High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox
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 sample...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2021-02-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/63167 |
| _version_ | 1811180580355702784 |
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| author | Rémi Allio Marie-Ka Tilak Celine Scornavacca Nico L Avenant Andrew C Kitchener Erwan Corre Benoit Nabholz Frédéric Delsuc |
| author_facet | Rémi Allio Marie-Ka Tilak Celine Scornavacca Nico L Avenant Andrew C Kitchener Erwan Corre Benoit Nabholz Frédéric Delsuc |
| author_sort | Rémi Allio |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T09:05:34Z |
| format | Article |
| id | doaj.art-f61a5cd1fa7a440f9e201b895c4a8a31 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-11T09:05:34Z |
| publishDate | 2021-02-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-f61a5cd1fa7a440f9e201b895c4a8a312022-12-22T04:32:39ZengeLife Sciences Publications LtdeLife2050-084X2021-02-011010.7554/eLife.63167High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared foxRémi Allio0https://orcid.org/0000-0003-3885-5410Marie-Ka Tilak1Celine Scornavacca2Nico L Avenant3Andrew C Kitchener4Erwan Corre5Benoit Nabholz6Frédéric Delsuc7https://orcid.org/0000-0002-6501-6287Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, FranceInstitut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, FranceInstitut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, FranceNational Museum and Centre for Environmental Management, University of the Free State, Bloemfontein, South AfricaDepartment of Natural Sciences, National Museums Scotland, Edinburgh, United KingdomCNRS, Sorbonne Université, CNRS, ABiMS, Station Biologique de Roscoff, Roscoff, FranceInstitut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France; Institut Universitaire de France (IUF), Paris, FranceInstitut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, FranceIn 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.https://elifesciences.org/articles/63167roadkillgenomicspopulation genomicsphylogenomicsspecies delimitationcarnivora |
| spellingShingle | Rémi Allio Marie-Ka Tilak Celine Scornavacca Nico L Avenant Andrew C Kitchener Erwan Corre Benoit Nabholz Frédéric Delsuc High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox eLife roadkill genomics population genomics phylogenomics species delimitation carnivora |
| title | High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox |
| title_full | High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox |
| title_fullStr | High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox |
| title_full_unstemmed | High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox |
| title_short | High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox |
| title_sort | high quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat eared fox |
| topic | roadkill genomics population genomics phylogenomics species delimitation carnivora |
| url | https://elifesciences.org/articles/63167 |
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