Skip to main content
SpringerLink
Log in

The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates

  • Original Article
  • Published:
Journal of Molecular Evolution Aims and scope Submit manuscript

Abstract

With the large collections of gene and genome sequences, there is a need to generate curated comparative genomic databases that enable interpretation of results in an evolutionary context. Such resources can facilitate an understanding of the co-evolution of genes in the context of a genome mapped onto a phylogeny, of a protein structure, and of interactions within a pathway. A phylogenetically indexed gene family database, the adaptive evolution database (TAED), is presented that organizes gene families and their evolutionary histories in a species tree context. Gene families include alignments, phylogenetic trees, lineage-specific dN/dS ratios, reconciliation with the species tree to enable both the mapping and the identification of duplication events, mapping of gene families onto pathways, and mapping of amino acid substitutions onto protein structures. In addition to organization of the data, new phylogenetic visualization tools have been developed to aid in interpreting the data that are also available, including TreeThrasher and TAED Tree Viewer. A new resource of gene families organized by species and taxonomic lineage promises to be a valuable comparative genomics database for molecular biologists, evolutionary biologists, and ecologists. The new visualization tools and database framework will be of interest to both evolutionary biologists and bioinformaticians.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Abbreviations

dN:

The normalized rate of nonsynonymous substitutions

dS:

The normalized rate of synonymous substitutions

TAED:

The adaptive evolution database

PAM:

Point accepted mutations, a measure of evolutionary distance

MPI:

Message passing interface

MSA:

Multiple sequence alignment

NHX:

The new Hampshire X format

NCBI:

National center for biotechnology information

BLAST:

Basic local alignment search tool

PAML:

Phylogenetic analysis using maximum-likelihood, software to estimate dN/dS

PDB:

Protein data bank

KEGG:

Kyoto encyclopedia of genes and genomes

References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  • Anisimova M, Yang Z (2007) Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol 24:1219–1228

    Article  CAS  PubMed  Google Scholar 

  • Anisimova M, Bielawski JP, Yang Z (2001) Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol 18:1585–1592

    Article  CAS  PubMed  Google Scholar 

  • Benner SA, Chamberlin SG, Liberles DA, Govindarajan S, Knecht L (2000) Functional inferences from reconstructed evolutionary biology involving rectified databases—an evolutionarily grounded approach to functional genomics. Res Microbiol 151:97–106

    Article  CAS  PubMed  Google Scholar 

  • Berglund-Sonnhammer AC, Steffansson P, Betts MJ, Liberles DA (2006) Optimal gene trees from sequences and species trees using a soft interpretation of parsimony. J Mol Evol 63:240–250

    Article  CAS  PubMed  Google Scholar 

  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235–242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cannarozzi GM, Schneider A (2012) Codon evolution: mechanisms and models. Oxford University Press, Oxford

    Book  Google Scholar 

  • Chamary JV, Parmley JL, Hurst LD (2006) Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 7:98–108

    Article  CAS  PubMed  Google Scholar 

  • Darriba D, Taboada GL, Doallo R, Posada D (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164–1165

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dasmeh P, Serohijos AWR, Kepp KP, Shakhnovich EI (2014) The influence of selection for protein stability on dN/dS estimations. Genome Biol Evol 6:2956–2967

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Drummond DA, Wilke CO (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341–352

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eöry L, Gilbert MTP, Li C, Li B, Archibald A, Aken BL, Zhang G, Jarvis E, Flicek P, Burt DW (2015) Avianbase: a community resource for bird genomics. Genome Biol 16:21

    Article  PubMed  PubMed Central  Google Scholar 

  • Fletcher W, Yang Z (2010) The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol 27:2257–2267

    Article  CAS  PubMed  Google Scholar 

  • Gharib WH, Robinson-Rechavi M (2013) The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC. Mol Biol Evol 30:1675–1686

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11:725–736

    CAS  PubMed  Google Scholar 

  • Gonnet GH, Hallett MT, Korostensky C, Bernardin L (2000) Darwin v. 2.0: an interpreted computer language for the biosciences. Bioinformatics 16:101–103

    Article  CAS  PubMed  Google Scholar 

  • Gouveia-Oliveira R, Sackett PW, Pedersen AG (2007) MaxAlign: maximizing usable data in an alignment. BMC Bioinformatics 8:312

