[Relationship between economy and ecology of Pearl River Delta Urban Agglomeration based on ecological footprint of net primary productivity]. / 基于生态足迹-å‡€åˆçº§ç”Ÿäº§åŠ›çš„ç ä¸‰è§’åŸŽå¸‚ç¾¤ç»æµŽä¸Žç”Ÿæ€çš„å ³ç³».

With the acceleration of regional economic integration, human activities have played an increasingly crucial role in regional sustainable development. In this study, MODIS remote sensing data and ecological footprint of net primary productivity (EF-NPP) were leveraged to calculate the equivalence factor and yield factor of the six major biologically productive land areas in the Pearl River Delta Urban Agglomeration. We analyzed the changes in per capita ecological footprint, per capita ecological carrying capacity, natural resource utilization efficiency and ecological moderate population from 2000 to 2020. Results showed that the per capita ecological footprint in the Pearl River Delta Urban Agglomeration continued to rise from 2000 to 2020. The ecological occupation of energy land was the highest. The ecological footprint was high in west, low in middle, and higher in northwest of the study area. The per capita ecological carrying capacity was relatively high in Zhaoqing and Jiangmen and low in Shenzhen, Dongguan, Foshan and Zhongshan. The gap between the ecological moderate population and the regional actual population widened over time, reaching 30.62 million in 2020. The regional actual population was much larger than the ecological moderate population, indicating huge population pressure. The natural resource utilization efficiency of the three main industries was high. The economic benefits created by the per capita ecological footprint increased by 36800 yuan·hm-2 during the research period, with an average annual growth rate of 1800 yuan·hm-2. The growth rate of the tertiary industry was the highest. Therefore, the results could provide reference for the study on natural resource utilization efficiency in medium and small-scale regions.

[Identification and restoration strategy of key areas for territorial space ecological restoration in Shanghai, China based on ecological security pattern]. / åŸºäºŽç”Ÿæ€å®‰å ¨æ ¼å±€çš„ä¸Šæµ·å›½åœŸç©ºé—´ç”Ÿæ€ä¿®å¤å ³é”®åŒºåŸŸè¯†åˆ«ä¸Žä¿®å¤ç­–ç•¥.

In the new era, ecological restoration of territorial space is the important task of maintaining regional ecological security, improving regional ecological quality and providing high-quality ecological products. From the perspective of ecological security, accurately determination of key areas to be restored in the territorial space is the primary work, and it is also a key and difficult problem to scientifically carry out ecological restoration. Based on the mainstream ecological security pattern theory, taking Shanghai as the research area, we integrated morphological spatial pattern analysis method and InVEST model to identify ecological sources, extracted ecological corridors, ecological "pinch points" and obstacle points with circuit theory, comprehensively determined the key areas to be restored, and proposed targeted restoration strategies. The results showed that the ecological sources of Shanghai were mainly distributed in the Yangtze River estuary, Chongming Island, Hangzhou Bay coast, and Dianshan Lake, accounting for about 17.9% of the study area. There were 103 key ecological corridors. The key areas to be repaired included 12 ecological "pinch points" and 54 ecological obstacle points, which were mainly distributed at the border of ecological source and ecological corridor, as well asthe intersection or turning point of ecological corridor and ecological corridor. According to the typical problems of key areas to be restored and land use conditions, three types of restoration strategy zones were proposed: ecological landscape reshaping, important corridor penetration, and ecological shoreline protection and restoration. The results could provide reference for compiling a territorial space ecological restoration plan in Shanghai and building a medium-scale ecological security pattern and carrying out systemic ecological restoration work in other regions of China.

Extended seed rain period of Adenostoma fasciculatum impacts diverse seed predators.

