Paige Miller

Portrait of Paige Miller
SEEDS Guide, CBSR Affiliate Researcher, Assistant Project Scientist, Marine Science Institute

My laboratory research pursues increasing our current understanding of the ecology of giant kelp forests by using molecular and population genetic studies to gain new information about the complex relationships of the diverse biotic community that relies on this important primary producer. We are studying the microbiome of multiple kelp (Macrocystis pyrifera) community organisms through Next-Generation Sequencing (NGS) of the 16s amplicon for bioinformatic analysis. My contributions to this work have include successful DNA extraction and preparation of a 16S NGS library for analysis. I currently use multiple bioinformatic tools and pipelines to study the completed NGS library dataset; including RStudio, Phyloseq, Geneious Prime, and Qiime2. Our first paper publishing important findings from this research is currently “In Press” at the journal Limnology and Oceanography Letters. I am also working with Watersipora, an invasive Bryozoan, which we are using as a model of dispersal of nonnative organisms on our coastline. To compare potential differences in dispersal, populations of the native scallop Crassadoma gigantea are also included in the study. At this time we are processing DNA from over 20 populations of these organisms for whole genome sequencing and genotype-by-sequencing analysis with SNPsaurus. We have already received whole genome sequence datasets for scallop, which I am currently running through quality control and using for initial alignments. I am also developing a genetic marker for giant kelp (Macrocystis pyrifera) that could be used in diet studies to detect kelp in the gut of organisms and augment the current understanding of the role of kelp in the food web. Our lab has also just started 2 new studies, one on population genetic structure of Silvetia compressa (AKA rockweed, a brown algae) which is becoming threatened on our coastline, and another using metabarcoding of prey gut contents from 4 species of rock crabs to determine their diet and possible links to domoic acid poisoning.