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ABSTRACT Landscape genomic approaches for detecting genotype‐environment associations (GEA), isolation by distance (IBD) and isolation by environment (IBE) have seen a dramatic increase in use, but there have been few thorough analyses of the influence of sampling strategy on their performance under realistic genomic and environmental conditions. We simulated 24,000 datasets across a range of scenarios with complex population dynamics and realistic landscape structure to evaluate the effects of the spatial distribution and number of samples on common landscape genomics methods. Our results show that common analyses are relatively robust to sampling scheme as long as sampling covers enough environmental and geographic space. We found that for detecting adaptive loci and estimatingIBE, sampling schemes that were explicitly designed to increase coverage of available environmental space matched or outperformed sampling schemes that only considered geographic space. When sampling does not cover adequate geographic and environmental space, such as with transect‐based sampling, we detected fewer adaptive loci and had higher error when estimatingIBDandIBE. We found thatIBDcould be detected with as few as nine sampling sites, while large sample sizes (e.g., greater than 100 individuals) were crucial for detecting adaptive loci andIBE. We also demonstrate that, even with optimal sampling strategies, landscape genomic analyses are highly sensitive to landscape structure and migration—when spatial autocorrelation and migration are weak, commonGEAmethods fail to detect adaptive loci.
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The Effects of Latitudinal Gradients, Climatic Anomalies, and Size‐Selective Harvesting on the Adaptive Potential of an Intertidal Gastropod
ABSTRACT Coastal organisms live in a dynamic environment where a myriad of environmental stressors, including climate change, ocean acidification, and human harvesting, act on variable spatio‐temporal scales. Each of these stressors may impose unique selective forces on a population, shaping a species' adaptive potential and its ability to persist under future climatic conditions. Genomic investigations of adaptive responses to environmental and anthropogenic disturbances remain rare, especially in marine systems. Here, we use whole genome sequencing data from the owl limpet,Lottia gigantea, and outlier detection methods to pinpoint signals of selection (1) across long‐standing environmental gradients spanning the species' distribution, (2) at the poleward edge of the species' range where it experienced a recent expansion, and (3) between sites vulnerable to or protected from human size‐selective harvesting within California. Loci associated with environmental gradients across the entire range show the strongest differentiation at the southern end of the species' range, potentially driven by adaptation to sea surface temperature and pH. Additionalad‐hocoutlier analyses revealed a distinct set of loci potentially under selection in the expanded range, with different functional roles than the range‐wide outliers. Despite demographic models suggesting that protection from harvesting has a positive impact on the abundance of large individuals, we did not find strong signals of selection or changes in genetic diversity between sites differing in harvesting vulnerability. Our findings suggest that range‐wide environmental selective signals established over longer time scales are distinct from those imposed by climatic anomalies at finer spatio‐temporal scales. We found that climatic variation has a stronger selective imprint than human harvesting, and thus conservation interventions should consider prioritizing the maintenance of climate‐related adaptive potential. Understanding how climatic trends and anomalies interact with anthropogenic pressures will allow us to make more informed decisions to sustain the evolutionary capacity ofL. giganteaand other key coastal species.
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- Award ID(s):
- 2023297
- PAR ID:
- 10660610
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Evolutionary Applications
- Volume:
- 18
- Issue:
- 9
- ISSN:
- 1752-4571
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
-
Accepted Manuscript
- Journal Article:
- https://doi.org/10.1111/eva.70159
