V.PhyloMaker2: An updated and enlarged R package that can generate very large phylogenies for vascular plants

Jin, Yi; Qian, Hong

doi:10.1016/j.pld.2022.05.005

Cited by 183 publications

(103 citation statements)

References 18 publications

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“…We used the package V.PhyloMaker2 (build.nodes.1; Jin & Qian, 2019, 2022) to generate a phylogeny for the 30,260 angiosperm species in our data set. V.PhyloMaker2 uses an updated and expanded version of the dated megaphylogeny GBOTB reported by Smith and Brown (2018) as a backbone to generate phylogenies.…”

Section: Methodsmentioning

confidence: 99%

“…V.PhyloMaker2 uses an updated and expanded version of the dated megaphylogeny GBOTB reported by Smith and Brown (2018) as a backbone to generate phylogenies. All families in our data set were resolved in the megaphylogeny (GBOTB.extended.TPL.tre; Jin & Qian, 2022). Of the 3,219 genera in our data set, 2,790 (87%) were included in the megaphylogeny.…”

Section: Methodsmentioning

confidence: 99%

“…Of the 3,219 genera in our data set, 2,790 (87%) were included in the megaphylogeny. We added the genera and species in our data set that were absent from the megaphylogeny to their respective families and genera using V.PhyloMaker2 (Scenario 3; Jin & Qian, 2022), which sets branch lengths of added taxa in a family by placing the nodes evenly between dated nodes and terminals within the family and placing a missing species at the mid‐point of the branch length of its genus. We pruned the megaphylogeny to generate a phylogenetic tree retaining only the angiosperm species present in China.…”

Section: Methodsmentioning

confidence: 99%

“…All families in our data set were resolved in the megaphylogeny (GBOTB.extended. TPL.tre; Jin & Qian, 2022). Of the 3,219 genera in our data set, 2,790 (87%) were included in the megaphylogeny.…”

Section: Phylogeny Constructionmentioning

confidence: 99%

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Phylogenetic structure of alien and native species in regional plant assemblages across China: Testing niche conservatism hypothesis versus niche convergence hypothesis

Qian

Sandel

2022

Global Ecol. Biogeogr.

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Aim The introduction of alien species may be influenced by the phylogenetic structure of the native assemblage, while at the same time altering that structure. Understanding these effects sheds light on both the factors influencing naturalization of introduced species and their impacts. Considering regional angiosperm assemblages across China, we ask the following questions: (a) Do geographic patterns and climate relationships of alien species richness and phylogenetic structure mirror those of natives? (b) Has the addition of alien species resulted in stronger phylogenetic clustering as predicted by Darwin's preadaptation hypothesis? (c) To what degree does the answer to these questions depend on phylogenetic scale? Location China. Time period Current. Taxon Angiosperms (flowering plants). Methods We divided China into 28 province‐level regions and collated native and naturalized alien species lists of angiosperms for each region. For each region, we computed two types of phylogenetic structure metrics [mean phylogenetic distance (MPD) and mean nearest neighbour distance (MNND), and their standardized effect sizes] for the native, alien and combined assemblages, and for angiosperms as a whole, 5 major clades and 10 well‐represented families. We then related these to climatic factors using correlation analyses. Results Richness of alien angiosperms is highest in regions with species rich and phylogenetically dispersed native assemblages. The standardized effect size of mean phylogenetic distance (MPDses) for aliens was positively correlated with that for natives. The introduction of alien species generally increased phylogenetic clustering of the combined assemblage compared to the natives for large phylogenetic extents, but effects within plant families were mixed. The MPDses was positively correlated with temperature and precipitation for both natives and aliens. Main conclusions The phylogenetic relationships at a lower level of phylogenetic scale may differ substantially from those at a higher level of phylogenetic scale. At the broadest phylogenetic extents, alien species tend to recapitulate the biogeographic patterns of natives, showing similar spatial patterns of species richness and phylogenetic structure, and tending to represent the same major angiosperm clades. This is highly consistent with Darwin's preadaptation hypothesis. Across narrower swaths of the phylogeny, these patterns are less clear, with a substantial number of plant families showing support for the biogeographic barrier hypothesis.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Phylogeny Constructionmentioning

confidence: 99%

See 2 more Smart Citations

Phylogenetic structure of alien and native species in regional plant assemblages across China: Testing niche conservatism hypothesis versus niche convergence hypothesis

Qian

Sandel

2022

Global Ecol. Biogeogr.

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“…Phylogenetic trees for the mangrove plants of this study and non-mangrove plants from previous studies 7,26 (Fig. S10, S11) were constructed separately using the R package V. PhyloMaker 55,56 . Plant names in the phylogenetic tree were referenced was not certified by peer review) is the author/funder.…”

Section: Samplingmentioning

confidence: 99%

Novel leaf-root coordination driven by leaf water storage tissues in mangroves

Cao

Qingpei

Chen

et al. 2022

Preprint

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Interactions among root and leaf traits (in particular, leaf hydraulic and leaf economics traits) are fundamental in generating diverse strategies in land plants, yet it remains a knowledge gap in mangrove plants that experiences saline stress distinct from most other vascular plants. Here, we tested the trait relationships in mangrove plants and compared them with typical land plants (non-mangrove). Consistent with non-mangrove plants, leaf hydraulic and economics traits were decoupled in mangrove plants. However, mangrove leaf economics traits correlated strongly with root hydraulic traits, which are normally decoupled in non-mangrove plants. Moreover, we observed a unique scaling relationship between leaf dry mass per area and root hydraulic traits in mangroves. The novel coordination between leaves and roots arises from the wide-presence of leaf water storage tissues in mangroves, and this potentially represents a new paradigm with which we look into the ecology, physiology and evolution of this important vegetation.

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Tropical–temperate comparisons in insect seed predation vary between study levels and years

Wang

Tao

et al. 2022

Ecology and Evolution

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The biotic interaction hypothesis, which states the species interaction becomes stronger in the tropics, is deeply rooted in classic ecological literature and widely accepted to contribute to the latitudinal gradients of biodiversity. Tests in latitudinal insect–plant interaction have emphasized leaf‐eating insects on a single or a few plant species rather than within an entire community and mixed accumulating evidence, leaving the biotic interaction hypothesis disputed. We aimed to test the hypothesis by quantifying insect seed predation in a pair of tropical and temperate forest communities with similar elevations. We applied a consistent study design to sample predispersal seeds with systematically set seed traps in 2019–2020 and examined internally feeding insects. The intensity of seed predation was measured and further applied to tropical versus temperate comparison at two levels (cross‐species and community‐wide). Our results showed every latitudinal pattern associated with different study levels and years, that is, negative (greater granivory in the tropics in community‐wide comparison in 2020), positive (less granivory in the tropics in community‐wide and cross‐species comparison in 2019), and missing (similar level of granivory in the tropics in cross‐species comparisons in 2020). The cross‐species level analyses ignore differences among species in seed production and weaken or even lose the latitudinal trend detected by community‐wide comparisons. The between‐year discrepancy in tropical–temperate comparisons relates to the highly variable annual seed composition in the temperate forest due to mast seeding of dominant species. Our study highlights that long‐term community‐level researches across biomes are essential to assess the latitudinal biotic interaction hypothesis.

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V.PhyloMaker2: An updated and enlarged R package that can generate very large phylogenies for vascular plants

Cited by 183 publications

References 18 publications

Phylogenetic structure of alien and native species in regional plant assemblages across China: Testing niche conservatism hypothesis versus niche convergence hypothesis

Phylogenetic structure of alien and native species in regional plant assemblages across China: Testing niche conservatism hypothesis versus niche convergence hypothesis

Novel leaf-root coordination driven by leaf water storage tissues in mangroves

Tropical–temperate comparisons in insect seed predation vary between study levels and years

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