Insular East Asia pig dispersal and vicariance inferred from Asian wild boar genetic evidence1

Abstract

The Formosan wild boar () is an endemic subspecies in Taiwan. Understanding the origins and spread of the Formosan wild boar could help clarify East Asian wild boar dispersion. Although in situ domestication of the wild boar occurred at a number of domestication centers across East Asia, corroborating archaeological and genetic evidence of pig domestication on Taiwan is lacking, leading to domestication being described as cryptic. This characterization applies to the Lanyu pig-a domestic pig breed found on Taiwan. To better understand pig domestication, this study examines the sympatric Formosan wild boar and domestic Lanyu pig to build a model of potential wild boar domestication on Taiwan and elucidate wild boar domestication patterns in the region. To this end, a comprehensive phylogenetic study of the Formosan wild boar and the Lanyu pig was conducted on animals sourced from Taiwan, Lanyu, and the Philippines. Phylogenetic analyses were conducted using full mitochondrial control-region sequences from 345 wild boars and domestic pigs. These were studied in concert with existing reports on 206 Asian wild boars. Genetic characteristics and Bayesian phylogenetic tree results identified 2 wild boar lineages of remote phylogenetic relationship. These were Formosan wild boar lineage (FWBL) and Formosan wild boar with Lanyu sign lineage (FWBLYL). Molecular clock analyses indicate that FWBLYL diverged earlier than other insular East Asia wild boars and show that FWBLYL and FWBL diverged approximately 0.60 million years ago. This result supports boars of FWBLYL being the earliest wild boars to have spread and become isolated in insular East Asia. In addition, the study proposes 6 Asian wild boar dispersion routes during glacial periods. At least 3 of these events occurred in insular East Asia with subsequent geographical isolation after glacial recession. This isolation potentially led to allopatric differentiation of wild boar subspecies. Also, the similar genetic signature and phylogenetic uniqueness of Lanyu pigs to wild boars of FWBLYL suggests such wild boars were the wild ancestor of domestic Lanyu pigs. This result indicates potential in situ domestication occurring on Taiwan. Finally, pigs possessing FWBLYL's genetic signatures were continuously distributed among Taiwan, Lanyu, and the Philippines. This pattern may signify human-mediated pig dispersal routes.

Genetic diversity and population structure analysis of Philippine native pigs highlight five priority populations for conservation

“…Furthermore, it revealed that the Cordillera Clade (which includes the Benguet [B] population) has ancestry distant from the general Asian clade (Banayo et al, 2023;Basilio Jr. et al, 2022), similar to the findings in the related Lanyu pig of Taiwan (Li et al, 2017;Wu et al, 2007). Moreover, PhNP interbreeds with endemic wild pigs of the Philippines, such as Sus philippensis, S. cebifrons, S. ahoenobarbus, S. olivieri, and S. sp.…”

“…Among the PhNP populations, the B population was the most differentiated according to the AMOVA results (Table 3). The high variance (Frt: 18%) between highland and lowland populations supports a long period of divergence, according to the assumptions of the SMM (Balloux & Goudet, 2002;Hardy et al, 2003;Li et al, 2017). However, their current low Ne elevates the risk of genetic erosion, similar to the related Lanyu pig of Taiwan (Chang et al, 2009;Wu et al, 2007).…”

“…However, their current low Ne elevates the risk of genetic erosion, similar to the related Lanyu pig of Taiwan (Chang et al, 2009;Wu et al, 2007). The Lanyu pig was previously reported to experience an increased rate of inbreeding and loss of heterozygosity (Chang et al, 2009), despite Lanyu islets being a potential domestication center (Li et al, 2017). Ethnic communities in the Cordillera region have long used the native pig in rituals and festivities, documented as early as 1902 in a folk epic called Hudhud (Lewis, 1992;Manuel, 1963).…”

Phylogeny and Genetic Diversity of Philippine Native Pigs (Sus scrofa) as Revealed by Mitochondrial DNA Analysis

“…Currently, the Cordillera is one of the most diverse and important biotas in the Philippines with many endemic genera (Heaney 2016;Heaney et al 2005). The Lanyu was estimated to have diverged at 0.6 MYA earlier than other East Asian wild boars (Li et al 2017). The CC haplotype was the major mtDNA signature of PhNP in Benguet, Mt.…”

Phylogeny and Genetic Diversity of Philippine Native Pigs (Sus scrofa) as Revealed by Mitochondrial DNA Analysis

“…Previous genetic studies have shown that native pigs from Batanes (Northern Philippines) (Li et al 2017 ), South Luzon (Dichoso et al 2022 ) and Visayas (Layos et al 2022a , b ) possess ancient mtDNA signatures initially found in the miniature Lanyu breed of Taiwan (Wu et al 2007a ). Layos et al ( 2022b ) further identified an A143T mutation that distinguishes the Philippine native from the Lanyu.…”