text:
Ltd./Mendeley Desktop/Downloaded/Turner, Foster - 2009 - The impact of forest conversion to oil palm on arthropod abundance and biomass in Sabah, Malaysia.pdf:pdf},
isbn = {0266-4674},
issn = {0266-4674},
journal = {Journal of Tropical Ecology},
keywords = {asplenium nidus,bird,deforestation,elaeis guineensis,logging,s nest fern},
pages = {23},
title = {{The impact of forest conversion to oil palm on arthropod abundance and biomass in Sabah, Malaysia}},
volume = {25},
year = {2009}
}
@article{Farwig2008,
abstract = {Tree plantations of native and exotic species are frequently used to compensate for forest loss in the tropics. However, these plantations may support lower species diversity and different communities than natural forest. We therefore investigated bird communities in stands of natural forest, different types of tree plantations and secondary forest in Kakamega Forest, western Kenya. We compared birds differing in habitat specialisation, i.e. forest specialists, generalists, and visitors. We recorded significant differences in mean species richness and number of individuals among the different forest types. Stands of natural forest and plantations of indigenous tree species comprised more species and individuals than plantations of exotic tree species and secondary forest. This was caused by a significant decline of forest specialists and generalists from natural forest and indigenous plantations to exotic plantations and secondary forest. Species composition of the bird communities did not differ between natural forest stands and plantations of a mixture of indigenous tree species, but clearly changed between natural forest and plantations of single tree species. These findings demonstrate that natural forest areas are needed for the conservation of forest bird diversity, but that plantations with a mixture of indigenous tree species can have similarly high conservation value. {\textcopyright} 2008 Elsevier B.V. All rights reserved.},
author = {Farwig, Nina and Sajita, Nixon and B{\"{o}}hning-Gaese, Katrin},
doi = {10.1016/j.foreco.2008.03.042},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Farwig, Sajita, B{\"{o}}hning-Gaese - 2008 - Conservation value of forest plantations for bird communities in western Kenya.pdf:pdf},
isbn = {0378-1127},
issn = {03781127},
journal = {Forest Ecology and Management},
keywords = {Africa,Forest avifauna,Kakamega Forest,Tropical rainforest},
pages = {3885--3892},
title = {{Conservation value of forest plantations for bird communities in western Kenya}},
volume = {255},
year = {2008}
}
@article{Fokkema2017,
abstract = {Identification of subgroups of patients for which treatment A is more e↵ective than treatment B, and vice versa, is of key importance to the development of personalized medicine. Several tree-based algorithms have been developed for the detection of such treatment-subgroup interactions. In many instances, however, datasets may have a clus-tered structure, where observations are clustered within, for example, research centers, studies or persons. In the current paper we propose a new algorithm, generalized linear mixed-e↵ects model (GLMM) trees, that allows for detection of treatment-subgroup in-teractions, as well as estimation of cluster-specific random e↵ects. The algorithm uses model-based recursive partitioning (MOB) to detect treatment-subgroup interactions, and a GLMM for the estimation of random-e↵ects parameters. In a simulation study, we evaluate the performance of GLMM tree and compare it with that of MOB without random-e↵ects estimation. GLMM tree was found to have a much lower Type I error rate than MOB trees without random e↵ects (4{\%} and 33{\%}, respectively). Furthermore, in datasets with treatment-subgroup interactions, GLMM tree recovered the true treatment subgroups much more often than MOB without random e↵ects (in 90{\%} and 61{\%} of the datasets, respectively). Also, GLMM tree predicted treatment outcome di↵erences more accurately than MOB without random e↵ects (average predictive accuracy of .94 and .88, respectively). We illustrate the application of GLMM tree on a patient-level dataset of a meta-analysis on the e↵ects of psycho-and pharmacotherapy for depression. We con-clude that GLMM tree is a promising algorithm for the detection of treatment-subgroup interactions in clustered datasets.},
author = {Fokkema, Marjolein and Smits, Niels and Zeileis, Achim and Hothorn, Torsten and Kelderman, Henk},
doi = {10.3758/s13428-017-0971-x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Fokkema et al. - 2017 - Detecting treatment-subgroup interactions in clustered data with generalized linear mixed-effects model trees.pdf:pdf},
isbn = {1342801709},
issn = {1554-3528},
journal = {Behavior Research Methods},
keywords = {classification and regression trees,generalized linear mixed-e↵ects model,model-based recursive partitioning,random ef-fects,treatment-subgroup interactions},
month = {oct},
pages = {1--32},
publisher = {Behavior Research Methods},
title = {{Detecting treatment-subgroup interactions in clustered data with generalized linear mixed-effects model trees}},
url = {http://eeecon.uibk.ac.at/{\%}0Ahttp://eeecon.uibk.ac.at/wopec/ http://link.springer.com/10.3758/s13428-017-0971-x},
year = {2017}
}
@article{Westling2011,
author = {Westling, Tatu},
file = {:C$\backslash$:/LocalStorage/References/2011/Westling{\_}2011{\_}Male organ and economic growth does size matter.pdf:pdf},
isbn = {3589191287},
keywords = {Male Organ},
mendeley-tags = {Male Organ},
number = {335},
title = {{Male organ and economic growth: does size matter?}},
url = {http://mpra.ub.uni-muenchen.de/32302/},
volume = {17},
year = {2011}
}
@article{Loh2005,
abstract = {The Living Planet Index was developed to measure the changing state of the world's biodiversity over time. It uses time-series data to calculate average rates of change in a large number of populations of terrestrial, freshwater and marine vertebrate species. The dataset contains about 3000 population time series for over 1100 species. Two methods of calculating the index are outlined: the chain method and a method based on linear modelling of log-transformed data. The dataset is analysed to compare the relative representation of biogeographic realms, ecoregional biomes, threat status and taxonomic groups among species contributing to the index. The two methods show very similar results: terrestrial species declined on average by 25{\%} from 1970 to 2000. Birds and mammals are over-represented in comparison with other vertebrate classes, and temperate species are over-represented compared with tropical species, but there is little difference in representation between threatened and non-threatened species. Some of the problems arising from over-representation are reduced by the way in which the index is calculated. It may be possible to reduce this further by post-stratification and weighting, but new information would first need to be collected for data-poor classes, realms and biomes.},
author = {Loh, Jonathan and Green, Rhys E and Ricketts, Taylor and Lamoreux, John and Jenkins, Martin and Kapos, Valerie and Randers, Jorgen},
doi = {10.1098/rstb.2004.1584},
file = {:C$\backslash$:/LocalStorage/References/2005/Loh et al.{\_}2005{\_}The Living Planet Index using species population time series to track trends in biodiversity.pdf:pdf},
isbn = {0962-8436 (Print)$\backslash$r0962-8436 (Linking)},
issn = {0962-8436},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
keywords = {Animals,Biodiversity,Conservation of Natural Resources,Conservation of Natural Resources: methods,Data Interpretation,Databases,Factual,International Cooperation,Linear Models,Population Dynamics,Research Design,Species Specificity,Statistical,Vertebrates},
month = {feb},
number = {1454},
pages = {289--95},
pmid = {15814346},
title = {{The Living Planet Index: using species population time series to track trends in biodiversity.}},
volume = {360},
year = {2005}
}
@article{Cardillo2008,
abstract = {Extinction risk varies among species, and comparative analyses can help clarify the causes of this variation. Here we present a phylogenetic comparative analysis of species-level extinction risk across nearly the whole of the class Mammalia. Our aims were to examine systematically the degree to which general predictors of extinction risk can be identified, and to investigate the relative importance of different types of predictors (life history, ecological, human impact and environmental) in determining extinction risk. A single global model explained 27.3{\%} of variation in mammal extinction risk, but explanatory power was lower for region-specific models (median R2=0.248) and usually higher for taxon-specific models (median R2=0.383). Geographical range size, human population density and latitude were the most consistently significant predictors of extinction risk, but otherwise there was little evidence for general, prescriptive indicators of high extinction risk across mammals. Our results therefore support the view that comparative models of relatively narrow taxonomic scope are likely to be the most precise.},
author = {Cardillo, Marcel and Mace, Georgina M and Gittleman, John L and Jones, Kate E and Bielby, Jon and Purvis, Andy},
doi = {10.1098/rspb.2008.0179},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Cardillo et al. - 2008 - The predictability of extinction biological and external correlates of decline in mammals.pdf:pdf},
isbn = {0962-8452 (Print)$\backslash$n0962-8452 (Linking)},
issn = {0962-8452},
journal = {Proceedings of the Royal Society B: Biological Sciences},
keywords = {phylogenetically independent contrasts,red list,supertree},
month = {jun},
number = {1641},
pages = {1441--1448},
pmid = {18367443},
title = {{The predictability of extinction: biological and external correlates of decline in mammals}},
url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2008.0179},
volume = {275},
year = {2008}
}
@article{Curtis2018,
abstract = {Global maps of forest loss depict the scale and magnitude of forest disturbance, yet companies, governments, and nongovernmental organizations need to distinguish permanent conversion (i.e., deforestation) from temporary loss from forestry or wildfire. Using satellite imagery, we developed a forest loss classification model to determine a spatial attribution of forest disturbance to the dominant drivers of land cover and land use change over the period 2001 to 2015. Our results indicate that 27{\%} of global forest loss can be attributed to deforestation through permanent land use change for commodity production. The remaining areas maintained the same land use over 15 years; in those areas, loss was attributed to forestry (26{\%}), shifting agriculture (24{\%}), and wildfire (23{\%}). Despite corporate commitments, the rate of commodity-driven deforestation has not declined. To end deforestation, companies must eliminate 5 million hectares of conversion from supply chains each year.},
author = {Curtis, Philip G. and Slay, Christy M. and Harris, Nancy L. and Tyukavina, Alexandra and Hansen, Matthew C.},
doi = {10.1126/science.aau3445},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Curtis et al. - 2018 - Classifying drivers of global forest loss.pdf:pdf},
issn = {0036-8075},
journal = {Science},
month = {sep},
number = {6407},
pages = {1108--1111},
pmid = {30213911},
title = {{Classifying drivers of global forest loss}},
url = {http://www.sciencemag.org/lookup/doi/10.1126/science.aau3445},
volume = {361},
year = {2018}
}
@article{Vellend2013,
abstract = {Global biodiversity is in decline. This is of concern for aesthetic and ethical reasons, but possibly also for practical reasons, as suggested by experimental studies, mostly with plants, showing that biodiversity reductions in small study plots can lead to compromised ecosystem function. However, inferring that ecosystem functions will decline due to biodiversity loss in the real world rests on the untested assumption that such loss is actually occurring at these small scales in nature. Using a global database of 168 published studies and {\textgreater}16,000 nonexperimental, local-scale vegetation plots, we show that mean temporal change in species diversity over periods of 5-261 y is not different from zero, with increases at least as likely as declines over time. Sites influenced primarily by plant species' invasions showed a tendency for declines in species richness, whereas sites undergoing postdisturbance succession showed increases in richness over time. Other distinctions among studies had little influence on temporal richness trends. Although maximizing diversity is likely important for maintaining ecosystem function in intensely managed systems such as restored grasslands or tree plantations, the clear lack of any general tendency for plant biodiversity to decline at small scales in nature directly contradicts the key assumption linking experimental results to ecosystem function as a motivation for biodiversity conservation in nature. How often real world changes in the diversity and composition of plant communities at the local scale cause ecosystem function to deteriorate, or actually to improve, remains unknown and is in critical need of further study.},
author = {Vellend, Mark and Baeten, Lander and Myers-Smith, Isla H and Elmendorf, Sarah C and Beausejour, R. and Brown, Carissa D and {De Frenne}, Pieter and Verheyen, Kris and Wipf, Sonja},
doi = {10.1073/pnas.1312779110},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Vellend et al. - 2013 - Global meta-analysis reveals no net change in local-scale plant biodiversity over time.pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
keywords = {20th Century,21st Century,Biodiversity,Conservation of Natural Resources,Conservation of Natural Resources: statistics {\&} nu,Ecosystem,History,Plants,Plants: genetics},
month = {nov},
number = {48},
pages = {19456--19459},
pmid = {24167259},
title = {{Global meta-analysis reveals no net change in local-scale plant biodiversity over time}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3845118{\&}tool=pmcentrez{\&}rendertype=abstract http://www.pnas.org/cgi/doi/10.1073/pnas.1312779110},
volume = {110},
year = {2013}
}
@article{Halekoh2014,
