Biases in demographic modelling affect our understanding of recent divergence

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: unknown

Published: Feb. 10, 2021

Testing among competing demographic models of divergence has become an important component evolutionary research in model and non-model organisms. However, the effect unaccounted events on choice parameter estimation remains largely unexplored. Using extensive simulations, we demonstrate that under realistic scenarios, failure to account for population size (Ne) changes daughter ancestral populations leads strong biases time estimates as well choice. We illustrate these issues reconstructing recent history North Sea Baltic turbots (Scophthalmus maximus) by testing 16 isolation with migration (IM) secondary contact (SC) modeling Ne effects linked selection barrier loci. Failure resulted selecting SC long periods strict times preceding formation Sea. In contrast, accounting suggest (<6 kya) constant gene flow. further show how interpreting genomic landscapes differentiation can help discerning models. For example, turbot data, islands signatures selective sweeps, rather than old resisting introgression. The results have broad implications study highlighting potential unmodeled inference. Tested should aim at representing scenarios target taxa, extreme caution always be exercised when modeling.

Language: Английский

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Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes

Evolution Letters, Journal Year: 2024, Volume and Issue: 8(4), P. 575 - 586

Published: April 23, 2024

Abstract Chromosomal rearrangements can lead to the coupling of reproductive barriers, but whether and how they contribute completion speciation remains unclear. Marine snails genus Littorina repeatedly form hybrid zones between populations segregating for multiple inversion arrangements, providing opportunities study their barrier effects. Here, we analyzed 2 adjacent transects across ecotypes fabalis (“large” “dwarf”) adapted different wave exposure conditions on a Swedish island. Applying whole-genome sequencing, found 12 putative inversions 9 17 chromosomes. Nine reached near differential fixation ecotypes, all were in strong linkage disequilibrium. These cover 20% genome carry 93% divergent single nucleotide polymorphisms (SNPs). Bimodal both indicated that maintain genetic phenotypic integrity following contact. The bimodality reflects clines extension effect whole genome. Demographic inference suggests arose during period allopatry has been maintained &gt; 1,000 generations after secondary Overall, this shows chromosomal contributes isolation. Notably, overlap with inverted genomic regions associated ecotype differences closely related species (Littorina saxatilis), suggesting same regions, similar structural variants, evolution distinct species.

Language: Английский

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Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister species complex

Molecular Ecology, Journal Year: 2019, Volume and Issue: 28(19), P. 4388 - 4403

Published: Sept. 4, 2019

In contrast to the plethora of studies focusing on genomic basis adaptive phenotypic divergence, role gene expression during speciation has been much less investigated and consequently understood. Yet, convergence differential patterns between closely related species-pairs might reflect natural selection process ecological speciation. Here, we test for intercontinental in transcriptional signatures limnetic benthic sympatric Lake Whitefish (Coregonus clupeaformis) its sister lineage, European lavaretus), using six replicated (two North America, two Norway Switzerland). We characterized both sequence variation transcribed regions species across continents. Our first finding was that differentially expressed genes (DEG) whitefish tend be enriched shared polymorphism among lineages. then used genotypes covariation order infer polygenic at level. identified parallel outliers DEG involving primarily overexpressed relative species. analysis finally revealed existence bases underlying from continents, such as a cis-eQTL affecting pyruvate kinase level involved glycolysis. results are consistent with long-standing maintaining trans-continental diversity traits whitefishes.

Language: Английский

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Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(9), P. 2087 - 2103

Published: Feb. 22, 2021

Abstract Hybridization, introgression, and reciprocal gene flow during speciation, specifically the generation of mitonuclear discordance, are increasingly observed as parts speciation process. Genomic approaches provide insight into where, when, how adaptation operates after can measure historical modern introgression. Whether adaptive or neutral in origin, hybridization cause discordance by placing mitochondrial genome one species (or population) nuclear background another species. The latter, introgressed may eventually have its own mtDNA replaced “captured” other across entire geographical range. Intermediate stages capture process should be observable. Two nonsister Australasian monarch‐flycatchers, Spectacled Monarch ( Symposiachrus trivirgatus ) mostly Australia Indonesia Spot‐winged S. guttula New Guinea, present an opportunity to observe this We analysed thousands single nucleotide polymorphisms (SNPs) derived from ultraconserved elements all subspecies both Mitochondrial DNA sequences Australian populations form two paraphyletic clades, being sister presumably despite little signal Population genetic analyses (e.g., tests for selection) support at least event between . also uncovered introgression Maluku Islands island population , resulting apparent paraphyly. find that demographic processes, not most likely these complex histories. suggest a Pleistocene extinction mainland resulted range expansion

Language: Английский

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Speciation‐by‐depth on coral reefs: Sympatric divergence with gene flow or cryptic transient isolation?

Journal of Evolutionary Biology, Journal Year: 2020, Volume and Issue: 34(1), P. 128 - 137

Published: Nov. 3, 2020

Abstract The distributions of many sister species in the sea overlap geographically but are partitioned along depth gradients. genetic changes leading to segregation may evolve geographic isolation as a prerequisite coexistence or emerge during primary divergence new species. These alternatives can now be distinguished via power endowed by thousands scorable loci provided second‐generation sequence data. Here, we revisit case two depth‐segregated, genetically isolated ecotypes nominal Caribbean candelabrum coral Eunicea flexuosa . Previous analyses based on handful markers could not distinguish between models exchange after period (consistent with secondary contact) and gene flow divergence). Analyses history isolation, population size 15,640 SNP derived from RNAseq data best support where began 800K BP include epochs flow, an intermediate transient isolation. Results also supported previous conclusion that recent occurs asymmetrically Shallow lineage Deep. Parallel other corals depth‐segregated populations ( Agaricia fragilis Pocillopora damicornis ) suggest begin symmetric exchange, epoch precedes more complete marked asymmetric introgression. Thus, while divergence‐with‐gene account for much differentiation separates closely related, species, it remains seen whether any critical steps speciation process only occur when isolated.

Language: Английский

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Highly Replicated Evolution of Parapatric Ecotypes

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(11), P. 4805 - 4821

Published: July 8, 2021

Abstract Parallel evolution of ecotypes occurs when selection independently drives the similar traits across environments. The multiple origins are often inferred based on a phylogeny that clusters populations according to geographic location and not by environment they occupy. However, use phylogenies infer parallel in closely related is problematic because gene flow incomplete lineage sorting can uncouple genetic structure at neutral markers from colonization history populations. Here, we demonstrate within an Australian wildflower, Senecio lautus. We observed strong as well phylogenetic clustering geography show this unlikely due between parapatric ecotypes, which was surprisingly low. further confirm analytically demonstrating distortion requires higher levels migration than those S. Our results imply repeatedly create phenotypes despite perceived homogenizing effects flow.

Language: Английский

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Genomic data support management of anadromous Arctic Char fisheries in Nunavik by highlighting neutral and putatively adaptive genetic variation

Evolutionary Applications, Journal Year: 2021, Volume and Issue: 14(7), P. 1880 - 1897

Published: May 8, 2021

Abstract Distinguishing neutral and adaptive genetic variation is one of the main challenges in investigating processes shaping population structure wild, landscape genomics can help identify signatures adaptation to contrasting environments. Arctic Char ( Salvelinus alpinus ) an anadromous salmonid most harvested fish species by Inuit people, including Nunavik (Québec, Canada), recently deglaciated regions world. Unlike many other salmonids, occupy coastal habitats near their natal rivers during short marine phase restricted summer ice‐free period. Our objective was document putatively genomic populations from bordering inform local fisheries management. We used genotyping sequencing (GBS) genotype 18,112 filtered single nucleotide polymorphisms (SNP) 650 individuals 23 sampling locations along >2000 km coastline. results reveal a hierarchical structure, whereby neighboring hydrographic systems harbor distinct grouped major oceanographic basins: Hudson Bay, Strait, Ungava Labrador Sea. found diversity differentiation be consistent both with expected postglacial recolonization history patterns isolation‐by‐distance reflecting contemporary gene flow. Results three gene–environment association methods supported hypothesis freshwater environments (strongest associations sea surface air temperatures salinity). support management strategy at regional scale, implications for hatchery projects climate change are discussed.

Language: Английский

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An Evolutionary Mosaic Challenges Traditional Monitoring of a Foundation Species in a Coastal Environment—The Baltic Fucus vesiculosus

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 17, 2025

ABSTRACT During periods of environmental change, genetic diversity in foundation species is critical for ecosystem function and resilience, but it remains overlooked monitoring. In the Baltic Sea, a key monitoring brown seaweed Fucus vesiculosus , which forms sublittoral 3D habitats providing shelter food fish invertebrates. Ecological distribution models predict significant loss F. due to ocean warming, unless populations can adapt. Genetic variation recombination during sexual reproduction are essential adaptation, studies have revealed large‐scale clonal within Sea. We analysed genome‐wide single nucleotide polymorphism (SNP) data from east Atlantic, “Transition zone,” found mosaic divergent lineages contrasting an outside dominance few groups. determined that previously described endemic radicans predominantly large female clone its northern distribution. two Estonian sites, however, individuals earlier referred as sexually reproductively isolated revealing separate lineage may diverged long before formation Monitoring without considering this complexity will fail prioritise with adaptive potential new climate conditions. From our genomic data, we extract informative diagnostic markers differentiate major entities. Such SNP panel provide straightforward tool spatial temporal informing management decisions actions.

Language: Английский

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Genetic Causes and Consequences of Sympatric Morph Divergence in Salmonidae: A Search for Mechanisms

Annual Review of Animal Biosciences, Journal Year: 2021, Volume and Issue: 10(1), P. 81 - 106

Published: Nov. 11, 2021

Repeatedly and recently evolved sympatric morphs exhibiting consistent phenotypic differences provide natural experimental replicates of speciation. Because such are observed frequently in Salmonidae, this clade provides a rare opportunity to uncover the genomic mechanisms underpinning Such insight is also critical for conserving salmonid diversity, loss which could have significant ecological economic consequences. Our review suggests that genetic differentiation among largely nonparallel apart from few key genes may be consistently driving morph differentiation. We discuss alternative levels parallelism likely underlying identify several factors temper incipient speciation between morphs, including glacial history contemporary selective pressures. synthesis demonstrates salmonids useful studying poses additional research questions answered by future study family.

Language: Английский

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Rapid adaptation through genomic and epigenomic responses following translocations in an endangered salmonid

Evolutionary Applications, Journal Year: 2021, Volume and Issue: 14(10), P. 2470 - 2489

Published: June 11, 2021

Identifying the molecular mechanisms facilitating adaptation to new environments is a key question in evolutionary biology, especially face of current rapid and human-induced changes. Translocations have become an important tool for species conservation, but attendant small population sizes ecological pressures might affect phenotypic genotypic variation trajectories dramatically unknown ways. In Scotland, European whitefish (

Language: Английский

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