Levels Of Microsatellite Diversity Research Articles

Genetic analysis of three remnant populations of the rufous hare-wallaby (Lagorchestes hirsutus) in arid Australia

The rufous hare-wallaby (Lagorchestes hirsutus) is now extinct in the wild on mainland Australia, but survives in captivity. However, endemic populations persist on Bernier and Dorre Islands, Western Australia. This study aimed to compare the genetic diversity and differentiation amongst three remaining rufous hare-wallaby populations using mitochondrial DNA (mtDNA) (cytochrome b, control region) sequence data and nuclear (microsatellite) markers. Levels of microsatellite diversity were low in both island populations but high in the captive mainland population. Levels of mtDNA diversity were low in all three populations. The mainland and island populations of L. hirsutus were found to be significantly differentiated for both microsatellite and mtDNA data, but the two island populations were significantly differentiated only for the microsatellite data. This pattern of differentiation is not consistent with the recognition of two separate island subspecies, but we recommend that the mainland and island populations be regarded as separate subspecies. The low diversity of the island populations and differentiation between island and mainland populations presents both challenges and opportunities for future management.

Lowered Diversity and Increased Inbreeding Depression within Peripheral Populations of Wild Rice Oryza rufipogon.

BackgroundThe distribution of genetic variability from the interior towards the periphery of a species’ range is of great interest to evolutionary biologists. Although it has been long presumed that population genetic variation should decrease as a species’ range is approached, results of empirical investigations still remain ambiguous. Knowledge regarding patterns of genetic variability as well as affected factors is particularly not conclusive in plants.Methodology/Principal FindingsTo determine genetic divergence in peripheral populations of the wild rice Oryza rufipogon Griff. from China, genetic diversity and population structure were studied in five northern & northeastern peripheral and 16 central populations using six microsatellite loci. We found that populations resided at peripheries of the species possessed markedly decreased microsatellite diversity than those located in its center. Population size was observed to be positively correlated with microsatellite diversity. Moreover, there are significantly positive correlations between levels of microsatellite diversity and distances from the northern and northeastern periphery of this species. To investigate genetic structure and heterozygosity variation between generations of O. rufipogon, a total of 2382 progeny seeds from 186 maternal families were further assayed from three peripheral and central populations, respectively. Peripheral populations exhibited significantly lower levels of heterozygosities than central populations for both seed and maternal generations. In comparisons with maternal samples, significantly low observed heterozygosity (HO) and high heterozygote deficit within populations (FIS) values were detected in seed samples from both peripheral and central populations. Significantly lower observed heterozygosity (HO) and higher FIS values were further observed in peripheral populations than those in central populations for seed samples. The results indicate an excess of homozygotes and thus high inbreeding depression in peripheral populations.Conclusions/SignificanceOur results together suggest that historical contraction of geographical range, demographic changes, and environmental conditions near the northern and northeastern margins of O. rufipogon favor inbreeding and possibly selfing, leading to the rapidly decreased effective population size. Genetic drift, reduced gene flow, and possible local selection, consequently lead to lowered gene diversity, accelerated genetic divergence and increased inbreeding depression found in peripheral populations of O. rufipogon. Given these characteristics observed, northern and northeastern peripheral populations deserve relatively different conservation strategies for either germplasm sampling of ex situ conservation or setting in situ reserves for the adaptation to possible environmental changes and the future germplasm utilization of wild rice.

Population differentiation of the European pond turtle (Emys orbicularis) in Poland inferred by the analysis of mitochondrial and microsatellite DNA: implications for conservation

We investigated the genetic diversity of Polish populations of the European pond turtle (Emys orbicularis) using complete sequences of the mitochondrial cytochrome b gene and allelic variation at thirteen microsatellite loci. We collected data from 146 turtles from 28 locations covering most of the species’ range in Poland. Our results showed a low haplotype diversity and high levels of microsatellite diversity in all populations. We applied two Bayesian approaches using the multilocus data and determined relationships of mtDNA haplotypes by constructing a parsimony network. We observed relatively consistent results of the two Bayesian clustering methods and largely concordant differentiation patterns between mitochondrial and microsatellite markers. All eastern Polish populations were assigned in a highly supported eastern group, while the majority of turtles from western Poland were joined in a distinct western group. The most probable number of population clusters corresponded to the number of native mtDNA lineages. Additionally, we detected a hierarchical structure within the eastern lineage splitting the populations into two subgroups. Polish populations generally constitute genetically homogenous groups, characterized by a low population admixture, with only negligible impact from allochthonous turtles.

Analysis of global and local population stratification of finless porpoises Neophocaena phocaenoides in Chinese waters

The existence of three distinct populations is widely accepted for the finless porpoise (Neophocaena phocaenoides) in Chinese waters: the Yellow Sea, Yangtze River, and South China Sea populations. Here, we use nine species-specific microsatellite loci, the complete mitochondrial DNA control region (912 bp), and the complete mitochondrial cytochrome b gene (1,140 bp) to further investigate potential population stratification in the Yellow Sea using 147 finless porpoise samples from the Bohai Sea and adjacent northern Yellow Sea, two regions that were largely underrepresented in previous genetic studies. Our F-statistics analyses confirm the previously described three populations, but further demonstrate significant genetic differentiation between the [Bohai + northern Yellow] Sea and the southern Yellow Sea. On the other hand, median-joining network analyses do not exhibit well-differentiated haplotype groups among different geographic populations, suggesting the existence of shared ancestral haplotypes. Levels of microsatellite diversity are moderate to high (mean HE = 0.794) among the 147 [Bohai + northern Yellow] Sea finless porpoises and no recent bottleneck was detected, whereas mtDNA control region and cytochrome b gene diversity is low to moderate. The microsatellite genotypic and mtDNA haplotypic data also confirm the presence of mother-calf pairs in single-net bycatch cases. The results presented here highlight the necessity to treat the [Bohai + northern Yellow] Sea population (highly impacted by anthropogenic threats) as a separate Management Unit.

Genetic structure of wild populations of the endangered Desert Pupfish complex (Cyprinodontidae: Cyprinodon)

Data from 10 microsatellite DNA loci were used to describe the genetic structure of the two extant species (Cyprinodon macularius and C. eremus) of the endangered Desert Pupfish complex of southwestern United States and northwestern Mexico. Variation at microsatellite loci was significantly correlated (Mantel test) with that of previous mtDNA results, both for the complex and for the relatively wide-ranging C. macularius alone. Both species showed unusually high levels of microsatellite diversity for non-marine fish (He = 0.84–0.93; AR = 11.9–17.0). There was evidence (RST > FST) that the two extant populations of C. eremus have been isolated sufficiently long for mutation to contribute significantly to genetic divergence, whereas divergence among the nine assayed populations of C. macularius could be attributed to genetic drift alone. Correspondingly, 10% of the diversity in C. eremus was attributable to differences between the two populations, whereas, for C. macularius, only 2.7% was attributable to among-population variation. Within C. macularius, a small (0.8%), but statistically significant, portion was attributable to differences between populations in the Salton Sea area and those on the lower Colorado River delta. The two populations of C. eremus and five groups of populations of C. macularius are recommended as management units for conservation genetics management of the two species.