abstract = {When testing for reduction of the mean value structure in linear mixed models, it is common to use an asymptotic ?2 test. Such tests can, however, be very poor for small and moderate sample sizes. The pbkrtest package implements two alternatives to such approximate ?2 tests: The package implements (1) a Kenward-Roger approximation for performing F tests for reduction of the mean structure and (2) parametric bootstrap methods for achieving the same goal. The implementation is focused on linear mixed models with independent residual errors. In addition to describing the methods and aspects of their implementation, the paper also contains several examples and a comparison of the various methods.},
archivePrefix = {arXiv},
arxivId = {arXiv:1501.0228},
author = {Halekoh, Ulrich and H{\o}jsgaard, S{\o}ren},
doi = {10.18637/jss.v059.i09},
eprint = {arXiv:1501.0228},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Halekoh, H{\o}jsgaard - 2014 - A Kenward-Roger Approximation and Parametric Bootstrap Methods for Tests in Linear Mixed Models - The R Pack.pdf:pdf},
isbn = {9781420065213},
issn = {1548-7660},
journal = {Journal of Statistical Software},
keywords = {adjusted degree of freedom,bartlett correction,denominator degree of freedom,f test,linear mixed,lme4,model,parametric bootstrap,r},
number = {9},
pages = {1--32},
pmid = {18291371},
title = {{A Kenward-Roger Approximation and Parametric Bootstrap Methods for Tests in Linear Mixed Models - The R Package pbkrtest}},
url = {http://www.jstatsoft.org/index.php/jss/article/view/v059i09/v59i09.pdf http://www.jstatsoft.org/v59/i09/},
volume = {59},
year = {2014}
}
@misc{MuMIn,
author = {Barto{\'{n}}, Kamil},
keywords = {R-Library},
mendeley-tags = {R-Library},
title = {{MuMIn: Multi-model inference.}},
url = {http://cran.r-project.org/package=MuMIn},
year = {2015}
}
@article{Tscharntke2012,
abstract = {Understanding how landscape characteristics affect biodiversity patterns and ecological processes at local and landscape scales is critical for mitigating effects of global environmental change. In this review, we use knowledge gained from human-modified landscapes to suggest eight hypotheses, which we hope will encourage more systematic research on the role of landscape composition and configuration in determining the structure of ecological communities, ecosystem functioning and services. We organize the eight hypotheses under four overarching themes. Section A: 'landscape moderation of biodiversity patterns' includes (1) the landscape species pool hypothesis-the size of the landscape-wide species pool moderates local (alpha) biodiversity, and (2) the dominance of beta diversity hypothesis-landscape-moderated dissimilarity of local communities determines landscape-wide biodiversity and overrides negative local effects of habitat fragmentation on biodiversity. Section B: 'landscape moderation of population dynamics' includes (3) the cross-habitat spillover hypothesis-landscape-moderated spillover of energy, resources and organisms across habitats, including between managed and natural ecosystems, influences landscape-wide community structure and associated processes and (4) the landscape-moderated concentration and dilution hypothesis-spatial and temporal changes in landscape composition can cause transient concentration or dilution of populations with functional consequences. Section C: 'landscape moderation of functional trait selection' includes (5) the landscape-moderated functional trait selection hypothesis-landscape moderation of species trait selection shapes the functional role and trajectory of community assembly, and (6) the landscape-moderated insurance hypothesis-landscape complexity provides spatial and temporal insurance, i.e. high resilience and stability of ecological processes in changing environments. Section D: 'landscape constraints on conservation management' includes (7) the intermediate landscape-complexity hypothesis-landscape-moderated effectiveness of local conservation management is highest in structurally simple, rather than in cleared (i.e. extremely simplified) or in complex landscapes, and (8) the landscape-moderated biodiversity versus ecosystem service management hypothesis-landscape-moderated biodiversity conservation to optimize functional diversity and related ecosystem services will not protect endangered species. Shifting our research focus from local to landscape-moderated effects on biodiversity will be critical to developing solutions for future biodiversity and ecosystem service management.},
author = {Tscharntke, Teja and Tylianakis, Jason M and Rand, Tatyana a and Didham, Raphael K and Fahrig, Lenore and Bat{\'{a}}ry, P{\'{e}}ter and Bengtsson, Janne and Clough, Yann and Crist, Thomas O and Dormann, Carsten F and Ewers, Robert M and Fr{\"{u}}nd, Jochen and Holt, Robert D and Holzschuh, Andrea and Klein, Alexandra M and Kleijn, David and Kremen, Claire and Landis, Doug a and Laurance, William and Lindenmayer, David and Scherber, Christoph and Sodhi, Navjot and Steffan-Dewenter, Ingolf and Thies, Carsten and van der Putten, Wim H and Westphal, Catrin},
doi = {10.1111/j.1469-185X.2011.00216.x},
file = {:C$\backslash$:/LocalStorage/References/2012/Tscharntke et al.{\_}2012{\_}Landscape moderation of biodiversity patterns and processes - eight hypotheses.pdf:pdf},
issn = {1469-185X},
journal = {Biological reviews of the Cambridge Philosophical Society},
keywords = {Animals,Biodiversity,Conservation of Natural Resources,Conservation of Natural Resources: methods,Ecosystem,Environmental Monitoring,Environmental Monitoring: methods,Hypotheses,Landscape,Plants,Review},
mendeley-tags = {Biodiversity,Hypotheses,Landscape,Review},
month = {aug},
number = {3},
pages = {661--85},
pmid = {22272640},
title = {{Landscape moderation of biodiversity patterns and processes - eight hypotheses.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22272640},
volume = {87},
year = {2012}
}
@article{Struebig2011,
abstract = {The potential for parallel impacts of habitat change on multiple biodiversity levels has important conservation implications. We report on the first empirical test of the 'species-genetic diversity correlation' across co-distributed taxa with contrasting ecological traits in the context of habitat fragmentation. In a rainforest landscape undergoing conversion to oil palm, we show that depauperate species richness in fragments is mirrored by concomitant declines in population genetic diversity in the taxon predicted to be most susceptible to fragmentation. This association, not seen in the other species, relates to fragment area rather than isolation. While highlighting the over-simplification of extrapolating across taxa, we show that fragmentation presents a double jeopardy for some species. For these, conserving genetic diversity at levels of pristine forest could require sites 15-fold larger than those needed to safeguard species numbers. Importantly, however, each fragment contributes to regional species richness, with larger ones tending to contain more species.},
author = {Struebig, Matthew J. and Kingston, Tigga and Petit, Eric J. and {Le Comber}, Steven C. and Zubaid, Akbar and Mohd-Adnan, Adura and Rossiter, Stephen J.},
doi = {10.1111/j.1461-0248.2011.01623.x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Struebig et al. - 2011 - Parallel declines in species and genetic diversity in tropical forest fragments.pdf:pdf},
isbn = {1461-0248},
issn = {1461023X},
journal = {Ecology Letters},
keywords = {Allelic richness,Bat,Biodiversity,Conservation value,Habitat fragmentation,Oil palm,SLOSS,Species-area relationship,Species-genetic diversity correlation},
month = {jun},
number = {6},
pages = {582--590},
pmid = {21564453},
title = {{Parallel declines in species and genetic diversity in tropical forest fragments}},
url = {http://doi.wiley.com/10.1111/j.1461-0248.2011.01623.x},
volume = {14},
year = {2011}
}
@article{Robinson2014a,
abstract = {Deforestation and degradation are tied to a complex array of socioeconomic and political factors. Many assume that among the most important of these are the particular bundles of rights regulating who can benefit from land (tenure form) and the overall assurance that those rights will be upheld (tenure security). This paper reviews literature that connects forest outcomes and land tenure to better understand broad interactions between tenure form, security and forest change. Papers from economic theory suggest tenure is embedded in a broader socioeconomic context, with the potential for either a positive or negative conservation impact on forested land. Empirically, we find 36 publications that link land cover change to tenure conditions while also controlling for other plausibly confounding variables. Publications often investigate more than one site and more than one form of tenure, so from these we derive 118 cases linking forest change with a specific tenure form in a particular location. From these cases, we find evidence that protected areas are associated with positive forest outcomes and that land tenure security is associated with less deforestation, regardless of the form of tenure. We conclude with a call for more robust identification of this relationship in future research, as well as set of recommendations for policymakers, particularly as forest carbon incentive programs such as REDD integrate further into national policies. ?? 2013 Elsevier Ltd. All rights reserved.},
author = {Robinson, Brian E. and Holland, Margaret B. and Naughton-Treves, Lisa},
doi = {10.1016/j.gloenvcha.2013.05.012},
file = {:C$\backslash$:/LocalStorage/References/2014/Robinson, Holland, Naughton-Treves{\_}2014{\_}Does secure land tenure save forests A meta-analysis of the relationship between land tenure and.pdf:pdf},
isbn = {0959-3780},
issn = {09593780},
journal = {Global Environmental Change},
keywords = {Deforestation,Degradation,Land tenure,Land tenure security,Meta-analysis,Protected areas},
month = {nov},
pages = {281--293},
publisher = {Elsevier Ltd},
title = {{Does secure land tenure save forests? A meta-analysis of the relationship between land tenure and tropical deforestation}},
url = {http://dx.doi.org/10.1016/j.gloenvcha.2013.05.012 http://linkinghub.elsevier.com/retrieve/pii/S0959378013000976},
volume = {29},
year = {2014}
}
@article{Peres2006,
abstract = {Tropical forests are beleaguered by an array of threats driven by different scales of anthropogenic perturbations, which vary in the degree to which they can be detected by remote sensing. The extent of different patterns of cryptic disturbance often far exceeds the total area deforested, as shown by two recent studies on selective logging in Amazonia. Here, we discuss different forms of disturbance in Amazonian forests and question how much of the apparently intact forest in this region remains relatively undisturbed.},
author = {Peres, Carlos A. and Barlow, Jos and Laurance, William F.},
doi = {10.1016/j.tree.2006.03.007},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Peres, Barlow, Laurance - 2006 - Detecting anthropogenic disturbance in tropical forests.pdf:pdf;:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Peres, Barlow, Laurance - 2006 - Detecting anthropogenic disturbance in tropical forests(2).pdf:pdf},
isbn = {0169-5347},
issn = {0169-5347},
journal = {Trends in Ecology {\&} Evolution},
keywords = {Brazil,Conservation of Natural Resources,Fires,Humans,Time Factors,Trees,Tropical Climate},
month = {may},
number = {5},
pages = {227--9},
pmid = {16697907},
title = {{Detecting anthropogenic disturbance in tropical forests.}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534706000942},
volume = {21},
year = {2006}
}
@article{Currie2004,
abstract = {Broad-scale variation in taxonomic richness is strongly correlated with climate. Many mechanisms have been hypothesized to explain these patterns; however, testable predictions that would distinguish among them have rarely been derived. Here, we examine several prominent hypotheses for climate–richness relationships, deriving and testing predictions based on their hypothesized mechanisms. The ?energy–richness hypothesis? (also called the ?more individuals hypothesis? ) postulates that more productive areas have more individuals and therefore more species. More productive areas do often have more species, but extant data are not consistent with the expected causal relationship from energy to numbers of individuals to numbers of species. We reject the energy–richness hypothesis in its standard form and consider some proposed modifications. The ?physiological tolerance hypothesis? postulates that richness varies according to the tolerances of individual species for different sets of climatic conditions. This hypothesis predicts that more combinations of physiological parameters can survive under warm and wet than cold or dry conditions. Data are qualitatively consistent with this prediction, but are inconsistent with the prediction that species should fill climatically suitable areas. Finally, the ?speciation rate hypothesis? postulates that speciation rates should vary with climate, due either to faster evolutionary rates or stronger biotic interactions increasing the opportunity for evolutionary diversification in some regions. The biotic interactions mechanism also has the potential to amplify shallower, underlying gradients in richness. Tests of speciation rate hypotheses are few (to date), and their results are mixed.},
author = {Currie, David J. and Mittelbach, Gary G. and Cornell, Howard V. and Field, Richard and Gu{\'{e}}gan, Jean Francois and Hawkins, Bradford a. and Kaufman, Dawn M. and Kerr, Jeremy T. and Oberdorff, Thierry and O'Brien, Eileen and Turner, J. R G},
doi = {10.1111/j.1461-0248.2004.00671.x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Currie et al. - 2004 - Predictions and tests of climate-based hypotheses of broad-scale variation in taxonomic richness.pdf:pdf},
isbn = {1461-023X},
issn = {1461023X},
journal = {Ecology Letters},
keywords = {Climatic gradients,Latitudinal gradients,Productivity,Speciation,Species richness,Species-energy theory},
number = {12},
pages = {1121--1134},
pmid = {231},
title = {{Predictions and tests of climate-based hypotheses of broad-scale variation in taxonomic richness}},
volume = {7},
year = {2004}
}
@article{Joppa2011,
author = {Joppa, L. N. and Pfaff, A.},
doi = {10.1098/rspb.2010.1713},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Joppa, Pfaff - 2011 - Global protected area impacts.pdf:pdf},
issn = {0962-8452},
journal = {Proceedings of the Royal Society B: Biological Sciences},
keywords = {conservation impacts,deforestation,land cover,matching,protected areas,redd},
month = {jun},
number = {1712},
pages = {1633--1638},
title = {{Global protected area impacts}},
url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2010.1713},
volume = {278},
year = {2011}