    Article  PubMed  PubMed Central  Google Scholar 

  • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321

    Article  CAS  PubMed  Google Scholar 

  • Hermansen RA, Mannakee BK, Knecht W, Liberles DA, Gutenkunst RN (2015) Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast. BMC Evol Biol 15:232

    Article  PubMed  PubMed Central  Google Scholar 

  • Hermansen RA, Hvidsten TR, Sandve SR, Liberles DA (2016) Extracting functional trends from whole genome duplication events using comparative genomics. Biol Proced Online 18:11

    Article  PubMed  PubMed Central  Google Scholar 

  • Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S et al (2016) Ensembl comparative genomics resources. Database. doi:10.1093/database/bav096

    Google Scholar 

  • Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al (2002) The Ensembl genome database project. Nucleic Acids Res 30:38–41

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hughes T, Hyun Y, Liberles DA (2004) Visualising very large phylogenetic trees in three dimensional hyperbolic space. BMC Bioinform 5:48

    Article  Google Scholar 

  • Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44:D457–D462

    Article  CAS  PubMed  Google Scholar 

  • Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Konrad A, Teufel AI, Grahnen JA, Liberles DA (2011) Toward a general model for the evolutionary dynamics of gene duplicates. Genome Biol Evol 3:1197–1209

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Letunic I, Bork P (2007) Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23:127–128

    Article  CAS  PubMed  Google Scholar 

  • Liberles DA (2007) Ancestral sequence reconstruction. Oxford University Press, Oxford

    Book  Google Scholar 

  • Liberles DA, Schreiber DR, Govindarajan S, Chamberlain SG, Benner SA (2001) The adaptive evolution database (TAED). Genome Biol Res 2(8):1–6

    Google Scholar 

  • Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A et al (2016) The Atlantic salmon genome provides insights into rediploidization. Nature 533:200–205

    Article  CAS  PubMed  Google Scholar 

  • Loytynoja A, Vilella AJ, Goldman N (2012) Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics 28:1684–1691

    Article  PubMed  PubMed Central  Google Scholar 

  • Matsen FA, Kodner RB, Armbrust EV (2010) Pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinform 11:538

    Article  Google Scholar 

  • Pervez MT, Babar ME, Nadeem A, Aslam M, Awan AR, Aslam N, Hussain T, Naveed N, Qadri S, Waheed U et al (2014) Evaluating the accuracy and efficiency of multiple sequence alignment methods. Evol Bioinform Online 10:205–217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pollock DD, Goldstein RA (2014) Strong evidence for protein epistasis, weak evidence against it. Proc Natl Acad Sci 111:E1450

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pollock DD, Thiltgen G, Goldstein RA (2012) Amino acid coevolution induces an evolutionary Stokes shift. Proc Natl Acad Sci USA 109:E1352–E1359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Proux E, Studer RA, Moretti S, Robinson-Rechavi M (2009) Selectome: a database of positive selection. Nucleic Acids Res 37:D404–D407

    Article  CAS  PubMed  Google Scholar 

  • Rosindell J, Harmon LJ (2012) OneZoom: a fractal explorer for the tree of life. PLoS Biol 10:e1001406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roth C, Liberles DA (2006) A systematic search for positive selection in higher plants (Embryophytes). BMC Plant Biol 6:12

    Article  PubMed  PubMed Central  Google Scholar 

  • Roth C, Betts MJ, Steffansson P, Saelensminde G, Liberles DA (2005) The adaptive evolution database (TAED): a phylogeny based tool for comparative genomics. Nucleic Acids Res 33:D495–D497

    Article  CAS  PubMed  Google Scholar 

  • Roth C, Rastogi S, Arvestad L, Dittmar K, Light S, Ekman D, Liberles DA (2007) Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms. J Exp Zool B 308:58–73

    Article  Google Scholar 

  • Sela I, Ashkenazy H, Katoh K, Pupko T (2015) GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Res 43:W7–W14

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shah P, McCandlish DM, Plotkin JB (2015) Contingency and entrenchment in protein evolution under purifying selection. Proc Natl Acad Sci 112:E3226–E3235

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Simonsen M, Mailund T, Pedersen CNS (2008) Rapid neighbour-joining. In: Crandall KA, Lagergren J (eds) Algorithms in bioinformatics: Proceeding of 8th International Workshop, WABI 2008, Karlsruhe, Germany. Springer, Berlin, pp 113–122, September 15–19 2008

