Dryad Data Packages

Data from: Substandard and falsified medicines in the UK: A retrospective review of drug alerts (2001–2011)

2013-06-19T19:52:27Z

Objective: To determine the extent of substandard and falsified medicines in the UK. Design: A retrospective review of drug alerts and company-led recalls. Setting: The Medicines and Healthcare Products Regulatory Agency (MHRA) website search for drug alerts issued between 2001 and 2011. Eligibility criteria: Drug alerts related to quality defect in medicinal products. Main outcome measure: Relevant data about defective medicines reported in drug alerts and company-led recalls, including description of the defect, type of formulation, year of the alert and category of the alert. Results: There were 280 substandard medicines of which 222 were recalled. The two most frequent problems were contamination (74 incidents) and issues related to packaging (98 incidents). Formulations for parenteral administration (117 incidents) were the formulation most frequently affected. There were 11 falsified medicines, as defined by the MHRA, reported over the 11 year period. The number of defective medicines reported by the MHRA increased tenfold from five in 2001 to 50 in 2011. Conclusions: Substandard medicines are a significant problem in the UK. It is uncertain whether the increasing number of reports relates to improved detection or an increase in the number of substandard medicines.

Data from: Leaf drop affects herbivory in oaks

2013-06-19T18:41:26Z

Leaf phenology is important to herbivores, but the timing and extent of leaf drop has not played an important role in our understanding of herbivore interactions with deciduous plants. Using phylogenetic general least squares regression, we compared the phenology of leaves of 55 oak species in a common garden with the abundance of leaf miners on those trees. Mine abundance was highest on trees with an intermediate leaf retention index, i.e. trees that lost most, but not all, of their leaves for 2–3 months. The leaves of more evergreen species were more heavily sclerotized, and sclerotized leaves accumulated fewer mines in the summer. Leaves of more deciduous species also accumulated fewer mines in the summer, and this was consistent with the idea that trees reduce overwintering herbivores by shedding leaves. Trees with a later leaf set and slower leaf maturation accumulated fewer herbivores. We propose that both leaf drop and early leaf phenology strongly affect herbivore abundance and select for differences in plant defense. Leaf drop may allow trees to dispose of their herbivores so that the herbivores must recolonize in spring, but trees with the longest leaf retention also have the greatest direct defenses against herbivores.

Data from: Nutrient regulation strategies differ between cricket morphs that trade-off dispersal and reproduction

2013-06-19T18:05:42Z

1. Nutrient regulation should covary with life history, but actual demonstrations of this connection are rare. 2. Here we use a wing-polymorphic cricket, Gryllus firmus, that trades-off dispersal and reproduction; the long-winged morph with functional flight muscles (LW(f)) is adapted for dispersal at the expense of egg production, while the short-winged (SW) morph is adapted for egg production at the expense of flight. We explore the extent to which these two morphs differentially regulate macronutrient intake to best match their life history strategy. 3. In a “choice” experiment, we offered female crickets of each morph (LW(f) and SW) two nutritionally complementary foods varying in protein and digestible carbohydrate content. In a second “no-choice” experiment, we confined crickets to one of five foods, each with a different protein-carbohydrate-ratio. In both experiments, and for both morphs, we measured food intake, mass gain, and lipid concentration. 4. In the “choice” experiments, LW(f) females selected a more carbohydrate-biased diet than SW females. The two morphs gained similar total mass, but the LW morph had higher lipid concentration. 5. In the no-choice experiment, the two morphs practiced different nutrient “consumption rules.” SW females ate similar total nutrient amounts (protein plus carbohydrate) across diets, while LW(f) females decreased intake as the protein-carbohydrate ratio of the available food became increasingly imbalanced. Overall mass gain was marginally higher in the SW morph, and lowest on the diets that were extremely carbohydrate-biased. LW(f) and SW females had similar lipid concentrations across the diets, even though LW(f) crickets ate less carbohydrate on the two carbohydrate-biased diets. Our data suggest that for LW(f) females there are costs of overeating nutrients in excess of requirements, but they are efficient at utilizing ingested nutrients. 6. Our results shed new light on how the nutritional environment interacts with the direct trade-off between dispersal and reproduction occurring in adult G. firmus crickets. Dispersal is linked to heightened diet selectivity and an emphasis on nutrients promoting flight fuel (lipid) storage over protein acquisition for egg-laying, such that nutritional regulation complements the metabolic mechanisms that generate this trade-off.

Data from: Projected climate-driven faunal movement routes

2013-06-19T16:32:51Z

Historically, many species moved great distances as climates changed. However, modern movements will be limited by the patterns of human-dominated landscapes. Here, we use a combination of projected climate-driven shifts in the distributions of 2903 vertebrate species, estimated current human impacts on the landscape, and movement models, to determine through which areas in the western hemisphere species will likely need to move to track suitable climates. Our results reveal areas with projected high densities of climate-driven movements – including, the Amazon Basin, the southeastern United States and southeastern Brazil. Some of these regions, such as southern Bolivia and northern Paraguay, contain relatively intact landscapes, whereas others such as the southeastern United States and Brazil are heavily impacted by human activities. Thus, these results highlight both critical areas for protecting lands that will foster movement, and barriers where human land-use activities will likely impede climate-driven shifts in species distributions.

Data from: A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

2013-06-19T16:24:53Z

Introduction: The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries. This is largely because the available versatile (“universal”) COI primers target the 658 barcoding region, whose size is considered too large for many NGS applications. Moreover, traditional barcoding primers are known to be poorly conserved across some taxonomic groups. Results: We first design a new PCR primer within the highly variable mitochondrial COI region, the “mlCOIintF” primer. We then show that this newly designed forward primer combined with the “jgHCO2198” reverse primer to target a 313 bp fragment performs well across metazoan diversity, with higher success rates than versatile primer sets traditionally used for DNA barcoding (i.e. LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment coupled with an efficient bioinformatics pipeline can be used to characterize species diversity from environmental samples by pyrosequencing. We examine the gut contents of three species of planktivorous and benthivorous coral reef fish (family: Apogonidae and Holocentridae). After the removal of dubious COI sequences, we obtained a total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla from 16 fish guts. Of these, 52.5% matched a reference barcode (>98% sequence similarity) and an additional 32% could be assigned to a higher taxonomic level using Bayesian assignment. Conclusions: The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies. We believe that this primer set will be a valuable asset for a range of applications from large-scale biodiversity assessments to food web studies.

Data from: A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs)

2013-06-19T16:07:21Z

Ray-finned fishes constitute the dominant radiation of vertebrates with over 32,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes.

Data from: Legume phylogeny and classification in the 21st century: progress, prospects and lessons for other species-rich clades

2013-06-18T18:02:51Z

The Leguminosae, the third-largest angiosperm family, has a global distribution and high ecological and economic importance. We examine how the legume systematic research community might join forces to produce a comprehensive phylogenetic estimate for the ca. 751 genera and ca. 19,500 species of legumes and then translate it into a phylogeny-based classification. We review the current state of knowledge of legume phylogeny and highlight where problems lie, for example in taxon sampling and phylogenetic resolution. We review approaches from bioinformatics and next-generation sequencing, which can facilitate the production of better phylogenetic estimates. Finally, we examine how morphology can be incorporated into legume phylogeny to address issues in comparative biology and classification. Our goal is to stimulate the research needed to improve our knowledge of legume phylogeny and evolution; the approaches that we discuss may also be relevant to other species-rich angiosperm clades.

