PATTERNS OF GENOMIC DIVERSITY WITHIN AND BETWEEN CRYPTIC SPECIES OF FIELD VOLES AND SURFCLAMS
Fletcher, Nicholas Keech
Understanding how genetic diversity is distributed within and between species is a fundamental goal of evolutionary biology and conservation. Cryptic species are an especially interesting challenge to study in this context as they lack the obvious morphological differentiation that provide clues to how genetic diversity may be partitioned. In this dissertation, I analyze genetic diversity in two unique cryptic species groups, voles in the genus Microtus and surfclams in the genus Spisula, at multiple levels of sampling both genomically and geographically. First, I analyze genome-wide single nucleotide polymorphism (SNP) data paired with environmental nice modeling (ENM) to understand how isolation glacial cycling has driven divergence in three cryptic European vole species formerly classified as Microtus agrestis. I find high levels of divergence distributed across the whole genome, with little evidence of ongoing gene flow well as divergence in environmental niches between species. There is a high level of predicted overlap between the niches of M. rozianus and M. lavernedii that has not resulted in any evidence in gene flow between these groups. These cryptic vole species have evolved high divergence across the genome in isolation during glacial cycling. Secondly, I use a dataset including microsatellite markers, mtDNA, and nuclear intron loci to examine patterns of genetic diversity in cryptic subspecies of the Atlantic surfclam, Spisula solidissima. Recently, isolated populations of the lesser-known southern Atlantic surfclam, S. s. similis, were found far north in the range of S. s. solidissima, a commercially important northern subspecies. To test a hypothesis of recency and isolation in the north, this newly found population of S. s. similis was sampled to provide the first population genetic comparison to a population in Georgia, as well as contrasts with S. s. solidissima. These recently discovered northern populations of S. s. similis showed a slight reduction in genetic diversity but high levels of connectivity with southern populations. Genetic differentiation was weak and only significant for microsatellite data. Based on coalescent modeling, I conclude that the northern S. s. similis populations most likely represent a post-glacial expansion, and it is hypothesized that there are unidentified stepping-stone populations connecting populations throughout its range. Finally, I explore a characteristic pattern of genomic variation within many species in Britain, dubbed the Celtic Fringe, which is generated by the two waves of colonization after the Last Glacial Maximum. Here I analyze low-coverage whole genome sequencing and full mitochondrial genomes from 11 populations and 124 individuals of the short-tailed field vole (Microtus agrestis), to explore patterns of genome-wide introgression and divergence across the Celtic Fringe. I find high genome-wide divergence between our northern and southern populations, with a strong signature of isolation by distance north to south. There is also a signature of mito-nuclear divergence in my genetic data, and the southern mitochondrial haplotype has not introgressed as far north as the southern nuclear DNA. I find no signature of selection in the data, and my results point to genetic drift the major evolutionary process driving divergence genome-wide between our populations. This study offers insights into the evolutionary and demographic processes that drive Celtic Fringe patterns in Britain and have led to contemporary patterns of genetic diversity after climatic cycling.
Cryptic Species; field vole; Genomics; Glacial Cycles; Population Genetics; surfclam
Searle, Jeremy B.
Hare, Matthew P.; Therkildsen, Nina Overgaard
Ecology and Evolutionary Biology
Ph. D., Ecology and Evolutionary Biology
Doctor of Philosophy
Attribution-NonCommercial-ShareAlike 4.0 International
dissertation or thesis
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