Phylogenomic approaches to detecting and characterizing introgression

Genetics, Journal Year: 2021, Volume and Issue: 220(2)

Published: Nov. 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.

Language: Английский

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The Role of Hybridization in Species Formation and Persistence

Cold Spring Harbor Perspectives in Biology, Journal Year: 2024, Volume and Issue: 16(12), P. a041445 - a041445

Published: March 4, 2024

Joshua V. Peñalba1, Anna Runemark2, Joana I. Meier3,4, Pooja Singh5,6, Guinevere O.U. Wogan7, Rosa Sánchez-Guillén8, James Mallet9, Sina J. Rometsch10,11, Mitra Menon12, Ole Seehausen5,6, Jonna Kulmuni13,14,16 and Ricardo Pereira15,16 1Museum für Naturkunde, Leibniz Institute for Evolution Biodiversity Science, Center Integrative Discovery, 10115 Berlin, Germany 2Department of Biology, Lund University, 22632 Lund, Sweden 3Tree Life, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom 4Department Zoology, University Cambridge, CB2 3EJ, 5Department Aquatic Ecology, Ecology Evolution, Bern, 3012 Switzerland 6Center & Biogeochemistry, Swiss Federal Science Technology (EAWAG), CH-8600 Kastanienbaum, 7Department Oklahoma State Stillwater, 74078, USA 8Red de Biología Evolutiva, INECOL, Xalapa, Veracruz, CP 91073, Mexico 9Organismal Evolutionary Harvard Massachusetts 02138, 10Department Yale New Haven, Connecticut 06511, 11Yale Biospheric Studies, 12Department California Davis, 95616, 13Department Population Ecosystem Dynamics, Amsterdam, 1098 XH The Netherlands 14Organismal Biology Research Programme, Helsinki, Biocenter 3, Finland 15Department Museum Natural History Stuttgart, Stuttgart 70191, Correspondence: ricardojn.pereira{at}gmail.com ↵16 These authors contributed equally to this work.

Language: Английский

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Ghost Introgression: Spooky Gene Flow in the Distant Past

BioEssays, Journal Year: 2020, Volume and Issue: 42(6)

Published: March 29, 2020

Abstract Evolution is a continuous trial and error process in which most lineages go extinct without leaving fossil remains. Many of these would be closely related occasionally hybridized with that gave rise to extant species. Hence, it likely one can find genetic signatures ancient introgression events present‐day genomes, so‐called ghost introgression. The increasing availability high‐quality genome assemblies for non‐model organisms the development more sophisticated methods detecting will undoubtedly reveal cases introgression, indicating Tree Life even reticulated than assumed. presence has important consequences study numerous evolutionary processes, including adaptation, speciation, macroevolutionary patterns. In addition, detailed studies introgressed regions could provide insights into morphology lineage, providing an unexpected link between genomics record. new take account need developed.

Language: Английский

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Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow

Systematic Biology, Journal Year: 2021, Volume and Issue: 70(5), P. 961 - 975

Published: March 30, 2021

Abstract Phylogenetic trees based on genome-wide sequence data may not always represent the true evolutionary history for a variety of reasons. One process that can lead to incorrect reconstruction species phylogenies is gene flow, especially if interspecific flow has affected large parts genome. We investigated phylogenetic relationships within clade comprising eight passerine birds (Phylloscopidae, Phylloscopus, leaf warblers) using one de novo genome assembly and 78 resequenced genomes. On basis hypothesis-exclusion trials D-statistics, network analysis, demographic inference we identified ancient affecting between ancestral lineage sister pair. This consistently caused erroneous phylogeny when amounts data. In contrast, were captured smaller analyzed, showing “winner-takes-all democratic majority tree” necessarily tree. Under this condition, sometimes avoid effects due stochastic sampling, as hidden reticulation histories are more likely emerge from use larger sets, whole-genome sets. addition, also found genomic regions by generally exhibited higher differentiation but lower recombination rate nucleotide diversity. Our study highlights importance considering in reconstructions era.[Bifurcation; introgression; recombination; reticulation; Phylloscopus.]

Language: Английский

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Evolution in the Genus Rhinella: A Total Evidence Phylogenetic Analysis of Neotropical True Toads (Anura: Bufonidae)

Bulletin of the American Museum of Natural History, Journal Year: 2021, Volume and Issue: 447(1)

Published: March 31, 2021

True toads of the genus Rhinella are among most common and diverse group Neotropical anurans. These widely distributed throughout South America, inhabiting a great diversity environments ecoregions. Currently, however, is defined solely on basis molecular characters, it lacks proper diagnosis. Although some phenetic species groups have traditionally been recognized within Rhinella, monophyly them rejected in previous phylogenetic analyses, many remain unassigned to these poorly groups. Additionally, identity taxonomy several problematic hinder specific recognition description undescribed taxa. In this work, we first perform analyses separate mitochondrial nuclear datasets test possible occurrence hybridization and/or genetic introgression genus. The comparative analysis both revealed unidirectional introgressions an unknown parental into R. horribilis ("ghost introgression") dorbignyi bernardoi; therefore, were considered separately subsequent analyses. We performed total-evidence that included revised (four five genes) phenotypic (90 characters) for 83 nominal plus multiple outgroups. Results demonstrate was nonmonophyletic due position ceratophrys, which recovered as sister taxon Rhaebo nasicus with strong support. Among our outgroups, strongly supported Anaxyrus + Incilius clade all other Rhinella. Once ceratophrys excluded, monophyletic, well supported, composed two major clades. One moderately includes former spinulosa Group (including gallardoi); monophyletic granulosa, crucifer, marina Groups; sequences horribilis. from non-monophyletic veraguensis margaritifera Groups, acrolopha Group, sternosignata. Consistent results, define eight mostly diagnosed by synapomorphies addition combination morphological character states. sternosignata only remains any group. also synonymize nine species, treat three subspecies full suggest 15 lineages represent putative species. Lastly, discuss apparently frequent hybridization, deep divergence, "ghost introgression"; incomplete evidence systems could be used future analyses); validity known fossil record source calibration points divergence dating

