mtDNA Variation and Human-Mediated Introgression of IndigenousSusPopulations on Several Indonesian Islands

Abstract

Abstract. To examine the genetic origin of the domestic pig, the distribution of wild boar, and human-mediated translocation of the domestic pig, we collected 223 samples from domestic pigs and wild boars from eight Indonesian islands, sequenced the control region of mitochondrial DNA (mtDNA) from each sample, and compared these sequences with previously determined sequences from East and Southeast Asian domestic pigs and wild boars. Three Sus species (S. scrofa, S. verrucosus, and S. celebensis) were identified on the Indonesian islands. The mtDNA sequences of three Indonesian Sus species were diverse, and they clustered into three lineages with low bootstrap values (an S. scrofa group including East and Southeast Asian domestic pigs and wild boars, a group including indigenous S. scrofa together with S. verrucosus from Sumatra and Java Islands, and an S. celebensis group from Sulawesi Island). The mtDNA haplotypes of S. scrofa wild boars from three (Sumbawa, Flores and New Guinea) islands and domestic pigs from two (Lombok and Timor) islands east of the Wallace Line, and some S. scrofa wild boars from Sumatra and Java Islands were related to Vietnamese pig mtDNA sequences in the East and Southeast Asian domestic pig and wild boar clade, supporting that ancient immigrants likely introduced domestic pigs from the Asian continent to east Indonesian islands. The mtDNA haplotypes of S. celebensis were broadly divided into three groups, which were distributed in the north and southwest areas, central area and southeast area of Sulawesi Island.

Genomic and Phenotypic Characterization of a Wild Medaka Population: Towards the Establishment of an Isogenic Population Genetic Resource in Fish

“…When interbreeding occurs, genotypes will be exchanged between populations that have separated some time ago, events that are referred to as introgression. Recent studies show that whole-genome data can illuminate ancient introgression events that are not visible by methods typing more limited numbers of loci ( Green et al 2010 ; Ishiguro et al 2012 ; Meyer et al 2012 ).…”

“…A prominent example of the successful application of this approach is the careful observations of allele frequencies between Neanderthals and modern humans [39] and subsequently between Denisovans and moderns humans [40]. The same approach has recently been applied successfully to trace introgression in Sus (Pig) species in Indonesia [41]. These studies show that whole genome data can illuminate ancient introgression events which are not visible by methods typing more limited numbers of loci.…”

Pigs as Pets: Early Human Relations with the Sulawesi Warty Pig (Sus celebensis)

“…The Wallacean archipelago (Wallacea) is located east of the Wallace Line, the biogeographical boundary delineating the easternmost distribution of the floral and faunal worlds of the Southeast Asian continental shelf (Sunda), and west of the Australia-New Guinea landmass (Sahul). The present-day distribution of the Sulawesi warty pig (S. celebensis), based on current assessments or conjecture (data sources: [14,28,29]), includes Sulawesi, where this suid taxon is an ancient component of the insular mammalian fauna, as well as Flores, Sawu, Rote, and Timor, all of which are Wallacean islands where S. celebensis is held to have been introduced by humans in pre-Neolithic times. The species is also reputed to have been translocated to New Guinea, and apparently as far west as Simeulue Island (and Nias).…”

Do Pleistocene rock paintings depict Sulawesi warty pigs (Sus celebensis) with a domestication character?

“…S. celebensis is undoubtedly endemic to Sulawesi, having been established on the island for at least 2 Myr (Frantz et al ., 2015, 2018). However, the species is also said to occur in Simeulue Island 2600 km to the west of Sulawesi, in New Guinea (Groves, 1981; Ishiguro et al ., 2012), and in the Lesser Sunda islands of Flores, Sawu, Rote and Timor (Groves, 1981; Macdonald, 1993). Suids identified as SWP may also be found in the Maluku islands of Halmahera, Buru, and Seram, but these reports are unconfirmed (Groves, 1981).…”

“…If so, then it is possible that the morphological anomaly represented in 16.4% of known cave art images of SWP documented by us may portray a lost character of “pure” S. celebensis . Current studies of S. celebensis have focused on mitochondrial DNA acquired from living samples (Hu et al ., 2016; Ishiguro et al ., 2012; Larson et al ., 2007). It will not be feasible to test this possibility, therefore, until a lot more is known about the genetic diversity of S. celebensis , requiring genome‐wide data sets and nuclear ancient genomes from fossil specimens.…”