2022, v2023). share trees each version. procedure, software, data stores generate public reproducible. presented here is Aves 1.3 can be easily updated with new information as published. demonstrate types large-scale analyses resource enables linking geographic phylogeny calculate regional diversity birds world. will release translation tables annually. procedure describe developing any group interest.

Language: Английский

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Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 3, 2024

The evolutionary histories of different genomic regions typically differ from each other and the underlying species phylogeny. This makes tree estimation challenging. Here, we examine performance phylogenomic methods using a well-resolved phylogeny that nevertheless contains many difficult nodes, living birds. We compared trees generated by maximum likelihood (ML) analysis concatenated data, gene summary methods, SVDquartets. also conduct first empirical test “new” method called METAL (Metric algorithm for Estimation Trees based on Aggregation Loci), which is distances calculated data. conducted this novel dataset comprising more than 4,000 ultraconserved element (UCE) loci almost all bird families two existing UCE intron datasets sampled avian orders. identified “reliable clades” very likely to be present in true used them assess performance. ML analyses data recovered reliable clades with less greater robustness missing methods. clades, but only performed well largest datasets. Gene (weighted ASTRAL weighted ASTRID) well; they required concatenation. SVDquartets exhibited worst tested. In addition methodological insights, study provides estimate 99% currently recognized families. Only one 181 examined was consistently resolved differently concatenation versus suggesting it may possible achieve consensus deep extant

Language: Английский

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Hummingbirds (Trochilidae)

Birds of the World, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 22, 2024

Language: Английский

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Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAcc

Integrative and Comparative Biology, Journal Year: 2024, Volume and Issue: 64(5), P. 1513 - 1525

Published: May 29, 2024

Synopsis Comparative genomics provides ample ways to study genome evolution and its relationship phenotypic traits. By developing testing alternate models of throughout a phylogeny, one can estimate rates molecular along different lineages in phylogeny link these with observations extant species, such as convergent phenotypes. Pipelines for work help identify when where genomic changes may be associated with, or possibly influence, We recently developed set called PhyloAcc, using Bayesian framework nucleotide substitution on branches phylogenetic tree evaluate their association pre-defined estimated PhyloAcc-ST PhyloAcc-GT both allow users define priori target then compare loci accelerating more lineages. Whereas ST considers only species across all input loci, GT topologies every locus. PhyloAcc-C simultaneously continuous trait evolution, allowing the user ask whether two are associated. Here, we describe provide tips workflows how prepare data run PhyloAcc.

Language: Английский

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Untangling the tree or unravelling the consensus? Recent developments in the quest to resolve the broad-scale relationships within Dinosauria

Journal of Systematic Palaeontology, Journal Year: 2024, Volume and Issue: 22(1)

Published: June 5, 2024

The phylogenetic relationships of the major lineages within Dinosauria have come under intense scrutiny in recent years. In 2017, a radical new hypothesis early dinosaur evolution, 'Ornithoscelida hypothesis', was proposed, prompting flurry work this area. However, instead untangling tree dinosaurs as hoped, further research unravelled scientific consensus on origins and their relationships. Multiple hypotheses now been including several that position 'traditionally' non-dinosaurian silesaurids Dinosauria. There is no sign an emerging consensus, with all possible combinations three clades (Ornithischia, Theropoda Sauropodomorpha) having recovered by analyses. existence 'wildcard taxa' uncertain affinities around base complicates efforts to differentiate these hypotheses. Recent studies suggested data sets used investigate might be fatally flawed. construction stronger focus logical underpinning characters, addition inclusion newly described or redescribed taxa, will likely hold key resolving debate.

Language: Английский

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