CASTER: Direct species tree inference from whole-genome alignments

Science, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 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.

Language: Английский

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Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 187, P. 107869 - 107869

Published: July 8, 2023

Language: Английский

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Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China

Cladistics, Journal Year: 2024, Volume and Issue: 40(4), P. 357 - 373

Published: Jan. 10, 2024

Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex in and observe variations across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution southwest China probably constitute syngameon. In this study, we mapped resequencing from different group Quercus aquifolioides reference genome obtain high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. reconstructed phylogenetic relationships, explored level pattern introgression these investigated tree variation using sliding windows. same or plastomes were found be shared extensively within specific geographical area. Phylogenomic analyses genome-wide SNP that most clade showed genetic coherence, but several connected by introgression. trees obtained windows are highly heterogeneous therefore obscured. Our study all form obscured observed empirically best explained conjunction incomplete lineage sorting.

Language: Английский

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The genome of the pygmy right whale illuminates the evolution of rorquals

BMC Biology, Journal Year: 2023, Volume and Issue: 21(1)

Published: April 12, 2023

Baleen whales are a clade of gigantic and highly specialized marine mammals. Their genomes have been used to investigate their complex evolutionary history decipher the molecular mechanisms that allowed them reach these dimensions. However, many unanswered questions remain, especially about early radiation rorquals how cancer resistance interplays with huge number cells. The pygmy right whale is smallest most elusive among baleen whales. It reaches only fraction body length compared its relatives it living member an otherwise extinct family. This placement makes genome interesting target update phylogenetic past whales, because splits up long branch leads rorquals. Apart from that, genomic data this species might help in large since not as important for other giant whales.Here, we present first de novo test potential phylogenomics research. To do so, constructed multi-species coalescent tree fragments whole-genome alignment quantified amount introgression evolution Furthermore, genome-wide comparison selection rates between small-bodied revealed small set conserved candidate genes connections resistance.Our results suggest best described hard polytomy rapid high levels introgression. lack shared positive selected different large-bodied supports previously proposed convergent gigantism hence

Language: Английский

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Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(17), P. 4844 - 4862

Published: July 29, 2023

Abstract Many organisms possess multiple discrete genomes (i.e. nuclear and organellar), which are inherited separately may have unique even conflicting evolutionary histories. Phylogenetic reconstructions from these can yield different patterns of relatedness, a phenomenon known as cytonuclear discordance. In many animals, mitonuclear discordance discordant histories between the mitochondrial genomes) has been widely documented, but its causes often considered idiosyncratic inscrutable. We show that case in Todiramphus kingfishers be explained by extensive genome‐wide incomplete lineage sorting (ILS), likely result explosive diversification history this genus. For kingfishers, quartet frequencies reveal genome is dominated topologies, with none internal branches our consensus tree recovered >50% gene trees. Meanwhile, lack inter‐species shared ancestry, non‐significant pairwise tests for flow, little evidence meaningful migration edges species, leads to conclusion flow cannot explain we observe. This combined discordance, hallmark ILS, us conclude observe results specifically deep coalescence genome. Based on study, hypothesize similar demographic other ‘great speciator’ taxa across Indo‐Pacific predispose groups high levels ILS likelihoods

Language: Английский

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Cladistic species definitions can lead to under-representation of biodiversity from adaptive radiations

Evolutionary Journal of the Linnean Society, Journal Year: 2024, Volume and Issue: 3(1)

Published: Jan. 1, 2024

Abstract Many species are paraphyletic, but current taxonomic practices often do not recognize this, and attempts made to apply a monophyletic concept. While allowing the recognition of ecomorphologically equivalent, or even phenotypically indistinguishable allopatric, taxa as species, this leads combining distinctive local forms (such cave-adapted populations) whole adaptive radiations (often in lakes) with widespread paraphyletic force monophyly. It is suggested that has negative consequences for our documentation understanding biodiversity, well conservation, through issues such lack IUCN red-listing.

Language: Английский

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Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)

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

Published: Feb. 27, 2024

Resolving the phylogeny of rapidly radiating lineages presents a challenge when building Tree Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that diversified at Pliocene-Pleistocene boundary.

Language: Английский

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Genome skimming for improved phylogenetics of Taiwanese phasmids (Insecta: Phasmatodea)

Molecular Phylogenetics and Evolution, Journal Year: 2025, Volume and Issue: unknown, P. 108292 - 108292

Published: Jan. 1, 2025

Language: Английский

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Species delimitation and molecular dating of southern African Tetramesa (Hymenoptera: Eurytomidae): An understudied microhymenopteran group

Austral Entomology, Journal Year: 2025, Volume and Issue: 64(2)

Published: April 19, 2025

Abstract The genus Tetramesa Walker (Hymenoptera: Eurytomidae) comprises over 200 species of herbivorous wasps that feed exclusively on grasses. Recent field surveys in South Africa for grass biological control programs have uncovered a large diversity potential African Here, mitochondrial (cytochrome c oxidase I [COI]) and nuclear (28S) genetic sequences were used to compare the outputs seven popular delimitation methods guide generation consensus boundaries putative taxa close relatives. Additionally, region was run dated analysis applied molecular clock rate. Consensus results found 35 operational taxonomic units (MOTUs) COI data 21 MOTUs 28S data. Of MOTUs, there 17 (16 novel southern 1 described Northern Hemisphere species, romana ), 13 which showed evidence specialisation single host plant. Comparatively, twenty‐one 5 (4 T. all specificity. suggested originated ~67.1 mya. There rapid diversification Southern clades between 15 mya, coincides with grassland expansions climatic fluctuations at time may driven specialisation. present provide valuable insights into broader scale evolutionary patterns this microhymenopteran group.

Language: Английский

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Genetic traceability, conservation effectiveness, and selection signatures analysis based on ancestral information: a case study of Beijing-You chicken

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: April 24, 2025

Genetic resources are essential components of biodiversity. As national strategy, the conservation genetic is crucial not only for biodiversity but also sustainable agriculture and cultural heritage. However, exact origin most local breeds remains unclear at genomic level. The efforts becoming more challenging as currently experiencing drift admixture, which may be further complicated by historical hybridizations. A typical example Beijing-You chicken, a breed renowned its excellent meat flavor unique appearance. With relatively recent history (~ 300 years), it displays mixed phenotypes have resulted from with yet to determined. Through comprehensive similarity analysis, we identified 12 donor chicken quantified their contributions, highest ancestry proportion coming Henan chickens. structure analyses suggest hybridization in formation this breed. Furthermore, innovatively used new material evaluation selection signature detection, demonstrating that over past decade been effective. Analysis signatures revealed genes regions associated polydactyly, egg production, intramuscular fat, spermatogenesis. By integrating various analytical strategies, developed novel framework traceability evaluation. Our results highlight effectiveness assessment offer valuable insights conservation, improvement, utilization breeds.

Language: Английский

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