The Clade Replacement Theory: a framework to study age-dependent extinction.

There is no scientific consensus about whether and how species' evolutionary age, or the elapsed time since their origination, might affect their probability of going extinct. Different age-dependent extinction (ADE) patterns have been proposed in theoretical and empirical studies, while the existence of a consistent and universal pattern across the tree of life remains debated. If evolutionary age predicts species extinction probability, then the study of ADE should comprise the elapsed time and the ecological process acting on species from their origin to their extinction or to the present for extant species. Additionally, given that closely related species share traits associated with fitness, evolutionary proximity could generate similar ADE patterns. Considering the historical context and extinction selectivity based on evolutionary relatedness, we build on previous theoretical work to formalize the Clade Replacement Theory (CRT) as a framework that considers the ecological and evolutionary aspects of species age and extinction probability to produce testable predictions on ADE patterns. CRT's domain is the diversification dynamics of two or more clades competing for environmental space throughout time, and its propositions or derived hypotheses are as follows: (i) incumbency effects by an early arriving clade that limit the colonization and the diversification of a younger clade leading to a negative ADE scenario (younger species more prone to extinction than older ones) and (ii) an ecological shift triggered by an environmental change that imposes a new selective regime over the environmental space and leads to a positive ADE scenario (extinction probability increasing with age). From these propositions, we developed the prediction that the ADE scenario would be defined by whether an ecological shift happens or not. We discuss how the CRT could be tested with empirical data and provide examples where it could be applied. We hope this article will provide a common ground to unify results from different fields and foster new empirical tests of the mechanisms derived here while providing insights into CRT theoretical structuration.

Patterns of energetic substrate modifications in response to feeding in boas, Boa constrictor (Serpentes, Boidae).

Ambush-foraging snakes that ingest large meals might undergo several months without eating when they use the internal reserves to support the energetic costs of living. Then, morphological and physiological processes might be orchestrated during the transition from fasting to the postprandial period to rapidly use the energetic stores while the metabolic rate is elevated in response to food intake. To understand the patterns of substrates deposition after feeding, we accessed the morphological and biochemical response in Boa constrictor snakes after two months of fasting and six days after feeding. We followed the plasma levels of glucose, total proteins, and total lipids, and we performed the stereological ultrastructural analysis of the liver and the proximal region of the intestine to quantify glycogen granules and lipid droplets. In the same tissues and stomach, we measured the activity of the enzyme fructose-1,6-biphosphatase (FBPase1) involved in the gluconeogenic pathway, and we measured pyruvate kinase (PK) and lactate dehydrogenase (LDH) enzymatic activities involved in the anaerobic pathway in the liver. Briefly, our results indicated an increase in boas' plasma glucose one day after meal intake compared to unfed snakes. The hepatic glycogen reserves were continuously restored within days after feeding. Also, the enzymes involved in the energetic pathways increased activity six days after feeding in the liver. These findings suggest a quick restoring pattern of energetic stores during the postprandial period.

Employment and Careers of European Chemists (ESEC2).

Employment conditions and career opportunities are in the focus of the new Employment Survey for European Chemists (ESEC2). Conditions and opportunities are individually analysed for all countries with a statistically significant number of responses. The results provide important clues for careers in these countries and in Europe as a whole. The importance of employer sectors varies very much between European countries. A chapter of this report is devoted to career planning of students and new graduates. This is the first general evaluation of the survey. It provides many details about the chemistry workforce in Europe and its development.

Niche analyses and the potential distribution of four invasive bumblebees worldwide.

The introduction of bees for agricultural production in distinct parts of the world and poor management have led to invasion processes that affect biodiversity, significantly impacting native species. Different Bombus species with invasive potential have been recorded spreading in different regions worldwide, generating ecological and economic losses. We applied environmental niche and potential distribution analyses to four species of the genus Bombus to evaluate the similarities and differences between their native and invaded ranges. We found that B. impatiens has an extended environmental niche, going from dry environmental conditions in the native range to warmer and wetter conditions in the invaded range. Bombus ruderatus also exhibited an extended environmental niche with drier and warmer conditions in the invaded range than in its native range. Bombus subterraneus expanded its environmental niche from cooler and wetter conditions in the native range to drier and warmer conditions in the invaded range. Finally, B. terrestris showed the most significant variation in the environmental niche, extending to areas with similar and different environmental conditions from its native range. The distribution models agreed with the known distributions for the four Bombus species, presenting geographic areas known to be occupied by each species in different regions worldwide. The niche analysis indicate shifts in the niches from the native to the invaded distribution area of the bee species. Still, niche similarities were observed in the areas of greatest suitability in the potential distribution for B. ruderatus, B. subterraneus, and B. terrestris, and to a lesser degree in the same areas with B. impatiens. These species require similar environmental conditions as in their native ranges to be established in their introduced ranges. Still, they can adapt to changes in temperature and humidity, allowing them to expand their ranges into new climatic conditions.

Morphological and physiological traits of the respiratory system in Iguana iguana and other non-avian reptiles.

Functional morphology considers form and function to be intrinsically related. To understand organismal functions, a detailed knowledge of morphological and physiological traits is necessary. Regarding the respiratory system, the combined knowledge about pulmonary morphology and respiratory physiology is fundamental to understand how animals exchange gases and regulate critical functions to sustain metabolic activity. In the present study, the paucicameral lungs of Iguana iguana were analyzed morphometrically through stereological analysis using light and transmission electron images and compared with unicameral and multicameral lungs of six other non-avian reptiles. The morphological data were combined with physiological information to perform a principal component analysis (PCA) and phylogenetic tests of the relationship of the respiratory system. Iguana iguana, Lacerta viridis, and Salvator merianae presented similar pulmonary morphologies and physiologies when compared to Varanus examthematicus, Gekko gecko, Trachemys scripta, and Crocodylus niloticus. The former species showed an elevated respiratory surface area (%AR), a high diffusion capacity, a low volume of total parenchyma (VP), a low percentage of parenchyma concerning the lung volume (VL), and a higher surface/volume ratio of the parenchyma (SAR/VP), with high respiratory frequency (fR) and consequently total ventilation. The total parenchymal surface area (SA), effective parenchymal surface-to-volume ratio (SAR/VP), respiratory surface area (SAR), and anatomical diffusion factor (ADF) showed a phylogenetic signal, evidence that the morphological traits are more strongly correlated with the species' phylogeny than the physiological traits. In sum, our results indicated that the pulmonary morphology is intrinsically related to physiological traits of the respiratory system. Furthermore, phylogenetic signal tests also indicate that morphological traits are more likely to be evolutionary conserved than physiological traits, suggesting that evolutive physiological adaptations in the respiratory system could happen faster than morphological changes.

The role of protected areas in maintaining natural vegetation in Brazil.

The destruction of natural vegetation in recent decades has been concentrated in the tropics, where ecosystem processes underpin global homeostasis and harbor most of the world's biodiversity. Protected areas (PAs) are the primary societal tool to avoid this destruction, yet their effectiveness is often questioned. Here, we quantified the impact of PAs and indigenous lands in avoiding 34 years of vegetation destruction in forested and nonforested biomes in Brazil. We showed that the odds of destruction in the PA network are four times lower than in unprotected areas, and generally, this positive effect extends to a buffer zone around PAs. Among the most effective groups of PAs are those that are older, larger, located in the Amazonian region, and indigenous lands. Despite recent setbacks for the Brazilian PA system, we highlight the benefits of PAs for biodiversity and climate if they were instead strengthened.

Development of Multi-Scale Carbon Nanofiber and Nanotube-Based Cementitious Composites for Reliable Sensing of Tensile Stresses.

In this work, multi-scale cementitious composites containing short carbon fibers (CFs) and carbon nanofibers (CNFs)/multi-walled carbon nanotubes (MWCNTs) were studied for their tensile stress sensing properties. CF-based composites were prepared by mixing 0.25, 0.5 and 0.75 wt.% CFs (of cement) with water using magnetic stirring and Pluronic F-127 surfactant and adding the mixture to the cement paste. In multi-scale composites, CNFs/MWCNTs (0.1 and 0.15 wt.% of cement) were dispersed in water using Pluronic F-127 and ultrasonication and CFs were then added before mixing with the cement paste. All composites showed a reversible change in the electrical resistivity with tensile loading; the electrical resistivity increased and decreased with the increase and decrease in the tensile load/stress, respectively. Although CF-based composites showed the highest stress sensitivity among all specimens at 0.25% CF content, the fractional change in resistivity (FCR) did not show a linear correlation with the tensile load/stress. On the contrary, multi-scale composites containing CNFs (0.15% CNFs with 0.75% CFs) and MWCNTs (0.1% MWCNTs with 0.5% CFs) showed good stress sensitivity, along with a linear correlation between FCR and tensile load/stress. Stress sensitivities of 6.36 and 11.82%/MPa were obtained for the best CNF and MWCNT-based multi-scale composite sensors, respectively.

Effects of polycyclic aromatic hydrocarbons on biomarker responses in Gambusia yucatana, an endemic fish from Yucatán Peninsula, Mexico.

Polycyclic aromatic hydrocarbons (PAHs) are petroleum components that, when dissolved in the aquatic environment, can disrupt normal animal physiological functions and negatively affect species populations. Gambusia yucatana is an endemic fish of the Yucatán Peninsula that seems to be particularly sensitive to the presence of PAHs dissolved in the water. Here, we examined PAH effects on gene expressions linked to endocrine disruption and biotransformation in this species. Specifically, we examined the expression of vitellogenin I (vtg1), vitellogenin II (vtg2), oestrogen receptor α (esr1), oestrogen receptor ß (esr2), aryl hydrocarbon receptor (AhR) and the cytochrome P4503A (CYP3A) genes. We exposed G. yucatana to different concentrations of PAHs (3.89, 9.27, 19.51 µg/L) over a period of 72 h and found changes associated with reproduction, such as increases in hepatic expression of vtg, esr, AhR and CYP3A, mainly at concentrations of 9.27 and 19.51 µg/L. Our results also indicate that benzo[a]pyrene was probably the main PAH responsible for the observed effects. The genes examined here can be used as molecular markers of endocrine-disrupting compounds, as the PAHs, present in the environment, as gene expression increases could be observed as early as after 24 h. These biomarkers can help researchers and conservationists rapidly identify the impacts of oil spills and improve mitigation before the detrimental effects of environmental stressors become irreversible.

Knowledge gaps hamper understanding the relationship between fragmentation and biodiversity loss: the case of Atlantic Forest fruit-feeding butterflies.

BACKGROUND: A key challenge for conservation biology in the Neotropics is to understand how deforestation affects biodiversity at various levels of landscape fragmentation. Addressing this challenge requires expanding the coverage of known biodiversity data, which remain to date restricted to a few well-surveyed regions. Here, we assess the sampling coverage and biases in biodiversity data on fruit-feeding butterflies at the Brazilian Atlantic Forest, discussing their effect on our understanding of the relationship between forest fragmentation and biodiversity at a large-scale. We hypothesize that sampling effort is biased towards large and connected fragments, which occur jointly in space at the Atlantic forest. METHODS: We used a comprehensive dataset of Atlantic Forest fruit-feeding butterfly communities to test for sampling biases towards specific geographical areas, climate conditions and landscape configurations. RESULTS: We found a pattern of geographical aggregation of sampling sites, independently of scale, and a strong sampling bias towards large and connected forest fragments, located near cities and roads. Sampling gaps are particularly acute in small and disconnected forest fragments and rare climate conditions. In contrast, currently available data can provide a fair picture of fruit-feeding butterfly communities in large and connected Atlantic Forest remnants. DISCUSSION: Biased data hamper the inference of the functional relationship between deforestation and biodiversity at a large-scale, since they are geographically clustered and have sampling gaps in small and disconnected fragments. These data are useful to inform decision-makers regarding conservation efforts to curb biodiversity loss in the Atlantic Forest. Thus, we suggest to expand sampling effort to small and disconnected forest fragments, which would allow more accurate evaluations of the effects of landscape modification.

Pathways to social inequality.

Social inequality is ubiquitous in contemporary human societies, and has deleterious social and ecological impacts. However, the factors that shape the emergence and maintenance of inequality remain widely debated. Here we conduct a global analysis of pathways to inequality by comparing 408 non-industrial societies in the anthropological record (described largely between 1860 and 1960) that vary in degree of inequality. We apply structural equation modelling to open-access environmental and ethnographic data and explore two alternative models varying in the links among factors proposed by prior literature, including environmental conditions, resource intensification, wealth transmission, population size and a well-documented form of inequality: social class hierarchies. We found support for a model in which the probability of social class hierarchies is associated directly with increases in population size, the propensity to use intensive agriculture and domesticated large mammals, unigeniture inheritance of real property and hereditary political succession. We suggest that influence of environmental variables on inequality is mediated by measures of resource intensification, which, in turn, may influence inequality directly or indirectly via effects on wealth transmission variables. Overall, we conclude that in our analysis a complex network of effects are associated with social class hierarchies.

