# Getting started: Simple tree searches

#### 2024-05-23

“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), and evaluate search progress (Whidden & Matsen, 2015):

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, 71(5), 1255–1270. doi:10.1093/sysbio/syab100
Smith, M. R. (2022b). Using information theory to detect rogue taxa and improve consensus trees. Systematic Biology, 71(5), 1088–1094. 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
Whidden, C., & Matsen, F. A. (2015). Quantifying MCMC exploration of phylogenetic tree space. Systematic Biology, 64(3), 472–491. doi:10.1093/sysbio/syv006