AIMS: The principal chaparral species in California, Adenostoma fasciculatum, an evergreen, sclerophyllous shrub, is broadly distributed and provides habitat and food resources for a large and diverse animal community. The effects of climate change, including elevated temperatures, fire frequency and severity, along with increased urban encroachment, have placed pressure on chaparral habitats in California. Our goal is to investigate aspects of reproductive ecology as a measure of the potential resiliency of A. fasciculatum. We focus on seed rain (all seed falling into the seed traps regardless of origin) and seed banks in the context of plant-animal interactions and regeneration. METHODS: Stand recovery following disturbance is achieved through both resprouting and germination from established persistent soil seed banks. In this study we focus on seed ecology using a series of experiments to document the length and quantity of seed rain, seed predation, parsing the importance of the community of granivores, and evaluating the connection between stand age and germination rate from soil seed banks. IMPORTANT FINDINGS: Our research documented an 8-month seed rain duration with over 1 million seeds per m2, multiple seed predators including passerines (songbirds) and rodents, and points to the possibility of native ants playing a role in the seed dispersal process. This is important given the recent advancement of the invasive Argentine ant (Linepthema humile) into Californian chaparral. This research demonstrates a clear relationship between A. fasciculatum and both resident and migratory granivores in the chaparral. We documented that a 39-year-old stand had higher germination rates than those which were 16, 20, 41 and 71 years old and how seed banks play a major role in assuring resiliency following fire. These findings are important for wildland managers to assure the continued resiliency of A. fasciculatum.

The Role of Stochasticity in Noise-Induced Tipping Point Cascades: A Master Equation Approach.

Tipping points have been shown to be ubiquitous, both in models and empirically in a range of physical and biological systems. The question of how tipping points cascade through systems has been less explored and is an important one. A study of noise-induced tipping, in particular, could provide key insights into tipping cascades. Here, we consider a specific example of a simple model system that could have cascading tipping points. This model consists of two interacting populations with underlying Allee effects and stochastic dynamics, in separate patches connected by dispersal, which can generate bistability. From an ecological standpoint, we look for rescue effects whereby one population can prevent the collapse of a second population. As a way to investigate the stochastic dynamics, we use an individual-based modeling approach rooted in chemical reaction network theory. Then, using continuous-time Markov chains and the theory of first passage times, we essentially approximate, or emulate, the original high-dimensional model by a Markov chain with just three states, where each state corresponds to a combination of population thresholds. Analysis of this reduced model shows when the system is likely to recover, as well as when tipping cascades through the whole system.

Histoecology: Applying Ecological Principles and Approaches to Describe and Predict Tumor Ecosystem Dynamics Across Space and Time.

Cancer cells exist within a complex spatially structured ecosystem composed of resources and different cell types. As the selective pressures imposed by this environment determine the fate of cancer cells, an improved understanding of how this ecosystem evolves will better elucidate how tumors grow and respond to therapy. State of the art imaging methods can now provide highly resolved descriptions of the microenvironment, yielding the data required for a thorough study of its role in tumor growth and treatment resistance. The field of landscape ecology has been studying such species-environment relationship for decades, and offers many tools and perspectives that cancer researchers could greatly benefit from. Here, we discuss one such tool, species distribution modeling (SDM), that has the potential to, among other things, identify critical environmental factors that drive tumor evolution and predict response to therapy. SDMs only scratch the surface of how ecological theory and methods can be applied to cancer, and we believe further integration will take cancer research in exciting new and productive directions. Significance: Here we describe how species distribution modeling can be used to quantitatively describe the complex relationship between tumor cells and their microenvironment. Such a description facilitates a deeper understanding of cancers eco-evolutionary dynamics, which in turn sheds light on the factors that drive tumor growth and response to treatment.

Characterizing the ecological and evolutionary dynamics of cancer.

Tumor initiation and progression are somatic evolutionary processes driven by the accumulation of genetic alterations, some of which confer selective fitness advantages to the host cell. This gene-centric model has shaped the field of cancer biology and advanced understanding of cancer pathophysiology. Importantly, however, each genotype encodes diverse phenotypic traits that permit acclimation to varied microenvironmental conditions. Epigenetic and transcriptional changes also contribute to the heritable phenotypic variation required for evolution. Additionally, interactions between cancer cells and surrounding stromal and immune cells through autonomous and non-autonomous signaling can influence competition for survival. Therefore, a mechanistic understanding of tumor progression must account for evolutionary and ecological dynamics. In this Perspective, we outline technological advances and model systems to characterize tumor progression through space and time. We discuss the importance of unifying experimentation with computational modeling and opportunities to inform cancer control.

Diving in uncharted waters: An updated genetics toolkit highlights the challenges of polyploidy in landscape genomics analyses.

As molecular ecologists, we have by necessity become adept at working across computational platforms. A diverse community of scientists has developed a broad array of analytical resources spanning command line to graphical user interface across Linux, Mac, and Windows environments and a dizzying array of program-specific input formats. In light of this, we often explore our data like free divers - filling our lungs with air and descending for a short period of time into one part of our data set before resurfacing, reformatting, and preparing for our next analysis. In this issue of Molecular Ecology Resources, Meirmans (2020) presents an updated version of GenoDive, a program with a toolkit that provides users with the opportunity to stay a while and delve deeper into the diverse portfolio of information provided by a genomic data set. The comprehensive nature of GenoDive coupled with its unique capability to handle both diploid and polyploid data also provides an opportunity to reflect on the unevenness of resources available for the analysis of polyploid versus diploid data. Since new updates include the addition of plug-ins for genotype-environment association analyses, we limit the observations presented here to the common tools used for landscape genomics analyses.

Innovating Governance for Planetary Health with Three Critically Informed Frames.

In May 2019, the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services warned that "around one million animal and plant species are now threatened with extinction." In September 2019, Naomi Klein, an astute writer on environmental change, described the interconnected social and ecological breakdowns on the planet in a new book. Ecological crises noted by these and other scholars speak well to the rise of planetary health as a new scholarship. Loss of biodiversity has manifold negative impacts on health, for example, rise of zoonotic infections and changes in healthy microbiome. But reducing our ecological footprints is not enough. We ought to change mindsets, the narrow science, and technology governance regimes that value nature and other life forms instrumentally by their usefulness to us. I describe three new, broader and critically informed, frames on governance for planetary health. First, I explain why we ought to acknowledge animal sentience, for example, as recognized in Article 13 of the Lisbon Treaty in 2009. I describe how political determinants of health, power, and agency operate at multiple sociological and planetary loci, not only among human beings but also at human and nonhuman animal interfaces. Second, planetary health calls for a shift toward ecological and political determinants beyond a narrow anthropocentric view, while resisting the entrenched dogma of exponential growth with finite planetary natural resources. Third, for critically informed governance of emerging technologies in planetary health (e.g., glycomics, artificial intelligence, health care robots), I refer to a question highlighted recently (Frodeman, 2019): "When Plato (more exactly, Juvenal) asked who guards the guardians, he was questioning whether any group can be trusted to look past its own interests for the common good." Hence, it is time we broaden the question "Who will guard the guardians?" beyond the scientific community, to actors in science policy as well. Policy questions cannot be limited to "which social issues emerge from a new technology?" but ought to include, "who should be framing science and technology policy, and why?" Youth leaders of the global climate movement such as Greta Thunberg and others are now rightly asking these epistemological questions that might contribute toward a new social contract on health for all sentient beings on planet Earth. While ecological changes accelerate and a new space industry is emerging, governance for planetary health will continue to be at the epicenter of systems thinking, responsible innovation and science policy in the 21st century.

Reproductive ecology of Otocinclus vittatus (Regan, 1904) in the Pantanal floodplain, upper Paraguay River basin / Ecologia reprodutiva de Otocinclus vittatus (Regan, 1904) na planície de inundação do Pantanal, bacia do alto rio Paraguai

Abstract We studied the reproductive biology of Otocinclus vittatus in the southern Pantanal, Brazil. A total of 1066 fishes were analyzed (490 males, 488 females and 88 individuals of undetermined sex), sampled with a rectangular sieve and a seine net from February/2009 to January/2011. Variations in the sex ratio, seasonality in reproduction, fecundity, and size at first maturity were estimated. No variations were detected in the total sex ratio for the study period as a whole; although ratio has varied over time. The gonadosomatic index varied according to the river level, but not according to water temperature and rainfall. The mean fecundity was estimated at 84.1 oocytes, with a positive correlation with standard length. The size at first maturity (L50) estimated was 18.7 mm for females and 20.1 mm for males.

Resumo Estudamos a biologia reprodutiva de Otocinclus vittatus no Pantanal Sul, Brasil. Um total de 1066 peixes foram analisados (490 machos, 488 fêmeas e 88 de sexo indeterminado), amostrados com tela de isca e rede de arrasto entre Fevereiro/2009 e Janeiro/2011. Foram estimadas as variações na proporção sexual, a sazonalidade na reprodução e o tamanho da primeira maturação. Não foi detectada variação na proporção sexual total para o período de estudo como um todo; embora a proporção tenha variado ao longo do tempo. O índice ganadossomático variou de acordo com o nível do rio, mas não de acordo com a temperatura da água e a pluviosidade. A média de fecundidade foi estimada em 84.1 ovócitos, com uma correlação positiva com o comprimento padrão. O tamanho de primeira maturação (L50) foi estimado em 18.7 mm para fêmeas e 20.1 mm para machos.

An overview of the applicability of functional diversity in Biological Conservation / Uma visão geral sobre a aplicabilidade da diversidade funcional na Conservação Biológica

Abstract Functional diversity is increasingly pointed as a useful approach to reach Biological Conservation goals. Here, we provide an overview of the functional diversity approach status in the Biological Conservation field. We sought for peer-reviewed papers published over a period of twenty years (from 1994 to 2014). First we used the general topic "functional diversity" and then refined our search using the key-word "conservation". We have identified the conservation strategies addressed, the organism studied, and the continent of study site in each paper. Thirteen classes of conservation strategies were identified. Plants were the most commonly studied organism group and most study-sites were located in Europe. The functional diversity approach was introduced in the Biological Conservation field in the early 2000's and its inclusion in conservation strategies is broadly advised. However, the number of papers that operationalise such inclusion by developing models and systems is still low. Functional diversity responds differently and eventually better than other measures to changes in land use and management, which suggests that this approach can potentially better predict the impacts. More studies are needed to corroborate this hypothesis. We pointed out knowledge gaps regarding identification of the responses for functional diversity about urban impacts and in research on the level of management intensity of land needed to maintain functional diversity. We recommend the use of functional diversity measures to find ecological indicators. Future studies should focus on the development of functional diversity measures of other taxa beyond plants as well as test hypothesis in tropical ecosystems.

Resumo A diversidade funcional é crescentemente apontada como uma abordagem útil para alcançar os objetivos da Conservação Biológica. Neste artigo, nós mostramos uma visão geral do status desta abordagem no campo da Conservação Biológica. Nós buscamos por artigos revisados por pares publicados ao longo de vinte anos (desde 1994 até 2014) usando, primeiramente, o tópico geral "functional diversity" e em seguida, refinamos a pesquisa com a palavra-chave "conservation". Identificamos a estratégia de conservação abordada, o organismo estudado e o continente da área de estudo de cada artigo. Treze classes de estratégias de conservação foram identificadas. As plantas foram o grupo de organismos mais amplamente estudado e a maior parte das áreas de estudo estavam localizadas no continente europeu. A abordagem da diversidade funcional entrou no campo da Conservação Biológica no início dos anos 2000 e sua inclusão nas estratégias de conservação é amplamente recomendada. Entretanto, o número de artigos que operacionalizam tal inclusão ainda é pequeno. A diversidade funcional responde diferentemente e, eventualmente, melhor do que as outras medidas às mudanças no uso da terra e no manejo, sugerindo que essa abordagem pode potencialmente prever melhor os impactos. Mais estudos são necessários para corroborar esta hipótese. Destacamos lacunas de conhecimento sobre a identificação das respostas da diversidade funcional aos impactos urbanos e sobre a busca pelo nível de intensidade de manejo da terra necessária para manter a diversidade funcional. Recomendamos o uso de medidas de diversidade funcional para encontrar indicadores ecológicos. Estudos futuros devem focar no desenvolvimento de medidas de diversidade funcional de outros taxa, além das plantas bem como testar hipóteses em ecossistemas tropicais.

An ecological risk assessment model for Arctic oil spills from a subsea pipeline.

There is significant risk associated with increased oil and gas exploration activities in the Arctic Ocean. This paper presents a probabilistic methodology for Ecological Risk Assessment (ERA) of accidental oil spills in this region. A fugacity approach is adopted to model the fate and transport of released oil, taking into account the uncertainty of input variables. This assists in predicting the 95th percentile Predicted Exposure Concentration (PEC95%) of pollutants in different media. The 5th percentile Predicted No Effect Concentration (PNEC5%) is obtained from toxicity data for 19 species. A model based on Dynamic Bayesian Network (DBN) is developed to assess the ecological risk posed to the aquatic community. The model enables accounting for the occurrence likelihood of input parameters, as well as analyzing the time-variable risk profile caused by seasonal changes. It is observed through the results that previous probabilistic methods developed for ERA can be overestimating the risk level.

GC-MS/MS determination and ecological risk assessment of pesticides in aquatic system: A case study in Hooghly River basin in West Bengal, India.

A liquid-liquid extraction (LLE) for water and modified QuEChERS (quick, easy, cheap, effective, rugged, and safe) method for sediment combined with gas chromatography-tandem mass spectrometry (GC-MS/MS) detection in multiple reaction monitoring (MRM) mode was standardized for determination of 31 pesticides. Performance characteristics for the selected pesticides were acceptable according to European Commission's (EC) guidelines for method validation (recovery 70-120%, RSD <20% and R2 value ≥ 0.99). River, pond and tubewell water and river sediment samples (64 nos.) were collected from Hooghly River basin in West Bengal, India during 2014-2016. About 42% of the samples showed the presence of 19 pesticides with the highest loading of total pesticides (T-pesticides) in river water (3.01 ng mL-1) followed by sediment (1.25 ng g-1), pond (0.40 ng mL-1) and tubewell (0.02 ng mL-1) water. The non-agricultural OC (organochlorine) insecticides were detected in all river water and sediment samples mainly due to HCHs (hexachlorocyclohexane) from old source and fresh use of DDTs (dichlorodiphenyltrichloroethane) in local areas. No OC insecticides were detected in pond and tubewell water. Maximum residues of some recommended pesticides in agriculture were obtained in pond water. Most of the river water samples (93.7%) were in excess of EC limit (0.50 ng mL-1) of T-pesticides for drinking followed by pond water samples (56.2%). Tubewell water samples were free from T-pesticide threat but exceeded the EC limit (0.10 ng mL-1) for single pesticide in case of chlorpyrifos only. Ecological risk on aquatic animals was observed for OCs in river and chlorpyrifos in pond aquatic ecosystem.

Ecological risk estimation of organophosphorus pesticides in riverine ecosystems.

Pesticides are of great concern because of their existence in ecosystems at trace concentrations. Worldwide pesticide use and its ecological impacts (i.e., altered environmental distribution and toxicity of pesticides) have increased over time. Exposure and toxicity studies are vital for reducing the extent of pesticide exposure and risk to the environment and humans. Regional regulatory actions may be less relevant in some regions because the contamination and distribution of pesticides vary across regions and countries. The risk quotient (RQ) method was applied to assess the potential risk of organophosphorus pesticides (OPPs), primarily focusing on riverine ecosystems. Using the available ecotoxicity data, aquatic risks from OPPs (diazinon and chlorpyrifos) in the surface water of the Langat River, Selangor, Malaysia were evaluated based on general (RQm) and worst-case (RQex) scenarios. Since the ecotoxicity of quinalphos has not been well established, quinalphos was excluded from the risk assessment. The calculated RQs indicate medium risk (RQm = 0.17 and RQex = 0.66; 0.1 ≤ RQ < 1) of overall diazinon. The overall chlorpyrifos exposure was observed at high risk (RQ ≥ 1) based on RQm and RQex at 1.44 and 4.83, respectively. A contradictory trend of RQs > 1 (high risk) was observed for both the general and worst cases of chlorpyrifos, but only for the worst cases of diazinon at all sites from downstream to upstream regions. Thus, chlorpyrifos posed a higher risk than diazinon along the Langat River, suggesting that organisms and humans could be exposed to potentially high levels of OPPs.

