bibliography.bib

@article{Webb_Exploring_2000,
  title = {Exploring the {{Phylogenetic Structure}} of {{Ecological Communities}}: {{An Example}} for {{Rain Forest Trees}}},
  shorttitle = {Exploring the {{Phylogenetic Structure}} of {{Ecological Communities}}},
  author = {Webb, null},
  year = {2000},
  month = aug,
  volume = {156},
  pages = {145--155},
  issn = {1537-5323},
  doi = {10.1086/303378},
  abstract = {Because of the correlation expected between the phylogenetic relatedness of two taxa and their net ecological similarity, a measure of the overall phylogenetic relatedness of a community of interacting organisms can be used to investigate the contemporary ecological processes that structure community composition. I describe two indices that use the number of nodes that separate taxa on a phylogeny as a measure of their phylogenetic relatedness. As an example of the use of these indices in community analysis, I compared the mean observed net relatedness of trees ({$>$}/=10 cm diameter at breast height) in each of 28 plots (each 0.16 ha) in a Bornean rain forest with the net relatedness expected if species were drawn randomly from the species pool (of the 324 species in the 28 plots), using a supertree that I assembled from published sources. I found that the species in plots were more phylogenetically related than expected by chance, a result that was insensitive to various modifications to the basic methodology. I tentatively infer that variation in habitat among plots causes ecologically more similar species to co-occur within plots. Finally, I suggest a range of applications for phylogenetic relatedness measures in community analysis.},
  journal = {The American Naturalist},
  language = {eng},
  number = {2},
  pmid = {10856198}
}
@article{Pavoine_Correlations_2013,
  title = {Correlations between Phylogenetic and Functional Diversity: Mathematical Artefacts or True Ecological and Evolutionary Processes?},
  shorttitle = {Correlations between Phylogenetic and Functional Diversity},
  author = {Pavoine, Sandrine and Gasc, Amandine and Bonsall, Michael B. and Mason, Norman W.H.},
  year = {2013},
  month = sep,
  volume = {24},
  pages = {781--793},
  issn = {1654-1103},
  doi = {10.1111/jvs.12051},
  abstract = {Questions Is phylogenetic diversity (PD) an accurate surrogate for functional diversity (FD)? How are FD:PD correlations affected by the diversity index used, covarying factors and/or the strength of the phylogenetic signal in ecological traits? Location Field study, coastal marsh plain Mekhada, Algeria, complemented by simulated data. Methods FD and PD indices might correlate simply because variation in species richness and evenness (referred to as co-factors) influences both FD and PD values. We partition FD and PD indices into components influenced by species richness, evenness and species' (functional and phylogenetic) characteristics. When a simple partition was not found, comparison to null models was used to remove the effects of co-factors. We examined correlations between ten FD and PD indices, among which several were shown to be connected using our mathematical partitioning approach and several were transformed by comparison with null models to control for effects of co-factors. In doing this, FD values were calculated using simulated trait values with varying phylogenetic signal. We then selected a subset of complementary FD and PD indices in exploring the influence of environmental variables on diversity across 75 plant assemblages in Mekhada. Results Altogether, mathematical partitioning and the comparison to null models successfully removed the effects of co-factors when comparing FD and PD. For all indices affected by species richness, FD:PD correlations approached 1, irrespective of the trait evolution model used. In contrast, simulations showed that FD:PD correlations measured with indices unaffected by co-factors decreased when the phylogenetic signal in traits decreased. Applied to plant assemblages in Mekhada, complementary diversity indices showed that, despite significant (but moderate) FD:PD correlation, FD but not PD was significantly correlated with the main stress gradient (salinity). Conclusions From both our simulations and analysis of plant community diversity, PD was a poor surrogate for FD. In Mekhada, PD was also less correlated with environmental variables than FD. Species richness was found to be a better surrogate for FD than PD in identifying the ecological processes that distribute species along the salinity gradient.},
  file = {/Users/Rekyt/Zotero/storage/RSB55GP5/Pavoine et al. - 2013 - Correlations between phylogenetic and functional d.pdf;/Users/Rekyt/Zotero/storage/H23UGMGS/abstract.html},
  journal = {Journal of Vegetation Science},
  keywords = {Assembly processes,biodiversity,biodiversity indices,environmental filtering,Environmental filtering,Niche complementarity,null model,Null model,Phylogenetic signal,Simpson index,species richness,Surrogates},
  language = {en},
  number = {5}
}
@article{Dobert_Logging_2017,
  title = {Logging Increases the Functional and Phylogenetic Dispersion of Understorey Plant Communities in Tropical Lowland Rain Forest},
  author = {D{\"o}bert, Timm F. and Webber, Bruce L. and Sugau, John B. and Dickinson, Katharine J. M. and Didham, Raphael K.},
  year = {2017},
  month = sep,
  volume = {105},
  pages = {1235--1245},
  publisher = {{John Wiley \& Sons, Ltd}},
  issn = {0022-0477},
  doi = {10.1111/1365-2745.12794},
