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Beetles, despite their remarkable biodiversity and a long history of research, remain lacking in reference genomes annotated with structural variations in 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 colouration. 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 homologues of nine and three candidate‐gene families that may be associated with the evolution of horn structure and body colouration 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. [ABSTRACT FROM AUTHOR]

Forest soil and leaf litter support diverse arthropod mesofauna for which diversity dynamics is challenging to study due to the high number of species and specimens, small body size and limited taxonomic knowledge.Immature stages (larvae) are even harder to identify than adults, as their morphology is largely unknown. Therefore, larvae are often ignored, even though they may form a substantial proportion of specimens collected, are less mobile than adults and their exclusion may provide an incomplete diversity profile.Here, we use Oxford Nanopore DNA barcoding to investigate whether the inclusion of larvae provides a more complete taxonomic, phylogenetic and functional diversity profiles in leaf litter beetles (Coleoptera) from a subtropical forest in Taiwan.Our results indicate that larvae represent up to 38% of beetle specimens per sample, but most of them belong to 2–3 common species. Larvae of most beetle species are rarely collected repeatedly or in multiple specimens, possibly due to special habitat requirements or high seasonality.Taxonomic, phylogenetic and incidence‐based functional diversity measures were not affected by the exclusion of larvae in the Staphylinidae dataset but were strongly biased in all‐beetle dataset, especially when only common or abundant species were considered. Taxonomic beta diversity was not affected by the omission of larvae.Our results indicate that immature stages may be omitted in ecological studies of arthropods in case both adults and larvae co‐occur in the same habitat, and the sites are sampled repeatedly. Caution is needed (1) in groups in which larvae and adults do not inhabit the same environment or strongly differ in biology, (2) when rare species are omitted or (3) when functional diversity is calculated from abundance data. [ABSTRACT FROM AUTHOR]

The evolutionary dynamics and phylogenetic utility of mitochondrial genomes (mitogenomes) have been of particular interest to systematists and evolutionary biologists. However, certain mitochondrial features, such as the molecular evolution of the control region in insects, remain poorly explored due to technological constraints. Using a combination of long- and short-read sequencing data, we assembled ten complete mitogenomes from ten Hercules beetles. We found large-sized mitogenomes (from 24 to 28 kb), which are among the largest in insects. The variation in genome size can be attributed to copy-number evolution of tandem repeats in the control region. Furthermore, one type of tandem repeat was found flanking the conserved sequence block in the control region. Importantly, such variation, which made up around 30% of the size of the mitogenome, may only become detectable should long-read sequencing technology be applied. We also found that, although different mitochondrial loci often inferred different phylogenetic histories, none of the mitochondrial loci statistically reject a concatenated mitochondrial phylogeny, supporting the hypothesis that all mitochondrial loci share a single genealogical history. We on the other hand reported statistical support for mito-nuclear phylogenetic discordance in 50% of mitochondrial loci. We argue that long-read DNA sequencing should become a standard application in the rapidly growing field of mitogenome sequencing. Furthermore, mitochondrial gene trees may differ even though they share a common genealogical history, and ND loci could be better candidates for phylogenetics than the commonly used COX1. [ABSTRACT FROM AUTHOR]