Extensive mitochondrial-DNA differentiation among European Red deer (Cervus elaphus) populations: implications for conservation and management (original) (raw)
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PLOS ONE, 2016
The trajectories of postglacial range expansions, the occurrence of lineage patches and the formation and maintenance of secondary contact between lineages may mostly reflect neutral demographic processes, including density blocking, that may leave long-lasting genetic signatures. However, a few studies have recently shown that climate may also play a role. We used red deer, a large, mobile herbivore that is assumed to be sensitive to climate change, to test hypotheses of possible selection on the mitochondrial DNA cytochrome b gene (mtDNA cytb) and competitive and/or density-blocking (using mtDNA control region). We searched for a possible link between the phylogeographic structure and abiotic climatic variables. Finally, we tested for isolation by distance and isolation by environment and assessed the impact of human-mediated translocations on the genetic structure of red deer. Our analysis of 30 red deer populations in Poland using the mtDNA control region (N = 357) and cytochrome b (N = 50) markers not only confirmed the presence of the Western and SouthEastern lineages of the species but also indicated the presence of a previously unnoticed, rare relic haplotype that grouped together C. e. italicus from Italy (the Mesola deer). No significant signs of positive selection were detected for the mtDNA cytb gene in the studied red deer. However, a significant signal for purifying selection was found in our study that may explain the narrowness of the contact zone because gene flow between the Western and SouthEastern lineages should drive relatively strong mito-nuclear incompatibilities. MtDNA control region differentiation among red deer populations in Poland correlated with different abiotic climatic variables. Strikingly, the southernmost ice sheet limits during the Elsterian was the most important factor, and it explained the largest amount of variation. However, neither isolation by distance (IBD) nor isolation by environment (IBE) were recorded, and a very limited impact of human translocations was evident. The abovementioned results suggest that in contemporary red deer populations in Poland, the phylogeographic pattern is well preserved, and long-term processes (density and/or competitive blocking) still play a major role.
Acta Theriologica, 2011
European red deer are known to show a conspicuous phylogeographic pattern with three distinct mtDNA lineages (western, eastern and North-African/ Sardinian). The western lineage, believed to be indicative of a southwestern glacial refuge in Iberia and southern France, nowadays covers large areas of the continent including the British Isles, Scandinavia and parts of central Europe, while the eastern lineage is primarily found in southeast-central Europe, the Carpathians and the Balkans. However, large parts of central Europe and the whole northeast of the continent were not covered by previous analyses. To close this gap, we produced mtDNA control region sequences from more than 500 red deer from
Acta biologica Hungarica, 2016
Recently, there has been considerable interest in genetic differentiation in the Cervidae family. A common tool used to determine genetic variation in different species, breeds and populations is mitochondrial DNA analysis, which can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We determined the complete mitochondrial genome of a Central European red deer, Cervus elaphus hippelaphus, from Hungary by a next generation sequencing technology. The mitochondrial genome is 16 354 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region, all of which are arranged similar as in other vertebra...
Mitochondrial Dna Variation in Roe Deer Population from Lithuania
2014
In order to investigate the roe deer population from Lithuania, data on the 457 bp mtDNA control region sequences were analysed. In the samples of 20 roe deer from Lithuania we found 6 different haplotypes, based on 38 variable sites, and observed haplotypes belonged to two haplogroups. Genetic diversity was estimated by haplotype diversity H d =0.800, nucleotide diversity P i =0.03031, average number of nucleotide differences k=13.853, and sequence conservation C=0.917. Haplotypes Hap_1 and Hap_2 were the most common in Lithuanian roe deer population. Comparative analysis of the data was performed using homologous mtDNA control region sequences downloaded in GenBank database. Analyses of control region mtDNA sequences indicated widespread introgression of Siberian roe deer ( C. pygargus ) mtDNA in the European roe deer genome, and introgressed individuals constituted 20% of the deer studied. Phylogenetic findings demonstrated distinction between two clades. Hap_2, Hap_3 and Hap_4 h...
