Analysis of MC1R genetic variation in Lepus species in Mediterranean refugia

Koutsogiannouli, Evagelia A.; Moutou, Katerina A.; Stamatis, Costas; Mamuris, Zissis

doi:10.1016/j.mambio.2012.01.005

Cited by 10 publications

(6 citation statements)

References 51 publications

(65 reference statements)

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“…This percentage fit well to earlier findings [62], [63], [67]. However, DQA genotype constitution did not differ between introgressed and non-introgressed hares, since introgressed individuals bore the most common alleles [ Leeu-DQA*30 (0.611), Leeu-DQA*14 (0.222), Leeu-DQA*52 (0.110) and Leeu-DQA*53 (0.066)].…”

Section: Resultssupporting

confidence: 91%

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Polarisation of Major Histocompatibility Complex II Host Genotype with Pathogenesis of European Brown Hare Syndrome Virus

et al. 2013

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A study was conducted in order to determine the occurrence of European Brown Hare Syndrome virus (EBHSV) in Denmark and possible relation between disease pathogenesis and Major Histocompatibility Complex (MHC) host genotype. Liver samples were examined from 170 brown hares (hunted, found sick or dead), collected between 2004 and 2009. Macroscopical and histopathological findings consistent with EBHS were detected in 24 (14.1%) hares; 35 (20.6%) had liver lesions not typical of the syndrome, 50 (29.4%) had lesions in other tissues and 61 (35.9%) had no lesions. Sixty five (38.2%) of 170 samples were found to be EBHSV-positive (RT-PCR, VP60 gene). In order to investigate associations between viral pathogenesis and host genotype, variation within the exon 2 DQA gene of MHC was assessed. DQA exon 2 analysis revealed the occurrence of seven different alleles in Denmark. Consistent with other populations examined so far in Europe, observed heterozygosity of DQA (H o = 0.1180) was lower than expected (H e = 0.5835). The overall variation for both nucleotide and amino acid differences (2.9% and 14.9%, respectively) were lower in Denmark than those assessed in other European countries (8.3% and 16.9%, respectively). Within the peptide binding region codons the number of nonsynonymous substitutions (dN) was much higher than synonymous substitutions (dS), which would be expected for MHC alleles under balancing selection. Allele frequencies did not significantly differ between EBHSV-positive and -negative hares. However, allele Leeu-DQA*30 was detected in significantly higher (P = 0.000006) frequency among the positive hares found dead with severe histopathological lesions than among those found sick or apparently healthy. In contrast, the latter group was characterized by a higher frequency of the allele Leeu-DQA*14 as well as the proportion of heterozygous individuals (P = 0.000006 and P = 0.027). These data reveal a polarisation between EBHSV pathogenesis and MHC class II genotype within the European brown hare in Denmark.

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Section: Resultssupporting

confidence: 91%

“…Hybridization followed by introgression of mtDNA between Lepus species in Europe is a common phenomenon [57]–[63]. We therefore verified whether introgressed individuals occurred among brown hares from Denmark, using methods of mtDNA analysis previously described [64], [65].…”

Section: Methodsmentioning

confidence: 99%

Polarisation of Major Histocompatibility Complex II Host Genotype with Pathogenesis of European Brown Hare Syndrome Virus

et al. 2013

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“…No specific results are available to interpret that phenotype/molecular data mismatch. Possibly, few introgressed genes underlying the addressed external characteristics (e.g., coat colour genes; Koutsogiannouli et al[122]) were not reflected by our overall microsatellite set. Notably, despite distinct coat colour differences, only shallow molecular divergence was observed among North African cape hares ( L .…”

Section: Discussionmentioning

confidence: 99%

Mitochondrial and nuclear DNA reveals reticulate evolution in hares (Lepus spp., Lagomorpha, Mammalia) from Ethiopia

