The relative performance of indel-coding methods in simulations

Simmons, Mark P.; Müller, Kai; Norton, Andrew

doi:10.1016/j.ympev.2007.04.001

Cited by 92 publications

(77 citation statements)

References 64 publications

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“…Previous research has suggested that alignment gaps can be a valuable source of phylogenetic signal (Egan and Crandall, 2008;Simmons et al, 2007). In order to code for gaps we treated each indel as a simple binary character (Simmons and Ochoterena, 2000).…”

Section: Methodsmentioning

confidence: 99%

Parsing polyphyletic Pueraria: Delimiting distinct evolutionary lineages through phylogeny

Egan

Vatanparast

Cagle³

2016

Molecular Phylogenetics and Evolution

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A taxon is defined as polyphyletic when it does not include the last common ancestor of all true members of the taxon, resulting in a number of subgroups not united by a common ancestor. Previous work has suggested Pueraria (Fabaceae) to be polyphyletic. Although several taxonomic treatments have recognized Pueraria as an unnatural grouping since its creation in 1825, and two have put forth taxonomic hypotheses, the polyphyly has never been resolved. The need for further biosystematic research has always been cited as the reason no changes were proposed. This project attempted to address this issue by sampling broadly across phaseoloid legumes with an initial target goal of 156 species including 15 species of Pueraria. Ultimately, 104 species across 69 genera were sampled for AS2 and 116 species across 64 genera for matK.Phylogeny reconstruction was carried out using maximum likelihood and Bayesian inference.Both analyses yielded congruent tree topologies and similar support values. Both previous taxonomic hypotheses show some congruence with the data, but discrepancies do occur. This work provides strong support for the existence of five separate clades within the genus Pueraria, requiring the resurrection of the genus Neustanthus for P. phaseoloides along with the need to create a new genus each for P. stricta, P. peduncularis, and P. wallichii. PARSING POLYPHYLETIC PUERARIA: DELIMITING DISTINCT EVOLUTIONARY LINEAGES THROUGH PHYLOGENY

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Section: Methodsmentioning

confidence: 99%

Parsing polyphyletic Pueraria: Delimiting distinct evolutionary lineages through phylogeny

Egan

Vatanparast

Cagle³

2016

Molecular Phylogenetics and Evolution

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“…We sampled the chain every 100 generations, and discarded the first 25% of the samples (which generally corresponded to when likelihood values became stationary) as the burn-in. Although utilization of gaps as character data can be phylogenetically informative in parsimony-based analyses, there are few well-tested methods for implementing gap information into model-based approaches to phylogenetic inference (Simmons et al, 2007, Phillips et al, 2000, and we thus treated all gaps as missing data. Although the majority of species were sequenced for all three loci (Table 1), because of logistical constraints (multiple failed sequencing attempts for some species-locus combinations), not all loci were sequenced for each species, and thus portions of our dataset were missing.…”

Section: Tree Constructionmentioning

confidence: 99%

Molecular phylogeny of the brachyuran crab superfamily Majoidea indicates close congruence with trees based on larval morphology

Hultgren

Stachowicz

2008

Molecular Phylogenetics and Evolution

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“…3. If different equally plausible alignments would lead to different (possibly spurious) synapomorphies, and it cannot be decided which one is preferable based on overall similarity of the Simmons et al 2007) was applied to those informative indels that could be placed with confidence. In a few cases, however, where short insertions of different size and/or different sequence suggesting a possibly different origin have been found in the same position relative to the majority of the taxa or where indels were caused by single nucleotide repeats of different lengths, we preferred to use a single multistate character.…”

Section: Introductionmentioning

confidence: 99%

A phylogenetic analysis of the Cryptocarya group (Lauraceae), and relationships of Dahlgrenodendron, Sinopora, Triadodaphne, and Yasunia

Rohwer¹,

Moraes

Rudolph

et al. 2014

Phytotaxa

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A phylogenetic analysis based on nuclear ITS and plastid trnK intron sequences confirms that Dahlgrenodendron, Sinopora, Triadodaphne, and Yasunia are members of the Cryptocarya group, as expected from morphology. Dahlgrenodendron from South Africa is sister to Aspidostemon from Madagascar. Triadodaphne inaequitepala is nested within Endiandra (both from Australasia), and Yasunia from South America is nested among South American Beilschmiedia species. Sinopora is a member of the Beilschmiedia clade, but its precise position is still uncertain. Among large genera of the group, Cryptocarya is clearly monophyletic, and Endiandra appears to be as well, if T. inaequitepala is included. Beilschmiedia is paraphyletic with respect to (at least) Potameia and Yasunia. Most wellsupported clades within genera are geographically homogeneous, except a clade including the Chilean Cryptocarya alba and two New Caledonian species. Both Beilschmiedia and Cryptocarya have reached the Americas more than once. Four-locular anthers are plesiomorphic in the Cryptocarya group; two-locular anthers have arisen by fusion of the two pollen sacs of a theca. In the plesiomorphic fruit type, the ovary is completely enclosed in receptacular tissue; a superior fruit, seated free on its pedicel, is a synapomorphy of the Beilschmiedia clade.

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The relative performance of indel-coding methods in simulations

Cited by 92 publications

References 64 publications

Parsing polyphyletic Pueraria: Delimiting distinct evolutionary lineages through phylogeny

Parsing polyphyletic Pueraria: Delimiting distinct evolutionary lineages through phylogeny

Molecular phylogeny of the brachyuran crab superfamily Majoidea indicates close congruence with trees based on larval morphology

A phylogenetic analysis of the Cryptocarya group (Lauraceae), and relationships of Dahlgrenodendron, Sinopora, Triadodaphne, and Yasunia

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