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 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.

Genetic Assessment of Fertile F1 Hybrids between Two Hercules Beetles, Dynastes maya Hardy and D. grantii Horn (Scarabaeidae).

Although hybridization may complicate taxonomic practices, it can be common between animal species. Animal hybridization not only can help with generating phenotypic and species diversity in nature, but also with understanding the genetic and genomic basis of phenotypic evolution in the laboratory. We assessed the genetic composition of captive bred F1 hybrids between two Hercules beetle species using mitochondrial CO1 and nuclear loci from a double-digest restriction-site associated DNA sequencing (ddRADseq) library. We showed that the F1 hybrids were genetically clustered with samples from the maternal species, D. grantii, based on CO1 data. Nuclear genome data, on the other hand, clearly showed that the F1 individuals were genetically intermediate between D. maya, the paternal species, and D. grantii, based on a principal component analysis. Our results also revealed that sampling design may have a major impact on the inferred genetic structure and hybrid individuals using ddRADseq data sets. We discuss the importance and potential from studying the genomics of this hybrid progeny in terms of understanding the origin and maintenance of both intraspecific and interspecific phenotypic divergence and convergence.

Long-read Sequencing Data Reveals Dynamic Evolution of Mitochondrial Genome Size and the Phylogenetic Utility of Mitochondrial DNA in Hercules Beetles (Dynastes; Scarabaeidae).

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.

Structure and membership of gut microbial communities in multiple fish cryptic species under potential migratory effects.

The animal gut microbiota evolves quickly towards a complex community and plays crucial roles in its host's health and development. Factors such as host genetics and environmental changes are regarded as important for controlling the dynamics of animal gut microbiota. Migratory animals are an important group for studying how these factors influence gut microbiota because they experience strong environmental perturbations during migration. The commercially important grey mullet, Mugil cephalus, is a cosmopolitan species complex that display reproductive migration behaviour. There are three cryptic species of M. cephalus fish distributed across the Northwest Pacific, and their spawning sites overlap in the Taiwan Strait. This extraordinary natural occurrence makes the grey mullet an ideal model organism for exploring the nature of wild animal-gut microbiota relationships and interactions. This study investigates the diversity and structure of the gut microbial community in three cryptic M. cephalus species using 16S rRNA amplicon sequencing. Gut microbial compositions from adult and juvenile fish samples were analysed. Our results indicate that gut microbial communities within the grey mullet share a core microbiome dominated by Proteobacteria, Firmicutes and Actinobacteria. However, the structures of gut microbial communities were more distinct between adult mullet groups than they were between juvenile ones. Intriguingly, we found that adult fish that migrate to different geographical tracts harbour gut microbiota similar to historical records of seawater microflora, along their respective migration routes. This observation provides new insights into the interaction between aquatic animal gut microbial communities and the environments along their hosts' migratory routes, and thus warrants future study.