Genetic Analysis of Turkish lynx (Lynx lynx) Based on Mitochondrial DNA Sequences

İbiş, Osman; Özcan, Servet; Kırmanoğlu, Cesur; Keten, Akif; Tez, Coşkun

doi:10.1134/s1022795419110061

Cited by 5 publications

(7 citation statements)

References 46 publications

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“…The resulting alignment of the concatenated sequences (cytb + COI 1770 bp; S = 19) contained our previously reported mitogenomic haplotypes, and the four haplotypes reported by İbİş et al. (2019).…”

Section: Methodsmentioning

confidence: 93%

“…Additionally, and in order to expand the geographical coverage of the study, we re‐analysed cytochrome b (cytb; 1140 pb; S = 7) and cytochrome oxidase I (COI; 630 pb; S = 5) sequences of Turkish lynx (İbİş et al., 2019), along with overlapping sequences in our mitogenome dataset. The resulting alignment of the concatenated sequences (cytb + COI 1770 bp; S = 19) contained our previously reported mitogenomic haplotypes, and the four haplotypes reported by İbİş et al.…”

Section: Methodsmentioning

confidence: 99%

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History, demography and genetic status of Balkan and Caucasian Lynx lynx (Linnaeus, 1758) populations revealed by genome‐wide variation

Bazzicalupo

Lucena-Pérez

Kleinman-Ruiz

et al. 2021

Diversity and Distributions

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Aim Genome‐wide genetic data can provide key input for both taxonomy and conservation, but its use in this context remains limited. In this study, we performed the first genome‐wide assessment of genetic variation in two populations of the Eurasian lynx, the Balkan population, the most threatened, and the Caucasian population, a possible glacial refugium, with the aim to place them in the context of the species, investigate their demographic history and evaluate their genetic status. Location The Balkans and the Caucasus. Methods We obtained whole genome resequencing data from seven Balkan and 12 Caucasian lynx, and analysed them along with novel and existing data from other populations. Based on a total 105 whole genome and 114 mitogenome sequences, we reconstructed phylogenetic and historical relationships, ancient and recent demography, and patterns of genetic diversity and inbreeding. Results Both the Balkan and the Caucasian lynx appear as distinct mitochondrial lineages that diverged from the rest of the Eurasian lynx lineages ca. 92.6 kya, and from each other ca. 46.4 kya. Autosomal data suggest, however, that the Balkan lynx is closely related with the Carpathian population, and revealing alarmingly low genetic diversity and high inbreeding. In contrast, the Caucasian lynx shows a longer history of relative isolation from the rest of lynx populations and high genetic diversity, consistent with its large long‐term effective population size. Main conclusions The taxonomic status of the Balkan lynx remains unresolved due to the evidence of long‐term isolation in the mitogenome, contrasting with extensive autosomal admixture and intense recent genetic drift in the nuclear genome. Our results alert on genetic risks and call for the consideration of genetic rescue from closely related Carpathian lynxes. In contrast, substantial mitogenomic and autosomal divergence with no signs of genetic drift supports the identification of the Caucasian lynx as a separate subspecies with good genetic health.

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Section: Methodsmentioning

confidence: 93%

Section: Methodsmentioning

confidence: 99%

History, demography and genetic status of Balkan and Caucasian Lynx lynx (Linnaeus, 1758) populations revealed by genome‐wide variation

Bazzicalupo

Lucena-Pérez

Kleinman-Ruiz

et al. 2021

Diversity and Distributions

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show abstract

“…These refugia were Iberia, Italy, and the Balkans [29], the latter connecting eastward to Turkey and possibly to the Caucasus [7,14,30,31]. Such high genetic diversity was confirmed in L. lynx populations living in Anatolia [32][33][34] and in the greater Caucasus [15], which renders these populations very important for elucidating the diversity and evolutionary history of Eurasian lynx. Furthermore, data from L. lynx populations from Central and Eastern Asia would also add essential information to the species evolutionary history.…”

Section: Introductionmentioning

confidence: 83%

Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx

Mengüllüoğlu

Ambarlı

Barlow

et al. 2021

Preprint

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Phylogenetic and phylogeographic assessments of species should ideally include individuals of all known populations. However, this is difficult for species with large distribution areas. Previous molecular studies of the wide-ranging Eurasian lynx Lynx lynx focused mainly on its northern Palearctic populations, with the consequence that the reconstruction of this species’ evolutionary history did not include genetic variation present in its southern Palearctic distribution. We sampled a previously not considered Asian subspecies (L. l. dinniki), added published data from another Asian subspecies (L. l. isabellinus), and reassessed the Eurasian lynx mtDNA phylogeny along with previously published data from northern Palearctic populations. Our mitogenome-based analyses revealed that the subspecies L. l. isabellinus harbours the most basal matriline, consistent with the origin of Lynx lynx in this subspecies’ current range. L. l. dinniki harbours the second-most basal matriline, which is related to, and may be the source of, the mtDNA diversity of the critically endangered Balkan lynx L. l. balcanicus. Our results suggest that the Anatolian peninsula was a glacial refugium for Eurasian lynx, with previously unconsidered implications for the colonization of Europe by this species. Genetic variation present in southern Palearctic populations of Lynx lynx is clearly important for elucidating the evolutionary history of this species.

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“…These refugia were Iberia, Italy, and the Balkans [32], with the Balkans connecting eastward to Turkey and possibly to the Caucasus [7,15,33,34]. Such high genetic diversity was confirmed in L. lynx populations living in Anatolia [35][36][37] and in the greater Caucasus [16], which renders these populations very important for elucidating the diversity and evolutionary history of Eurasian lynx.…”

Section: Introductionmentioning

confidence: 85%

Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx

Mengüllüoğlu

Ambarlı

Barlow

et al. 2021

Genes

View full text Add to dashboard Cite

Previous molecular studies of the wide-ranging Eurasian lynx Lynx lynx focused mainly on its northern Palearctic populations, with the consequence that the reconstruction of this species’ evolutionary history did not include genetic variation present in its southern Palearctic distribution. We sampled a previously not considered Asian subspecies (L. l. dinniki), added published data from another Asian subspecies (L. l. isabellinus), and reassessed the Eurasian lynx mtDNA phylogeny along with previously published data from northern Palearctic populations. Our mitogenome-based analyses revealed the existence of three major clades (A: Central Asia, B: SE Europe/SW Asia, C: Europe and Northern Asia) and at least five lineages, with diversification in Lynx lynx commencing at least 28kyr earlier than hitherto estimated. The subspecies L. l. isabellinus harbors the most basal matriline, consistent with the origin of Lynx lynx in this subspecies’ current range. L. l. dinniki harbors the second most basal matriline, which is related to, and may be the source of, the mtDNA diversity of the critically endangered Balkan lynx L. l. balcanicus. Our results suggest that the Anatolian peninsula was a glacial refugium for Eurasian lynx, with previously unconsidered implications for the colonization of Europe by this species.

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Genetic Analysis of Turkish lynx (Lynx lynx) Based on Mitochondrial DNA Sequences

Cited by 5 publications

References 46 publications

History, demography and genetic status of Balkan and Caucasian Lynx lynx (Linnaeus, 1758) populations revealed by genome‐wide variation

History, demography and genetic status of Balkan and Caucasian Lynx lynx (Linnaeus, 1758) populations revealed by genome‐wide variation

Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx

Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx

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