Ecology and Evolution Publishes Issue 3.12

ECE 3 12The latest issue of Ecology and Evolution is now live! Over 20 excellent articles free to read, download and share. The cover image has been taken from the article ‘Daphnia predation on the amphibian chytrid fungus and its impacts on disease risk in tadpoles’ by Catherine L. Searle, Joseph R. Mendelson III, Linda E. Green and Meghan A. Duffy. Below are some highlights from this issue:

purple_lock_open Functional similarity and molecular divergence of a novel reproductive transcriptome in two male-pregnant Syngnathus pipefish species by Clayton M. Small, April D. Harlin-Cognato, and Adam G. Jones
Summary: Evolutionary studies have revealed that reproductive proteins in animals and plants often evolve more rapidly than the genome-wide average. The causes of this pattern, which may include relaxed purifying selection, sexual selection, sexual conflict, pathogen resistance, reinforcement, or gene duplication, remain elusive. Investigative expansions to additional taxa and reproductive tissues have the potential to shed new light on this unresolved problem. Here, we embark on such an expansion, in a comparison of the brood-pouch transcriptome between two male-pregnant species of the pipefish genus Syngnathus.

purple_lock_open Drosophila rely on learning while foraging under semi-natural conditions by Vukašin Zrelec, et al.
Summary: Learning is predicted to affect manifold ecological and evolutionary processes, but the extent to which animals rely on learning in nature remains poorly known, especially for short-lived non-social invertebrates. This is in particular the case for Drosophila, a favourite laboratory system to study molecular mechanisms of learning. Here we tested whether Drosophila melanogaster use learned information to choose food while free-flying in a large greenhouse emulating the natural environment.

purple_lock_open Strong species-environment feedback shapes plant community assembly along environmental gradients by Jiang Jiang and Donald L. DeAngelis
Summary: An aim of community ecology is to understand the patterns of competing species assembly along environmental gradients. All species interact with their environments. However, theories of community assembly have seldom taken into account the effects of species that are able to engineer the environment. In this modeling study, we integrate the species’ engineering trait together with processes of immigration and local dispersal into a theory of community assembly.

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The British Ecological Society Celebrates Open Access Week

This post has been reposted from the Methods in Ecology and Evolution Blog

BESThis week is international Open Access Week, which aims to raise the awareness of open access publishing within the scientific and academic community, and provides an opportunity to hear about its potential benefits and the latest policies and opinions. Institutions and universities from all over the world are involved and there’s an extensive calendar of events that you can have a look at to see what’s happening in your area.

What open access options do Methods and the other BES Journals offer?

In addition to the above open access options, all of our content is made freely available 2 years after publication. We’re also pleased to be able to offer readers free access to all Application papers, which are citable descriptions of new methods and techniques in ecology and evolution.

Read Ecology and Evolution Issue 3.10

ECE 3 10The latest issue of Ecology and Evolution is now live! Over 30 excellent articles free to read, download and share. ‘Interior Least Tern (Sternula antillarum) breeding distribution and ecology: implications for population-level studies and the evaluation of alternative management strategies on large, regulated rivers’ by Casey A. Lott et al. Below are some highlights from this issue:

purple_lock_open Dramatic response to climate change in the Southwest: Robert Whittaker’s 1963 Arizona Mountain plant transect revisited by Richard C. Brusca, et al.
Summary: Models analyzing how Southwestern plant communities will respond to climate change predict that increases in temperature will lead to upward elevational shifts of montane species. We tested this hypothesis by reexamining Robert Whittaker’s 1963 plant transect in the Santa Catalina Mountains of southern Arizona, finding that this process is already well underway. Our survey, five decades after Whittaker’s, reveals large changes in the elevational ranges of common montane plants, while mean annual rainfall has decreased over the past 20 years, and mean annual temperatures increased 0.25°C/decade from 1949 to 2011 in the Tucson Basin. Although elevational changes in species are individualistic, significant overall upward movement of the lower elevation boundaries, and elevational range contractions, have occurred. This is the first documentation of significant upward shifts of lower elevation range boundaries in Southwestern montane plant species over decadal time, confirming that previous hypotheses are correct in their prediction that mountain communities in the Southwest will be strongly impacted by warming, and that the Southwest is already experiencing a rapid vegetation change.

purple_lock_open Did the house mouse (Mus musculus L.) shape the evolutionary trajectory of wheat (Triticum aestivum L.)? by C. F. Morris, et al.
Summary: Wheat (Triticum aestivum L.) is one of the most successful domesticated plant species in the world. The majority of wheat carries mutations in the Puroindoline genes that result in a hard kernel phenotype. An evolutionary explanation, or selective advantage, for the spread and persistence of these hard kernel mutations has yet to be established. Here, we demonstrate that the house mouse (Mus musculus L.) exerts a pronounced feeding preference for soft over hard kernels. When allele frequencies ranged from 0.5 to 0.009, mouse predation increased the hard allele frequency as much as 10-fold. Studies involving a single hard kernel mixed with ~1000 soft kernels failed to recover the mutant kernel. Nevertheless, the study clearly demonstrates that the house mouse could have played a role in the evolution of wheat, and therefore the cultural trajectory of humankind.