Data from: Scale-dependent foraging ecology of a marine top predator modelled using passive acoustic data

2013-06-18T14:08:19Z

1. Understanding which environmental factors drive foraging preferences is critical for the development of effective management measures, but resource use patterns may emerge from processes that occur at different spatial and temporal scales. Direct observations of foraging are also especially challenging in marine predators, but passive acoustic techniques provide opportunities to study the behavior of echolocating species over a range of scales. 2. We used an extensive passive acoustic dataset to investigate the distribution and temporal dynamics of foraging in bottlenose dolphins using the Moray Firth (Scotland, UK). Echolocation buzzes were identified with a mixture model of detected echolocation inter-click intervals, and used as a proxy of foraging activity. A robust modelling approach accounting for autocorrelation in the data was then used to evaluate which environmental factors were associated with the observed dynamics at two different spatial and temporal scales. 3. At a broad scale, foraging varied seasonally, and was also affected by sea-bed slope and shelf-sea fronts. At a finer scale, we identified variation in seasonal use and local interactions with tidal processes. Foraging was best predicted at a daily scale, accounting for site-specificity in the shape of the estimated relationships. 4. This study demonstrates how passive acoustic data can be used to understand foraging ecology in echolocating species, and provides a robust analytical procedure for describing spatio-temporal patterns. Associations between foraging and environmental characteristics varied according to spatial and temporal scale, highlighting the need for a multi-scale approach. Our results indicate that dolphins respond to coarser-scale temporal dynamics, but have a detailed understanding of finer-scale spatial distribution of resources.

Data from: Are shy individuals less behaviorally variable? Insights from a captive population of mouse lemurs

2013-06-17T19:55:25Z

Increasingly, individual variation in personality has become a focus of behavioral research in animal systems. Boldness and shyness, often quantified as the tendency to explore novel situations, are seen as personality traits important to the fitness landscape of individuals. Here we tested for individual differences within and across contexts in behavioral responses of captive mouse lemurs (Microcebus murinus) to novel objects, novel foods, and handling. We report consistent differences in behavioral responses for objects and handling. We also found that the responses to handling and novel objects were correlated and repeatable. Lastly, we show that shyer individuals may show less variability in their behavioral responses. This study provides new information on the potential for behavioral syndromes in this species and highlights differences in the degree to which behavioral types (e.g., shy/bold) vary in their behavioral responses.

Data from: Condition-dependent expression of pre- and postcopulatory sexual traits in guppies

2013-06-17T19:09:09Z

Female choice can impose persistent directional selection on male sexually selected traits, yet such traits often exhibit high levels of phenotypic variation. One explanation for this paradox is that if sexually selected traits are costly, only the fittest males are able to acquire and allocate the resources required for their expression. Furthermore, because male condition is dependent on resource allocation, condition dependence in sexual traits is expected to underlie trade-offs between reproduction and other life-history functions. In this study we test these ideas by experimentally manipulating diet quality (carotenoid levels) and quantity in the guppy (Poecilia reticulata), a livebearing freshwater fish that is an important model for understanding relationships between pre- and post-copulatory sexually selected traits. Specifically, we test for condition dependence in the expression of pre- and postcopulatory sexual traits (behavior, ornamentation, sperm traits) and determine whether diet manipulation mediates relationships among these traits. Consistent with prior work we found a significant effect of diet quantity on the expression of both pre- and postcopulatory male traits; diet-restricted males performed fewer sexual behaviors and exhibited significant reductions in color ornamentation, sperm quality, sperm number, and sperm length than those fed ad libitum. However, contrary to our expectations, we found no significant effect of carotenoid manipulation on the expression of any of these traits, and no evidence for a trade-off in resource allocation between pre- and postcopulatory episodes of sexual selection. Our results further underscore the sensitivity of behavioral, ornamental, and ejaculate traits to dietary stress, and highlight the important role of condition dependence in maintaining the high variability in male sexual traits.

Data from: Phylogeny of salmonids (salmoniformes: Salmonidae) and its molecular dating: analysis of mtDNA data

2013-06-17T18:46:47Z

Phylogenetic relationships among 41 species of salmonid fish and some aspects of their diversification-time history were studied using the GenBank and original mtDNA data. The position of the root of the Salmonidae phylogenetic tree was uncertain. Among the possible variants, the most reasonable seems to be that in which thymallins are grouped into the same clade as coregonins and the lineage of salmonins occupied a basal position relative to this clade. The genera of Salmoninae formed two distinct clades, i.e., (Brachymystax, Hucho) and (Salmo, Parahucho, (Salvelinus, (Parasalmo, Oncorhynchus)). Furthermore, the genera Parasalmo and Oncorhynchus were reciprocally monophyletic. The congruence of Salmonidae phylogenetic trees obtained using different types of phylogenetic markers is discussed. According to Bayesian dating, ancestral lineages of salmonids and their sister esocoids diverged about 106 million years ago. Sometime after, probably 100–70 million years ago, the salmonid-specific whole genome duplication took place. The divergence of salmonid lineages on the genus level occurred much later, within the time interval of 42–20 million years ago. The main wave of the diversification of salmonids at the species level occurred during the last 12 million years. The possible effect of genome duplication on the Salmonidae diversification pattern is discussed.

Data from: Inferences of evolutionary history of a widely distributed mangrove species, Bruguiera gymnorrhiza, in the Indo-West Pacific region

2013-06-17T18:20:16Z

Inference of genetic structure and demographic history is fundamental issue in evolutionary biology. We examined the levels and patterns of genetic variation of a widespread mangrove species in the Indo-West Pacific region, Bruguiera gymnorrhiza, using ten nuclear gene regions. Genetic variation of individual populations covering its distribution range was low, but as the entire species it was comparable to other plant species. Genetic differentiation among the investigated populations was high. They could be divided into two genetic clusters: the West and East clusters of the Malay Peninsula. Our results indicated that these two genetic clusters derived from their ancestral population whose effective size of which was much larger compared to the two extant clusters. The point estimate of speciation time between B. gymnorrhiza and Bruguiera sexangula was two times older than that of divergence time between the two clusters. Migration from the West cluster to the East cluster was much higher than the opposite direction but both estimated migration rates were low. The past Sundaland and/or the present Malay Peninsula are likely to prevent gene flow between the West and East clusters and function as a geographical or land barrier.

Data from: Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets

2013-06-17T17:19:46Z

DNA barcoding-type studies assemble single-locus data from large samples of individuals and species, and have provided new kinds of data for evolutionary surveys of diversity. An important goal of many such studies is to delimit evolutionarily significant species units, especially in biodiversity surveys from environmental DNA samples. The Generalized Mixed Yule Coalescent (GMYC) method is a likelihood method for delimiting species by fitting within- and between-species branching models to reconstructed gene trees. Although the method has been widely used, it has not previously been described in detail or evaluated fully against simulations of alternative scenarios of true patterns of population variation and divergence between species. Here, we present important reformulations to the GMYC method as originally specified, and demonstrate its robustness to a range of departures from its simplifying assumptions. The main factor affecting the accuracy of delimitation is the mean population size of species relative to divergence times between them. Other departures from the model assumptions, such as varying population sizes among species, alternative scenarios for speciation and extinction, and population growth or subdivision within species, have relatively smaller effects. Our simulations demonstrate that support measures derived from the likelihood function provide a robust indication of when the model performs well and when it leads to inaccurate delimitations. Finally, the so-called single threshold version of the method outperforms the multiple threshold version of the method on simulated data: we argue that this represents a fundamental limit due to the nature of evidence used to delimit species in this approach. Together with other studies comparing its performance relative to other methods, our findings support the robustness of GMYC as a tool for delimiting species when only single-locus information is available.

