Species-genus ratios reflect a global history of diversification and range expansion in marine bivalves

The distribution of marine bivalve species among genera and higher taxa takes the form of the classic hollow curve, wherein few lineages are species rich and many are species poor. The distribution of species among genera (S/G ratio) varies with latitude, with temperate S/G's falling within the null expectation, and tropical and polar S/G's exceeding it. Here, we test several hypotheses for this polar overdominance in the species richness of small numbers of genera. We find a significant positive correlation between the latitudinal range of a genus and its species richness, both globally and within regions. Genus age and species richness are also positively related, but this relationship breaks down when the analysis is limited to genera endemic to climate zones or with narrow latitudinal ranges. The data suggest a link between speciation and range-expansion, with genera expanding out of the tropical latitudinal bins tending to speciate more prolifically, both globally and regionally. These genera contain more species within climate zones than taxa endemic to that zone. Range expansion thus appears to be fundamentally coupled with speciation, producing the skewed distribution of species among genera, both globally and regionally, whereas clade longevity is achieved through extinction -- resistance conferred by broad geographical ranges.     

Modelling the development and arrangement of the primary vascular structure in plants

Background and Aims

The process of vascular development in plants results in the formation of a specific array of bundles that run throughout the plant in a characteristic spatial arrangement. Although much is known about the genes involved in the specification of procambium, phloem and xylem, the dynamic processes and interactions that define the development of the radial arrangement of such tissues remain elusive.

Methods

This study presents a spatially explicit reaction–diffusion model defining a set of logical and functional rules to simulate the differentiation of procambium, phloem and xylem and their spatial patterns, starting from a homogeneous group of undifferentiated cells.

Key Results

Simulation results showed that the model is capable of reproducing most vascular patterns observed in plants, from primitive and simple structures made up of a single strand of vascular bundles (protostele), to more complex and evolved structures, with separated vascular bundles arranged in an ordered pattern within the plant section (e.g. eustele).

Conclusions

The results presented demonstrate, as a proof of concept, that a common genetic–molecular machinery can be the basis of different spatial patterns of plant vascular development. Moreover, the model has the potential to become a useful tool to test different hypotheses of genetic and molecular interactions involved in the specification of vascular tissues.     

Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional‐scale disturbance

Much attention is paid in conservation planning to the concept of a species, to ensure comparability across studies and regions when classifying taxa against criteria of endangerment and setting priorities for action. However, various jurisdictions now allow taxonomic ranks below the level of species and nontaxonomic intraspecific divisions to be factored into conservation planning—subspecies, key populations, evolutionarily significant units, or designatable units. Understanding patterns of genetic diversity and its distribution across the landscape is a key component in the identification of species boundaries and determination of substantial geographic structure within species. A total of 12,532 reliable polymorphic SNP loci were generated from 63 populations (286 individuals) covering the distribution of the Australian eastern three‐lined skink, Bassiana duperreyi, to assess genetic population structure in the form of diagnosable lineages and their distribution across the landscape, with particular reference to the recent catastrophic bushfires of eastern Australia. Five well‐supported diagnosable operational taxonomic units (OTUs) existed within B. duperreyi. Low levels of divergence of B. duperreyi between mainland Australia and Tasmania (no fixed allelic differences) support the notion of episodic exchange of alleles across Bass Strait (ca 60 m, 25 Kya) during periods of low sea level during the Upper Pleistocene rather than the much longer period of isolation (1.7 My) indicated by earlier studies using mitochondrial sequence variation. Our study provides foundational work for the detailed taxonomic re‐evaluation of this species complex and the need for biodiversity assessment to include an examination of cryptic species and/or cryptic diversity below the level of species. Such information on lineage diversity within species and its distribution in the context of disturbance at a regional scale can be factored into conservation planning regardless of whether a decision is made to formally diagnose new species taxonomically and nomenclaturally.     

