TY - JOUR
T1 - Genetic comparisons yield insight into the evolution of enamel thickness during human evolution
AU - Horvath, Julie E.
AU - Ramachandran, Gowri L.
AU - Fedrigo, Olivier
AU - Nielsen, William J.
AU - Babbitt, Courtney C.
AU - St. Clair, Elizabeth M.
AU - Pfefferle, Lisa W.
AU - Jernvall, Jukka
AU - Wray, Gregory A.
AU - Wall, Christine E.
N1 - Funding Information:
This paper is dedicated to Charles A. Lockwood. We thank Jennifer An, Annie Chen, Sujoy Ghosh, Michael Granatosky, Amy Heilman, Rich Kay, Anthony Moore, Christina Sheedy, Maxx Toler and Christine Wu for helpful discussions and interactions. We also thank the reviewers and editors for discussion and comments that greatly improved the manuscript. We thank Dr. Lucia Carbone and Alan Mootnik for providing gibbon genomic DNA samples. For training in phylogenetic comparative methods, we thank the AnthroTree Workshop, which is supported by the NSF (BCS-0923791) and the National Evolutionary Synthesis Center (NSF grant EF-0905606). This study was funded by NSF-BCS-08-27552 HOMIND (GAW and CEW) , the Wenner-Gren Foundation for Anthropological Research (CEW) ( Grant 3832395 ) and the Duke Primate Genomics Initiative (JEH and GAW) .
PY - 2014/8
Y1 - 2014/8
N2 - Enamel thickness varies substantially among extant hominoids and is a key trait with significance for interpreting dietary adaptation, life history trajectory, and phylogenetic relationships. There is a strong link in humans between enamel formation and mutations in the exons of the four genes that code for the enamel matrix proteins and the associated protease. The evolution of thick enamel in humans may have included changes in the regulation of these genes during tooth development. The cis-regulatory region in the 5' flank (upstream non-coding region) of MMP20, which codes for enamelysin, the predominant protease active during enamel secretion, has previously been shown to be under strong positive selection in the lineages leading to both humans and chimpanzees. Here we examine evidence for positive selection in the 5' flank and 3' flank of AMELX, AMBN, ENAM, and MMP20. We contrast the human sequence changes with other hominoids (chimpanzees, gorillas, orangutans, gibbons) and rhesus macaques (outgroup), a sample comprising a range of enamel thickness. We find no evidence for positive selection in the protein-coding regions of any of these genes. In contrast, we find strong evidence for positive selection in the 5' flank region of MMP20 and ENAM along the lineage leading to humans, and in both the 5' flank and 3' flank regions of MMP20 along the lineage leading to chimpanzees. We also identify putative transcription factor binding sites overlapping some of the species-specific nucleotide sites and we refine which sections of the up- and downstream putative regulatory regions are most likely to harbor important changes. These non-coding changes and their potential for differential regulation by transcription factors known to regulate tooth development may offer insight into the mechanisms that allow for rapid evolutionary changes in enamel thickness across closely-related species, and contribute to our understanding of the enamel phenotype in hominoids.
AB - Enamel thickness varies substantially among extant hominoids and is a key trait with significance for interpreting dietary adaptation, life history trajectory, and phylogenetic relationships. There is a strong link in humans between enamel formation and mutations in the exons of the four genes that code for the enamel matrix proteins and the associated protease. The evolution of thick enamel in humans may have included changes in the regulation of these genes during tooth development. The cis-regulatory region in the 5' flank (upstream non-coding region) of MMP20, which codes for enamelysin, the predominant protease active during enamel secretion, has previously been shown to be under strong positive selection in the lineages leading to both humans and chimpanzees. Here we examine evidence for positive selection in the 5' flank and 3' flank of AMELX, AMBN, ENAM, and MMP20. We contrast the human sequence changes with other hominoids (chimpanzees, gorillas, orangutans, gibbons) and rhesus macaques (outgroup), a sample comprising a range of enamel thickness. We find no evidence for positive selection in the protein-coding regions of any of these genes. In contrast, we find strong evidence for positive selection in the 5' flank region of MMP20 and ENAM along the lineage leading to humans, and in both the 5' flank and 3' flank regions of MMP20 along the lineage leading to chimpanzees. We also identify putative transcription factor binding sites overlapping some of the species-specific nucleotide sites and we refine which sections of the up- and downstream putative regulatory regions are most likely to harbor important changes. These non-coding changes and their potential for differential regulation by transcription factors known to regulate tooth development may offer insight into the mechanisms that allow for rapid evolutionary changes in enamel thickness across closely-related species, and contribute to our understanding of the enamel phenotype in hominoids.
KW - AMBN
KW - AMELX
KW - ENAM
KW - MMP20
KW - Primate comparative genomics
UR - https://www.scopus.com/pages/publications/84905746729
UR - https://www.scopus.com/pages/publications/84905746729#tab=citedBy
U2 - 10.1016/j.jhevol.2014.01.005
DO - 10.1016/j.jhevol.2014.01.005
M3 - Article
C2 - 24810709
AN - SCOPUS:84905746729
SN - 0047-2484
VL - 73
SP - 75
EP - 87
JO - Journal of Human Evolution
JF - Journal of Human Evolution
ER -