Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Feb 18:10:e63167.
doi: 10.7554/eLife.63167.

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

Rémi Allio  1 , Marie-Ka Tilak  1 , Celine Scornavacca  1 , Nico L Avenant  2 , Andrew C Kitchener  3 , Erwan Corre  4 , Benoit Nabholz  1   5 , Frédéric Delsuc  1
Affiliations

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

Rémi Allio et al. Elife. .

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.

Keywords: carnivora; evolutionary biology; genetics; genomics; phylogenomics; population genomics; roadkill; species delimitation.

PubMed Disclaimer

Conflict of interest statement

RA, MT, CS, NA, AK, EC, BN, FD No competing interests declared

Figures

Figure 1.
Figure 1.. Disjunct distributions of the aardwolf (Proteles cristatus) and the bat-eared fox (Otocyon megalotis) in Eastern and Southern Africa.
Within each species, two subspecies have been recognized based on their distributions and morphological differences (Clark, 2005; Koehler and Richardson, 1990). Picture credits: Southern aardwolf (P. cristatus cristatus) copyright Dominik Käuferle; Southern bat-eared fox (O. megalotis megalotis) copyright Derek Keats.
Figure 2.
Figure 2.. Representation of the mitochondrial genetic diversity within the Carnivora with (a) the mitogenomic phylogeny inferred from 142 complete Carnivora mitogenomes, including those of the two populations of aardwolf (Proteles cristatus) and bat-eared fox (Otocyon megalotis) and (b) intraspecific (orange) and the interspecific (red) genetic diversities observed for the two mitochondrial markers COX1 and CYTB.
Silhouettes from http://phylopic.org/.
Figure 3.
Figure 3.. Genetic differentiation indexes obtained from a comparison of intraspecific (orange values) and interspecific (red values) polymorphisms in four pairs of well-defined.
Carnivora species and for the subspecies of aardwolf (Proteles cristatus) and bat-eared fox (Otocyon megalotis) (gray values). Silhouettes from http://phylopic.org/.
Figure 3—figure supplement 1.
Figure 3—figure supplement 1.. Genetic differentiation indexes obtained from a comparison of intraspecific and interspecific polymorphisms after having homogenized the depth-of-coverage in all species (at about 15x).
The estimates were calculated for four pairs of well-defined Carnivora species and for the subspecies of aardwolf (Proteles cristatus) and bat-eared fox (Otocyon megalotis). Silhouettes from http://phylopic.org/.
Figure 3—figure supplement 2.
Figure 3—figure supplement 2.. Genetic differentiation indexes obtained from the comparison of intraspecific and interspecific polymorphisms for the pair Ursus arctos/Ursus maritimus (~10 replicates per species).
GDI is estimated for each pair of individuals. Each vertical bar represents the variance in GDI obtained (from 10 replicates x 10 regions of 100 kb) by comparing one pair of individuals. This result demonstrates that randomly picking only three individuals (out of 10) is sufficient to accurately estimate the level of genetic differentiation between the two species.
Figure 4.
Figure 4.. PSMC estimates of changes in effective population size over time for the Eastern (orange) and Southern (blue and purple) populations of (a) bat-eared fox and (b) aardwolf.
mu = mutation rate of 10−8 mutations per site per generation and g = generation time of 2 years. Vertical red lines indicate 20 kyrs and 40 kyrs. Silhouettes from http://phylopic.org/.
Figure 5.
Figure 5.. Phylogenomic tree reconstructed from the nucleotide supermatrix composed of 14,307 single-copy orthologous genes for 52 species of Carnivora plus one outgroup (Manis javanica).
The family names in the legend are ordered as in the phylogeny. Silhouettes from http://phylopic.org/.
Figure 6.
Figure 6.. Phenotypic comparisons, highlighting the differences in fur coloration and stripe pattern, between captive individuals of Eastern (P. septentrionalis) and Southern (P. cristatus) aardwolves held at Hamerton Zoo Park (UK).
All pictures copyright and used with permission from Rob Cadd.
Appendix 1—figure 1.
