Search results for "ANCIENT DNA"
showing 4 items of 124 documents
Defining the Island Dwarfing Rate of an Extinct Sicilian Elephant Using Ancient DNA
2020
Evolution on islands, and the often extreme phenotypic changes associated with it, has attracted much interest from evolutionary biologists. However, measuring the rate of change of a particular phenotypic trait of extinct animals can be challenging, due to the incompleteness of the fossil record. Here, we use combined molecular and fossil evidence to define the minimum and maximum rate of dwarfing in an extinct Mediterranean dwarf elephant from Puntali Cave (Sicily). Despite the challenges associated with recovering ancient DNA from warm climates, we successfully retrieved a mitogenome from a sample with an estimated age between 147,000 and 50,000 years. Our results suggest that this speci…
Atlas: analysis tools for low-depth and ancient samples
2017
AbstractSummaryPost-mortem damage (PMD) obstructs the proper analysis of ancient DNA samples and can currently only be addressed by removing or down-weighting potentially damaged data. Here we present ATLAS, a suite of methods to accurately genotype and estimate genetic diversity from ancient samples, while accounting for PMD. It works directly from raw BAM files and enables the building of complete and customized pipelines for the analysis of ancient and other low-depth samples in a very user-friendly way. Based on simulations we show that, in the presence of PMD, a dedicated pipeline of ATLAS calls genotypes more accurately than the state-of-the-art pipeline of GATK combined with mapDamag…
Absence of the lactase-persistence-associated allele in early Neolithic Europeans.
2007
Lactase persistence (LP), the dominant Mendelian trait conferring the ability to digest the milk sugar lactose in adults, has risen to high frequency in central and northern Europeans in the last 20,000 years. This trait is likely to have conferred a selective advantage in individuals who consume appreciable amounts of unfermented milk. Some have argued for the “culture-historical hypothesis,” whereby LP alleles were rare until the advent of dairying early in the Neolithic but then rose rapidly in frequency under natural selection. Others favor the “reverse cause hypothesis,” whereby dairying was adopted in populations with preadaptive high LP allele frequencies. Analysis based on the cons…
Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation
2022
©. This manuscript version is made available under the CC-BY 4.0 license http://creativecommons.org/licenses/by/4.0/ This document is the Published manuscript version of a Published Work that appeared in final form in FEMS Microbes. To access the final edited and published work see DOI: 10.1093/femsmc/xtac006 The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied p…