pinecone/core-2020-05-10-deduplication huggingface dataset:
Plant invasion and speciation along elevational gradients on the oceanic island La Palma, Canary Islands.

Ecosystems that provide environmental opportunities but are poor in species and functional richness generally support speciation as well as invasion processes. These processes are expected not to be equally effective along elevational gradients due to specific ecological, spatial, and anthropogenic filters, thus controlling the dispersal and establishment of species. Here, we investigate speciation and invasion processes along elevational gradients. We assess the vascular plant species richness as well as the number and percentage of endemic species and non- native species systematically along three elevational gradients covering large parts of the climatic range of La Palma, Canary Islands. Species richness was negatively correlated with elevation, while the percentage of Canary endemic species showed a positive relationship. However, the percentage of Canary–Madeira endemics did not show a relationship with elevation. Non- native species richness (indicating invasion) peaked at 500 m elevation and showed a consistent decline until about 1,200 m elevation. Above that limit, no non- native species were present in the studied elevational gradients. Ecological, anthropo- genic, and spatial filters control richness, diversification, and invasion with elevation. With increase in elevation, richness decreases due to species–area relationships. Ecological limitations of native ruderal species related to anthropogenic pressure are in line with the absence of non- native species from high elevations indicating direc- tional ecological filtering. Increase in ecological isolation with elevation drives diversi- fication and thus increased percentages of Canary endemics. The best preserved eastern transect, including mature laurel forests, is an exception. The high percentage of Canary–Madeira endemics indicates the cloud forest’s environmental uniqueness— and thus ecological isolation—beyond the Macaronesian islands
Heterogeneous tempo and mode of evolutionary diversification of compounds in lizard chemical signals

Important part of the multivariate selection shaping social and interspecific interactions among and within animal species emerges from communication. Therefore, understanding the diversification of signals for animal communication is a central endeavor in evolutionary biology. Over the last decade, the rapid development of phylogenetic approaches has promoted a stream of studies investigating evolution of communication signals. However, comparative research has primarily focused on visual and acoustic signals, while the evolution of chemical signals remains largely unstudied. An increasing interest in understanding the evolution of chemical communication has been inspired by the realization that chemical signals underlie some of the major interaction channels in a wide range of organisms. In lizards, in particular, chemosignals play paramount roles in female choice and male–male competition, and during community assembly and speciation. Here, using phylogenetic macro-evolutionary modeling, we show for the very first time that multiple compounds of scents for communication in lizards have diversified following highly different evolutionary speeds and trajectories. Our results suggest that cholesterol, α-tocopherol, and cholesta-5,7-dien-3-ol have been subject to stabilizing selection (Ornstein–Uhlenbeck model), whereas the remaining compounds are better described by Brownian motion modes of evolution. Additionally, the diversification of the individual compounds has accumulated substantial relative disparity over time. Thus, our study reveals that the chemical components of lizard chemosignals have proliferated across different species following compound-specific directions
Prevalence dependence in model goodness measures with special emphasis on true skill statistics

It has long been a concern that performance measures of species distribution models react to attributes of the modeled entity arising from the input data structure rather than to model performance. Thus, the study of Allouche et al. (Journal of Applied Ecology, 43, 1223, 2006) identifying the true skill statistics (TSS) as being independent of prevalence had a great impact. However, empirical experience questioned the validity of the statement. We searched for technical reasons behind these observations. We explored possible sources of prevalence dependence in TSS including sampling constraints and species characteristics, which influence the calculation of TSS. We also examined whether the widespread solution of using the maximum of TSS for comparison among species introduces a prevalence effect. We found that the design of Allouche et al. (Journal of Applied Ecology, 43, 1223, 2006) was flawed, but TSS is indeed independent of prevalence if model predictions are binary and under the strict set of assumptions methodological studies usually apply. However, if we take realistic sources of prevalence dependence, effects appear even in binary calculations. Furthermore, in the widespread approach of using maximum TSS for continuous predictions, the use of the maximum alone induces prevalence dependence for small, but realistic samples. Thus, prevalence differences need to be taken into account when model comparisons are carried out based on discrimination capacity. The sources we identified can serve as a checklist to safely control comparisons, so that true discrimination capacity is compared as opposed to artefacts arising from data structure, species characteristics, or the calculation of the comparison measure (here TSS). © 2017 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd
Effects of biotic interactions on modeled species' distribution can be masked by environmental gradients

A fundamental goal of ecology is to understand the determinants of species' distributions (i.e., the set of locations where a species is present). Competition among species (i.e., interactions among species that harms each of the species involved) is common in nature and it would be tremendously useful to quantify its effects on species' distributions. An approach to studying the large-scale effects of competition or other biotic interactions is to fit species' distributions models (SDMs) and assess the effect of competitors on the distribution and abundance of the species of interest. It is often difficult to validate the accuracy of this approach with available data. Here, we simulate virtual species that experience competition. In these simulated datasets, we can unambiguously identify the effects that competition has on a species' distribution. We then fit SDMs to the simulated datasets and test whether we can use the outputs of the SDMs to infer the true effect of competition in each simulated dataset. In our simulations, the abiotic environment influenced the effects of competition. Thus, our SDMs often inferred that the abiotic environment was a strong predictor of species abundance, even when the species' distribution was strongly affected by competition. The severity of this problem depended on whether the competitor excluded the focal species from highly suitable sites or marginally suitable sites. Our results highlight how correlations between biotic interactions and the abiotic environment make it difficult to infer the effects of competition using SDMs
Integrating biogeography, threat and evolutionary data to explore extinction crisis in the taxonomic group of cycads

Will the ongoing extinction crisis cause a severe loss of evolutionary information
accumulated over millions of years on the tree of life? This question has been largely
explored, particularly for vertebrates and angiosperms. However, no equivalent effort
has been devoted to gymnosperms. Here, we address this question focusing on cycads,
the gymnosperm group exhibiting the highest proportion of threatened species in the
plant kingdom. We assembled the first complete phylogeny of cycads and assessed
how species loss under three scenarios would impact the cycad tree of life. These
scenarios are as follows: (1) All top 50% of evolutionarily distinct (ED) species are lost;
(2) all threatened species are lost; and (3) only all threatened species in each IUCN
category are lost. Finally, we analyzed the biogeographical pattern of cycad diversity
hotspots and tested for gaps in the current global conservation network. First, we
showed that threatened species are not significantly clustered on the cycad tree of
life. Second, we showed that the loss of all vulnerable or endangered species does not
depart significantly from random loss. In contrast, the loss of all top 50% ED, all
threatened or all critically endangered species, would result in a greater loss of PD
(Phylogenetic Diversity) than expected. To inform conservation decisions, we defined
five hotpots of diversity, and depending on the diversity metric used, these hotspots
are located in Southern Africa, Australia, Indo-Pacific,
and Mexico and all are found
within protected areas. We conclude that the phylogenetic diversity accumulated over
millions of years in the cycad tree of life would not survive the current extinction crisis.
As such, prioritizing efforts based on ED and concentrating efforts on critically
endangered species particularly in southern Africa, Australia, Indo-Pacific,
and Mexico are required to safeguarding the evolutionary diversity in the cycad tree of life.National Research Foundation, South Africa,
Grant/Award Number: 103944http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)2045-7758am2017Plant Scienc
Abundance distributions for tree species in Great Britain: a two-stage approach to modeling abundance using species distribution modeling and random forest

High-quality abundance data are expensive and time-consuming\ud
to collect and often highly limited in availability. Nonetheless, accurate, high-resolution abundance distributions are essential for many ecological applications ranging from species conservation to epidemiology. Producing models that can predict abundance well, with good resolution over large areas, has therefore been an important aim in ecology, but poses considerable challenges. We present a two-stage approach to modeling abundance, combining two established techniques. First, we produce ensemble species distribution models (SDMs) of trees in Great Britain at a fine resolution, using much more\ud
common presence–absence data and key environmental variables. We then use random forest regression to predict abundance by linking the results of the SDMs to a\ud
much smaller amount of abundance data. We show that this method performs well in predicting the abundance of 20 of 25 tested British tree species, a group that is generally\ud
considered challenging for modeling distributions due to the strong influence of human activities. Maps of predicted tree abundance for the whole of Great Britain are provided at 1 km2 resolution. Abundance maps have a far wider variety of applications than presence-only maps, and these maps should allow improvements to aspects of woodland management and conservation including analysis of habitats and ecosystem functioning, epidemiology, and disease management, providing a useful contribution to the protection of British trees. We also provide complete R scripts to facilitate application of the approach to other scenarios
Invasive termites in a changing climate: A global perspective.

