I have a broad interest in investigating how environmental change drives evolution at the population and species level, and in combining genomic and ecological techniques to connect processes at the population level to macroevolutionary patterns. Variation in climatic conditions in space and time is a key driver of speciation and patterns of biodiversity. However, the links between local or regional environmental conditions and resulting patterns in species richness are currently poorly understood—theory predicts more variable climates to lead to diversification in some cases and species extinction or collapse in others, while directional shifts in climate can also lead to either diversification via ecological opportunity or species extinction by their inability to adapt. A population’s ability to evolve and adapt is essential to survival in a changing environment, and I believe that understanding these links between the environment and evolution will be critical for maintaining biodiversity in the coming decades.
Phylogenetics and population history of Lates species in Lake Tanganyika
In the fall of 2016, I began my PhD research focusing on the genomics of evolution and speciation in fish radiations as a member of the Wagner Lab at the University of Wyoming. My research involves investigating the phylogenetics of endemic Lates (Nile perch) species in Lake Tanganyika, including divergence times, phylogenetic relationships, and population histories, as a method of contextualizing current declines in these fisheries-important fishes. In addition to work on Lates species, I am involved in projects researching Lake Tanganyika dagaa (sardines) and local Wyoming fish as well.
Reference bias in SNP-based phylogenetics
Analysis of genomic data requires researchers to make a priori decisions on which data to retain and which to filter out, which can introduce biases into the data used in analyses. It is important to understand biases introduced by these data processing steps, which can substantially affect subsequent analyses. There has been little investigation into biases introduced by the choice of which reference genome(s) to use for aligning reads when using reduced-representation or whole genome resequencing data, yet these early steps may substantially alter inferences by systematically biasing which genetic loci are retained after processing. Together with Dr. Chad Brock, I am using simulations to investigate the effects of the distance from a reference genome to the in-group taxa (i.e., whether the reference genome is an in- or outgroup individual) and the manner in which this interacts with bioinformatic filtering choices made before analysis even begins in earnest.
MINNESOTA WOLF POPULATION GENETIC ASSESSMENT
In this portion of my research, I used microsatellite genotyping to infer the genetic diversity and population genetic structure of the Minnesota wolf population in two sampling years spanning an increase in anthropogenic mortality corresponding to the delisting of wolves under the Endangered Species Act and the onset of legal wolf harvest in Minnesota. I focused on compensation (for increased mortality) in the wolf system via dispersal and immigration, to provide a baseline for answering questions related to the genetic consequences of disturbances-- specifically, anthropogenic mortality-- in this wolf system.
Related publication: Rick, JA, RA Moen, JD Erb, JL Strasburg. 2017. Temporal changes in population genetics and structure of a newly harvested wolf (Canis lupus) population in Minnesota. Conservation Genetics 18(5): 1091–1104
Related presentations: MN/WI Chapter of The Wildlife Society Annual Meeting (February 2015), Midwest PopGen Conference (July 2015), Annual Conference of The Wildlife Society (October 2015), UMD Biology Department Seminar Series (November 2015)
WOLF-COYOTE HYBRIDIZATION IN MINNESOTA
The second part of my research focuses more narrowly on hybridization, a known consequence of reductions in wolf numbers in some areas of the United States and Canada. In this study, I sequenced two uni-parentally inherited genetic markers (one mtDNA, and one on the Y-chromosome) in a subset of the harvested wolves from 2012 and 2013 to assess the evidence for historical or contemporary wolf-coyote hybridization in Minnesota and to analyze how the phylogeography based on these markers compares to the population structure observed using microsatellite loci.
Related publication: Rick, JA, SM Grewenow, RA Moen, JL Strasburg. In prep. Phylogenetics and hybridization of wolves (Canis lupus) in Minnesota using mitochondrial and Y chromosome haplotyping.
Capture-Recapture population assessment in Leech Lake (MN)
As a side project during my master's, I was involved in conducting the lab work for a pilot study using noninvasive capture-recapture to estimate the population size and density of wolves living on the Leech Lake Reservation in Minnesota. This project involved collaborating with tribal biologists and optimizing laboratory processes for working with low-quality and low-quantity DNA sources (ie. wolf scat), processing the first two years of samples for the project.