Medzhitov R, Janeway CA: Innate Immunity: The virtues of a nonclonal system of recognition. Cell. 1997, 91: 295-298. 10.1016/S0092-8674(00)80412-2.
Article
PubMed
CAS
Google Scholar
Smith KD, Andersen-Nissen E, Hayashi F, Strobe K, Bergman MA, Barrett SL, Cookson BT, Aderem A: Toll-like receptor 5 recognizes a conserved site on flagellin required for protofilament formation and bacterial motility. Nat Immunol. 2004, 4: 1247-1253.
Article
Google Scholar
Mukherjee S, Sarkar-Roy N, Wagener DK, Majumder PP: Signatures of natural selection are not uniform across genes of innate immune system, but purifying selection is the dominant signature. Proc Natl Acad Sci USA. 2009, 106: 7073-7078. 10.1073/pnas.0811357106.
Article
PubMed
PubMed Central
Google Scholar
Barreiro LB, Ben-Ali M, Quach H, Laval G, Patin E, Pickrell JK, Bouchier C, Tichit M, Neyrolles O, Gicquel B, Kidd JR, Kidd KK, Alcais A, Ragimbeau J, Pellegrini S, Abel L, Casanova JL, Quintana-Murci L: Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense. PLoS Genet. 2009, 5: e1000562-10.1371/journal.pgen.1000562.
Article
PubMed
PubMed Central
Google Scholar
Sackton TB, Lazzaro BP, Schlenke TA, Evans JD, Hultmark D, Clark AG: Dynamic evolution of the innate immune system in Drosophila. Nat Genet. 2007, 39: 1461-1468. 10.1038/ng.2007.60.
Article
PubMed
CAS
Google Scholar
Ferrer-Admetlla A, Bosch E, Sikora M, Marque's-Bonet T, Ramı'rez-Soriano A, Muntasell A, Navarro A, Lazarus R, Calafell F, Bertranpetit J, Casals F: Balancing selection is the main force shaping the evolution of innate immunity genes. J Immunol. 2008, 181: 1315-1322.
Article
PubMed
CAS
Google Scholar
Arora P, Porcelli SA: A glycan shield for bacterial sphingolipids. Chem Biol. 2008, 15: 642-644. 10.1016/j.chembiol.2008.07.001.
Article
PubMed
CAS
Google Scholar
Nakajima T, Ohtani H, Satta Y, Uno Y, Akari H, Ishida T, Kimura A: Natural selection in the TLR-related genes in the course of primate evolution. Immunogenetics. 2008, 60: 727-735. 10.1007/s00251-008-0332-0.
Article
PubMed
CAS
Google Scholar
Wlasiuk G, Khan S, Switzer WM, Nachman MW: A history of recurrent positive selection at the toll-like receptor 5 in primates. Mol Biol Evol. 2009, 26: 937-949. 10.1093/molbev/msp018.
Article
PubMed
CAS
PubMed Central
Google Scholar
Wlasiuk G, Nachman MW: Adaptation and constraint at toll-like receptors in primates. Mol Biol Evol. 2010, 27: 2172-2186. 10.1093/molbev/msq104.
Article
PubMed
CAS
PubMed Central
Google Scholar
Jann OC, Werling D, Chang JS, Haig D, Glass EJ: Molecular evolution of bovine Toll-like receptor 2 suggests substitutions of functional relevance. BMC Evol Biol. 2008, 8: 288-10.1186/1471-2148-8-288.
Article
PubMed
PubMed Central
Google Scholar
Yilmaz A, Shen S, Adelson DL, Xavier S, Zhu JJ: Identification and sequence analysis of chicken Toll-like receptors. Immunogenetics. 2005, 56: 743-753. 10.1007/s00251-004-0740-8.
Article
PubMed
CAS
Google Scholar
Alcaide M, Edwards SV: Molecular evolution of the Toll-like receptor multigene 1 family in birds. Mol Biol Evol. 2011, 28: 1703-1715. 10.1093/molbev/msq351.
Article
PubMed
CAS
Google Scholar
Chen JS, Wang TY, Tzeng TD, Wang CY, Wang D: Evidence for positive selection in the TLR9 gene of teleosts. Fish Shellfish Immunol. 2008, 24: 234-242. 10.1016/j.fsi.2007.11.005.
Article
PubMed
CAS
Google Scholar
Ortiz M, Kaessmann H, Zhang K, Bashirova A, Carrington M, Quintana-Murci L, Telenti A: The evolutionary history of the CD209 (DC-SIGN) family in humans and nonhuman primates. Genes and Immunity. 2008, 9: 483-492. 10.1038/gene.2008.40.
Article
PubMed
CAS
PubMed Central
Google Scholar
Thewissen JGM, Cooper LN, Clementz MT, Bajpai S, Tiwari BN: Whales originated from aquatic artiodactyls in the Eocene epoch of India. Nature. 2007, 450: 1190-1194. 10.1038/nature06343.
