Population Genetics Structure and Gut Microbiome Metagenomics Analyses of the Endangered Proboscis Monkey (Nasalis larvatus) in Malaysian Borneo.

Norfarhana, Mazlan (2021) Population Genetics Structure and Gut Microbiome Metagenomics Analyses of the Endangered Proboscis Monkey (Nasalis larvatus) in Malaysian Borneo. Masters thesis, UNIVERSITI MALAYSIA SARAWAK.

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Abstract

Numerous researches on population genetics have been done assessing the genetic variation and population structure to understand the effect of evolutionary and environmental changes within a species. Such biological data is significant particularly to the species that are facing threats leading towards extinction. Likewise, the gut microbial composition within their gastrointestinal (GI) tract carries similar importance as much as their genetic variation, ensuring long-term fitness of the animals to better adapt and survive in changing environments. While discovering the gut bacterial diversity aids in the digestion processes, pathogenic bacteria may as well be found that probably harmful to animals and humans. The information obtained will enlighten our interpretation of human-animal conflicts. Hence, to assess those criteria, the endemic proboscis monkey, Nasalis larvatus, is an ideal species model for this research. Nasalis larvatus that are only confined to the island of Borneo, is listed in the IUCN Red List as Endangered with a decreasing population trend. Nevertheless, the biological information on their genetic diversity of the species and gut microbe composition is still incomplete. Its fragmented distribution poses difficulties in gathering genetic samples along with its widespread distribution across Borneo. This study aims to determine the genetic variation and structure of N. larvatus with an emphasis on Malaysian Borneo populations to elucidate its gene flow and to discover the microbe diversity present within the GI tract. For this purpose, genetic materials were obtained from faecal samples, collected across Sarawak and Sabah. The population genetics analyses of N. larvatus were examined using 50 sequences of the 1,434-bp COI gene region of mitochondrial DNA. The COI sequences revealed low genetic variation among N. larvatus populations in Malaysian Borneo, which could be the result of inbreeding pressure that may have occurred due to the absence of population expansion in this species over the last 30,000 years. This is supported in our analysis of molecular variance, which showed that groups of N. larvatus are significantly differentiated possibly due to natural geographic barriers. Whereas, the study on gut microbial composition was carried out using a metagenomics approach. The amplicon sequencing of 16S rRNA successfully generated over two million raw reads of bacteria (98%) and archaea (2%) which covers 4030 OTUs. The diversity and abundance of gut microbiota vary comparing different types of population, e.g.: wild, semi-wild and captive, proven to be affected mainly by their food resource availability, besides the environmental factors which contribute to the diversity. The shift in the microbe diversity observed between habitats becomes evidence of the effect of habitat alteration on the microbes found in the GI tract of N. larvatus. On the other hand, this study also discovered numerous pathogens from the proboscis’ faecal samples and among the most significant findings are from genera Campylobacter, Helicobacter, and Comamonas. The prevalence of the pathogenic bacteria gives an insight into the risk of human interactions with primates which requires attentive management of public health. In brief, the study on population genetics provides baseline information on the genetic diversity among N. larvatus populations in Borneo for the future genetic assessment of the species, and the crucial information on gut microbiome determined the mutualistic relationship between the organisms and the gut microbes that helps the species in the adaptation process. Keywords: 16S rRNA, cytochrome oxidase I, gut microbiota, Nasalis larvatus, population genetics.

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