  abstract = {Summary Logging is a major driver of tropical forest degradation, with severe impacts on plant richness and composition. Rarely have these effects been considered in terms of their impact on the functional and phylogenetic diversity of understorey plant communities, despite the direct relevance to community reassembly trajectories. Here, we test the effects of logging on functional traits and evolutionary relatedness, over and above effects that can be explained by changes in species richness alone. We hypothesised that strong environmental filtering will result in more clustered (under-dispersed) functional and phylogenetic structures within communities as logging intensity increases. We surveyed understorey plant communities at 180 locations across a logging intensity gradient from primary to repeatedly logged tropical lowland rain forest in Sabah, Malaysia. For the 691 recorded plant taxa, we generated a phylogeny to assess plot-level phylogenetic relatedness. We quantified 10 plant traits known to respond to disturbance and affect ecosystem functioning, and tested the influence of logging on functional and phylogenetic structure. We found no significant effect of forest canopy loss or road configuration on species richness. By contrast, both functional dispersion and phylogenetic dispersion (net relatedness index) showed strong gradients from clustered towards more randomly assembled communities at higher logging intensity, independent of variation in species richness. Moreover, there was a significant nonlinear shift in the trait dispersion relationship above a logging intensity threshold of c. 65\% canopy loss ({$\pm$}17\% CL). All functional traits showed significant phylogenetic signals, suggesting broad concordance between functional and phylogenetic dispersion, at least below the logging intensity threshold. Synthesis. We found a strong logging signal in the functional and phylogenetic structure of understorey plant communities, over and above species richness, but this effect was opposite to that predicted. Logging increased, rather than decreased, functional and phylogenetic dispersion in understorey plant communities. This effect was particularly pronounced for functional response traits, which directly link disturbance with plant community reassembly. Our study provides novel insights into the way logging affects understorey plant communities in tropical rain forest and highlights the importance of trait-based approaches to improve our understanding of the broad range of logging-associated impacts.},
  file = {/Users/Rekyt/Zotero/storage/Z5IVRFGL/Döbert et al. - 2017 - Logging increases the functional and phylogenetic .pdf;/Users/Rekyt/Zotero/storage/H4KEH4Y4/1365-2745.html},
  journal = {Journal of Ecology},
  keywords = {above-ground biomass,Borneo,carbon storage,dipterocarp forest,disturbance gradient,land-use change,logging intensity,phylogenetic signal,plant functional traits,response diversity},
  number = {5}
}
@misc{Dobert_Data_2018,
  title = {Data from: {{Logging}} Increases the Functional and Phylogenetic Dispersion of Understorey Plant Communities in Tropical Lowland Rainforest},
  shorttitle = {Data From},
  author = {D{\"o}bert, Timm F. and Webber, Bruce L. and Sugau, John B. and Dickinson, Katharine J. M. and Didham, Raphael K.},
  year = {2018},
  pages = {387472 bytes},
  publisher = {{Dryad}},
  doi = {10.5061/DRYAD.F77P7},
  abstract = {1. Logging is a major driver of tropical forest degradation, with severe impacts on plant richness and composition. Rarely have these effects been considered in terms of their impact on the functional and phylogenetic diversity of understorey plant communities, despite the direct relevance to community reassembly trajectories. Here, we test the effects of logging on functional traits and evolutionary relatedness, over and above effects that can be explained by changes in species richness alone. We hypothesised that strong environmental filtering will result in more clustered (under-dispersed) functional and phylogenetic structures within communities as logging intensity increases. 2. We surveyed understorey plant communities at 180 locations across a logging intensity gradient from primary to repeatedly-logged tropical lowland rainforest in Sabah, Malaysia. For the 691 recorded plant taxa, we generated a phylogeny to assess plot-level phylogenetic relatedness. We quantified 10 plant traits known to respond to disturbance (dispersal mode, fruit type, life-history mode, pollination syndrome, reproduction strategy and seed number) and affect ecosystem functioning (plant growth form, plant height, specific leaf area and wood density), and tested the influence of logging on functional and phylogenetic structure. 3. We found no significant effect of local- or landscape-scale forest canopy loss, or configuration of logging roads on species richness. By contrast, both the trait dispersion index (FDis) and net relatedness index (NRI) for phylogenetic dispersion showed strong gradients from clustered towards more randomly-assembled communities at higher logging intensity, independent of variation in species richness. All functional traits showed significant phylogenetic signals, indicating strong concordance between functional and phylogenetic dispersion. 4. Synthesis. We found a strong logging signal in the functional and phylogenetic structure of understorey plant communities, over and above species richness, but this effect was opposite to that predicted. Logging increased, rather than decreased, functional and phylogenetic dispersion in understorey plant communities. This effect was particularly pronounced for functional response traits, which directly link disturbance with plant community reassembly. Our study provides novel insight into the way logging affects understorey plant communities in tropical rainforest and highlights the importance of trait-based approaches to improve our understanding of the broad range of logging-associated impacts.},
  copyright = {Creative Commons Zero v1.0 Universal},
  keywords = {Above-ground biomass,Determinants of plant community diversity and structure,Dipterocarp forest,disturbance gradient,Land-use change,logging intensity,phylogenetic signal,plant functional traits,response diversity},
  language = {en}
}
@article{Lavorel_Predicting_2002,
  title = {Predicting Changes in Community Composition and Ecosystem Functioning from Plant Traits: Revisiting the {{Holy Grail}}},
  shorttitle = {Predicting Changes in Community Composition and Ecosystem Functioning from Plant Traits},
  author = {Lavorel, S. and Garnier, E.},
  year = {2002},
  volume = {16},
  pages = {545--556},
  issn = {1365-2435},
  doi = {10.1046/j.1365-2435.2002.00664.x},
  abstract = {1 The concept of plant functional type proposes that species can be grouped according to common responses to the environment and/or common effects on ecosystem processes. However, the knowledge of relationships between traits associated with the response of plants to environmental factors such as resources and disturbances (response traits), and traits that determine effects of plants on ecosystem functions (effect traits), such as biogeochemical cycling or propensity to disturbance, remains rudimentary. 2 We present a framework using concepts and results from community ecology, ecosystem ecology and evolutionary biology to provide this linkage. Ecosystem functioning is the end result of the operation of multiple environmental filters in a hierarchy of scales which, by selecting individuals with appropriate responses, result in assemblages with varying trait composition. Functional linkages and trade-offs among traits, each of which relates to one or several processes, determine whether or not filtering by different factors gives a match, and whether ecosystem effects can be easily deduced from the knowledge of the filters. 3 To illustrate this framework we analyse a set of key environmental factors and ecosystem processes. While traits associated with response to nutrient gradients strongly overlapped with those determining net primary production, little direct overlap was found between response to fire and flammability. 4 We hypothesize that these patterns reflect general trends. Responses to resource availability would be determined by traits that are also involved in biogeochemical cycling, because both these responses and effects are driven by the trade-off between acquisition and conservation. On the other hand, regeneration and demographic traits associated with response to disturbance, which are known to have little connection with adult traits involved in plant ecophysiology, would be of little relevance to ecosystem processes. 5 This framework is likely to be broadly applicable, although caution must be exercised to use trait linkages and trade-offs appropriate to the scale, environmental conditions and evolutionary context. It may direct the selection of plant functional types for vegetation models at a range of scales, and help with the design of experimental studies of relationships between plant diversity and ecosystem properties.},
  annotation = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-2435.2002.00664.x},
  file = {/Users/Rekyt/Zotero/storage/JRPT4CIG/Lavorel et Garnier - 2002 - Predicting changes in community composition and ec.pdf;/Users/Rekyt/Zotero/storage/2HXJHW7Q/j.1365-2435.2002.00664.html},
  journal = {Functional Ecology},
  keywords = {Biogeochemical cycles,disturbance,effect traits,fire,resource gradient,response traits,scaling-up,trade-offs},
  language = {en},
  number = {5}
}
@article{Laliberte_distancebased_2010,
  title = {A Distance-Based Framework for Measuring Functional Diversity from Multiple Traits},
  author = {Lalibert{\'e}, Etienne and Legendre, Pierre},
  year = {2010},
  volume = {91},
  pages = {299--305},
  issn = {1939-9170},
  doi = {10.1890/08-2244.1},
  abstract = {A new framework for measuring functional diversity (FD) from multiple traits has recently been proposed. This framework was mostly limited to quantitative traits without missing values and to situations in which there are more species than traits, although the authors had suggested a way to extend their framework to other trait types. The main purpose of this note is to further develop this suggestion. We describe a highly flexible distance-based framework to measure different facets of FD in multidimensional trait space from any distance or dissimilarity measure, any number of traits, and from different trait types (i.e., quantitative, semi-quantitative, and qualitative). This new approach allows for missing trait values and the weighting of individual traits. We also present a new multidimensional FD index, called functional dispersion (FDis), which is closely related to Rao's quadratic entropy. FDis is the multivariate analogue of the weighted mean absolute deviation (MAD), in which the weights are species relative abundances. For unweighted presence\textendash absence data, FDis can be used for a formal statistical test of differences in FD. We provide the ``FD'' R language package to easily implement our distance-based FD framework.},
  copyright = {\textcopyright{} 2010 by the Ecological Society of America},
  file = {/Users/Rekyt/Zotero/storage/5K6N9NPQ/08-2244.html},
  journal = {Ecology},
  keywords = {functional composition,functional dispersion,functional divergence,functional diversity,functional evenness,functional identity,functional richness,functional trait,multivariate dispersion},
  language = {en},
  number = {1}
}