Redundancy analysis: A Swiss Army Knife for landscape genomics

Methods in Ecology and Evolution, Journal Year: 2021, Volume and Issue: 12(12), P. 2298 - 2309

Published: Sept. 20, 2021

Abstract Landscape genomics identifies how spatial and environmental factors structure the amount distribution of genetic variation among populations. genomic analyses have been applied across diverse taxonomic groups ecological settings, are increasingly used to analyse datasets composed large numbers markers multiple predictors. It is in this context that multivariate methods show their strengths. Redundancy analysis (RDA) a constrained ordination that, landscape framework, models linear relationships environment predictors variation, effectively identifying covarying allele frequencies associated with environment. RDA can be at both individual population levels, include covariates account for confounding directly infer genotype–environment associations on landscape. The modelling response explanatory variables allows accommodate complexity found nature, producing powerful efficient tool genomics. In review, we outline uses genomics, including variable selection, variance partitioning, associations, calculation adaptive indices offset. To illustrate these applications, use published dataset lodgepole pine includes genomic, phenotypic data. We provide an introduction statistical basis RDA, tutorial its interpretation discuss limitations guidelines avoid misuse. This review comprehensive resource community improve understanding as encourage appropriate applications. truly Swiss Army Knife genomics: multipurpose, adaptable versatile approach identifying, evaluating forecasting between variation.

Language: Английский

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Aquatic Landscape Genomics and Environmental Effects on Genetic Variation

Trends in Ecology & Evolution, Journal Year: 2019, Volume and Issue: 34(7), P. 641 - 654

Published: March 20, 2019

Language: Английский

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Copy number variants outperform SNPs to reveal genotype–temperature association in a marine species

Molecular Ecology, Journal Year: 2020, Volume and Issue: 29(24), P. 4765 - 4782

Published: Aug. 17, 2020

Abstract Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. To date, our knowledge evolution has largely been acquired by means single nucleotide polymorphism (SNPs) analyses. Until recently, the adaptive role structural (SVs) particularly that CNVs overlooked wild populations, partly due to their challenging identification. Here, we document usefulness Rapture, derived reduced‐representation shotgun sequencing approach, detect investigate copy alongside SNPs American lobster ( Homarus americanus ) populations. We conducted comparative study examine potential local adaptation 1,141 lobsters from 21 sampling sites within southern Gulf St. Lawrence, which experiences highest yearly thermal variance Canadian marine coastal waters. Our results demonstrated account for higher genetic differentiation than SNP markers. Contrary SNPs, no significant genetic–environment association was found, 48 CNV candidates were significantly associated with annual sea surface temperature, leading clustering locations despite geographic separation. Altogether, provide strong empirical case putatively contribute species unveil stronger spatial signal population structure SNPs. provides nonmodel highlights importance considering enhance understanding ecological evolutionary processes shaping structure.

Language: Английский

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Incorporating putatively neutral and adaptive genomic data into marine conservation planning

Conservation Biology, Journal Year: 2020, Volume and Issue: 35(3), P. 909 - 920

Published: Aug. 12, 2020

Abstract The availability of genomic data for an increasing number species makes it possible to incorporate evolutionary processes into conservation plans. Recent studies show how genetic can inform spatial prioritization (SCP), but they focus on metrics diversity and distinctness derived primarily from neutral sets. Identifying adaptive markers provide important information regarding the capacity populations adapt environmental change. Yet, effect including based SCP in comparison more widely used has not been explored. We existing a commercially exploited species, giant California sea cucumber ( Parastichopus californicus ), perform coastal region British Columbia (BC), Canada. Using RAD‐seq set 717 P. individuals across 24 sampling locations, we identified putatively (i.e., candidate) single nucleotide polymorphisms (SNPs) genotype–environment associations with seafloor temperature. calculated various both candidate SNPs compared outcomes independent combinations metrics. Priority areas varied depending whether or were specific metric used. For example, targeting sites high frequency warm‐temperature‐associated alleles support persistence under future warming prioritized southern region. In contrast, expected heterozygosity at loci uncertainty north. When combining metrics, all scenarios generated intermediate solutions, protecting that span latitudinal thermal gradients. Our results demonstrate distinguishing between affect solutions emphasize importance defining objectives when choosing among SCP.

Language: Английский

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Rare, long‐distance dispersal underpins genetic connectivity in the pink sea fan, Eunicella verrucosa

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(3)

Published: March 1, 2024

Abstract Characterizing patterns of genetic connectivity in marine species is critical importance given the anthropogenic pressures placed on environment. For sessile species, population can be shaped by many processes, such as pelagic larval duration, oceanographic boundaries and currents. This study combines restriction‐site associated DNA sequencing (RADseq) passive particle dispersal modelling to delineate pink sea fan, Eunicella verrucosa , a temperate octocoral. Individuals were sampled from 20 sites covering most species' northeast Atlantic range, site northwest Mediterranean Sea inform across Atlantic‐Mediterranean transition. Using 7510 neutral SNPs, geographic cline clusters was detected, partitioning into Ireland, Britain, France, Spain (Atlantic), Portugal (Mediterranean). Evidence significant inbreeding detected at all sites, finding not previous this based microsatellite loci. Genetic characterized an isolation distance pattern (IBD) ( r 2 = 0.78, p < 0.001), which persisted Mediterranean‐Atlantic boundary. In contrast, exploration ancestral assignment using program ADMIXTURE indicated Bay Biscay, we suggest represents natural break possibly linked lack suitable habitat. As duration (PLD) unknown, simulations run for 14 21 days. both modelled PLDs, inter‐annual variations trajectories suggested that long‐lived, range‐wide IBD driven rare, longer events act maintain gene flow. These results may facilitate stepping‐stone E. highlight oceanography breaks range should considered designation ecologically coherent MPA networks.

