Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 14-Day Trial for You or Your Team.

Learn More →

Molecular homology and multiple-sequence alignment: an analysis of concepts and practice

Molecular homology and multiple-sequence alignment: an analysis of concepts and practice Sequence alignment is just as much a part of phylogenetics as is tree building, although it is often viewed solely as a necessary tool to construct trees. However, alignment for the purpose of phylogenetic inference is primarily about homology, as it is the procedure that expresses homology relationships among the characters, rather than the historical relationships of the taxa. Molecular homology is rather vaguely defined and understood, despite its importance in the molecular age. Indeed, homology has rarely been evaluated with respect to nucleotide sequence alignments, in spite of the fact that nucleotides are the only data that directly represent genotype. All other molecular data represent phenotype, just as do morphology and anatomy. Thus, efforts to improve sequence alignment for phylogenetic purposes should involve a more refined use of the homology concept at a molecular level. To this end, we present examples of molecular-data levels at which homology might be considered, and arrange them in a hierarchy. The concept that we propose has many levels, which link directly to the developmental and morphological components of homology. Of note, there is no simple relationship between gene homology and nucleotide homology. We also propose terminology with which to better describe and discuss molecular homology at these levels. Our over-arching conceptual framework is then used to shed light on the multitude of automated procedures that have been created for multiple-sequence alignment. Sequence alignment needs to be based on aligning homologous nucleotides, without necessary reference to homology at any other level of the hierarchy. In particular, inference of nucleotide homology involves deriving a plausible scenario for molecular change among the set of sequences. Our clarifications should allow the development of a procedure that specifically addresses homology, which is required when performing alignment for phylogenetic purposes, but which does not yet exist. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Australian Systematic Botany CSIRO Publishing

Molecular homology and multiple-sequence alignment: an analysis of concepts and practice

Download PDF
17 pages

Loading next page...
 
/lp/csiro-publishing/molecular-homology-and-multiple-sequence-alignment-an-analysis-of-N1GTUTOJ6R

References

References for this paper are not available at this time. We will be adding them shortly, thank you for your patience.

Publisher
CSIRO Publishing
Copyright
Copyright © The Author(s). Published by CSIRO Publishing
ISSN
1030-1887
eISSN
1446-4701
DOI
10.1071/SB15001
Publisher site
See Article on Publisher Site

Abstract

Sequence alignment is just as much a part of phylogenetics as is tree building, although it is often viewed solely as a necessary tool to construct trees. However, alignment for the purpose of phylogenetic inference is primarily about homology, as it is the procedure that expresses homology relationships among the characters, rather than the historical relationships of the taxa. Molecular homology is rather vaguely defined and understood, despite its importance in the molecular age. Indeed, homology has rarely been evaluated with respect to nucleotide sequence alignments, in spite of the fact that nucleotides are the only data that directly represent genotype. All other molecular data represent phenotype, just as do morphology and anatomy. Thus, efforts to improve sequence alignment for phylogenetic purposes should involve a more refined use of the homology concept at a molecular level. To this end, we present examples of molecular-data levels at which homology might be considered, and arrange them in a hierarchy. The concept that we propose has many levels, which link directly to the developmental and morphological components of homology. Of note, there is no simple relationship between gene homology and nucleotide homology. We also propose terminology with which to better describe and discuss molecular homology at these levels. Our over-arching conceptual framework is then used to shed light on the multitude of automated procedures that have been created for multiple-sequence alignment. Sequence alignment needs to be based on aligning homologous nucleotides, without necessary reference to homology at any other level of the hierarchy. In particular, inference of nucleotide homology involves deriving a plausible scenario for molecular change among the set of sequences. Our clarifications should allow the development of a procedure that specifically addresses homology, which is required when performing alignment for phylogenetic purposes, but which does not yet exist.