Allozyme analyses of the genus Trisopterus: taxonomic status and population structure of the poor cod

Genetic analysis of the four Trisopterus (Gadidae) taxa suggests that the interrelationships of the two morphs of poor cod ( T. minutus minutus in the Atlantic and T. minutus capelanus in the Mediterranean) should be reconsidered. The Mediterranean poor cod T. m. capelanus is more closely related to bib T. luscus than to the Atlantic poor cod, so the population structure in the Atlantic and Mediterranean poor cod must be considered separately. Among 635 Atlantic individuals there was some evidence of poor cod population differentiation (allele frequency heterogeneity test P <0·0005; F _ST=0·0135, P ≤0·0005). Levels of genetic variation were similar to those reported for related gadoid species. Some differentiation was present on the Norwegian coast (samples from Trondheimsfjord) and between the Faeroe Islands (Faeroe Bank) and the adjacent European coastal location. In contrast no statistically significant population differentiation was evident in Mediterranean poor cod, but fewer samples and individuals were screened.     

The geographic, taxonomic and temporal distribution of determinate growth in marine gastropods

Many marine gastropods are characterized by determinate growth, as inferred from the presence of unique terminal elaborations of the shell's aperture. Although determinate growth has evolved repeatedly in most major gastropod clades, it is especially frequent among siphonate caenogastropods. Analyses of shallow-water assemblages show that the incidence of species with determinate growth is far higher in the tropics (especially the tropical Pacific and Indian Oceans) than at higher latitudes. Compilations of fossil assemblages from warm-water environments indicate that, although determinate growth occurred in some Palaeozoic gastropods, it became widespread only in the Neogene. In some groups, terminal apertural elaborations arose in lineages whose growth was more or less continuous and indeterminate, but in others it was derived either from or was ancestral to episodic growth. The hypothesis that periodic or terminal apertural elaborations evolved as a means to dispose of calcium carbonate once growth in the spiral direction ceased is rejected in favour of functional interpretations. Among the latter, the roles of modified apertures in defence and in mate recognition are explored, but no firm conclusion regarding the latter possibility can be drawn owing to our ignorance of mate recognition in gastropods.     

Toward a conceptual framework for managing and conserving marine habitats: A case study of kelp forests in the Salish Sea

Kelp forests are in decline across much of their range due to place‐specific combinations of local and global stressors. Declines in kelp abundance can lead to cascading losses of biodiversity and productivity with far‐reaching ecological and socioeconomic consequences. The Salish Sea is a hotspot of kelp diversity where many species of kelp provide critical habitat and food for commercially, ecologically, and culturally important fish and invertebrate species. However, like other regions, kelp forests in much of the Salish Sea are in rapid decline. Data gaps and limited long‐term monitoring have hampered attempts to identify and manage for specific drivers of decline, despite the documented urgency to protect these important habitats. To address these knowledge gaps, we gathered a focus group of experts on kelp in the Salish Sea to identify perceived direct and indirect stressors facing kelp forests. We then conducted a comprehensive literature review of peer‐reviewed studies from the Salish Sea and temperate coastal ecosystems worldwide to assess the level of support for the pathways identified by the experts, and we identified knowledge gaps to prioritize future research. Our results revealed major research gaps within the Salish Sea and highlighted the potential to use expert knowledge for making informed decisions in the region. We found high support for the pathways in the global literature, with variable consensus on the relationship between stressors and responses across studies, confirming the influence of local ecological, oceanographic, and anthropogenic contexts and threshold effects on stressor–response relationships. Finally, we prioritized areas for future research in the Salish Sea. This study demonstrates the value expert opinion has to inform management decisions. These methods are readily adaptable to other ecosystem management contexts, and the results of this case study can be immediately applied to kelp management.     

Differential extinction and the contrasting structure of polar marine faunas

Background

The low taxonomic diversity of polar marine faunas today reflects both the failure of clades to colonize or diversify in high latitudes and regional extinctions of once-present clades. However, simple models of polar evolution are made difficult by the strikingly different faunal compositions and community structures of the two poles.

Methodology/Principal Findings

A comparison of early Cenozoic Arctic and Antarctic bivalve faunas with modern ones, within the framework of a molecular phylogeny, shows that while Arctic losses were randomly distributed across the tree, Antarctic losses were significantly concentrated in more derived families, resulting in communities dominated by basal lineages. Potential mechanisms for the phylogenetic structure to Antarctic extinctions include continental isolation, changes in primary productivity leading to turnover of both predators and prey, and the effect of glaciation on shelf habitats.

