text:
agenda for conserving biodiversity in human-modified tropical landscapes}},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1744-7429.2008.00471.x/full},
volume = {41},
year = {2008}
}
@article{Whitmee2013,
author = {Whitmee, Sarah and Orme, C. David L.},
doi = {10.1111/j.1365-2656.2012.02030.x},
editor = {Humphries, Murray},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Whitmee, Orme - 2013 - Predicting dispersal distance in mammals a trait-based approach.pdf:pdf},
issn = {00218790},
journal = {Journal of Animal Ecology},
month = {jan},
number = {1},
pages = {211--221},
title = {{Predicting dispersal distance in mammals: a trait-based approach}},
url = {http://doi.wiley.com/10.1111/j.1365-2656.2012.02030.x},
volume = {82},
year = {2013}
}
@article{McRae2017,
abstract = {As threats to species continue to increase, precise and unbiased measures of the impact these pressures are having on global biodiversity are urgently needed. Some existing indicators of the status and trends of biodiversity largely rely on publicly available data from the scientific and grey literature, and are therefore prone to biases introduced through over-representation of well-studied groups and regions in monitoring schemes. This can give misleading estimates of biodiversity trends. Here, we report on an approach to tackle taxonomic and geographic bias in one such indicator (Living Planet Index) by accounting for the estimated number of species within biogeographical realms, and the relative diversity of species within them. Based on a proportionally weighted index, we estimate a global population decline in vertebrate species between 1970 and 2012 of 58{\%} rather than 20{\%} from an index with no proportional weighting. From this data set, comprising 14,152 populations of 3,706 species from 3,095 data sources, we also find that freshwater populations have declined by 81{\%}, marine populations by 36{\%}, and terrestrial populations by 38{\%} when using proportional weighting (compared to trends of -46{\%}, +12{\%} and +15{\%} respectively). These results not only show starker declines than previously estimated, but suggests that those species for which there is poorer data coverage may be declining more rapidly.},
author = {McRae, Louise and Deinet, Stefanie and Freeman, Robin},
doi = {10.1371/journal.pone.0169156},
editor = {Doi, Hideyuki},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/McRae, Deinet, Freeman - 2017 - The Diversity-Weighted Living Planet Index Controlling for Taxonomic Bias in a Global Biodiversity Indic.pdf:pdf},
isbn = {1111111111},
issn = {1932-6203},
journal = {PLOS ONE},
month = {jan},
number = {1},
pages = {e0169156},
pmid = {28045977},
title = {{The Diversity-Weighted Living Planet Index: Controlling for Taxonomic Bias in a Global Biodiversity Indicator}},
url = {http://dx.plos.org/10.1371/journal.pone.0169156},
volume = {12},
year = {2017}
}
@article{Frund2010,
abstract = {In the face of global decline in biodiversity, the relationship between diversity and species interactions deserves particular attention. If pollinators are strongly dependent on floral diversity due to mutual specialization, declines in plant diversity, e.g. caused by land use intensification, may be associated with linked extinctions of pollinators. However, the general extent of pollinator specialization is still poorly known. To explore the dependence of local bee and hoverfly communities on flower diversity, we recorded flower supply and flower-visiting insects on 27 meadows with varying flower diversity in southern Germany and analyzed (a) whether the diversity of flower visitors is correlated with flower diversity, (b) whether the degree of dietary specialization of flower visitors changes with flower diversity and (c) whether flower preferences of individual flower visitor species are constant or variable between different communities. Flower–visitor interaction webs were compiled during a single day on each meadow. This approach prevents relating pollinator species to flowers they never encounter because of non-overlapping phenology or spatial segregation. (a) Flower diversity and flower visitor diversity were positively correlated. (b) Flower visitor assemblies were significantly specialized at a relatively high level, contrasting to the opinion that plant–pollinator webs are highly generalized, and providing a possible explanation for the positive diversity correlation. However, the level of specialization did not change significantly across the gradient of flower diversity, suggesting that pollinators are partitioned to a similar extent in each meadow. (c) In the analysis of ten common flower visitor species previously categorized as generalists, strong evidence was found for both, consistent preferences and preferences that differ between sites. These results indicate a flexibility in flower preferences and a dynamic resource partitioning among pollinators. Generally, our findings highlight the complexity of plant–pollinator interactions and confirm the importance of flower diversity for bee and hoverfly communities.},
author = {Fr{\"{u}}nd, Jochen and Linsenmair, Karl Eduard and Bl{\"{u}}thgen, Nico},
doi = {10.1111/j.1600-0706.2010.18450.x},
file = {:C$\backslash$:/LocalStorage/References/2010/Fr{\"{u}}nd, Linsenmair, Bl{\"{u}}thgen{\_}2010{\_}Pollinator diversity and specialization in relation to flower diversity.pdf:pdf},
issn = {00301299},
journal = {Oikos},
keywords = {Community,Paper,Pollination,diversity,network analyses},
mendeley-tags = {Paper},
month = {oct},
number = {10},
pages = {1581--1590},
publisher = {Wiley Online Library},
title = {{Pollinator diversity and specialization in relation to flower diversity}},
url = {http://doi.wiley.com/10.1111/j.1600-0706.2010.18450.x http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0706.2010.18450.x/pdf},
volume = {119},
year = {2010}
}
@article{Steffan-Dewenter2001,
author = {Steffan-Dewenter, Ingolf and Tscharntke, Teja},
doi = {10.1034/j.1600-0587.2001.240110.x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Steffan-Dewenter, Tscharntke - 2001 - Succession of bee communities on fallows.pdf:pdf},
issn = {09067590},
journal = {Ecography},
keywords = {Bee,Pollination},
mendeley-tags = {Bee,Pollination},
month = {feb},
number = {1},
pages = {83--93},
title = {{Succession of bee communities on fallows}},
url = {http://doi.wiley.com/10.1034/j.1600-0587.2001.240110.x},
volume = {24},
year = {2001}
}
@article{Kerr2001,
abstract = {Although there is no shortage of potential explanations for the large-scale patterns of biological diversity, the hypothesis that energy-related factors are the primary determinants is perhaps most extensively supported, especially in cold-temperate regions. By using unusually high-resolution biodiversity and environmental data that have not previously been available, we demonstrate that habitat heterogeneity, as measured by remotely sensed land cover variation, explains Canadian butterfly richness better than any energy-related variable we measured across spatial scales. Although species-richness predictability declines with progressively smaller quadrat sizes, as expected, we demonstrate that most variability ({\textgreater}90{\%}) in butterfly richness may be explained by habitat heterogeneity with secondary contributions from climatic energy. We also find that patterns of community similarity across Canada are strongly related to patterns of habitat composition but not to differences in energy-related factors. Energy should still be considered significant but its main role may be through its effects on within-habitat diversity and perhaps, indirectly, on the sorts of habitats that may be found in a region. Effects of sampling intensity and spatial autocorrelation do not alter our findings.},
author = {Kerr, Jeremy T and Southwood, T R E and Cihlar, Josef},
doi = {10.1073/pnas.201398398},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Kerr, Southwood, Cihlar - 2001 - Remotely sensed habitat diversity predicts butterfly species richness and community similarity in Canad.pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
month = {sep},
number = {20},
pages = {11365--11370},
pmid = {11553792},
title = {{Remotely sensed habitat diversity predicts butterfly species richness and community similarity in Canada}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.201398398},
volume = {98},
year = {2001}
}
@article{Hurlbert1971,
abstract = {The recent literature on species diversity contains many semantic, conceptual, and technical problems. It is suggested that, as a result of these problems, species diversity has become a meaningless concept, that the term be abandoned, and that ecologists take a more critical approach to species?number relations and rely less on information theoretic and other analogies. As multispecific collections of organisms possess numerous statistical properties which conform to the conventional criteria for diversity indices, such collections are not intrinsically arrangeable in linear order along some diversity scale. Several such properties or "species composition parameters" having straightforward biological interpretations are presented as alternatives to the diversity approach. The two most basic of these are simply ?1=[n/n?1][1?$\Sigma$i(N{\_}i/{\_}N)2] =the proportion of potential interindividual encounters which is interspecific (as opposed to intraspecific), assuming every individual in the collection can encounter all other individuals, E(Sn) = $\Sigma$i [1?(N?Nin)/(Nn)] =the expected number of species in a sample of n individuals selected at random from a collection containing N individuals, S species, and Ni individuals in the ith species. See full-text article at JSTOR},
author = {Hurlbert, Stuart H},
doi = {10.2307/1934145},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Hurlbert - 1971 - The Nonconcept of Species Diversity A Critique and Alternative Parameters.pdf:pdf},
isbn = {0012-9658},
issn = {00129658},
journal = {Ecology},
month = {jul},
number = {4},
pages = {577--586},
pmid = {1484},
title = {{The Nonconcept of Species Diversity: A Critique and Alternative Parameters}},
url = {http://www.jstor.org/stable/1934145 http://doi.wiley.com/10.2307/1934145},
volume = {52},
year = {1971}
}
@article{McKinney1999,
abstract = {Human activities are not random in their negative and positive impacts on biotas. Emerging evidence shows that most species are declining as a result of human activities ('losers') and are being replaced by a much smaller number of expanding species that thrive in human-altered environments ('winners'). The result will be a more homogenized biosphere with lower diversity at regional and global scales. Recent data also indicate that the many losers and few winners tend to be non-randomly distributed among higher taxa and ecological groups, enhancing homogenization.},
author = {McKinney, Ml and Lockwood, Jl},
file = {:C$\backslash$:/LocalStorage/References/1999/McKinney, Lockwood{\_}1999{\_}Biotic homogenization a few winners replacing many losers in the next mass extinction.pdf:pdf},
issn = {0169-5347},
journal = {Trends in ecology {\&} evolution},
keywords = {Biotic Homogenization,Drivers of Homogenization,Homogenization,Paper,Study,biotic homogenization,divers},
mendeley-tags = {Biotic Homogenization,Homogenization,Paper,Study},
month = {nov},
number = {11},
pages = {450--453},
pmid = {10511724},
title = {{Biotic homogenization: a few winners replacing many losers in the next mass extinction.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10511724},
volume = {14},
year = {1999}
}
@article{Stanton2018,
abstract = {Globally, agriculture has intensified during the past 50 years due to increased mechanization, changes in the timing of farming operations, grassland conversion to cropland, and increased agrochemical inputs. Birds associated with farmlands and grasslands in North America have experienced severe declines over the last several decades, prompting the need for a comprehensive review of the drivers, mechanisms and magnitude of effects on bird populations. Here we evaluated changes in North American farmland bird populations over time and conducted a systematic review and analysis of the published literature to identify the major causes. Based on North American Breeding Bird Survey data, populations of 57 of 77 (74{\%}) farmland-associated species decreased from 1966 to 2013. Multiple species exhibited highly congruent declines during the 1960s-1980s − a period with rapid changes in farming practices to low tillage systems, heavy pesticide use and widespread conversion of grassland habitat to cropland. The most severe declines occurred in aerial insectivorous birds (average change of −39.5{\%} from 1966 to 2013), followed by grassland (‐20.8{\%}) and shrubland (‐16.5{\%}) bird species. Direct agricultural drivers impacting bird abundance, survival, and reproduction include loss of natural habitats, interference from farming equipment, and direct mortality or sublethal effects from pesticide exposure. Subtle interference with behaviour or physiology are reported through indirect drivers such as reduced food supplies, sublethal pesticide toxicity, habitat fragmentation and alteration, and disturbance. Indirect effects are likely significant for many species, particularly aerial insectivores, but detailed mechanistic studies are lacking. Our review of 122 studies found that pesticides (42{\%} of all studies), followed by habitat loss or alterations (27{\%}), were most predominant in negatively affecting farmland birds, with pesticides (93{\%} negative) and mowing/harvesting (81{\%} negative) having the most consistently negative effects. Modifications to farmland management such as reducing pesticide inputs through integrated pest management and maintaining or restoring uncultivated field margins and native habitat could positively influence farmland birds without significantly reducing agricultural crop yields.},
author = {Stanton, R.L. and Morrissey, C.A. and Clark, R.G.},
doi = {10.1016/j.agee.2017.11.028},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Stanton, Morrissey, Clark - 2018 - Analysis of trends and agricultural drivers of farmland bird declines in North America A review.pdf:pdf},
issn = {01678809},
journal = {Agriculture, Ecosystems {\&} Environment},
keywords = {Aerial insectivores,Agricultural intensification,Avian declines,Farmland birds,Grassland birds,Habitat loss,Pesticides},
month = {feb},
number = {November 2017},
pages = {244--254},
publisher = {Elsevier},
title = {{Analysis of trends and agricultural drivers of farmland bird declines in North America: A review}},
