Faculty Opinions recommendation of Maximum-likelihood phylogenetic analysis under a covarion-like model.

Author(s):  
John Huelsenbeck
Phytotaxa ◽  
2014 ◽  
Vol 159 (4) ◽  
pp. 241 ◽  
Author(s):  
Yu-lan Peng ◽  
Yu Zhang ◽  
Xin-fen Gao ◽  
Lin-jing Tong ◽  
Liang Li ◽  
...  

The systematic position of Paraixeris humifusa (Asteraceae) is hard to define, because the circumscription of Paraixeris, Youngia and Crepidiastrum, three closely related genera in subtribe Crepidinae (Cichorieae), is not clear. This paper reports on the relationships between 30 species in subtribe Crepidinae, based on an analysis of nucleotides from one nuclear (ITS) and three chloroplast DNA regions ( trnL-F, rps16 and atpB-rbcL). The phylogenetic analyses used maximum parsimony with maximum likelihood inference. The monophyly of Crepidiastrum in the most recent generic classification of Shih & Kilian (2011) is explored. The results show that 12 species in Crepidiastrum constitute a monophyletic group, and that Paraixeris humifusa should be treated as Youngia humifusa.


Zootaxa ◽  
2020 ◽  
Vol 4869 (3) ◽  
pp. 387-403
Author(s):  
ELYNTON ALVES DO NASCIMENTO ◽  
TAMIRES DINIZ BRESSAN ◽  
MILADA BOCAKOVA

A new genus of Neotropical Lycidae, Currhaeus gen. nov., is herein proposed as the second Eurrhacini genus lacking parameres in male genitalia. Seven new species are described: Currhaeus striatus sp. nov., C. nigroapicalis sp. nov., C. championi sp. nov., C. tabascensis sp. nov., C. ruschii sp. nov., C. polegattoi sp. nov., and C. paranaensis sp. nov. Illustrations of diagnostic characters and a key to species identification are presented. Parsimony and maximum likelihood analyses of morphological data demonstrated that Currhaeus gen. nov. belongs in the crown Eurrhacini. Implied weighting parsimony trees recovered Currhaeus as sister to Eurrhacus Waterhouse. 


2011 ◽  
Vol 8 (2) ◽  
pp. 299-303 ◽  
Author(s):  
Michael S. Y. Lee ◽  
Trevor H. Worthy

The widespread view that Archaeopteryx was a primitive (basal) bird has been recently challenged by a comprehensive phylogenetic analysis that placed Archaeopteryx with deinonychosaurian theropods. The new phylogeny suggested that typical bird flight (powered by the front limbs only) either evolved at least twice, or was lost/modified in some deinonychosaurs. However, this parsimony-based result was acknowledged to be weakly supported. Maximum-likelihood and related Bayesian methods applied to the same dataset yield a different and more orthodox result: Archaeopteryx is restored as a basal bird with bootstrap frequency of 73 per cent and posterior probability of 1. These results are consistent with a single origin of typical (forelimb-powered) bird flight. The Archaeopteryx –deinonychosaur clade retrieved by parsimony is supported by more characters (which are on average more homoplasious), whereas the Archaeopteryx –bird clade retrieved by likelihood-based methods is supported by fewer characters (but on average less homoplasious). Both positions for Archaeopteryx remain plausible, highlighting the hazy boundary between birds and advanced theropods. These results also suggest that likelihood-based methods (in addition to parsimony) can be useful in morphological phylogenetics.


2019 ◽  
Author(s):  
Kirill V. Mikhailov ◽  
Viatcheslav N. Ivanenko

AbstractReanalysis of the dataset used by Khodami et al. (2017) reveals low support values for the key nodes of the copepod (Crustacea) phylogeny and fails to reproduce the results obtained in the study. Maximum likelihood (ML) and Bayesian analyses with the dataset produce phylogenies that are inconsistent with the branching of copepod groups proposed by Khodami et al. (2017). The proposed phylogeny is refuted by the approximately unbiased (AU) statistical test, which undermines several conclusions drawn from the original study.


ZooKeys ◽  
2021 ◽  
Vol 1046 ◽  
pp. 189-206
Author(s):  
Lin-Lin Yang ◽  
Hou-Hun Li

The genus Pelecystola Meyrick, 1920 and the species Pelecystola strigosa (Moore, 1888) are newly recorded from China, and Pelecystola peculiarissp. nov. is described as new to science. Adults, head, venation, and genitalia of the two species are illustrated. A molecular phylogenetic analysis is presented to ascertain the generic affiliation of the new species. Forty-four species of 38 genera in Tineidae are analyzed using maximum likelihood methods based on one mitochondrial (COI) and two nuclear gene fragments (CAD and wingless). DNA barcodes of the two species are provided, and the genetic distance of barcode divergence among four species of Pelecystola is calculated.


Phytotaxa ◽  
2018 ◽  
Vol 369 (2) ◽  
pp. 80 ◽  
Author(s):  
XU LU ◽  
YAN-HONG MU ◽  
HAI-SHENG YUAN

Two new species of Tomentella from the Lesser Xingan Mts. of northeastern China, T. pallidocastanea and T. tenuirhizomorpha, are described and illustrated using morphological characteristics and molecular phylogenetic analysis. T. pallidocastanea is characterized by mucedinoid basidiocarps adherent to the substrate, a light reddish brown to pinkish grey hymenophoral surface, absence of rhizomorphs and cystidia, generative hyphae with clamps, rarely with simple septa and echinulate, and subglobose to lobed basidiospores (echinuli up to 1.5 μm long). T. tenuirhizomorpha is characterized by mucedinoid basidiocarps separable from the substrate, a greyish brown to dark brown hymenophoral surface, thin rhizomorphs in the subiculum and margins, an absence of cystidia, generative hyphae with clamps rarely with simple septa and echinulate, and subglobose to globose basidiospores (echinuli up to 1.5 μm long). Molecular analyses using Maximum Likelihood, Maximum Parsimony and Bayesian Analysis confirm the phylogenetic position of the two new species. The discriminating characters of these two new species and their closely related species are discussed in this study.


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