Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis)

Abstract

BackgroundLong-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of which most are restricted to small islands of Southeast Asia. In contrast, the common long-tailed macaque (M. f. fascicularis) is distributed over large parts of the Southeast Asian mainland and the Sundaland region. To shed more light on the phylogeny of M. f. fascicularis, we sequenced complete mitochondrial (mtDNA) genomes of 40 individuals from all over the taxon’s range, either by classical PCR-amplification and Sanger sequencing or by DNA-capture and high-throughput sequencing.ResultsBoth laboratory approaches yielded complete mtDNA genomes from M. f. fascicularis with high accuracy and/or coverage. According to our phylogenetic reconstructions, M. f. fascicularis initially diverged into two clades 1.70 million years ago (Ma), with one including haplotypes from mainland Southeast Asia, the Malay Peninsula and North Sumatra (Clade A) and the other, haplotypes from the islands of Bangka, Java, Borneo, Timor, and the Philippines (Clade B). The three geographical populations of Clade A appear as paraphyletic groups, while local populations of Clade B form monophyletic clades with the exception of a Philippine individual which is nested within the Borneo clade. Further, in Clade B the branching pattern among main clades/lineages remains largely unresolved, most likely due to their relatively rapid diversification 0.93-0.84 Ma.ConclusionsBoth laboratory methods have proven to be powerful to generate complete mtDNA genome data with similarly high accuracy, with the DNA-capture and high-throughput sequencing approach as the most promising and only practical option to obtain such data from highly degraded DNA, in time and with relatively low costs. The application of complete mtDNA genomes yields new insights into the evolutionary history of M. f. fascicularis by providing a more robust phylogeny and more reliable divergence age estimations than earlier studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1437-0) contains supplementary material, which is available to authorized users.

Three Divergent Subpopulations of the Malaria ParasitePlasmodium knowlesi

“…It is likely that allopatric divergence occurred as a result of the ocean barrier between Borneo and mainland Southeast Asia, established at the end of the last ice age ≈13,000 years ago, which prevents the movement of wild macaque reservoir hosts ( 31 ). However, one of the old laboratory lines that was recently sequenced is labeled as having originally been isolated from a long-tailed macaque in “Philippines,” and this sequence is clearly assigned to cluster 3 along with the parasites from peninsular Malaysia ( 16 ), although the islands of the Philippines have never been connected to peninsular Malaysia or any other part of mainland Southeast Asia ( 32 ).…”

“…However, one of the old laboratory lines that was recently sequenced is labeled as having originally been isolated from a long-tailed macaque in “Philippines,” and this sequence is clearly assigned to cluster 3 along with the parasites from peninsular Malaysia ( 16 ), although the islands of the Philippines have never been connected to peninsular Malaysia or any other part of mainland Southeast Asia ( 32 ). Unless there was a historical mislabeling or previous mixup of parasite material, this finding suggests that wider sampling of P. knowlesi in wild macaques will give a more complete understanding of divergence within this zoonotic parasite species ( 31 , 33 – 35 ). Similarly, the observation that a minority of P. knowlesi parasites in long-tailed macaques from peninsular Malaysia are assigned to cluster 2, which has otherwise been seen only in samples from Malaysian Borneo, indicates that additional sampling of macaques from different areas may uncover more features of the parasite population structure.…”

Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist

“…rodents [7], Macaca spp. [48,49], masked palm civet [5] and common palm civet [8]. In the case of the two Catopuma species, it is conceivable that following the split into the northern Indochinese ( =  temminckii ) and the southern Sundaic ( =  badia ) populations, the latter specialized and became more adapted to tropical evergreen rainforests, whereas the northern population remained a more generalistic species due to the higher habitat diversity in Indochina.…”

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

“…This resulted in a 1,082 bp alignment. Samples from Penang, Malaysia (Rovie‐Ryan et al, ) as well as Liedigk et al's () samples also included both HVI and HVII, while all other GenBank samples were restricted to HVII alone with the exception of samples from Smith et al (), which only included HVI. In addition to curating sequences via GBlocks, we also generated alignments trimmed to HVI only and HVII only, as well as completely unedited alignments to test for any systematic biases introduced due to variable sizes of GenBank sequences across studies relative to each other, as well as to the two datasets presented here.…”