Article
PubMed
CAS
Google Scholar
Nikaido M, Rooney AP, Okada N: Phylogenetic relationships among cetartiodactyls based on insertions of short and long interspersed elements: hippopotamuses are the closest extant relatives of whales. Proc Natl Acad Sci USA. 1999, 96: 10261-10266. 10.1073/pnas.96.18.10261.
Article
PubMed
CAS
PubMed Central
Google Scholar
Thewissen JGM, Cooper LN, George JC, Bajpai S: From land to water: the origin of whales, dolphins, and porpoises. Evol Edu Outreach. 2009, 2: 272-288. 10.1007/s12052-009-0135-2.
Article
Google Scholar
Williams EM: Synopsis of the earliest cetaceans. The emergence of whales: evolutionary patterns in the origin of Cetacea. Edited by: Thewissen JGM. 1998, New York: Plenum, 1-28.
Chapter
Google Scholar
Uhen M: The origin (s) of whales. Annu Rev Earth Planet Sci. 2010, 38: 189-219. 10.1146/annurev-earth-040809-152453.
Article
CAS
Google Scholar
Geisler JH, Sanders AE: Morphological evidence for the phylogeny of Cetacea. J Mammal Evol. 2003, 10: 23-129. 10.1023/A:1025552007291.
Article
Google Scholar
Thewissen JGM, Williams EM: The early evolution of Cetacea (whales, dolphins, and porpoises). Ann Rev Ecol Syst. 2002, 33: 73-90. 10.1146/annurev.ecolsys.33.020602.095426.
Article
Google Scholar
Fordyce RE, de Muizon C: Evolutionary history of cetaceans: a review. Secondary adaptation of tetrapods to life in water. Edited by: Mazin JM, de Buffr'enil V. 2001, 169-233.
Google Scholar
Steeman M, Hebsgaard MB, Fordyce RE, Ho SYW, Rabosky DL, Nielsen R, Rahbek C, Glenner H: SØrensen MV, Willerslev E: Radiation of extant cetaceans driven by restructuring of the oceans. Syst Biol. 2009, 58: 573-585. 10.1093/sysbio/syp060.
Article
PubMed
PubMed Central
Google Scholar
Rice DW: Marine mammals of the world: systematics and distribution. 1998, Society of Marine Mammalogy Special Publication Number 4
Hoelzel AR: Marine mammal biology: an evolutionary approach. 2002, Oxford, United Kingdom: Blackwell Publishing Ltd.
Google Scholar
Slater GJ, Price SA, Santini F, Alfaro ME: Diversity versus disparity and the radiation of modern cetaceans. Proc R Soc B. 2010, 277: 3097-3104. 10.1098/rspb.2010.0408.
Article
PubMed
PubMed Central
Google Scholar
Poltorak A, He X, Smirnova I, Liu MY, Huffel CV, Du X, Birdwell D, Alejos E, Silva M, Galanos C, Freudenberg M, Ricciardi-Castagnoli P, Layton B, Beutler B: Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice: mutations in Tlr4 gene. Science. 1998, 282: 2085-2088.
Article
PubMed
CAS
Google Scholar
Kumar H, Kawai T, Akira S: Pathogen recognition in the innate immune response. Biochem J. 2009, 420: 1-16. 10.1042/BJ20090272.
Article
PubMed
CAS
Google Scholar
da Silva Correia J, Soldau K, Christen U, Tobias PS, Ulevitch RJ: Lipopolysaccharide is in close proximity to each of the proteins in its membrane receptor complex. Transfer from cd14 to tlr4 and md-2. J Biol Chem. 2001, 276: 21129-21135. 10.1074/jbc.M009164200.
Article
PubMed
CAS
Google Scholar
Agnarsson I, May-Collado LJ: The phylogeny of Cetartiodactyla: the importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogenies. Mol Phylogenet Evol. 2008, 48: 964-985. 10.1016/j.ympev.2008.05.046.
Article
PubMed
CAS
Google Scholar
Xiong Y, Brandley MC, Xu S, Zhou K, Yang G: Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales. BMC Evol Biol. 2009, 9: 20-10.1186/1471-2148-9-20.
Article
PubMed
PubMed Central
Google Scholar
Zhou X, Xu S, Yang Y, Zhou K, Yang G: Phylogenomic analyses and improved resolution of Cetartiodactyla. Mol Phyloget Evol. 2011, 61: 255-264. 10.1016/j.ympev.2011.02.009.
Article
Google Scholar
Yampolsky LY, Stoltzfus A: The exchangeability of amino acids in proteins. Genetics. 2005, 170: 1459-1472. 10.1534/genetics.104.039107.
Article
PubMed
CAS
PubMed Central
Google Scholar
Zhang J, Nielsen R, Yang Z: Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 2005, 22: 1-8.
