Population Genetics of Freshwater Pearl Mussel (Margaritifera margaritifera) in Central Massachusetts and Implications for Conservation

Date of Award


Degree Type


Degree Name

Master of Science in Biology



Chief Instructor

John G. Gibbons

Second Reader

John A. Baker

Third Reader

Susan A. Foster


The freshwater pearl mussel Margaritifera margaritifera is an ecologically-important globally-endangered species, yet little is known about biodiversity and population genetics in North American populations. We focused our study on M. margaritifera from central and eastern Massachusetts, USA, to better understand the historical impact of damming and habitat fragmentation on local population structure and genetic diversity. In order to examine the local population genetics of M. margaritifera, we generated ~300 informative single nucleotide polymorphisms (SNPs) from 59 individuals across 6 geographic locations, using the RAD-seq approach. We also gleaned genotypes from publicly available RNA-seq data of 23 French M. margaritifera samples. The 6 Massachusetts sites were located in varying stream systems and separated by dams which could influence gene flow and genetic diversity. Population structure predictions using Discriminant Analysis of Principle Components (DAPC) and fastStructure both indicate the existence of a single genetic population in central and eastern Massachusetts, and a clear separation from French individuals. This hypothesis is supported by frequency-based population genetics calculations performed using GenAlEx, indicating near-complete admixture and a high number of migrants between Massachusetts sites. Our results suggest that the effects of habitat fragmentation from damming in the past century have not radiated through Massachusetts populations of M. margaritifera, potentially due to the species' long lifespan and generation time. However, the population has similar levels of genetic diversity compared to endangered populations in Europe, and conservationists should consider these factors when creating management plans.

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