Microsatellite cross-species amplification in the genus Littorina and detection of null alleles in Littorina saxatilis

Abstract

Microsatellite DNA is widely used as population genetic marker, but the cost of using microsatellites is high, as they usually need to be developed and optimized for each species separately. Cross-species amplification of microsatellites is therefore commonly applied to bring down the cost, but it can also involve genotyping errors. We studied cross-species amplification of microsatellites in four species of the Atlantic group of Littorina (Neritrema ): L. saxatilis (Olivi, 1792), L. obtusata (Linnaeus, 1758), L. fabalis (Turton, 1825) and L. arcana Hannaford Ellis, 1978 to investigate whether markers originally developed for a more distantly related Pacific species [L. subrotundata (Carpenter, 1864)] suffered from more amplification problems than markers developed for one of the species in the Atlantic group (L. saxatilis ). We also compared variation in amplification success among the species and among different regions in the NE Atlantic. Approximately half of the 12 primers developed for L. subrotundata and the seven primers developed for L. saxatilis were successfully amplified in other species of the subgenus. The success was dependent on phylogenetic distance among species within the subgenus. On the other hand, the variation in performance of the loci between geographically remote populations of the same species was as high as variation among the species. In earlier studies statistical analyses indicated that several loci showed a heterozygote deficiency due to null alleles. The presence of null alleles was confirmed by a segregation analysis of the microsatellite loci in eight half-sib families of L. saxatilis.

Genetic characterization of Mytilus coruscus and M. galloprovincialis using microsatellite markers

“…Deviations from HWE have been previously reported in MS marker analyses of M. coruscus (Xu et al, 2010), M. galloprovincia (Diz and Presa, 2008), and other mollusk species (Hedgecock et al, 2004;Li et al, 2006;Panova et al, 2008). These deviations might arise because of one or a combination of factors, such as the substructure of samples caused by the pooling of samples from several different sites, inbreeding, or the presence of null alleles (Zouros and Foltz, 1984).…”

Development of microsatellite markers for a hard-shelled mussel, Mytilus coruscus, and cross-species transfer

“…Although heterozygote deficiency can result from diverse factors such as inbreeding, the Wahlund effect, and selection, the main cause is generally the presence of non-amplifying PCR null alleles (Hoffman and Amos, 2005;Selkoe and Toonen, 2006), as the non-amplified heterozygotes are scored as homozygotes. Null alleles are usually suspected when the deviation from Hardy-Weinberg equilibrium occurs only in a particular locus (Panova et al, 2008).…”

“…Although they fertilize by releasing eggs and sperm that can travel some distance, little genetic exchange with other population is expected. The possible genetic isolation of this population and the reasons for the homozygote excess could be further explored by comparing its genetic structure with that of other populations or by using statistical methods (Panova et al, 2008).…”

Characterization of polymorphic microsatellites for the rough periwinkle gastropod, Littorina saxatilis (Olivi, 1792) and their cross-amplification in four congeners

“…Additional studies involving larger sample sizes and additional populations are required to disentangle the effects of these possible factors. Null alleles were found to be relatively common for microsatellites previously developed for L. saxatilis (e.g., Panova et al 2008). Even if null alleles are present in certain loci/samples, their presence can be accounted for in population genetic studies given new statistical approaches now implemented in a number of routinely used software (e.g., FreeNA, Structure, Geneland), which reduce the bias associated with them (e.g., Chapuis and Estoup 2007;Falush et al 2007;Guillot et al 2008).…”

“…Seven loci cross-amplified in L. saxatilis' sister-species L. compressa and six loci cross-amplified in L. fabalis and L. obtusata. A lack of conservation of microsatellite primer binding sites tends to increase with increasing genetic distance (Panova et al 2008;McInerney et al 2009). Not The number of alleles is listed in successful amplification and their size range described in parenthesis '-' indicates no scorable PCR product Conserv Genet surprisingly then given larger genetic differences, just three loci cross-amplified in L. littorea, nonetheless they were polymorphic (N A = 9).…”