The Stone laboratory is working on applications of population genetics to questions concerning the origins, population history and evolution of humans and the great apes. At present, our research focuses on the biological history of Native South Americans and on the evolution and genetic diversity of the genus Pan, which includes chimpanzees and bonobos. We are also working on projects to examine genetic susceptibility to tuberculosis in Native Americans and to investigate the evolutionary history of tuberculosis using ancient DNA.

Graduate Student Projects:

The evolutionary significance of copy number variation on the human and chimpanzee sex chromosomes (PJ Perry)

It has recently been recognized that copy number variants (CNVs; large duplications and deletions of genomic sequence) are common among normal humans. Some of these variants are likely involved in human phenotypic diversity, including traits of longstanding interest to anthropologists. Additionally, between-species copy number differences have had a greater per base impact than single nucleotide substitutions on genomic differences between humans and chimpanzees, and between-species copy number variation may have contributed to the evolution of phenotypes that distinguish us from our closest relatives. In the proposed study, within- and between-species CNVs on the X and Y chromosomes will be identified in humans and chimpanzees. These data will be compared to nucleotide sequence variation data and to existing gene expression and single nucleotide polymorphism (SNP) datasets in order to test models of neutral evolution and to characterize the phenotypic consequences of copy number variation. This study will make important contributions to anthropology through a better understanding of the significance of copy number variation in the evolutionary histories of humans and chimpanzees.

This project is funded by the Leakey Foundation and the Wenner-Gren Foundation for Anthropological Research.

The biological evidence from the San Pau Chu site and its implication for Austronesian migrations (Hsiuman Lin)

The general aim of this research is to characterize genetic variation in ancient native populations in Taiwan as a tool to test hypotheses about population relationships and possible migrations in the southern Pacific. The presence of one distinctive decorated pottery style in the Pacific Island realm represents a unique cultural development, the “Lapita cultural complex,” which corresponds to the spread of Austronesian-speaking peoples. In order to refine reconstructed migrations of the Lapita culture, Oceania has been geographically separated into Near Oceania and Remote Oceania.. To date, the biological, archaeological, and linguistic evidence primarily suggests that Southeast Asian islanders, including the indigenous Taiwanese, culturally, linguistically, and biologically contributed to the peopling of Oceania. Therefore, this research attempts to illuminate the ancestral homeland of Austronesian-speaking populations by using prehistoric human skeletal samples from the San-Pau-Chu (SPC) and Wu-Chen-Tsu South (WCTS) sites in Taiwan. To date, bone samples have been collected from 33 individuals from the San-Pau-Chu (SPC) site and from 12 individuals from the Wu-Chen-Tzu South site in the Tainan Industrial Science-base Park, Taiwan. Mitochondrial DNA hypervariable region sequencing and haplogroup marker analysis is underway for these samples; dental metric and non-metric trait measurements and analyses are mostly complete for these samples. Intra-observer control study shows insignificant statistic errors. Additional sample collection is underway for these sites and sites from the sample time period around this area. MtDNA results for the San-Pau Chu site were presented at the 2003 meeting of the American Association of Physical Anthropologists in Tempe, AZ.

This project is funded by NSF (BCS #0321795), the Wenner Gren Foundation for Anthropological Research, and the Deutscher Akademischer Austausch Dienst (DAAD).