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Abstract Genetic diversity plays a key role in maintaining population viability by preventing inbreeding depression and providing the building blocks for adaptation. Understanding how genetic diversity varies across space is, therefore, of key interest in conservation and population genetics.Here, we introducewingen, anrpackage for calculating continuous maps of genetic diversity, including nucleotide diversity, allelic richness, and heterozygosity, from standard genotypic and spatial data using a spatial moving window approach. We provide functions to account for variation in sample size across space using rarefaction, to create kriging‐interpolated maps of genetic diversity, and to mask any areas that are outside the area of interest.Tests with simulated and empirical datasets demonstrate thatwingencan successfully capture variation in genetic diversity across landscapes from both reduced‐representation and whole genome sequencing datasets. For reduced‐representation datasets,wingen's functions can be run easily on a standard laptop computer, and we provide options for parallelization to increase the efficiency of running larger whole genome datasets.wingenprovides novel and computationally tractable tools for creating informative maps of genetic diversity with applications for conservation prioritization as well as population and landscape genetic analyses.
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Individual‐based landscape genomics for conservation: An analysis pipeline
Abstract Landscape genomics can harness environmental and genetic data to inform conservation decisions by providing essential insights into how landscapes shape biodiversity. The massive increase in genetic data afforded by the genomic era provides exceptional resolution for answering critical conservation genetics questions. The accessibility of genomic data for non‐model systems has also enabled a shift away from population‐based sampling to individual‐based sampling, which now provides accurate and robust estimates of genetic variation that can be used to examine the spatial structure of genomic diversity, population connectivity and the nature of environmental adaptation. Nevertheless, the adoption of individual‐based sampling in conservation genetics has been slowed due, in large part, to concerns over how to apply methods developed for population‐based sampling to individual‐based sampling schemes. Here, we discuss the benefits of individual‐based sampling for conservation and describe how landscape genomic methods, paired with individual‐based sampling, can answer fundamental conservation questions. We have curated key landscape genomic methods into a user‐friendly, open‐source workflow, which we provide as a new R package, A Landscape Genomics Analysis Toolkit in R (algatr). Thealgatrpackage includes novel added functionality for all of the included methods and extensive vignettes designed with the primary goal of making landscape genomic approaches more accessible and explicitly applicable to conservation biology.
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- Award ID(s):
- 1845682
- PAR ID:
- 10512104
- Editor(s):
- Grueber, Catherine E
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Molecular Ecology Resources
- ISSN:
- 1755-098X
- Subject(s) / Keyword(s):
- conservation biology conservation genetics genetic diversity landscape genomics population structure spatial analysis
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1111/1755-0998.13884
