We describe four extensions to existing Bayesian methods for the analysis of genetic structure in populations: (i) use of beta distributions to approximate the posterior distribution of f and theta(B); (ii) use of an entropy statistic to describe the amount of information about a parameter derived from the data; (iii) use of the Deviance Information Criterion (DIC) as a model choice criterion for determining whether there is evidence for inbreeding within populations or genetic differentiation among populations; and (iv) use of samples from the posterior distributions for f and theta(B) derived from different data sets to determine whether the estimates are consistent with one another. We illustrate each of these extensions by applying them to data derived from previous allozyme and random amplified polymorphic DNA surveys of an endangered orchid, Platanthera leucophaea, and we conclude that differences in theta(B) from the two data sets may represent differences in the underlying mutational processes.

Species that have become rare or endangered due to human disturbance are at increased risk of extinction as a result of environmental, demographic, and genetic stochasticity. Smaller populations, which can be typical of endangered species, are especially vulnerable to loss of variation through stochastic events. For 10 populations of Platanthera leucophaea (Nuttall) Lindley (Orchidaceae), a threatened species, genetic variation at allozyme and random amplified polymorphic DNA (RAPD) loci was measured to assess the potential effects of fragmentation and reduced population size on the future viability of populations. Allozymes revealed very low levels of diversity (AP = 1.18; PP = 12%; HO = 0.008) and high levels of population differentiation (FST = 0.75). Additionally, inbreeding coefficients were very high in five of the 10 populations surveyed, due largely to the fixation of alternative alleles at two loci in different populations. In contrast, every individual displayed a unique RAPD fingerprint, yielding higher levels of polymorphism (PP = 45%) and gene diversity (Nei's H = 0.159). Estimates of population differentiation based on RAPD are moderate as measured by amova (ΦST = 0.21), Wright's F‐statistics (GST = 0.26), or Shannon's information index (Hamong = 0.30). However, genetic and geographic distances are not significantly correlated, suggesting a lack of interpopulation gene flow and/or genetic drift within populations. Population size is not a good predictor of genetic variation in the present study, and it is hypothesized that plant dormancy patterns and chaotic fluctuations in population size from year to year may buffer against stochastic events, especially in small populations.

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Microsatellites occur in all plant genomes and provide useful markers for studies of genetic diversity and structure. Chloroplast microsatellites (cpSSRs) are frequently targeted because they are more easily isolated than nuclear microsatellites. Here, we quantified the frequency and uses of cpSSRs based on a literature review of over 400 studies published 1995–2013. These markers are an important and economical tool for plant biologists and continue to be used alongside modern genomics approaches to study genetic diversity and structure, evolutionary history, and hybridization in native and agricultural species. Studies using species-specific primers reported a greater number of polymorphic loci than those employing universal primers. A major disadvantage to cpSSRs is fragment size homoplasy; therefore, we documented its occurrence at several cpSSR loci within and between species of Acmispon (Fabaceae). Based on our empirical data set, we recommend targeted sequencing of a subset of samples combined with fragment genotyping as a cost-efficient, data-rich approach to the use of cpSSRs and as a test of homoplasy. The availability of genomic resources for plants aids in the development of primers for new study systems, thereby enhancing the utility of cpSSRs across plant biology.

Spread of the invasive cactus-feeding moth Cactoblastis cactorum has been well documented since its export from Argentina to Australia as a biocontrol agent, and records suggest that all non-native populations are derived from a single collection in the moth's native range. The subsequent global spread of the moth has been complex, and previous research has suggested multiple introductions into North America. There exists the possibility of additional emigrations from the native range in nursery stock during the late twentieth century. Here, we present mitochondrial gene sequence data (COI) from South America (native range) and North America (invasive range) to test the hypothesis that the rapid invasive spread in North America is enhanced by unique genetic combinations from isolated portions of the native range. We found that haplotype richness in the native range of C. cactorum is high and that there was 90% lower richness in Florida than in Argentina. All Florida C. cactorum haplotypes are represented in a single, well-defined clade, which includes collections from the reported region of original export from Argentina. Thus, our data are consistent with the documented history suggesting a single exportation of C. cactorum from the eastern region of the native range. Additionally, the presence of geographic structure in three distinct haplotypes within the same clade across Florida supports the hypothesis of multiple introductions into Florida from a location outside the native range. Because the common haplotypes in Florida are also known to occur in the neighboring Caribbean Islands, the islands are a likely source for independent North American colonization events. Our data show that rapid and successful invasion within North America cannot be attributed to unique genetic combinations. This suggests that successful invasion of the southeastern US is more likely the product of a fortuitous introduction into favorable abiotic conditions and/or defense responses of specific Opuntia hosts, rapid adaptation, or a release from native enemies.

Stalk-eyed flies (Diptera: Diopsidae) possess eyes at the ends of elongated peduncles, and exhibit dramatic variation in eye span, relative to body length, among species. In some sexually dimorphic species, evidence indicates that eye span is under both intra- and intersexual selection. Theory predicts that isolated populations should evolve differences in sexually selected traits due to drift. To determine if eye span changes as a function of divergence time, 1370 flies from 10 populations of the sexually dimorphic species, Cyrtodiopsis dalmanni and Cyrtodiopsis whitei, and one population of the sexually monomorphic congener, Cyrtodiopsis quinqueguttata, were collected from Southeast Asia and measured. Genetic differentiation was used to assess divergence time by comparing mitochondrial (cytochrome oxidase II and 16S ribosomal RNA gene fragments) and nuclear (wingless gene fragment) DNA sequences for c. five individuals per population. Phylogenetic analyses indicate that most populations cluster as monophyletic units with up to 9% nucleotide substitutions between populations within a species. Analyses of molecular variance suggest a high degree of genetic structure within and among the populations; > 97% of the genetic variance occurs between populations and species while < 3% is distributed within populations, indicating that most populations have been isolated for thousands of years. Nevertheless, significant change in the allometric slope of male eye span on body length was detected for only one population of either dimorphic species. These results are not consistent with genetic drift. Rather, relative eye span appears to be under net stabilizing selection in most populations of stalk-eyed flies. Given that one population exhibited dramatic evolutionary change, selection, rather than genetic variation, appears to constrain eye span evolution.

G(ST) is a genetic statistic describing differentiation of populations and has frequently been compared with Hamrick and Godt's (1989) review of the plant literature. We show here that some comparisons may be inappropriate if G(ST) was calculated in a different way than that used by Hamrick and Godt (HG). An alternative method advocated by Nei is mathematically different from the HG technique, occasionally resulting in different G(ST) values. We reviewed 695 studies that appeared between 1990 and September 1999 that cited Hamrick and Godt (1989) and found that many of these calculated G(ST) according to Nei's method (46%), with the majority of these papers (61%) including comparisons to Hamrick and Godt's review. We suggest that if G(ST) estimates are compared across studies, it is most appropriate to calculate them the same way. However, we found that in most cases, the magnitude of difference in G(ST) values was small, suggesting that qualitative comparisons of G(ST) estimates between most studies are probably valid. Nevertheless, we have identified theoretical and empirical situations in which large differences in G(ST) values are likely to arise. Thus, we advise future investigators to carefully consider which method to use in calculating G(ST) for a given data set.