Size homoplasy and mutational processes of interrupted microsatellites in two bee species, Apis mellifera and Bombus terrestris (Apidae)

Similar microsatellite electromorphs (PCR products of the same size) can arise from independent mutational events. Such alleles are not identical by descent. This phenomenon, termed size homoplasy, was studied by sequencing electromorphs of two microsatellite loci in which the stretch of basic repeats is interrupted by different short (1-2 bp) DNA motifs. The number and position of these interruptions were established for electromorphs from closely and distantly related populations of honeybees and bumblebees. No sequence difference was found when electromorphs came from the same subspecies or from closely related subspecies, suggesting that they were probably identical by descent. In contrast, sequence differences were often detected in distantly related subspecies, showing that size homoplasy frequently occurs at this level of population differentiation. Size homoplasy is increased by limits to free length variation of alleles, a phenomenon that seems to act on interrupted microsatellites when comparing distantly related taxa, that is, honeybee subspecies from different evolutionary lineages. Electromorph sequences suggest that, within the scope of these limits, large mutation events have occurred frequently at both interrupted loci studied. In good agreement with the molecular data, computations based on the observed heterozygosity and number of electromorphs and simulation studies showed that neither locus fits the one-step stepwise mutant model (SMM). We speculate that interrupted microsatellites in general could be characterized by a higher variance in repeat number and consequently a lower homoplasy rate than pure ones. Hence, interrupted microsatellites should be most appropriate for investigating population differentiation and evolutionary relationship between relatively distant populations.      

Macroinvertebrate communities associated with duckweed (Lemnaceae) in two Eastern Cape rivers,South Africa

The functional feeding groups and diversity of macroinvertebrate communities associated with duckweed mats in the New Years River (two sites) and Bloukrans River (two sites), Eastern Cape province, South Africa, were assessed. Duckweed (Lemnaceae) is a ubiquitous family of floating macrophytes. A total of 41 macroinvertebrate families were collected monthly over a six-month period from February to July 2014. Duckweed biomass in both rivers was highly variable both temporally and spatially. The majority of identified macroinvertebrate taxa were predators and detritivores, with a small percentage of herbivores. An average of approximately 26% of the macroinvertebrate taxa found were from families that include species from more than one functional feeding group. Although overall measures of diversity and ecosystem health (Fisher’s α and Simpson’s index) remained constant over time in the New Years River, significant differences in macroinvertebrate community structure were seen between sites and months on both rivers, with dissimilarity being driven by a larger number of species in the New Years River. This high variability within macroinvertebrate assemblages probably reflects a combination of heterogeneous duckweed distribution, variation in physico-chemistry, opportunistic behaviours of macroinvertebrate predators and/or successional colonisation of duckweed mats.     

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

Despite their importance to host health and development, the communities of microorganisms associated with humans and other animals are characterized by a large degree of unexplained variation across individual hosts. The processes that drive such inter-individual variation are not well understood. To address this, we surveyed the microbial communities associated with the intestine of the zebrafish, Danio rerio, over developmental time. We compared our observations of community composition and distribution across hosts with that predicted by a neutral assembly model, which assumes that community assembly is driven solely by chance and dispersal. We found that as hosts develop from larvae to adults, the fit of the model to observed microbial distributions decreases, suggesting that the relative importance of non-neutral processes, such as microbe-microbe interactions, active dispersal, or selection by the host, increases as hosts mature. We also observed that taxa which depart in their distributions from the neutral prediction form ecologically distinct sub-groups, which are phylogenetically clustered with respect to the full metacommunity. These results demonstrate that neutral processes are sufficient to generate substantial variation in microbiota composition across individual hosts, and suggest that potentially unique or important taxa may be identified by their divergence from neutral distributions.     

Developing indices of relative abundance for monitoring cave and ground wētā (Orthoptera) in southern beech forest,New Zealand

We sampled populations of forest-floor dwelling cave and ground wētā using footprint tracking tunnels and spotlight transect counts in southern beech forest, New Zealand. Samples were compared to estimates of wētā density based on mark–recapture estimates from 25?m² enclosures. Both activity indices captured variability in cave wētā in time and space, were strongly correlated with each other, and have the potential for monitoring cave wētā activity levels. Comparisons between indices and cave wētā density estimates were equivocal, as recapture rates were too low to calculate high-resolution density estimates. We also found that cave wētā counts had a curved relationship increasing with temperature, and a negative relationship with increasing shrub and woody debris cover. Based on these preliminary results, tracking tunnels could be a viable method of monitoring cave wētā as they appear more efficient than transect counts and are relatively inexpensive. However, further calibration trials are needed to determine if indices mirror robust population density estimates.     

Genetic analysis of the two zebrafish patched homologues identifies novel roles for the hedgehog signaling pathway

Background  

Aberrant activation of the Hedgehog (Hh) signaling pathway in different organisms has shown the importance of this family of morphogens during development. Genetic screens in zebrafish have assigned specific roles for Hh in proliferation, differentiation and patterning, but mainly as a result of a loss of its activity. We attempted to fully activate the Hh pathway by removing both receptors for the Hh proteins, called Patched1 and 2, which are functioning as negative regulators in this pathway.     

A Bayesian approach for constructing genetic maps when markers are miscoded

The advent of molecular markers has created opportunities for a better understanding of quantitative inheritance and for developing novel strategies for genetic improvement of agricultural species, using information on quantitative trait loci (QTL). A QTL analysis relies on accurate genetic marker maps. At present, most statistical methods used for map construction ignore the fact that molecular data may be read with error. Often, however, there is ambiguity about some marker genotypes. A Bayesian MCMC approach for inferences about a genetic marker map when random miscoding of genotypes occurs is presented, and simulated and real data sets are analyzed. The results suggest that unless there is strong reason to believe that genotypes are ascertained without error, the proposed approach provides more reliable inference on the genetic map.