Data from: Emsian Ammonoidea and the age of the Hunsrück Slate (Rhenish Mountains, Western Germany)

2013-06-19T15:26:26Z

The ammonoids from the well-studied German Fossillagerstätte of the Hunsrück Slate have the reputation of being the oldest known representatives of this cephalopod group. This material is of great interest not only because of the global scarcity of the earliest ammonoids, but also because it includes the first record of stratigraphically-controlled specimens, which could be assigned to the middle Kaub Formation in the Bundenbach/Gemünden area. Accordingly, some of the Hunsrück Slate ammonoids are indeed the stratigraphically oldest ammonoids because they are associated with the index dacryoconarid Nowakia praecursor and thus derive from the Nowakia zlichovensis Biozone of the early Emsian (Zlíchovian), while younger dacryoconarids and other ammonoid samples (Mimagoniatites fecundus, Mimosphinctes tripartitus) indicate the Nowakia barrandei to N. elegans biozones. In spite of this special importance, these Early Devonian cephalopods have never been revised comprehensively.Our study includesmore than 300 Hunsrück Slate specimens from both public and private collections. For the first time, ammonoids from the Altlay Hunsrück Slate in the Northern Hunsrück/Mosel region are reported, while all the materials from older collections derive from the middle Kaub Formation of the Central Hunsrück Basin (central Hunsrück, Taunus). These early ammonoids thus prove to be a valuable source of information for biostratigraphic correlation within the Hunsrück Slate and with early Emsian occurrences in other regions. Based on conch characters (geometry, ornament, suture lines) and ontogenetic traits, we describe the species Metabactrites fuchsi n. sp., Ivoites hunsrueckianus (Erben 1960), Ivoites schindewolfi n. sp., ?Ivoites sp., ?Ivoites opitzi n. sp., Anetoceras mittmeyeri n. sp., Erbenoceras advolvens (Erben 1960), Erbenoceras solitarium (Barrande 1865), Chebbites sp., Mimosphinctes primigenitus (Erben 1965), Mimosphinctes tripartitus Eichenberg, 1931, Gyroceratites heinricherbeni n. sp., ?Teicherticeras sp., and Mimagoniatites fecundus (Barrande 1865). Supposedly endemic species of the Hunsrück Slate such as “Anetoceras recticostatum Erben, 1962” and “Mimagoniatites falcistria (Fuchs 1915)” are here synonymized with the widely distributed species Erbenoceras solitarium and Mimagoniatites fecundus, both known to occur also outside Europe. Furthermore, we studied their taphonomy and assigned them to sevengroups of preservation.Theresults of this taphonomic study corroborate previous interpretations of the depositional environment and diagenesis. We also discuss the evolution of the shell in the earliest ammonoids and their closest relatives as well as structures (“Opitzian pits”) possibly caused by parasitic infestations of these early Emsian ammonoids.

Data from: Genotypic and phenotypic variation in transmission traits of a complex life cycle parasite

2013-06-13T18:55:59Z

Characterizing genetic variation in parasite transmission traits and its contribution to parasite vigor is essential for understanding the evolution of parasite life-history traits. We measured genetic variation in output, activity, survival, and infection success of clonal transmission stages (cercaria larvae) of a complex life cycle parasite (Diplostomum pseudospathaceum). We further tested if variation in host nutritional stage had an effect on these traits by keeping hosts on limited or ad libitum diet. The traits we measured were highly variable among parasite genotypes indicating significant genetic variation in these life-history traits. Traits were also phenotypically variable, for example, there was significant variation in the measured traits over time within each genotype. However, host nutritional stage had no effect on the parasite traits suggesting that a short-term reduction in host resources was not limiting the cercarial output or performance. Overall, these results suggest significant interclonal and phenotypic variation in parasite transmission traits that are not affected by host nutritional status.

Data from: Metapopulation dynamics of the mistletoe and its host in savanna areas with different fire occurrence

2013-06-13T18:47:17Z

Mistletoes are aerial hemiparasitic plants which occupy patches of favorable habitat (host trees) surrounded by unfavorable habitat and may be possibly modeled as a metapopulation. A metapopulation is defined as a subdivided population that persists due to the balance between colonization and extinction in discrete habitat patches. Our aim was to evaluate the dynamics of the mistletoe Psittacanthus robustus and its host Vochysia thyrsoidea in three Brazilian savanna areas using a metapopulation approach. We also evaluated how the differences in terms of fire occurrence affected the dynamic of those populations (two areas burned during the study and one was fire protected). We monitored the populations at six-month intervals. P. robustus population structure and dynamics met the expected criteria for a metapopulation: i) the suitable habitats for the mistletoe occur in discrete patches; (ii) local populations went extinct during the study and (iii) colonization of previously non-occupied patches occurred. The ratio of occupied patches decreased in all areas with time. Local mistletoe populations went extinct due to two different causes: patch extinction in area with no fire and fire killing in the burned areas. In a burned area, the largest decrease of occupied patch ratios occurred due to a fire event that killed the parasites without, however, killing the host trees. The greatest mortality of V. thyrsoidea occurred in the area without fire. In this area, all the dead trees supported mistletoe individuals and no mortality was observed for parasite-free trees. Because P. robustus is a fire sensitive species and V. thyrsoidea is fire tolerant, P. robustus seems to increase host mortality, but its effect is lessened by periodic burning that reduces the parasite loads.

Data from: Female mate preferences for male body size and shape promote sexual isolation in threespine sticklebacks

2013-06-13T18:39:56Z

Female mate preferences for ecologically relevant traits may enhance natural selection, leading to rapid divergence. They may also forge a link between mate choice within species and sexual isolation between species. Here, we examine female mate preference for two ecologically important traits: body size and body shape. We measured female preferences within and between species of benthic, limnetic, and anadromous threespine sticklebacks (Gasterosteus aculeatus species complex). We found that mate preferences differed between species and between contexts (i.e., within vs. between species). Within species, anadromous females preferred males that were deep bodied for their size, benthic females preferred larger males (as measured by centroid size), and limnetic females preferred males that were more limnetic shaped. In heterospecific mating trials between benthics and limnetics, limnetic females continued to prefer males that were more limnetic like in shape when presented with benthic males. Benthic females showed no preferences for size when presented with limnetic males. These results show that females use ecologically relevant traits to select mates in all three species and that female preference has diverged between species. These results suggest that sexual selection may act in concert with natural selection on stickleback size and shape. Further, our results suggest that female preferences may track adaptation to local environments and contribute to sexual isolation between benthic and limnetic sticklebacks.

Data from: Switching between apparently redundant iron-uptake mechanisms benefits bacteria in changeable environments

2013-06-13T18:31:32Z

Bacteria often possess multiple siderophore-based iron uptake systems for scavenging this vital resource from their environment. However, some siderophores seem redundant, because they have limited iron-binding efficiency and are seldom expressed under iron limitation. Here, we investigate the conundrum of why selection does not eliminate this apparent redundancy. We focus on Pseudomonas aeruginosa, a bacterium that can produce two siderophores—the highly efficient but metabolically expensive pyoverdine, and the inefficient but metabolically cheap pyochelin. We found that the bacteria possess molecular mechanisms to phenotypically switch from mainly producing pyoverdine under severe iron limitation to mainly producing pyochelin when iron is only moderately limited. We further show that strains exclusively producing pyochelin grew significantly better than strains exclusively producing pyoverdine under moderate iron limitation, whereas the inverse was seen under severe iron limitation. This suggests that pyochelin is not redundant, but that switching between siderophore strategies might be beneficial to trade off efficiencies versus costs of siderophores. Indeed, simulations parameterized from our data confirmed that strains retaining the capacity to switch between siderophores significantly outcompeted strains defective for one or the other siderophore under fluctuating iron availabilities. Finally, we discuss how siderophore switching can be viewed as a form of collective decision-making, whereby a coordinated shift in behaviour at the group level emerges as a result of positive and negative feedback loops operating among individuals at the local scale.

Data from: Comparative analyses of reproductive structures in harvestmen (Opiliones) reveal multiple transitions from courtship to precopulatory antagonism

2013-06-13T18:26:44Z

Explaining the rapid, species-specific diversification of reproductive structures and behaviors is a long-standing goal of evolutionary biology, with recent research tending to attribute reproductive phenotypes to the evolutionary mechanisms of female mate choice or intersexual conflict. Progress in understanding these and other possible mechanisms depends, in part, on reconstructing the direction, frequency and relative timing of phenotypic evolution of male and female structures in species-rich clades. Here we examine evolution of reproductive structures in the leiobunine harvestmen or “daddy long-legs” of eastern North America, a monophyletic group that includes species in which males court females using nuptial gifts and other species that are equipped for apparent precopulatory antagonism (i.e., males with long, hardened penes and females with sclerotized pregenital barriers). We used parsimony- and Bayesian likelihood-based analyses to reconstruct character evolution in categorical reproductive traits and found that losses of ancestral gift-bearing penile sacs are strongly associated with gains of female pregenital barriers. In most cases, both events occur on the same internal branch of the phylogeny. These coevolutionary changes occurred at least four times, resulting in clade-specific designs in the penis and pregenital barrier. The discovery of convergent origins and/or enhancements of apparent precopulatory antagonism among closely related species offers an unusual opportunity to investigate how major changes in reproductive morphology have occurred. We propose new hypotheses that attribute these enhancements to changes in ecology or life history that reduce the duration of breeding seasons, an association that is consistent with female choice, sexual conflict, and/or an alternative evolutionary mechanism.

