Abstract
Recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves. Null alleles have been associated with heterozygous deficits in many studies. While several studies have tested for its presence using different analytical tools, few have empirically tested for its consequences in estimating population structure and differentiation. We characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam, Donax trunculus. We carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles. We tested the robustness of microsatellite genotyping for population assignment by showing that well-recognised biogeographic regions of the south Atlantic and south Mediterranean coast of Spain harbour genetically different populations.
Highlights
Recent studies have reported an unusually high frequency of non-amplifying alleles, known as null alleles, at microsatellite loci in bivalves (Hargrove et al, 2015; Chiesa et al, 2016) including the wedge clam (Nantón et al, 2014)
There were a total of 85 contigs (31.8%) we identified as PAL of di- or tri-nucleotide microsatellites and 182 contigs (68.2%) as nonPAL
When running STRUCTURE with the complete data set without a different locus at a time for each run, our results showed that three microsatellite loci were very informative (D.tru4, D.tru29 and D.tru32; Fig. S1, Table S2 )
Summary
Recent studies have reported an unusually high frequency of non-amplifying alleles, known as null alleles, at microsatellite loci in bivalves (Hargrove et al, 2015; Chiesa et al, 2016) including the wedge clam (Nantón et al, 2014). Null alleles occur when mutations in the binding site of the targeted DNA sequence prevent the efficient annealing of at least one primer resulting in failure of amplification during the PCR reaction. Null alleles can occur via segmental aneuploidy, where one chromosome has a deletion containing the primer binding site. In a study of allelic BAC sequences in the Pacific oyster obtained by the Oyster Genome Consortium, 42 of 101 microsatellite loci were found to occur in the hemizygous state, owing to indels of various sizes Null alleles can occur in homozygous state when the samples produce no
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