Repurposing Legacy Reduced-Representation Genomic Datasets for Conservation Biogeography: Lessons From Hercules Beetles Across Neotropical Ecoregions

Abstract

Aim

The study aimed to explore the opportunities and challenges of repurposing previously published reduced-representation genomic datasets for conservation biogeography post the Kunming-Montreal Agreement. Specifically, the study evaluates how historical climate fluctuations, habitat size, and recent anthropogenic disturbances may be associated with differences in genetic diversity among charismatic Hercules beetles across ecoregions.

Location

Northern Neotropics.

Methods

Combining site frequency spectrum and linkage disequilibrium based approaches with preexisting population genomic data and a reference genome, I assessed how historical climate fluctuations and recent anthropogenic forest exploitation shaped the observed genomic diversity. Additionally, continental, island and captive-bred samples were included to evaluate the performance of different indices for measuring genomic diversity.

Results

During the Pleistocene, although climatic fluctuations occurred frequently, most species maintained stable or increasing effective population sizes (Ne). In contrast, recent demographic inferences reveal fluctuating and uncertain Ne trajectories. Interestingly, the Central American species, D. septentrionalis, shows a possible recent Ne increase when the full dataset was used; however, this pattern became less clear when SNP subsampling was applied. Individuals of continental species generally exhibit higher genetic diversity than insular species; however, such patterns may depend on sequence quality as well as the filtering methods applied to the data.

Main Conclusions

Historical forest dynamics shape current genomic diversity in Neotropical beetles, but their impacts on genetic diversity differ across time. Importantly, results from the Central America species imply that forest protection and restoration may lead to demographic recovery, although caution should be applied because of the uncertainty associated with estimating recent demographic history. This study shows that previously published reduced-representation genome-wide datasets originally designed for other study foci can be repurposed for comparative conservation genomics as high-quality reference genomes become increasingly available.