Origin of YAP+ Lineages of the Human Y-Chromosome CLAUDIO M. BRAVI, GRACIELA BAILLIET, VERO ´ NICA L. MARTI ´NEZ-MARIGNAC, AND NE ´ STOR O. BIANCHI* Multidisciplinary Institute of Cell Biology (IMBICE), 1900 La Plata, Argentina KEY WORDS YAP+ chromosomes; YAP+ lineages; Y-specific Alu inserts ABSTRACT We screened a total of 841 Y-chromosomes representing 36 human populations of wide geographical distribution for the presence of a Y-specific Alu insert (YAP+ chromosomes). The Alu element was found in 77 cases. We tested 5 biallelic and 8 polyallelic markers in 70 out of the 77 YAP+ chromosomes. We could identify the existence of a hierarchical and chrono- logical structuring of ancestral and derived YAP+ lineages, giving rise to 4 haplogroups, 14 subhaplogroups and 60 haplotypes. Moreover, we propose a monophyletic origin for each one of the YAP+ lineages. Out-of-Africa and out-of-Asia models have been suggested to explain the origin and evolution of ancestral and derived YAP+ elements. We analyze the evidence supporting these two hypotheses, and we conclude that the information available does not allow one to decide between the out-of-Asia or out-of-Africa models. Am J Phys Anthropol 112:149 –158, 2000. © 2000 Wiley-Liss, Inc. The Y-specific region of Y-chromosomes is haploid and patrilineally transmitted along generations. As this region does not undergo recombination, all Y-specific genes and markers are in linkage disequilibrium, with mutations being the only potential source of variation between the male ancestor and his male offspring. Several Alu inserts known to occur in hu- mans after the human/ape divergence have been extensively used to infer the evolution of modern human populations (Batzer et al., 1994; Stoneking et al., 1997; Hammer, 1994, 1995; Whitfield et al., 1995). Among these human-specific elements, one of them is particularly interesting due to its location in the nonrecombinant region (DYS287 locus) of the human Y-chromosome; YAP+ and YAP- acronyms identify the presence or absence (ancestral state) of the insert re- spectively (Hammer, 1994; Spurdle et al., 1994). YAP+ chromosomes appear at low fre- quency (10%) in some Asian, Oceanian, and Amerindian populations, at intermedi- ate frequency (11–30%) in Caucasians and Japanese, and at high frequency (31%) in Tibetans and several African populations (Altheide and Hammer, 1997; Hammer, 1994; Hammer et al., 1998; Spurdle et al., 1994; Bianchi et al., 1997; Karafet et al., 1997; Thomas et al., 1998). Since its origin, this Alu domain accumulated several bial- lelic additional mutations: two C  T tran- sitions at 338 bp (PN1) and 1,682 bp (PN2) loci, and a deletion of the Poly-A tail (S for short tail). Finally, outside the Alu domain, two other mutations, a G  A transition at 4,064 bp of the SRY domain (Whitfield et al., 1995) and an A  G transition at the 168 bp position of the DYS271 locus (Seielstad et al., 1994) were also informative (Hammer, Grant sponsor: National Council of Research, Argentina; Grant sponsor: Research Commission of the province of Buenos Aires, Argentina; Grant sponsor: Argentine-Brazilian Center for Biotechnology; Grant sponsor: National Agency for the Develop- ment of Science and Technology, Argentina. *Correspondence to: Dr. Ne ´ stor O.Bianchi, IMBICE, Calle 526 e/10 y 11, 1900 La Plata, Argentina. E-mail: imbice@satlink.com or bianchi@satlink.com Received 4 January 1999; accepted 24 January 2000. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 112:149 –158 (2000) © 2000 WILEY-LISS, INC.