Phylogenomic approaches to detecting and characterizing introgression

Genetics, Год журнала: 2021, Номер 220(2)

Опубликована: Ноя. 11, 2021

Abstract Phylogenomics has revealed the remarkable frequency with which introgression occurs across tree of life. These discoveries have been enabled by rapid growth methods designed to detect and characterize from whole-genome sequencing data. A large class phylogenomic makes use data species infer based on expectations multispecies coalescent. range simple tests, such as D-statistic, model-based approaches for inferring phylogenetic networks. Here, we provide a detailed overview various signals that different modes are expected leave in genome, how current them. We discuss strengths pitfalls these identify areas future development, highlighting introgression, power each method conclude discussion challenges they could potentially be addressed.

Язык: Английский

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Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes

Systematic Biology, Год журнала: 2024, Номер 73(4), С. 666 - 682

Опубликована: Май 11, 2024

Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring may be hindered by complexities homology determination in taxa. We use simulations to show that phasing alleles from allopolyploid individuals improve network inference under multispecies coalescent obtaining true with fewer loci compared haplotype consensus sequences or heterozygous bases represented as ambiguity codes. Phased allelic data also divergence time estimates networks, which is helpful evaluating speciation hypotheses and proposing mechanisms speciation. To achieve these outcomes empirical data, we present novel pipeline leverages recently developed algorithm reliably phase polyploids. This especially appropriate target enrichment where depth coverage typically high enough entire loci. an example North American Dryopteris fern complex demonstrates phased well challenges inference. establish our (PATÉ: Alleles Target Enrichment data) capable recovering proportion both diploids These using assemblies accurately direction gene flow, but statistical nonidentifiability poses barrier evolutionary history complexes.

Язык: Английский

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Hybridization and Transgressive Evolution Generate Diversity in an Adaptive Radiation of Anolis Lizards

Systematic Biology, Год журнала: 2023, Номер 72(4), С. 874 - 884

Опубликована: Апрель 25, 2023

Abstract Interspecific hybridization may act as a major force contributing to the evolution of biodiversity. Although generally thought reduce or constrain divergence between 2 species, can, paradoxically, promote by increasing genetic variation providing novel combinations alleles that selection can upon move lineages toward new adaptive peaks. Hybridization may, then, play key role in radiation allowing diversify into ecological space. Here, we test for signatures historical Anolis lizards Puerto Rico and evaluate hypotheses facilitating radiation—the hybrid swarm origins hypothesis syngameon hypothesis. Using whole genome sequences from all 10 species Rican anoles, calculated D f-statistics (from ABBA-BABA tests) introgression across employed multispecies network coalescent methods reconstruct phylogenetic networks allow hybridization. We then analyzed morphological data these patterns consistent with transgressive evolution, phenomenon which trait lineage is found outside range its parents. Our analyses uncovered strong evidence at multiple stages radiation, including support an ancient origin clade comprising half extant anole species. Moreover, detected significant signals ecologically important traits, head length toepad width, latter has been described innovation Anolis. [Adaptive radiation; introgression; coalescent; phenotypic evolution; network; reticulation; syngameon; segregation.]

Язык: Английский

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Widespread reticulate evolution in an adaptive radiation

Evolution, Год журнала: 2023, Номер 77(4), С. 931 - 945

Опубликована: Янв. 21, 2023

A fundamental assumption of evolutionary biology is that phylogeny follows a bifurcating process. However, hybrid speciation and introgression are becoming more widely documented in many groups. Hybrid inference studies have been historically limited to small sets taxa, while exploration the prevalence trends reticulation at deep time scales remains unexplored. We study history an adaptive radiation 109 gemsnakes Madagascar (Pseudoxyrhophiinae) identify potential instances introgression. Using several network methods, we find 12 events within 22-million-year gemsnakes, producing 28% diversity for group, including one resulted diversification 18 species radiation. These reticulations found nodes with high gene tree discordance occurred among parental lineages distributed along north-south axis share similar ecologies. Younger hybrids occupy intermediate contact zones between parent showing post-speciation dispersal this group has not eroded spatial signatures Reticulations accumulated consistently over time, despite drops overall rates during Pleistocene. This suggests may decline as result accumulation environmental change, by hybridization be robust these processes.

