The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections

Abstract

Museum collections are essential for reconstructing and understanding past biodiversity. Many museum specimens are, however, challenging to identify. Museum samples may be incomplete, have an unusual morphology, or represent juvenile individuals, all of which complicate accurate identification. In some cases, inaccurate identification can lead to false biogeographic reconstructions with cascading impacts on paleontological and paleoecological research. Here, we analyzed an unusual Equid mandible found in the Far North of the Taymyr peninsula that was identified morphologically as Equus hemionus, an ancestor of present‐day Asiatic wild asses. If correct, this identification represents the only finding of a putative Late Pleistocene hemione in the Arctic region, and is therefore critical to understanding wild ass evolution and paleoecology. To confirm the accuracy of this specimen's taxonomic assignment, we used ancient DNA and mitochondrial hybridization capture to identify and place this specimen in the larger equid phylogeny. We find that the specimen is actually a member of E. caballus, the ancestor of domestic horses. Our study demonstrates the utility of ancient DNA to validate morphological identification, in particular of incomplete, otherwise problematic, or taxonomically unusual museum specimens.

Reconstructing mitochondrial genomes from ancient DNA through iterative mapping: an evaluation of software, parameters, and bait reference

“…CC-BY-NC-ND 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted December 17, 2021. ; https://doi.org/10.1101/2021.12.16.472923 doi: bioRxiv preprint iterative mapping tools are available; mapping interactive assembler (MIA) was originally designed to assemble a number of Neandertal and early modern human mitochondria (Green et al, 2008), but has been used for non-human species (Vershinina et al, 2020). Despite its utility, when using a more distant bait reference, MIA requires much more memory and CPU time than MITObim (Hahn et al, 2013), and is therefore not as suitable for species when only relatively divergent bait references are available, such as the datasets tested here.…”

Genomics of natural history collections for understanding evolution in the wild

“…In these cases, molecular identification using aDNA can provide an unequivocal identification (Miller, 2007). Vershinina and collaborators provide an example of how aDNA from NHC specimens can help us correctly identify samples and avoid false biogeographic reconstructions (Vershinina, Kapp, Baryshnikov, & Shapiro, 2019). Using ancient DNA, they corrected a morphological misidentification made from a partial jaw of an Equid, initially described as Equus hemionus, the Asiatic wild ass (Cucchi et al., 2017; Vershinina et al., 2019).…”

“…Vershinina and collaborators provide an example of how aDNA from NHC specimens can help us correctly identify samples and avoid false biogeographic reconstructions (Vershinina, Kapp, Baryshnikov, & Shapiro, 2019). Using ancient DNA, they corrected a morphological misidentification made from a partial jaw of an Equid, initially described as Equus hemionus, the Asiatic wild ass (Cucchi et al., 2017; Vershinina et al., 2019). Molecular results showed that the partial jaw belonged to E. caballus, motivating a substantial reinterpretation of the evolutionary history of Equids, which in addition to wild asses includes horses, zebras, kiangs and donkeys (Cucchi et al., 2017; Vershinina et al., 2019).…”

“…Using ancient DNA, they corrected a morphological misidentification made from a partial jaw of an Equid, initially described as Equus hemionus, the Asiatic wild ass (Cucchi et al., 2017; Vershinina et al., 2019). Molecular results showed that the partial jaw belonged to E. caballus, motivating a substantial reinterpretation of the evolutionary history of Equids, which in addition to wild asses includes horses, zebras, kiangs and donkeys (Cucchi et al., 2017; Vershinina et al., 2019). This study highlights the relevance of molecular identification in challenging cases and how it can clarify the evolutionary trajectories of species.…”

Optimized and affordable high‐throughput sequencing workflow for preserved and nonpreserved small zooplankton specimens

“…However, these protocols are primarily optimized to deal with poor DNA quality due to contamination and fragmentation (Rohland, Harney, Mallick, Nordenfelt, & Reich, 2015), designed to enrich endogenous DNA over contaminations (Horn, 2012) and therefore target only specific parts of the genome (Knyshov, Gordon, & Weirauch, 2019;Suchan et al, 2016). Many of the protocols also still require higher amounts of input DNA or tissue than used in this study (Gamba et al, 2016;Shapiro et al, 2019;Tsai et al, 2019;Vershinina, Kapp, Baryshnikov, & Shapiro, 2020). Therefore, these methods are more targeted to fragmented DNA and less cost-and time-efficient compared to the presented workflow.…”