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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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Toward ecologically realistic predictions of species distributions: A cross‐time example from tropical montane cloud forests
Abstract There is an urgent need for more ecologically realistic models for better predicting the effects of climate change on species’ potential geographic distributions. Here we build ecological niche models usingMAXENTand test whether selecting predictor variables based on biological knowledge and selecting ecologically realistic response curves can improve cross‐time distributional predictions. We also evaluate how the method chosen for extrapolation into nonanalog conditions affects the prediction. We do so by estimating the potential distribution of a montane shrew (Mammalia, Soricidae,Cryptotis mexicanus) at present and the Last Glacial Maximum (LGM). Because it is tightly associated with cloud forests (with climatically determined upper and lower limits) whose distributional shifts are well characterized, this species provides clear expectations of plausible vs. implausible results. Response curves for theMAXENTmodel made using variables selected via biological justification were ecologically more realistic compared with those of the model made using many potential predictors. This strategy also led to much more plausible geographic predictions for upper and lower elevational limits of the species both for the present and during theLGM. By inspecting the modeled response curves, we also determined the most appropriate way to extrapolate into nonanalog environments, a previously overlooked factor in studies involving model transfer. This study provides intuitive context for recommendations that should promote more realistic ecological niche models for transfer across space and time.
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- Award ID(s):
- 1650241
- PAR ID:
- 10053966
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Global Change Biology
- Volume:
- 24
- Issue:
- 4
- ISSN:
- 1354-1013
- Page Range / eLocation ID:
- p. 1511-1522
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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