Getting started: Simple tree searches

Martin R. Smith

2022-05-11

“TreeSearch” is an R package that allows, among other things, parsimony search on morphological datasets that contain inapplicable data, using the algorithm proposed by Brazeau, Guillerme and Smith (2019) and implemented in the ‘MorphyLib’ C library (Brazeau, Smith, & Guillerme, 2017) (details).

Getting started

A companion vignette gives details on installing the package and getting up and running.

Launch an interactive ‘app’ in your browser by typing TreeSearch::EasyTrees() at the R / RStudio command line.

This will allow you to load data from a file, modify search settings, and explore the distribution of most parsimonious trees in tree space.

Starting parsimony search

View a consensus tree and explore the position of rogue taxa (Smith, 2022b):

Visualizing position of rogue taxon on search result consensus tree

Explore the distribution of trees (whether found by search or loaded from file) in tree space (Smith, 2022a):

Evaluating search progress using tree space

Map characters on a chosen tree, using character and taxon notes imported from a Nexus file, if present. (This is designed to be interoperable with MorphoBank matrices.)

Mapping character reconstructions

Trees can be saved as images, or in Nexus/Newick for further analysis.

Implied weighting

Equal weights produces trees that are less accurate and less precise than implied weights (Smith, 2019); equally weighted analysis should never be conducted without also considering the results of implied weights (Goloboff, 1993, 1997), ideally under a range of concavity constants (cf. Smith & Ortega-Hernández, 2014).

Implied weights can be activated by simply specifying a value of the concavity constant, k:

iwTrees <- MaximizeParsimony(vinther, concavity = 10)
par(mar = rep(0.25, 4), cex = 0.75) # make plot easier to read
plot(ape::consensus(iwTrees))

Note that we recommend a default value of 10, somewhat higher than the default of 3 in TNT; this low default gives poorer results in many settings (Goloboff, Torres, & Arias, 2018; Smith, 2019). Better still is to use multiple values and compare the results, perhaps in Tree space. Even better (?) is to use profile parsimony.

References

Brazeau, M. D., Guillerme, T., & Smith, M. R. (2019). An algorithm for morphological phylogenetic analysis with inapplicable data. Systematic Biology, 68, 619–631. doi:10.1093/sysbio/syy083
Brazeau, M. D., Smith, M. R., & Guillerme, T. (2017). MorphyLib: A library for phylogenetic analysis of categorical trait data with inapplicability. doi:10.5281/zenodo.815372
Goloboff, P. A. (1993). Estimating character weights during tree search. Cladistics, 9(1), 83–91. doi:10.1111/j.1096-0031.1993.tb00209.x
Goloboff, P. A. (1997). Self-weighted optimization: tree searches and character state reconstructions under implied transformation costs. Cladistics, 13(3), 225–245. doi:10.1111/j.1096-0031.1997.tb00317.x
Goloboff, P. A., Torres, A., & Arias, J. S. (2018). Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology. Cladistics, 34(4), 407–437. doi:10.1111/cla.12205
Smith, M. R. (2019). Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets. Biology Letters, 15(2), 20180632. doi:10.1098/rsbl.2018.0632
Smith, M. R. (2022a). Robust analysis of phylogenetic tree space. Systematic Biology, syab100. doi:10.1093/sysbio/syab100
Smith, M. R. (2022b). Using information theory to detect rogue taxa and improve consensus trees. Systematic Biology, syab099. doi:10.1093/sysbio/syab099
Smith, M. R., & Ortega-Hernández, J. (2014). Hallucigenia’s onychophoran-like claws and the case for Tactopoda. Nature, 514(7522), 363–366. doi:10.1038/nature13576
Vinther, J., Van Roy, P., & Briggs, D. E. G. (2008). Machaeridians are Palaeozoic armoured annelids. Nature, 451(7175), 185–188. doi:10.1038/nature06474