url = {https://doi.org/10.1016/j.agee.2017.11.028 http://linkinghub.elsevier.com/retrieve/pii/S016788091730525X},
volume = {254},
year = {2018}
}
@article{Kennedy2014,
author = {Kennedy, Robert E and Andr{\'{e}}fou{\"{e}}t, Serge and Cohen, Warren B and G{\'{o}}mez, Cristina and Griffiths, Patrick and Hais, Martin and Healey, Sean P and Helmer, Eileen H and Hostert, Patrick and Lyons, Mitchell B and Meigs, Garrett W and Pflugmacher, Dirk and Phinn, Stuart R and Powell, Scott L and Scarth, Peter and Sen, Susmita and Schroeder, Todd A and Schneider, Annemarie and Sonnenschein, Ruth and Vogelmann, James E and Wulder, Michael A and Zhu, Zhe},
doi = {10.1890/130066},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Kennedy et al. - 2014 - Bringing an ecological view of change to Landsat-based remote sensing.pdf:pdf},
issn = {1540-9295},
journal = {Frontiers in Ecology and the Environment},
month = {aug},
number = {6},
pages = {339--346},
title = {{Bringing an ecological view of change to Landsat-based remote sensing}},
url = {http://www.esajournals.org/doi/abs/10.1890/130066},
volume = {12},
year = {2014}
}
@book{Venables2002,
abstract = {S-PLUS is a powerful environment for the statistical and graphical analysis of data. It provides the tools to implement many statistical ideas which have been made possible by the widespread availability of workstations having good graphics and computational ...},
address = {New York, New York, USA},
author = {Venables, W N and Ripley, B D},
booktitle = {New York},
edition = {4},
isbn = {0387954570},
publisher = {Springer},
title = {{Modern applied statistics with S}},
url = {http://www.stats.ox.ac.uk/pub/MASS4},
year = {2002}
}
@misc{Forkel2015,
author = {Forkel, Matthias and Wutzler, Thomas},
keywords = {Greening,Greening-to-browning reversal,r},
title = {{greenbrown - land surface phenology and trend analysis. A package for the R software}},
url = {http://greenbrown.r-forge.r-project.org/},
year = {2015}
}
@article{Martin2013,
abstract = {Both REDD+ and the Convention on Biological Diversity aim to enhance carbon stocks and biodiversity through tropical forest restoration. However, we lack evidence of the effectiveness of such management. Using data from tropical forest chronosequence and restoration studies we investigate the recovery of carbon pools and plant biodiversity in recovering forests and determine factors limiting recovery.},
author = {Martin, P. A. and Newton, A. C. and Bullock, J. M.},
doi = {10.1098/rspb.2013.2236},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Martin, Newton, Bullock - 2013 - Carbon pools recover more quickly than plant biodiversity in tropical secondary forests.pdf:pdf},
isbn = {0962-8452$\backslash$r1471-2954},
issn = {0962-8452},
journal = {Proceedings of the Royal Society B: Biological Sciences},
keywords = {ecology,environmental science},
month = {nov},
number = {1773},
pages = {20132236--20132236},
pmid = {24197410},
title = {{Carbon pools recover more quickly than plant biodiversity in tropical secondary forests}},
url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2013.2236},
volume = {280},
year = {2013}
}
@article{Elith2008,
abstract = {1. Ecologists use statistical models for both explanation and prediction, and need techniques that are flexible enough to express typical features of their data, such as nonlinearities and interactions. 2. This study provides a working guide to boosted regression trees (BRT), an ensemble method for fitting statistical models that differs fundamentally from conventional techniques that aim to fit a single parsimonious model. Boosted regression trees combine the strengths of two algorithms: regression trees (models that relate a response to their predictors by recursive binary splits) and boosting (an adaptive method for combining many simple models to give improved predictive performance). The final BRT model can be understood as an additive regression model in which individual terms are simple trees, fitted in a forward, stagewise fashion. 3. Boosted regression trees incorporate important advantages of tree-based methods, handling different types of predictor variables and accommodating missing data. They have no need for prior data transformation or elimination of outliers, can fit complex nonlinear relationships, and automatically handle interaction effects between predictors. Fitting multiple trees in BRT overcomes the biggest drawback of single tree models: their relatively poor predictive performance. Although BRT models are complex, they can be summarized in ways that give powerful ecological insight, and their predictive performance is superior to most traditional modelling methods. 4. The unique features of BRT raise a number of practical issues in model fitting. We demonstrate the practicalities and advantages of using BRT through a distributional analysis of the short-finned eel (Anguilla australis Richardson), a native freshwater fish of New Zealand. We use a data set of over 13 000 sites to illustrate effects of several settings, and then fit and interpret a model using a subset of the data. We provide code and a tutorial to enable the wider use of BRT by ecologists.},
author = {Elith, J and Leathwick, J R and Hastie, T},
doi = {10.1111/j.1365-2656.2008.01390.x},
file = {:C$\backslash$:/LocalStorage/References/2008/Elith, Leathwick, Hastie{\_}2008{\_}A working guide to boosted regression trees.pdf:pdf},
issn = {1365-2656},
journal = {The Journal of animal ecology},
keywords = {Anguilla,Anguilla: growth {\&} development,Anguilla: physiology,Animals,BRT,Biological,Boosted Regression Tree,Decision Trees,Ecology,Ecology: statistics {\&} numerical data,Method-Paper,Models,Regression Analysis,Statistical,Statistics as Topic},
mendeley-tags = {BRT,Boosted Regression Tree,Method-Paper},
month = {jul},
number = {4},
pages = {802--13},
pmid = {18397250},
title = {{A working guide to boosted regression trees.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18397250},
volume = {77},
year = {2008}
}
@article{Samain2008,
abstract = {The goal of this study is to demonstrate the asset in using a Kalman filter to improve the spatial coherence and time consistency of surface Bidirectional Reflectance Distribution Function (BRDF) and albedo retrievals from moderate resolution sensor data sets. For this purpose, we use a simple surface model describing BRDF seasonal evolution for the land cover classes of the ECOCLIMAP database. The application of temporal composition windows used so far for BRDF retrieval is limited in regions characterized by a high frequency of cloud coverage, which induces a lot of gaps in the temporal series. Instead, the present method ensures a continuous production of surface BRDF parameters thanks to the Kalman filter recursive data processing. An application of the method is performed with SPOT/VEGETATION data over the western Africa equatorial region for the year 2003. Compared to presently available products from VEGETATION and MODIS instruments, this new approach allows to fill the gaps and improves the retrieved parameters time consistency. Another interesting possibility of the Kalman filter is the production of surface biophysical variables in quasi-real-time for applications that require a frequent update of the surface parameters. ?? 2007 Elsevier Inc. All rights reserved.},
author = {Samain, O and Roujean, J and Geiger, B},
doi = {10.1016/j.rse.2007.07.007},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Samain, Roujean, Geiger - 2008 - Use of a Kalman filter for the retrieval of surface BRDF coefficients with a time-evolving model based.pdf:pdf},
issn = {00344257},
journal = {Remote Sensing of Environment},
keywords = {Kalman filter,Land surface BRDF},
month = {apr},
number = {4},
pages = {1337--1346},
title = {{Use of a Kalman filter for the retrieval of surface BRDF coefficients with a time-evolving model based on the ECOCLIMAP land cover classification}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0034425707003264},
volume = {112},
year = {2008}
}
@article{Hansen2014,
abstract = {Tropek et al. critique the Hansen et al. global forest loss paper in terms of its utility and accuracy. Both criticisms suffer from a miscomprehension of the definition of forest employed as well as the requirements of product validation. Utility of the product is enhanced through its integration with forest type, carbon stock, protected area status, and other ancillary data.},
archivePrefix = {arXiv},
arxivId = {1011.1669v3},
author = {Hansen, M and Potapov, P and Margono, B and Stehman, S and Turubanova, S and Tyukavina, A},
doi = {10.1126/science.1248817},
eprint = {1011.1669v3},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Hansen et al. - 2014 - Response to comment on High-resolution global maps of 21st-century forest cover change.pdf:pdf},
isbn = {1095-9203 (Electronic)$\backslash$n0036-8075 (Linking)},
issn = {1095-9203},
journal = {Science},
keywords = {Conservation of Natural Resources,Geographic Mapping,Maps as Topic,Trees},
number = {6187},
pages = {981},
pmid = {24876488},
title = {{Response to comment on "High-resolution global maps of 21st-century forest cover change".}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24876488},
volume = {344},
year = {2014}
}
@article{McCain2009,
abstract = {Aim Elevational gradients distributed across the globe are a powerful test system for understanding biodiversity. Here I use a comprehensive set of bird elevational gradients to test the main drivers of diversity, including sampling, area, mid-domain effect, temperature, temperature and water availability, and hypotheses of evolutionary history. Location Seventy-eight elevational gradients of bird diversity from mountains in both hemispheres spanning 24.5° S to 48.2° N, including gradients from various climates, biogeographical regions and habitat types. Methods Data on bird elevational diversity were taken from the literature. Of the 150 datasets found or compiled, only those with a high, unbiased sampling effort were used in analyses. Datasets sampled all birds, all breeding birds or all forest birds; a few studies detailed seasonal, elevational shifts. Eighteen predictions of diversity theory were tested, including three sets of interactions. Results Birds display four distinct diversity patterns in nearly equal frequency on mountains: decreasing diversity, low-elevation plateaus, low-elevation plateaus with mid-peaks, and unimodal mid-elevational peaks. Bird elevational diversity strongly supports current climate as the main driver of diversity, particularly combined trends in temperature and water availability. Bird diversity on humid mountains is either decreasing or shows a low-elevation plateau in diversity, while on dry mountains it is unimodal or a broad, low-elevation plateau usually with a mid-elevation maximum. The predictions of sampling, area and mid-domain effect were not consistently supported globally. The only evolutionary hypothesis with preliminary support was niche conservatism. Main conclusions Both water and temperature variables are needed to comprehensively predict elevational diversity patterns for birds. This result is consistent for breeding and forest birds, for both hemispheres, and for local- or regional-scale montane gradients. More analyses are needed to discern whether the mechanism underlying these relationships is ecological, based on direct physiological limitations or indirect food resource limitations, or historical, based on phylogenetic niche conservation or other evolutionary trends related to climate. The species–area and mid-domain effects are not supported as primary drivers of elevational diversity in birds.},
author = {McCain, Christy M.},
doi = {10.1111/j.1466-8238.2008.00443.x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/McCain - 2009 - Global analysis of bird elevational diversity.pdf:pdf},
isbn = {1466822X$\backslash$n14668238},
issn = {1466822X},
journal = {Global Ecology and Biogeography},
keywords = {Avian,Climate,Environmental gradient,Evolutionary history,Mid-domain effect,Mountains,Species richness,Species-area relationship,Temperature,Water availability},
month = {may},
number = {3},
pages = {346--360},
pmid = {3206},
title = {{Global analysis of bird elevational diversity}},
url = {http://doi.wiley.com/10.1111/j.1466-8238.2008.00443.x},
volume = {18},
year = {2009}
}
@article{Ellis2015a,
abstract = {Humans, unlike any other multicellular species in Earth's history, have emerged as a global force that is transforming the ecology of an entire planet. It is no longer possible to understand, predict, or successfully manage ecological pattern, process or change without understanding why and how humans reshape these over the long-term. Here, a general causal theory is presented to explain why human societies gained the capacity to globally alter the patterns, processes and dynamics of ecology and how these anthropogenic alterations unfold over time and space as societies themselves change over human generational time. Building on existing theories of ecosystem engineering, niche construction, inclusive inheritance, cultural evolution, ultrasociality, and social change, this theory of anthroecological change holds that sociocultural evolution of subsistence regimes based on ecosystem engineering, social specialization and nonkin exchange, or "sociocultural niche construction", is the main cause of both the long-term upscaling of human societies and their unprecedented transformation of the biosphere. Human sociocultural niche construction can explain, where classic ecological theory cannot, the sustained transformative effects of human societies on biogeography, ecological succession, ecosystem processes, and the ecological patterns and processes of landscapes, biomes and the biosphere. Anthroecology theory generates empirically testable hypotheses on the forms and trajectories of long-term anthropogenic ecological change that have significant theoretical and practical implications across the subdisciplines of ecology and conservation. Though still at an early stage of development, anthroecology theory aligns with and integrates established theoretical frameworks including social-ecological systems, social metabolism, countryside biogeography, novel ecosystems and anthromes. The "fluxes of nature" are fast becoming "cultures of nature". To investigate, understand, and address the ultimate causes of anthropogenic ecological change, not just the consequences, human sociocultural processes must become as much a part of ecological theory and practice as biological and geophysical processes are now. Strategies for achieving this goal and for advancing ecological science and conservation in an increasingly anthropogenic biosphere are presented.},
