Genomic tools for comparative conservation genetics among three recently diverged stag beetles (Lucanus, Lucanidae)

We are witnessing a rapid decline in global biodiversity. International protocols and local conservation laws have been installed to counter such an unprecedented rate of decline. However, quantitatively evaluating how much biodiversity has been lost due to climatic and anthropogenic effects and how much biodiversity has been restored due to conservation efforts remain challenging. We applied a comparative conservation genomic approach to statistically and quantitatively address these questions using three geographical taxa from a stag beetle species complex. We found that the three sky-island taxa formed three independently evolving units without detectable post-divergence gene flow; furthermore, the three taxa, which have been divergent from each other since the mid-Pleistocene, have experienced episodes of demographic decline in the past.  More importantly, even though idiosyncratic anthropogenic exploitations have been hypothesized to impact the recent demographic history (<..., , , , # Supplementary data for \"Genomic tools for comparative conservation genetics: Objectively evaluating the impacts of anthropogenic exploitation and informing an immediate conservation plan among three recently diverged stag beetles (Lucanus, Lucanidae).\"

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These folders have the supplementary data for our study, in which we analyzed the population trends of tree stag beetles (genus Lucanus) sister species in Taiwan.

## Description of the data and file structure

bootstrapped_sites: this folder has the results of the sites bootstrapping for evaluating parameter estimates (see [https://speciationgenomics.github.io/fastsimcoal2/](https://speciationgenomics.github.io/fastsimcoal2/) for understanding how they are made and how they are used through Bash scripts for generating blocks of sites for bootstrapping). Therefore, each \"sites\" file contains around 6667 sites from the original Variant Call Format (VCF) file of each population, which is contained in the \"AllSites\" file. \"header\" fi...