purple_lock_open Quantitative genetic analysis of responses to larval food limitation in a polyphenic butterfly indicates environment- and trait-specific effects by Marjo Saastamoinen, et al.
Summary: Different components of heritability, including genetic variance (VG), are influenced by environmental conditions. Here, we assessed phenotypic responses of life-history traits to two different developmental conditions, temperature and food limitation. The former represents an environment that defines seasonal polyphenism in our study organism, the tropical butterfly Bicyclus anynana, whereas the latter represents a more unpredictable environment. We quantified heritabilities using restricted maximum likelihood (REML) procedures within an “Information Theoretical” framework in a full-sib design. Whereas development time, pupal mass, and resting metabolic rate showed no genotype-by-environment interaction for genetic variation, for thorax ratio and fat percentage the heritability increased under the cool temperature, dry season environment. Additionally, for fat percentage heritability estimates increased under food limitation. Hence, the traits most intimately related to polyphenism in B. anynana show the most environmental-specific heritabilities as well as some indication of cross-environmental genetic correlations. This may reflect a footprint of natural selection and our future research is aimed to uncover the genes and processes involved in this through studying season and condition-dependent gene expression.

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Ecology and Evolution Publishes issue 3.9. Read the Highlights Here!

ECE 3 9The latest issue of Ecology and Evolution is now live! Over 30 excellent articles free to read, download and share. The cover image has been taken from the article ‘Different modes of evolution in males and females generate dichromatism in fairy-wrens (Maluridae)’ by Allison E. Johnson, J. J. Price, and S. Pruett-Jones. Below are some highlights from this issue:

purple_lock_open Different modes of evolution in males and females generate dichromatism in fairy-wrens (Maluridae) by Allison E. Johnson, J. Jordan Price, Stephen Pruett-Jones
Summary: Sexual dichromatism in birds is often attributed to selection for elaboration in males. However, evolutionary changes in either sex can result in plumage differences between them, and such changes can result in either gains or losses of dimorphism. We reconstructed the evolution of plumage colors in both males and females of species in Maluridae, a family comprising the fairy-wrens (Malurus, Clytomias, Sipodotus), emu-wrens (Stipiturus), and grasswrens (Amytornis). Our results show that, across species, males and females differ in their patterns of color evolution. Male plumage has diverged at relatively steady rates, whereas female coloration has changed dramatically in some lineages and little in others. Accordingly, in comparisons against evolutionary models, plumage changes in males best fit a Brownian motion (BM) model, whereas plumage changes in females fit an Ornstein Uhlenbeck (OU) multioptimum model, with different adaptive peaks corresponding to distributions in either Australia or New Guinea. Levels of dichromatism were significantly associated with latitude, with greater dichromatism in more southerly taxa. Our results suggest that current patterns of plumage diversity in fairy-wrens are a product of evolutionary changes in both sexes, driven in part by environmental differences across the distribution of the family.

purple_lock_open Tropical rain forest conservation and the twin challenges of diversity and rarity by Stephen P. Hubbell
Summary: Data from a global network of large, permanent plots in lowland tropical forests demonstrate (1) that the phenomenon of tropical tree rarity is real and (2) that almost all the species diversity in such forests is due to rare species. Theoretical and empirically based reasoning suggests that many of these rare species are not as geographically widespread as previously thought. These findings suggest that successful strategies for conserving global tree diversity in lowland tropical forests must pay much more attention to the biogeography of rarity, as well as to the impact of climate change on the distribution and abundance of rare species. Because the biogeography of many tropical tree species is poorly known, a high priority should be given to documenting the distribution and abundance of rare tropical tree species, particularly in Amazonia, the largest remaining tropical forested region in the world.

purple_lock_open Nonconsumptive effects in a multiple predator system reduce the foraging efficiency of a keystone predator by Jon M. Davenport, David R. Chalcraft
Summary: Many studies have demonstrated that the nonconsumptive effect (NCE) of predators on prey traits can alter prey demographics in ways that are just as strong as the consumptive effect (CE) of predators. Less well studied, however, is how the CE and NCE of multiple predator species can interact to influence the combined effect of multiple predators on prey mortality. We examined the extent to which the NCE of one predator altered the CE of another predator on a shared prey and evaluated whether we can better predict the combined impact of multiple predators on prey when accounting for this influence. We conducted a set of experiments with larval dragonflies, adult newts (a known keystone predator), and their tadpole prey. We quantified the CE and NCE of each predator, the extent to which NCEs from one predator alters the CE of the second predator, and the combined effect of both predators on prey mortality. We then compared the combined effect of both predators on prey mortality to four predictive models. Dragonflies caused more tadpoles to hide under leaf litter (a NCE), where newts spend less time foraging, which reduced the foraging success (CE) of newts. Newts altered tadpole behavior but not in a way that altered the foraging success of dragonflies. Our study suggests that we can better predict the combined effect of multiple predators on prey when we incorporate the influence of interactions between the CE and NCE of multiple predators into a predictive model. In our case, the threat of predation to prey by one predator reduced the foraging efficiency of a keystone predator. Consequently, the ability of a predator to fill a keystone role could be compromised by the presence of other predators.

