Abstract
Detailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.
Highlights
Precise information on the delineation of evolutionary lineages, their genetic composition and population substructure is imperative for guiding population restoration and the long-term preservation of biodiversity[1]
It has been shown that some freshwater mussel species utilize different host fishes in different river s ystems[13,14], and research has shown that mussel larvae transform to juveniles at higher rates on sympatric populations of host-fish s pecies[13,15], indicating that the relationship between obligate parasitic mussel larvae and host fishes may be reinforced by co-evolutionary forces
STACKS parameter exploration identified a combination of assembly parameters (− m = 3, − M = 2, − n = 3, − max_locus_stacks = 3, with single nucleotide polymorphisms (SNP) model) as the best performing parameters, and this parameter setting was chosen for de novo ddRADseq assembly and SNP discovery, and for downstream genetic analyses
Summary
Precise information on the delineation of evolutionary lineages, their genetic composition and population substructure is imperative for guiding population restoration and the long-term preservation of biodiversity[1]. The life cycle of North American freshwater mussels includes a larval stage, called a glochidium, that must attach to a host fish to complete their development[10]. The freshwater mussel genus Cyprogenia inhabits high-gradient streams within the Mississippi faunal province which includes the Eastern, Ozark, and Ouachita highland regions of North A merica[16]. Phylogenetic research based on mitochondrial DNA (mtDNA)[20,21] indicated that the two species of Cyprogenia were not reciprocally monophyletic, and that the divergent mitochondrial clades recovered in analyses were associated with the color of the conglutinate lures used by mussels to attract and infest host fishes[22]. Population genetic research using microsatellite markers[21,23] supported the recognition of both C. aberti and C. stegaria, as allopatric species inhabiting the Western and Eastern highland regions respectively. The taxonomic status of these species while clearer was still not fully resolved, and C. aberti has been assessed as Data Deficient due to these ongoing taxonomic issues (http://www.iucnredlist.org/details/6182/0)
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