author = {Ellis, Erle C.},
doi = {10.1890/14-2274.1},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Ellis - 2015 - Ecology in an anthropogenic biosphere.pdf:pdf;:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Ellis - 2015 - Ecology in an anthropogenic biosphere(2).pdf:pdf},
issn = {0012-9615},
journal = {Ecological Monographs},
keywords = {anthropocene,anthropogenic landscapes,anthrosequence,archaeology,biodiversity,centennial paper,cultural inheritance,disturbance,ecosystems,extended evolutionary synthesis,human ecology,human impacts,human-dominated,it would be difficult,natural history,not to say impossible,to draw a},
number = {3},
pages = {287--331},
title = {{Ecology in an anthropogenic biosphere}},
url = {http://www.esajournals.org/doi/abs/10.1890/14-2274.1 http://www.esajournals.org/doi/10.1890/14-2274.1},
volume = {85},
year = {2015}
}
@article{Fritz2015,
author = {Fritz, Steffen and See, Linda and Mccallum, Ian a N and You, Liangzhi and Bun, Andriy and Moltchanova, Elena and Duerauer, Martina and Albrecht, Fransizka and Schill, Christian and Perger, Christoph and Havlik, Petr and Mosnier, Aline and Thornton, Philip and Wood-Sichra, Ulrike and Herrero, Mario and Becker-, Inbal and Becker-Reshef, Inbal and Justice, Chris and Hansen, Matthew and Gong, Peng and {Abdel Aziz}, Sheta and Cipriani, Anna and Cumani, Renato and Cecchi, Giuliano and Conchedda, Giulia and Ferreira, Stefanus and Gomez, Adriana and Haffani, Myriam and Kayitakire, Francois and Malanding, Jaiteh and Mueller, Rick and Newby, Terence and Nonguierma, Andre and Olusegun, Adeaga and Ortner, Simone and Rajak, D. Ram and Rocha, Jansle and Schepaschenko, Dmitry and Schepaschenko, Maria and Terekhov, Alexey and Tiangwa, Alex and Vancutsem, Christelle and Vintrou, Elodie and Wenbin, Wu and van der Velde, Marijn and Dunwoody, Antonia and Kraxner, Florian and Obersteiner, Michael},
doi = {10.1111/gcb.12838},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Fritz et al. - 2015 - Mapping global cropland and field size.pdf:pdf;:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Fritz et al. - 2015 - Mapping global cropland and field size(2).pdf:pdf},
issn = {13541013},
journal = {Global Change Biology},
keywords = {8 december 2014,agricultural intensity,cropland,data fusion,field size,land cover,november 2014 and accepted,received 29 july 2014,revised version received 30,synergy map},
month = {may},
number = {5},
pages = {1980--1992},
title = {{Mapping global cropland and field size}},
url = {http://doi.wiley.com/10.1111/gcb.12838},
volume = {21},
year = {2015}
}
@article{VANDERGAST2006,
author = {Vandergast, Amy G. and Bohonak, Andrew J. and Weissman, David B. and Fisher, Robert N.},
doi = {10.1111/j.1365-294X.2006.03216.x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Vandergast et al. - 2006 - Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history phyl.pdf:pdf},
issn = {09621083},
journal = {Molecular Ecology},
keywords = {2006,accepted 30 october 2006,anthropogenic habitat fragmentation,gene flow,genetic population structure,insect,quaternary inundation,received 14 july 2006,revision received 9 october,stenopelmatus,urbanization},
month = {dec},
number = {5},
pages = {977--992},
title = {{Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus)}},
url = {http://doi.wiley.com/10.1111/j.1365-294X.2006.03216.x},
volume = {16},
year = {2006}
}
@article{Sweet2015,
abstract = {The physical and biological responses to rapid arctic warming are proving acute, and as such, there is a need to monitor, understand, and predict ecological responses over large spatial and temporal scales. The use of the normalized difference vegetation index (NDVI) acquired from airborne and satellite sensors addresses this need, as it is widely used as a tool for detecting and quantifying spatial and temporal dynamics of tundra vegetation cover, productivity, and phenology. Such extensive use of the NDVI to quantify vegetation characteristics suggests that it may be similarly applied to characterizing primary and secondary consumer communities. Here, we develop empirical models to predict canopy arthropod biomass with canopy-level measurements of the NDVI both across and within distinct tundra vegetation communities over four growing seasons in the Arctic Foothills region of the Brooks Range, Alaska, USA. When canopy arthropod biomass is predicted with the NDVI across all four growing seasons, our over...},
author = {Sweet, Shannan K. and Asmus, Ashley and Rich, Matthew E. and Wingfield, John and Gough, Laura and Boelman, Natalie T.},
doi = {10.1890/14-0632.1},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Sweet et al. - 2015 - NDVI as a predictor of canopy arthropod biomass in the Alaskan arctic tundra.pdf:pdf},
issn = {1051-0761},
journal = {Ecological Applications},
keywords = {Alaska,Arctic region,Brooks Range foothills,Canopy arthropod biomass,Canopy reflectance,Landscape heterogeneity,Normalized difference vegetation index (NDVI),Tundra,USA},
month = {apr},
number = {3},
pages = {779--790},
title = {{NDVI as a predictor of canopy arthropod biomass in the Alaskan arctic tundra}},
url = {http://doi.wiley.com/10.1890/14-0632.1},
volume = {25},
year = {2015}
}
@article{Sørensen2011,
abstract = {In this paper, we develop a method, termed the Interaction Distribution (ID) method, for analysis of quantitative ecological network data. In many cases, quantitative network data sets are under-sampled, i.e. many interactions are poorly sampled or remain unobserved. Hence, the output of statistical analyses may fail to differentiate between patterns that are statistical artefacts and those which are real characteristics of ecological networks. The ID method can support assessment and inference of under-sampled ecological network data.In the current paper, we illustrate and discuss the ID method based on the properties of plant-animal pollination data sets of flower visitation frequencies. However, the ID method may be applied to other types of ecological networks. The method can supplement existing network analyses based on two definitions of the underlying probabilities for each combination of pollinator and plant species: (1), pi,j: the probability for a visit made by the i'th pollinator species to take place on the j'th plant species; (2), qi,j: the probability for a visit received by the j'th plant species to be made by the i'th pollinator. The method applies the Dirichlet distribution to estimate these two probabilities, based on a given empirical data set. The estimated mean valuesfor pi,jand qi,jreflect the relative differences between recorded numbers of visits for different pollinator and plant species, and the estimated uncertainty of pi,jand qi,jdecreases with higher numbers of recorded visits.},
author = {S{\o}rensen, Peter B and Damgaard, Christian F and Strandberg, Beate and Dupont, Yoko L and Marianne, B and Carvalheiro, Luisa G and Biesmeijer, Jacobus C and Olsen, Jens Mogens and Hagen, Melanie and Potts, G},
file = {:C$\backslash$:/LocalStorage/References/2011/S{\o}rensen et al.{\_}2011{\_}A method for under - sampled ecological network data analysis plant - pollination as case study.pdf:pdf},
journal = {Journal of Pollination Ecology},
keywords = {Bayesian method,Ecological network,plant-animal pollination data analysis,under-sampled data sets},
number = {December},
pages = {129--139},
title = {{A method for under - sampled ecological network data analysis: plant - pollination as case study}},
volume = {6},
year = {2011}
}
@article{Bowman2015,
author = {Bowman, David M.J.S. and Perry, George L.W. and Marston, J.B.},
doi = {10.1016/j.tree.2015.03.005},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Bowman, Perry, Marston - 2015 - Feedbacks and landscape-level vegetation dynamics.pdf:pdf},
issn = {01695347},
journal = {Trends in Ecology {\&} Evolution},
number = {5},
pages = {255--260},
publisher = {Elsevier Ltd},
title = {{Feedbacks and landscape-level vegetation dynamics}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534715000646},
volume = {30},
year = {2015}
}
@article{Vogt2007,
abstract = {We use morphological image process- ing for classifying spatial patterns at the pixel le- vel on binary land-cover maps. Land-cover pattern is classified as ‘perforated,' ‘edge,' ‘patch,' and ‘core' with higher spatial precision and the- matic accuracy compared to a previous approach based on image convolution, while retaining the capability to label these features at the pixel level for any scale of observation. The implementation of morphological image processing is explained and then demonstrated, with comparisons to results from image convolution, for a forest map of the Val Grande National Park in North Italy. Keywords},
author = {Vogt, Peter and Riitters, Kurt H. and Estreguil, Christine and Kozak, Jacek and Wade, Timothy G. and Wickham, James D.},
doi = {10.1007/s10980-006-9013-2},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Vogt et al. - 2007 - Mapping Spatial Patterns with Morphological Image Processing.pdf:pdf},
isbn = {0921-2973},
issn = {0921-2973},
journal = {Landscape Ecology},
keywords = {Forest fragmentation,Morphological image processing,Spatial pattern},
month = {jan},
number = {2},
pages = {171--177},
title = {{Mapping Spatial Patterns with Morphological Image Processing}},
url = {http://link.springer.com/10.1007/s10980-006-9013-2},
volume = {22},
year = {2007}
}
@article{Tsendbazar2015,
author = {Tsendbazar, Nandin-Erdene and de Bruin, Sytze and Fritz, Steffen and Herold, Martin},
doi = {10.3390/rs71215804},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Tsendbazar et al. - 2015 - Spatial Accuracy Assessment and Integration of Global Land Cover Datasets.pdf:pdf},
issn = {2072-4292},
journal = {Remote Sensing},
keywords = {data integration,geostatistics,global land cover,reference dataset,spatial accuracy},
month = {nov},
number = {12},
pages = {15804--15821},
title = {{Spatial Accuracy Assessment and Integration of Global Land Cover Datasets}},
url = {http://www.mdpi.com/2072-4292/7/12/15804},
volume = {7},
year = {2015}
}
@article{Nakagawa2013,
abstract = {1. The use of both linear and generalized linear mixed-effects models (LMMs and GLMMs) has become popular not only in social and medical sciences, but also in biological sciences, especially in the field of ecology and evolution. Information criteria, such as Akaike Information Criterion (AIC), are usually presented as model comparison tools for mixed-effects models. 2. The presentation of ‘variance explained' (R2) as a relevant summarizing statistic of mixed-effects models, however, is rare, even though R2 is routinely reported for linear models (LMs) and also generalized linear models (GLMs). R2 has the extremely useful property of providing an absolute value for the goodness-of-fit of a model, which cannot be given by the information criteria. As a summary statistic that describes the amount of variance explained, R2 can also be a quantity of biological interest. 3. One reason for the under-appreciation of R2 for mixed-effects models lies in the fact that R2 can be defined in a number of ways. Furthermore, most definitions of R2 for mixed-effects have theoretical problems (e.g. decreased or negative R2 values in larger models) and/or their use is hindered by practical difficulties (e.g. implementation). 4. Here, we make a case for the importance of reporting R2 for mixed-effects models. We first provide the common definitions of R2 for LMs and GLMs and discuss the key problems associated with calculating R2 for mixed-effects models. We then recommend a general and simple method for calculating two types of R2 (marginal and conditional R2) for both LMMs and GLMMs, which are less susceptible to common problems. 5. This method is illustrated by examples and can be widely employed by researchers in any fields of research, regardless of software packages used for fitting mixed-effects models. The proposed method has the potential to facilitate the presentation of R2 for a wide range of circumstances.},
author = {Nakagawa, Shinichi and Schielzeth, Holger},
doi = {10.1111/j.2041-210x.2012.00261.x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Nakagawa, Schielzeth - 2013 - A general and simple method for obtaining R 2 from generalized linear mixed-effects models.pdf:pdf},
isbn = {2041-210X},
issn = {2041210X},
journal = {Methods in Ecology and Evolution},
keywords = {Coefficient of determination,Goodness-of-fit,Heritability,Information criteria,Intra-class correlation,Linear models,Method-Paper,Model fit,Repeatability,Statistic,Variance explained},
mendeley-tags = {Method-Paper,Statistic},
month = {feb},
number = {2},
pages = {133--142},
title = {{A general and simple method for obtaining R 2 from generalized linear mixed-effects models}},
volume = {4},
year = {2013}
}
@article{Zhu2017,
abstract = {The free and open access to all archived Landsat images in 2008 has completely changed the way of using Landsat data. Many novel change detection algorithms based on Landsat time series have been developed We present a comprehensive review of four important aspects of change detection studies based on Landsat time series, including frequencies, preprocessing, algorithms, and applications. We observed the trend that the more recent the study, the higher the frequency of Landsat time series used. We reviewed a series of image preprocessing steps, including atmospheric correction, cloud and cloud shadow detection, and composite/fusion/metrics techniques. We divided all change detection algorithms into six categories, including thresholding, differencing, segmentation, trajectory classification, statistical boundary, and regression. Within each category, six major characteristics of different algorithms, such as frequency, change index, univariate/multivariate, online/offline, abrupt/gradual change, and sub-pixel/pixel/spatial were analyzed. Moreover, some of the widely-used change detection algorithms were also discussed. Finally, we reviewed different change detection applications by dividing these applications into two categories, change target and change agent detection.},
author = {Zhu, Zhe},
doi = {10.1016/j.isprsjprs.2017.06.013},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Zhu - 2017 - Change detection using landsat time series A review of frequencies, preprocessing, algorithms, and applications.pdf:pdf},
issn = {09242716},
journal = {ISPRS Journal of Photogrammetry and Remote Sensing},
keywords = {Change detection,Landsat,Review,Time series},
