Population genetic structure of an estuarine and a reef fish species exploited by Brazilian artisanal fishing

In this study, we used microsatellite markers to examine the genetic structures of Centropomus undecimalis (Bloch, 1792) and Epinephelus marginatus (Lowe, 1834) populations collected from artisanal fishing sites along a stretch of coastline in southeastern Brazil. Based on F-statistics, there was no significant genetic differentiation evident in any C. undecimalis samples (FST=0.012). However, Bayesian clustering, principal component analysis (PCA) and discriminant analysis of principal components (DAPC) results suggested that there were most likely two clusters, with no relation to geographic areas. The bottleneck results showed no significant values and the effective population sizes (Ne) for the two genetically differentiated groups were large and similar. In contrast, for E. marginatus populations, the microsatellite loci showed no population subdivisions. The FST value was low and non-significant (FST=0.008), a Bayesian analysis indicated one cluster, and a PCA showed that all samples from different geographical sites shared the same genetic structure. The bottleneck results exhibited significant differences, and a low Ne was observed. The results of the genetic study of these two species along the southeastern Brazilian coast suggest that the distinct genetic structure of each species should be taken into account as management units for the conservation of their genetic diversities.

Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies

We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations (“admixture linkage disequilibium”). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.

DNA polymorphism in a subdivided population: the expected number of segregating sites in the two-subpopulation model.

Using the two subpopulation model, the expected numbers of segregating sites in a number of DNA sequences randomly sampled from a subdivided population were examined for several types of population subdivisions. It is shown that, in the case where the pattern of migration is symmetrical such as the finite island model, the expected number of segregating sites is independent of the migration rate when two or three DNA sequences are randomly sampled from the same subpopulation, but depends on the migration rate when more than three DNA sequences are sampled. It is also shown that the population subdivision can increase the amount of DNA polymorphism even in a subpopulation in some cases.

The Allelic Correlation Structure of Gainj- and Kalam-Speaking People. II. The Genetic Distance Between Population Subdivisions

ABSTRACT The patterning of allele frequency variability among 18 local groups of Gainj and Kalam speakers of highland Papua New Guinea is investigated using new genetic distance methods. The genetic distances proposed here are obtained by decomposing Sewall Wright's coefficient FST into a set of coefficients corresponding to all pairs of population subdivisions. Two statistical methods are given to estimate these quantities. One method provides estimates weighted by sample sizes, while the other method does not use sample size weighting. Both methods correct for the within-individual and between-individual-within-groups sums of squares. Genetic distances among the Gainj and Kalam subdivisions are analyzed with respect to demographic, geographic, and linguistic variables. We find that a demographic feature, group size, has the greatest demonstrable association with the patterning of genetic distances. The pattern of geographic distances among groups displays a weak congruence with the pattern of genetic distances, and the association of genetic and linguistic diversity is very low. An effect of differences in group size on genetic distances is not surprising, from basic theoretical considerations, but genetic distances have not often been analyzed with respect to these variables in the past. The lack of correspondence between genetic distances and linguistic and geographic differences is an unusual feature that distinguishes the Gainj and Kalam from most other tribal populations.