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.

ABSTRACT.Little is known about the classification and phylogenetic relationships of the leaf monkeys (Presbytis). We analyzed mitochondrial DNA sequences of cytochrome b (Cyt b) and 12S rRNA to determine the phylogenetic relationships of the genus Presbytis. Gene fragments of 388 and 371 bp of Cyt b and 12S rRNA, respectively, were sequenced from samples of Presbytis melalophos (subspecies femoralis, siamensis, robinsoni, and chrysomelas), P. rubicunda and P. hosei. The genus Trachypithecus (Cercopithecidae) was used as an outgroup. The Cyt b NJ and MP phylogeny trees showed P. m. chrysomelas to be the most primitive, followed by P. hosei, whereas 12S rRNA tree topology only indicated that these two species have close relationships with the other members of the genus. In our analysis, chrysomelas, previously classified as a subspecies of P. melalophos, was not included in either the P. m. femoralis clade or the P. m. siamensis clade. Whether or not there should be a separation at the species level remains to be clarified. The tree topologies also showed that P. m. siamensis is paraphyletic with P. m. robinsoni, and P. m. femoralis with P. rubicunda, in two different Phylogenetic relationships of Presbytis clades. Cyt b and 12S rRNA are good gene candidates for the study of phylogenetic relationships at the species level. However, the systematic relationships of some subspecies in this genus remain unclear.

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ABSTRACT. Mitochondrial DNA cytochrome c oxidase II (COII) gene sequences of Malaysian Cercopithecidae were examined to ascertain their phylogenetic relationships. Colobinae were represented by the genera Presbytis, Trachypithecus and Nasalis, while the genus Macaca represented Cercopithecinae. DNA amplification and sequencing of the COII gene was performed on 16 samples. Symphalangus syndactylus (Hylobatidae) was used as the outgroup. Data were analyzed using both character (maximum parsimony) and distance (neighbor-joining) methods. Tree topologies indicated that Colobinae and Cercopithecinae have their own distinct monophyletic clade. This result was well supported by bootstrap values and genetic distances derived from the Kimura-2-parameter algorithm. Separation of Macaca nemestrina from M. fascicularis was also well supported by bootstrap values. In addition, tree topologies indicate a good resolution of the Colobinae phylogenetic relationships at the intergeneric level, but with low bootstrap support. The position of Nasalis remained problematic in both trees. Overall, COII is a good gene candidate for portraying the phylogenetic relationships of Malaysian primates at the inter-and intra-subfamily levels.

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Presbytis chrysomelas chrysomelas endemic only in Sarawak and Kalimantan was categorized by IUCN as a critically endangered primate that require special attention from research and conservation perspectives. A qualitative study on ranging patterns of P. c. chrysomelas was conducted in the Samunsam Wildlife Sanctuary, Sarawak. The study was conducted over a period of 13 months from December 2004 to December 2005 with 213 days of observation. Behavioural observation covered 17 groups with special emphasis on two main groups and 1 subadult group. Scanning and focal sampling were employed as the observation methods. Results indicated that P. c. chrysomelas had vertical, straight horizontal, and cross-horizontal types of movement patterns. P. c. chrysomelas was recorded to have a short movement distance (31.8–54.3 m). Distribution, abundance types, and food resources might be the factors that shaped the patterns of movement and distance in P. c. chrysomelas.

Abstract. Md-Zain BM, Abid-Kamal SNA, Aifat NR, Abdul-Latiff MAB, Mohd-Hashim A, Ampeng A, Yaakop S, Samat A. 2018.Molecular identification of shark fins in Malaysian Borneo’s local markets. Biodiversitas 19: 1035-1043. A molecular study was carriedout to investigate the potential of the cytochrome c oxidase subunit I (COI) gene as a molecular marker for the genetic identification ofshark fin samples that have gone through various preservation processes. A total number of 17 shark fin samples were collected fromlocal markets in Sabah and Sarawak (Malaysian Borneo). The DNA sequences of the 17 samples were amplified by using polymerasechain reaction. The results from the analysis showed that, in the 17 sequences, there were 16 haplotypes present, with 244 sites from 688bp of the sequences. For phylogeny analysis, tree topologies were reconstructed using the neighbor-joining (NJ) and maximumparsimony (MP) methods. DNA barcoding technique successfully identifies shark fins collected in local markets in Malaysian Borneo atspecies level employed during this study. Phylogenetic analysis showed that there were four clades that distinguish the four differentorders present in the sample species. These clades had bootstrap values higher than 80. In addition, results indicated that 88.2% of theindividuals are listed as endangered (Lamiopsis tephrodes, Sphyrna mokarran, and Sphyrna lewini), vulnerable (Alopias pelagicus andRhynchobatus australiae), and near threatened (Carcharhinus limbatus, Chiloscyllium griseum, Carcharhinus sorrah, and Carcharhinusbrevipinna), in the International Union for Conservation of Nature (IUCN) Red Data List.

Biophysical and socio-cultural factors have jointly shaped the distribution of global biodiversity, yet relatively few studies have quantitatively assessed the influence of social and ecological landscapes on wildlife distributions. We sought to determine whether social and ecological covariates shape the distribution of a cultural keystone species, the bearded pig (Sus barbatus). Drawing on a dataset of 295 total camera trap locations and 25,755 trap days across 18 field sites and three years in Sabah and Sarawak, Malaysian Borneo, we fitted occupancy models that incorporated socio-cultural covariates and ecological covariates hypothesized to influence bearded pig occupancy. We found that all competitive occupancy models included both socio-cultural and ecological covariates. Moreover, we found quantitative evidence supporting Indigenous pig hunting rights: predicted pig occupancy was positively associated with predicted high levels of Indigenous pig-hunting groups in low-accessibility areas, and predicted pig occupancy was positively associated with predicted medium and low levels of Indigenous pig-hunting groups in high-accessibility areas. These results suggest that bearded pig populations in Malaysian Borneo should be managed with context-specific strategies, promoting Indigenous pig hunting rights. We also provide important baseline information on bearded pig occupancy levels prior to the 2020–2021 outbreak of African Swine Fever (ASF), which caused social and ecological concerns after mass dieoffs of bearded pigs in Borneo. The abstract provided in Malay is in the Supplementary file.