Potential of microsatellites for individual assignment: the North Atlantic redfish (genus Sebastes) species complex as a case study

We used the four redfish taxa (genus Sebastes) from the North Atlantic to evaluate the potential of multilocus genotype information obtained from microsatellites in assigning individuals at two different levels of group divergence. We first tested the hypothesis that microsatellites can diagnostically discriminate individual redfish from different groups. Second, we compared two different methods to quantify the effect of number of loci and likelihood stringency levels on the power of microsatellites for redfish group membership. The potential of microsatellites to discriminate individuals from different taxa was illustrated by a shared allele distance tree in which four major clusters corresponding to each taxa were defined. Concomitant with this strong discrimination, microsatellites also proved to be powerful in reclassifying specimens to the taxon of origin, using either an empirical or simulated method of estimating assignment success. By testing for the effect of both the number of loci and the level of stringency on the assignment success, we found that 95% of all specimens were still correctly reclassified with only four loci at the most commonly used criterion of log0. In contrast, the results obtained at the population level within taxa highlighted several problems of assignment that may occur at low levels of divergence. Namely, a drastic decrease of success with increasing stringency illustrated the lack of power of our set of loci. Strong discrepancy was observed between results obtained from the empirical and simulated methods. Finally, the highest assignment success was obtained when reducing the number of loci used, an observation previously reported in studies of human populations.     

Genetic variation within a fragmented population of swietenia humilis zucc

With large tracts of once continuous forest now modified by human use to leave reduced and highly fragmented stands of trees, the determination of the genetic consequences of forest fragmentation is a priority for ascertaining the conservation value of resultant stands, and in formulating sustainable management strategies. The levels and distribution of genetic diversity over 10 microsatellite loci were investigated within a fragmented population of the neotropical tree Swietenia humilis Zucc. High levels of genetic variation, typical of a highly outcrossing species, were found in all fragments at all loci (mean HE = 0.548). The majority of the variation was within rather than between fragments (RST = 0.032), giving high indirect estimates of gene flow (Nm = 8.9), probably reflecting the genetic structure of the trees present under more continuous forest. A high proportion of loci also showed significant departures from Hardy-Weinberg equilibrium with associated significant levels of FIS. The initial effects of fragmentation were, however, seen in the fragments through the loss of low-frequency alleles present in the continuous 'control' stand. The percentage of this allelic loss increased with a decrease in fragment size.     

Phylogeography and conservation genetics of the Iowa pleistocene snail

The Iowa Pleistocene snail, Discus macclintocki, is an endangered species that survives only in relictual populations on algific (cold-air) talus slopes in northeast Iowa and northwest Illinois in the central region of the USA. These populations are believed to have been isolated since the temperatures began to warm at the end of the last glacial period around 16 500 years ago. DNA sequencing of the 16s rRNA gene of the mitochondria was used to determine the genetic relationship among 10 populations and the genetic diversity within these populations. Genetic diversity is extremely high within this species with 40 haplotypes spread across the 10 populations sampled within a 4000 km2 region. Phylogenetic analyses showed that haplotypes formed monophyletic groups by the watershed on which they were found, suggesting that watersheds were important historical avenues of gene flow. Genetic distances were strongly related to the geographical distance among all populations, but this relationship was dependent on the scale being considered.     

Random amplified polymorphic DNA (RAPD) markers detect a single phenotype in lysimachia minoricensis J.J. Rodr. (Primulaceae), A wild extinct plant

Lysimachia minoricensis is a Mediterranean (Balearic Islands) endemic that is extinct in the wild but extant in botanical gardens. Previously, no variation at 22 isozyme loci was revealed in more than 150 analysed plants. Random amplified polymorphic DNA (RAPD) analysis was used to examine genetic variation among five individuals from each of eight botanical garden accessions (40 plants). No polymorphisms were detected at 201 amplified bands. This is the first report of RAPD monomorphism in a nonapomictic vascular plant. The lack of detectable genetic variation suggests that an extremely reduced gene pool was recovered in the field before its extinction. Although the screening of other genomic markers is feasible, it is suggested that the knowledge of biological and autoecological features should be prioritized before new re-introductions are attempted.     

