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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A genomic timescale for placental mammal evolution

Science, Journal Year: 2023, Volume and Issue: 380(6643)

Published: April 27, 2023

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis genetic variation across an alignment 241 mammal genome assemblies, addressing prior concerns regarding limited genomic sampling species. compared neutral genome-wide phylogenomic signals using concatenation coalescent-based approaches, interrogated chromosomes, analyzed extensive catalogs structural variants. Interordinal relationships exhibit relatively low rates conflict diverse datasets analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades radiated during the Cenozoic. Genomic time trees reveal accumulation cladogenic before immediately after Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance K-Pg extinction in radiation.

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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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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Karyotypic stasis and swarming influenced the evolution of viral tolerance in a species-rich bat radiation

Cell Genomics, Journal Year: 2024, Volume and Issue: 4(2), P. 100482 - 100482

Published: Jan. 17, 2024

The emergence of COVID-19 and severe acute respiratory syndrome (SARS) has prioritized understanding bats' viral tolerance. Myotis bats are exceptionally species rich have evolved They also exhibit swarming, a cryptic behavior where large, multi-species assemblages gather for mating, which been hypothesized to promote interspecific hybridization. To resolve the coevolution genome architecture their unusual antiviral tolerance, we undertook phylogenomic analysis 60 Old World genomes. We demonstrate an extensive history introgressive hybridization that replaced phylogeny across 17%-93% except pericentromeric regions macrochromosomes. Introgression tracts were enriched on microchromosome containing key pathway genes overexpressed during challenge experiments. Together, these results suggest karyotype may selectively position immune-related in high recombining genomic prone introgression divergent alleles, including diversity interleukin loci responsible release pro-inflammatory cytokines.

Language: Английский

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Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: June 26, 2024

The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, schrenkii, Sander vitreus along with additional percid reference genomes, we provide an evolutionary comparative genomic analysis their sex-determination systems.

Language: Английский

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Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements

BMC Ecology and Evolution, Journal Year: 2021, Volume and Issue: 21(1)

Published: Nov. 22, 2021

Abstract Background Divergence time estimation is fundamental to understanding many aspects of the evolution organisms, such as character evolution, diversification, and biogeography. With development sequence technology, improved analytical methods, knowledge fossils for calibration, it possible obtain robust molecular dating results. However, while phylogenomic datasets show great promise in phylogenetic estimation, best ways leverage large amounts data divergence has not been well explored. A potential solution focus on a subset which can significantly reduce computational burdens avoid problems with heterogeneity that may bias Results In this study, we obtained thousands ultraconserved elements (UCEs) from 130 extant galliform taxa, including representatives all genera, determine times throughout history. We tested effects different “gene shopping” schemes using carefully, previously validated, set fossils. Our results found commonly used clock-like be suitable UCE (or other types) where some loci have little information. suggest use partitioning (e.g., PartitionFinder) selection tree-like partitions good strategies select UCEs. tree largely consistent clock studies mitochondrial nuclear loci. our increased taxon sampling, well-resolved topology, carefully vetted fossil calibrations, high quality tree. Conclusions provide backbone combined more records further facilitate Galliformes resource comparative biogeographic group.

Language: Английский

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Phylogenetic definitions for 25 higher-level clade names of birds

Avian Research, Journal Year: 2022, Volume and Issue: 13, P. 100027 - 100027

Published: Jan. 1, 2022

Knowledge of the higher-level phylogenetic relationships birds has grown substantially during past two decades due to application genomic data. However, nomenclature taxa not become more stable, lack regulation taxon names above level superfamily by ICZN, and usage rank-based nomenclature, which is tied clades in a phylogeny. Lack instability impede effective communication among systematists. We review support for avian using set 10 phylogenomic data sets, identify that are supported congruency at least four these. provide formal definitions these based on rules recently published PhyloCode. The 25 here defined minimum-crown-clade (n ​= ​23), minimum-clade ​1) maximum-crown-clade definitions. Five new introduced here: Dinocrypturi, Pteroclimesites, Musophagotides, Phaethoquornithes Pelecanes. also diagnostic apomorphies relevant clades, known synonyms homonyms. By establishing link between well-supported hypotheses, our will solid basis stabilization nomenclature.

Language: Английский

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Ancient proteins resolve controversy over the identity ofGenyorniseggshell

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(43)

Published: May 24, 2022

The realization that ancient biomolecules are preserved in “fossil” samples has revolutionized archaeological science. Protein sequences survive longer than DNA, but their phylogenetic resolution is inferior; therefore, careful assessment of the research questions required. Here, we show potential proteins Pleistocene eggshell addressing a longstanding controversy human and animal evolution: identity extinct bird laid large eggs which were exploited by Australia’s indigenous people. had been originally attributed to iconic flightless Genyornis newtoni (†Dromornithidae, Galloanseres) subsequently dated before 50 ± 5 ka Miller et al. [ Nat. Commun. 7, 10496 (2016)]. This was taken represent likely extinction date for this endemic megafaunal species thus implied role humans its demise. A contrasting hypothesis, according mound-builder megapode (Megapodiidae, Galliformes), would therefore acquit responsibility . Ancient protein reconstructed used assess evolutionary proximity undetermined extant birds, rejecting hypothesis. Authentic DNA could not be confirmed from these highly degraded samples, morphometric data also support attribution When triangulation address well-defined hypotheses, paleoproteomics powerful tool reconstructing history samples. In addition clarification placement, provide more nuanced understanding modes interactions between environment.

Language: Английский

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