Utility of microsatellites and mitochondrial DNA for species delimitation in the spruce budworm (Choristoneura fumiferana) species complex (Lepidoptera: Tortricidae)

Species identifications have been historically difficult in the Choristoneura fumiferana group, an important insect pest complex. We examined the utility of simple sequence repeats (SSRs, also referred to as microsatellites) and mitochondrial DNA (mtDNA) for delimiting and identifying eight currently recognized species sampled across North America. Four of these species formed discrete clusters using SSRs, while only two species were delimited with mtDNA. There was evidence for hybridization or incomplete lineage sorting between several species pairs. An integrative approach, using both phenotypic traits and molecular markers, allowed for the discrimination of more biologically relevant species units than did the use of molecular markers alone. As species are currently identified using putatively adaptive phenotypic traits, the differences observed between recognized species and neutral SSRs or mtDNA suggests that these species (or evolutionary significant units) have diverged via natural selection in spite of some gene flow.     

Les néandertaliens de la Caverna delle Fate (Finale Ligure,Italie). II – Les dents

The neandertalian remains discovered in the Caverna delle Fate, Finale Ligure (Italy) gave up a majority of dental material: 10 isolated teeth and six teeth upon arcade or included in the adult mandible Fate 3 and in the child mandible 8–10 years old, Fate 2. Until now, this assemblage is the most numerous of neandertalian teeth excavated in Italy, with archeostratigraphic and paleoenvironmental accurate context. No decidual tooth, lost naturally, has been recognized. The dental material is well preserved, not much altered by wear. The morphometric data confirm the possibility of presence of a gracile neandertalian population living along the mediterranean septentrional European shore. These populations were present since the MIS 5.1, between 80,000 and 70,000 years. This gracility can be explained by the geographic impact and not by the evolutive stage.     

Mating patterns influence vulnerability to the extinction vortex

Earth's biodiversity is undergoing mass extinction due to anthropogenic compounding of environmental, demographic and genetic stresses. These different stresses can trap populations within a reinforcing feedback loop known as the extinction vortex, in which synergistic pressures build upon one another through time, driving down population viability. Sexual selection, the widespread evolutionary force arising from competition, choice and reproductive variance within animal mating patterns could have vital consequences for population viability and the extinction vortex: (a) if sexual selection reinforces natural selection to fix ‘good genes’ and purge ‘bad genes’, then mating patterns encouraging competition and choice may help protect populations from extinction; (b) by contrast, if mating patterns create load through evolutionary or ecological conflict, then population viability could be further reduced by sexual selection. We test between these opposing theories using replicate populations of the model insect Tribolium castaneum exposed to over 10 years of experimental evolution under monogamous versus polyandrous mating patterns. After a 95‐generation history of divergence in sexual selection, we compared fitness and extinction of monogamous versus polyandrous populations through an experimental extinction vortex comprising 15 generations of cycling environmental and genetic stresses. Results showed that lineages from monogamous evolutionary backgrounds, with limited opportunities for sexual selection, showed rapid declines in fitness and complete extinction through the vortex. By contrast, fitness of populations from the history of polyandry, with stronger opportunities for sexual selection, declined slowly, with 60% of populations surviving by the study end. The three vortex stresses of (a) nutritional deprivation, (b) thermal stress and (c) genetic bottlenecking had similar impacts on fitness declines and extinction risk, with an overall sigmoid decline in survival through time. We therefore reveal sexual selection as an important force behind lineages facing extinction threats, identifying the relevance of natural mating patterns for conservation management.     

Cellular settings mediating Src Substrate switching between focal adhesion kinase tyrosine 861 and CUB-domain-containing protein 1 (CDCP1) tyrosine 734

Reciprocal interactions between Src family kinases (SFKs) and focal adhesion kinase (FAK) are critical during changes in cell attachment. Recently it has been recognized that another SFK substrate, CUB-domain-containing protein 1 (CDCP1), is differentially phosphorylated during these events. However, the molecular processes underlying SFK-mediated phosphorylation of CDCP1 are poorly understood. Here we identify a novel mechanism in which FAK tyrosine 861 and CDCP1-Tyr-734 compete as SFK substrates and demonstrate cellular settings in which SFKs switch between these sites. Our results show that stable CDCP1 expression induces robust SFK-mediated phosphorylation of CDCP1-Tyr-734 with concomitant loss of p-FAK-Tyr-861 in adherent HeLa cells. SFK substrate switching in these cells is dependent on the level of expression of CDCP1 and is also dependent on CDCP1-Tyr-734 but is independent of CDCP1-Tyr-743 and -Tyr-762. In HeLa CDCP1 cells, engagement of SFKs with CDCP1 is accompanied by an increase in phosphorylation of Src-Tyr-416 and a change in cell morphology to a fibroblastic appearance dependent on CDCP1-Tyr-734. SFK switching between FAK-Tyr-861 and CDCP1-Tyr-734 also occurs during changes in adhesion of colorectal cancer cell lines endogenously expressing these two proteins. Consistently, increased p-FAK-Tyr-861 levels and a more epithelial morphology are seen in colon cancer SW480 cells silenced for CDCP1. Unlike protein kinase Cδ, FAK does not appear to form a trimeric complex with Src and CDCP1. These data demonstrate novel aspects of the dynamics of SFK-mediated cell signaling that may be relevant during cancer progression.     

