pinecone/core-2020-05-10-deduplication huggingface dataset:
Genome-wide analyses suggest parallel selection for universal traits may eclipse local environmental selection in a highly mobile carnivore

Ecological and environmental heterogeneity can produce genetic differentiation in highly mobile species. Accordingly, local adaptation may be expected across comparatively short distances in the presence of marked environmental gradients. Within the European continent, wolves (Canis lupus) exhibit distinct north-south population differentiation. We investigated more than 67-K single nucleotide polymorphism (SNP) loci for signatures of local adaptation in 59 unrelated wolves from four previously identified population clusters (northcentral Europe n=32, Carpathian Mountains n=7, Dinaric-Balkan n=9, Ukrainian Steppe n=11). Our analyses combined identification of outlier loci with findings from genome-wide association study of individual genomic profiles and 12 environmental variables. We identified 353 candidate SNP loci. We examined the SNP position and neighboring megabase (1Mb, one million bases) regions in the dog (C. lupus familiaris) genome for genes potentially under selection, including homologue genes in other vertebrates. These regions included functional genes for, for example, temperature regulation that may indicate local adaptation and genes controlling for functions universally important for wolves, including olfaction, hearing, vision, and cognitive functions. We also observed strong outliers not associated with any of the investigated variables, which could suggest selective pressures associated with other unmeasured environmental variables and/or demographic factors. These patterns are further supported by the examination of spatial distributions of the SNPs associated with universally important traits, which typically show marked differences in allele frequencies among population clusters. Accordingly, parallel selection for features important to all wolves may eclipse local environmental selection and implies long-term separation among population clusters.201
Maternal response to environmental unpredictability

This study was funded by a postdoctoral fellowship to MB (SFRH/BPD/82259/2011) and with a “Bolsista CAPES/BRASIL,” (Project A058/2013) to AMVMS.Mothers are expected to use environmental cues to modify maternal investment to optimize their fitness. However, when the environment varies unpredictably, cues may not be an accurate proxy of future conditions. Under such circumstances, selection favors a diversifying maternal investment strategy. While there is evidence that the environment is becoming more uncertain, the extent to which mothers are able to respond to this unpredictability is generally unknown. In this study, we test the hypothesis that Daphnia magna increase the variance in maternal investment in response to unpredictable variation in temperature consistent with global change predictions. We detected significant variability across temperature treatments in brood size, neonate size at birth, and time between broods. The estimated variability within-brood size was higher (albeit not statistically significant) in mothers reared in unpredictable temperature conditions. We also detected a cross-generational effect with the temperature history of mothers modulating the phenotypic response of F1's. Notably, our results diverged from the prediction that increased variability poses a greater risk to organisms than changes in mean temperature. Increased unpredictability in temperature had negligible effects on fitness-correlated traits. Mothers in the unpredictable treatment, survived as long, and produced as many F1's during lifetime as those produced in the most fecund treatment. Further, increased unpredictability in temperature did not affect the probability of survival of F1's. Collectively, we provide evidence that daphnia respond effectively to thermal unpredictability. But rather than increasing the variance in maternal investment, daphnia respond to uncertainty by being a jack of all temperatures, master of none. Importantly, our study highlights the essential need to examine changes in variances rather than merely on means, when investigating maternal responses.Publisher PDFPeer reviewe
Release from belowground enemies and shifts in root traits as interrelated drivers of alien plant invasion success : a hypothesis\ud

Our understanding of the interrelated mechanisms driving plant invasions, such as the interplay between enemy release and resource-acquisition traits, is biased by an aboveground perspective. To address this bias, I hypothesize that plant release from belowground enemies (especially fungal pathogens) will give invasive plant species a fitness advantage in the alien range, via shifts in root traits (e.g., increased specific root length and branching intensity) that increase resource uptake and competitive ability compared to native species in the alien range, and compared to plants of the invader in its native range. Such root-trait changes could be ecological or evolutionary in nature. I explain how shifts in root traits could occur as a consequence of enemy release and contribute to invasion success of alien plants, and how they could be interrelated with other potential belowground drivers of invasion success (allelopathy, mutualist enhancement). Finally, I outline the approaches that could be taken to test whether belowground enemy release results in increased competitive ability and nutrient uptake by invasive alien plants, via changes in root traits in the alien range
Evolution along the Great Rift Valley: phenotypic and genetic differentiation of East African white-eyes (Aves, Zosteropidae)

