Analysis of Evolution and Ethnic Diversity at Glucose-Associated SNPs of Circadian Clock-Related Loci with Cryptochrome 1, Cryptochrome 2, and Melatonin receptor 1B

Diabetes shows high heritability and, worldwide, causes significant health problems including cardiovascular disease and stroke. There is significant variation in the frequency of diabetes between different populations. Both Cryptochromes and Melatonin have a major role to regulate the circadian clock. Circadian clock failure causes metabolic dysfunctions including diabetes and obesity. Variations in the Cryptochrome 1, the Cryptochrome 2, and the Melatonin receptor 1B (MTNR1B) genes show associations with fasting glucose, and are also related to circadian clock. Here, we analyzed evidence for genetic selection and ethnic diversity at circadian clock- and glucose-related gene loci associated with Cryptochrome 1, Cryptochrome 2, and MTNR1B. We carried out a 3-step genetic method to investigate genetic selection at the Cryptochrome 1, Cryptochrome 2, and MTNR1B on four populations from the 1000 Genomes Project and HapMap. First we used F-statistics to quantify genetic population differences and find ethnic diversity. Then we applied a long-range haplotype test to detect significant extreme long haplotypes, and then the integrated haplotype score (iHS) to find genetic selection at Cryptochrome 1, Cryptochrome 2, and MTNR1B. We observed genetic population differences and ethnic diversity at one glucose-associated Cryptochrome 1 single-nucleotide polymorphism (SNP) (rs8192440), one glucose-associated Cryptochrome 2 SNP (rs11605924), and one glucose-associated MTNR1B SNP (rs10830963) by F-statistics. Both Cryptochrome 1 and MTNR1B also showed selection by the iHS. These observations show new evidence for evolution at Cryptochrome 1, Cryptochrome 2 and MTNR1B. Further investigation should continue to examine the evolution of circadian clock- and glucose-related genes.