Ancient sequences
-
Investigating population continuity with ancient DNA under a spatially explicit simulation framework
Recent advances in sequencing technologies have allowed for the retrieval of ancient DNA data (aDNA) from skeletal remains, providing direct genetic snapshots from diverse periods of human prehistory.
13p vinarcissa 21-03-2023 6 1 Download
-
Sesame is an important and ancient oil crop in tropical and subtropical areas. China is one of the most important sesame producing countries with many germplasm accessions and excellent cultivars.
15p vinarcissa 21-03-2023 4 1 Download
-
Ancient DNA (aDNA) is the first step material in studying the genetic information of ancient samples, as such, it is of great significance. A number of methods have been developed worldwide; however, the contamination of modern human DNA (hDNA) is a problem that causes difficulties for the laboratories in Vietnam. In this study, we have successfully developed an effective and economical aDNA extraction/sequencing method.
7p viellenkullman 13-05-2022 8 1 Download
-
Population demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at the genome level. The present study represents an in-depth genomic analysis of a Pan African set of individuals, which emphasizes their complex relationships and demographic history at population level.
15p vigalileogalilei 27-02-2022 10 1 Download
-
How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over deep timescales. A second approach focuses on the direct identification of genomic changes at a shorter timescale by sequencing ancient DNA preserved in subfossil remains.
17p vigalileogalilei 27-02-2022 9 1 Download
-
The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. Results: Here we introduce EAGER, a time-efficient pipeline, which greatly simplifies the analysis of large-scale genomic data sets. EAGER provides features to preprocess, map, authenticate, and assess the quality of ancient DNA samples. Additionally, EAGER comprises tools to genotype samples to discover, filter, and analyze variants.
14p viaristotle 29-01-2022 7 0 Download
-
We report a method called ContamLD for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA.
22p viarchimedes 26-01-2022 5 0 Download
-
During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications.
18p viarchimedes 26-01-2022 7 0 Download
-
Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochondrial analyses have revealed important insights into the evolutionary history of canids. Utilizing a recently published dog Y-chromosome reference, we analyzed Y-chromosome sequence across a diverse collection of canids and determined the Y haplogroup of three ancient European dogs.
9p vibeauty 23-10-2021 8 0 Download
-
Sample index cross-talk can result in false positive calls when massively parallel sequencing (MPS) is used for sensitive applications such as low-frequency somatic variant discovery, ancient DNA investigations, microbial detection in human samples, or circulating cell-free tumor DNA (ctDNA) variant detection. Therefore, the limit-of-detection of an MPS assay is directly related to the degree of index cross-talk.
10p vibeauty 23-10-2021 7 1 Download
-
In this study, we investigated the quantitative impacts of sequence variations on the structural evolution of homologues in 68 ancient protein superfamilies that exist widely in sequenced eukaryotic, bacterial and archaeal genomes.
9p vitzuyu2711 29-09-2021 5 1 Download
-
It is believed that natural selection acts on the phenotypical changes caused by mutations. Phenotypically, from fishes to amphibians to reptiles, the emergence of limbs greatly facilitates the landing of ancient vertebrates, but the causal mutations and evolutionary trajectory of this process remain unclear.
11p vitzuyu2711 29-09-2021 9 1 Download
-
Originally developed for the genomic analysis of highly degraded ancient DNA, single-stranded DNA (ssDNA) library preparation methods are gaining popularity in the field of cfDNA analysis due to their efficiency and ability to convert short, fragmented DNA into sequencing libraries without altering DNA ends. However, current ssDNA methods are costly and time-consuming.
14p vijeeni2711 24-07-2021 7 0 Download
-
Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis Complex (MTBC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre-Columbian mummies of Peru, sparking debate over the origin and frequency of tuberculosis in the Americas prior to European colonization.
13p vijeeni2711 24-07-2021 6 0 Download
-
The current growth in DNA sequencing techniques makes of genome annotation a crucial task in the genomic era. Traditional gene finders focus on protein-coding sequences, but they are far from being exhaustive.
10p vijeeni2711 24-07-2021 8 0 Download
-
Recent advances in the next-generation sequencing (NGS) allowed the metagenomic analyses of DNA from many different environments and sources, including thousands of years old skeletal remains. It has been shown that most of the DNA extracted from ancient samples is microbial.
14p vijeeni2711 24-07-2021 13 0 Download
-
After over a decade of developments in field collection, laboratory methods and advances in highthroughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.
10p vijeeni2711 30-06-2021 12 1 Download
-
Duplicated gene pairs produced by ancient polyploidy maintain high sequence similarity over a long period of time and may result from illegitimate recombination between homeologous chromosomes.
19p vilichoo2711 25-06-2021 5 1 Download
-
Bud dormancy is a strategic mechanism plants developed as an adaptation to unfavorable environments. The grapevine (Vitis vinifera) is one of the most ancient fruit vine species and vines are planted all over the world due to their great economic benefits.
20p vijichea2711 28-05-2021 8 1 Download
-
Modern DNA sequencing methods produce vast amounts of data that often requires mapping to a reference genome. Most existing programs use the number of mismatches between the read and the genome as a measure of quality.
17p vikentucky2711 26-11-2020 11 0 Download