purple_lock_open  Functional traits, the phylogeny of function, and ecosystem service vulnerability by Sandra Díaz, Andy Purvis, Johannes H. C. Cornelissen, Georgina M. Mace, Michael J. Donoghue, Robert M. Ewers, Pedro Jordano, William D. Pearse
Summary: People depend on benefits provided by ecological systems. Understanding how these ecosystem services – and the ecosystem properties underpinning them – respond to drivers of change is therefore an urgent priority. We address this challenge through developing a novel risk-assessment framework that integrates ecological and evolutionary perspectives on functional traits to determine species’ effects on ecosystems and their tolerance of environmental changes. We define Specific Effect Function (SEF) as the per-gram or per capita capacity of a species to affect an ecosystem property, and Specific Response Function (SRF) as the ability of a species to maintain or enhance its population as the environment changes. Our risk assessment is based on the idea that the security of ecosystem services depends on how effects (SEFs) and tolerances (SRFs) of organisms – which both depend on combinations of functional traits – correlate across species and how they are arranged on the species’ phylogeny. Four extreme situations are theoretically possible, from minimum concern when SEF and SRF are neither correlated nor show a phylogenetic signal, to maximum concern when they are negatively correlated (i.e., the most important species are the least tolerant) and phylogenetically patterned (lacking independent backup). We illustrate the assessment with five case studies, involving both plant and animal examples. However, the extent to which the frequency of the four plausible outcomes, or their intermediates, apply more widely in real-world ecological systems is an open question that needs empirical evidence, and suggests a research agenda at the interface of evolutionary biology and ecosystem ecology.

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Ecology and Evolution has received its first Impact Factor of 1.184, ranking 99/136 in Ecology!

ECE 3 7Following on from the release of Ecology and Evolution’s first Impact Factor, the latest issue of Ecology and Evolution is now live! Over 30 excellent articles free to read, download and share. The cover image has been taken from the article Inbreeding reveals mode of past selection on male reproductive characters in Drosophila melanogaster by Outi Ala-Honkola et al. Below are some highlights from this issue:

 purple_lock_open An age–size reaction norm yields insight into environmental interactions affecting life-history traits: a factorial study of larval development in the malaria mosquitoAnopheles gambiae sensu stricto by Conan Phelan and Bernard D. Rotiberg
Summary: Environmental factors frequently act nonindependently to determine growth and development of insects. Because age and size at maturity strongly influence population dynamics, interaction effects among environmental variables complicate the task of predicting dynamics of insect populations under novel conditions. We reared larvae of the African malaria mosquito Anopheles gambiae sensu stricto (s.s.) under three factors relevant to changes in climate and land use: food level, water depth, and temperature. Each factor was held at two levels in a fully crossed design, for eight experimental treatments. Larval survival, larval development time, and adult size (wing length) were measured to indicate the importance of interaction effects upon population-level processes. For age and size at emergence, but not survival, significant interaction effects were detected for all three factors, in addition to sex. Some of these interaction effects can be understood as consequences of how the different factors influence energy usage in the context of a nonindependent relationship between age and size. Experimentally assessing interaction effects for all potential future sets of conditions is intractable. However, considering how different factors affect energy usage within the context of an insect’s evolved developmental program can provide insight into the causes of complex environmental effects on populations.

purple_lock_open  Foraging area fidelity for Kemp’s ridleys in the Gulf of Mexico by Donna J. Shaver, Kristen M. Hart, Ikuko Fujisaki, Cynthia Rubio, Autumn R. Sartain, Jaime Peña, Patrick M. Burchfield, Daniel Gomez Gamez and Jaime Ortiz
Summary: For many marine species, locations of key foraging areas are not well defined. We used satellite telemetry and switching state-space modeling (SSM) to identify distinct foraging areas used by Kemp’s ridley turtles (Lepidochelys kempii) tagged after nesting during 1998–2011 at Padre Island National Seashore, Texas, USA (PAIS;= 22), and Rancho Nuevo, Tamaulipas, Mexico (RN;= 9). Overall, turtles traveled a mean distance of 793.1 km (±347.8 SD) to foraging sites, where 24 of 31 turtles showed foraging area fidelity (FAF) over time (= 22 in USA,= 2 in Mexico). Multiple turtles foraged along their migratory route, prior to arrival at their “final” foraging sites. We identified new foraging “hotspots” where adult female Kemp’s ridley turtles spent 44% of their time during tracking (i.e., 2641/6009 tracking days in foraging mode). Nearshore Gulf of Mexico waters served as foraging habitat for all turtles tracked in this study; final foraging sites were located in water <68 m deep and a mean distance of 33.2 km (±25.3 SD) from the nearest mainland coast. Distance to release site, distance to mainland shore, annual mean sea surface temperature, bathymetry, and net primary production were significant predictors of sites where turtles spent large numbers of days in foraging mode. Spatial similarity of particular foraging sites selected by different turtles over the 13-year tracking period indicates that these areas represent critical foraging habitat, particularly in waters off Louisiana. Furthermore, the wide distribution of foraging sites indicates that a foraging corridor exists for Kemp’s ridleys in the Gulf. Our results highlight the need for further study of environmental and bathymetric components of foraging sites and prey resources contained therein, as well as international cooperation to protect essential at-sea foraging habitats for this imperiled species.

