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1.  The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts 
Hudson, Lawrence N | Newbold, Tim | Contu, Sara | Hill, Samantha L L | Lysenko, Igor | De Palma, Adriana | Phillips, Helen R P | Senior, Rebecca A | Bennett, Dominic J | Booth, Hollie | Choimes, Argyrios | Correia, David L P | Day, Julie | Echeverría-Londoño, Susy | Garon, Morgan | Harrison, Michelle L K | Ingram, Daniel J | Jung, Martin | Kemp, Victoria | Kirkpatrick, Lucinda | Martin, Callum D | Pan, Yuan | White, Hannah J | Aben, Job | Abrahamczyk, Stefan | Adum, Gilbert B | Aguilar-Barquero, Virginia | Aizen, Marcelo A | Ancrenaz, Marc | Arbeláez-Cortés, Enrique | Armbrecht, Inge | Azhar, Badrul | Azpiroz, Adrián B | Baeten, Lander | Báldi, András | Banks, John E | Barlow, Jos | Batáry, Péter | Bates, Adam J | Bayne, Erin M | Beja, Pedro | Berg, Åke | Berry, Nicholas J | Bicknell, Jake E | Bihn, Jochen H | Böhning-Gaese, Katrin | Boekhout, Teun | Boutin, Céline | Bouyer, Jérémy | Brearley, Francis Q | Brito, Isabel | Brunet, Jörg | Buczkowski, Grzegorz | Buscardo, Erika | Cabra-García, Jimmy | Calviño-Cancela, María | Cameron, Sydney A | Cancello, Eliana M | Carrijo, Tiago F | Carvalho, Anelena L | Castro, Helena | Castro-Luna, Alejandro A | Cerda, Rolando | Cerezo, Alexis | Chauvat, Matthieu | Clarke, Frank M | Cleary, Daniel F R | Connop, Stuart P | D'Aniello, Biagio | da Silva, Pedro Giovâni | Darvill, Ben | Dauber, Jens | Dejean, Alain | Diekötter, Tim | Dominguez-Haydar, Yamileth | Dormann, Carsten F | Dumont, Bertrand | Dures, Simon G | Dynesius, Mats | Edenius, Lars | Elek, Zoltán | Entling, Martin H | Farwig, Nina | Fayle, Tom M | Felicioli, Antonio | Felton, Annika M | Ficetola, Gentile F | Filgueiras, Bruno K C | Fonte, Steven J | Fraser, Lauchlan H | Fukuda, Daisuke | Furlani, Dario | Ganzhorn, Jörg U | Garden, Jenni G | Gheler-Costa, Carla | Giordani, Paolo | Giordano, Simonetta | Gottschalk, Marco S | Goulson, Dave | Gove, Aaron D | Grogan, James | Hanley, Mick E | Hanson, Thor | Hashim, Nor R | Hawes, Joseph E | Hébert, Christian | Helden, Alvin J | Henden, John-André | Hernández, Lionel | Herzog, Felix | Higuera-Diaz, Diego | Hilje, Branko | Horgan, Finbarr G | Horváth, Roland | Hylander, Kristoffer | Isaacs-Cubides, Paola | Ishitani, Masahiro | Jacobs, Carmen T | Jaramillo, Víctor J | Jauker, Birgit | Jonsell, Mats | Jung, Thomas S | Kapoor, Vena | Kati, Vassiliki | Katovai, Eric | Kessler, Michael | Knop, Eva | Kolb, Annette | Kőrösi, Ádám | Lachat, Thibault | Lantschner, Victoria | Le Féon, Violette | LeBuhn, Gretchen | Légaré, Jean-Philippe | Letcher, Susan G | Littlewood, Nick A | López-Quintero, Carlos A | Louhaichi, Mounir | Lövei, Gabor L | Lucas-Borja, Manuel Esteban | Luja, Victor H | Maeto, Kaoru | Magura, Tibor | Mallari, Neil Aldrin | Marin-Spiotta, Erika | Marshall, E J P | Martínez, Eliana | Mayfield, Margaret M | Mikusinski, Grzegorz | Milder, Jeffrey C | Miller, James R | Morales, Carolina L | Muchane, Mary N | Muchane, Muchai | Naidoo, Robin | Nakamura, Akihiro | Naoe, Shoji | Nates-Parra, Guiomar | Navarrete Gutierrez, Dario A | Neuschulz, Eike L | Noreika, Norbertas | Norfolk, Olivia | Noriega, Jorge Ari | Nöske, Nicole M | O'Dea, Niall | Oduro, William | Ofori-Boateng, Caleb | Oke, Chris O | Osgathorpe, Lynne M | Paritsis, Juan | Parra-H, Alejandro | Pelegrin, Nicolás | Peres, Carlos A | Persson, Anna S | Petanidou, Theodora | Phalan, Ben | Philips, T Keith | Poveda, Katja | Power, Eileen F | Presley, Steven J | Proença, Vânia | Quaranta, Marino | Quintero, Carolina | Redpath-Downing, Nicola A | Reid, J Leighton | Reis, Yana T | Ribeiro, Danilo B | Richardson, Barbara A | Richardson, Michael J | Robles, Carolina A | Römbke, Jörg | Romero-Duque, Luz Piedad | Rosselli, Loreta | Rossiter, Stephen J | Roulston, T'ai H | Rousseau, Laurent | Sadler, Jonathan P | Sáfián, Szabolcs | Saldaña-Vázquez, Romeo A | Samnegård, Ulrika | Schüepp, Christof | Schweiger, Oliver | Sedlock, Jodi L | Shahabuddin, Ghazala | Sheil, Douglas | Silva, Fernando A B | Slade, Eleanor M | Smith-Pardo, Allan H | Sodhi, Navjot S | Somarriba, Eduardo J | Sosa, Ramón A | Stout, Jane C | Struebig, Matthew J | Sung, Yik-Hei | Threlfall, Caragh G | Tonietto, Rebecca | Tóthmérész, Béla | Tscharntke, Teja | Turner, Edgar C | Tylianakis, Jason M | Vanbergen, Adam J | Vassilev, Kiril | Verboven, Hans A F | Vergara, Carlos H | Vergara, Pablo M | Verhulst, Jort | Walker, Tony R | Wang, Yanping | Watling, James I | Wells, Konstans | Williams, Christopher D | Willig, Michael R | Woinarski, John C Z | Wolf, Jan H D | Woodcock, Ben A | Yu, Douglas W | Zaitsev, Andrey S | Collen, Ben | Ewers, Rob M | Mace, Georgina M | Purves, Drew W | Scharlemann, Jörn P W | Purvis, Andy
Ecology and Evolution  2014;4(24):4701-4735.
Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – http://www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
doi:10.1002/ece3.1303
PMCID: PMC4278822  PMID: 25558364
Data sharing; global change; habitat destruction; land use
2.  Mapping Functional Traits: Comparing Abundance and Presence-Absence Estimates at Large Spatial Scales 
PLoS ONE  2012;7(8):e44019.
Efforts to quantify the composition of biological communities increasingly focus on functional traits. The composition of communities in terms of traits can be summarized in several ways. Ecologists are beginning to map the geographic distribution of trait-based metrics from various sources of data, but the maps have not been tested against independent data. Using data for birds of the Western Hemisphere, we test for the first time the most commonly used method for mapping community trait composition – overlaying range maps, which assumes that the local abundance of a given species is unrelated to the traits in question – and three new methods that as well as the range maps include varying degrees of information about interspecific and geographic variation in abundance. For each method, and for four traits (body mass, generation length, migratory behaviour, diet) we calculated community-weighted mean of trait values, functional richness and functional divergence. The maps based on species ranges and limited abundance data were compared with independent data on community species composition from the American Christmas Bird Count (CBC) scheme coupled with data on traits. The correspondence with observed community composition at the CBC sites was mostly positive (62/73 correlations) but varied widely depending on the metric of community composition and method used (R2: 5.6×10−7 to 0.82, with a median of 0.12). Importantly, the commonly-used range-overlap method resulted in the best fit (21/22 correlations positive; R2: 0.004 to 0.8, with a median of 0.33). Given the paucity of data on the local abundance of species, overlaying range maps appears to be the best available method for estimating patterns of community composition, but the poor fit for some metrics suggests that local abundance data are urgently needed to allow more accurate estimates of the composition of communities.
doi:10.1371/journal.pone.0044019
PMCID: PMC3432103  PMID: 22952859
3.  Emergent Global Patterns of Ecosystem Structure and Function from a Mechanistic General Ecosystem Model 
PLoS Biology  2014;12(4):e1001841.
This paper presents the first mathematical model that attempts to represent the biology and behavior of all individual organisms globally, taking us a step closer to holistic ecological and conservation science founded on mechanistic predictions.
Anthropogenic activities are causing widespread degradation of ecosystems worldwide, threatening the ecosystem services upon which all human life depends. Improved understanding of this degradation is urgently needed to improve avoidance and mitigation measures. One tool to assist these efforts is predictive models of ecosystem structure and function that are mechanistic: based on fundamental ecological principles. Here we present the first mechanistic General Ecosystem Model (GEM) of ecosystem structure and function that is both global and applies in all terrestrial and marine environments. Functional forms and parameter values were derived from the theoretical and empirical literature where possible. Simulations of the fate of all organisms with body masses between 10 µg and 150,000 kg (a range of 14 orders of magnitude) across the globe led to emergent properties at individual (e.g., growth rate), community (e.g., biomass turnover rates), ecosystem (e.g., trophic pyramids), and macroecological scales (e.g., global patterns of trophic structure) that are in general agreement with current data and theory. These properties emerged from our encoding of the biology of, and interactions among, individual organisms without any direct constraints on the properties themselves. Our results indicate that ecologists have gathered sufficient information to begin to build realistic, global, and mechanistic models of ecosystems, capable of predicting a diverse range of ecosystem properties and their response to human pressures.
Author Summary
Ecosystems across the world are being rapidly degraded. This threatens their provision of natural goods and services, upon which all life depends. To be able to reduce—and one day reverse—this damage, we need to be able to predict the effects of human actions on ecosystems. Here, we present the first example of a General Ecosystem Model (GEM)—called the Madingley Model—a novel class of computational model that can be applied to any ecosystem, marine or terrestrial, and can be simulated at any spatial scale from local up to global. It covers almost all organisms in ecosystems, from the smallest to the largest, encoding the underlying biology and behaviour of individual organisms to capture the interactions between them and with the environment, to model the fate of each individual organism, and to make predictions about ecosystem structure and function. Predictions made by the Madingley Model broadly resemble what we observe in real-world ecosystems across scales from individuals through to communities, ecosystems, and the world as a whole. Our results show that ecologists can now begin modelling all nonhuman life on earth, and we suggest that this type of approach may hold promise for predicting the ecological implications of different future trajectories of human activity on our shared planet.
doi:10.1371/journal.pbio.1001841
PMCID: PMC3995663  PMID: 24756001
4.  Ecological traits affect the response of tropical forest bird species to land-use intensity 
Land-use change is one of the main drivers of current and likely future biodiversity loss. Therefore, understanding how species are affected by it is crucial to guide conservation decisions. Species respond differently to land-use change, possibly related to their traits. Using pan-tropical data on bird occurrence and abundance across a human land-use intensity gradient, we tested the effects of seven traits on observed responses. A likelihood-based approach allowed us to quantify uncertainty in modelled responses, essential for applying the model to project future change. Compared with undisturbed habitats, the average probability of occurrence of bird species was 7.8 per cent and 31.4 per cent lower, and abundance declined by 3.7 per cent and 19.2 per cent in habitats with low and high human land-use intensity, respectively. Five of the seven traits tested affected the observed responses significantly: long-lived, large, non-migratory, primarily frugivorous or insectivorous forest specialists were both less likely to occur and less abundant in more intensively used habitats than short-lived, small, migratory, non-frugivorous/insectivorous habitat generalists. The finding that species responses to land use depend on their traits is important for understanding ecosystem functioning, because species' traits determine their contribution to ecosystem processes. Furthermore, the loss of species with particular traits might have implications for the delivery of ecosystem services.
doi:10.1098/rspb.2012.2131
PMCID: PMC3574433  PMID: 23173205
birds; functional traits; land-use change; likelihood-based model; tropical forest
5.  How Stand Productivity Results from Size- and Competition-Dependent Growth and Mortality 
PLoS ONE  2011;6(12):e28660.
Background
A better understanding of the relationship between stand structure and productivity is required for the development of: a) scalable models that can accurately predict growth and yield dynamics for the world's forests; and b) stand management regimes that maximize wood and/or timber yield, while maintaining structural and species diversity.
Methods
We develop a cohort-based canopy competition model (“CAIN”), parameterized with inventory data from Ontario, Canada, to examine the relationship between stand structure and productivity. Tree growth, mortality and recruitment are quantified as functions of diameter and asymmetric competition, using a competition index (CAIh) defined as the total projected area of tree crowns at a given tree's mid-crown height. Stand growth, mortality, and yield are simulated for inventoried stands, and also for hypothetical stands differing in total volume and tree size distribution.
