An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure

Qian, Hong; Jin, Yi

doi:10.1093/jpe/rtv047

Cited by 403 publications

(405 citation statements)

References 40 publications

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“…Here we conduct the fi rst phylogenetically structured tests of the correlations among leaf margin entirety (mostly due to the presence/absence of marginal teeth), leaf thickness, and latitude on a global basis, superimposing data for all traits gleaned from Royer et al (2009) on a broad-scale angiosperm phylogeny provided by Zanne et al (2014) and a more inclusive phylogeny to increase the match of species using S.PhyloMaker ( Qian and Jin, 2015 ). Branch lengths are those given by the authors and based on time.…”

Section: Hypothetical Advantages Of Non-entire Leaf Marginsmentioning

confidence: 99%

“…Toothed leaves are signifi cantly associated with ring-porous wood ( Royer et al, 2012 ), whose wide vessels can easily embolize during frosts or drought; entire margins are associated with diff use-porous wood with narrower vessels less susceptible to cavitation. However, large numbers of tropical plants possess hydathodes ( Roth, 1990 ), many arctic and alpine shrubs exposed to frequent frost lack teeth of any kind ( Bailey and Sinnott, 1916 ), species with toothed leaves oft en do not produce root pressure ( Edwards et al, 2016 ), most temperate plants produce root pressure only briefl y before the buds FIGURE 3 Leaf thickness and marginal type superimposed on the Qian-Jin molecular angiosperm phylogeny ( Qian and Jin, 2015 ), showing repeated evolution of thin leaves with non-entire margins. Branch lengths related to extent of genetic divergence in ultrametric tree.…”

Section: Hypothetical Advantages Of Non-entire Leaf Marginsmentioning

confidence: 99%

“…Such tundra species, however, may accord with the support-supply hypothesis TABLE 1. Numbers and percentages of species with diff erent kinds of leaf (or leafl et) margins from Royer et al (2012) that were overlaid on the Qian and Jin (2015) tree. Third column indicates the percentages of species with nonentire leaf margins that are toothed only, lobed and toothed, or lobed only.…”

Section: Hypothetical Advantages Of Non-entire Leaf Marginsmentioning

confidence: 99%

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Causes of ecological gradients in leaf margin entirety: Evaluating the roles of biomechanics, hydraulics, vein geometry, and bud packing

Givnish

Kriebel

2017

American J of Botany

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PREMISE OF THE STUDY:A recent commentary by Edwards et al. (Am. J. Bot. 103: 975–978) proposed that constraints imposed by the packing of young leaves in buds could explain the positive association between non‐entire leaf margins and latitude but did not thoroughly consider alternative explanations.METHODS:We review the logic and evidence underlying six major hypotheses for the functional significance of marginal teeth, involving putative effects on (1) leaf cooling, (2) optimal support and supply of the areas served by major veins, (3) enhanced leaf‐margin photosynthesis, (4) hydathodal function, (5) defense against herbivores, and (6) bud packing.KEY RESULTS:Theoretical and empirical problems undermine all hypotheses except the support–supply hypothesis, which implies that thinner leaves should have non‐entire margins. Phylogenetically structured analyses across angiosperms, the El Yunque flora, and the genus Viburnum all demonstrate that non‐entire margins are indeed more common in thinner leaves. Across angiosperms, the association of leaf thickness with non‐entire leaf margins is stronger than that of latitude.CONCLUSION:We outline a synthetic model showing how biomechanics, hydraulics, vein geometry, rates of leaf expansion, and length of development within resting buds, all tied to leaf thickness, drive patterns in the distribution of entire vs. non‐entire leaf margins. Our model accounts for dominance of entire margins in the tropics, Mediterranean scrub, and tundra, non‐entire margins in cold temperate deciduous forests and tropical vines and early‐successional trees, and entire leaf margins in monocots. Spinose‐toothed leaves should be favored in short‐statured evergreen trees and shrubs, primarily in Mediterranean scrub and related semiarid habitats.

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Section: Hypothetical Advantages Of Non-entire Leaf Marginsmentioning

confidence: 99%

Section: Hypothetical Advantages Of Non-entire Leaf Marginsmentioning

confidence: 99%

Section: Hypothetical Advantages Of Non-entire Leaf Marginsmentioning

confidence: 99%

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Causes of ecological gradients in leaf margin entirety: Evaluating the roles of biomechanics, hydraulics, vein geometry, and bud packing

Givnish

Kriebel

2017

American J of Botany

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“…1) was assembled using the 'S.PhyloMaker' function implemented for R (provided in the Supplementary Data; Qian and Jin, 2016) in combination with the BLADJ algorithm (as in Phylocom). The supertree was constructed based on an updated megaphylogeny of vascular plants (PhytoPhylo; Qian and Jin, 2016). The resulting phylogenetic tree had 50 tips and 47 internal nodes (Fig.…”

Section: Phylogenetic Signal and Community Structurementioning

confidence: 99%

Disturbance by an endemic rodent in an arid shrubland is a habitat filter: effects on plant invasion and taxonomical, functional and phylogenetic community structure

Escobedo

Ríos

Salgado‐Luarte

et al. 2017

Ann Bot

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Background and Aims Disturbance often drives plant invasion and may modify community assembly. However, little is known about how these modifications of community patterns occur in terms of taxonomic, functional and phylogenetic structure. This study evaluated in an arid shrubland the influence of disturbance by an endemic rodent on community functional divergence and phylogenetic structure as well as on plant invasion. It was expected that disturbance would operate as a habitat filter favouring exotic species with short life cycles.Methods Sixteen plots were sampled along a disturbance gradient caused by the endemic fossorial rodent Spalacopus cyanus, measuring community parameters and estimating functional divergence for life history traits (functional dispersion index) and the relative contribution to functional divergence of exotic and native species. The phylogenetic signal (Pagel's lambda) and phylogenetic community structure (mean phylogenetic distance and mean nearest taxon phylogenetic distance) were also estimated. The use of a continuous approach to the disturbance gradient allowed the identification of non-linear relationships between disturbance and community parameters.Key Results The relationship between disturbance and both species richness and abundance was positive for exotic species and negative for native species. Disturbance modified community composition, and exotic species were associated with more disturbed sites. Disturbance increased trait convergence, which resulted in phylogenetic clustering because traits showed a significant phylogenetic signal. The relative contribution of exotic species to functional divergence increased, while that of natives decreased, with disturbance. Exotic and native species were not phylogenetically distinct.Conclusions Disturbance by rodents in this arid shrubland constitutes a habitat filter over phylogeny-dependent life history traits, leading to phylogenetic clustering, and drives invasion by favouring species with short life cycles. Results can be explained by high phenotypic and phylogenetic resemblance between exotic and native species. The use of continuous gradients when studying the effects of disturbance on community assembly is advocated.

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“…We used the most comprehensive phylogenetic tree for land plants [17,43] that comprises 31,389 species. Taxonomic information for our phylogenetic tree was run through Taxonstand …”

Section: Seed Mass and Phylogenetic Datasetmentioning

confidence: 99%

Seed size and its rate of evolution correlate with species diversification across angiosperms

Igea

Miller

Papadopulos

et al. 2016

Preprint

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Species diversity varies greatly across the different taxonomic groups that comprise the Tree of Life (ToL). This imbalance is particularly conspicuous within angiosperms, but is largely unexplained. Seed mass is one trait that may help clarify why some lineages diversify more than others because it confers adaptation to different environments, which can subsequently influence speciation and extinction. The rate at which seed mass changes across the angiosperm phylogeny may also be linked to diversification by increasing reproductive isolation and allowing access to novel ecological niches. However, the magnitude and direction of the association between seed mass and diversification has not been assessed across the angiosperm phylogeny. Here, we show that absolute seed size and the rate of change in seed size are both associated with variation in diversification rates. Based on the largest available angiosperm phylogenetic tree, we found that smaller-seeded plants had higher rates of diversification, possibly due to improved colonisation potential. The rate of phenotypic change in seed size was also strongly positively correlated with speciation rates, providing rare, large-scale evidence that rapid morphological change is associated with species divergence. Our study now reveals that variation in morphological traits and, importantly, the rate at which they evolve can contribute to explaining the extremely uneven distribution of diversity across the ToL. Author summaryWhy are some groups of flowering plants extremely diverse while others are very poor in species? Are the traits of species and the rate at which they evolve important in generating this uneven distribution of biodiversity? By using the largest available phylogenetic tree of plants coupled with an unparalleled trait dataset, we analysed how seed size and its rate of change across the phylogeny are correlated with the rate of species formation. Seed size is crucial to plant evolution because it is related to adaptation to environment and influences many aspects of plant life history, including dispersal, resistance to damage and colonisation potential. We found that faster rates of seed size change were associated with faster rates of speciation, probably by fostering the appearance of reproductive barriers between lineages. We also found that smaller seeded species speciated faster than larger seeded ones. These results underscore the importance of morphological traits, and particularly their rate of evolution, in promoting species divergence across one of the largest radiations of organisms on the planet.

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An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure

Cited by 403 publications

References 40 publications

Causes of ecological gradients in leaf margin entirety: Evaluating the roles of biomechanics, hydraulics, vein geometry, and bud packing

Causes of ecological gradients in leaf margin entirety: Evaluating the roles of biomechanics, hydraulics, vein geometry, and bud packing

Disturbance by an endemic rodent in an arid shrubland is a habitat filter: effects on plant invasion and taxonomical, functional and phylogenetic community structure

Seed size and its rate of evolution correlate with species diversification across angiosperms

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