Whole‐genome resequencing reveals recent divergence of geographic populations of the dung beetle Phelotrupes auratus with color variation

Abstract

Knowledge of population divergence history is key to understanding organism diversification mechanisms. The geotrupid dung beetle Phelotrupes auratus, which inhabits montane forests and exhibits three color forms (red, green, and indigo), diverged into five local populations (west/red, south/green, south/indigo, south/red, and east/red) in the Kinki District of Honshu, Japan, based on the combined interpretation of genetic cluster and color-form data. Here, we estimated the demographic histories of these local populations using the newly assembled draft genome sequence of P. auratus and whole-genome resequencing data obtained from each local population. Using coalescent simulation analysis, we estimated P. auratus population divergences at ca. 3800, 2100, 600, and 200 years ago, with no substantial gene flow between diverged populations, implying the existence of persistent barriers to gene flow. Notably, the last two divergence events led to three local populations with different color forms.The initial divergence may have been affected by climatic cooling around that time, and the last three divergence events may have been associated with the increasing impact of human activities. Both climatic cooling and increasing human activity may have caused habitat fragmentation and a reduction in the numbers of large mammals supplying food (dung) for P. auratus, thereby promoting the decline, segregation, and divergence of local populations. Our research demonstrates that geographic population divergence in an insect with conspicuous differences in traits such as body color may have occurred rapidly under the influence of human activity.

The sacred deer conflict of management after a 1000‐year history: Hunting in the name of conservation or loss of their genetic identity

“…Over the past several 100 years, hunting pressure has resulted in the decline and fragmentation of the distribution range of sika deer in the Japanese archipelago (Iijima et al, 2023; Tsujino et al, 2010). This has also affected the population dynamics of other species, for example, on the Kii Peninsula, the speciation of dung beetles ( Phelotrupes auratus ), which feed heavily on deer dung (Araki & Sota, 2023), coincided with the fragmentation of deer populations (Takagi et al, 2023). The recent re‐expansion of deer populations in the area surrounding Nara and their contact with the Nara Park population may indicate that deer are experiencing a release from the negative influence of human hunting of the past 2000 years.…”

Population Genomics of Tetraopes texanus (Coleoptera: Cerambycidae)

“…Conversion also requires an estimate of the mutation rate (μ). No μ estimates are available, so following other genome-scale studies of beetles, including Cerambycidae (Cui et al, 2022;Araki & Sota, 2023;DeVito et al, 2023), we applied a rate of 2.9 × 10 −9 per site per generation from Heliconius melpone (Keightley et al 2015). Although this rate will not be exact, this value falls within the range reported for many insects (e.g., Chironomus = 2.1× 10 −9 , Bombus = 3.4 × 10 −9 , Drosophila = 2.8-3.5 × 10 −9 ) (Keightly et al, 2014;Oppold & Pfenninger, 2017;Liu et al, 2017).…”