month = {aug},
pages = {370--384},
publisher = {International Society for Photogrammetry and Remote Sensing, Inc. (ISPRS)},
title = {{Change detection using landsat time series: A review of frequencies, preprocessing, algorithms, and applications}},
url = {http://dx.doi.org/10.1016/j.isprsjprs.2017.06.013 http://linkinghub.elsevier.com/retrieve/pii/S092427161730103X},
volume = {130},
year = {2017}
}
@article{Aizen2012,
abstract = {The loss of interactions from mutualistic networks could foreshadow both plant and animal species extinctions. Yet, the characteristics of interactions that predispose them to disruption are largely unknown. We analyzed 12 pollination webs from isolated hills ("sierras"), in Argentina, ranging from tens to thousands of hectares. We found evidence of nonrandom loss of interactions with decreasing sierra size. Low interaction frequency and high specialization between interacting partners contributed additively to increase the vulnerability of interactions to disruption. Interactions between generalists in the largest sierras were ubiquitous across sierras, but many of them lost their central structural role in the smallest sierras. Thus, particular configurations of interaction networks, along with unique ecological relations and evolutionary pathways, could be lost forever after habitat reduction.},
author = {Aizen, Marcelo a. and Sabatino, Malena and Tylianakis, JM Jason M.},
doi = {10.1126/science.1215320},
file = {:C$\backslash$:/LocalStorage/References/2012/Aizen, Sabatino, Tylianakis{\_}2012{\_}Specialization and rarity predict nonrandom loss of interactions from mutualist networks.pdf:pdf},
isbn = {0036-8075},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
keywords = {Animals,Argentina,Biodiversity,Biological Evolution,Ecosystem,Food Chain,Insects,Plant-Animal Network,Plants,Pollination,Population Dynamics,Symbiosis},
mendeley-tags = {Plant-Animal Network,Pollination},
month = {mar},
number = {6075},
pages = {1486--9},
pmid = {22442482},
title = {{Specialization and rarity predict nonrandom loss of interactions from mutualist networks.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22442482 http://www.sciencemag.org/content/335/6075/1486.short},
volume = {335},
year = {2012}
}
@article{Decocq2016,
author = {Decocq, Guillaume and Andrieu, Emilie and Brunet, J{\"{o}}rg and Chabrerie, Olivier and {De Frenne}, Pieter and {De Smedt}, Pallieter and Deconchat, Marc and Diekmann, Martin and Ehrmann, Steffen and Giffard, Brice and Mifsud, Elena Gorriz and Hansen, Karin and Hermy, Martin and Kolb, Annette and Lenoir, Jonathan and Liira, Jaan and Moldan, Filip and Prokofieva, Irina and Rosenqvist, Lars and Varela, Elsa and Vald{\'{e}}s, Alicia and Verheyen, Kris and Wulf, Monika},
doi = {10.1007/s40725-016-0028-x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Decocq et al. - 2016 - Ecosystem Services from Small Forest Patches in Agricultural Landscapes.pdf:pdf},
issn = {2198-6436},
journal = {Current Forestry Reports},
month = {jan},
title = {{Ecosystem Services from Small Forest Patches in Agricultural Landscapes}},
url = {http://link.springer.com/10.1007/s40725-016-0028-x},
volume = {In press},
year = {2016}
}
@misc{IUCN2016a,
abstract = {IUCN 2016. IUCN Red List of Threatened Species. Version 2016.1. {\textless}www.iucnredlist.org{\textgreater}.},
author = {IUCN},
pages = {www.iucnredlist.org},
title = {{IUCN 2016. The IUCN Red List of Threatened Species. Version 2016.1}},
url = {www.iucnredlist.org},
urldate = {2016-06-16},
year = {2016}
}
@article{Buckland2008,
abstract = {In many bird monitoring surveys, no attempt is made to estimate bird densities or abundance. Instead, counts of one form or another are made, and these are assumed to correlate with bird density. Unless complete counts on sample plots are feasible, this approach can easily lead to false conclusions, because detectability of birds varies by species, habitat, observer and many other factors. Trends in time of counts often reflect trends in detectability, rather than trends in abundance. Conclusions are further compromised when surveys are conducted at unrepresenta- tive sites. We consider how to avoid these problems. We give a brief description of distance sampling methods, which allow detectability to be estimated. We consider strategies to ease their implementation, to enhance their reliability, to adapt the methods for difficult species, and to deal with circumstances in which representative sampling is problematic. We also consider some of the common problems encountered, and suggest solutions.},
author = {Buckland, Stephen T. and Marsden, Stuart J. and Green, Rhys E.},
doi = {10.1017/S0959270908000294},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Buckland, Marsden, Green - 2008 - Estimating bird abundance making methods work.pdf:pdf},
isbn = {0959-2709},
issn = {0959-2709},
journal = {Bird Conservation International},
month = {sep},
number = {S1},
pages = {91--108},
title = {{Estimating bird abundance: making methods work}},
url = {http://www.journals.cambridge.org/abstract{\_}S0959270908000294},
volume = {18},
year = {2008}
}
@article{Jamali2015,
abstract = {Although satellite-based sensors have made vegetation data series available for several decades, the detection of vegetation trend and change is not yet straightforward. This is partly due to the scarcity of available change detection algorithms suitable for identifying and characterizing both abrupt and non-abrupt changes, without sacrificing accuracy or computational speed. We propose a user-friendly program for analysing vegetation time series, with two main application domains: generalising vegetation trends to main features, and characterizing vegetation trend changes. This program, Detecting Breakpoints and Estimating Segments in Trend (DBEST) uses a novel segmentation algorithm which simplifies the trend into linear segments using one of three user-defined parameters: a generalisation-threshold parameter ??, the m largest changes, or a threshold ?? for the magnitude of changes of interest for detection. The outputs of DBEST are the simplified trend, the change type (abrupt or non-abrupt), and estimates for the characteristics (time and magnitude) of the change. DBEST was tested and evaluated using simulated Normalized Difference Vegetation Index (NDVI) data at two sites, which included different types of changes. Evaluation results demonstrate that DBEST quickly and robustly detects both abrupt and non-abrupt changes, and accurately estimates change time and magnitude.DBEST was also tested using data from the Global Inventory Modeling and Mapping Studies (GIMMS) NDVI image time series for Iraq for the period 1982-2006, and was able to detect and quantify major change over the area. This showed that DBEST is able to detect and characterize changes over large areas. We conclude that DBEST is a fast, accurate and flexible tool for trend detection, and is applicable to global change studies using time series of remotely sensed data sets.},
author = {Jamali, Sadegh and J{\"{o}}nsson, Per and Eklundh, Lars and Ard{\"{o}}, Jonas and Seaquist, Jonathan},
doi = {10.1016/j.rse.2014.09.010},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Jamali et al. - 2015 - Detecting changes in vegetation trends using time series segmentation.pdf:pdf},
isbn = {0034-4257},
issn = {00344257},
journal = {Remote Sensing of Environment},
keywords = {Change detection,DBEST,GIMMS,NDVI,Satellite imagery,Segmentation,Time series,Trend analysis,Vegetation dynamics},
month = {jan},
pages = {182--195},
publisher = {Elsevier Inc.},
title = {{Detecting changes in vegetation trends using time series segmentation}},
url = {http://dx.doi.org/10.1016/j.rse.2014.09.010 http://linkinghub.elsevier.com/retrieve/pii/S0034425714003538},
volume = {156},
year = {2015}
}
@article{Bolker2009,
author = {Bolker, Benjamin M. and Brooks, Mollie E. and Clark, Connie J. and Geange, Shane W. and Poulsen, John R. and Stevens, M. Henry H. and White, Jada-Simone S.},
doi = {10.1016/j.tree.2008.10.008},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Bolker et al. - 2009 - Generalized linear mixed models a practical guide for ecology and evolution.pdf:pdf},
issn = {01695347},
journal = {Trends in Ecology {\&} Evolution},
month = {mar},
number = {3},
pages = {127--135},
title = {{Generalized linear mixed models: a practical guide for ecology and evolution}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534709000196},
volume = {24},
year = {2009}
}
@article{Newton2014,
author = {Newton, Erica J. and Pond, Bruce a. and Brown, Glen S. and Abraham, Kenneth F. and Schaefer, James a.},
doi = {10.1007/s00300-014-1472-3},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Newton et al. - 2014 - Remote sensing reveals long-term effects of caribou on tundra vegetation.pdf:pdf},
issn = {0722-4060},
journal = {Polar Biology},
keywords = {Exploitation ecosystem hypothesis,Grazing,NDVI,Normalized Difference Vegetation Index,Rangifer tarandus,Time lag},
month = {may},
number = {5},
pages = {715--725},
title = {{Remote sensing reveals long-term effects of caribou on tundra vegetation}},
url = {http://link.springer.com/10.1007/s00300-014-1472-3},
volume = {37},
year = {2014}
}
@article{Devictor2008,
abstract = {Aim Worldwide, functional homogenization is now considered to be one of the most prominent forms of biotic impoverishment induced by current global changes. Yet this process has hardly been quantified on a large scale through simple indices, and the connection between landscape disturbance and functional homogenization has hardly been established. Here we test whether changes in land use and landscape fragmentation are associated with functional homogenization of bird communities at a national scale. Location France. Methods We estimated functional homogenization of a community as the average specialization of the species present in that community. We studied the spatial variation of this community specialization index (CSI) using 1028 replicates from the French Breeding Bird Survey along spatial gradients of landscape fragmentation and recent landscape disturbance, measured independently, and accounting for spatial autocorrelation. Results The CSI was very sensitive to both measures of environmental degradation: on average, 23{\%} of the difference in the CSI values between two sample sites was attributed to the difference in fragmentation and the disturbance between sites. This negative correlation between CSI and sources of landscape degradation was consistent over various habitats and biogeographical zones. Main conclusions We demonstrate that the functional homogenization of bird communities is strongly positively correlated to landscape disturbance and fragmentation. We suggest that the CSI is particularly effective for measuring functional homogenization on both local and global scales for any sort of organism and with abundance or presence–absence data.},
author = {Devictor, Vincent and Julliard, Romain and Clavel, Joanne and Jiguet, Fr{\'{e}}d{\'{e}}ric and Lee, Alexandre and Couvet, Denis},
doi = {10.1111/j.1466-8238.2007.00364.x},
file = {:C$\backslash$:/LocalStorage/References/2008/Devictor et al.{\_}2008{\_}Functional biotic homogenization of bird communities in disturbed landscapes.pdf:pdf},
issn = {1466-822X},
journal = {Global Ecology and Biogeography},
keywords = {2010 target,Biodiversity indicator,Biotic Homogenization,France,Paper,biotic homogenization,bird,breeding bird survey,community,landscape disturbance,landscape fragmentation,specialization},
mendeley-tags = {Biotic Homogenization,Paper},
month = {mar},
number = {2},
pages = {252--261},
title = {{Functional biotic homogenization of bird communities in disturbed landscapes}},
url = {http://doi.wiley.com/10.1111/j.1466-8238.2007.00364.x},
volume = {17},
year = {2008}
}
@article{Fernandez2016,
author = {Fern{\'{a}}ndez, N{\'{e}}stor and Rom{\'{a}}n, Jacinto and Delibes, Miguel},
doi = {10.1098/rspb.2015.2998},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Fern{\'{a}}ndez, Rom{\'{a}}n, Delibes - 2016 - Variability in primary productivity determines metapopulation dynamics.pdf:pdf},
isbn = {0000000296458},
issn = {0962-8452},
journal = {Proceedings of the Royal Society B: Biological Sciences},
month = {apr},
number = {1828},
pages = {20152998},
title = {{Variability in primary productivity determines metapopulation dynamics}},
url = {http://rspb.royalsocietypublishing.org/lookup/doi/10.1098/rspb.2015.2998},
volume = {283},
year = {2016}
}
@article{Petermann2010,
abstract = {1. The consequences of species loss on ecosystem functioning within a single trophic level have been extensively studied. However, the loss of basal species is likely to have profound impacts on the abundance, richness and ecosystem functioning of species at higher trophic levels. 2. Here, we used experimentally established plant communities with a species richness gradient to study the effects of plant species loss on a multi-trophic insect community in the field. We measured densities and species richness of aphids and parasitic wasps (primary, secondary and facultative tertiary parasitoids of aphids) that naturally colonized the grassland plots. 3. Furthermore, we calculated two ecosystem functions: aphid load (the number of aphid individuals per host plant biomass used as a proxy for herbivory) and parasitism rate. We used structural equation models to explore pathways of direct and indirect effects of plant species richness on higher trophic levels. 4. We found that the densities and richness of species at all trophic levels were influenced by changes in plant species richness. The effects were rarely direct, but instead mediated by the abundance and species richness of aphid host plants and subsequent trophic levels. 5. The herbivore and primary parasitoid levels were most directly affected by changes in plant species richness, with highest insect densities and species richness occurring at intermediate plant species richness. The densities and species richness of secondary parasitoids declined linearly with plant species richness owing to sparser resources, resulting in shorter food chains in communities with the highest plant species richness. 6. Aphid load was highest at intermediate plant species richness and negatively affected by both host plant biomass and host plant species richness. Parasitism rate was mostly affected indirectly via aphid density and overall only weakly negatively related to plant species richness. 7. Our results demonstrate that plant species richness can have strong cascading effects up to high trophic levels. However, their direction may differ at the lower and higher ends of the plant species richness spectrum, cautioning against simplifying consequences of plant species loss for specialist food webs that may become limited by sparse resources at high plant richness.},