Appendix 1—figure 1.. Plot of the quality of Nanopore long reads base-called with either the fast or the high accuracy option of Guppy v3.1.5.
The quality of the base-calling step has a large impact on the final quality of the assemblies by reducing the number of contigs and increasing the N50 value.
Appendix 1—figure 2.
Appendix 1—figure 2.. Comparison of 503 mammalian genome assemblies from 12 taxonomic groups using bean plots of the (a) number of scaffolds, and (b) scaffold N50 values ranked by median values.
Thick black lines show the medians, dashed black lines represent individual data points, and polygons represent the estimated density of the data. Note the log scale on the Y axes. The bat-eared fox (Otocyon megalotis megalotis) and aardwolf (Proteles cristatus cristatus) assemblies produced in this study using SOAPdenovo and MaSuRCA are indicated by asterisks. Bean plots were computed using BoxPlotR (Spitzer et al., 2014).
Appendix 1—figure 3.
Appendix 1—figure 3.. BUSCO completeness assessment of 67 Carnivora genome assemblies visualized as bar charts representing percentages of complete single-copy (light blue), complete duplicated (dark blue), fragmented (yellow), and missing (red) genes ordered by increasing percentage of total complete genes.
The bat-eared fox (Otocyon megalotis megalotis) and aardwolf (Proteles cristatus cristatus) assemblies produced in this study using MaSuRCA and SOAPdenovo are indicated by asterisks.
Appendix 2—figure 1.
Appendix 2—figure 1.. Unicolored fur of an Eastern aardwolf from Ethiopia (NMS.Z.1877.15.5) (A) and bicolored fur of a Southern aardwolf of South African origin (NMS.Z.2020.44) (B).
Appendix 2—figure 2.
Appendix 2—figure 2.. Box and jitter plot of (A) post-orbital breadths of Proteles taxa: cristatus (left) and septentrionalis (right) and (B) condylobasal lengths of skull of Proteles taxa: cristatus (left) and septentrionalis (right).
Graph generated with BoxPlotR (http://shiny.chemgrid.org/boxplotr/).
Appendix 3—figure 1.
Appendix 3—figure 1.. Definition of the genetic differentiation index (GDI) based on the F-statistic (FST).
The main difference between these two indexes is the use of heterozygous allele states for GDI rather than real polymorphism for the FST. Green = πwithin, Orange = πbetween, Blue = Population A, Red = Population A+B.
Appendix 4—figure 1.
Appendix 4—figure 1.. Graphical representation (BlobPlot) of the results of contamination analyses performed with BlobTools for (a) the aardwolf (Proteles cristatus cristatus) and (b) the bat-eared fox (Otocyon megalotis megalotis) genome assemblies.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, Ribeca P, Capella-Gutiérrez S, Rodríguez JM, Câmara F, Lowy E, Cozzuto L, Erb I, Tress ML, Rodriguez-Ales JL, Ruiz-Orera J, Reverter F, Casas-Marce M, Soriano L, Arango JR, Derdak S, Galán B, Juie B, Gut M, Lorente-Galdos B, Andrés-Nieto M, López-Otín C, Valencia A, Gut I, García JL, Guigó R, Murphy WJ, Ruiz-Herrera A, Marques-Bonet T, Roma G, Notredame C, Mailund T, Albà MM, Gabaldón T, Alioto T, Godoy JA. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered iberian Lynx. Genome Biology. 2016;17:251. doi: 10.1186/s13059-016-1090-1. - DOI - PMC - PubMed
    1. Agnarsson I, Kuntner M, May-Collado LJ. Dogs, cats, and kin: a molecular species-level phylogeny of carnivora. Molecular Phylogenetics and Evolution. 2010;54:726–745. doi: 10.1016/j.ympev.2009.10.033. - DOI - PubMed
    1. Allen JA, Tjader R, Lang H. Mammals from british East Africa, collected by the tjäder expedition of 1906. Bulletin of the AMNH. 1909;26:12
    1. Allen R, Ryan H, Davis BW, King C, Frantz L, Irving-Pease E, Barnett R, Linderholm A, Loog L, Haile J, Lebrasseur O, White M, Kitchener AC, Murphy WJ, Larson G. A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids. Proceedings of the Royal Society B: Biological Sciences. 2020;287:20200690. doi: 10.1098/rspb.2020.0690. - DOI - PMC - PubMed
    1. Allio R, Schomaker-Bastos A, Romiguier J, Prosdocimi F, Nabholz B, Delsuc F. MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Molecular Ecology Resources. 2020a;20:892–905. doi: 10.1111/1755-0998.13160. - DOI - PMC - PubMed

Publication types

LinkOut - more resources