The Evolution of Comparative Phylogeography: Putting the Geography (and More) into Comparative Population Genomics

Genome Biology and Evolution, Год журнала: 2021, Номер 14(1)

Опубликована: Авг. 3, 2021

Comparative population genomics is an ascendant field using genomic comparisons between species to draw inferences about forces regulating genetic variation. phylogeography, by contrast, focuses on the shared lineage histories of codistributed geographically and decidedly organismal in perspective. phylogeography approximately 35 years old, and, some metrics, showing signs reduced growth. Here, we contrast goals methods comparative argue that offers important perspective evolutionary history succeeds integrating with landscape evolution ways complement suprageographic genomics. Focusing primarily terrestrial vertebrates, review its milestones ongoing conceptual innovations, increasingly global focus, status as a bridge process speciation. We also that, science strong "sense place," abundant "place-based" educational opportunities focus geography natural history, well for collaboration local communities indigenous peoples. Although does not yet require whole-genome sequencing many goals, conclude it nonetheless plays role grounding our interpretation variation fundamentals Earth history.

Язык: Английский

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Comparative genomics approach to evolutionary process connectivity

Evolutionary Applications, Год журнала: 2020, Номер 13(6), С. 1320 - 1334

Опубликована: Апрель 15, 2020

The influence of species life history traits and historical demography on contemporary connectivity is still poorly understood. However, these factors partly determine the evolutionary responses to anthropogenic landscape alterations. Genetic its outcomes depend a variety spatially dependent processes, such as population structure, local adaptation, genetic admixture, speciation. Over last years, genomic studies have been interrogating processes with increasing resolution, revealing large diversity structured landscapes. In parallel, multispecies meta-analyses usually based low-genome coverage data provided fundamental insights into ecological determinants connectivity, key structure. comparative lack thorough integration macro- micro-evolutionary scales fully realize their potential. Here, I present how genomics framework may provide deeper understanding process connectivity. This relies coupling inference long-term demographic selective an assessment consequences Standardizing this approach across several occupying same should help understand spatial environmental heterogeneity has shaped patterns in different taxa contrasted traits. will argue that reasonable amount genome sequence can be sufficient resolve connect complex histories. Ultimately, implementing varied taxonomic groups expected improve scientific guidelines for conservation management policies.

Язык: Английский

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Reduced‐Representation Sequencing Detects Trans‐Arctic Connectivity and Local Adaptation in Polar Cod (Boreogadus saida)

Molecular Ecology, Год журнала: 2025, Номер unknown

Опубликована: Март 5, 2025

Information on connectivity and genetic structure of marine organisms remains sparse in frontier ecosystems such as the Arctic Ocean. Filling these knowledge gaps becomes increasingly urgent, is undergoing rapid physical, ecological socio-economic changes. The abundant widely distributed polar cod (Boreogadus saida) highly adapted to waters, its larvae juveniles live close association with sea ice. Through a reduced-representation sequencing approach, this study explored spatial at circum-Arctic scale. Genomic variation was partitioned into neutral adaptive components respectively investigate local adaptation. Based 922 high-quality single nucleotide polymorphism (SNP) markers genotyped 611 cod, broad-scale differentiation detected among three groups: (i) Beaufort -Chukchi seas, (ii) all regions connected by Transpolar Drift, ranging from Laptev Sea Iceland, including European (iii) West Greenland. Patterns suggested broadscale oceanographic ice drift features (i.e., Gyre Drift) important drivers connectivity. 35 outlier loci indicated divergence Greenland Beaufort-Chukchi Seas populations, possibly driven environmental conditions. decline changing ocean currents can alter or disrupt between groups, potentially undermining their resilience climate change, even putative refugia, Central Ocean Archipelago.