author = {Petermann, Jana S and M{\"{u}}ller, Christine B and Weigelt, Alexandra and Weisser, Wolfgang W and Schmid, Bernhard},
doi = {10.1111/j.1365-2656.2010.01674.x},
file = {:C$\backslash$:/LocalStorage/References/2010/Petermann et al.{\_}2010{\_}Effect of plant species loss on aphid-parasitoid communities.pdf:pdf},
issn = {1365-2656},
journal = {The Journal of animal ecology},
keywords = {Animals,Aphids,Aphids: parasitology,Biodiversity,Host-Parasite Interactions,Paper,Plants,Plants: classification,Plants: genetics,Study,Wasps,Wasps: physiology},
mendeley-tags = {Paper,Study},
month = {may},
number = {3},
pages = {709--20},
pmid = {20202014},
title = {{Effect of plant species loss on aphid-parasitoid communities.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20202014},
volume = {79},
year = {2010}
}
@article{Wood2013,
abstract = {The problem of testing smooth components of an extended generalized additive model for equality to zero is considered. Confidence intervals for such components exhibit good across-the-function coverage probabilities if based on the approximate result $\backslash$hat f(i) {\~{}} N{\{}f(i),V{\_}f(i,i){\}}, where f is the vector of evaluated values for the smooth component of interest and V{\_}f is the covariance matrix for f according to the Bayesian view of the smoothing process. Based on this result, a Wald-type test of f=0 is proposed. It is shown that care must be taken in selecting the rank used in the test statistic. The method complements previous work by extending applicability beyond the Gaussian case, while considering tests of zero effect rather than testing the parametric hypothesis given by the null space of the component's smoothing penalty. The proposed p-values are routine and efficient to compute from a fitted model, without requiring extra model fits or null distribution simulation.},
author = {Wood, Simon N.},
doi = {10.1093/biomet/ass048},
issn = {0006-3444},
journal = {Biometrika},
keywords = {-spline,Hypothesis test,Model selection,Semiparametric regression,Spline},
month = {mar},
number = {1},
pages = {221--228},
title = {{On p-values for smooth components of an extended generalized additive model}},
url = {https://academic.oup.com/biomet/article-lookup/doi/10.1093/biomet/ass048},
volume = {100},
year = {2013}
}
@article{LeMaire2014,
abstract = {Short-rotation plantations are extending worldwide due to the increased demand for pulp and wood. Reliable estimations of recent expansion of short-rotation plantation areas and associated land use changes are a prerequisite to assess their environmental impact on regional carbon and water cycles, and on climate. A binary classification methodology using MODerate resolution Imaging Spectroradiometer (MODIS) 16-day 250. m NDVI time series was developed and applied to classify Eucalyptus plantations across Brazil. The identification of Eucalyptus plantations specific patterns in the time series was based on the calculation of matching functions between the NDVI time series and a {\~{}}. 2. years long reference time series. Among the seven tested matching functions, the bounding envelope was the most successful. This method was robust to residual noise on the NDVI time series, and a threshold coefficient for the binary classification was adjusted using an omission-commission criteria. With this method, it was possible to detect any presence of Eucalyptus between 2003 and 2009 at monthly time-steps, including the periods of bare soils between two rotations that are typically 6-7 years long. The dates of first afforestation, of clear-cut at the end of a rotation, and of re-planting at the beginning of a new rotation were retrieved from the NDVI time series with a precision of {\~{}}. 66. days. The final almost continuous tri-dimensional map (space and time) was validated with three different datasets, from local to regional data. All three datasets gave similarly high global accuracy statistics, but a global underestimation of Eucalyptus areas compared to large scales census was observed. Discrepancies and way to improve the Eucalyptus area estimates were discussed in this study. The developed methodology could be applied to other short-rotation tree plantations. {\textcopyright} 2014 Elsevier Inc.},
author = {le Maire, Guerric and Dupuy, St{\'{e}}phane and Nouvellon, Yann and Loos, Rodolfo Araujo and Hakamada, Rodrigo},
doi = {10.1016/j.rse.2014.05.015},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/le Maire et al. - 2014 - Mapping short-rotation plantations at regional scale using MODIS time series Case of eucalypt plantations in Br.pdf:pdf},
isbn = {0034-4257},
issn = {00344257},
journal = {Remote Sensing of Environment},
keywords = {Bounding envelope,Eucalypt,Fast-growing plantations,Landsat,MOD13Q1,Mining time series data,Pattern recognition,Subsequence matching,Time series pattern analysis,Vegetation indices},
pages = {136--149},
publisher = {Elsevier Inc.},
title = {{Mapping short-rotation plantations at regional scale using MODIS time series: Case of eucalypt plantations in Brazil}},
url = {http://dx.doi.org/10.1016/j.rse.2014.05.015},
volume = {152},
year = {2014}
}
@article{Jarzyna2017,
abstract = {Assessments of spatial patterns of biodiversity change are essential to detect a signature of anthropogenic impacts, inform monitoring and conservation programs, and evaluate implications of biodiversity loss to humans. While taxonomic diversity (TD) is the most commonly assessed attribute of biodiversity, it misses the potential functional or phylogenetic implications of species losses or gains for ecosystems. Functional (FD) and phylogenetic (PD) diversity are able to capture these important trait-based and phylogenetic attributes of species, but their changes have to date only been evaluated over limited spatial and temporal extents. Employing a novel framework for addressing detectability, we here comprehensively assess a near half century of changes in local TD, FD, and PD of breeding birds across much of North America to examine levels of congruency in changes among these biodiversity facets and their variation across spatial and environmental gradients. Time-series analysis showed significant and continuous increases in all three biodiversity attributes until ca. 2000, followed by a slow decline since. Comparison of avian diversity at the beginning and end of the temporal series revealed net increase in TD, FD, and PD, but changes in TD were larger than those in FD and PD, suggesting increasing biotic homogenization of avian assemblages throughout the US. Changes were greatest at high elevations and latitudes—consistent with purported effects of ongoing climate change on biodiversity. Our findings highlight the potential of combining new types of data with novel statistical models to enable a more integrative monitoring and assessment of the multiple facets of biodiversity.},
author = {Jarzyna, Marta A. and Jetz, Walter},
doi = {10.1111/gcb.13571},
issn = {13652486},
journal = {Global Change Biology},
keywords = {biodiversity,birds,detectability,functional diversity,imperfect detection,occupancy modeling,phylogenetic diversity},
month = {aug},
number = {8},
pages = {2999--3011},
pmid = {27860064},
title = {{A near half-century of temporal change in different facets of avian diversity}},
url = {http://doi.wiley.com/10.1111/gcb.13571},
volume = {23},
year = {2017}
}
@article{Bluthgen2008,
abstract = {The structure of ecological interaction networks is often interpreted as a product of meaningful ecological and evolutionary mechanisms that shape the degree of specialization in community associations. However, here we show that both unweighted network metrics (connectance, nestedness, and degree distribution) and weighted network metrics (interaction evenness, interaction strength asymmetry) are strongly constrained and biased by the number of observations. Rarely observed species are inevitably regarded as "specialists," irrespective of their actual associations, leading to biased estimates of specialization. Consequently, a skewed distribution of species observation records (such as the lognormal), combined with a relatively low sampling density typical for ecological data, already generates a "nested" and poorly "connected" network with "asymmetric interaction strengths" when interactions are neutral. This is confirmed by null model simulations of bipartite networks, assuming that partners associate randomly in the absence of any specialization and any variation in the correspondence of biological traits between associated species (trait matching). Variation in the skewness of the frequency distribution fundamentally changes the outcome of network metrics. Therefore, interpretation of network metrics in terms of fundamental specialization and trait matching requires an appropriate control for such severe constraints imposed by information deficits. When using an alternative approach that controls for these effects, most natural networks of mutualistic or antagonistic systems show a significantly higher degree of reciprocal specialization (exclusiveness) than expected under neutral conditions. A higher exclusiveness is coherent with a tighter coevolution and suggests a lower ecological redundancy than implied by nested networks.},
author = {Bl{\"{u}}thgen, Nico and Fr{\"{u}}nd, Jochen and V{\'{a}}zquez, Diego P DP and Menzel, Florian and Biology, Tropical and Hubland, Am},
file = {:C$\backslash$:/LocalStorage/References/2008/Bl{\"{u}}thgen et al.{\_}2008{\_}What do interaction network metrics tell us about specialization and biological traits.pdf:pdf},
issn = {0012-9658},
journal = {Ecology},
keywords = {Adaptation,Animals,Biodiversity,Biological,Biological Evolution,Computer Simulation,Demography,Ecosystem,Food Chain,Interaction Networks,Method-Paper,Models,Physiological,Population Density,Population Dynamics,Population Growth,Species Specificity,abundance distribution,biological traits,connectance,degree distribution,ecological,interaction diversity,interaction strength,nestedness,networks,null models,specialization},
mendeley-tags = {Interaction Networks,Method-Paper},
month = {dec},
number = {12},
pages = {3387--99},
pmid = {19137945},
title = {{What do interaction network metrics tell us about specialization and biological traits?}},
url = {http://www.esajournals.org/doi/pdf/10.1890/07-2121.1 http://www.ncbi.nlm.nih.gov/pubmed/19137945},
volume = {89},
year = {2008}
}
@article{Ahlering2012,
abstract = {We investigated the genetic metapopulation structure of elephants across the trans Rift Valley region of Kenya and Tanzania, one of the remaining strongholds for savannah elephants (Loxodonata africana) in East Africa, using microsatellite and mitochondrial DNA (mtDNA) markers. We then examined this population structure to determine the source population for a recent colonization event of savannah elephants on community-owned land within the trans rift valley region. Four of the five sampled populations showed significant genetic differentiation (p{\textless}0.05) as measured with both mtDNA haplotypes and microsatellites. Only the samples from the adjacent Maasai Mara and Serengeti ecosystems showed no significant differentiation. A phylogenetic neighbour-joining tree constructed from mtDNA haplotypes detected four clades. Clade four corresponds to the F clade of previous mtDNA studies that reported to have originated in forest elephants (Loxodonta cyclotis) but to also be present in some savannah elephant populations. The split between clade four and the other three clades corresponded strongly to the geographic distribution of mtDNA haplotypes across the rift valley in the study area. Clade four was the dominant clade detected on the west side of the rift valley with rare occurrences on the east side. Finally, the strong patterns of population differentiation clearly indicated that the recent colonists to the community-owned land in Kenya came from the west side of the rift valley. Our results indicate strong female philopatry within the isolated populations of the trans rift valley region, with gene flow primarily mediated via male movements. The recent colonization event from Maasai Mara or Serengeti suggests there is hope for maintaining connectivity and population viability outside formal protected areas in the region.},
author = {Ahlering, Marissa a and Eggert, Lori S and Western, David and Estes, Anna and Munishi, Linus and Fleischer, Robert and Roberts, Melissa and Maldonado, Jesus E},
doi = {10.1371/journal.pone.0052288},
file = {:C$\backslash$:/LocalStorage/References/2012/Ahlering et al.{\_}2012{\_}Identifying source populations and genetic structure for savannah elephants in human-dominated landscapes and prote.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
month = {jan},
number = {12},
pages = {e52288},
pmid = {23300634},
title = {{Identifying source populations and genetic structure for savannah elephants in human-dominated landscapes and protected areas in the Kenya-Tanzania borderlands.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3530563{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {7},
year = {2012}
}
@article{Sugiura2012,
abstract = {BACKGROUND: The positive relationship between habitat area and species number is considered a fundamental rule in ecology. This relationship predicts that the link number of species interactions increases with habitat area, and structure is related to habitat area. Biological invasions can affect species interactions and area relationships. However, how these relationships change at different spatial scales has remained unexplored. We analysed understory plant-pollinator networks in seven temperate forest sites at 20 spatial scales (radius 120-2020 m) to clarify scale-associated relationships between forest area and plant-pollinator networks. RESULTS: The pooled data described interactions between 18 plant (including an exotic) and 89 pollinator (including an exotic) species. The total number of species and the number of interaction links between plant and pollinator species were negatively correlated with forest area, with the highest correlation coefficient at radii of 1520 and 1620 m, respectively. These results are not concordant with the pattern predicted by species-area relationships. However, when associations with exotic species were excluded, the total number of species and the number of interaction links were positively correlated with forest area (the highest correlation coefficient at a radius of 820 m). The network structure, i.e., connectance and nestedness, was also related to forest area (the highest correlation coefficients at radii of 720-820 m), when associations with exotics were excluded. In the study area, the exotic plant species Alliaria petiolata, which has invaded relatively small forest patches surrounded by agricultural fields, may have supported more native pollinator species than initially expected. Therefore, this invasive plant may have altered the original relationships between forest area and plant-pollinator networks. CONCLUSIONS: Our results demonstrate scale-dependent effects of forest area on the size and structure of plant-pollinator networks. We also suggest that a single exotic plant species can impact plant-pollinator networks, even in temperate continental habitats.},
