1. Evolutionary Biology
  2. Genetics and Genomics
Download icon

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

  1. Rémi Allio  Is a corresponding author
  2. Marie-Ka Tilak
  3. Celine Scornavacca
  4. Nico L Avenant
  5. Andrew C Kitchener
  6. Erwan Corre
  7. Benoit Nabholz
  8. Frédéric Delsuc  Is a corresponding author
  1. CNRS, IRD, EPHE, Université de Montpellier, France
  2. National Museum and Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa, France
  3. National Museums Scotland, United Kingdom
  4. CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680 Roscoff, France, France
  5. UMR 5554 ISEM (Université de Montpellier-CNRS-IRD-EPHE), France
  6. CNRS - Université de Montpellier, France
Research Article
  • Cited 0
  • Views 218
  • Annotations
Cite this article as: eLife 2021;10:e63167 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.

Article and author information

Author details

  1. Rémi Allio

    Institut des Sciences de l Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
    For correspondence
    rem.allio@yahoo.fr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3885-5410

  2. Marie-Ka Tilak

    Institut des Sciences de l Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
    Competing interests
    The authors declare that no competing interests exist.

  3. Celine Scornavacca

    Institut des Sciences de l Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, France, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
    Competing interests
    The authors declare that no competing interests exist.

  4. Nico L Avenant

    Department of Mammalogy, National Museum and Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa, Montpellier, France
    Competing interests
    The authors declare that no competing interests exist.

  5. Andrew C Kitchener

    Department of Natural Sciences, National Museums Scotland, Edinburgh, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  6. Erwan Corre

    Informatics and Bioinformatics, CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680 Roscoff, France, Montpellier, France
    Competing interests
    The authors declare that no competing interests exist.

  7. Benoit Nabholz

    UMR 5554 ISEM (Université de Montpellier-CNRS-IRD-EPHE), Montpellier, France
    Competing interests
    The authors declare that no competing interests exist.

  8. Frédéric Delsuc

    Institut des Sciences de l'Evolution, CNRS - Université de Montpellier, Montpellier, France
    For correspondence
    frederic.delsuc@umontpellier.fr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6501-6287

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

  1. George H Perry, Pennsylvania State University, United States

Publication history

  1. Received: September 16, 2020
  2. Accepted: February 16, 2021
  3. Accepted Manuscript published: February 18, 2021 (version 1)

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.

Metrics

  • 218
    Page views
  • 40
    Downloads
  • 0
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Categories and tags

Further reading

    1. Evolutionary Biology
    2. Genetics and Genomics

    Evolutionary dynamics of transposable elements in bdelloid rotifers

    Reuben W Nowell et al.
    Research Article Updated

    Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates in which males are thus far unknown. Contrary to expectations, we find a variety of active TEs in bdelloid genomes, at an overall frequency within the range seen in sexual species. We find no evidence that TEs are spread by cryptic recombination or restrained by unusual DNA repair mechanisms. Instead, we find that that TE content evolves relatively slowly in bdelloids and that gene families involved in RNAi-mediated TE suppression have undergone significant expansion, which might mitigate the deleterious effects of active TEs and compensate for the consequences of long-term asexuality.

    1. Computational and Systems Biology
    2. Evolutionary Biology

    Repeated outbreaks drive the evolution of bacteriophage communication

    Hilje M Doekes et al.
    Research Article Updated

    Recently, a small-molecule communication mechanism was discovered in a range of Bacillus-infecting bacteriophages, which these temperate phages use to inform their lysis-lysogeny decision. We present a mathematical model of the ecological and evolutionary dynamics of such viral communication and show that a communication strategy in which phages use the lytic cycle early in an outbreak (when susceptible host cells are abundant) but switch to the lysogenic cycle later (when susceptible cells become scarce) is favoured over a bet-hedging strategy in which cells are lysogenised with constant probability. However, such phage communication can evolve only if phage-bacteria populations are regularly perturbed away from their equilibrium state, so that acute outbreaks of phage infections in pools of susceptible cells continue to occur. Our model then predicts the selection of phages that switch infection strategy when half of the available susceptible cells have been infected.

    1. Evolutionary Biology
    2. Genetics and Genomics

    Emergence and diversification of a highly invasive chestnut pathogen lineage across southeastern Europe

    Lea Stauber et al.
    Research Article

    Invasive microbial species constitute a major threat to biodiversity, agricultural production and human health. Invasions are often dominated by one or a small number of genotypes, yet the underlying factors driving invasions are poorly understood. The chestnut blight fungus Cryphonectria parasitica first decimated the North American chestnut, and a more recent outbreak threatens European chestnut stands. To unravel the chestnut blight invasion of southeastern Europe, we sequenced 230 genomes of predominantly European strains. Genotypes outside of the invasion zone showed high levels of diversity with evidence for frequent and ongoing recombination. The invasive lineage emerged from the highly diverse European genotype pool rather than a secondary introduction from Asia or North America. The expansion across southeastern Europe was mostly clonal and is dominated by a single mating type, suggesting a fitness advantage of asexual reproduction. Our findings show how an intermediary, highly diverse bridgehead population gave rise to an invasive, largely clonally expanding pathogen.