}
@article{Rocchini2016,
abstract = {Assessing the level of diversity in plant communities from field-based data is difficult for a number of practical reasons: (1) establishing the number of sam-pling units to be investigated can be difficult; (2) the choice of sample design can impact on results; and (3) defining the population of concern can be chal-lenging. Satellite remote sensing (SRS) is one of the most cost-effective approaches to identify biodiversity hotspots and predict changes in species composition. This is because, in contrast to field-based methods, it allows for complete spatial coverages of the Earth's surface under study over a short per-iod of time. Furthermore, SRS provides repeated measures, thus making it pos-sible to study temporal changes in biodiversity. Here, we provide a concise review of the potential of satellites to help track changes in plant species diver-sity, and provide, for the first time, an overview of the potential pitfalls associ-ated with the misuse of satellite imagery to predict species diversity. Our work shows that, while the assessment of alpha-diversity is relatively straightforward, calculation of beta-diversity (variation in species composition between adjacent locations) is challenging, making it difficult to reliably estimate gamma-diversity (total diversity at the landscape or regional level). We conclude that an increased collaboration between the remote sensing and biodiversity communi-ties is needed in order to properly address future challenges and developments.},
author = {Rocchini, Duccio and Boyd, Doreen S and F{\'{e}}ret, Jean-Baptiste and Foody, Giles M and He, Kate S and Lausch, Angela and Nagendra, Harini and Wegmann, Martin and Pettorelli, Nathalie},
doi = {10.1002/rse2.9},
editor = {Skidmore, Andrew and Chauvenet, Alienor},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Rocchini et al. - 2016 - Satellite remote sensing to monitor species diversity potential and pitfalls.pdf:pdf},
isbn = {20563485},
issn = {20563485},
journal = {Remote Sensing in Ecology and Conservation},
keywords = {alpha-diversity,beta-diversity,biodiversity,distance decay models,remote sensing},
month = {feb},
number = {1},
pages = {25--36},
title = {{Satellite remote sensing to monitor species diversity: potential and pitfalls}},
url = {http://doi.wiley.com/10.1002/rse2.9},
volume = {2},
year = {2016}
}
@article{Martay2017,
abstract = {Climate change has had well-documented impacts on the distribution and phenology of species across many taxa, but impacts on species' abundance, which relates closely to extinction risk and ecosystem function, have not been assessed across taxa. In the most comprehensive multi-taxa comparison to date, we modelled variation in national population indices of 501 mammal, bird, aphid, butterfly and moth species as a function of annual variation in weather variables, which through time allowed us to identify a component of species' population growth that can be associated with post-1970s climate trends. We found evidence that these climate trends have significantly affected population trends of 15.8{\%} of species, including eight with extreme ({\textgreater} 30{\%} decline per decade) negative trends consistent with detrimental impacts of climate change. The modelled effect of climate change could explain 48{\%} of the significant across-species population decline in moths and 63{\%} of the population increase in winged aphids. The other taxa did not have significant across-species population trends or consistent climate change responses. Population declines in species of conservation concern were linked to both climatic and non-climatic factors respectively accounting for 42 and 58{\%} of the decline. Evident differential impacts of climate change between trophic levels may signal the potential for future ecosystem disruption. Climate change has therefore already driven large-scale population changes of some species, had significant impacts on the overall abundance of some key invertebrate groups and may already have altered biological communities and ecosystems in Great Britain.},
author = {Martay, B. and Brewer, M. J. and Elston, D. A. and Bell, J. R. and Harrington, R. and Brereton, T. M. and Barlow, K. E. and Botham, M. S. and Pearce-Higgins, J. W.},
doi = {10.1111/ecog.02411},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Martay et al. - 2017 - Impacts of climate change on national biodiversity population trends.pdf:pdf},
isbn = {0039022643407},
issn = {09067590},
journal = {Ecography},
month = {oct},
number = {10},
pages = {1139--1151},
title = {{Impacts of climate change on national biodiversity population trends}},
url = {http://doi.wiley.com/10.1111/ecog.02411},
volume = {40},
year = {2017}
}
@article{Wulder2009,
author = {Wulder, Michael A. and White, Joanne C. and Andrew, Margaret E. and Seitz, Nicole E. and Coops, Nicholas C.},
doi = {10.1016/j.foreco.2009.07.041},
issn = {03781127},
journal = {Forest Ecology and Management},
keywords = {landscape composition},
month = {oct},
number = {9},
pages = {1938--1949},
title = {{Forest fragmentation, structure, and age characteristics as a legacy of forest management}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0378112709005131},
volume = {258},
year = {2009}
}
@article{EVANNO2009,
abstract = {We examined the spatial and temporal variation of species diversity and genetic diversity in a metacommunity comprising 16 species of freshwater gastropods. We monitored species abundance at five localities of the Ain river floodplain in southeastern France, over a period of four years. Using 190 AFLP loci, we monitored the genetic diversity of Radix balthica, one of the most abundant gastropod species of the metacommunity, twice during that period. An exceptionally intense drought occurred during the last two years and differentially affected the study sites. This allowed us to test the effect of natural disturbances on changes in both genetic and species diversity. Overall, local (alpha) diversity declined as reflected by lower values of gene diversity H(S) and evenness. In parallel, the among-sites (beta) diversity increased at both the genetic (F(ST)) and species (F(STC)) levels. These results suggest that disturbances can lead to similar changes in genetic and community structure through the combined effects of selective and neutral processes.},
author = {EVANNO, GUILLAUME and CASTELLA, EMMANUEL and ANTOINE, C{\'{E}}LINE and PAILLAT, GABRIELLE and GOUDET, J{\'{E}}R{\^{O}}ME},
doi = {10.1111/j.1365-294X.2009.04102.x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/EVANNO et al. - 2009 - Parallel changes in genetic diversity and species diversity following a natural disturbance.pdf:pdf},
isbn = {09621083$\backslash$n1365294X},
issn = {09621083},
journal = {Molecular Ecology},
keywords = {Beta diversity,Biodiversity,Disturbance,Floodplain,Gastropods,Genetic structure},
month = {mar},
number = {6},
pages = {1137--1144},
pmid = {19226317},
title = {{Parallel changes in genetic diversity and species diversity following a natural disturbance}},
url = {http://doi.wiley.com/10.1111/j.1365-294X.2009.04102.x},
volume = {18},
year = {2009}
}
@article{Harrison2011,
abstract = {1. Carry-over effects occur when processes in one season influence the success of an individual in the following season. This phenomenon has the potential to explain a large amount of variation in individual fitness, but so far has only been described in a limited number of species. This is largely due to difficulties associated with tracking individuals between periods of the annual cycle, but also because of a lack of research specifically designed to examine hypotheses related to carry-over effects. 2. We review the known mechanisms that drive carry-over effects, most notably macronutrient supply, and highlight the types of life histories and ecological situations where we would expect them to most often occur. We also identify a number of other potential mechanisms that require investigation, including micronutrients such as antioxidants. 3. We propose a series of experiments designed to estimate the relative contributions of extrinsic and intrinsic quality effects in the pre-breeding season, which in turn will allow an accurate estimation of the magnitude of carry-over effects. To date this has proven immensely difficult, and we hope that the experimental frameworks described here will stimulate new avenues of research vital to advancing our understanding of how carry-over effects can shape animal life histories. 4. We also explore the potential of state-dependent modelling as a tool for investigating carry-over effects, most notably for its ability to calculate optimal rates of acquisition of a multitude of resources over the course of the annual cycle, and also because it allows us to vary the strength of density-dependent relationships which can alter the magnitude of carry-over effects in either a synergistic or agonistic fashion. 5. In conclusion carry-over effects are likely to be far more widespread than currently indicated, and they are likely to be driven by a multitude of factors including both macro- and micronutrients. For this reason they could feasibly be responsible for a large amount of the observed variation in performance among individuals, and consequently warrant a wealth of new research designed specifically to decompose components of variation in fitness attributes related to processes across and within seasons.},
author = {Harrison, Xavier a. and Blount, Jonathan D. and Inger, Richard and Norris, D. Ryan and Bearhop, Stuart},
doi = {10.1111/j.1365-2656.2010.01740.x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Harrison et al. - 2011 - Carry-over effects as drivers of fitness differences in animals.pdf:pdf},
isbn = {0021-8790},
issn = {00218790},
journal = {Journal of Animal Ecology},
keywords = {Density dependence,Micronutrients,Population dynamics,Reproductive threshold,Seasonal interactions,State-dependent modelling},
month = {jan},
number = {1},
pages = {4--18},
pmid = {20726924},
title = {{Carry-over effects as drivers of fitness differences in animals}},
url = {http://doi.wiley.com/10.1111/j.1365-2656.2010.01740.x},
volume = {80},
year = {2011}
}
@article{Pysek2010,
abstract = {The accelerating rates of international trade, travel, and transport in the latter half of the twentieth century have led to the progressive mixing of biota from across the world and the number of species introduced to new regions continues to increase. The importance of biogeographic, climatic, economic, and demographic factors as drivers of this trend is increasingly being realized but as yet there is no consensus regarding their relative importance. Whereas little may be done to mitigate the effects of geography and climate on invasions, a wider range of options may exist to moderate the impacts of economic and demographic drivers. Here we use the most recent data available from Europe to partition between macroecological, economic, and demographic variables the variation in alien species richness of bryophytes, fungi, vascular plants, terrestrial insects, aquatic invertebrates, fish, amphibians, reptiles, birds, and mammals. Only national wealth and human population density were statistically significant predictors in the majority of models when analyzed jointly with climate, geography, and land cover. The economic and demographic variables reflect the intensity of human activities and integrate the effect of factors that directly determine the outcome of invasion such as propagule pressure, pathways of introduction, eutrophication, and the intensity of anthropogenic disturbance. The strong influence of economic and demographic variables on the levels of invasion by alien species demonstrates that future solutions to the problem of biological invasions at a national scale lie in mitigating the negative environmental consequences of human activities that generate wealth and by promoting more sustainable population growth.},
author = {Pysek, Petr and Jarosik, V. and Hulme, P. E. and Kuhn, I. and Wild, Jan and Arianoutsou, Margarita and Bacher, Sven and Chiron, F. and Didziulis, Viktoras and Essl, Franz and Genovesi, Piero and Gherardi, Francesca and Hejda, Martin and Kark, Salit and Lambdon, Philip W. and Desprez-Loustau, M.-L. and Nentwig, Wolfgang and Pergl, Jan and Poboljsaj, Katja and Rabitsch, Wolfgang and Roques, Alain and Roy, David B. and Shirley, Susan and Solarz, Wojciech and Vila, M. and Winter, Marten},
doi = {10.1073/pnas.1002314107},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Pysek et al. - 2010 - Disentangling the role of environmental and human pressures on biological invasions across Europe.pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
keywords = {Animals,Biodiversity,Biological,Climate,Ecosystem,Environment,Europe,Fungi,Fungi: growth {\&} development,Geography,Human Activities,Humans,Invertebrates,Invertebrates: growth {\&} development,Mammals,Mammals: growth {\&} development,Models,Plant Development,Population Density,Population Dynamics,Regression Analysis},
month = {jul},
number = {27},
pages = {12157--12162},
pmid = {20534543},
title = {{Disentangling the role of environmental and human pressures on biological invasions across Europe}},
url = {http://www.pnas.org/content/107/27/12157.short http://www.pnas.org/cgi/doi/10.1073/pnas.1002314107},
volume = {107},
year = {2010}
}
@article{Walther2002,
abstract = {There is now ample evidence of the ecological impacts of recent climate change, from polar terrestrial to tropical marine environments. The responses of both flora and fauna span an array of ecosystems and organizational hierarchies, from the species to the community levels. Despite continued uncertainty as to community and ecosystem trajectories under global change, our review exposes a coherent pattern of ecological change across systems. Although we are only at an early stage in the projected trends of global warming, ecological responses to recent climate change are already clearly visible.},
author = {Walther, Gian-Reto and Post, Eric and Convey, Peter and Menzel, Annette and Parmesan, Camille and Beebee, Trevor J C and Fromentin, Jean-Marc and Hoegh-Guldberg, Ove and Bairlein, Franz},
doi = {10.1038/416389a},
file = {:C$\backslash$:/LocalStorage/References/2002/Walther et al.{\_}2002{\_}Ecological responses to recent climate change.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
keywords = {Animals,Climate,Climate-Change,Ecology,Environment,Humans,Plants},
mendeley-tags = {Climate-Change},
month = {mar},
number = {6879},
pages = {389--95},
pmid = {11919621},
title = {{Ecological responses to recent climate change.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3145734{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {416},
year = {2002}
}
@article{Fahrig2003a,
abstract = {The literature on effects of habitat fragmentation on biodiversity is huge. It is also very diverse, with different authors measuring fragmentation in different ways and, as a consequence, drawing different conclusions regarding both the magnitude and direction of its effects. Habitat fragmentation is usually defined as a landscape-scale process involving both habitat loss and the breaking apart of habitat. Results of empirical studies of habitat fragmentation are often difficult to interpret because (a) many researchers measure fragmentation at the patch scale, not the landscape scale and (b) most researchers measure fragmentation in ways that do not distinguish between habitat loss and habitat fragmentation per se, i.e., the breaking apart of habitat after controlling for habitat loss. Empirical studies to date suggest that habitat loss has large, consistently negative effects on biodiversity. Habitat fragmentation per se has much weaker effects on biodiversity that are at least as likely to be positive as negative. Therefore, to correctly interpret the influence of habitat fragmentation on biodiversity, the effects of these two components of fragmentation must be measured independently. More studies of the independent effects of habitat loss and fragmentation per se are needed to determine the factors that lead to positive versus negative effects of fragmentation per se. I suggest that the term "fragmentation" should be reserved for the breaking apart of habitat, independent of habitat loss.},
author = {Fahrig, Lenore},
doi = {10.1146/annurev.ecolsys.34.011802.132419},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Fahrig - 2003 - Effects of Habitat Fragmentation on Biodiversity.pdf:pdf},
isbn = {00664162 (ISSN)},
issn = {1543-592X},
journal = {Annual Review of Ecology, Evolution, and Systematics},
keywords = {Fragmentation,Review,diverse,extinction threshold,fragmentation in dif-,fragmentation on biodiversity is,habitat,habitat configuration,habitat loss,huge,isolation,it is also very,landscape complementation,landscape scale,on effects of habitat,patch,patch isolation,patch size,s abstract the literature,with different authors measuring},
mendeley-tags = {Fragmentation,Review},
month = {nov},
number = {1},
pages = {487--515},
pmid = {220102000018},
title = {{Effects of Habitat Fragmentation on Biodiversity}},
url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.34.011802.132419 http://www.jstor.org/stable/30033784{\%}5Cnhttp://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.34.011802.132419},
volume = {34},
year = {2003}
}
@article{Smit2011,
author = {Smit, Izak P. J.},
doi = {10.1111/j.1600-0587.2010.06029.x},
file = {:C$\backslash$:/LocalStorage/References/2011/Smit{\_}2011{\_}Resources driving landscape-scale distribution patterns of grazers in an African savanna.pdf:pdf},
issn = {09067590},
journal = {Ecography},
month = {feb},
number = {1},
pages = {67--74},
title = {{Resources driving landscape-scale distribution patterns of grazers in an African savanna}},
url = {http://doi.wiley.com/10.1111/j.1600-0587.2010.06029.x},
volume = {34},
year = {2011}
}
@article{VERBURG2011,
author = {Verburg, Peter H. and Neumann, Kathleen and Nol, Linda},
doi = {10.1111/j.1365-2486.2010.02307.x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Verburg, Neumann, Nol - 2011 - Challenges in using land use and land cover data for global change studies.pdf:pdf},
issn = {13541013},
journal = {Global Change Biology},
keywords = {31 july 2010,climate change,emission inventory,integrated assessment,july 2010 and accepted,land cover,land use,received 19 april 2010,revised version received 26,spatial data},
month = {feb},
number = {2},
pages = {974--989},
title = {{Challenges in using land use and land cover data for global change studies}},
url = {http://doi.wiley.com/10.1111/j.1365-2486.2010.02307.x},
volume = {17},
year = {2011}
}
@article{Chase2013,
abstract = {There is little consensus about how natural (e.g. productivity, disturbance) and anthropogenic (e.g. invasive species, habitat destruction) ecological drivers influence biodiversity. Here, we show that when sampling is standardised by area (species density) or individuals (rarefied species richness), the measured effect sizes depend critically on the spatial grain and extent of sampling, as well as the size of the species pool. This compromises comparisons of effects sizes within studies using standard statistics, as well as among studies using meta-analysis. To derive an unambiguous effect size, we advocate that comparisons need to be made on a scale-independent metric, such as Hurlbert's Probability of Interspecific Encounter. Analyses of this metric can be used to disentangle the relative influence of changes in the absolute and relative abundances of individuals, as well as their intraspecific aggregations, in driving differences in biodiversity among communities. This and related approaches are necessary to achieve generality in understanding how biodiversity responds to ecological drivers and will necessitate a change in the way many ecologists collect and analyse their data.},
author = {Chase, Jonathan M. and Knight, Tiffany M.},
doi = {10.1111/ele.12112},
file = {:C$\backslash$:/LocalStorage/References/2013/Chase, Knight{\_}2013{\_}Scale-dependent effect sizes of ecological drivers on biodiversity Why standardised sampling is not enough.pdf:pdf},
isbn = {1461-023X},
issn = {1461023X},
journal = {Ecology Letters},
keywords = {Biodiversity,Effect size,Intraspecific aggregation,Modelling,Probability of interspecific encounter,Rarefaction,Species abundance distribution,Species-accumulation curve},
mendeley-tags = {Biodiversity,Modelling},
month = {may},
pages = {17--26},
pmid = {23679009},
title = {{Scale-dependent effect sizes of ecological drivers on biodiversity: Why standardised sampling is not enough}},
volume = {16},
year = {2013}
}
@article{Rosa2014,
abstract = {Land-use and land-cover (LULC) change is one of the largest drivers of biodiversity loss and carbon emissions globally. We use the tropical rainforests of the Amazon, the Congo basin and South-East Asia as a case study to investigate spatial predictive models of LULC change. Current predictions differ in their modelling approaches, are highly variable and often poorly validated. We carried out a quantitative review of 48 modelling methodologies, considering model spatio-temporal scales, inputs, calibration and validation methods. In addition, we requested model outputs from each of the models reviewed and carried out a quantitative assessment of model performance for tropical LULC predictions in the Brazilian Amazon. We highlight existing shortfalls in the discipline and uncover three key points that need addressing to improve the transparency, reliability and utility of tropical LULC change models: (1) a lack of openness with regard to describing and making available the model inputs and model code; (2) the difficulties of conducting appropriate model validations; and (3) the difficulty that users of tropical LULC models face in obtaining the model predictions to help inform their own analyses and policy decisions. We further draw comparisons between tropical LULC change models in the tropics and the modelling approaches and paradigms in other disciplines, and suggest that recent changes in the climate change and species distribution modelling communities may provide a pathway that tropical LULC change modellers may emulate to further improve the discipline. Climate change models have exerted considerable influence over public perceptions of climate change and now impact policy decisions at all political levels. We suggest that tropical LULC change models have an equally high potential to influence public opinion and impact the development of land-use policies based on plausible future scenarios, but, to do that reliably may require further improvements in the discipline.},
author = {Rosa, Isabel M D and Ahmed, Sadia E. and Ewers, Robert M.},
doi = {10.1111/gcb.12523},
file = {:C$\backslash$:/LocalStorage/References/2014/Rosa, Ahmed, Ewers{\_}2014{\_}The transparency, reliability and utility of tropical rainforest land-use and land-cover change models.pdf:pdf},
isbn = {1365-2486},
issn = {13652486},
journal = {Global Change Biology},
keywords = {Amazon,Input data,Land use,Model comparison,Modelling framework,Prediction,Spatio-temporal scales,Tropical,Tropical LULC change,Validation methods},
mendeley-tags = {Land use,Prediction,Tropical},
pages = {1707--1722},
pmid = {24399778},
title = {{The transparency, reliability and utility of tropical rainforest land-use and land-cover change models}},
volume = {20},
year = {2014}
}
@article{Yan2016,
author = {Yan, L. and Roy, D.P.},
doi = {10.1016/j.rse.2015.10.034},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Yan, Roy - 2016 - Conterminous United States crop field size quantification from multi-temporal Landsat data.pdf:pdf},
issn = {00344257},
journal = {Remote Sensing of Environment},
keywords = {Agriculture,Fields,Landsat,Object extraction,WELD},
month = {jan},
pages = {67--86},
publisher = {The Authors},
title = {{Conterminous United States crop field size quantification from multi-temporal Landsat data}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0034425715301851},
volume = {172},
year = {2016}
}
@article{Levis2017,
author = {Levis, C. and Costa, F. R. C. and Bongers, F. and Pe{\~{n}}a-Claros, M. and Clement, C. R. and Junqueira, A. B. and Neves, E G and Tamanaha, E K and Figueiredo, F O G and Salom{\~{a}}o, R P and Castilho, C V and Magnusson, W. E. and Phillips, O. L. and Guevara, J. E. and Sabatier, D. and Molino, J.-F. and L{\'{o}}pez, D. C{\'{a}}rdenas and Mendoza, A. M. and Pitman, N. C. A. and Duque, A. and Vargas, P. N{\'{u}}{\~{n}}ez and Zartman, C E and Vasquez, R and Andrade, A and Camargo, J L and Feldpausch, T R and Laurance, S. G. W. and Laurance, W. F. and Killeen, T. J. and Nascimento, H. E. Mendon{\c{c}}a and Montero, J. C. and Mostacedo, B. and Amaral, I. L. and {Guimar{\~{a}}es Vieira}, I. C. and Brienen, R. and Castellanos, H. and Terborgh, J. and Carim, M. de Jesus Veiga and Guimar{\~{a}}es, J. R. da Silva and Coelho, L De Souza and Matos, F D De Almeida and Wittmann, F and Mogoll{\'{o}}n, H F and Damasco, G and D{\'{a}}vila, N. and Garc{\'{i}}a-Villacorta, R. and Coronado, E. N. H. and Emilio, T. and Filho, D. de Andrade Lima and Schietti, J. and Souza, P. and Targhetta, N. and Comiskey, J. A. and Marimon, B. S. and Marimon, B.-H. and Neill, D. and Alonso, A. and Arroyo, L. and Carvalho, F. A. and de Souza, F. C. and Dallmeier, F. and Pansonato, M. P. and Duivenvoorden, J. F. and Fine, P. V. A. and Stevenson, P. R. and Araujo-Murakami, A. and {Aymard C.}, G. A. and Baraloto, C. and do Amaral, D. D. and Engel, J. and Henkel, T. W. and Maas, P. and Petronelli, P. and Revilla, J. D. Cardenas and Stropp, J. and Daly, D. and Gribel, R. and Paredes, M. R{\'{i}}os and Silveira, M. and Thomas-Caesar, R. and Baker, T. R. and da Silva, N. F. and Ferreira, L. V. and Peres, C. A. and Silman, M. R. and Cer{\'{o}}n, C. and Valverde, F. C. and {Di Fiore}, A. and Jimenez, E. M. and Mora, M. C. Pe{\~{n}}uela and Toledo, M. and Barbosa, E. M. and Bonates, L. C. de Matos and Arboleda, N. C. and Farias, E. de Sousa and Fuentes, A. and Guillaumet, J.-L. and J{\o}rgensen, P. M{\o}ller and Malhi, Y. and {de Andrade Miranda}, I. P. and Phillips, J. F. and Prieto, A. and Rudas, A. and Ruschel, A. R. and Silva, N. and von Hildebrand, P. and Vos, V. A. and Zent, E. L. and Zent, S. and Cintra, B. B. L. and Nascimento, M. T. and Oliveira, A. A. and Ramirez-Angulo, H. and Ramos, J. F. and Rivas, G. and Sch{\"{o}}ngart, J. and Sierra, R. and Tirado, M. and van der Heijden, G. and Torre, E. V. and Wang, O. and Young, K. R. and Baider, C. and Cano, A. and Farfan-Rios, W. and Ferreira, C. and Hoffman, B. and Mendoza, C. and Mesones, I. and Torres-Lezama, A. and Medina, M. N. U. and van Andel, T. R. and Villarroel, D. and Zagt, R. and Alexiades, M. N. and Balslev, H. and Garcia-Cabrera, K. and Gonzales, T. and Hernandez, L. and Huamantupa-Chuquimaco, I. and Manzatto, A. G. and Milliken, W. and Cuenca, W. P. and Pansini, S. and Pauletto, D. and Arevalo, F. R. and Reis, N. F. Costa and Sampaio, A. F. and Giraldo, L. E. Urrego and Sandoval, E. H. Valderrama and Gamarra, L. Valenzuela and Vela, C. I. A. and ter Steege, H.},
doi = {10.1126/science.aal0157},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Levis et al. - 2017 - Persistent effects of pre-Columbian plant domestication on Amazonian forest composition.pdf:pdf},
issn = {0036-8075},
journal = {Science},
month = {mar},
number = {6328},
pages = {925--931},
title = {{Persistent effects of pre-Columbian plant domestication on Amazonian forest composition}},
url = {http://www.sciencemag.org/lookup/doi/10.1126/science.aal0157},
volume = {355},
year = {2017}
}
@article{Bai2003,
abstract = {In a recent paper, Bai and Perron (1998) considered theoretical issues related to the limiting distribution of estimators and test statistics in the linear model with multiple structural changes. In this companion paper, we consider practical issues for the empirical applications of the procedures. We first address the problem of estimation of the break dates and present an efficient algorithm to obtain global minimizers of the sum of squared residuals. This algorithm is based on the principle of dynamic programming and requires at most least-squares operations of order O(T2) for any number of breaks. Our method can be applied to both pure and partial structural change models. Second, we consider the problem of forming confidence intervals for the break dates under various hypotheses about the structure of the data and the errors across segments. Third, we address the issue of testing for structural changes under very general conditions on the data and the errors. Fourth, we address the issue of estimating the number of breaks. Finally, a few empirical applications are presented to illustrate the usefulness of the procedures. All methods discussed are implemented in a GAUSS program.},
author = {Bai, Jushan and Perron, Pierre},
doi = {10.1002/jae.659},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Bai, Perron - 2003 - Computation and analysis of multiple structural change models.pdf:pdf},
isbn = {08837252},
issn = {0883-7252},
journal = {Journal of Applied Econometrics},
month = {jan},
number = {1},
pages = {1--22},
pmid = {15795132},
title = {{Computation and analysis of multiple structural change models}},
url = {http://doi.wiley.com/10.1002/jae.659},
volume = {18},
year = {2003}
}
@article{GuilleraArroita2019,
author = {Guillera‐Arroita, Gurutzeta and K{\'{e}}ry, Marc and Lahoz‐Monfort, Jos{\'{e}} J.},
doi = {10.1002/ece3.4821},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Guillera‐Arroita, K{\'{e}}ry, Lahoz‐Monfort - 2019 - Inferring species richness using multispecies occupancy modeling Estimation performance a.pdf:pdf},
issn = {2045-7758},
journal = {Ecology and Evolution},
keywords = {sempach,swiss ornithological institute},
month = {jan},
number = {2},
pages = {780--792},
title = {{Inferring species richness using multispecies occupancy modeling: Estimation performance and interpretation}},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.4821},
volume = {9},
year = {2019}
}
@article{Oldeland2010,
abstract = {Different approaches for the assessment of biodiversity by means of remote sensing were developed over the last decades. A new approach, based on the spectral variation hypothesis, proposes that the spectral heterogeneity of a remotely sensed image is correlated with landscape structure and complexity which also reflects habitat heterogeneity which itself is known to enhance species diversity. In this context, previous studies only applied species richness as a measure of diversity. The aim of this paper was to analyze the relationship of richness and abundance-based diversity measures with spectral variability and compare the results at two scales. At three different test sites in Central Namibia, measures of vascular plant diversity was sampled at two scales - 100 m2 and 1000 m2. Hyperspectral remote sensing data were collected for the study sites and spectral variability, was calculated at plot level. Ordinary least square regression was used to test the relationship between species richness and the abundance-based Shannon Index and spectral variability. We found that Shannon Index permanently achieved better results at all test sites especially at 1000 m2, Even when all sites where pooled together, Shannon Index was still significantly related with spectral variability at 1000 m2. We suggest incorporating abundance-based diversity measures in studies of relationships between ecological and spectral variability. The contribution made by the high spectral and spatial resolution of the hyperspectral sensor is discussed. {\textcopyright} 2009 Elsevier Ltd. All rights reserved.},
author = {Oldeland, Jens and Wesuls, Dirk and Rocchini, Duccio and Schmidt, Michael and J{\"{u}}rgens, Norbert},
doi = {10.1016/j.ecolind.2009.07.012},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Oldeland et al. - 2010 - Does using species abundance data improve estimates of species diversity from remotely sensed spectral heteroge.pdf:pdf},
isbn = {1470-160X},
issn = {1470160X},
journal = {Ecological Indicators},
keywords = {Hyperspectral,Savannah,Scale,Shannon Index,Species richness,Spectral variation hypothesis},
number = {2},
pages = {390--396},
title = {{Does using species abundance data improve estimates of species diversity from remotely sensed spectral heterogeneity?}},
volume = {10},
year = {2010}
}
@article{Granger1969,
author = {Granger, C. W. J.},
doi = {10.2307/1912791},
file = {:C$\backslash$:/LocalStorage/References/1912791.pdf:pdf},
issn = {00129682},
journal = {Econometrica},
month = {aug},
number = {3},
pages = {424},
title = {{Investigating Causal Relations by Econometric Models and Cross-spectral Methods}},
url = {https://www.jstor.org/stable/1912791?origin=crossref},
volume = {37},
year = {1969}
}
@article{Hermosilla2015a,
author = {Hermosilla, Txomin and Wulder, Michael A. and White, Joanne C. and Coops, Nicholas C. and Hobart, Geordie W.},
doi = {10.1016/j.rse.2015.09.004},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Hermosilla et al. - 2015 - Regional detection, characterization, and attribution of annual forest change from 1984 to 2012 using Landsat.pdf:pdf},
issn = {00344257},
journal = {Remote Sensing of Environment},
keywords = {Change detection,Image compositing,Landsat,Object based change,Temporal analysis},
month = {dec},
pages = {121--132},
publisher = {Elsevier Inc.},
title = {{Regional detection, characterization, and attribution of annual forest change from 1984 to 2012 using Landsat-derived time-series metrics}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0034425715301279},
volume = {170},
year = {2015}
}
@article{Rufin2015,
abstract = {Monitoring changes in land use intensity of grazing systems in the Amazon is an important prerequisite to study the complex political and socio-economic forces driving Amazonian deforestation. Remote sensing offers the potential to map pasture vegetation over large areas, but mapping pasture conditions consistently through time is not a trivial task because of seasonal changes associated with phenology and data gaps from clouds and cloud shadows. In this study, we tested spectral-temporal metrics derived from intra-annual Landsat time series to distinguish between grass-dominated and woody pastures. The abundance of woody vegetation on pastures is an indicator for management intensity, since the duration and intensity of land use steer secondary succession rates, apart from climate and soil conditions. We used the developed Landsat-based metrics to analyze pasture intensity trajectories between 1985 and 2012 in Novo Progresso, Brazil, finding that woody vegetation cover generally decreased after four to ten years of grazing activity. Pastures established in the 80s and early 90s showed a higher fraction of woody vegetation during their initial land use history than pastures established in the early 2000s. Historic intensity trajectories suggested a trend towards more intensive land use in the last decade, which aligns well with regional environmental policies and market dynamics. This study demonstrates the potential of dense Landsat time series to monitor land-use intensification on Amazonian pastures.},
author = {Rufin, Philippe and M{\"{u}}ller, Hannes and Pflugmacher, Dirk and Hostert, Patrick},
doi = {10.1016/j.jag.2015.04.010},
file = {:C$\backslash$:/LocalStorage/References/2015/Rufin et al.{\_}2015{\_}Land use intensity trajectories on Amazonian pastures derived from Landsat time series.pdf:pdf;:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Rufin et al. - 2015 - Land use intensity trajectories on Amazonian pastures derived from Landsat time series.pdf:pdf},
issn = {03032434},
journal = {International Journal of Applied Earth Observation and Geoinformation},
keywords = {Amazon pastures,Land use intensity,Landsat,Phenology,Time series,Vegetation dynamics},
month = {sep},
pages = {1--10},
publisher = {Elsevier B.V.},
title = {{Land use intensity trajectories on Amazonian pastures derived from Landsat time series}},
url = {http://dx.doi.org/10.1016/j.jag.2015.04.010 http://linkinghub.elsevier.com/retrieve/pii/S0303243415000896},
volume = {41},
year = {2015}
}
@article{Gibbs2015,
author = {Gibbs, H.K. and Salmon, J.M.},
doi = {10.1016/j.apgeog.2014.11.024},
file = {:C$\backslash$:/LocalStorage/References/2015/Gibbs, Salmon{\_}2015{\_}Mapping the world's degraded lands.pdf:pdf},
issn = {01436228},
journal = {Applied Geography},
month = {feb},
pages = {12--21},
publisher = {Elsevier Ltd},
title = {{Mapping the world's degraded lands}},
url = {http://dx.doi.org/10.1016/j.apgeog.2014.11.024 http://linkinghub.elsevier.com/retrieve/pii/S0143622814002793},
volume = {57},
year = {2015}
}
@article{Brown2004,
author = {Brown, James H. and Gillooly, James F. and Allen, Andrew P. and Savage, Van M. and West, Geoffrey B.},
doi = {10.1890/03-9000},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Brown et al. - 2004 - Toward a metabolic theory of ecology.pdf:pdf},
isbn = {0012-9658},
issn = {0012-9658},
journal = {Ecology},
keywords = {allometry,biogeochemical cycles,body size,development,ecological interactions,ecological theory,metabolism,population growth,production,stoichiometry,temperature,trophic},
month = {jul},
number = {7},
pages = {1771--1789},
pmid = {21915553},
title = {{Toward a metabolic theory of ecology}},
url = {http://doi.wiley.com/10.1890/03-9000},
volume = {85},
year = {2004}
}
@article{Grundel2010,
abstract = {Given bees' central effect on vegetation communities, it is important to understand how and why bee distributions vary across ecological gradients. We examined how plant community composition, plant diversity, nesting suitability, canopy cover, land use, and fire history affected bee distribution across an open-forest gradient in northwest Indiana, USA, a gradient similar to the historic Midwest United States landscape mosaic. When considered with the other predictors, plant community composition was not a significant predictor of bee community composition. Bee abundance was negatively related to canopy cover and positively to recent fire frequency, bee richness was positively related to plant richness and abundance of potential nesting resources, and bee community composition was significantly related to plant richness, soil characteristics potentially related to nesting suitability, and canopy cover. Thus, bee abundance was predicted by a different set of environmental characteristics than was bee species richness, and bee community composition was predicted, in large part, by a combination of the significant predictors of bee abundance and richness. Differences in bee community composition along the woody vegetation gradient were correlated with relative abundance of oligolectic, or diet specialist, bees. Because oligoleges were rarer than diet generalists and were associated with open habitats, their populations may be especially affected by degradation of open habitats. More habitat-specialist bees were documented for open and forest/scrub habitats than for savanna/woodland habitats, consistent with bees responding to habitats of intermediate woody vegetation density, such as savannas, as ecotones rather than as distinct habitat types. Similarity of bee community composition, similarity of bee abundance, and similarity of bee richness between sites were not significantly related to proximity of sites to each other. Nestedness analysis indicated that species composition in species-poor sites was not merely a subset of species composition at richer sites. The lack of significant proximity or nestedness effects suggests that factors at a small spatial scale strongly influence bees' use of sites. The findings indicate that patterns of plant diversity, nesting resource availability, recent fire, and habitat shading, present at the scale of a few hundred meters, are key determinants of bee community patterns in the mosaic open-savanna-forest landscape.},
author = {Grundel, Ralph and Jean, RP Robert P and Frohnapple, Krystalynn J and Glowacki, Gary a and Scott, Peter E and Pavlovic, Noel B and Survey, U S Geological and Lakes, Great and Haute, Terre},
file = {:C$\backslash$:/LocalStorage/References/2010/Grundel et al.{\_}2010{\_}Floral and nesting resources, habitat structure, and fire influence bee distribution across an open-forest gradient.pdf:pdf},
issn = {1051-0761},
journal = {Ecological applications : a publication of the Ecological Society of America},
keywords = {Animals,Bees,Bees: physiology,Demography,Ecosystem,Fires,Flowers,Flowers: physiology,Forests,Nesting Behavior,Paper,Time Factors,Trees,bee abundance,bee diversity,fire,habitat specialists,indiana dunes,land use,nestedness,nesting resources,oak savanna,oligolectic,plant richness,species density},
mendeley-tags = {Forests,Paper},
month = {sep},
number = {6},
pages = {1678--92},
pmid = {20945767},
title = {{Floral and nesting resources, habitat structure, and fire influence bee distribution across an open-forest gradient.}},
url = {http://www.esajournals.org/doi/abs/10.1890/08-1792.1 http://www.ncbi.nlm.nih.gov/pubmed/20945767},
volume = {20},
year = {2010}
}
@article{Gilbert2012,
abstract = {Reproducibility is the benchmark for results and conclusions drawn from scientific studies, but systematic studies on the reproducibility of scientific results are surprisingly rare. Moreover, many modern statistical methods make use of 'random walk' model fitting procedures, and these are inherently stochastic in their output. Does the combination of these statistical procedures and current standards of data archiving and method reporting permit the reproduction of the authors' results? To test this, we reanalysed data sets gathered from papers using the software package STRUCTURE to identify genetically similar clusters of individuals. We find that reproducing structure results can be difficult despite the straightforward requirements of the program. Our results indicate that 30{\%} of analyses were unable to reproduce the same number of population clusters. To improve this, we make recommendations for future use of the software and for reporting STRUCTURE analyses and results in published works.},
author = {Gilbert, Kimberly J and Andrew, Rose L and Bock, Dan G and Franklin, Michelle T and Kane, Nolan C and Moore, Jean-S{\'{e}}bastien and Moyers, Brook T and Renaut, S{\'{e}}bastien and Rennison, Diana J and Veen, Thor and Vines, Timothy H},
doi = {10.1111/j.1365-294X.2012.05754.x},
file = {:C$\backslash$:/LocalStorage/References/2012/Gilbert et al.{\_}2012{\_}Recommendations for utilizing and reporting population genetic analyses the reproducibility of genetic clustering us.pdf:pdf},
issn = {1365-294X},
journal = {Molecular ecology},
keywords = {Bayes Theorem,Cluster Analysis,Computational Biology,Computational Biology: methods,Data Interpretation,Databases,Genetic,Genetics,Population,Population: methods,Reproducibility of Results,Software,Statistical},
month = {oct},
number = {20},
pages = {4925--30},
pmid = {22998190},
title = {{Recommendations for utilizing and reporting population genetic analyses: the reproducibility of genetic clustering using the program STRUCTURE.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22998190},
volume = {21},
year = {2012}
}
@book{Pickett1985,
address = {New York, NY},
author = {Pickett, S. T. A. and White, PS},
isbn = {0-12-554520-7},
publisher = {Academic Press},
title = {{The Ecology of Natural Disturbance and Patch Dynamics}},
year = {1985}
}
@article{KleinGoldewijk2013,
