Incomplete lineage sorting and phenotypic evolution in marsupials

Cell, Год журнала: 2022, Номер 185(10), С. 1646 - 1660.e18

Опубликована: Апрель 20, 2022

Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that leads to incongruent phenotypic variation. Here, performed phylogenomic analyses show the South American monito del monte is sister of all Australian marsupials, although over 31% its genome closer Diprotodontia than other groups due ancient radiation. Pervasive conflicting signals across whole are consistent with some morphological variation among extant marsupials. We detected hundreds genes experienced stochastic fixation ILS, encoding same amino acids non-sister species. Using functional experiments, confirm how may have directly contributed hemiplasy traits were established marsupial ca. 60 mya.

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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Genomic evidence for homoploid hybrid speciation in a marine mammal apex predator

Science Advances, Год журнала: 2023, Номер 9(18)

Опубликована: Май 3, 2023

Hybridization is widespread and constitutes an important source of genetic variability evolution. In animals, its role in generating novel independent lineages (hybrid speciation) has been strongly debated, with only a few cases supported by genomic data. The South American fur seal (SAfs) Arctocephalus australis marine apex predator Pacific Atlantic waters, disjunct set populations Peru Northern Chile [Peruvian (Pfs)] controversial taxonomic status. We demonstrate, using complete genome reduced representation sequencing, that the Pfs genetically distinct species admixed originated from hybridization between SAfs Galapagos (Arctocephalus galapagoensis) ~400,000 years ago. Our results support origin homoploid hybrid speciation over alternative introgression scenarios. This study highlights promoting species-level biodiversity large vertebrates.

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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Charting the course of pinniped evolution: insights from molecular phylogeny and fossil record integration

Evolution, Год журнала: 2024, Номер 78(7), С. 1212 - 1226

Опубликована: Апрель 22, 2024

Abstract Pinnipeds (seals, sea lions, walruses, and their fossil relatives) are one of the most successful mammalian clades to live in oceans. Despite a well-resolved molecular phylogeny global record, complete understanding macroevolutionary dynamics remains hampered by lack formal analyses that combine these 2 rich sources information. We used meta-analytic approach infer densely sampled pinniped date (36 recent 93 taxa) phylogenetic paleobiological methods study diversification biogeographic history. mostly diversified at constant rates. Walruses, however, experienced rapid turnover which extinction rates ultimately exceeded speciation from 12 6 Ma, possibly due changing levels and/or competition with otariids (eared seals). Historical analyses, including data, allowed us confidently identify North Pacific Atlantic (plus or minus Paratethys) as ancestral ranges Otarioidea seals + walrus) crown phocids (earless seals), respectively. Yet, despite novel addition stem pan-pinniped taxa, region origin for Pan-Pinnipedia remained ambiguous. These results suggest further avenues pinnipeds provide framework investigating other groups substantial extinct extant diversity.

Язык: Английский

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Phylogenomics reveal extensive phylogenetic discordance due to incomplete lineage sorting following the rapid radiation of alpine butterflies (Papilionidae: Parnassius)

Systematic Entomology, Год журнала: 2023, Номер 48(4), С. 585 - 599

Опубликована: Апрель 3, 2023

Abstract Under rapid radiation, the earliest components of evolutionary divergence are often difficult to resolve, which were always driven by characteristics taxa and limitations alternative analytical methods. The origin radiation alpine butterfly Parnassius , a high‐altitude mountainous insect group, can be attributed uplift Qinghai‐Tibet Plateau. Despite detailed phylogenetic analyses genus, deep relationships among major subgenera remain recalcitrant. In this study, 102 individuals from 10 representative species sampled resolve based on nuclear mitochondrial genome datasets. Gene‐tree/species‐tree conflicts detected concatenation multispecies coalescent (MSC) approaches. We recovered well‐supported tree, despite these conflicts, considerable discordance genomic regions. main explanation for topological was extensive incomplete lineage sorting (ILS), whereas introgression events not prominent. explosive (i.e., succession speciation events) in late Miocene associated with environmental plateau led short internal branches, thereby increasing ILS especially closely related subgenera. Our results also suggested that MSC approaches (SNP AFLP Package Phylogenetic analysis [SNAPP] SVDquartets) accurate superior approach; particular, SVDquartets explicitly accommodate gene‐tree/species‐tree caused high demonstrate strong robustness. Finally, we explored phylogenomic data testing multiple sources conflict clarify strengths different approaches, while considering signal variation loci. anticipate phylogeny described here will backbone future studies genus provide insight into due radiation.

Язык: Английский

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PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance

Molecular Biology and Evolution, Год журнала: 2023, Номер 40(9)

Опубликована: Сен. 1, 2023

An important goal of evolutionary genomics is to identify genomic regions whose substitution rates differ among lineages. For example, experiencing accelerated molecular evolution in some lineages may provide insight into links between genotype and phenotype. Several comparative methods have been developed accelerations species, including a Bayesian method called PhyloAcc, which models shifts rate multiple target on phylogeny. However, few consider the possibility discordance trees individual loci species tree due incomplete lineage sorting, might cause false positives. Here, we present PhyloAcc-GT, extends PhyloAcc by modeling gene heterogeneity. Given tree, adopt multispecies coalescent model as prior distribution trees, use Markov chain Monte Carlo (MCMC) for inference, design novel MCMC moves sample efficiently. Through extensive simulations, show that PhyloAcc-GT outperforms other identifying lineage-specific detecting complex patterns shifts, robust specification population size parameters. usually more conservative than calling convergent because it identifies ancestral terminal branches. We apply two examples evolution: flightlessness ratites marine mammal adaptations, tool associated with specific while accounting sorting.

Язык: Английский

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Reconciling Gene Tree Discordance and Biogeography in European Crows

Molecular Ecology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 10, 2025

ABSTRACT Reconstructing the evolutionary history of young lineages diverging with gene flow is challenging due to factors like incomplete lineage sorting, introgression, and selection causing tree discordance. The European crow hybrid zone between all‐black carrion crows grey‐coated hooded exemplifies this challenge. Most genome in Western Central populations near‐identical crows, but differs substantially from their Iberian congeners. A notable exception a single major‐effect colour‐locus under sexual aligning ‘species’ tree. To understand underlying processes, we reconstructed biogeographic species complex. During Pleistocene took refuge Peninsula Middle East, respectively. Allele‐sharing likewise black at represents last trace ancestry, resisting expanding that have homogenised most genome. model introgression an ancestor into near Pyrenées was significantly less supported. We found no positive relationship recombination rate consistent absence genome‐wide, polygenic barriers Overall, study portrays scenario where few large‐effect loci, subject divergent selection, resist rampant asymmetric exchange. This underscores importance integrating population demography biogeography accurately interpret patterns discordance following divergence.

Язык: Английский

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Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria

Systematic Biology, Год журнала: 2023, Номер 72(3), С. 694 - 712

Опубликована: Фев. 24, 2023

Abstract Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due widespread horizontal gene transfers (HGTs). Consequently, representing relationships prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among derived from phylogenomic data sets have shown these can result artifacts or processes other than HGT, such incomplete lineage sorting, low phylogenetic signal, and systematic errors substitution model misspecification. Here, we present results an extensive exploration in cyanobacterial order Nostocales, for which previous inferred strongly supported conflicting when using different concatenated sets. We found most concentrated deep clusters short internodes Nostocales phylogeny, where great majority individual resolving power. then networks detect HGT events while also accounting sorting. Our indicate likely sorting linked ancient rapid radiation, rather HGTs. Moreover, this radiation fit expectations anomaly zone, i.e., a region tree parameter space species is discordant with its tree. demonstrated concatenation loci recover up 17 distinct well-supported within putative zone corresponding observed based on studies. findings highlight important role radiations potential cause bacteria. propose polytomies may appropriate representation part zones, especially all possible genomic markers infer phylogenies. [Anomaly zone; bacteria; transfer; sorting; Nostocales; conflict; radiation; Rhizonema.]

Язык: Английский

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Disentangling sources of gene tree discordance for Hordeum species via target-enriched sequencing assays

Molecular Phylogenetics and Evolution, Год журнала: 2024, Номер 199, С. 108160 - 108160

Опубликована: Июль 16, 2024

Язык: Английский

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