The 81st Annual Meeting of the American Association of Physical Anthropologists (2012)


Recombination networks as genetic markers in a human variation study of the Old World

FRANCESC CALAFELL1, MARTA MELÉ1, ASIF JAVED2, MARC PYBUS1, PIERRE ZALLOUA3, MARC HABER3, DAVID COMAS1, MIHAI G. NETEA4, OLEG BALANOVSKY5, OLGA BALANOVSKA5, LI JIN6, YAJUN YANG6, GANESH ARUNKUMAR7, RAMASAMY PITCHAPPAN7,8, JAUME BERTRANPETIT1, LAXMI PARIDA2 and THE GENOGRAPHIC CONSORTIUM9.

1Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, 2Computational Biology Center, IBM T J Watson Research, Yorktown, USA, 3School of Medicine, Lebanese American University, Beirut, Lebanon, 4Department of Medicine and Nijmegen Institute for Infection, Inflammation, and Immunity, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands, 5Research Cenetr for, Medical Genetics, Moscow, Russia, 6MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China, 7School of Biological Sciences, Madurai Kamaraj University, Madurai, India, 8Chettinad Academy of Research & Education, Chettinad Health City, Rajiv Gandhi Salai, Kelampakkam, Chennai, India, 9The Genographic Project, National Geographic Society

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We have analyzed human genetic diversity in 33 Old World populations including 23 populations obtained through Genographic Project studies. A set of 1536 SNPs in five gene-free X-chromosome regions were genotyped in 1288 individuals (mostly males). We use a novel analysis employing subARG network construction with recombining chromosomal segments, by using the IRiS software (freely available at https://researcher.ibm.com/researcher/view_project.php?id=2303). A subARG is constructed independently for each of five regions and the results are aggregated across them. The observed population structure supports genome-wide frequency-based analyses: African populations show higher genetic diversity, and the general trend of shared variation is seen across the globe from Africa through Middle East, Europe, Central Asia, Southeast Asia, and East Asia in broad patterns. The recombinational analysis was also compared with established methods based on SNPs and haplotypes.

We also estimated effective population sizes; Sub-Saharan African populations have effective population sizes that are ~4 times greater than those of non-African populations. Outside of Africa, South Asian populations had the largest effective sizes. Additionally, recombination diversity correlated with distance out of Africa through a South Arabian, but not a Sinai, route, and, within Eurasian populations, recombination distance correlated with distance from Southern India.

Our recombinational analysis suggested a southern migration route out of Africa, and it also supports a single, rapid human expansion from Africa to East Asia through South Asia, with a a larger role than previously envisaged for South Asia in the demographic history and population expansions of anatomically modern humans out of Africa.

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