Functional implications of structural differences between variants A and B of bovine beta-lactoglobulin

The structure of the trigonal crystal form of bovine beta-lactoglobulin variant B at pH 7.1 has been determined by X-ray diffraction methods at a resolution of 2.22 A and refined to values for R and Rfree of 0.239 and 0.286, respectively. By comparison with the structure of the trigonal crystal form of bovine beta-lactoglobulin variant A at pH 7.1, which was determined previously [Qin BY et al., 1998, Biochemistry 37:14014-14023], the structural consequences of the sequence differences D64G and V118A of variants A and B, respectively, have been investigated. Only minor differences in the core calyx structure occur. In the vicinity of the mutation site D64G on loop CD (residues 61-67), there are small changes in main-chain conformation, whereas the substitution V118A on beta-strand H is unaccompanied by changes in the surrounding structure, thereby creating a void volume and weakened hydrophobic interactions with a consequent loss of thermal stability relative to variant A. A conformational difference is found for the loop EF, implicated in the pH-dependent conformational change known as the Tanford transition, but it is not clear whether this reflects differences intrinsic to the variants in solution or differences in crystallization.     

Gene mapping by linkage and association analysis

Genetic analysis is used to map genes, including disease loci, to positions within the human genome. Linkage analysis depends on the co-segregation of a gene (locus) and a phenotype through a pedigree, while association analysis, or linkage disequilibrium mapping, depends on measuring deviation from the random occurrence of alleles in a haplotype in unrelated individuals or nuclear families. Complex computer programs may be used in both forms of analysis. In recent years most interest has focused on identifying genes involved in common, multifactorial diseases. Here I review some current and developing techniques of genetic analysis and give references to where further information can be obtained.     

Modeling heterogeneity in nest survival data

Current statistical methods for estimating nest survival rates assume that nests are identical in their propensity to succeed. However, there are several biological reasons to question this assumption. For example, experience of the nest builder, number of nest helpers, genetic fitness of individuals, and site effects may contribute to an inherent disparity between nests with respect to their daily mortality rates. Ignoring such heterogeneity can lead to incorrect survival estimates. Our results show that constant survival models can seriously underestimate overall survival in the presence of heterogeneity. This paper presents a flexible random-effects approach to model heterogeneous nest survival data. We illustrate our methods through data on redwing blackbirds.     

Power and sample size for testing homogeneity of relative risks in prospective studies

Power and sample-size formulas for testing the homogeneity of relative risks using the score method are presented. The homogeneity score test (Gart, 1985, Biometrika 72, 673-677) is formally equivalent to the Pearson chi-square test, although they look different. Results of this paper may be useful in assessing the validity of the model of a common relative risk before combining several 2 x 2 tables or in designing a prospective study for detecting heterogeneity of relative risks.     

Reduced sensitivity to hidden bias at upper quantiles in observational studies with dilated treatment effects

When a treatment has a dilated effect, with larger effects when responses are higher, there can be much less sensitivity to bias at upper quantiles than at lower quantiles; i.e., small, plausible hidden biases might explain the ostensible effect of the treatment for many subjects, and yet only quite large hidden biases could explain the effect on a few subjects having dramatically elevated responses. An example concerning kidney function of cadmium workers is discussed in detail. In that example, the treatment effect is far from additive: It is plausibly zero at the lower quartile of responses to control, and it is large and fairly insensitive to bias at the upper quartile.     

Statistical inference for self-designing clinical trials with a one-sided hypothesis

In the process of monitoring clinical trials, it seems appealing to use the interim findings to determine whether the sample size originally planned will provide adequate power when the alternative hypothesis is true, and to adjust the sample size if necessary. In the present paper, we propose a flexible sequential monitoring method following the work of Fisher (1998), in which the maximum sample size does not have to be specified in advance. The final test statistic is constructed based on a weighted average of the sequentially collected data, where the weight function at each stage is determined by the observed data prior to that stage. Such a weight function is used to maintain the integrity of the variance of the final test statistic so that the overall type I error rate is preserved. Moreover, the weight function plays an implicit role in termination of a trial when a treatment difference exists. Finally, the design allows the trial to be stopped early when the efficacy result is sufficiently negative. Simulation studies confirm the performance of the method.