 purple_lock_open A new method for identifying rapid decline dynamics in wild vertebrate populations by Martina Di Fonzo, Ben Collen and Georgina M. Mace
Summary: Tracking trends in the abundance of wildlife populations is a sensitive method for assessing biodiversity change due to the short time-lag between human pressures and corresponding shifts in population trends. This study tests for proposed associations between different types of human pressures and wildlife population abundance decline-curves and introduces a method to distinguish decline trajectories from natural fluctuations in population time-series. First, we simulated typical mammalian population time-series under different human pressure types and intensities and identified significant distinctions in population dynamics. Based on the concavity of the smoothed population trend and the algebraic function which was the closest fit to the data, we determined those differences in decline dynamics that were consistently attributable to each pressure type. We examined the robustness of the attribution of pressure type to population decline dynamics under more realistic conditions by simulating populations under different levels of environmental stochasticity and time-series data quality. Finally, we applied our newly developed method to 124 wildlife population time-series and investigated how those threat types diagnosed by our method compare to the specific threatening processes reported for those populations. We show how wildlife population decline curves can be used to discern between broad categories of pressure or threat types, but do not work for detailed threat attributions. More usefully, we find that differences in population decline curves can reliably identify populations where pressure is increasing over time, even when data quality is poor, and propose this method as a cost-effective technique for prioritizing conservation actions between populations.

purple_lock_open Estimating resource selection with count data by Ryan M. Nielson and Hall Sawyer
Summary: Resource selection functions (RSFs) are typically estimated by comparing covariates at a discrete set of “used” locations to those from an “available” set of locations. This RSF approach treats the response as binary and does not account for intensity of use among habitat units where locations were recorded. Advances in global positioning system (GPS) technology allow animal location data to be collected at fine spatiotemporal scales and have increased the size and correlation of data used in RSF analyses. We suggest that a more contemporary approach to analyzing such data is to model intensity of use, which can be estimated for one or more animals by relating the relative frequency of locations in a set of sampling units to the habitat characteristics of those units with count-based regression and, in particular, negative binomial (NB) regression. We demonstrate this NB RSF approach with location data collected from 10 GPS-collared Rocky Mountain elk (Cervus elaphus) in the Starkey Experimental Forest and Range enclosure. We discuss modeling assumptions and show how RSF estimation with NB regression can easily accommodate contemporary research needs, including: analysis of large GPS data sets, computational ease, accounting for among-animal variation, and interpretation of model covariates. We recommend the NB approach because of its conceptual and computational simplicity, and the fact that estimates of intensity of use are unbiased in the face of temporally correlated animal location data.

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Ecology and Evolution Publishes Issue 3.6

ECE 3 6The latest issue of Ecology and Evolution is now live! Over 30 excellent articles free to read, download and share. The cover image is taken from ‘Ejaculate investment and attractiveness in the stalk-eyed fly, Diasemopsis meigenii by Elisabeth Harley et al. Below are some highlights from this issue:

purple_lock_open Belowground interactions shift the relative importance of direct and indirect genetic effects by Mark A. Genung, Joseph K. Bailey and Jennifer A. Schweitzer
Summary: Intraspecific genetic variation can affect decomposition, nutrient cycling, and interactions between plants and their associated belowground communities. However, the effects of genetic variation on ecosystems can also be indirect, meaning that genes in a focal plant may affect ecosystems by altering the phenotype of interacting (i.e., neighboring) individuals. We manipulated genotype identity, species identity, and the possibility of belowground interactions between neighboring Solidago plants. We hypothesized that, because our plants were nitrogen (N) limited, the most important interactions between focal and neighbor plants would occur belowground. More specifically, we hypothesized that the genotypic identity of a plant’s neighbor would have a larger effect on belowground biomass than on aboveground biomass, but only when neighboring plants were allowed to interact belowground.

