Search

Metabolomes, as chemical phenotypes of organisms, are likely not only shaped by the environment but also by common ancestry. If this is the case, we expect that closely related species of pines will tend to reach similar metabolomic solutions to the same environmental stressors. We examined the metabolomes of two sympatric subspecies of Pinus sylvestris in Sierra Nevada (southern Iberian Peninsula), in summer and winter and exposed to folivory by the pine processionary moth. The overall metabolomes differed between the subspecies but both tended to respond more similarly to folivory. The metabolomes of the subspecies were more dissimilar in summer than in winter, and iberica trees had higher concentrations of metabolites directly related to drought stress. Our results are consistent with the notion that certain plant metabolic responses associated with folivory have been phylogenetically conserved. The larger divergence between subspecies metabolomes in summer is likely due to the warmer and drier conditions that the northern iberica subspecies experience in Sierra Nevada. Our results provide crucial insights into how iberica populations would respond to the predicted conditions of climate change under an increased defoliation in the Mediterranean Basin.

Most of the Earth's vegetated surface is fireprone but the relevance of fire in understanding how nature works is not always recognized. We aim to show that, by adding the fire dimension to observations on biological phenomena, interpretations can be improved; how fire-related research can be used to answer 'fundamental' questions in ecology; and how theories/models developed for fireprone ecosystems can be applied to advancing disturbance ecology, biogeography and evolutionary biology more generally. We compiled lists from the world-wide web of the most highly cited papers in fire ecology, and examined papers that had been approached from multiple viewpoints, including fire. We show that great advances over the last 20 years have been made in our understanding of the pivotal role of fire as a driver of many ecological processes and a powerful selective agent/evolutionary trigger among biota. We document 21 sets of observations originally interpreted in the context of the two traditional dimensions, prevailing environment and biotic interactions, but can also be shown to have a strong, if not dominant, historical link to fire. We note that fire-related research is able to address 55 of the 100 questions considered 'fundamental' in ecology and that many have already received some attention in fireprone ecosystems. We show how theories/models that had their origins in fireprone systems can be applied to other disturbance-prone systems and thus have wide application in ecology and evolutionary biology. Fire and other disturbances should be included as variables in research about possible critical environmental and biotic constraints controlling ecosystem function in general. Adding this third dimension to research endeavours greatly enriches our understanding of how nature works at the global scale in an era where ecosystems are changing rapidly and novel species-environmental interactions are emerging. [ABSTRACT FROM AUTHOR]

Non-uniform rates of morphological evolution and evolutionary increases in organismal complexity, captured in metaphors like “adaptive zones”, “punctuated equilibrium” and “blunderbuss patterns”, require more elaborate explanations than a simple gradual accumulation of mutations. Here we argue that non-uniform evolutionary increases in phenotypic complexity can be caused by a threshold-like response to growing ecological pressures resulting from evolutionary diversification at a given level of complexity. Acquisition of a new phenotypic feature allows an evolving species to escape this pressure but can typically be expected to carry significant physiological costs. Therefore, the ecological pressure should exceed a certain level to make such an acquisition evolutionarily successful. We present a detailed quantitative description of this process using a microevolutionary competition model as an example. The model exhibits sequential increases in phenotypic complexity driven by diversification at existing levels of complexity and a resulting increase in competitive pressure, which can push an evolving species over the barrier of physiological costs of new phenotypic features. [ABSTRACT FROM AUTHOR]

Mutualisms may be “key innovations” that spur lineage diversification by augmenting niche breadth, geographic range, or population size, thereby increasing speciation rates or decreasing extinction rates. Whether mutualism accelerates diversification in both interacting lineages is an open question. Research suggests that plants that attract ant mutualists have higher diversification rates than non-ant associated lineages. We ask whether the reciprocal is true: does the interaction between ants and plants also accelerate diversification in ants, i.e. do ants and plants cooperate-and-radiate? We used a novel text-mining approach to determine which ant species associate with plants in defensive or seed dispersal mutualisms. We investigated patterns of lineage diversification across a recent ant phylogeny using BiSSE, BAMM, and HiSSE models. Ants that associate mutualistically with plants had elevated diversification rates compared to non-mutualistic ants in the BiSSE model, with a similar trend in BAMM, suggesting ants and plants cooperate-and-radiate. However, the best-fitting model was a HiSSE model with a hidden state, meaning that diversification models that do not account for unmeasured traits are inappropriate to assess the relationship between mutualism and ant diversification. Against a backdrop of diversification rate heterogeneity, the best-fitting HiSSE model found that mutualism actually decreases diversification: mutualism evolved much more frequently in rapidly diversifying ant lineages, but then subsequently slowed diversification. Thus, it appears that ant lineages first radiated, then cooperated with plants. [ABSTRACT FROM AUTHOR]

Exploration and exploitation are contradictory in differential evolution (DE) algorithm. In order to balance the search behavior between exploitation and exploration better, a novel self-adaptive dual-strategy differential evolution algorithm (SaDSDE) is proposed. Firstly, a dual-strategy mutation operator is presented based on the “DE/best/2” mutation operator with better global exploration ability and “DE/rand/2” mutation operator with stronger local exploitation ability. Secondly, the scaling factor self-adaption strategy is proposed in an individual-dependent and fitness-dependent way without extra parameters. Thirdly, the exploration ability control factor is introduced to adjust the global exploration ability dynamically in the evolution process. In order to verify and analyze the performance of SaDSDE, we compare SaDSDE with 7 state-of-art DE variants and 3 non-DE based algorithms by using 30 Benchmark test functions of 30-dimensions and 100-dimensions, respectively. The experiments results demonstrate that SaDSDE could improve global optimization performance remarkably. Moreover, the performance superiority of SaDSDE becomes more significant with the increase of the problems’ dimension. [ABSTRACT FROM AUTHOR]

In the absence of constraints, preference for larger mates is expected to evolve, as larger individuals are typical of higher potential fitness. Large females are often more fecund and carry larger eggs (which result in higher number and better quality of offspring), whereas large males usually have more conspicuous ornaments and are better at defending resources. However, intrasexual competition can constrain the access to larger partners, especially when opportunities for mate takeover abound. Here we investigate the relationship between individual’s size and mate choice in relation to one’s own size and their respective mate’s size using the sailfin tetra, a sexually dimorphic Amazonian fish species. We show that ornaments of larger males are exponentially more conspicuous, and larger females are more fecund and carry larger eggs. Contrary to expectation, neither males nor females associated for longer with the larger of two offered potential mates. Instead, individuals of both genders chose opposite-sex individuals of similar sizes to themselves. Additionally, similar-sized pairs were more likely to spawn than couples with higher size asymmetries. Grounded on field observations, we propose that prudent choice should be particularly important in this system, since courtship is long (often taking several days), which offers opportunities for mate takeover. Intrasexual competition, however, cannot readily explain female choice for similar-sized males. We thus suggest that such preference might be best explained by avoidance of filial cannibalism. [ABSTRACT FROM AUTHOR]

Differential Evolution (DE) is powerful for global optimization problems. Among DE algorithms, JADE and its variants, whose mutation strategy is DE/current-to-pbest/1 with optional archive, have good performance. A significant feature of the above mutation strategy is that one individual for difference operation comes from the union of the optional external archive and the population. In existing DE algorithms based on the mutation strategy—JADE and its variants, individuals eliminated from the population are send to the archive. In this paper, we propose a scheme for managing the optional external archive. According to our scheme, two subpopulations are maintained in the population. Each of them regards the other as the archive. In experiments, our scheme is applied in JADE and two of its variants—SHADE and L-SHADE. Experimental results show that our scheme can enhance JADE and its variants. Moreover, it can be seen that L-SHADE with our scheme performs significantly better than four DE algorithms, CoBiDE, MPEDE, EDEV, and MLCCDE. [ABSTRACT FROM AUTHOR]

