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Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects

Citation

Chaturvedi, Samridhi et al. (2022), Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects, Dryad, Dataset, https://doi.org/10.5061/dryad.51c59zwbr

Abstract

Evolution can repeat itself, resulting in parallel adaptations in independent lineages occupying similar environments. Moreover, parallel evolution sometimes, but not always, uses the same genes. Two main hypotheses have been put forth to explain the probability and extent of parallel evolution. First, parallel evolution is more likely when shared ecologies result in similar patterns of natural selection in different taxa. Second, parallelism is more likely when genomes are similar, because of shared standing variation and similar mutational effects in closely related genomes. Here we combine ecological, genomic, experimental, and phenotypic data with Bayesian modeling and randomization tests to quantify the degree of parallelism and its relationship with ecology and genetics. Our results show that the extent to which genomic regions associated with climate are parallel among species of Timema stick insects is shaped collectively by shared ecology and genomic background. Specifically, the extent of genomic parallelism decays with divergence in climatic conditions (i.e., habitat or ecological similarity) and genomic similarity. Moreover, we find that climate-associated loci are likely subject to selection in a field experiment, overlap with genetic regions associated with cuticular hydrocarbon traits, and are not strongly shaped by introgression between species. Our findings shed light on when evolution is most expected to repeat itself.

Methods

This dataset contains files used for different analyses associated with this study. These are specific analysis which use various formats of genomic data. The data has been processed using various programs such as custom perl scripts and programs such as BayPass, Entropy, and Treemix.

Usage Notes

Any basic text editor can be used to open these data files. Alternatively, the less, head, tail, cat commands can be used on the UNIX command line to look at the files. 

Funding

HORIZON EUROPE European Research Council, Award: 770826 EE-Dynamics

National Science Foundation, Award: DEB 1844941

National Science Foundation, Award: 1638997

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Award: Postdoc mobility PBBSP3_141367

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Award: Postdoc mobility P300P3_147888