<i>MonoPhy</i>: a simple R package to find and visualize monophyly issues

Schwery, Orlando; O’Meara, Brian C.

doi:10.7717/peerj-cs.56

Cited by 32 publications

(8 citation statements)

References 24 publications

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“…We inspected the initial Sanger phylogeny to identify any remaining rogues or names that needed updating in the taxonomic database. We checked for monophyly at taxonomic levels at or above genus using the MonoPhy R package v1.3 ( Schwery and O’Meara, 2016 ). We updated our taxonomic database if the molecular data clearly indicated the current usage of a synonym was incorrect (e.g., a taxonomic intruder into an otherwise expected monophyletic genus with a synonym available for that genus; expected monophyly follows Pteridophyte Phylogeny Group I, 2016 ).…”

Section: Methodsmentioning

confidence: 99%

An open and continuously updated fern tree of life

et al. 2022

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Ferns, with about 12,000 species, are the second most diverse lineage of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated. Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use a curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification. The current FTOL includes 5,582 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 51 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies. FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anyone studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.

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Section: Methodsmentioning

confidence: 99%

An open and continuously updated fern tree of life

et al. 2022

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“…We applied phylocom's bladj() function (Webb, Ackerly, & Kembel, 2008) to the Raxml phylogeny based on 36 fossil calibration dates (Bell, Soltis, & Soltis, 2010;Gastauer & Meira-Neto, 2016). We used the R package monophy (Schwery & O'Meara, 2016) to test the monophyly of genera. For this analysis, we maintained supported nodes and collapsed unsupported nodes (bootstrap support <63) to polytomies (Farris, Albert, Kallersjo, Lipscomb, & Kluge, 1996).…”

Section: Estimation Of Community Phylogenymentioning

confidence: 99%

Plant DNA‐barcode library and community phylogeny for a semi‐arid East African savanna

Gill

Musili

Kurukura

et al. 2019

Molecular Ecology Resources

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Applications of DNA barcoding include identifying species, inferring ecological and evolutionary relationships between species, and DNA metabarcoding. These applications require reference libraries that are not yet available for many taxa and geographic regions. We collected, identified, and vouchered plant specimens from Mpala Research Center in Laikipia, Kenya, to develop an extensive DNA‐barcode library for a savanna ecosystem in equatorial East Africa. We amassed up to five DNA barcode markers (rbcL, matK, trnL‐F, trnH–psbA, and ITS) for 1,781 specimens representing up to 460 species (~92% of the known flora), increasing the number of plant DNA barcode records for Africa by ~9%. We evaluated the ability of these markers, singly and in combination, to delimit species by calculating intra‐ and interspecific genetic distances. We further estimated a plant community phylogeny and demonstrated its utility by testing if evolutionary relatedness could predict the tendency of members of the Mpala plant community to have or lack “barcode gaps”, defined as disparities between the maximum intra‐ and minimum interspecific genetic distances. We found barcode gaps for 72%–89% of taxa depending on the marker or markers used. With the exception of the markers rbcL and ITS, we found that evolutionary relatedness was an important predictor of barcode‐gap presence or absence for all of the markers in combination and for matK, trnL‐F, and trnH–psbA individually. This plant DNA barcode library and community phylogeny will be a valuable resource for future investigations.

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“…We inspected the initial Sanger phylogeny to identify any remaining rogues or names that needed updating in the taxonomic database. We checked for monophyly at taxonomic levels at or above genus using the MonoPhy R package v1.3 (Schwery and O’Meara, 2016). We updated our taxonomic database if the molecular data clearly indicated the current usage of a synonym was incorrect ( e.g ., a taxonomic intruder into an otherwise expected monophyletic genus with a synonym available for that genus; expected monophyly follows PPG I, 2016).…”

Section: Methodsmentioning

confidence: 99%

An Open and Continuously Updated Fern Tree of Life

Nitta

Schuettpelz

Ramírez‐Barahona

et al. 2022

Preprint

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Ferns, with about 12,000 species, are the second most diverse clade of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated. Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use an curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification. The current FTOL includes 5,563 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 65 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies. FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anybody studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.

show abstract

MonoPhy: a simple R package to find and visualize monophyly issues

Cited by 32 publications

References 24 publications

An open and continuously updated fern tree of life

An open and continuously updated fern tree of life

Plant DNA‐barcode library and community phylogeny for a semi‐arid East African savanna

An Open and Continuously Updated Fern Tree of Life

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