In 1989, he joined the Human Genome Center at the Lawrence Berkeley Laboratory, Berkeley, as a Staff Scientist. Then he worked as an Associate Research Scientist at the Department of Human Genetics, Cetus Corporation, Emeryville, California for a year. In 1990, he entered the faculty of Assistant Professor the Department of Anthropology, Pennsylvania State University as Assistant Professor. He was promoted to Associate Professor in 1994 and a full professor in 1998. During 1996-1997 he served as a Visiting Professor at the Zoology Institute, University of Munich, Germany. In 1999, he got an appointment in the Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, as the Group Leader. He concurrently serves as an Honorary Professor of Biological Anthropology at the University of Leipzig.
He has been an Associate Editor of the Journal of Human Evolution, Human Biology, BioEssays, Anthropological Science,, Evolutionary Biology, BMC Genetics, Gene, Investigative Genetics, EMBO Reports, and Language Dynamics and Change. He is also Senior Editor of the Annals of Human Genetics from 2008 to present. He has been in the Technical Working Group, DNA Analysis Methods of FBI between 1993 and 1998, Defense Science Board Task Force on DNA Technology for Identification of Ancient Remains, Wellcome Trust Bioarchaeology Panel, Steering Committee for National Energy Research Council Program on Environmental Factors and the Chronology of Human Evolution and Dispersal . He is also a member of the Advisory Committee, The Role of Culture in Early Expansions of Humans, Heidelberg Academy of Sciences since 2008; Advisory Board, US National Evolutionary Synthesis Center since 2011; and Chair, Scientific Advisory Committee of the Program on Forensics and Ethnicity, Philippine Genome Center, since 2011.
Legacy
Mitochondrial Eve
Stoneking came to prominence both in the academic and media circles with his work on mitochondrial DNA variation among different human populations. He started under the supervision of Allan Wilson and following the pioneering work of his senior graduate student, Rebecca Cann. Cann had collected data from different human populations, including those of Asians, Africans, and Europeans. Then Stoneking added data from aboriginal Australians and New Guineans. In 1987, after a year of pending, their paper was published in Nature in which their findings indicated that all living humans were descended through a single mother, who lived ~200,000 years ago in Africa. The common hypothetical mother is dubbed Mitochondrial Eve, and the concept directly implies recent African origin of modern humans, hence, the underpinning of the so-called "Recent Out of Africa" theory. In spite of criticisms, and religious antagonisms, even after two decades he still holds this view to be as valid as any scientific theory since a number independent research also corroborates their original human mtDNA phylogenetic tree.
Other aspects of human evolution
Awards and honours
National Science Foundation Graduate Fellowship, 1977-1978, 1979-1981
Pennsylvania State University Graduate Fellowship, 1978-1979