Plant Diversity ›› 2023, Vol. 45 ›› Issue (03): 347-352.DOI: 10.1016/j.pld.2022.12.007
• Short communications • Previous Articles Next Articles
Yi Jina, Hong Qianb
Received:
2022-11-19
Revised:
2022-12-16
Online:
2023-07-06
Contact:
Yi Jin,E-mail:codon@126.com;Hong Qian,E-mail:hong.qian@illinoisstatemuseum.org
Supported by:
Yi Jina, Hong Qianb
通讯作者:
Yi Jin,E-mail:codon@126.com;Hong Qian,E-mail:hong.qian@illinoisstatemuseum.org
基金资助:
Yi Jin, Hong Qian. U.PhyloMaker:An R package that can generate large phylogenetic trees for plants and animals[J]. Plant Diversity, 2023, 45(03): 347-352.
Yi Jin, Hong Qian. U.PhyloMaker:An R package that can generate large phylogenetic trees for plants and animals[J]. Plant Diversity, 2023, 45(03): 347-352.
[1] Angiosperm Phylogeny Group, 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants:APG IV. Bot. J. Linn. Soc. 181, 1-20. [2] Cavender-Bares, J., Kozak, K.H., Fine, P.V.A., et al., 2009. The merging of community ecology and phylogenetic biology. Ecol. Lett. 12, 693-715. [3] Faith, D.P., 1992. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 61, 1-10. [4] Freiberg, M., Winter, M., Gentile, A., et al., 2020. LCVP, the Leipzig catalogue of vascular plants, a new taxonomic reference list for all known vascular plants. Sci. Data 7, 416. [5] Govaerts, R., Nic Lughadha, E., Black, N., et al., 2021. The World Checklist of Vascular Plants, a continuously updated resource for exploring global plant diversity. Sci. Data 8, 215. [6] Jetz, W., Pyron, R.A., 2018. The interplay of past diversification and evolutionary isolation with present imperilment across the amphibian tree of life. Nat. Ecol. Evol. 2, 850-858. [7] Jetz, W., Thomas, G.H., Joy, J.B., et al., 2012. The global diversity of birds in space and time. Nature 491, 444-448. [8] Jin, Y., Qian, H., 2019. V.PhyloMaker:an R package that can generate very large phylogenies for vascular plants. Ecography 42, 1353-1359. [9] Jin, Y., Qian, H., 2022. V.PhyloMaker2:An updated and enlarged R package that can generate very large phylogenies for vascular plants. Plant Divers. 44, 335-339. [10] Li, D., Trotta, L., Marx, H.E., Allen, J.M., Sun, M., Soltis, D.E., Soltis, P.S., Guralnick, R.P., Baiser, B., 2019. For common community phylogenetic analyses, go ahead and use synthesis phylogenies. Ecology 100, e02788. [11] Nitta, J.H., Schuettpelz, E., Ramirez-Barahona, S., et al., 2022. An open and continuously updated fern tree of life. Front. Plant Sci. 13, 909768. [12] Paradis, E., Claude, J., Strimmer, K., 2004. APE:analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289-290. [13] Qian, H., 2023. Patterns of phylogenetic relatedness of non-native plants across the introduction-naturalization-invasion continuum in China. Plant Divers. (in press). [14] Qian, H., Jin, Y., 2016. An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure. J. Plant Ecol. 9, 233-239. [15] Qian, H., Jin, Y., 2021. Are phylogenies resolved at the genus level appropriate for studies on phylogenetic structure of species assemblages? Plant Divers. 43, 255-263. [16] Qian, H., Cao, Y., Li, D., et al., 2020. Geographic patterns and environmental correlates of phylogenetic relatedness and diversity for freshwater fish assemblages in North America. Ecography 43, 1814-1824. [17] Qian, H., Kessler, M., Deng, T., et al. 2021. Patterns and drivers of phylogenetic structure of pteridophytes in China. Global Ecol. Biogeogr. 30, 1835-1846. [18] Qian, H., Zhang, J., 2016. Are phylogenies derived from family-level supertrees robust for studies on macroecological patterns along environmental gradients? Journal of Systematics and Evolution 54, 29-36. [19] R Core Team, 2016. R:A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/. [20] Rabosky, D.L., Chang, J., Title, P.O., et al., 2018. An inverse latitudinal gradient in speciation rate for marine fishes. Nature 559, 392-395. [21] RStudio Team, 2015. RStudio:Integrated Development for R. RStudio, Inc., Boston, MA, USA. URL http://www.rstudio.com/. [22] Smith, S.A., Brown, J.W., 2018. Constructing a broadly inclusive seed plant phylogeny. Am. J. Bot. 105, 302-314. [23] Testo, W., Sundue, M., 2016. A 4000-species dataset provides new insight into the evolution of ferns. Mol. Phylogenet. Evol. 105, 200-211. [24] Tonini, J.F.R., Beard, K.H., Ferreira, R.B., et al., 2016. Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status. Biol. Conserv. 204, 23-31. [25] Upham, N.S., Esselstyn, J.A., Jetz., W., 2019. Inferring the mammal tree:Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biol. 17, e3000494. [26] Webb, C.O., 2000. Exploring the phylogenetic structure of ecological communities:an example for rain forest trees. Am. Nat. 156, 145-155. [27] Webb, C.O., Ackerly, D.D., McPeek, M.A., et al., 2002. Phylogenies and community ecology. Annu. Rev. Ecol. Syst. 33, 475-505. [28] Webb, C.O., Donoghue, M.J., 2005. Phylomatic:tree assembly for applied phylogenetics. Mol. Ecol. Notes 5, 181-183. [29] Wickham, H., Hester, J., Chang, W., 2018. devtools:Tools to Make Developing R Packages Easier. R package version 1.13.6. https://CRAN.R-project.org/package=devtools [30] Yue, J., Li, R., 2021. Phylogenetic relatedness of woody angiosperm assemblages and its environmental determinants along a subtropical elevational gradient in China. Plant Divers. 43, 111-116. [31] Zanne, A.E., Tank, D.C., Cornwell, W.K., et al., 2014. Three keys to the radiation of angiosperms into freezing environments. Nature 506, 89-92. [32] Zhang, J., Qian, H., 2022. U.Taxonstand:An R package for standardizing scientific names of plants and animals. Plant Diversity. https://doi.org/10.1016/j.pld.2022.09.001. [33] Zhang, Y.-Z., Qian, L.-S., Spalink, D., et al., 2021. Spatial phylogenetics of two topographic extremes of the Hengduan Mountains in southwestern China and its implications for biodiversity conservation. Plant Divers. 43, 181-191. [34] Zhou, Y.-D., Qian, H., Jin, Y., et al., 2023. Geographic patterns of taxonomic and phylogenetic β-diversity of aquatic angiosperms in China. Plant Divers. (in press). |
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