Assessing the genetic diversity in Argopecten nucleus (Bivalvia: Pectinidae), a functional hermaphrodite species with extremely low population density and self‐fertilization: Effect of null alleles

Abstract

Argopecten nucleus is a functional hermaphroditic pectinid species that exhibits self‐fertilization, whose natural populations have usually very low densities. In the present study, the genetic diversity of a wild population from Neguanje Bay, Santa Marta (Colombia), was estimated using microsatellite markers, and the effect of the presence of null alleles on this estimation was assessed. A total of 8 microsatellite markers were developed, the first described for this species, and their amplification conditions were standardized. They were used to determine the genotype of 48 wild individuals from Naguanje Bay, and 1,010 individuals derived from the offspring of 38 directed crosses. For each locus, the frequencies of the identified alleles, including null alleles, were estimated using the statistical package Micro‐Checker, and the parental genotypes were confirmed using segregation analysis. Three to 8 alleles per locus with frequencies from 0.001 to 0.632 were detected. The frequencies of null alleles ranged from 0.10 to 0.45, with Ho from 0.0 to 0.79, and He from 0.53 to 0.80. All loci were in H‐W disequilibrium. The null allele frequencies values were high, with lower estimations using segregation analysis than estimated using Micro‐Checker. The present results show high levels of population genetic diversity and indicate that null alleles were not the only cause of deviation from H‐W equilibrium in all loci, suggesting that the wild population under study presents signs of inbreeding and Wahlund effect.

Genetic Diversity and Population Structure Revealed by SSR Markers on Endemic Species Osmanthusserrulatus Rehder from Southwestern Sichuan Basin, China

“…The mating system, that is, functional androdioecy, and the contrasting levels of gene flow might explain the high genetic diversity of this narrowly distributed species in some way [44,45]. The presence of null and dropout alleles will lead to a high deviation between Ho and He, and a high frequency of null alleles will cause the deviation from HWE in all loci [42,46]. In this study, all values of Ho were much smaller than He among the ten populations as well as among the 18 loci (except Os35), which may be caused by the high frequency of null alleles at all loci (0.017-0.966, mean Fn = 0.556), and further lead to an underestimation of population genetic diversity [46].…”

“…The presence of null and dropout alleles will lead to a high deviation between Ho and He, and a high frequency of null alleles will cause the deviation from HWE in all loci [42,46]. In this study, all values of Ho were much smaller than He among the ten populations as well as among the 18 loci (except Os35), which may be caused by the high frequency of null alleles at all loci (0.017-0.966, mean Fn = 0.556), and further lead to an underestimation of population genetic diversity [46]. Meanwhile, the significant HWE deviation (p < 0.001) might present signs of inbreeding, which suggests high heterozygosity deficiency and nonrandom mating among individuals [47].…”

Genetic structure and trait variation within a maple hybrid zone underscore North China as an overlooked diversity hotspot

“…Six loci were reported to have null alleles, but no large allele dropouts. Since there were two genetic types in the DHS populations with reduced gene flow between types (see results), it might be no surprise to find null alleles in more than half of the loci 51 . Previous studies have tested the probability of null alleles for the same set of SSR loci in the same species, and no null alleles were found 10,31 .…”

Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA

“…albopictus native range with microsatellites ( Beebe et al 2013 ), and may reflect the local breeding structure of this container mosquito ( Black et al 1988 ). Alternatively, the increase in homozygosity relative to the expected Hardy-Weinberg equilibrium diagnostic of inbreeding may also be the result of a Wahlund effect or the presence of null alleles, and distinguishing among those mechanisms is not trivial ( Barros et al 2020 ). We detected putative null alleles at low frequencies (0.02 – 0.22) at all but one of the 15 loci used in this study.…”