TNT version 1.5, including a full implementation of phylogenetic morphometrics (original) (raw)

TNT, a free program for phylogenetic analysis

Cladistics, 2008

The main features of the phylogeny program TNT are discussed. Windows versions have a menu interface, while Macintosh and Linux versions are command‐driven. The program can analyze data sets with discrete (additive, non‐additive, step‐matrix) as well as continuous characters (evaluated with Farris optimization). Effective analysis of large data sets can be carried out in reasonable times, and a number of methods to help identifying wildcard taxa in the case of ambiguous data sets are implemented. A variety of methods for diagnosing trees and exploring character evolution is available in TNT, and publication‐quality tree‐diagrams can be saved as metafiles. Through the use of a number of native commands and a simple but powerful scripting language, TNT allows the user an enormous flexibility in phylogenetic analyses or simulations.© The Willi Hennig Society 2008.

Phylogenetic morphometrics (I): the use of landmark data in a phylogenetic framework

Cladistics, 2010

A method for the direct use of aligned landmark data (2D or 3D coordinates of comparable points) in phylogenetic analysis is described. The approach is based on finding, for each of the landmark points, the ancestral positions that minimize the distance between the ancestor/descendant points along the tree. Doing so amounts to maximizing the degree to which similar positions of the landmarks in different taxa can be accounted for by common ancestry, i.e. parsimony. This method requires no transformation of the aligned data or the results: the data themselves are the x, y, z coordinates of the landmarks, and the output of mapping a character onto a given tree is the x, y, z coordinates for the hypothetical ancestors. In the special case of collinear points, the results are identical to those of optimization of (continuous) additive characters.

Visual TreeCmp : Comprehensive Comparison of Phylogenetic Trees on the Web

Methods in Ecology and Evolution, 2020

The construction of phylogenetic trees helps to understand evolutionary processes as mechanisms leading to genetic diversity. These trees allow an easy visualization of genetic relationships between populations or biological sequence sets. There are many methods for constructing such trees (e.g. maximum likelihood, maximum parsimony or Bayesian method) and most of them return not one but numerous sets of phylogenetic relations for the same input data. The comparison of the obtained set of trees requires the use of methods determining the distance between them, i.e. metrics. An alternative application of these metrics is related to the assessment of the accuracy of phylogenetic tree reconstruction, especially when developing a new method (Price, Dehal, & Arkin, 2010; Sul, Matthews, & Williams, 2009). The phylogenetic metrics are also used to build supertrees (Bansal, Burleigh, Eulenstein, & Fernández-Baca, 2010) and to define the consensus and median point of tree sets (Bryant, 1997). Another use of these methods is an efficient search for phylogenetic databases (Chen, Burleigh, Bansal, & Fernández-Baca, 2008). It is difficult to find a tool to compare large-size phylogenetic trees easily and efficiently in a comprehensive manner. The Visual TreeCmp Web application, which is a successor of the command line utility TreeCmp (Bogdanowicz, Giaro, & Wróbel, 2012), has been designed to fill this gap.

Landmarks, localization, and the use of morphometrics in phylogenetic analysis

Topics in geobiology, 2001

The analysis of morphology is crucial to the study of phylogeny in many ancient and modern organismal groups. Recently a number of arguments have been made in favor of regarding certain kinds of morphometric variables as putatively homologous characters and allowing them to participate, along with other non-morphometric variables, in parsimony-based cladistic analyses. These arguments rest on the assumptions that geometric landmarks incorporate the concept of biological homology and that partial warp and principal warp morphometric variables uniquely incorporate and operationalize the concept of spatial localization, thus providing investigators with the ability to assess patterns and directions of geometrical variation in unmeasured regions of organic forms. Literature review, coupled with empirical investigations of similarities and differences among three different morphometric data analysis methods on two different datasets suggest that there is no support for these assertions. Geometric landmarks, which form the basis for all morphometric measurements and latent shape variables, have no necessary correspondence to biological homology. Partial warp variables, coordinate-point eigenshape variables, and inter-landmark distance-based singular vector shape-change variables all express localized (= regionally-weighted) geometric deformations. However, none of these deformation patterns are localized in the sense of being truly independent from globally-distributed aspects of shape change. All three of the morphometric data analysis methods investigated are capable of inferring patterns of shape change in remote regions of the form so long as a spatially adequate array of landmarks is used as the basis for the shape analysis. Based on these results it is concluded that: (1) all types of morphometric procedures are potentially useful in phylogenetic inference to the extent that they are able to summarize patterns of biotic shape change within the Euclidean space of the original measurements; (2) morphometric interpretations are strengthened by using alternative analytic approaches to probe the geometric system in a hypothetico-deductive manner and achieve a robust and consistent interpretation of underlying differences among operational taxonomic units (OTU s); and (3) while deformationbased morphometric variables can be used to analyze the distribution of organic shapes in a variety of measurement and latent variable spaces, they represent abstract investigative tools that are tied irreducibly to particular samples and data. Such variables can be used to study morphological characters, refine character and character state definitions, and aid in the assignment of character states to OTU s. However, they are not characters themselves and may not be suitable for phylogenetic analyses directly. In addition, a new morphometric data analysis technique coordinate-point eigenshape analysis is described and its use illustrated.

Visual TreeCmp: Comprehensive Comparison1of Phylogenetic Trees on the Web

Methods in Ecology and Evolution, 2020

Phylogenetic signals in morphometric data

Morphology, shape and …, 2002

a new method of subdivided relative warp analysis (described herein) performs very well at recognizing simulated morphological character states and recovering a simulated morphological phylogenetic hierarchy. Based on these results it is concluded that the potential of morphometric data analysis methods (especially relative warp-based methods) to contribute to phylogenetic-systematic investigations should be explored further.

Nine Easy Steps for Constructing Reliable Trees from Published Phylogenetic Analyses 1

Annals of the Missouri Botanical Garden, 2007

Classification and biogeography should be informed by reliable phylogenetic reconstruction. This may be recovered from the mainly speculative literature by a nine-step protocol of critical methods, the ''operative transform.'' Piecemeal total evidence is attained by combining separately published support values for the same branch arrangement with Bayes' Formula. Joint probability correction is advanced for multiple test problems of conclusions of monophyly necessarily regarded as sets. Tables are given for conversion of nonparametric bootstrap values and decay indexes into probabilities, based on four-taxon simulations. Uncontested morphology-based branch arrangements are assigned high priors. Probabilities associated with unaccounted assumptions are addressed by a general correction factor. A probabilistic calculation allows the inference of two or more reliable internodes from a series of less well-supported internodes. A patristic distance of at least two internodes is used to support inference from molecular data alone of an intermediate lineage for recognition of supraspecific segregate taxonomic entities. Recognizing paraphyletic taxa when appropriate preserves attributes of inferred functional evolution providing taxic unity and value. Evolutionary Lazarus taxa contravening Dollo's Rule against re-evolution of complex traits justify interpretations of reticulation. This method of evaluation of the decisiveness of published molecular studies is exemplified with previously published cladograms focused on Malpighiales and the moss family Pottiaceae. Additional consideration of evolutionary process not reflected in phylogenetic analysis leads to reliable hypotheses of evolutionary relationship.

The Growth of Phylogenetic Information and the Need for a Phylogenetic Data Base

Systematic Biology, 1993

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TNT version 1.5, including a full implementation of phylogenetic morphometrics (original) (raw)

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