scholarly journals A Memetic Algorithm for Phylogenetic Reconstruction with Maximum Parsimony

2009 ◽  
pp. 164-175 ◽  
Author(s):  
Jean-Michel Richer ◽  
Adrien Goëffon ◽  
Jin-Kao Hao
Keyword(s):  
Maximum Parsimony ◽  
Memetic Algorithm ◽  
Phylogenetic Reconstruction

scholarly journals An experimental study comparing linguistic phylogenetic reconstruction methods

Diachronica ◽  
2013 ◽  
Vol 30 (2) ◽  
pp. 143-170 ◽  
Author(s):  
François Barbançon ◽  
Steven N. Evans ◽  
Luay Nakhleh ◽  
Don Ringe ◽  
Tandy Warnow
Keyword(s):  
Experimental Study ◽  
Simulation Study ◽  
Maximum Parsimony ◽  
Phylogenetic Reconstruction ◽  
Phylogeny Reconstruction ◽  
Neighbor Joining ◽  
Reconstruction Methods

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 and maximum compatibility if the characters with high weights exhibit low homoplasy.

scholarly journals The limitations of ontogenetic data in phylogenetic analyses

2002 ◽  
Vol 71 (1-3) ◽  
pp. 47-65 ◽  
Author(s):  
Stefan Koenemann ◽  
Frederick R. Schram
Keyword(s):  
Maximum Parsimony ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Real Data ◽  
Linear Type ◽  
Molecular Sequence Data ◽  
Event Sequences ◽  
Coding Method

The analysis of consecutive ontogenetic stages, or events, introduces a new class of data to phylogenetic systematics that are distinctly different from traditional morphological characters and molecular sequence data. Ontogenetic event sequences are distinguished by varying degrees of both a collective and linear type of dependence and, therefore, violate the criterion of character independence. We applied different methods of phylogenetic reconstruction to ontogenetic data including maximum parsimony and distance (cluster) analyses. Two different data sets were investigated: (1) four simulated ontogenies with defined phylogenies of six hypothetical taxa, and (2) a set of “real” data comprising sequences of 29 ontogenetic events from 11 vertebrate taxa. We confirm that heterochronic event sequences do contain a phylogenetic signal. However, based on our results we argue that maximum parsimony is a biased method to analyze such developmental sequence data. Ontogenetic events require a special analytical algorithm that would not neglect instances of chronological (horizontal) dependence of this type of data. One coding method, “event-pairing”, appeared to fulfill this requirement in the vertebrate analyses. However, to accurately analyze ontogenetic sequence data, a more sophisticated coding method and algorithm are needed, for example, measuring distances of dependent events.

A new species of Contomastix (Squamata, Teiidae) supported by total evidence, with remarks on diagnostic characters defining the genus

2019 ◽  
pp. 23-36
Author(s):  
Mario. R. Cabrera
Keyword(s):  
New Species ◽  
Geographic Distribution ◽  
Phylogenetic Reconstruction ◽  
Total Evidence ◽  
Molecular Evidence ◽  
Proximal Margin ◽  
Diagnostic Characters ◽  
Morphological Differences ◽  
A New Species ◽  
Molecular Characters

Formerly Cnemidophorus was thought to be the most speciose genus of Teiidae. This genus comprised four morphological groups that were later defined as four different genera, Ameivula, Aurivela, Cnemidophorus and Contomastix. The last appears as paraphyletic in a recent phylogenetic reconstruction based on morphology, but monophyletic in a reconstruction using molecular characters. Six species are allocated to Contomastix. One of them, C. lacertoides, having an extensive and disjunct geographic distribution in Argentina, Uruguay and Brazil. Preliminary analyses revealed morphological differences among its populations, suggesting that it is actually a complex of species. Here, we describe a new species corresponding to the Argentinian populations hitherto regarded as C. lacertoides, by integrating morphological and molecular evidence. Furthermore, we demonstrate that the presence of notched proximal margin of the tongue is a character that defines the genus Contomastix.

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