Conceptual and empirical bridges between micro- and macroevolution

Nature Ecology & Evolution, Journal Year: 2023, Volume and Issue: 7(8), P. 1181 - 1193

Published: July 10, 2023

Language: Английский

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The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics

PLoS Genetics, Journal Year: 2024, Volume and Issue: 20(1), P. e1011110 - e1011110

Published: Jan. 18, 2024

In the presence of recombination, evolutionary relationships between a set sampled genomes cannot be described by single genealogical tree. Instead, are related complex, interwoven collection genealogies formalized in structure called an ancestral recombination graph (ARG). An ARG extensively encodes ancestry genome(s) and thus is replete with valuable information for addressing diverse questions biology. Despite its potential utility, technological methodological limitations, along lack approachable literature, have severely restricted awareness application ARGs evolution research. Excitingly, recent progress reconstruction simulation made ARG-based approaches feasible many systems. this review, we provide accessible introduction exploration ARGs, survey breakthroughs, describe to further existing goals open avenues inquiry that were previously inaccessible genomics. Through discussion, aim more widely disseminate promise genomics encourage broader development adoption inference.

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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Impacts of marine heat extremes on bivalves

Frontiers in Marine Science, Journal Year: 2023, Volume and Issue: 10

Published: June 8, 2023

As the global ocean continues to experience consequences of an increase in frequency and intensity heat waves, trend is expected persist into 21st century, with a projected tripling waves by 2040. This phenomenon poses significant threat marine ecosystems survival organisms, including ecologically economically vital bivalves. Bivalves are vulnerable harm from stress at various levels biological organization, their growth can be negatively impacted high temperatures, potentially leading mass mortalities posing ecosystem quality food security. In light these concerns, this review aims provide comprehensive examination effects on It summarizes physiological biochemical changes that bivalves undergo response extreme events offers overview strategies they employ mitigate impacts. A better understanding underlying mechanisms bivalve responses crucial order fully appreciate impact organisms. synthesizes current knowledge highlights importance further research area. By providing during use its impact, support development more effective approaches minimize

Language: Английский

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Genomics of plant speciation

Plant Communications, Journal Year: 2023, Volume and Issue: 4(5), P. 100599 - 100599

Published: April 12, 2023

Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study other organisms while also additional ways which can form. Now, ability to sequence genomes at an unprecedented pace and scale allowed biologists settle decades-long debates tackle emerging challenges research. Here, we review these recent genome-enabled developments plant speciation. We discuss complications related identification reproductive isolation (RI) loci using analyses landscape genomic divergence highlight important role that structural variants speciation, as increasingly revealed by sequencing technologies. Further, genomics advanced what know routes formation, like hybridization or whole-genome duplication, casting doubt others, population bottlenecks genetic drift. While fast-track genes mutations confer RI, emphasize follow-up molecular field experiments remain critical. Nonetheless, clarified outsized ancient rather than mutations, particularly early during conclude highlighting promising avenues future study. These include expanding so far about epigenetic changes broadening scope taxonomic breadth studies, synthesizing information from extensive data already generated community.

Language: Английский

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Structural Variants and Speciation: Multiple Processes at Play

Cold Spring Harbor Perspectives in Biology, Journal Year: 2023, Volume and Issue: 16(3), P. a041446 - a041446

Published: Dec. 5, 2023

Emma L. Berdan1,2, Thomas G. Aubier3,4, Salvatore Cozzolino5, Rui Faria6,7, Jeffrey Feder8, Mabel D. Giménez9,10, Mathieu Joron11, Jeremy B. Searle12 and Claire Mérot13 1Department of Marine Sciences, Gothenburg University, 40530, Sweden 2Bioinformatics Core, Department Biostatistics, Harvard T.H. Chan School Public Health, Medical School, Boston, Massachusetts 02115, USA 3Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, 31077 Toulouse, France 4Department Biology, University North Carolina at Chapel Hill, 27599, 5Department Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Napoli, Italia 6CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal 7BIOPOLIS Program in Genomics, Biodiversity Land Planning, CIBIO, 4485-661 8Department Biological Notre Dame, Indiana 46556, 9Consejo Nacional Investigaciones Científicas y Técnicas (CONICET), Instituto Genética Humana Misiones (IGeHM), Parque la Salud Provincia "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina 10Facultad Ciencias Exactas, Químicas Naturales, Universidad N3300LQH 11Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, CNRS, EPHE, IRD, 12Department Ecology Evolutionary Cornell Ithaca, New York 14853, 13CNRS, 6553 Ecobio, OSUR, Rennes, 35000 Correspondence: claire.merot{at}gmail.com; emma.berdan{at}gmail.com

Language: Английский

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The Ecology of Hybrid Incompatibilities

