CONSEL: for assessing the confidence of phylogenetic tree
  selection

Shimodaira, Hidetoshi; Hasegawa, Masami

doi:10.1093/bioinformatics/17.12.1246

Cited by 1,953 publications

(1,376 citation statements)

References 16 publications

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“…bicolor Hewitt, 1926. Per-site log-likelihoods were calculated for each of the tested topologies under GTR + G model in RAxML; then, these likelihood values were used to estimate statistical significance in CONSEL v.0.2 (Shimodaira and Hasegawa, 2001). …”

Section: Applying the Algorithm E-ins-i (Recommended For Less Then 200mentioning

confidence: 99%

The phylogenetic position and diversity of the enigmatic mongrel frog Nothophryne Poynton, 1963 (Amphibia, Anura)

Bittencourt-Silva

Conradie

Siu-Ting

et al. 2016

Molecular Phylogenetics and Evolution

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Highlights• Using a two-tiered phylogenetic approach proves to be an efficient way to add new taxa into phylogenies.• Nothophryne is a member of Pyxicephalidae and is the sister group of Tomopterna.• First phylogeny to include representatives of all pyxicephalid genera.• Cryptic diversity of Nothophryne species revealed. 2 Graphical abstract AbstractThe phylogenetic relationships of the African mongrel frog genus Nothophryne are poorly understood. We provide the first molecular assessment of the phylogenetic position of, and diversity within, this monotypic genus from across its range -the Afromontane regions of Malawi and Mozambique. Our analysis using a two-tiered phylogenetic approach allowed us to place the genus in Pyxicephalidae. Within the family, Nothophryne grouped with Tomopterna, a hypothesis judged significantly better than alternative hypotheses proposed based on morphology. Our analyses of populations across the range of Nothophryne suggest the presence of several cryptic species, at least one species per mountain. Formal recognition of these species is pending but there is a major conservation concern for these narrowly distributed populations in an area impacted by major habitat change. The phylogenetic tree of pyxicephalids is used to examine evolution of life history, ancestral habitat, and biogeography of this group.

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Section: Applying the Algorithm E-ins-i (Recommended For Less Then 200mentioning

confidence: 99%

The phylogenetic position and diversity of the enigmatic mongrel frog Nothophryne Poynton, 1963 (Amphibia, Anura)

Bittencourt-Silva

Conradie

Siu-Ting

et al. 2016

Molecular Phylogenetics and Evolution

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show abstract

“…The site likelihood values were computed for both the constrained and unconstrained ML trees by the software RAxML with the same model mentioned above. The likelihood values obtained were analyzed using the approximately unbiased (AU) and Shimodaira-Hasegawa (SH) tests with CONSEL v.0.1j software (Shimodaira and Hasegawa, 2001). …”

Section: Sequence Alignment and Phylogenetic Analysesmentioning

confidence: 99%

Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohymenophorea

Feng

Jiang

Warren

et al. 2015

Molecular Phylogenetics and Evolution

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“…To this end, the approximately unbiased (AU) test in CONSEL ver. 0.1k (Shimodaira 2002(Shimodaira , 2008Shimodaira and Hasegawa 2001) was applied. A p-value of < 0.05 was chosen for rejection of the null hypothesis.…”

Section: Topology Hypothesis Testingmentioning

confidence: 99%

Morphologic and molecular description of Metopus fuscus Kahl from North America and new rDNA sequences from seven metopids (Armophorea, Metopidae)

Bourland

Wendell

Hampikian

2014

European Journal of Protistology

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Most species in the large ciliate genus Metopus Claparède & Lachmann, 1858 lack detailed descriptions based on modern morphologic and molecular methods. This lack of data for the vast majority of species hampers application of a morphospecies approach to the taxonomy of Metopus and other armophorids. In this report we redescribe the large species, Metopus fuscus Kahl, 1927 based on in vivo observation, silver impregnation, scanning electron microscopy, and single-cell 18S rDNA sequencing of a freshwater North American (Idaho) population. Metopus fuscus invariably has a perinuclear envelope of endosymbiotic bacteria not found in other species. Unlike the original description of a single row of coarse granules between ciliary rows, the Idaho population has five loose rows of small interkinetal granules. We discuss the possible importance of this character in metopids. We also provide a phylogenetic analysis including setosus form a fully supported clade, challenging previous morphospecies groupings. We discuss some ambiguities of armophorid morphologic terminology in the earlier literature. Our phylogenetic analysis of Idaho metopids indicates that the genera Metopus and Brachonella are both nonmonophyletic.

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CONSEL: for assessing the confidence of phylogenetic tree selection

Abstract: shimo@ism.ac.jp

Cited by 1,953 publications

References 16 publications

The phylogenetic position and diversity of the enigmatic mongrel frog Nothophryne Poynton, 1963 (Amphibia, Anura)

The phylogenetic position and diversity of the enigmatic mongrel frog Nothophryne Poynton, 1963 (Amphibia, Anura)

Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohymenophorea

Morphologic and molecular description of Metopus fuscus Kahl from North America and new rDNA sequences from seven metopids (Armophorea, Metopidae)

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