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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Hybridization increases population variation during adaptive radiation

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(46), P. 23216 - 23224

Published: Oct. 28, 2019

Adaptive radiations are prominent components of the world's biodiversity. They comprise many species derived from one or a small number ancestral in geologically short time that have diversified into variety ecological niches. Several authors proposed introgressive hybridization has been important generation new morphologies and even species, but how happens throughout evolutionary history is not known. Interspecific gene exchange expected to greatest impact on variation if it occurs after diverged genetically phenotypically before genetic incompatibilities arise. We use dated phylogeny infer populations Darwin's finches Galápagos became more variable morphological traits through time, consistent with hypothesis, then declined reaching peak. Some vary substantially than others. Phylogenetic inferences supported by field observations contemporary hybridization. Morphological effects investigated island Daphne Major documenting changes hybridizing Geospiza fortis scandens over 30-y period. G. showed evidence admixture Beaks progressively blunter, while length increased, depth decreased. These imply independent introgression 2, correlated, beak dimensions. Our study shows can alter ecologically traits, increase as radiation proceeds, enhance potential for future evolution changing environments.

Language: Английский

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Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae)

Systematic Biology, Journal Year: 2019, Volume and Issue: 69(1), P. 91 - 109

Published: May 21, 2019

Abstract Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity an already situation. Dactylorhiza (Orchidaceae: Orchidinae) a genus much affected by allopolyploid speciation and reticulate relationships. Here, we use genetic variation at tens thousands genomic positions to unravel convoluted evolutionary history Dactylorhiza. We first investigate circumscription species using coalescent maximum likelihood methods, then group 16 allotetraploids affiliation their putative parental diploids, implementing method based on genotype likelihoods. The direction hybrid crosses inferred allotetraploid information maternally inherited plastid RADseq loci. Starting age estimates taxa, relative ages these entities quantifying similarity diploids numbers private alleles compared allotetraploids. Whereas northwestern Europe dominated young postglacial origins, comparatively older distributed further south, where climatic conditions remained relatively stable during Pleistocene glaciations. Our bioinformatics approach should prove effective study other naturally occurring, nonmodel, polyploid plant complexes.

Language: Английский

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Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut

Molecular Biology and Evolution, Journal Year: 2019, Volume and Issue: 36(11), P. 2451 - 2461

Published: April 26, 2019

Persian walnut (Juglans regia) is cultivated worldwide for its high-quality wood and nuts, but origin has remained mysterious because in phylogenies it occupies an unresolved position between American black walnuts Asian butternuts. Equally unclear the of only butternut, J. cinerea. We resequenced whole genome 80 individuals from 19 22 species Juglans assembled relatives Pterocarya stenoptera Platycarya strobilacea. Using phylogenetic-network analysis single-copy nuclear genes, genome-wide site pattern probabilities, Approximate Bayesian Computation, we discovered that regia (and landrace sigillata) arose as a hybrid lineages cinerea resulted massive introgression immigrating butternut into walnut. Computation modeling placed late Pliocene, ∼3.45 My, with both parental since having gone extinct Europe.

Language: Английский

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The genic view of hybridization in the Anthropocene

Evolutionary Applications, Journal Year: 2021, Volume and Issue: 14(10), P. 2342 - 2360

Published: March 13, 2021

Human impact is noticeable around the globe, indicating that a new era might have begun: Anthropocene. Continuing human activities, including land-use changes, introduction of non-native species and rapid climate change, are altering distributions countless species, often giving rise to human-mediated hybridization events. While interbreeding different populations or can detrimental effects, such as genetic extinction, it be beneficial in terms adaptive introgression an increase diversity. In this paper, I first review mechanisms outcomes anthropogenic based on literature from last five years (2016-2020). The most common leading previously isolated taxa include habitat change (51% studies) (34% intentional 19% unintentional). These human-induced events result (80%). high incidence exchange between hybridizing indicates application genic view speciation (and introgression) provide crucial insights how address This perspective considers genome dynamic collection loci with distinct evolutionary histories, heterogenous genomic landscape differentiation introgression. First, understanding lead better selection diagnostic markers characterize hybrid populations. Second, describing patterns vary across help predict likelihood negative processes, demographic swamping, well positive outcomes, It especially important not only quantify much material introgressed, but also what has been exchanged. Third, comparing pre-Anthropocene current cases novel into swamping collapse during event. However, comparative approach remains tested before applied practice. Finally, combined conservation studies determine legal status hybrids take appropriate measures manage interplay genomics will constant ideas these fields which improve our knowledge origin conserve protect them.