Cold Spring Harbor Perspectives in Biology, Journal Year: 2023, Volume and Issue: 16(9), P. a041440 - a041440

Published: Dec. 27, 2023

Ecologically mediated selection against hybrids, caused by hybrid phenotypes fitting poorly into available niches, is typically viewed as distinct from epistatic Dobzhansky-Muller incompatibilities. Here, we show how transgressive in hybrids manifests incompatibility. After outlining our logic, summarize current approaches for studying ecology-based on hybrids. We then quantitatively review QTL-mapping studies and find traits differing between parent taxa are polygenic. Next, describe verbal models of translate to phenotypic genetic fitness landscapes, highlighting emerging detecting polygenic Finally, a synthesis published data, report that trait transgression-and thus possibly extrinsic incompatibility hybrids-escalates with the divergence parents. discuss conceptual implications conclude ecological basis will facilitate new discoveries about mechanisms speciation.

Language: Английский

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RIDGE, a tool tailored to detect gene flow barriers across species pairs

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(4)

Published: Feb. 28, 2024

Abstract Characterizing the processes underlying reproductive isolation between diverging lineages is central to understanding speciation. Here, we present RIDGE—Reproductive Isolation Detection using Genomic polymorphisms—a tool tailored for quantifying gene flow barrier proportion and identifying relevant genomic regions. RIDGE relies on an Approximate Bayesian Computation with a model‐averaging approach accommodate diverse scenarios of lineage divergence. It captures heterogeneity in effective migration rate along genome while accounting variation linked selection recombination. The detection test numerous summary statistics compute Bayes factor, offering robust statistical framework that facilitates cross‐species comparisons. Simulations revealed RIDGE's efficiency capturing signals ongoing migration. Model averaging proved particularly valuable high model uncertainty where no or homogeneity can be wrongly assumed, typically recent divergence times <0.1 2 N e generations. Applying four published crow data sets, first validated our by well‐known large region associated mate choice patterns. Second, identified significant overlap outlier loci traditional scans, results suggest substantial portion previously outliers are likely false positives. Outlier allele differentiation, relative measures count shared polymorphisms fixed differences. Our analyses also highlight value incorporating multiple including newly developed ones useful challenging conditions.

Language: Английский

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Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives

Cold Spring Harbor Perspectives in Biology, Journal Year: 2023, Volume and Issue: 15(10), P. a041607 - a041607

Published: Sept. 11, 2023

Radka Reifová1, S. Lorena Ament-Velásquez2, Yann Bourgeois3, Jenn Coughlan4, Jonna Kulmuni5,6, Agnieszka P. Lipinska7,8, Genta Okude9, Laurie Stevison10, Kohta Yoshida9 and Jun Kitano9 1Department of Zoology, Faculty Science, Charles University, 128 00 Prague, Czech Republic 2Department Stockholm 106 91 Stockholm, Sweden 3DIADE, University Montpellier, CIRAD, IRD, 34090 France 4Department Ecology & Evolutionary Biology, Yale New Haven, Connecticut 06520, USA 5Institute for Biodiversity Ecosystem Dynamics, Department Population Amsterdam, 1012 The Netherlands 6Organismal Biology Research Programme, Helsinki, 00100 Finland 7Department Algal Development Evolution, Max Planck Institute 72076 Tuebingen, Germany 8CNRS, UMR 8227, Integrative Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680 9Department Genomics National Genetics, Mishima, Shizuoka 411-8540, Japan 10Department Biological Sciences, Auburn Auburn, Alabama 36849, Correspondence: radka.reifova{at}natur.cuni.cz; jkitano{at}nig.ac.jp

Language: Английский

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Divergent Selection in Low Recombination Regions Shapes the Genomic Islands in Two Incipient Shorebird Species

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(2)

Published: Jan. 16, 2024

Abstract Speciation in the face of gene flow is usually associated with a heterogeneous genomic landscape divergence nascent species pairs. However, multiple factors, such as divergent selection and local recombination rate variation, can influence formation these islands. Examination landscapes pairs that are still early stages speciation provides an insight into this conundrum. In study, population analyses were undertaken using wide range sampling whole-genome resequencing data from 96 unrelated individuals Kentish plover (Charadrius alexandrinus) white-faced dealbatus). We suggest two exhibit varying levels admixture along Chinese coast on Taiwan Island. Genome-wide for introgression indicate ancient had occurred population, ongoing mainland coastal populations. Furthermore, we identified few regions significant interspecific differentiation suppression, which contain several genes potentially disease resistance, coloration, regulation plumage molting thus may be relevant to phenotypic ecological species. Overall, our findings low main force shaping islands incipient shorebird

Language: Английский

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