abstract = {Land use and land-use change play an important role in global integrated assessments. However, there are still many uncertainties in the role of current and historical land use in the global carbon cycle as well as in other dimensions of global environmental change. Although databases of histor- ical land use are frequently used in integrated assess- ments and climate studies, they are subject to considerable uncertainties that often are ignored. This paper examines a number of the most important uncertainties related to the process of reconstructing historical land use. We discuss the origins of different types of uncertainty and the sensitivity of land-use reconstructions to these uncertainties. The results indicate that uncertainties not only arise as result of the large temporal and spatial variation in historical population data, but also relate to assumptions on the relationship between population and land use used in the reconstructions. Improving empirical data to better specify and validate the assumptions about the rela- tionship between population and land use, while accounting for the spatial and temporal variation, could reduce uncertainties in the reconstructions. Such empirical evidence could be derived from local case studies, such as those conducted in landscape ecology, environmental history, archeology and paleoecology.},
author = {{Klein Goldewijk}, Kees and Verburg, Peter H.},
doi = {10.1007/s10980-013-9877-x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Klein Goldewijk, Verburg - 2013 - Uncertainties in global-scale reconstructions of historical land use An illustration using the HYDE da.pdf:pdf},
isbn = {0921-2973},
issn = {09212973},
journal = {Landscape Ecology},
keywords = {Global,Historic land use,Land cover,Reconstructions,Uncertainty},
pages = {861--877},
title = {{Uncertainties in global-scale reconstructions of historical land use: An illustration using the HYDE data set}},
volume = {28},
year = {2013}
}
@article{Thomas2004,
abstract = {Climate change over the past approximately 30 years has produced numerous shifts in the distributions and abundances of species and has been implicated in one species-level extinction. Using projections of species' distributions for future climate scenarios, we assess extinction risks for sample regions that cover some 20{\%} of the Earth's terrestrial surface. Exploring three approaches in which the estimated probability of extinction shows a power-law relationship with geographical range size, we predict, on the basis of mid-range climate-warming scenarios for 2050, that 15-37{\%} of species in our sample of regions and taxa will be 'committed to extinction'. When the average of the three methods and two dispersal scenarios is taken, minimal climate-warming scenarios produce lower projections of species committed to extinction ( approximately 18{\%}) than mid-range ( approximately 24{\%}) and maximum-change ( approximately 35{\%}) scenarios. These estimates show the importance of rapid implementation of technologies to decrease greenhouse gas emissions and strategies for carbon sequestration.},
author = {Thomas, Chris D and Cameron, Alison and Green, Rhys E and Bakkenes, Michel and Beaumont, Linda J and Collingham, Yvonne C and Erasmus, Barend F N and {De Siqueira}, Marinez Ferreira and Grainger, Alan and Hannah, Lee and Hughes, Lesley and Huntley, Brian and {Van Jaarsveld}, Albert S and Midgley, Guy F and Miles, Lera and Ortega-Huerta, Miguel a and Peterson, a Townsend and Phillips, Oliver L and Williams, Stephen E},
doi = {10.1038/nature02121},
file = {:C$\backslash$:/LocalStorage/References/2004/Thomas et al.{\_}2004{\_}Extinction risk from climate change.pdf:pdf},
isbn = {0028083614764},
issn = {0028-0836},
journal = {Nature},
keywords = {Animals,Biodiversity,Carbon,Carbon: metabolism,Conservation of Natural Resources,Extinction,Geography,Greenhouse Effect,Models,Risk Assessment,Species Specificity,Theoretical,Time Factors},
mendeley-tags = {Extinction},
month = {jan},
number = {6970},
pages = {145--148},
pmid = {14712274},
title = {{Extinction risk from climate change.}},
volume = {427},
year = {2004}
}
@article{Putz2014,
abstract = {Tropical forests play an important role in the global carbon cycle, as they store a large amount of carbon (C). Tropical forest deforestation has been identified as a major source of CO2 emissions, though biomass loss due to fragmentation—the creation of additional forest edges—has been largely overlooked as an additional CO2 source. Here, through the combination of remote sensing and knowledge on ecological processes, we present long-term carbon loss estimates due to fragmentation of Neotropical forests: within 10 years the Brazilian Atlantic Forest has lost 69 (±14) Tg C, and the Amazon 599 (±120) Tg C due to fragmentation alone. For all tropical forests, we estimate emissions up to 0.2 Pg C y−1 or 9 to 24{\%} of the annual global C loss due to deforestation. In conclusion, tropical forest fragmentation increases carbon loss and should be accounted for when attempting to understand the role of vegetation in the global carbon balance.},
author = {P{\"{u}}tz, Sandro and Groeneveld, J{\"{u}}rgen and Henle, Klaus and Knogge, Christoph and Martensen, Alexandre Camargo and Metz, Markus and Metzger, Jean Paul and Ribeiro, Milton Cezar and de Paula, Mateus Dantas and Huth, Andreas},
doi = {10.1038/ncomms6037},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/P{\"{u}}tz et al. - 2014 - Long-term carbon loss in fragmented Neotropical forests.pdf:pdf},
isbn = {2041-1723 (Electronic)$\backslash$r2041-1723 (Linking)},
issn = {2041-1723},
journal = {Nature Communications},
month = {oct},
number = {iDiv},
pages = {5037},
pmid = {25289858},
title = {{Long-term carbon loss in fragmented Neotropical forests}},
url = {http://www.nature.com/doifinder/10.1038/ncomms6037{\%}5Cnhttp://dx.doi.org/10.1038/ncomms6037{\%}5Cn10.1038/ncomms6037 http://www.nature.com/doifinder/10.1038/ncomms6037},
volume = {5},
year = {2014}
}
@article{McGarigal1995,
abstract = {This report describes a program, FRAGSTATS, developed to quantify landscape structure. FRAGSTATS offers a comprehensive choice of landscape metrics and was designed to be as versatile as possible. The program is almost completely automated and thus requires little technical training. Two separate versions of FRAGSTATS exist: one for vector images and one for raster images. The vector version is an Arc/Info AML that accepts Arc/Info polygon coverages. The raster version is a C program that accepts ASCII image files, 8- or 16-bit binary image files, Arc/Info SVF files, Erdas image files, and IDRISI image files. Both versions of FRAGSTATS generate the same array of metrics, including a variety of area metrics, patch density, size and variability metrics, edge metrics, shape metrics, core area metrics, diversity metrics, and contagion and interspersion metrics. The raster version also computes several nearest neighbor metrics. In this report, each metric calculated by FRAGSTATS is described in terms of its ecological application and limitations. Example landscapes are included, and a dis- cussion is provided of each metric as it relates to the sample landscapes. Several important concepts and definitions critical to the assessment of landscape structure are discussed. The appendices include a complete list of algorithms, the units and ranges of each metric, examples of the FRAGSTATS output files, and a users guide describing how to install and run FRAGSTATS.},
author = {McGarigal, Kevin and Marks, Barbara J.},
journal = {General Technical Report PNW-GTR-351. US {\ldots}},
number = {503},
pages = {134},
title = {{FRAGSTATS: Spatial Pattern Analysis Program for Quantifying Landscape Structure}},
volume = {97331},
year = {1995}
}
@article{Yates2018,
abstract = {Predictive models are central to many scientific disciplines and vital for informing management in a rapidly changing world. However, limited understanding of the accuracy and precision of models transferred to novel conditions (their ‘transferability') undermines confidence in their predictions. Here, 50 experts identified priority knowledge gaps which, if filled, will most improve model transfers. These are summarized into six technical and six fundamental challenges, which underlie the combined need to intensify research on the determinants of ecological predictability, including species traits and data quality, and develop best practices for transferring models. Of high importance is the identification of a widely applicable set of transferability metrics, with appropriate tools to quantify the sources and impacts of prediction uncertainty under novel conditions.},
author = {Yates, Katherine L. and Bouchet, Phil J. and Caley, M. Julian and Mengersen, Kerrie and Randin, Christophe F. and Parnell, Stephen and Fielding, Alan H. and Bamford, Andrew J. and Ban, Stephen and Barbosa, A. M{\'{a}}rcia and Dormann, Carsten F. and Elith, Jane and Embling, Clare B. and Ervin, Gary N. and Fisher, Rebecca and Gould, Susan and Graf, Roland F. and Gregr, Edward J. and Halpin, Patrick N. and Heikkinen, Risto K. and Hein{\"{a}}nen, Stefan and Jones, Alice R. and Krishnakumar, Periyadan K. and Lauria, Valentina and Lozano-Montes, Hector and Mannocci, Laura and Mellin, Camille and Mesgaran, Mohsen B. and Moreno-Amat, Elena and Mormede, Sophie and Novaczek, Emilie and Oppel, Steffen and {Ortu{\~{n}}o Crespo}, Guillermo and Peterson, A. Townsend and Rapacciuolo, Giovanni and Roberts, Jason J. and Ross, Rebecca E. and Scales, Kylie L. and Schoeman, David and Snelgrove, Paul and Sundblad, G{\"{o}}ran and Thuiller, Wilfried and Torres, Leigh G. and Verbruggen, Heroen and Wang, Lifei and Wenger, Seth and Whittingham, Mark J. and Zharikov, Yuri and Zurell, Damaris and Sequeira, Ana M.M.},
doi = {10.1016/j.tree.2018.08.001},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Yates et al. - 2018 - Outstanding Challenges in the Transferability of Ecological Models.pdf:pdf},
isbn = {1600-0706},
issn = {01695347},
journal = {Trends in Ecology {\&} Evolution},
keywords = {Predictive modeling,extrapolation,generality,habitat models,model transfers,species distribution models,uncertainty},
month = {oct},
number = {10},
pages = {790--802},
pmid = {30166069},
publisher = {Elsevier Ltd},
title = {{Outstanding Challenges in the Transferability of Ecological Models}},
url = {https://doi.org/10.1016/j.tree.2018.08.001 https://linkinghub.elsevier.com/retrieve/pii/S0169534718301812},
volume = {33},
year = {2018}
}
@article{Yang2012,
abstract = {Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. The advancement of sequencing technologies has taken phylogenetic analysis to a new height. Phylogenies have permeated nearly every branch of biology, and the plethora of phylogenetic methods and software packages that are now available may seem daunting to an experimental biologist. Here, we review the major methods of phylogenetic analysis, including parsimony, distance, likelihood and Bayesian methods. We discuss their strengths and weaknesses and provide guidance for their use.},
author = {Yang, Ziheng and Rannala, Bruce},
doi = {10.1038/nrg3186},
file = {:C$\backslash$:/LocalStorage/References/2012/Yang, Rannala{\_}2012{\_}Molecular phylogenetics principles and practice.pdf:pdf},
issn = {1471-0064},
journal = {Nature reviews. Genetics},
keywords = {Base Sequence,Biological,Female,Humans,Male,Models,Molecular Sequence Data,Phylogeny,Software,Statistical},
month = {may},
number = {5},
pages = {303--14},
pmid = {22456349},
publisher = {Nature Publishing Group},
title = {{Molecular phylogenetics: principles and practice.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22456349},
volume = {13},
year = {2012}
}
@article{Tilman1997,
abstract = {JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact support@jstor.org. Abstract.-An analytical model of competitive coexistence in spatial habitats, modified to ad-dress habitat destruction, predicts that the most abundant species can be among the first species driven extinct by habitat destruction, given that abundant species are the poorest dispersers and best competitors. This contrasts with the classical view of biased extinction of rare species. Here we explore the robustness of this prediction both analytically and in spatially explicit simulations of more realistic cases. The prediction proved surprisingly robust. The poorest dispersers, which in this model generally are the best competitors and may be the most abundant species, were among the first driven extinct by habitat destruction whether they were abundant or rare, had short or long range dispersal, or reproduced continuously or periodically; whether competitive displacement was immediate or gradual; whether habitat destruction was clumped, uniform, or random and whether destruction occurred at once or progressively; and whether the habitat was large or small. The amount of destruction sufficient to produce extinctions changed considerably as model assumptions changed, but the biased extinction remained. The underlying reason for the robustness of our conclusions is the broad assumption that inferior competitors persist by virtue of greater dispersal ability and/or lower mortality rates. Further work on the forces allowing multispecies coexistence is thus essential for understanding the effects of habitat destruction on extinction. Habitat destruction has long been thought to lead to the biased extinctions of rare species. It directly causes the immediate extinction of rare endemic species},
author = {Tilman, David and Lehman, Clarence L. and Yin, Chengjun},
doi = {10.1086/285998},
file = {:C$\backslash$:/LocalStorage/References/285998.pdf:pdf},
issn = {0003-0147},
journal = {The American Naturalist},
month = {mar},
number = {3},
pages = {407--435},
title = {{Habitat Destruction, Dispersal, and Deterministic Extinction in Competitive Communities}},
url = {https://www.journals.uchicago.edu/doi/10.1086/285998},
volume = {149},
year = {1997}
}
@article{Riitters2015,
author = {Riitters, Kurt and Wickham, James and Costanza, Jennifer K. and Vogt, Peter},
doi = {10.1007/s10980-015-0270-9},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Riitters et al. - 2016 - A global evaluation of forest interior area dynamics using tree cover data from 2000 to 2012.pdf:pdf},
issn = {0921-2973},
journal = {Landscape Ecology},
keywords = {Assessment,Forest fragmentation,Monitoring,Spatial analysis},
month = {jan},
number = {1},
pages = {137--148},
publisher = {Springer Netherlands},
title = {{A global evaluation of forest interior area dynamics using tree cover data from 2000 to 2012}},
