Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes

Funder: Sapienza Università di RomaAbstract: Although ancient DNA data have become increasingly more important in studies about past populations, it is often not feasible or practical to obtain high coverage genomes from poorly preserved samples. While methods of accurate genotype imputation from > 1 × coverage data have recently become a routine, a large proportion of ancient samples remain unusable for downstream analyses due to their low coverage. Here, we evaluate a two-step pipeline for the imputation of common variants in ancient genomes at 0.05–1 × coverage. We use the genotype likelihood input mode in Beagle and filter for confident genotypes as the input to impute missing genotypes. This procedure, when tested on ancient genomes, outperforms a single-step imputation from genotype likelihoods, suggesting that current genotype callers do not fully account for errors in ancient sequences and additional quality controls can be beneficial. We compared the effect of various genotype likelihood calling methods, post-calling, pre-imputation and post-imputation filters, different reference panels, as well as different imputation tools. In a Neolithic Hungarian genome, we obtain ~ 90% imputation accuracy for heterozygous common variants at coverage 0.05 × and > 97% accuracy at coverage 0.5 ×. We show that imputation can mitigate, though not eliminate reference bias in ultra-low coverage ancient genomes

Patterns of Inter-Chromosomal Gene Conversion on the Male-Specific Region of the Human Y Chromosome

The male-specific region of the human Y chromosome (MSY) is characterized by the lack of meiotic recombination and it has long been considered an evolutionary independent region of the human genome. In recent years, however, the idea that human MSY did not have an independent evolutionary history begun to emerge with the discovery that inter-chromosomal gene conversion (ICGC) can modulate the genetic diversity of some portions of this genomic region. Despite the study of the dynamics of this molecular mechanism in humans is still in its infancy, some peculiar features and consequences of it can be summarized. The main effect of ICGC is to increase the allelic diversity of MSY by generating a significant excess of clustered single nucleotide polymorphisms (SNPs) (defined as groups of two or more SNPs occurring in close proximity and on the same branch of the Y phylogeny). On the human MSY, 13 inter-chromosomal gene conversion hotspots (GCHs) have been identified so far, involving donor sequences mainly from the X-chromosome and, to a lesser extent, from autosomes. Most of the GCHs are evolutionary conserved and overlap with regions involved in aberrant X–Y crossing-over. This review mainly focuses on the dynamics and the current knowledge concerning the recombinational landscape of the human MSY in the form of ICGC, on how this molecular mechanism may influence the evolution of the MSY, and on how it could affect the information enclosed within a genomic region which, until recently, appeared to be an evolutionary independent unit

Bone adhered sediments as a source of target and environmental DNA and proteins

In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, however, sediments are not always collected during excavation. In this study, we analyzed an overlooked but abundant resource in archaeological collections - sediments adhered to bone. We performed metagenomics and metaproteomics analysis on sediment from several human skeletal elements, originating from Neolithic to Medieval sites in England. We were able to reconstruct a partial human genome, the genetic profile of which matches that recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular, we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material that is usually ignored or discarded, can be used to reveal information about the individual and the environmental conditions at the time of their death

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, today infects a majority of adults globally1, yet no ancient HSV-1 genomes have yet been published. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups2, 3 has suggested that the virus co-diverged with anatomically modern humans migrating out of Africa4, although a much younger origin has also been proposed5. The lack of ancient HSV-1 genomes, high rates of recombination, and high mobility of humans in the modern era have impeded the understanding of HSV-1’s evolutionary history. Here we present three full ancient European HSV-1 genomes and one partial genome, dating to between the 3rd and 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. These HSV-1 strains fall within modern Eurasian diversity. We estimate a mean mutation rate of 7.6 × 10-7Introduction Results - Retrieved genomes are likely from typical infections - Demographic history of HSV-1 in a global context Discussion Material and Methods - Ethics statement - Sampling - Generation of aDNA libraries - Sequencing - aDNA authentication - Metagenomic screening - Targeted capture of HSV-1 - Alignment of viral data to the reference sequence - Genotyping - HSV-1 linkage disequilibrium and population genetic analysis - Compilation of comparative HSV data - Preparation of genome sequences - HSV-1 phylogenetic analysis and recombination filtering - Phylogenetic dating - Alignment of human data to the reference sequence and quality control - Genetic sex estimation, mtDNA, and Y haplotyping - Human variant calling and imputation of genotype

Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes

Funder: Sapienza Università di RomaAbstract: Although ancient DNA data have become increasingly more important in studies about past populations, it is often not feasible or practical to obtain high coverage genomes from poorly preserved samples. While methods of accurate genotype imputation from > 1 × coverage data have recently become a routine, a large proportion of ancient samples remain unusable for downstream analyses due to their low coverage. Here, we evaluate a two-step pipeline for the imputation of common variants in ancient genomes at 0.05–1 × coverage. We use the genotype likelihood input mode in Beagle and filter for confident genotypes as the input to impute missing genotypes. This procedure, when tested on ancient genomes, outperforms a single-step imputation from genotype likelihoods, suggesting that current genotype callers do not fully account for errors in ancient sequences and additional quality controls can be beneficial. We compared the effect of various genotype likelihood calling methods, post-calling, pre-imputation and post-imputation filters, different reference panels, as well as different imputation tools. In a Neolithic Hungarian genome, we obtain ~ 90% imputation accuracy for heterozygous common variants at coverage 0.05 × and > 97% accuracy at coverage 0.5 ×. We show that imputation can mitigate, though not eliminate reference bias in ultra-low coverage ancient genomes

Progetto, realizzazione e caratterizzazione sperimentale di una cella di ammettenza per misure di permettività in bassa frequenza

In questo lavoro vengono presentati il progetto e la caratterizzazione di una cella di ammettenza a piatti piani paralleli, da utilizzarsi per la misura di permettività in bassa frequenza di sostanze liquide. La cella è stata realizzata con materiali che ne consentano l’utilizzo con svariate tipologie di liquidi, senza che avvengano fenomeni di corrosione, ed è stata progettata con le armature prive di anello di guardia per renderne possibile l’impiego con la serie più ampia possibile di impedenzimetri. Il fattore correttivo necessario per epurare le misure dall’effetto ai bordi (capacità di “fringing”) è stato ricavato tramite opportune simulazioni elettromagnetiche della struttura. Una serie di test sperimentali su liquidi di riferimento in condizioni controllate ha rivelato scarti massimi nella permettività misurata, rispetto ai dati di letteratura, contenuti entro il 6%. Tale dato, corroborato anche da una analisi teorica dell’incertezza di misura, è in linea con l’accuratezza tipica delle soluzioni commerciali, ma con costi nettamente più contenuti (circa un ordine di grandezza inferiori)

Genetic diversity at three palindromic sequences of the human Y chromosome

One of the most striking structural features of the male specific region of the human Y chromosome (MSY) is the presence, within the ampliconic sequences, of eight massive palindromes (P1-P8). Each palindrome is composed of two large inverted repeats (arms) separated by a small “spacer” sequence at the centre. These elements, ranging from 30 kb to 2.9 Mb, contain many testis-specific genes and typically exhibit > 99.9% intra-palindromic (arm-to-arm) sequence identity. It has been hypothesized that the high observed sequence similarity is due to abundant gene conversion events between the arms of each palindrome. Although the occurrence of arm-to-arm gene conversion has been clearly demonstrated, the effect of this molecular mechanism on the genetic diversity of palindromes, as well as its rate and extension, remain largely unexplored. To gain new insights into the evolutionary history of the human Y chromosome palindromic sequences and to shed light into the dynamics of intra-palindrome gene conversion, we analysed by high-coverage next- generation sequencing (50x) the shortest known palindromes (P6, P7 and P8) and their relative spacers (for a total of about 0.3 Mb) in 158 samples chosen to represent most of the independent evolutionary lineages (haplogroups) of the MSY. By this analysis we identified several gene conversion events and a peculiar mutational pattern of the palindrome arms with respect to the spacer. Moreover, we found few phylogenetically conserved paralogous sequence variants (PSVs), suggestive of a high arm-to-arm gene conversion activity. Because Y chromosomes are clonally inherited from father to son, it has been possible to capture their evolutionary relationships in a robust phylogenetic tree with known age of each node. By mapping gene conversion events across a Y tree based on thousands of stable mutations obtained from 3.3 Mb of single copy MSY sequences, we were able to calculate a precise Y-Y gene conversion rate for each of the palindromes here analysed

Permittivity measurement on construction materials through free space method

This paper presents the validation and test of an experimental set-up for complex permittivity measurements of construction materials. Measurements on reference materials like Plexiglas® and PVC in an anechoic chamber and in a laboratory set up give results in agreement with literature data. The proposed set up is able to accommodate walls made with different construction materials and to measure their complex permittivity as a function of the frequency in the 2 - 6 GHz range

Misura della permettività di materiali edili con il metodo in spazio libero

In questo lavoro è stata presentata la caratterizzazione di un metodo in spazio libero per la misura dei valori di permettività di pareti in muratura. Il set-up sperimentale è stato impiegato per analizzare l’andamento in frequenza della permettività di materiali da costruzione diversi