purple_lock_open Reevaluation of a classic phylogeographic barrier: new techniques reveal the influence of microgeographic climate variation on population divergence by J. Angel Soto-Centeno, Lisa N. Barrow, Julie M. Allen and David L. Reed
Summary: We evaluated the mtDNA divergence and relationships within Geomys pinetis to assess the status of formerly recognized Geomys taxa. Additionally, we integrated new hypothesis-based tests in ecological niche models (ENM) to provide greater insight into causes for divergence and potential barriers to gene flow in Southeastern United States (Alabama, Florida, and Georgia). Our DNA sequence dataset confirmed and strongly supported two distinct lineages within G. pinetis occurring east and west of the ARD. Divergence date estimates showed that eastern and western lineages diverged about 1.37 Ma (1.9 Ma–830 ka). Predicted distributions from ENMs were consistent with molecular data and defined each population east and west of the ARD with little overlap. Niche identity and background similarity tests were statistically significant suggesting that ENMs from eastern and western lineages are not identical or more similar than expected based on random localities drawn from the environmental background.

purple_lock_open Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments by Luke R. Thompson, Chris Field, Tamara Romanuk, David Kamanda Ngugi, Rania Siam, Hamza El Dorry and Ulrich Sting
Summary: Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux.

purple_lock_open Forecasting deforestation and carbon emissions in tropical developing countries facing demographic expansion: a case study in Madagascar by Ghislain Vieilledent, Clovis Grinand and Romuald Vaudry
Summary: Anthropogenic deforestation in tropical countries is responsible for a significant part of global carbon dioxide emissions in the atmosphere. To plan efficient climate change mitigation programs (such as REDD+, Reducing Emissions from Deforestation and forest Degradation), reliable forecasts of deforestation and carbon dioxide emissions are necessary. Although population density has been recognized as a key factor in tropical deforestation, current methods of prediction do not allow the population explosion that is occurring in many tropical developing countries to be taken into account. Here, we propose an innovative approach using novel computational and statistical tools, including R/GRASS scripts and the new phcfM R package, to model the intensity and location of deforestation including the effect of population density. We used the model to forecast anthropogenic deforestation and carbon dioxide emissions in five large study areas in the humid and spiny-dry forests of Madagascar. Using our approach, we were able to demonstrate that the current rapid population growth in Madagascar (+3.39% per year) will significantly increase the intensity of deforestation by 2030 (up to +1.17% per year in densely populated areas).

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Read issue 3.5 of Ecology and Evolution now!

ECE 3 5 coverThe latest issue of Ecology and Evolution is now live! Over 20 excellent articles free to read, download and share. The cover image is taken from Non-linear feeding functional responses in the Greater Flamingo (Phoenicopterus roseus) predict immediate negative impact of wetland degradation on this flagship species by Anne-Sophie Deville et al. Below are some highlights from this issue:

purple_lock_open Taxonome: a software package for linking biological species data by Thomas A. Kluyver and Colin P. Osborne
Summary: Online databases of biological information offer tremendous potential for evolutionary and ecological discoveries, especially if data are combined in novel ways. However, the different names and varied spellings used for many species present major barriers to linking data. Taxonome is a software tool designed to solve this problem by quickly and reproducibly matching biological names to a given reference set. It is available both as a graphical user interface (GUI) for simple interactive use, and as a library for more advanced functionality with programs written in Python. Taxonome also includes functions to standardize distribution information to a well-defined set of regions, such as the TDWG World Geographical Scheme for Recording Plant Distributions. In combination, these tools will help biologists to rapidly synthesize disparate datasets, and to investigate large-scale patterns in species traits.

purple_lock_open Interpretations arising from Wrightian and Malthusian fitness under strong frequency dependent selection by Bin Wu, Chaitanya S. Gokhale, Matthijs van Veelen, Long Wang and Arne  Traulsen
Summary: Fitness is the central concept in evolutionary theory. It measures a phenotype’s ability to survive and reproduce. There are different ways to represent this measure: Malthusian fitness and Wrightian fitness. One can go back and forth between the two, but when we characterize model properties or interpret data, it can be important to distinguish between them. Here, we discuss a recent experiment to show how the interpretation changes if an alternative definition is used.

purple_lock_open Anthropogenic extinction threats and future loss of evolutionary history in reef corals by Danwei Huang and Kaustuv Roy
Summary: Extinction always results in loss of phylogenetic diversity (PD), but phylogenetically selective extinctions have long been thought to disproportionately reduce PD. Recent simulations show that tree shapes also play an important role in determining the magnitude of PD loss, potentially offsetting the effects of clustered extinctions. While patterns of PD loss under different extinction scenarios are becoming well characterized in model phylogenies, analyses of real clades that often have unbalanced tree shapes remain scarce, particularly for marine organisms. Here, we use a fossil-calibrated phylogeny of all living scleractinian reef corals in conjunction with IUCN data on extinction vulnerabilities to quantify how loss of species in different threat categories will affect the PD of this group. Our analyses reveal that predicted PD loss in corals varies substantially among different threats, with extinctions due to bleaching and disease having the largest negative effects on PD. In general, more phylogenetically clustered extinctions lead to larger losses of PD in corals, but there are notable exceptions; extinction of rare corals from distantly-related old and unique lineages can also result in substantial PD loss. Thus our results show that loss of PD in reef corals is dependent on both tree shape and the nature of extinction threats.

