Kawasaki K, Buchanan AV, Weiss KM. Biomineralization in humans: making the hard choices in life. Annu Rev Genet. 2009;43:119–42.
Article
CAS
Google Scholar
Kawasaki K. The SCPP gene family and the complexity of hard tissues in vertebrates. Cells Tissues Organs. 2011;194:108–12.
Article
Google Scholar
Kawasaki K, Weiss KM. Mineralized tissue and vertebrate evolution: the secretory. Proc Natl Acad Sci USA. 2003;100:4060–5.
Article
CAS
Google Scholar
Sire J-Y, Davit-Béal T, Delgado S, Gu X. The origin and evolution of enamel mineralization genes. Cells Tissues Organs. 2007;186:25–48.
Article
Google Scholar
Bosshardt DD, Lang NP. The junctional epithelium: from health to disease. J Dent Res. 2005;84:9–20.
Article
CAS
Google Scholar
Moffatt P, Smith CE, St-Arnaud R, Nanci A. Characterization of Apin, a secreted protein highly expressed in tooth-associated epithelia. J Cell Biochem. 2008;103:941–56.
Article
CAS
Google Scholar
Lee H-K, Lee D-S, Ryoo H-M, Park J-T, Park S-J, Bae H-S, Cho M-I, Park J-C. The odontogenic ameloblast-associated protein (ODAM) cooperates with RUNX2 and modulates enamel mineralization via regulation of MMP-20. J Cell Biochem. 2010;111:755–67.
Article
CAS
Google Scholar
Lee H-K, Ji S, Park S-J, Choung H-W, Choi Y, Lee H-J, Park S-Y, Park J-C. Odontogenic ameloblast-associated protein (ODAM) mediates junctional epithelium attachment to teeth via integrin-ODAM-rho guanine nucleotide exchange factor 5 (ARHGEF5)-RhoA signaling. J Biol Chem. 2015;290:14740–53.
Nishio C, Wazen R, Kuroda S, Moffatt P, Nanci A. Expression pattern of odontogenic ameloblast-associated and amelotin during formation and regeneration of the junctional epithelium. Eur Cells Mater. 2010;20:393–402.
Article
CAS
Google Scholar
Fouillen A, Dos Santos Neves J, Charline M, Castonguay J-D, Moffatt P, Baron C, Nanci A. Inactivation of AMTN, ODAM and SCPPPQ1 proteins of a specialized basal lamina that attaches epithelial cells to tooth mineral. Sci Rep. 2017;7:46683.
Article
Google Scholar
Park J-C, Park J-T, Son H-H, Kim H-J, Jeong M-J, Lee C-S, Dey R, Cho M-I. The amyloid protein APin is highly expressed during enamel mineralization and maturation in rat incisors. Eur J Oral Sci. 2007;115:153–60.
Article
CAS
Google Scholar
Ikeda Y, Neshatian M, Holcroft J, Ganss B. The enamel protein ODAM promotes mineralization in a collagen matrix. Connect Tissue Res. 2018;59(sup1):62–6.
Article
CAS
Google Scholar
Wazen RM, Moffatt P, Ponce KJ, Kuroda S, Nishio C, Nanci A. Inactivation of the odontogenic ameloblast-associated gene affects the integrity of the junctional epithelium and gingival healing. Eur Cells Mater. 2015;30:187–99.
Article
CAS
Google Scholar
Kestler DP, Foster JS, Macy SD, Murphy CL, Weiss DT, Solomon A. Expression of odontogenic ameloblast-associated protein (ODAM) in dental and other epithelial neoplasms. Mol Med. 2008;14:318–26.
Article
CAS
Google Scholar
Lee HK, Park SJ, Oh HJ, Kim JW, Bae HS, Park JC. Expression pattern, subcellular localization, and functional implications of ODAM in ameloblasts, odontoblasts, osteoblasts, and various cancer cells. Gene Expr Patterns. 2012;12:102–8.
Article
CAS
Google Scholar
Sire J-Y, Delgado S, Girondot M. Hen’s teeth with enamel cap: from dream to impossibility. BMC Evol Biol. 2008;8:e246.
Article
Google Scholar
Davit-Béal T, Tucker AS, Sire J-Y. Loss of teeth and enamel in tetrapods: fossil record, genetic data and morphological adaptations. J Anat. 2009;214:477–501.
Article
Google Scholar
Al-Hashimi N, Lafont A-G, Delgado S, Kawasaki K, Sire J-Y. The enamelin genes in lizard, crocodile, and frog and the pseudogene in the chicken provide new insights on enamelin evolution in tetrapods. Mol Biol Evol. 2010;27:2078–94.
Article
CAS
Google Scholar
Meredith RW, Zhang G, Gilbert MTP, Jarvis ED, Springer MS. Evidence for a single loss of mineralized teeth in the common avian ancestor. Science. 2014;346:1254390.
Article
Google Scholar
Meredith RW, Gatesy J, Springer MS. Molecular decay of enamel matrix protein genes in turtles and other edentulous amniotes. BMC Evol Biol. 2013;13:20.
Article
CAS
Google Scholar
Deméré TA, McGowen MR, Berta A, Gatesy J. Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in mysticete whales. Syst Biol. 2008;57:15–37.
Article
Google Scholar
McKnight DA, Fisher LW. Molecular evolution of dentin phosphoprotein among toothed and toothless animals. BMC Evol Biol. 2009;9:299.
Article
Google Scholar
Meredith RW, Gatesy J, Murphy WJ, Ryder OA, Springer MS. Molecular decay of the tooth gene enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals. PLoS Genet. 2009;5:1–12.
Article
Google Scholar
Meredith RW, Gatesy J, Cheng J, Springer MS. Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales. Proc R Soc B. 2011;278:993–1002.
Article
CAS
Google Scholar
Kawasaki K, JC-C H, Simmer JP. Evolution of Klk4 and enamel maturation in eutherians. Biol Chem. 2014;395:1003–13.
Article
CAS
Google Scholar
Springer MS, Signore AV, Paijmans JLA, Vélez-Juarbe J, Domning DP, Bauer CE, He K, Crerar L, Campos PF, Murphy WJ, Meredith RW, Gatesy J, Willerslev E, MacPhee RDE, Hofreiter M, Campbell KL. 2015 Interordinal gene capture, the phylogenetic position of Steller’s sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia. Mol Phylogenet Evol. 2015;91:178–93.
Article
Google Scholar
Springer MS, Starrett J, Morin PA, Lanzetti A, Hayashi C, Gatesy J. Inactivation of C4orf26 in toothless placental mammals. Mol Phylogenet Evol. 2016;95:34–45.
Article
CAS
Google Scholar
Sharma V, Hecker N, Roscito JG, Foerster L, Langer BE, Hiller M. A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nat Commun. 2018;9:1215.
Article
Google Scholar
Gasse B, Silvent J, Sire J-Y. Evolutionary analysis suggests that AMTN is enamel-specific and a candidate for AI. J Dent Res. 2012;91:1085–9.
Article
CAS
Google Scholar
Delsuc F, Gasse B, Sire J-Y. Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta. BMC Evol Biol. 2015;15:148.
Article
Google Scholar
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Mentjies P, Drummond A. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28:1647–9.
Article
Google Scholar
Katoh K, Misawa K, Kuma K, Miyata TMAFFT. A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–66.
Article
CAS
Google Scholar
Katoh K. Stanley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.
Article
CAS
Google Scholar
Ranwez V, Harispe S, Delsuc F, Douzery EJP. MACSE: multiple alignment of coding SEquences accounting for frameshifts and stop codons. PLoS One. 2011;6:e22594.
Article
CAS
Google Scholar
Ranwez V, Douzery EJP, Cambon C, Chantret N, Delsuc F. MACSE v2: toolkit for the alignment of coding sequences accounting for frameshifts and stop codons. Mol Biol Evol. 2018;35:2582–4.
Article
Google Scholar
Swofford DL, PAUP*. Phylogenetic analysis using parsimony (* and other methods). Sinauer associates, Sunderland Massachusetts: Sinauer Associates; 2002.
Google Scholar
Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688–90.
Article
CAS
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 201;30;1312–1313.
Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES science gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop. 2010:1–8.
Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol. 2008;57:758–71.
Article
Google Scholar
Lartillot N, Poujol R. A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters. Mol Biol Evol. 2010;28:729–44.
Article
Google Scholar
Lartillot N, Delsuc F. Joint reconstruction of divergence times and life-history evolution in placental mammals using a phylogenetic covariance model. Evolution. 2012;66:1773–87.
Article
Google Scholar
Teeling EC, Springer MS, Madsen O, Bates P, O’Brien SJ. Murphy WJ. A molecular phylogeny for bats illuminates biogeography and the fossil record. Science. 2005;307:580–4.
Article
CAS
Google Scholar
Meredith RW, Janecka JE, Gatesy J, Ryder OA, Fisher CA, Teeling EC, Goodbla A, Eizirik E, Simão TLL, Stadler T, Rabosky DL, Honeycutt RL, Flynn JJ, Ingram CM, Steiner C, Williams TL, Robinson TJ, Burk-Herrick A, Westerman M, Ayoub NA, Springer MS, Murphy WJ. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science. 2011;334:521–4.
