Pablo A. Goloboff

National Scientific and Technical Research Council | conicet

A small species of the spider genus Actinopus Perty 1833 from Copo National Park in Argentina is described—Actinopus chilikuti sp. nov. The new species belongs to a small group that in Argentina previously comprised three morphologically homogeneous species. Detailed morphological descriptions of both sexes, illustrations and geographic distributio...

This note describes the implementation and use of wincladtree , a TNT script to plot publication‐quality tree‐diagrams. This is intended to assist analysis of morphological datasets, where displaying the synapomorphies for the different groups in a compact “Hennigian” style is the norm.

Wheeler (Cladistics 2023, 39, 475) recently suggested that the issues with inapplicable characters in phylogenetic analysis can be dealt with directly by treating observed absences of a feature not in a separate absence/presence character but as insertion/deletion events in a complex character that describes the feature in all its variation; and th...

This paper discusses methods to take into account interactions between characters, in the context of parsimony analysis. These interactions can be in the form of some characters becoming inapplicable given certain states of other, primary characters; in the form of only certain states being allowed in some characters when a given state or set of st...

Gene-tree-inference error can cause species-tree-inference artefacts in summary phylogenomic coalescent analyses. Here we integrate two ways of accommodating these inference errors: collapsing arbitrarily or dubiously resolved gene-tree branches, and subsampling gene trees based on their pairwise congruence. We tested the effect of collapsing gene-...

A new graphical user interface (GUI) for the parsimony program TNT is presented that works under the Linux and Mac operating systems, as well as the Cygwin environment (which runs under Windows). The new interface is based on the GIMP Tool Kit, GTK (version 3). Formerly, only Windows versions of TNT had a GUI. The new interface improves upon the ex...

Phylogenetic inference, which involves time-consuming calculations, is a field where parallelization can speed up the resolution of many problems. TNT (a widely used program for phylogenetic analysis under parsimony) allows parallelization under the PVM system (Parallel Virtual Machine). However, as the basic aspects of the implementation remain un...

Areas of endemism characterize geographical regions by their unique biotas, providing the basis for studies on the ecological and historical drivers of these biologically distinct units. Tribe Bignonieae (Bignoniaceae) are a highly diverse clade of lianas distributed throughout the Neotropics, representing an excellent model for studying the driver...

Competing morphology-based phylogenetic analyses are routinely compared and evaluated only by a posteriori phylogenetic topology and group support, with little or no analysis of a priori data sources responsible for differing results. Although discordant characters and character-state scores are usually key to differing results (more so than variat...

We discuss here the use of TNT (Tree Analysis using New Technology) for phylogenomic analysis. For such data, parsimony is a useful alternative to model-based analyses, which frequently utilize models that make unrealistic assumptions (e.g. low heterotachy), struggle with high levels of missing data, etc. Parsimony and model-based methods often yie...

This paper examines the implementation of parsimony methods in the programs PAUP*, MEGA and MPBoot, and compares them with TNT. PAUP* implements standard, well-tested algorithms, and flexible search strategies and options for handling trees; its main drawback is the lack of advanced search algorithms, which makes it difficult to find most parsimoni...

Humanity is currently facing the challenge of two devastating pandemics, caused by two very different RNA viruses: HIV-1, which has been with us for decades, and SARS-CoV-2, which has swept the world in the course of a single year. The same evolutionary strategies that drive HIV-1 evolution are at play in SARS-CoV-2. Single nucleotide mutations, mu...

Evidence for phylogenetic analysis comes in the form of observed similarities, and trees are selected to minimize the number of similarities that cannot be accounted for by homology (homoplasies). Thus, the classical argument for parsimony directly links homoplasy with explanatory power. When characters are hierarchically related, a first character...

Assessing the effect of methodological decisions on the resulting hypotheses is critical in phylogenetics. Recent studies have focused on evaluating how model selection, orthology definition and confounding factors affect phylogenomic results. Here, we compare the results of three concatenated phylogenetic methods (Maximum Likelihood, ML; Bayesian...