The moist and cool cloud forests of East Africa represent a network of isolated habitats that are separated by dry and warm lowland savannah, offering an opportunity to investigate how strikingly different selective regimes affect species diversification. Here, we used the passerine genus Zosterops (white-eyes) from this region as our model system. Species of the genus occur in contrasting distribution settings, with geographical mountain isolation driving diversification, and savannah interconnectivity preventing differentiation. We analyze (1) patterns of phenotypic and genetic differentiation in high- and lowland species (different distribution settings), (2) investigate the potential effects of natural selection and temporal and spatial isolation (evolutionary drivers), and (3) critically review the taxonomy of this species complex. We found strong phenotypic and genetic differentiation among and within the three focal species, both in the highland species complex and in the lowland taxa. Altitude was a stronger predictor of phenotypic patterns than the current taxonomic classification. We found longitudinal and latitudinal phenotypic gradients for all three species. Furthermore, wing length and body weight were significantly correlated with altitude and habitat type in the highland species Z.poliogaster. Genetic and phenotypic divergence showed contrasting inter- and intraspecific structures. We suggest that the evolution of phenotypic characters is mainly driven by natural selection due to differences in the two macro-habitats, cloud forest and savannah. In contrast, patterns of neutral genetic variation appear to be rather driven by geographical isolation of the respective mountain massifs. Populations of the Z.poliogaster complex, as well as Z.senegalensis and Z.abyssinicus, are not monophyletic based on microsatellite data and have higher levels of intraspecific differentiation compared to the currently accepted species
A spatially explicit capture-recapture estimator for single-catch traps

This work was part-funded by EPSRC grant EP/I000917/1.1. Single-catch traps are frequently used in live-trapping studies of small mammals. Thus far a likelihood for single-catch traps has proven elusive and usually the likelihood for multi-catch traps is used for spatially explicit capture-recapture (SECR) analyses of such data. Previous work found the multi-catch likelihood to provide a robust estimator of average density. 2. We build on a recently developed continuous-time model for SECR to derive a likelihood for single-catch traps. We use this to develop an estimator based on observed capture times and compare its performance by simulation to that of the multi-catch estimator for various scenarios with non-constant density surfaces. 3. While the multi-catch estimator is found to be a surprisingly robust estimator of average density, its performance deteriorates with high trap saturation and increasing density gradients. Moreover, it is found to be a poor estimator of the height (but not range) of the detection function. By contrast, the single catch estimators of density, distribution and detection function parameters are found to be unbiased or nearly unbiased in all scenarios considered. This gain comes at the cost of higher variance, so that despite the lower bias of the single-catch estimator of the density surface over space, its root mean squared error is similar to that of the multi-catch estimator. 4. If there is no interest in interpreting the detection function parameters themselves, and if density is expected to be fairly constantover the survey region, then the multi-catch estimator performs well with single-catch traps. However if accurate estimation of the detection function is of interest, or if density is expected to vary substantially in space, then there is merit in using the single-catch estimator when trap saturation is above about 60%. The estimator’s performance is improved if care is taken to place traps so as to span the range of variables that affect animal distribution. As a single-catch likelihood with unknown capture times remains intractable for now, researchers using single-catch traps should aim to incorporate timing devices with their traps.Publisher PDFPeer reviewe
Ocean acidification and temperature increase impact mussel shell shape and thickness : problematic for protection?

Ocean acidification threatens organisms that produce calcium carbonate shells by potentially generating an under-saturated carbonate environment. Resultant reduced calcification and growth, and subsequent dissolution of exoskeletons, would raise concerns over the ability of the shell to provide protection for the marine organism under ocean acidification and increased temperatures. We examined the impact of combined ocean acidification and temperature increase on shell formation of the economically important edible mussel Mytilus edulis. Shell growth and thickness along with a shell thickness index and shape analysis were determined. The ability of M. edulis to produce a functional protective shell after 9 months of experimental culture under ocean acidification and increasing temperatures (380, 550, 750, 1000 μatm pCO2, and 750, 1000 μatm pCO2 + 2°C) was assessed. Mussel shells grown under ocean acidification conditions displayed significant reductions in shell aragonite thickness, shell thickness index, and changes to shell shape (750, 1000 μatm pCO2) compared to those shells grown under ambient conditions (380 μatm pCO2). Ocean acidification resulted in rounder, flatter mussel shells with thinner aragonite layers likely to be more vulnerable to fracture under changing environments and predation. The changes in shape presented here could present a compensatory mechanism to enhance protection against predators and changing environments under ocean acidification when mussels are unable to grow thicker shells. Here, we present the first assessment of mussel shell shape to determine implications for functional protection under ocean acidification
Predator-driven elemental cycling: the impact of predation and risk effects on ecosystem stoichiometry