Google Scholar
Shishido R, Ohishia K, Suzukic R, Takishitaa K, Ohtsud D, Okutsud K, Tokutaked K, Katsumatae E, Bandof T, Fujise Y, Murayamag T, Maruyamaa T: Cetacean Toll-like receptor 4 and myeloid differentiation factor 2, and possible cetacean-specific responses against Gram-negative bacteria. Comp Immunol Microb. 2010, 33: 89-98. 10.1016/j.cimid.2010.03.003.
Article
Google Scholar
May-Collado LJ, Agnarsson I, Wartzok D: Phylogenetic review of tonal sound production in whales in relation to sociality. BMC Evol Biol. 2007, 7: 136-10.1186/1471-2148-7-136.
Article
PubMed
PubMed Central
Google Scholar
Gatesy J: More DNA support for a Cetacea/Hippopotamidae clade: the blood-clotting protein gene gamma-fibrinogen. Mol Biol Evol. 1997, 14: 537-543. 10.1093/oxfordjournals.molbev.a025790.
Article
PubMed
CAS
Google Scholar
McGowen MR, Spaulding M, Gatesy J: Divergence date estimation and a comprehensive molecular tree of extant cetaceans. Mol Phylogenet Evol. 2009, 53: 891-906. 10.1016/j.ympev.2009.08.018.
Article
PubMed
CAS
Google Scholar
Janeway CA, Medzhitov R: Innate immune recognition. Annu Rev Immunol. 2002, 20: 197-216. 10.1146/annurev.immunol.20.083001.084359.
Article
PubMed
CAS
Google Scholar
Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci USA. 1988, 85: 2444-2448. 10.1073/pnas.85.8.2444.
Article
PubMed
CAS
PubMed Central
Google Scholar
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32: 1792-1797. 10.1093/nar/gkh340.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kumar S, Dudley J, Nei M, Tamura K: MEGA: a biologistcentric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 2008, 9: 299-306. 10.1093/bib/bbn017.
Article
PubMed
CAS
PubMed Central
Google Scholar
Ronquist F, Huelsenbeck JP: MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003, 19: 1572-1574. 10.1093/bioinformatics/btg180.
Article
PubMed
CAS
Google Scholar
Whelan S, Goldman N: A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 2001, 18: 691-699. 10.1093/oxfordjournals.molbev.a003851.
Article
PubMed
CAS
Google Scholar
Posada D: jModelTest: phylogenetic model averaging. Mol Biol Evol. 2008, 25: 1253-1256. 10.1093/molbev/msn083.
Article
PubMed
CAS
Google Scholar
Kimura M: The neutral theory of molecular evolution. 1983, New York: Cambridge University Press
Chapter
Google Scholar
Ohta T: The nearly neutral theory of molecular evolution. Ann Rev Ecol Syst. 1992, 23: 263-286. 10.1146/annurev.es.23.110192.001403.
Article
Google Scholar
Yang Z, Nielsen R, Goldman N, Pedersen AMK: Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 2000, 155: 431-449.
PubMed
CAS
PubMed Central
Google Scholar
Yang Z: PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007, 24: 1586-1591. 10.1093/molbev/msm088.
Article
PubMed
CAS
Google Scholar
Pond SLK, Frost SDW: Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics. 2005, 21: 2531-2533. 10.1093/bioinformatics/bti320.
Article
PubMed
CAS
Google Scholar
Pond SLK, Frost SDW: Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 2005, 22: 1208-1222. 10.1093/molbev/msi105.
Article
CAS
Google Scholar
Yang Z: Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol. 1998, 15: 568-573. 10.1093/oxfordjournals.molbev.a025957.
Article
PubMed
CAS
Google Scholar
Yang Z, Nielsen R: Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol. 2002, 19: 908-917. 10.1093/oxfordjournals.molbev.a004148.
Article
PubMed
CAS
Google Scholar
Maddison WP, Maddison DR: Mesquite: A modular system for evolutionary analysis, version 1.01. [http://mesquiteproject.org]
Pride DT: SWAAP: a tool for analyzing substitutions and similarity in multiple alignments. Version 1.0.2. [http://www.bacteriamuseum.org/SWAAP/SwaapPage.htm]
Hulo N, Bairoch A, Bulliard V, Cerutti L, Cuche BA, Castro Ed, Lachaize C, Langendijk-Genevaux PS, Sigrist CJA: The 20 years of PROSITE. Nucleic Acids Res. 2008, 36: 245-249.
Article
Google Scholar
Schultz J, Copley RR, Doerks T, Ponting CP, Bork P: SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res. 2000, 28: 231-234. 10.1093/nar/28.1.231.
Article
PubMed
CAS
PubMed Central
Google Scholar
R Development Core Team: R: A language and environment for statistical computing. 2010, R Foundation for Statistical Computing, Vienna, Austria, ISBN 3-900051-07-0, URL http://www.R-project.org/.
Google Scholar