Conclusions/Significance

These results show that phylogenetic consequences of past extinctions can vary substantially among regions and thus shape regional faunal structures, even when due to similar drivers, here global cooling, and provide the first phylogenetic support for the “retrograde” hypothesis of Antarctic faunal evolution.     

Lack of definition of mathematical terms in ecology: The case of the sigmoid class of functions in macro‐ecology

Defining mathematical terms and objects is a constant issue in ecology; often definitions are absent, erroneous, or imprecise. Through a bibliographic prospection, we show that this problem appears in macro‐ecology (biogeography and community ecology) where the lack of definition for the sigmoid class of functions results in difficulties of interpretation and communication. In order to solve this problem and to help harmonize papers that use sigmoid functions in ecology, herein we propose a comprehensive definition of these mathematical objects. In addition, to facilitate their use, we classified the functions often used in the ecological literature, specifying the constraints on the parameters for the function to be defined and the curve shape to be sigmoidal. Finally, we interpreted the different properties of the functions induced by the definition through ecological hypotheses in order to support and explain the interest of such functions in ecology and more precisely in biogeography.     

Species pool structure determines the level of generalism of island parasitoid faunas

Aim To examine whether island parasitoid faunas are biased towards generalists when compared with the mainland and their species pool, and to evaluate the effects of climate, island characteristics and regional factors on the relative proportions of idiobionts (i.e. generalists) and koinobionts (i.e. specialists) of two parasitic wasp families, Braconidae and Ichneumonidae. Location Seventy‐three archipelagos distributed world‐wide. Methods We used data on the distribution and biology obtained from a digital catalogue and several literature sources. We related level of generalism, measured as the ratio between the number of idiobiont and koinobiont species, to climatic, physiographic and regional factors using generalized linear models. We compared models by means of Akaike weighting, and evaluated the spatial structure of their residuals. We used partial regressions to determine whether the final models account for all latitudinal structure in the level of generalism. Results Islands host comparatively more idiobionts than continental areas. Although there is a latitudinal gradient in the level of generalism of island faunas correlating with both environmental factors and island characteristics, the most important determinant of island community structure is their source pool. This effect is stronger for ichneumonids, where generalism is higher in the Indomalayan region, arguably due to the higher diversity of endophytic hosts in its large rain forests. Main conclusions The level of generalism of island parasitoid faunas is largely constrained by regional factors, namely by the structure of the species pool, which emphasizes the importance of including regional processes in our understanding of the functioning of ecological communities. The fact that generalist species are more predominant in islands with a large cover of rain forests pinpoints the importance of the indirect effects of ecological requirements on community structure, highlighting the complex nature of geographical gradients of diversity.     

Long-term temporal variation in the organization of an ant–plant network

Background and Aims

Functional groups of species interact and coevolve in space and time, forming complex networks of interacting species. A long-term study of temporal variation of an ant–plant network is presented with the aims of: (1) depicting its structural changes over a 20-year period; (2) detailing temporal variation in network topology, as revealed by nestedness and modularity analysis and other parameters (i.e. connectance, niche overlap); and (3) identifying long-term turnover in taxonomic structure (i.e. switches in ant resource use or plant visitor assemblages according to taxa).

Methods

Fieldwork was carried out at La Mancha, Mexico, and ant–plant interactions were observed between 1989 and 1991, between 1998 and 2000, and between May 2010 and 2011. Occurrences of ants on extrafloral nectaries (EFNs) were recorded. The resulting ant–plant networks were constructed from qualitative presence–absence data determined by a species–species matrix defined by the frequency of occurrence of each pairwise ant–plant interaction.

Key Results

Network variation across time was stable and a persistent nested structure may have contributed to the maintenance of resilient and species-rich communities. Modularity was lower than expected, especially in the most recent networks, indicating that the community exhibited high overlap among interacting species (e.g. few species were hubs in the more recent network, being partly responsible for the nested pattern). Structurally, the connections created among modules by super-generalists gave cohesion to subsets of species that otherwise would remain unconnected. This may have allowed an increasing cascade-effect of evolutionary events among modules. Mutualistic ant–plant interactions were structured 20 years ago mainly by the subdominant nectarivorous ant species Camponotus planatus and Crematogaster brevispinosa, which monopolized the best extrafloral nectar resources and out-competed other species with broader feeding habits. Through time, these ants, which are still present, lost their position as network hubs and diminished in their importance in structuring the network; simultaneously, plants gained in importance.

