GUIDANCE: a web server for assessing alignment confidence scores

Penn, Osnat; Privman, Eyal; Ashkenazy, Haim; Landan, Giddy; Graur, Dan; Pupko, Tal

doi:10.1093/nar/gkq443

Cited by 572 publications

(425 citation statements)

References 26 publications

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“…The nucleotide sequences of each gene were aligned separately on the GUIDANCE web server (Penn et al., 2010) using the algorithm MAFFT (Katoh & Standley, 2013). In the alignment of the wsp gene, columns with GUIDANCE scores lower than 0.93 were considered to be unreliable and were removed.…”

Section: Methodsmentioning

confidence: 99%

Revisiting the phylogeny ofWolbachiain Collembola

Chen

et al. 2017

Ecology and Evolution

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The endosymbiont Wolbachia has been detected in a few parthenogenetic collembolans sampled in Europe and America, including three species of Poduromorpha, two species of Entomobryomorpha, and two species of Neelipleona. Based on 16S rRNA and ftsZ gene sequences, most of the Wolbachia infecting parthenogenetic collembolans were characterized as members of supergroup E and showed concordant phylogeny with their hosts. However, the two neelipleonan symbionts form another unique group, indicating that Wolbachia has infected parthenogenetic collembolans multiple times. In this study, five parthenogenetic collembolan species were identified as hosts of Wolbachia, and four new Wolbachia strains were reported for four collembolan species sampled in China, respectively, including a neelipleonan strain from Megalothorax incertus (wMinc). Our results demonstrated that the Wolbachia multilocus sequence typing (MLST) system is superior to the 16S rRNA + ftsZ approach for phylogenetic analyses of collembolan Wolbachia. The MLST system assigned these Wolbachia of parthenogenetic collembolans to supergroup E as a unique clade, which included wMinc, supporting the monophyletic origin of Wolbachia in parthenogenetic collembolan species. Moreover, our data suggested supergroup E as one of the most divergent lineages in Wolbachia and revealed the discrepancy between the phylogenies of Wolbachia from parthenogenetic collembolans and their hosts, which may result from the high level of genetic divergence between collembolan Wolbachia, in association with the geographic differentiation of their hosts, or the possible horizontal transmission of Wolbachia between different collembolan species.

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Section: Methodsmentioning

confidence: 99%

Revisiting the phylogeny ofWolbachiain Collembola

Chen

et al. 2017

Ecology and Evolution

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“…Both datasets were aligned using the stand-alone version of GUIDANCE (version 1.5, Penn et al, 2010) with the MAFFT multiple sequence alignment algorithm (version 7, Katoh and Standley, 2013). The following GUIDANCE parameters were used: GUIDANCE score algorithm; 100 bootstrap replicates; a sequence cutoff score of 0.0 (no sequence removal); a column cutoff score of 0.0 (no columns removal); global pair alignment.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): Defining modern subfamilies and tribes

Lopes‐Lima

Froufe

et al. 2017

Molecular Phylogenetics and Evolution

144

130

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a b s t r a c t Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problems and a lack of detailed ecological data. This highlights the urgent need for advances in the areas of systematics and evolutionary relationships within the Unionida. This study presents the most comprehensive phylogeny to date of the larger Unionida family, i.e., the Unionidae. The phylogeny is based on a combined dataset of 1032 bp (COI + 28S) of 70 species in 46 genera, with 7 of this genera being sequenced for the first time. The resulting phylogeny divided the Unionidae into 6 supported subfamilies and 18 tribes, three of which are here named for the first time (i.e., Chamberlainiini nomen novum, Cristariini nomen novum and Lanceolariini nomen novum). Molecular analyses were complemented by investigations of selected morphological, anatomical and behavioral characters used in traditional phylogenetic studies. No single morphological, anatomical or behavioral character was diagnostic at the subfamily level and few were useful at the tribe level. However, within subfamilies, many tribes can be recognized based on a subset of these characters. The geographical distribution of each of the subfamilies and tribes is also presented. The present study provides important advances in the systematics of these extraordinary taxa with implications for future ecological and conservation studies.

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“…Forward and reverse sequences were assembled and edited using Sequencher 4.01 (Gene Codes, Ann Arbor, MI, USA). Contigs were aligned using Clustal W (Larkin et al, 2007) and GUIDANCE (Penn et al, 2010), and the alignments obtained were manually refined using PhyDE (Müller et al, 2006). Regions of incomplete data at the 3 0 and 5 0 ends of the target loci were excluded from subsequent analyses.…”

Section: Taxon and Molecular Samplingmentioning

confidence: 99%

Is the sword moss (Bryoxiphium) a preglacial Tertiary relict?

Patiño

Goffinet

Sim‐Sim

et al. 2016

Molecular Phylogenetics and Evolution

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a b s t r a c tThe disjunction of floras between East Asia, Southeast North America, West North America, and Southwest Eurasia has been interpreted in terms of the fragmentation of a once continuous mixed mesophytic forest that occurred throughout the Northern Hemisphere due to the climatic and geological changes during the late Tertiary. The sword moss, Bryoxiphium, exhibits a distribution that strikingly resembles that of the mesophytic forest elements such as Liriodendron and is considered as the only living member of an early Tertiary flora in Iceland. These hypotheses are tested here using molecular dating analyses and ancestral area estimations. The results suggest that the extant range of Bryoxiphium results from the fragmentation of a formerly wider range encompassing North America and Southeast Asia about 10 million years ago. The split of continental ancestral populations is too recent to match with a continental drift scenario but is spatially and temporally remarkably congruent with that observed in Tertiary angiosperm relict species. The timing of the colonization of Iceland from Macaronesian ancestors, about two million years ago, is, however, incompatible with the hypothesis that Bryoxiphium is the only living member of an early Tertiary flora of the island. Alaska was recurrently colonized from East Asia. The ability of Bryoxiphium to overcome large oceanic barriers is further evidenced by its occurrence on remote oceanic archipelagos. In particular, Madeira was colonized twice independently from American and East Asian ancestors, respectively. The striking range disjunction of Bryoxiphium is interpreted in terms of its mating system, as the taxon exhibits a very singular pattern of spatial segregation of the sexes.

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GUIDANCE: a web server for assessing alignment confidence scores

Cited by 572 publications

References 26 publications

Revisiting the phylogeny ofWolbachiain Collembola

Revisiting the phylogeny ofWolbachiain Collembola

Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): Defining modern subfamilies and tribes

Is the sword moss (Bryoxiphium) a preglacial Tertiary relict?

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