Climate change is amongst the main threats to biodiversity. Considering extant mammals endured Quaternary climate change, we analyzed the extent to which this past change predicts current mammals’ extinction risk at global and biogeographical scales. We accessed range dynamics by modeling the potential distribution of all extant terrestrial mammals in the Last Glacial Maximum (LGM, 21,000 years ago) and in current climate conditions and used extinction risk from IUCN red list. We built General Linear Mixed-Effects Models to test the magnitude with which the variation in geographic range (ΔRange) and a proxy for abundance (ΔSuitability) between the LGM and present-day predicts current mammal’s extinction risk. We found past climate change most strongly reduced the geographical range and climatic suitability of threatened rather than non-threatened mammals. Quaternary range contractions and reduced suitability explain around 40% of species extinction risk, particularly for small-bodied mammals. At global and biogeographical scales, all groups that suffered significant Quaternary range contractions now contain a greater proportion of threatened species when compared to groups whose ranges did not significantly contract. This reinforces the importance of using historical range contractions as a key predictor of extinction risk for species in the present and future climate change scenarios and supports current efforts to fight climate change for biodiversity conservation. [ABSTRACT FROM AUTHOR]

Natural microbial communities perform many functions that are crucial for human well-being. Yet we have very little control over them, and we do not know how to optimize their functioning. One idea is to breed microbial communities as we breed dogs: by comparing a set of microbiomes and allowing the best-performing ones to generate new communities, and so on. Although this idea seems simple, designing such a selection experiment brings with it many decisions with surprising outcomes. Xie and colleagues developed a computational model that reveals this complexity and shows how different experimental design decisions can impact the success of such an experiment. [ABSTRACT FROM AUTHOR]

Climate change represents one of the most significant threats to human and wildlife communities on the planet. Populations at range margins or transitions between biomes can be particularly instructive for observing changes in biological communities that may be driven by climate change. Avian communities in lowland boreal habitats in the Adirondack Park, located at the North American boreal-temperate ecotone, have been the focus of long-term monitoring efforts since 2007. By documenting long-term changes in community structure and composition, such datasets provide an opportunity to understand how boreal species are responding differently to climate change, and which habitat characteristics may be best able to retain boreal avian communities. We examined three specific questions in order to address how well current biological communities in Adirondack boreal wetland habitats are being maintained in a changing climate: (1) how do trends in occupancy vary across species, and what guilds or characteristics are associated with increasing or decreasing occupancy? (2) how is avian community composition changing differently across sites, and (3) what distinguishes sites which are retaining boreal birds to a higher degree than other sites? Our analysis revealed that (1) boreal species appear to exhibit the largest changes in occupancy among our study locations as compared to the larger avian community, (2) dynamics of community change are not uniform across sites and habitat structure may play an important role in driving observed changes, and (3) the particular characteristics of large open peatlands may allow them to serve as refugia for boreal species in the context of climate change. [ABSTRACT FROM AUTHOR]

Humans depend on microbial communities for numerous ecosystem services such as global nutrient cycles, plant growth and their digestive health. Yet predicting dynamics and functioning of these complex systems is hard, making interventions to enhance functioning harder still. One simplifying approach is to assume that functioning can be predicted from the set of enzymes present in a community. Alternatively, ecological and evolutionary dynamics of species, which depend on how enzymes are packaged among species, might be vital for predicting community functioning. I investigate these alternatives by extending classical chemostat models of bacterial growth to multiple species that evolve in their use of chemical resources. Ecological interactions emerge from patterns of resource use, which change as species evolve in their allocation of metabolic enzymes. Measures of community functioning derive in turn from metabolite concentrations and bacterial density. Although the model shows considerable functional redundancy, species packaging does matter by introducing constraints on whether enzyme levels can reach optimum levels for the whole system. Evolution can either promote or reduce functioning compared to purely ecological models, depending on the shape of trade-offs in resource use. The model provides baseline theory for interpreting emerging data on evolution and functioning in real bacterial communities. [ABSTRACT FROM AUTHOR]

Species diversity in the genus Ulva remains understudied worldwide. Using molecular analyses we investigated the species composition, diversity, distribution, and relative frequencies of the genus Ulva along the entire coast of Jeju Island, off the southern tip of Korea. Species identification was performed for 215 samples collected from 23 sites, based on comprehensive phylogenetic and model-based species delimitation analyses using the sequences of two molecular markers, chloroplast elongation factor Tu (tufA) and nuclear rDNA internal transcribed spacer (ITS). We identified 193 specimens as nine Ulva species, 14 specimens as Blidingia spp., and eight samples undetermined, based on the combined analysis of tufA and ITS phylogenies. Two model-based approaches generally supported nine groups of Ulva species. Previously documented species complex, such as U. ohnoi−U. spinulosa and U. procera−U. linza showed discordant relationships between the two phylogenies. The occurrence of U. torta on Jeju Island was first observed, despite its existence on the mainland previously reported. Ulva australis [16 of 23 sites; 34.4% (relative frequency)], U. ohnoi (16; 21.9%), and U. procera (11; 14%) were found to be the predominant species. Our study highlights that molecular analysis is critical for species delimitation in the genus Ulva and provides fundamental information for an understanding of green-tide assemblages on the “biological hotspot” coastal ecosystem, Jeju Island in Korea. This study will also help to monitor and manage local green tides at the areas that are currently encountering rapid climate changes. [ABSTRACT FROM AUTHOR]

Citizen science is mainstream: millions of people contribute data to a growing array of citizen science projects annually, forming massive datasets that will drive research for years to come. Many citizen science projects implement a “leaderboard” framework, ranking the contributions based on number of records or species, encouraging further participation. But is every data point equally “valuable?” Citizen scientists collect data with distinct spatial and temporal biases, leading to unfortunate gaps and redundancies, which create statistical and informational problems for downstream analyses. Up to this point, the haphazard structure of the data has been seen as an unfortunate but unchangeable aspect of citizen science data. However, we argue here that this issue can actually be addressed: we provide a very simple, tractable framework that could be adapted by broadscale citizen science projects to allow citizen scientists to optimize the marginal value of their efforts, increasing the overall collective knowledge. [ABSTRACT FROM AUTHOR]

Uniting diverse stakeholders through communication, education or building a collaborative ‘common vision’ for biodiversity management is a recommended approach for enabling effective conservation in regions with multiple uses. However, socially focused strategies such as building a collaborative vision can require sharing scarce resources (time and financial resources) with the on-ground management actions needed to achieve conservation outcomes. Here we adapt current prioritisation tools to predict the likely return on the financial investment of building a stakeholder-led vision along with a portfolio of on-ground management strategies. Our approach brings together and analyses expert knowledge to estimate the cost-effectiveness of a common vision strategy and on-ground management strategies, before any investments in these strategies are made. We test our approach in an intensively-used Australian biodiversity hotspot with 179 threatened or at-risk species. Experts predicted that an effective stakeholder vision for the region would have a relatively low cost and would significantly increase the feasibility of on-ground management strategies. As a result, our analysis indicates that a common vision is likely to be a cost-effective investment, increasing the expected persistence of threatened species in the region by 9 to 52%, depending upon the strategies implemented. Our approach can provide the maximum budget that is worth investing in building a common vision or another socially focused strategy for building support for on-ground conservation actions. The approach can assist with decisions about whether and how to allocate scarce resources amongst social and ecological actions for biodiversity conservation in other regions worldwide. [ABSTRACT FROM AUTHOR]

Resilience theory aims to understand and predict ecosystem state changes resulting from disturbances. Non-native species are ubiquitous in ecological communities and integrated into many described ecological interaction networks, including mutualisms. By altering the fitness landscape and rewiring species interactions, such network invasion may carry important implications for ecosystem resistance and resilience under continued environmental change. Here, I hypothesize that the tendency of established non-native species to be generalists may make them more likely than natives to occupy central network roles and may link them to the resistance and resilience of the overall network. I use a quantitative research synthesis of 58 empirical pollination and seed dispersal networks, along with extinction simulations, to examine the roles of known non-natives in networks. I show that non-native species in networks enhance network redundancy and may thereby bolster the ecological resistance or functional persistence of ecosystems in the face of disturbance. At the same time, non-natives are unlikely to partner with specialist natives, thus failing to support the resilience of native species assemblages. Non-natives significantly exceed natives in network centrality, normalized degree, and Pollination Service Index. Networks containing non-natives exhibit lower connectance, more links on average, and higher generality and vulnerability than networks lacking non-natives. As environmental change progresses, specialists are particularly likely to be impacted, reducing species diversity in many communities and network types. This work implies that functional diversity may be retained but taxonomic diversity decline as non-native species become established in networks worldwide. [ABSTRACT FROM AUTHOR]

Insect herbivores and their hostplants constitute much of Earth's described biological diversity, but how these often-specialized associations diversify is not fully understood. We combined detailed hostplant data and comparative phylogenetic analyses of the lepidopteran family Momphidae to explore how shifts in the use of hostplant resources, not just hostplant taxon, contribute to the diversification of a phytophagous insect lineage. We inferred two phylogenetic hypotheses emphasizing relationships among species in the nominate genus, Mompha Hübner. A six-gene phylogeny was constructed with reared exemplars and collections from hostplants in the family Onagraceae from western and southwestern USA, and a cytochrome c oxidase subunit 1 (COI) phylogeny was inferred from collections and publicly available accessions in the Barcode of Life Data System. Species delimitation analyses combined with morphological data revealed ca. 56 undescribed species-level taxa, many of which are hostplant specialists on Onagraceae in the southwestern USA. Our phylogenetic reconstructions divided Momphidae into six major clades: 1) an Onagraceae flower- and fruit-boring clade, 2) a Melastomataceae-galling clade, 3) a leafmining clade A, 4) a leafmining clade B, 5) a Zapyrastra Meyrick clade, and 6) a monobasic lineage represented by Mompha eloisella (Clemens). Ancestral trait reconstructions using the COI phylogeny identified leafmining on Onagraceae as the ancestral state for Momphidae. Our study finds that shifts along three hostplant resource axes (plant taxon, plant tissue type, and larval feeding mode) have contributed to the evolutionary success and diversification of momphids. [ABSTRACT FROM AUTHOR]

Termites (Isoptera) are important ecosystem engineers of tropical ecosystems. However, they are notoriously difficult to identify, which hinders ecological research. To overcome these problems, we comparatively studied termite assemblages in the two major West African ecosystems, savannah and forest, both under natural settings and along disturbance gradients. We identified all species using morphological as well as molecular markers. We hypothesized species richness to be higher in the forest than the savannah and that it declines with disturbance in both ecosystems. Overall we found more species in the forest than in the savannah. However, alpha diversity per site did not differ between both ecosystems with on average around ten species. For both ecosystems, species diversity did not decrease along the studied disturbance gradient but encounter rates did. For the forest, we did not detect a decline in soil feeding termites and an increase of fungus grower Macrotermitinae with disturbance as some other studies did. Yet, soil feeders were generally rare. Strikingly, the set of morphologically difficult-to-identify Macrotermitinae (Microtermes and Ancistrotermes) was as high in the forest as in the savannah with little species overlap between both ecosystems. Using phylogenetic community analyses, we found little evidence for strong structuring mechanisms such as environmental filtering or interspecific competition. Most local assemblages did not differ significantly from random assemblages of the regional species pool. Our study is the most comprehensive of its kind. It provides the most reliable termite species list for West Africa that builds the basis for further ecological studies. [ABSTRACT FROM AUTHOR]

One measure of habitat quality is a species’ demographic performance in a habitat and the gold standard metric of performance is reproduction. Such a measure, however, may be misleading if individual quality is a fitness determinant. We report on factors affecting lifetime reproduction (LR), the total number of lifetime fledglings produced by an individual, and long-term territory-specific reproduction in a multi-generational study of northern goshawks (Accipiter gentilis). LR increased with longer lifespans and more breeding attempts and was strongly correlated with the number of recruits in two filial generations indicating that LR was a good fitness predictor. Extensive differences in LR attested to heterogeneity in individual quality, a requisite for the ideal pre-emptive distribution model (IPD) of habitat settling wherein high quality individuals get the best habitats forcing lower quality individuals into poorer habitats with lower reproduction. In response to 7‒9-year prey abundance cycles, annual frequency of territory occupancy by breeders was highly variable and low overall with monotonic increases in vacancies through low prey years. Occupancy of territories by breeders differed from random; some appeared preferred while others were avoided, producing a right-skewed distribution of total territory-specific fledgling production. However, mean fledglings per nest attempt was only slightly lower in less versus more productive territories, and, contrary to IPD predictions of increases in annual territory-specific coefficients of variation (CV) in reproduction as breeder densities increase, the CV of production decreased as density increased. Rather than habitat quality per se, conspecific attraction elicited territory selection by prospecting goshawks as 70% of settlers comprised turnovers on territories, resulting in occupancy continuity and increased territory-specific reproduction. Top-producing territories had as few as 2 long-lived (high LR) and up to 6 short-lived (low LR) sequential breeders. While individual quality appeared to effect territory-specific heterogeneity in reproductive performance, our data suggests that differences in individual quality may be washed-out by a random settling of prospectors in response to conspecific attraction. [ABSTRACT FROM AUTHOR]

Hybridization is common in many ferns and has been a significant factor in fern evolution and speciation. However, hybrids are rare between the approximately 30 species of Dicksonia tree ferns world-wide, and none are well documented. In this study we examine the relationship of a newly-discovered Dicksonia tree fern from Whirinaki, New Zealand, which does not fit the current taxonomy of the three species currently recognized in New Zealand. Our microsatellite genotyping and ddRAD-seq data indicate these plants are F1 hybrids that have formed multiple times between D. fibrosa and D. lanata subsp. lanata. The Whirinaki plants have intermediate morphology between D. fibrosa and D. lanata subsp. lanata and their malformed spores are consistent with a hybrid origin. The Whirinaki plants–Dicksonia fibrosa × D. lanata subsp. lanata–are an example of hybridization between distantly related fern lineages, with the two parent species estimated to have diverged 55–25 mya. Our chloroplast sequencing indicates asymmetric chloroplast inheritance in the Whirinaki morphology with D. lanata subsp. lanata always contributing the chloroplast genome. [ABSTRACT FROM AUTHOR]

Phytoplankton are the oceans’ principal source of polyunsaturated fatty acids that support the growth and reproduction of consumers such as copepods. Previous studies have demonstrated ocean acidification (OA) can change the availability of polyunsaturated fatty acids to consumer diets which may affect consumer reproduction. Two laboratory experiments were conducted to examine the effects of feeding high-pCO2-reared phytoplankton on copepod egg production, hatching success, and naupliar survival. Marine phytoplankton Rhodomonas salina, Skeletonema marinoi, Prorocentrum micans, and Isochrysis galbana were exponentially grown in semi-continuous cultures at present (control) (400 ppm CO2, pH~8.1) and future (1,000 ppm CO2, pH~7.8) conditions and provided to Acartia tonsa copepods over 4 consecutive days as either nitrogen-limited (Exp. I) or nitrogen-depleted (Exp. II) mixed assemblage of phytoplankton. The composition of FAs in the phytoplankton diet was affected by pCO2 concentration and nitrogen deficiency; the ratio of essential fatty acids to total polyunsaturated fatty acids decreased in phytoplankton grown under high pCO2 and the mass of total fatty acids increased under nitrogen depletion. Additionally, total concentrations of essential fatty acids and polyunsaturated fatty acids in the diet mixtures were less under the high-pCO2 compared to the control-pCO2 treatments. Median egg production, hatching success, and naupliar survival were 48–52%, 4–87%, and 9–100% lower, respectively, in females fed high-pCO2 than females fed low-pCO2 phytoplankton, but this decrease in reproductive success was less severe when fed N-depleted, but fatty acid-rich cells. This study demonstrates that the effects of OA on the nutritional quality of phytoplankton (i.e., their cellular fatty acid composition and quota) were modified by the level of nitrogen deficiency and the resulting negative reproductive response of marine primary consumers. [ABSTRACT FROM AUTHOR]

Molecular morphometrics is an emerging third dimensional aspect of fungal species delimitation. They have been demonstrated to be more informative than conventional barcoding methods. Hence in this study, foliar endophytic fungal (FEF) assemblages in three Magnoliopsida plants were delimited using nuclear ribosomal internal transcribed spacer 2 (ITS2) sequence—secondary structural features based phylogenetic analysis, also known as molecular morphometrics. A total of 392 FEF isolates were obtained from the Aglaia elaeagnoidea, Flacourtia inermis, and Premna serratifolia leaves and grouped into 98 morphotypes. Among these host plants, P. serratifolia showed the maximum percentage of colonization frequency. Representatives of each morphotype was sequenced and subjected to further molecular characterization. The results revealed that morphotypes were belonged to the phylum of Ascomycota, distributed over two classes (Sordariomycetes (68.59%) and Dothideomycetes (31.41%)), 6 orders and 19 genera. Based on compensatory base changes (CBC) analysis and absolute identity of ITS2 structure, 21, 20 and 23 species were recognized from A. elaeagnoidea, F. inermis, and P. serratifolia respectively. Diversity indices were higher in A. elaeagnoidea, despite it accounted for a modest 16.8% of total isolates recorded in this study. The genus Colletotrichum was predominant in A. elaeagnoidea (39%) and P. serratifolia (48%). Similarly, Diaporthe (43%) was dominant in F. inermis. Several host-specific species were also observed. This study concludes that these plants host diverse species of Ascomycota. To the best of our knowledge, this is the first detailed report on FEF diversity from these plants. Also, the inclusion of ITS2 secondary structure information along with the sequence provides a further dimension to resolve the inherent problems in identification of fungal species. [ABSTRACT FROM AUTHOR]

Information on species distribution is recognized as a crucial input for biodiversity conservation and management. To that end, considerable resources have been dedicated towards increasing the quantity and availability of species occurrence data, boosting their use in species distribution modeling and online platforms for their dissemination. Currently, those platforms face the challenge of bringing biology into modeling by making informed decisions that result in meaningful models, based on limited occurrence and ecological data. Here we describe BioModelos, a modeling approach supported by an online system and a core team of modelers, whereby a network of experts contributes to the development of species distribution models by assessing the quality of occurrence data, identifying potentially limiting environmental variables, establishing species’ accessible areas and validating modeling predictions qualitatively. Models developed through BioModelos become freely and publicly available once validated by experts, furthering their use in conservation applications. Our approach has been implemented in Colombia since 2013 and it currently consist of a network of nearly 500 experts that collaboratively contribute to enhance the knowledge on the distribution of a growing number of species and it has aided the development of several decision support products such as national risk assessments and biodiversity compensation manuals. BioModelos is an example of operationalization of an essential biodiversity variable at a national level through the implementation of a research infrastructure that enhances the value of open access species data. [ABSTRACT FROM AUTHOR]

Invasive alien species are a major threat to native insular species. Eradicating invasive mammals from islands is a feasible and proven approach to prevent biodiversity loss. We developed a conceptual framework to identify globally important islands for invasive mammal eradications to prevent imminent extinctions of highly threatened species using biogeographic and technical factors, plus a novel approach to consider socio-political feasibility. We applied this framework using a comprehensive dataset describing the distribution of 1,184 highly threatened native vertebrate species (i.e. those listed as Critically Endangered or Endangered on the IUCN Red List) and 184 non-native mammals on 1,279 islands worldwide. Based on extinction risk, irreplaceability, severity of impact from invasive species, and technical feasibility of eradication, we identified and ranked 292 of the most important islands where eradicating invasive mammals would benefit highly threatened vertebrates. When socio-political feasibility was considered, we identified 169 of these islands where eradication planning or operation could be initiated by 2020 or 2030 and would improve the survival prospects of 9.4% of the Earth’s most highly threatened terrestrial insular vertebrates (111 of 1,184 species). Of these, 107 islands were in 34 countries and territories and could have eradication projects initiated by 2020. Concentrating efforts to eradicate invasive mammals on these 107 islands would benefit 151 populations of 80 highly threatened vertebrates and make a major contribution towards achieving global conservation targets adopted by the world’s nations. [ABSTRACT FROM AUTHOR]

Amphibians are sensitive to anthropogenic habitat alterations but also respond to natural drivers of assemblage composition at many levels. Additionally, they are usually hard to detect in field inventories. We used a multiscale approach, from microhabitat to the landscape levels, to try to understand the effects of natural changes, and try to distinguish them from the effects of landscape level anthropogenic changes, on dynamic and diverse anuran assemblages, taking imperfect detection into account. We conducted thorough field inventories in 16 streams at Serra do Cipó, in the southern portion of Espinhaço Mountain Range, southeastern Brazil, during two time periods separated by 16 years. We compared species richness and diversity between periods, sampling both tadpoles and adult frogs. We quantified tadpole microhabitat availability, alterations in immediate riparian vegetation, and changes in classes of land cover within buffers around streams (adult habitats) to test for their effects on species composition. We also tested for effects of human occupancy around streams on nestedness and turnover components of species diversity. Microhabitats and riparian vegetation explained some of the changes in species composition (or detection) between time periods. Nestedness seemed to be influenced by the stability of the landscape. Detectabilities were too low to support robust occupancy estimates for most species. Natural changes in local habitats occupied by anurans in montane meadows are likely to influence species distribution. Some species with robust estimates experienced change in their occupancy over the studied 16-year interval, although no anthropogenic causes could be directly associated with such changes. The low detectability of most species, even with thorough sampling effort, makes it very hard to detect amphibian declines and possibly tell them apart from natural population fluctuations. New techniques are needed that improve species detectability in such diverse tropical habitats. [ABSTRACT FROM AUTHOR]

A longstanding question in ecology concerns the prediction of the fate of mountain species under climate change, where climatic and geomorphic factors but also endogenous species characteristics are jointly expected to control species distributions. A significant step forward would single out reliably landscape effects, given their constraining role and relative ease of theoretical manipulation. Here, we address population dynamics in ecosystems where the substrates for ecological interactions are mountain landscapes subject to climate warming. We use a minimalist model of metapopulation dynamics based on virtual species (i.e. a suitable assemblage of focus species) where dispersal processes interact with the spatial structure of the landscape. Climate warming is subsumed by an upward shift of species habitat altering the metapopulation capacity of the landscape and hence species viability. We find that the landscape structure is a powerful determinant of species survival, owing to the specific role of the predictably evolving connectivity of the various habitats. Range shifts and lags in tracking suitable habitat experienced by virtual species under warming conditions are singled out in different landscapes. The range of parameters is identified for which these virtual species (characterized by comparable viability thus restricting their possible fitnesses and niche widths) prove unable to cope with environmental change. The statistics of the proportion of species bound to survive is identified for each landscape, providing the temporal evolution of species range shifts and the related expected occupation patterns. A baseline dynamic model for predicting species fates in evolving habitats is thus provided. [ABSTRACT FROM AUTHOR]

