Environmental Epigenetic Variation During Giraffe Speciation and Evolution
The current study was designed to examine the potential role of environmental epigenetics (DNA methylation) in the phenotypic variation between two species of giraffe and a related species okapi (Okapi johnstoni). The Angolan giraffe (Giraffa giraffa angolensis), subspecies of the southern giraffe (G. giraffa), has a longer neck, and is more muscular and larger in size than the Kordofan giraffe (Giraffa camelopardalis antiquorum), subspecies of the northern giraffe (G. camelopardalis). Epigenetic changes generally have orders of magnitude higher frequency compared to genetic mutations and have been shown to regulate physiological traits in all species examined, from insects to humans. Observations obtained identify differences in the DNA methylation between the two giraffe species. The related okapi (Okapi johnstoni) is also epigenetically distinct from the giraffes. A role for environmental epigenetics in the speciation of giraffes is suggested and supporting data presented. Although genetic mutation change will also have a role, it occurs less frequently than epigenetic change. Genetic single nucleotide polymorphisms (SNPs) were found to have significantly lower frequency than epigenetic differences. Conclusions that environmental induced change in epigenetics will have a significant role in the evolution and speciation of these giraffes is consistent to the observations made in other species such as Darwin's finches. Observations further support the Unified Theory of Evolution and Extended Evolutionary Synthesis, which integrates neo-Lamarckian and neo-Darwinian concepts. Overall design: Buccal samples were collected from the Angolan giraffe (Giraffa giraffa angolensis), the Kordofan giraffe (Giraffa camelopardalis antiquorum)  and the related okapi (Okapi johnstoni). Methylated DNA immunoprecipitation (MeDIP) was performed on the buccal cell DNA samples. The MeDIP was followed by DNA sequencing (MeDIP-Seq). Differential DNA methylation regions (DMRs) were identified between the two giraffe species, seperately for males and females. Some Samples are missing processed data for one of two reasons. First, the initial study plan was to collect additional Okapi samples, however that did not end up being feasable. The two samples collected were insufficient to perform a quality DMR analysis. They are included in the submission since they may be useful for other researchers. Other samples without processed data did not have sufficient read depth to include in the analysis.