Incorporating information from length-mutational events into phylogenetic analysis.

With the growing number of phylogenetic studies that use length variable DNA sequences, incorporating information from length-mutational events into phylogenetic analysis is becoming increasingly important. A new method, modified complex indel coding is described that aims at maximizing the phylogenetic information retained from unambiguously aligned sequence regions or regions where the principal relative position of gaps to one another can be safely established. An algorithm is described that allows application of the method to all theoretically possible gap-nucleotide patterns. A platform-independent computer program is introduced that automates the new method as well as several previously published coding schemes. Differences to previously published indel coding approaches as well as to the integration of ambiguously aligned regions into phylogenetic analysis are discussed.

[1]  I. Olivieri,et al.  Evolution of annual species of the genus Medicago: a molecular phylogenetic approach. , 1998, Molecular phylogenetics and evolution.

[2]  M T Clegg,et al.  Evolution of a noncoding region of the chloroplast genome. , 1993, Molecular phylogenetics and evolution.

[3]  Jerrold I. Davis,et al.  Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences. , 1998, Systematic biology.

[4]  Anders Gorm Pedersen,et al.  RevTrans: multiple alignment of coding DNA from aligned amino acid sequences , 2003, Nucleic Acids Res..

[5]  Mark P. Simmons,et al.  Gaps as characters in sequence-based phylogenetic analyses. , 2000, Systematic biology.

[6]  Olivier Poch,et al.  A comprehensive comparison of multiple sequence alignment programs , 1999, Nucleic Acids Res..

[7]  K. Müller,et al.  Characterisation of the Chloroplast DNA psbT‐H Region and the Influence of Dyad Symmetrical Elements on Phylogenetic Reconstructions , 2003 .

[8]  D. Geiger,et al.  Stretch Coding and Block Coding: Two New Strategies to Represent Questionably Aligned DNA Sequences , 2001, Journal of Molecular Evolution.

[9]  S. Kelchner,et al.  Hairpins create minute inversions in non-coding regions of chloroplast DNA , 1996, Current Genetics.

[10]  Makoto Kato,et al.  Evolution and phylogenetic utility of alignment gaps within intron sequences of three nuclear genes in bumble bees (Bombus). , 2003, Molecular biology and evolution.

[11]  Peter C. Hoch,et al.  A Phylogenetic Analysis of Epilobium (Onagraceae) Based on Nuclear Ribosomal DNA Sequences , 1994 .

[12]  W. Barthlott,et al.  Evolution of carnivory in Lentibulariaceae and the Lamiales. , 2004, Plant biology.

[13]  Burkhard Morgenstern,et al.  DIALIGN2: Improvement of the segment to segment approach to multiple sequence alignment , 1999, German Conference on Bioinformatics.

[14]  K. Müller.  SeqState: primer design and sequence statistics for phylogenetic DNA datasets. , 2005, Applied bioinformatics.

[15]  W C Wheeler,et al.  On gaps. , 1999, Molecular phylogenetics and evolution.

[16]  W. Wheeler,et al.  The Triangle Inequality and Character Analysis , 1993 .

[17]  R. Olmstead,et al.  Microstructural Changes in Noncoding Chloroplast DNA: Interpretation, Evolution, and Utility of Indels and Inversions in Basal Angiosperm Phylogenetic Inference , 2000, International Journal of Plant Sciences.

[18]  K. Müller,et al.  Phylogenetics of Utricularia (Lentibulariaceae) and molecular evolution of the trnK intron in a lineage with high substitutional rates , 2004, Plant Systematics and Evolution.

[19]  Michael S. Y. Lee.  Unalignable sequences and molecular evolution , 2001 .

[20]  Michael Brudno,et al.  Fast and sensitive multiple alignment of large genomic sequences , 2003, BMC Bioinformatics.

[21]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[22]  S. Kelchner.  Group II introns as phylogenetic tools: structure, function, and evolutionary constraints. , 2002, American journal of botany.

[23]  J. Braverman,et al.  Patterns and relative rates of nucleotide and insertion/deletion evolution at six chloroplast intergenic regions in new world species of the Lecythidaceae. , 2003, Molecular biology and evolution.

[24]  Elga,et al.  Incorporation , Relative Homoplasy , and Effect of Gap Characters in Sequence-Based Phylogenetic Analyses , 2001 .

[25]  K. Kjer,et al.  Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. , 1995, Molecular phylogenetics and evolution.

[26]  D. Ord,et al.  PAUP:Phylogenetic analysis using parsi-mony , 1993 .

[27]  Mark W. Chase,et al.  Analysis of Mitochondrial nad1b-c Intron Sequences in Orchidaceae: Utility and Coding of Length-change Characters , 2009 .

[28]  D. Maddison,et al.  NEXUS: an extensible file format for systematic information. , 1997, Systematic biology.

[29]  S. Kelchner,et al.  Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae). , 1997, Molecular phylogenetics and evolution.

[30]  Fixed Character States and the Optimization of Molecular Sequence Data , 1999 .

[31]  Lars Vogt.  Weighting indels as phylogenetic markers of 18S rDNA sequences in Diptera and Strepsiptera , 2002 .

[32]  W. Applequist,et al.  Deletions in the plastid trnT–trnL intergenic spacer define clades within Cactaceae subfamily Cactoideae , 2002, Plant Systematics and Evolution.

[33]  P. Wagner,et al.  Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. , 2000, Systematic biology.

[34]  V. Barriel,et al.  [Molecular phylogenies and nucleotide insertion-deletion]. , 1994, Comptes rendus de l'Academie des sciences. Serie III, Sciences de la vie.

[35]  H. Štorchová,et al.  Hairpins involving both inverted and direct repeats are associated with homoplasious indels in non-coding chloroplast DNA of Taraxacum (Lactuceae: Asteraceae). , 2000, Genome.

[36]  M. Simmons,et al.  The effects of increasing genetic distance on alignment of, and tree construction from, rDNA internal transcribed spacer sequences. , 2003, Molecular phylogenetics and evolution.

[37]  John Healy,et al.  GapCoder automates the use of indel characters in phylogenetic analysis , 2003, BMC Bioinformatics.

[38]  Robert R. Sokal,et al.  Advances in Cladistics, Proceedings of the First Meeting of the Willi Hennig Society , 1982 .

[39]  T. Borsch,et al.  Molecular evolution and phylogenetic utility of the petD group II intron: a case study in basal angiosperms. , 2005, Molecular biology and evolution.

[40]  S. Kelchner.  The Evolution of Non-Coding Chloroplast DNA and Its Application in Plant Systematics , 2000 .

[41]  Gary Benson,et al.  Reconstructing the Duplication History of a Tandem Repeat , 1999, ISMB.

[42]  V. Barriel,et al.  Phylogénies moléculaires et insertions-délétions de nucléotides , 1994 .

[43]  Gary Benson.  Sequence Alignment with Tandem Duplication , 1997, J. Comput. Biol..