Journal

Australian Systematic Botany – CSIRO Publishing

Published: Sep 10, 2015

References

  • Developmental genetics and homology: a hierarchical approach.
    Abouheif E
  • Quantitative tests of primary homology.
    Agnarsson I Coddington JA
  • Evolution of protein indels in plants, animals and fungi.
    Ajawatanawong P Baldauf SL
  • Issues in bioinformatics benchmarking: the case study of multiple sequence alignment.
    Aniba MR Poch O Thompson JD
  • Finding the balance between the mathematical and biological optima in multiple sequence alignment.
    Anisimova M Cannarozzi GM Liberles DA
  • StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction.
    Arunapuram P Edvardsson I Golden M Anderson JWJ Novak Á Sükösd Z Hein J
  • Are homology and synapomorphy the same or different?
    Assis LCS
  • Homology assessment in parsimony and model-based analyses: two sides of the same coin.
    Assis LCS
  • Combining evidence using P -values: application to sequence homology searches.
    Bailey TL Gribskov M
  • The potential value of indels as phylogenetic markers: position of trichomonads as a case study.
    Bapteste E Philippe H
  • Networks: expanding evolutionary thinking.
    Bapteste E van Iersel L Janke A Kelchner S Kelk S McInerney JO Morrison DA Nakhleh L Steel M Stougie L Whitfield J
  • Investigating phylogenetic relationships within the Apicomplexa using sequence data: the search for homology.
    Barta JR
  • A review of long-branch attraction.
    Bergsten J
  • Widespread horizontal transfer of mitochondrial genes in flowering plants.
    Bergthorsson U Adams KL Thomason B Palmer JD
  • Class of multiple sequence alignment algorithm affects genomic analysis.
    Blackburne BP Whelan S
  • Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis.
    Bonham-Carter O Steele J Bastola D
  • Homology in comparative, molecular, and evolutionary developmental biology: the radiation of a concept.
    Brigandt I
  • Homology and errors.
    Brower AVZ de Pinna MCC
  • Three steps of homology assessment.
    Brower AVZ Schawaroch V
  • Rfam 11.0: 10 years of RNA families.
    Burge SW Daub J Eberhardt R Tate J Barquist L Nawrocki EP Eddy SR Gardner PP Bateman A
  • Defining sameness: historical, biological, and generative homology.
    Butler AB Saidel WM
  • Next-generation phylogenomics.
    Chan CX Ragan MA
  • Inferring phylogenies of evolving sequences without multiple sequence alignment.
    Chan CX Bernard G Poirion O Hogan JM Ragan MA
  • The evolution of small insertions and deletions in the coding genes of Drosophila melanogaster .
    Chong Z Zhai W Li C Gao M Gong Q Ruan J Li J Jiang L Lv X Hungate E Wu C-I
  • Phylogeny and evo-devo: characters, homology, and the historical analysis of the evolution of development.
    Cracraft J
  • The roots of phylogeny: how did Haeckel build his trees?
    Dayrat B
  • Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy, not minimization of operationally defined total cost or minimization of equally weighted transformations.
    De Laet J
  • Concepts and tests of homology in the cladistic paradigm.
    de Pinna MCC
  • A memory efficient method for structure-based RNA multiple alignment.
    DeBlasio D Bruand J Zhang S
  • Indel information eliminates trivial sequence alignment in maximum likelihood phylogenetic analysis.
    Denton JSS Wheeler WC
  • Phylogenetic assessment of alignments reveals neglected tree signal in gaps.
    Dessimov C Gil M
  • Molecules and morphology: where’s the homology?
    Dickinson WJ
  • Alignment-free detection of local similarity among viral and bacterial genomes.
    Domazet-Loöo M Haubold B
  • Similar amino acid sequences: chance or common ancestry?
    Doolittle RF
  • Phylogenetic inference under varying proportions of indel-induced alignment gaps.
    Dwivedi B Gadagkar SR
  • MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
    Edgar RC
  • Quality measures for protein alignment benchmarks.
    Edgar RC
  • Incorporating gaps as phylogenetic characters across either DNA regions: ramifications for North American
    Egan AN Crandall KA
  • Effects of sequence alignment on the phylogeny of Sarcocystis deduced from 18S rDNA sequences.
    Ellis J Morrison DA
  • Homology and misdirection.
    Farris JS
  • The Pfam protein families database.
    Finn RD Bateman A Clements J Coggill P Eberhardt RY Eddy SR Heger A Hetherington K Holm L Mistry J Sonnhammer ELL Tate J Punta M
  • Distinguishing homologous from analogous proteins.
    Fitch WM
  • Homology: a personal view on some of the problems.
    Fitch WM
  • Characters, states and homology.
    Freudenstein JV
  • From basepairs to birdsongs: phylogenetic data in the age of genomics.
    Freudenstein JV Pickett KM Simmons MP Wenzel JW
