Landscape genomics of tropical high altitude plant species

Mastretta-Yanes, Alicia (2014) Landscape genomics of tropical high altitude plant species. Doctoral thesis, University of East Anglia.

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Abstract

Changes to species distributions involve demographic processes that occur over generations and affect allele frequencies within populations, leading to patterns of genetic restructuring. The specific genetic structuring patterns that will be observed as a consequence depend on explicit geographical features, such as topography and latitude. Over the first decades of phylogeography, the effect of climate history and geography on species genomes was examined at low resolution with DNA sequences and other traditional molecular markers. However, During the last five years it has become feasible to obtain genomic data for non-model organisms and large sample sizes.
The present thesis spans the transition years between phylogeographic studies being restricted to low resolution molecular markers, and new methods facilitating the generation of genomic data for non-model species. As such, this thesis focuses on two main points. First, on the methodological aspects of utilising double digest RAD-seq (ddRAD) for individual-based population genetics and phylogeography of plant species. Second, on applying the obtained data to examine one of the classic. but as yet not fully explained, biodiversity patterns: the biodiversity excess within tropical mountains.
The main contributions of this thesis at the methodological level are; (1) demonstrating the utility of DNA replicates for the estimation of genotyping error and optimisation of de novo assembly; (2) proposing a method for identifying paralogous loci resulting from recent gene duplications; and (3) showing that such logi provide a measure of population differentiation. Regarding the drivers of biodiversity excess within tropical mountains, I used landscape genomic analyses and ddRAD data to examine two plant species from the alpine grasslands of the Transmexican Volcanic Belt. As a main result, this thesis supports from a population-level perspective that tropical mountains; (1) allow for long-term in situ population persistence; and (2) promote population differentiation as a function of topographic isolation.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: Brian Watkins
Date Deposited: 02 Feb 2015 17:17
Last Modified: 03 Feb 2015 16:42
URI: https://ueaeprints.uea.ac.uk/id/eprint/52157
DOI:

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