Evolution and recent adaptation of the domestic water buffalo

Davies, Luke 2024. Evolution and recent adaptation of the domestic water buffalo. PhD Thesis, Cardiff University. Item availability restricted.

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Abstract

Domestication has underpinned the development of human civilization. A growing human population and increasingly complex societies have created intensification pressures upon the livestock industry. Favouring of highly productive breeds at the expense of the loss of locally adapted rarer breeds will have implications for future food security due to the loss of genomic resources. With the recent availability of accessible genomic resources for domestic water buffalo (Bubalus bubalis), this thesis seeks to contribute towards quantifying their genetic variation and adaptive potential. In Chapter Two, ancestry of two UK populations was tracked to Italian origins and was shown to have retained the majority of genetic diversity since importation. Such levels of genetic diversity provide the opportunity for effective selection programmes focused on production-based QTLs. Chapter Three analysed and compared novel data from an Indian murrah buffalo population to wider global populations to detect selective sweeps indicative of recent selection. Loci under selection in non-Indian murrah were associated with genes linked to draught and meat traits instead of the typical focus on milk. SNP array data is incredibly useful for genomic selection; however, inherent ascertainment bias creates challenges for evolutionary studies. Chapter Four attempted to understand the bias in the AxiomTM Buffalo Genotyping Array when analysing river and swamp buffaloes. Results showed that patterns of variation were inconsistent between river and swamp species, and between array and sequencing data. Shared polymorphic markers in the array are likely ancestral SNPs and targets of balancing selection, thus distorting evolutionary inferences between the two species. Chapter Five modelled the evolutionary history of domestic buffaloes revealing further support for a Pleistocene divergence of river and swamp species. Dispersal of river buffalo from India is likely linked to maritime trade early in the Common Era. Furthermore, artificial selection appears to be a driving force for regions of divergence between river and swamp buffalo.

Item Type:	Thesis (PhD)
Date Type:	Completion
Status:	Unpublished
Schools:	Biosciences
Subjects:	Q Science > Q Science (General)
Date of First Compliant Deposit:	13 December 2024
Last Modified:	13 Dec 2024 14:46
URI:	https://orca.cardiff.ac.uk/id/eprint/174719

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