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Abstract Genomic data and machine learning approaches have gained interest due to their potential to identify adaptive genetic variation across populations and to assess species vulnerability to climate change. By identifying gene–environment associations for putatively adaptive loci, these approaches project changes to adaptive genetic composition as a function of future climate change (genetic offsets), which are interpreted as measuring the future maladaptation of populations due to climate change. In principle, higher genetic offsets relate to increased population vulnerability and therefore can be used to set priorities for conservation and management. However, it is not clear how sensitive these metrics are to the intensity of population and individual sampling. Here, we use five genomic datasets with varying numbers of SNPs (NSNPs = 7006–1,398,773), sampled populations (Npop = 23–47) and individuals (Nind = 185–595) to evaluate the estimation sensitivity of genetic offsets to varying degrees of sampling intensity. We found that genetic offsets are sensitive to the number of populations being sampled, especially with less than 10 populations and when genetic structure is high. We also found that the number of individuals sampled per population had small effects on the estimation of genetic offsets, with more robust results when five or more individuals are sampled. Finally, uncertainty associated with the use of different future climate scenarios slightly increased estimation uncertainty in the genetic offsets. Our results suggest that sampling efforts should focus on increasing the number of populations, rather than the number of individuals per populations, and that multiple future climate scenarios should be evaluated to ascertain estimation sensitivity.
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Sparse modeling for climate variable selection across trophic levels
Abstract Understanding how populations respond to climate is fundamentally important to many questions in ecology, evolution, and conservation biology. Climate is complex and multifaceted, with aspects affecting populations in different and sometimes unexpected ways. Thus, when measuring the changing climate it is important to consider the complexity of the phenomenon and the number of ways it can be characterized through different metrics. We used a Bayesian sparse modeling approach to select among 80 metrics of climate and applied the approach to 19 datasets of bird, insect, and plant population responses to abiotic conditions as case studies of how the method can be applied for climate variable selection in a time series context. For phenological datasets, mean spring temperature was frequently selected as an important climate driver, while selected predictors were more diverse for population metrics such as abundance or reproductive success. The climate variable selection approach presented here can help to identify potential climate metrics when there is limited physiological or mechanistic information to make ana priorivariable selection, and is broadly applicable across studies on population responses to climate.
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- Award ID(s):
- 2114793
- PAR ID:
- 10537305
- Publisher / Repository:
- Ecological Society of America
- Date Published:
- Journal Name:
- Ecology
- Volume:
- 105
- Issue:
- 3
- ISSN:
- 0012-9658
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1002/ecy.4231
