Sequential fragmentation of Pleistocene forests in an East Africa biodiversity hotspot: chameleons as a model to track forest history

Background

The Eastern Arc Mountains (EAM) is an example of naturally fragmented tropical forests, which contain one of the highest known concentrations of endemic plants and vertebrates. Numerous paleo-climatic studies have not provided direct evidence for ancient presence of Pleistocene forests, particularly in the regions in which savannah presently occurs. Knowledge of the last period when forests connected EAM would provide a sound basis for hypothesis testing of vicariance and dispersal models of speciation. Dated phylogenies have revealed complex patterns throughout EAM, so we investigated divergence times of forest fauna on four montane isolates in close proximity to determine whether forest break-up was most likely to have been simultaneous or sequential, using population genetics of a forest restricted arboreal chameleon, Kinyongia boehmei.

Methodology/Principal Findings

We used mitochondrial and nuclear genetic sequence data and mutation rates from a fossil-calibrated phylogeny to estimate divergence times between montane isolates using a coalescent approach. We found that chameleons on all mountains are most likely to have diverged sequentially within the Pleistocene from 0.93–0.59 Ma (95% HPD 0.22–1.84 Ma). In addition, post-hoc tests on chameleons on the largest montane isolate suggest a population expansion ∼182 Ka.

Conclusions/Significance

Sequential divergence is most likely to have occurred after the last of three wet periods within the arid Plio-Pleistocene era, but was not correlated with inter-montane distance. We speculate that forest connection persisted due to riparian corridors regardless of proximity, highlighting their importance in the region''s historic dispersal events. The population expansion coincides with nearby volcanic activity, which may also explain the relative paucity of the Taita''s endemic fauna. Our study shows that forest chameleons are an apposite group to track forest fragmentation, with the inference that forest extended between some EAM during the Pleistocene 1.1–0.9 Ma.     

The effects of substratum on locomotor performance in lacertid lizards

Locomotion is important to animals because it has direct implications for fitness through its role in predator escape, prey capture, and territory defence. Despite significant advances in our understanding of animal locomotion, studies exploring how substrate properties affect locomotor performance remain scant. In the present study, we explore how variation in substrate (sand, slate, cork) affects locomotor performance in lacertid lizards that differ in morphology. Moreover, we explore whether substrate effects are the same for different types of locomotor performance (speed, acceleration, and stamina). Our results show that the substrate affected most types of locomotor performance studied but not always in the same way. Although substrate effects were species‐dependent for the maximal speed over 50 cm and the distance run to exhaustion, this was not the case for acceleration capacity. These results suggest that substrate texture differentially affects burst performance vs. longer duration measures of locomotor performance. Finally, straightforward relationships between habitat use and the substrate on which performance was maximized were not observed. This suggests that the evolution of locomotor capacity is complex and that animals may show compromise phenotypes allowing them to deal with a variety of substrates in their natural environment. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●●, ●●–●●.     

Evaluation of coagulation activation after Rhinovirus infection in patients with asthma and healthy control subjects: an observational study

Background

Asthma exacerbations are frequently triggered by rhinovirus infections. Both asthma and respiratory tract infection can activate haemostasis. Therefore we hypothesized that experimental rhinovirus-16 infection and asthmatic airway inflammation act in synergy on the haemostatic balance.

Methods

28 patients (14 patients with mild allergic asthma and 14 healthy non-allergic controls) were infected with low-dose rhinovirus type 16. Venous plasma and bronchoalveolar lavage fluid (BAL fluid) were obtained before and 6 days after infection to evaluate markers of coagulation activation, thrombin-antithrombin complexes, von Willebrand factor, plasmin-antiplasmin complexes, plasminogen activator inhibitor type-1, endogenous thrombin potential and tissue factor-exposing microparticles by fibrin generation test, in plasma and/or BAL fluid. Data were analysed by nonparametric tests (Wilcoxon, Mann Whitney and Spearman correlation).

Results

13 patients with mild asthma (6 females, 19-29 y) and 11 healthy controls (10 females, 19-31 y) had a documented Rhinovirus-16 infection. Rhinovirus-16 challenge resulted in a shortening of the fibrin generation test in BAL fluid of asthma patients (t = -1: 706 s vs. t = 6: 498 s; p = 0.02), but not of controls (t = -1: 693 s vs. t = 6: 636 s; p = 0.65). The fold change in tissue factor-exposing microparticles in BAL fluid inversely correlated with the fold changes in eosinophil cationic protein and myeloperoxidase in BAL fluid after virus infection (r = -0.517 and -0.528 resp., both p = 0.01).Rhinovirus-16 challenge led to increased plasminogen activator inhibitor type-1 levels in plasma in patients with asthma (26.0 ng/mL vs. 11.5 ng/mL in healthy controls, p = 0.04). Rhinovirus-16 load in BAL showed a linear correlation with the fold change in endogenous thrombin potential, plasmin-antiplasmin complexes and plasminogen activator inhibitor type-1.