  • Large-scale assignment of orthology: back to phylogenetics?
    Gabaldón T
  • Divergence and convergence in enzyme evolution.
    Galperin MY Koonin EV
  • Generating implied alignments under direct optimization using POY.
    Giribet G
  • Mind the gaps: evidence of bias in estimates of multiple sequence alignments.
    Golubchik T Wise MJ Easteal S Jermiin LS
  • Microstructural changes in noncoding chloroplast DNA: interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference.
    Graham SW Reeves PA Burns ACF Olmstead RG
  • A pluralistic account of homology: adapting the models to the data.
    Haggerty LS Jachiet P-A Hanage WP Fitzpatrick D Lopez P O’Connell MJ Pisani D Wilkinson M Bapteste E McInerney JO
  • Homology and homoplasy: dichotomy or continuum?
    Hall BK
  • Primary homology assessment, characters and character states.
    Hawkins JA Hughes CE Scotland RW
  • The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence.
    Hickson RE Simon C Perrey SW
  • Is multiple-sequence alignment required for accurate inference of phylogeny?
    Höhl M Ragan MA
  • The history of the homology concept and the ‘Phylogenetisches Symposium’.
    Hoßfeld U Olsson L
  • Evolutionary analysis of amino acid repeats across the genomes of 12 Drosophila species.
    Huntley MA Clark AG
  • Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.
    Iantorno S Gori K Goldman N Gil M Dessimoz C
  • The concept of homology in biology.
    Jardine N
  • The observational and theoretical components of homology: a study based on the morphology of the dermal skull-roofs of rhipidistian fishes.
    Jardine N
  • MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
    Katoh K Standley DM
  • The evolution of non-coding chloroplast DNA and its application in plant systematics.
    Kelchner SA
  • Group II introns as phylogenetic tools: structure, function, and evolutionary constraints.
    Kelchner SA
  • Phylogenetic models and model selection for noncoding DNA.
    Kelchner SA
  • Molecular evolution and phylogenetic utility of the rpl16 intron in Chusquea and the
    Kelchner SA Clark LG
  • Hairpins create minute inversions in non-coding regions of chloroplast DNA.
    Kelchner SA Wendel JF
  • Upcoming challenges for multiple sequence alignment methods in the high-throughput era.
    Kemena C Notredame C
  • PSAR-Align: improving multiple sequence alignment using probabilistic sampling.
    Kim J Ma J
  • Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs.
    Kjer KM
  • The formation of the theory of homology in biological sciences.
    Kleisner K
  • Origin and evolution of SINEs in eukaryotic genomes.
    Kramerov DA Vassetzky NS
  • Relative rates of gene fusion and fission in multi-domain proteins.
    Kummerfeld SK Teichmann SA
  • On the use of the term homology in modern zoology, and the distinction between homogenetic and homoplastic agreements.
    Lankester ER
  • Clustal W and Clustal X version 2.0.
    Larkin MA Blackshields G Brown NP Chenna R McGettigan PA McWilliam H Valentin F Wallace IM Wilm A Lopez R Thompson JD Gibson TJ Higgins DG
  • Quality assessment of multiple alignment programs.
    Lassmann T Sonnhammer ELL
  • Automatic assessment of alignment quality.
    Lassmann T Sonnhammer ELL
  • Homology in development and the development of the homology concept.
    Laubichler MD
  • Legume phylogeny and classification in the 21st century: progress, prospects and lessons for other species-rich clades.
    Legume Phylogeny Working Group
  • The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods.
    Letsch HO Kück P Stocsits RR Misof B
  • A survey of sequence alignment algorithms for next-generation sequencing.
    Li H Homer N
  • Treelength optimization for phylogeny estimation.
    Liu K Warnow T
  • Functional homology and homology of function: biological concepts and philosophical consequences.
    Love AC
  • Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.
    Löytynoja A Goldman N
  • Posttranscriptional recoding by RNA editing.
    Maas S
  • Unsorted homology within locus and species trees.
    Mallo D de Oliveira Martins L Posada D
  • Homology: a definition.
    Margoliash E
  • Using genetic networks and homology to understand the evolution of phenotypic traits.
    McCune AR Schimenti JC
  • Detecting sequence homology at the gene cluster level with MultiGeneBlast.
    Medema MH Takano E Breitling R
  • The majority of recent short DNA insertions in the human genome are tandem duplications.
    Messer PW Arndt PF
  • Similarity and congruence as criteria for molecular homology.
    Mindell DP
  • Homology evolving.
    Mindell DP Meyer A
  • The dynamics and evolutionary potential of domain loss and emergence.
