Fish population genomics

Fish are entertaining to watch, fun to catch, and can be delicious to eat. However, uninformed fisheries management strategies that fail to consider population structure can result in severe consequences for reproductive capacity and stock rebuilding. My lab uses genomic data to deepen our understanding of fish population dynamics, with a particular focus on data that will be relevant to conservation and management.

Atlantic Cod

Gadus morhua

Atlantic cod has been and continues to be an important economic resource in the North Atlantic. Since 2000, Atlantic cod total catch in New England has decreased by approximately 6-fold resulting in a significant economic and ecosystem loss. Within the species there is evidence of the evolution of substocks that differ in their migratory behavior, spawning time, or salinity tolerance. Cod present an interesting system for genomic research because these differences have been localized to multiple inversions within their genomes.

We have used whole-genome sequencing to study the genomic basis of differences between ecotypes in the Gulf of Maine and Iceland. This project was started by my former graduate student Sara Schaal and is being prepared for publication.

Now, we are really digging into these genomic sequences and using them to test theoretical predictions regarding the evolution of inversions. Undergraduate Leila Curtis is cataloging all the structual variants in the cod genome as part of their Honor's Thesis.

Collaborator: Sara Schaal (NOAA)

Gulf of Maine Collaborators: Jon Grabowski (Northeastern University), Graham Sherwood (GMRI), Lisa Kerr (GMRI)

Graduate students, dreaming about catching cod.

Genomes are a lot like the Matryoshka, or Russian Doll. There are chromosomes within individuals, structural variants within chromosomes, and single nucleotide polymorphisms within structual variants. We develop new statistical methods to summarize and visualize this data.

Black Sea Bass

Centropristis striata

Warming seawater temperatures in the Gulf of Maine has resulted in the northern range of some fishery species to move further northward. One such species that is shifting rapidly is the northern stock of black sea bass, which historically ranged from Cape Hatteras to Cape Cod, but is now common in the Gulf of Maine (GOM). While this range expansion presents a new opportunity for fisheries, it has also been a source of contention because resource managers have struggled to keep pace with rapidly shifting species distributions in New England and other regions globally where coastal seawater temperatures are rising rapidly.

We previously received funding from NOAA to quantify population genetic structure of black sea bass and the fisher perceptions of black sea bass population increases. This information will be crucial to ongoing efforts to manage black sea bass at the northern edge of their range.

Currently, this project is led by Remy Gatins (former lab postdoc, currently faculty at Northeastern University), who is using this rapid range expansion to test evolutionary predictions of increased deleterious mutation load in the expanded range.

Collaborators: Jonathan Grabowski and Steven Scyphers (Northeastern University), Marissa McMahan (Senior Fisheries Scientist, Manomet), Remy Gatins (Northeastern University)

Previous research

Pacific Rockfish

Sebastes spp.

Many species of Pacific rockfish are long-lived (50-100 years) and have high catch-and-release mortality, characteristics that makes it difficult for them to recover from overfishing. Many rockfish species have suffered severe declines since the 1980’s due to fishing, which has spurred several recent management efforts through marine reserves and closures in both the US and Canada. Understanding both how rockfish populations are connected via dispersal and how the reproductive success of rockfish populations depends on the ocean environment is crucial for recovery efforts, however little is still known about these processes in rockfish.

We studied the population dynamics of Sebastes melanops (black rockfish, pictured left) and other rockfish species in Barkley Sound, British Columbia and across the US-Canada border from 2005-2014. We used Standard Measuring Units for the Recruitment of Fish (SMURF’s) and visual surveys to monitor rockfish recruitment. Our previous research has unexpectedly shown that the abundance of recruits was not correlated with the number of parents that produced them. We explained this counterintuitive result by showing how oceanographic processes shaped the reproductive success of adults and survival of larvae (Lotterhos and Markel 2012). In a larger scale study we found that Rockfish Conservation Areas in Canada and the US were largely unconnected by dispersal due to a lack of reserves near the US border (Lotterhos et al. 2014). We have also synthesizing spatial recruitment data with data on adult abundances to test hypotheses about the spatial and habitat drivers of abundance (Lotterhos and Markel 2017), and about the importance of strong year classes for the fishery (Haggarty et al 2017).

Did you know that black rockfish can live to be over 50 years old?

Bluefin tuna

Thunnus thynnus

In 2024, we started a new project with The Bluefin Collaborative, a non-profit organization that works with fishers to advance science for Bluefin Tuna. Bluefin Tunas are one of the fastest fish in the ocean and support an important fishery in the North Atlantic. We are currently setting the foundation for a state-of-the-art citizen science sampling program with interactive apps for data collection. Our program will collect and store genomic DNA from tuna where they are caught in the field. These samples will enable genomic studies on population structure, population assignment, close-kin mark recapture, responses to climate change, and tests of evolutionary theory.

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