The Role of Epigenetic Modications and Microbiome Evolution in Bovid Adaptation to Environmental Changes

Abstract

Ancient DNA (aDNA) techniques have demonstrated its power to reveal past events and reconstruct the evolutionary histories of animals. However, many questions regarding the rapid adaptation of animals cannot be solely explained by genomic evidence and thus remain to be further investigated. Gut bacterial communities (microbiota) perform essential functions for their hosts, including nutrient synthesis, dietary toxin degradation, and host immunity development. Epigenetics, including DNA methylation and microRNAs (miRNAs), participates in the regulation of the gene expression as well as many critical cellular processes. These non-genomic mechanisms tend to be highly dynamic and susceptible to internal (i.e., genetics) and external factors (i.e., environmental cues). It is possible that microbiota alterations and epigenetic modifications swiftly transfer external cues to animal phenotypic alterations and exert durative influence on animal fitness and adaptation, whereas the evidence from modern animal models remains scarce and controversial. The most recently developed aDNA techniques allowed the recovery of microbiomic and epigenomic information from ancient animal remains. In this thesis, I employed advanced ancient DNA (aDNA) techniques to explore the role of nongenomic mechanisms in bovid adaptation to environmental changes over an evolutionary timescale. Two bovid taxa, Myotragus and Bison, were used for case studies to explore the possible roles of microbiota and epigenetics in animal adaption. In the first case study, I was able to find evidence suggesting the gut microbiota of Myotragus facilitate its adaptation to a toxic diet; in the second case study, the potential methylation hotspots responding to mammal-environment interactions were identified. Furthermore, novel protocols and bioinformatics tools were developed and optimised to retrieve ancient epigenetic and microbial information from extremely degraded and contaminated DNA sources. Overall, these studies suggest the microbiota and epigenetic modifications play a role in the adaption to the environment of the past animals. These findings also highlight the potential of aDNA techniques for resolving long-standing evolutionary questions.