Empirical evidence is beginning to show that predators can be important drivers of elemental cycling within ecosystems by propagating indirect effects that determine the distribution of elements among trophic levels as well as determine the chemical content of organic matter that becomes decomposed by microbes. These indirect effects can be propagated by predator consumptive effects on prey, nonconsumptive (risk) effects, or a combination of both. Currently, there is insufficient theory to predict how such predator effects should propagate throughout ecosystems. We present here a theoretical framework for exploring predator effects on ecosystem elemental cycling to encourage further empirical quantification. We use a classic ecosystem trophic compartment model as a basis for our analyses but infuse principles from ecological stoichiometry into the analyses of elemental cycling. Using a combined analytical-numerical approach, we compare how predators affect cycling through consumptive effects in which they control the flux of nutrients up trophic chains; through risk effects in which they change the homeostatic elemental balance of herbivore prey which accordingly changes the element ratio herbivores select from plants; and through a combination of both effects. Our analysis reveals that predators can have quantitatively important effects on elemental cycling, relative to a model formalism that excludes predator effects. Furthermore, the feedbacks due to predator nonconsumptive effects often have the quantitatively strongest impact on whole ecosystem elemental stocks, production and efficiency rates, and recycling fluxes by changing the stoichiometric balance of all trophic levels. Our modeling framework predictably shows how bottom-up control by microbes and top-down control by predators on ecosystems become interdependent when top predator effects permeate ecosystems
Persistence of distinctive morphotypes in the native range of the CITES-listed Aldabra giant tortoise

Understanding the extent of morphological variation in the wild population of Aldabra giant tortoises is important for conservation, as morphological variation in captive populations has been interpreted as evidence for lingering genes from extinct tortoise lineages. If true, this could impact reintroduction programmes in the region. The population of giant tortoises on Aldabra Atoll is subdivided and distributed around several islands. Although pronounced morphological variation was recorded in the late 1960s, it was thought to be a temporary phenomenon. Early researchers also raised concerns over the future of the population, which was perceived to have exceeded its carrying capacity. We analyzed monthly monitoring data from 12 transects spanning a recent 15-year period (1998–2012) during which animals from four subpopulations were counted, measured, and sexed. In addition, we analyzed survival data from individuals first tagged during the early 1970s. The population is stable with no sign of significant decline. Subpopulations differ in density, but these differences are mostly due to differences in the prevailing vegetation type. However, subpopulations differ greatly in both the size of animals and the degree of sexual dimorphism. Comparisons with historical data reveal that phenotypic differences among the subpopulations of tortoises on Aldabra have been apparent for the last 50 years with no sign of diminishing. We conclude that the giant tortoise population on Aldabra is subject to varying ecological selection pressures, giving rise to stable morphotypes in discrete subpopulations. We suggest therefore that (1) the presence of morphological differences among captive Aldabra tortoises does not alone provide convincing evidence of genes from other extinct species; and (2) Aldabra serves as an important example of how conservation and management in situ can add to the scientific value of populations and perhaps enable them to better adapt to future ecological pressures
Don't let spurious accusations of pseudoreplication limit our ability to learn from natural experiments (and other messy kinds of ecological monitoring)

Pseudoreplication is defined as the use of inferential statistics to test for treatment effects where treatments are not replicated and/or replicates are not statistically independent. It is a genuine but controversial issue in ecology particularly in the case of costly landscape-scale manipulations, behavioral studies where ethics or other concerns may limit sample sizes, ad hoc monitoring data, and the analysis of natural experiments where chance events occur at a single site. Here key publications on the topic are reviewed to illustrate the debate that exists about the conceptual validity of pseudoreplication. A survey of ecologists and case studies of experimental design and publication issues are used to explore the extent of the problem, ecologists’ solutions, reviewers’ attitudes, and the fate of submitted manuscripts. Scientists working across a range of ecological disciplines regularly come across the problem of pseudoreplication and build solutions into their designs and analyses. These include carefully defining hypotheses and the population of interest, acknowledging the limits of statistical inference and using statistical approaches including nesting and random effects. Many ecologists face considerable challenges getting their work published if accusations of pseudoreplication are made – even if the problem has been dealt with. Many reviewers reject papers for pseudoreplication, and this occurs more often if they haven't experienced the issue themselves. The concept of pseudoreplication is being applied too dogmatically and often leads to rejection during review. There is insufficient consideration of the associated philosophical issues and potential statistical solutions. By stopping the publication of ecological studies, reviewers are slowing the pace of ecological research and limiting the scope of management case studies, natural events studies, and valuable data available to form evidence-based solutions. Recommendations for fair and consistent treatment of pseudoreplication during writing and review are given for authors, reviewers, and editors
Oxidative stress and life histories: unresolved issues and current needs.

