Considerations for measuring genetic variation and population structure with multilocus fingerprinting

Multilocus DNA fingerprinting provides a cost-effective means to rapidly assay genetic variation at many loci. While this makes the technique particularly attractive for studies of evolution and conservation biology, fingerprint data can be difficult to interpret. Measurement errors inherent with the technique force investigators to group similar-sized alleles (bands) into discrete bins before estimating genetic parameters. If too little error is accounted for in this process homologous alleles will not be grouped in a common bin, whereas overestimated error can produce bins with homoplasic alleles. We used simulations and empirical data for two frog species ( Rana luteiventris and Hyla regilla ) to demonstrate that mean band-sharing ( S¯_xy ) and heterozygosity ( H ¯_E) are a function of both bin width and band profile complexity (i.e. number and distribution of bands). These estimators are also sensitive to the number of lanes included in the analysis when bin width is wide and a floating bin algorithm is employed. Multilocus estimates of H ¯_E were highly correlated with S¯_xy and thus provide no additional information about genetic variation. Estimates of population subdivision ( F ^ and Φ^_ST) appeared robust to changes in bin size. We also examined the issue of statistical independence for band-sharing data when comparisons are made among all samples. This analysis indicated that the covariance between band-sharing statistics was very small and not statistically different from zero. We recommend that sensitivity analyses for bin size be used to improve confidence in the biological interpretation of multilocus fingerprints, and that the covariance structure for band-sharing statistics be examined.     

A new phytoplasma associated with little leaf disease in azalea: multilocus sequence characterization reveals a distinct lineage within the aster yellows phytoplasma group

An azalea little leaf (AzLL) disease characterised by abnormally small leaves, yellowing and witches'‐broom growth symptoms was observed in suburban Kunming, southwest China. Transmission electron microscopic observations of single‐membrane‐bound, ovoid to spherical bodies in phloem sieve elements of diseased plants and detection of phytoplasma‐characteristic 16S rRNA gene sequence in DNA samples from diseased plants provided evidence linking the disease to infection by a phytoplasma. Results from restriction fragment length polymorphism, phylogenetic and comparative structural analyses of multiple genetic loci containing 16S rRNA, rpsS, rplV, rpsC and secY genes indicated that the AzLL phytoplasma represented a distinct, new 16Sr subgroup lineage, designated as 16SrI‐T, in the aster yellows phytoplasma group. The genotyping also revealed that the AzLL phytoplasma represented new rp and secY gene lineages [rp(I)‐P and secY(I)‐O, respectively]. Phylogenetic analyses of secY and rp gene sequences allowed clearer distinctions between AzLL and closely related strains than did analysis of 16S rDNA.     

Microsatellite Markers Reveal Genetic Variation within Sclerotinia sclerotiorum Populations in Irrigated Dry Bean Crops in Brazil

Microsatellites are powerful markers to infer population genetic parameters. We used 10 microsatellite loci to characterize the genetic diversity and structure of 79 samples of Sclerotinia sclerotiorum isolated from four Brazilian dry bean populations and observed that eight of them were polymorphic within populations. We identified 102 different haplotypes ranging from 6 to 18 per locus. Analyses based on genetic diversity and fixation indices indicated variability among and within populations of 28.79% (F_ST = 28793) and 71.21%, respectively. To examine genetic relatedness among S. sclerotiorum isolates, we used internal spacer (ITS1‐5.8S‐ITS2) restriction fragment length polymorphism (PCR‐RFLP) and sequencing analysis. PCR‐RFLP analysis of these regions failed to show any genetic differences among isolates. However, we detected variability within the sequence, which does not support the hypothesis of clonal populations within each population. High variability within and among populations may indicate the introduction of new genotypes in the areas analysed, in addition to the occurrence of clonal and sexual reproduction in the populations of S. sclerotiorum in the Brazilian Cerrado.     

Isolation‐driven divergence: speciation in a widespread North American songbird (Aves: Certhiidae)

Lineage, or true ‘species’, trees may differ from gene trees because of stochastic processes in molecular evolution leading to gene‐tree heterogeneity. Problems with inferring species trees because of excessive incomplete lineage sorting may be exacerbated in lineages with rapid diversification or recent divergences necessitating the use of multiple loci and individuals. Many recent multilocus studies that investigate divergence times identify lineage splitting to be more recent than single‐locus studies, forcing the revision of biogeographic scenarios driving divergence. Here, we use 21 nuclear loci from regional populations to re‐evaluate hypotheses identified in an mtDNA phylogeographic study of the Brown Creeper (Certhia americana), as well as identify processes driving divergence. Nuclear phylogeographic analyses identified hierarchical genetic structure, supporting a basal split at approximately 32°N latitude, splitting northern and southern populations, with mixed patterns of genealogical concordance and discordance between data sets within the major lineages. Coalescent‐based analyses identify isolation, with little to no gene flow, as the primary driver of divergence between lineages. Recent isolation appears to have caused genetic bottlenecks in populations in the Sierra Madre Oriental and coastal mountain ranges of California, which may be targets for conservation concerns.