Veterinarski arhiv, 2019
Fallow deer (Dama dama) are one of the most important game species in Europe and approximately 5 million animals are raised on farms globally. These deer are considered to be indigenous in Europe, but during the last ice age became extinct from most of their range except Sicily, the Balkan Peninsula and Anatolia. Research suggests that after the Middle Ages the indigenous population only survived in Anatolia (today's Turkey and Iran), so all present worldwide fallow deer populations were reintroduced from there. In Croatia, the species is mostly kept in fenced areas, while breeding in open hunting grounds or farms is rare. The goal of our research was to analyze the genetic diversity of fallow deer that live in the open grasslands of the Croatian island Veliki Brijun on an area of 5.72 km 2. DNA was isolated from the muscle tissue of 22 animals and 405 base pairs of mitochondrial DNA control region were sequenced. One polymorphic site and two haplotypes were detected, both matching sequences from Germany, while one of the haplotypes was also previously detected in fallow deer in Hungary and Italy. The mtDNA diversity of Dama dama from Brijuni National park was rather low but, considering the island's isolation, the obtained results were in accordance with the diversity of previously researched European continental populations of fallow deer.
PLoS ONE, 2014
In the last years several phylogeographic studies of both extant and extinct red deer populations have been conducted. Three distinct mitochondrial lineages (western, eastern and North-African/Sardinian) have been identified reflecting different glacial refugia and postglacial recolonisation processes. However, little is known about the genetics of the Alpine populations and no mitochondrial DNA sequences from Alpine archaeological specimens are available. Here we provide the first mitochondrial sequences of an Alpine Copper Age Cervus elaphus. DNA was extracted from hair shafts which were part of the remains of the clothes of the glacier mummy known as the Tyrolean Iceman or Ö tzi (5,350-5,100 years before present). A 2,297 base pairs long fragment was sequenced using a mixed sequencing procedure based on PCR amplifications and 454 sequencing of pooled amplification products. We analyzed the phylogenetic relationships of the Alpine Copper Age red deer's haplotype with haplotypes of modern and ancient European red deer. The phylogenetic analyses showed that the haplotype of the Alpine Copper Age red deer falls within the western European mitochondrial lineage in contrast with the current populations from the Italian Alps belonging to the eastern lineage. We also discussed the phylogenetic relationships of the Alpine Copper Age red deer with the populations from Mesola Wood (northern Italy) and Sardinia.
Biodiversity and Conservation, 2014
Native red deer (Cervus elaphus) in Western Europe might at least partially derive from refugial populations which survived in the Iberian Peninsula during the last glacial maximum, and that expanded northwards at the onset of the Holocene. However, the phylogeny and genetic structure of red deer populations in the Iberian Peninsula are still poorly known. This study was planned, in a first step, to reconstruct the phylogenetic relationship of the main red deer populations extant in Spain by the analyses of an extensive sample of mitochondrial DNA sequences. Results indicate that sequences from these populations can be assigned to one of two deeply divergent mtDNA lineages (South-Western and Central-Eastern) with molecular divergence nearby the 2 %. In each lineage were respectively found sixteen and thirteen different haplotypes. It was evidenced that they may be allopatrically distributed in Spain with 86.6 % sequences of the South-Western lineage at the South-Western side and the 65 % sequences of Central-Eastern lineage in the Central-Eastern side. These mitochondrial lineages might have originated in two distinct refugial populations during the last glacial maximum. Genetic data also reveal instances of admixture between native populations and translocated European red deer, which belong to at least three distinct subspecies. Gene introgression was mainly due to red Electronic supplementary material The online version of this article (
Gene Reports
The complete mitochondrial genome of Eld's deer (Rucervus eldii eldii) has been sequenced, assembled and characterized for the first time using 25 sets of published primers. The Eld's deer, famously known as Sangai or Manipur's brow-antlered deer belongs to the family cervidae and is critically endangered species in India which needs immediate attention and concern for wildlife conservation. The 16,357 bp long complete mitogenome of R. e. eldii was very similar to most vertebrates in organisation with 13 protein-coding genes, 22 transfer RNA, 2 ribosomal RNA and a typical non-coding control region. Its protein-coding region exhibits codon usage common to all mammals. A detailed characterization of the available mitogenomes of Artiodactyla suggested conserved nature of gene organisation, codon usage, gene orientation and evolutionary rates of proteins. A detailed characterization of the available mitogenomes of Artiodactyla, suggested conserved nature of gene organisation, codon usage, gene orientation and evolutionary rates of proteins. The complete mitogenome and proteincoding genes of R. e. eldii were found to be highly A+T biased. Rate of protein evolution was highest in nad6 and lowest in cox1. The phylogenetic analyses based on concatenated amino acid and nucleotide sequences of 13 protein-coding genes provided a well-supported broader outline of cervidae, which agree with the previously described traditional morphological classification. Besides, the well supported phylogeny of artiodactyls mitochondrial genomes helped to resolve relationships between Rucervus eldii eldii (India) and Rucervus eldii hainanus (China) being the other two Eld's deer species remains unresolved ie. Rucervus eldii thamin (Myanmar)