Data from: The effects of model choice and mitigating bias on the ribosomal tree of life

2013-06-13T18:17:26Z

Deep-level relationships within Bacteria, Archaea, and Eukarya as well as the relationships of these three domains to each other require resolution. The ribosomal machinery, universal to all cellular life, represents a protein repertoire resistant to horizontal gene transfer, which provides a largely congruent signal necessary for reconstructing a tree suitable as a backbone for life’s reticulate history. Here, we generate a ribosomal tree of life from a robust taxonomic sampling of Bacteria, Archaea, and Eukarya to elucidate deep-level intra-domain and inter-domain relationships. Lack of phylogenetic information and systematic errors caused by inadequate models (that cannot account for substitution rate or compositional heterogeneities) or improper model selection compound conflicting phylogenetic signals from HGT and/or paralogy. Thus, we tested several models of varying sophistication on three different datasets, performed removal of fast-evolving or long-branched Archaea and Eukarya, and employed three different strategies to remove compositional heterogeneity to examine their effects on the topological outcome. Our results support a two-domain topology for the tree of life, where Eukarya emerges from within Archaea as sister to a Korarchaeota/Thaumarchaeota (KT) or Crenarchaeota/KT clade for all models under all or at least one of the strategies employed. Taxonomic manipulation allows single-matrix and certain mixture models to vacillate between two-domain and three-domain phylogenies. We find that models vary in their ability to resolve different areas of the tree of life, which does not necessarily correlate with model complexity. For example, both single-matrix and some mixture models recover monophyletic Crenarchaeota and Euryarchaeota archaeal phyla. In contrast, the most sophisticated model recovers a paraphyletic Euryarchaeota but detects two large clades that comprise the Bacteria, which were recovered separately but never together in the other models. Overall, models recovered consistent topologies despite dataset modifications due to the removal of compositional bias, which reflects either ineffective bias reduction or robust datasets that allow models to overcome reconstruction artifacts. We recommend a comparative approach for evolutionary models to identify model weaknesses as well as consensus relationships.

Data from: pavo: an R package for the analysis, visualization and organization of spectral data

2013-06-13T15:52:50Z

1. Recent technical and methodological advances have led to a dramatic increase in the use of spectrometry to quantify reflectance properties of biological materials, as well as models to determine how these colours are perceived by animals, providing important insights into ecological and evolutionary aspects of animal visual communication. 2. Despite this growing interest, a unified cross-platform framework for analyzing and visualizing spectral data has not been available. We introduce pavo, an R package that facilitates the organization, visualization, and analysis of spectral data in a cohesive framework. pavo is highly flexible, allowing users to (a) organize and manipulate data from a variety of sources, (b) visualize data using R's state-of-the-art graphics capabilities, and (c) analyze data using spectral curve shape properties and visual system modeling for a broad range of taxa. 3. In this paper, we present a summary of the functions implemented in pavo and how they integrate in a workflow to explore and analyze spectral data. We also present an exact solution for the calculation of colour volume overlap in colourspace, thus expanding previously published methodologies. 4. As an example of pavo's capabilities, we compare the colour patterns of three African Glossy Starling species, two of which have diverged very recently. We demonstrate how both colour vision models and direct spectral measurement analysis can be used to describe colour attributes and differences between these species. Different approaches to visual models and several plotting capabilities exemplify the package's versatility and streamlined workflow. 5. pavo provides a cohesive environment for handling spectral data and addressing complex sensory ecology questions, while integrating with R's modular core for a broader and comprehensive analytical framework, automated management of spectral data, and reproducible workflows for colour analysis.

Data from: Major histocompatibility complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3

2013-06-12T19:27:32Z

Genes of the Major Histocompatibility Complex (MHC) have become an important marker for the investigation of adaptive genetic variation in vertebrates because of their critical role in pathogen resistance. However, despite significant advances in the last few years the characterization of MHC variation in non-model species still remains a challenging task due to the redundancy and high variation of this gene complex. Here we report the utility of a single pair of primers for the cross-amplification of the third exon of MHC class I genes, which encodes the more polymorphic half of the peptide-binding region (PBR), in oscine passerines (songbirds; Aves: Passeriformes), a group especially challenging for MHC characterization due to the presence of large and complex MHC multigene families. In our survey, although the primers failed to amplify exon 3 from two suboscine passerine birds, they amplified exon 3 of multiple MHC class I genes in all 16 species of oscine songbirds tested, yielding a total of 120 sequences. The 16 songbird species belong to 14 different families, primarily within the Passerida, but also in the Corvida. Using a conservative approach based on the analysis of cloned amplicons (n = 16) from each species, we found between 3 and 10 MHC sequences per individual. Each allele repertoire was highly divergent, with the overall number of polymorphic sites per species ranging from 33 to 108 (out of 264 sites) and the average number of nucleotide differences between alleles ranging from 14.67 to 43.67. Our survey in songbirds allowed us to compare macroevolutionary dynamics of exon 3 between songbirds and non-passerine birds. We found compelling evidence of positive selection acting specifically upon peptide-binding codons across birds, and we estimate the strength of diversifying selection in songbirds to be about twice that in non-passerines. Analysis using comparative methods suggest weaker evidence for a higher GC content in the 3rd codon position of exon 3 in non-passerine birds, a pattern that contrasts with among-clade GC patterns found in other avian studies and may suggests different mutational mechanisms. Our primers represent a useful toolfor the characterization of functional and evolutionarily relevant MHC variation across the hyperdiverse songbirds.

Data from: Group formation, relatedness, and the evolution of multicellularity

2013-06-12T19:14:25Z

The evolution of multicellular organisms represents one of approximately eight major evolutionary transitions that have occurred on earth. The major challenge raised by this transition is to explain why single cells should join together and become mutually dependent, in a way that leads to a more complex multicellular life form that can only replicate as a whole. It has been argued that a high genetic relatedness (r) between cells played a pivotal role in the evolutionary transition from single-celled to multicellular organisms, because it leads to reduced conflict and an alignment of interests between cells. We tested this hypothesis with a comparative study, comparing the form of multicellularity in species where groups are clonal (r = 1) to species where groups are potentially nonclonal (r ≤ 1). We found that species with clonal group formation were more likely to have undergone the major evolutionary transition to obligate multicellularity and had more cell types, a higher likelihood of sterile cells, and a trend toward higher numbers of cells in a group. More generally, our results unify the role of group formation and genetic relatedness across multiple evolutionary transitions and provide an unmistakable footprint of how natural selection has shaped the evolution of life.

Data from: Key ornamental innovations facilitate diversification in an avian radiation

2013-06-12T18:55:50Z

Patterns of biodiversity are often explained by ecological processes, where traits that promote novel ways of interacting with the environment (key innovations) play a fundamental role in promoting diversification. However, sexual selection and social competition can also promote diversification through rapid evolution of ornamental traits. Because selection can operate only on existing variation, the tendency of ornamental traits to constrain or enable the production of novel phenotypes is a crucial but often overlooked aspect of diversification. Starlings are a speciose group characterized by diverse iridescent colors produced by nanometer-scale arrays of melanin-containing organelles (melanosomes) that play a central role in sexual selection and social competition. We show that evolutionary lability of these colors is associated with both morphological and lineage diversification in African starlings. The solid rod-like melanosome morphology has evolved in a directional manner into three more optically complex forms that can produce a broader range of colors than the ancestral form, resulting in (i) faster color evolution, (ii) the occupation of novel, previously unreachable regions of colorspace, and ultimately (iii) accelerated lineage diversification. As in adaptive radiations, key innovations in ornament production can provide high phenotypic trait variability, leading to dramatic effects on the tempo and mode of diversification.

