The Population History of Extant and Extinct Hyenas

Rohland, Nadin; Pollack, Joshua L.; Nagel, Doris; Beauval, Cédric; Airvaux, Jean; Pääbo, Svante; Hofreiter, Michael

doi:10.1093/molbev/msi244

Cited by 131 publications

(103 citation statements)

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“…Panthera tigris) indicate that the genetic distance between the cave and the spotted hyena is in the range of that exhibited between sub-species or even different specimens from the same sub-species (electronic supplementary material, table S4). The close phylogenetic position of the cave and spotted hyena mitochondrial genome sequences is in line with the observation that one of the four Crocuta clades characterized using a fragment of the cytb gene included cave as well as extant spotted hyena specimens [13]. The cave and spotted hyena cytb sequences of the current study belong to this clade.…”

Section: Resultssupporting

confidence: 86%

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Coprolites as a source of information on the genome and diet of the cave hyena

Bon

Berthonaud

Maksud³

et al. 2012

Proc. R. Soc. B.

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We performed high-throughput sequencing of DNA from fossilized faeces to evaluate this material as a source of information on the genome and diet of Pleistocene carnivores. We analysed coprolites derived from the extinct cave hyena (Crocuta crocuta spelaea), and sequenced 90 million DNA fragments from two specimens. The DNA reads enabled a reconstruction of the cave hyena mitochondrial genome with up to a 158-fold coverage. This genome, and those sequenced from extant spotted (Crocuta crocuta) and striped (Hyaena hyaena) hyena specimens, allows for the establishment of a robust phylogeny that supports a close relationship between the cave and the spotted hyena. We also demonstrate that high-throughput sequencing yields data for cave hyena multi-copy and single-copy nuclear genes, and that about 50 per cent of the coprolite DNA can be ascribed to this species. Analysing the data for additional species to indicate the cave hyena diet, we retrieved abundant sequences for the red deer (Cervus elaphus), and characterized its mitochondrial genome with up to a 3.8-fold coverage. In conclusion, we have demonstrated the presence of abundant ancient DNA in the coprolites surveyed. Shotgun sequencing of this material yielded a wealth of DNA sequences for a Pleistocene carnivore and allowed unbiased identification of diet.

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Section: Resultssupporting

confidence: 86%

“…Coprolite samples were screened by PCR using primers (electronic supplementary material, table S1) designed from the partial cytb sequence of the cave hyena [13]. Initially, all samples were amplified using primer pair 1, which yields an 84 bp fragment.…”

Section: Methodsmentioning

confidence: 99%

Coprolites as a source of information on the genome and diet of the cave hyena

Bon

Berthonaud

Maksud³

et al. 2012

Proc. R. Soc. B.

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“…This type of eastern/southern split is also seen in many mammal species, including carnivores (Rohland et al 2005;Freeman et al 2001;Dubach et al 2005;Barnett et al 2006), and large ungulates (Flagstad et al 2001;Moodley and Bruford 2007;Muwanika et al 2003;Arctander et al 1999;Brown et al 2007).…”

Section: Historical Causes Of Diversificationmentioning

confidence: 86%

Phylogeographic analysis of nuclear and mtDNA supports subspecies designations in the ostrich (Struthio camelus)

et al. 2010

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We investigated the phylogeography and subspecies classification of the ostrich (Struthio camelus) by assessing patterns of variation in mitochondrial DNA control region (mtDNA-CR) sequence and across fourteen nuclear microsatellite loci. The current consensus taxonomy of S. camelus names five subspecies based on morphology, geographic range, mtDNA restriction fragment length polymorphism and mtDNA-CR sequence analysis: S. c. camelus, S. c. syriacus, S. c. molybdephanes, S. c. massaicus and S. c. australis. We expanded a previous mtDNA dataset from 18 individual mtDNA-CR sequences to 123 sequences, including sequences from all five subspecies. Importantly, these additional sequences included 43 novel sequences of the red-necked ostrich, S. c. camelus, obtained from birds from Niger. Phylogeographic reconstruction of these sequences matches previous results, with three well-supported clades containing S. c. camelus/syriacus, S. c. molybdophanes, and S. c. massaicus/australis, respectively. The 14 microsatellite loci assessed for 119 individuals of four subspecies (all but S. c. syriacus) showed considerable variation, with an average of 13.4 (±2.0) alleles per locus and a mean observed heterozygosity of 55.7 (±5.3)%. These data revealed high levels of variation within most subspecies, and a structure analysis revealed strong separation between each of the four subspecies. The level of divergence across both marker types suggests the consideration of separate species status for S. c. molybdophanes, and perhaps also for S. c. camelus/syriacus. Both the mtDNA-CR and microsatellite analyzes also suggest that there has been no recent hybridization between the subspecies. These findings are of importance for management of the highly endangered red-necked subspecies (S. c. camelus) and may warrant its placement onto the IUCN red list of threatened animals.

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“…The fossils were retrieved from anoxic saltwater, and were found to contain substantial collagen [20], suggesting at least the potential for DNA preservation. Although samples from temperate saltwater deposits have yielded endogenous DNA [21,22], the validity of a recent report on aDNA from a Mexican underwater cave [23] has been questioned [24]. Thus, the preservation potential of DNA in tropical aquatic or water-logged environments is poorly understood.…”

Section: Introductionmentioning

confidence: 99%

Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoiseChelonoidis alburyorum

et al. 2017

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Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1 000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island. Phylogenetic and molecular clock analyses place this extinct species as closely related to Galápagos (C. niger complex) and Chaco tortoises (C. chilensis), and provide evidence for repeated overseas dispersal in this tortoise group. The ancestors of extant Chelonoidis species arrived in South America from Africa only after the opening of the Atlantic Ocean and dispersed from there to the Caribbean and the Galápagos Islands. Our results also suggest that the anoxic, thermally buffered environment of blue holes may enhance DNA preservation, and thus are opening a window for better understanding evolution and population history of extinct tropical species, which would likely still exist without human impact.

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The Population History of Extant and Extinct Hyenas

Cited by 131 publications

References 50 publications

Coprolites as a source of information on the genome and diet of the cave hyena

Coprolites as a source of information on the genome and diet of the cave hyena

Phylogeographic analysis of nuclear and mtDNA supports subspecies designations in the ostrich (Struthio camelus)

Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoiseChelonoidis alburyorum

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