Conclusions

The long-term network analysis reveals a decrease in attended plant species richness, a notable increase in plant species participation from 1990 to 2010 (sustained by less plant taxonomic similarity in the older 1990 network), an increase in the number of ant species and a diminishing dominance of super-generalist ants. The structure of the community has remained highly nested and connected with low modularity, suggesting overall a more participative, homogeneous, cohesive interaction network. Although previous studies have suggested that interactions between ants and EFN-bearing plants are susceptible to seasonality, abiotic factors and perturbation, this cohesive structure appears to be the key for biodiversity and community maintenance.     

Solution structure and backbone dynamics of Calsensin, an invertebrate neuronal calcium-binding protein

Calsensin is an EF-hand calcium-binding protein expressed by a subset of peripheral sensory neurons that fasciculate into a single tract in the leech central nervous system. Calsensin is a 9-kD protein with two EF-hand calcium-binding motifs. Using multidimensional NMR spectroscopy we have determined the solution structure and backbone dynamics of calcium-bound Calsensin. Calsensin consists of four helices forming a unicornate-type four-helix bundle. The residues in the third helix undergo slow conformational exchange indicating that the motion of this helix is associated with calciumbinding. The backbone dynamics of the protein as measured by (15)N relaxation rates and heteronuclear NOEs correlate well with the three-dimensional structure. Furthermore, comparison of the structure of Calsensin with other members of the EF-hand calcium-binding protein family provides insight into plausible mechanisms of calcium and target protein binding.     

Effects of age,sex, and ENSO phase on foraging and flight performance in Nazca boobies

Age‐related changes in survival and reproduction are common in seabirds; however, the underlying causes remain elusive. A lack of experience for young individuals, and a decline in foraging performance for old birds, could underlie age‐related variation in reproduction because reproductive success is connected closely to provisioning offspring. For seabirds, flapping flight during foraging trips is physiologically costly; inexperience or senescent decline in performance of this demanding activity might cap delivery of food to the nest, providing a proximate explanation for poor breeding success in young and old age, respectively. We evaluated the hypothesis that young and old Nazca boobies (Sula granti), a Galápagos seabird, demonstrate deficits in foraging outcomes and flight performance. We tagged incubating male and female adults across the life span with both accelerometer and GPS loggers during the incubation periods of two breeding seasons (years), during the 2015 El Niño and the following weak La Niña. We tested the ability of age, sex, and environment to explain variation in foraging outcomes (e.g., mass gained) and flight variables (e.g., wingbeat frequency). Consistent with senescence, old birds gained less mass while foraging than middle‐aged individuals, a marginal effect, and achieved a slower airspeed late in a foraging trip. Contrary to expectations, young birds showed no deficit in foraging outcomes or flight performance, except for airspeed (contingent on environment). Young birds flew slower than middle‐aged birds in 2015, but faster than middle‐aged birds in 2016. Wingbeat frequency, flap–glide ratio, and body displacement (approximating wingbeat strength) failed to predict airspeed and were unaffected by age. Sex influenced nearly all aspects of performance. Environment affected flight performance and foraging outcomes. Boobies'' foraging outcomes were better during the extreme 2015 El Niño than during the 2016 weak La Niña, a surprising result given the negative effects tropical seabirds often experience during extreme El Niños.     