    Moore AD Bornberg-Bauer E
  • Inference of molecular homology and sequence alignment by direct optimization.
    Morgan MJ Kelchner SA
  • Multiple sequence alignment for phylogenetic purposes.
    Morrison DA
  • A framework for phylogenetic sequence alignment.
    Morrison DA
  • Why would phylogeneticists ignore computerized sequence alignment?
    Morrison DA
  • Is sequence alignment an art or a science?
    Morrison DA
  • Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of Apicomplexa.
    Morrison DA Ellis JT
  • DACTAL: divide-and-conquer
    Nelesen S Liu K Wang LS Linder CR Warnow T
  • Patterns of gene expression: homology or homocracy?
    Nielsen C Martinez P
  • On homology.
    Nixon KC Carpenter JM
  • Recent evolutions of multiple sequence alignment algorithms.
    Notredame C
  • The accuracy of several multiple sequence alignment programs for proteins.
    Nuin PAS Wang Z Tillier ERM
  • Assessing the efficiency of multiple sequence alignment programs.
    Pais FS-M Ruy PC Oliveira G Coimbra RS
  • Homology in classical and molecular biology.
    Patterson C
  • The contemporary concepts of homology in biology: a theoretical review.
    Pavlinov IY
  • Multiple protein sequence alignment.
    Pei J
  • PROMALS: towards accurate multiple sequence alignments of distantly related proteins.
    Pei J Grishin NV
  • Multiple sequence alignment in phylogenetic analysis.
    Phillips A Janies D Wheeler W
  • Philosophy and the transformation of cladistics.
    Platnick NJ
  • On character coding for phylogeny reconstruction.
    Pleijel F
  • Molecular evolution of the trn LUAA intron in bryophytes.
    Quandt D Stech M
  • SINEs of a nearly perfect character.
    Ray DA Xing J Salem A-H Batzer MA
  • ‘Homology’ in proteins and nucleic acids: a terminology muddle and a way out of it.
    Reeck GR de Haën C Teller DC Doolittle RF Fitch WM Dickerson RE Chambon P McLachlan AD Margoliash E Jukes TH Zuckerkandl E
  • Multiple alignment-free sequence comparison.
    Ren J Song K Sun F Deng M Reinert G
  • Homologies in phylogenetic analyses: concept and test.
    Richter S
  • The language of systematics, and the philosophy of ‘total evidence’.
    Rieppel O
  • Similarity.
    Rieppel O Kearney M
  • Homology and hierarchies: problems solved and unresolved.
    Roth VL
  • Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation.
    Roth FP Hughes JD Estep PW Church GM
  • Evo-devo and the search for homology (‘sameness’) in biological systems.
    Rutishauser R Moline P
  • PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach.
    Sahraeian SME Yoo B-J
  • Evolution of 5S RNA and the non-randomness of base replacement.
    Sankoff D Morel C Cedergren RJ
  • A fundamental problem with amino-acid-sequence characters for phylogenetic analyses.
    Simmons MP
  • Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses.
    Simmons MP Ochoterena H Carr TG
  • Alignment-free genome comparison with feature frequency
    Sims GE Jun S-R Wu GA Kim S-H
  • RNA structure prediction from evolutionary patterns of nucleotide composition.
    Smit S Knight R Heringa J
  • Plant taxonomy and biosystematics: does DNA provide all the answers?
    Stace CA
  • Prevalence of multinucleotide replacements in evolution of primates and Drosophila .
    Terekhanova NV Bazykin GA Neverov A Kondrashov AS Seplyarskiy VB
  • Gene family evolution and homology: genomics meets phylogenetics.
    Thornton JW DeSalle R
  • Alignment-free sequence comparison: a review.
    Vinga S Almeida J
  • The biological homology concept.
    Wagner GP
  • Parallel evolution.
    Went FW
  • Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search.
    Wheeler WC
  • POY version 5: phylogenetic analysis using dynamic homologies under multiple optimality criteria.
    Wheeler WC Lucaroni N Hong L Crowley LM Varón A
  • Bringing molecules back into molecular evolution.
    Wilke C
  • A comparison of two methods of character construction.
    Wilkinson M
  • An enhanced RNA alignment benchmark for sequence alignment programs.
    Wilm A Mainz I Steger G
  • Alignment uncertainty and genomic analysis.
    Wong KM Suchard MA Huelsenbeck JP
  • Gaps in structurally similar proteins: towards improvement of multiple sequence alignment.
    Wrabl JO Grishin NV
  • When is homology not homology?
    Wray GA Abouheif E
  • Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA.
    Wuyts J Van de Peer Y De Wachter R
  • Host adaptation and host-parasite co-evolution in Cryptosporidium : implications for taxonomy and public health.
    Xiao L Sulaiman IM Ryan UM Zhou L Atwill ER Tischler ML Zhang X Fayer R Lal AA
  • Simultaneous phylogeny reconstruction and multiple sequence alignment.
    Yue F Shi J Tang J