Defining the speciation continuum

Evolution, Journal Year: 2021, Volume and Issue: 75(6), P. 1256 - 1273

Published: March 23, 2021

A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe too long study from start finish. The idea continuum provides something solution this problem; rather than observing the entire process, we can simply reconstruct multitude events surround us. But what do really mean when talk about continuum, and help us understand speciation? We explored these questions using literature review online survey researchers. Although most researchers were familiar with concept thought was useful, revealed extensive disagreement actually tells This due partly lack clear definition. Here, provide an explicit definition compatible Biological Species Concept. That is, reproductive isolation. After outlining logic in light alternatives, explain why attempts process present-day populations will ultimately fail. then outline how think continue act as foundation for isolation surrounds

Language: Английский

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What is reproductive isolation?

Journal of Evolutionary Biology, Journal Year: 2022, Volume and Issue: 35(9), P. 1143 - 1164

Published: Sept. 1, 2022

Abstract Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since modern synthesis and basis by which biological species are defined. Despite this, term used seemingly different ways, attempts to quantify RI have very approaches. After showing that field lacks clear definition term, we attempt clarify key issues, including what is, how it can be quantified principle, measured practice. Following other definitions with genetic focus, propose quantitative measure effect differences between populations on gene flow. Specifically, compares flow neutral alleles presence these without any such differences. thus greater than zero when reduce populations. We show range scenarios. A conclusion depends strongly circumstances—including spatial, temporal genomic context—making difficult compare across systems. reviewing methods for estimating from data, conclude discuss our findings light goals encourage use integrate organismal biology ways efforts data vastly In this paper, issues about RI,

Language: Английский

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Taxon-specific, phased siRNAs underlie a speciation locus in monkeyflowers

Science, Journal Year: 2023, Volume and Issue: 379(6632), P. 576 - 582

Published: Feb. 10, 2023

Taxon-specific small RNA loci are widespread in eukaryotic genomes, yet their role lineage-specific adaptation, phenotypic diversification, and speciation is poorly understood. Here, we report that a locus monkeyflowers (Mimulus), YELLOW UPPER (YUP), contains an inverted repeat region produces interfering RNAs (siRNAs) phased pattern. Although the derived from partial duplication of protein-coding gene not involved flower pigmentation, one siRNAs targets represses master regulator floral carotenoid pigmentation. YUP emerged with two genes control other aspects coloration as "superlocus" subclade Mimulus has contributed to subsequent diversification pollinator-mediated descendant species.

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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On the causes of geographically heterogeneous parallel evolution in sticklebacks

Nature Ecology & Evolution, Journal Year: 2020, Volume and Issue: 4(8), P. 1105 - 1115

Published: June 22, 2020

Language: Английский

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Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(7), P. 2750 - 2766

Published: March 2, 2021

Abstract The relative importance of introgression for diversification has long been a highly disputed topic in speciation research and remains an open question despite the great attention it received over past decade. Gene flow leaves traces genome similar to those created by incomplete lineage sorting (ILS), identification quantification gene presence ILS is challenging requires knowledge about true phylogenetic relationship among species. We use whole nuclear, plastid, organellar genomes from 12 species rapidly radiated, ecologically diverse, actively hybridizing genus peatmoss (Sphagnum) reconstruct phylogeny quantify using suite phylogenomic methods. found extensive discordance nuclear phylogenies, as well across nodes tree, best explained following rapid radiation rather than postspeciation introgression. Our analyses support idea ancient ancestral lineages followed ILS, whereas recent restricted widespread interspecific hybridization known group. results contribute understanding how proceeds groups, demonstrate that employing combination diverse methods can facilitate untangling complex patterns

Language: Английский

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Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes

Genetics, Journal Year: 2020, Volume and Issue: 215(3), P. 779 - 797

Published: May 2, 2020

Abstract As a genetic mutation is passed down across generations, it distinguishes those genomes that have inherited from not, providing glimpse of the genealogical tree relating to each other at site. Statistical summaries variation therefore also describe underlying genealogies. We use this correspondence define general framework efficiently computes single-site population statistics using succinct sequence encoding genealogies and genome sequence. The approach accumulates sample weights within position on genome, which are then combined summary function; different result choices weight function. Results can be reported in three ways: by site, corresponds calculated as usual sequence; branch, gives expected value dual site statistic under infinite sites model mutation, node, summarizes contribution ancestor these statistics. implement many currently defined (making statistics’ relationship trees concrete explicit), well corresponding branch shape. evaluate computational performance simulated data, show calculating sequences several orders magnitude more efficient than optimized matrix-based methods terms both run time memory requirements. explore how duality between holds practice inferred 1000 Genomes Project data set, discuss ways deviations may encode interesting biological signals.

Language: Английский

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DILS: Demographic inferences with linked selection by using ABC

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 21(8), P. 2629 - 2644

Published: Jan. 15, 2021

We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single-population or two-population sets (multilocus fasta sequences) and performs three types of analyses in hierarchical manner, identifying: (a) the best model to study importance gene flow size change on genetic patterns polymorphism divergence, (b) determine whether effective Ne migration rate N, m are heterogeneously distributed along genome (implying selection) (c) loci regions most associated barriers flow. Also available via Web interface, objective is facilitate collaborative research speciation genomics. Here, we show performance limitations by simulations finally apply method published divergence continuum composed 28 pairs Mytilus mussel populations/species.

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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Genomic evidence for domestication selection in three hatchery populations of Chinook salmon, Oncorhynchus tshawytscha

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(2)

Published: Feb. 1, 2024

Fish hatcheries are widely used to enhance fisheries and supplement declining wild populations. However, substantial evidence suggests that hatchery fish subject differential selection pressures compared their counterparts. Domestication selection, or adaptation the environment, poses a risk populations if traits specific success in environment have genetic component there is subsequent introgression between fish. Few studies investigated domestication on genomic level, even fewer done so parallel across multiple hatchery-wild population pairs. In this study, we low-coverage whole-genome sequencing investigate signals of three separate Chinook salmon,

Language: Английский

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