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.

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.

Onthophagus acernorus (Coleoptera: Scarabaeidae: Scarabaeinae: Onthophagini), a new dung beetle species from Jalisco, Mexico

The Onthophagus chevrolati Harold, 1869 (Coleoptera: Scarabaeidae: Scarabaeinae: Onthophagini) species complex was recently studied, and a majority of its species were newly described or redescribed (see Moctezuma Halffter 2020). Onthophagus viridichevrolati Moctezuma Halffter, 2020 was the only species within the O. chevrolati species complex recognized to occur in the Mexican state of Jalisco (Moctezuma Halffter 2020). Recently, new material belonging to the O. chevrolati species complex was collected from the maple (Acer; Sapindaceae) forests of Talpa de Allende, Jalisco, Mexico. The examination of these specimens showed that they are morphologically similar to O. chevrolati Harold, 1869 and belong to an undescribed species. In this study, we provide photographs of the habitus (male and female) and male genitalia of O. acernorus new species; an identification key to separate it from O. chevrolati, and an updated distribution map of the O. chevrolati species complex.

Species Redescriptions and New Species of the Onthophagus mexicanus Species Group (Coleoptera: Scarabaeidae), with Notes on Distribution and Rodent-dung Beetle Associations

The Onthophagus mexicanus species group includes at least 18 species: O. anewtoni Howden and Génier, O. arnetti Howden and Cartwright, O. browni Howden, O. cartwrighti Howden, O. championi Bates, O. concinnus Castelnau, O. cynomysi Brown, O. eulophus Bates, O. guatemalensis Bates, O. hecate (Panzer), O. mcclevei Howden and Génier, O. medorensis Brown, O. mexicanus Bates, O. orpheus (Panzer), O. polyphemi Hubbard, O. pseudoguatemalensis sp. n., O. totonacus sp. n. and O. velutinus Howden and Cartwright. Onthophagus pseudoguatemalensis sp. n. and O. totonacus sp. n. are described from Mexico (Jalisco and Veracruz, respectively). Onthophagus cartwrighti, O. championi, O. eulophus and O. guatemalensis are redescribed, while lectotypes are designated herein for O. championi and O. eulophus. The distribution of O. cartwrighti is clarified; a new country record is provided for O. championi (Honduras); new state records are reported for O. championi (Oaxaca and Veracruz, Mexico) and O. guatemalensis (Oaxaca, Mexico). The accurate distribution of O. eulophus remains unknown since its original description. Updated distribution maps are included for all the species within the group. An updated determination key to species of the O. mexicanus species group is provided. The rarity of O. eulophus and O. totonacus in the entomological collections is thought to be a consequence of their trophic habits; both species are suggested to be inquilines of rodent nests or burrows.

The integration processes of the distributional patterns in the Mexican Transition Zone: Phyletic, paleogeographic and ecological factors of a case study

In this study, we take the Onthophagus chevrolati species group, likely a monophyletic species group as an example to analyze the processes that led to the biogeographic integration of the Holarctic fauna in the mountains of the Mexican Transition Zone to test our biogeographic hypotheses. We propose a change from the status of subspecies to species for O. oaxacanus Zunino Halffter, 1988 new status; O. howdeni Zunino Halffter, 1988 new status; O. jaliscensis Zunino Halffter, 1988 new status; O. longecarinatus Zunino Halffter, 1988 new status; O. omiltemius Bates, 1889 revised status; and O. retusus Harold, 1869 revised status. Consequently, the O. chevrolati group of species is currently made up of 47 species belonging to four species lines: O. vespertilio, O. hippopotamus, O. cyanellus and O. chevrolati. The diversification of the Onthophagus chevrolati species group in this region resulted from three hypothetical stages of evolution. In the first, the penetration and expansion of the ancestor of the O. chevrolati species group occurred before the Miocene and the Trans-Mexican Volcanic Belt arose. During the second stage, the O. hippopotamus species line expanded and evolved, integrating with the paleogeographic changes and the formation of the Trans-Mexican Volcanic Belt, as a consequence of volcanism during the Miocene-Pliocene. In the third and most recent stage, the O. chevrolati species line used the existing mountain systems and interglacial climate fluctuations of the Pleistocene to expand and diversify. Thus, the mountains of the Mexican Transition Zone are not simply periglacial refugia. The entomofauna of Holarctic origin present in the region evolved while the Earth's geological processes were underway.

