High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox
- CNRS, IRD, EPHE, Université de Montpellier, France
- National Museum and Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa, France
- National Museums Scotland, United Kingdom
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680 Roscoff, France, France
- UMR 5554 ISEM (Université de Montpellier-CNRS-IRD-EPHE), France
- CNRS - Université de Montpellier, France
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.
Data availability
Genome assemblies, associated Illumina and Nanopore sequence reads, and mitogenomes have been submitted to the National Center for Biotechnology Information (NCBI) and will be available after publication under BioProject number PRJNA681015. The full analytical pipeline, phylogenetic datasets (mitogenomic and genomic), corresponding trees, and other supplementary materials are available from zenodo.org (DOI: 10.5281/zenodo.4479226).
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Article and author information
Author details
Funding
H2020 European Research Council (ERC‐2015‐CoG‐683257)
- Frédéric Delsuc
Agence Nationale de la Recherche (ANR‐10‐LABX‐25‐01)
- Rémi Allio
- Marie-Ka Tilak
- Celine Scornavacca
- Benoit Nabholz
- Frédéric Delsuc
Agence Nationale de la Recherche (ANR‐10‐LABX‐0004)
- Rémi Allio
- Marie-Ka Tilak
- Celine Scornavacca
- Benoit Nabholz
- Frédéric Delsuc
Agence Nationale de la Recherche (ANR-11-INBS-0013)
- Erwan Corre
National Research Foundation (86321)
- Nico L Avenant
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- George H Perry, Pennsylvania State University, United States
Version history
- Received: September 16, 2020
- Accepted: February 16, 2021
- Accepted Manuscript published: February 18, 2021 (version 1)
- Version of Record published: March 15, 2021 (version 2)
- Version of Record updated: April 1, 2021 (version 3)
Copyright
© 2021, Allio et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox
eLife 10:e63167.
https://doi.org/10.7554/eLife.63167
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