New species and records of saprophytic ascomycetes (Myxotrichaceae) from decaying logs in the boreal forest

Decayed wood from fallen white spruce (Picea glauca) and trembling aspen (Populus tremuloides) collected in northeastern Alberta, Canada, was the source of new isolates of species in the ascomycete generaGymnostellatospora andPseudogymnoascus. In addition to new reports ofG. japonica, G. frigida andP. roseus, two new species are described.Gymnostellatospora canadensis sp. nov. resemblesG. japonica but differs in producing brown ascomata and in the formation of an arthroconidial anamorph.Gymnostellatospora subnuda sp. nov. is distinct in lacking differentiated peridial hyphae.Gymnostellatospora alpina was not found in decayed wood but is reviewed based on extralimital material. A dichtomous key to the five species ofGymnostellatospora is provided.     

Non-iterative, regression-based estimation of haplotype associations with censored survival outcomes

The general availability of reliable and affordable genotyping technology has enabled genetic association studies to move beyond small case-control studies to large prospective studies. For prospective studies, genetic information can be integrated into the analysis via haplotypes, with focus on their association with a censored survival outcome. We develop non-iterative, regression-based methods to estimate associations between common haplotypes and a censored survival outcome in large cohort studies. Our non-iterative methods--weighted estimation and weighted haplotype combination--are both based on the Cox regression model, but differ in how the imputed haplotypes are integrated into the model. Our approaches enable haplotype imputation to be performed once as a simple data-processing step, and thus avoid implementation based on sophisticated algorithms that iterate between haplotype imputation and risk estimation. We show that non-iterative weighted estimation and weighted haplotype combination provide valid tests for genetic associations and reliable estimates of moderate associations between common haplotypes and a censored survival outcome, and are straightforward to implement in standard statistical software. We apply the methods to an analysis of HSPB7-CLCNKA haplotypes and risk of adverse outcomes in a prospective cohort study of outpatients with chronic heart failure.     

Multiwave validation sampling for error-prone electronic health records

Electronic health record (EHR) data are increasingly used for biomedical research, but these data have recognized data quality challenges. Data validation is necessary to use EHR data with confidence, but limited resources typically make complete data validation impossible. Using EHR data, we illustrate prospective, multiwave, two-phase validation sampling to estimate the association between maternal weight gain during pregnancy and the risks of her child developing obesity or asthma. The optimal validation sampling design depends on the unknown efficient influence functions of regression coefficients of interest. In the first wave of our multiwave validation design, we estimate the influence function using the unvalidated (phase 1) data to determine our validation sample; then in subsequent waves, we re-estimate the influence function using validated (phase 2) data and update our sampling. For efficiency, estimation combines obesity and asthma sampling frames while calibrating sampling weights using generalized raking. We validated 996 of 10,335 mother-child EHR dyads in six sampling waves. Estimated associations between childhood obesity/asthma and maternal weight gain, as well as other covariates, are compared to naïve estimates that only use unvalidated data. In some cases, estimates markedly differ, underscoring the importance of efficient validation sampling to obtain accurate estimates incorporating validated data.     

Effects of heme on the structure of the denatured state and folding kinetics of cytochrome b562

Heme-linked proteins, such as cytochromes, are popular subjects for protein folding studies. There is the underlying question of whether the heme affects the structure of the denatured state by cross-linking it and forming other interactions, which would perturb the folding pathway. We have studied wild-type and mutant cytochrome b562 from Escherichia coli, a 106 residue four-alpha-helical bundle. The holo protein apparently refolds with a half-life of 4 micros in its ferrous state. We have analysed the folding of the apo protein using continuous-flow fluorescence as well as stopped-flow fluorescence and CD. The apo protein folded much more slowly with a half-life of 270 micros that was unaffected by the presence of exogenous heme. We examined the nature of the denatured states of both holo and apo proteins by NMR methods over a range of concentrations of guanidine hydrochloride. The starting point for folding of the holo protein in concentrations of denaturant around the denaturation transition was a highly ordered native-like species with heme bound. Fully denatured holo protein at higher concentrations of denaturant consisted of denatured apo protein and free heme. Our results suggest that the very fast folding species of denatured holo protein is in a compact state, whereas the normal folding pathway from fully denatured holo protein consists of the slower folding of the apo protein followed by the binding of heme. These data should be considered in the analysis of folding of heme proteins.