Haplotype Network and Molecular Evolution of Clarias batrachus in Sumatera Based COI Gene.

<b>Background and Objective:</b> <i> Clarias batrachus</i> is native to Asia, Sumatra was one of the islands that were divided due to the division of Sundaland because of a transgression event. The Bukit Barisan Mountains divide Sumatra into two parts: West and East. Therefore, it is important to research <i>C. batrachus</i> phylogeography. One of the mtDNA genes that can be used for phylogeographic is the CO1 gene. This study examined the association between geographic isolation in Sumatra's Eastern and Western watersheds and the phylogenetic relationships between <i>C. batrachus</i> populations in Sumatra and other Southeast Asia using the CO1 gene. <b>Materials and Methods:</b> <i>Clarias batrachus</i> samples were collected from five populations 7 (Mungo River, Sinamar River, Agam River, Anai River and Lubuak Paraku River) from West Sumatra. The method of this research used the molecular method. The DNA isolation based on the COI gene follows the Invitrogen PureLink^TM Genomic DNA Mini Kit protocol. Haplotype network using software Popart v.1.7 and molecular evolution analysis using software MEGA. <b>Results:</b> Based on a total of 28 sequences (including comparisons and outgroups) with 504 base pairs of the CO1 gene from <i>C. batrachus</i>, three haplogroups and 19 haplotypes were identified using the haplotype analysis. Speciation events between haplogroup 1 estimates are 0.41 Mya haplogroup 2 estimates are 0.50 Mya. <b>Conclusion:</b> The separation of Sundaland and the separation in Sumatra's Eastern and Western watersheds affects the kinship relationship of these populations with variations in subspecies level.

Phylogenetic Relationships of Sun Bear (Helarctos malayanus) Based on Mitochondrial DNA from Sumatra and Other Southeast Asian Regions.

<b>Background and Objective:</b> The <i>Helarctos malayanus</i> is the sole bear species-living in Indonesia (Sumatra and Borneo). The available biological data for sun bears (<i>H. malayanus</i>) in Sumatra is limited, especially for morphological and genetic data. A morphological approach is difficult to do. Therefore, a molecular approach is the most likely choice. Phylogenetic analysis was carried out on <i>H. malayanus</i> in Central Sumatra (Dharmasraya, South Solok and Riau) using the Cytochrome B gene. <b>Materials and Methods:</b> Blood samples from three individuals of <i>H. malayanus</i> were obtained at the Sumatran Tiger Rehabilitation Center, Dharmasraya. Three <i>H. malayanus</i> Central Sumatra sequences and 62 GenBank sequences were used in the analysis. The DNA sequences were analyzed using the DNA Star, AliView, Bioedit, DNA SP, haplotype network, IQ Tree and MEGA software. <b>Results:</b> Forty-one haplotypes were identified in 65 sequences, with 17 haplotypes belonging to <i>H. malayanus</i>. Haplotype network analysis divides <i>H. malayanus</i> into Haplogroup I (Sundaland) and Haplogroup II (Mainland). All individuals of <i>H. malayanus</i> in Central Sumatra have the same haplotype as Peninsular Malaysia sequence. The sun bear (<i>H. malayanus</i>) has a monophyletic relationship with other bear species. The <i>H. malayanus</i> has a higher genetic distance between the two lineages (1.0-2.3%) than the genetic distance within the subpopulations of each lineage. <b>Conclusion:</b> The study results supported sun bear (<i>H. malayanus</i>) divided into two different lineages: Mainland (subcluster 1) and Sundaland (subcluster 2 and 3). The geographic isolation causes the absence of gene flow, which results in high genetic distance between sun bears (<i>H. malayanus</i>) in Sundaland and Mainland lineages.

Faecal DNA to the rescue: Shotgun sequencing of non-invasive samples reveals two subspecies of Southeast Asian primates to be Critically Endangered species.

A significant number of Southeast Asian mammal species described in the 19th and 20th century were subsequently synonymized and are now considered subspecies. Many are affected by rapid habitat loss which creates an urgent need to re-assess the conservation status based on species boundaries established with molecular data. However, such data are lacking and difficult to obtain for many populations and subspecies. We document via a literature survey and empirical study how shotgun sequencing of faecal DNA is a still underutilized but powerful tool for accelerating such evaluations. We obtain 11 mitochondrial genomes for three subspecies in the langur genus Presbytis through shotgun sequencing of faecal DNA (P. femoralis femoralis, P. f. percura, P. siamensis cf. cana). The genomes support the resurrection of all three subspecies to species based on multiple species delimitation algorithms (PTP, ABGD, Objective Clustering) applied to a dataset covering 40 species and 43 subspecies of Asian colobines. For two of the newly recognized species (P. femoralis, P. percura), the results lead to an immediate change in IUCN status to Critically Endangered due to small population sizes and fragmented habitats. We conclude that faecal DNA should be more widely used for clarifying species boundaries in endangered mammals.