The presence of Balkan and Iberian red deer ( Cervus elaphus ) mitochondrial DNA lineages in the Carpathian Basin

Frank, Krisztián; Bleier, Norbert; Tóth, Bálint; Sugár, László; Horn, Peter A.; Barta, Endre; Orosz, László; Stéger, Viktor

doi:10.1016/j.mambio.2017.04.005

Cited by 8 publications

(11 citation statements)

References 30 publications

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“…mitochondrial) lineages showed that after the last ice age red deer migrated into the Carpathian Basin from two different directions, from the West (Iberian refuge) and from the South (Balkan refuge). The corresponding maternal genetic footprints are present in today’s regional deer populations in southwestern versus northeastern Hungary [ 40 ]. Here, we tested these with nuclear microsatellites, including autosomal, X- and Y-chromosomal STRs, combined in various setups.…”

Section: Discussionmentioning

confidence: 99%

“…Our previous study on maternal (i.e. mitochondrial) lineages showed that after the last ice age, red deer migrated into the Carpathian Basin from two different directions, from an Iberian refuge and a Balkan refuge [ 40 ]. The corresponding maternal genetic footprints are present in today’s regional deer populations in southwestern versus northeastern Hungary.…”

Section: Discussionmentioning

confidence: 99%

“…huge unbroken flooded lands, sandy-hill regions and steppe between and along the two big rivers, the Danube and the Tisza; later industrialization and the main rail- and highways). After the last glacial period deer migrated into the two sampling regions from different refugia [ 40 ]. Of the samples, 87 were collected in southwestern (SW) Hungary and 36 in northeastern (NE) Hungary ( Fig 1 ).…”

Section: Methodsmentioning

confidence: 99%

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Mining the red deer genome (CerEla1.0) to develop X-and Y-chromosome-linked STR markers

et al. 2020

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Microsatellites are widely applied in population and forensic genetics, wildlife studies and parentage testing in animal breeding, among others, and recently, high-throughput sequencing technologies have greatly facilitated the identification of microsatellite markers. In this study the genomic data of Cervus elaphus (CerEla1.0) was exploited, in order to identify microsatellite loci along the red deer genome and for designing the cognate primers. The bioinformatics pipeline identified 982,433 microsatellite motifs genome-wide, assorted along the chromosomes, from which 45,711 loci mapped to the X- and 1096 to the Y-chromosome. Primers were successfully designed for 170,873 loci, and validated with an independently developed autosomal tetranucleotide STR set. Ten X- and five Y-chromosome-linked microsatellites were selected and tested by two multiplex PCR setups on genomic DNA samples of 123 red deer stags. The average number of alleles per locus was 3.3, and the average gene diversity value of the markers was 0.270. The overall observed and expected heterozygosities were 0.755 and 0.832, respectively. Polymorphic Information Content (PIC) ranged between 0.469 and 0.909 per locus with a mean value of 0.813. Using the X- and Y-chromosome linked markers 19 different Y-chromosome and 72 X-chromosome lines were identified. Both the X- and the Y-haplotypes split to two distinct clades each. The Y-chromosome clades correlated strongly with the geographic origin of the haplotypes of the samples. Segregation and admixture of subpopulations were demonstrated by the use of the combination of nine autosomal and 16 sex chromosomal STRs concerning southwestern and northeastern Hungary. In conclusion, the approach demonstrated here is a very efficient method for developing microsatellite markers for species with available genomic sequence data, as well as for their use in individual identifications and in population genetics studies.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Mining the red deer genome (CerEla1.0) to develop X-and Y-chromosome-linked STR markers

et al. 2020

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“…The Carpathian Mountains represent the largest highmountain system of Central and Eastern Europe, with a key role in the phylogeography of many species (Schmitt 2009;Frank et al 2017). This region harbours one of the largest wolf populations in Europe, estimated to number ca.…”

