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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Origin and Evolution of Birds

Fascinating life sciences, Journal Year: 2023, Volume and Issue: unknown, P. 1 - 154

Published: Jan. 1, 2023

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 region of suppressed recombination misleads neoavian phylogenomics

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(15)

Published: April 1, 2024

Genomes are typically mosaics of regions with different evolutionary histories. When speciation events closely spaced in time, recombination makes the sharing same history small, and changes rapidly as we move along genome. examining rapid radiations such early diversification Neoaves 66 Mya, no consistent is observed across segments exceeding kilobases Here, report an exception. We found that a 21-Mb region avian genomes, mapped to chicken chromosome 4, shows extremely strong discordance-free signal for from inferred species tree. Such signal, indicative suppressed many millions base pairs, not elsewhere genome any deep relationships. Although long have been documented recently diverged species, our results pertain relationships dating circa 65 Mya. provide evidence this may be due ancient rearrangement blocked remained polymorphic several million years prior fixation. show presence has misled previous phylogenomic efforts lower taxon sampling, showing interplay between locus sampling. predict similar rearrangements confound phylogenetic analyses other clades, pointing need new analytical models incorporate possibility events.

Language: Английский

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Data Types and the Phylogeny of Neoaves

Birds, Journal Year: 2021, Volume and Issue: 2(1), P. 1 - 22

Published: Jan. 5, 2021

The phylogeny of Neoaves, the largest clade extant birds, has remained unclear despite intense study. difficulty associated with resolving early branches in Neoaves is likely driven by rapid radiation this group. However, conflicts among studies may be exacerbated data type analyzed. For example, analyses coding exons typically yield trees that place Strisores (nightjars and allies) sister to remaining while non-coding where Mirandornites (flamingos grebes) Neoaves. Our understanding effects hampered fact previous have used different taxa, loci, types data. Herein, we provide strong corroboration hypothesis for comparing based on derived from same taxa gene regions. A simple analytical method known minimize biases due base composition (coding nucleotides as purines pyrimidines) resulted exon increased congruence topology using concatenated analyses. These results improve our resolution neoavian point a challenge—data effects—that an important factor phylogenetic birds (and many other taxonomic groups). Using results, summary identifies well-corroborated relationships highlights specific nodes future efforts should focus.

Language: Английский

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What Have We Learned from the First 500 Avian Genomes?

Annual Review of Ecology Evolution and Systematics, Journal Year: 2021, Volume and Issue: 52(1), P. 611 - 639

Published: Sept. 9, 2021

The increased capacity of DNA sequencing has significantly advanced our understanding the phylogeny birds and proximate ultimate mechanisms molding their genomic diversity. In less than a decade, number available avian reference genomes to over 500—approximately 5% bird diversity—placing in privileged position advance fields phylogenomics comparative, functional, population genomics. Whole-genome sequence data, as well indels rare changes, are further resolving tree life. accumulation genomes, increasingly with long-read greatly improves resolution features such germline-restricted chromosomes W chromosome, is facilitating comparative integration genotypes phenotypes. Community-based initiatives Bird 10,000 Genomes Project Vertebrate Genome playing fundamental role amplifying coalescing vibrant international program

Language: Английский

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The avian respiratory system: implications for anaesthesia

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 380(1920)

Published: Feb. 27, 2025

Anaesthesia is not a natural state for any animal, including birds. The unique anatomic and physiological attributes of the class Aves that have made it possible birds to inhabit every continent on this planet live in variety environments, some considered challenging if inhospitable mammals, pose challenges their anaesthetic management. Indeed, more than management reality substantiated by fact risk anaesthesia-related death up 20 times higher dogs cats. This article highlights those (respiratory system, renal–portal system), (gas exchange, respiratory control mechanisms brainstem peripheral chemoreceptor areas, intrapulmonary chemoreceptors) pharmacological (pharmacokinetics pharmacodynamics) make management, both inhalant injectable anaesthesia, challenging, how are managed. part theme issue ‘The biology avian system’.

Language: Английский

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Biogeographic mechanisms involved in the colonization of Madagascar by African vertebrates: Rifting, rafting and runways

Journal of Biogeography, Journal Year: 2020, Volume and Issue: 48(3), P. 492 - 510

Published: Dec. 9, 2020

Abstract Aim For 80 years, popular opinion has held that most of Madagascar's terrestrial vertebrates arrived from Africa by transoceanic dispersal (i.e. rafting or swimming). We reviewed this proposition, focussing on three ad hoc hypotheses proposed to render unlikely scenario more feasible: (a) Could hibernation have helped mammals reach Madagascar? (b) the aquatic abilities hippopotamuses enabled them swim Mozambique Channel? (c) How valid is Ali‐Huber model predicting eastward Palaeogene surface currents allowed rafts Madagascar in 3–4 weeks? Finally, we explored alternative hypothesis geodispersal via short‐lived land bridges between and Madagascar. Location East Africa, Madagascar, Channel. Taxa Fish, amphibians, reptiles, birds, mammals. Methods established colonization timeframes using molecular divergence dates estimated for Malagasy vertebrate lineages. likelihood “torpid waif” “swimming hippopotamus” hypotheses, re‐investigated Ali Huber's Eocene jet‐like tracking particle trajectories simulated Institut Pierre‐Simon Laplace Earth System Model. summarized recent geological findings Channel, used compile palaeosedimentological maps PLACA4D. Results fauna complex origins. Hibernation probably an adaptation hypervariable climate, rather than a facilitator mammal dispersal. Hippopotamus physiology precludes ability cross oceanic channel deeper 4 m hundreds km wide. The considerably underestimated time required Channel under palaeogeographic conditions. New data indicate existence at 66–60 Ma, 36–30 Ma 12–05 Ma. Main conclusion Cenozoic afford grounded extant biota swimming, although vicariance, island hopping limited also played role.

Language: Английский

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A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths

Molecular Phylogenetics and Evolution, Journal Year: 2021, Volume and Issue: 158, P. 107091 - 107091

Published: Feb. 3, 2021

Language: Английский

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Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi

Systematic Biology, Journal Year: 2022, Volume and Issue: 71(3), P. 741 - 757

Published: Jan. 31, 2022

Whole genome sequences are beginning to revolutionize our understanding of phylogenetic relationships. Yet, even whole can fail resolve the evolutionary history most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure group. To overcome such challenges, one emerging strategy is integrate results across different methods. Most approaches have been implemented on reduced representation genomic data sets, but genomes should provide maximum possible evidence approach. Here, we test ability single nucleotide polymorphisms extracted from resequencing data, in an integrative approach, key nodes phylogeny mbuna, rock-dwelling cichlid fishes Lake Malaŵi, which epitomize intractability that often accompanies explosive diversification. This monophyletic radiation has diversified at unparalleled rate into several hundred species less than 2 million years. Using array phylogenomic methods, consistently recovered four major clades a large basal polytomy among them. Although introgression between apparently contributed challenge reconstruction, reduction set nonintrogressed sites still did not help polytomy. On hand, relationships six congeneric pairs were resolved without ambiguity, case existing led us predict resolution would be difficult. We conclude bursts diversification earliest stages mbuna may phylogenetically unresolvable, regions tree clearly supported. Integration multiple will continue increase confidence inferred these whole-genome sets. [Incomplete sorting; introgression; linkage disequilibrium; multispecies coalescence; rapid radiation; soft polytomy.].

Language: Английский

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