Population genetics of freshwater pearl mussel (Margaritifera margaritifera) in central Massachusetts and implications for conservation

Abstract

1. The freshwater pearl mussel Margaritifera margaritifera is an ecologically important globally endangered species, yet little is known about its biodiversity and population genetics in North American populations. This study focused on M. margaritifera from six locations within two stream systems in central and eastern Massachusetts, USA, to understand the historical impact of damming and habitat fragmentation on local population structure and genetic diversity. 2. Approximately 300 informative single nucleotide polymorphisms were generated from 59 individuals across six geographical locations, using the restriction-siteassociated DNA sequencing approach. Genotypes were also gleaned from publicly available RNA sequencing data of 23 French M. margaritifera samples. 3. Predictions of population structure using discriminant analysis of principal components and fastStructure both indicate the existence of a single genetic population in central and eastern Massachusetts, and a clear separation from French individuals. This observation is further supported by frequency-based calculations of population genetics, which indicate near-complete admixture and a high number of migrants between Massachusetts sites. 4. These results suggest that the effects of habitat fragmentation from damming in the past century have not radiated through the Massachusetts population of M. margaritifera, potentially because of the long lifespan and generation time of the species. However, the Massachusetts population has similar levels of genetic diversity to the endangered populations in Europe, and these factors should be considered by conservationists when creating conservation and management plans. 5. The findings of this study suggest that populations in North America are reasonably healthy and diverse and that, as one population, the study area represents one conservation unit. This indicates that dam removal, habitat restoration, and captive breeding programmes may be viable options to increase the small population numbers and retain a substantial portion of genetic diversity without sacrificing local adaptation.

Applying genomic approaches to delineate conservation strategies: a case study using the freshwater mussel Margaritifera margaritifera in the Iberian Peninsula

“…These inconsistencies may be associated with the lower number of loci analyzed in microsatellites studies when compared to SNP datasets, hence SNPs re ect genome-wide genetic diversity of populations more accurately than microsatellites [6]. The overall low genetic diversity values found for M. margaritifera are commonly found in other endangered freshwater organisms, such as Australian freshwater crocodiles and Mexican golden trout [44] [45] and have also been estimated for North American M. margaritifera [24] and M. hembeli [25], suggesting a strong relation between the loss of genetic diversity and the poor conservation status of these species. The low genetic diversity values found in the Iberian populations have been explained by strong genetic drift effects due to population bottlenecks [20] [21].…”

“…High degrees of population structure have also been identi ed in central and northern European populations of freshwater pearl mussels, but in this case the degree of genetic diversity was variable, often with higher values [22] [23]. Contrary to these genetic patterns, North American populations of M. margaritifera are characterized by high levels of genetic diversity and low degree of genetic differentiation, and its conservation status is not as precarious as the one of European populations [24]. Studies based on SNP markers for Iberian M. margaritifera populations have not been performed yet.…”

“…Studies based on SNP markers for Iberian M. margaritifera populations have not been performed yet. Only two SNP-based studies for Margaritifera were performed in a restricted area of North America (M. margaritifera: [24]; M. hembeli: [25], as well as one study in the unionid genus Cyprogenia, endemic to North America [26].…”

The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

“…Despite the cultural significance and poor conservation status of the freshwater pearl mussel, the availability of genomic resources to study this species is still limited [13, [18][19][20][21][22]. Also, almost nothing is known about the molecular mechanism governing the regulation and functioning of its many relevant biological features.…”