Using Gene Expression to Investigate Differences Between Clam Populations

Gene expression can point to the presence of pathogens, contaminants, nutrients, and physiological stresses. None of these were found to impact the two populations of clams differently.

This study introduces an application of new technology (gene expression) to investigate an ecosystem-level problem: Why were similar clam beaches experiencing very different population abundance trends? Two adjacent populations of Pacific razor clams (Siliqua patula) were studied--one on the east side of Cook Inlet, Alaska, the other on the west side. The east-side population had supported a sport and personal-use fishery, but has been closed since 2015 due to declines in abundance. The west-side population continues to support commercial and sport fisheries. We wanted to know why the east-side population hasn't recovered and the west-side population continues to sustain harvest. We wondered if there was something different about the ecosystems on the east side compared to the west.

We sampled clams from both sites over two years. The genes we evaluated generally respond to a wide variety of environmental stressors commonly associated with coastal marine habitats. But we found no differences of gene expression between east and west populations. Our results suggest that pathogens, contaminants, nutrients, or physiological stress are not driving population abundance of razor clams at the scale of Cook Inlet. This led us to two potential conclusions: (1) differences exist but were not detected in the genes we analyzed, or (2) physiological processes do not account for the differences in abundance, and other factors such as predation or changes in habitat may be impacting the east Cook Inlet population.

We did not directly measure predation pressure exerted by sea otters on our sampled beaches (sea otters are prevalent on the east side of Cook Inlet, but not on the west side). We are looking into that now. If sea otters were a main contributor to the decline of razor clams on the east side, monitoring the expansion of sea otters as they reoccupy habitat along the west coast of Cook Inlet will be important to improve management of the clam harvest by anticipating and responding to changes.

Gene Expression Profiles in Two Razor Clam Populations: Discerning Drivers of Population Status

Abstract

With rapidly changing marine ecosystems, shifts in abundance and distribution are being documented for a variety of intertidal species. We examined two adjacent populations of Pacific razor clams (Siliqua patula) in lower Cook Inlet, Alaska. One population (east) supported a sport and personal use fishery, but this has been closed since 2015 due to declines in abundance, and the second population (west) continues to support commercial and sport fisheries. We used gene expression to investigate potential causes of the east side decline, comparing razor clam physiological responses between east and west Cook Inlet. The target gene profile used was developed for razor clam populations in Alaska based on physiological responses to environmental stressors. In this study, we identified no differences of gene expression between east and west populations, leading to two potential conclusions: (1) differences in factors capable of influencing physiology exist between the east and west and are sufficient to influence razor clam populations but are not detected by the genes in our panel, or (2) physiological processes do not account for the differences in abundance, and other factors such as predation or changes in habitat may be impacting the east Cook Inlet population.

Coletti, H. A., L. Bowen, B. E. Ballachey, T. L. Wilson, S. Waters, M. Booz, K. L. Counihan, T. E. Hollmen, and B. Pister. 2021. Gene expression profiles in two razor clam populations: Discerning drivers of population status. Life 11(12): 1288.