Cultural transmission and ecological opportunity jointly shaped global patterns of reliance on agriculture.

The evolution of agriculture improved food security and enabled significant increases in the size and complexity of human groups. Despite these positive effects, some societies never adopted these practices, became only partially reliant on them, or even reverted to foraging after temporarily adopting them. Given the critical importance of climate and biotic interactions for modern agriculture, it seems likely that ecological conditions could have played a major role in determining the degree to which different societies adopted farming. However, this seemingly simple proposition has been surprisingly difficult to prove and is currently controversial. Here, we investigate how recent agricultural practices relate both to contemporary ecological opportunities and the suitability of local environments for the first species domesticated by humans. Leveraging a globally distributed dataset on 1,291 traditional societies, we show that after accounting for the effects of cultural transmission and more current ecological opportunities, levels of reliance on farming continue to be predicted by the opportunities local ecologies provided to the first human domesticates even after centuries of cultural evolution. Based on the details of our models, we conclude that ecology probably helped shape the geography of agriculture by biasing both human movement and the human-assisted dispersal of domesticates.

The role of ecological niche evolution on diversification patterns of birds distinctly distributed between the Amazonia and Atlantic rainforests.

The Amazonian and Atlantic Forest share several organisms that are currently isolated but were continuously distributed during the Quaternary period. As both biomes are under different climatic regimes, paleoclimatic events may have modulated species' niches due to a lack of gene flow and imposing divergent selection pressure. Here, we assessed patterns of ecological niche overlap in 37 species of birds with disjunct ranges between the Amazonian and Brazilian Atlantic Forests. We performed niche overlap analysis and ecological niche modeling using four machine-learning algorithms to evaluate whether species' ecological niches evolved or remained conserved after the past South American biogeographic events. We found a low niche overlap among the same species populations in the two biomes. However, niche similarity tests showed that, for half of the species, the overlap was higher than the ones generated by our null models. These results lead us to conclude that niche conservatism was not enough to avoid ecological differentiation among species even though detected in many species. In sum, our results support the role of climatic changes in late-Pleistocene-that isolated Amazon and the Atlantic Forest-as a driving force of ecological differences among the same species populations and potential mechanism of current diversification in both regions.

Integrating Computational Methods to Investigate the Macroecology of Microbiomes.

Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as "everything is everywhere, but the environment selects") as well as applied ecological problems, such as those posed by human induced global environmental changes.

Hindcasting global population densities reveals forces enabling the origin of agriculture.

The development and spread of agriculture changed fundamental characteristics of human societies1-3. However, the degree to which environmental and social conditions enabled the origins of agriculture remains contested4-6. We test three hypothesized links between the environment, population density and the origins of plant and animal domestication, a prerequisite for agriculture: (1) domestication arose as environmental conditions improved and population densities increased7 (surplus hypothesis); (2) populations needed domestication to overcome deteriorating environmental conditions (necessity hypothesis)8,9; (3) factors promoting domestication were distinct in each location10 (regional uniqueness hypothesis). We overcome previous data limitations with a statistical model, in which environmental, geographic and cultural variables capture 77% of the variation in population density among 220 foraging societies worldwide. We use this model to hindcast potential population densities across the globe from 21,000 to 4,000 years before present. Despite the timing of domestication varying by thousands of years, we show that improving environmental conditions favoured higher local population densities during periods when domestication arose in every known agricultural origin centre. Our results uncover a common, global factor that facilitated one of humanity's most significant innovations and demonstrate that modelling ancestral demographic changes can illuminate major events deep in human history.

The global geography of human subsistence.

How humans obtain food has dramatically reshaped ecosystems and altered both the trajectory of human history and the characteristics of human societies. Our species' subsistence varies widely, from predominantly foraging strategies, to plant-based agriculture and animal husbandry. The extent to which environmental, social and historical factors have driven such variation is currently unclear. Prior attempts to resolve long-standing debates on this topic have been hampered by an over-reliance on narrative arguments, small and geographically narrow samples, and by contradictory findings. Here we overcome these methodological limitations by applying multi-model inference tools developed in biogeography to a global dataset (818 societies). Although some have argued that unique conditions and events determine each society's particular subsistence strategy, we find strong support for a general global pattern in which a limited set of environmental, social and historical factors predicts an essential characteristic of all human groups: how we obtain our food.