et al. 2017

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For hares (Lepus spp., Leporidae, Lagomorpha, Mammalia) from Ethiopia no conclusive molecular phylogenetic data are available. To provide a first molecular phylogenetic model for the Abyssinian Hare (Lepus habessinicus), the Ethiopian Hare (L. fagani), and the Ethiopian Highland Hare (L. starcki) and their evolutionary relationships to hares from Africa, Eurasia, and North America, we phylogenetically analysed mitochondrial ATPase subunit 6 (ATP6; n = 153 / 416bp) and nuclear transferrin (TF; n = 155 / 434bp) sequences of phenotypically determined individuals. For the hares from Ethiopia, genotype composition at twelve microsatellite loci (n = 107) was used to explore both interspecific gene pool separation and levels of current hybridization, as has been observed in some other Lepus species. For phylogenetic analyses ATP6 and TF sequences of Lepus species from South and North Africa (L. capensis, L. saxatilis), the Anatolian peninsula and Europe (L. europaeus, L. timidus) were also produced and additional TF sequences of 18 Lepus species retrieved from GenBank were included as well. Median joining networks, neighbour joining, maximum likelihood analyses, as well as Bayesian inference resulted in similar models of evolution of the three species from Ethiopia for the ATP6 and TF sequences, respectively. The Ethiopian species are, however, not monophyletic, with signatures of contemporary uni- and bidirectional mitochondrial introgression and/ or shared ancestral polymorphism. Lepus habessinicus carries mtDNA distinct from South African L. capensis and North African L. capensis sensu lato; that finding is not in line with earlier suggestions of its conspecificity with L. capensis. Lepus starcki has mtDNA distinct from L. capensis and L. europaeus, which is not in line with earlier suggestions to include it either in L. capensis or L. europaeus. Lepus fagani shares mitochondrial haplotypes with the other two species from Ethiopia, despite its distinct phenotypic and microsatellite differences; moreover, it is not represented by a species-specific mitochondrial haplogroup, suggesting considerable mitochondrial capture by the other species from Ethiopia or species from other parts of Africa. Both mitochondrial and nuclear sequences indicate close phylogenetic relationships among all three Lepus species from Ethiopia, with L. fagani being surprisingly tightly connected to L. habessinicus. TF sequences suggest close evolutionary relationships between the three Ethiopian species and Cape hares from South and North Africa; they further suggest that hares from Ethiopia hold a position ancestral to many Eurasian and North American species.

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“…A large number of studies over the last 20 years have focused on its distribution, ecology, biology, population dynamics and evolutionary history and have helped us to better understand fundamental issues concerning mammalian micro- and macro-evolution, conservation biology and local adaptations. Data that were based on nuclear DNA markers have supported relatively high rates of gene flow across large geographical ranges, whereas mitochondrial DNA (mtDNA) analysis has revealed a higher degree of spatial partitioning [ 4 , 5 ]. A comprehensive phylogeographic analysis, based on mtDNA variability of >1200 individuals from Europe, Asia Minor, Middle East and Cyprus identified three major haplogroups with a clear phylogeographic signal that reflected the presence of late-Pleistocene refugia in the central⁄southern Balkans and in Anatolia ([ 4 ]; unpublished data).…”

Section: Introductionmentioning

confidence: 99%

SNP Identification through Transcriptome Analysis of the European Brown Hare (Lepus europaeus): Cellular Energetics and Mother’s Curse

et al. 2016

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The European brown hare (Lepus europaeus, Pallas 1778) is an important small game species in Europe. Due to its size and position in the food chain, as well as its life history, phenotypic variation and the relatively recent speciation events, brown hare plays an important role in the structure of various ecosystems and has emerged as an important species for population management and evolutionary studies. In order to identify informative SNPs for such studies, heart and liver tissues of three samples from the European lineage and a three-sample pool from the Anatolian lineage were subjected to RNA-Sequencing analysis. This effort resulted in 9496 well-assembled protein-coding sequences with close homology to human. After applying very stringent filtering criteria, 66185 polymorphic sites were identified in 7665 genes/cds and 2050 of those polymorphic sites are potentially capable of distinguishing the European from the Anatolian lineage. From these distinguishing mutations we focused on those in genes that are involved in cellular energy production, namely the glycolysis, Krebs cycle and the OXPHOS machinery. A selected set of SNPs was also validated by Sanger sequencing. By simulating the three European individuals as one pool, no substantial informative-SNP identification was lost, making it a cost-efficient approach. To our knowledge this is the first attempt to correlate the differentiation in both nuclear and mitochondrial genome between the two different lineages of L. europaeus with the observed spatial partitioning of the lineages of the species, proposing a possible mechanism that is maintaining the reproductive isolation of the lineages.

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Analysis of MC1R genetic variation in Lepus species in Mediterranean refugia

Cited by 10 publications

References 51 publications

Polarisation of Major Histocompatibility Complex II Host Genotype with Pathogenesis of European Brown Hare Syndrome Virus

Polarisation of Major Histocompatibility Complex II Host Genotype with Pathogenesis of European Brown Hare Syndrome Virus

Mitochondrial and nuclear DNA reveals reticulate evolution in hares (Lepus spp., Lagomorpha, Mammalia) from Ethiopia

SNP Identification through Transcriptome Analysis of the European Brown Hare (Lepus europaeus): Cellular Energetics and Mother’s Curse

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