pinecone/core-2020-05-10-deduplication huggingface dataset:
Toward a methodical framework for comprehensively assessing forest multifunctionality

Biodiversity-ecosystem functioning (BEF) research has extended its scope from communities that are short-lived or reshape their structure annually to structurally complex forest ecosystems. The establishment of tree diversity experiments poses specific methodological challenges for assessing the multiple functions provided by forest ecosystems. In particular, methodological inconsistencies and nonstandardized protocols impede the analysis of multifunctionality within, and comparability across the increasing number of tree diversity experiments. By providing an overview on key methods currently applied in one of the largest forest biodiversity experiments, we show how methods differing in scale and simplicity can be combined to retrieve consistent data allowing novel insights into forest ecosystem functioning. Furthermore, we discuss and develop recommendations for the integration and transferability of diverse methodical approaches to present and future forest biodiversity experiments. We identified four principles that should guide basic decisions concerning method selection for tree diversity experiments and forest BEF research: (1) method selection should be directed toward maximizing data density to increase the number of measured variables in each plot. (2) Methods should cover all relevant scales of the experiment to consider scale dependencies of biodiversity effects. (3) The same variable should be evaluated with the same method across space and time for adequate larger-scale and longer-time data analysis and to reduce errors due to changing measurement protocols. (4) Standardized, practical and rapid methods for assessing biodiversity and ecosystem functions should be promoted to increase comparability among forest BEF experiments. We demonstrate that currently available methods provide us with a sophisticated toolbox to improve a synergistic understanding of forest multifunctionality. However, these methods require further adjustment to the specific requirements of structurally complex and long-lived forest ecosystems. By applying methods connecting relevant scales, trophic levels, and above- and belowground ecosystem compartments, knowledge gain from large tree diversity experiments can be optimized
Nitrogen loss from karst area in China in recent 50 years: An in-situ simulated rainfall experiment's assessment

Karst topography covers more than 1/3 of the People's Republic of China in area. The porous, fissured, and soluble nature of the underlying karst bedrock (primarily dolomite and limestone) leads to the formation of underground drainage systems. Karst conduit networks dominate this system, and rainfall takes a crucial role on water cycle at China karst area. Nitrogen loss from the karst system is of particular concern, with regard to nutrient use efficiency as well as water quality, as much of the karst system, including steeply sloping terrain, is used for intensive agriculture. We use simulated rainfall experiments to determine the relationship between rainfall and nitrogen loss at typical karst slope land and then estimate nitrogen loss from the karst soil. The results show that both surface runoff and subsurface runoff have a significant linear correlation with rainfall at all studied sites. Subsurface runoff is larger than surface runoff at two karst sites, while the opposite is true at the non‐karst site. Exponential function satisfactorily described the correlation between rainfall and nitrogen concentrations in runoff. Nitrates accounted for 60%–95% of the dissolved nitrogen loss (DN, an index of N‐loss in this research). The estimated annual N‐loss load varies between 1.05 and 1.67 Tg N/year in the whole karst regions of China from 1961 to 2014. Approximately, 90% of the N‐loss load occurred during the wet season, and 90% of that passed through the subsurface. Understanding the processes and estimating N‐loss is highly valuable in determining long‐term soil security and sustainability in karst regions.&nbsp
Population genomics of the Asian tiger mosquito, Aedes albopictus: insights into the recent worldwide invasion

Aedes albopictus, the “Asian tiger mosquito,” is an aggressive biting mosquito native to Asia that has colonized all continents except Antarctica during the last ~30–40 years. The species is of great public health concern as it can transmit at least 26 arboviruses, including dengue, chikungunya, and Zika viruses. In this study, using double-digest Restriction site-Associated DNA (ddRAD) sequencing, we developed a panel of ~58,000 single nucleotide polymorphisms (SNPs) based on 20 worldwide Ae. albopictus populations representing both the invasive and the native range. We used this\ud
genomic-based approach to study the genetic structure and the differentiation of Ae. albopictus populations and to understand origin(s) and dynamics of the recent invasions. Our analyses indicated the existence of two major genetically differentiated population clusters, each one including both native and invasive populations. The detection of additional genetic structure within each major cluster supports that these NPs can detect differentiation at a global and local scale, while the similar levels of genomic diversity between native and invasive range populations support the scenario of multiple invasions or colonization by a large number of propagules. Finally, our results revealed the possible source(s) of the recent invasion in Americas, Europe, and Africa, a finding with important implications for vector-control strategies
Rainfall can explain adaptive phenotypic variation with high gene flow in the New Holland Honeyeater (Phylidonyris novaehollandiae)