Nowhere to run, rabbit: the cold-war calculus of disease ecology.

During the cold war, Frank Fenner (protégé of Macfarlane Burnet and René Dubos) and Francis Ratcliffe (associate of A. J. Nicholson and student of Charles Elton) studied mathematically the coevolution of host resistance and parasite virulence when myxomatosis was unleashed on Australia's rabbit population. Later, Robert May called Fenner the "real hero" of disease ecology for his mathematical modeling of the epidemic. While Ratcliffe came from a tradition of animal ecology, Fenner developed an ecological orientation in World War II through his work on malaria control (with Ratcliffe and Ian Mackerras, among others)-that is, through studies of tropical medicine. This makes Fenner at least a partial exception to other senior disease ecologists in the region, most of whom learned their ecology from examining responses to agricultural challenges and animal husbandry problems in settler colonial society. Here I consider the local ecologies of knowledge in southeastern Australia during this period, and describe the particular cold-war intellectual niche that Fenner and Ratcliffe inhabited.

A guide to phylogenetic metrics for conservation, community ecology and macroecology.

The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify 'anchor' representatives: for α-diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.

Bioecology and movements of bull sharks, Carcharhinus leucas, caught in a long-term longline survey off northeastern Brazil

A robust understanding of habitat usage by coastal shark species, and how it overlaps with human presence in densely-populated regions is needed to inform the development of efficient conservation strategies for these important top predators. An intensive longline survey conducted in nearshore waters off northeastern Brazil from 2004 through 2014 caught a total of 18 bull sharks (Carcharhinus leucas) (male-female ratio = 0.63:1), which can be dangerous to humans. Although most sharks were sexually mature, there was no evidence that this region could be used as a parturition or nursery area. Prey items identified in the guts of the sharks comprised teleosts, mollusks and elasmobranchs. Additionally, one satellite-tagged bull shark covered a great distance (> 3,000 km) in 75 days at liberty, making most use of shallow waters (< 20 m depth) and presumably also entering an estuarine area. Although bull sharks are not an important fishery resource in this region, such a reduced abundance coupled with its affinity for coastal and inshore habitats highlights the potential vulnerability of C. leucas to deleterious anthropic interferences off northeastern Brazil.(AU)

Um melhor entendimento sobre a utilização de hábitat das espécies de tubarões costeiros, e como ela se sobrepõe à presença humana em regiões altamente populosas, se faz necessário a fim de subsidiar o desenvolvimento de eficientes medidas de conservação para esses importantes predadores de topo. Um estudo intensivo utilizando espinhel, conduzido em águas costeiras do nordeste do Brasil entre os anos de 2004 e 2014, capturou um total de 18 tubarões cabeça-chata (Carcharhinus leucas) (proporção macho-fêmea = 0,63:1), os quais podem ser perigosos para humanos. Apesar da maioria dos tubarões estarem sexualmente maduros, não houve evidências de que essa região esteja sendo utilizada como uma área de parto ou berçário. Entre os itens alimentares identificados foram encontrados teleósteos, moluscos e elasmobrânquios. Além disso, um tubarão cabeça-chata marcado com um transmissor satélite percorreu uma grande distância (> 3.000 km) em 75 dias em liberdade, fazendo o uso de águas superficiais (< 20 m profundidade) e presumivelmente entrando em uma área estuarina. Apesar de os tubarões cabeça-chata não corresponderem a um recurso pesqueiro importante nessa região, tal reduzida abundância juntamente com a sua afinidade por hábitats costeiros reforçam a potencial vulnerabilidade de C. leucas às interferências antrópicas deletérias ao longo da costa nordeste do Brasil.(AU)

Proteomics in evolutionary ecology.

Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein modifications and protein interactions of interest with high accuracy and assess protein diversity and function. Therefore, proteomic technologies can be viewed as providing evolutionary biologist with exciting novel opportunities to understand very early events in functional variation of cellular molecular machinery that are acting as part of evolutionary processes.

Trends and biases in global scientific literature about ecological niche models / Tendências e vieses na literatura científica mundial sobre modelos de nicho ecológico

Abstract Recently, ecological niche models have been employed to investigate the potential geographical distribution of species. However, it is necessary to analyze the vast number of publications on this topic to understand the trends and biases of research using ecological niche models (ENMs). Therefore, this study aims to investigate trends in the scientific literature regarding studies on ENMs. For the quantitative analysis of the literature on ENMs, we performed a search in the Thomson ISI (Web of Science) database between 1991 and 2013. The search identified 3042 papers containing preselected keywords in either the title or abstract. The results showed that the number of papers has increased over the years (r=0.77, P<0.001), with a sharp increase in recent years, highlighting the widespread use of the ENMs. There was an increase in the diversity of journals that published papers about ENMs (r=0.97, P<0.001). The research was conducted in different countries, predominantly the United States of America (550 papers), and the most commonly used method was the Maximum Entropy method (312 papers). Regarding the taxonomic group, most research has been conducted on plants (402 papers, or 28.36% of the total). There was no relationship between the modeling method used and the taxonomic group studied (χ2=4.8, P=0.15). Finally, the wide availability of biological, environmental and computational resources has elicited the broad use of tools for ENMs. Despite the conceptual discussions of the ENMs, this method is currently the most effective way to evaluate the potential geographical distribution of species, and to predict the distribution under different environmental conditions (i.e., future or past scenarios).

Resumo Recentemente, modelos de nicho têm sido empregados para investigar a distribuição geográfica potencial de espécies. Porém, é necessário analisar a vasta quantidade de publicações sobre o referido tema, a fim de compreender as tendências e vieses das pesquisas que usam modelos de nicho ecológico (MNEs). Portanto, esse trabalho tem por objetivo investigar as tendências da literatura científica de trabalhos sobre MNEs. Para a análise quantitativa das publicações sobre MNEs, foi realizada uma busca na base de dados Thomson ISI (Web of Science), entre o período de 1991 a 2013. A pesquisa agrupou 3042 documentos que continham nas palavras-chave, no título ou no resumo os termos selecionados para a busca. Os resultados mostraram que de forma geral o número de artigos tem aumentado ao longo dos anos (r=0,77, P<0,001), com um acentuado crescimento nos anos mais recentes, destacando o amplo uso de MNEs. Ao longo dos anos percebeu-se um aumento da diversidade de revistas que publicam sobre o assunto (r=0,97, P<0,001). As pesquisas têm sido desenvolvidas em diferentes países, com predomínio dos Estados Unidos (550 artigos) e o método mais utilizado foi o de Máxima Entropia (312 artigos). Quanto ao grupo taxonômico, a maioria dos estudos tem ocorrido com plantas (402 artigos ou 28,36% do total de artigos). Não houve relação entre método de modelagem e grupo taxonômico (χ2=4,8, P=0,15). Por fim, a ampla disponibilidade de dados biológicos, ambientais e recursos computacionais tem propiciado um amplo uso de MNEs. Apesar das discussões conceituais sobre MNEs, o método atualmente é o mais eficaz para conhecer a distribuição geográfica potencial das espécies e ainda projetar essa distribuição sob diferentes condições ambientais (i.e. cenários futuros, passado).