Data from: The effect of elevated CO2 on growth and competition in experimental phytoplankton communities

2013-06-12T18:37:47Z

We report an experiment designed to identify the effect of elevated CO2 on species of phytoplankton in a simple laboratory system. Major taxa of phytoplankton differ in their ability to take up CO2, which might lead to predictable changes in the growth rate of species and thereby shifts in the composition of phytoplankton communities in response to rising CO2. Six species of phytoplankton belonging to three major taxa (cyanobacteria, diatoms and chlorophytes) were cultured in atmospheres whose CO2 concentration was gradually increased from ambient levels to 1000 parts per million over about 100 generations and then maintained for a further 200 generations at elevated CO2. The experimental design allowed us to trace a predictive sequence, from physiological features to the growth response of species to elevated CO2 in pure culture, from the growth response in pure culture to competitive ability in pairwise mixtures and from pairwise competitive ability to shifts in the relative abundance of species in the full community of all six species. CO2 altered the dynamics of growth in a fashion consistent with known differences among major taxa in their ability to take up and use CO2. This pure-culture response was partly successful in predicting the outcome of competition in pairwise mixtures, especially the enhanced competitive ability of chlorophytes relative to cyanobacteria, although generally statistical support was weak. The competitive response in pairwise mixtures was a good predictor of changes in competitive ability in the full community. Hence, there is a potential for forging a logical chain of inferences for predicting how phytoplankton communities will respond to elevated CO2. Clearly further extensive experiments will be required to validate this approach in the greater complexity found in diverse communities and environments of natural systems.

Data from: Parasites affect food web structure primarily through increased diversity and complexity

2013-06-12T17:36:42Z

Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity), particularly when including concomitant links (links from predators to parasites of their prey). However, we clarify prior claims that parasites “dominate” food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites' roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites' feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic organization, identifies limitations of current food web models, and provides direction for future structural and dynamical models.

Data from: Horizontal transmission of the father’s song in the Zebra Finch (Taeniopygia guttata)

2013-06-12T16:26:14Z

As is the case for human speech, birdsong is transmitted across generations by imitative learning. Although transfer of song patterns from adults to juveniles typically occurs via vertical or oblique transmission, there is also evidence of horizontal transmission between juveniles of the same generation. Here, we show that a young male zebra finch (Taeniopygia guttata) that has been exposed to its father during the sensitive period for song learning can lead a brother, that has never heard the paternal song, to imitate some sounds of the father. Moreover, song similarity between the two brothers was higher than the similarity measured between the paternal song and the song of the brother that had a week-long exposure to the father. We speculate that the phenomenon of within-generation song learning among juveniles may be more widespread than previously thought and that when a juvenile evaluates potential models for imitative learning, a sibling may be as salient as an adult.

Data from: Turtle embryos move to optimal thermal environments within the egg

2013-06-12T16:06:38Z

A recent study demonstrated that the embryos of soft-shelled turtles can reposition themselves within their eggs to exploit locally warm conditions. In the current paper, we ask whether turtle embryos actively seek out optimal thermal environments for their development, as do post-hatching individuals. Specifically, (1) do reptile embryos move away from dangerously-high temperatures, as well as towards warm temperatures? and (2) is such embryonic movement due to active thermoregulation, or (more simply) to passive embryonic repositioning caused by local heat-induced changes in viscosity of fluids within the egg? Our experiments with an emydid turtle (Chinemys reevesii) show that embryos avoid dangerously high temperatures by moving to cooler regions of the egg. The repositioning of embryos is an active not passive process: live embryos move toward a heat source, whereas dead ones do not. Overall, our results suggest that behavioural thermoregulation by turtle embryos is an active process, genuinely analogous to the thermoregulatory behaviour exhibited by post-hatching ectotherms.

Data from: Plasticity of parental care under the risk of predation: how much should parents reduce care?

2013-06-12T15:57:53Z

Predation can be an important agent of natural selection shaping parental care behaviours, and can also favor behavioural plasticity. Parent birds often decrease the rate that they visit the nest to provision offspring when perceived risk is high. Yet the plasticity of such responses may differ among species as a function of either their relative risk of predation, or the mean rate of provisioning. Here, we report parental provisioning responses to experimental increases in the perceived risk of predation. We tested responses of 10 species of birds in north temperate Arizona and subtropical Argentina that differed in their ambient risk of predation. All species decreased provisioning rates in response to the nest predator but not to a control. However, provisioning rates decreased more in species that had greater ambient risk of predation on natural nests. These results support theoretical predictions that the extent of plasticity of a trait that is sensitive to nest predation risk should vary among species in accordance with predation risk.

Data from: Complex phylogeography in Rhinoclemmys melanosterna: conflicting mitochondrial and nuclear evidence suggests past hybridization (Testudines: Geoemydidae)

2013-06-12T15:35:06Z

We examined differentiation within the Colombian wood turtle Rhinoclemmys melanosterna, and among R. melanosterna and the closely allied species R. diademata, R. funerea and R. punctularia, based on 1060 base pairs of the mitochondrial cyt b gene. We also assessed the phylogenetic relationships among these species using 2050 bp of mtDNA (partial cyt b, 12S and 16S genes) and 3620 bp of nuclear DNA (partial Rag 1, Rag 2, C-mos, R35 and ODC genes). There is considerable phylogeographic structuring within R. melanosterna, with seven distinct clades distributed across the species’ range. These clades correspond to some extent with previously described differences in the dorsal pattern of head coloration. Individual and combined analyses of mitochondrial and nuclear DNA indicated contradictory relationships among R. melanosterna, R. diademata, R. funerea and R. punctularia. Mitochondrial DNA sequences revealed R. melanosterna to be non-monophyletic with respect to R. diademata, R. funerea and R. punctularia. In contrast, R. melanosterna constituted a well-supported monophyletic clade using nuclear DNA. This conflict between mitochondrial and nuclear data suggests past gene flow among the allopatrically and parapatrically distributed species R. melanosterna, R. diademata, R. funerea and R. punctularia. Compared to the other Rhinoclemmys species, the taxa under study are weakly differentiated. To assess their taxonomic status, further research is warranted using additional nuclear markers and additional samples of R. diademata, R. funerea and R. punctularia. For the time being, a continued classification of R. melanosterna, R. diademata, R. funerea and R. punctularia as distinct species is justified owing to their allopatric and parapatric distributions, and to conserve the established usage of names that is based on characteristic and distinct phenotypes associated with each species.

Data from: Rapidly fluctuating environments constrain coevolutionary arms races by impeding selective sweeps

2013-06-12T15:02:45Z

Although pervasive, the impact of temporal environmental heterogeneity on coevolutionary processes is poorly understood. Productivity is a key temporally heterogeneous variable, and increasing productivity has been shown to increase rates of antagonistic arms race coevolution, and lead to the evolution of more broadly resistant hosts and more broadly infectious parasites. We investigated the effects of the grain of environmental heterogeneity, in terms of fluctuations in productivity, on bacteria–phage coevolution. Our findings demonstrate that environmental heterogeneity could constrain antagonistic coevolution, but that its effect was dependent upon the grain of heterogeneity, such that both the rate and extent of coevolution were most strongly limited in fine-grained, rapidly fluctuating heterogeneous environments. We further demonstrate that rapid environmental fluctuations were likely to have impeded selective sweeps of resistance alleles, which occurred over longer durations than the fastest, but not the slowest, frequency of fluctuations used. Taken together our results suggest that fine-grained environmental heterogeneity constrained the coevolutionary arms race by impeding selective sweeps.

Data from: Dietary macronutrients modulate the fatty acyl composition of rat liver mitochondrial cardiolipins

2013-06-12T15:16:46Z

The interaction of dietary fats and carbohydrates on liver mitochondria were examined in male FBNF1 rats fed 20 different low-fat, isocaloric diets. Animal growth rates and mitochondrial respiratory parameters were essentially unaffected, but mass spectrometry-based, mitochondrial lipidomics profiling revealed increased levels of cardiolipins (CLs), a family of phospholipids essential for mitochondrial structure and function, in rats fed saturated or trans fat-based diets with a high glycemic index. These mitochondria showed elevated monolysocardiolipins (a CL precursor/product of CL degradation), elevated ratio of trans PC (18:1/18:1) to cis PC (18:1/18:1) (a marker of thiyl radical stress), and decreased ubiquinone Q9 -- the latter two of which imply a low-grade mitochondrial redox abnormality. Extended analysis demonstrated: (i) dietary fats and, to a lesser extent, carbohydrates induce changes in the relative abundance of specific CL species; (ii) Fatty acid (FA) incorporation into mature CLs undergoes both positive (>400-fold) and negative (2.5-fold) regulation; and, (iii) dietary lipid abundance and incorporation of FAs into both the CL pool and specific mature tetra-acyl CLs are inversely related, suggesting previously unobserved compensatory regulation. This study reveals previously unobserved complexity/regulation of the central lipid in mitochondrial metabolism.