Язык: Английский

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Ten years of demographic modelling of divergence and speciation in the sea

Evolutionary Applications, Год журнала: 2022, Номер 16(2), С. 542 - 559

Опубликована: Июнь 6, 2022

Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry considered necessary most events because geographical barriers seemed largely absent sea, and many marine have high dispersal capacities. Combining genome-wide data with demographic modelling infer history of has introduced new ways address this classical issue. These models assume an ancestral splits into two subpopulations diverging according different scenarios allow tests periods gene flow. Models can also test heterogeneities sizes migration rates along genome account, respectively, background selection against introgressed ancestry. To investigate how flow arise we compiled studies organisms extracted preferred together estimates parameters. show do exist but occur without isolation. Heterogeneity detected pairs suggesting predominance semipermeable during divergence. We found weak positive relationship between fraction experiencing reduced levels differentiation. Furthermore, upper bound 'grey zone speciation' our dataset extended beyond before, implying taxa possible at higher than previously thought. Finally, list recommendations further strengthening use research. include more balanced representation taxa, consistent comprehensive modelling, clear reporting results simulation rule out nonbiological explanations general results.

Язык: Английский

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Spatial coalescent connectivity through multi-generation dispersal modelling predicts gene flow across marine phyla

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Окт. 4, 2022

Abstract Gene flow governs the contemporary spatial structure and dynamic of populations as well their long-term evolution. For species that disperse using atmospheric or oceanic flows, biophysical models allow predicting migratory component gene flow, which facilitates interpretation broad-scale inferred from observed allele frequencies among populations. However, frequent mismatches between dispersal estimates genetic diversity prevent an operational synthesis for eco-evolutionary projections. Here we use extensive compilation 58 population studies 47 phylogenetically divergent marine sedentary over Mediterranean basin to assess how differentiation is predicted by Isolation-By-Distance, single-generation multi-generation models. Unlike previous approaches, latter unveil explicit parents-to-offspring links (filial connectivity) implicit siblings a common ancestor (coalescent connectivity). We find almost 70 % variance in explained coalescent connectivity multiple generations, significantly outperforming other Our results offer great promises untangle forces shape anticipate climate-driven redistributions, altogether improving conservation planning.

Язык: Английский

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Opportunities and inherent limits of using environmental DNA for population genetics

Environmental DNA, Год журнала: 2023, Номер 5(5), С. 1048 - 1064

Опубликована: Авг. 9, 2023

Abstract Molecular techniques using DNA retrieved from community or environmental samples, in particular (eDNA), are becoming increasingly popular for detecting individual species, assessing biodiversity, and quantifying ecological indices. More recently, eDNA has also been proposed as a template population genetics, several studies have already tested the feasibility of this approach, mostly looking at vertebrate species. Their results along with general opportunities offered by these types “community‐based” such possibility to target multiple species same time, generated great enthusiasm expectations genetics. However, not every aspect genetics can be addressed eDNA‐based data some inherent limitations may challenge its conclusions. Here, we firstly review state current knowledge samples Then, focusing on eDNA, summarize but detail four main use population‐level inferences, namely, (1) difficulty retrieve species‐specific dataset, (2) potential lack correlation between observed true allelic frequencies, (3) loss information multi‐locus genotyping linkage loci, (4) uncertainty about individuals contributing sampled pool (e.g., number, life‐stage, sex). Some might overcome development new technologies models that account specificities eDNA. Others, however, inherent, their effect inferences must thoroughly evaluated. The gaining insights into genetic diversity structure is appealing scientists, conservation managers, other practitioners. Yet, avoid false incorrect it imperative known considered alongside advantages.

