Gaps as characters in sequence-based phylogenetic analyses.

By Mark P. Simmons, H. Ochoterena. Systematic Biology, 2000

2,571 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Paleontology

View Paper: https://www.semanticscholar.org/paper/240d27a99d634528e10a25e323955882a0b65572

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In Ecology, Evolution, Behavior and Systematics

In Paleontology

Citations in the corpus

A novel phylogeny-based generic classification for Chenopodium sensu lato, and a tribal rearrangement of Chenopodioideae (Chenopodiaceae) (2012, methodology): “2003; müller & Borsch 2005). the trnL-F and matK/trnK data sets were combined for phylogenetic analysis. indels were coded with the Simple indel coding method (Simmons & ochoterena 2000) using the program Seq State 1.40 (müller 2005a).”
FastML: a web server for probabilistic reconstruction of ancestral sequences (2012, methodology): “To account for the dependence of insertions and deletions among sites, the FastML server ﬁrst employs the simple indel coding scheme (17) to code all indels in the data as binary (presence\absence) characters, each of which may represent a gap of multiple sites.”
Phylogeny of Nymphaea (Nymphaeaceae): Evidence from Substitutions and Microstructural Changes in the Chloroplast trnT‐trnF Region (2007, methodology): “To overcome this, Simmons and Ochoterena (2000) suggested calculating stepwise matrices that consider the stepwise mutational process and applying a parsimony principle to reconstruct the simplest sequence of mutational steps, a concept recently extended and incorporated into software by Müller…”
A comprehensive phylogeny of the bumble bees (Bombus) (2007, methodology): “Gap regions of unambiguous alignment were coded as separate binary characters following the methods of Simmons & Ochoterena (2000) and Simmons, Ochoterena & Carr (2001), incorporating only the regions that were parsimony informative in collective analyses.”
Phylogeny and Systematics of Lemnaceae, the Duckweed Family (2009, methodology): “This procedure is similar to the ‘‘simple indel coding’’ method of Simmons and Ochoterena (2000).”
A new subfamilial and tribal classification of the pantropical flowering plant family Annonaceae informed by molecular phylogenetics (2012, positive): “Gaps in the alignment shared by two or more taxa were coded as a single binary character (presence/absence) according to the simple indel coding method of Simmons & Ochoterena (2000).”
Morphology, phylogeny and taxonomy of South American bothropoid pitvipers (Serpentes, Viperidae) (2012, methodology): “Gaps were treated as a fifth state, instead of missing data, as they can carry useful phylogenetic information (Simmons & Ochoterena 2000; Ogden & Rosenberg 2007; Simmons et al. 2008).”
Phylogenetic relationships in subtribe Poinae (Poaceae, Poeae) based on nuclear ITS and plastid trnT-trnL-trnF sequences (2008, methodology): “Unambiguous parsimony informative insertions and deletions (indels) were coded as separate presence/absence characters using the simple indel coding method of Simmons and Ochoterena (2000) , with overlapping indels coded as in Graham et al. (2000).”
Systematics of Pipevines: Combining Morphological and Fast‐Evolving Molecular Characters to Investigate the Relationships within Subfamily Aristolochioideae (Aristolochiaceae) (2006, methodology): “Thereafter, indels were automatically coded employing the simple indel coding algorithm (SIC) (Simmons and Ochoterena 2000), via SeqState (Müller 2005) using the PhyDeplugin option.”
Phylogeny and Biogeography of Cercis (Fabaceae): Evidence from Nuclear Ribosomal ITS and Chloroplast ndhF Sequence Data (2009, methodology): “…positions were treated as missing by PAUP*, but we included potentially parsimony-informative indels in the analyses as binary characters, following the reasoning of Simmons and Ochoterena (2000) that we implemented by using a gap-coding script distributed by R. Ree (Harvard University Herbaria).”