Rare Deep-Rooting Y Chromosome Lineages in Humans: Lessons for Phylogeography

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Rare Deep-Rooting Y Chromosome Lineages in Humans: Lessons for Phylogeography

Michael E. Weale^a, Tina Shah^a, Abigail L. Jones^a, John Greenhalgh^a, James F. Wilson^b, Pagbajabyn Nymadawa^c, David Zeitlin^d, Bruce A. Connell^e, Neil Bradman^a, and Mark G. Thomas^a
^a The Centre for Genetic Anthropology, Department of Biology, University College, London WC1E 6BT, United Kingdom,
^b Department of Biology, University College, London WC1E 6BT, United Kingdom,
^c Subassembly of Medical Sciences, Mongolian Academy of Sciences, Ulaanbaatar-13, Mongolia,
^d Centre for Social Anthropology and Computing, Department of Anthropology, University of Kent, Canterbury CT2 7NS, United Kingdom
^e Department of Languages, Literatures and Linguistics, York University, Toronto, Ontario M3J 1P3, Canada

Corresponding author: Mark G. Thomas, Department of Biology, University College, Gower St., London WC1E 6BT, United Kingdom., m.thomas{at}ucl.ac.uk (E-mail)

Communicating editor: Z. YANG

There has been considerable debate on the geographic originof the human Y chromosome Alu polymorphism (YAP). Here we reporta new, very rare deep-rooting haplogroup within the YAP clade,together with data on other deep-rooting YAP clades. The newhaplogroup, found so far in only five Nigerians, is the least-derivedYAP haplogroup according to currently known binary markers.However, because the interior branching order of the Y chromosomegenealogical tree remains unknown, it is impossible to imputethe origin of the YAP clade with certainty. We discuss the problemspresented by rare deep-rooting lineages for Y chromosome phylogeography.