Identifying environmentally driven changes in traits that serve an ecological function is essential for predicting evolutionary outcomes of climate change. We examined population genetic structure, sex-specific dispersal patterns, and morphology in relation to rainfall patterns across an island and three peninsulas in South Australia. The study system was the New Holland Honeyeater (Phylidonyris novaehollandiae), a nectarivorous passerine that is a key pollinator species. We predicted that rainfall-related mechanisms would be driving local adaptation of morphological traits, such that in areas of lower rainfall, where nectar is less available, more insectivorous traits – shorter, deeper bills, longer tarsi, and longer wings – would be favored. The study populations differed in phenotype across the Eyre, Yorke, and Fleurieu Peninsulas and Kangaroo Island despite high gene flow (single continuous population) and sex-biased dispersal (males were philopatric and females dispersed). We tested the role of rainfall in shaping the observed phenotypic differences, and found strong support for our predicted relationships: birds in areas of higher rainfall had higher condition indices, as well as longer bill-head length, deeper bills, and shorter tarsi. Bill depth in males in high-rainfall sites showed signals of stabilizing selection, suggesting local adaptation. In addition to these local indications of selection, a global pattern of directional selection toward larger size for bill-head length, bill-nostril length, and wing length was also observed. We suggest this pattern may reflect an adaptive response to the relatively dry conditions that South Australia has experienced over the last decade. We conclude that rainfall has shaped aspects of phenology in P. novaehollandiae, both locally, with different patterns of stabilizing and directional selection, and globally, with evidence of adaptive divergence at a landscape scale.Steven A. Myers, Stephen Donnellan and Sonia Kleindorfe
The origins of Atlantic salmon (Salmo salar L.) recolonizing the River Mersey in northwest England.

notes: PMCID: PMC3492779types: Journal Article© 2012 The Authors. Ecology and Evolution published by Blackwell Publishing Ltd.

This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.By the 1950s, pollution had extirpated Atlantic salmon in the river Mersey in northwest England. During the 1970s, an extensive restoration program began and in 2001, an adult salmon was caught ascending the river. Subsequently, a fish trap was installed and additional adults are now routinely sampled. In this study, we have genotyped 138 adults and one juvenile salmon at 14 microsatellite loci from across this time period (2001-2011). We have used assignment analysis with a recently compiled pan-European microsatellite baseline to identify their most probable region of origin. Fish entering the Mersey appear to originate from multiple sources, with the greatest proportion (45-60%, dependent on methodology) assigning to rivers in the geographical region just north of the Mersey, which includes Northwest England and the Solway Firth. Substantial numbers also appear to originate from rivers in western Scotland, and from rivers in Wales and Southwest England; nonetheless, the number of fish originating from proximal rivers to the west of the Mersey was lower than expected. Our results suggest that the majority of salmon sampled in the Mersey are straying in a southerly direction, in accordance with the predominantly clockwise gyre present in the eastern Irish Sea. Our findings highlight the complementary roles of improving water quality and in-river navigability in restoring salmon to a river and underlines further the potential benefits of restoration over stocking as a long-term solution to declining fish stocks.The Environment Agency (England & Wales)The Game and Wildlife Conservation TrustThe Westcountry Rivers TrustThe University of Exete
Inducing broadcast coral spawning ex situ: Closed system mesocosm design and husbandry protocol.

For many corals, the timing of broadcast spawning correlates strongly with a number of environmental signals (seasonal temperature, lunar, and diel cycles). Robust experimental studies examining the role of these putative cues in triggering spawning have been lacking until recently because it has not been possible to predictably induce spawning in fully closed artificial mesocosms. Here, we present a closed system mesocosm aquarium design that utilizes microprocessor technology to accurately replicate environmental conditions, including photoperiod, seasonal insolation, lunar cycles, and seasonal temperature from Singapore and the Great Barrier Reef (GBR), Australia. Coupled with appropriate coral husbandry, these mesocosms were successful in inducing, for the first time, broadcast coral spawning in a fully closed artificial ex situ environment. Four Acropora species (A. hyacinthus, A. tenuis, A. millepora, and A. microclados) from two geographical locations, kept for over 1 year, completed full gametogenic cycles ex situ. The percentage of colonies developing oocytes varied from ~29% for A. hyacinthus to 100% for A. millepora and A. microclados. Within the Singapore mesocosm, A. hyacinthus exhibited the closest synchronization to wild spawning, with all four gravid colonies releasing gametes in the same lunar month as wild predicted dates. Spawning within the GBR mesocosm commenced at the predicted wild spawn date but extended over a period of 3 months. Gamete release in relation to the time postsunset for A. hyacinthus, A. millepora, and A. tenuis was consistent with time windows previously described in the wild. Spawn date in relation to full moon, however, was delayed in all species, possibly as a result of external light pollution. The system described here could broaden the number of institutions on a global scale, that can access material for broadcast coral spawning research, providing opportunities for institutions distant from coral reefs to produce large numbers of coral larvae and juveniles for research purposes and reef restoration efforts
Receptor uptake arrays for vitamin B12, siderophores and glycans shape
  bacterial communities

Molecular variants of vitamin B12, siderophores and glycans occur. To take up
variant forms, bacteria may express an array of receptors. The gut microbe
Bacteroides thetaiotaomicron has three different receptors to take up variants
of vitamin B12 and 88 receptors to take up various glycans. The design of
receptor arrays reflects key processes that shape cellular evolution.
Competition may focus each species on a subset of the available nutrient
diversity. Some gut bacteria can take up only a narrow range of carbohydrates,
whereas species such as B.~thetaiotaomicron can digest many different complex
glycans. Comparison of different nutrients, habitats, and genomes provide
opportunity to test hypotheses about the breadth of receptor arrays. Another
important process concerns fluctuations in nutrient availability. Such
fluctuations enhance the value of cellular sensors, which gain information
about environmental availability and adjust receptor deployment. Bacteria often
adjust receptor expression in response to fluctuations of particular
carbohydrate food sources. Some species may adjust expression of uptake
receptors for specific siderophores. How do cells use sensor information to
control the response to fluctuations? That question about regulatory wiring
relates to problems that arise in control theory and artificial intelligence.
Control theory clarifies how to analyze environmental fluctuations in relation
to the design of sensors and response systems. Recent advances in deep learning
studies of artificial intelligence focus on the architecture of regulatory
wiring and the ways in which complex control networks represent and classify
environmental states. I emphasize the similar design problems that arise in
cellular evolution, control theory, and artificial intelligence. I connect
those broad concepts to testable hypotheses for bacterial uptake of B12,
siderophores and glycans.Comment: Added many new references, edited throughou
Mind the gap! Integrating taxonomic approaches to assess ant diversity at the southern extreme of the Atlantic Forest

Understanding patterns of species diversity rely on accurate taxonomy which can only be achieved by long-term natural history research and the use of complementary information to establish species boundaries among cryptic taxa. We used DNA barcoding to characterize the ant diversity of Iguazú National Park (INP), a protected area of the Upper Paraná Atlantic Forest ecoregion, located at the southernmost extent of this forest. We assessed ant diversity using both cytochrome c oxidase subunit 1 (COI) sequences and traditional morphological approaches and then compared the results of these two methods. We successfully obtained COI sequences for 312 specimens belonging to 124 species, providing a DNA barcode reference library for nearly 50% of the currently known ant fauna of INP. Our results evidenced a clear barcode gap for all but two species, with a mean intraspecific divergence of 0.72%, and an average congeneric distance of 17.25%. Congruently, the library assembled here was remarkably useful for the discrimination of the ants of INP and even allowed us to link unidentified males and queens to their worker castes. To detect overlooked diversity, we classified the DNA barcodes into Molecular Operational Taxonomic Units (MOTUs) using three different clustering algorithms and then compared their number and composition to that of reference species identified based on morphology. The MOTU count was always higher than that of reference species regardless of the method, suggesting that the diversity of ants at INP could be between 6% and 10% higher than currently recognized. Lastly, our survey contributed with 78 new barcode clusters to the global DNA barcode reference library, and added 36 new records of ant species for the INP, being 23 of them new citations for Argentina.Fil: Hanisch, Priscila Elena. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaFil: Lavinia Oblanca, Pablo Damián. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaFil: Suarez, Andrew. University of Illinois; Estados UnidosFil: Lijtmaer, Dario Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaFil: Leponce, Maurice. Royal Belgian Institute of Natural Sciences; BélgicaFil: Paris, Carolina Ivon. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; ArgentinaFil: Tubaro, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentin
Predictions of response to temperature are contingent on model choice and data quality

