YBYRÁ facilitates comparison of large phylogenetic trees

Machado, Denis Jacob

doi:10.1186/s12859-015-0642-9

Cited by 35 publications

(29 citation statements)

References 14 publications

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“…Results were visualized using Mesquite v.3.03 (Maddison and Maddison, ). Lists of phenotypic synapomorphies were generated with YBYRÁ (Machado, ) using TNT. YBYRÁ categorizes character transformation events from any source of data given all possible optimization schemes in a set of trees.…”

Section: Methodsmentioning

confidence: 99%

A total evidence analysis of the phylogeny of hatchet‐faced treefrogs (Anura: Hylidae: Sphaenorhynchus)

et al. 2019

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The Neotropical hylid genus Sphaenorhynchus includes 15 species of small, greenish treefrogs widespread in the Amazon and Orinoco basins, and in the Atlantic Forest of Brazil. Although some studies have addressed the phylogenetic relationships of the genus with other hylids using a few exemplar species, its internal relationships remain poorly understood. In order to test its monophyly and the relationships among its species, we performed a total evidence phylogenetic analysis of sequences of three mitochondrial and three nuclear genes, and 193 phenotypic characters from all species of Sphaenorhynchus. Our results support the monophyly of Sphaenorhynchus with molecular and phenotypic evidence, with S. pauloalvini as the earliest diverging taxon, followed by S. carneus, as the sister taxon of all remaining species of the genus. We recognize three species groups in Sphaenorhynchus (the S. lacteus, S. planicola and S. platycephalus groups), to facilitate its taxonomic study; only three species (S. carneus, S. pauloalvini and S. prasinus) remain unassigned to any group. Sequence data were not available for only two species (S. bromelicola and S. palustris) for which we scored phenotypic data; wildcard behaviour was detected only in S. bromelicola nested inside the S. platycephalus group. On the basis of the resulting phylogenetic hypothesis, we discuss the evolution of oviposition site and a number of phenotypic characters that could be associated with heterochronic events in the evolutionary history of this group.

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Section: Methodsmentioning

confidence: 99%

A total evidence analysis of the phylogeny of hatchet‐faced treefrogs (Anura: Hylidae: Sphaenorhynchus)

et al. 2019

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“…These relative Goodman‐Bremer values were not considered for the selection of the optimal trees of each weighting scheme. The optimal trees of each weighting scheme were compared using the software YBYRÁ (Machado, ), which allows for a visual congruence analysis (illustrated through colored square plots) among all trees generated for the study. YBYRÁ generates color‐coded boxes to indicate whether synapomorphies are unambiguous (non‐homoplastic), or also occur in other clades (homoplastic) and if they are shared by all terminals in a given clade (unique) or are subsequently transformed into one or more different states within that clade (non‐unique).…”

Section: Methodsmentioning

confidence: 99%

A species‐level total evidence phylogeny of the microteiid lizard family Alopoglossidae (Squamata: Gymnophthalmoidea)

et al. 2020

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Alopoglossidae is a family of Neotropical lizards composed of 23 species allocated in two genera (Alopoglossus and Ptychoglossus). There is a lack of knowledge about the phylogenetic relationships and systematics of this family. Published phylogenies that include alopoglossid species have very low taxon coverage within the family, and are usually based on limited character sampling. Considering these shortcomings, we infer the phylogenetic relationships of Alopoglossidae-including all but one species in the family-based on the combined analyses of DNA sequences and morphological characters. We use four loci (the mitochondrial 12S, 16S and ND4; the nuclear C-mos) and a matrix of 143 phenotypic characters from scutellation, tongue morphology, hemipenis morphology, and osteology. The dataset is analyzed with Maximum Parsimony, with four alternative weighting schemes: three under Extended Implied Weighting, and one with equal weighting. The respective resulting topologies are compared in a sensitivity analysis framework. Our analyses support the paraphyly of Ptychoglossus, with Alopoglossus nested within it. We provide an updated classification for the family, where Ptychoglossus Boulenger, 1890 is considered a junior synonym of Alopoglossus Boulenger, 1885.

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“…This script considered 1,000 replicates with 10 repetitions of ratchet and drift [ 41 , 42 ] in constrained searches and the remaining default parameters. Finally, putative transformations for selected branches were compiled using the consensus tree obtained by TNT with YBYRÁ [ 47 ].…”

Section: Methodsmentioning

confidence: 99%

“…The first partition was analyzed in POY as described above and COI was only analyzed in TNT with the same settings as before. Selected clades were diagnosed using YBYRÁ [ 47 ] within each partition.…”

Section: Methodsmentioning

confidence: 99%

Systematics and diversification of Anindobothrium Marques, Brooks & Lasso, 2001 (Eucestoda: Rhinebothriidea)

2017

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Tapeworms of the genus Anindobothrium Marques, Brooks & Lasso, 2001 are found in both marine and Neotropical freshwater stingrays of the family Potamotrygonidae. The patterns of host association within the genus support the most recent hypothesis about the history of diversification of potamotrygonids, which suggests that the ancestor of freshwater lineages of the Potamotrygonidae colonized South American river systems through marine incursion events. Despite the relevance of the genus Anindobothrium to understand the history of colonization and diversification of potamotrygonids, no additional efforts were done to better investigate the phylogenetic relationship of this taxon with other lineages of cestodes since its erection. This study is a result of recent collecting efforts to sample members of the genus in marine and freshwater potamotrygonids that enabled the most extensive documentation of the fauna of Anindobothrium parasitizing species of Styracura de Carvalho, Loboda & da Silva, Potamotrygon schroederi Fernández-Yépez, P. orbignyi (Castelnau) and P. yepezi Castex & Castello from six different countries, representing the eastern Pacific Ocean, Caribbean Sea, and river basins in South America (Rio Negro, Orinoco, and Maracaibo). The newly collected material provided additional specimens for morphological studies and molecular samples for subsequent phylogenetic analyses that allowed us to address the phylogenetic position of Anindobothrium and provide molecular and morphological evidence to recognize two additional species for the genus. The taxonomic actions that followed our analyses included the proposition of a new family, Anindobothriidae fam. n., to accommodate the genus Anindobothrium in the order Rhinebothriidea Healy, Caira, Jensen, Webster & Littlewood, 2009 and the description of two new species—one from the eastern Pacific Ocean, A. carrioni sp. n., and the other from the Caribbean Sea, A. inexpectatum sp. n. In addition, we also present a redescription of the type species of the genus, A. anacolum (Brooks, 1977) Marques, Brooks & Lasso, 2001, and of A. lisae Marques, Brooks & Lasso, 2001. Finally, we discuss the paleogeographical events mostly linked with the diversification of the genus and the protocols adopted to uncover cryptic diversity in Anindobothrium.

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YBYRÁ facilitates comparison of large phylogenetic trees

Cited by 35 publications

References 14 publications

A total evidence analysis of the phylogeny of hatchet‐faced treefrogs (Anura: Hylidae: Sphaenorhynchus)

A total evidence analysis of the phylogeny of hatchet‐faced treefrogs (Anura: Hylidae: Sphaenorhynchus)

A species‐level total evidence phylogeny of the microteiid lizard family Alopoglossidae (Squamata: Gymnophthalmoidea)

Systematics and diversification of Anindobothrium Marques, Brooks & Lasso, 2001 (Eucestoda: Rhinebothriidea)

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