Data from: Reduction of leaf area and symptom severity as proxies of disease-induced plant mortality: the example of the Cauliflower mosaic virus infecting two Brassicaceae hosts.

2013-06-12T14:15:18Z

Disease induced effects on host survival are important to understand the evolution of parasitic virulence and host resistance/tolerance. Unfortunately, experiments evaluating such effects are in most cases logistically demanding justifying the measurement of survival proxies. For plant hosts commonly used proxies are leaf area and the nature and severity of visual qualitative disease symptoms. In this study we tested whether these traits are indeed correlated to the host mortality rate induced by viral infection. We infected Brassica rapa and Arabidopsis thaliana plants with different natural isolates of Cauliflower mosaic virus (CaMV) and estimated over time the development of symptoms and the relative reduction of leaf area compared to healthy plants and followed plant mortality. We observed that the mortality of infected plants was correlated with the relative reduction of leaf area of both B. rapa and A. thaliana. Measures of mortality were also correlated with the severity of visual qualitative symptoms but the magnitude of the correlations and the time frame at which they were significant depended on the host plant: stronger and earlier correlations were observed on A. thaliana.

Data from: On the importance of shrub encroachment by sprouters, climate, species richness and anthropic factors for ecosystem multifunctionality in semi-arid mediterranean ecosystems

2013-06-11T18:36:40Z

One of the most important changes taking place in drylands worldwide is the increase of the cover and dominance of shrubs in areas formerly devoid of them (shrub encroachment). A large body of research has evaluated the causes and consequences of shrub encroachment for both ecosystem structure and functioning. However, there are virtually no studies evaluating how shrub encroachment affects the ability of ecosystems to maintain multiple functions and services simultaneously (multifunctionality). We aimed to do so by gathering data from ten ecosystem functions linked to the maintenance of primary production and nutrient cycling and storage (organic C, activity of β-glucosidase, pentoses, hexoses, total N, total available N, amino acids, proteins, available inorganic P, and phosphatase activity), and summarizing them in a multifunctionality index (M). We assessed how climate, species richness, anthropic factors (distance to the nearest town, sandy and asphalted road, and human population in the nearest town at several historical periods) and encroachment by sprouting shrubs impacted both the functions in isolation and M along a regional (ca. 350 km) gradient in Mediterranean grasslands and shrublands dominated by a non-sprouting shrub. Values of M were higher in those grasslands and shrublands containing sprouting shrubs (43 and 62%, respectively). A similar response was found when analyzing the different functions in isolation, as encroachment by sprouting shrubs increased functions by 2–80% compared to unencroached areas. Encroachment was the main driver of changes in M along the regional gradient evaluated, followed by anthropic factors and species richness. Climate had little effects on M in comparison to the other factors studied. Similar responses were observed when evaluating the functions in isolation. Overall, our results showed that M was higher at sites with higher sprouting shrub cover, longer distance to roads and higher perennial plant species richness. Our study is the first documenting that ecosystem multifunctionality in shrublands is enhanced by encroaching shrubs differing in size and leaf attributes. Our findings reinforce the idea that encroachment effects on ecosystem functioning cannot be generalized, and that are largely dependent on the traits of the encroaching shrub relative to those of the species being replaced.

Data from: Causes and evolutionary consequences of population subdivision of an Iberian mountain lizard, Iberolacerta monticola

2013-06-10T19:55:18Z

Aim: The study of the factors that influence population connectivity and spatial distribution of genetic variation is crucial for understanding speciation and for predicting the effects of landscape modification and habitat fragmentation, which are considered severe threats to global biodiversity. This dual perspective is obtained from analyses of subalpine mountain species, whose present distribution may have been shaped both by cyclical climate changes over ice ages and anthropogenic perturbations of their habitats. Here, we examine the phylogeography, population structure and genetic diversity of the lacertid lizard Iberolacerta monticola, an endemism considered to be facing a high risk of extinction in several populations. Location: Northwestern quadrant of the Iberian Peninsula. Methods: We analyzed the mtDNA variation at the control region (454 bp) and the cytochrome b (598 bp) loci, as well as at 10 nuclear microsatellite loci from 17 populations throughout the distribution range of the species. Results: According to nuclear markers, most sampling sites are defined as distinct, genetically differentiated populations, and many of them show traces of recent bottlenecks. Mitochondrial data identify a relatively old, geographically restricted lineage, and four to six younger geographically vicariant sister clades, whose origin may be traced back to the mid-Pleistocene revolution, with several subclades possibly associated to the mid-Bruhnes transition. Geographic range fragmentation of one of these clades, which includes lowland sites, is very recent, and most likely due to the accelerated loss of Atlantic forests by human intervention. Main Conclusions: Altogether, the data fit a “refugia within refugia” model, some lack of pattern uniformity notwithstanding, and suggest that these mountains might be the cradles of new species of Iberolacerta. However, the changes operated during the Holocene severely compromise the long-term survival of those genetic lineages more exposed to the anthropogenic perturbations of their habitats.

Data from: Predator-prey interactions shape thermal patch use in a newt larvae-dragonfly nymph model

2013-06-10T19:37:25Z

Thermal quality and predation risk are considered important factors influencing habitat patch use in ectothermic prey. However, how the predator’s food requirement and the prey’s necessity to avoid predation interact with their respective thermoregulatory strategies remains poorly understood. The recently developed ‘thermal game model’ predicts that in the face of imminent predation, prey should divide their time equally among a range of thermal patches. In contrast, predators should concentrate their hunting activities towards warmer patches. In this study, we test these predictions in a laboratory setup and an artificial environment that mimics more natural conditions. In both cases, we scored thermal patch use of newt larvae (prey) and free-ranging dragonfly nymphs (predators). Similar effects were seen in both settings. The newt larvae spent less time in the warm patch if dragonfly nymphs were present. The patch use of the dragonfly nymphs did not change as a function of prey availability, even when the nymphs were starved prior to the experiment. Our behavioral observations partially corroborate predictions of the thermal game model. In line with asymmetric fitness pay-offs in predator-prey interactions (the ‘life-dinner’ principle), the prey’s thermal strategy is more sensitive to the presence of predators than vice versa.

Data from: Evolution mediates the effects of apex predation on aquatic food webs

2013-06-10T19:29:42Z

Ecological and evolutionary mechanisms are increasingly thought to shape local community dynamics. Here, I evaluate if the local adaptation of a meso-predator to an apex predator alters local food webs. The marbled salamander (Ambystoma opacum) is an apex predator that consumes both the spotted salamander (Ambystoma maculatum) and shared zooplankton prey. Common garden experiments reveal that spotted salamander populations which co-occur with marbled salamanders forage more intensely than those that face other predator species. These foraging differences, in turn, alter the diversity, abundance and composition of zooplankton communities in common garden experiments and natural ponds. Locally adapted spotted salamanders exacerbate prey biomass declines associated with apex predation, but dampen the top-down effects of apex predation on prey diversity. Countergradient selection on foraging explains why locally adapted spotted salamanders exacerbate prey biomass declines. The two salamander species prefer different prey species, which explains why adapted spotted salamanders buffer changes in prey composition owing to apex predation. Results suggest that local adaptation can strongly mediate effects from apex predation on local food webs. Community ecologists might often need to consider the evolutionary history of populations to understand local diversity patterns, food web dynamics, resource gradients and their responses to disturbance.

