Asia-wide phylogeography of wild boar (Sus scrofa) based on mitochondrial DNA and Y-chromosome: Revising the migration routes of wild boar in Asia

Abstract

Genetics of pigs has been well studied in Europe and Asia, but most of previous studies of molecular phylogeny of Sus scrofa have been based on sequences of both wild and domestic forms. In this study we analysed genetic traits of Sus scrofa from 13 regions in Asia (including previously undisclosed Eastern Caucasus and Trans-Baikal regions) using purely wild boar samples. Mitochondrial control region and Y-chromosome genes (AMELY & USP9Y) were employed to resolve phylogeographic relationships. We discussed spatiotemporal dynamics of wild boar distribution and compared molecular data to morphological and cytogenetic data on wild boar variability and taxonomy. A total of 51 haplotypes were detected in mtDNA control region and five haplotypes were found in combined sequences of Y-chromosome genes. The phylogeography of Asia-wide wild boars supported a hypothesis of migration from SouthEast Asia to South Asia, followed by migration to East and West Asia. We present a hypothesis about independent dispersal of wild boars into West Asia from South and NorthEast Asia. Mitochondrial DNA phylogeny generally fits the morphologically based intraspecies taxonomy. Distribution of chromosomal variants of wild boar presently does not show clear correlation with mtDNA clades.

Clear phylogeographic pattern and genetic structure of wild boar Sus scrofa population in Central and Eastern Europe

“…The species has also been introduced by humans to all other continents (except Antarctica) and many islands 1 . Wild boar evolved in South-Eastern Asia, and then colonized northern, central and western parts of Eurasia in several migration waves 2 , 3 . Omnivorous and ecologically flexible, the species occurs in many different temperate and tropical habitats from forests, marshes and grasslands to semi-deserts 1 , 4 .…”

“…There have been several phylogenetic studies performed on wild boar in Eurasia 2 , 3 , 19 – 22 , which revealed two or three main mtDNA lineages of wild boar: the Asian (or East Asian and Near Eastern) and the European one divided further into clades. However, the phylogenetic positions of these lineages and clades varied among studies due to different length, number, and geographic distribution of analysed sequences (comp.…”

“…However, the phylogenetic positions of these lineages and clades varied among studies due to different length, number, and geographic distribution of analysed sequences (comp. e.g., 2 , 3 , 20 . The contact zone of the European and the Asian lineages of wild boar occurs in the vicinity of the Caspian Sea in Iran 20 and the Caucasian Mountains 21 .…”

Genetic Diversity, Admixture and Analysis of Homozygous-by-Descent (HBD) Segments of Russian Wild Boar

“…The use of molecular genetic methods makes it possible to characterize animal populations and determine the degree of their genetic differentiation. Various types of DNA markers are used to characterize the wild boar populations from Russia: mitochondrial DNA [ 10 , 11 , 12 ], Y-chromosome [ 12 , 13 ], STR [ 14 , 15 , 16 , 17 ], SNP [ 18 , 19 , 20 ].…”

Spatial Genetic Structure and Demographic History of the Wild Boar in the Qinling Mountains, China

“…In East Asia, many previous studies have focused on the origin and the recolonization history of domestic pigs [ 16 , 17 ]. The phylogeography of the Asia-wide wild boar revealed that the wild boar migrated from South-East Asia to South Asia, followed by migration to East and West Asia [ 18 ]. Geographical barriers, such as the complex topography of mountains and islands in east and central China, long-term gene flow and population history, play an important role in driving the formation of complex spatial genetic structure of wild boar in East Asia [ 19 ].…”