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Genetic Population Structure, History, and Ancestry

Understanding the spatial patterns of human genetic diversity is crucial for comprehending the origin and distribution of disease associated and causing genetic variation. Furthermore it is relevant to address open questions in human evolution and population history, and provides the scientific basis for genetic ancestry testing in various applications. We therefore explore genetic-geographic structure of human populations, develop statistical methods to improve its detectability, and use spatial patterns of human genetic diversity to answer questions about human origin and migration history. Based on this knowledge, we develop and apply highly informative sets of DNA markers for inferring individual bio-geographic ancestry from DNA as is useful for finding unknown perpetrators not identifiable via current forensic DNA profiling. Depending on the research question, we are using paternally inherited Y-chromosome DNA, maternally inherited mitochondrial DNA, or genome-wide autosomal DNA markers. For instance, our earlier work highlighted that Pacific Islanders are of dual genetic origin in East Asia and Melanesia and the mixing of both groups likely occurred in a sex-biased way before the occupation of the Pacific. Our genome-wide work showed that there is a strong correlation between genetic and geographic distance across Europe, as well – albeit much less so – within European countries such as the Netherlands, and that the origin of European Romani is in northwestern India with different levels of non-Romani European admixture seen in Romani groups across Europe.

Selected relevant publications (last 5 years only):

Chaitanya et al. Simultaneous Whole Mitochondrial genome sequencing with short overlapping amplicons suitable for degraded DNA using the Ion Torrent Personal Genome Machine. Hum Mutat. 2015 36: 1236-47. [PubMed: 26387877]

Genome of the Netherlands Consortium. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat Genet. 2014 46: 818-25. [PubMed: 24974849]

van Oven et al. Human genetics of the Kula Ring: Y-chromosome and mitochondrial DNA variation in the Massim of Papua New Guinea. Eur J Hum Genet. 2014 22: 1393-403. [PubMed: 24619143]

Lao et al. GAGA: a new algorithm for genomic inference of geographic ancestry reveals fine level population substructure in Europeans. PLoS Comput Biol. 2014 10:e1003480. [PubMed: 24586132]

Malaspinas et al. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil. Curr Biol. 2014 24: R1035-R1037. [PubMed: 25455029]

Lao et al. Clinal distribution of human genomic diversity across the Netherlands despite archaeological evidence for genetic discontinuities in Dutch population history. Investig Genet. 2013 4: 9. [PubMed: 23687922]

Mendizabal et al. Reconstructing the Population History of European Romani from Genome-wide Data. Curr Biol. 2012 22: 2342-9. [PubMed: 23219723]

Delfin et al. Bridging Near and Remote Oceania: mtDNA and NRY Variation in the Solomon Islands. Mol Biol Evol. 2012 29: 545-64. [PubMed: 21771715]

van Oven et al. Unexpected island effects at an extreme: reduced Y chromosome and mitochondrial DNA diversity in Nias. Mol Biol Evol. 2011 28: 1349-61. [PubMed: 21059792]

Kayser, M., de Knijff, P. Improving human forensics through advances in genetics, genomics and molecular biology. Nat Rev Genet. 2011 12: 179-92. [PubMed: 21331090]

Kayser M. The human genetic history of Oceania: near and remote views of dispersal. Curr Biol. 2010 20: R194-201. [PubMed: 20178767]

Wollstein et al. Demographic history of Oceania inferred from genome-wide data. Curr Biol. 2010 20: 1983-92. [PubMed: 21074440]

Lao, O. et al. Evaluating self-declared ancestry of U.S. Americans with autosomal, Y-chromosomal and mitochondrial DNA. Hum Mutat. 2010 31: E1875-93. [PubMed: 20886636]