scholarly journals Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences

BMC Biology ◽  
2018 ◽  
Vol 16 (1) ◽  
Author(s):  
Cesare de Filippo ◽  
Matthias Meyer ◽  
Kay Prüfer
Keyword(s):  
Ancient Dna ◽  
Dna Sequences

Systematic benchmark of ancient DNA read mapping

2021 ◽  
Author(s):  
Adrien Oliva ◽  
Raymond Tobler ◽  
Alan Cooper ◽  
Bastien Llamas ◽  
Yassine Souilmi
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Population Genetic ◽  
Reference Genome ◽  
Population Data ◽  
Human Populations ◽  
Current Standard ◽  
Read Mapping ◽  
Reference Bias ◽  
The Impact

Abstract The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA ‘reads’) against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30–80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software—BWA-aln, BWA-mem, NovoAlign and Bowtie2—and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.

Hybridization capture of Larix candidate adaptive genes from sedimentary ancient DNA.

2021 ◽  
Author(s):  
Stefano Meucci ◽  
Luise Schulte ◽  
Kathleen R. Stoof-Leichsenring ◽  
Stefan Kruse ◽  
Konstantin Krutovsky ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Environmental Changes ◽  
Genetic Material ◽  
Siberian Larch ◽  
Shotgun Sequencing ◽  
Adaptive Genetic Variation ◽  
Hybridization Capture ◽  
Sequencing Method ◽  
Larch Species

<p>Siberian larch forests dominate large areas of northern Russia and contribute important roles for the world´s ecosystem. In order to understand the past dynamics of larches and their adaptive genetic variation, sedimentary ancient DNA (sedaDNA) extracted from lake sediment cores is a crucial source of genetic material. The difficulty of retrieving extremely rare DNA sequences from samples reaching back up to 25000 years in age, is challenging. Previous studies (Schulte et al.) showed that the hybridization capture allowed an enrichment of targeted sequences by several orders of magnitude in comparison to shotgun sequencing method. Therefore, we established for the first time, a hybridization capture method targeting 65 candidate adaptive genes laying on the Larix nuclear genome. Our preliminary results showed the ability of our newly established method to enrich extremely rare DNA sequences of the targeted Larix candidate adaptive genes, which were not retrieved by shotgun sequencing method applied on the same samples. Furthermore, the results allowed to detect and compare specific nucleotide polymorphism of adaptive candidate genes among sedaDNA samples distributed in space and time. The establishment of this new method is laying the basis to investigate possible adaptive variation of larch species acquired across the dry and cold conditions of the Last Glacial Maximum (LGM); as well as their possible advantages or disadvantages in relation to the current environmental changes toward dry and warm conditions.</p>

scholarly journals Resurrecting phenotypes from ancient DNA sequences: promises and perspectives

2015 ◽  
Vol 93 (9) ◽  
pp. 701-710 ◽  
Author(s):  
K.L. Campbell ◽  
M. Hofreiter
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Cell Biology ◽  
Genome Engineering ◽  
Ectopic Expression ◽  
Evolutionary Transitions ◽  
Extinct Species ◽  
Evolutionary Origins ◽  
Structural And Functional Properties

Anatomical changes in extinct mammalian lineages over evolutionary time, such as the loss of fingers and teeth and the rapid increase in body size that accompanied the late Miocene dispersal of the progenitors of Steller’s sea cows (Hydrodamalis gigas (Zimmermann, 1780)) into North Pacific waters and the convergent development of a thick pelage and accompanying reductions in ear and tail surface area of woolly mammoths (Mammuthus primigenius (Blumenbach, 1799)) and woolly rhinoceros (Coelodonta antiquitatis (Blumenbach, 1799)), are prime examples of adaptive evolution underlying the exploitation of new habitats. It is likely, however, that biochemical specializations adopted during these evolutionary transitions were of similar or even greater biological importance. As these “living” processes do not fossilize, direct information regarding the physiological attributes of extinct species has largely remained beyond the range of scientific inquiry. However, the ability to retrieve genomic sequences from ancient DNA samples, combined with ectopic expression systems, now permit the evolutionary origins and structural and functional properties of authentic prehistoric proteins to be examined in great detail. Exponential technical advances in ancient DNA retrieval, enrichment, and sequencing will soon permit targeted generation of complete genomes from hundreds of extinct species across the last one million years that, in combination with emerging in vitro expression, genome engineering, and cell differentiation techniques, promises to herald an exciting new trajectory of evolutionary research at the interface of biochemistry, genomics, palaeontology, and cell biology.

scholarly journals Ancient DNA sequences of rice from the low Yangtze reveal significant genotypic divergence

2011 ◽  
Vol 56 (28-29) ◽  
Author(s):  
LongJiang Fan ◽  
YiJie Gui ◽  
YunFei Zheng ◽  
Yu Wang ◽  
DaGuang Cai ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Dna Sequences

scholarly journals Phylogenetic relationships of Chacodelphys (Marsupialia: Didelphidae: Didelphinae) based on “ancient” DNA sequences