Language: Английский

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Seascape genomics of eastern oyster (Crassostrea virginica) along the Atlantic coast of Canada

Evolutionary Applications, Journal Year: 2018, Volume and Issue: 12(3), P. 587 - 609

Published: Nov. 28, 2018

Interactions between environmental factors and complex life-history characteristics of marine organisms produce the genetic diversity structure observed within species. Our main goal was to test for differentiation among eastern oyster populations from coastal region Canadian Maritimes against expected homogeneity caused by historical events, taking into account spatial (temperature, salinity, turbidity) variation. This achieved genotyping 486 individuals originating 13 locations using RADSeq. A total 11,321 filtered SNPs were used in a combination population genomics association analyses. We revealed significant neutral (mean FST = 0.009) sampling locations, occurrence six major clusters studied system. Redundancy analyses (RDAs) that variables explained 3.1% 4.9% variation 38.6% 12.2% putatively adaptive variation, respectively. These results indicate these play role distribution both Moreover, polygenic selection suggested genotype-environment analysis correlations additive scores temperature salinity. discuss our context their conservation management implications oyster.

Language: Английский

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Putatively adaptive genetic variation in the giant California sea cucumber (Parastichopus californicus) as revealed by environmental association analysis of restriction‐site associated DNA sequencing data

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(24), P. 5035 - 5048

Published: Nov. 14, 2018

Abstract Understanding the spatial scale of local adaptation and factors associated with adaptive diversity are important objectives for ecology evolutionary biology, have significant implications effective conservation management wild populations natural resources. In this study, we used an environmental association analysis to identify bioclimatic variables correlated putatively genetic variation in a benthic marine invertebrate—the giant California sea cucumber ( Parastichopus californicus )—spanning coastal British Columbia southeastern Alaska. We redundancy (RDA) 3,699 single nucleotide polymorphisms (SNPs) obtained using RAD sequencing detect candidate markers 11 variables, including bottom surface conditions, across two scales (entire study area within subregions). At broadest scale, RDA revealed 59 SNPs, 86% which were mean temperature. Similar patterns identified when population structure was accounted for. Additive polygenic scores, provide measure cumulative signal all strongly temperature, consistent spatially varying selection thermal gradient. finer 23 SNPs detected, primarily salinity (26%) current velocity (17%). Our findings suggest that may play role as drivers P. . These results context future studies evaluate basis help inform relevant situ field putative invertebrates.

Language: Английский

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Population epigenetic divergence exceeds genetic divergence in the Eastern oyster Crassostrea virginica in the Northern Gulf of Mexico

Evolutionary Applications, Journal Year: 2019, Volume and Issue: 13(5), P. 945 - 959

Published: Dec. 23, 2019

Populations may respond to environmental heterogeneity via evolutionary divergence or phenotypic plasticity. While occurs through DNA sequence differences among populations, plastic populations be generated by changes in the epigenome. Here, we present results of a genome-wide comparison methylation patterns and genetic structure four Eastern oyster (

Language: Английский

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Asymmetrical gene flow in five co-distributed syngnathids explained by ocean currents and rafting propensity

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2020, Volume and Issue: 287(1926)

Published: May 6, 2020

Ocean circulation driving macro-algal rafting is believed to serve as an important mode of dispersal for many marine organisms, leading predictions on population-level genetic connectivity and the directionality effective dispersal. Here, we use genome-wide single nucleotide polymorphism data investigate whether gene flow in two seahorses ( Hippocampus ) three pipefishes Syngnathus follows predominant ocean patterns Gulf Mexico northwestern Atlantic. In addition, explore magnitudes are predicted by traits related active ability habitat preference. We inferred demographic histories these co-distributed syngnathid species, coalescent model-based estimates indicate that agreement with predicts eastward northward transport. However, magnitude which currents influence this pattern appears strongly dependent species-specific propensity preferences. Higher levels stronger observed erectus , floridae louisianae closely associated pelagic macro-algae Sargassum spp., compared zosterae scovelli / fuscus sister-species pair, prefer near shore habitats weakly . This study highlights how combination population genomic inference together can help explain structure diversity ecosystems.

Language: Английский

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Population Genomics Applied to Fishery Management and Conservation

Population genomics, Journal Year: 2019, Volume and Issue: unknown, P. 399 - 421

Published: Jan. 1, 2019

Language: Английский

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