This is the final version of the article. Available from the publisher via the DOI in this record.Life-history theory concerns the trade-offs that mold the patterns of investment by animals between reproduction, growth, and survival. It is widely recognized that physiology plays a role in the mediation of life-history trade-offs, but the details remain obscure. As life-history theory concerns aspects of investment in the soma that influence survival, understanding the physiological basis of life histories is related, but not identical, to understanding the process of aging. One idea from the field of aging that has gained considerable traction in the area of life histories is that life-history trade-offs may be mediated by free radical production and oxidative stress. We outline here developments in this field and summarize a number of important unresolved issues that may guide future research efforts. The issues are as follows. First, different tissues and macromolecular targets of oxidative stress respond differently during reproduction. The functional significance of these changes, however, remains uncertain. Consequently there is a need for studies that link oxidative stress measurements to functional outcomes, such as survival. Second, measurements of oxidative stress are often highly invasive or terminal. Terminal studies of oxidative stress in wild animals, where detailed life-history information is available, cannot generally be performed without compromising the aims of the studies that generated the life-history data. There is a need therefore for novel non-invasive measurements of multi-tissue oxidative stress. Third, laboratory studies provide unrivaled opportunities for experimental manipulation but may fail to expose the physiology underpinning life-history effects, because of the benign laboratory environment. Fourth, the idea that oxidative stress might underlie life-history trade-offs does not make specific enough predictions that are amenable to testing. Moreover, there is a paucity of good alternative theoretical models on which contrasting predictions might be based. Fifth, there is an enormous diversity of life-history variation to test the idea that oxidative stress may be a key mediator. So far we have only scratched the surface. Broadening the scope may reveal new strategies linked to the processes of oxidative damage and repair. Finally, understanding the trade-offs in life histories and understanding the process of aging are related but not identical questions. Scientists inhabiting these two spheres of activity seldom collide, yet they have much to learn from each other.This study was the result of a week-long workshop sponsored
by the Rank prize funds attended by all the authors.
We are grateful to the Rank prize funds for supporting
this meetin
Evolutionary patterns of volatile terpene emissions across 202 tropical tree species

International audiencePlant responses to natural enemies include formation of secondary metabolites acting as direct or indirect defenses. Volatile terpenes represent one of the most diverse groups of secondary metabolites. We aimed to explore evolutionary patterns of volatile terpene emission. We measured the composition of damage-induced volatile terpenes from 202 Amazonian tree species, spanning the angiosperm phylogeny. Volatile terpenes were extracted with solid-phase micro extraction and desorbed in a gas chromatography–mass spectrometry for compound identification. The chemical diversity of the terpene blend showed a strong phylogenetic signal as closely related species emitted a similar number of compounds. Closely related species also tended to have compositionally similar blends, although this relationship was weak. Meanwhile, the ability to emit a given compound showed no significant phylogenetic signal for 200 of 286 compounds, indicating a high rate of diversification in terpene synthesis and/or great variability in their expression. Three lineages (Magnoliales, Laurales, and Sapindales) showed exceptionally high rates of terpene diversification. Of the 70 compounds found in >10% of their species, 69 displayed significant correlated evolution with at least one other compound. These results provide insights into the complex evolutionary history of volatile terpenes in angiosperms, while highlighting the need for further research into this important class of compounds
Local and neighboring patch conditions alter sex-specific movement in banana weevils

Understanding the mechanisms underlying the movements and spread of a species over time and space is a major concern of ecology. Here, we assessed the effects of an individual's sex and the density and sex ratio of conspecifics in the local and neighboring environment on the movement probability of the banana weevil, Cosmopolites sordidus. In a “two patches” experiment, we used radiofrequency identification tags to study the C. sordidus movement response to patch conditions. We showed that local and neighboring densities of conspecifics affect the movement rates of individuals but that the density-dependent effect can be either positive or negative depending on the relative densities of conspecifics in local and neighboring patches. We demonstrated that sex ratio also influences the movement of C. sordidus, that is, the weevil exhibits nonfixed sex-biased movement strategies. Sex-biased movement may be the consequence of intrasexual competition for resources (i.e., oviposition sites) in females and for mates in males. We also detected a high individual variability in the propensity to move. Finally, we discuss the role of demographic stochasticity, sex-biased movement, and individual heterogeneity in movement on the colonization process. (Résumé d'auteur