url = {http://link.springer.com/10.1007/s10980-015-0270-9},
volume = {31},
year = {2016}
}
@article{Trimble2009,
abstract = {Environmentally induced variation in survival and fecundity generates demographic fluctuations that affect population growth rate. However, a general pattern of the comparative influence of variation in fecundity and juvenile survival on elephant population dynamics has not been investigated at a broad scale. We evaluated the relative importance of conception, gestation, first year survival and subsequent survivorship for controlling demographic variation by exploring the relationship between past environmental conditions determined by integrated normalized difference vegetation index (INDVI) and the shape of age distributions at 17 sites across Africa. We showed that, generally, INDVI during gestation best explained anomalies in age structure. However, in areas with low mean annual rainfall, INDVI during the first year of life was critical. The results challenge Eberhardt's paradigm for population analysis that suggests that populations respond to limited resource availability through a sequential decrease in juvenile survival, reproductive rate and adult survival. Contrastingly, elephants appear to respond first through a reduction in reproductive rate. We conclude that this discrepancy is likely due to the evolutionary significance of extremely large body size – an adaptation that increases survival rate but decreases reproductive potential. Other megaherbivores may respond similarly to resource limitation due to similarities in population dynamics. Knowing how vital rates vary with changing environmental conditions will permit better forecasts of the trajectories of megaherbivore populations.},
author = {Trimble, M. J. and Ferreira, S. M. and van Aarde, R. J.},
doi = {10.1111/j.1469-7998.2009.00560.x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Trimble, Ferreira, van Aarde - 2009 - Drivers of megaherbivore demographic fluctuations inference from elephants.pdf:pdf},
isbn = {0952-8369},
issn = {09528369},
journal = {Journal of Zoology},
keywords = {African elephant,Conception,Dynamics,Elephant,Gestation,INDVI,Megaherbivore,Population,Population dynamics,Survival},
mendeley-tags = {Dynamics,Elephant,INDVI,Population},
month = {sep},
number = {1},
pages = {18--26},
pmid = {6513},
title = {{Drivers of megaherbivore demographic fluctuations: inference from elephants}},
url = {http://doi.wiley.com/10.1111/j.1469-7998.2009.00560.x},
volume = {279},
year = {2009}
}
@article{Wang2014,
author = {Wang, Xianli and Blanchet, F. Guillaume and Koper, Nicola},
doi = {10.1111/2041-210X.12198},
editor = {Tatem, Andrew},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Wang, Blanchet, Koper - 2014 - Measuring habitat fragmentation An evaluation of landscape pattern metrics.pdf:pdf},
issn = {2041210X},
journal = {Methods in Ecology and Evolution},
month = {jul},
number = {7},
pages = {634--646},
title = {{Measuring habitat fragmentation: An evaluation of landscape pattern metrics}},
url = {http://doi.wiley.com/10.1111/2041-210X.12198},
volume = {5},
year = {2014}
}
@article{Green2005,
abstract = {World food demand is expected to more than double by 2050. Decisions about how to meet this challenge will have profound effects on wild species and habitats. We show that farming is already the greatest extinction threat to birds (the best known taxon), and its adverse impacts look set to increase, especially in developing countries. Two competing solutions have been proposed: wildlife-friendly farming (which boosts densities of wild populations on farmland but may decrease agricultural yields) and land sparing (which minimizes demand for farmland by increasing yield). We present a model that identifies how to resolve the trade-off between these approaches. This shows that the best type of farming for species persistence depends on the demand for agricultural products and on how the population densities of different species on farmland change with agricultural yield. Empirical data on such density-yield functions are sparse, but evidence from a range of taxa in developing countries suggests that high-yield farming may allow more species to persist.},
author = {Green, Rhys E and Cornell, Stephen J and Scharlemann, J{\"{o}}rn P W and Balmford, Andrew},
doi = {10.1126/science.1106049},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Green et al. - 2005 - Farming and the fate of wild nature.pdf:pdf},
isbn = {0036-8075},
issn = {0036-8075},
journal = {Science (New York, N.Y.)},
number = {5709},
pages = {550--555},
pmid = {15618485},
title = {{Farming and the fate of wild nature.}},
volume = {307},
year = {2005}
}
@article{Breitbach2010,
abstract = {Only few studies have analysed the relationship between biodiversity and ecosystem function at the landscape scale although relationships and mechanisms known from experimental studies might be different in natural systems. We quantified bird diversity and seed removal from 38 wild cherry trees (Prunus avium) along a human land-use gradient from forest to structurally diverse to simple agricultural systems. High human land-use intensity led to low species richness and total abundance of the local bird community around wild cherry trees, as expected from previous studies. Nevertheless, trees in structurally simple agroecosystems were visited as frequently as trees in structurally complex landscapes and in forests. Furthermore, the number of seeds removed per tree did not decline with increasing human land-use intensity. Thus, ecosystem function was robust in spite of locally reduced bird diversity. The reason might be that movement behaviour and movement distances of birds changed along the human land-use gradient. It appears that birds moved longer distances to forage in fruiting cherry trees in structurally simple agroecosystems. This suggests that for systems where ecosystem function is mediated by highly mobile organisms, movement behaviour and distances are of considerable importance. Increases in movement distances with increasing human land-use intensity might also be common in other systems in which ecosystem function depends on mobile links.},
author = {Breitbach, Nils and Laube, Irina and Steffan-Dewenter, Ingolf and B{\"{o}}hning-Gaese, Katrin},
doi = {10.1007/s00442-009-1547-y},
file = {:C$\backslash$:/LocalStorage/References/2010/Breitbach et al.{\_}2010{\_}Bird diversity and seed dispersal along a human land-use gradient high seed removal in structurally simple farmlan.pdf:pdf},
issn = {1432-1939},
journal = {Oecologia},
keywords = {Agriculture,Animals,Biodiversity,Birds,Birds: physiology,Feeding Behavior,Feeding Behavior: physiology,Geography,Germany,Population Dynamics,Prunus,Prunus: growth {\&} development,Prunus: physiology,Seed-Dispersal,Seeds,Seeds: physiology,Study,Time Factors},
mendeley-tags = {Seed-Dispersal,Study},
month = {apr},
number = {4},
pages = {965--76},
pmid = {20049479},
title = {{Bird diversity and seed dispersal along a human land-use gradient: high seed removal in structurally simple farmland.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20049479},
volume = {162},
year = {2010}
}
@article{Martin2016,
abstract = {Globally, mature forests appear to be increasing in biomass density (BD). There is disagreement whether these increases are the result of increases in atmospheric CO 2 concentrations or a legacy effect of previous land-use. Recently, it was suggested that a threshold of 450 years should be used to define mature forests and that many forests increasing in BD may be younger than this. However, the study making these suggestions failed to account for the interactions between forest age and climate. Here we revisit the issue to identify: (1) how climate and forest age control global forest BD and (2) whether we can set a threshold age for mature forests. Using data from previously published studies we modelled the impacts of forest age and climate on BD using linear mixed effects models. We examined the potential biases in the dataset by comparing how representative it was of global mature forests in terms of its distribution, the climate space it occupied, and the ages of the forests used. BD increased with forest age, mean annual temperature and annual precipitation. Importantly, the effect of forest age increased with increasing temperature, but the effect of precipitation decreased with increasing temperatures. The dataset was biased towards northern hemisphere forests in relatively dry, cold climates. The dataset was also clearly biased towards forests {\textless}250 years of age. Our analysis suggests that there is not a single threshold age for forest maturity. Since climate interacts with forest age to determine BD, a threshold age at which they reach equilibrium can only be determined locally. We caution against using BD as the only determinant of forest maturity since this ignores forest biodiversity and tree size structure which may take longer to recover. Future research should address the utility and cost-effectiveness of different methods for determining whether forests should be classified as mature.},
author = {Martin, Philip and Jung, Martin and Brearley, Francis Q. and Ribbons, Relena R. and Lines, Emily R. and Jacob, Aerin L.},
doi = {10.7717/peerj.1595},
issn = {2167-8359},
journal = {PeerJ},
month = {feb},
pages = {e1595},
title = {{Can we set a global threshold age to define mature forests?}},
url = {https://peerj.com/articles/1595},
volume = {4},
year = {2016}
}
@misc{Christensen2015,
author = {Christensen, RHB},
keywords = {R-Library,ordinal},
mendeley-tags = {R-Library,ordinal},
title = {{ordinal---Regression Models for Ordinal Data}},
url = {http://www.cran.r-project.org/package=ordinal},
year = {2015}
}
@article{Tamburello2015,
abstract = {locomotion strategy, foraging dimension, trophic guild, and prey size together explain 80{\%} of the variation in home-range size across vertebrates when controlling for phylogeny and tracking method. Within carnivores, smaller relative prey size among gape-limited fishes contributes to shallower scaling relative to other predators. Our study reveals how simple morphological traits and prey-handling ability can profoundly influence individual space use},
author = {Tamburello, Natascia and C{\^{o}}t{\'{e}}, Isabelle M. and Dulvy, Nicholas K.},
doi = {10.1086/682070},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Tamburello, C{\^{o}}t{\'{e}}, Dulvy - 2015 - Energy and the Scaling of Animal Space Use.pdf:pdf},
isbn = {1860255485},
issn = {0003-0147},
journal = {The American Naturalist},
keywords = {allometry,home range,metabolic theory,prey handling,prey size,spatial ecology},
month = {aug},
number = {2},
pages = {196--211},
pmid = {17820973},
title = {{Energy and the Scaling of Animal Space Use}},
url = {http://www.journals.uchicago.edu/doi/10.1086/682070},
volume = {186},
year = {2015}
}
@article{KATTGE2011,
abstract = {Here, we investigated the impact of temperature on the carbon economy of two Plantago species from contrasting habitats. The lowland Plantago major and the alpine Plantago euryphylla were grown hydroponically at three constant temperatures: 13, 20 and 27 degrees C. Rates of photosynthetic CO(2) uptake (P) and respiratory CO(2) release (R) in shoots and R in roots were measured at the growth temperature using intact plants. At each growth temperature, air temperatures were changed to establish short-term temperature effects on the ratio of R to P (R/P). In both species, R/P was essentially constant in plants grown at 13 and 20 degrees C. However, R/P was substantially greater in 27 degrees C-grown plants, particularly in P. euryphylla. The increase in R/P at 27 degrees C would have been even greater had biomass allocation to roots not decreased with increasing growth temperature. Short-term increases in air temperature increased R/P in both species, with the effects of air temperature being most pronounced in 13 degrees C-grown plants. We conclude that temperature-mediated changes in biomass allocation play an important role in determining whole-plant R/P values, and, while homeostasis of R/P is achieved across moderate growth temperatures, homeostasis is not maintained when plants are exposed to growth temperatures higher than usually experienced in the natural habitat.},
author = {Kattge, J. and D{\'{i}}az, S. and Lavorel, S. and Prentice, i. c. and Leadley, P. and B{\"{o}}nisch, G. and Garnier, E. and Westoby, M. and Reich, p. b. and Wright, i. j. and Cornelissen, j. h. c. and Violle, C. and Harrison, s. p. and Van bodegom, p. m. and Reichstein, M. and Enquist, b. j. and Soudzilovskaia, n. a. and Ackerly, d. d. and Anand, M. and Atkin, O. and Bahn, M. and Baker, t. r. and Baldocchi, D. and Bekker, R. and Blanco, c. c. and Blonder, B. and Bond, w. j. and Bradstock, R. and Bunker, d. e. and Casanoves, F. and Cavender-bares, J. and Chambers, j. q. and Chapin iii, f. s. and Chave, J. and Coomes, D. and Cornwell, w. k. and Craine, j. m. and Dobrin, b. h. and Duarte, L. and Durka, W. and Elser, J. and Esser, G. and Estiarte, M. and Fagan, w. f. and Fang, J. and Fern{\'{a}}ndez-m{\'{e}}ndez, F. and Fidelis, A. and Finegan, B. and Flores, O. and Ford, H. and Frank, D. and Freschet, g. t. and Fyllas, n. m. and Gallagher, r. v. and Green, w. a. and Gutierrez, a. g. and Hickler, T. and Higgins, s. i. and Hodgson, j. g. and Jalili, A. and Jansen, S. and Joly, c. a. and Kerkhoff, a. j. and Kirkup, D. and Kitajima, K. and Kleyer, M. and Klotz, S. and Knops, j. m. h. and Kramer, K. and K{\"{u}}hn, I. and Kurokawa, H. and Laughlin, D. and Lee, t. d. and Leishman, M. and Lens, F. and Lenz, T. and Lewis, s. l. and Lloyd, J. and Llusi{\`{a}}, J. and Louault, F. and Ma, S. and Mahecha, m. d. and Manning, P. and Massad, T. and Medlyn, b. e. and Messier, J. and Moles, a. t. and M{\"{u}}ller, s. c. and Nadrowski, K. and Naeem, S. and Niinemets, {\"{U}}. and N{\"{o}}llert, S. and N{\"{u}}ske, A. and Ogaya, R. and Oleksyn, J. and Onipchenko, v. g. and Onoda, Y. and Ordo{\~{n}}ez, J. and Overbeck, G. and Ozinga, w. a. and Pati{\~{n}}o, S. and Paula, S. and Pausas, j. g. and Pe{\~{n}}uelas, J. and Phillips, o. l. and Pillar, V. and Poorter, H. and Poorter, L. and Poschlod, P. and Prinzing, A. and Proulx, R. and Rammig, A. and Reinsch, S. and Reu, B. and Sack, L. and Salgado-negret, B. and Sardans, J. and Shiodera, S. and Shipley, B. and Siefert, A. and Sosinski, E. and Soussana, J.-f. and Swaine, E. and Swenson, N. and Thompson, K. and Thornton, P. and Waldram, M. and Weiher, E. and White, M. and White, S. and Wright, s. j. and Yguel, B. and Zaehle, S. and Zanne, a. e. and Wirth, C.},
