Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila
- Department of Biology, Stanford University, United States
- Wellcome Sanger Institute, United Kingdom
- Department of Biology, University of Virginia, United States
- Department of Biology, University of Pennsylvania, United States
- Department of Genetics, University of Georgia, United States
- Institute of Population Genetics, Vetmeduni Vienna, Austria
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, United Kingdom
- Department of Biology, University of Fribourg, Switzerland
- Institute of Evolutionary Biology, CSIC- Universitat Pompeu Fabra, Spain
- Department of Biology, University of Utah, United States
- Taras Shevchenko National University of Kyiv, Ukraine
- National Antarctic Scientific Centre of Ukraine, Taras Shevchenko Blvd., Ukraine
- Department of Entomology, Cornell University, United States
- Department of Chemistry & Biochemistry, Laurentian University, Canada
- Laboratory of Genetics, University of Wisconsin-Madison, United States
- Department of Ecology and Evolutionary Biology, University of Kansas, United States
- Department of Biology, The Pennsylvania State University, United States
Figures
Figure 1 with 2 supplements
Sampling times, localities, and basic population structure of samples used in this study.
(A) Distribution of collection times during the spring (red) and fall (blue) in relation to latitude. For samples where the collection month, but not day, was recorded, we specified the 15th of the …
Figure 1—figure supplement 1
All sampling localities collected.
Sampling localities in (A) North America and (B) Europe for all samples collected, regardless of use in the present analysis. Sizes of circles reflect number of samples per locality.
Figure 1—figure supplement 2
Effect of filtering monomorphic variants on allele frequency distributions.
Distributions of the mean spring (A, B) and mean fall (C, D) allele frequencies for the dataset before (A, C) and after (B, D) filtering SNP found to be monomorphic in any population.
Figure 2 with 4 supplements
Signals of seasonal adaptation.
(A) p-value distribution of GLM seasonal regression (red line), permutations (solid black lines, 50/500 plotted), and expected values (dashed black line). (B) Comparison of seasonal test statistics …
Figure 2—figure supplement 1
Enrichment of seasonal SNPs by chromosome and significance threshold.
Enrichment is calculated as the observed number of seasonal SNPs over the number of seasonal SNPs in each permutation (median of 500 permutations). Error bars are 95% confidence intervals, and …
Figure 2—figure supplement 2
Comparison of bayenv and GLM seasonal analyses.
(A) Proportion of SNPs found highly seasonal in both the GLM and the bayenv seasonal analyses. (B) Seasonal and latitudinal concordance for both the GLM and the bayenv analyses.
Figure 2—figure supplement 3
Artificial sample size increases for GLM and RFM methods.
The effect of artificial increases of sample size on the Core20 seasonal analysis using (A, C) the RFM and (B, D) the GLM analyses. Top row: sample size inflated by a fixed amount. Bottom row: …
Figure 2—figure supplement 4
Comparison of the GLM and the Bayenv model for assessing clinal and seasonal concordance.
(A) The ‘joint quantile threshold’ is the quantile threshold for both the seasonal and the clinal analysis, and includes all SNPs at that quantile or less. (B) The ‘joint quantile bin’ includes only …
Figure 3
The thermal limit model.
The thermal limit model argues that weather in the weeks prior to sampling can explain variation in the predictability of allele frequency change. (A) Each line represents the comparison between one …
Additional files
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Supplementary file 1
Sample metadata.
(A) Population information. (B) Top 1% of seasonal SNPs (regression beta and p-values). Coordinates are in D. melanogaster reference v5.5.
- https://cdn.elifesciences.org/articles/67577/elife-67577-supp1-v2.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/67577/elife-67577-transrepform-v2.docx