Language: Английский

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Consequences of Hybridization in Mammals: A Systematic Review

Genes, Journal Year: 2021, Volume and Issue: 13(1), P. 50 - 50

Published: Dec. 24, 2021

Hybridization, defined as breeding between two distinct taxonomic units, can have an important effect on the evolutionary patterns in cross-breeding taxa. Although interspecific hybridization has frequently been considered a maladaptive process, which threatens species genetic integrity and survival via swamping outbreeding depression, some cases introduce novel adaptive variation increase fitness. Most studies to date focused documenting events analyzing their causes, while relatively little is known about consequences of its impact parental species. To address this knowledge gap, we conducted systematic review mammals published 2010-2021, identified 115 relevant studies. Of 13 categories described these studies, most common negative consequence (21% studies) was positive (8%) gain variation. The total frequency (49%) higher than (13%) neutral (38%) consequences. These frequencies are biased by detection possibilities microsatellite loci, markers used papers assessed. As outcomes typically easier demonstrate ones (e.g., extinction vs hybrid speciation), they may be over-represented publications. Transition towards genomic involving both will provide better insight into real impacts hybridization.

Language: Английский

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Epigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Oct. 7, 2021

Abstract Mutations are the source of genetic variation and substrate for evolution. Genome-wide mutation rates appear to be affected by selection probably adaptive. Mutation also known vary along genomes, possibly in response epigenetic modifications, but causality is only assumed. In this study we determine direct impact modifications temperature stress on mitotic a fungal pathogen using accumulation approach. Deletion mutants lacking confirm that histone mark H3K27me3 increases whereas H3K9me3 decreases rate. Furthermore, cytosine methylation transposable elements (TE) rate 15-fold resulting significantly less TE mobilization. Also accessory chromosomes have higher rates. Finally, find substantially elevates Taken together, environmental conditions modify location spontaneous mutations genome alter its evolutionary trajectory.

Language: Английский

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Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance

Systematics and Biodiversity, Journal Year: 2020, Volume and Issue: 18(3), P. 269 - 280

Published: April 2, 2020

Species are a fundamental unit of biodiversity that delimited via genetic data and coalescent-based methods with increasing frequency. Despite the widespread use species delimitation, we do not fully understand sensitivity these to potential sources bias violations their underlying assumptions. One implicit assumption delimitation is geographic sampling adequate representative variation among populations within lineage interest. Yet exhaustive logistically difficult, if impossible, for many taxa span large expanses or occupy remote regions. Here, examine impact on output Bayes-factor SNAPP, popular pipeline. First, demonstrate problematic nature sparse isolation by distance using simulated sets connected different levels gene flow. We then whether similar trends present in an empirical dataset Andesiops mayflies (Ephemeroptera: Baetidae) from high elevation transect Ecuadorian Andes. In both analyses, systematically exclude geographically intermediate sites quantify delimitation. find removing genetically admixed individuals incorrectly favors multi-species scenarios. Oversplitting especially pronounced when strong, but exists even flow neighboring relatively high. These findings highlight importance urge caution interpreting such species' distributions sparsely sampled systems characterized strong patterns distance.

Language: Английский

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Stable species boundaries despite ten million years of hybridization in tropical eels

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: March 18, 2020

Abstract Genomic evidence is increasingly underpinning that hybridization between taxa commonplace, challenging our views on the mechanisms maintain their boundaries. Here, we focus seven catadromous eel species (genus Anguilla ) and use genome-wide sequence data from more than 450 individuals sampled across tropical Indo-Pacific, morphological information, three newly assembled draft genomes to compare contemporary patterns of with signatures past introgression a time-calibrated phylogeny. We show have remained distinct for up 10 million years find current frequencies pairs contrast genomic introgression. Based near-complete asymmetry in directionality decreasing later-generation hybrids, suggest cytonuclear incompatibilities, hybrid breakdown, purifying selection as can support cohesion even when has been pervasive throughout evolutionary history clades.

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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