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Current Research Projects

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Uncovering the genomic architecture of Atlantic cod ecotype evolution in the Gulf of Maine and Iceland

Supervised by Dr. Katie E. Lotterhos, Northeastern University

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In the Gulf of Maine, we have three putative groups: coastal-red cod, olive spring-spawning cod, and olive winter-spawning cod. Initial work has shown genetic differences between spring and winter-spawning olive cod, but how red cod are diverging from these two olive spawning groups and whether these groups correspond to resident and migratory cod found elsewhere is still not well understood. In Iceland, two genetically distinct ecotypes exist: frontal (offshore) cod and coastal cod. However, little work has been done using high-resolution genomics methods in conjunction with phenotypes and environmental conditions to determine what are the major drivers of their evolution. Additionally, by comparing across geographic locations we can identify whether the same suite of markers underlie ecotype evolution between populations.

 

In our study, frontal and coastal Atlantic cod samples were collected from two geographic locations in Iceland (see map below) and red cod and olive cod were collected from two locations in the Gulf of Maine (GOM). Within the GOM, we additionally split the Massachusetts Bay olive cod into spring and winter spawners. For each sample, fin

Understanding the way in which populations are distributed in space and revealing the drivers of population assembly is a major priority of evolutionary and conservation biology. In Atlantic cod (Gadus morhua), intra-specific variation has been identified in the form of migratory and resident life-history strategies within many populations across the species range and recent molecular work has uncovered that these are genetically distinct forms (i.e. ecotypes) of the species in certain populations.

clips were preserved for genomic analysis, otoliths were extracted for aging, growth and stable isotope analysis, photographs were taken for morphometric analysis, and gonad and liver weights were taken for gonadosomatic and condition indices, respectively.

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With these data, we intend to characterize phenotypic variation both within the two geographic locations and between them. These data will then be used to carry out a genome-wide association study (GWAS) to identify regions in the genome linked to variation in the phenotypes. In addition, we will characterize the thermal history of each individual using oxygen stable isotopes collected from the otoliths. These data will be used to conduct a genetic-environment analysis to determine regions in the genome linked to variation in thermal environment.

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Historic reconstruction of the thermal and trophic conditions experienced by Icelandic cod ecotypes over the last millennial 

Supervised by Dr. Katie E. Lotterhos, Northeastern University Marine Science Center 

Collaboration with Drs. Guðbjörg Ásta Ólafsdóttir, Ragnar Edvardsson, and Steven Campana, University of Iceland and Dr. Jessica Lueders-Dumont, Princeton University 

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Atlantic cod ecotypes are found within populations across the distributional range of the species. However, little is known about the environmental conditions experienced by each ecotype both in contemporary samples and historically. Characterizing the environment experienced by a highly-mobile fish species can be a challenge due to the range in conditions that could potentially be experienced by a single individual throughout its lifetime. The otoliths or "earstones" of a fish are an imporant resource that researchers can use to circumvent this issue. An otolith grows similarly to tree rings where daily growth rings are laid down that capture the chemical composition of the organisms surroundings at the time. Using otolith microchemistry, we can measure specific isotopic signatures at yearly increments in the otolith to determine what temperature water a fish experienced throughout ontogeny and whether the trophic level varies between ecotypes through time. 

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Using a set of >150 historic Icelandic cod otoliths that we collected from middens, trash heaps, found beside historic fishing houses in the Westfjords of Iceland, we are reconstructing the ecotype composition (otolith shape analysis), thermal environment (δ  O), trophic level (δ  N) and growth rates of Icelandic cod over the last 1000 years. By identifying the thermal conditions experienced by individuals at multiple life-stages and through this historic time series we are able to shed light on stage-specific selection pressures and the potential role of temporally-stable, thermal-selection pressures on the evolution of ecotypes in sympatry. 

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Genetic data reveal non-local juvenile recruitment and variable seasonal movement of a highly mobile marine fish across Alaska
Supervised by Drs. Wes Larson and Ingrid Spies, NOAA Alaska Fisheries Science Center 

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Whole genome sequencing can be prohibitive costly for large-scale studies on hundreds to thousands of individuals. However, targeted sequencing methods (e.g., amplicon sequencing) provide a powerful and cost-effective alternative by scaling down the number of genomic markers and scaling up the number of samples for efficiently answering many research questions. In this work, we developed a Genotyping-in-the-Thousands by Sequencing (GT-seq) panel for Pacific cod (Gadus macrocephalus) ​in order to both address questions related to movement dynamics across ontogeny in Pacific cod and also provide a useful genomic resource for future questions related to Pacific cod. The panel was designed based on the findings of four unique genetic stocks present in whole-genome sequencing data from spawning adults throughout the Gulf of Alaska and Bering Sea. The panel that identifies these stocks at >95% confidence was then applied to individuals of unknown origin to address two major research questions: 1) what is the seasonal variation in the stock-specific adult habitat use? and 2) what is the stock-specific habitat use of juvenile Pacific cod throughout the GOA? This work has identified little seasonal variation in mixing of genetically distinct stocks with the exception of two stocks mixing in the Northern Bering Sea in the summer (non-spawning) season. At the juvenile stage, we have highlighted year-to-year variation in juvenile movement between regions in the Gulf of Alaska that may be due to variation in oceanographic conditions transporting larvae throughout the Gulf of Alaska.


Exploration of How Historical Climate Events Impacted Pacific Cod (Gadus macrocephalus) Evolution and Fishery Use
Supervised by Drs. Courtney Hofman, Catherine West, and Ingrid Spies, University of Oklahoma, Boston University, and NOAA Alaska Fisheries Science Center ​

The world's oceans are experiencing unprecedented changes in environmental conditions, and the impacts these changes have on marine species are often unknown and difficult to predict. However, by looking into the past and evaluating how populations have responded to previous environmental changes, researchers can better understand and predict how species will fare in a changing ocean. These research efforts are especially vital for species with both ecological and economic importance. Pacific cod (Gadus macrocephalus), an apex marine predator found throughout the North Pacific Ocean, has been an important fishery for coastal communities for thousands of years, and previous archeological studies suggest that Pacific cod in the western Gulf of Alaska (GOA) have fluctuated in availability over this time period. However, the causes, magnitude, and evolutionary consequences of these fluctuations are not well understood. Therefore, the main objective of this research project is to investigate how two late Holocene climatic events affected Pacific cod populations throughout the last millennium. We are testing the hypothesis that these climatic events caused significant population declines followed by population recovery, evidenced by loss of genetic diversity, increased genomic adaptation, trophic level shifts, and variation in the seasonality of fishery use. 

We are combining zooarchaeological, archaeogenomic, and isotopic data from Pacific cod bones excavated from archaeological sites in three locations across the North Pacific: Prince Edward Island in the Eastern Gulf, Mink Island in Amalik Bay near the Kodiak archipelago in the western GOA, and Amchitka Island in the Aleutian Islands. The archaeological samples date to three main time periods: pre-Medieval Warm Period (MWP; ca. 2000-1500 BP), post-MWP/pre-Little Ice Age (LIA; ca. ~1000 BP), and end of the LIA (ca. ~500-200 BP). With these data we are working to 1) characterize the population genetic structure, genetic diversity, and effective population sizes of Pacific cod populations over the last millennium; 2) identify genomic signatures of selection in response to historical climatic events and compare to adaptive regions found in modern Aleutian Islands Pacific cod; 3) determine whether there is evidence for genomic evolution following past climatic events related to a change in trophic level; and 4) compare and contrast the seasonality of fishing on fishing grounds between modern and historical time periods.

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