Genomics to aid conservation and restoration of the yellow lampmussel (Lampsilis cariosa) and tidewater mucket (Atlanticoncha ochracea)
Dates
Start Date
2024-04-01
End Date
2026-09-30
Summary
The yellow lampmussel (YLM; Lampsilis cariosa) occurs in the Saint Lawrence River system and the Atlantic Slope drainages, from Nova Scotia to Georgia. While most mussel species occur only in lotic habitats (rivers and streams), a few occur in lentic habitats (ponds and lakes). The YLM is unusual as it occurs in both lotic and lentic habitats, including large rivers of the Atlantic drainage as well as pools that resemble lentic environments (Haag 2012). The YLM is listed as threatened, endangered, or imperiled in nine states and is considered a species of special concern in Canada. Outside of Canada, there has been no comprehensive assessment of the species’ biological needs, including information on host fishes, population status, [...]
Summary
The yellow lampmussel (YLM; Lampsilis cariosa) occurs in the Saint Lawrence River system and the Atlantic Slope drainages, from Nova Scotia to Georgia. While most mussel species occur only in lotic habitats (rivers and streams), a few occur in lentic habitats (ponds and lakes). The YLM is unusual as it occurs in both lotic and lentic habitats, including large rivers of the Atlantic drainage as well as pools that resemble lentic environments (Haag 2012). The YLM is listed as threatened, endangered, or imperiled in nine states and is considered a species of special concern in Canada. Outside of Canada, there has been no comprehensive assessment of the species’ biological needs, including information on host fishes, population status, habitat usage and availability, and threats.
The tidewater mucket (TM; Atlanticoncha ochracea = Leptodea ochracea) occurs largely in the tidal sections of the Northern Atlantic province from Nova Scotia (Cape Breton) to Georgia (Savannah River) (Martel et al. 2010), inhabiting tidal freshwater regions with sand or mud bottoms. In the eastern US, it can be found in a wide variety of substrates such as clay, cobble, gravel, sand, and silt (Nedeau et al 2000). Dispersal is restricted to coastal plains rivers and ponds with connectivity to the Atlantic Ocean (NatureServer). Populations in Canada have declined. The TM is considered vulnerable to critically endangered along its distribution in the US. and is considered extirpated from Pennsylvania. The TM is listed as vulnerable by NatureServe, special concern by the American Fisheries Society (Williams et al. 1993) and near threated on the IUCN Red List. The reason for the decline in mussel numbers is unknown.
Both the YLM and TM are in decline across their ranges and have been extirpated from many areas where they historically occurred (see Appendix 1, attached, for a summary of species distributions). In addition, identification by shell morphology alone makes it difficult for biologists to accurately determine presence and abundance of these two species. While shell morphology is still the most common method used to identify mussels (Inoue et al. 2013), many species have similar, almost indistinguishable shells. For example, while the YLM generally has an oval shell shape, there is variation between sexes and life stages and mature female shells tend to be more rounded than male and immature female shells, which are of a more elongated shape. The YLM has a swollen umbo with a doubled-looped pattern (Bogan and Alderman 2008; Nedeau and Victoria 2003). The YLM, however, is sometimes difficult to distinguish from TM (Nedeau and Victoria 2003). In the Delaware and Potomac River basins, L. cariosa shells are similar to L. ovata (https://www.naturalheritage.state.pa). This makes it difficult for biologists to confirm L. cariosa sightings. In the Potomac, hybridization may be occurring with L. cardium. The TM has an ovate shape with thick laterally inflated shells. TM is often confused with YLM and eastern lampmussel (L. radiata) (Nedeau and Victoria 2003). Genetic analyses are less ambiguous and have been used to complement morphological analysis in the identification of species (e.g., Inoue et al., 2013; 2015).
Currently, there is a lack of information about genetic diversity across the range of both species. The estimation of genetic diversity is important for conservation because it is related to evolutionary fitness. In mussel species where populations are large enough, it is important to understand the genetic diversity and structuring among populations to select an appropriate source stock that can be released in a specific area for targeted augmentation. Hence, hatchery-reared juveniles that are ready to be released in streams need to be both ecologically and genetically appropriate for the stream in question to avoid the potential decrease of genetic diversity and stock mixing which could result in extinction (Haag and Williams 2014). For the YLM, estimation of genetic diversity and population structure in the northern portion of its range (Maine) has been assessed with microsatellites by Kelly et al. (2005), where genetic diversity was estimated for three river drainages (Kennebec, Penobscot, and Saint George) using seven microsatellites that were developed for Lampsilis abrupta (Eackles and King 2002). Significant differences were detected within and among drainages, suggesting that drainages may represent separate management units. In the central portion of the distribution of YLM (Virginia), genetic diversity has been estimated for Dan, Nottoway and South Flat River using 6 microsatellites loci (Olivera-Hyde and Hallerman 2018), where population structuring was found among some of the studied populations. Given the population structuring detected in portions of the YLM range, a more comprehensive population genetic survey is needed to guide conservation and management decisions.
The current project will characterize genome wide levels of genetic diversity and determine units of conservation through genotyping of 1000s of Single Nucleotide Polymorphisms (SNPs) using ddRAD methodology. These results will help expand capacity for conducting surveys across the species range and improve detection efficiencies and accuracy.
Objectives:
Use genome skimming to obtain mitochondrial genomes and ribosomal DNA of L. cariosa and A. ochracea as well as other related species for phylogenomic analysis to clarify relationships among morphologically similar species and assure correct morphological identifications.
Determine levels of genetic diversity within and potential genetic structuring among YLM and TM populations across the species ranges.
Develop quantitative PCR markers for L. cariosa and A. ochracea to be used for eDNA analysis.
Participate in an Interagency Forum for biologists and managers to identify conservation needs for L. cariosa and A. ochracea.
