Phylogenetic plant community structure along elevation is lineage specific

Ndiribe, Charlotte; Pellissier, Loïc; Antonelli, Silvia; Dubuis, Anne; Pottier, Julien; Vittoz, Pascal; Guisan, Antoine; Salamin, Nicolas

doi:10.1002/ece3.868

Cited by 33 publications

(38 citation statements)

References 68 publications

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“…Phylogenetic patterns can vary widely when including only members of specific clades, such as the most diverse families at a site, in agreement with the findings of Ndiribe et al (2013) and others who found that community phylogenetic structure can be lineage specific. Our study, which covers a broader range of communities and clades, represents further evidence that patterns can be lineage specific.…”

Section: Questionsupporting

confidence: 90%

Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

Jantzen

Whitten

Neubig

et al. 2019

Ecology and Evolution

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The amount and patterns of phylodiversity in a community are often used to draw inferences about the local and historical factors affecting community assembly and can be used to prioritize communities and locations for conservation. Because measures of phylodiversity are based on the topology and branch lengths of phylogenetic trees, which are affected by the number and diversity of taxa in the tree, these analyses may be sensitive to changes in taxon sampling and tree reconstruction methods. To investigate the effects of taxon sampling and tree reconstruction methods on measures of phylodiversity, we investigated the community phylogenetics of the Ordway‐Swisher Biological Station (Florida), which is home to over 600 species of vascular plants. We studied the effects of (a) the number of taxa included in the regional phylogeny; (b) random versus targeted sampling of species to assemble the regional species pool; (c) including only species from specific clades rather than broad sampling; (d) using trees reconstructed directly for the taxa under study compared to trees pruned from a larger reconstructed tree; and (e) using phylograms compared to chronograms. We found that including more taxa in a study increases the likelihood of observing significantly nonrandom phylogenetic patterns. However, there were no consistent trends in the phylodiversity patterns based on random taxon sampling compared to targeted sampling, or within individual clades compared to the complete dataset. Using pruned and reconstructed phylogenies resulted in similar patterns of phylodiversity, while chronograms in some cases led to significantly different results from phylograms. The methods commonly used in community phylogenetic studies can significantly impact the results, potentially influencing both inferences of community assembly and conservation decisions. We highlight the need for both careful selection of methods in community phylogenetic studies and appropriate interpretation of results, depending on the specific questions to be addressed.

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Section: Questionsupporting

confidence: 90%

Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

Jantzen

Whitten

Neubig

et al. 2019

Ecology and Evolution

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“…Another post‐modeling functionality, nicely complementing the SESAM framework (e.g. to set phylogenetic constraints on assemblages), is the function to predict phylogenetic diversity in geographic space from the stacked predictions of species distribution models (Pio et al , ), which can also be used for simple pre‐modeling analyses based on raw observations (Ndiribe et al , , Pellissier et al , b).…”

Section: Introductionmentioning

confidence: 99%

“…The calculation of phylogenetic diversity measures on observed (pre‐modeling) or predicted (post‐modeling) coarse species assemblages (as in Pio et al , ) or local communities (Ndiribe et al , ), provides a comprehensive list of indices and optimized calculations for large data sets (which are then important for producing maps). The function ecospat.calculate.pd() uses a phylogenetic tree, a presence or absence (binary) matrix for each species in each location or grid cell (direct observations, S‐SDM binary predictions or SESAM predictions), and different phylogenetic diversity measures (Schweiger et al ).…”

Section: Introductionmentioning

confidence: 99%

ecospat: an R package to support spatial analyses and modeling of species niches and distributions

et al. 2017

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The aim of the ecospat package is to make available novel tools and methods to support spatial analyses and modeling of species niches and distributions in a coherent workflow. The package is written in the R language (R Development Core Team) and contains several features, unique in their implementation, that are complementary to other existing R packages. Pre‐modeling analyses include species niche quantifications and comparisons between distinct ranges or time periods, measures of phylogenetic diversity, and other data exploration functionalities (e.g. extrapolation detection, ExDet). Core modeling brings together the new approach of ensemble of small models (ESM) and various implementations of the spatially‐explicit modeling of species assemblages (SESAM) framework. Post‐modeling analyses include evaluation of species predictions based on presence‐only data (Boyce index) and of community predictions, phylogenetic diversity and environmentally‐constrained species co‐occurrences analyses. The ecospat package also provides some functions to supplement the ‘biomod2’ package (e.g. data preparation, permutation tests and cross‐validation of model predictive power). With this novel package, we intend to stimulate the use of comprehensive approaches in spatial modelling of species and community distributions.

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“…We also looked at the effect of the dominant species on relatedness patterns among different taxonomic groups because phylogenetic diversity of lineages has different patterns within large clades (Cavender‐Bares, Keen & Miles ; Cadotte & Strauss ; Lanier, Edwards & Knowles ; Ndiribe et al . ; Elliott, Waterway & Davies ) and because species with different ecological characteristics have different responses to selective pressure (such as competition; Cardillo ). Thus, thirdly we hypothesized that the closely related species within different taxonomic groups (e.g.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic diversity reveals hidden patterns related to population source and species pools during restoration

Khalil

Gibson

Baer

2016

Journal of Applied Ecology

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Summary A phylogenetic perspective of community assembly can reveal new insights into how variation within dominant species interacts with the local species pool to influence the structure of restored plant communities. Many studies have examined the effect of dominant species in structuring plant communities, but few have investigated their effect on phylogenetic diversity (PD). We established grassland in a post‐agricultural field using two population sources (cultivars and local ecotypes) of three dominant grasses (Sorghastrum nutans, Andropogon gerardii and Schizachyrium scoparium) with three unique pools of subordinate species that varied in PD but not taxonomic or life‐form diversity. We tested the effect of the population source treatment on two metrics of community PD (net relatedness index [NRI] and nearest taxon index [NTI]) during the first 4 years of restoration. The NRI measures the overall pairwise phylogenetic distance between all pairs of taxa in a community. By contrast, NTI measures the pairwise distance between closely related taxa in a community. Population sources had a transitory effect on community phylogenetic structure over time. Local ecotypes decreased the abundance of closely related eudicots, monocots (low +NRI and +NTI values) and volunteer species (−NTI) more than cultivars. However, population sources did not affect ecologically conservative species (i.e. species with intermediate‐to‐poor ecological tolerance and a high degree of fidelity to prairie habitats). Thus, cultivars might have a positive effect on community phylogenetic diversity more than local ecotypes by decreasing the abundance of a phylogenetically diverse community of less closely related volunteer species. Differences in PD of seed mixes were maintained in the community of high‐fidelity species, but did not affect PD of the unsown (volunteer) species in the assembling community. Synthesis and applications. This is the first experiment to show consequences of using different seed sources on phylogenetic diversity (PD) in grassland restoration. Phylogenetics can reveal the effects of population sources on the abundance of volunteer species not evident through traditional analyses of species diversity. The PD of seed mixes or establishing communities, or other assessments of phylogenetic relationships, by restoration practitioners is recommended as a metric to allow consequences of the evolutionary patterns among species to be included in conservation planning. Increased accessibility of phylogenetic tools will allow the application of PD in restoration monitoring.

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Phylogenetic plant community structure along elevation is lineage specific

Cited by 33 publications

References 68 publications

Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

ecospat: an R package to support spatial analyses and modeling of species niches and distributions

Phylogenetic diversity reveals hidden patterns related to population source and species pools during restoration

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