author = {Sugiura, Shinji and Taki, Hisatomo},
doi = {10.1186/1472-6785-12-11},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Sugiura, Taki - 2012 - Scale-dependent effects of habitat area on species interaction networks invasive species alter relationships.pdf:pdf},
isbn = {1472-6785},
issn = {1472-6785},
journal = {BMC ecology},
keywords = {Animals,Biota,Ecosystem,Insects,Insects: physiology,Introduced Species,Invasion biology,Ontario,Plants,Pollination,Trees},
mendeley-tags = {Invasion biology},
month = {jan},
number = {1},
pages = {11},
pmid = {22817690},
title = {{Scale-dependent effects of habitat area on species interaction networks: invasive species alter relationships.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22817690 http://www.biomedcentral.com/content/pdf/1472-6785-12-11.pdf http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3521176{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {12},
year = {2012}
}
@article{Oksanen1981,
author = {Oksanen, Lauri and Fretwell, Stephen D and Arruda, Joseph and Niemela, Pekka},
doi = {10.1086/283817},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Oksanen et al. - 1981 - Exploitation Ecosystems in Gradients of Primary Productivity.pdf:pdf},
isbn = {0003-0147},
issn = {0003-0147},
journal = {The American Naturalist},
month = {aug},
number = {2},
pages = {240--261},
title = {{Exploitation Ecosystems in Gradients of Primary Productivity}},
url = {http://www.journals.uchicago.edu/doi/10.1086/283817},
volume = {118},
year = {1981}
}
@article{Egli2018,
archivePrefix = {arXiv},
arxivId = {arXiv:physics/0608246v3},
author = {Egli, Lukas and Meyer, Carsten and Scherber, Christoph and Kreft, Holger and Tscharntke, Teja},
doi = {10.1111/gcb.14076},
eprint = {0608246v3},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Egli et al. - 2018 - Winners and losers of national and global efforts to reconcile agricultural intensification and biodiversity conser.pdf:pdf},
isbn = {0000000154871},
issn = {13541013},
journal = {Global Change Biology},
month = {feb},
number = {10},
pages = {3218--3221},
pmid = {27935037},
primaryClass = {arXiv:physics},
title = {{Winners and losers of national and global efforts to reconcile agricultural intensification and biodiversity conservation}},
url = {http://doi.wiley.com/10.1111/gcb.14076},
volume = {12},
year = {2018}
}
@article{Schmidtlein2017,
author = {Schmidtlein, Sebastian and Fassnacht, Fabian Ewald},
doi = {10.1016/j.rse.2017.01.036},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Schmidtlein, Fassnacht - 2017 - The spectral variability hypothesis does not hold across landscapes.pdf:pdf},
issn = {00344257},
journal = {Remote Sensing of Environment},
keywords = {Biodiversity,Floristic survey,Plant species richness,SVH,Spatial non-stationarity,Zoning effects},
month = {apr},
pages = {114--125},
publisher = {Elsevier Inc.},
title = {{The spectral variability hypothesis does not hold across landscapes}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0034425717300482},
volume = {192},
year = {2017}
}
@article{Laurance2014b,
abstract = {The human population is projected to reach 11 billion this century, with the greatest increases in tropical developing nations. This growth, in concert with rising per-capita consumption, will require large increases in food and biofuel production. How will these megatrends affect tropical terrestrial and aquatic ecosystems and biodiversity? We foresee (i) major expansion and intensification of tropical agriculture, especially in Sub-Saharan Africa and South America; (ii) continuing rapid loss and alteration of tropical old-growth forests, woodlands, and semi-arid environments; (iii) a pivotal role for new roadways in determining the spatial extent of agriculture; and (iv) intensified conflicts between food production and nature conservation. Key priorities are to improve technologies and policies that promote more ecologically efficient food production while optimizing the allocation of lands to conservation and agriculture.},
author = {Laurance, William F and Sayer, Jeffrey and Cassman, Kenneth G},
doi = {10.1016/j.tree.2013.12.001},
file = {:C$\backslash$:/LocalStorage/References/2014/Laurance, Sayer, Cassman{\_}2014{\_}Agricultural expansion and its impacts on tropical nature.pdf:pdf},
issn = {1872-8383},
journal = {Trends in ecology {\&} evolution},
keywords = {001,0169-5347,10,1016,12,2013,agricultural intensification,all rights reserved,biodiversity,biodiversity hotspots,carbon,deforestation,doi,dx,http,j,land sparing,org,see front matter,species extinctions,storage,tree,{\ss} 2013 elsevier ltd},
month = {feb},
number = {2},
pages = {107--16},
pmid = {24388286},
publisher = {Elsevier Ltd},
title = {{Agricultural expansion and its impacts on tropical nature.}},
volume = {29},
year = {2014}
}
@article{Knutson2010,
author = {Knutson, Thomas R. and McBride, John L. and Chan, Johnny and Emanuel, Kerry and Holland, Greg and Landsea, Chris and Held, Isaac and Kossin, James P. and Srivastava, A. K. and Sugi, Masato},
doi = {10.1038/ngeo779},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Knutson et al. - 2010 - Tropical cyclones and climate change.pdf:pdf},
isbn = {1752-0894},
issn = {1752-0894},
journal = {Nature Geoscience},
month = {mar},
number = {3},
pages = {157--163},
pmid = {15666689},
title = {{Tropical cyclones and climate change}},
url = {http://www.nature.com/ngeo/journal/vaop/ncurrent/full/ngeo779.html http://www.nature.com/doifinder/10.1038/ngeo779},
volume = {3},
year = {2010}
}
@article{Meli2017,
author = {Meli, Paula and Holl, Karen D. and {Rey Benayas}, Jos{\'{e}} Mar{\'{i}}a and Jones, Holly P. and Jones, Peter C. and Montoya, Daniel and {Moreno Mateos}, David},
doi = {10.1371/journal.pone.0171368},
editor = {Joseph, Shijo},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Meli et al. - 2017 - A global review of past land use, climate, and active vs. passive restoration effects on forest recovery.pdf:pdf},
isbn = {1111111111},
issn = {1932-6203},
journal = {PLOS ONE},
month = {feb},
number = {2},
pages = {e0171368},
pmid = {28158256},
title = {{A global review of past land use, climate, and active vs. passive restoration effects on forest recovery}},
url = {http://dx.plos.org/10.1371/journal.pone.0171368},
volume = {12},
year = {2017}
}
@article{Essl2015a,
abstract = {Location Global. Results Effects of change in environmental forcing are transmitted along a ser- ies of linked cause–effect relationships which act on different biodiversity com- ponents (e.g. individuals, populations, species, communities). We show that lagged responses to environmental forcing are caused by different mechanisms (e.g. metapopulation dynamics, dispersal limitation, successional dynamics), which operate sequentially on these intermediary links. Lags manifest them- selves on the respective biodiversity component which changes over time; the full relaxation time of a focal system will therefore depend on the aggregate length of different lags. We elucidate key mechanisms and circumstances which are likely to cause cumulative lagged responses, and propose research avenues to improve understanding of cumulative biodiversity lags. Main conclusions The failure to give adequate consideration to widespread cumulative time-lags often masks the full extent of biodiversity changes that have already been triggered. Effects that are particularly relevant for human livelihoods (e.g. changes in the provision of ecosystem services) may emerge with the most pronounced delay. Accordingly, the consideration of appropriate temporal scales should become a key topic in future work at the science–policy interface.},
author = {Essl, Franz and Dullinger, Stefan and Rabitsch, Wolfgang and Hulme, Philip E. and Py{\v{s}}ek, Petr and Wilson, John R U and Richardson, David M.},
doi = {10.1111/ddi.12312},
editor = {Kueffer, Christoph},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Essl et al. - 2015 - Historical legacies accumulate to shape future biodiversity in an era of rapid global change.pdf:pdf},
isbn = {1472-4642},
issn = {13669516},
journal = {Diversity and Distributions},
keywords = {Biological invasions,Framework,Global change,Invasion debt,Management,Thresholds,Time-lags,extinction debt},
month = {may},
number = {5},
pages = {534--547},
pmid = {16769436},
title = {{Historical legacies accumulate to shape future biodiversity in an era of rapid global change}},
url = {http://doi.wiley.com/10.1111/ddi.12312},
volume = {21},
year = {2015}
}
@article{Oehri2017,
author = {Oehri, Jacqueline and Schmid, Bernhard and Schaepman-Strub, Gabriela and Niklaus, Pascal A.},
doi = {10.1073/pnas.1703928114},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Oehri et al. - 2017 - Biodiversity promotes primary productivity and growing season lengthening at the landscape scale.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
month = {sep},
pages = {201703928},
pmid = {28874547},
title = {{Biodiversity promotes primary productivity and growing season lengthening at the landscape scale}},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1703928114},
year = {2017}
}
@article{Dupouey2002,
author = {Dupouey, J. L. and Dambrine, E and Laffite, J D and Moares, C},
doi = {10.2307/3071833},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Dupouey et al. - 2002 - Irreversible Impact of past Land Use on Forest Soils and Biodiversity.pdf:pdf},
issn = {00129658},
journal = {Ecology},
keywords = {archaeology,biodiversity,forest,forest soils,france,lorrain limestone plateau,past land use,phosphorus,plant diversity},
month = {nov},
number = {11},
pages = {2978},
title = {{Irreversible Impact of past Land Use on Forest Soils and Biodiversity}},
url = {http://www.jstor.org/stable/3071833?origin=crossref},
volume = {83},
year = {2002}
}
@article{Bengtsson2003,
abstract = {In a world increasingly modified by human activities, the conservation of biodiversity is essential as insurance to maintain resilient ecosystems and ensure a sustainable flow of ecosystem goods and services to society. However, existing reserves and national parks are unlikely to incorporate the long-term and large-scale dynamics of ecosystems. Hence, conservation strategies have to actively incorporate the large areas of land that are managed for human use. For ecosystems to reorganize after large-scale natural and human-induced disturbances, spatial resilience in the form of ecological memory is a prerequisite. The ecological memory is composed of the species, interactions and structures that make ecosystem reorganization possible, and its components may be found within disturbed patches as well in the surrounding landscape. Present static reserves should be complemented with dynamic reserves, such as ecological fallows and dynamic successional reserves, that are part of ecosystem management mimicking natural disturbance regimes at the landscape level.},
author = {Bengtsson, Janne and Angelstam, Per and Elmqvist, Thomas and Emanuelsson, Urban and Folke, Carl and Ihse, Margareta and Moberg, Fredrik and Nystr{\"{o}}m, Magnus},
doi = {10.1579/0044-7447-32.6.389},
file = {:C$\backslash$:/LocalStorage/References/4315407.pdf:pdf},
isbn = {0044-7447},
issn = {0044-7447},
journal = {Ambio},
number = {6},
pages = {389--396},
pmid = {14627367},
title = {{Reserves, Resilience and Dynamic Landscapes}},
url = {http://www.bioone.org/doi/abs/10.1579/0044-7447-32.6.389},
volume = {32},
year = {2003}
}
@article{Olesen2002,
abstract = {Recent reviews of plant–pollinator mutualistic networks showed that generalization is a common pattern in this type of interaction. Here we examine the ecological correlates of generalization patterns in plant–pollinator networks, especially how interaction patterns covary with latitude, elevation, and insularity. We review the few published analyses of whole networks and include unpublished material, analyzing 29 complete plant–pollinator networks that encompass arctic, alpine, temperate, Mediterranean, and subtropical–tropical areas. The number of interactions observed (I) was a linear function of network size (M) the maximum number of interactions: ln I = 0.575 + 0.61 ln M; R2 = 0.946. The connectance (C), the fraction of observed interactions relative to the total possible, decreased exponentially with species richness, the sum of animal and plant species in each community (A + P): C = 13.83 exp[−0.003(A + P)]. After controlling for species richness, the residual connectance was significantly lower in highland ({\textgreater}1500 m elevation) than in lowland networks and differed marginally among biogeographic regions, with both alpine and tropical networks showing a trend for lower residual connectance. The two Mediterranean networks showed the highest residual connectance. After correcting for variation in network size, plant species were shown to be more generalized at higher latitude and lowland habitats, but showed increased specialization on islands. Oceanic island networks showed an impoverishment of potential animal pollinators (lower ratio of animal to plant species, A : P, compared to mainland networks) associated with this trend of increased specialization. Plants, but not their flower-visiting animals, supported the often-repeated statements about higher specificity in the tropics than at higher latitudes. The pattern of interaction build-up as diversity increases in pollination networks does not differ appreciably from other mutualisms, such as plant–seed disperser networks or more complex food webs.},
author = {Olesen, JM and Jordano, P},
file = {:C$\backslash$:/LocalStorage/References/2002/Olesen, Jordano{\_}2002{\_}Geographic patterns in plant-pollinator mutualistic networks.pdf:pdf},
journal = {Ecology},
