Continental Monophyly and Molecular Divergence of Peninsular Malaysia’sMacaca fascicularis fascicularis

Abstract

The phylogenetic relationships of long-tailed macaque (Macaca fascicularis fascicularis) populations distributed in Peninsular Malaysia in relation to other regions remain unknown. The aim of this study was to reveal the phylogeography and population genetics of Peninsular Malaysia's M. f. fascicularis based on the D-loop region of mitochondrial DNA. Sixty-five haplotypes were detected in all populations, with only Vietnam and Cambodia sharing four haplotypes. The minimum-spanning network projected a distant relationship between Peninsular Malaysian and insular populations. Genetic differentiation (F ST, Nst) results suggested that the gene flow among Peninsular Malaysian and the other populations is very low. Phylogenetic tree reconstructions indicated a monophyletic clade of Malaysia's population with continental populations (NJ = 97%, MP = 76%, and Bayesian = 1.00 posterior probabilities). The results demonstrate that Peninsular Malaysia's M. f. fascicularis belonged to Indochinese populations as opposed to the previously claimed Sundaic populations. M. f. fascicularis groups are estimated to have colonized Peninsular Malaysia ~0.47 million years ago (MYA) directly from Indochina through seaways, by means of natural sea rafting, or through terrestrial radiation during continental shelf emersion. Here, the Isthmus of Kra played a central part as biogeographical barriers that then separated it from the remaining continental populations.

Investigating biogeographic boundaries of the Sunda shelf: A phylogenetic analysis of two island populations of Macaca fascicularis

“…Our results for HVII corroborate previous phylogenetic analyses of M. fascicularis mtDNA (Abdul‐Latiff et al, ; Blancher et al, ; Rovie‐Ryan et al, ; Schillaci et al, ; Shiina et al, ; Tosi & Coke, ) in that we recovered M. fascicularis as a monophyletic unit (ML bootstrapping 90%; Bayesian posterior probability 99) with two major mitochondrial lineages—an “insular” clade (Group I; 83%; 100) that includes Bali, Sumatra, Java, East Malaysia, Borneo, Lombok, Timor, and the Philippines populations and a predominately “continental” clade (Group II; 72%; n/s) that includes broadly Indochinese, Cambodia, Vietnam, peninsular Malaysia, and Singapore populations along with a small subset of samples from Indonesia and northern Sumatra (Figure ). Within the “insular” clade, all four subgroups defined in Blancher et al () are recovered with either maximum likelihood bootstrap support (>50%), Bayesian support (>80), or both (subgroup: ML bootstrapping %, Bayesian posterior probability): two general Indonesia clades (I‐3 and I‐4), one primarily Philippine clade (I‐1), with all Bali samples falling within the clade including both Lombok samples as well as two broadly Indonesian samples (I‐2) and five samples from Java.…”

“…The analysis of Y DNA from Bali, Indonesia M. fascicularis , reveals that polymorphism in Y DNA haplotypes is not restricted to long‐tailed macaques in Sumatra and Mauritius, and instead extends much deeper into the Indonesian archipelago than previously documented (Tosi & Coke, ). The mtDNA clade distributions also show greater island‐specific differentiation of mitochondrial D‐loop than previously shown (Abdul‐Latiff et al, ; Blancher et al, ; Shiina et al, ; Smith et al, ; Tosi & Coke, ). Such divergence maintained between islands among mtDNA clades strongly suggests that introgression of “continental” Y DNA haplotypes is not recent, nor is it the result of human movement as was the case for the Mauritius macaques.…”

“…Extensive work has documented the evolutionary history of the genus Macaca , with particular attention being paid to both M. fascicularis and M. mulatta (Badhan, Eichstaedt, Almond, Knapp, & Rose, ; Blancher et al, ; Bonhomme, Cuartero, Blancher, & Crouau‐Roy, ; Hayasaka, Fujii, & Horai, ; Osada et al, ; Shiina et al, ; Smith, McDonough, & George, ; Tosi & Coke, ; Tosi, Morales, & Melnick, ). Only recently, however, has this work been extended to include wild macaque populations (Abdul‐Latiff et al, ; Bunlungsup et al, , ; Hasan et al, ; Rovie‐Ryan et al, ; Schillaci, Saravia, Lee, & Matheson, ; Schillaci et al, ) with none utilizing all available sequence data in a meta‐analysis to examine how the inclusion of newly sampled wild populations impacts the overall phylogeographic relationships across Southeast Asia. While most studies report mtDNA monophyly of M. fascicularis lineages (Blancher et al, ; Hayasaka et al, ; Rovie‐Ryan et al, ; Schillaci et al, ; Shiina et al, ; Smith et al, ; Tosi and Coke, ; Tosi, Morales, and Melnick, ), Y DNA analysis supports paraphyly with evident introgression of M. mulatta Y haplotypes into M. fascicularis populations across an Indochinese hybrid zone (Bonhomme et al, ; Osada et al, ; Stevison & Kohn, ; Tosi et al, ; Tosi & Coke, ).…”

“…However, sparse sampling of the islands surrounding Sumatra has limited the extent to which Y DNA introgression into the archipelago could be adequately assessed. Moreover, until recently, samples from peninsular Malaysia were unavailable to further resolve mitochondrial lineages across the Sundaic region (Abdul‐Latiff et al, ; Rovie‐Ryan et al, ), leaving a major gap in the geographic sampling between the Indochinese populations North of the Isthmus of Kra and insular populations.…”

Is Malaysia’s banded langur, Presbytis femoralis femoralis, actually Presbytis neglectus neglectus? Taxonomic revision with new insights on the radiation history of the Presbytis species group in Southeast Asia

“…All available sequences of the Presbytis species group, such as P. thomasi, P. rubicunda, P. frontata, P. potenziani, P. comata, and P. hosei, and the outgroup T. obscurus, were extracted from GenBank for comparative analysis purposes and as a calibration point for the molecular clock rate (Raaum et al 2005;Meyer et al 2011;Abdul-Latiff et al 2014b; Table 1).…”