Trait probability density (<scp>TPD</scp>): measuring functional diversity across scales based on <scp>TPD</scp> with R

Carmona, Carlos P.; Bello, Francesco de; Mason, Norman W. H.; Lepš, Jan

doi:10.1002/ecy.2876

Cited by 111 publications

(214 citation statements)

References 43 publications

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“…We used the following packages in R software ver. 3.3.3 (<http://www.r-project.org>): TPD (Carmona ) for calculating trait probability distributions, functional diversity indices, functional dissimilarity and functional uniqueness measures; FD (Laliberté et al ) for calculating CWMs, betapart (Baselga et al ) for beta diversity analyses; lme4 (Bates et al ) for linear mixed‐effects models; MASS (Venables and Ripley ) for NMDS; and ggplot2 (Wickham ) for graphics.…”

Section: Methodsmentioning

confidence: 99%

The cryptic impacts of invasion: functional homogenization of tropical ant communities by invasive fire ants

Wong

Guénard²,

Lewis

2020

Oikos

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The diversity and distribution of traits in an ecological community shapes its responses to change and the ecosystem processes it modulates. This ‘functional diversity’, however, is not necessarily a direct outcome of taxonomic diversity. Invasions by exotic insects occur in ecosystems worldwide, but there is limited understanding of how they impact functional diversity. We present the first comprehensive trait‐based investigation of the impacts of an ant invasion, and the first incorporating intraspecific polymorphisms in species‐level functional diversity. The fire ant Solenopsis invicta is an invasive species with a global distribution. Focusing on invaded and uninvaded plots in tropical grasslands of Hong Kong, we investigated how the presence of S. invicta affects the diversity and distribution of ant species and traits within and across communities, the functional identities of communities, and functionally unique species. Using trait probability density functions, we built trait spaces for 29 different species, and scaled up these components to calculate functional diversity at community and landscape levels. We found that invasion had limited effects on species and functional richness but pronounced effects on functional composition. Specifically, invaded communities had fewer functionally‐unique individuals, and were characterized by species with narrower heads and bodies and shorter mandibles. Moreover, invaded communities showed substantially higher levels of functional redundancy (+56%) due to a clustering of trait values. Consequently, across the landscape, invaded communities displayed 23% less functional turnover than uninvaded communities despite showing comparable levels of taxonomic turnover – a result confirming theoretical predictions of the effects of high local functional redundancy. In sum, the presence of S. invicta alters the functional properties of multiple local communities selectively, resulting in functional homogenization across the landscape. The disparities between taxonomic and functional impacts of invasion highlight the need to consider how trait diversity across ecological scales shapes biodiversity and its responses to change.

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Section: Methodsmentioning

confidence: 99%

The cryptic impacts of invasion: functional homogenization of tropical ant communities by invasive fire ants

Wong

Guénard²,

Lewis

2020

Oikos

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“…We retained the four first axes of the PCoA, that represented 65.6% of the total variation in the trait matrix, and used the scores of the species in these axes to estimate functional diversity indices. For this, we used the R package TPD 74,75 to obtain a trait probability density function (TPD) for each species and assemblage. TPD functions reflect the abundance of the different trait combinations in each community and can be used to estimate several aspects of functional diversity 56,72 .…”

Section: Data Analysis Full Inventory Completeness Was Reported As Tmentioning

confidence: 99%

Contrasting functional structure of saproxylic beetle assemblages associated to different microhabitats

Micó

Ramilo

Thorn

et al. 2020

Sci Rep

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Saproxylic beetles depend on diverse microhabitats that are exploited by different species assemblages. We focused on analysing the functional trait patterns and functional diversity components of two main assemblages that were collected with window traps (Wts) and hollow emergence traps (Hets) respectively, between three protected areas of the iberian peninsula. for that we measured phenological, physiological, morphological, and ecological traits. Results showed that the main microhabitats exploited by each assemblage (Wt and Het) constrain most of the morphological traits and trophic guilds. in addition, relative elytra length and predator guild, together with adult activity period, responded to differences at the habitat level (among study areas). HET assemblages were less taxonomically diverse but more functionally diverse than those of Wts, enhancing the functional relevance of tree hollows. Additionally, niche filtering dominated WT assemblages, which were characterised by a narrower functional space and a higher redundancy. in contrast, in the Het assemblages the coexistence of functionally dissimilar species is driven by the niche heterogeneity. HET and WT assemblages differed in the functional space occupied by each within areas, but both assemblages reflected coincident patterns among areas that pointed to a reduction of functional space with management.Saproxylic beetles are one of the main components of the forest fauna. They are highly diverse and provide important ecosystem services related to nutrient recycling and the decomposition of wood 1,2 ; forest pest control, through the action of saproxylic predators on primary xylophagous beetles (i.e., Scolytinae) 3,4 ; and pollination, as many adult saproxylic beetles are flower visitors. In spite of the functional importance of saproxylic beetle communities, few studies have included a functional trait approach 5-10 , and most have focused on how they respond to environmental change.Saproxylic beetles depend, directly or indirectly, on a number of distinct microhabitats provided by living and dead trees that can host specific assemblages of co-occurring beetle species 1,11 . Moreover, each assemblage is formed by species belonging to different trophic guilds that interact among themselves and with the substrate in different ways 11,12 . Species richness and composition vary between woody microhabitats 6,13,14 ; however, studies focused on the different saproxylic assemblages -understood as a taxonomically related group of species that occur together in space and time 15 -or on their assemblage mechanisms are scarce 6 .The most commonly used method for studying saproxylic beetles is flight intercept traps, such as window traps (WTs), which collect a species assemblage representing a broad set of ecologies 6 . WTs primarily catch flying adults arriving from several tree microhabitats (e.g., decaying branches, bark, or tree hollows) but also from other woody resources within the woodland environment, such as dead wood on the ground (e.g., snags, logs) [1...

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“…By developing robust functions for estimating the primary facets of FD-the richness, divergence, and regularity components (Pavoine & Bonsall, 2011;Tucker et al, 2017),-we open up the potential to fully exploit the strengths of the Hutchinsonian niche concept in functional ecology research (Blonder, 2019). As in the case of other frameworks for estimating FD (e.g., Mouchet et al, 2010;Junker, Kuppler, Bathke, Schreyer, & Trutschnig, 2016;Carmona et al, 2019), these new functions can be used to answer a large assortment of questions. Alpha and beta FD allow us to understand the richness of a functional hyperspace, and in which components multiple functional hyperspaces differ, namely the pairwise richness or replacement difference in term of functional traits.…”

Section: Discussionmentioning

confidence: 99%

“…This function allows the user to calculate functional richness in a kernel context. Alpha FD is simply the total volume of the functional niche hyperspace-but see Carmona et al (2016bCarmona et al ( , 2016aCarmona et al ( , 2019 for an alternative estimation based on trait probability density (TPD). & Gomes, 2012;Carvalho, Cardoso, Borges, Schmera, & Podani, 2013) in a similar way as already proposed for functional trees .…”

Section: Kernelalphamentioning

confidence: 99%

Functional diversity metrics using kernel densityn-dimensional hypervolumes

Mammola¹,

Cardoso

2020

Preprint

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Equal contribution: both authors conceived the idea, developed the code, contributed critically to the drafts, and gave final approval for publication. 1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 1718 Summary 1. The use of kernel density n-dimensional hypervolumes [Global Ecol. Biogeogr. 23(5):595-609] in traitbased ecology is rapidly increasing. By representing the functional space of a species or community as a Hutchinsonian niche space, this relatively new approach is showing great potential for the advance of functional ecology theory.2. Functions for calculating the standard set of functional diversity (FD) indexes-richness, divergence, and regularity-have not been developed in the context of kernel density hypervolumes yet. This gap is delaying a full exploitation of the kernel density n-dimensional hypervolumes framework in functional ecology, meanwhile preventing the possibility to compare its performance with that of other FD methods.3. We develop a set of functions to calculate FD indices based on kernel density n-dimensional hypervolumes, including alpha (richness), beta (and respective components), dispersion, evenness, contribution, and originality. Altogether, these indexes provide a coherent framework to explore the primary mathematical components of FD within a kernel density setting. These new functions can work either with Hypervolumes objects, HypervolumeList objects, or raw data (species presence or abundance and their traits) as input data, and are versatile in terms of computation speed, which is achieved by controlling the number of stochastic points to be used in the different estimations. 4. These newly developed functions are implemented within the R package BAT, an open platform for biodiversity assessments. As a coherent corpus of functional indexes based on a common algorithm, it opens up the possibility to fully explore the strengths of the Hutchinsonian niche concept in community ecology research.

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Trait probability density (TPD): measuring functional diversity across scales based on TPD with R

Cited by 111 publications

References 43 publications

The cryptic impacts of invasion: functional homogenization of tropical ant communities by invasive fire ants

The cryptic impacts of invasion: functional homogenization of tropical ant communities by invasive fire ants

Contrasting functional structure of saproxylic beetle assemblages associated to different microhabitats

Functional diversity metrics using kernel densityn-dimensional hypervolumes

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