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Ecology and Evolution publishes its latest issue

Ecology and Evolution 3 2 coverThe latest issue of Ecology and Evolution is now live! Over 20 excellent articles free to read, download and share. The cover image is taken from The bacterial parasite Pasteuria ramosa is not killed if it fails to infect: implications for coevolution by Kayla C. King, et al.

Below are some highlights from this issue:

Extinction hazards in experimental Daphnia magna populations: effects of genotype diversity and environmental variation by John D. Robinson, John P. Wares, and John M. Drake
Summary: Extinction is ubiquitous in natural systems and the ultimate fate of all biological populations. However, the factors that contribute to population extinction are still poorly understood, particularly genetic diversity and composition. A laboratory experiment was conducted to examine the influences of environmental variation and genotype diversity on persistence in experimental Daphnia magna populations. Populations were initiated in two blocks with one, two, three, or six randomly selected and equally represented genotypes, fed and checked for extinction daily, and censused twice weekly over a period of 170 days.

Simulating evolutionary responses of an introgressed insect resistance trait for ecological effect assessment of transgene flow: a model for supporting informed decision-making in environmental risk assessment by Matthias S. Meier, Miluse Trtikova, Matthias Suter, Peter J. Edwards and Angelika Hilbeck
Summary: Predicting outcomes of transgene flow from arable crops requires a system perspective that considers ecological and evolutionary processes within a landscape context. In Europe, the arable weed Raphanus raphanistrum is a potential hybridization partner of oilseed rape, and the two species are ecologically linked through the common herbivores Meligethes spp. Observations in Switzerland show that high densities of Meligethes beetles maintained by oilseed rape crops can lead to considerable damage on R. raphanistrum. We asked how increased insect resistance in R. raphanistrum – as might be acquired through introgression from transgenic oilseed rape – would affect seed production under natural herbivore pressure.

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Wiley signs Open Access Agreements with Helmholtz Association and University of Manitoba

Ten institutes of the Helmholtz Association and the University of Manitoba have signed up for Wiley Open Access Accounts.   These agreements provide active financial support and a streamlined process for authors to ensure open access to their published research in Wiley-Blackwell journals.  Authors affiliated with the Univesity of Manitoba and the institutes of the Helmholtz Association listed below can now benefit from these arrangements when publishing articles in Wiley Open Access journals.

Alfred-Wegener-Institut für Polar- und Meeresforschung
Deutsches Elektronen-Synchrotron DESY
Deutsches Krebsforschungszentrum
Deutsches Zentrum für Luft- und Raumfahrt
Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)
Forschungszentrum Jülich
GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel
Helmholtz-Zentrum für Infektionsforschung
Helmholtz-Zentrum für Umweltforschung – UFZ
Karlsruher Institut für Technologie

The University of Manitoba and the Helmholtz Association insitutions join a number of funders who have opened a Wiley Open Access Account since this was launched. Browse our listing to see the institutions / funders who have an account or partnership with Wiley Open Access.

More information about our open access options for funders and institutions can be found here.

Ecology and Evolution Publishes the Final Issue of 2012

ECE 2 12The latest issue of Ecology and Evolution is now live! Over 20 excellent articles free to read, download and share. The cover image is taken from Permeability of the landscape matrix between amphibian breeding sites by Josh Van Buskirk. This is the final issue in what has been another fantastic volume for Ecology and Evolution.

Below are the editors’ highlights from this issue:

 Diversity of birds in eastern North America shifts north with global warming by Kenneth W. McDonald, Christopher J. W. McClure, Brian W. Rolek and Geoffrey E. Hill
Summary: Here, we report that bird diversity in North America increased and shifted northward between 1966 and 2010. This change in the relationship of diversity to the latitudinal gradient is, likely, primarily influenced by range expansions of species that winter in the eastern United States as opposed to species which migrate to this area from wintering grounds in the tropics. This increase in diversity and its northward expansion is best explained by an increase in regional prebreeding season temperature over the past 44 years.

 Evidence of stable genetic structure across a remote island archipelago through self-recruitment in a widely dispersed coral reef fish by Mark A. Priest, Andrew R. Halford and Jennifer L. McIlwain
Summary: For the majority of marine organisms a pelagic larval stage provides the primary mechanism for dispersal amongst often spatially fragmented habitat patches. The degree to which larvae disperse and populations are subsequently connected may have a profound influence on the population dynamics of a species. We used microsatellite markers to assess the population genetic structure of the scribbled rabbitfish Siganus spinus in the western Pacific. This species is a culturally important food fish in the Mariana Archipelago and subject to high fishing pressure. Our results confirm the relative isolation of the southern Mariana Islands population and highlight how local processes can act to isolate populations that, by virtue of their broad-scale distribution, have been subject to traditionally high gene flows.

