Evolution of the melanocortin-1 receptor gene (MC1R) in chamois (Rupicapra spp.)

Phylogenetic Analysis of the Complete Mitochondrial Genomes in the Ten Rupicapra Subspecies and Implications for the Existence of Multiple Glacial Refugia in Europe

Simple Summary

The successive glaciations that took place during the Pleistocene shaped de distribution of temperate species in Europe, both plants and animals. Traditionally, it has been hypothesized that during the coldest periods, species took refuge in three areas of southern Europe (Iberian, Italian and Balkan peninsulas) and then recolonized the north when temperatures rose and conditions were more favorable. In the present work, the complete mitochondrial sequences of the ten described chamois populations have been analyzed to identify which areas of the continent have served as refuges for the species during the glaciations. The results of the present work are consistent with the existence of multiple glacial refugia across Europe, revealing a much more complex picture of the effect of glaciations on the genetics of temperate species than is commonly accepted, giving us a better understanding of how past events determine the present species.

Abstract

The current distribution of populations in Europe is marked by the effects of glaciations that occurred during the Pleistocene. Temperate species were isolated in glacial refugia that were the sources of postglacial recolonization. The traditional glacial refuge areas were the Iberian, the Italian and the Balkan peninsulas. Here we revisit the evolutionary history of chamois (Rupicapra genus) to evaluate other sites in continental Europe and Anatolia that have been suggested as potential refuges. We have obtained the complete mitochondrial sequence of seven chamois, including the subspecies parva, carpatica, caucasica, and asiatica whose mitochondrial genome had not been yet reported. These, together with the other fourteen sequences already in the GenBank, represent the different geographical populations of the Rupicapra genus. The phylogenetic analysis showed the three old clades, dating from the early Pleistocene, already reported: mtW in the Iberian Peninsula, mtC in the Appenines and the Massif of Chartreuse, and mtE comprising all the population from the Alps to the east. The genomes within each of the clades mtW and mtE, showed divergence times larger than 300 thousand years. From here, it can be argued that the present-day lineages across Europe are very old and their split dates back to the middle Pleistocene.

Evolution and phylogenetic application of the MC1R gene in the Cobitoidea (Teleostei: Cypriniformes)

Fish of the superfamily Cobitoidea sensu stricto (namely loaches) exhibit extremely high diversity of color patterns, but so far little is known about their evolutionary mechanism. Melanocortin 1 receptor gene (MC1R) plays an important role during the synthesis of melanin and formation of animal body color patterns. In this study, we amplified and sequenced the partial MC1R gene for 44 loach individuals representing 31 species of four families. Phylogenetic analyses yielded a topology congruent with previous studies using multiple nuclear loci, showing that each of the four families was monophyletic with sister relationships of Botiidae+ (Cobitidae+(Balitoridae+Nemacheilidae)). Gene evolutionary analyses indicated that MC1R in loaches was under purifying selection pressure, with various sites having different dN/dS values. Both Botiidae and Cobitidae had lower dN/dS values than those of background lineages, suggesting their evolution might be strongly affected by purifying selection pressure. For Balitoridae and Nemacheilidae, both had larger dN/dS values than those of background lineages, suggesting they had a faster evolutionary rate under more relaxed selection pressure. Consequently, we inferred that the relatively stable color patterns in Botiidae and Cobitidae might result from the strong purifying selection pressure on the MC1R gene, whereas the complicated and diverse color patterns in Balitoridae and Nemacheilidae might be associated with the relaxed selection pressure. Given the easy experimental procedure for the partial MC1R gene and its excellent performance in reconstructing phylogeny, we suggest this gene could be used as a good molecular marker for the phylogenetic study of fish species.

