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Genomic signatures of local adaptation reveal source-sink dynamics in a high gene flow fish species.

ABSTRACT: Understanding source-sink dynamics is important for conservation management, particularly when climatic events alter species' distributions. Following a 2011 'marine heatwave' in Western Australia, we observed high recruitment of the endemic fisheries target species Choerodon rubescens, towards the cooler (southern) end of its distribution. Here, we use a genome wide set of 14 559 single-nucleotide polymorphisms (SNPs) to identify the likely source population for this recruitment event. Most loci (76%) showed low genetic divergence across the species' range, indicating high levels of gene flow and confirming previous findings using neutral microsatellite markers. However, a small proportion of loci showed strong patterns of differentiation and exhibited patterns of population structure consistent with local adaptation. Clustering analyses based on these outlier loci indicated that recruits at the southern end of C. rubescens' range originated 400?km to the north, at the centre of the species' range, where average temperatures are up to 3?°C warmer. Survival of these recruits may be low because they carry alleles adapted to an environment different to the one they now reside in, but their survival is key to establishing locally adapted populations at and beyond the range edge as water temperatures increase with climate change.

SUBMITTER: Cure K

PROVIDER: S-EPMC5561064 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Genomic signatures of local adaptation reveal source-sink dynamics in a high gene flow fish species.

Cure Katherine K Thomas Luke L Hobbs Jean-Paul A JA Fairclough David V DV Kennington W Jason WJ

Scientific reports 20170817 1

Understanding source-sink dynamics is important for conservation management, particularly when climatic events alter species' distributions. Following a 2011 'marine heatwave' in Western Australia, we observed high recruitment of the endemic fisheries target species Choerodon rubescens, towards the cooler (southern) end of its distribution. Here, we use a genome wide set of 14 559 single-nucleotide polymorphisms (SNPs) to identify the likely source population for this recruitment event. Most loc ...[more]

PMID: 28819230

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Project description:When populations of a rare species are small, isolated and declining under climate change, some populations may become locally maladapted. Detecting this maladaptation may allow effective rapid conservation interventions, even if based on incomplete knowledge. Population maladaptation may be estimated by finding genome-environment associations (GEA) between allele frequencies and environmental variables across a local species range, and identifying populations whose allele frequencies do not fit with these trends. We can then design assisted gene flow strategies for maladapted populations, to adjust their allele frequencies, entailing lower levels of intervention than with undirected conservation action. Here, we investigate this strategy in Scottish populations of the montane plant dwarf birch (Betula nana). In genome-wide restriction site-associated single nucleotide polymorphism (SNP) data, we found 267 significant associations between SNP loci and environmental variables. We ranked populations by maladaptation estimated using allele frequency deviation from the general trends at these loci; this gave a different prioritization for conservation action than the Shapely Index, which seeks to preserve rare neutral variation. Populations estimated to be maladapted in their allele frequencies at loci associated with annual mean temperature were found to have reduced catkin production. Using an environmental niche modelling (ENM) approach, we found annual mean temperature (35%), and mean diurnal range (15%), to be important predictors of the dwarf birch distribution. Intriguingly, there was a significant correlation between the number of loci associated with each environmental variable in the GEA and the importance of that variable in the ENM. Together, these results suggest that the same environmental variables determine both adaptive genetic variation and species range in Scottish dwarf birch. We suggest an assisted gene flow strategy that aims to maximize the local adaptation of dwarf birch populations under climate change by matching allele frequencies to current and future environments.

Project description:BackgroundThe scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species.ResultsAfter stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise FST estimates revealed low differentiation among populations (pairwise FST range?=?-?0.0008 - 0.0021). Analysis of genetic variation using putatively directional FST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p?<?0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise FST range?=?0.0288-0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus.ConclusionsFindings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes.

Dataset Information

Genomic signatures of local adaptation reveal source-sink dynamics in a high gene flow fish species.

Publications

Genomic signatures of local adaptation reveal source-sink dynamics in a high gene flow fish species.

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