Analysis of MC1R genetic variation in Lepus species in Mediterranean refugia

Melanization, α-melanocyte stimulating hormone and steroid hormones in male western fence lizards from nine populations

Hormones can mediate suites of correlated traits. Melanocortins regulate melanin synthesis and elements of the melanocortin system can directly, and indirectly, affect a number of other traits, such as stress reactivity. Trait correlations within the melanocortin system have been studied mainly in birds and mammals but less so in reptiles. We examined adult male western fence lizards (Sceloporus occidentalis) and if melanization was correlated with plasma levels of three hormones, including peptide hormone α-melanocyte stimulating hormone (α-MSH), testosterone and corticosterone, and ectoparasite loads. This lizard is darker at higher elevations in California, and we compared five high-elevation and four low-elevation populations during comparable periods of the breeding season at each site. We first validated use of an α-MSH assay kit with lizard plasma. Since Anolis carolinensis is one of the few species with published values for α-MSH plasma levels, we assayed both Anolis and Sceloporus plasma and compared hormone values to those we generated for Anolis to the publish values. We also evaluated effects of different methods of storing spiked plasma pools on resulting α-MSH concentrations. Plasma levels of α-MSH did not differ significantly, but some populations differed significantly in mean corticosterone and mean testosterone. Combining all individuals from the nine populations, we found that individual variation in α-MSH was not associated with individual variation in melanization, but levels of α-MSH were positively associated with plasma testosterone and negatively associated with corticosterone. The lack of association between individual levels of melanization and expression of most other traits differs from a growing number of within-population studies of melanization, and we discuss what differences in physiological mechanisms could produce different hypothetical patterns. Circulating levels of -MSH are only one element of the melanocortin system; in situ synthesis of α-MSH by the skin and the diversity of melanocortin receptors could also contribute to variation in traits mediated by the melanocortin system and should be examined.

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

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.

Mitogenomic analysis in European brown hare (Lepus europaeus) proposes genetic and functional differentiation between the distinct lineages

European brown hare is a small game species spreading across Europe to Asia Minor, with important economic traits. Population genetics studies using mitochondrial DNA markers have revealed the existence of two major phylogeographic lineages, the European and the Anatolian. European lineage is further divided in the European type halpogroup and south-eastern European type halpogroup, while Anatolian consists only by the Anatolian/Middle Eastern type halpogroup. All three haplogroups show a discrete geographical distribution, with an overlapping zone forming in North-East Greece and Bulgaria, forming a contact zone. Despite the existence of a contact zone, European haplotype was never detected in Anatolia and vice versa, proposing the presence of genetic barriers responsible for this phenomenon. In this study, we analyzed the whole mitochondrial genomes of specimens originating from both lineages, aiming to detect the genetic and functional differentiation of the oxidative phosphorylation complexes that are encoded by mtDNA that could lead gradually to the reproductive isolation of the lineages.

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

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.

Polarisation of major histocompatibility complex II host genotype with pathogenesis of European Brown Hare syndrome virus

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.