The girl with finches: a unique post-medieval burial in Tunel Wielki Cave, southern Poland
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ABSTRACT:
PROVIDER: PRJEB49644 | ENA |
REPOSITORIES: ENA
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Project description:The prevailing theory for the molecular basis of evolution involves genetic mutations that ultimately generate the heritable phenotypic variation on which natural selection acts. However, epigenetic transgenerational inheritance of phenotypic variation may also play an important role in evolutionary change. A growing number of studies have demonstrated the presence of epigenetic inheritance in a variety of different organisms that can persist for hundreds of generations. The possibility that epigenetic changes could accumulate over macroevolutionary time has been considered, but not yet seldom been tested empirically. The current study was designed to compare epigenetic changes among several closely related species of Darwin’s finches, a well-known example of adaptive radiation. Erythrocyte DNA was obtained from five species of sympatric Darwin's finches that vary in phylogenetic relatedness. Genome wide alterations in genetic mutations using copy number variation (CNV) were compared to epigenetic alterations associated with differential DNA methylation regions (epimutations). Epimutations were more common than genetic CNV mutations among the five species; furthermore, the number of epimutations increased monotonically with phylogenetic distance. Interestingly, the number of genetic CNV mutations did not consistently increase with phylogenetic distance. The number, chromosomal locations, regional clustering, and lack of overlap of epimutations and genetic mutations suggests that epigenetic changes are distinct and that they correlate with the evolutionary history of Darwin’s finches. The potential functional significance of the epimutations was explored by comparing their locations on the genome to the location of evolutionarily important genes and cellular pathways in birds. Specific epimutations were associated with genes related to the bone morphogenic protein (BMP), toll receptor, and melanogenesis signaling pathways. Species- specific epimutations were significantly over-represented in these pathways. Since environmental factors are known to rapidly alter heritable changes in the epigenome, it is possible that epigenetic changes have played a contributing role in the molecular basis of the evolution of Darwin's finches.
2014-06-10 | GSE58334 | GEO
Project description:The molecular basis of evolutionary change is assumed to be genetic variation. However, growing evidence suggests that epigenetic mechanisms, such as DNA methylation, may also be involved in evolutionary change. An important first step in evaluating this hypothesis is to test for the presence of epigenetic variation between natural populations living under different environmental conditions. In the current study we explored variation between populations of Darwin’s finches living in adjacent “urban” and “rural” environments on Santa Cruz Island in the Galápagos. We tested for morphological, genetic, and epigenetic differences between the urban and rural populations of each of two species of ground finches, Geospiza fortis and G. fuliginosa. Using data collected from more than 1000 birds, we found significant morphological differences between populations of G. fortis, but not G. fuliginosa. We did not find genetic differences between populations of either species, based on comparisons of copy number variation (CNV). In contrast, we did find epigenetic differences between the urban and rural populations of both species, based on DNA methylation analysis. We explored genomic features and gene associations of the differentially methylated regions (DMR), as well as their possible functional significance. In summary, our study documents local population epigenetic variation within species of Darwin’s finches.
2017-01-07 | GSE87825 | GEO
Project description:Regenerating feathers of the Gouldian finches were collected from heads of moulting individuals from an Australian captive population. Affymetrix microarrays were used to examine gene expression differences between black and red morphs.
2019-03-01 | GSE125295 | GEO
Project description:Epigenetics and the Evolution of Darwin’s Finches
| PRJNA252020 | ENA
Project description:Many animals exhibit typical color patterns that have been linked to key adaptive functions, yet the developmental mechanisms establishing these crucial designs remain unclear. Here, we surveyed color distribution in the plumage across a large number of passerine finches. Despite extreme apparent pattern diversity, we identified a small set of conserved color regions whose combinatory association can explain all observed patterns. We found these domains are instructed by signals from embryonic somites and lateral plate mesoderm, and through profiling and comparative analyses, produced a molecular map marking putative color domains in the developing skin. This revealed cryptic pre-patterning common to differently colored species, uncovering a simple molecular landscape underlying extensive color pattern variation.
2024-01-18 | GSE165119 | GEO
Project description:We used five different species of Darwins Finches (G. magnirostris, G. conirostris, G. fortis, G. scandens, G. difficilis). G. difficilis was used as a common reference and we polled RNA from 9 unrelated individuals of this species to lower variation. We used at least two unrelated individual embryos from each of the more derived species. We first made cDNA library from the upper beak primordia tissue, which was used to print microarrays. Next, we collected upper beak primordia from stage 26 embryos of 5 species of Darwins Finches that differed in their beak morphology, for making Cy3- and Cy5-labeled probes with the most basal species, the Sharp-beaked Finch, serving as a reference. We then clustered the obtained expression profiles to find transcripts that were expressed in a species- and/or size-specific manner.
2022-11-21 | E-MEXP-702 | biostudies-arrayexpress
Project description: Not available
| S-EPMC8626500 | biostudies-literature
Project description: Not available
| S-EPMC7479612 | biostudies-literature
Project description:Epigenetic variation between urban and rural populations of Darwin’s finches
| PRJNA347828 | ENA
Project description: Not available
| S-EPMC7341330 | biostudies-literature