title: Deep haplotype divergence and long-range linkage disequilibrium at xp21.1 provide evidence that humans descend from a structured ancestral population.
abstract: Fossil evidence links human ancestry with populations that evolved from modern gracile morphology in Africa 130,000-160,000 years ago. Yet fossils alone do not provide clear answers to the question of whether the ancestors of all modern Homo sapiens comprised a single African population or an amalgamation of distinct archaic populations. DNA sequence data have consistently supported a single-origin model in which anatomically modern Africans expanded and completely replaced all other archaic hominin populations. Aided by a novel experimental design, we present the first genetic evidence that statistically rejects the null hypothesis that our species descends from a single, historically panmictic population. In a global sample of 42 X chromosomes, two African individuals carry a lineage of noncoding 17.5-kb sequence that has survived for >1 million years without any clear traces of ongoing recombination with other lineages at this locus. These patterns of deep haplotype divergence and long-range linkage disequilibrium are best explained by a prolonged period of ancestral population subdivision followed by relatively recent interbreeding. This inference supports human evolution models that incorporate admixture between divergent African branches of the genus Homo.
authors.affiliation: Genomic Analysis and Technology Core, University of Arizona, Tucson, Arizona 85721, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Garrigan
authors.forename: Zahra
authors.initials: Z
authors.lastname: Mobasher
authors.forename: Sarah B
authors.initials: SB
authors.lastname: Kingan
authors.forename: Jason A
authors.initials: JA
authors.lastname: Wilder
authors.forename: Michael F
authors.initials: MF
authors.lastname: Hammer
mesh_terms: D005075:Biological Evolution; D041321:Chromosomes, Human, X; D005580:Fossils; D005828:Genetics, Population; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium