Search

Biodiversity conservation is a top priority in the face of global environmental change, and the practical restoration of biodiversity has emerged as a key objective. Nevertheless, the question of how to effectively contribute to biodiversity restoration and identify suitable systems for such efforts continues to present major challenges. By using genome-wide SNP data, our study revealed that populations from different mountain ranges of the Formosan Long-Arm Scarab beetle, a flagship species that receives strict protection, exhibited a single genetic cluster with no subdivision. Additionally, our result implied an association between the demographic history and historical fluctuations in climate and environmental conditions. Furthermore, we showed that, despite a stable and moderately sized effective population over recent history, all the individuals we studied exhibited signs of genetic inbreeding. We argued that the current practice of protecting the species as one evolutionarily significant unit remains the best conservation plan and that recent habitat change may have led to the pattern of significant inbreeding. We closed by emphasizing the importance of conservation genetic studies in guiding policy decisions and highlighting the potential of genomic data for identifying ideal empirical systems for genetic rescue, or assisted gene flow studies. [ABSTRACT FROM AUTHOR]

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]

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]

Character displacement that leads to divergent phenotypes between sympatric species has been hypothesized to facilitate coexistence and promote the accumulation of biodiversity. However, there are alternative evolutionary mechanisms that may also lead to the evolution of phenotypic divergence between sympatric species; one of the mechanisms is evolutionary contingency. We studied the evolution of the presence and absence of a major male horn phenotype, which may have ecological implications for promoting coexistence between sympatric beetles, across geographic populations from different Xylotrupes beetles. By using a previously published phylogeny with 80 Xylotrupes taxa, we estimated the transition rates between the two phenotypic states (i.e., presence vs. absence of a major male phenotype). Based on the estimated transition rates, we then simulated possible phenotypic outcomes between sympatric species. We found that sympatric species were equally likely to evolve the same versus distinct phenotypic states based on the estimated transition rates given the phylogeny. The empirically observed number of sympatric species showing different phenotypic states can be explained by evolutionary contingency alone. We discussed the importance of applying phylogenetic comparative methods when studying phenotypic evolution and more generally to investigate the effect of stochastic processes before making deterministic inferences. [ABSTRACT FROM AUTHOR]

Consistent and objective species delimitation is crucial to biodiversity studies, but challenges remain when conflicting taxonomic decisions have been made because different data sets and analytical methods were used to delineate species. In the rhinoceros beetle, Xylotrupes siamensis , the use of different morphological characters has resulted in taxonomic disagreement between studies. We used three molecular loci (mitochondrial CO1 and nuclear ITS2 and H3) to investigate the genetic divergence between populations exhibiting different male horn phenotypes. We also applied an approximate Bayesian computation approach to test alternative historical hypotheses that might explain the present genetic diversity among geographical populations. Furthermore, we used species distribution models to estimate the temporal variation in the geographical distribution of suitable habitats. The results show that the two phenotypic taxa within X. siamensis are not genetically structured and that their genetic structure can be explained using isolation by geographical distance. The emergence of the two phenotypic taxa might have been associated with historical isolation in separate refugia. However, spatial expansion and genetic interchange between populations might have gradually eroded the spatial genetic structure. We demonstrate that understanding the historical processes responsible for phenotypic divergence and genetic diversity among current populations could help with making evolutionarily coherent taxonomic decisions. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Biotic interchange between geographic regions can promote rapid diversification. However, what are the important factors that determine the rate of diversification (e.g., trait-dependent diversification) vary between study systems. The evolutionary history of Dynastes beetles, which can be found in both North and South Americas and exhibit two different altitudinal preferences (highland and lowland) is tested for the effects of biotic interchange between continents and different ecological preferences on the rate of species diversification. Additionally, the hypotheses of geological time-dependent and lineage specific diversification rates are also tested. Results from this study indicate that in Dynastes beetles a pre-landbridge dispersal hypothesis from South to North America is preferred and that the speciation rates estimated using BAMM are similar between lineages of different geographic origins and different altitudinal preferences (i.e., diversification rate is not trait-dependent). On the other hand, my result from marcoevolutionary cohort analysis based on BAMM outputs suggests that the rate of speciation in Dynastes beetles is, instead of trait-dependent (geographic and ecological), lineage specific. Furthermore, a steadily increasing speciation rate can be found in Pliocene and Pleistocene, which implies that geological and climatic events, i.e., colonizing North America, habitat reformation in the Amazonia, and forest contraction in Pleistocene, may have together shaped the current biodiversity pattern in Dynastes beetles. [ABSTRACT FROM AUTHOR]