Museum phylogenomics of extinctOryctesbeetles from the Mascarene Islands

Abstract

The evolution of island systems is characterized by processes that result in extreme morphological diversity, high endemism and high extinction rates. These dynamics can make phylogenetic reconstruction difficult, i.e. the extinct flightless Dodo from Mauritius was assigned to the family of doves only through DNA analysis of subfossils. Many insect species on islands have gone extinct through habitat loss, and face similar challenges to decipher their evolutionary history, however historical specimens have not yet been harnessed for phylogenomic reconstructions. Here, we employed historical museum specimens from the Mascarene Islands to generate the first whole-genome based phylogeny of three presumably extinct species of the rhinoceros beetle genus Oryctes . We compared their genomes with those of an extant Oryctes species from the island of Réunion, as well as a flightless Réunion-based species previously placed into the supposedly unrelated genus Marronus . We found that Marronus borbonicus belongs instead to the genus Oryctes and that the two Réunion-based species ( O. borbonicus and M. borbonicus ) are not sister taxa, suggesting two independent colonizations. The divergence time between them (<3Myr) overlaps with the volcanic formation of Réunion, likely indicating that M. borbonicus became flightless in situ . Our study showcases the power of genomes from insect museum specimens to address evolutionary questions in light of increasing extinction rates.

A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros)

“…Namely, we identified seven Sigma GST genes in two clusters in our O. rhinoceros annotation (Supplemental file 1), and this matches the structure in the red flour beetle, T. castaneum [54]. Considering that the initial O. borbonicus assembly contained divergent haplotypes that were not correctly haploidized [38], it was difficult (if not impossible) for Meyer and colleagues to avoid erroneous inference of gene duplications. Our O. rhinoceros assembly, on the other hand, enabled the annotation of the Sigma GST gene family that is consistent with other Coleoptera; moreover, the proteins they code show the highest amino-acid sequence similarity to the proteins of another scarab beetle ( O. taurus , Figure 5).…”

A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros)

“…Of note is that the original assembly for O. borbonicus , generated with the short-read Illumina technology, was first reported to be 518 Mb [ 37 ], but refinement with the 10X Genomics data led to a 28% reduction in size (removal of more than 140 Mb). The inflated size of the initial assembly was explained as a consequence of an incorrect haploidization of the assembly i.e., divergent haplotypes were assembled separately across many parts of the genome [ 38 ]. This exemplifies the difficulties of the assembly process based on the short-read sequencing of samples that have high genome-wide variability.…”

“…Based on this pattern, they hypothesized that the expansion of Sigma GST genes occurred specifically in the beetle lineage containing Oryctes species. Assuming that initial O. borbonicus assembly contained divergent haplotypes that were not correctly haploidized [ 38 ], the likelihood of an erroneous inference of gene duplications in this taxon is high. Our O. rhinoceros assembly and annotation recovered nine Sigma GST genes grouped on two contigs (Fig.…”

A linked‐read approach to museomics: Higher quality de novo genome assemblies from degraded tissues

“…These methods allow the assembly of pseudo‐long reads up to tens of kb from short‐read data, and with higher accuracy compared to true long‐read sequencing (Jiao & Schneeberger, 2017). Initially introduced by Illumina (Kuleshov et al, 2014; McCoy et al, 2014), there are few but increasing numbers of publications using linked‐read methods, particularly in the field of museomics (Etherington et al, 2019; Latorre et al, 2020; Lutgen et al, 2020). 10× Genomics (Zheng et al, 2016), a newer technology loosely based on innovations developed by the Illumina SLR technique, offers several advantages for museum science applications.…”