Termites are ubiquitous insects in tropical, subtropical, and warm temperate regions and play an important role in ecosystems. Several termite species are also significant economic pests, mainly in urban areas where they attack human-made structures, but also in natural forest habitats. Worldwide, approximately 28 termite species are considered invasive and have spread beyond their native ranges, often with significant economic consequences. We used predictive climate modeling to provide the first global risk assessment for 13 of the world's most invasive termites. We modeled the future distribution of 13 of the most serious invasive termite species, using two different Representative Concentration Pathways (RCPs), RCP 4.5 and RCP 8.5, and two projection years (2050 and 2070). Our results show that all but one termite species are expected to significantly increase in their global distribution, irrespective of the climatic scenario and year. The range shifts by species (shift vectors) revealed a complex pattern of distributional changes across latitudes rather than simple poleward expansion. Mapping of potential invasion hotspots in 2050 under the RCP 4.5 scenario revealed that the most suitable areas are located in the tropics. Substantial parts of all continents had suitable environmental conditions for more than four species simultaneously. Mapping of changes in the number of species revealed that areas that lose many species (e.g., parts of South America) are those that were previously very species-rich, contrary to regions such as Europe that were overall not among the most important invasion hotspots, but that showed a great increase in the number of potential invaders. The substantial economic and ecological damage caused by invasive termites is likely to increase in response to climate change, increased urbanization, and accelerating economic globalization, acting singly or interactively
A simulation approach to assessing environmental risk of sound exposure to marine mammals

Intense underwater sounds caused by military sonar, seismic surveys, and pile driving can harm acoustically sensitive marine mammals. Many jurisdictions require such activities to undergo marine mammal impact assessments to guide mitigation. However, the ability to assess impacts in a rigorous, quantitative way is hindered by large knowledge gaps concerning hearing ability, sensitivity, and behavioral responses to noise exposure. We describe a simulation-based framework, called SAFESIMM (Statistical Algorithms For Estimating the Sonar Influence on Marine Megafauna), that can be used to calculate the numbers of agents (animals) likely to be affected by intense underwater sounds. We illustrate the simulation framework using two species that are likely to be affected by marine renewable energy developments in UK waters: gray seal (Halichoerus grypus) and harbor porpoise (Phocoena phocoena). We investigate three sources of uncertainty: How sound energy is perceived by agents with differing hearing abilities; how agents move in response to noise (i.e., the strength and directionality of their evasive movements); and the way in which these responses may interact with longer term constraints on agent movement. The estimate of received sound exposure level (SEL) is influenced most strongly by the weighting function used to account for the specie's presumed hearing ability. Strongly directional movement away from the sound source can cause modest reductions (~5 dB) in SEL over the short term (periods of less than 10 days). Beyond 10 days, the way in which agents respond to noise exposure has little or no effect on SEL, unless their movements are constrained by natural boundaries. Most experimental studies of noise impacts have been short-term. However, data are needed on long-term effects because uncertainty about predicted SELs accumulates over time. Synthesis and applications. Simulation frameworks offer a powerful way to explore, understand, and estimate effects of cumulative sound exposure on marine mammals and to quantify associated levels of uncertainty. However, they can often require subjective decisions that have important consequences for management recommendations, and the basis for these decisions must be clearly described.Publisher PDFPeer reviewe
Differential timing of gene expression regulation between leptocephali of the two Anguilla eel species in the Sargasso Sea

The unique life-history characteristics of North Atlantic catadromous eels have long intrigued evolutionary biologists, especially with respect to mechanisms that could explain their persistence as two ecologically very similar but reproductively and geographically distinct species. Differential developmental schedules during young larval stages have commonly been hypothesized to represent such a key mechanism. We performed a comparative analysis of gene expression by means of microarray experiments with American and European eel leptocephali collected in the Sargasso Sea in order to test the alternative hypotheses of (1) differential timing of gene expression regulation during early development versus (2) species-specific differences in expression of particular genes. Our results provide much stronger support for the former hypothesis since no gene showed consistent significant differences in expression levels between the two species. In contrast, 146 genes showed differential timings of expression between species, although the observed expression level differences between the species were generally small. Consequently, species-specific gene expression regulation seems to play a minor role in species differentiation. Overall, these results show that the basis of the early developmental divergence between the American and European eel is probably influenced by differences in the timing of gene expression regulation for genes involved in a large array of biological functions.Publisher PDFPeer reviewe
"Menage à trois": the presence/absence of thyme shapes the mutualistic interaction between the host plant [i]Medicago truncatula[/i] (Fabaceae) and its symbiotic bacterium [i]Sinorhizobium meliloti[/i]

