Adaptation to chasmophytic habitats therefore appears to have occurred independently, as a result of convergent evolution within the group. We confirmed that seven of the ten chasmophyte species in the section are not related to each other but are, instead, genetically closer to geographically nearby species belonging to Italicae yet growing in open habitats. The delimitation of other species (e.g., Silene nemoralis, S. Despite the use of a small number of genes, the large number of sequenced samples allowed confident delimitation of 50% of the species. We investigate species delimitation within this section using 500 specimens sequenced for one nuclear and two plastid markers. Silene section Italicae (Caryophyllaceae) has been taxonomically controversial, with about 30 species described. Recent divergence can obscure species boundaries among closely related taxa. Imputation of ancient Sus scrofa holds potential but should be approached with caution due to these biases, and suggests that there is no universal approach for imputation of non-human ancient species.
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This demonstrates that the current reference panel does not possess the full diversity needed for accurate imputation of ancient Sus, due to missing variations from Near Eastern and Mesolithic wild boar. Despite this high concordance the sources of diversity present in the genotypes called in the original high coverage genomes were not equally imputed leading to biases in downstream analyses a trend toward genotypes most common in the reference panel is observed. We achieved genotype concordance in most cases reaching above 90% with the highest being 98% with ∼2,000,000 variants recovered using GLIMPSE. We evaluate a variety of imputation methods, including Beagle5, GLIMPSE, and Impute5 with varying filters, pipelines, and variant calling methods. We show how issues like genetic architecture and, reference panel divergence, composition and size affect imputation accuracy. In this study we report results of a systematic evaluation of imputation of three whole genome ancient Sus scrofa samples from the Early and Late Neolithic (∼7,100-4,500 BP), to test the utility of imputation. Ancient imputation beyond humans has not been investigated.
Imputing missing genotypes can potentially increase information content and quality of ancient data, but requires different computational approaches than modern DNA imputation. Sequencing ancient DNA to high coverage is often limited by sample quality and cost. This would be of enormous utility in dietary recommendations for precision nutrition both at population and individual level. This is a first of its kind of study on baseline variations in genes that could govern cuisine designs, dietary preferences and health outcomes. Examples include ADCY10, TRPV1, RGS6, OR7D4, ITPR3, OPRM1, TCF7L2, and RUNX1. We also identified 1,184 variants that exhibit differences in frequency of derived alleles and high population differentiation (FST ≥0.3) in Indian populations compared to European, East Asian and African populations. Three predominant ancestry groups within IndiGen were identified based on population structure analysis. Across species, receptors for bitter taste were the most diverse compared to others. Genes associated with olfaction harbored most SNPs followed by those associated with differences in perception of salt and pungent tastes. 137,760 SNPs including common and rare variants were identified in IndiGenomes with 62,950 novel (46%) and 48% shared with the 1,000 Genomes. Population genetics approaches were used to infer ancestry of IndiGen individuals, gene divergence and extent of differentiation among studied populations. SNPs from 80 chemosensory genes were studied in whole genomes of 1,029 IndiGen samples and 2054 from the 1000 Genomes project. We aimed to study the variation landscape of chemosensory genes involved in perception of taste, texture, odour, temperature and burning sensations through analysis of 1,029 genomes of the IndiGen project and diverse continental populations. Inherent differences in chemosensory genes, ethnicity, geo-climatic conditions, and sociocultural practices are other determinants. Perception and preferences for food and beverages determine dietary behaviour and health outcomes.
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