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Background  We analyzed a combined segment (2032-bp) of the sex-determining region and the testis-specific protein of the Y-chromosome (Y-DNA) gene to clarify the gene flow and phylogenetic relationships of the long-tailed macaques ( Macaca fascicularis ) in Southeast Asia. Phylogenetic relationships were constructed using the maximum likelihood, Bayesian inference, and the median-joining network from a total of 164 adult male  M. fascicularis  from 62 localities in Malaysia, including sequences from the other regions from previous studies.    Results  Based on Y-DNA, we confirm the presence of two lineages of  M. fascicularis : the Indochinese and Sundaic lineages. The Indochinese lineage is represented by  M. fascicularis  located northwards of the Surat Thani-Krabi depression region and is introgressed by the  Macaca mulatta  Y-DNA. The Sundaic lineage is free from such hybridization event, thus defined as the original carrier of the  M. fascicularis  Y-DNA. We further revealed that the Sundaic lineage differentiated into two forms: the insular and the continental forms. The insular form, which represents the ancestral form of  M. fascicularis , consists of two haplotypes: a single homogenous haplotype occupying the island of Borneo, Philippines, and southern Sumatra; and the Javan haplotype .  The more diverse continental form consists of 17 haplotypes in which a dominant haplotype was shared by individuals from southern Thai Peninsular (south of Surat Thani-Krabi depression), Peninsular Malaysia, and Sumatra. Uniquely, Sumatra contains both the continental and insular Y-DNA which can be explained by a secondary contact hypothesis.    Conclusions  Overall, the findings in this study are important: (1) to help authority particularly in Malaysia on the population management activities including translocation and culling of conflict  M. fascicularis , (2) to identify the unknown origin of captive  M. fascicularis  used in biomedical research, and; (3) the separation between the continental and insular forms warrants for the treatment as separate management units.

Evolutionary pattern of Macaca fascicularis in Southeast Asia inferred using Y-chromosomal gene