Top 10 Biorxiv Papers Today in Ecology


2.015 Mikeys
#1. Risks to pollinators from different land-use transitions: bee species' responses to agricultural expansion show strong phylogenetic signal
Adriana De Palma, Michael Kuhlmann, William D Pearse, Emma Flynn, Stuart P.M. Roberts, Simon G Potts, Andy Purvis
Bee species worldwide are facing a future of further land-use change and intensification. Populations of closely-related species with similar ecological characteristics are likely to respond similarly to such pressures. Such phylogenetic signal in species' responses could undermine the stability of pollination services in agricultural and natural systems. We use abundance data from a global compilation of bee assemblages in different land uses to assess the sensitivity of 573 bee species to agricultural expansion, intensification and urbanization; and combine the results with the Bee Tree of Life to assess phylogenetic signal. In addition, we assess whether variation in species' sensitivity to land-use change is better explained by phylogenetic or available functional trait differences. Bee species show strong phylogenetic signal in sensitivity to agricultural land expansion but only a weak signal in sensitivity to agricultural intensification and urbanisation. Sensitivities were usually best explained by a combination of...
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biorxivpreprint: Risks to pollinators from different land-use transitions: bee species' responses to agricultural expansion show strong phylogenetic signal https://t.co/BlvqiCbGO9 #bioRxiv
biorxiv_ecology: Risks to pollinators from different land-use transitions: bee species' responses to agricultural expansion show strong phylogenetic ... https://t.co/sz3GyGH9h9 #biorxiv_ecology
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Sample Sizes : None.
Authors: 7
Total Words: 8697
Unqiue Words: 3420

2.014 Mikeys
#2. Landscape-scale simulations as a tool in multi-criteria decision making for agri-environment schemes
Chris Topping, Lars Dalby, Jose Valdez
Increasing concerns over the environmental impacts of agriculture in Europe has led to the introduction of agri-environment schemes (AES) to help mitigate biodiversity loss. However, effectiveness of AES has been mixed and only partially successful in achieving desired outcomes. To improve effectiveness and reduce high costs, multi-criteria decision analysis (MCDA) can help support decision-making and determine the most effective management action. Although MCDA has great potential for evaluating policy measures, it rarely considers the context-dependency of species responses to management practices across different landscapes. Landscape simulations can, therefore, be valuable for reducing the uncertainties when predicting the consequences of management actions. A potential suitable simulation system is the Animal, Landscape and Man Simulation System (ALMaSS), a mechanistic simulation with can improve MCDA with the automatic integration of a species ecology and behaviour and landscape context. The aim of this study was to...
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biorxivpreprint: Landscape-scale simulations as a tool in multi-criteria decision making for agri-environment schemes https://t.co/RzdNUsRaH3 #bioRxiv
biorxiv_ecology: Landscape-scale simulations as a tool in multi-criteria decision making for agri-environment schemes https://t.co/sABnuIFcM3 #biorxiv_ecology
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Sample Sizes : None.
Authors: 3
Total Words: 8551
Unqiue Words: 2930

2.013 Mikeys
#3. Metabolic rates of prokaryotic microbes may inevitably rise with global warming
Thomas P Smith, Thomas J H Thomas, Bernardo Garcia-Carreras, Sofia Sal, Gabriel Yvon-Durocher, Thomas Bell, Samraat Pawar
Understanding how the metabolic rates of prokaryotes respond to temperature is fundamental to our understanding of how ecosystem functioning will be altered by climate change, as these micro-organisms are major contributors to global carbon efflux. Ecological metabolic theory suggests that species living at higher temperatures evolve higher growth rates than those in cooler niches due to thermodynamic constraints. Here, using a global prokaryotic dataset, we find that maximal growth rate at thermal optimum increases with temperature for mesophiles (temperature optima ≲ 45°C), but not thermophiles (≳ 45°C). Furthermore, short-term (within-day) thermal responses of prokaryotic metabolic rates are typically more sensitive to warming than those of eukaryotes. Given that climatic warming will mostly impact ecosystems in the mesophilic temperature range, we conclude that as microbial communities adapt to higher temperatures, their metabolic rates and therefore, carbon efflux, will inevitably rise. Using a mathematical model, we...
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biorxivpreprint: Metabolic rates of prokaryotic microbes may inevitably rise with global warming https://t.co/7fwygBr7eD #bioRxiv
biorxiv_ecology: Metabolic rates of prokaryotic microbes may inevitably rise with global warming https://t.co/jWYPfGwqaA #biorxiv_ecology
kztakemoto: Metabolic rates of prokaryotic microbes may inevitably rise with global warming https://t.co/BPioKiZN92
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Authors: 7
Total Words: 9556
Unqiue Words: 3102

