Generating continuous maps of genetic diversity using moving windows

Bishop, Anusha P; Chambers, E. Anne; Wang, Ian

doi:10.1111/2041-210x.14090

Cited by 8 publications

(2 citation statements)

References 22 publications

(38 reference statements)

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“…Genetic diversity metrics are sensitive to sample size, a problem that rarefaction has been shown to resolve (Kalinowski 2004; Bishop et al 2023). We therefore removed any nodes with sample sizes less than 15 and randomly subsampled larger nodes down to 15 to have consistency in sample size.…”

Section: Methodsmentioning

confidence: 99%

Genetic network analysis uncovers spatial variation in diversity and connectivity of a species presenting a continuous distribution

Fournier,

Manseau,

Redquest

et al. 2024

Preprint

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The conservation of genetic diversity and connectivity is essential for the long-term persistence and adaptive ability of a species. Recent calls have been made for the inclusion of genetic diversity and differentiation measures in the assessment, management, and conservation of species. However, the literature often lacks direction on how to do so for species with continuous distributions or no distinct breaks in genetic connectivity. There are many considerations to overcome when investigating genetic diversity and connectivity of such species. We combine multiple genetic network methodologies with more traditional population genetic analyses within a single framework to address the challenges of investigating population structure and quantifying variation in genetic diversity and connectivity of wide-ranging species with continuous distributions. We demonstrate the efficacy and applicability of our framework through a study on woodland caribou (Rangifer tarandus) occupying the boreal forest of Canada; a species of significant conservation concern. The dataset consisted of 4911 unique individuals genotyped at 9 microsatellite loci, which were subsequently partitioned into 103 spatial nodes to create a population-based genetic network. The Walktrap community detection algorithm was used to detect hierarchical population genetic structure within the study area and node-based network metrics such as mean inverse edge weight and clustering coefficient were used to quantify the variation in genetic connectivity across the range. Lastly, genetic diversity was assessed by calculating allelic richness and heterozygosity of the nodes making up the network. The community detection analysis identified two communities at the coarsest scale to nine communities at the optimal partition. A strong pattern of Isolation by Distance (IBD) was found across the range at multiple scales. Furthermore, signs of genetic erosion along the study area's southern boundaries were depicted by nodes presenting low genetic diversity and low centrality values. These results are important to the species status assessments in providing previously unavailable information on connectivity and diversity within and beyond the current local population units used in management. Our approach to quantify the patterns and extent of connectivity across the boreal range is comprehensive and could easily be adapted to other species. The results are robust and provide a solid foundation for the continued monitoring and recovery of the species.

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Section: Methodsmentioning

confidence: 99%

Genetic network analysis uncovers spatial variation in diversity and connectivity of a species presenting a continuous distribution

Fournier,

Manseau,

Redquest

et al. 2024

Preprint

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“…Once MLLs had been established, genotypic richness (R)the inverse of clonality-was calculated according to Dorken and Eckert (2001): R = (number of MLLs-1) / (number of samples-1) for each meadow, each identified genetic cluster (see below) and each coast (Figure 1). Genotypic richness values were then plotted as a heatmap, using the R package "wingen 1.1.0" (Bishop et al, 2023). We excluded the site Gottskär (GOT) from the interpolated heatmap because of the low number of successfully sequenced samples at this site (Table 1).…”

Section: Genotypic Richness (R)mentioning

confidence: 99%

Genetic structure and diversity of the seagrass Zostera marina along a steep environmental gradient, with implications for genetic monitoring

Ries,

Faust,

Johannesson

et al. 2023

Front. Clim.

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Zostera marina (eelgrass) is a foundation species in coastal zones in the northern hemisphere. Eelgrass is declining across its distribution, a trend likely to accelerate under climate change. In Sweden, eelgrass is a species of particular concern in management and conservation. Here, we provide information on genetic variation, an important component for the potential persistence and adaptation of any species in a changing environment. In particular, the steep salinity gradient over which eelgrass is distributed along the Swedish coast (26 psu on the west coast to 5 psu on the east coast) calls for a better understanding of genetic diversity, connectivity, and potential for local adaptation. To assess genetic variation and population genetic structure, we genotyped individuals with 2,138 single nucleotide polymorphisms (SNPs) from 15 eelgrass meadows spanning the whole Swedish distribution. We found a geographic population genetic structure from west to east parallel to the salinity gradient and with a clear genetic break at the entrance to the Baltic Sea. Meadows along the low salinity east coast consisted of a few or only one clone. Eelgrass on the west coast had higher genotypic richness, higher genetic variation, and showed population differentiation on smaller geographic scales. With their low genetic variation, the east coast meadows are especially threatened amidst global changes. Lack of sexual reproduction and the capacity to generate new genotypes is an issue that needs to be seriously considered in management and conservation. In addition, the lack of sexual reproduction renders clonal eelgrass less likely to recover and recolonize after disturbance, and more challenging to restore. The here provided information on genetic clusters, clonality, and genetic variation can be included for prioritizing meadows for conservation and for identifying meadows for restoration purposes. Most importantly, genetic monitoring is urgently needed to assess temporal genetic changes of eelgrass along the Swedish coast and elsewhere facing climate change.

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Distinct spatial patterns of genetic structure and diversity in the butterfly Marbled White (Melanargia galathea) inhabiting fragmented grasslands

Terzer,

Schmid,

Bauert

et al. 2023

Conserv Genet

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We adopted a landscape-scale approach to analyze the genetic patterns (diversity, structure, and differentiation) of the Marbled White (Melanargia galathea). This butterfly species is characteristic of semi-dry grasslands, which have substantially declined in Switzerland during past decades. We sampled individuals on a regular grid of the established Biodiversity Monitoring program of Switzerland over five consecutive years, obtaining 1639 genotyped individuals from 185 locations. Results showed that M. galathea populations cluster into five spatially aggregated clusters that largely coincide with the biogeographic regions of Switzerland. Genetic diversity (allelic richness) was higher in the South of the Alps, likely related to immigration dynamics that suggest recolonisation from the South after the last glaciation. Demographic history resulted in distinct isolation by distance (IBD) and by cumulative elevational difference (isolation by altitude, IBA) at large scale, while regional IBD and IBA were less pronounced. This pattern was likely induced by the barrier effect of the high mountains of the Alps impeding continuous northward migration after the last glacial maximum. A temporal analysis revealed that regional genetic diversity did not change strongly during the five sampling years. This result indicates that the genetic diversity pattern in M. galathea has not been noticeably affected by historical land-use change or that the sampling period of five years is too short to detect any changes. Our findings highlight the regionally, topography-induced distinct genetic clusters, relevant for consideration as conservation units and likely reflecting genetic structures similar to those found in other butterfly species of conservation concern.

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Generating continuous maps of genetic diversity using moving windows

Cited by 8 publications

References 22 publications

Genetic network analysis uncovers spatial variation in diversity and connectivity of a species presenting a continuous distribution

Genetic network analysis uncovers spatial variation in diversity and connectivity of a species presenting a continuous distribution

Genetic structure and diversity of the seagrass Zostera marina along a steep environmental gradient, with implications for genetic monitoring

Distinct spatial patterns of genetic structure and diversity in the butterfly Marbled White (Melanargia galathea) inhabiting fragmented grasslands

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