Abstract. We report the results of one of the first intrageneric analyses to simultaneously survey mitochondrial, Ychromosomal, and autosomal loci from the same individuals representing the same taxa. Phylogenetic trees were constructed for each of these genetic systems from a pool of 63 macaques, representing all 19 recognized species in this genus, and eight outgroup taxa. The mitochondrial locus analyzed here (1.5 Kb) spans the 3Ј end of 12S rDNA, tRNA-VAL, and the 5Ј end of 16S rDNA; the Y chromosome dataset (3.1 Kb) consists of the genes SRY and TSPY; the two autosomal datasets include IRBP intron 3 (1.6 Kb) and the 5Ј half of C4 ''long'' intron 9 (3.3 Kb). A total of 1.35 million bases were read, revealing 682 variable sites within the genus Macaca. With regard to earlier unresolved issues of macaque evolution, a comparison of topologies reconstructed from each of the three genetic systems suggests:(1) four monophyletic species groups; (2) an initial bifurcation among Asian macaques between the silenus group progenitor and a M. fascicularis-like taxon, with the latter representing the probable common ancestor to all nonsilenus group Asian macaques; (3) a possible hybrid origin of M. arctoides from proto-M. assamensis/thibetana and proto-M. fascicularis; and (4) contemporary introgression between M. mulatta and M. fascicularis in Indochina. Inferences 3 and 4 are of particular interest, because episodes of reticulate evolution often go undetected in analyses employing a single genetic system. Finally, divergence calculations suggest that, in female-philopatric taxa, mitochondrial bifurcations may typically predate Y-chromosomal divergences at the same node. The Old World monkey genus Macaca is one of the most successful extant primate radiations. Members of this highly speciose group are found in over 20 Asian countries and parts of northern Africa (Fig. 1), covering an area of more than five million km 2 (Fa 1989). Fossil data suggest macaques arose in northeast Africa around 7 million years ago (mya;Delson 1975Delson , 1980 and subsequently spread through most of continental Asia by 5.5 mya (Delson 1996) where they then diversified into four species groups (Fig. 1), defined according to distinct forms of male reproductive anatomy (Fooden 1976(Fooden , 1980 (Tosi et al. 2000), have proposed scenarios to explain the radiation of Macaca. Despite general consensus, these works disagree on a number of issues regarding the finer details of macaque evolution. First, although the ''nuclear'' studies agree on the monophyly of four macaque species groups (sensu Delson 1980), the mitochondrial analyses suggest paraphyletic relationships among sinica (Hayasaka et al. 1996) or fascicularis group 2 Present address: Molecular Anthropology Laboratory, New York University, 25 Waverly Place, New York, New York 10003; E-mail: ajt5@nyu.edu. members (Morales and Melnick 1998). Second, nearly all of these works propose a different phylogenetic position of M. arctoides, a taxon unique in reproductive behavior and morphology. ...