Язык: Английский

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PhyloCoalSimulations: A Simulator for Network Multispecies Coalescent Models, Including a New Extension for the Inheritance of Gene Flow

Systematic Biology, Год журнала: 2023, Номер 72(5), С. 1171 - 1179

Опубликована: Май 31, 2023

We consider the evolution of phylogenetic gene trees along species networks, according to network multispecies coalescent process, and introduce a new model with correlated inheritance flow. This generalizes two traditional versions coalescent: independent or common inheritance. At each reticulation, multiple lineages given locus are inherited from parental populations chosen at random, either independently across positive correlation Dirichlet process. process may account for locus-specific probabilities inheritance, example. implemented simulation under these models in Julia package PhyloCoalSimulations, which depends on PhyloNetworks its powerful manipulation tools. Input phylogenies can be read extended Newick format, numbers generations units. Simulated written way that preserves information about their embedding within network. used downstream purposes, such as simulate species-specific processes like rate variation species, other scenarios illustrated this note. should useful studies simulation-based inference methods. The software is available open source documentation tutorial https://github.com/cecileane/PhyloCoalSimulations.jl.

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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Genome-wide data reveal extensive gene flow during the diversification of the western rattlesnakes (Viperidae: Crotalinae: Crotalus)

Molecular Phylogenetics and Evolution, Год журнала: 2021, Номер 165, С. 107313 - 107313

Опубликована: Сен. 17, 2021

Язык: Английский

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RF-Net 2: fast inference of virus reassortment and hybridization networks

Bioinformatics, Год журнала: 2022, Номер 38(8), С. 2144 - 2152

Опубликована: Фев. 7, 2022

A phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g. hybridization, reassortment, recombination) evolution. The standard approach inference of hybridization networks (i) reconstruct rooted gene trees (ii) leverage tree discordance for inference. Recently, we introduced method called RF-Net accurate virus reassortment from input in the presence errors commonly found trees. While demonstrated ability accurately infer up four reticulations erroneous trees, its application was limited by number it could handle reasonable amount time. This limitation particularly restrictive history segmented RNA viruses such as influenza (IAV), where one major mechanisms shaping evolution these pathogens.

Язык: Английский

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Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade)

Systematic Biology, Год журнала: 2023, Номер 72(4), С. 739 - 752

Опубликована: Апрель 25, 2023

In this study we detangled the evolutionary history of Patagonian lizard clade Liolaemus kingii, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear mitochondrial data (restriction site-associated DNA sequencing cytochrome b) to hypothesize evaluate species limits, phylogenetic relationships, demographic histories. complemented these analyses with posterior predictive simulations assess fit genomic multispecies coalescent model. also employed a approach time-calibrate network. Our results show several instances mito-nuclear discordance consistent support for reticulated history, supporting view that complex kingii is characterized by extensive gene flow rapid diversification events. discuss our findings in contexts "gray zone" speciation, phylogeographic patterns region, taxonomic outcomes. [Model adequacy; coalescent; network phylogenomics; delimitation.].

Язык: Английский

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Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2021, Номер unknown

Опубликована: Май 4, 2021

Abstract Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring may be hindered by complexities homology determination in taxa. We use simulations to show that phasing alleles from allopolyploid individuals improve network inference under multispecies coalescent obtaining true with fewer loci compared haplotype consensus sequences or heterozygous bases represented as ambiguity codes. Phased allelic data also divergence time estimates networks, which is helpful evaluating speciation hypotheses and proposing mechanisms speciation. To achieve these outcomes empirical data, we present novel pipeline leverages recently developed algorithm reliably phase polyploids. This especially appropriate target enrichment where depth coverage typically high enough entire loci. an example North American Dryopteris fern complex demonstrates phased well challenges inference. establish our (PATÉ: Alleles Target Enrichment data) capable recovering proportion both diploids These using assemblies accurately direction gene flow, but statistical non-identifiability poses barrier evolutionary history complexes.

Язык: Английский

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