  • Studer RA, Penel S, Duret L, Robinson-Rechavi M (2008) Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res 18:1393–1402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suchard MA, Redelings BD (2006) BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics 22:2047–2048

    Article  CAS  PubMed  Google Scholar 

  • Suyama M, Torrents D, Bork P (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34:W609–W612

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tellgren Å, Berglund A-C, Savolainen P, Janis CM, Liberles DA (2004) Myostatin rapid sequence evolution in ruminants predates domestication. Mol Phylogenet Evol 33:782–790

    Article  CAS  PubMed  Google Scholar 

  • Tellgren-Roth Å, Dittmar K, Massey SE, Kemi C, Tellgren-Roth C, Savolainen P, Lyons LA, Liberles DA (2009) Keeping the blood flowing—plasminogen activator genes and feeding behavior in vampire bats. Naturwissenschaften 96:39–47

    Article  CAS  PubMed  Google Scholar 

  • The Genomes Project C (2015) A global reference for human genetic variation. Nature 526:68–74

    Article  Google Scholar 

  • Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E (2009) EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 19:327–335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wallace IM, O’Sullivan O, Higgins DG, Notredame C (2006) M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res 34:1692–1699

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis SE, Rost B, Goldberg T (2016) MSAViewer: interactive JavaScript visualization of multiple sequence alignments. Bioinformatics 32:3501–3503

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591

    Article  CAS  PubMed  Google Scholar 

  • Yang Z, Nielsen R (1998) Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol 46:409–418

    Article  CAS  PubMed  Google Scholar 

  • Yang Z, Nielsen R (2008) Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol 25:568–579

    Article  CAS  PubMed  Google Scholar 

  • Yang Z, Kumar S, Nei M (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641–1650

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yang Z, Nielsen R, Goldman N, Pedersen AM (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431–449

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors would like to thank Jason Davies and Ken-ichi Ueda for generating the base code for the D3 tree visualization software. The authors would also like to thank the Advanced Research Computing Center (ARCC) at the University of Wyoming for technical assistance in implementing the TAED pipeline. The authors would additionally like to thank Jessica Siltberg-Liberles and Dietlind Gerloff for feedback on data quality during database development. Lastly, the authors would like to thank National Science Foundation Grants DBI-0743374 and DBI-1355846 for support as well as the University of Wyoming INBRE Award P20 RR016474.

Author information

Author notes

  1. Benjamin P. Oswald

    Present address: IBEST Computational Resources Core, University of Idaho, Moscow, ID, 83844, USA

  2. Stormy Knight

    Present address: Supercomputer Systems Group, National Center for Atmospheric Research, Cheyenne, WY, 82009, USA

  3. Katharine L. Korunes

    Present address: Department of Biology, Duke University, Durham, NC, 27708, USA

  4. Stephen N. Michel

    Present address: College of Biological Sciences, University of Minnesota, Saint Paul, MN, 55108, USA

Authors and Affiliations

  1. Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA

    Russell A. Hermansen, Stephen D. Shank, David Northover & David A. Liberles

  2. Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA

    Russell A. Hermansen, Benjamin P. Oswald, Stormy Knight, Katharine L. Korunes, Stephen N. Michel & David A. Liberles

Authors
  1. Russell A. Hermansen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Benjamin P. Oswald
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Stormy Knight
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Stephen D. Shank
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. David Northover
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Katharine L. Korunes
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Stephen N. Michel
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. David A. Liberles
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

RAH and DAL conceived of the study. RAH built the pipeline to generate the database, built the database, executed most of the analysis, and wrote the first draft of the manuscript. DAL supervised the project and contributed significantly to the writing of the manuscript. BPO wrote TAED Tree Viewer, adapted OneZoom for TAED use, and also contributed to the pipeline and data analysis. SK wrote TreeThrasher. SDS contributed to database construction and function, including the protein viewer. DN wrote the API. KLK and SM contributed to running the pipeline and database analysis. All authors contributed to final writing of the manuscript.

Corresponding author

Correspondence to David A. Liberles.

Ethics declarations

Conflict of interest

The authors declare that they have no competing interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hermansen, R.A., Oswald, B.P., Knight, S. et al. The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates. J Mol Evol 85, 46–56 (2017). https://doi.org/10.1007/s00239-017-9806-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00239-017-9806-8

Keywords

Search

Navigation