Язык: Английский

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Comparative phylogeography in the genomic age: Opportunities and challenges

Journal of Biogeography, Год журнала: 2022, Номер 49(12), С. 2130 - 2144

Опубликована: Окт. 5, 2022

Abstract Aim We consider the opportunities and challenges comparative phylogeography (CP) faces in genomic age to determine: (1) how we can maximise potential of big CP analyses advance biogeographic macroevolutionary theory; (2) what can, will struggle, achieve using approaches this era genomics. Location World‐wide. Taxon All. Methods review literature discuss future ‐ particularly examining insights enabled by genomics that may not be possible for single species and/or few molecular markers. focus on geography species' natural histories interact yield congruent incongruent patterns neutral adaptive processes context both historical recent rapid evolution. also data are being stored, accessed, shared. Results With widespread availability data, shift from a single‐ multi‐locus perspective is resulting detailed inferences an improved statistical rigour phylogeography. However, time effort required collecting co‐distributed accruing species‐specific ecological knowledge continue limiting factors. Bioinformatic skills user‐friendly analytical tools, alongside computational infrastructure limiting. Main conclusions Over last ~35 years, there has been much progress understanding intraspecific genetic variation geographically distributed. The next major steps incorporate evolutionary community perspectives account responses among across temporal scales, including those related anthropogenic change. full only realised if employ robust study designs within sound framework. advocate phylogeographers adopt such consistent enhance comparisons present‐day findings.

Язык: Английский

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The influence of fragmented landscapes on speciation

Journal of Evolutionary Biology, Год журнала: 2024, Номер 37(12), С. 1499 - 1509

Опубликована: Апрель 3, 2024

Abstract In the face of unprecedented global transformations, unravelling intricate mechanisms governing biodiversity patterns is imperative for predicting and interpreting species responses. An important element in this interplay fragmentation spatial mosaic or arrangement suitable sites within landscape. Beyond its well-documented impact on loss, fragmented landscapes also influence origin biodiversity, by influencing speciation dynamics. This research employs a model that integrates configuration dispersal abilities individuals to investigate landscape species’ evolutionary trajectories. Specifically, we propose microevolutionary where are characterized their ability genome, allowing population evolution diversification. Space explicitly unsuitable define landscapes. Our demonstrates how intermediate enhance However, simulations more result lower total number percentage occupied individuals, particularly when have limited abilities. Furthermore, found levels can stimulate greater richness, while higher extinction events tend occur under fragmentations. results show non-monotonic dependence richness dispersal, supporting hypothesis as promotor diversification, demonstrating synergistic effects processes speciation, extinction, poses real challenge context dynamic world.

Язык: Английский

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Restricted dispersal in a sea of gene flow

Proceedings of the Royal Society B Biological Sciences, Год журнала: 2021, Номер 288(1951), С. 20210458 - 20210458

Опубликована: Май 18, 2021

How far do marine larvae disperse in the ocean? Decades of population genetic studies have revealed generally low levels structure at large spatial scales (hundreds kilometres). Yet this result, typically based on discrete sampling designs, does not necessarily imply extensive dispersal. Here, we adopt a continuous strategy along 950 km coast northwestern Mediterranean Sea to address question four species. In line with expectations, observe weak scale. Nevertheless, our uncovers pattern isolation by distance small (few tens kilometres) two Individual-based simulations indicate that signal is an expected signature restricted At other extreme connectivity spectrum, pairs individuals are closely related genetically were found more than 290 apart, indicating long-distance Such combination dispersal rare events supported high-resolution biophysical model larval study area, and posit it may be common Our results bridge direct implications for design reserve networks.

Язык: Английский

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Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics

Proceedings of the Royal Society B Biological Sciences, Год журнала: 2021, Номер 288(1957), С. 20211252 - 20211252

Опубликована: Авг. 25, 2021

Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances sequencing and analysis aDNA from range organisms have enabled detailed processes such as past demography, introgression, domestication, adaptation speciation. However, to date with notable exception microbiomes sediments, most studies focused on single taxa or taxonomic groups, making study changes at community level challenging. This is rather surprising because current analytical approaches allow us obtain analyse multiple source materials. When combined, these data can enable simultaneous through space time, could thus provide more comprehensive ecosystem-wide changes. It therefore timely develop an integrative approach by combining substrates. In this review, we discuss various applications, associated challenges future prospects approach.

Язык: Английский

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