2.009 Mikeys
#4. Ponds, puddles, floodplains and dams in the Upper Xingu Basin: could we be witnessing the 'lentification' of deforested Amazonia?
Luis Cesar Schiesari, Paulo R. Ilha, Daniel Din Betin Negri, Paulo Inácio Prado, Britta Grillitsch
Hydrological change is a conspicuous signal of land use intensification in human-dominated landscapes. We hypothesized that land conversion and land use change increase the availability of lentic habitats and associated biodiversity in Southern Amazonian landscapes through at least four drivers. River damming promotes the formation of reservoirs, which are novel permanent lentic water bodies. A rise in the water table driven by local deforestation promotes the expansion of shallow riparian floodplains. Soil compaction and the deliberate construction of cattle and drainage ponds promote the increase in temporary water bodies in interfluvia. We tested these hypotheses using data on habitat characterization and biological surveys of amphibians and fish in forests, pastures and soybean fields in the headwaters of the Xingu River in Mato Grosso, Brazil. Lentic habitat availability sharply increased in deforested land, with consequences to freshwater biodiversity. Reservoir formation influenced both fish and amphibian assemblage...
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biorxivpreprint: Ponds, puddles, floodplains and dams in the Upper Xingu Basin: could we be witnessing the 'lentification' of deforested Amazonia? https://t.co/iYlog5MuhJ #bioRxiv
biorxiv_ecology: Ponds, puddles, floodplains and dams in the Upper Xingu Basin: could we be witnessing the 'lentification' of deforested Amazonia? https://t.co/OKKsGr9C9U #biorxiv_ecology
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Sample Sizes : [18]
Authors: 5
Total Words: 11061
Unqiue Words: 3887

2.008 Mikeys
#5. The Regime Shift Detector: a model to identify changes in dynamic rules governing populations
Christie A Bahlai, Elise F Zipkin
Environmental factors may interact with internal rules of population regulation, sometimes perturbing systems to alternate dynamic states. Yet, pinpointing when state changes occur in naturally fluctuating populations is difficult. An analytical approach that can identify the timing and magnitude of such changes, or "regime shifts", would facilitate understanding of abrupt ecological transitions with potential to inform conservation and management of species. We developed a generalizable model, the "Regime Shift Detector", for identifying changes in the parameters of a simple density dependent model governing the temporal fluctuations of a population. The model is a tool comprised of a suite of functions for examining population time series data for the presence, location, and magnitude of parameter shifts. The model uses an iterative approach to fitting subsets of time series data, then ranks the fit of a particular break point combination using model selection and assigns a relative weight to each break. We examined the...
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biorxivpreprint: The Regime Shift Detector: a model to identify changes in dynamic rules governing populations https://t.co/e1CHkfMLib #bioRxiv
biorxiv_ecology: The Regime Shift Detector: a model to identify changes in dynamic rules governing populations https://t.co/Y1BtISxh4s #biorxiv_ecology
cbahlai: The Regime Shift Detector: a model to identify changes in dynamic rules governing populations https://t.co/bBrr8oB3a4
cbahlai: RT @biorxivpreprint: The Regime Shift Detector: a model to identify changes in dynamic rules governing populations https://t.co/e1CHkfMLib…
cbahlai: RT @biorxiv_ecology: The Regime Shift Detector: a model to identify changes in dynamic rules governing populations https://t.co/Y1BtISxh4s…
ZipkinLab: RT @cbahlai: The Regime Shift Detector: a model to identify changes in dynamic rules governing populations https://t.co/bBrr8oB3a4
Github