UMR 1334 AGAP : Equipe DAVEM Diversité et adaptation de la vigne et des espèces méditerranéennesThe long-term maintenance of specialized mutualisms remains an evolutionary puzzle. Recent focus has been on factors governing the stability of these mutualisms, including sanctions by the host, partner choice, and coevolutionary constraint, that is, the genetic correlation (r(G)) between fitness of both partners. So far these studies have been typically carried out in a single environment. Here, we ask if the genetic correlation between fitness of the host plant Medicago truncatula (Fabaceae) and its bacterial symbiont Sinorhizobium meliloti is affected by the presence/absence of a monoterpene (carvacrol) leached into the soil by Thymus vulgaris-a common plant of the Mediterranean vegetation, often co-occuring with Medicago. We show that the presence of carvacrol in the soil dramatically affects fitness of the rhizobial partner and increases the magnitude of rG between plant and rhizobia fitness (r(G) = 0.02 +/- 0.05 vs. r(G) = 0.57 +/- 0.02). This finding emphasizes the importance of heterogeneity in the biotic environment for understanding the evolution of species interactions
Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change

Climate change can influence soil microorganisms directly by altering their growth and activity but also indirectly via effects on the vegetation, which modifies the availability of resources. Direct impacts of climate change on soil microorganisms can occur rapidly, whereas indirect effects mediated by shifts in plant community composition are not immediately apparent and likely to increase over time. We used molecular fingerprinting of bacterial and fungal communities in the soil to investigate the effects of 17 years of temperature and rainfall manipulations in a species-rich grassland near Buxton, UK. We compared shifts in microbial community structure to changes in plant species composition and key plant traits across 78 microsites within plots subjected to winter heating, rainfall supplementation, or summer drought. We observed marked shifts in soil fungal and bacterial community structure in response to chronic summer drought. Importantly, although dominant microbial taxa were largely unaffected by drought, there were substantial changes in the abundances of subordinate fungal and bacterial taxa. In contrast to short-term studies that report high resistance of soil fungi to drought, we observed substantial losses of fungal taxa in the summer drought treatments. There was moderate concordance between soil microbial communities and plant species composition within microsites. Vector fitting of community-weighted mean plant traits to ordinations of soil bacterial and fungal communities showed that shifts in soil microbial community structure were related to plant traits representing the quality of resources available to soil microorganisms: the construction cost of leaf material, foliar carbon-to-nitrogen ratios, and leaf dry matter content. Thus, our study provides evidence that climate change could affect soil microbial communities indirectly via changes in plant inputs and highlights the importance of considering long-term climate change effects, especially in nutrient-poor systems with slow-growing vegetation
Composition of riparian litter input regulates organic matter decomposition: Implications for headwater stream functioning in a managed forest landscape

Although the importance of stream condition for leaf litter decomposition has been extensively studied, little is known about how processing rates change in response to altered riparian vegetation community composition. We investigated patterns of plant litter input and decomposition across 20 boreal headwater streams that varied in proportions of riparian deciduous and coniferous trees. We measured a suite of in-stream physical and chemical characteristics, as well as the amount and type of litter inputs from riparian vegetation, and related these to decomposition rates of native (alder, birch, and spruce) and introduced (lodgepole pine) litter species incubated in coarse- and fine-mesh bags. Total litter inputs ranged more than fivefold among sites and increased with the proportion of deciduous vegetation in the riparian zone. In line with differences in initial litter quality, mean decomposition rate was highest for alder, followed by birch, spruce, and lodgepole pine (12, 55, and 68% lower rates, respectively). Further, these rates were greater in coarse-mesh bags that allow colonization by macroinvertebrates. Variance in decomposition rate among sites for different species was best explained by different sets of environmental conditions, but litter-input composition (i.e., quality) was overall highly important. On average, native litter decomposed faster in sites with higher-quality litter input and (with the exception of spruce) higher concentrations of dissolved nutrients and open canopies. By contrast, lodgepole pine decomposed more rapidly in sites receiving lower-quality litter inputs. Birch litter decomposition rate in coarse-mesh bags was best predicted by the same environmental variables as in fine-mesh bags, with additional positive influences of macroinvertebrate species richness. Hence, to facilitate energy turnover in boreal headwaters, forest management with focus on conifer production should aim at increasing the presence of native deciduous trees along streams, as they promote conditions that favor higher decomposition rates of terrestrial plant litter.Full Tex