A new phylogenetic comparative method called DUALCOR is presented to evaluate the evolutionary response of a character to non‐evolving external factors, such as environmental variables. The method treats the character as a typical evolving feature of an organism that is reconstructed on a given tree, whereas the external factor is treated as unrela...

We analyzed 769 242 occurrence records for 115 424 species of terrestrial arthropods, from three biodiversity repositories (Global Biodiversity Information Facility (GBIF), Natural History Museum, London, and “Sistema de Informação Distribuído para Coleções Biológicas” (SpeciesLink)), to test the use of global‐scale data points for quantitative ass...

Uncertainties in the phylogeny of birds (Avialae) and their closest relatives have impeded deeper understanding of early theropod flight. To help address this, we produced an updated evolutionary hypothesis through an automated analysis of the Theropod Working Group (TWiG) coelurosaurian phylogenetic data matrix. Our larger, more resolved, and bett...

Evolution of birds from non-flying theropod dinosaurs is a classic evolutionary transition, but a deeper understanding of early flight has been frustrated by disagreement on the relationships between birds (Avialae) and their closest theropod relatives. We address this through a larger, more resolved evolutionary hypothesis produced by a novel auto...

Motivation: TNT (a widely used program for phylogenetic analysis) includes an interpreter for a scripting language, but that implementation is non-standard and uses several conventions of its own. This paper describes the implementation and basic usage of a C-interpreter (with all the ISO essentials) now included in TNT. A phylogenetic library inc...

The spider family Migidae Simon, 1889 is represented in Chile by three genera: Calathotarsus Simon, 1903, Mallecomigas Goloboff & Platnick, 1987 and Goloboffia Griswold & Ledford, 2001. In the present study, four new species of Goloboffia from Chile are described, increasing the known diversity and geographic distribution of the genus. Goloboffia m...

Several slowly evolving characters are evaluated with the main objective of reinforcing the higher classiication of Embioptera. An embiopteran femoral auditory organ, described here for the irst time, exhibits diferences in shape and position that provide diagnostic criteria for higher taxonomic groups in the order. New characters on silk ejectors,...

Incomplete data sampling, bias, and like properties of distribution datasets that potentially introduce uncertainty in biogeographical analyses and blur biogeographical patterns; therefore, it is important to understand their influence. Despite their relevance, these problems have been largely overlooked in biogeography, where concepts such as ambi...

A likelihood method that approximates the behaviour of implied weighting is described. This approach provides a likelihood perspective on several aspects of implied weighting, such as guidance for the choice of concavity values, a justification to use different concavities for different numbers of taxa, and a natural basis for extended implied weig...

The Mkv evolutionary model, based on minor modifications to models of molecular evolution, is being increasingly used to infer phylogenies from discrete morphological data, often producing different results from parsimony. The critical difference between Mkv and parsimony is the assumption of a "common mechanism" in the Mkv model, with branch lengt...

The genus Actinopus Perty, 1833, is revised for Argentina, comprising a total of 23 species. The female of A. insignis (Holmberg, 1881) is described for the first time; the species is found in northern Buenos Aires, southern Santa Fe, and Uruguay. The female of A. longipalpis (Koch, 1842), previously known only from the male type from Uruguay, is d...

This paper discusses the problem of whether creating a matrix with all the character state combinations that have a fixed number of steps (or extra steps) on a given tree T, produces the same tree T when analyzed with maximum parsimony or maximum likelihood. Exhaustive enumeration of cases up to 20 taxa for binary characters, and up to 12 taxa for...

One of the lasting controversies in phylogenetic inference is the degree to which specific evolutionary models should influence the choice of methods. Model-based approaches to phylogenetic inference (likelihood, Bayesian) are defended on the premise that without explicit statistical models there is no science, and parsimony is defended on the grou...

Aim Understanding patterns of endemism is a key to deciphering the history of biotas and setting conservation priorities, but resolving the complexity of distributional patterns quantitatively into areas of endemism is often a difficult task. We report here an analysis of a comprehensive biodiversity dataset for the study of endemism, including vir...