A new tool for detecting changes in dynamic rules in population time series data

Repository: monarch_regime
User: cbahlai
Language: R
Stargazers: 2
Subscribers: 2
Forks: 1
Open Issues: 0
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Authors: 2
Total Words: 7799
Unqiue Words: 2309

2.0 Mikeys
#6. Dominant coral bacterium Endozoicomonas acroporae metabolizes DMSP
Kshitij Tandon, Pei-Wen Chiang, Chih-Ying Lu, Shan-Hua Yang, Ya-Fan Chen, Naohisa Wada, Ping-Yun Chen, Hsiao-Yu Chang, Ming-Shean Chou, Wen-Ming Chen, Sen-Lin Tang
Dominant coral associated Endozoicomonas bacteria species have been long hypothesized to play a role in the global sulfur cycle by metabolizing Dimethylsulfoniopropionate (DMSP) into Dimethylsulfide (DMS), which releases sulfur into the atmosphere; however, no sequenced genome to date harbors genes for this process. We assembled high-quality (>95 % complete) genomes of two new strains (Acr-1 and Acr-5) of a recently added species Endozoicomonas acroporae isolated from the coral Acropora muricata . We identified and functionally characterized the first DMSP lyase;a dddD gene homolog found in all E. acroporae , capable of metabolizing DMSP into DMS via the DddD cleavage pathway using qPCR and GC-MS. Comparative genomic analysis identified that Endozoicomonas has high genomic divergence and a high percentage oxidative stress responsive genes and that E. acroporae strains have the highest number of Type III secretion system genes (T3SS) in the genus. This study confirms the role of the genus Endozoicomonas in the global sulfur cycle.
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biorxivpreprint: Dominant coral bacterium Endozoicomonas acroporae metabolizes DMSP https://t.co/xLzUddSRM4 #bioRxiv
biorxiv_ecology: Dominant coral bacterium Endozoicomonas acroporae metabolizes DMSP https://t.co/uJazBIH7lW #biorxiv_ecology
jcamthrash: Dominant coral bacterium Endozoicomonas acroporae metabolizes DMSP https://t.co/vbsEdyyRfP
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Authors: 11
Total Words: 2496
Unqiue Words: 1138

1.999 Mikeys
#7. Mosquito and primate ecology predict human risk of yellow fever virus spillover in Brazil
Marissa L Childs, Nicole Nova, Justine Colvin, Erin A Mordecai
Many (re)emerging infectious diseases in humans arise from pathogen spillover from wildlife or livestock, and accurately predicting pathogen spillover is an important public health goal. In the Americas, yellow fever in humans primarily occurs following spillover from non-human primates via mosquitoes. Predicting yellow fever spillover can improve public health responses through vector control and mass vaccination. Here, we develop and test a mechanistic model of pathogen spillover to predict human risk for yellow fever in Brazil. Our environmental risk model, based on the ecology of mosquito vectors and non-human primate hosts, distinguished municipality-months with yellow fever spillover from 2001 to 2016 with high accuracy (AUC = 0.71). Incorporating hypothesized cyclical dynamics of infected primates improved accuracy (AUC = 0.79). Using boosted regression trees to identify gaps in the mechanistic model, we found that important predictors include current and lagged (mechanistic) environmental risk, vaccine coverage, population...
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morde: New preprint: Mosquito and primate ecology predict human risk of yellow fever virus spillover in Brazil. Combines heterogeneous data sources to model each of the key bottlenecks on spillover https://t.co/JsiPSvuQcq
DiogoProvete: RT @biorxiv_ecology: Mosquito and primate ecology predict human risk of yellow fever virus spillover in Brazil https://t.co/fKKn0AyOJ5 #bi…
Github

Code and data for "Mosquito and primate ecology predict human risk of yellow fever virus spillover in Brazil"

