Indo-European phylogenetics with R

Abstract The last twenty or so years have witnessed a dramatic increase in the use of computational methods for inferring linguistic phylogenies. Although the results of this research have been controversial, the methods themselves are an undeniable boon for historical and Indo-European linguistics, if for no other reason than that they allow the field to pursue questions that were previously intractable. After a review of the advantages and disadvantages of computational phylogenetic methods, I introduce the following methods of phylogenetic inference in R: maximum parsimony; distance-based methods (UPGMA and neighbor joining); and maximum likelihood estimation. I discuss the strengths and weaknesses of each of these methods and in addition explicate various measures associated with phylogenetic estimation, including homoplasy indices and bootstrapping. Phylogenetic inference is carried out on the Indo-European dataset compiled by Don Ringe and Ann Taylor, which includes phonological, morphological, and lexical characters.

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Optimized Fuzzy Cmeans – Fuzzy Covariance – Fuzzy Maximum Likelihood Estimation Clustering Method Based on Deferential Evolutionary Optimization Algorithm for Identification of Rock Mass Discontinuities Sets

Periodica Polytechnica Civil Engineering ◽

10.3311/ppci.13885 ◽

2019 ◽

Author(s):

Akbar Esmaeilzadeh ◽

Kourosh Shahriar

Keyword(s):

Rock Mass ◽

Maximum Likelihood ◽

Maximum Likelihood Estimation ◽

Field Data ◽

Likelihood Estimation ◽

Clustering Methods ◽

Clustering Method ◽

Advantages And Disadvantages ◽

Differential Evolutionary Algorithm ◽

Clustering Quality

Detecting of joint sets (clusters) is one of the most important processes in determining properties of fractures. Joints clustering and consequently, determination of the mean value representing each cluster is applicable to most rock mass studies. It is clear that the accuracy of the clustering process plays a key role in analyzing stability of infrastructures such as dams and tunnels and so on. Hence, in this paper, by reviewing several methods proposed for clustering fractures and considering their advantages and disadvantages, a three-stage hybrid method is developed which contains Fuzzy c-means, Fuzzy covariance and Fuzzy maximum likelihood estimation that by utilizing the modified orientation matrix had been optimized. This method is optimized by the Differential Evolutionary algorithm using a new and strong cost function which is defined as the computation core. In addition, using three clustering quality comparing criteria, the new developed method of differential evolutionary optimized of fuzzy cmeans - fuzzy covariance - fuzzy maximum likelihood estimation clustering method (DEF3) is compared with other base and common methods using field data. After doing the calculations, the developed method by giving the best values for all the criteria provided the best results and good stability in meeting different criteria. The DEF3 method was validated using actual field data which mapped in Rudbar Lorestan dam site. The results revealed that DEF3 acquired the best rank among the other method by getting the value of 0.5721 of Davis-Bouldin criterion, 1403.1 of Calinski-Harabasz criterion, and 0.83482 of Silihotte as comparing criteria of clustering methods.

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Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2016.2290 ◽

2017 ◽

Vol 284 (1846) ◽

pp. 20162290 ◽

Cited By ~ 75

Author(s):

Mark N. Puttick ◽

Joseph E. O'Reilly ◽

Alastair R. Tanner ◽

James F. Fleming ◽

James Clark ◽

...

Keyword(s):

Maximum Likelihood ◽

Maximum Likelihood Estimation ◽

Likelihood Estimation ◽

Accurate Method ◽

Morphological Data ◽

Or Groups ◽

Phenotype Data ◽

Bayesian Implementation ◽

Phylogenetic Estimation ◽

The Impact

Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured but recent studies have shown that these approaches are less accurate than the Bayesian implementation of the Mk model. Here we expand on these findings in several ways: we assess the impact of tree shape and maximum-likelihood estimation using the Mk model, as well as analysing data composed of both binary and multistate characters. We find that all methods struggle to correctly resolve deep clades within asymmetric trees, and when analysing small character matrices. The Bayesian Mk model is the most accurate method for estimating topology, but with lower resolution than other methods. Equal weights parsimony is more accurate than implied weights parsimony, and maximum-likelihood estimation using the Mk model is the least accurate method. We conclude that the Bayesian implementation of the Mk model should be the default method for phylogenetic estimation from phenotype datasets, and we explore the implications of our simulations in reanalysing several empirical morphological character matrices. A consequence of our finding is that high levels of resolution or the ability to classify species or groups with much confidence should not be expected when using small datasets. It is now necessary to depart from the traditional parsimony paradigms of constructing character matrices, towards datasets constructed explicitly for Bayesian methods.

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