Currently accepting PhD student applications (email: frederic_chain[at]uml.edu)
Info on PhD program in Applied Biology at UMass Lowell

genome evolution, ecological adaptation and speciation

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Genome-wide variation in recently diverged populations can reveal molecular signatures reflecting the processes driving adaptive evolution and speciation. The three-spined stickleback is a useful vertebrate model to investigate genome evolution during population differentiation and ecological adaptation; freshwater colonization has repeatedly occurred since the last glaciation giving rise to recurrent phenotypic diversification and locally-adapted ecotypes.

As part of a consortium headed by Manfred Milinski, we carried out comparative & population genomics analyses and immunological transcriptomics to assess the extent of genome-wide differentiation among pairs of lake-river ecotypes. Results indicate that selection is a major contributor to the observed heterogeneous patterns of genomic divergence, and that structural variation substantially contributes to genetic variation. Young genes such as recently duplicated genes are overrepresented among copy-number variations (CNVs), and are enriched with functional roles related to environmental response. These young duplicates provide ample raw genetic material that may be used for adaptation to novel environments.

Current investigations include the emergence of new genes across populations and the role of epigenetics in determining the regulation and evolutionary fate of new genes. 

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duplicate gene evolution

Photo of Xenopus by Ben Evans

Gene and genome duplications can facilitate genetic innovation, reduce pleiotropy and catalyze reproductive incompatibilities and speciation. Therefore, the molecular and transcriptional fate of duplicate genes play important roles in the evolutionary trajectory of populations and species.

Using the polyploid African clawed frog (Xenopus) in Ben Evans' lab, we found that multiple different mechanisms explain the retention of duplicate genes, and that genes with greater and broader expression are less likely to be lost following whole genome duplication. Substantial gene expression divergence was observed despite purifying selection on amino acid sequences, potentially reflecting adaptation or even the early stages of pseudogenization. Younger duplicate genes in diploid frogs also had significantly higher levels of sex-biased expression.

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mutation rates and environmental stress

Environmental factors such as radiation and sunlight are known to cause mutations. Despite the interest in understanding long-term health effects of such stressors, little is known about the extent to which stressful environmental conditions accelerate mutation rates and the genetic load of populations. Moreover, most studies on mutation rates focus on point mutations rather than large-scale deletions and duplications (copy-number variations or CNVs), which have mutational mechanisms potentially more readily induced by stress.

Work in Melania Cristescu's lab was conducted with Daphnia mutation accumulation (MA) lines, permitting us to directly detect all but sub-lethal mutations due to repetitive bottlenecking that reduces effective population size. MA lines that were exposed to the highest levels of heavy metals showed significantly higher rates of large-scale mutations, potentially caused by an increase in error-prone double strand break repair. Compared to MA lines, isolates evolving in a non-MA population had far fewer mutations, including point mutations, suggesting that selection on new mutations is strong in small populations.

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gene-environment effects on transcriptomic diversity

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Gene expression responses to environmental cues can vary based on the genetic background. Our work in Daphnia has found that genetic lineages display different regulation responses to copper exposure, not only in transcriptional levels but also in patterns of alternative splicing.

Gene knockout experiments can help reveal gene functions and pathways, but the environmental conditions of the experiment affect regulatory processes and observable phenotypes. In collaboration with Dr. Myre's lab at UML, we show that in the model slime mold Dictyostelium, gene expression across development is largely unaffected by growth condition in wildtype cells, but substantially modified in knockout cells (Figure). We are now investigating gene expression responses to iron deficiency in huntingtin knockouts, and screening mutants for second site suppressors of autophagic defects and other huntingtin-associated phenotypes.

genetic approaches for environmental assessment

fish elevator in Lowell

Lowell canals

Due to growing threats to biodiversity and ecosystems from globalization, genetic methods to monitor biodiversity are in pressing demand. 

As part of the Canadian Aquatic Invasive Species Network (CAISN), we developed a metabarcoding pipeline to monitor zooplankton communities for the early detection of non-indigenous species. Metabarcoding is useful for detecting low-abundance organisms, but current genetic and bioinformatic methods pose limitations. Our work tries to improve these approaches and apply them to monitor urban waterways.

We are currently using eDNA in an environmental monitoring project on the Merrimack watershed, also in association with an alewife migration monitoring program led by the Lowell Parks & Conservation Trust.