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Immune Mediators in Cancer pp 313–343Cite as

Phylogenetic Analyses of Chemokine Receptors from Sequence Retrieval to Phylogenetic Trees

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2108))

Abstract

Phylogenetic trees are an essential requisite for comparative biology studies where hypotheses regarding the evolution of genes can be investigated. Trees provide visual and statistical guides to characterize the degree of relatedness among biological entities from genes to species. In a tree, ancestor-descendant relationships are represented by connections, and closely related entities share most of these links. In this chapter, I outlined a method to retrieve and label amino acid and nucleotide sequences of chemokine receptors, align them in sequence matrices, determine their best-model of molecular evolution, and estimate the corresponding phylogenetic trees with distance and maximum likelihood approaches. Most of these analyses are performed within the R environment, and all of these methods use open-source software.

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References

  1. Felsenstein J (2004) Inferring phylogenies. Sinauer Associates, Sunderland, MA

    Google Scholar 

  2. Gluckman P, Beedle A, Hanson M (2009) Principles of evolutionary medicine, 1st edn. Oxford University Press, Inc., New York

    Google Scholar 

  3. Garland T, Bennett AF, Rezende EL (2004) Phylogenetic approaches in comparative physiology. J Exp Biol 208:3015–3035

    Article  Google Scholar 

  4. Baum D (2008) Reading a phylogenetic tree: the meaning of monophyletic groups. Nat Educ 1(1):190

    Google Scholar 

  5. Rosenberg M (2008) Sequence alignment: methods, models, concepts, and strategies. University of California Press, Berkeley, CA

    Google Scholar 

  6. R_Core_Team (2019) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. https://www.r-project.org/

    Google Scholar 

  7. Bachelerie F, Ben-Baruch A, Burkhardt AM, Combadiere C, Farber JM, Graham GJ, Horuk R, Sparre-Ulrich AH, Locati M, Luster AD, Mantovani A, Matsushima K, Murphy PM, Nibbs R, Nomiyama H, Power CA, Proudfoot AEI, Rosenkilde MM, Rot A, Sozzani S, Thelen M, Yoshie O, Zlotnik A (2014) International Union of Pharmacology. LXXXIX. Update on the extended family of chemokine receptors and introducing a new nomenclature for atypical chemokine receptors. Pharmacol Rev 66(1):1–79. https://doi.org/10.1124/pr.113.007724

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Bateman A, Martin MJ, O’Donovan C, Magrane M, Apweiler R, Alpi E, Antunes R, Ar-Ganiska J, Bely B, Bingley M, Bonilla C, Britto R, Bursteinas B, Chavali G, Cibrian-Uhalte E, Da Silva A, De Giorgi M, Dogan T, Fazzini F, Gane P, Cas-Tro LG, Garmiri P, Hatton-Ellis E, Hieta R, Huntley R, Legge D, Liu WD, Luo J, MacDougall A, Mutowo P, Nightin-Gale A, Orchard S, Pichler K, Poggioli D, Pundir S, Pureza L, Qi GY, Rosanoff S, Saidi R, Sawford T, Shypitsyna A, Turner E, Volynkin V, Wardell T, Watkins X, Watkins CA, Figueira L, Li WZ, McWilliam H, Lopez R, Xenarios I, Bougueleret L, Bridge A, Poux S, Redaschi N, Aimo L, Argoud-Puy G, Auchincloss A, Axelsen K, Bansal P, Baratin D, Blatter MC, Boeckmann B, Bolleman J, Boutet E, Breuza L, Casal-Casas C, De Castro E, Coudert E, Cuche B, Doche M, Dornevil D, Duvaud S, Estreicher A, Famiglietti L, Feuermann M, Gasteiger E, Gehant S, Gerritsen V, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, Jungo F, Keller G, Lara V, Lemercier P, Lieberherr D, Lombardot T, Martin X, Masson P, Morgat A, Neto T, Nouspikel N, Paesano S, Pedruzzi I, Pilbout S, Pozzato M, Pruess M, Rivoire C, Roechert B, Schneider M, Sigrist C, Sonesson K, Staehli S, Stutz A, Sundaram S, Tognolli M, Verbregue L, Veuthey AL, Wu CH, Arighi CN, Arminski L, Chen CM, Chen YX, Garavelli JS, Huang HZ, Laiho KT, McGarvey P, Natale DA, Suzek BE, Vinayaka CR, Wang QH, Wang YQ, Yeh LS, Yerramalla MS, Zhang J, UniProt C (2015) UniProt: a hub for protein information. Nucleic Acids Res 43(D1):D204–D212. https://doi.org/10.1093/nar/gku989

    Article  CAS  Google Scholar 

  9. Wickham H, Hester J, Chang W (2019) devtools: tools to make developing R packages easier. R package version 2.0.2. https://cran.r-project.org/package=devtools

  10. Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oles AK, Pages H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015) Orchestrating high-throughput genomic analysis with bioconductor. Nat Methods 12(2):115–121. https://doi.org/10.1038/nmeth.3252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge YC, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang JH (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5(10):16. https://doi.org/10.1186/gb-2004-5-10-r80

    Article  Google Scholar 

  12. Gentleman R (2019) annotate: annotation for microarrays. R package version 1.60.1

    Google Scholar 

  13. Paradis E, Schliep K (2018) ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35:526–528

    Article  Google Scholar 

  14. Paradis E (2012) Analysis of phylogenetics and evolution with R, 2nd edn. Springer, New York

    Book  Google Scholar 

  15. Schliep KP (2011) phangorn: phylogenetic analysis in R. Bioinformatics 27(4):592–593

    Article  CAS  PubMed  Google Scholar 

  16. Winter DJ (2017) rentrez: an R package for the NCBI eUtils API. The R Journal 9(2):520–526

    Google Scholar 

  17. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST plus: architecture and applications. BMC Bioinformatics 10:9. https://doi.org/10.1186/1471-2105-10-421

    Article  CAS  Google Scholar 

  18. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li WZ, Lopez R, McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:6. https://doi.org/10.1038/msb.2011.75

    Article  Google Scholar 

  19. Goujon M, McWilliam H, Li WZ, Valentin F, Squizzato S, Paern J, Lopez R (2010) A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res 38:W695–W699. https://doi.org/10.1093/nar/gkq313

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27(2):221–224. https://doi.org/10.1093/molbev/msp259

    Article  CAS  PubMed  Google Scholar 

  21. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797. https://doi.org/10.1093/nar/gkh340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312–1313. https://doi.org/10.1093/bioinformatics/btu033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9(8):772–772. https://doi.org/10.1038/nmeth.2109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. 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(3):307–321. https://doi.org/10.1093/sysbio/syq010

    Article  CAS  PubMed  Google Scholar 

  25. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial-DNA in humans and chimpanzees. Mol Biol Evol 10(3):512–526

    CAS  PubMed  Google Scholar 

  26. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8(3):275–282

    CAS  PubMed  Google Scholar 

  27. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21–132

    Chapter  Google Scholar 

  28. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376

    Article  CAS  PubMed  Google Scholar 

  29. Saitou N, Nei M (1987) The neighbor-joining method—a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425

    CAS  PubMed  Google Scholar 

  30. Maddison WP, Maddison DR (2018) Mesquite: a modular system for evolutionary analysis. Version 3.51. http://www.mesquiteproject.org/

  31. Yu GC, Smith DK, Zhu HC, Guan Y, Lam TTY (2017) GGTREE: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 8(1):28–36. https://doi.org/10.1111/2041-210x.12628

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Biological Sciences, College of Liberal Arts and Sciences, St. John’s University, Queens, NY, USA

    Juan C. Santos

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  1. Juan C. Santos
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Correspondence to Juan C. Santos .

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Editors and Affiliations

  1. Department of Biological Sciences, St. John’s University, Queens, NY, USA

    Ivana Vancurova

  2. Department of Biological Sciences, St. John’s University, Queens, NY, USA

    Yan Zhu

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Santos, J.C. (2020). Phylogenetic Analyses of Chemokine Receptors from Sequence Retrieval to Phylogenetic Trees. In: Vancurova, I., Zhu, Y. (eds) Immune Mediators in Cancer. Methods in Molecular Biology, vol 2108. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0247-8_27

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  • DOI: https://doi.org/10.1007/978-1-0716-0247-8_27

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0246-1

  • Online ISBN: 978-1-0716-0247-8

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