Local search for the generalized tree alignment problem

Varón, Andrés; Wheeler, Ward C.

doi:10.1186/1471-2105-14-66

Cited by 18 publications

(10 citation statements)

References 32 publications

(43 reference statements)

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“…(; see also Kluge and Grant, ; Grant and Kluge, ), we employed direct optimization (e.g. Sankoff, ; Wheeler, ; Varón and Wheeler, , ) in the program POY v.5.1.1 (Wheeler et al., ), which tests hypotheses of nucleotide homology dynamically by optimizing unaligned DNA sequences directly onto alternative topologies (Kluge and Grant, ; Wheeler et al., ; Grant and Kluge, ) while simultaneously optimizing prealigned transformation series (e.g. morphology) as standard matrices.…”

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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“…direct optimization or dynamic homology; e.g. Sankoff, ; Wheeler, ; Varón and Wheeler, , ). The method tested hypotheses of nucleotide homology dynamically by optimizing unaligned DNA sequences directly onto alternative topologies (Kluge and Grant, ; Wheeler et al., ; Grant and Kluge, ) while simultaneously optimizing prealigned transformation series as standard static matrices.…”

Section: Methodsmentioning

confidence: 99%

Phylogeny of Riama (Squamata: Gymnophthalmidae), impact of phenotypic evidence on molecular datasets, and the origin of the Sierra Nevada de Santa Marta endemic fauna

et al. 2017

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Riama is the most speciose genus of the Neotropical lizard family Gymnophthalmidae. Its more than 30 montane species occur throughout the northern Andes, the Cordillera de la Costa (CC) in Venezuela, and Trinidad. We present the most comprehensive phylogenetic analysis of Riama to date based on a total evidence (TE) approach and direct optimization of molecular and morphological evidence. Analyses use DNA sequences from four loci and 35 phenotypic characters. The dataset consists of 55 ingroup terminals representing 25 of the 30 currently recognized species of Riama plus five undescribed taxa, including an endemic species from the Sierra Nevada de Santa Marta (SNSM) in Colombia, and 66 outgroup terminals of 47 species. Analysis results in a well-supported hypothesis in which Riama is polyphyletic, with its species falling into three clades. The Tepuian Anadia mcdiarmidi nests within one clade of Riama, and the recently resurrected Pantodactylus nests within Cercosaura. Accordingly, we propose a monophyletic taxonomy that reflects historical relationships. Analysis of character evolution indicates that the presence/absence of prefrontals-a cornerstone of the early genus-level taxonomy of cercosaurines-is optimally explained as having been plesiomorphically present in the most recent common ancestor of Cercosaurinae and lost in that of the immediately less inclusive clade. Multiple independent reversals to present and subsequent returns to absent occur within this clade. To evaluate the impact of phenotypic evidence on our results, we compare our TE results with results obtained from analyses using only molecular data. Although phenotypic evidence comprises only 1.2% of the TE matrix, its inclusion alters both the topology and support values of the clades that do not differ. Finally, current phylogenetic evidence reveals a SNSM-CC-Trinidad-tepuis biogeographical link. We hypothesize that an ancient connection facilitated the exchange of species between the SNSM and the CC.

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“…Parsimony jackknife absolute frequencies (Farris et al, 1996) were estimated using new technology requesting 10 hits with driven searches under search level 15, for a total of 1,000 replicates. Alignment files were merged and exported in different formats using SequenceMatrix (Vaidya et al, 2011). Trees were edited with FigTree (Rambaut, 2014).…”

Section: Phylogenetic Analysismentioning

confidence: 99%

On the Monophyly and Relationships of Several Genera of Hylini (Anura: Hylidae: Hylinae), with Comments on Recent Taxonomic Changes in Hylids

Faivovich

Pereyra

Luna

et al. 2018

South American Journal of Herpetology

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We present a molecular phylogenetic analysis of the hylid tribe Hylini, with the goals of testing the monophyly of the genera Duellmanohyla, Isthmohyla, and Ptychohyla and providing a discussion on the monophyly of Bromeliohyla, Charadrahyla, Ecnomiohyla, Exerodonta, Megastomatohyla, and Sarcohyla. Our results indicate the paraphyly of Ptychohyla, with Bromeliohyla and Duellmanohyla nested within it, and, as in previous analyses, the paraphyly of Duellmanohyla (due to Ptychohyla legleri and P. salvadorensis being nested within it). To resolve this situation, we restrict the contents of Ptychohyla, redelimit those of Duellmanohyla and Bromeliohyla, and erect two new genera, one to include the former Ptychohyla panchoi and P. spinipollex, and the other for the former Ptychohyla acrochorda, P. sanctaecrucis, P. zoque, and tentatively, P. erythromma. Exerodonta as currently defined is not monophyletic, inasmuch as Exerodonta juanitae is nested within Charadrahyla. Consequently, we transfer this species and, tentatively, E. pinorum to Charadrahyla. Also, we discuss some possible taxonomic problems within Exerodonta. Our results indicate that Isthmohyla is polyphyletic, the bromeliad-dwelling Isthmohyla melacaena being the sister taxon of our only exemplar of Bromeliohyla, B. bromeliacia. For this reason, we transfer I. melacaena to Bromeliohyla, rendering Isthmohyla monophyletic. The former Isthmohyla pictipes Group is shown to be paraphyletic due to having the non-monophyletic I. pseudopuma Group within it. Accordingly, we recognize a redelimited I. pseudopuma Group (contents: I. infucata and I. pseudopuma), an I. zeteki Group (contents: I. picadoi and I. zeteki), and a newly defined I. tica Group (contents: I. angustilineata, I. calypsa, I. debilis, I. graceae, I. lancasteri, I. pictipes, I. tica, I. rivularis, and, tentatively, I. insolita and I. xanthosticta). The three groups of Isthmohyla are supported by molecular evidence with jackknife support values > 90%, and two of them by putative morphological synapomorphies. We discuss the recognition of Dryophytes, Hyliola, Rheohyla, and Sarcohyla and whether it is useful to recognize Anotheca, Diaglena, and Triprion as three distinct, monotypic genera. Finally, we discuss a recent taxonomic proposal involving changes in rank and from ranked to unranked names in hylids that overall we consider to have been poorly justified and only superficially discussed.

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Local search for the generalized tree alignment problem

Cited by 18 publications

References 32 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)

Phylogeny of Riama (Squamata: Gymnophthalmidae), impact of phenotypic evidence on molecular datasets, and the origin of the Sierra Nevada de Santa Marta endemic fauna

On the Monophyly and Relationships of Several Genera of Hylini (Anura: Hylidae: Hylinae), with Comments on Recent Taxonomic Changes in Hylids

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