Mitochondrial phylogeography of the European wild boar: the effect of climate on genetic diversity and spatial lineage sorting across Europe

Abstract

Aim Climate changes in the past had a deep impact on the evolutionary history of many species and left genetic signatures that are often still detectable today. We investigated the geographical pattern of mitochondrial DNA diversity in the European wild boar (Sus scrofa). Our final aims were to clarify the influence of present and past climatic conditions, infer the geographical position of glacial refugia, and suggest post-glacial spatial dynamics.Location Europe.Methods D-loop sequences were obtained for 763 individuals from Portugal to western Russia. Phylogenetic, multivariate and interpolation methods were used to describe the genetic and geographical patterns. Climatic suitability during the Last Glacial Maximum (LGM) was predicted using MaxEnt. The effect of present and past suitability on the observed patterns of diversity was evaluated by multiple linear regression. ResultsWe confirmed the existence of a ubiquitous mitochondrial clade in Europe (E1), an endemic clade in Italy (E2) and a few East Asian haplotypes (A), presumably introgressed from domestic pigs. No Near Eastern haplotypes were detected. Genetic divergence was not simply related to geographical distance. A clear south-north decreasing gradient of diversity was observed, with maximum levels in putative glacial refugia. Latitudinal variation in climatic conditions during the LGM was shown to be a good predictor of current genetic diversity. Moreover, an unexpected similarity between Iberia and eastern Europe was observed, while central European populations showed a higher affinity to the Italian gene pool. Main conclusionsThe current distribution of mitochondrial genetic diversity was highly influenced by past climatic events, especially those related to the LGM, and is consistent with a major contribution of the Italian peninsula and the Balkans to the post-glacial recolonization of northern areas. More recent processes, such as restocking and extensive hunting, probably acted at rather local scales, without great impact on the global pattern of mitochondrial diversity.

Size matters: A comparative analysis of pig domestication

“…The Italian clade was found only in the Peninsula and in Sardinia, probably because of a stronger isolation of the Italian populations (Vilaça et al, 2014). Further analysis is necessary to strengthen our contention that the Italian haplotypes are uncommon in domestic context because of their small size, which still persists today.…”

Like a pig out of water: seaborne spread of domestic pigs in Southern Italy and Sardinia during the Bronze and Iron Ages

“…The presence of the two haplotypes in Southern Italy (E1 A-side and C-side) together with previously published Mesolithic data (the Italian E2 haplotype reported in Larson et al, 2007) further points to the high variability of mtDNA of this geographical region before the domestication and the human manipulation. This bolsters the idea that southernmost Europe acted as a genetic reservoir for the species during the last glaciation (Hewitt, 2004;Alexandri et al, 2012;Vilaça et al, 2014).…”

Maternal genomic variability of the wild boar (Sus scrofa) reveals the uniqueness of East‐Caucasian and Central Italian populations

“…Most genetic studies on the diversity or phylogenetics of wild boar were based on partial D-loop sequences of mitochondrial DNA (mtDNA; less than 7% of the whole mtDNA genome), or cytochrome b sequences (Fang & Andersson, 2006;Kusza et al, 2014;Larson et al, 2005;Ramíres et al, 2009;Scandura et al, 2008;Veličković et al, 2015Veličković et al, , 2016Vilaça et al, 2014), which occupies less than 7% of the whole mtDNA genome, sometimes in combination with another region (e.g., cytochrome b). Most genetic studies on the diversity or phylogenetics of wild boar were based on partial D-loop sequences of mitochondrial DNA (mtDNA; less than 7% of the whole mtDNA genome), or cytochrome b sequences (Fang & Andersson, 2006;Kusza et al, 2014;Larson et al, 2005;Ramíres et al, 2009;Scandura et al, 2008;Veličković et al, 2015Veličković et al, , 2016Vilaça et al, 2014), which occupies less than 7% of the whole mtDNA genome, sometimes in combination with another region (e.g., cytochrome b).…”