A new genus of the subfamily Euagrinae is described from Chile, Vilchura calderonigen. et sp. nov. this is the second euagrine genus described for South America. The genus is distinguished from other euagrine genera by its short and recurved fovea, the presence of a megaspine on both male tibiae I and II, and the female spermathecae divided in...

This paper describes two types of problems related to tree shapes, as well as algorithms that can be used to solve these problems. The first problem is that of comparing the similarity of the unlabelled shapes instead of merely their degree of balance, in a manner analogous to that routinely used to compare topologies for labelled trees. There are...

We present a phylogenetic analysis of spiders using a dataset of 932 spider species, representing 115 families (only the family Synaphridae is unrepresented), 700 known genera, and additional representatives of 26 unidentified or undescribed genera. Eleven genera of the orders Amblypygi, Palpigradi, Schizomida and Uropygi are included as outgroups....

Version 1.5 of the computer program TNT completely integrates landmark data into phylogenetic analysis. Landmark data consist of coordinates (in two or three dimensions) for the terminal taxa; TNT reconstructs shapes for the internal nodes such that the difference between ancestor and descendant shapes for all tree branches sums up to a minimum; th...

Quantitative analyses of areas of endemism have rarely considered higher taxa. This paper discusses aspects related to the use of higher taxa in the analysis of areas of endemism, and computer implementations. An example of the application of the method is provided, with a data set for Nearctic mammals, showing that some of the areas recognized by...

This paper describes an efficient implementation of triplet-based measures of stability, in the program TNT. The only available implementations of such measures are much slower than the present one, either because of an inefficient implementation (Phyutility, Thor) or because the stability is evaluated with quartets (RogueNaRok, requiring O(t(4)),...

This paper examines a recent proposal to calculate supertrees by minimizing the sum of subtree prune-and-regraft distances to the input trees. The supertrees thus calculated may display groups present in a minority of the input trees but contradicted by the majority, or groups that are not supported by any input tree or combination of input trees....

When doing a bootstrap analysis with a single tree saved per pseudoreplicate, biased search algorithms may influence support values more than actual properties of the data set. Two methods commonly used for finding phylogenetic trees consist of randomizing the input order of species in multiple addition sequences followed by branch swapping, or usi...

Three different types of data sets, for which the uniquely most parsimonious tree can be known exactly but is hard to find with heuristic tree search methods, are studied. Tree searches are complicated more by the shape of the tree landscape (i.e. the distribution of homoplasy on different trees) than by the sheer abundance of homoplasy or characte...

In recent years, several publications in computer science journals have proposed new heuristic methods for parsimony analysis. This contribution discusses those papers, including methods highly praised by their authors, such as Hydra, Sampars and GA + PR + LS. Trees of comparable or better scores can be obtained using the program TNT, but from one...

Resumen Se presenta una breve síntesis del conocimiento de las especies argentinas de las familias de arañas migalomorfas agrupadas en el clado Rastelloidina (Actinopodidae, Migidae, Idiopidae y Cyrtaucheniidae), conocidas usualmente como “arañas albañiles”. Se trata de arañas robustas, sedentarias, de patas relativamente cortas y fuertemente armad...

Resumen Se revisa el conocimiento taxonómico de las familias de arañas migalomorfas Nemesiidae y Microstigmatidae en la fauna argentina. Ambas comparten un cefalotórax más bien bajo, uñas tarsales superiores anchas y bipectinadas, uña del palpo de la hembra con dientes en el promargen, y las hileras más cortas que en Dipluridae. Las Microstigmatida...

Resumen Las familias de arañas Mecicobothriidae, Hexathelidae y Dipluridae comprenden arañas migalomorfas tejedoras de telas en forma de sábana con embudos, de tamaño variable y similares superficialmente por la presencia de hileras laterales largas a muy largas. Las Mecicobothriidae (cuatro géneros y nueve especies descriptas, siete de ellas exclu...

Oblong, a program with very low memory requirements, is presented. It is designed for parsimony analysis of data sets comprising many characters for moderate numbers of taxa (the order of up to a few hundred). The program can avoid using vast amounts of RAM by temporarily saving data to disk buffers, only parts of which are periodically read back i...