doi = {10.1111/j.1365-2486.2011.02451.x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Kattge et al. - 2011 - TRY - a global database of plant traits.pdf:pdf},
isbn = {1365-2486},
issn = {13541013},
journal = {Global Change Biology},
keywords = {Comparative ecology,Database,Environmental gradient,FUNCTIONAL TRAITS,Functional diversity,Global analysis,Global change,HAWAIIAN METROSIDEROS-POLYMORPHA,Interspecific variation,Intraspecific variation,LEAF ECONOMICS SPECTRUM,LITTER DECOMPOSITION RATES,OLD-FIELD SUCCESSION,Plant attribute,Plant functional type,Plant trait,RELATIVE GROWTH-RATE,SUB-ARCTIC FLORA,TERRESTRIAL BIOSPHERE,TROPICAL RAIN-FOREST,Vegetation model,WIDE-RANGE,comparative ecology,database,environmental gradient,functional diversity,global analysis,global change,interspecific variation,intraspecific variation,plant attribute,plant functional type,plant trait,vegetation model},
month = {sep},
number = {9},
pages = {2905--2935},
pmid = {17388899},
title = {{TRY - a global database of plant traits}},
url = {http://doi.wiley.com/10.1111/j.1365-2486.2011.02451.x},
volume = {17},
year = {2011}
}
@article{Gwinn2015,
author = {Gwinn, Daniel C. and Allen, Michael S. and Bonvechio, Kimberly I. and {V. Hoyer}, Mark and Beesley, Leah S.},
doi = {10.1111/2041-210X.12462},
editor = {O'Hara, Robert B.},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Gwinn et al. - 2015 - Evaluating estimators of species richness the importance of considering statistical error rates.pdf:pdf},
issn = {2041210X},
journal = {Methods in Ecology and Evolution},
month = {sep},
pages = {n/a--n/a},
title = {{Evaluating estimators of species richness: the importance of considering statistical error rates}},
url = {http://doi.wiley.com/10.1111/2041-210X.12462},
year = {2015}
}
@article{Iwao2006,
author = {Iwao, Koki and Nishida, Kenlo and Kinoshita, Tsuguki and Yamagata, Yoshiki},
doi = {10.1029/2006GL027768},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Iwao et al. - 2006 - Validating land cover maps with Degree Confluence Project information.pdf:pdf},
issn = {0094-8276},
journal = {Geophysical Research Letters},
keywords = {degree confluence project,doi:10.1029/2006GL027768,http://dx.doi.org/10.1029/2006GL027768,land cover map,validation},
month = {dec},
number = {23},
pages = {L23404},
title = {{Validating land cover maps with Degree Confluence Project information}},
url = {http://doi.wiley.com/10.1029/2006GL027768},
volume = {33},
year = {2006}
}
@article{lme4,
abstract = {Maximum likelihood or restricted maximum likelihood (REML) estimates of the parameters in linear mixed-effects models can be determined using the lmer function in the lme4 package for R. As for most model-fitting functions in R, the model is described in an lmer call by a formula, in this case including both fixed- and random-effects terms. The formula and data together determine a numerical representation of the model from which the profiled deviance or the profiled REML criterion can be evaluated as a function of some of the model parameters. The appropriate criterion is optimized, using one of the constrained optimization functions in R, to provide the parameter estimates. We describe the structure of the model, the steps in evaluating the profiled deviance or REML criterion, and the structure of classes or types that represents such a model. Sufficient detail is included to allow specialization of these structures by users who wish to write functions to fit specialized linear mixed models, such as models incorporating pedigrees or smoothing splines, that are not easily expressible in the formula language used by lmer.},
archivePrefix = {arXiv},
arxivId = {10.18637/jss.v067.i01},
author = {Bates, Douglas M. and Maechler, Martin and Bolker, Ben and Walker, Steve},
eprint = {jss.v067.i01},
file = {:C$\backslash$:/LocalStorage/References/2015/Bates et al.{\_}2015{\_}lme4 linear mixed-effects models using S4 classes.pdf:pdf},
journal = {Journal of statistical software},
keywords = {R-Library},
mendeley-tags = {R-Library},
month = {jun},
number = {1},
pages = {1--48},
primaryClass = {10.18637},
title = {{lme4: linear mixed-effects models using S4 classes}},
url = {http://dx.doi.org/10.18637/jss.v067.i01},
volume = {67},
year = {2015}
}
@article{Peres2001,
author = {Peres, Carlos a.},
doi = {10.1046/j.1523-1739.2001.01089.x},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Peres - 2001 - Synergistic Effects of Subsistence Hunting and Habitat Fragmentation on Amazonian Forest Vertebrates.pdf:pdf},
issn = {08888892},
journal = {Conservation Biology},
month = {dec},
number = {6},
pages = {1490--1505},
title = {{Synergistic Effects of Subsistence Hunting and Habitat Fragmentation on Amazonian Forest Vertebrates}},
url = {http://doi.wiley.com/10.1046/j.1523-1739.2001.01089.x},
volume = {15},
year = {2001}
}
@article{Kaplan2017,
abstract = {Anthropogenic land cover change (ALCC) is the most important transformation of the Earth system that occurred in the preindustrial Holocene, with implications for carbon, water and sediment cycles, biodiversity and the provision of ecosystem services and regional and global climate. For example, anthropogenic deforestation in preindustrial Eurasia may have led to feedbacks to the climate system: both biogeophysical, regionally amplifying winter cold and summer warm temperatures, and biogeochemical, stabilizing atmospheric CO 2 concentrations and thus influencing global climate. Quantification of these effects is difficult, however, because scenarios of anthropogenic land cover change over the Holocene vary widely, with increasing disagreement back in time. Because land cover change had such widespread ramifications for the Earth system, it is essential to assess current ALCC scenarios in light of observations and provide guidance on which models are most realistic. Here, we perform a systematic evaluation of two widely-used ALCC scenarios (KK10 and HYDE3.1) in northern and part of central Europe using an independent, pollen-based reconstruction of Holocene land cover (REVEALS). Considering that ALCC in Europe primarily resulted in deforestation, we compare modeled land use with the cover of non-forest vegetation inferred from the pollen data. Though neither land cover change scenario matches the pollen-based reconstructions precisely, KK10 correlates well with REVEALS at the country scale, while HYDE systematically underestimates land use with increasing magnitude with time in the past. Discrepancies between modeled and reconstructed land use are caused by a number of factors, including assumptions of per-capita land use and socio-cultural factors that cannot be predicted on the basis of the characteristics of the physical environment, including dietary preferences, long-distance trade, the location of urban areas and social organization.},
author = {Kaplan, Jed and Krumhardt, Kristen and Gaillard, Marie-Jos{\'{e}} and Sugita, Shinya and Trondman, Anna-Kari and Fyfe, Ralph and Marquer, Laurent and Mazier, Florence and Nielsen, Anne},
doi = {10.3390/land6040091},
file = {:C$\backslash$:/LocalStorage/References/land-06-00091.pdf:pdf},
issn = {2073-445X},
journal = {Land},
keywords = {environmental history,human-environment interactions,land use,paleoecology},
month = {dec},
number = {4},
pages = {91},
title = {{Constraining the Deforestation History of Europe: Evaluation of Historical Land Use Scenarios with Pollen-Based Land Cover Reconstructions}},
url = {http://www.mdpi.com/2073-445X/6/4/91},
volume = {6},
year = {2017}
}
@article{Kabir2007,
abstract = {In managed landscapes, tree-dominated habitats often show promise for biodiversity conservation. In Bangladesh where natural forest cover is less than 10 percent, homegardens, which are maintained by at least 20 millions households, represent one possible strategy for biodiversity conservation. This study investigated the floristic and structural diversity of 402 homegardens from six regions across southwestern Bangladesh. All plants were censused, totaling 419 species (59{\%} native), including six IUCN Red Listed. The median homegarden (800 m 2) contained a mean of 34 species. Each region contained a mean of 293 species in a mean of 67 homegardens. A total of 49,478 individuals (107 per homegarden and 1003 per hectare) of trees and shrubs were counted from 45.2 ha total sampled area. Thus, significant botanical richness was exhibited in the homegardens across southwestern Bangladesh. However, most species were rare: 82 percent of all species including 189 native were found in 50 or fewer homegardens, and 63 species (36 native) were found in only one or two homegardens. Sixty percent of all tree and shrub species had 50 or fewer individuals each. Thus, whereas richness across the landscape was high, serious effort must be made to increase the populations of most species. We propose three main conservation activities: (1) awareness building; (2) protection of existing individuals of rare species; and (3) propagation. Overlaying all of these activities is the inclusion of local communities in the process, who were the ones to retain these species in homegardens in the first place, and the stakeholders who will determine whether homegardens indeed act as long-term repositories to biodiversity conservation. {\textcopyright} 2007 The Author(s).},
author = {Kabir, Md Enamul and Webb, Edward L.},
doi = {10.1111/j.1744-7429.2007.00346.x},
file = {:C$\backslash$:/LocalStorage/References/2008/Kabir, Webb{\_}2008{\_}Can homegardens conserve biodiversity in Bangladesh.pdf:pdf},
isbn = {0006-3606},
issn = {00063606},
journal = {Biotropica},
keywords = {Agroforestry,Composition,Conservation,Ex situ,Patch,Structure,Tropical},
mendeley-tags = {Agroforestry},
month = {aug},
number = {1},
pages = {95--103},
title = {{Can homegardens conserve biodiversity in Bangladesh?}},
volume = {40},
year = {2008}
}
@article{Pfeifer2012,
author = {Pfeifer, Marion and Burgess, Neil D. and Swetnam, Ruth D. and Platts, Philip J. and Willcock, Simon and Marchant, Robert},
doi = {10.1371/journal.pone.0039337},
editor = {Hayward, Matt},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Pfeifer et al. - 2012 - Protected Areas Mixed Success in Conserving East Africa's Evergreen Forests.pdf:pdf},
issn = {1932-6203},
journal = {PLoS ONE},
month = {jun},
number = {6},
pages = {e39337},
title = {{Protected Areas: Mixed Success in Conserving East Africa's Evergreen Forests}},
url = {http://dx.plos.org/10.1371/journal.pone.0039337},
volume = {7},
year = {2012}
}
@article{Gamon1995,
abstract = {In a range of plant species from three Californian vegetation types, we examined the widely used "normalized difference vegetation index" (NDVI) and "simple ratio" (SR) as indicators of canopy structure, light absorption, and photosynthetic activity. These indices, which are derived from canopy reflectance in the red and near-infrared wavebands, highlighted phenological differences between evergreen and deciduous cano- pies. They were poor indicators of total canopy biomass due to the varying abundance of non-green standing biomass in these vegetation types. However, in sparse canopies (leaf area index [LAI] 0-2), NDVI was a sensitive indicator of canopy structure and chemical content (green biomass, green leaf area index, chlorophyll content, and foliar nitrogen content). At higher canopy green LAI values ({\textgreater}2; typical of dense shrubs and trees), NDVI was relatively insensitive to changes in canopy structure. Compared to SR, NDVI was better correlated with indicators of canopy structure and chemical content, but was equivalent to the logarithm of SR. In agreement with theoretical expectations, both NDVI and SR ex- hibited near-linear correlations with fractional PAR intercepted by green leaves over a wide range of canopy densities. Maximum daily photosynthetic rates were positively correlated with NDVI and SR in annual grassland and semideciduous shrubs where canopy devel- opment and photosynthetic activity were in synchrony. The indices were also correlated with peak springtime canopy photosynthetic rates in evergreens. However, over most of the year, these indices were poor predictors of photosynthetic performance in evergreen species due to seasonal reductions in photosynthetic radiation-use efficiency that occurred without substantial declines in canopy greenness. Our results support the use of these vegetation indices as remote indicators of PAR absorption, and thus potential photosynthetic activity, even in heterogeneous landscapes. To provide accurate estimates of vegetation- atmosphere},
author = {Gamon, John A and Field, Christopher B and Goulden, Michael L and Griffin, Kevin L and Hartley, Anne E and Joel, Geeske and Penuelas, Josep and Valentini, Riccardo},
doi = {10.2307/1942049},
file = {:C$\backslash$:/Users/mj291/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Gamon et al. - 1995 - Relationships Between NDVI, Canopy Structure, and Photosynthesis in Three Californian Vegetation Types.pdf:pdf},
issn = {10510761},
journal = {Ecological Applications},
keywords = {absorbed photosynthetically active radiation,biomass,chlorophyll content,content,dry mat-,leaf area index,net primary production,nitrogen,normalized difference vegetation index,photosynthesis,photosynthetic radiation-use efficiency,simple ratio,spectral vegetation in-,ter yield},
month = {feb},
number = {1},
pages = {28--41},
title = {{Relationships Between NDVI, Canopy Structure, and Photosynthesis in Three Californian Vegetation Types}},
url = {http://www.jstor.org/stable/1942049 http://doi.wiley.com/10.2307/1942049},
volume = {5},
year = {1995}
}
@article{Ray2013,
abstract = {The world's agricultural systems face the challenge of meeting the rising demands from population$\backslash$n growth, changing dietary preferences, and expanding biofuel use. Previous studies have put forward$\backslash$n strategies for meeting this growing demand by increasing global crop production, either expanding$\backslash$n the area under cultivation or intensifying the crop yields of our existing agricultural lands.$\backslash$n However, another possible means for increasing global crop production has received less attention:$\backslash$n increasing the frequency of global cropland harvested each year. Historically, many of the world's$\backslash$n croplands were left fallow, or had failed harvests, each year, foregoing opportunities for$\backslash$n delivering crop production. Furthermore, many regions, particularly in the trop