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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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, Год журнала: 2023, Номер 187, С. 107869 - 107869

Опубликована: Июль 8, 2023

Язык: Английский

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

Cladistics, Год журнала: 2024, Номер 40(4), С. 357 - 373

Опубликована: Янв. 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.

Язык: Английский

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

BMC Biology, Год журнала: 2023, Номер 21(1)

Опубликована: Апрель 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

Язык: 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, Год журнала: 2023, Номер 32(17), С. 4844 - 4862

Опубликована: Июль 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

Язык: Английский

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

Evolutionary Journal of the Linnean Society, Год журнала: 2024, Номер 3(1)

Опубликована: Янв. 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.

Язык: Английский

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Phylogenomic Analyses Show Repeated Evolution of Hypertrophied Lips Among Lake Malawi Cichlid Fishes

Genome Biology and Evolution, Год журнала: 2022, Номер 14(4)

Опубликована: Апрель 1, 2022

Abstract Cichlid fishes have repeatedly evolved an astounding diversity of trophic morphologies. For example, hypertrophied lips multiple times in both African and Neotropical cichlids could even convergently within single species assemblages such as Lake Malawi cichlids. However, the extremely high diversification rate extensive potential for hybridization has cast doubt on whether genome-level phylogenetic reconstructions delineate if these types adaptations once or times. To examine evolution this iconic trait using protein-coding noncoding nucleotide polymorphisms (SNPs), we analyzed genomes 86 cichlid species, including 33 de novo resequenced genomes. Surprisingly, genome-wide SNPs exhibited enough informativeness to reconstruct interspecific intraspecific relationships lip cichlids, although provided better support. thinning indicated most discrepancies come from relatively smaller number sites not fundamental differences their informativeness. Both coding showed that several “sand-dwelling” sampled intraspecifically, form a clade interspersed with few other nonhypertrophied lineages. We also recovered Abactochromis labrosus rock-dwelling “mbuna” lineage, starkly contrasting affinities taxa found largely sand-dwelling “nonmbuna” component radiation. Comparative analyses coupled tests introgression indicate there is no widespread between lineages taken together suggest phenotype likely at least twice independently within-lake Malawi.

Язык: Английский

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

BMC Biology, Год журнала: 2024, Номер 22(1)

Опубликована: Фев. 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.

Язык: Английский

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Replicated Functional Evolution in Cichlid Adaptive Radiations

The American Naturalist, Год журнала: 2024, Номер 204(3), С. 242 - 257

Опубликована: Май 17, 2024

AbstractAdaptive radiations highlight the mechanisms by which species and traits diversify extent to these patterns are predictable. We used 1,110 high-speed videos of suction feeding study functional morphological diversification in 300 cichlid from three African Great Lake varying ages (Victoria, Malawi, Tanganyika) an older, spatially dispersed continental radiation Neotropics. Among radiations, standing diversity was reflective time. Morphological variance Victoria, youngest radiation, a subset that within itself nested older Tanganyikan radiation. However, Neotropical cichlids often lower than Tanganyika, despite being much older. These two broadly overlapped, but each diversified into novel trait spaces not found lake radiations. Evolutionary rates across were inversely related age, suggesting extremely rapid evolution at early stages, particularly Despite this support for bursts, other inconsistent with expectations adaptive This work suggests has played out strikingly similar fashion different contingencies eventually resulting lineage-specific novelties.

Язык: Английский

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

Molecular Phylogenetics and Evolution, Год журнала: 2025, Номер unknown, С. 108292 - 108292

Опубликована: Янв. 1, 2025

Язык: Английский

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