The Species as a Reproductive Community Emerging From the Past DOI Creative Commons
Wayne P. Maddison, Jeannette Whitton

Bulletin of the Society of Systematic Biologists, Год журнала: 2023, Номер 2(1), С. 1 - 35

Опубликована: Дек. 8, 2023

Biologists and philosophers of science have been unable to fully resolve the decades-long controversy as what kind unit living biodiversity should receive valued label “species”: reproductive communities (among sexual organisms), genealogical groups, or clusters organisms that share traits. Among these choices, which represent a spectrum from process history observable outcome (respectively), latter (more operationalist) concepts are not viable. Species must embody imply cohesive integrating processes such interbreeding shared ecological pressures if they sufficient power bear burden we give them: predict explain traits across genome among organisms. This commitment is needed whether biologists use species taxonomic containers synthesize data, minimal phylogenetic units, actors in evolutionary diversification. These varied uses can be satisfied via concept community, but strict Biological Concept (BSC). Its two drawbacks focus on contemporary restriction intrinsic factors. Current compatibility may future matings, it does well genes already have. The alive today were shaped by isolating factors past, those present, whatever extent differ. most broadly-useful therefore see retrospectively, past. As well, BSC’s exclusion extrinsic renders each its units incomplete explanation synthesis. Reproductive nature isolated just (genetic) differences, also purely (e.g., geographic) Such real, natural entities whose integrated self-reinforcing constrained descent aligned distribution many Retrospective Community (RRCC), formalized mathematically multispecies coalescent models, justifies traditional practice taxonomists using morphological data seek echoes past cohesion. However, naturally deserve ranked species, demes populations, vexing question. There no natural, discrete broadly informative rank applies universally, perhaps even usually. To justified, justified for asexual sexuals. presence absence sex one example variability confront. Because vary clades, useful broadly-applicable cannot specify detailed mechanisms. Nor perfectly align named taxonomy with evolution, because structured match taxonomy’s partition boxes. Taxonomic approximate, only units. Settling retrospection, letting go meaning rank, accepting approximation allow biology turn far more daunting task: listening world understand interacting built distinction identity, emerging out into present day.

Язык: Английский

Conceptual and empirical bridges between micro- and macroevolution DOI
Jonathan Rolland, L. Francisco Henao‐Díaz, Michael Doebeli

и другие.

Nature Ecology & Evolution, Год журнала: 2023, Номер 7(8), С. 1181 - 1193

Опубликована: Июль 10, 2023

Язык: Английский

Процитировано

50
Impacts of marine heat extremes on bivalves DOI Creative Commons
Fortunatus Masanja, Ke Yang, Yang Xu

и другие.

Frontiers in Marine Science, Год журнала: 2023, Номер 10

Опубликована: Июнь 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

Язык: Английский

Процитировано

44
The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics DOI Creative Commons
Alexander L. Lewanski, Michael C. Gründler, Gideon S. Bradburd

и другие.

PLoS Genetics, Год журнала: 2024, Номер 20(1), С. e1011110 - e1011110

Опубликована: Янв. 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.

Язык: Английский

Процитировано

37
The Role of Hybridization in Species Formation and Persistence DOI
Joshua V. Peñalba, Anna Runemark, Joana I. Meier

и другие.

Cold Spring Harbor Perspectives in Biology, Год журнала: 2024, Номер 16(12), С. a041445 - a041445

Опубликована: Март 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.

Язык: Английский

Процитировано

19
Genomics of plant speciation DOI Creative Commons
Dan G. Bock,

Zhe Cai,

Cassandra Elphinstone

и другие.

Plant Communications, Год журнала: 2023, Номер 4(5), С. 100599 - 100599

Опубликована: Апрель 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.

Язык: Английский

Процитировано

39
Structural Variants and Speciation: Multiple Processes at Play DOI
Emma L. Berdan, Thomas G. Aubier, Salvatore Cozzolino

и другие.

Cold Spring Harbor Perspectives in Biology, Год журнала: 2023, Номер 16(3), С. a041446 - a041446

Опубликована: Дек. 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

Язык: Английский

Процитировано

20
The Ecology of Hybrid Incompatibilities DOI
Ken Thompson, Yaniv Brandvain,

Jenn M. Coughlan

и другие.

Cold Spring Harbor Perspectives in Biology, Год журнала: 2023, Номер 16(9), С. a041440 - a041440

Опубликована: Дек. 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.

Язык: Английский

Процитировано

17
Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives DOI
Radka Reifová, S. Lorena Ament‐Velásquez, Yann Bourgeois

и другие.

Cold Spring Harbor Perspectives in Biology, Год журнала: 2023, Номер 15(10), С. a041607 - a041607

Опубликована: Сен. 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

Язык: Английский

Процитировано

14
RIDGE, a tool tailored to detect gene flow barriers across species pairs DOI Creative Commons
Ewen Burban, Maud I. Tenaillon, Sylvain Glémin

и другие.

Molecular Ecology Resources, Год журнала: 2024, Номер 24(4)

Опубликована: Фев. 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.

Язык: Английский

Процитировано

6
Gregor Johann Mendel and the development of modern evolutionary biology DOI Creative Commons
Nils Chr. Stenseth, Leif Andersson, Hopi E. Hoekstra

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2022, Номер 119(30)

Опубликована: Июль 18, 2022

Microbial communities are found throughout the biosphere, from human guts to glaciers, soil activated sludge. Understanding statistical properties of such diverse can pave way elucidate common mechanisms ...Multiple ecological forces act together shape composition microbial communities. Phyloecology approaches—which combine phylogenetic relationships between species with community ecology—have potential disentangle but often ...

Язык: Английский

Процитировано

18