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).
-
Admixture mapping identifies introgressed genomic regions in North American canids.SRR8926747, SRR8926748, SRR7976426.
-
Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears.PB43 : SRR942203, SRR942290, SRR942298; PB28: SRR942211, SRR942287, SRR942295; Brown Bear: SRR935591, SRR935625, SRR935627.
-
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.Lynx pardinus LYNX11 : ERR1255591-ERR1255594; Lynx lynx LYNX8: ERR1255579-ERR1255582SRRXXX; Lynx lynx LYNX23: ERR1255540-ERR1255549.
-
Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assemblySRR10009886, SRR836361, SRR3041424.
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.
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
-
- 2,124
- views
-
- 238
- downloads
-
- 18
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
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)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
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
Further reading
-
- Evolutionary Biology
The majority of highly polymorphic genes are related to immune functions and with over 100 alleles within a population, genes of the major histocompatibility complex (MHC) are the most polymorphic loci in vertebrates. How such extraordinary polymorphism arose and is maintained is controversial. One possibility is heterozygote advantage (HA), which can in principle maintain any number of alleles, but biologically explicit models based on this mechanism have so far failed to reliably predict the coexistence of significantly more than ten alleles. We here present an eco-evolutionary model showing that evolution can result in the emergence and maintenance of more than 100 alleles under HA if the following two assumptions are fulfilled: first, pathogens are lethal in the absence of an appropriate immune defence; second, the effect of pathogens depends on host condition, with hosts in poorer condition being affected more strongly. Thus, our results show that HA can be a more potent force in explaining the extraordinary polymorphism found at MHC loci than currently recognized.
-
- Evolutionary Biology
Spatial patterns in genetic diversity are shaped by individuals dispersing from their parents and larger-scale population movements. It has long been appreciated that these patterns of movement shape the underlying genealogies along the genome leading to geographic patterns of isolation by distance in contemporary population genetic data. However, extracting the enormous amount of information contained in genealogies along recombining sequences has, until recently, not been computationally feasible. Here we capitalize on important recent advances in genome-wide gene-genealogy reconstruction and develop methods to use thousands of trees to estimate per-generation dispersal rates and to locate the genetic ancestors of a sample back through time. We take a likelihood approach in continuous space using a simple approximate model (branching Brownian motion) as our prior distribution of spatial genealogies. After testing our method with simulations we apply it to Arabidopsis thaliana. We estimate a dispersal rate of roughly 60km2 per generation, slightly higher across latitude than across longitude, potentially reflecting a northward post-glacial expansion. Locating ancestors allows us to visualize major geographic movements, alternative geographic histories, and admixture. Our method highlights the huge amount of information about past dispersal events and population movements contained in genome-wide genealogies.
