Examining microspatial genetic variation in an intertidal marine invertebrate, a commercial fish species, and a benthic invertebrate community [electronic resource]

As the pace of environmental change increases, it becomes more important than ever to understand the processes of natural selection that lead to adaptation to environmental change. Local adaptation, or the differential adaptive response of subpopulations within a species diverging in adaptive traits across an environmental gradient, is thought to be an important mechanism in the preservation of genetic diversity within species, as different alleles will be most fit (and thus under positive selection) in different portions of a species range. It is the maintenance of this standing genetic variation that is the fuel for rapid adaptation to new environmental conditions, but the geographic location of these differently adaptive alleles is a critical component of the adaptability of populations. When environmental conditions change significantly and newly adaptive alleles are located far away, it may take several generations for dispersal to bring significant numbers of these alleles to fill in the newly changed environment. However, if small-scale variability in environmental conditions occurs within a 'local' habitat, then adaptive alleles may be much closer to the new environment, and adaptation may occur much faster. While we are beginning to understand the processes of local adaptation in marine environments, little is known about how genetic diversity distributes across environmental variability at very small spatial scales. In Chapter 1, I examined the spatial scale of genetic variability in the California mussel, Mytilus californianus, at the spatial scale of one to two meters. By using transcriptomic techniques, we identified a suite of candidate single nucleotide polymorphisms (SNPs) that appeared to have different frequencies of alleles between mussels living in sun-exposed and shaded beds within the same region of the intertidal zone. Further validation of these candidate loci revealed many false positive outlier identifications, though genetic differentiation remained within a critical thermal tolerance gene, HSP70kDa 12B, at these spatial scales. In Chapter 2, I extend the concept of small-scaled spatial genetic variability to spatiotemporal genetic variability in the Atlantic cod, Gadus morhua, within the Gulf Maine. Using deep DNA sequencing of a small number of individuals, we showed that three previously known 'islands of divergence' in cod that have been examined across ocean basins and between ecotypes of cod are present and segregating between mating cohorts within the same bay. Using the newly assembled genome, we go further and describe the genic content of those islands of divergence and argue that they may be supergenes, as one of these regions is highly enriched for genes coding for chromatin structuring proteins and chromatin alteration genes. Lastly, in Chapter 3 I expand the concept of genetic variability to include community variability at small spatial scales, by investigating the community structure of coralline algae encrusted cobbles sampled within the same kelp forest canopy in Pacific Grove, CA. By using both morphological taxonomic techniques and DNA metabarcoding on the same samples, we were able to compare both of these methods directly. We found that, while all samples were dominated by malacostracans and polychaetes, subtle differences remained between samples taken at different depths within the same 'community.' Together, these studies show that the spatial scale of sampling can make significant differences in the findings of both intra-species genetic diversity and community composition, and environmental variability at these small scales should be taken into account when sampling at these scales.

Keywords: Biology.
Advisor: Palumbi Stephen R.
Denny Mark W.
Peay Kabir
Somero George N. advisor. Thesis advisor