A NGS approach to trophic dynamics and energy flow in benthic systems

We are developing a combination of next generation sequencing and compound-specific stable isotope techniques to understand the trophic dynamics of invasive species and herbivorous reef fish. For omnivorous species, such as invasive green crabs (Carcinus maenas), traditional diet analyses are biased towards food items that have hard parts, and often give low taxonomic resolution because of the difficulty of visually identifying partially digested food items. Similarly, several groups of coral reef fish focus their feeding activities on a thin layer of reef surface, and includes filamentous seaweeds, bacterial films, even the coral rock itself. What are fish targeting within this complex, amorphous, and highly productive resource? What role do herbivorous reef fish play in transferring this highly productive resource to higher trophic levels? Sequencing environmental DNA in animal guts provides unprecedented resolution of the diversity of ingested food items.  These data, coupled with stable isotope signals generated from consumer tissues, can provide new insights into the primary foods that are assimilated by consumers and potentially available to higher trophic levels.

Genotype and phenotype in a green crab hybrid zone

Mitochondrial DNA played a foundational role in the field of phylogeography, and is often assumed to have “neutral” behavior with respect to phenotypic traits that affect fitness. The honors work of Aidan Coyle ’17 and Sam Walkes ’18, and independent research of Hugh Cipperone ’19, in my lab has found the opposite, that mitochondrial haplotypes have large effects on traits that affect both thermal tolerance and feeding behavior. We are currently working on a series of papers from experimental work that has leveraged the genomic diversity found in the Carcinus maenus hybrid zone in the northern Gulf of Maine, and the experimental capabilities of the Schiller Coastal Studies Center’s new seawater laboratory.

Reef fish hybrid zone dynamics in the Tropical Eastern Pacific

Hybrid zones, or geographic regions where distinct populations or species meet and mate, have provided important tests of theories and processes that are important to the origin and maintenance of new species. The green crab hybrid zone in the Gulf of Maine provides an excellent local system to study the dynamics of this fundamental evolutionary process, and our work with mitochondrial and nuclear DNA has important implications for the role of natural selection in determining the spread of unique genetic lineages, and the ecological consequences of gene flow among distinct populations. In warmer seas, we have been documenting a more complex set of hybrid zones that involve a complex of three evolutionary “old” parrotfish species that mate and produce fertile offspring. The geographic extent of this hybrid complex is quite large, spanning the latitude of the entire Tropical Eastern Pacific. Our first manuscript based on mitochondrial and nuclear DNA is approaching submission, and we are working on a second based on targeted sequence capture of ultra-conserved elements (UCEs).