For ambiguous data sets, methods to determine areas of endemism based on an optimality criterion may result in large numbers of candidate areas, and thus some kind of consensus technique is required to summarize those results. This paper presents a formal description of two possible algorithms or rules for area consensus, which merge candidate area...

Several extensions to implied weighting, recently implemented in TNT, allow a better treatment of data sets combining morphological and molecular data sets, as well as those comprising large numbers of missing entries (e.g. palaeontological matrices, or combined matrices with some genes sequenced for few taxa). As there have been recent suggestions...

This paper presents a pipeline, implemented in an open-source program called GB→TNT (GenBank-to-TNT), for creating large molecular matrices, starting from GenBank files and finishing with TNT matrices which incorporate taxonomic information in the terminal names. GB→TNT is designed to retrieve a defined genomic region from a bulk of sequences inclu...

Several new species of Hexathelidae Simon (1892) from Chile are described. In Scotinoecus Simon (1892), a new species (S. ruiles) is described using females; a new species (S. major) is proposed for the male previously misidentified as S. cinereopilosus (Simon, 1889), and females are described; the male of S. cinereopilosus is described for the fir...

The idea of an area of endemism implies that different groups of plants and animals should have largely coincident distributions. This paper analyses an area of 1152 000 km2, between parallels 21 and 32°S and meridians 70 and 53°W to examine whether a large and taxonomically diverse data set actually displays areas supported by different groups. Th...

All methods proposed to date for mapping landmark configurations on a phylogenetic tree start from an alignment generated by methods that make no use of phylogenetic information, usually by superimposing all configurations against a consensus configuration. In order to properly interpret differences between landmark configurations along the tree as...

Based on Hovenkamp’s ideas on historical biogeography, we present a method for analysis of taxon history, spatial analysis of vicariance, which uses observed distributions as data, thus requiring neither predefined areas nor assumptions of hierarchical relations between areas. The method is based on identifying sister nodes with disjunct (allopatri...

This paper describes algorithms for optimizing two- or three-dimensional landmark data onto trees directly. The method is based on a first approximation using grids, and subsequent iterative refinement of the initial point estimates. Details of the implementation are discussed, as well as an empirical example. © The Willi Hennig Society 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...

A new phylogenetic comparative method is proposed, based on mapping two continuous characters on a tree to generate data pairs for regression or correlation analysis, which resolves problems of multiple character reconstructions, phylogenetic dependence, and asynchronous responses (evolutionary lags). Data pairs are formed in two ways (tree-down an...

The 27th meeting of the Willi Hennig Society was held at the Sierras de San Javier, Tucumán (27–31 October 2008), jointly with the VIII Reunión Argentina de Cladística y Biogeografía. This was the second Hennig meeting held in South America and the third in Latin America. The event was attended by 129 participants from 16 countries, with the strong...

The main purpose of this study is to analyze whether areas of endemism can be characterized quantitatively by using insects, which are typically much more poorly sampled than vertebrates or plants. For this, an optimality criterion in the search for endemic areas was used to analyze approximately 1,100 georeferences from 288 species of holometabolo...

The main purpose of this study is to analyze whether areas of endemism can be characterized quantitatively by using insects, which are typically much more poorly sampled than vertebrates or plants. For this, an optimality criterion in the search for endemic areas was used to analyze approximately 1,100 georeferences from 288 species of holometabolo...

Obtaining a well supported schema of phylogenetic relationships among the major groups of living organisms requires considering as much taxonomic diversity as possible, but the computational cost of calculating large phylogenies has so far been a major obstacle. We show here that the parsimony algorithms implemented in TNT can successfully process...

Azilia leucostigma Mello-Leitão 1941 considered by Mello-Leitão as a metine (Tetragnathidae), is transferred to the gnaphosoid family Gallieniellidae, as the type species of the new genus Galianoella. The obliquely depressed endites, the flattened irregular posterior median eyes, and the conical anterior lateral spinnerets retaining a sclerotized d...

