The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests

Beetles, despite their remarkable biodiversity and a long history of
research, remain lacking in reference genomes annotated with structural
variations of loci of adaptive significance. We sequenced and assembled
high-quality chromosome-level genomes of four Hercules beetles which
exhibit divergence in male horn size and shape, and body coloration. The
four Hercules beetle genomes were assembled to 11 pseudo-chromosomes,
where the three genomes assembled using Nanopore data (Dynastes grantii,
D. hyllus, and D. tityus) were mapped to the genome assembled using PacBio
+ Hi-C data (D. maya). We demonstrated a striking similarity in genome
structure among the four species. This conservative genome structure may
be attributed to our use of the D. maya assembly as the reference;
however, it is worth noting that such a conservative genome structure is a
recurring phenomenon among scarab beetles. We further identified homologs
of nine and three candidate-gene families that may be associated with the
evolution of horn structure and body coloration, respectively. Structural
variations in Scr and Ebony2 were detected and discussed for their
putative impacts on generating morphological diversity in beetles. We also
reconstructed the demographic histories of the four Hercules beetles using
heterozygosity information from the diploid genomes. We found that the
demographic histories of the beetles closely recapitulated historical
changes in suitable forest habitats driven by climate shifts.