Data from: Long-term storage effects in steroid metabolite extracts from baboon (Papio sp.) faeces – a comparison of three commonly applied storage methods

2013-06-10T18:20:17Z

1. The measurement of steroid hormone metabolites from faeces in wild animal populations is a powerful, non-invasive tool in behavioural endocrinology of all major vertebrate taxa. However, because such research is often done in remote areas with limited infrastructure, storage of samples for hormone analysis over long periods at high temperature is a critical issue in field endocrinology. Previous studies have indicated that storage of alcoholic faecal extracts is more reliable than storage of unprocessed faeces if no freezer is available, but a standard method has not been established yet. 2. We tested the validity of three commonly applied storage conditions - liquid extracts, dried extracts, and extracts placed on solid phase extraction (SPE)-cartridges - to preserve concentrations of glucocorticoid and androgen metabolites from faecal extracts of olive baboons (Papio anubis) at high temperature over one year. 3. Temporal variation in concentrations was detected for all metabolites and all storage conditions, including values measured from the control condition, i.e. extracts stored at 20°C. This suggested that most variation was due to inter-assay variability, corroborated by comparisons of variation in ‘quality controls’ and samples. 4. Compared to frozen control samples, liquid extracts were stable for up to 24 weeks, extracts on SPE-cartridges were stable for up to 50 weeks, while steroid metabolite concentrations in dried extracts decreased slightly over time. 5. If steroid samples have to be stored at ambient temperature, we suggest storage of liquid extracts for up to 24 weeks in a dark and cool place. For longer periods, SPE-cartridges should be applied as evaporation, a potential confound arising with long-term storage of liquid extracts at higher temperatures, is not a problem in this storage condition. Storage of dried extracts is more cost-effective, but may result in small time-dependent changes in steroid concentrations.

Data from: The link between host density and egg production in a parasitoid insect: comparison between agricultural and natural habitats

2013-06-10T17:00:40Z

1. Theory predicts that organisms should invest in overcoming a factor that may limit their reproductive success in direct proportion to their probability of being limited by it. The occurrence of egg limitation (where female insects deplete their eggs while oviposition opportunities are still available) is predicted to impose selection for increased fecundity at the expense of other fitness components. 2. We tested the hypothesis that the fecundity of a proovigenic parasitoid (where females emerge with their full egg load) should be positively correlated with the mean expectation for oviposition opportunities in the environment. More specifically, we tested whether females from agricultural systems, where hosts are often relatively abundant, emerge with more eggs than those from natural habitats. 3. We studied the proovigenic parasitoid wasp Anagrus daanei, which parasitizes eggs of leafhoppers of the genus Erythroneura. Erythroneura spp. leafhoppers feed on Vitis spp. (grapes) and are major pests of commercial vineyards as well as common herbivores of wild Vitis californica, which grows in riparian habitats. We sampled leafhoppers and parasitoids from eight vineyards and eight riparian habitats in central California. 4. We found that leafhopper density was higher at vineyards than in riparian habitats, whereas leafhopper egg size and parasitoid body size did not differ among these habitat types. Parasitoids from vineyards had higher egg loads than parasitoids from wild grapes, and fecundity was positively related to host density across field sites. Parasitoid egg volume was larger in natural sites; however, this variation was not significantly correlated with host density across field sites. Within a single population of parasitoids collected from a vineyard, parasitoid egg load was negatively correlated with longevity, suggesting a trade-off between reproduction and lifespan. 5. The results may be explained by a rapid evolution of reproductive traits in response to oviposition opportunities; or alternatively, by the occurrence of maternal effects on the fecundity of daughters based on the foraging experience of their mothers. 6. The ability of parasitoid fecundity to track mean host availability may strengthen the ability of parasitoids to suppress the population densities of their hosts, and hence may represent an important ecological or eco-evolutionary feedback.

Data from: Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus)

2013-06-17T14:50:45Z

Species are a fundamental unit for biological studies, yet no uniform guidelines exist for determining species limits in an objective manner. Given the large number of species concepts available, defining species can be both highly subjective and biased. Although morphology has been commonly used to determine species boundaries, the availability and prevalence of genetic data has allowed researchers to use such data to make inferences regarding species limits. Genetic data also have been used in the detection of cryptic species, where other lines of evidence (morphology in particular) may underestimate species diversity. In this study, we investigate species limits in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus) from California. Multiple approaches were used to determine species boundaries in this highly genetically fragmented group, including both multilocus discovery and validation approaches (plus a chimeric approach). Additionally, we introduce a novel tree-based discovery approach using species trees. Results suggest that this complex includes multiple cryptic species, with two groupings consistently recovered across analyses. Due to incongruence across analyses for the remaining samples, we take a conservative approach and recognize a three species complex, and formally describe two new species (Aliatypus roxxiae, sp. nov. and Aliatypus starretti, sp. nov.). This study helps to clarify species limits in a genetically fragmented group and provides a framework for identifying and defining the cryptic lineage diversity that prevails in many organismal groups.

Data from: Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation

2013-06-10T14:15:17Z

Several evolutionary theories predict that rates of morphological change should be positively associated with the rate at which new species arise. For example, the theory of punctuated equilibrium proposes that phenotypic change typically occurs in rapid bursts associated with speciation events. However, recent phylogenetic studies have found little evidence linking these processes in nature. Here we demonstrate that rates of species diversification are highly correlated with the rate of body size evolution across the 30,000+ living species of ray-finned fish that comprise the majority of vertebrate biological diversity. This coupling is a general feature of fish evolution and transcends vast differences in ecology and body-plan organization. Our results may reflect a widespread speciational mode of character change in living fishes. Alternatively, these findings are consistent with the hypothesis that phenotypic ‘evolvability’ – the capacity of organisms to evolve – shapes the dynamics of speciation through time at the largest phylogenetic scales.

Data from: Population growth in a wild bird is buffered against phenological mismatch

2013-06-07T15:50:10Z

Broad-scale environmental changes are altering patterns of natural selection in the wild, but few empirical studies have quantified the demographic cost of sustained directional selection in response to these changes. We tested whether population growth in a wild bird is negatively affected by climate change–induced phenological mismatch, using almost four decades of individual-level life-history data from a great tit population. In this population, warmer springs have generated a mismatch between the annual breeding time and the seasonal food peak, intensifying directional selection for earlier laying dates. Interannual variation in population mismatch has not, however, affected population growth. We demonstrated a mechanism contributing to this uncoupling, whereby fitness losses associated with mismatch are counteracted by fitness gains due to relaxed competition. These findings imply that natural populations may be able to tolerate considerable maladaptation driven by shifting climatic conditions without undergoing immediate declines.

Data from: Disentangling the effects of geographic and ecological isolation on genetic differentiation

2013-06-07T15:16:29Z

Populations can be genetically isolated by both geographic distance and by differences in their ecology or environment that decrease the rate of successful migration. Empirical studies often seek to investigate the relationship between genetic differentiation and some ecological variable(s) while accounting for geographic distance, but common approaches to this problem (such as the partial Mantel test) have a number of drawbacks. In this article, we present a Bayesian method that enables users to quantify the relative contributions of geographic distance and ecological distance to genetic differentiation between sampled populations or individuals. We model the allele frequencies in a set of populations at a set of unlinked loci as spatially correlated Gaussian processes, in which the covariance structure is a decreasing function of both geographic and ecological distance. Parameters of the model are estimated using a Markov chain Monte Carlo algorithm. We call this method Bayesian Estimation of Differentiation in Alleles by Spatial Structure and Local Ecology (BEDASSLE), and have implemented it in a user-friendly format in the statistical platform R. We demonstrate its utility with a simulation study and empirical applications to human and teosinte datasets.