Adaptive population structure shifts in invasive parasitic mites,Varroa destructor

Comparative studies of genetic diversity and population structure can shed light on the ecological and evolutionary factors governing host–parasite interactions. Even though invasive parasites are considered of major biological importance, little is known about their adaptative potential when infesting the new hosts. Here, the genetic diversification of Varroa destructor, a novel parasite of Apis mellifera originating from Asia, was investigated using population genetics to determine how the genetic structure of the parasite changed in distinct European populations of its new host. To do so, mites infesting two categories of hosts in four European regions were compared: (a) adapted hosts surviving through means of natural selection, thereby expected to impose strong selective pressure on the mites, and (b) treated host populations, surviving mite infestations because acaricides are applied, therefore characterized by a relaxed selection imposed by the host on the mites. Significant genetic divergence was found across regions, partially reflecting the invasion pattern of V. destructor throughout Europe and indicating local adaptation of the mite to the host populations. Additionally, varying degrees of genotypic changes were found between mites from adapted and treated colonies. Altogether, these results indicate that V. destructor managed to overcome the genetic bottlenecks following its introduction in Europe and that host‐mediated selection fostered changes in the genetic structure of this mite at diverse geographic scales. These findings highlight the potential of parasites to adapt to their local host populations and confirm that adaptations developed within coevolutionary dynamics are a major determinant of population genetic changes.     

Statistical ecology comes of age

The desire to predict the consequences of global environmental change has been the driver towards more realistic models embracing the variability and uncertainties inherent in ecology. Statistical ecology has gelled over the past decade as a discipline that moves away from describing patterns towards modelling the ecological processes that generate these patterns. Following the fourth International Statistical Ecology Conference (1–4 July 2014) in Montpellier, France, we analyse current trends in statistical ecology. Important advances in the analysis of individual movement, and in the modelling of population dynamics and species distributions, are made possible by the increasing use of hierarchical and hidden process models. Exciting research perspectives include the development of methods to interpret citizen science data and of efficient, flexible computational algorithms for model fitting. Statistical ecology has come of age: it now provides a general and mathematically rigorous framework linking ecological theory and empirical data.     

Network robustness and structure depend on the phenological characteristics of plants and pollinators

Many structural patterns have been found to be important for the stability and robustness of mutualistic plant–pollinator networks. These structural patterns are impacted by a suite of variables, including species traits, species abundances, their spatial configuration, and their phylogenetic history. Here, we consider a specific trait: phenology, or the timing of life history events. We expect that timing and duration of activity of pollinators, or of flowering in plants, could greatly affect the species'' roles within networks in which they are embedded. Using plant–pollinator networks from 33 sites in southern British Columbia, Canada, we asked (a) how phenological species traits, specifically timing of first appearance in the network and duration of activity in a network, were related to species'' roles within a network, and (b) how those traits affected network robustness to phenologically biased species loss. We found that long duration of activity increased connection within modules for both pollinators and plants and among modules for plants. We also found that date of first appearance was positively related to interaction strength asymmetry in plants but negatively related to pollinators. Networks were generally more robust to the loss of pollinators than plants, and robustness increased if the models allow new interactions to form when old ones are lost, constrained by overlapping phenology of plants and pollinators. Robustness declined with the loss of late‐flowering plants, which tended to have higher interaction strength asymmetry. In addition, robustness declined with loss of early‐flying or long‐duration pollinators. These pollinators tended to be among‐module connectors. Our results point to networks being limited by early‐flying pollinators. If plants flower earlier due to climate change, plant fitness may decline as they will depend on early emerging pollinators, unless pollinators also emerge earlier.     

Crystal structure of the capsular polysaccharide synthesizing protein CapE of Staphylococcus aureus

Enzymes synthesizing the bacterial CP (capsular polysaccharide) are attractive antimicrobial targets. However, we lack critical information about the structure and mechanism of many of them. In an effort to reduce that gap, we have determined three different crystal structures of the enzyme CapE of the human pathogen Staphylococcus aureus. The structure reveals that CapE is a member of the SDR (short-chain dehydrogenase/reductase) super-family of proteins. CapE assembles in a hexameric complex stabilized by three major contact surfaces between protein subunits. Turnover of substrate and/or coenzyme induces major conformational changes at the contact interface between protein subunits, and a displacement of the substrate-binding domain with respect to the Rossmann domain. A novel dynamic element that we called the latch is essential for remodelling of the protein–protein interface. Structural and primary sequence alignment identifies a group of SDR proteins involved in polysaccharide synthesis that share the two salient features of CapE: the mobile loop (latch) and a distinctive catalytic site (MxxxK). The relevance of these structural elements was evaluated by site-directed mutagenesis.