Language: Английский

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Systematics of the avian family Alaudidae using multilocus and genomic data

Avian Research, Journal Year: 2023, Volume and Issue: 14, P. 100095 - 100095

Published: Jan. 1, 2023

The family Alaudidae, larks, comprises 93–100 species (depending on taxonomy) that are widely distributed across Africa and Eurasia, with single extending their ranges to North northernmost South America Australia. A decade-old molecular phylogeny, comprising ∼80% of the species, revealed multiple cases parallel evolution large variation in rates morphological evolution, which had misled taxonomists into creating many non-monophyletic genera. Here, we reconstruct phylogeny using a dataset covering one mitochondrial 16 nuclear loci all except currently recognised as well several recently proposed new (in total 133 taxa; not available for species). We provide additional support genome-wide markers infer genus-level based near-complete generic sampling 51 samples 44 taxa 40 Our results confirm previous findings rampant convergence divergence, reveal paraphyletic propose subfamily classification, also genus Mirafra is divided four genera produce more balanced classification Alaudidae. study supports splits some recent lumps, while questioning latter. This comprehensive will form an important basis future studies, such comparative studies lark natural history, ecology, conservation.

Language: Английский

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Candidate‐species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones

Ecology and Evolution, Journal Year: 2022, Volume and Issue: 12(2)

Published: Feb. 1, 2022

Dusky Salamanders (genus

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Ghost admixture in eastern gorillas

Nature Ecology & Evolution, Journal Year: 2023, Volume and Issue: 7(9), P. 1503 - 1514

Published: July 27, 2023

Abstract Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic been identified in chimpanzees bonobos but the possibility of not explored other species. Here, we address this question using high-coverage whole-genome sequences all four extant gorilla subspecies, six newly sequenced eastern gorillas previously unsampled geographic regions. Using approximate Bayesian computation neural networks to model demographic history gorillas, find signature an ‘ghost’ lineage common ancestor western gorillas. We infer that up 3% genome these individuals is introgressed diverged more than 3 million years ago This introgression event took place before split mountain lowland probably 40 thousand may have influenced perception bitter taste When comparing landscapes humans bonobos, consistent depletion fragments X chromosome However, protein-coding content detectable possibly consequence stronger genetic drift

Language: Английский

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Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(9), P. 2087 - 2103

Published: Feb. 22, 2021

Abstract Hybridization, introgression, and reciprocal gene flow during speciation, specifically the generation of mitonuclear discordance, are increasingly observed as parts speciation process. Genomic approaches provide insight into where, when, how adaptation operates after can measure historical modern introgression. Whether adaptive or neutral in origin, hybridization cause discordance by placing mitochondrial genome one species (or population) nuclear background another species. The latter, introgressed may eventually have its own mtDNA replaced “captured” other across entire geographical range. Intermediate stages capture process should be observable. Two nonsister Australasian monarch‐flycatchers, Spectacled Monarch ( Symposiachrus trivirgatus ) mostly Australia Indonesia Spot‐winged S. guttula New Guinea, present an opportunity to observe this We analysed thousands single nucleotide polymorphisms (SNPs) derived from ultraconserved elements all subspecies both Mitochondrial DNA sequences Australian populations form two paraphyletic clades, being sister presumably despite little signal Population genetic analyses (e.g., tests for selection) support at least event between . also uncovered introgression Maluku Islands island population , resulting apparent paraphyly. find that demographic processes, not most likely these complex histories. suggest a Pleistocene extinction mainland resulted range expansion

Language: Английский

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An overview of speciation and species limits in birds

Ornithology, Journal Year: 2021, Volume and Issue: 138(2)

Published: April 6, 2021

Abstract Accurately determining avian species limits has been a challenge and work in progress for most of century. It is fascinating but difficult problem. Under the biological concept, only lineages that remain essentially independent when they are sympatry clearly species. Otherwise, there no clear line yet found marks pair diverging (e.g., allopatry) become different enough to warrant full status. Also, with more data, often require reevaluation. The process divergence speciation itself very complex focus intense research. Translating what we understand into taxonomic names can be challenging. A series issues important. Single-locus criteria unlikely convincing. Genetic independence not requirement, degree (gene flow) needs considered opportunity gene flow complete. Time-based (limits determined by time separation) unsatisfactory, though integrating effectively our datasets warranted. We need disentangle data signal due neutral processes vs. selection prioritize latter as main driver speciation. Assortative mating also likely an adequate criterion limits. Hybridization important than ever, condition being treated evenly taxonomy: evolutionary trysts 2 or stuck together through just short over long periods. Comparative methods use occurs between good contact infer among allopatric forms gold standard, inaccurate controversial. Species-level taxonomy birds unsettled some time. While study never exciting dynamic, silver bullet delimitation, nor it will ever one. Careful using integrative comparative framework promising way forward.

Language: Английский

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