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

Saber Khederzadeh,Nikica Šprem,Ya‐Ping Zhang,Cui‐Ping Huang,Hai‐Bing Xie,Massimo Scandura,Ivan V Seryodkin,Ali Esmailizadeh,Nickolay Markov,Elmar Babaev,Ladislav Paule,Szilvia Kusza

doi:10.1002/ece3.5415

Abstract

The phylogeography of the European wild boar was mainly determined by postglacial recolonization patterns from Mediterranean refugia after the last ice age. Here we present the first analysis of SNP polymorphism within the complete mtDNA genome of West Russian (n = 8), European (n = 64), and North African (n = 5) wild boar. Our analyses provided evidence of unique lineages in the East‐Caucasian (Dagestan) region and in Central Italy. A phylogenetic analysis revealed that these lineages are basal to the other European mtDNA sequences. We also show close connection between the Western Siberian and Eastern European populations. Also, the North African samples were clustered with the Iberian population. Phylogenetic trees and migration modeling revealed a high proximity of Dagestan sequences to those of Central Italy and suggested possible gene flow between Western Asia and Southern Europe which was not directly related to Northern and Central European lineages. Our results support the presence of old maternal lineages in two Southern glacial refugia (i.e., Caucasus and the Italian peninsula), as a legacy of an ancient wave of colonization of Southern Europe from an Eastern origin.

Highlights

Wild boar (Sus scrofa) is widely distributed all over the world, and their population is almost four million, considered the sec‐ ond most abundant ungulate species in Europe and a pest in sev‐ eral regions (Apollonio, Andersen, & Putman, 2010; Bobek, 2018)
Wild boars have an intermediate level of mitochondrial DNA (mtDNA) D‐ loop variability (Djan et al, 2013), and little information is available about their complete mtDNA genome diversity (Chen et al, 2018; Kijas & Andersson, 2001; Ni et al, 2018; Tan et al, 2018)
We studied the SNPs of complete mtDNA genome and variability of wild boars from West Siberia, Eastern Caucasus, Europe, and North Africa to provide new data on the species' ge‐ netic diversity and phylogenetic patterns

Summary

Introduction

Wild boar (Sus scrofa) is widely distributed all over the world, and their population is almost four million, considered the sec‐ ond most abundant ungulate species in Europe and a pest in sev‐ eral regions (Apollonio, Andersen, & Putman, 2010; Bobek, 2018). Some authors have attributed their range expansion to climate change (mild winters with no or low snow cover, triggering the necessity for higher food intake; Jędrzejewska, Jędrzejewski, Bunevich, Miłkowski, & Krasiński, 1997; Root et al, 2003; Vetter, Ruf, Bieber, & Arnold, 2015) Others argue that this population in‐ crease has been caused by intensive crop production, changes in agricultural practices, reduced number of predator species, declined hunting pressure, human activities such as supplementary feeding, intentional releases for hunting purposes, and hybridization with do‐ mestic pigs (Apollonio, Scandura, & Šprem, 2014; Baskin & Danell, 2003; Bieber & Ruf, 2005; Geisser & Reyer, 2004, 2006; Iacolina, Corlatti, Buzan, Safner, & Šprem, 2019; Jędrzejewska et al, 1997; Leaper, Massei, Gorman, & Aspinall, 1999; Massei & Genov, 2004; Massei et al, 2015; Sáez‐Royuela & Tellería, 1986). Previous studies revealed the complex genetic structure of wild boar populations in Eurasia, including multiple domestication events and gene flow between wild boar and domestic pig breeds (Iacolina et al, 2016; Larson et al, 2005; Ramíres et al, 2009; Ribani et al, 2019; Šprem et al, 2014)

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