The Onthophagus fuscus (Coleoptera: Scarabaeidae) species complex: an update and the description of a new species

The Onthophagus fuscus Boucomont, 1932 (Coleoptera: Scarabaeidae: Scarabaeinae: Onthophagini) species complex has a total of eight species, one of which is a new species (Onthophagus orizabensis new species) and three are elevated from the subspecies level (O. canescens Zunino Halffter, 1988 new rank; O. mycetorum Zunino Halffter, 1988 new rank; O. parafuscus Zunino Halffter, 2005 new rank). Onthophagus navarretorum Delgado Capistan, 1996 is included, while Onthophagus semiopacus has been removed from the species complex. The distribution map and key for the identification of species in this species complex are updated. Habitat preferences, ecological tolerance, and the restriction of this species complex to the mountains of the Mexican Transition Zone are discussed.

A New Species of Vindex Kaup (Coleoptera: Scarabaeoidea: Passalidae: Passalinae: Proculini) from Oaxaca, Mexico

Vindex chimalapensis Ariza-Marín, Reyes-Castillo, Moctezuma & Sánchez-Huerta, a new species, is described from the cloud forest in Oaxaca, México. Vindex chimalapensis is like V. sculptilis Bates in the form of lateral elytral punctures and glabrous epipleura, but has dorsal punctures in the pronotum and the form of the aedeagus differs on the basal piece. Male genitalia, female genitalia, and head are shown in photographs. Vindex chimalapensis is the only species known from this genus with dorsal punctures on the pronotum. Ecology, distribution, and biogeography of Vindex and the Mountain Mesoamerican distribution pattern are discussed, with emphasis on V. chimalapensis.

Two new species of Ateuchus with remarks on ecology, distributions, and evolutionary relationships (Coleoptera, Scarabaeidae, Scarabaeinae)

Two new species of the genus Ateuchus Weber are described from the region of Los Chimalapas, Oaxaca, Mexico: A.benitojuarezisp. n. and A.colossussp. n. A diagnosis for distinguishing these new species from the other species of this genus in North America is included. This paper is illustrated with pictures of the dorsal habitus and the male genitalia of the new species. The evolutionary relationships of the species are discussed, as well as their distribution and ecology. It is considered that the species of the genus Ateuchus present in North and Central America correspond to the Typical Neotropical and Mountain Mesoamerican distribution patterns.

Two new species of the Phanaeus endymion species group (Coleoptera, Scarabaeidae, Scarabaeinae)

Phanaeusbravoensissp. n. is described from the coniferous-oak forests in the state of Guerrero, and P.huicholsp. n. from coniferous-oak forests and cloud forests in Jalisco and Nayarit. The new species are closely related to P.halffterorum and P.zoque respectively. Morphological trait combination, geographic distribution, and trophic habits show important differences among the studied species. A distribution map and an updated key to separate the species are included.

A contribution to the knowledge of the mountain entomofauna of Mexico with a description of two new species of Onthophagus Latreille, 1802 (Coleoptera, Scarabaeidae, Scarabaeinae)

Recent intensive samplings carried out across the mountainous regions of El Pinal (Puebla, Mexico) have provided new insights into the main environmental factors that affect the geographic distribution of the scarabaeinae beetles of the Trans-Mexican Volcanic Belt above 2500 m a.s.l. This study is part of an ongoing project investigating the diversity and biogeography of copro-necrophagous beetles (Scarabaeinae, Aphodiinae, Geotrupinae and Silphidae) in the easternmost areas of the Trans-Mexican Volcanic Belt.

Previous experience allows us to propose a series of predictions that we expect will provide possible explanations for current distribution patterns observed in Scarabaeinae and other groups of insects found in the Trans-Mexican Volcanic Belt. This mountain range has a primarily biogeographic importance, limiting the Mexican High Plateau in the South and connecting the western and eastern Sierra Madre mountain chains, which are considered the most important routes for dispersal of mountain fauna of northern origin. The taxonomic and biogeographic study of the species collected so far in El Pinal (including Onthophagusclavijeroisp. n. and Onthophagusmartinpieraisp. n. described here), along with their possible relationships with other known species, allows us to answer the preliminary assumptions proposed.

A new species of Onthophagus (Scarabaeoidea: Scarabaeinae) from the Mexican Transition Zone, with remarks on its relationships and distribution

A new American Onthophagus of the chevrolati species-group is described (Onthophagus bolivari sp. nov.), providing also identification keys to the aztecus complex. Dorsal habitus and genital structures of the new species are illustrated. The relationships and geographical distribution of the aztecus complex are discussed, giving particular attention to the evolutionary history of O. bolivari.