Complexity of avian evolution revealed by family-level genomes

Nature, Год журнала: 2024, Номер 629(8013), С. 851 - 860

Опубликована: Апрель 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.

Язык: Английский

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A region of suppressed recombination misleads neoavian phylogenomics

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(15)

Опубликована: Апрель 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.

Язык: Английский

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CASTER: Direct species tree inference from whole-genome alignments

Science, Год журнала: 2025, Номер unknown

Опубликована: Янв. 23, 2025

Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference tree life. While genome-wide data are routinely used for discordance-aware phylogenomic analyses, due to modeling and scalability limitations, current practice leaves out large chunks genomes. As more high-quality genomes become available, we urgently need methods infer directly from a multiple genome alignment. Here, introduce CASTER, theoretically justified site-based method that eliminates predefine recombination-free loci. CASTER is scalable hundreds mammalian whole We demonstrate accuracy in simulations include recombination apply several biological datasets, showing its per-site scores can reveal both artefactual patterns discordance across genome.

Язык: Английский

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The avian respiratory system: implications for anaesthesia

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2025, Номер 380(1920)

Опубликована: Фев. 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’.

Язык: Английский

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Conserved gene content and unique phylogenetic history characterize the 'bloopergene' underlying Triturus' balanced lethal system

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 25, 2024

Abstract In a balanced lethal system, half the reproductive output succumbs. Triturus newts are best-known example. Their chromosome 1 comes in two distinct versions and embryos carrying same version twice experience developmental arrest. Those possessing different survive, suggesting that each carries something uniquely vital. With target capture we obtain over 7,000 nuclear DNA markers across genus all main lineages of Salamandridae (the family to which belongs) investigate evolutionary history Triturus’ versus other chromosomes. Dozens genes completely missing from either one or . Furthermore, unique gene content 1A 1B is remarkably similar species, system evolved before radiated. The tree topology differs rest genome, presumably due pervasive, ancient hybridization between ancestor newt lineages. Our findings accentuate complex nature – ‘bloopergene’ driving evolutionarily enigmatic system.

Язык: Английский

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NewtCap: an efficient target capture approach to boost genomic studies in Salamandridae (True Salamanders and Newts)

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 25, 2024

Abstract Salamanders have large and complex genomes, hampering whole genome sequencing, but reduced representation sequencing provides a feasible alternative. We present NewtCap: sequence capture bait set that targets c.7k coding regions across the genomes of all True Newts (the family Salamandridae, also known as ‘salamandrids’). test efficacy NewtCap, originally designed for Eurasian Triturus newts, in 30 species, belonging to 17 different genera, cover main Salamandridae lineages. NewtCap two other salamander families. discover performs well lineages (but not families Ambystomatidae Hynobiidae). As expected, amount genetic divergence from genus correlates negatively mapping success. However, this does impede our downstream analyses. showcase potential contexts of; 1) phylogenomics, by reconstructing phylogeny 2) phylogeography, four closely related species comprising Taricha , 3) hybrid zone analysis, genotyping Lissotriton classes interspecific hybrids, 4) conservation genetics, comparing ivanbureschi samples several wild populations one captive-bred population. Overall, has boost straightforward, reproducible, affordable genomic studies, tackling both fundamental applied research questions salamandrids.

Язык: Английский

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Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants

Systematic Biology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 8, 2025

Abstract While some relationships in phylogenomic studies have remained stable since the Sanger sequencing era, many challenging nodes remain, even with genome-scale data. Incongruence or lack of resolution era is frequently attributed to inadequate data modeling and analytical issues that lead systematic biases. However, few investigate potential for random error establish expectations level achievable a given empirical dataset integrate uncertainties across methods when faced conflicting results. Ants are most species-rich lineage social insects one ecologically important terrestrial animals. Consequently, ants garnered significant research attention, including their systematics. Despite this, there has been no comprehensive genus-level phylogeny inferred using genomic thoroughly evaluates both signal strength incongruence. In this study, we provide insight into quantify uncertainty ant tree life by utilizing taxonomically Ultraconserved Elements date, 277 (81%) recognized genera from all 16 extant subfamilies, representing over 98% described species. We use simulations resolution, identify branches less-than-expected concordance, dissect effects model selection on recalcitrant nodes. Simulations show hundreds loci needed resolve our phylogeny. This demonstrates continued role studies. Our analyses picture support incongruence phylogeny, while offering more nuanced depiction significantly expanding generic sampling. consensus approach different find assumptions about root age exert substantial influence divergence dating. results suggest advancing understanding will require not only but also refined phylogenetic models. workflow identifying under-supported concatenation analyses, outline pragmatic way reconcile phylogenomics, introduce user-friendly locus tool

Язык: Английский

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Evaluating UCE data adequacy and integrating uncertainty in a comprehensive phylogeny of ants

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 5, 2024

Abstract While some relationships in phylogenomic studies have remained stable since the era of Sanger sequencing, many challenging nodes elude resolution, even with genome-scale data. As early grappled random error and insufficient information, incongruence or lack resolution phylogenomics is generally associated inadequate modeling biological phenomena combined analytical issues leading to systematic biases. Few studies, however, explore potential for establish an expectation what level should be expected from a given empirical dataset. In presenting incongruent results, phylogeneticists face choice providing diverse array results different approaches single preferred tree, few attempting integrate uncertainties across methods. Recent phylogenetic work has uncovered well-supported often novel relationships, as well more contentious findings, phylogeny ants. Ants are most species-rich lineage social insects among ecologically important terrestrial animals. result, they attracted much research, including regarding systematics. To date, there been no comprehensive genus-level ants inferred using genomic data effort evaluate signal throughout. Here we provide deeper insight into quantify uncertainty ant tree life. We accomplish this taxonomically Ultraconserved Elements dataset 277 (81%) recognized genera all 16 extant subfamilies, representing over 98% described species-level diversity. use simulations expectations identify branches less-than-expected concordance, dissect effects model selection on recalcitrant nodes. also construct consensus integrating multiple analyses. Simulations show that hundreds loci needed resolve our phylogeny, under best-case scenario known parameters without bias. This demonstrates continues play role phylogenomics. Our analyses picture support topology congruent recent study subfamily-level, while rendering realistic significantly expanding generic sampling. divergence dating find assumptions about root age significant impact dates inferred. suggest improved understanding will require both better models. workflow under-supported concatenation analyses, outline pragmatic way reconcile conflicting phylogenomics, introduce user-friendly locus tool dating.

Язык: Английский

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The Lithornithiformes (Aves) from the early Eocene London Clay of Walton‐on‐the‐Naze (Essex, UK)

Papers in Palaeontology, Год журнала: 2025, Номер 11(1)

Опубликована: Янв. 1, 2025

Abstract We describe multiple partial skeletons and isolated bones of the palaeognathous Lithornithiformes from early Eocene London Clay Walton‐on‐the‐Naze (Essex, UK). The well‐preserved specimens are assigned to at least four species taxa Lithornis Pseudocrypturus. Two identified as L. nasi cf. grandei . latter species, which was established for fossils North American Green River Formation, initially monotypic taxon Calciavis , is here considered synonymous with further new tentatively referred Pseudocrypturus described ? P. danielsi gracilipes In previous analyses, lithornithiforms most often resulted sister either Tinamiformes or all crown group Palaeognathae. detail that current morphological evidence conforms best a position these birds outside Palaeognathae discuss previously unrecognized plesiomorphic features foot pelvis, support this phylogenetic placement.

Язык: Английский

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Disentangling a genome-wide mosaic of conflicting phylogenetic signals in Western Rattlesnakes

Molecular Phylogenetics and Evolution, Год журнала: 2025, Номер unknown, С. 108309 - 108309

Опубликована: Фев. 1, 2025

Язык: Английский

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