High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox.

Rémi Allio,Benoit Nabholz,Celine Scornavacca,Marie-Ka Tilak,Erwan Corre,Andrew C Kitchener,Nico L Avenant,Frédéric Delsuc

doi:10.7554/elife.63167

Abstract

In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is essential for conservation. The thousands of yearly mammalian roadkill provide a useful source material for genomic surveys. To illustrate the potential of this underexploited resource, we used roadkill samples to study the genomic diversity of the bat-eared fox (Otocyon megalotis) and the aardwolf (Proteles cristatus), both having subspecies with similar disjunct distributions in Eastern and Southern Africa. First, we obtained reference genomes with high contiguity and gene completeness by combining Nanopore long reads and Illumina short reads. Then, we showed that the two subspecies of aardwolf might warrant species status (P. cristatus and P. septentrionalis) by comparing their genome-wide genetic differentiation to pairs of well-defined species across Carnivora with a new Genetic Differentiation index (GDI) based on only a few resequenced individuals. Finally, we obtained a genome-scale Carnivora phylogeny including the new aardwolf species.

Highlights

In the context of worldwide erosion of biodiversity, obtaining large-scale genomic resources from wildlife is essential for biodiversity assessment and species conservation
Our results show that high-quality reference mammalian genomes could be obtained through a combination of short- and long-read sequencing methods providing opportunities for large-scale population genomic studies of mammalian wildlife usingsequencing of samples collected from roadkill
Mitochondrial diversity within Carnivora The first dataset, composed of complete carnivoran mitogenomes available in GenBank combined with the newly generated sequences of the two subspecies of P. cristatus, the two subspecies of O. megalotis, Parahyaena brunnea, Speothos venaticus and Vulpes vulpes, plus the sequences extracted from Ultra Conserved Elements (UCE) libraries for Bdeogale nigripes, Fossa fossana, and Viverra tangalunga, comprised

Summary

Introduction

In the context of worldwide erosion of biodiversity, obtaining large-scale genomic resources from wildlife is essential for biodiversity assessment and species conservation. But potentially useful, source of material for genomics is the many thousands of annual wildlife fatalities due to collisions with cars. Developed to measure the impact of roads on wildlife, these web-based systems highlight the numbers of car-wildlife collisions. The possibility of retrieving DNA from roadkill tissue samples (Etherington et al, 2020; Maigret, 2019) could provide new opportunities in genomics by giving access to a large number of specimens of commonly encountered species, and to more elusive and endangered species that might be difficult to sample otherwise

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