Multilocus Intron Trees Reveal Extensive Male-Biased Homogenization of Ancient Populations of Chamois (Rupicapra spp.) across Europe during Late Pleistocene

The inferred phylogenetic relationships between organisms often depend on the molecular marker studied due to the diverse evolutionary mode and unlike evolutionary histories of different parts of the genome. Previous studies have shown conflicting patterns of differentiation of mtDNA and several nuclear markers in chamois (genus Rupicapra) that indicate a complex evolutionary picture. Chamois are mountain caprine that inhabit most of the medium to high altitude mountain ranges of southern Eurasia. The most accepted taxonomical classification considers two species, R. pyrenaica (with the subspecies parva, pyrenaica and ornata) from southwestern Europe and R. rupicapra (with the subspecies cartusiana, rupicapra, tatrica, carpatica, balcanica, asiatica and caucasica) from northeastern Europe. Phylogenies of mtDNA revealed three very old clades (from the early Pleistocene, 1.9 Mya) with a clear geographical signal. Here we analyze a set of 23 autosomal introns, comprising 15,411 nucleotides, in 14 individuals covering the 10 chamois subspecies. Introns offered an evolutionary scenario that contrasts with mtDNA. The nucleotidic diversity was 0.0013± 0.0002, at the low range of what is found in other mammals even if a single species is considered. A coalescent multilocus analysis with *BEAST indicated that introns diversified 88 Kya, in the late Pleistocene, and the effective population size at the root was lower than 10,000 individuals. The dispersal of some few migrant males should have rapidly spread trough the populations of chamois, given the homogeneity of intron sequences. The striking differences between mitochondrial and nuclear markers can be attributed to strong female philopatry and extensive male dispersal. Our results highlight the need of analyzing multiple and varied genome components to capture the complex evolutionary history of organisms.

Survival by genotype: patterns at Mc1r are not black and white at the White Sands ecotone

Measuring links among genotype, phenotype and survival in the wild has long been a focus of studies of adaptation. We conducted a 4-year capture-recapture study to measure survival by genotype and phenotype in the Southwestern Fence Lizard (Sceloporus cowlesi) at the White Sands ecotone (transition area between white sands and dark soil habitats). We report several unanticipated findings. First, in contrast with previous work showing that cryptic blanched coloration in S. cowlesi from the heart of the dunes is associated with mutations in the melanocortin-1 receptor gene (Mc1r), ecotonal S. cowlesi showed minimal association between colour phenotype and Mc1r genotype. Second, the frequency of the derived Mc1r allele in ecotonal S. cowlesi appeared to decrease over time. Third, our capture-recapture data revealed a lower survival rate for S. cowlesi individuals with the derived Mc1r allele. Thus, our results suggest that selection at the ecotone may have favoured the wild-type allele in recent years. Even in a system where a genotype-phenotype association appeared to be black and white, our study suggests that additional factors - including phenotypic plasticity, epistasis, pleiotropy and gene flow - may play important roles at the White Sands ecotone. Our study highlights the importance of linking molecular, genomic and organismal approaches for understanding adaptation in the wild. Furthermore, our findings indicate that dynamics of natural selection can be particularly complex in transitional habitats like ecotones and emphasize the need for future research that examines the patterns of ongoing selection in other ecological 'grey' zones.

The shared mitochondrial genome of Rupicapra pyrenaica ornata and Rupicapra rupicapra cartusiana: old remains of a common past

Mitochondrial DNA (mtDNA) has largely been used for species delimitation. However, mtDNA introgression across species boundaries can lead to inconsistent phylogenies. Partial sequences of the mitochondrial genome in the chamois, genus Rupicapra, show the presence of three well differentiated clades, West (mtW), Central (mtC) and East (mtE), each with a geographically restricted distribution. The complete mtDNAs of the clades mtW and mtE (main representatives of the two currently considered species R. pyrenaica and R. rupicapra respectively) have been reported. In the present study, we sequenced the clade mtC present in populations from both species inhabiting the central area of Europe: the Apennines (R. pyrenaica ornata) and the Chartreuse Mountains (R. rupicapra cartusiana). The phylogenetic comparison with the genomes of Caprini highlights the ancient presence of chamois in Europe relative to the fossil record, and the old age of the chamois clade mtC that was split from the clade mtW in the early Pleistocene. The separation of R. pyrenaica ornata and R. rupicapra cartusiana female lineages was recent, dating of the late Pleistocene. Our data represent an example of mtDNA introgression of resident females of Chartreuse Mountains into immigrant males of R. rupicapra due to male-biased migration and female phylopatry.