keywords = {Community Network,Geography,Review,animal interaction,food web,geographic variation,insects,interaction-web connectance,mutualism,networks,plant,pollination,specialization},
mendeley-tags = {Community Network,Geography,Review},
number = {9},
pages = {2416--2424},
title = {{Geographic patterns in plant-pollinator mutualistic networks}},
url = {http://www.esajournals.org/doi/pdf/10.1890/0012-9658(2002)083[2416:GPIPPM]2.0.CO;2 http://www.esajournals.org/doi/abs/10.1890/0012-9658(2002)083[2416:GPIPPM]2.0.CO;2?journalCode=ecol},
volume = {83},
year = {2002}
}
@article{Wood2017,
author = {Wood, Sylvia L. R. and Rhemtulla, Jeanine M. and Coomes, Oliver T.},
doi = {10.1002/eap.1462},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Wood, Rhemtulla, Coomes - 2017 - Cropping history trumps fallow duration in long-term soil and vegetation dynamics of shifting cultivati.pdf:pdf},
issn = {10510761},
journal = {Ecological Applications},
keywords = {biodiversity,cropping,fallow length,land-use history,shifting cultivation,soil properties},
month = {mar},
number = {2},
pages = {519--531},
title = {{Cropping history trumps fallow duration in long-term soil and vegetation dynamics of shifting cultivation systems}},
url = {http://doi.wiley.com/10.1002/eap.1462},
volume = {27},
year = {2017}
}
@misc{Developers2014,
author = {Developers, Signal},
publisher = {{\{}http://r-forge.r-project.org/projects/signal/}},
title = {{signal: Signal processing}},
url = {http://r-forge.r-project.org/projects/signal/},
year = {2014}
}
@article{Benali2017,
author = {Benali, Akli and Mota, Bernardo and Carvalhais, Nuno and Oom, Duarte and Miller, Lee M and Campagnolo, Manuel L and Pereira, Jos{\'{e}} M. C.},
doi = {10.1111/geb.12586},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Benali et al. - 2017 - Bimodal fire regimes unveil a global-scale anthropogenic fingerprint.pdf:pdf},
issn = {1466822X},
journal = {Global Ecology and Biogeography},
month = {jul},
number = {7},
pages = {799--811},
title = {{Bimodal fire regimes unveil a global-scale anthropogenic fingerprint}},
url = {http://doi.wiley.com/10.1111/geb.12586},
volume = {26},
year = {2017}
}
@article{GIL-TENA2009,
author = {GIL-TENA, ASSU and BROTONS, LLU{\'{I}}S and SAURA, SANTIAGO},
doi = {10.1111/j.1365-2486.2008.01730.x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/GIL-TENA, BROTONS, SAURA - 2009 - Mediterranean forest dynamics and forest bird distribution changes in the late 20th century.pdf:pdf},
issn = {13541013},
journal = {Global Change Biology},
keywords = {bird species,dispersal,forest maturation,forest spread,generalist and specialist forest,hierarchical modelling,land abandonment,mixed models,regional processes,spatial autocorrelation},
month = {feb},
number = {2},
pages = {474--485},
title = {{Mediterranean forest dynamics and forest bird distribution changes in the late 20th century}},
url = {http://doi.wiley.com/10.1111/j.1365-2486.2008.01730.x},
volume = {15},
year = {2009}
}
@article{Rowhani2008,
abstract = {Habitat transformations and climate change are among the most important drivers of biodiversity loss. Understanding the factors responsible for the unequal distribution of species richness is a major challenge in ecology. Using data from the North American Breeding Bird Survey to measure species richness and a change metric extracted from the MODerate resolution Imaging Spectroradiometer (MODIS), we examined the influence of energy variability on the geographic distribution of avian richness across the conterminous U.S. and in the different ecoregions, while controlling for energy availability. The analysis compared three groups of birds: all species, Neotropical migrants, and permanent residents. We found that interannual variability in available energy explained more than half of the observed variation in bird richness in some ecoregions. In particular, energy variability is an important factor in explaining the patterns of overall bird richness and of permanent residents, in addition to energy availability. Our results showed a decrease in species richness with increasing energy variability and decreasing energy availability, suggesting that more species are found in more stable and more productive environments. However, not all ecoregions followed this pattern. The exceptions might reflect other biological factors and environmental conditions. With more ecoclimatic variability predicted for the future, this study provides insight into how energy variability influences the geographical patterns of species richness.},
author = {Rowhani, Pedram and Lepczyk, Christopher a. and Linderman, Marc a. and Pidgeon, Anna M. and Radeloff, Volker C. and Culbert, Patrick D. and Lambin, Eric F.},
doi = {10.1007/s10021-008-9165-9},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Rowhani et al. - 2008 - Variability in Energy Influences Avian Distribution Patterns Across the USA.pdf:pdf},
isbn = {1432-9840},
issn = {1432-9840},
journal = {Ecosystems},
keywords = {Avian ecology,Biodiversity,Breeding Bird Survey (BBS),Energy variability,MODIS,Richness patterns},
month = {sep},
number = {6},
pages = {854--867},
title = {{Variability in Energy Influences Avian Distribution Patterns Across the USA}},
url = {http://link.springer.com/10.1007/s10021-008-9165-9},
volume = {11},
year = {2008}
}
@article{Ackerly2010,
author = {Ackerly, D. D. and Loarie, S. R. and Cornwell, W. K. and Weiss, S. B. and Hamilton, H. and Branciforte, R. and Kraft, N. J. B.},
doi = {10.1111/j.1472-4642.2010.00654.x},
file = {:C$\backslash$:/LocalStorage/References/2010/Ackerly et al.{\_}2010{\_}The geography of climate change implications for conservation biogeography.{\_}2010{\_}dive:{\_}2010{\_}dive},
issn = {13669516},
journal = {Diversity and Distributions},
keywords = {climate change,climatic heterogeneity,conservation,protected area networks,spatial heterogeneity,spatial scale,topoclimate},
month = {apr},
number = {3},
pages = {476--487},
title = {{The geography of climate change: implications for conservation biogeography}},
url = {http://doi.wiley.com/10.1111/j.1472-4642.2010.00654.x},
volume = {16},
year = {2010}
}
@article{OConnor2014,
abstract = {The term ‘carryover effect' originally arose from repeated measures clinical experiments. However, the term has more recently been applied to ecological and evolutionary studies, often in migratory systems, which has led to an emphasis on non-lethal effects across seasons. In this article, we suggest that ecological carryover effects can also occur between life-history stages, developmental stages, physiological states, or social situations, and each will be associated with a discrete time-scale. Therefore, we propose the working definition: In an ecological context, carryover effects occur in any situation in which an individual's previous history and experience explains their current performance in a given situation. This concept of carryover effects provides an explicit but highly flexible context for examining the mechanisms that drive non-lethal interactions between distinct periods of an organism's lifetime, and unites the currently disparate fields investigating these effects in ecological systems. Greater communication among research fields and identifying mechanisms of carryover effects at different time scales will ultimately lead to a better understanding of the factors influencing variation in individual fitness.},
author = {O'Connor, Constance M. and Norris, D. Ryan and Crossin, Glenn T. and Cooke, Steven J.},
doi = {10.1890/ES13-00388.1},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/O'Connor et al. - 2014 - Biological carryover effects linking common concepts and mechanisms in ecology and evolution.pdf:pdf},
isbn = {2150-8925},
issn = {2150-8925},
journal = {Ecosphere},
keywords = {2014,accepted 17 december 2013,article distributed under the,c,carry over effect,commons,connor et al,copyright,corresponding editor,d,delayed effect,february 2014,final version received 11,latent effect,life-history trade-off,maternal effect,p,peters,published 13 march,received 13 december 2013,reproductive trade-off,terms of the creative,this is an open-access,{\'{o}} 2014 o},
month = {mar},
number = {3},
pages = {28},
title = {{Biological carryover effects: linking common concepts and mechanisms in ecology and evolution}},
url = {http://doi.wiley.com/10.1890/ES13-00388.1},
volume = {5},
year = {2014}
}
@article{Harris2008,
abstract = {Small geographical range size is the single best predictor of threat of extinction in terrestrial species. Knowing how small a species' range has to be before authorities consider it threatened with extinction would allow prediction of a species' risk from continued deforestation and warming climates and provide a baseline for conservation and management strategies aspiring to mitigate these threats. To determine the threshold at which forest-dependent bird species become threatened with extinction, we compared the range sizes of threatened and nonthreatened species. In doing so, we present a simple, repeatable, and practical protocol to quantify range size. We started with species' ranges published in field guides or comparable sources. We then trimmed these ranges, that is, we included only those parts of the ranges that met the species' requirements of elevation and types of forest preferred. Finally, we further trimmed the ranges to the amount of forest cover that remains. This protocol generated an estimate of the remaining suitable range for each species. We compared these range estimates with those from the World Conservation Union Red List. We used the smaller of the two estimates to determine the threshold, 11,000 km2, below which birds should be considered threatened. Species considered threatened that have larger ranges than this qualified under other (nonspatial) red list criteria. We identified a suite of species (18) that have not yet qualified as threatened but that have perilously small ranges--about 11{\%} of the nonthreatened birds we analyzed. These birds are likely at risk of extinction and reevaluation of their status is urgently needed.},
author = {Harris, Grant and Pimm, Stuart L.},
doi = {10.1111/j.1523-1739.2007.00798.x},
file = {:C$\backslash$:/LocalStorage/References/2008/Harris, Pimm{\_}2008{\_}Range size and extinction risk in forest birds.pdf:pdf},
isbn = {0888-8892},
issn = {1523-1739},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
keywords = {Animals,Biological,Birds,Birds: physiology,Central America,Conservation of Natural Resources,Demography,Ecosystem,Extinction,Models,Risk Factors,Trees},
mendeley-tags = {Birds,Extinction},
month = {feb},
number = {1},
pages = {163--71},
pmid = {18254861},
title = {{Range size and extinction risk in forest birds.}},
volume = {22},
year = {2008}
}
@article{Aronson2014,
abstract = {Urbanization contributes to the loss of the world's biodiversity and the homogenization of its biota. However, comparative studies of urban biodiversity leading to robust generalities of the status and drivers of biodiversity in cities at the global scale are lacking. Here, we compiled the largest global dataset to date of two diverse taxa in cities: birds (54 cities) and plants (110 cities). We found that the majority of urban bird and plant species are native in the world's cities. Few plants and birds are cosmopolitan, the most common being Columba livia and Poa annua. The density of bird and plant species (the number of species per km2) has declined substantially: {\&} 2014 The Author(s) Published by the Royal Society. All rights reserved. Downloaded from rspb.royalsocietypublishing.org on March 11, 2014 only 8{\%} of native bird and 25{\%} of native plant species are currently present compared with estimates of non-urban density of species. The current density of species in cities and the loss in density of species was best explained by anthropogenic features (landcover, city age) rather than by non-anthropogenic factors (geography, climate, topography). As urbanization continues to expand, efforts directed towards the conservation of intact vegetation within urban landscapes could support higher concentrations of both bird and plant species. Despite declines in the density of species, cities still retain endemic native species, thus providing opportunities for regional and global biodiversity conservation, restoration and education.},
author = {Aronson, Myla F J and {La Sorte}, F. A. and Nilon, Charles H and Katti, Madhusudan and Goddard, Mark A and Lepczyk, Christopher A and Warren, Paige S and Williams, N. S. G. and Cilliers, Sarel and Clarkson, Bruce and Dobbs, Cynnamon and Dolan, Rebecca and Hedblom, Marcus and Klotz, Stefan and Kooijmans, Jip Louwe and Kuhn, I. and MacGregor-Fors, I. and McDonnell, M. and Mortberg, U. and Pysek, Petr and Siebert, Stefan and Sushinsky, Jessica and Werner, Peter and Winter, Marten},
doi = {10.1098/rspb.2013.3330},
file = {:C$\backslash$:/LocalStorage/References/2014/Aronson et al.{\_}2014{\_}A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers.pdf:pdf},
issn = {0962-8452},
journal = {Proceedings of the Royal Society B: Biological Sciences},
month = {feb},
number = {1780},
pages = {20133330--20133330},
title = {{A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers}},
url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2013.3330},
volume = {281},
year = {2014}
}
@article{Bardsen2012,
abstract = {1. Recent studies have shown that optimal reproductive allocation depends on both climatic conditions and population density. We tested this hypothesis using six years of demographic data from eight reindeer (Rangifer tarandus) populations coupled with data on population abundance and vegetation greenness [measured using the Enhanced Vegetation Index (EVI)]. 2. Female spring body mass positively affected summer body mass gain, and lactating females were unable to compensate for harsh winters as efficiently as barren ones. Female spring body mass was highly sensitive to changes in population abundance and vegetation greenness and less dependent on previous autumn body mass and reproductive status. Lactating females were larger than barren females in the spring. Moreover, female autumn body mass was positively related to female autumn body mass and reproductive success and was not very sensitive to changes in vegetation greenness and population abundance. 3. Offspring autumn body mass was positively related to both maternal spring and autumn body mass, and as predicted from theory, offspring were more sensitive to changes in vegetation greenness and population abundance than adult females. A lagged cost of reproduction was present as larger females who were barren, the previous year produced larger offspring than equally sized females that successfully reproduced the previous year. 4. Reproductive success was negatively related to female autumn body mass and positively related to female spring body mass. Moreover, females who successfully reproduced the previous year experienced the highest reproductive success. The fact that negative density-dependence was only present for females that had successfully reproduced the previous year further support the hypothesis that reproduction is costly. 5. This study shows that female reindeer buffer their reproductive allocation according to expected winter conditions and that their buffering abilities were limited by population abundance and a lagged cost of reproduction and enhanced by vegetation greenness.},
