Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology.

By F. Lutzoni, P. Wagner, Valérie Reeb, Stefan Zoller. Systematic Biology, 2000

380 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/b2e29006d155a5b223481b6f332a323f017d20d3

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Citations in the corpus

Phylogenetic Relationships and Evolution of Extant Horsetails, Equisetum, Based on Chloroplast DNA Sequence Data (rbcL and trnL‐F) (2003, methodology): “Ambiguously aligned regions (e.g., regions of uncertain homology among taxa) of the trnL intron and trnL-F spacer were delimited following the method of Lutzoni et al. (2000).”
Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA (2006, methodology): “F or p er so na l u se o nl y. ANRV292-ES37-20 ARI 17 October 2006 7:32 information in indels has been quantified separately and added into phylogenetic analyses later (Kjer et al. 2001, Lutzoni et al. 2000).”
Tribal phylogenetic relationships within Vespertilioninae (Chiroptera: Vespertilionidae) based on mitochondrial and nuclear sequence data (2010, methodology): “Regions appearing to violate the assumption of positional homology were recognized and excluded from phylogenetic analyses based on the procedures of Lutzoni et al. (2000).”
Most species of Lepraria and Leproloma form a monophyletic group closely related to Stereocaulon (2002, methodology): “Parsimony-based methods have been described that could potentially overcome part of the problem (e.g. Wheeler 1999, Lutzoni et al. 2000 ).”
A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion. (2009, methodology): “To test ALISCORE’s performance on real data, we used the original concatenated data (18S + 28S recombinant DNA) of Mallatt et al. (2004). The complete data without anymodifications were used as provided by the authors (http://chuma.”
Phylogenetic analysis of morphology in Prunus reveals extensive homoplasy (2006, methodology): “Because some regions of ITS are highly divergent at the generic level in Rosaceae we also explored the use of the approach described by Lutzoni et al. (2000) and implemented in their software INAASE.”
GapCoder automates the use of indel characters in phylogenetic analysis (2003, methodology): “The third method to be considered is the multistate gap region method [4,18–20].”
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. (2007, background): “A third, intermediate option, is the recoding of such regions us-ing different strategies (Geiger, 2002; Lutzoni et al., 2000; Young and Healy, 2003), which allows the use of at least part of the information.”
Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. (2004, methodology): “Alignments of nucSSU, nucLSU, and mitSSU rDNA sequences and delimitation of ambiguously aligned regions were done accordingly to Lutzoni et al. (2000) and Reeb et al. (2004) using the secondary structure model (Kjer, 1995) of Saccharomyces cerevisiae (U53879, V00704, X07799, X07800, X14966)…”
Phylogenetic Revision of the Genus Peltigera (Lichen‐Forming Ascomycota) Based on Morphological, Chemical, and Large Subunit Nuclear Ribosomal DNA Data (2000, methodology): “The secondary structure of the LSU nrDNA of Saccharomyces cerevisiae (Larsen et al. 1993) was used to verify the alignment and to provide an additional criterion to delimit ambiguously aligned regions (Lutzoni et al. 2000).”
A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales (2009, methodology): “Ambiguously-aligned regions were recoded using INAASE v3.0 ( Lutzoni et al., 2000 ), and were reintegrated as new characters as outlined by Reeb et al. (2004) and Gaya et al. (2008).”
Molecular Evidence for the Major Clades of Placental Mammals (2001, methodology): “Ambiguously aligned regions of the 12S rRNA-tRNA valine-16S rRNA alignment were excluded from phylogenetic analyses following Madsen et al. (2001) [see Wheeler et al. (1995) and Lutzoni et al. (2000) for alternate strategies to deal with ambiguously aligned regions].”
Phylogeny and biogeography of the ant subfamily Myrmeciinae (Hymenoptera: Formicidae) (2003, neutral): “Although some useful information is undoubtedly discarded by this exclusion procedure (Lee 2001a), such a conservative approach reduces the chances of spurious homology assignment due to alignment errors in hypervariable regions (Lutzoni 1997; Lutzoni et al. 2000).”
Phylogeny of caddisflies (Insecta, Trichoptera) (2002, methodology): “With a fauna of some 10 000 described extant species, distributed among 45 families (Morse 1997a), the order is diverse in terms of the microhabitats and trophic niches occupied by the species (Mackay & Wiggins 1979). We collected sequence data and re-evaluated a morphological dataset from Frania & ”
Relationships among the major lineages of Dictyoptera: the effect of outgroup selection on dictyopteran tree topology (2008, methodology): “…as the most accurate method available for aligning ribosomal data (Ellis & Morrison, 1995; Kjer, 1995, 2004; Hickson et al., 1996, 2000; Titus & Frost, 1996; Morrison & Ellis, 1997; Lutzoni et al., 2000; Mugridge et al., 2000; Gillespie et al., 2005; Deans et al., 2006; Morse & Normark, 2006).”