TreeSearch: Morphological Phylogenetic Analysis in R

Abstract

TreeSearch is an R package for phylogenetic analysis, optimized for discrete character data. Tree search may be conducted using equal or implied step weights with an explicit (albeit inexact) allowance for inapplicable character entries, avoiding some of the pitfalls inherent in standard parsimony methods. Profile parsimony and user-specified optimality criteria are supported. A graphical interface, which requires no familiarity with R, is designed to help a user to improve the quality of datasets through critical review of underpinning character codings; and to obtain additional information from results by identifying and summarizing clusters of similar trees, mapping the distribution of trees, and removing 'rogue' taxa that obscure underlying relationships. Taken together, the package aims to support methodological rigour at each step of data collection, analysis, and the exploration of phylogenetic results.

An enigmatic Cretaceous beetle with possible affinity to Erotylidae (Coleoptera: Cucujiformia)

“…The analyses were performed under both equal and implied weights, using R 4.1.0 ( R Core Team, 2019 ) and the R package TreeSearch 1.3.1 ( Smith, 2023 ). The concavity constant in weighted analysis was set to 12, following the suggestion by Goloboff et al (2018) and Smith (2019) .…”

Kekveus brevisulcatus sp. nov., a new featherwing beetle from mid-Cretaceous amber of northern Myanmar (Coleoptera: Ptiliidae)

“…The parsimony analyses were performed under implied weights with R 4.1.0 ( R Core Team, 2021 ) and the R package TreeSearch 1.0.1 ( Smith, 2023 ). Parsimony analyses achieve highest accuracy under a moderate weighting scheme ( i.e., when concavity constants, K, are between 5 and 20) ( Goloboff, Torres & Arias, 2018 ; Smith, 2019 ).…”

An unusual lineage of Helotidae in mid-Cretaceous amber from northern Myanmar (Coleoptera: Nitiduloidea)

“…4.1.0, R Foundation for Statistical Computing, Vienna, Austria, see https://www.R-project.org) and the R package TreeSearch (ver. 1.0.1, see https://cran.r-project.org/package=TreeSearch; Smith 2023) (). Parsimony analyses achieve highest accuracy under a moderate weighting scheme (i.e.…”