author = {B{\aa}rdsen, B{\aa}rd-J{\o}rgen and Tveraa, Torkild},
doi = {10.1111/j.1365-2656.2011.01913.x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/B{\aa}rdsen, Tveraa - 2012 - Density-dependence vs. density-independence - linking reproductive allocation to population abundance and veget.pdf:pdf},
isbn = {0021-8790},
issn = {00218790},
journal = {Journal of Animal Ecology},
keywords = {Environmental unpredictability,Foraging,Herbivore,Individual quality,Life history,Moderate Resolution Imaging Spectroradiometer,Normalized Difference Vegetation Index,Norway,Phenotypic plasticity,Risk sensitivity},
month = {mar},
number = {2},
pages = {364--376},
pmid = {21985598},
title = {{Density-dependence vs. density-independence - linking reproductive allocation to population abundance and vegetation greenness}},
url = {http://doi.wiley.com/10.1111/j.1365-2656.2011.01913.x},
volume = {81},
year = {2012}
}
@article{Kremen2015,
author = {Kremen, Claire and M'Gonigle, Leithen K.},
doi = {10.1111/1365-2664.12418},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Kremen, M'Gonigle - 2015 - Small-scale restoration in intensive agricultural landscapes supports more specialized and less mobile pollin.pdf:pdf},
issn = {00218901},
journal = {Journal of Applied Ecology},
pages = {n/a--n/a},
title = {{Small-scale restoration in intensive agricultural landscapes supports more specialized and less mobile pollinator species}},
url = {http://doi.wiley.com/10.1111/1365-2664.12418},
year = {2015}
}
@article{Tucker1979,
abstract = {In situ collected spectrometer data were used to evaluate and quantify the relationships between various linear combinations of red and photographic infrared radiances and experimental plot biomass, leaf water content, and chlorophyll content. The radiance variables evaluated included the red and photographic infrared (IR) radiance and the linear combinations of the IR/red ratio, the square root of the IR/red ratio, the IR-red difference, the vegetation index, and the transformed vegetation index. In addition, the corresponding green and red linear combinations were evaluated for comparative purposes. Three data sets were used from June, September, and October sampling periods. Regression analysis showed the increased utility of the IR and red linear combinations vis-{\`{a}}-vis the same green and red linear combinations. The red and IR linear combinations had 7{\%} and 14{\%} greater regression significance than the green and red linear combinations for the June and September sampling periods, respectively. The vegetation index, transformed vegetation index, and square root of the IR/red ratio were the most significant, followed closely by the IR/red ratio. Less than a 6{\%} difference separated the highest and lowest of these four ER and red linear combinations. The use of these linear combinations was shown to be sensitive primarily to the green leaf area or green leaf biomass. As such, these linear combinations of the red and photographic IR radiances can be employed to monitor the photosynthetically active biomass of plant canopies. {\textcopyright} 1979.},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Tucker, Compton J.},
doi = {10.1016/0034-4257(79)90013-0},
eprint = {arXiv:1011.1669v3},
isbn = {0034-4257},
issn = {00344257},
journal = {Remote Sensing of Environment},
month = {may},
number = {2},
pages = {127--150},
pmid = {175},
title = {{Red and photographic infrared linear combinations for monitoring vegetation}},
url = {http://linkinghub.elsevier.com/retrieve/pii/0034425779900130},
volume = {8},
year = {1979}
}
@article{Tuck2014,
abstract = {Remotely sensed data – available at medium to high resolution across global spatial and temporal scales – are a valuable resource for ecologists. In particular, products from NASA's MODerate-resolution Imaging Spectroradiometer (MODIS), providing twice-daily global coverage, have been widely used for ecological applications. We present MODISTools, an R package designed to improve the accessing, downloading, and processing of remotely sensed MODIS data. MODISTools automates the process of data downloading and processing from any number of locations, time periods, and MODIS products. This automation reduces the risk of human error, and the researcher effort required compared to manual per-location downloads. The package will be particularly useful for ecological studies that include multiple sites, such as meta-analyses, observation networks, and globally distributed experiments. We give examples of the simple, reproducible workflow that MODISTools provides and of the checks that are carried out in the process. The end product is in a format that is amenable to statistical modeling. We analyzed the relationship between species richness across multiple higher taxa observed at 526 sites in temperate forests and vegetation indices, measures of aboveground net primary productivity. We downloaded MODIS derived vegetation index time series for each location where the species richness had been sampled, and summarized the data into three measures: maximum time-series value, temporal mean, and temporal variability. On average, species richness covaried positively with our vegetation index measures. Different higher taxa show different positive relationships with vegetation indices. Models had high R2 values, suggesting higher taxon identity and a gradient of vegetation index together explain most of the variation in species richness in our data. MODISTools can be used on Windows, Mac, and Linux platforms, and is available from CRAN and GitHub (https://github.com/seantuck12/MODISTools).},
author = {Tuck, Sean L and Phillips, Helen R.P. and Hintzen, Rogier E and Scharlemann, J{\"{o}}rn P.W. and Purvis, Andy and Hudson, Lawrence N},
doi = {10.1002/ece3.1273},
file = {:C$\backslash$:/LocalStorage/References/2014/Tuck et al.{\_}2014{\_}MODISTools - downloading and processing MODIS remotely sensed data in R.pdf:pdf},
issn = {20457758},
journal = {Ecology and Evolution},
keywords = {Conservation biology,PREDICTS,earth observation,global change,land processes,macroecology,remote-sensing,satellite imagery},
number = {24},
pages = {4658--4668},
title = {{MODISTools - downloading and processing MODIS remotely sensed data in R}},
volume = {4},
year = {2014}
}
@article{Faith1987,
author = {Faith, Daniel P. and Minchin, Peter R. and Belbin, Lee},
doi = {10.1007/BF00038687},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Faith, Minchin, Belbin - 1987 - Compositional dissimilarity as a robust measure of ecological distance.pdf:pdf},
issn = {0042-3106},
journal = {Vegetatio},
keywords = {dissimilarity measure,ecological distance,hybrid multidimensional scaling,multidimensional,nonmetric,ordination,robustness,scaling,simulation},
month = {apr},
number = {1-3},
pages = {57--68},
title = {{Compositional dissimilarity as a robust measure of ecological distance}},
url = {http://link.springer.com/10.1007/BF00038687},
volume = {69},
year = {1987}
}
@article{Metzger2009,
abstract = {Time-lagged responses of biological variables to landscape modifications are widely recognized, but rarely considered in ecological studies. In order to test for the existence of time-lags in the response of trees, small mammals, birds and frogs to changes in fragment area and connectivity, we studied a fragmented and highly dynamic landscape in the Atlantic forest region. We also investigated the biological correlates associated with differential responses among taxonomic groups. Species richness and abundance for four taxonomic groups were measured in 21 secondary forest fragments during the same period (2000-2002), following a standardized protocol. Data analyses were based on power regressions and model selection procedures. The model inputs included present (2000) and past (1962, 1981) fragment areas and connectivity, as well as observed changes in these parameters. Although past landscape structure was particularly relevant for trees, all taxonomic groups (except small mammals) were affected by landscape dynamics, exhibiting a time-lagged response. Furthermore, fragment area was more important for species groups with lower dispersal capacity, while species with higher dispersal ability had stronger responses to connectivity measures. Although these secondary forest fragments still maintain a large fraction of their original biodiversity, the delay in biological response combined with high rates of deforestation and fast forest regeneration imply in a reduction in the average age of the forest. This also indicates that future species losses are likely, especially those that are more strictly-forest dwellers. Conservation actions should be implemented to reduce species extinction, to maintain old-growth forests and to favour the regeneration process. Our results demonstrate that landscape history can strongly affect the present distribution pattern of species in fragmented landscapes, and should be considered in conservation planning. ?? 2009 Elsevier Ltd. All rights reserved.},
author = {Metzger, Jean Paul and Martensen, Alexandre Camargo and Dixo, Marianna and Bernacci, Luis Carlos and Ribeiro, Milton Cezar and Teixeira, Ana Maria Godoy and Pardini, Renata},
doi = {10.1016/j.biocon.2009.01.033},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Metzger et al. - 2009 - Time-lag in biological responses to landscape changes in a highly dynamic Atlantic forest region.pdf:pdf},
isbn = {0006-3207},
issn = {00063207},
journal = {Biological Conservation},
keywords = {Anura,Atlantic Forest,Aves,Connectivity,Corridor,Extinction debt,Fragmentation,Mammalia,Secondary forest,South America,Temporal dynamics,abundance,biodiversity,biotic factor,connectivity,conservation planning,deforestation,dispersal,ecosystem response,extinction risk,habitat corridor,habitat fragmentation,landscape change,landscape history,old-growth forest,regeneration,secondary forest,species richness,temporal variation},
month = {jun},
number = {6},
pages = {1166--1177},
publisher = {Elsevier Ltd},
title = {{Time-lag in biological responses to landscape changes in a highly dynamic Atlantic forest region}},
url = {http://dx.doi.org/10.1016/j.biocon.2009.01.033 http://www.scopus.com/inward/record.url?eid=2-s2.0-63349093285{\&}partnerID=40{\&}md5=fbe0d0462afc9a233286b7796cb2396b{\%}5Cnfiles/34989/display.html http://linkinghub.elsevier.com/retrieve/pii/S0006320709000780},
volume = {142},
year = {2009}
}
@article{Gao2000,
abstract = {For a better evaluation of the accuracy of VIs in estimating biophysical parameters, a "true" VI value attributed only to the vegetation signal and free of any contamination is needed. In this article, pure vegetation spectra were extracted from a set of open and closed canopies by unmixing the green vegetation signal from the background component. Canopy model-simulation and reflectances derived from graph-based linear extrapolation were used to unmix and derive a "true" vegetation signal, equivalent to a perfect absorber (free boundary) canopy background reflectance condition. Optical-biophysical relationships were then derived for a variety of canopy structures with differences in foliage clumping, horizontal heterogeneity, and leaf type. A 3-dimensional canopy radiative transfer model and a hybrid geometric optical-radiative transfer model (GORT) were used to simulate the directional-hemispherical reflectances from agricultural, grassland, and forested canopies (cereal and broadleaf crop, grass, needleleaf, and broadleaf forest). The relationships of the extracted red and near-intimated reflectances and derived vegetation indices (VIs) to various biophysical parameters (leaf area index, fraction of absorbed photosynthetically active radiation, and percent ground cover) were examined for the pure vegetation spectra. The results showed normalized difference vegetation index (NDVI) relationships with biophysical parameters to become more asymptotic over the pure vegetation condition. The extraction of pure vegetation signals had little effect on the soil-adjusted vegetation index (SAVI), which had values equivalent to those obtained with the presence of a background signal. NDVI values were fairly uniform across the different canopy types, whereas the SAVI values had pronounced differences among canopy types, particularly between the broadleaf and cereal/needleleaf structural types. These results were useful not only in selecting suitable vegetation indices to characterize specific canopy biophysical parameters, but also in understanding a "true" VI behavior, free of background noise. ??2000 Elsevier Science Inc.},
author = {Gao, Xiang and Huete, Alfredo R. and Ni, Wenge and Miura, Tomoaki},
doi = {10.1016/S0034-4257(00)00150-4},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Gao et al. - 2000 - Optical-biophysical relationships of vegetation spectra without background contamination.pdf:pdf},
isbn = {0034-4257},
issn = {00344257},
journal = {Remote Sensing of Environment},
month = {dec},
number = {3},
pages = {609--620},
title = {{Optical-biophysical relationships of vegetation spectra without background contamination}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0034425700001504},
volume = {74},
year = {2000}
}
@incollection{DePalma2018,
author = {{De Palma}, Adriana and {Sanchez Ortiz}, Katia and Martin, Phillip A. and Chadwick, Amy and Gilbert, Guillermo and Bates, Amanda E. and B{\"{o}}rger, Luca and Contu, Sara and Hill, Samantha L.L. and Purvis, Andy},
booktitle = {Next Generation Biomonitoring: Part 1},
doi = {10.1016/bs.aecr.2017.12.004},
edition = {1},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/De Palma et al. - 2018 - Challenges With Inferring How Land-Use Affects Terrestrial Biodiversity Study Design, Time, Space and Synthesis.pdf

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib