4.8 Article

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

Journal

ELIFE
Volume 10, Issue -, Pages -

Publisher

eLIFE SCIENCES PUBL LTD
DOI: 10.7554/eLife.63167

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Funding

  1. H2020 European Research Council [ERC -2015 -CoG -683257]
  2. Agence Nationale de la Recherche [ANR -10 -LABX -25 -01, ANR -10 -LABX -0004, ANR-11-INBS-0013]
  3. National Research Foundation [86321]
  4. Agence Nationale de la Recherche (ANR) [ANR-10-LABX-0004] Funding Source: Agence Nationale de la Recherche (ANR)

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In the context of ongoing biodiversity erosion, genomic resources from wildlife are crucial for conservation efforts. This study utilized roadkill samples to investigate the genetic diversity of the bat-eared fox and aardwolf, revealing potential new species within the aardwolf taxon through a novel Genetic Differentiation index. The research also generated a genome-wide Carnivora phylogeny that includes the newly identified aardwolf species.
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.

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