Grant and Kluge have recently stated that Bremer support and their own REP (“relative explanatory power”), are the only objective measures of group support. This paper discusses their claim, showing that their philosophical arguments have no basis, and that their own numerical examples actually serve to illustrate shortcomings of REP.

The problem of character weighting in cladistic analysis is revisited. The finding that, in large molecular data sets, removal of third positions (with more homoplasy) decreases the number of well supported groups has been interpreted by some authors as indicating that weighting methods are unjustified. Two arguments against that interpretation are...

The SPR distance between two trees is the minimum number of SPR moves required to convert one tree into the other. It has been proven as an NP-complete problem. A heuristic to calculate SPR distances between trees is described. It performs favorably when compared with other existing heuristics, RIATA-HGT and EEEP. Compared with RIATA-HGT, the new m...

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 set...

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 ...

Roshan et al. recently described a "divide-and-conquer" technique for parsimony analysis of large data sets, Rec-I-DCM3, and stated that it compares very favorably to results using the program TNT. Their technique is based on selecting subsets of taxa to create reduced data sets or subproblems, finding most-parsimonious trees for each reduced data...

We performed a phylogenetic analysis of 2359 hemagglutinin sequences of influenza A. We find multiple host shifts of all polarities among swine, humans, and birds. We also describe novel methods to assess the quality of surveillance and apply these methods to the public sequence record.

Quantitative and continuous characters have rarely been included in cladistic analyses of morphological data; when included, they have always been discretized, using a variety of ad hoc methods. As continuous characters are typically additive, they can be optimized with well known algorithms, so that with a proper implementation they could be easil...

Description of the male of Missulena tussulena Goloboff 1994 (Araneae, Mygalomorphae, Actinopodidae). The male of the Chilean actinopodid spider Missulena tussulena Goloboff 1994 is described for the first time. The species has been assigned tentatively to the genus Missulena Walckenaer (otherwise exclusively Australian), on the basis of the long f...

New examples are presented, showing that supertree methods such as matrix representation with parsimony, minimum flip trees, and compatibility analysis of the matrix representing the input trees, produce supertrees that cannot be interpreted as displaying the groups present in the majority of the input trees. These methods may produce a supertree d...

It is often assumed that homoplasy makes cladistic results uncertain. The minimum values that the consistency index C (Kluge and Farris, 1969) can achieve on most parsimonious trees decrease with number of taxa and have a more complex dependence with number of characters. Those minimum values have never been calculated, and therefore it is not know...

A method to assess the cost of character state transformations based on their congruence is proposed. Measuring the distortion of different transformations with a convex increasing function of the number of transformations, and choosing those reconstructions which minimize the distortion for all transformations, may provide a better optimality crit...

Abstract Cladistic data are more decisive when the possible trees differ more in tree length. When all the possible dichotomous trees have the same length, no one tree is better supported than the others, and the data are completely undecisive. From a rule for recursively generating undecisive matrices for different numbers of taxa, formulas to cal...

Algorithms to speed up tree searches under Sankoff parsimony are described. For T terminal taxa, an exact algorithm allows calculating length during searches T to 2T times faster than a complete down-pass optimization. An approximate but accurate method is from 3T to 8T times faster than a down-pass. Other algorithms that provide additional increas...

Abstract — Several algorithms to speed up branch swapping searches for most parsimonious trees are described. The method for indirect tree length calculation when moving a clipped clade, based on final states for the divided tree, is expanded to take into account polymorphic characters, and to include the possibility of rejecting several locations...

A method that allows estimating consensus trees without exhaustive searches is described. The method consists of comparing the results of different independent superficial searches. The results of the searches are then summarized through a majority rule, consensed with the strict consensus tree of the best trees found overall. This assumes that to...

Methods of phylogeny reconstruction are often divided into statistical methods (which require an explicit model of evolution) and non-statistical methods. Among methods with an explicit statist-ical justification, the most widely used are the methods of maximum likelihood, resulting from Felsenstein's (1973, 1981c) work, and more recently, Bayesian...