Delsuc F, Gibb GC, Kuch M, Billet G, Hautier L, Southon J, Rouillard J-M, Fernicola JC, Vizcaíno SF, MacPhee RDE, Poinar HN. The phylogenetic affinities of the extinct glyptodonts. Curr Biol. 2016;26:R141–56.
Article
Google Scholar
Foley NM, Springer MS, Teeling EC. Mammal madness: is the mammal tree of life not yet resolved? Philos Trans R Soc B. 2016;371:20150140.
Article
Google Scholar
Emerling CA, Huynh HT, Nguyen MA, Meredith RW, Springer MS. Spectral shifts of mammalian ultraviolet-sensitive pigments (short wavelength-sensitive opsin 1) are associated with eye length and photic niche evolution. Proc Roy Soc B. 2015;282:20151817.
Jones KE, Bielby J, Cardillo M, Fritz SA, O'Dell J, Orme CDL, Safi K, Sechrest W, Boakes EH, Carbone C, Connolly C, Cutts MJ, Foster JK, Grenyer R, Habib M, Plaster CA, Price SA, Rigby EA, Rist J, Teacher A, Bininda-Emonds ORP, Gittleman JL, Mace GM, Purvis A. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology. 2009;90:2648.
Article
Google Scholar
Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24:1586–91.
Article
CAS
Google Scholar
Thorne JL, Kishono H, Painter IS. Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol. 1998;15:1647–57.
Article
CAS
Google Scholar
Yeo G, Burge CB. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comp Biol. 2004;11:377–94.
Article
CAS
Google Scholar
Nitsche A, Rose D, Fasold M, Reiche K, Stadler PF. Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved. RNA. 2015;21:1–12.
Article
Google Scholar
Springer MS, Meredith RW, Gatesy J, Emerling CA, Park J, Rabosky DL, Stadler T, Steiner C, Ryder OA, Janecka JE, Fisher CA, Murphy WJ. Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS One. 2012;7:e49521.
Article
CAS
Google Scholar
Gaubert P, Antunes A, Meng H, Miao L, Peigné S, Justy F, Njiokou F, Dufour S, Danquah E, Alahakoon J, Verheyen E. The complete phylogeny of pangolins: scaling up resources for the molecular tracing of the most trafficked mammals on earth. J Heredity. 2017;109:347–59.
Article
Google Scholar
Prudent X, Parra G, Schwede P, Roscito JG, Hiller M. Controlling for phylogenetic relatedness and evolutionary rates improves the discovery of associations between species’ phenotypic and genomic differences. Mol Biol Evol. 2016;33:2135–50.
Article
CAS
Google Scholar
Madsen O, Scally M, Douady CJ, Kao DJ, DeBry RW, Adkins R, Amrine HM, Stanhope MJ, de Jong WW, Springer MS. Parallel adaptive radiations in two major clades of placental mammals. Nature. 2001;409:610–4.
Article
CAS
Google Scholar
Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O’Brien SJ. Molecular phylogenetics and the origins of placental mammals. Nature. 2001;409:614–8.
Article
CAS
Google Scholar
Murphy WJ, Eizirik E, O’Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001;294:2348–51.
Article
CAS
Google Scholar
Scally M, Madsen O, Douady CJ, de Jong WW, Stanhope MJ, Springer MS. Molecular evidence for the major clades of placental mammals. J Mammal Evol 2001;8:239–277.
Waddell PJ, Kishino H. Ota R. A phylogenetic foundation for comparative mammalian genomics. Genome Informatics. 2001;12:141–54.
CAS
PubMed
Google Scholar
Delsuc F, Scally M, Madsen O, Stanhope MJ, de Jong W, Catzeflis FM, Springer MS, Douzery EJP. Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting. Mol Biol Evol. 2002;19:1656–71.
Article
CAS
Google Scholar
Springer MS, Murphy WJ, Eizirik E, O’Brien SJ. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc Natl Acad Sci U S A. 2003;100:1056–61.
Springer MS, Stanhope MJ, Madsen O, de Jong WW. Molecules consolidate the placental mammal tree. Trends Ecol Evol. 2004;19:430–8.
Article
Google Scholar
Springer MS, Murphy WJ, Eizirik E, O’Brien SJ. Evidence for major placental clades. In: Rose KD, Archibald JK, editors. The rise of placental mammals: origins and relationships of the major extant clades. Baltimore: Johns Hopkins University Press; 2005. p. 37–49.
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.
