Avoiding inaccuracies in tree calibration and phylogenetic community analysis using Phylocom 4.2

Gastauer, Markus; Meira‐Neto, João Augusto Alves

doi:10.1016/j.ecoinf.2013.03.005

Cited by 50 publications

(46 citation statements)

References 20 publications

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“…According to a recent census, 520 species from 13 well studied genera or families are already registered in Itacolomi State Park's campos rupestres; the overall richness of vascular plants is estimated to 1100 species, the majority of which are angiosperms (Gastauer & Meira-Neto 2013). However, a checklist of all angiosperms from the Itacolomi State Park is not available at present, although it would give further valuable insights in evolutionary aspects of campo rupestre community assembly.…”

Section: Discussionmentioning

confidence: 99%

Environmental severity promotes phylogenetic clustering in campo rupestre vegetation

2015

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The stress-dominance hypothesis postulates that the importance of competition in plant communities declines with increasing environmental stress while the importance of environmental filters increases. To test this hypothesis for campo rupestre vegetation, we analyzed phylogenetic diversity and community structure of angiosperm communities at two study sites within the Itacolomi State Park, Minas Gerais, Brazil. Plots representing more favorable habitats, such as those with a higher percentage of rocky outcrops that might permit the tapping of deeper water and nutrient resources as well as higher contents of clay and loam thereby increasing water and nutrient availability, show higher phylogenetic diversity and therefore lower phylogenetic clustering than plots with more sever habitats. This observation is consistent with the stress-dominance hypothesis if we assume ecological niches to be conserved within evolutionary niches. However, more comprehensive studies including tests for phylogenetic signal of ecological niches are necessary before generalizations for larger regions may be carried out.

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Section: Discussionmentioning

confidence: 99%

Environmental severity promotes phylogenetic clustering in campo rupestre vegetation

2015

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“…PD is phylogenetic diversity) and measures of phylogenetic community structure (NRI is net relatedness index, NTI is nearest taxon index and ses.PD is standard effect size of PF) calculated using R20160415.new and age estimates from Bell et al (2010, exponential distribution) and Magallón et al (2015, penalized likelihood). from 0.7 to 0.9 indicate differences in the outcomes of the two calibration sets, which could certainly lead to ecological misinterpretation (Gastauer & Meira-Neto 2013). Furthermore, the finding that all measures, except Faith's PD, exhibited slopes less than one, indicates that outcomes computed using age estimates from Bell et al (2010) tend to underestimate phylogenetic community structure, and especially NRI and NTI values.…”

Section: Resultsmentioning

confidence: 88%

“…More recently, the use of phylogenetic diversity to describe the amount of evolutionary history represented within a sample has gained importance as an indicator for conservation purposes (Forest et al 2007;Huang et al 2016;Arponen & Zupan 2016). The correct computation of these measures demands an accurately calibrated high-resolution phylogeny comprising the entire taxonomic group under study (Gastauer & Meira-Neto 2013).…”

Section: Introductionmentioning

confidence: 99%

Updated angiosperm family tree for analyzing phylogenetic diversity and community structure

Gastauer

Neto

2017

Acta Bot. Bras.

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Th e computation of phylogenetic diversity and phylogenetic community structure demands an accurately calibrated, high-resolution phylogeny, which refl ects current knowledge regarding diversifi cation within the group of interest. Herein we present the angiosperm phylogeny R20160415.new, which is based on the topology proposed by the Angiosperm Phylogeny Group IV, a recently released compilation of angiosperm diversifi cation. R20160415.new is calibratable by diff erent sets of recently published estimates of mean node ages. Its application for the computation of phylogenetic diversity and/or phylogenetic community structure is straightforward and ensures the inclusion of up-to-date information in user specifi c applications, as long as users are familiar with the pitfalls of such handmade supertrees.

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“…This command fixes the root node (angiosperms, 179 Ma) and other nodes to specified ages based on Wikstr€ om et al (2001). Inconsistencies in syntax between internal node labels of the phylogeny and the ages file were modified manually to ensure a better performance of the node calibration using bladj (Gastauer & Meira-Neto, 2013). To determine if PD metrics are affected by phylogenetic resolution, we compared our results generated using the PHYLOCOM phylogeny with those using a phylogeny of Amazonian tree genera generated from DNA sequences of rbcL and matK plastid genes (K. G. Dexter & J. Chave, unpublished data).…”

Section: Phylogenetic Treesmentioning

confidence: 99%

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2015

Diversity and Distributions

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Aim To examine variation in the phylogenetic diversity (PD) of tree communities across geographical and environmental gradients in Amazonia.Location Two hundred and eighty-three c. 1 ha forest inventory plots from across Amazonia.Methods We evaluated PD as the total phylogenetic branch length across species in each plot (PDss), the mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardized for species richness (ses.PDss, ses.MPD, ses.MNTD). We compared PD of tree communities growing (1) on substrates of varying geological age; and (2) in environments with varying ecophysiological barriers to growth and survival.Results PDss is strongly positively correlated with species richness (SR), whereas MNTD has a negative correlation. Communities on geologically young-and intermediate-aged substrates (western and central Amazonia respectively) have the highest SR, and therefore the highest PDss and the lowest MNTD. We find that the youngest and oldest substrates (the latter on the Brazilian and Guiana Shields) have the highest ses.PDss and ses.MNTD. MPD and ses.MPD are strongly correlated with how evenly taxa are distributed among the three principal angiosperm clades and are both highest in western Amazonia. Meanwhile, seasonally dry tropical forest (SDTF) and forests on white sands have low PD, as evaluated by any metric. Amazonia results from its favourable, easy-to-colonize environment, whereas high values in the Brazilian and Guianan Shields may be due to accumulation of lineages over a longer period of time. White-sand forests and SDTF are dominated by close relatives from fewer lineages, perhaps reflecting ecophysiological barriers that are difficult to surmount evolutionarily. Because MPD and ses.MPD do not reflect lineage diversity per se, we suggest that PDss, ses.PDss and ses.MNTD may be the most useful diversity metrics for setting large-scale conservation priorities.

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Avoiding inaccuracies in tree calibration and phylogenetic community analysis using Phylocom 4.2

Cited by 50 publications

References 20 publications

Environmental severity promotes phylogenetic clustering in campo rupestre vegetation

Environmental severity promotes phylogenetic clustering in campo rupestre vegetation

Updated angiosperm family tree for analyzing phylogenetic diversity and community structure

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