Creating the CIPRES Science Gateway for inference of large phylogenetic trees

Miller, Mark A.; Pfeiffer, Wayne; Schwartz, Terri

doi:10.1109/gce.2010.5676129

Cited by 9,428 publications

(6,938 citation statements)

References 12 publications

Supporting

Mentioning

6,891

Contrasting

Unclassified

Order By: Relevance

“…For maximum likelihood, we used RAxML-VI-HPC2 v7.2.7 on teragrid at the CIPRES Science Gateway (www.phylo.org) 19,42 . For each data set, analyses were conducted using 100 alternative runs with nonparametric bootstrap analysis (500 replicates) used to provide branch support values for the most likely tree.…”

Section: Methodsmentioning

confidence: 99%

Dynamic evolution of venom proteins in squamate reptiles

2012

View full text Add to dashboard Cite

Phylogenetic analyses of toxin gene families have revolutionised our understanding of the origin and evolution of reptile venoms, leading to the current hypothesis that venom evolved once in squamate reptiles. However, because of a lack of homologous squamate non-toxin sequences, these conclusions rely on the implicit assumption that recruitments of protein families into venom are both rare and irreversible. Here we use sequences of homologous non-toxin proteins from two snake species to test these assumptions. Phylogenetic and ancestral-state analyses revealed frequent nesting of 'physiological' proteins within venom toxin clades, suggesting early ancestral recruitment into venom followed by reverse recruitment of toxins back to physiological roles. These results provide evidence that protein recruitment into venoms from physiological functions is not a one-way process, but dynamic, with reversal of function and/or co-expression of toxins in different tissues. This requires a major reassessment of our previous understanding of how animal venoms evolve.

show abstract

Section: Methodsmentioning

confidence: 99%

Dynamic evolution of venom proteins in squamate reptiles

2012

View full text Add to dashboard Cite

show abstract

“…Nucleotide sequences were translated into amino acids, imported into the CIPRES Science Gateway 45 and aligned using the E-INS-i search strategy in MAFFT 46 . Alignments were converted into relaxed phylip format.…”

Section: Identification and Phylogenetic Analysis Of Nbs-lrr Genesmentioning

confidence: 99%

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

et al. 2013

View full text Add to dashboard Cite

“…All Bayesian and ML analyses were run in the Cyberinfrastructure for Phylogenetic Research (Cipres Science Gateway; Miller et al, 2010). All MP strict consensus trees, ML trees, and Bayesian 50% majority-rule consensus trees were visualized and partially edited in FigTree v.1.4 (Rambaut, 2012).…”

Section: Alignment and Phylogenetic Analysesmentioning

confidence: 99%

A molecular phylogeny reveals the Cuban enigmatic genus Behaimia as a new piece in the Brongniartieae puzzle of papilionoid legumes

Queiroz

São-Mateus

Delgado‐Salinas

et al. 2017

Molecular Phylogenetics and Evolution

View full text Add to dashboard Cite

This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. E-mail address: luciano.paganucci@gmail.com (L.P. de Queiroz). ABSTRACTThe papilionoid legume tribe Brongniartieae comprises a collection of 13 genera with disparate morphologies that were previously positioned in at least three remotely related tribes. The Brongniartieae displays a wide geographical disjunction between Australia and the New World and previous phylogenetic studies had provided conflicting results about the relationships between the American and Australian genera. We carry out phylogenetic analyses of (1) a plastid matK dataset extensively sampled across legumes to solve the enigmatic relationship of the Cuban-endemic monospecific genus Behaimia; and (2) multilocus datasets with focus on all genera ever referred toBrongniartieae. These analyses resulted in a well-resolved and strongly-supported phylogenetic tree of the Brongniartieae. Increased molecular sampling in papilionoid legume phylogeny has dramatically changed our understanding of the evolution and taxonomic classification in this species rich lineage of economically and ecologically important legumes (family Leguminosae).The prevailing traditional hypotheses of generic relationships assumed that the papilionate flower would be a signature of the most "derived" groups, whereas the more caesalpinioid and mimosoid-like floral organizations, involving undifferentiated petals and free stamens, marked mostly the "primitive" tribes within the subfamily Papilionoideae (Polhill, 1981a). Hence, such an evolutionary perspective has largely influenced the way in which the modern subfamily, tribe, and even genus-level classification of legumes was built (LPWG, 2013(LPWG, , 2017. In the past 15 years, molecular phylogenetic studies have underpinned dramatic taxonomic changes after revealing unexpected relationships, suggesting that floral architecture is relatively labile in the early-branching papilionoid lineages (e.g. Pennington et al., 2001;Wojciechowski et al., 2004; Cardoso et al., 2012aCardoso et al., , 2013aCardoso et al., , 2015Ramos et al., 2016).The recent examples of broad phylogenetic re-alignments that were unexpectedly revealed in the early-branching genera of Papilionoideae (Cardoso et al., 2012a(Cardoso et al., , 2012b(Cardoso et al., , 2012c(Cardoso et al., , 2013a(Cardoso et al., , 2017Ramos et al., 2016; Castellanos et al., in press) are not an exception across legumes. For example, dramatic shuffling in the placement of genera has also been necessary within the species-rich canavanine-accumulating clade (Wojciechowski et al., 2004;Silva et al., 2012;Sirichamorn et al., ...

show abstract

Creating the CIPRES Science Gateway for inference of large phylogenetic trees

Cited by 9,428 publications

References 12 publications

Dynamic evolution of venom proteins in squamate reptiles

Dynamic evolution of venom proteins in squamate reptiles

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

A molecular phylogeny reveals the Cuban enigmatic genus Behaimia as a new piece in the Brongniartieae puzzle of papilionoid legumes

Contact Info

Product

Resources

About