Repository: YellowFeverSpillover
User: marissachilds
Language: R
Stargazers: 0
Subscribers: 0
Forks: 0
Open Issues: 0
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Authors: 4
Total Words: 8809
Unqiue Words: 2702

1.998 Mikeys
#8. Disharmony of the world's island floras
Christian Koenig, Patrick Weigelt, Amanda Taylor, Anke Stein, Wayne Dawson, Franz Essl, Jan Pergl, Petr Pysek, Mark van Kleunen, Marten Winter, Cyrille Chatelain, Jan J. Wieringa, Pavel Krestov, Holger Kreft
Disharmony is a key concept in island biology that describes the biased representation of higher taxa on islands compared to their mainland source regions. Although differential colonization success of taxa is predicted by selective dispersal, environmental and biotic filtering, the empirical evidence for disharmony remains largely anecdotal. Here, we develop a novel method for delineating island source regions and present the first global quantitative assessment of island disharmony. We analyzed the overall compositional bias of 320 island floras and examined the over- or under-representation on islands for 450 plant families. We found that the compositional bias of island floras is strongly predicted by geographical and climatic island characteristics (isolation, area, geologic origin, temperature, precipitation), whereas the representation of individual families is only weakly related to family-specific characteristics (family size, family age, taxonomic group, functional traits), indicating that the taxonomic scope of the...
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biorxivpreprint: Disharmony of the world's island floras https://t.co/2uv2MUEnOS #bioRxiv
biorxiv_ecology: Disharmony of the world's island floras https://t.co/eBiQ52G7w0 #biorxiv_ecology
Ana_Maria_BU: RT @biorxiv_ecology: Disharmony of the world's island floras https://t.co/eBiQ52G7w0 #biorxiv_ecology
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Authors: 14
Total Words: 8968
Unqiue Words: 2957

1.998 Mikeys
#9. Understanding the variation in wood densities of trees and its implications for carbon assessments
Karthik Teegalapalli, Chandan Kumar Pandey, Anand Osuri, Jayashree Ratnam, Mahesh Sankaran
Aims: Wood density is a key functional trait used to estimate aboveground biomass (AGB) and carbon stocks. A common practice in forest AGB and carbon estimation is to substitute genus averages (across species with known wood densities) in cases where wood densities of particular species are unknown. However, the extent to which genus-level averages are reflective of species wood densities across tree genera is uncertain, and understanding this is critical for estimating the accuracy of carbon stock estimates. Using primary field data from India and secondary data from a published global dataset, we quantified the extent to which wood density varied among individuals within species (intraspecific variation) at the regional scale and among species within genera (interspecific variation) at regional to global scales. Methods: We used a published global database with wood density data for 7743 species belonging to 1741 genera. Linear models were used to compare the species values with the genera averages and the individual values with...
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Authors: 5
Total Words: 4469
Unqiue Words: 1199

1.996 Mikeys
#10. Changes in fungal communities across a forest disturbance gradient
Lingling Shi, Dossa G.O Gbadamassi, Paudel Ekananda, Huadong Zang, Jianchu Xu, Rhett D Harrison
Deforestation has a substantial impact on above ground biodiversity, but the response of below ground soil fungi remains poorly understood. In a tropical montane rainforest in southwestern China, plots were established along a forest degradation gradient ranging from mature and regenerated forests to open land to examine the impacts of forest degradation and deforestation on ecosystem diversity and function. Here, we evaluate the changes in below ground fungal diversity and community composition using a metabarcoding approach. Soil saprotrophic fungal richness declined with increasing forest disturbance. For example, Penicillium spp (Phosphorus (P) solubilizing fungi) dominated in mature forest, but were less abundant in regenerating forest and showed the lowest abundance in open land sites. Conversely, the abundance of facultative pathogenic fungi increased along the disturbance gradient. The decline in soil saprophytic fungi may be a direct result of forest disturbance or it may be associated with increased availability of soil...
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Sample Sizes : None.
Authors: 6
Total Words: 9862
Unqiue Words: 3725

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