Data from: Decay of ecosystem differences and decoupling of tree community-soil environment relationships at ecotones

2013-06-06T18:08:47Z

Ecotones are important landscape features where there is a transition between adjoining ecosystems. However, there are few generalized hypotheses about the response of communities to ecotones, except for a proposed increase in species richness that receives varying empirical support. Based on the assumption that transport of abiotic material and dispersal of organism propagules across ecotones are independent processes, we propose the new hypothesis that ecotones decouple community-environment relationships, increasing the importance of spatial structure that is independent of the environment. We tested this hypothesis by examining the effects of ecotones on relationships between trees and soil properties in a temperate deciduous forest. The study area included different landforms defined by topography, hydrology, and geomorphology, which we designated upland, bottomland, and riparian forests. The site also included a mowed herbaceous corridor. We found that soil properties and tree community composition significantly differed among landforms, and thus they could be treated as differing ecosystem types. However, inclusion of plots near ecotones significantly reduced the variance explained by landform due to introduction of increased noise, increased similarity of ecotone plots in different landforms, or both. To examine tree community-soil environment relationships, factorial kriging analysis was used to decompose variation in soil properties into structures associated with differing spatial scales, which were then used as predictors of tree composition using redundancy analysis. In agreement with the ecotone-decoupling hypothesis, we found that ecotones introduced significant unexplained variation into correlations between tree community composition and soil properties. In addition, spatial variation in tree community composition that was independent of soil properties was only detected when ecotones were included in the analysis, and little variation in tree community composition was attributed to small-scale soil property structures. Together, these results indicate that dispersal limitation and mass effects in the tree community take on increased importance near ecotones. We found no consistent changes in tree species richness associated with ecotones, and suggest that the ecotone-decoupling hypothesis may correspond with a more general community-level pattern that warrants further testing. Decoupling of community-environment relationships near ecotones also has important implications for accuracy of models predicting community distributions from abiotic information.

Data from: Transient dominance in a central African rain forest

2013-06-06T17:59:13Z

The large-crowned emergent tree Microberlinia bisulcata dominates rainforest groves at Korup, along with two co-dominants Tetraberlinia bifoliolata and T. korupensis. M. bisulcata has a pronounced modal size frequency distribution ~100 cm stem diameter: its recruitment potential is very poor. It is a long-lived light-demanding species, one of many found in African forests. Tetraberlinia spp. lack modality, are more shade-tolerant and recruit better. All three species are ectomycorrhizal. M. bisulcata dominates grove basal area, even though it has similar numbers of trees ({greater than or equal to} 50 cm stem diameter) as each of the other two species. This situation presented a conundrum which prompted a long-term study of grove dynamics. Enumerations of two plots (82.5 and 56.25 ha) between 1990 and 2010 showed mortality and recruitment of M. bisulcata to be very low (both rates ~0.2%/yr) compared with Tetraberlinia (2.4, 0.8%/yr), and M. bisulcata grows twice as fast as the Tetraberlinia. Ordinations indicated that these three species determined community structure by their strong negative associations whilst other species showed almost none. Ranked species abundance curves fitted the Zipf-Mandelbrot model well, and allowed 'over-dominance' of M. bisulcata to be estimated. Spatial analysis indicated strong repulsion by clusters of large (50 - < 100 cm) and very large (> 100 cm) M. bisulcata of their own medium-sized (10 -< 50 cm) trees and all sizes of Tetraberlinia. This was interpreted as competition by M. bisulcata increasing its dominance, but also inhibition of its own replacement potential. Stem coring showed a modal age of ~200 year for M. bisulcata, but with large size variation (50 - 150 cm). Fifty-year model projections suggested little change in medium, decreases in large, and increases in very large trees of M. bisulcata, accompanied by overall decreases in medium and large trees of Tetraberlinia spp. Realistically increasing very large-tree mortality led to grove collapse without short-term replacement. M. bisulcata most likely depends on climatic events to rebuild its stands: the ratio of disturbance interval to median species' longevity is important. A new theory of transient dominance explains how M. bisulcata may be cycling in abundance over time and displaying non-equilibrium dynamics.

Data from: A novel hearing specialization in the New Zealand bigeye, Pempheris adspersa

2013-06-06T17:23:26Z

The New Zealand bigeye, Pempheris adspersa, is a nocturnal planktivore and has recently been found to be an active sound producer. The rostral end of the swim bladder lies adjacent to Baudelot's ligament which spans between the bulla and the cleithrum bone of the pectoral girdle. The aim of this study was to use the auditory evoked potential technique to physiologically test the possibility that this structure provides an enhanced sensitivity to sound pressure in the bigeye. At 100 Hz, bigeye had hearing sensitivity similar to that of goldfish (species with a mechanical connection between the swim bladder and the inner ear mediated by the Weberian ossicles) and were much more sensitive than other teleosts without ancillary hearing structures. Severing Baudelot's ligament bilaterally resulted in a marked decrease in hearing sensitivity, as did swim bladder puncture or lateral line blockage. These results show that bigeye have an enhanced sensitivity to sound pressure and provide experimental evidence that the functional basis of this sensitivity represents a novel hearing specialization in fish involving the swim bladder, Baudelot's ligament and the lateral line.

Data from: Facial attractiveness is related to women’s cortisol and body fat, but not with immune responsiveness

2013-06-06T17:16:16Z

Recent studies suggest that facial attractiveness indicates immune responsiveness in men and that this relationship is moderated by stress hormones which interact with testosterone levels. However, studies testing whether facial attractiveness in women signals their immune responsiveness are lacking. Here, we photographed young Latvian women, vaccinated them against hepatitis B and measured the amount of specific antibodies produced, cortisol levels and percentage body fat. Latvian men rated the attractiveness of the women's faces. Interestingly, in women, immune responsiveness (amount of antibodies produced) did not predict facial attractiveness. Instead, plasma cortisol level was negatively associated with attractiveness, indicating that stressed women look less attractive. Fat percentage was curvilinearly associated with facial attractiveness, indicating that being too thin or too fat reduces attractiveness. Our study suggests that in contrast to men, facial attractiveness in women does not indicate immune responsiveness against hepatitis B, but is associated with two other aspects of long-term health and fertility: circulating levels of the stress hormone cortisol and percentage body fat.

Data from: The genetic architecture of methotrexate toxicity is similar in Drosophila melanogaster and humans

2013-06-06T15:56:41Z

The severity of the toxic side effects of chemotherapy varies among patients and much of this variation is likely genetically based. Here, we use the model system Drosophila melanogaster to genetically dissect toxicity of methotrexate (MTX), a drug used primarily to treat childhood acute lymphoblastic leukemia and rheumatoid arthritis. We utilize the Drosophila Synthetic Population Resource (DSPR), a panel of recombinant inbred lines derived from a multiparent advanced intercross, and quantify MTX toxicity as a reduction in female fecundity. We identify three QTL affecting MTX toxicity; two co-localize with the fly orthologs of human genes believed to mediate MTX toxicity, and one is a novel MTX toxicity gene with a human ortholog. A fourth suggestive QTL spans a centromere. Local single marker association scans of candidate gene exons fail to implicate amino acid variants as the causative SNPs, and we therefore hypothesize the causative variation is regulatory. In addition, the effects at our mapped QTL do not conform to a simple biallelic pattern, suggesting multiple causative factors underlie the QTL mapping results. Consistent with this observation, no single SNP located in or near a candidate gene can explain the QTL mapping signal. Overall, our results validate D. melanogaster as a model for uncovering the genetic basis of chemotoxicity and suggest the genetic basis of MTX toxicity is due to a handful of genes each harboring multiple segregating regulatory factors.

Data from: Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino-acid replacement in mitochondrial genomes of mammals and birds

2013-06-06T15:28:20Z

The nearly-neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of non-synonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino-acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc and 3 life-history traits, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared to dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly-neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step towards a more comprehensive phylogenetic reconstruction of the evolution of life-history and of the population-genetics environment.

Data from: Fruit evolution and diversification in campanulid angiosperms

2013-06-14T18:55:00Z

With increases in both the size and scope of phylogenetic trees, we are afforded a renewed opportunity to address long standing comparative questions, such as whether particular fruit characters account for much of the variation in diversity among flowering plant clades. Studies to date have reported conflicting results, largely as a consequence of taxonomic scale and a reliance on potentially conservative statistical measures. Here we examine a larger and older angiosperm clade, the Campanulidae, and infer the rates of character transitions among the major fruit types, emphasizing the evolution of the achene fruits that are most frequently observed within the group. Our analyses imply that campanulids likely originated bearing capsules, and that all subsequent fruit diversity was derived from various modifications of this dry fruit type. We also found that the preponderance of lineages bearing achenes is a consequence of not only being a fruit type that is somewhat irreversible once it evolves, but one that also seems to have a positive association with diversification rates. While these results imply the achene fruit type is a significant correlate of diversity patterns observed across campanulids, we conclude that it remains difficult to confidently and directly view this character state as the actual cause of increased diversification rates.