Spatial structure and genetic diversity of three tropical tree species with different habitat preferences within a natural forest

Analyses of the spatial distribution pattern, spatial genetic structure and genetic diversity were carried out using a 33-ha plot in a hill dipterocarp forest for three dipterocarps with different habitat preferences, i.e. Shorea curtisii on the ridges, Shorea leprosula in the valleys and Shorea macroptera both on the ridges and in the valleys. The significant spatial aggregation in small-diameter trees of all the three species was explained by limited seed dispersal. At the large-diameter trees, only S. macroptera showed random distribution and this might further prove that S. macroptera is habitat generalist, whilst S. curtisii and S. leprosula are habitat specific. The levels of genetic diversity estimated based on five microsatellite loci were high and comparable in all the three studied species. As the three studied species reproduced mainly through outcrossing, the observed high levels of genetic diversity might support the fact that the plant mating system can be used as guideline to infer the levels of genetic diversity, regardless of whether the species is habitat specific or habitat generalist. The lack of spatial genetic structure but significant aggregation in the small-diameter trees of all the three species might indicate limited seed dispersal but extensive pollen flow. Hence, if seed dispersal is restricted but pollen flow is extensive, significant spatial aggregation but no spatial genetic structure will be observed at the small-diameter trees, regardless of whether the species is habitat specific or habitat generalist. The inferred extensive pollen flow might indicate that energetic pollinators are involved in the pollination of Shorea species in the hill dipterocarp forests.     

Impact of agricultural land use on aquatic insect assemblages in the Garonne river catchment (SW France)

The impact of agricultural land use on the composition and structure of aquatic insect assemblages (i.e., taxa of Ephemeroptera, Plecoptera, Trichoptera, and Coleoptera (EPTC)) was investigated in tributary streams of the Garonne river basin, southern France. The self-organizing map (SOM) method was applied to compare both instream environmental conditions and EPTC assemblages between forest and agricultural streams. According to the SOM model, the study sites were classified into three main clusters corresponding to distinct EPTC assemblages. The SOM cluster associated with most of the agricultural sites had lower EPTC species richness and diversity. This cluster was also characterized by high levels of total dissolved solids, nitrate (NO₃), and chemical oxygen demand. Overall, our study shows that agricultural streams when compared with forest streams had lower biological integrity. In accordance with the European Water Framework Directive, our results indicate that the sites most impacted by agricultural land use should be restored and that the least-impacted forest sites could serve as reference conditions.     

Why do parasitized hosts look different? Resolving the “chicken-egg” dilemma

Phenotypic differences between infected and non-infected hosts are often assumed to be the consequence of parasite infection. However, pre-existing differences in hosts’ phenotypes may promote differential susceptibility to infection. The phenotypic variability observed within the host population may therefore be a cause rather than a consequence of infection. In this study, we aimed at disentangling the causes and the consequences of parasite infection by calculating the value of a phenotypic trait (i.e., the growth rate) of the hosts both before and after infection occurred. That procedure was applied to two natural systems of host–parasite interactions. In the first system, the infection level of an ectoparasite (Tracheliastes polycolpus) decreases the growth rate of its fish host (the rostrum dace, Leuciscus leuciscus). Reciprocally, this same phenotypic trait before infection modulated the future level of host sensitivity to the direct pathogenic effect of the parasite, namely the level of fin degradation. In the second model, causes and consequences linked the growth rate of the fish host (the rainbow smelt, Osmerus mordax) and the level of endoparasite infection (Proteocephalus tetrastomus). Indeed, the host’s growth rate before infection determined the number of parasites later in life, and the parasite biovolume then decreased the host’s growth rate of heavily infected hosts. We demonstrated that reciprocal effects between host phenotypes and parasite infection can occur simultaneously in the wild, and that the observed variation in the host phenotype population was not necessarily a consequence of parasite infection. Disentangling the causality of host–parasite interactions should contribute substantially to evaluating the role of parasites in ecological and evolutionary processes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Calpain cleavage within dysferlin exon 40a releases a synaptotagmin-like module for membrane repair

Dysferlin and calpain are important mediators of the emergency response to repair plasma membrane injury. Our previous research revealed that membrane injury induces cleavage of dysferlin to release a synaptotagmin-like C-terminal module we termed mini-dysferlin_C72. Here we show that injury-activated cleavage of dysferlin is mediated by the ubiquitous calpains via a cleavage motif encoded by alternately spliced exon 40a. An exon 40a–specific antibody recognizing cleaved mini-dysferlin_C72 intensely labels the circumference of injury sites, supporting a key role for dysferlin_Exon40a isoforms in membrane repair and consistent with our evidence suggesting that the calpain-cleaved C-terminal module is the form specifically recruited to injury sites. Calpain cleavage of dysferlin is a ubiquitous response to membrane injury in multiple cell lineages and occurs independently of the membrane repair protein MG53. Our study links calpain and dysferlin in the calcium-activated vesicle fusion of membrane repair, placing calpains as upstream mediators of a membrane repair cascade that elicits cleaved dysferlin as an effector. Of importance, we reveal that myoferlin and otoferlin are also cleaved enzymatically to release similar C-terminal modules, bearing two C2 domains and a transmembrane domain. Evolutionary preservation of this feature highlights its functional importance and suggests that this highly conserved C-terminal region of ferlins represents a functionally specialized vesicle fusion module.     

Ensemble modelling of species distribution: the effects of geographical and environmental ranges

The aim of this study was to analyse the effects of species geographical and environmental ranges on the predictive performances of species distribution models (SDMs). We explored the usefulness of ensemble modelling approaches and tested whether species attributes influenced the outcomes of such approaches. Eight SDMs were used to model the current distribution of 35 fish species at 1110 stream sections in France. We first quantified the consensus among the resulting set of predictions for each fish species. Next, we created an average model by taking the average of the individual model predictions and tested whether the average model improved the predictive performances of single SDMs. Lastly, we described the ranges of fish species along four gradients: latitudinal, thermal, stream gradient (i.e. upstream‐downstream) and elevation. After accounting for the effects of phylogenetic relatedness and species prevalence, these four species attributes were related to the observed variations in both consensus among SDMs and predictive performances by using generalized estimation equations. Our results highlight the usefulness of ensemble approaches for identifying geographical areas of agreement among predictions. Although the geographical extent of species had no effect on the performances of SDMs, we demonstrated that more consensual and accurate predictions were obtained for species with low thermal and elevation ranges, validating the hypothesis that specialist species yield models with higher accuracy than generalist ones. We emphasized that significant improvements in the accuracy of SDMs can be achieved by using an average model. Furthermore, these improvements were higher for species with smaller ranges along the four gradients studied. The geographical extent and ranges of species along environmental gradients provide promising insights into our understanding of uncertainties in species distribution modelling.     

Temporal Patterns of Larval Fish Occurrence in a Large Subtropical River

Knowledge of temporal patterns of larval fish occurrence is limited in south China, despite its ecological importance. This research examines the annual and seasonal patterns of fish larval presence in the large subtropical Pearl River. Data is based on samples collected every two days, from 2006 to 2013. In total, 45 taxa representing 13 families and eight orders were sampled. The dominant larval family was Cyprinidae, accounting for 27 taxa. Squaliobarbus curriculus was the most abundant species, followed by Megalobrama terminalis, Xenocypris davidi, Cirrhinus molitorella, Hemiculter leuscisculus and Squalidus argentatus. Fish larvae abundances varied significantly throughout the seasons (multivariate analyses: Cluster, SIMPROF and ANOSIM). The greatest numbers occurred between May and September, peaking from June through August, which corresponds to the reproductive season. In this study, redundancy analysis was used to describe the relationship between fish larval abundance and associated environmental factors. Mean water temperature, river discharge, atmospheric pressure, maximum temperature and precipitation play important roles in larval occurrence patterns. According to seasonal variations, fish larvae occurrence is mainly affected by water temperature. It was also noted that the occurrence of Salanx reevesii and Cyprinus carpio larvae is associated with higher dissolved oxygen (DO) concentrations, higher atmospheric pressure and lower water temperatures which occur in the spring. On the other hand, M. terminalis, X. davidi, and C. molitorella are associated with high precipitation, high river discharge, low atmospheric pressure and low DO concentrations which featured during the summer months. S. curriculus also peaks in the summer and is associated with peak water temperatures and minimum NH₃–N concentrations. Rhinogobius giurinus occur when higher atmospheric pressure, lower precipitation and lower river discharges occur in the autumn. Dominant fish species stagger their spawning period to avoid intraspecific competition for food resources during early life stages; a coexistence strategy to some extent. This research outlines the environmental requirements for successful spawning for different fish species. Understanding processes such as those outlined in this research paper is the basis of conservation of fish community diversity which is a critical resource to a successful sustainable fishery in the Pearl River.     

The uncertain road towards genomic medicine

Cheap, high-throughput approaches to generating biological data are transforming biology into a data-driven science and promise to similarly transform medicine. However, the road to genomic medicine is paved with challenges and uncertainty.     

Axon-bearing and axon-less horizontal cell subtypes are generated consecutively during chick retinal development from progenitors that are sensitive to follistatin

Background  

Horizontal cells are retinal interneurons that modulate the output from photoreceptors. A rich literature on the morphological classification and functional properties of HCs in different animals exists, however, the understanding of the events underlying their development is still limited. In most vertebrates including chicken, two main horizontal cell (HC) subtypes are identified based on the presence or absence of an axon.