Current Research Projects
Uncovering the genomic architecture of Atlantic cod ecotype evolution in the Gulf of Maine and Iceland
Supervised by Dr. Katie E. Lotterhos, Northeastern University (2015 - Present)
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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.
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 (2015 - Present)
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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Inversion invasions! Understanding the conditions in which inversion polymorphisms arise and persist in populations undergoing environmental adaptation
Supervised by Dr. Katie E. Lotterhos, Northeastern University Marine Science Center (2015 - Present)
Collaboration with Dr. Benjamin Haller
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Inversion polymorphisms have been implicated in the evolution of coexisting phenotypes and behaviors in a number of species. Within Atlantic cod, some studies have implicated inversions polymorphisms in the evolution of the migratory and stationary ecotypes found throughout their distributional range. Although theory has suggested that a reason that inversions evolve is due to the reduction in recombination between alleles captured within an inversion, little work has explored the range in conditions (e.g. levels of migration & selection, genomic redundancy, inversion size, etc.) necessary for inversions to arise and persist in a population.
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Using evolutionary simulations built using the SLiM evolutionary software, we are testing a range of parameters in a two population model undergoing stabilizing selection on a single trait to better understand when inversions arise and how often they persist in a population. Using these models, we are additionally exploring whether inversions are more likely to persist if they capture already established adaptive mutations or if they arise neutral and accumulate mutations over time. Finally, because we still do not fully understand how well our current statistical methods perform when identifying structural rearrangements linked to adaptation, our results will be used to test whether genome scan methods can identify neutral vs. adaptive inversion polymorphisms in the genome.
SLiM