Alternative transcriptional initiation (ATI) refers to the frequent observation that one gene has multiple transcription start sites (TSSs). Although this phenomenon is thought to be adaptive, the specific advantage is rarely known. Here, we propose that each gene has one optimal TSS and that ATI arises primarily from imprecise transcriptional initiation that could be deleterious. This error hypothesis predicts that (i) the TSS diversity of a gene reduces with its expression level; (ii) the fractional use of the major TSS increases, but that of each minor TSS decreases, with the gene expression level; and (iii) cis-elements for major TSSs are selectively constrained, while those for minor TSSs are not. By contrast, the adaptive hypothesis does not make these predictions a priori. Our analysis of human and mouse transcriptomes confirms each of the three predictions. These and other findings strongly suggest that ATI predominantly results from molecular errors, requiring a major revision of our understanding of the precision and regulation of transcription. [ABSTRACT FROM AUTHOR]

Identifying the species that are at risk of local extinction in highly diverse ecosystems is a big challenge for conservation science. Assessments of species status are costly and difficult to implement in developing countries with diverse ecosystems due to a lack of species-specific surveys, species-specific data, and other resources. Numerous techniques are devised to determine the threat status of species based on the availability of data and budgetary limits. On this basis, we developed a framework that compared occurrence data of historically exploited reef species in Kenya from existing disparate data sources. Occurrence data from archaeological remains (750-1500CE) was compared with occurrence data of these species catch assessments, and underwater surveys (1991-2014CE). This comparison indicated that only 67 species were exploited over a 750 year period, 750-1500CE, whereas 185 species were landed between 1995 and 2014CE. The first step of our framework identified 23 reef species as threatened with local extinction. The second step of the framework further evaluated the possibility of local extinction with Bayesian extinction analyses using occurrence data from naturalists’ species list with the existing occurrence data sources. The Bayesian extinction analysis reduced the number of reef species threatened with local extinction from 23 to 15. We compared our findings with three methods used for assessing extinction risk. Commonly used extinction risk methods varied in their ability to identify reef species that we identified as threatened with local extinction by our comparative and Bayesian method. For example, 12 of the 15 threatened species that we identified using our framework were listed as either least concern, unevaluated, or data deficient in the International Union for the Conservation of Nature red list. Piscivores and macro-invertivores were the only functional groups found to be locally extinct. Comparing occurrence data from disparate sources revealed a large number of historically exploited reef species that are possibly locally extinct. Our framework addressed biases such as uncertainty in priors, sightings and survey effort, when estimating the probability of local extinction. Our inexpensive method showed the value and potential for disparate data to fill knowledge gaps that exist in species extinction assessments. [ABSTRACT FROM AUTHOR]

Nine wild Iberian provenances of Castanea sativa Mill. grouped in two gene pools, North Iberian Peninsula and Mediterranean, were evaluated for several adaptive traits in two provenance–progeny trials with the aim of evaluating the role of natural selection in shaping adaptive variation and increasing our understanding of the genetic structure of this species, as well as reporting complete information on the genetic variation among and within the studied populations. An annual growth rhythm experiment was evaluated during the first 3 years after establishment for phenology, growth, stem form and survival, and a periodic drought-stress experiment was evaluated for dry weight, growth, survival and other related drought traits in both well-watered and drought-stress treatments. The high genetic variability reported in both trials is largely due to the genetic variation among populations. The significant differences reported between quantitative genetic and neutral marker differentiation indicated the local adaptation of these populations through directional selection, mainly for phenology, growth and biomass allocation. A clinal variation among populations was determined through correlations of phenology with latitude and xerothermic index of the provenances, showing that central and southern Mediterranean populations had earlier phenology than northern populations and that drought played a relevant role in this differentiation. The significant correlation between phenological traits and the ancestry values in the Mediterranean gene pool supported the different pattern of behavior between both gene pools and also indicated the existence of two ecotypes: xeric and mesophytic ecotypes, corresponding to Mediterranean and North Iberian gene pools, respectively. The results obtained in the drought-stress experiment confirmed that, in general terms, xeric populations showed a greater adaptability to drought, with more developed root systems and higher survival than northern populations. Moreover, the genetic variability observed within populations indicated the potential response capacity of Iberian C. sativa populations to undergo fast adaptive evolution. [ABSTRACT FROM AUTHOR]

Both ecological theory and empirical evidence suggest that negative frequency dependent feedbacks structure plant communities, but integration of these findings has been limited. Here we develop a generic model of frequency dependent feedback to analyze coexistence and invasibility in random theoretical and real communities for which frequency dependence through plant-soil feedbacks (PSFs) was determined empirically. We investigated community stability and invasibility by means of mechanistic analysis of invasion conditions and numerical simulations. We found that communities fall along a spectrum of coexistence types ranging from strict pair-wise negative feedback to strict intransitive networks. Intermediate community structures characterized by partial intransitivity may feature “keystone competitors” which disproportionately influence community stability. Real communities were characterized by stronger negative feedback and higher robustness to species loss than randomly assembled communities. Partial intransitivity became increasingly likely in more diverse communities. The results presented here theoretically explain why more diverse communities are characterized by stronger negative frequency dependent feedbacks, a pattern previously encountered in observational studies. Natural communities are more likely to be maintained by strict negative plant-soil feedback than expected by chance, but our results also show that community stability often depends on partial intransitivity. These results suggest that plant-soil feedbacks can facilitate coexistence in multi-species communities, but that these feedbacks may also initiate cascading effects on community diversity following from single-species loss. [ABSTRACT FROM AUTHOR]

Research in applied ecology provides scientific evidence to guide conservation policy and management. Applied ecology is becoming increasingly quantitative and model selection via information criteria has become a common statistical modeling approach. Unfortunately, parameters that contain little to no useful information are commonly presented and interpreted as important in applied ecology. I review the concept of an uninformative parameter in model selection using information criteria and perform a literature review to measure the prevalence of uninformative parameters in model selection studies applying Akaike’s Information Criterion (AIC) in 2014 in four of the top journals in applied ecology (Biological Conservation, Conservation Biology, Ecological Applications, Journal of Applied Ecology). Twenty-one percent of studies I reviewed applied AIC metrics. Many (31.5%) of the studies applying AIC metrics in the four applied ecology journals I reviewed had or were very likely to have uninformative parameters in a model set. In addition, more than 40% of studies reviewed had insufficient information to assess the presence or absence of uninformative parameters in a model set. Given the prevalence of studies likely to have uninformative parameters or with insufficient information to assess parameter status (71.5%), I surmise that much of the policy recommendations based on applied ecology research may not be supported by the data analysis. I provide four warning signals and a decision tree to assist authors, reviewers, and editors to screen for uninformative parameters in studies applying model selection with information criteria. In the end, careful thinking at every step of the scientific process and greater reporting standards are required to detect uninformative parameters in studies adopting an information criteria approach. [ABSTRACT FROM AUTHOR]

Taxonomy of Geastrum species in the neotropics has been subject to divergent opinions among specialists. In our study, type collections were reassessed and compared with recent collections in order to delimit species in Geastrum, sect. Myceliostroma, subsect. Epigaea. A thorough review of morphologic features combined with barcode and phylogenetic analyses (ITS and LSU nrDNA) revealed six new species (G. neoamericanum, G. rubellum, G. brunneocapillatum, G. baculicrystallum, G. rubropusillum and G. courtecuissei). In additon, the presence of hairs on the exoperidium, a commonly used feature to diagnose Geastrum species, proved to be ineffective because it is a derived character within subsect. Epigaea. [ABSTRACT FROM AUTHOR]

Our intestine is a melting pot of interactions between microbial and human cells. This gene-rich ecosystem modulates our health, but questions remain unanswered regarding its genetic structure, such as, “How rapid is evolutionary change in the human gut microbiome? How can its function be maintained?” Much research on the microbiome has characterized the species it contains. Yet the high growth rate and large population sizes of many species, and the mutation rate of most microbes (approximately 10−3 per genome per generation), could imply that evolution might be happening in our gut along our lifetime. In support of this view, Garud and colleagues present an analysis that begins to unravel the pattern of short- and long-term evolution of dozens of gut species. Even with limited longitudinal short-read sequence data, significant evolutionary dynamics—shaped by both positive and negative selection—can be detected on human microbiomes. This may only be the tip of the iceberg, as recent work on mice suggests, and its full extent should be revealed with dense time series long-read sequence data and new eco-evolutionary theory. [ABSTRACT FROM AUTHOR]

Maximum growth rate per individual (r) and carrying capacity (K) are key life-history traits that together characterize the density-dependent population growth and therefore are crucial parameters of many ecological and evolutionary theories such as r/K selection. Although r and K are generally thought to correlate inversely, both r/K tradeoffs and trade-ups have been observed. Nonetheless, neither the conditions under which each of these relationships occur nor the causes of these relationships are fully understood. Here, we address these questions using yeast as a model system. We estimated r and K using the growth curves of over 7,000 yeast recombinants in nine environments and found that the r–K correlation among genotypes changes from 0.53 to −0.52 with the rise of environment quality, measured by the mean r of all genotypes in the environment. We respectively mapped quantitative trait loci (QTLs) for r and K in each environment. Many QTLs simultaneously influence r and K, but the directions of their effects are environment dependent such that QTLs tend to show concordant effects on the two traits in poor environments but antagonistic effects in rich environments. We propose that these contrasting trends are generated by the relative impacts of two factors—the tradeoff between the speed and efficiency of ATP production and the energetic cost of cell maintenance relative to reproduction—and demonstrate an agreement between model predictions and empirical observations. These results reveal and explain the complex environment dependency of the r–K relationship, which bears on many ecological and evolutionary phenomena and has biomedical implications. [ABSTRACT FROM AUTHOR]

Patterns of trait distribution among competing species can potentially reveal the processes that allow them to coexist. It has been recently proposed that competition may drive the spontaneous emergence of niches comprising clusters of similar species, in contrast with the dominant paradigm of greater-than-chance species differences. However, current clustering theory relies largely on heuristic rather than mechanistic models. Furthermore, studies of models incorporating demographic stochasticity and immigration, two key players in community assembly, did not observe clusters. Here we demonstrate clustering under partitioning of resources, partitioning of environmental gradients, and a competition-colonization tradeoff. We show that clusters are robust to demographic stochasticity, and can persist under immigration. While immigration may sustain clusters that are otherwise transient, too much dilutes the pattern. In order to detect and quantify clusters in nature, we introduce and validate metrics which have no free parameters nor require arbitrary trait binning, and weigh species by their abundances rather than relying on a presence-absence count. By generalizing beyond the circumstances where clusters have been observed, our study contributes to establishing them as an update to classical trait patterning theory. [ABSTRACT FROM AUTHOR]

Heritability and evolvability estimates of adult traits from free-living bird populations can be used to gauge the ability of populations to respond to selection, but are rare due to difficulties in gathering detailed pedigree information. The capacity to respond to selection is particularly important for species occupying managed habitats such as agricultural grasslands because of the potential for humans to accidentally influence traits. We calculated heritability and evolvability of six morphological traits in a population of Savannah Sparrows (Passerculus sandwichensis) breeding in a large agricultural landscape. We used microsatellite analysis to determine a genetic pedigree, revealing a high level of extra-pair paternity (63%) within a relatively philopatric population. For the entire population, heritabilities varied from low to high (bill width: 0.160±0.182 to tarsus length: 0.651±0.155), while evolvabilities were low across all traits (wing length: 0.035±0.013 to body mass: 0.066±0.106). Our results indicate that any directional selection from agricultural management practices will produce negligible changes in basic morphometrics of Savannah sparrow populations occupying the Champlain Valley of Vermont, USA. [ABSTRACT FROM AUTHOR]

The generation of the high species diversity of insects in Japan was profoundly influenced by the formation of the Japanese Archipelago. We explored the species diversification and biogeographical history of the Nemouridae Billberg, 1820 family in the Japanese Archipelago using mitochondrial DNA and nuclear DNA markers. We collected 49 species among four genera: Indonemoura Baumann, 1975; Protonemura Kempny, 1898; Amphinemura, Ris 1902 and Nemoura Latreille, 1796 in Japan, China, South Korea and North America. We estimated their divergence times—based on three molecular clock node calibrations—using Bayesian phylogeography approaches. Our results suggested that Japanese Archipelago formation events resulted in diversification events in the middle of the Cretaceous (<120 Ma), speciation in the Paleogene (<50 Ma) and intra-species diversification segregated into eastern and western Japan of the Fossa Magna region at late Neogene (20 Ma). The Indonemoura samples were genetically separated into two clades—that of Mainland China and that of Japan. The Japanese clade clustered with the Nemouridae species from North America, suggesting the possibility of a colonisation event prior to the formation of the Japanese Archipelago. We believe that our results enhanced the understanding both of the origin of the species and of local species distribution in the Japanese Archipelago. [ABSTRACT FROM AUTHOR]

Rare bacterial species have recently attracted interest due to their many potential beneficial functions. However, only little is known about their cultivability. In this study we test the hypotheses that the use of flow cell-sorting for cultivation results in a high proportion of rare soil bacterial isolates relative to bacterial taxa that are abundant in soil. Moreover, we investigate whether different oligotrophic cultivation media and a prolonged incubation time increase the number of cultivated rare species. In a cultivation study we used flow cell sorting to select for small cells and to separate single cells, and grew bacteria on different oligotrophic media with prolonged incubation times. The abundance of the isolates in the field was assessed by comparing them to a 454-sequencing dataset from the same soil. Consequentially, all bacterial isolates were classified as either rare (<0.01% relative abundance) or abundant (>0.01% relative abundance) in the field soil. We found more bacterial taxa among the isolates that were abundant in soil than would be expected by the proportion of abundant species in the field. Neither incubation time nor growth medium had an influence on the recovery of rare species. However, we did find differences in time until visible growth on the plate between different phylogenetic classes of the isolates. These results indicate that rare cultivable species are active and not more likely to be dormant than abundant species, as has been suggested as a reason for their rarity. Moreover, future studies should be aware of the influence incubation time might have on the phylogenetic composition of the isolate collection. [ABSTRACT FROM AUTHOR]

In ant communities, species coexist by using different foraging strategies. We developed an adaptive dynamics model to gain a better understanding of the factors that promote the emergence and maintenance of strategy diversity. We analysed the consequences of both interspecific competition and resource distribution for the evolutionary dynamics of social foraging in ants. The evolution of social foraging behaviour was represented using a stochastic mutation-selection process involving interactions among colonies. In our theoretical community, ant colonies inhabit an environment where resources are limited, and only one resource type is present. Colony interactions depend on colony-specific foraging strategies (defined as the degree of collective foraging), resource distribution patterns, and the degree of competition asymmetry. At the ecological timescale, we have created a model of foraging processes that reflects trade-offs between resource discovery and resource exploitation and between resource discovery and ant behavioural dominance. At the evolutionary timescale, we have identified the conditions of competition and resource distribution that can lead to the emergence and coexistence of both collective and individual foraging strategies. We suggest that asymmetric competition is an essential component in the emergence of diverse foraging strategies in a sympatric ant community. [ABSTRACT FROM AUTHOR]

Chirality in shape and motility can evolve rapidly in microbes and cancer cells. To determine how chirality affects cell fitness, we developed a model of chiral growth in compact aggregates such as microbial colonies and solid tumors. Our model recapitulates previous experimental findings and shows that mutant cells can invade by increasing their chirality or switching their handedness. The invasion results either in a takeover or stable coexistence between the mutant and the ancestor depending on their relative chirality. For large chiralities, the coexistence is accompanied by strong intermixing between the cells, while spatial segregation occurs otherwise. We show that the competition within the aggregate is mediated by bulges in regions where the cells with different chiralities meet. The two-way coupling between aggregate shape and natural selection is described by the chiral Kardar-Parisi-Zhang equation coupled to the Burgers’ equation with multiplicative noise. We solve for the key features of this theory to explain the origin of selection on chirality. Overall, our work suggests that chirality could be an important ecological trait that mediates competition, invasion, and spatial structure in cellular populations. [ABSTRACT FROM AUTHOR]

Persistent seed banks are predicted to have an important impact on population genetic processes by increasing effective population size and storing past genetic diversity. Accordingly, persistent seed banks may buffer genetic effects of disturbance, fragmentation and/or selection. However, empirical studies surveying the relationship between aboveground and seed bank genetics under changing environments are scarce. Here, we compared genetic variation of aboveground and seed bank cohorts in 15 populations of the partially cleistogamous Viola elatior in two contrasting early and late successional habitats characterized by strong differences in light-availability and declining population size. Using AFLP markers, we found significantly higher aboveground than seed bank genetic diversity in early successional meadow but not in late successional woodland habitats. Moreover, individually, three of eight woodland populations even showed higher seed bank than aboveground diversity. Genetic differentiation among populations was very strong (фST = 0.8), but overall no significant differentiation could be detected between above ground and seed bank cohorts. Small scale spatial genetic structure was generally pronounced but was much stronger in meadow (Sp-statistic: aboveground: 0.60, seed bank: 0.32) than in woodland habitats (aboveground: 0.11; seed bank: 0.03). Our findings indicate that relative seed bank diversity (i.e. compared to aboveground diversity) increases with ongoing succession and despite decreasing population size. As corroborated by markedly lower small-scale genetic structure in late successional habitats, we suggest that the observed changes in relative seed bank diversity are driven by an increase of outcrossing rates. Persistent seed banks in Viola elatior hence will counteract effects of drift and selection, and assure a higher chance for the species’ long term persistence, particularly maintaining genetic variation in declining populations of late successional habitats and thus enhancing success rates of population recovery after disturbance events. [ABSTRACT FROM AUTHOR]

The coevolutionary process among free-living mutualists with extremely long matching traits may favor the formation of mutualistic interaction networks through coevolutionary escalation, complementarity and convergence. These networks may be geographically structured; the links among the species of a local network are shaped by the biotic composition of the community, thus creating selection mosaics at broader geographical scales. Therefore, to fully understand a coevolutionary process, it is crucial to visualize the geographical structure of the interaction network across the landscape. In this study we focused on the poorly known interaction system between Ensifera ensifera and its guild of long-flowered plant species. We combined occurrence data and environmental variables to predict E. ensifera distribution, in addition to range polygons available for plant species in order to evaluate the geographical variation in bill length and plant species richness. A positive relationship between bill length and plant species richness within the E. ensifera range suggests a geographical structuring of the interaction networks. At mid-latitude locations of E. ensifera range, where hummingbirds attained the longest bills, richness of long-flowered plant species was higher than at low latitude locations. These locations likely represent coevolutionary vortices where long-lasting reciprocal selection probably drove the evolution of long traits, consequently drawing new plant species into the coevolutionary network. Conversely, areas where the sword-billed hummingbird was absent or had shorter bills probably represent coevolutionary coldspots. Our results provide a first insight into this phenotypically specialized plant-pollinator network across the landscape and show candidate areas to test the predictions of the coevolutionary hypothesis, such as reciprocal selection. [ABSTRACT FROM AUTHOR]

Copy number variants (CNVs) are a pervasive source of genetic variation and evolutionary potential, but the dynamics and diversity of CNVs within evolving populations remain unclear. Long-term evolution experiments in chemostats provide an ideal system for studying the molecular processes underlying CNV formation and the temporal dynamics with which they are generated, selected, and maintained. Here, we developed a fluorescent CNV reporter to detect de novo gene amplifications and deletions in individual cells. We used the CNV reporter in Saccharomyces cerevisiae to study CNV formation at the GAP1 locus, which encodes the general amino acid permease, in different nutrient-limited chemostat conditions. We find that under strong selection, GAP1 CNVs are repeatedly generated and selected during the early stages of adaptive evolution, resulting in predictable dynamics. Molecular characterization of CNV-containing lineages shows that the CNV reporter detects different classes of CNVs, including aneuploidies, nonreciprocal translocations, tandem duplications, and complex CNVs. Despite GAP1’s proximity to repeat sequences that facilitate intrachromosomal recombination, breakpoint analysis revealed that short inverted repeat sequences mediate formation of at least 50% of GAP1 CNVs. Inverted repeat sequences are also found at breakpoints at the DUR3 locus, where CNVs are selected in urea-limited chemostats. Analysis of 28 CNV breakpoints indicates that inverted repeats are typically 8 nucleotides in length and separated by 40 bases. The features of these CNVs are consistent with origin-dependent inverted-repeat amplification (ODIRA), suggesting that replication-based mechanisms of CNV formation may be a common source of gene amplification. We combined the CNV reporter with barcode lineage tracking and found that 102–104 independent CNV-containing lineages initially compete within populations, resulting in extreme clonal interference. However, only a small number (18–21) of CNV lineages ever constitute more than 1% of the CNV subpopulation, and as selection progresses, the diversity of CNV lineages declines. Our study introduces a novel means of studying CNVs in heterogeneous cell populations and provides insight into their dynamics, diversity, and formation mechanisms in the context of adaptive evolution. [ABSTRACT FROM AUTHOR]

The alsodid ground frogs of the Eupsophus genus are divided into two groups, the roseus (2n = 30) and vertebralis (2n = 28), which are distributed throughout the temperate Nothofagus forests of South America. Currently, the roseus group is composed by four species, while the vertebralis group consists of two. Phylogenetic relationships and species delimitation within each group are controversial. In fact, previous analyses considered that the roseus group was composed of between four to nine species. In this work, we evaluated phylogenetic relationships, diversification times, and species delimitation within the roseus group using a multi-locus dataset. For this purpose, mitochondrial (D-loop, Cyt b, and COI) and nuclear (POMC and CRYBA1) partial sequences from 164 individuals were amplified, representing all species. Maximum Likelihood (ML) and Bayesian approaches were used to reconstruct phylogenetic relationships. Species tree was estimated using BEAST and singular value decomposition scores for species quartets (SVDquartets). Species limits were evaluated with six coalescent approaches. Diversification times were estimated using mitochondrial and nuclear rates with LogNormal relaxed clock in BEAST. Nine well-supported monophyletic lineages were recovered in Bayesian, ML, and SVDquartets, including eight named species and a lineage composed by specimens from the Villarrica population (Bootstrap:>70, PP:> 0.99). Single-locus species delimitation analyses overestimated the species number in E. migueli, E. calcaratus, and E. roseus lineages, while multi-locus analyses recovered as species the nine lineages observed in phylogenetic analyses (Ctax = 0.69). It is hypothesized that Eupsophus diversification occurred during Mid-Pleistocene (0.42–0.14 Mya), with most species having originated after the Last Southern Patagonian Glaciation (0.18 Mya). Our results revitalize the hypothesis that the E. roseus group is composed of eight species and support the Villarrica lineage as a new putative species. [ABSTRACT FROM AUTHOR]

In the past few years, miniature light-level geolocators have been developed for tracking wild bird species that were previously too small to track during their full annual cycle. Geolocators offer an exciting opportunity to study the full annual cycle for many species. However, the potential detrimental effects of carrying geolocators are still poorly understood, especially for small-bodied birds. Here, we deployed light-level geolocators on common yellowthroat warblers (Geothlypis trichas). Over two years, we monitored return rates and neighborhood demography for 40 warblers carrying a geolocator and 20 reference birds that did not carry a geolocator. We compared the two groups with long-term data from 108 unmanipulated birds breeding at the same location in previous and subsequent years. Overall, we found that individuals carrying a geolocator were less likely to return to the study site in the following year (21% to 33% returned, depending on inclusion criteria) than either contemporaneous controls (55%) or long-term controls (55%). Among birds marked with geolocators, we also detected viability selection for greater wing length, whereas this pattern was not present in control birds. Finally, in each year after geolocator deployment, inexperienced breeders colonized vacant territories and this demographic effect persisted for two years after deployment. Sexual selection and ornamentation are strongly age-dependent in this system, and behavioral data collected after geolocator deployment is likely to differ systematically from natural conditions. Clearly geolocators will continue to be useful tools, but we suggest that future studies should carefully consider the potential for biased returns and the ecological validity of behavioral data collected from geolocator marked populations. [ABSTRACT FROM AUTHOR]

