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.

Why Are X Autosome Rearrangements so Frequent in Beetles? A Study of 50 Cases

Amongst the 460 karyotypes of Polyphagan Coleoptera that we studied, 50 (10.8%) were carriers of an X autosome rearrangement. In addition to mitotic metaphase analysis, the correct diagnosis was performed on meiotic cells, principally at the pachytene stage. The percentages of these inter-chromosomal rearrangements, principally fusions, varied in relation to the total diploid number of chromosomes: high (51%) below 19, null at 19, low (2.7%) at 20 (the ancestral and modal number), and slightly increasing from 7.1% to 16.7% from 22 to above 30. The involvement of the X in chromosome fusions appears to be more than seven-fold higher than expected for the average of the autosomes. Examples of karyotypes with X autosome rearrangements are shown, including insertion of the whole X in the autosome (ins(A;X)), which has never been reported before in animals. End-to-end fusions (Robertsonian translocations, terminal rearrangements, and pseudo-dicentrics) are the most frequent types of X autosome rearrangements. As in the 34 species with a 19,X formula, there was no trace of the Y chromosome in the 50 karyotypes with an X autosome rearrangement, which demonstrates the dispensability of this chromosome. In most instances, C-banded heterochromatin was present at the X autosome junction, which suggests that it insulates the gonosome from the autosome portions, whose genes are subjected to different levels of expression. Finally, it is proposed that the very preferential involvement of the X in inter-chromosome rearrangements is explained by: (1) the frequent acrocentric morphology of the X, thus the terminal position of constitutive heterochromatin, which can insulate the attached gonosomal and autosomal components; (2) the dispensability of the Y chromosome, which considerably minimizes the deleterious consequences of the heterozygous status in male meiosis, (3) following the rapid loss of the useless Y chromosome, the correct segregation of the X autosome-autosome trivalent, which ipso facto is ensured by a chiasma in its autosomal portion.

Holocene Population Decline and Conservation Implication for the Western Hercules Beetle, Dynastes grantii (Coleoptera, Scarabaeidae)

The Western Hercules beetle (Dynastes grantii) is endemic to the highland forest habitats of southwestern United States and northern Mexico. The habitats harbor many endemic species, but are being threatened by rapid climate change and urban development. In this study, the genetic structure of D. grantii populations from southwestern United States was investigated. Specifically, genomic data from double-digest restriction-site-associated DNA sequencing libraries were utilized to test whether geographically distant populations from the Mogollon Rim (Arizona [N = 12 individuals] and New Mexico [N = 10 individuals]) are genetically structured. The study also estimated the effective population size of the Mogollon Rim populations based on genetic diversity. The results indicated that the 2 geographic populations from the Mogollon Rim were not genetically structured. A population size reduction was detected since the end of the last glacial period, which coincided with a reduction of forest habitat in the study area. The results implied that the connectivity and the size of highland forest habitats in the Mogollon Rim could have been the major factors shaping the population genetic structure and demographic history of D. grantii. The Western Hercules beetle could be a useful flagship species for local natural history education and to promote the conservation of highland forest habitats.

Annotated catalog and bibliography of the cyclocephaline scarab beetles (Coleoptera, Scarabaeidae, Dynastinae, Cyclocephalini)

Cyclocephaline scarab beetles represent the second largest tribe of the subfamily Dynastinae, and the group includes the most speciose genus of dynastines, Cyclocephala. The period following publication of Sebő Endrődi's The Dynastinae of the World has seen a huge increase in research interest on cyclocephalines, and much of this research has not been synthesized. The objective of this catalog and bibliography is to compile an exhaustive list of taxa in Cyclocephalini. This paper provides an updated foundation for understanding the taxonomy and classification of 14 genera and over 500 species in the tribe. It discusses the history of cataloging dynastine species, clarifies issues surrounding the neotype designations in Endrődi's revision of Cyclocephalini, synthesizes all published distribution data for cyclocephaline species, and increases accessibility to the voluminous literature on the group by providing an easily searchable bibliography for each species. We propose the nomen novum Cyclocephala rogerpauli, new replacement name, for C. nigra Dechambre.

Chromosome comparison of 17 species / sub-species of African Goliathini (Coleoptera, Scarabaeidae, Cetoniinae)

The mitotic karyotypes of 17 species of African Goliathini (Cetoniinae) are described using various chromosome banding techniques. All but one are composed of 20 chromosomes, mostly metacentric, forming a karyotype assumed to be close to that of the Polyphaga ancestor. The most derived karyotypes are those of Goliathus goliatus Drury, 1770, with eight pairs of acrocentrics and Chlorocana africana Drury, 1773, with only14 chromosomes. In species of the genera Cyprolais Burmeister, 1842, Megalorhina Westwood, 1847, Stephanocrates Kolbe, 1894 and Stephanorrhina Burmeister, 1842, large additions of variable heterochromatin are observed on both some particular autosomes and the X chromosome. Species of the genera Eudicella White, 1839 and Dicronorrhina Burmeister, 1842 share the same sub-metacentric X. Although each species possesses its own karyotype, it remains impossible to propose robust phylogenetic relationships on the basis of chromosome data only.

The Species versus Subspecies Conundrum: Quantitative Delimitation from Integrating Multiple Data Types within a Single Bayesian Approach in Hercules Beetles

With the recent attention and focus on quantitative methods for species delimitation, an overlooked but equally important issue regards what has actually been delimited. This study investigates the apparent arbitrariness of some taxonomic distinctions, and in particular how species and subspecies are assigned. Specifically, we use a recently developed Bayesian model-based approach to show that in the Hercules beetles (genus Dynastes) there is no statistical difference in the probability that putative taxa represent different species, irrespective of whether they were given species or subspecies designations. By considering multiple data types, as opposed to relying exclusively on genetic data alone, we also show that both previously recognized species and subspecies represent a variety of points along the speciation spectrum (i.e., previously recognized species are not systematically further along the continuum than subspecies). For example, based on evolutionary models of divergence, some taxa are statistically distinguishable on more than one axis of differentiation (e.g., along both phenotypic and genetic dimensions), whereas other taxa can only be delimited statistically from a single data type. Because both phenotypic and genetic data are analyzed in a common Bayesian framework, our study provides a framework for investigating whether disagreements in species boundaries among data types reflect (i) actual discordance with the actual history of lineage splitting, or instead (ii) differences among data types in the amount of time required for differentiation to become apparent among the delimited taxa. We discuss what the answers to these questions imply about what characters are used to delimit species, as well as the diverse processes involved in the origin and maintenance of species boundaries. With this in mind, we then reflect more generally on how quantitative methods for species delimitation are used to assign taxonomic status.