Biology subjects

Gunter, N.

Publications and source records attributed to Gunter, N..

3 recordsLinked to original sources

bioRxiv2023

From museum drawer to tree: historical DNA phylogenomics clarifies the systematics of rare dung beetles (Coleoptera: Scarabaeinae) from museum collections

Although several methods exist for extracting and sequencing historical DNA originating from drypreserved insect specimens deposited in natural history museums, no consensus exists as to what is the optimal approach. We demonstrate that a customized, low-cost archival DNA extraction protocol ([~] {euro}10 per sample), in combination with Ultraconserved Elements (UCEs), is an effective tool for insect phylogenomic studies. We successfully tested our approach by sequencing DNA from scarab dung beetles preserved in both wet and dry collections, including unique primary type and rare historical specimens from internationally important natural history museums in London, Paris and Helsinki. The focal specimens comprise enigmatic dung beetle genera (Nesosisyphus, Onychotechus and Helictopleurus) that varied in age and preservation. The oldest specimen, the holotype of the now possibly extinct Mauritian endemic Nesosisyphus rotundatus, was collected in 1944. We obtained high-quality DNA from all studied specimens to enable the generation of a UCE-based dataset that revealed an insightful and well-supported phylogenetic tree of dung beetles. The resulting phylogeny suggested the reclassification of Onychotechus (previously incertae sedis) within the tribe Coprini. Our approach demonstrates the feasibility and effectiveness of combining DNA data from historic and recent museum specimens to provide novel insights. The proposed archival DNA protocol is available at DOI 10.17504/protocols.io.81wgbybqyvpk/v1 HighlightsO_LIWe combined custom low-cost archival DNA extractions and Ultraconserved Element phylogenomics C_LIO_LIDNA from rare museum specimens of enigmatic dung beetles revealed their phylogenetic connections C_LIO_LIGenomic data was obtained from the holotype of a potentially extinct monoinsular endemic species C_LIO_LIGenomic data allowed a rare and enigmatic species of previously unknown affinity to be classified C_LIO_LIThe morphology of museum specimens remained intact following non-destructive DNA extraction C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/564347v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@34aad0org.highwire.dtl.DTLVardef@1ba597dorg.highwire.dtl.DTLVardef@1493c2dorg.highwire.dtl.DTLVardef@10dd2eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2023

To design or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design

Tailoring ultraconserved element (UCE) probe set design to focal taxa has been demonstrated to improve locus recovery and phylogenomic inference. However, beyond conducting expensive in vitro testing, it remains unclear how best to determine whether an existing UCE probe set is likely to suffice for phylogenomic inference, or if tailored probe design will be desirable. Here we investigate the utility of eight different UCE probe sets for the in silico phylogenomic inference of scarabaeoid beetles. Probe sets tested differed in terms of (1) how phylogenetically distant from Scarabaeoidea taxa those used during probe design are, (2) breadth of phylogenetic inference probe set was designed for, and (3) method of probe design. As part of this study, two new UCE probe sets are produced for the beetle family Scarabaeidae and superfamily Hydrophiloidea. We find that, predictably, probe set utility decreases with increasing phylogenetic distance of design taxa from focal taxa, as well as with narrower breadth of phylogenetic inference probes were designed for. We also confirm previous findings regarding ways to optimize UCE probe design. Finally, we make suggestions regarding assessment of need for de novo probe design and reinforce previous proposed methods for maximizing UCE probe design to improve phylogenomic inference.

evolutionary biology↗

bioRxiv2022

Metagenomics reveals that Dung Beetles (Coleoptera: Scarabaeinae) broadly feed on Reptile dung and could feed on that of Dinosaurs

According to traditional views, the evolution of dung beetles (Coleoptera: Scarabaeinae) and their feeding habits are largely attributed to mammal dung. In this paper, we challenge this view and provide evidence that many dung beetle communities are actually associated with the dung of reptiles and birds (= Sauropsida). In turn, this indicates that sauropsid dung may have played a crucial evolutionary role that was previously underestimated. We argue that it is physiologically realistic to consider that coprophagy in dung beetles could have evolved during the Cretaceous in response to the massive amount of dung produced by dinosaurs. Furthermore, we demonstrate that sauropsid dung may be one of the major factors driving the emergence of insular dung beetle communities across the globe. We support our findings with amplicon-metagenomic analyses, trapping experiments, and meta-analysis of the published literature.

evolutionary biology↗