Reproductive site selection is a key determinant of fitness in many taxa. However, if the site characteristics that enhance offspring survival are detrimental to the parent’s survival or mating success, then complex evolutionary trade-offs occur. In the Brazilian Atlantic Forest, males of the treefrog species Aparasphenodon arapapa use the temporary water bodies in forest-floor bromeliads to court and mate. Males fit tightly into the plant with the head blocking the access and after mating, stay in the bromeliad with the offspring. Since evaporation of the temporary water body inside the bromeliad results in reproductive failure, we expected that males would simply choose the largest bromeliad tanks with the most water. We found that although this was generally true, males seemed to avoid both very large bromeliads and very high water volumes. Field observations suggested a trade-off mechanism for this pattern, whereby very large and water-filled tanks would reduce the male’s ability to effectively seal the tank entrance, avoid predation, or call to mating females. Males also avoided bromeliads with leaf litter and preferred slightly inclined plants. Our results indicate that during reproductive site selection, this bromeliad-breeder needs to engage in complex trade-offs between selection pressures, balancing water requirements against the need for defense and potentially, the ability to attract a mate. [ABSTRACT FROM AUTHOR]

The Community Assembly by Trait Selection (CATS) model of community assembly predicts species abundances along environmental gradients in relatively undisturbed vegetation. Here we ask whether this model, when calibrated with data from natural plant communities, can predict the abundances of five dominant grass species (Bouteloua gracilis, Elymus elymoides, Festuca arizonica, Muhlenbergia montana, and Poa fendleriana) in a greenhouse experiment that manipulated light and soil properties. To address this question, we used generalized additive models (GAMs) to model community-weighted mean (CWM) seed mass, mean Julian flowering date, and specific root length (SRL) as non-linear functions of two environmental variables (soil pH and pine basal area) in natural vegetation. The model-fitted CWM traits were then used as constraints in the CATS model to predict the relative abundance of the five grass species that were seeded in a mixture at equal densities into a 2×2 factorial experiment with soil parent material and light level as crossed factors. Light was the most important factor influencing seedling community composition, especially the abundances of Bouteloua gracilis and Poa fendleriana. The model-predicted relative abundances were significantly correlated with the observed relative abundances, and the model accurately predicted the dominant species in every treatment. P. fendleriana was correctly predicted to be the most abundant species in both shade treatments and the sun-basalt treatment, and B. gracilis was correctly predicted to be the most abundant species in the sun-limestone treatment. Our results provide experimental evidence that environmental filtering of the species pool occurs in the early stages of community assembly (including germination, emergence, and early growth), and that trait-based models calibrated with data from natural plant communities can be used to predict the outcome of the early stages of community assembly under experimental conditions. [ABSTRACT FROM AUTHOR]

Current biodiversity loss is mostly caused by anthropogenic habitat loss and fragmentation, climate change, and resource exploitation. Measuring the balance of species loss and gain in remaining fragmented landscapes throughout time entails a central research challenge. We resurveyed in 2013 plant species richness in the same plots of a previous sampling conducted in 2003 across 18 forest fragments of different sizes of the Chaco Serrano forest in Argentina. While the area of these forest remnants was kept constant, their surrounding forest cover changed over this time period. We compared plant species richness of both sampling years and calculated the proportion of species loss and gain at forest edges and interiors. As in 2003, we found a positive relationship between fragment area and plant richness in 2013 and both years showed a similar slope. However, we detected a net decrease of 24% of species’ richness across all forest fragments, implying an unprecedentedly high rate and magnitude of species loss driven mainly by non-woody, short-lived species. There was a higher proportion of lost and gained species at forest edges than in forest interiors. Importantly, fragment area interacted with percent change in surrounding forest cover to explain the proportion of species lost. Small forest fragments showed a relatively constant proportion of species loss regardless of any changes in surrounding forest cover, whereas in larger fragments the proportion of species lost increased when surrounding forest cover decreased. We show that despite preserving fragment area, habitat quality and availability in the surroundings is of fundamental importance in shaping extinction and immigration dynamics of plant species at any given forest remnant. Because the Chaco Serrano forest has already lost 94% of its original cover, we argue that plant extinctions will continue through the coming decades unless active management actions are taken to increase native forest areas. [ABSTRACT FROM AUTHOR]

The threatened thin-spined porcupine (Chaetomys subspinosus), a forest-specialist endemic to the Brazilian Atlantic forest, was rarely detected in the wild during the 20th century. Previous geographic distribution assessments were carried out nearly three decades ago and were based on interview data. We performed extensive field surveys (based on active search and interviews), a literature review, and species distribution modeling to predict and validate a more reliable picture of its geographic distribution and environmental suitability gradient. We identified the main predictors of species’ incidence, its conservation status, and pinpointed key areas for species conservation. Our results indicated that C. subspinosus is distributed continuously in the Atlantic forest from southeastern Espirito Santo to central-eastern Sergipe state, totaling 104,326 km2 of occurrence area, although only 3,299 km2 (13.3%) is currently represented by native forests (species habitat). C. subspinosus was absent or at least so rare that it was not detected in more than half of the locations sampled by interviews (53.5%). Our results suggest that populations are sensitive to climatic conditions and habitat loss, becoming abruptly rarer when the remaining forest cover reaches less than 10% area within a region (~ 5,000 km2 scale). This result indicates that the high deforestation level of the Atlantic forest is already close to the limit of regional species resistance. Bahia state still harbors the bulk of the remaining forest with high climatic suitability, and generally under low levels of legal protection. Herein we highlight priority areas and research gaps that could guide decision makers to promote conservation strategies for this threatened species. [ABSTRACT FROM AUTHOR]

Because parental care is costly, conflict between mates over their roles in reproduction seems unavoidable unless they both benefit from parental labour split equally between partners. In the current paper we analyse the division of parental investment in the Blackcap (Sylvia atricapilla), a species that experiences high nest predation. We show that both sexes invest in the incubation of eggs as well as feeding and brooding nestlings at a similar level. We also found that pairs which divided feeding duties more equally produced nestlings that grew faster. Faster nestling development enables earlier fledging in case of predation attempts at the end of nesting period. Thus parents who more evenly participate in provisioning may benefit from higher breeding success. Our findings suggest that in species under high risk of nest predation disparity in parental investment may not provide much benefit to parent’s residual reproductive value and that equality in parental duties constitutes a winning strategy. [ABSTRACT FROM AUTHOR]

The olive moth -Prays oleae Bern.- remains a significant pest of olive trees showing situation dependent changes in population densities and in severity of damages. The genetic variability of olive moth was assessed on three main olive orchards regions in Portugal by three different markers (COI, nad5 and RpS5), suggesting high species diversity albeit with no obvious relation with a regional pattern nor to an identified ecological niche. Selected COI sequences obtained in this study were combined with those available in the databases for Prays genus to generate a global dataset. The reconstruction of the Prays phylogeny based on this marker revealed the need to revise Prays oleae to confirm its status of single species: COI data suggests the co-existence of two sympatric evolutionary lineages of morphologically cryptic olive moth. We show, however, that the distinct mitochondrial subdivision observed in the partial COI gene fragment is not corroborated by the other DNA sequences. There is the need of understanding this paradigm and the extent of Prays variability, as the disclosure of lineage-specific differences in biological traits between the identified lineages is fundamental for the development of appropriate pest management practices. [ABSTRACT FROM AUTHOR]