Investigating the Evolutionary History of Catarrhine Primates using Whole Genome Data

by Lakshmi Seshadri
Doctoral thesis
Date of Examination:2024-12-11
Date of issue:2025-05-08
Advisor:Prof. Dr. Lutz Walter
Referee:Prof. Dr. Lutz Walter
Referee:Prof. Dr. Rolf Daniel
Persistent Address: http://dx.doi.org/10.53846/goediss-11238

 

 

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Abstract

English

The aim of my PhD project is to investigate the evolutionary history and adaptive potential of diverse catarrhine primates using whole genome sequencing data, with a focus on Bale monkey (Chlorocebus djamdjamensis) and baboons (Papio sp.). Advancements in high- quality reference genomes and sequencing data have enabled extensive genetic studies over the past decade. In chapter 1, I used whole genome sequence of the Bale monkey (C. djamdjamensis) along with data of the other five Chlorocebus species. The Bale monkey is a food specialist (primarily bamboo) of the Ethiopian highland, and occurs in two disjunct populations, one in continuous forest (CF) and the other in fragmented forest (FF). Phenotypic and mitochondrial studies suggest that the population in the fragmented forest has experienced introgression from paraptric species. I reconstructed and evaluated phylogenetic relationships to trace the evolutionary history of Bale monkeys. Using various statistical methods, I found evidence for gene flow between FF and C. aethiops. Additionally, I performed gene enrichment analysis to identify genes and KEGG pathways potentially involved in adaptation to high-altitude and bamboo metabolism. Our findings revealed SNPs in genes such as EPAS1 (altitude adaptation), TST, and MPST (cyanide detoxification) and TAS2R16 (bitter taste receptor) which may contribute to these adaptations. In chapter 2, I contributed to the Baboon Genome Project, which investigates the genome wide co-ancestry resulting from both recent and ancient male-driven reticulation in baboons. Baboons consist of six species known for extensive hybridisation, both ancient and recent, leading to a complex evolutionary history marked by repeated introgression and gene flow across Africa. I worked on identifying gene flow events and also constructing consensus phylogenetic trees using window-based methods from 118 male X-chromosome data representing 18 populations. My thesis also explores genetic diversity and the genetic basis of adaptive evolution in non-human primates. Over the past decade, the availability of high-quality reference genomes and sequencing data has grown exponentially, facilitating numerous genetic studies. I therefore aim to provide a brief overview of current knowledge on genetic diversity and the genetic basis of adaptive evolution in non-human primates including the Bale monkey and baboons, while also highlighting the lack of genomic studies in certain primate groups, such as Strepsirrhini.
Keywords: Genomics; Whole Genome; Hybridization; Introgression; Genomic Adaptations
 
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