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Genomic architecture of parallel ecological divergence in Galician Littorina saxatilis ecotypes

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Title: Genomic architecture of parallel ecological divergence in Galician Littorina saxatilis ecotypes
Author: Kess, Joseph Anthony
Department: Department of Integrative Biology
Program: Integrative Biology
Advisor: Boulding, Elizabeth
Abstract: Similar ecological forces have been shown to produce parallel phenotypes, indicating constraint and directionality in evolution. Genomic changes may mirror phenotypic evolution, with limited potential genetic solutions to ecological challenges. The timing and source of gene flow may constrain the variety of available trait architectures that evolve during local adaptation. The distinct ecology and evolutionary history of the marine snail Littorina saxatilis enables study of the genomic patterns underlying parallel ecological adaptations with potential gene flow. In exposed shores of northwestern Spain, morphologically and genetically divergent pairs of ecotypes inhabit overlapping intertidal zones with different environmental selective forces (crab-predation, wave-action). To survey genome-wide variation between ecotype pairs in three populations, I developed a novel double-digest restriction associated DNA sequencing (ddRAD) protocol. I used this method to genotype L. saxatilis ecotypes, to test whether shared divergence corresponded to observed population structure. I identified substantial sharing of divergent genomic regions between close sites (30%), which declined with distance (8-13%). Analyses of population structure revealed isolation by distance determining variation between groups, but a stronger role for local ecotype differentiation than previously identified. Population clustering indicated isolation between ecotypes may be more extensive than previously estimated with other molecular markers, as only 12 of 166 putative hybrids exhibited recent admixture. I then measured shell variation between ecotypes to conduct genome-wide association analysis (GWA), to determine the role of potential gene flow in shaping genetic architecture. I identified variation in shell shape corresponding to ecotype differentiation, but also uncovered variation in shell shape associated with distinct populations. Polygenic trait architectures with many small effect alleles were common among 137 identified loci associated with shell shape variation, but a subset of these loci exhibited high levels of pleiotropy, and large effect size alleles corresponding to variation in shell morphology associated with ecotype survival. My work in this thesis aids in elucidating the role of gene flow in shaping genomic evolution. I demonstrate that possibility of gene flow between populations may affect rates of repeatable genomic divergence, but potential for maladaptive gene flow between ecotypes may not be the driving factor in genetic architecture evolution.
Date: 2017-10-06

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