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

Abstract

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.

A Mother’s Story, Mitogenome Relationships in the Genus Rupicapra

“…The phylogeny and taxonomy of Rupicapra species remain controversial despite the improvements in molecular methods over the decades and are still an intriguing question, with important implications on both the evolution and conservation of this species complex [ 2 , 9 ]. Initial molecular investigations using electrophoresis in the 1980s supported the subdivision into an Alpine lineage separated from the Apennine and Pyrenean one [ 48 ].…”

“…Initial molecular investigations using electrophoresis in the 1980s supported the subdivision into an Alpine lineage separated from the Apennine and Pyrenean one [ 48 ]. Later studies, however, revealed a much more complex phylogenetic history with contrasting nuclear, Y-chromosome, and mitochondrial patterns [ 5 , 6 , 7 , 18 ], whereas more recent findings provide support to the hypothesis of ancient hybridization among lineages [ 8 , 9 ]. Although differences among markers in phylogenetic reconstructions are not unusual, due to the evolutionary mode of each marker and the fact that they represent either matrilineal (mitochondrial), patrilineal (Y-chromosome), or biparental (nuclear) evolutionary histories, what is intriguing with Rupicapra is that the same marker, in this case, mitochondrial DNA, led to contrasting conclusions on the number and composition of lineages at different times, depending on the methodological approach (restriction fragment length polymorphisms or sequencing) and the region analyzed (coding, non-coding, a combination or the whole mitogenome) [ 2 , 18 ].…”

“…Overall, our results provide increased resolution compared to the available literature, confirm the phylogeny previously reported for both whole and partial mitochondrial sequences and the discrepancy among markers in phylogenetic reconstruction of the genus. Pérez and colleagues [ 9 ] explained the differences among nuclear, mitochondrial, and Y-chromosome phylogenies with male-mediated introgression and female philopatry. Hybridization is a particularly controversial aspect for this genus, since both natural and human-mediated hybridization have been repeatedly hypothesized or anecdotally reported on several occasions, but confirmed on few [ 19 ].…”

“…Previous studies relying on cytochrome b ( cytb ) identified three lineages geographically separated, a western clade in the Western Alps and Iberia, a central clade in the Apennines and the Chartreuse Massif, and an eastern clade covering all regions east of the Alps [ 6 ]. This subdivision, later confirmed by a combination of mitochondrial regions [ 7 ], differs from the pattern observed with microsatellites, mitochondrial pseudogenes, and introns [ 7 , 8 , 9 ]. The analyses using nuclear markers, although recognizing geographically structured clades, more closely resemble the subspecies subdivision based on morphological characteristics and highlight a complex population history strongly shaped by male-biased dispersal [ 7 , 8 , 9 ], as confirmed by Y-chromosome lineages [ 5 ].…”

“…This subdivision, later confirmed by a combination of mitochondrial regions [ 7 ], differs from the pattern observed with microsatellites, mitochondrial pseudogenes, and introns [ 7 , 8 , 9 ]. The analyses using nuclear markers, although recognizing geographically structured clades, more closely resemble the subspecies subdivision based on morphological characteristics and highlight a complex population history strongly shaped by male-biased dispersal [ 7 , 8 , 9 ], as confirmed by Y-chromosome lineages [ 5 ]. However, mitochondrial genes evolution rates differ [ 10 , 11 , 12 ], with mutations accumulating faster in non-coding than in coding regions, and are strongly influenced by energetic demands [ 12 , 13 , 14 ], thus using the whole mitochondrial genome (mitogenome) could help to address different phylogenetic aspects [ 15 , 16 ].…”