Hydrobates spp. – Circadian locomotor output cycles kaput (Clock) gene poly-glutamine repeats

Annual cues in the environment result in physiological changes that allow organisms to time reproduction during periods of optimal resource availability. Understanding how circadian rhythm genes sense these environmental cues and stimulate the appropriate physiological changes in response is important for determining the adaptability of species, especially in the advent of changing climate. A first step involves characterizing the environmental correlates of natural variation in these genes. Band-rumped and Leach’s storm-petrels (Hydrobates spp.) are pelagic seabirds that breed across a wide range of latitudes. Importantly, some populations have undergone allochronic divergence, in which sympatric populations use the same breeding sites at different times of year. We investigated the relationship between variation in key functional regions of four genes that play an integral role in the cellular clock mechanism – Clock, Bmal1, Cry2 and Per2 – with both breeding season and absolute latitude in these two species complexes.  We discovered that allele frequencies in two genes, Clock and Bmal1, differed between seasonal populations in one archipelago, and also correlated with absolute latitude of breeding colonies. These results indicate that variation in these circadian rhythm genes may be involved in allochronic speciation, as well as adaptation to photoperiod at breeding locations.

Methods
This dataset contains Clock allele length information for samples of band-rumped storm-petrel (Hydrobates castro) and Leach's storm-petrel (Hydrobates leucorhoa) populations located throughout the Atlantic and Pacific oceans. The data were collected from 1995 to 2011. The data were collected by the following individuals:

Yuliana Bedolla-Guzman
Petra Quillfeldt
Juan F. Masello
Petra Deane
Vicki L. Friesen

Polymerase Chain Reaction (PCR) was performed to isolate the Clock gene for all samples in the study. Sequences were aligned using BioEdit (v7.0.9) to confirm amplification of the intended target. A Beckman-Coulter CEQ 8000 was then used to screen for variation in allele lengths in all individuals. The Beckman-Coulter CE 8000 Genetic Analysis software was used to score the resulting chromatograms. Clock allele lengths and sequences of 10 individuals were compared to determine the corresponding number of polyQ repeats based on allele length. Basic Local Alignment Search Tool (BLAST) searches on GenBank were used to confirm that the target genes were correctly amplified.