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The Evolution of Author Guidelines

Congratulations are due to PeerJ for succeeding in bringing into focus an essential publisher service that has been little publicised in the past.

The journal opened for submissions on December 3rd, and many tweets and blogs have been spawned by the following passage in the Instructions for Authors:

We want authors spending their time doing science, not formatting.

We include reference formatting as a guide to make it easier for editors, reviewers, and PrePrint readers, but will not strictly enforce the specific formatting rules as long as the full citation is clear.

Styles will be normalized by us if your manuscript is accepted.

Of course, it would be ridiculous to assert that every manuscript ever submitted up to this point had perfectly formatted references in journal style; in fact it is relatively rare to make no edits at all on a reference list. Journal Production Editors have been converting reference formats since journal publishing began; laboriously at first, but the digital revolution has certainly helped in recent years, with more automated processes and specialist typesetters taking on much of the tedium.

 As the PeerJ guidelines correctly state, a requirement for a particular style can help the editorial and review process, and I would go further in saying that it can impose some rigour on the creation of the reference list, helping to ensure that all critical elements are present. However, it has been the case for some time that publishers have barely batted an eye if an article happens to arrive in the incorrect format, as long as all of the important content was present.

 At Wiley, we took this a stage further on the launch of our Wiley Open Access program back in May 2011. We made a point of paring the formatting requirements down to a bare minimum for the entire article. The Author Guidelines state:

 We place very few restrictions on the way in which you prepare your article, and it is not necessary to try to replicate the layout of the journal in your submission. We ask only that you consider your reviewers by supplying your manuscript in a clear, generic and readable layout, and ensure that all relevant sections are included. Our production process will take care of all aspects of formatting and style.

And with respect to the references:

 As with the main body of text, the completeness and content of your reference list is more important than the format chosen. A clear and consistent, generic style will assist the accuracy of our production processes and produce the highest quality published work, but it is not necessary to try to replicate the journal’s own style, which is applied during the production process. If you use bibliographic software to generate your reference list, select a standard output style, and check that it produces full and comprehensive reference listings…The final journal output will use the ‘Harvard’ style of reference citation. If your manuscript has already been prepared using the ‘Vancouver’ system, we are quite happy to receive it in this form. We will perform the conversion from one system to the other during the production process.

There is no doubt that this service, which has been quietly in operation in most journals for some time, has now been thrown much more into the limelight, and this can only be positive because it showcases one of the valuable services that professional publishing can provide.

Reading through the blogs, I see that the more overt adoption of this service as a point of policy is already spreading to more journals, as it has to eLife, and Elsevier’s Free Radical Biology & Medicine.

 This can only be a good thing.

Will Wilcox, Journals Content Management Director for Life Sciences

Ecology and Evolution at the British Ecological Society Annual Meeting

ECE 2 11 coverTo celebrate the new partnership with the British Ecological Society, Ecology and Evolution will be sponsoring the Welcome Mixer quiz at this year’s British Ecological Society Annual Meeting.

This year’s BES Annual Meeting is taking place between 17th and 20th December and with more abstracts submitted and delegates registered than any year over the past decade, this meeting will be one of the biggest and best for some time! There will be a number of networking opportunities throughout the Meeting, starting with the Welcome Mixer on Monday 17th, 19:30-21:30, at the spectacular Birmingham Museum and Art Gallery – photos to follow!

BES President Professor Georgina Mace will be introducing the Annual Meeting at this Welcome Mixer, and announcing that the BES journals have joined other high-impact titles in offering authors a rapid manuscript transferral system which maintains the highest standards of peer review while increasing the efficiency of the process. Both Ecology and Evolution Editors-in-Chief, Andrew Beckerman and Allen Moore, and a number of other BES Journal Editors will be attending both the Welcome Mixer, and the Annual Meeting.

Ecology and Evolution Publishes Issue 2.11

ECE 2 11 coverThe latest issue of Ecology and Evolution is now live! Over 20 excellent articles free to read, download and share. The cover image is taken from Philopatry drives genetic differentiation in an island archipelago: comparative population genetics of Galapagos Nazca boobies (Sula granti) and great frigatebirds (Fregata minor) by Iris I. Levin and Patricia G. Parker.

