U.PhyloMaker:An R package that can generate large phylogenetic trees for plants and animals

doi:10.1016/j.pld.2022.12.007

Abstract

Abstract: The previously released packages of the PhyloMaker series (i.e. S.PhyloMaker, V.PhyloMaker, and V.PhyloMaker2) have been broadly used to generate phylogenetic trees for ecological and biogeographical studies. Although these packages can be used to generate phylogenetic trees for any groups of plants and animals for which megatrees are available, they focus on generating phylogenetic trees for plants based on the megatrees provided by the packages. How to use these packages to generate phylogenetic trees based on other megatrees is not straightforward. Here, we present a new tool, which is called 'U.PhyloMaker', and a simple R script that can be used to easily generate large phylogenetic trees for both plants and animals at a relatively fast speed.

Key words: Animals, Community phylogenetics, Megatree, Phylogeny, Plants, Species list

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.

References

[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).