Article
CAS
Google Scholar
Gatesy J, Geisler JH, Chang J, Buell C, Berta A, Meredith RW, Springer MS, McGowen MR. A phylogenetic blueprint for a modern whale. Mol Phylogenet Evol. 2013;66:479–506.
Article
Google Scholar
Teeling EC, Madsen O, Van Den Bussche RA, de Jong WW, Stanhope MJ, Springer MS. Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats. Proc Natl Acad Sci U S A. 2002;99:1431–6.
Article
CAS
Google Scholar
Roca AL, Bar-Gal GK, Eizirik E, Helgen KM, Maria R, Springer MS, O’Brien SJ, Murphy WJ. Mesozoic origin for West Indian insectivores. Nature. 2004;429:649–51.
Springer MS, Murphy WJ, Roca AL. Appropriate fossil calibrations and tree constraints uphold the Mesozoic divergence of solenodons from other extant mammals. Mol Phylogenet Evol. 2018;121:158–65.
Article
Google Scholar
Shoshani J, Walter RC, Abraha M, Berhe S, Tassy P, Sanders WJ, Marchant GH, Libeskal Y, Ghirmai T, Zinner D. A proboscidean from the late Oligocene of Eritrea, a “missing link” between early Elephantiformes and Elephantimorpha, and biogeographic implications. Proc Natl Acad Sci U S A. 2006;103:17296–301.
Article
CAS
Google Scholar
Palkopoulou E, Lipson M, Mallick S, Nielsen S, Rohland N, Baleka N, Karpinski S, Ivancevic AM, To T-H, Kortschak RD, Raison JM, Qu Z, Chin T-J, Alt KW, Claesson S, Dalén L, MacPhee RDE, Meller H, Roca AL, Ryder OA, Heiman D, Young S, Breen M, Williams C, Aken BL, Ruffier M, Karlsson E, Johnson J, Di Palma F, Alfordi J, Adelson DL, Mailund T, Munch K, Lindblad-Toh K, Hofreiter M, Poiner H, Reich D. A comprehensive genomic history of extinct and living elephants. Proc Natl Acad Sci U S A. 2018;115:E2566–74.
Article
CAS
Google Scholar
Sharma V, Elghafari A, Hiller M. Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation. Nucleic Acids Res. 2016;44:e103.
Article
Google Scholar
Oliver B, Parisi M, Clark D. Gene expression neighborhoods. J Biol. 2002;1:4.
Article
Google Scholar
Franzen JL. The implications of the numerical dating of the Messel fossil deposit (Eocene, Germany) for mammalian biochronology. Ann Paleontol. 2005;91:329–35.
Article
Google Scholar
Rosenberger AL. Loss of incisor enamel in marmosets. J Mammal. 1978;59:207–8.
Article
Google Scholar
Ishiyama M. Enamel structure in odontocete whales. Scan Microsc. 1987;1:1071–9.
CAS
Google Scholar
Loch C, Duncan W, Simões-Lopes PC, Kieser JA, Fordyce RE. Ultrastructure of enamel and dentine in extant dolphins (Cetacea: Delphinoidea and Inioidea). Zoomorphology. 2013;132:215–25.
Article
Google Scholar
Loch C, Kieser JA, Fordyce RE. Enamel ultrastructure in fossil cetaceans (Cetacea: Archaeoceti and Odontoceti). PLoS One. 2015;10:e0116557.
Article
Google Scholar
Koenigswald W, Rensberger JM, Pretzschner HU. Changes in the tooth enamel of early Paleocene mammals allowing increased diet diversity. Nature. 1987;328:150–2.
Article
Google Scholar
Domning DP. Marching teeth of the manatee. Nat Hist. 1983;92:8–12.
Google Scholar
Rohland N, Reich D, Mallick S, Meyer M, Green RE, Georgiadis NJ, Roca AL, Hofreiter M. Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants. PLoS Biol. 2010;8:e1000564.
Article
CAS
Google Scholar
Seo TK, Kishino H, Thorne JL. Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. Mol Biol Evol. 2004;21:1201–13.
Article
CAS
Google Scholar
Krishnan J, Rohner N. Cavefish and the basis for eye loss. Philos Trans Roy Soc B. 2017;372:20150487.
Article
Google Scholar
Tokita M, Chaeychomsri W, Siruntawineti J. Developmental basis of toothlessness in turtles: insight into convergent evolution of vertebrate morphology. Evolution. 2013;67:260–73.
Article
Google Scholar
Emerling CA, Widjaja AD, Nguyen NN, Springer MS. Their loss is our gain: regressive evolution in vertebrates provides genomic models for uncovering human disease loci. J Med Genet. 2017;54:787–94.
Article
Google Scholar