Results
For a given diameter, tree growth decreases as CAIh increases, whereas the probability of mortality increases. For a given CAIh, diameter growth exhibits a humped pattern with respect to diameter, whereas mortality exhibits a U-shaped pattern reflecting senescence of large trees. For a fixed size distribution, stand growth increases asymptotically with total density, whereas mortality increases monotonically. Thus, net productivity peaks at an intermediate volume of 100–150 m3/ha, and approaches zero at 250 m3/ha. However, for a fixed stand volume, mortality due to senescence decreases if the proportion of large trees decreases as overall density increases. This size-related reduction in mortality offsets the density-related increase in mortality, resulting in a 40% increase in yield.
Conclusions
Size-related variation in growth and mortality exerts a profound influence on the relationship between stand structure and productivity. Dense stands dominated by small trees yield more wood than stands dominated by fewer large trees, because the relative growth rate of small trees is higher, and because they are less likely to die.
doi:10.1371/journal.pone.0028660
PMCID: PMC3236764  PMID: 22174861
6.  Influences of Forest Structure, Climate and Species Composition on Tree Mortality across the Eastern US 
PLoS ONE  2010;5(10):e13212.
Few studies have quantified regional variation in tree mortality, or explored whether species compositional changes or within-species variation are responsible for regional patterns, despite the fact that mortality has direct effects on the dynamics of woody biomass, species composition, stand structure, wood production and forest response to climate change. Using Bayesian analysis of over 430,000 tree records from a large eastern US forest database we characterised tree mortality as a function of climate, soils, species and size (stem diameter). We found (1) mortality is U-shaped vs. stem diameter for all 21 species examined; (2) mortality is hump-shaped vs. plot basal area for most species; (3) geographical variation in mortality is substantial, and correlated with several environmental factors; and (4) individual species vary substantially from the combined average in the nature and magnitude of their mortality responses to environmental variation. Regional variation in mortality is therefore the product of variation in species composition combined with highly varied mortality-environment correlations within species. The results imply that variation in mortality is a crucial part of variation in the forest carbon cycle, such that including this variation in models of the global carbon cycle could significantly narrow uncertainty in climate change predictions.
doi:10.1371/journal.pone.0013212
PMCID: PMC2954149  PMID: 20967250
7.  The demography of range boundaries versus range cores in eastern US tree species 
Regional species–climate correlations are well documented, but little is known about the ecological processes responsible for generating these patterns. Using the data from over 690 000 individual trees I estimated five demographic rates—canopy growth, understorey growth, canopy lifespan, understorey lifespan and per capita reproduction—for 19 common eastern US tree species, within the core and the northern and southern boundaries, of the species range. Most species showed statistically significant boundary versus core differences in most rates at both boundary types. Differences in canopy and understorey growth were relatively small in magnitude but consistent among species, being lower at the northern (average −17%) and higher at the southern (average +12%) boundaries. Differences in lifespan were larger in magnitude but highly variable among species, except for a marked trend for reduced canopy lifespan at the northern boundary (average −49%). Differences in per capita reproduction were large and statistically significant for some species, but highly variable among species. The rate estimates were combined to calculate two performance indices: R0 (a measure of lifetime fitness in the absence of competition) was consistently lower at the northern boundary (average −86%) whereas Z* (a measure of competitive ability in closed forest) showed no sign of a consistent boundary–core difference at either boundary.
doi:10.1098/rspb.2008.1241
PMCID: PMC2677233  PMID: 19324819
biogeography; climate change; forest dynamics; mortality; range shifts; species migrations
8.  Crown Plasticity and Competition for Canopy Space: A New Spatially Implicit Model Parameterized for 250 North American Tree Species 
PLoS ONE  2007;2(9):e870.
Background
Canopy structure, which can be defined as the sum of the sizes, shapes and relative placements of the tree crowns in a forest stand, is central to all aspects of forest ecology. But there is no accepted method for deriving canopy structure from the sizes, species and biomechanical properties of the individual trees in a stand. Any such method must capture the fact that trees are highly plastic in their growth, forming tessellating crown shapes that fill all or most of the canopy space.
Methodology/Principal Findings
We introduce a new, simple and rapidly-implemented model–the Ideal Tree Distribution, ITD–with tree form (height allometry and crown shape), growth plasticity, and space-filling, at its core. The ITD predicts the canopy status (in or out of canopy), crown depth, and total and exposed crown area of the trees in a stand, given their species, sizes and potential crown shapes. We use maximum likelihood methods, in conjunction with data from over 100,000 trees taken from forests across the coterminous US, to estimate ITD model parameters for 250 North American tree species. With only two free parameters per species–one aggregate parameter to describe crown shape, and one parameter to set the so-called depth bias–the model captures between-species patterns in average canopy status, crown radius, and crown depth, and within-species means of these metrics vs stem diameter. The model also predicts much of the variation in these metrics for a tree of a given species and size, resulting solely from deterministic responses to variation in stand structure.