Enchytraeid abundance in Araucaria Mixed Forest determined by cold and hot wet extraction / Abundância de enquitreídeos na Floresta Ombrófila Mista determinada por extração úmida quente e fria

Abstract Enchytraeids are small oligochaetes found worldwide in soils with sufficient moisture and organic matter, but scarcely studied in the Southern hemisphere. This is the third study on enchytraeid abundance in Brazil using wet extraction and the first carried out in Araucaria Mixed Forest (subtropical region). The sampling and extraction were based on the standard method ISO 23611-3/2007 using an adapted split soil corer and wet extraction with and without heat to assess the abundance of enchytraeids in a forest fragment at Embrapa Forestry in Colombo, Paraná State. The samplings were performed in 3 occasions between September 2011 and April 2012. The average numbers estimated by each method varied from appr. 2.000-12.000 (cold) and 5.000-12.000 ind./ m2 (hot), respectively, with a maximum of 44.000 ind./ m2 in one of the samples, the highest value reported so far in Brazil. The hot extraction was more advantageous, given the speed and preservation of the specimens in vivo, allowing taxonomic identification. Advantages and disadvantages of wet extractions compared to handsorting and formol methods are also discussed. Guaranidrilus, Hemienchytraeus, Enchytraeus, Fridericia and Achaeta were the genera identified in the samples.

Resumo Os enquitreídeos são pequenos oligoquetas encontrados no mundo todo em solos com suficiente umidade e matéria orgânica, porém muito pouco estudados no hemisfério Sul. Este é o terceiro estudo sobre a abundância de enquitreídeos no Brasil utilizando o método de extração úmida e o primeiro realizado em Floresta Ombrófila Mista (região subtropical). A amostragem e extração foram baseadas no método padrão ISO 23611-3/2007, utilizando-se um trado desmontável adaptado e extração úmida com e sem aquecimento para acessar a abundância de enquitreídeo em um fragmento de floresta na Embrapa Florestas em Colombo, Paraná. As amostragens foram realizadas em três ocasiões entre setembro, 2011 e abril 2012. Os números médios estimados através de cada método variaram de 2.000-12.000 (frio) e 5.000-12.000 ind./ m2 (quente), respectivamente, e o máximo de 44.000 ind./ m2 em uma das amostras, o mais alto já relatado no Brasil. A extração quente foi a mais vantajosa, considerando a rapidez e preservação dos exemplares in vivo. As vantagens e desvantagens das extrações úmidas comparadas aos métodos de triagem manual e extração com formol foram discutidas. Os gêneros Guaranidrilus, Hemienchytraeus, Enchytraeus, Fridericia e Achaeta foram identificados nas amostras.

A New Method for Noninvasive Genetic Sampling of Saliva in Ecological Research.

Noninvasive samples for genetic analyses have become essential to address ecological questions. Popular noninvasive samples such as faeces contain degraded DNA which may compromise genotyping success. Saliva is an excellent alternative DNA source but scarcity of suitable collection methods makes its use anecdotal in field ecological studies. We develop a noninvasive method of collection that combines baits and porous materials able to capture saliva. We report its potential in optimal conditions, using confined dogs and collecting saliva early after deposition. DNA concentration in saliva extracts was generally high (mean 14 ng µl(-1)). We correctly identified individuals in 78% of samples conservatively using ten microsatellite loci, and 90% of samples using only eight loci. Consensus genotypes closely matched reference genotypes obtained from hair DNA (99% of identification successes and 91% of failures). Mean genotyping effort needed for identification using ten loci was 2.2 replicates. Genotyping errors occurred at a very low frequency (allelic dropout: 2.3%; false alleles: 1.5%). Individual identification success increased with duration of substrate handling inside dog's mouth and the volume of saliva collected. Low identification success was associated with baits rich in DNA-oxidant polyphenols and DNA concentrations <1 ng µl(-1). The procedure performed at least as well as other noninvasive methods, and could advantageously allow detection of socially low-ranked individuals underrepresented in sources of DNA that are involved in marking behaviour (faeces or urine). Once adapted and refined, there is promise for this technique to allow potentially high rates of individual identification in ecological field studies requiring noninvasive sampling of wild vertebrates.