2015 ◽  
Vol 97 (2) ◽  
pp. 394-404 ◽  
Author(s):  
Juan F. Díaz-Nieto ◽  
Sharon A. Jansa ◽  
Robert S. Voss
Keyword(s):  
Soft Tissue ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Morphological Character ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Taxon ◽  
Evolutionary Relationships ◽  
Fresh Material

Abstract Morphological character data are inadequate to resolve the evolutionary relationships of the didelphid genus Chacodelphys , which previous phylogenetic analyses have alternatively suggested might be the sister taxon of Lestodelphys and Thylamys (tribe Thylamyini) or of Monodelphis (tribe Marmosini) in the subfamily Didelphinae. Because fresh material of Chacodelphys is unavailable, we extracted DNA from microscopic fragments of soft tissue adhering to the 95-year-old holotype skull of C. formosa. Phylogenetic analyses of the resulting sequence data convincingly resolve Chacodelphys as the sister taxon of Cryptonanus , a genus with which it had not previously been thought to be closely related. This novel clade ( Chacodelphys + Cryptonanus ) belongs to an unnamed thylamyine lineage with Gracilinanus and Lestodelphys + Thylamys , but relationships among these taxa remain to be convincingly resolved. Los análisis basados en caracteres morfológicos han sido inadecuados para resolver las relaciones evolutivas del género marsupial didélfido Chacodelphys . Previos análisis filogenéticos han sugerido como hipótesis alternativas que Chacodelphys sea el grupo hermano de Lestodelphys y Thylamys (tribu Thylamyini) o de Monodelphis (tribu Marmosini), todos estos géneros pertenecientes a la subfamilia Didelphinae. Debido a la ausencia de material fresco de Chacodelphys , extrajimos ADN de fragmentos microscópicos de tejido adherido al cráneo de 95 años del holotipo de C. formosa . Análisis filogenéticos de las secuencias obtenidas resuelven convincentemente la posición filogenética de Chacodelphys como el taxón hermano de Cryptonanus , un género con el cual nunca antes se había pensado que estuviera cercanamente relacionado. Aunque reconocemos a este nuevo clado ( Chacodelphys + Cryptonanus ) junto con Gracilinanus y Lestodelphys + Thylamys pertenecientes a un linaje sin nombre, las relaciones entre estas taxa siguen sin estar convincentemente resueltas.

scholarly journals Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

2016 ◽  
Vol 113 (24) ◽  
pp. 6707-6712 ◽  
Author(s):  
Faisal Almathen ◽  
Pauline Charruau ◽  
Elmira Mohandesan ◽  
Joram M. Mwacharo ◽  
Pablo Orozco-terWengel ◽  
...  
Keyword(s):  
Gene Flow ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Arabian Peninsula ◽  
Long Distance ◽  
Ecological Zones ◽  
Genotype Information ◽  
Mitochondrial Genotype ◽  
History Of ◽  
Approximate Bayesian

Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species’ range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the “restocking from the wild” hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments.

A Blind Testing Design for Authenticating Ancient DNA Sequences

1997 ◽  
Vol 7 (2) ◽  
pp. 261-265 ◽  
Author(s):  
Hong Yang ◽  
Edward M. Golenberg ◽  
Jeheskel Shoshani
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Testing Design

Complete mitochondrial genome of wild aurochs (Bos primigenius) reconstructed from ancient DNA

2013 ◽  
Vol 16 (2) ◽  
pp. 265-273 ◽  
Author(s):  
J. Zeyland ◽  
Ł. Wolko ◽  
J. Bocianowski ◽  
M. Szalata ◽  
R. Słomski ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Demographic History ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Genetic Material ◽  
Gradual Process ◽  
Mtdna Sequence ◽  
History Of

Abstract Extinct aurochs (Bos primigenius), accepted as the ancestor of domestic cattle, was one of the largest wild animals inhabiting Europe, Asia and North Africa. The gradual process of aurochs extinction finished in Poland in 1627, were the last recorded aurochs, a female, died. Some aspects of cattle domestication history and the distribution of aurochs genetic material among modern cattle breeds still remain unclear. Analyses of ancient DNA (aDNA) from bone sample deliver new genetic information about extinct wild aurochs as well as modern cattle phylogeny. DNA was extracted from a fragment of aurochs fossil bone found in the Pisz Forest, Poland. The sample was radiocarbon- dated to about 1500 yBP. The aDNA was used for Whole Genome Amplification in order to form a DNA bank. Auroch mitochondrial DNA sequences were amplified using sets of 41 primers overlapping the whole mtDNA, cloned and sequenced. The sequence of the whole mitochondrial genome was reconstructed and deposed in GenBank [GenBank:JQ437479]. Based on the phylogenetic analyses of the Bovine mitochondrial genomes, a phylogenetic tree was created. As expected, the tree clearly shows that the mtDNA sequence of the analyzed PWA (Polish Wild Aurochs) individual belongs to haplogroup P. In the course of the comparative mtDNA analysis we identified 30 nucleotide marker positions for haplogroup P and nine unique PWA differences compared to the two remaining haplotype P representatives. Our analysis provides the next step to the reconstruction of the demographic history of this extinct but still exciting species.

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