Below are some highlights from this issue:

purple_lock_open Warming off southwestern Japan linked to distributional shifts of subtidal canopy-forming seaweeds by Kouki Tanaka, Seiya Taino, Hiroko Haraguchi, Gabrielle Prendergast and Masanori Hiraoka.
Summary: To assess distributional shifts of species in response to recent warming, historical distribution records are the most requisite information. The surface seawater temperature (SST) of Kochi Prefecture, southwestern Japan on the western North Pacific, has significantly risen, being warmed by the Kuroshio Current. Past distributional records of subtidal canopy-forming seaweeds (Laminariales and Fucales) exist at about 10-year intervals from the 1970s, along with detailed SST datasets at several sites along Kochi’s >700 km coastline. In order to provide a clear picture of distributional shifts of coastal marine organisms in response to warming SST, we observed the present distribution of seaweeds and analyzed the SST datasets to estimate spatiotemporal SST trends in this coastal region.

purple_lock_open Extreme climatic events drive mammal irruptions: regression analysis of 100-year trends in desert rainfall and temperature by Aaron C. Greenville, Glenda M. Wardle and Chris R. Dickman.
Summary: Extreme climatic events, such as flooding rains, extended decadal droughts and heat waves have been identified increasingly as important regulators of natural populations. Climate models predict that global warming will drive changes in rainfall and increase the frequency and severity of extreme events. Consequently, to anticipate how organisms will respond we need to document how changes in extremes of temperature and rainfall compare to trends in the mean values of these variables and over what spatial scales the patterns are consistent.

Read other top articles in this issue >

Submit your paper to Ecology and Evolution here >

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Ecology and Evolution Accepted for Indexing by Institute for Scientific Information (ISI)

2012 has been a hugely successful year for Ecology and Evolution and is ending on a high with the news that the journal has been accepted for indexing by the Institute for Scientific Information (ISI) in Current Contents/Agriculture, Biology & Environmental Sciences, the Journal Citation Report, and Science Citation Index Expanded with coverage to begin from volume 1 issue 1.  Ecology and Evolution should receive its first Impact Factor in 2013.  We are delighted with this result as it reflects the growth and increased visibility of the journal in its field and the hard work and support given by our Editorial Board and in-house staff.  This follows the exciting news last week of the partnership with the British Ecological Society (BES) which has brought the number of high profile journals supporting the open access title to 16. Eleven of these partner titles are ranked in the top 20 ecology journals by ISI. 

To support and drive the further growth of Ecology and Evolution, we are also expanding its editorial expertise with the appointment of new editor Dr Andrew Beckerman, from the University of Sheffield, UK, who joins Allen Moore, from the University of Georgia, USA, in leading the journal.

The journal has been extremely well supported by the communities it serves and we are very grateful to the large number of scientists who have chosen to publish in the journal since its launch in September 2011.

Please visit the journal’s website  for further information and future updates.

British Ecological Society Partners With Wiley Open Access Journal Ecology and Evolution

Ecology and EvolutionJohn Wiley & Sons, Inc., has announced a new partnership between the British Ecological Society (BES) and the Wiley Open Access journal Ecology and Evolution. This latest partnership brings the number of high profile journals supporting the open access title to 16. Eleven of these partner titles are ranked in the top 20 ecology journals by the Institute for Scientific Information (ISI).

BES journals will join other high impact titles in offering authors a rapid manuscript transferal system which maintains the integrity of peer review and allows authors to meet the requirements of their funders.

Since the inaugural issue of Ecology and Evolution in September 2011, more than 250 papers have been published in the journal. The support of the five BES journal titles, all of which rank in the top 20% of ecology journals (ISI), will ensure Ecology and Evolution continues to attract the latest prestigious research from across the discipline.

Ecology and Evolution publishes papers under the Creative Commons Attribution (CC-BY) License, which permits use, distribution and reproduction, provided the original work is properly cited. An article publication charge (APC) is payable by authors on acceptance of their articles and under this new partnership BES members can take advantage of a 10% discount on this charge.

“Having published ecological journals for 100 years, we are delighted to announce this partnership as we embark on the BES’s centenary year,” said Georgina Mace, President of the BES. “Our established journals receive increasing numbers of high quality submissions each year and this involvement with Ecology and Evolution will enable us to further serve our ecological community by publishing more of this important ecological research.”

Ecology and Evolution is also expanding its editorial expertise with the appointment of new editor Dr Andrew Beckerman, from the University of Sheffield, UK, who joins Allen Moore, from the University of Georgia, USA, in leading the journal.

Dr Beckerman is a Senior Lecturer in the Department of Animal and Plant Sciences. His research links genetics, behaviour and life history to the distribution and abundance of organisms and the structure and dynamics of communities. Andrew has previously served as an Associate Editor for the Journal of Animal Ecology and Ecology Letters.

“I am excited to join Allen and the team on this journal with its broad subject coverage cutting across ecology and evolution, and to become part of an interesting venture in open access publishing,” said Dr Beckerman.

“We are thrilled that the BES has chosen to extend our 60-year relationship by collaborating with us on the open access journal, Ecology and Evolution,” said Liz Ferguson, Editorial Director, Life Science, Wiley. “This new partnership is a great fit for the editorial ambitions of Ecology and Evolution and we are also delighted to welcome Andrew at this critical stage of the Journal’s development.”

Please visit the journal’s website  for further information and future updates.