Annals of Human Genetics

The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations

P. A. UNDERHILL a1c1, G. PASSARINO a1a5, A. A. LIN a1, P. SHEN a2, M. MIRAZÓN LAHR a3a4, R. A. FOLEY a3, P. J. OEFNER a2 and L. L. CAVALLI-SFORZA a1
a1 Department of Genetics, Stanford University, 300 Pasteur Dr., Stanford, CA 94305–5120, USA
a2 Stanford DNA Sequencing and Technology Center, 855 California Ave, Palo Alto, CA 94304, USA
a3 Department of Biological Anthropology, University of Cambridge, Downing Street Cambridge CB2 3DZ, UK
a4 Departamento de Biologia, Inst. de Biociencas, Universidad de São Paulo, Rua do Matão, Travessa 14, No. 321, 05508–900 Cidade Universitária, São Paulo, Brasil
a5 Department of Cell Biology, Calabria University, Rende, Italy


Although molecular genetic evidence continues to accumulate that is consistent with a recent common African ancestry of modern humans, its ability to illuminate regional histories remains incomplete. A set of unique event polymorphisms associated with the non-recombining portion of the Y-chromosome (NRY) addresses this issue by providing evidence concerning successful migrations originating from Africa, which can be interpreted as subsequent colonizations, differentiations and migrations overlaid upon previous population ranges. A total of 205 markers identified by denaturing high performance liquid chromatography (DHPLC), together with 13 taken from the literature, were used to construct a parsimonious genealogy. Ancestral allelic states were deduced from orthologous great ape sequences. A total of 131 unique haplotypes were defined which trace the microevolutionary trajectory of global modern human genetic diversification. The genealogy provides a detailed phylogeographic portrait of contemporary global population structure that is emblematic of human origins, divergence and population history that is consistent with climatic, paleoanthropological and other genetic knowledge.

(Received August 24 00)
(Accepted November 16 00)

c1 Correspondence: P. A. Underhill. E-mail: