The shared mitochondrial genome of Rupicapra pyrenaica ornata and Rupicapra rupicapra cartusiana: Old remains of a common past

Pérez, Trinidad; González, Iago; Essler, Sabine E.; Fernández, Mónica; Domínguez, Ana

doi:10.1016/j.ympev.2014.07.004

Cited by 17 publications

(16 citation statements)

References 23 publications

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“…On the other hand, the extinction of several other ungulates since the 1800s has ultimately been linked to indiscriminate poaching. This is surely the case of the Saudi gazelle, the South African bluebuck (Hippotragus leucophaeus), the Queen of Sheba's gazelle or Yemen gazelle (Gazella bilkis), and the Schomburgk's deer (Rucervus schomburgki), while other heavily hunted taxa such as the Barbary deer (Cervus elaphus barbarous: Kingdon et al 2013), the Alpine ibex (Grossen et al 2017) and the Apennine chamois (Rupicapra pyrenaica ornata: Pérez et al 2014) were rescued from the brink of extinction thanks to last resort conservation initiatives.…”

Section: Discussionmentioning

confidence: 99%

Demography reveals populational expansion of a recently extinct Iberian ungulate

Forcina¹,

Woutersen²,

Sánchez‐Ramírez³

et al. 2021

ZSE

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Reconstructing the demographic history of endangered taxa is paramount to predict future fluctuations and disentangle the contributing factors. Extinct taxa or populations might also provide key insights in this respect by means of the DNA extracted from museum specimens. Nevertheless, the degraded status of biological material and the limited number of records may pose some constraints. For this reason, identifying all available sources, including private and public biological collections, is a crucial step forward. In this study, we reconstructed the demographic history based on cytochrome-b sequence data of the Pyrenean ibex (Capra pyrenaica pyrenaica), a charismatic taxon of the European wildlife that became extinct in the year 2000. Moreover, we built a database of the museum specimens available in public biological collections worldwide and genotyped a privately owned 140-year-old trophy from the Spanish Pyrenees to confirm its origin. We found that the population of the Pyrenean ibex underwent a recent expansion approximately 20,000 years ago, after which trophy hunting and epizootics triggered a relentless population decline. Our interpretations, based on the genetic information currently available in public repositories, provide a solid basis for more exhaustive analyses relying on all the new sources identified. In particular, the adoption of a genome-wide approach appears a fundamental prerequisite to disentangle the multiple contributing factors associated with low genetic diversity, including inbreeding depression, acting as extinction drivers.

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Section: Discussionmentioning

confidence: 99%

Demography reveals populational expansion of a recently extinct Iberian ungulate

Forcina¹,

Woutersen²,

Sánchez‐Ramírez³

et al. 2021

ZSE

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“…This huge difference cannot be accounted for by differences in the nuclear and mitochondrial clock, as becomes evident from the comparison of the estimated age of the root in years after calibration. The age of the mtDNA MRCA of Rupicapra was estimated to 1.93 MYA (1.56–2.33 CI, 95% HDP) [ 25 ]. In contrast, Rupicapra introns are remarkably young, 292 ky (95% HDP 241–527 ky), according to data based on concatenation and much more recent following the species tree method.…”

Section: Discussionmentioning

confidence: 99%

“…But recently, more ancient fossils were discovered in the Balkans in a biostratigraphic zone that corresponds to between 780 and 750 Kya [ 27 ]. Diversification time estimates between mitochondrial lineages based on partial sequences [ 18 – 20 , 24 , 68 ] or in complete mitochondrial genomes [ 25 ] were older, between 1.5 and 2.1 mya. Following the comparison of complete mitochondrial genomes, the MRCA of Rupicapra occurred at 1.93 MYA (1.56–2.33 CI, 95%HPD) [ 25 ].…”

Section: Discussionmentioning

confidence: 99%

“…Diversification time estimates between mitochondrial lineages based on partial sequences [ 18 – 20 , 24 , 68 ] or in complete mitochondrial genomes [ 25 ] were older, between 1.5 and 2.1 mya. Following the comparison of complete mitochondrial genomes, the MRCA of Rupicapra occurred at 1.93 MYA (1.56–2.33 CI, 95%HPD) [ 25 ]. This age corresponds to the boundary between the Gelasian and the Calabrian Stages at the Early Pleistocene (following the recent “Formal Subdivisions of the Pleistocene Series/Epoch” of the subcommission on Quaternary Stratigraphy, former Plio-Pleistocen boundary).…”

Section: Discussionmentioning

confidence: 99%

“…With regard to the timing of differentiation of Rupicapra , the divergence between the main mtDNA clades has been estimated around 1.9 mya [ 19 , 24 , 25 ], at the Early Pleistocene following the recent “Formal Subdivisions of the Pleistocene Series/Epoch” of the subcommission on Quaternary Stratigraphy [ 26 ] that we will adopt along the paper. This is by far older than the age of the most ancient Rupicapra fossils in Europe that were discovered in the Balkans and correspond to the beginning of the middle Pleistocene, between 780 and 750 Kya [ 27 ].…”

Section: Introductionmentioning

confidence: 99%

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Multilocus Intron Trees Reveal Extensive Male-Biased Homogenization of Ancient Populations of Chamois (Rupicapra spp.) across Europe during Late Pleistocene

et al. 2017

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The inferred phylogenetic relationships between organisms often depend on the molecular marker studied due to the diverse evolutionary mode and unlike evolutionary histories of different parts of the genome. Previous studies have shown conflicting patterns of differentiation of mtDNA and several nuclear markers in chamois (genus Rupicapra) that indicate a complex evolutionary picture. Chamois are mountain caprine that inhabit most of the medium to high altitude mountain ranges of southern Eurasia. The most accepted taxonomical classification considers two species, R. pyrenaica (with the subspecies parva, pyrenaica and ornata) from southwestern Europe and R. rupicapra (with the subspecies cartusiana, rupicapra, tatrica, carpatica, balcanica, asiatica and caucasica) from northeastern Europe. Phylogenies of mtDNA revealed three very old clades (from the early Pleistocene, 1.9 Mya) with a clear geographical signal. Here we analyze a set of 23 autosomal introns, comprising 15,411 nucleotides, in 14 individuals covering the 10 chamois subspecies. Introns offered an evolutionary scenario that contrasts with mtDNA. The nucleotidic diversity was 0.0013± 0.0002, at the low range of what is found in other mammals even if a single species is considered. A coalescent multilocus analysis with *BEAST indicated that introns diversified 88 Kya, in the late Pleistocene, and the effective population size at the root was lower than 10,000 individuals. The dispersal of some few migrant males should have rapidly spread trough the populations of chamois, given the homogeneity of intron sequences. The striking differences between mitochondrial and nuclear markers can be attributed to strong female philopatry and extensive male dispersal. Our results highlight the need of analyzing multiple and varied genome components to capture the complex evolutionary history of organisms.

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Northern Chamois Rupicapra rupicapra (Linnaeus, 1758) and Southern Chamois Rupicapra pyrenaica Bonaparte, 1845

Corlatti

Herrero

Ferretti

et al. 2022

Handbook of the Mammals of Europe

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The shared mitochondrial genome of Rupicapra pyrenaica ornata and Rupicapra rupicapra cartusiana: Old remains of a common past

Cited by 17 publications

References 23 publications

Demography reveals populational expansion of a recently extinct Iberian ungulate

Demography reveals populational expansion of a recently extinct Iberian ungulate

Multilocus Intron Trees Reveal Extensive Male-Biased Homogenization of Ancient Populations of Chamois (Rupicapra spp.) across Europe during Late Pleistocene

Northern Chamois Rupicapra rupicapra (Linnaeus, 1758) and Southern Chamois Rupicapra pyrenaica Bonaparte, 1845

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