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Research Projects
Quantitative genetics of blue crabs: Are fisheries making crabs smaller?
Blue crabs (Callinectes sapidus) are a commercially important crustacean worth ~$200 million annually. The fishery is regulated based on crab size, which might apply a pressure on crabs to mature at smaller sizes to avoid being taken by watermen. Indeed, there is anecdotal evidence that blue crabs are smaller today than a few decades ago. In addition, so-called "pygmy females," sexually mature females that are the size of juveniles, are becoming more widespread. This study aims to characterize the genetic architecture of size variation in blue crabs with hopes to develop statistical models to project how fishery pressures might be driving blue crabs to be smaller over time.
Pygmy female.
Whole genome assembly of the shovel bug (Lepidactylus dysticus)
Shovel bugs (Haustoriidae: Amphipoda) are small crustaceans that live on sandy beaches. They have remarkably variable genome sizes, ranging from 2-14 Gb. Past research has identified that a large fraction of the shovel bug genome is devoted to transposable elements that have rapidly proliferated in the past few million years. This project aims to fully sequence one species (Lepidactylus dysticus) which has a genome size ~7 Gb
using MinION long-read sequencing at 30x coverage. With this draft genome in hand, we can begin to sequence more individuals at lower coverage to characterize both repeat and structural variation in hopes of understanding the evolutionary dynamics of rapid genome expansion.
Population variation in gene expression patterns in the mud fiddler crab
Mud fiddler crabs (Minuca pugnax) are ubiquitous on the Georgia coastline. Males have one large, showy claw that they wave at females to get their attention. However, as ectotherms, fiddlers are sensitive to high temperatures and so have a limited display window before they must return to their burrows to cool off. A current hypothesis is that larger claws might help dissipate heat. This study aims to characterize differential patterns of gene expression of the heat shock protein (HSP70) under varying temperature regimes, and whether that variation is correlated to claw size.
Alfred Brehm (1887). Public domain.
sandwrm: Statistical population genetic inference methods
Most of the statistical tools for inferring effective population size (Ne), a critical measure of the rate of genetic drift in a population, are built under the assumption of discrete structure with random mating. However, most species are distributed across continuous landscapes. A goal of the lab is to develop more sophisticated and landscape-aware techniques for accurate estimation of population genetic parameters of interest. These projects will build on an existing R package that Dr. Hancock developed, called sandwrm, which jointly estimates Wright's neighborhood size and the "species-level" effective population size. Future versions will include asymmetric gene flow and linear-population models.