Molecular characterization of the freshwater snail Lymnaea natalensis (Gastropoda: Lymnaeidae) on Madagascar with an observation of an unusual polymorphism in ribosomal small subunit genes

Abstract

Recent characterization of nuclear ribosomal small subunit (SSU) genes has shown that variant nucleotides within this region could be useful for species and species group identification within the genus Lymnaea (Gastropoda: Lymnaeidae). This study aimed to characterize a range of populations of Lymnaea natalensis Krauss, 1848 on Madagascar, and addressed two related questions. First, is there any evidence of intraspecific variation of the SSU and, if so, what might be its significance? Secondly, might this variation jeopardize the use of SSU for lymnaeid taxonomy and phylogeny? Lymnaea natalensis (n = 212) was collected from 17 sampling localities, spanning the northern and southern ends of the island. Variation within a selected region of the SSU known to vary between species, the V1 and V2, was assayed by polymerase chain reaction (PCR) linked restriction fragment length polymorphism (RFLP) and denaturing gradient gel electrophoresis (DGGE) analysis. The PCR-RFLP profiles indicated a striking dimorphism across populations at two restriction site loci (CfoI & MspI) within the E10-1 helix of the V2 region. The observed RFLP variation was confirmed by direct sequencing and by genomic digestion with subsequent hybridization. Putative heterozygotes were also encountered and in these individuals the SSU arrays composed of two distinct types approximately 1% divergent. A severe departure from Hardy–Weinberg equilibrium with a highly statistically significant (P < 10^-5) heterozygote deficiency was found and genetic variation among populations was highly structured (F_st = 0.53). The geographic distribution of the variants was mapped, revealing that one variant was restricted to higher, predominately colder environments and was thought to be an adaptation. The molecular basis of the SSU variation was caused by single nucleotide polymorphisms (SNPs). To test for the possibility of cryptic taxa, an analysis of individuals representative of the SSU variant types with isoenzyme analysis (ISA), randomly amplified polymorphic DNA (RAPDs) and PCR-RFLP analysis of the ribosomal Internal Transcribed Spacer (ITS) was performed. Little variation was revealed and none that correlated to the groups suggested by SSU, confirming that the SSU variation was intraspecific. The levels of intraspecific divergence of the V1 and V2 within Lymnaea were not appreciably different (1%) from interspecific and would therefore question the validity of these data for lymnaeid taxonomy and phylogeny.