Section: Introductionmentioning

confidence: 99%

The origin and population genetics of wolves in the north Hungarian mountains

Fehér

Frank

Gombkötő³

et al. 2022

Mamm Biol

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The grey wolf (Canis lupus) is one of the most challenging species to conserve in our modern and crowded world. Due to various factors, most European wolf populations are currently growing. In Hungary, numbers have increased since the 2000s. Although spontaneous recolonisation from Slovakia is considered to be the most likely mechanism by the majority of experts, some stakeholders claim that hand-reared individuals have been released. To determine the origin of wolves in northern Hungary, we analysed samples of free-ranging wolves collected in Slovakia and Hungary as well as samples from wolves in private enclosures in the region. We also included reference samples from domestic dogs. All samples were genotyped at 14 canine autosomal tetranucleotide microsatellite loci (STR) and analysed using multivariate, Bayesian methods. Hungarian wolf samples were also analysed using kinship methods. In the free-ranging wolf samples, all loci were polymorphic with 3–12 alleles. The overall observed (Ho) and unbiased expected (uHE) heterozygosities were 0.60–0.66 and 0.69–0.71, respectively. Parental and sibling relationships were also found among Hungarian individuals: three generations of a pack in the Bükk Mountains were identified. Samples from free-ranging wolves clustered separately from those of captive wolves and dogs. However, genetic similarities were found between Slovakian and Hungarian wolf samples. Our analyses indicate a Slovakian origin of the sampled Hungarian wolves, and we found no evidence that individuals originating in captivity have played any role in the recolonisation process. Kinship relationships and moderate genetic diversity suggest that there is ongoing gene flow across the Slovakian–Hungarian border.

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“…Studies on the genetic structure of European mammals, including red deer, based on mitochondrial DNA (mtDNA) sequences (Ludt et al 2004;Skog et al 2009;Niedziałkowska et al 2011;Meiri et al 2013;Frank et al 2017;Rey-Iglesia et al 2017;Queirós et al 2019) as well as on microsatellites (Zachos et al 2016;Frantz et al 2017;Queirós et al 2019) have shown the large-scale genetic pattern shaped by the Late Pleistocene and Holocene glacial-interglacial cycles. Local or regional red deer populations have also been extensively studied from a population genetic point of view, often taking into account anthropogenic influences (Kuehn et al 2003;Zachos et al 2003;Frantz et al 2006;Hajji et al 2008;Haanes et al 2010;Dellicour et al 2011;Radko et al 2014;Krojerová-Prokešová et al 2015;Borowski et al 2016;Carranza et al 2016;Hoffmann et al 2016;Willems et al 2016;Galarza et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Genetic traces of dispersal and admixture in red deer (Cervus elaphus) populations from the Carpathian Basin

et al. 2022

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After the last glacial, the Carpathian Basin was repopulated from either eastward or northward colonisation routes for various species; one of these was the emblematic member of the European megafauna, the red deer, Cervus elaphus. We analysed 303 red deer individuals from the middle of the region, in seven Hungarian game reserves, at ten microsatellite loci (C01, C229, T26, T108, T123, T156, T172, T193, T501, T507), to investigate the genetic diversity of these subpopulations. We discovered high levels of genetic diversity of red deer subpopulations; allelic richness values ranging 4.99–7.01, observed heterozygosity 0.729–0.800, polymorphic information content 0.722–0.806, and Shannon’s information index 1.668–2.064. Multi-locus analyses indicated population admixtures of various degrees that corresponded to geographical location, and complex genetic structures were shown by clustering. Populations in the south-western and the north-eastern parts of the region formed two highly separated groups, and the red deer from populations in between them were highly admixed (in western Pannonia/Transdanubia, where the Danube flows into the Carpathian Basin). This pattern corresponds to the distribution of mitochondrial as well as Y-chromosome lineages. Assignment tests showed that a large fraction of individuals (29.4%) are found outside of their population of origin, indicating that the dispersal of red deer is rather common, which could be expected considering the life course of the species.

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The presence of Balkan and Iberian red deer ( Cervus elaphus ) mitochondrial DNA lineages in the Carpathian Basin

Cited by 8 publications

References 30 publications

Mining the red deer genome (CerEla1.0) to develop X-and Y-chromosome-linked STR markers

Mining the red deer genome (CerEla1.0) to develop X-and Y-chromosome-linked STR markers

The origin and population genetics of wolves in the north Hungarian mountains

Genetic traces of dispersal and admixture in red deer (Cervus elaphus) populations from the Carpathian Basin

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