Download Using genomics to understand megalopae abundance to predict

Case Study: Using genomics to understand how megalopae abundance
can be used to predict future commercial catches of Dungeness Crabs
(Cancer magister) in Oregon
Contact:

Kathleen O’Malley ([email protected])
Topic:
Genomics
Background:
Over the past six decades, there have been large fluctuations in commercial landings
of Dungeness crab off the west coast of the United States. Given the continuous increase in
number of crab pots fished throughout this period, it is believed that large fluctuations in
landings are likely due to varying ocean conditions (i.e. water temperature, food availability,
and ocean currents) and not a result of harvest patterns.
Understanding how ocean conditions influence larval dispersal and ultimately adult
recruitment of Dungeness crab is of interest to researchers, fishery managers, and
commercial fishermen. The timing of Dungeness crab life history events varies with
seasonally changing ocean conditions. In the California Current (CC) system, Dungeness
crab mate in the spring and females store sperm until egg extrusion in the fall. Egg
development takes three to four months with hatching occurring near the coast in the
winter (Strathmann 1987). The larval period, which consists of five zoeae stages and a
megalopal stage, ranges from three to four months. As larvae develop, they are found
progressively further from shore. By the megalopal stage, larvae are typically found in CC
waters, seaward of the continental shelf, and often >100 km from shore. To survive to
adults, megalopae must migrate from offshore back to the coast and settle in shallow water
(Wild & Tasto 1983). In Oregon, megalopae begin returning to shore, on average, in April.
For 12 years (1997-2001, 2006-2012), Dr. A. Shanks (University of Oregon) and
colleagues have measured the daily abundance of Dungeness crab megalopae in Coos Bay,
Oregon to explore the possibility of predicting the commercial catch of Dungeness crabs
from the abundance of returning megalopae and evaluate how inter-annual variation in
ocean conditions impact megalopae abundance. One notable observation throughout these
studies is how long the megalopae settlement season lasts. In many years, megalopae are
captured from early spring through the entire summer and some years into the fall.
However, along the coast from California to Washington, peak larval release occurs between
January and February. Considering a 5-month larval period, all megalopae should settle by
July. Alternatively, peak larval release in British Columbia occurs in April and even later
further north (Strathmann 1987) which may allow southward currents to transport larvae
hatched in Canadian waters to Oregon.
Preliminary results from a Dungeness crab population genetics study provide some
evidence for reduced genetic connectivity between adult Dungeness crab sampled off the
Oregon coast and Dungeness crab sampled off the coast of British Columbia (O’Malley et al.
In prep). To advance this research, we have initiated a two-year study to examine fine-scale
patterns of genetic connectivity among adult Dungeness crab sampled in the California
Current system. To date, no study has examined the genetic diversity of recruiting
Dungeness crab megalopae. However, with the establishment of a baseline genetic data set
for adult Dungeness crab in the California Current and evidence for genetic differentiation
between Oregon and British Columbia Dungeness crab, we are now able to test the
hypothesis that late season pulses of megalopae observed in Oregon originate from
Canadian waters and tend to increase during years in which the Pacific Decadal Oscillation
(PDO) is negative. The primary objectives of this study are to 1) examine intra-annual
genetic diversity of recruiting megalopae using a genomic approach and 2) evaluate
the influence of ocean conditions (i.e. timing of spring transition, PDO, and upwelling)
on the genetic diversity of recruiting megalopae. Results from this study will be used to
improve our understanding of larval dispersal and recruitment and ultimately enhance our
ability to predict future commercial catches of Dungeness crab in Oregon.
Existing Data:
Adult Dungeness crab genetic baseline, time series of adult landings, time series of
megalopae abundance, oceanographic data (e.g. timing of spring transition, PDO phase,
amount of upwelling), Lagangrian particle tracking model for the CC (Rasmuson et al. in
prep)
Data Needs:
Whole-genome sequencing of pools of early (N = 100) and late recruiting megalopae (N =
100) collected in 2014 following the approach described by Scholtterer et al. (2014).
Collection of a second year of early and late recruiting megalopae samples to study interannual variation.
Desired Area(s) of Expertise for Students:
Genomics, Computer Science, Statistics, Ocean Modeling
References
O’Malley KG, Jackson TM, Jacobson DP, Roegner GC (In prep) Assessing population
connectivity in a widely dispersing marine invertebrate.
Schlotterer C, Tobler R, Kofler R, Nolte V (2014) Sequencing pools of individuals – mining
genome-wide polymorphism data without big funding. Nature Reviews Genetics 15:
749-763.
Shanks AL, Roegner GC (2007) Recruitment limitation in Dungeness crab populations is
driven by variation in atmospheric forcing. Ecology 88:1726–1737.
Shanks AL, Roegner GC, Miller J (2010) Using megalopae abundance to predict future
commercial catches of Dungeness crabs (Cancer magister) in Oregon. California
Cooperative Fisheries Investigations Report 51:1–13.
Shanks AL (2013) Atmospheric forcing drives recruitment variation in the Dungeness crab
(Cancer magister), revisited. Fisheries Oceanography 22: 263-272.
Strathmann MF (1987) Reproduction and Development of Marine Invertebrates of the
Northern Pacific Coast. University of Washington, Seattle.
Wild PW, Tasto RN (1983) Life history, environment, and mariculture studies of Dungeness
crab with emphasis on the central California fishery resource. California Department
of Fish and Game, Fish Bulletin 172: 1-352.