We give an explicit construction to solve a conjecture of Mike Steel and David Penny that any phylogeny involving N taxa can be recovered unambiguously using on the order of log N binary characters and the method of maximum parsimony. Biologically, this means that homoplasy need not be a deterrent to parsimony methods. Some patterns of homoplasy are phylogenetically informative and can exponent...

Fehr and Schmidt (1999) introduced an influential utility function for individuals in interpersonal contexts that captures self-centered inequity aversion. The power of this utility function lies in its good balance between parsimony and fit. This paper provides a preference foundation for exactly the model of Fehr and Schmidt (FS), so that the preference conditions satisfy exactly FS’s balance...

This paper reports a simulation study comparing and evaluating the performance of different linguistic phylogeny reconstruction methods on model datasets for which the true trees are known. UPGMA performed least well, then (in ascending order) neighbor joining, the method of Gray & Atkinson and finally maximum parsimony. Weighting characters greatly improves the accuracy of maximum parsimony an...

The cost/benefit analysis is standard fare in contemporary ontology: we measure how a theory performs along a variety of dimensions (simplicity, coherence with intuitions etc.) and then – having completed this for all theories currently being evaluated – we opt for the theory that has, overall, the best cost-benefit profile. §1 is a more detailed exposition of this methodology. One of those the...

Despite the introduction of likelihood-based methods for estimating phylogenetic trees from phenotypic data, parsimony remains the most widely-used optimality criterion for building trees from discrete morphological data. However, it has been known for decades that there are regions of solution space in which parsimony is a poor estimator of tree topology. Numerous software implementations of l...

Inferring positive selection at single amino acid sites is of biological and medical importance. Parsimony-based and likelihood-based methods have been developed for this purpose, but the reliabilities of these methods are not well understood. Because the evolutionary models assumed in these methods are only rough approximations to reality, it is desirable that the methods are not very sensitiv...

When the rate variation among sites is described by a gamma distribution, an important problem is how to estimate the shape parameter 01, which is an index of the degree of among-site rate variation. The parsimony-based methods for estimating (Y are simple but biased, i.e., (Y tends to be overestimated. On the other hand, the likelihood-based methods are asymptotically unbiased but take a huge ...

Hybridization events generate reticulate species relationships, giving rise to species networks rather than species trees. We report a comparative study of consensus, maximum parsimony, and maximum likelihood methods of species network reconstruction using gene trees simulated assuming a known species history. We evaluate the role of the divergence time between species involved in a hybridizati...

Termites are highly abundant and vital insects that directly indirectly influence local soils. The present study investigated the morphological molecular phylogenetics of termite species collected from fields in southern Haryana, India, 2020 to 2021. Samples were subjected integrated systematic analyses, taking into account mandible features soldiers for systematics 16S rRNA gene-based phylogen...