Conclusions

Experimental rhinovirus infection induces procoagulant changes in the airways of patients with asthma through increased activity of tissue factor-exposing microparticles. These microparticle-associated procoagulant changes are associated with both neutrophilic and eosinophilic inflammation. Systemic activation of haemostasis increases with Rhinoviral load.

Trial registration

This trial was registered at the Dutch trial registry (http://www.trialregister.nl): NTR1677.     

Postglacial climate changes and rise of three ecotypes of harbour porpoises,Phocoena phocoena,in western Palearctic waters

Despite no obvious barriers to gene flow in the marine realm, environmental variation and ecological specializations can lead to genetic differentiation in highly mobile predators. Here, we investigated the genetic structure of the harbour porpoise over the entire species distribution range in western Palearctic waters. Combined analyses of 10 microsatellite loci and a 5085 base‐pair portion of the mitochondrial genome revealed the existence of three ecotypes, equally divergent at the mitochondrial genome, distributed in the Black Sea (BS), the European continental shelf waters, and a previously overlooked ecotype in the upwelling zones of Iberia and Mauritania. Historical demographic inferences using approximate Bayesian computation (ABC) suggest that these ecotypes diverged during the last glacial maximum (c. 23–19 kilo‐years ago, kyrbp ). ABC supports the hypothesis that the BS and upwelling ecotypes share a more recent common ancestor (c. 14 kyrbp ) than either does with the European continental shelf ecotype (c. 28 kyrbp ), suggesting they probably descended from the extinct populations that once inhabited the Mediterranean during the glacial and post‐glacial period. We showed that the two Atlantic ecotypes established a narrow admixture zone in the Bay of Biscay during the last millennium, with highly asymmetric gene flow. This study highlights the impacts that climate change may have on the distribution and speciation process in pelagic predators and shows that allopatric divergence can occur in these highly mobile species and be a source of genetic diversity.     

Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method

It is well recognized that Escherichia coli consists of a number of distinct phylo-groups and that strains of the different phylo-groups vary in their ecological niches, life-history characteristics and propensity to cause disease. Consequently, much can be learnt by assigning a strain of E. coli to one of the recognized phylo-groups. A triplex PCR-based method that enables strains of E. coli to be assigned to a phylo-group using a dichotomous key approach based on the presence or absence of two genes (chuA and yjaA) and an anonymous DNA fragment (TSPE4.C2) has been developed. However, the accuracy with which this method assigns strains to their correct phylo-group has not been adequately evaluated. Consequently, 662 strains of E. coli were characterized using a multi-locus sequence typing approach. Unsupervised population assignment algorithms were used to assign strains to phylo-groups based on the multi-locus sequence typing data. The analyses revealed that 85-90% of E. coli strains can be assigned to a phylo-group and that 80-85% of the phylo-group memberships assigned using the Clermont method are correct. However, the accuracy with which strains are assigned to the correct phylo-group depends on their Clermont genotype. For example, strains yielding a Clermont genotype consistent with phylo-groups B1 and B2 are assigned correctly 95% of the time. Strains failing to yield any PCR products using the Clermont method are seldom members of phylo-group A and strains with such a genotype should not be assigned to a phylo-group.     

Integrins regulate the intracellular distribution of eukaryotic initiation factor 4E in platelets. A checkpoint for translational control.

Recent evidence from our laboratory demonstrates that platelets synthesize numerous proteins in a signal-dependent fashion (Pabla, R., Weyrich, A. S., Dixon, D. A., Bray, P. F., McIntyre, T. M., Prescott, S. M., and Zimmerman, G. A. (1999) J. Cell Biol. 144, 175-184; Weyrich, A. S., Dixon, D. A., Pabla, R., Elstad, M. R., McIntyre, T. M., Prescott, S. M., and Zimmerman, G. A. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 5556-5561). Protein synthesis in platelets is controlled at the translational level; however, the mechanisms of regulation are not known. Here we demonstrate that translation initiation factors are redistributed to mRNA-rich areas in aggregated platelets, an event that induces protein synthesis. Interrogation of cDNA arrays revealed that platelet-derived mRNAs are primarily associated with the cytoskeletal core. In contrast, eukaryotic initiation factor 4E (eIF4E), the essential mRNA cap-binding protein that controls global translation rates, is localized in the membrane skeleton and soluble fraction of platelets, physically separated from most mRNAs. Platelet activation redistributes eIF4E to the cytoskeleton and increases interactions of eIF4E with mRNA cap structures. Redistribution of eIF4E to the mRNA-rich cytoskeleton coincides with a marked increase in protein synthesis, a process that is blocked when intracellular actin is disrupted. Additional studies demonstrated that beta(3) integrins are the primary membrane receptor that distributes eIF4E within the cell. These results imply that integrins link receptor-mediated pathways with mRNA-rich cytoskeletal domains and thereby modulate the organization of intracellular translational complexes. They also indicate that the functional status of eIF4E is regulated by its intracellular distribution.     

