The genetic mosaic suggests a new role for hitchhiking in ecological speciation

Early in ecological speciation, the genomically localized effects of divergent selection cause heterogeneity among loci in divergence between incipient species. We call this pattern of genomic variability in divergence the 'genetic mosaic of speciation'. Previous studies have used F(ST) outliers as a way to identify divergently selected genomic regions, but the nature of the relationship between outlier loci and quantitative trait loci (QTL) involved in reproductive isolation has not yet been quantified. Here, we show that F(ST) outliers between a pair of incipient species are significantly clustered around QTL for traits that cause ecologically based reproductive isolation. Around these key QTL, extensive 'divergence hitchhiking' occurs because reduced inter-race mating and negative selection decrease the opportunity for recombination between chromosomes bearing different locally adapted QTL alleles. Divergence hitchhiking is likely to greatly increase the opportunity for speciation in populations that are sympatric, regardless of whether initial divergence was sympatric or allopatric. Early in ecological speciation, analyses of population structure, gene flow or phylogeography based on different random or arbitrarily chosen neutral markers should be expected to conflict--only markers in divergently selected genomic regions will reveal the evolutionary history of adaptive divergence and ecologically based reproductive isolation. Species retain mosaic genomes for a very long time, and gene exchange in hybrid zones can vary dramatically among loci. However, in hybridizing species, the genomic regions that affect ecologically based reproductive isolation are difficult to distinguish from regions that have diverged for other reasons.     

A model of niche overlap and interaction in ecological systems

Ecological niches are the result of ecosystem element (compartment) interaction under the influence of environmental factors. The competence model is devised to map this interaction. It includes the assumption of an overall physiological state of a compartment depending only on intensive environmental factors, expressions for the adaptedness and competence of the compartment in interaction. Consequently, niches are environmental factor domains of superior competence. The situation of niches (niche structure) and competence maxima are extensively studied in the fundamental case of two interacting compartments and in the special case of n concentric compartments. The impact of one immigrating compartment is discussed. All detailed investigations made involve only one intensive environmental factor and the special assumption of similar physiological state functions of all compartments.     

The genetic structure of crossbills suggests rapid diversification with little niche conservatism

Conservatism of ecological niches can cause geographical ranges or the formation of new species to be constrained, and might be expected in situations where strong trade‐offs result in ecological specialization. Here we address the flexibility of resource use in European crossbills by comparing the ecological and genetic similarities between four Mediterranean and three northern European crossbill populations, all specialized in feeding on a different resource. We used sequence data of one mitochondrial and two nuclear genes from between 211 and 256 individuals. The northern crossbills were genetically too similar to infer which population was more related to the southern ones. Crossbills from the island of Mallorca showed genetic signatures of a stable and isolated population, supporting their past treatment as a locally (co)evolving taxon, and seem to have evolved from an ecologically distinct ancestor. Previous studies in other populations also suggest that genetic similarity does not predict morphological and resource similarity. We estimate that the divergence of all western European crossbills has occurred within the last 11 000 years. Overall, it appears that crossbills can diversify rapidly and with little niche conservatism, but that such potentially reproductively isolated specialists are evolutionarily short‐lived. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 908–922.     

A synthesis of transplant experiments and ecological niche models suggests that range limits are often niche limits

Global change has made it important to understand the factors that shape species’ distributions. Central to this area of research is the question of whether species’ range limits primarily reflect the distribution of suitable habitat (i.e. niche limits) or arise as a result of dispersal limitation. Over‐the‐edge transplant experiments and ecological niche models are commonly used to address this question, yet few studies have taken advantage of a combined approach for inferring the causes of range limits. Here, we synthesise results from existing transplant experiments with new information on the predicted suitability of sites based on niche models. We found that individual performance and habitat suitability independently decline beyond range limits across multiple species. Furthermore, inferences from transplant experiments and niche models were generally concordant within species, with 31 out of 40 cases fully supporting the hypothesis that range limits are niche limits. These results suggest that range limits are often niche limits and that the factors constraining species’ ranges operate at scales detectable by both transplant experiments and niche models. In light of these findings, we outline an integrative framework for addressing the causes of range limits in individual species.     

Food niche overlap and ecological separation in a multi-species community of shrews in the Siberian taiga

An investigation of the feeding habits and prey availability in a community of seven species of shrew (Insectivora: Soricidae) inhabiting the taiga of Central Siberia was carried out with the aim of quantifying levels of niche overlap and elucidating modes of ecological separation amongst these coexisting species. All species took a wide range of invertebrate prey, and overlap in the numbers of shared prey taxa was high, but differences in dietary composition of certain taxa reduced overlap between most species. Small species fed almost exclusively on small arthropods, mostly Araneae, Chilopoda and Coleoptera, while medium and large-sized species took high proportions of oligochaetes. Prey were mostly taken in proportions approximately equal to their availability, although certain prey appeared to be selected. All shrews took prey in a range of sizes, and the high dietary occurrence of small invertebrates reflected their availability and high encounter rate in field samples. Dietary occurrence of small prey was negatively correlated, and large prey positively correlated, with body size of shrew. Smaller shrews were predominantly ground-surface foragers while larger species were more subterranean, with body size and dietary occurrence of soil prey being positively correlated. Differences in prey size and foraging mode reduced niche overlap between shrew species of widely differing sizes. Each shrew species did not occupy a separate, well-defined food niche. Instead, the community was sub-divided into three functional groups: large and small species which tended towards specialization with relatively low levels of overlap, and intermediate, generalist species with higher levels of overlap.     

The ecological niche of a specialized subterranean spider

Hypogean habitats offer unique opportunities for ecological studies because they are characterized by low abundance and diversity of organisms, they receive low energy inputs, they are relatively stable from a climatic point of view, and they are quite easily modeled. However, given the harsh conditions of the working environment and difficulty of access, very few studies have investigated in detail the ecology of subterranean species directly in the field. In this study, we describe the ecological niche of the subterranean spider Troglohyphantes vignai (Araneae, Linyphiidae). We monitored the population of T. vignai in a disused graphite mine in the Western Italian Alps over 1 year, and recorded the main biotic and abiotic parameters characterizing each sampling plot (i.e., temperature, humidity, prey availability, illuminance, and structural complexity). The ecological niche of T. vignai was modeled through polynomial generalized linear mixed models (GLMM) and illustrated graphically by means of three‐dimensional plots and GIS techniques. The environmental range in which the probability of presence of T. vignai was higher was consistent with a trade‐off between climatic stability and food availability. Neither temporal nor spatial variation of the niche of T. vignai was detected through the year. The methodology used here may be easily adapted to other hypogean sites, paving the way to a novel understanding of niche partitioning in subterranean ecosystems.     

闽江口主要渔获鱼类的生态位宽度与重叠

根据2015年闽江口4个季度月(1、5、8、11月)的渔业资源底拖网调查资料,通过相对重要性指数确定主要渔获鱼类,对主要渔获鱼类的生态位宽度、生态位重叠进行分析.结果表明: 4个航次总共渔获鱼类137种,隶属16目37科,以鲈形目、鲱形目、鲽形目和鲀形目等为主.主要渔获鱼类有15种,其中优势种6种,分别为六指马鲅、龙头鱼、白姑鱼、鹿斑仰口鲾、短舌鳎和凤鲚,其余9种为重要种.时空生态位宽度值达到1以上的种类有7种,从大到小依次为短舌鳎、棘头梅童鱼、鹿斑仰口鲾、六丝钝尾虾虎鱼、赤鼻棱鳀、凤鲚、龙头鱼.主要渔获鱼类的生态位变动在闽江口受季节变化的影响比较明显.闽江口主要渔获鱼类种对的时空生态位重叠达有意义水平的种对占比较高,达81.9%,其中重叠显著的有6个种对,说明闽江口主要渔获鱼类间在时空二维上的分布普遍相似,在资源利用上存在竞争关系.时空生态位重叠值最大的种对为日本绯鲤-沙带鱼,重叠值最小的种对为日本绯鲤-棘头梅童鱼,时空生态位重叠受季节变化的影响比较明显.     

The niche of Salsuginus thalkeni, a gill parasite of Fundulus zebrinus

Distribution of a monogenean parasitic helminth Salsuginus thalkeni on the gills of the fish Fundulus zebrinus is described by calculation of mean positions and niche breadths on the linear spatial resource gradients gill filament length, gill arch length and arch number. All distributions are given for parasites in the presence and absence of various combinations of potential competitors, namely the 6 other parasite species that occupy the same host species. Filament niche breadth was narrowest in the absence of potential competitors; breadth on arch was widest in the presence of potential competitors. Breadth on both resources was correlated positively with mean number of parasites per individual. Arch breadth exhibited cyclic seasonal changes, being lowest in early to mid-summer. Mean position exhibited no repeated pattern of variation on either resource. The results are considered consistent with predictions about the niche structures of species in unsaturated noninteractive specialist communities.     

The structure of FtsZ filaments in vivo suggests a force-generating role in cell division

In prokaryotes, FtsZ (the filamentous temperature sensitive protein Z) is a nearly ubiquitous GTPase that localizes in a ring at the leading edge of constricting plasma membranes during cell division. Here we report electron cryotomographic reconstructions of dividing Caulobacter crescentus cells wherein individual arc-like filaments were resolved just underneath the inner membrane at constriction sites. The filaments' position, orientation, time of appearance, and resistance to A22 all suggested that they were FtsZ. Predictable changes in the number, length, and distribution of filaments in cells where the expression levels and stability of FtsZ were altered supported that conclusion. In contrast to the thick, closed-ring-like structure suggested by fluorescence light microscopy, throughout the constriction process the Z-ring was seen here to consist of just a few short (approximately 100 nm) filaments spaced erratically near the division site. Additional densities connecting filaments to the cell wall, occasional straight segments, and abrupt kinks were also seen. An 'iterative pinching' model is proposed wherein FtsZ itself generates the force that constricts the membrane in a GTP-hydrolysis-driven cycle of polymerization, membrane attachment, conformational change, depolymerization, and nucleotide exchange.     

The role of taste in food selection by African apes: implications for niche separation and overlap in tropical forests

Ripe fruit eating shapes the behavior of most of the apes. Gorillas (Gorilla gorilla) and chimpanzees (Pan troglodytes) are very different sizes and, consequently, have been traditionally viewed as ecologically distinct, but few studies have explored the behavioral and physiological foundations of their diets. Debate continues on the extent that large-bodied gorillas may be less selective and more opportunistic fruit eaters than chimpanzees. Taste responses have been predicted to relate to body size and digestive strategies. This study employs laboratory research on taste perception and discrimination among captive zoo-housed chimpanzees and relates it to previous work on gorillas to better characterize diets and niche separation among these apes. During the captive trials, differences were recorded in consumption patterns of water and varying concentrations of dilute aqueous fructose (sweet) and tannic acid solutions (astringent), compounds commonly found in wild foods. The chimpanzees exhibited similar preference thresholds for fructose (50 mM) to other primates studied. They exhibited slightly lower inhibition thresholds for tannic acid solutions than gorillas, but higher than smaller primates studied to date. These preliminary findings suggest that tannin tolerance may well be mediated by body size, though possible species differences in salivary proteins or other sensory differences remain to be explored. This research furthers our efforts to understand the roles of body size and physiological adaptations in shaping diet and niche separation of chimpanzees and gorillas.     

The structure of Antirrhinum centroradialis protein (CEN) suggests a role as a kinase regulator

Expression of the plant protein centroradialis (CEN) leads to a morphological switch between shoot growth and the development of flower structures (inflorescence). We have determined the crystal structure of Antirrhinum CEN to 1.9 A resolution. This structure confirms the CEN proteins as a subset of the family of phosphatidylethanolamine-binding proteins (PEBP), as predicted from sequence homology. Mammalian forms of PEBP have been found to act as inhibitors of MAP kinase signalling, a central signalling cascade regulating cell differentiation. CEN and PEBP proteins share a similar topology dominated by a large central beta-sheet. The strong conservation of a binding pocket at one end of this sheet which is capable of binding phosphoryl ligands, suggests the biological effects of CEN, like PEBP, arise from the ability of this region to form complexes with phosphorylated ligands, hence interfering with kinases and their effectors.     

The crystal structure of Escherichia coli MoaB suggests a probable role in molybdenum cofactor synthesis

The crystal structure of Escherichia coli MoaB was determined by multiwavelength anomalous diffraction phasing and refined at 1.6-A resolution. The molecule displayed a modified Rossman fold. MoaB is assembled into a hexamer composed of two trimers. The monomers have high structural similarity with two proteins, MogA and MoeA, from the molybdenum cofactor synthesis pathway in E. coli, as well as with domains of mammalian gephyrin and plant Cnx1, which are also involved in molybdopterin synthesis. Structural comparison between these proteins and the amino acid conservation patterns revealed a putative active site in MoaB. The structural analysis of this site allowed to advance several hypothesis that can be tested in further studies.     

The evolutionarily conserved trimeric structure of CutA1 proteins suggests a role in signal transduction

CutA1 are a protein family present in bacteria, plants, and animals, including humans. Escherichia coli CutA1 is involved in copper tolerance, whereas mammalian proteins are implicated in the anchoring of acetylcholinesterase in neuronal cell membranes. The x-ray structures of CutA1 from E. coli and rat were determined. Both proteins are trimeric in the crystals and in solution through an inter-subunit beta-sheet formation. Each subunit consists of a ferredoxin-like (beta1alpha1beta2beta3alpha2beta4) fold with an additional strand (beta5), a C-terminal helix (alpha3), and an unusual extended beta-hairpin involving strands beta2 and beta3. The bacterial CutA1 is able to bind copper(II) in vitro through His2Cys coordination in a type II water-accessible site, whereas the rat protein precipitates in the presence of copper(II). The evolutionarily conserved trimeric assembly of CutA1 is reminiscent of the architecture of PII signal transduction proteins. This similarity suggests an intriguing role of CutA1 proteins in signal transduction through allosteric communications between subunits.     

Modeling the ecological niche of long-term land use changes: The role of biophysical factors

Land use/land cover changes (LULCCs) represent the result of the complex interaction between biophysical factors and human activity, acting over a wide range of temporal and spatial scales. The aim of this work is to quantify the role of biophysical factors in constraining the trajectories of land abandonment and urbanization in the last 50 years. A habitat suitability model borrowed from animal ecology was used to analyze the ecological niche of the following LULCC trajectories occurred in Emilia-Romagna (northern Italy) during 1954–2008: (i) land abandonment (LA) and (ii) urbanization (URB), both from agricultural areas (URB_agr) and from semi-natural areas (URB_for). Results showed that the different LULCC trajectories were driven by different combinations of biophysical factors, such as climate, topography and soil quality. In particular, slope and elevation resulted as the main driving factors for rural processes, while slope and temperatures resulted as the main constraints underlying urban processes. This approach may represent a conceptual and technical step toward the systematic assessment of LULCC processes, thus providing an effective support tool to inform decision makers about land use transformations, their underlying causes, as well as their possible implications.     

Robustness of the outcome of adult bumblebee infection with a trypanosome parasite after varied parasite exposures during larval development

The outcome of defence by the invertebrate immunity has recently been shown to be more complex than previously thought. In particular, the outcome is affected by biotic and abiotic environmental variation, host genotype, parasite genotype and their interaction. Knowledge of conditions under which environmental variation affects the outcome of an infection is one important question that relates to this complexity. We here use the model system of the bumblebee, Bombus terrestris, infected by the trypanosome, Crithidia bombi, combined with a split-colony design to test the influence of the parasite environment during larval rearing on adult resistance. We find that genotype-specific interactions are maintained and adult resistance is not influenced. This demonstrates that environmental dependence of bumblebee-trypanosome interactions is not ubiquitous, and yet unknown constraints will maintain standard coevolutionary dynamics under such environmental deviations.     

The crystal structure of the Escherichia coli lipocalin Blc suggests a possible role in phospholipid binding

Lipocalins form a large multifunctional family of small proteins (15-25 kDa) first discovered in eukaryotes. More recently, several types of bacterial lipocalins have been reported, among which Blc from Escherichia coli is an outer membrane lipoprotein. As part of our structural genomics effort on proteins from E. coli, we have expressed, crystallized and solved the structure of Blc at 1.8 A resolution using remote SAD with xenon. The structure of Blc, the first of a bacterial lipocalin, exhibits a classical fold formed by a beta-barrel and a alpha-helix similar to that of the moth bilin binding protein. Its empty and open cavity, however, is too narrow to accommodate bilin, while the alkyl chains of two fatty acids or of a phospholipid could be readily modeled inside the cavity. Blc was reported to be expressed under stress conditions such as starvation or high osmolarity, during which the cell envelope suffers and requires maintenance. These data, together with our structural interpretation, suggest a role for Blc in storage or transport of lipids necessary for membrane repair or maintenance.     

Neonicotinoids override a parasite exposure impact on hibernation success of a key bumblebee pollinator

1. Seasonal adaptations enabling the bridging of periodic challenging abiotic conditions are taxonomically widespread. However, sensitivity to other environmental stresses can be heightened during these periods. 2. Several temperate insects with over‐wintering strategies play key ecosystem and economic roles, including wild bee pollinators. For example, hibernation survival in temperate bumblebees is crucial, as only new queens of future social colonies over‐winter. These bees are also faced with other abiotic and biotic stressors, some of which have been linked to recent pollinator declines, such as exposure to pesticides and parasites. 3. Using a fully crossed experiment, the influence of dietary exposure to neonicotinoid insecticides (thiamethoxam and clothianidin) and/or the prevalent bumblebee parasite Crithidia bombi on hibernation survival and hibernation weight change of Bombus terrestris bumblebee queens was investigated. 4. Both neonicotinoid and C. bombi exposures reduced hibernation success individually, but no additive or synergistic effects between the stressors were found. Further, effects were asynchronous, with early neonicotinoid effects on hibernation mortality overriding later parasite effects under combined exposures. Neonicotinoid exposure also increased hibernation weight loss of surviving queens. 5. Diapause periods, employed by numerous temperate organisms, are likely to be especially vulnerable to environmental stresses, besides the seasonal challenge for which these periods are an adaptation. Thus, diapause requires inclusion during the consideration of the impacts of such stresses. Accordingly, it is demonstrated here that naturally relevant exposures of pesticides and parasites have important detrimental effects on bumblebees during a critical hibernation period, with potential consequences for populations of these key wild pollinators.