<scp>POY</scp> version 5: phylogenetic analysis using dynamic homologies under multiple optimality criteria

Wheeler, Ward C.; Lucaroni, Nicholas; Lin, Hong; Crowley, Louise M.; Varón, Andrés

doi:10.1111/cla.12083

Cited by 78 publications

(55 citation statements)

References 45 publications

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“…In the case of DNA, standard models of sequence evolution do not consider indels (let alone more complex transformations such as gene rearrangements! ); thus, it is far from obvious how to decide which is preferable: a more accurate description of substitions excluding indels, or a more simplistic analysis of substitutions and indels together (as in Poy, Wheeler et al., ). That likelihoodists may have the hopes that substitutions alone (when gaps in appropriate alignments are considered as missing data) will suffice to guarantee consistency (Truszkowski and Goldman, ) is besides the point, especially when considering that, in practice, different programs for sequence alignment produce very different results, and that phylogeneticists are indeed interested in understanding the evolution of sequences, not just substitutions.…”

Section: Discussionmentioning

confidence: 99%

Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology

2017

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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 grounds that it provides the best rationalization of the data, while refraining from assigning specific probabilities to trees or character‐state reconstructions. Authors who favour model‐based approaches often focus on the statistical properties of the methods and models themselves, but this is of only limited use in deciding the best method for phylogenetic inference—such decision also requires considering the conditions of evolution that prevail in nature. Another approach is to compare the performance of parsimony and model‐based methods in simulations, which traditionally have been used to defend the use of models of evolution for DNA sequences. Some recent papers, however, have promoted the use of model‐based approaches to phylogenetic inference for discrete morphological data as well. These papers simulated data under models already known to be unfavourable to parsimony, and modelled morphological evolution as if it evolved just like DNA, with probabilities of change for all characters changing in concert along tree branches. The present paper discusses these issues, showing that under reasonable and less restrictive models of evolution for discrete characters, equally weighted parsimony performs as well or better than model‐based methods, and that parsimony under implied weights clearly outperforms all other methods.

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Section: Discussionmentioning

confidence: 99%

Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology

2017

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“…Limits of different regions were marked with # and matrices were analyzed under maximum parsimony direct optimization. Direct optimization analyses were carried out in the computer program POY v 5.1.1b [53]. We used a search strategy based on iterated timed searches (multiple Wagner trees followed by SPR + TBR + ratchet and tree fusing) for 4–6 h as described in [54].…”

Section: Methodsmentioning

confidence: 99%

Multigene phylogenetic analysis redefines dung beetles relationships and classification (Coleoptera: Scarabaeidae: Scarabaeinae)

Tarasov

Dimitrov

2016

BMC Evol Biol

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BackgroundDung beetles (subfamily Scarabaeinae) are popular model organisms in ecology and developmental biology, and for the last two decades they have experienced a systematics renaissance with the adoption of modern phylogenetic approaches. Within this period 16 key phylogenies and numerous additional studies with limited scope have been published, but higher-level relationships of this pivotal group of beetles remain contentious and current classifications contain many unnatural groupings. The present study provides a robust phylogenetic framework and a revised classification of dung beetles.ResultsWe assembled the so far largest molecular dataset for dung beetles using sequences of 8 gene regions and 547 terminals including the outgroup taxa. This dataset was analyzed using Bayesian, maximum likelihood and parsimony approaches. In order to test the sensitivity of results to different analytical treatments, we evaluated alternative partitioning schemes based on secondary structure, domains and codon position. We assessed substitution models adequacy using Bayesian framework and used these results to exclude partitions where substitution models did not adequately depict the processes that generated the data. We show that exclusion of partitions that failed the model adequacy evaluation has a potential to improve phylogenetic inference, but efficient implementation of this approach on large datasets is problematic and awaits development of new computationally advanced software. In the class Insecta it is uncommon for the results of molecular phylogenetic analysis to lead to substantial changes in classification. However, the results presented here are congruent with recent morphological studies and support the largest change in dung beetle systematics for the last 50 years. Here we propose the revision of the concepts for the tribes Deltochilini (Canthonini), Dichotomiini and Coprini; additionally, we redefine the tribe Sisyphini. We provide and illustrate synapomorphies and diagnostic characters supporting the new concepts to facilitate diagnosability of the redefined tribes. As a result of the proposed changes a large number of genera previously assigned to these tribes are now left outside the redefined tribes and are treated as incertae sedis.ConclusionsThe present study redefines dung beetles classification and gives new insight into their phylogeny. It has broad implications for the systematics as well as for various ecological and evolutionary analyses in dung beetles.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0822-x) contains supplementary material, which is available to authorized users.

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“…Other programs compete with TNT for the analysis of sequence data (especially POY: Wheeler et al., ; RaxML: Stamatakis, ; MrBayes: Ronquist et al., ) and are widely used. However, no other program includes TNT's array of options for morphological data sets, in terms of optimality criteria, analytical options, diagnostic facilities and data types.…”

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confidence: 99%

TNT version 1.5, including a full implementation of phylogenetic morphometrics

2016

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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; this sum is used as tree score. Landmark data can be analysed alone or in combination with standard characters; all the applicable commands and options in TNT can be used transparently after reading a landmark data set. The program continues implementing all the types of analyses in former versions, including discrete and continuous characters (which can now be read at any scale, and automatically rescaled by TNT). Using algorithms described in this paper, searches for landmark data can be made tens to hundreds of times faster than it was possible before (from T to 3T times faster, where T is the number of taxa), thus making phylogenetic analysis of landmarks feasible even on standard personal computers.

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POY version 5: phylogenetic analysis using dynamic homologies under multiple optimality criteria

Cited by 78 publications

References 45 publications

Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology

Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology

Multigene phylogenetic analysis redefines dung beetles relationships and classification (Coleoptera: Scarabaeidae: Scarabaeinae)

TNT version 1.5, including a full implementation of phylogenetic morphometrics

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