Interactive response of the horn fly (Diptera: Muscidae) and selected breeds of beef cattle

Statistically significant differences were observed in the population density of the horn fly, Haematobia irritans irritans (L.), on different breeds of beef cattle. The European breed Chianina had a population density of horn flies generally less than or equal to 50% than that of the British cattle breeds (Angus, Hereford, Polled Hereford, and Red Poll) and another European breed (Charolais). Generally, no significant difference existed among numbers of horn flies on Hereford, Polled Hereford, and Red Poll cows in 1988 or among Angus, Hereford, Polled Hereford, and Red Poll cows in 1989. Factors other than color appeared to be involved in the selective process between the horn fly and its host. Population densities on two white European breeds (Charolais and Chianina) were significantly different on all weekly intervals except for 4 wk in both 1988 and 1989. No significant difference existed among Charolais and British breeds except during 4 wk in 1988 and 3 wk in 1989. When weaning weights of all calves were adjusted for the effects of age to 205 d, sex of calf, and age of dam, the indirect effect of the horn fly on weaning weight showed a significant linear regression. Each 100 flies per cow caused a reduction of 8.1 kg in calf weaning weight. Cows within each breed with low numbers of horn flies weaned significantly heavier calves than cows with higher numbers of horn flies.     

Effects of CO2 enrichment and water stress on gas exchange of Liquidambar styraciflua and Pinus taeda seedlings grown under different irradiance levels

Summary The effects of CO₂ enrichment and water stress on gas exchange of Liquidambar styraciflua L. (sweetgum) and Pinus taeda L. (loblolly pine) seedlings were examined for individuals grown from seed under high (1000 mol·m^-2·s^-1) and low (250 mol·m^-2·s^-1) photosynthetic photon flux density at 350, 675 and 1000 l·l^-1 CO₂. At 8 weeks of age, half the seedlings in each CO₂-irradiance treatment were subjected to a drying cycle which reduced plant water potential to about -2.5 MPa in the most stressed plants, while control plants remained well-watered (water potentials of -0.3 and -0.7 MPa for sweetgum and loblolly pine, respectively). During this stress cycle, whole seedling net photosynthesis, transpiration and stomatal conductance of plants from each CO₂-irradiance-water treatment were measured under respective growth conditions.For both species, water stress effects on gas exchange were greatest under high irradiance conditions. Waterstressed plants had significantly lower photosynthesis rates than well-watered controls throughout most of the drying cycle, with the most severe inhibition occurring for low CO₂, high irradiance-grown sweetgum seedlings. Carbon dioxide enrichment had little effect on gas exchange rates of either water-stressed or well-watered loblolly pine seedlings. In contrast, water stress effects were delayed for sweetgum seedlings grown at elevated CO₂, particularly in the 1000 l·l^-1 CO₂, high irradiance treatment where net photosynthesis, transpiration and conductance of stressed plants were 60, 36 and 33% of respective control values at the end of the drying cycle. Development of internal plant water deficits was slower for stressed sweetgum seedlings grown at elevated CO₂. As a result, these seedlings maintained higher photosynthetic rates over the drying cycle than stressed sweetgum seedlings grown at 350 l·l^-1 CO₂ and stressed loblolly pine seedlings grown at ambient and enriched CO₂ levels. In addition, water-stressed sweetgum seedlings grown at elevated CO₂ exhibited a substantial increase in water use efficiency.The results suggest that with the future increase in atmospheric CO₂ concentration, sweetgum seedlings should tolerate longer exposure to low soil moisture, resulting in greater first year survival of seedlings on drier sites of abandoned fields in the North Carolina piedmont.     

Cyclic variations in nitrogen uptake rate in soybean plants

Uptake of NO₃⁻ by nonnodulated soybean plants (Glycine max L. Merr. cv Ransom) growing in flowing hydroponic culture at 22 and 14°C root temperatures was measured daily during a 31-day growth period. Ion chromatography was used to determine removal of NO₃⁻ from solution during each 24-hour period. At both root-zone temperatures, rate of NO₃⁻ uptake per plant oscillated with a periodicity of 3 to 5 days. The rate of NO₃⁻ uptake per plant was consistently lower at 14°C than 22°C. The lower rate of NO₃⁻ uptake at 14°C during the initial 5 to 10 days was caused by reduced uptake rates per gram root dry weight, but with time uptake rates per gram root became equal at 14 and 22°C. Thereafter, the continued reduction in rate of NO₃⁻ uptake per plant at 14°C was attributable to slower root growth.