The equations used to account for the temperature dependence of biological processes, including growth and metabolic rates, are the foundations of our predictions of how global biogeochemistry and biogeography change in response to global climate change. We review and test the use of 12 equations used to model the temperature dependence of biological processes across the full range of their temperature response, including supra- and suboptimal temperatures. We focus on fitting these equations to thermal response curves for phytoplankton growth but also tested the equations on a variety of traits across a wide diversity of organisms. We found that many of the surveyed equations have comparable abilities to fit data and equally high requirements for data quality (number of test temperatures and range of response captured) but lead to different estimates of cardinal temperatures and of the biological rates at these temperatures. When these rate estimates are used for biogeographic predictions, differences between the estimates of even the best-fitting models can exceed the global biological change predicted for a decade of global warming. As a result, studies of the biological response to global changes in temperature must make careful consideration of model selection and of the quality of the data used for parametrizing these models
Gut microbiota composition is associated with environmental landscape in honey bees.

There is growing recognition that the gut microbial community regulates a wide variety of important functions in its animal hosts, including host health. However, the complex interactions between gut microbes and environment are still unclear. Honey bees are ecologically and economically important pollinators that host a core gut microbial community that is thought to be constant across populations. Here, we examined whether the composition of the gut microbial community of honey bees is affected by the environmental landscape the bees are exposed to. We placed honey bee colonies reared under identical conditions in two main landscape types for 6 weeks: either oilseed rape farmland or agricultural farmland distant to fields of flowering oilseed rape. The gut bacterial communities of adult bees from the colonies were then characterized and compared based on amplicon sequencing of the 16S rRNA gene. While previous studies have delineated a characteristic core set of bacteria inhabiting the honey bee gut, our results suggest that the broad environment that bees are exposed to has some influence on the relative abundance of some members of that microbial community. This includes known dominant taxa thought to have functions in nutrition and health. Our results provide evidence for an influence of landscape exposure on honey bee microbial community and highlight the potential effect of exposure to different environmental parameters, such as forage type and neonicotinoid pesticides, on key honey bee gut bacteria. This work emphasizes the complexity of the relationship between the host, its gut bacteria, and the environment and identifies target microbial taxa for functional analyses
Nutrient stoichiometry and land use rather than species richness determine plant functional diversity

Ajuts: Deutsche Forschungsgemeinschaft. Grant Numbers: FI 1246/6‐1, HO 3830/2‐1, KL 2265/5‐1 - TRY initiative on plant traits DIVERSITAS/Future Earth and the German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig - Open Access Publication Fund of University of Muenster.Plant functional traits reflect individual and community ecological strategies. They allow the detection of directional changes in community dynamics and ecosystemic processes, being an additional tool to assess biodiversity than species richness. Analysis of functional patterns in plant communities provides mechanistic insight into biodiversity alterations due to anthropogenic activity. Although studies have consi‐dered of either anthropogenic management or nutrient availability on functional traits in temperate grasslands, studies combining effects of both drivers are scarce. Here, we assessed the impacts of management intensity (fertilization, mowing, grazing), nutrient stoichiometry (C, N, P, K), and vegetation composition on community‐weighted means (CWMs) and functional diversity (Rao's Q) from seven plant traits in 150 grasslands in three regions in Germany, using data of 6 years. Land use and nutrient stoichiometry accounted for larger proportions of model variance of CWM and Rao's Q than species richness and productivity. Grazing affected all analyzed trait groups; fertilization and mowing only impacted generative traits. Grazing was clearly associated with nutrient retention strategies, that is, investing in durable structures and production of fewer, less variable seed. Phenological variability was increased. Fertilization and mowing decreased seed number/mass variability, indicating competition‐related effects. Impacts of nutrient stoichiometry on trait syndromes varied. Nutrient limitation (large N:P, C:N ratios) promoted species with conservative strategies, that is, investment in durable plant structures rather than fast growth, fewer seed, and delayed flowering onset. In contrast to seed mass, leaf‐economics variability was reduced under P shortage. Species diversity was positively associated with the variability of generative traits. Synthesis. Here, land use, nutrient availability, species richness, and plant functional strategies have been shown to interact complexly, driving community composition, and vegetation responses to management intensity. We suggest that deeper understanding of underlying mechanisms shaping community assembly and biodiversity will require analyzing all these parameters