Kuang-ti Li

Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania

Human settlement of Oceania marked the culmination of a global colonization process that began when humans first left Africa at least 90,000 years ago. The precise origins and dispersal routes of the Austronesian peoples and the associated Lapita culture remain contentious, and numerous disparate models of dispersal (based primarily on linguistic, genetic, and archeological data) have been proposed. Here, through the use of mtDNA from 781 modern and ancient Sus specimens, we provide evidence for an early human-mediated translocation of the Sulawesi warty pig (Sus celebensis) to Flores and Timor and two later separate human-mediated dispersals of domestic pig (Sus scrofa) through Island Southeast Asia into Oceania. Of the later dispersal routes, one is unequivocally associated with the Neolithic (Lapita) and later Polynesian migrations and links modern and archeological Javan, Sumatran, Wallacean, and Oceanic pigs with mainland Southeast Asian S. scrofa. Archeological and genetic evidence shows these pigs were certainly introduced to islands east of the Wallace Line, including New Guinea, and that so-called “wild” pigs within this region are most likely feral descendants of domestic pigs introduced by early agriculturalists. The other later pig dispersal links mainland East Asian pigs to western Micronesia, Taiwan, and the Philippines. These results provide important data with which to test current models for human dispersal in the region.

Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency

The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index (FST) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu’s inbred populations. Inbreeding values (FIS) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity (HE) or FST, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, FST and D-scores were used. Only 6 to 8 markers ranking HE, FST or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, FST and allelic number of close lineage populations.

Tooth Ablation in Early Neolithic Skeletons from Taiwan

Nankuanli East Site Sample • Earliest Neolithic (5000-4500 BP) skeletons from Taiwan (see map) • Excavations in Tainan Science Park (TSP), southwestern Taiwan from 2002-2003 • Extended supine burials with associated pottery and other funerary objects including domesticated and wild animals • Subsistence: extensive marine exploitation, hunting, plant collecting, & early farming including the cultivation of foxtail millet Tooth Ablation in Indigenous Peoples of Taiwan

A genetic analysis of taoyuan pig and its phylogenetic relationship to eurasian pig breeds.

Taoyuan pig is a native Taiwan breed. According to the historical record, the breed was first introduced to Taiwan from Guangdong province, Southern China, around 1877. The breed played an important role in Taiwan’s early swine industry. It was classified as an indigenous breed in 1986. After 1987, a conserved population of Taoyuan pig was collected and reared in isolation. In this study, mitochondrial DNA sequences and 18 microsatellite markers were used to investigate maternal lineage and genetic diversity within the Taoyuan pig population. Population differentiation among Taoyuan, Asian type, and European type pig breeds was also evaluated using differentiation indices. Only one D-loop haplotype of the Taoyuan pig was found. It clustered with Lower Changjiang River Basin and Central China Type pig breeds. Based on the polymorphism of microsatellite markers, a positive fixation index value (FIS) indicates that the conserved Taoyuan population suffers from inbreeding. In addition, high FST values (>0.2105) were obtained, revealing high differentiation among these breeds. Non-metric multi-dimensional scaling showed a clear geometric structure among 7 breeds. Together these results indicate that maternally Taoyuan pig originated in the Lower Changjiang River Basin and Central China; however, since being introduced to Taiwan differentiation has occurred. In addition, Taoyuan pig has lost genetic diversity in both its mitochondrial and nuclear genomes.

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

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 FWBLYLs genetic signatures were continuously distributed among Taiwan, Lanyu, and the Philippines. This pattern may signify human-mediated pig dispersal routes.