† Present address: Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, D-69117 Heidelberg, Germany
Forums, H&C, Research Papers, Perspective (EDE)
Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus
Article first published online: 30 MAR 2012
© 2012 Wiley Periodicals, Inc.
Evolution & Development
Volume 14, Issue 2, pages 152–167, March / April 2012
How to Cite
Garfield, D., Haygood, R., Nielsen, W. J. and Wray, G. A. (2012), Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus. Evolution & Development, 14: 152–167. doi: 10.1111/j.1525-142X.2012.00532.x
- Issue published online: 30 MAR 2012
- Article first published online: 30 MAR 2012
- NSF. Grant Number: DIG 0910121
- NSF Bioinformatics Postdoctoral Fellowship
- NSF. Grant Number: DEB 02-35152
- NASA. Grant Number: NAG-2-1583
Despite the fact that noncoding sequences comprise a substantial fraction of functional sites within all genomes, the evolutionary mechanisms that operate on genetic variation within regulatory elements remain poorly understood. In this study, we examine the population genetics of the core, upstream cis-regulatory regions of eight genes (AN, CyIIa, CyIIIa, Endo16, FoxB, HE, SM30 a, and SM50) that function during the early development of the purple sea urchin, Strongylocentrotus purpuratus. Quantitative and qualitative measures of segregating variation are not conspicuously different between cis-regulatory and closely linked “proxy neutral” noncoding regions containing no known functional sites. Length and compound mutations are common in noncoding sequences; conventional descriptive statistics ignore such mutations, under-representing true genetic variation by approximately 28% for these loci in this population. Patterns of variation in the cis-regulatory regions of six of the genes examined (CyIIa, CyIIIa, Endo16, FoxB, AN, and HE) are consistent with directional selection. Genetic variation within annotated transcription factor binding sites is comparable to, and frequently greater than, that of surrounding sequences. Comparisons of two paralog pairs (CyIIa/CyIIIa and AN/HE) suggest that distinct evolutionary processes have operated on their cis-regulatory regions following gene duplication. Together, these analyses provide a detailed view of the evolutionary mechanisms operating on noncoding sequences within a natural population, and underscore how little is known about how these processes operate on cis-regulatory sequences.