Early Neolithic genomes from the eastern Fertile Crescent.
Science 353(6298):499 (2016)
We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially...
Early farmers from across Europe directly descended from Neolithic Aegeans.
PNAS 113(25):6886 (2016)
Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local for...
The Kalash Genetic Isolate? The Evidence for Recent Admixture.
The American Journal of Human Genetics 98(2):396 (2016)
The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape
Current Biology 25(21):2878 (2015)
The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape.
Current Biology 25(19):2518 (2015)
Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient humans across West Eurasia, demonstrating the presence of large-...
Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference.
PLoS Genetics 11(8):e1005397 (2015)
The Ari peoples of Ethiopia are comprised of different occupational groups that can be distinguished genetically, with Ari Cultivators and the socially marginalised Ari Blacksmiths recently shown to have a similar level of genetic differentiation between them (FST ≈ 0.023 - 0.04) as that observe...
Evidence for negative selection of gene variants that increase dependence on dietary choline in a Gambian cohort.
FASEB Journal 29(8):3426 (2015)
Choline is an essential nutrient, and the amount needed in the diet is modulated by several factors. Given geographical differences in dietary choline intake and disparate frequencies of single-nucleotide polymorphisms (SNPs) in choline metabolism genes between ethnic groups, we tested the hypot...
The fine-scale genetic structure of the British population.
Nature 519(7543):309 (2015)
Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide single nucleotide polymorphism (SNP) data from a c...
The genomic and phenotypic diversity of Schizosaccharomyces pombe.
Nature Genetics 47(3):235 (2015)
Natural variation within species reveals aspects of genome evolution and function. The fission yeast Schizosaccharomyces pombe is an important model for eukaryotic biology, but researchers typically use one standard laboratory strain. To extend the usefulness of this model, we surveyed the genom...
Human Dispersal Out of Africa: A Lasting Debate.
Evolutionary Bioinformatics 11(Suppl 2):57 (2015)
Unraveling the first migrations of anatomically modern humans out of Africa has invoked great interest among researchers from a wide range of disciplines. Available fossil, archeological, and climatic data offer many hypotheses, and as such genetics, with the advent of genome-wide genotyping and...
Unravelling the hidden ancestry of American admixed populations.
Nature Communications 6:6596 (2015)
The movement of people into the Americas has brought different populations into contact, and contemporary American genomes are the product of a range of complex admixture events. Here we apply a haplotype-based ancestry identification approach to a large set of genome-wide SNP data from a variet...
A genetic atlas of human admixture history.
Science 343(6172):747 (2014)
Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at f...
Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
Nature Genetics 45(11):1353 (2013)
Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (P < 1.0 × 10(-4)). In a replication phase, we combined these data with previous genome-w...
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
Nature Genetics 45(10):1150 (2013)
Schizophrenia is an idiopathic mental disorder with a heritable component and a substantial public health impact. We conducted a multi-stage genome-wide association study (GWAS) for schizophrenia beginning with a Swedish national sample (5,001 cases and 6,243 controls) followed by meta-analysis ...
Inference of population structure using dense haplotype data.
PLoS Genetics 8(1):e1002453 (2012)
The advent of genome-wide dense variation data provides an opportunity to investigate ancestry in unprecedented detail, but presents new statistical challenges. We propose a novel inference framework that aims to efficiently capture information on population structure provided by patterns of hap...
Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population.
PLoS Genetics 8(3):e1002504 (2012)
In spite of its evolutionary significance and conservation importance, the population structure of the common chimpanzee, Pan troglodytes, is still poorly understood. An issue of particular controversy is whether the proposed fourth subspecies of chimpanzee, Pan troglodytes ellioti, from parts o...
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
Nature 476(7359):214 (2011)
Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that ...
The major histocompatibility complex and multiple sclerosis: a smoking gun?
Brain 134(Pt 3):638 (2011)
Inferring human colonization history using a copying model.
PLoS Genetics 4(5):e1000078 (2008)
Genome-wide scans of genetic variation can potentially provide detailed information on how modern humans colonized the world but require new methods of analysis. We introduce a statistical approach that uses Single Nucleotide Polymorphism (SNP) data to identify sharing of chromosomal segments be...
msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots.
We have incorporated both crossover and gene conversion hotspots into an existing coalescent-based program for simulating genetic variation data for a sample of chromosomes from a population.
The source code for msHOT is available at http://home.uchicago.edu/~rhudson1, along with accompanying in...