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Cooperative care influences genome-wide levels of DNA methylation in nestling chestnut-crowned babblers

ABSTRACT: Here, using whole-genome methylation sequencing, we measured how additional carers influence DNA methylation in nestlings of chestnut-crowned babblers (Pomatostomus ruficeps). Comparing nestlings raised by just their parents and those raised by parents plus additional helpers revealed that additional care is associated with genome-wide differences in DNA methylation. Overall, we saw more methylated in nestlings reared by groups. Sites associated with genes integral for metabolism, growth, sociality, and coping with stressors were differentially methylated between the groups.

ORGANISM(S): Pomatostomus ruficeps

PROVIDER: GSE310508 | GEO | 2026/03/31

REPOSITORIES: GEO

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	GSE310508_all_fledge_filtered_for_model_2025_v1.csv.gz	Csv

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Project description:Proteomics has become a popular method for investigating diet and cuisine in well-preserved ancient food remains, and calcified deposits like dental calculus. However, foodcrusts (the typically charred residues on the surface of pottery) have not been extensively explored as a source of dietary proteins. We remain ignorant of the impact of cooking and burial on the protein extractome, and crucially, the extent to which palaeoproteomic extractomes actually reflect the composition of input ingredients and cuisines. Therefore, through cooking and burial experiments we investigate the impact of these processes on protein preservation in foodcrusts and accompanying ceramics. Here, we aim to identify proteins that persist throughout the cooking process and become embedded in foodcrusts and ceramics, as well as those that persist through six months burial in soil, using ‘typical’ Mesolithic ingredients of Cervus elaphus (red deer), Salmo salar (Atlantic salmon) and Castanea sativa (sweet chestnut). Specifically, we seek to understand why particular proteins persist through cooking and burial. Hence we examine a range of physiochemical properties which have been theorised to aid protein preservation. The results reveal that proteins were much more likely to be detected in foodcrusts than ceramics using the methodology employed, with dietary proteins identified in all buried deer and salmon foodcrust replicates and most chestnut replicates, tentatively indicating that extraction of protein from ancient foodcrusts may be successful, while in contrast, dietary proteins were rarely identified in cooked or buried ceramics of any input ingredient. It was apparent that the input ingredient strongly influenced frequency of protein and peptide identifications, with chestnut surviving poorly compared to other ingredients, revealing that the detection of ingredients is biassed by the ingredients themselves. The results also reveal that degradation is not universal nor linear between proteins, indicating that protein physiochemical properties are at play. While certain properties appear to aid protein preservation such as hydrophobicity, none was seen to single-handedly explain why particular proteins/peptides survive in buried foodcrusts, with results indicating that certain properties act on protein preservation in complex ways requiring further investigation. These results have implications on archaeological analyses, by demonstrating the utility of foodcrusts as a good target sample for proteomics, while cautioning the interpretation of foodcrust extractomes: which should not be expected to reflect the initial input extractome.

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Cooperative care influences genome-wide levels of DNA methylation in nestling chestnut-crowned babblers

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