Conclusions/Significance
This new model, with parameters for US tree species, opens up new possibilities for understanding and modeling forest dynamics at local and regional scales, and may provide a new way to interpret remote sensing data of forest canopies, including LIDAR and aerial photography.
doi:10.1371/journal.pone.0000870
PMCID: PMC1964803  PMID: 17849000
9.  Different but equal: the implausible assumption at the heart of neutral theory 
The Journal of Animal Ecology  2010;79(6):1215-1225.
1.The core assumption of neutral theory is that all individuals in a community have equal fitness regardless of species, and regardless of the species composition of the community. But, real communities consist of species exhibiting large trait differences; hence these differences must be subject to perfect fitness-equalizing trade-offs for neutrality to hold.
2.Here we explain that perfect equalizing trade-offs are extremely unlikely to occur in reality, because equality of fitness among species is destroyed by: (i) any deviation in the functional form of the trade-off away from the one special form that gives equal fitness; (ii) spatial or temporal variation in performance; (iii) random species differences in performance.
3.In the absence of the density-dependent processes stressed by traditional niche-based community ecology, communities featuring small amounts of (i) or (ii) rapidly lose trait variation, becoming dominated by species with similar traits, and exhibit substantially lower species richness compared to the neutral case. Communities featuring random interspecific variation in traits (iii) lose all but a few fortuitous species.
4.Thus neutrality should be viewed, a priori, as a highly improbable explanation for the long-term co-occurrence of measurably different species within ecological communities. In contrast, coexistence via niche structure and density dependence, is robust to species differences in baseline fitness, and so remains plausible.
5.We conclude that: (i) co-occurring species will typically exhibit substantial differences in baseline fitness even when (imperfect) equalizing trade-offs have been taken into account; (ii) therefore, communities must be strongly niche structured, otherwise they would lose both trait variation and species richness; (iii) nonetheless, even in strongly niche-structured communities, it is possible that the abundance of species with similar traits are at least partially free to drift.
doi:10.1111/j.1365-2656.2010.01738.x
PMCID: PMC3025117  PMID: 20726922
biodiversity; coexistence; community ecology; density dependence; ecological drift; ecosystem function; life-history manifold; null model; trait variation
10.  Quantifying variation in forest disturbance, and its effects on aboveground biomass dynamics, across the eastern United States 
Global Change Biology  2013;19(5):1504-1517.
The role of tree mortality in the global carbon balance is complicated by strong spatial and temporal heterogeneity that arises from the stochastic nature of carbon loss through disturbance. Characterizing spatio-temporal variation in mortality (including disturbance) and its effects on forest and carbon dynamics is thus essential to understanding the current global forest carbon sink, and to predicting how it will change in future. We analyzed forest inventory data from the eastern United States to estimate plot-level variation in mortality (relative to a long-term background rate for individual trees) for nine distinct forest regions. Disturbances that produced at least a fourfold increase in tree mortality over an approximately 5 year interval were observed in 1–5% of plots in each forest region. The frequency of disturbance was lowest in the northeast, and increased southwards along the Atlantic and Gulf coasts as fire and hurricane disturbances became progressively more common. Across the central and northern parts of the region, natural disturbances appeared to reflect a diffuse combination of wind, insects, disease, and ice storms. By linking estimated covariation in tree growth and mortality over time with a data-constrained forest dynamics model, we simulated the implications of stochastic variation in mortality for long-term aboveground biomass changes across the eastern United States. A geographic gradient in disturbance frequency induced notable differences in biomass dynamics between the least- and most-disturbed regions, with variation in mortality causing the latter to undergo considerably stronger fluctuations in aboveground stand biomass over time. Moreover, regional simulations showed that a given long-term increase in mean mortality rates would support greater aboveground biomass when expressed through disturbance effects compared with background mortality, particularly for early-successional species. The effects of increased tree mortality on carbon stocks and forest composition may thus depend partly on whether future mortality increases are chronic or episodic in nature.
doi:10.1111/gcb.12152
PMCID: PMC3657128  PMID: 23505000
CAIN; carbon fluxes; forest inventory and analysis; hierarchical Bayes; mortality; simulation modeling; tree demography

Results 1-10 (10)