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Environmental Epigenetic Variation During Giraffe Speciation and Evolution

ABSTRACT: 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.

ORGANISM(S): Giraffa camelopardalis antiquorum Okapia johnstoni Giraffa giraffa angolensis

PROVIDER: GSE312624 | GEO | 2025/12/09

REPOSITORIES: GEO

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			Action	DRS
		Other
	GSE312624_female.results.csv.gz	Csv
	GSE312624_male.results.csv.gz	Csv

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Project description:Plumage color plays a prominent role in reproductive isolation and thus understanding the genetic basis of pigmentation patterns can provide critical insight into speciation. Subspecies of the dark-eyed junco (Junco hyemalis) show marked differences in melanic plumage coloration known to have evolved rapidly since the Last Glacial Maximum just 18,000 years ago. To understand this rapid radiation we studied the pigment composition and the genetic basis of coloration in two divergent subspecies, the slate-colored and Oregon juncos. We used HPLC and light microscopy to investigate pigment deposition patterns in feathers from four body areas. RNA-seq data generated under common garden experimental conditions were then used to compare the relative roles of differential gene expression in growing feathers and sequence divergence in loci expressed during feather development. Junco feathers were found to differ in eumelanin and pheomelanin content and distribution, producing a range of black, gray and brown colors. Transcriptomic data revealed marked regulatory differences among subspecies and among body-parts within subspecies in known melanin-pathway genes (including PMEL, TYR, TYRP1, OCA2, MLANA), but also in several novel or poorly known loci (EDAR, VPS33B, HPS1). Within subspecies, lighter feathers expressed less melanin synthesis genes, more ASIP, and showed differential expression of Wnt signaling genes. Feathers from different body regions also showed differential expression of Hox genes. The two subspecies differed in expression of ASIP and three other genes (MFSD12, KCNJ13, HAND2) previously associated with color development. Sequence variation in the expressed genes was not related to color differences between junco subspecies. Our findings suggest that differential expression of a few genes can account for marked differences in plumage color and pattern, a mechanism that can account for the rapid diversification of juncos. Several novel candidate pigmentation genes found in juncos may contribute to the expression of melanic coloration in other vertebrates.

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Environmental Epigenetic Variation During Giraffe Speciation and Evolution

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