Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

Letunić, Ivica; Bork, Peer

doi:10.1093/nar/gkw290

Cited by 4,411 publications

(3,565 citation statements)

References 15 publications

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“…The outer ring of colored circles refers to habitat preferences: blue, lentic; green, lotic; yellow, cave; red, burrow. Figure was created using iTOL version 3 (Letunic and Bork 2016). …”

Section: Resultsmentioning

confidence: 99%

Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead‐end

et al. 2017

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Caves are perceived as isolated, extreme habitats with a uniquely specialized biota, which long ago led to the idea that caves are “evolutionary dead‐ends.” This implies that cave‐adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independently evolved cave‐dwelling groups. Here, we use the freshwater crayfish, a group with dozens of cave‐dwelling species in multiple lineages, as a system to test this hypothesis. We consider historical patterns of lineage diversification and habitat transition as well as current patterns of geographic range size. We find that while cave‐dwelling lineages have small relative range sizes and rarely transition back to the surface, they exhibit remarkably similar diversification patterns to those of other habitat types and appear to be able to maintain a diversity of lineages through time. This suggests that cave adaptation is not a “dead‐end” for freshwater crayfish, which has positive implications for our understanding of biodiversity and conservation in cave habitats.

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“…The outer ring of colored circles refers to habitat preferences: blue, lentic; green, lotic; yellow, cave; red, burrow. Figure was created using iTOL version 3 (Letunic and Bork 2016). …”

Section: Resultsmentioning

confidence: 99%

Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead‐end

et al. 2017

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“…UPGMA trees were calculated in Geneious R9 (Kearse et al., 2012). The RAxML BlackBox Web server was used to run ML analysis with default settings (Stamatakis, Hoover, & Rougemont, 2008), and trees were uploaded to iTOL for annotation (Letunic & Bork, 2016). The Eurasian white oaks ( Q. petraea , Q. robur , Q. fabri , and Q. aliena ) were used to root the ML tree for purposes of visualization.…”

Section: Methodsmentioning

confidence: 99%

A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

Fitzek

Delcamp

Guichoux

et al. 2018

Ecology and Evolution

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DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restrictionsite‐associated DNA sequencing (RAD‐seq) to develop an economical single nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with postclustering bioinformatic tools to generate a list of 291 potential SNPs, 80 of which were included in a barcoding toolkit that is easily implemented using MassARRAY mass spectrometry technology. As a proof‐of‐concept, we used the genotyping toolkit to infer potential hybridization between North American white oaks transplanted outside of their native range (Q. michauxii, Q. montana, Q muehlenbergii/Q. prinoides, and Q. stellata) into a horticultural collection surrounded by natural forests of locally native trees (Q. alba and Q. macrocarpa) in the living collection at The Morton Arboretum (Lisle, IL, USA). Phylogenetic and clustering analyses suggested low rates of hybridization between cultivated and native species, with the exception of one Q. michauxii mother tree, the acorns of which exhibited high admixture from either Q. alba or Q. stellata and Q. macrocarpa, and a hybrid between Q. stellata that appears to have backcrossed almost exclusively to Q. alba. Together, RAD‐seq and MassARRAY technologies allow for efficient development and implementation of a multispecies barcode for one of the more challenging forest tree genera.

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“…Phylogenetic trees were generated from alignments using 1,000 ultrafast bootstrap iterations. The Fad tree was visualized using Figtree (v1.4.3) (http://tree.bio.ed.ac.uk/software/figtree/), and the Elovl tree was visualized using Interactive Tree Of Life (v3) (Letunic & Bork, 2016). …”

Section: Methodsmentioning

confidence: 99%

Insights into the phylogenetic and molecular evolutionary histories of Fad and Elovl gene families in Actiniaria

Surm

Toledo

Prentis

et al. 2018

Ecology and Evolution

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The biosynthesis of long‐chain polyunsaturated fatty acids (LC‐PUFAs, ≥ C20) is reliant on the action of desaturase and elongase enzymes, which are encoded by the fatty acyl desaturase (Fad) and elongation of very long‐chain fatty acid (Elovl) gene families, respectively. In Metazoa, research investigating the distribution and evolution of these gene families has been restricted largely to Bilateria. Here, we provide insights into the phylogenetic and molecular evolutionary histories of the Fad and Elovl gene families in Cnidaria, the sister phylum to Bilateria. Four model cnidarian genomes and six actiniarian transcriptomes were interrogated. Analysis of the fatty acid composition of a candidate cnidarian species, Actinia tenebrosa, was performed to determine the baseline profile of this species. Phylogenetic analysis revealed lineage‐specific gene duplication in actiniarians for both the Fad and Elovl gene families. Two distinct cnidarian Fad clades clustered with functionally characterized Δ5 and Δ6 proteins from fungal and plant species, respectively. Alternatively, only a single cnidarian Elovl clade clustered with functionally characterized Elovl proteins (Elovl4), while two additional clades were identified, one actiniarian‐specific (Novel ElovlA) and the another cnidarian‐specific (Novel ElovlB). In actiniarians, selection analyses revealed pervasive purifying selection acting on both gene families. However, codons in the Elovl gene family show patterns of nucleotide variation consistent with the action of episodic diversifying selection following gene duplication events. Significantly, these codons may encode amino acid residues that are functionally important for Elovl proteins to target and elongate different precursor fatty acids. In A. tenebrosa, the fatty acid analysis revealed an absence of LC‐PUFAs > C20 molecules and implies that the Elovl enzymes are not actively contributing to the elongation of these LC‐PUFAs. Overall, this study has revealed that actiniarians possess Fad and Elovl genes required for the biosynthesis of some LC‐PUFAs, and that these genes appear to be distinct from bilaterians.

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Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

Cited by 4,411 publications

References 15 publications

Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead‐end

Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead‐end

A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

Insights into the phylogenetic and molecular evolutionary histories of Fad and Elovl gene families in Actiniaria

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