Spatial relationships between above-ground biomass and bird species biodiversity in Palawan, Philippines.

This study maps distribution and spatial congruence between Above-Ground Biomass (AGB) and species richness of IUCN listed conservation-dependent and endemic avian fauna in Palawan, Philippines. Grey Level Co-Occurrence Texture Matrices (GLCMs) extracted from Landsat and ALOS-PALSAR were used in conjunction with local field data to model and map local-scale field AGB using the Random Forest algorithm (r = 0.92 and RMSE = 31.33 Mg·ha-1). A support vector regression (SVR) model was used to identify the factors influencing variation in avian species richness at a 1km scale. AGB is one of the most important determinants of avian species richness for the study area. Topographic factors and anthropogenic factors such as distance from the roads were also found to strongly influence avian species richness. Hotspots of high AGB and high species richness concentration were mapped using hotspot analysis and the overlaps between areas of high AGB and avian species richness was calculated. Results show that the overlaps between areas of high AGB with high IUCN red listed avian species richness and endemic avian species richness were fairly limited at 13% and 8% at the 1-km scale. The overlap between 1) low AGB and low IUCN richness, and 2) low AGB and low endemic avian species richness was higher at 36% and 12% respectively. The enhanced capacity to spatially map the correlation between AGB and avian species richness distribution will further assist the conservation and protection of forest areas and threatened avian species.

Using ecological niche models and niche analyses to understand speciation patterns: the case of sister neotropical orchid bees.

The role of past connections between the two major South American forested biomes on current species distribution has been recognized a long time ago. Climatic oscillations that further separated these biomes have promoted parapatric speciation, in which many species had their continuous distribution split, giving rise to different but related species (i.e., different potential distributions and realized niche features). The distribution of many sister species of orchid bees follow this pattern. Here, using ecological niche models and niche analyses, we (1) tested the role of ecological niche differentiation on the divergence between sister orchid-bees (genera Eulaema and Eufriesea) from the Amazon and Atlantic forests, and (2) highlighted interesting areas for new surveys. Amazonian species occupied different realized niches than their Atlantic sister species. Conversely, species of sympatric but distantly related Eulaema bees occupied similar realized niches. Amazonian species had a wide potential distribution in South America, whereas Atlantic Forest species were more limited to the eastern coast of the continent. Additionally, we identified several areas in need of future surveys. Our results show that the realized niche of Atlantic-Amazonian sister species of orchid bees, which have been previously treated as allopatric populations of three species, had limited niche overlap and similarity. These findings agree with their current taxonomy, which treats each of those populations as distinct valid species.

Body size, extinction risk and knowledge bias in New World snakes.

Extinction risk and body size have been found to be related in various vertebrate groups, with larger species being more at risk than smaller ones. We checked whether this was also the case for snakes by investigating extinction risk-body size relationships in the New World's Colubroidea species. We used the IUCN Red List risk categories to assign each species to one of two broad levels of threat (Threatened and Non-Threatened) or to identify it as either Data Deficient or Not-Evaluated by the IUCN. We also included the year of description of each species in our analysis as this could affect the level of threat assigned to it (earlier described species had more time to gather information about them, which might have facilitated their evaluation). Also, species detectability could be a function of body size, with larger species tending to be described earlier, which could have an impact in extinction risk-body size relationships. We found a negative relationship between body size and description year, with large-bodied species being described earlier. Description year also varied among risk categories, with Non-Threatened species being described earlier than Threatened species and both species groups earlier than Data Deficient species. On average, Data Deficient species also presented smaller body sizes, while no size differences were detected between Threatened and Non-Threatened species. So it seems that smaller body sizes are related with species detectability, thus potentially affecting both when a species is described (smaller species tend to be described more recently) as well as the amount of information gathered about it (Data Deficient species tend to be smaller). Our data also indicated that if Data Deficient species were to be categorized as Threatened in the future, snake body size and extinction risk would be negatively related, contrasting with the opposite pattern commonly observed in other vertebrate groups.