Adam Siepel

Biological Statistics & Computational Biology
Cornell Center for Comparative and Population Genomics
Cornell University

Bayesian inference of ancient human demography from individual genome sequences

Monday, December 5, 2011
AA-G008, 5:00 PM

Abstract

Whole-genome sequences provide a rich source of information about human evolution. Here we describe an effort to estimate key evolutionary parameters based on the whole-genome sequences of six individuals from diverse human populations. We use a Bayesian, coalescent-based approach to obtain information about ancestral population sizes, divergence times, and migration rates from inferred genealogies at many neutrally evolving loci across the genome. We introduce new methods for accommodating gene flow between populations and integrating over possible phasings of diploid genotypes. We also describe a custom pipeline for genotype inference to mitigate biases from heterogeneous sequencing technologies and coverage levels. Our analysis indicates that the San of Southern Africa diverged from other human populations 108–157 thousand years ago (kya), that Eurasians diverged from an ancestral African population 38–64 kya, and that the effective population size of the ancestors of all modern humans was ~9,000.

Biography

Adam Siepel is an Associate Professor in the Department of Biological Statistics and Computational Biology at Cornell University. His research focuses on comparative genomics, particularly of mammals, and includes a mixture of statistical modeling, algorithms development, software implementation, and scientific discovery. Siepel received a B.S. in Agricultural and Biological Engineering from Cornell in 1994, then worked in software development for bioinformatics for several years in the late 1990s, first at Los Alamos National Laboratory and then at the National Center for Genome Resources in Santa Fe. In 2001, he received an M.S. in Computer Science from the University of New Mexico, and, in 2005, a Ph.D. in Computer Science from UC Santa Cruz. Siepel is a winner of a Microsoft Research New Faculty Fellowship, a Packard Fellowship, a Sloan Fellowship, and a National Science Foundation CAREER Award. He currently serves as an associate editor for PLoS Computational Biology, as Director of Graduate Studies for Cornell’s Computational Biology graduate program, and as an associate director for the Cornell Center for Comparative and Population Genomics (3CPG). He has also served on the editorial board of Genome Research, on review panels for the National Science Foundation and the National Institutes of Health, and on advisory committees for the National Human Genome Research Institute. Siepel teaches courses in computational genomics and machine learning at Cornell, and is a member of the graduate fields of Computational Biology, Computer Science, Biometry, Applied Mathematics, and Genetics & Development.

Readings

• Siepel, Adam. 2009. “Phylogenomics of primates and their ancestral populations.” Genome Research, 19:1929-1941. [Review article; PDF]
• Gronau, Ilan; Hubisz, Melissa J.; Gulko, Brad; Danko, Charles G.; and Siepel, Adam. 2011. “Bayesian inference of ancient human demography from individual genome sequences.” Nature Genetics. In press. [Research article; abstract here; full text available under Course Reserves in the Blackboard group for BIOL 480S/680S]