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https://www.readbyqxmd.com/read/28444234/inferring-allele-frequency-trajectories-from-ancient-dna-indicates-that-selection-on-a-chicken-gene-coincided-with-changes-in-medieval-husbandry-practices
#1
Liisa Loog, Mark G Thomas, Ross Barnett, Richard Allen, Naomi Sykes, Ptolemaios D Paxinos, Ophelie Lebrasseur, Keith Dobney, Joris Peters, Andrea Manica, Greger Larson, Anders Eriksson
Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele frequency changes to temporal shifts in environment or cultural practices. However, analyses have often been hampered by uneven sampling and uncertainties in sample dating, as well as being confounded by demographic processes. Here we present a Bayesian statistical framework for quantifying the timing and strength of selection using ancient DNA that explicitly addresses these challenges. We applied this method to time series data for two loci: TSHR and BCDO2, both argued to have undergone strong and recent selection in domestic chickens...
April 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28441401/ancient-genes-establish-stress-induced-mutation-as-a-hallmark-of-cancer
#2
Luis Cisneros, Kimberly J Bussey, Adam J Orr, Milica Miočević, Charles H Lineweaver, Paul Davies
Cancer is sometimes depicted as a reversion to single cell behavior in cells adapted to live in a multicellular assembly. If this is the case, one would expect that mutation in cancer disrupts functional mechanisms that suppress cell-level traits detrimental to multicellularity. Such mechanisms should have evolved with or after the emergence of multicellularity. This leads to two related, but distinct hypotheses: 1) Somatic mutations in cancer will occur in genes that are younger than the emergence of multicellularity (1000 million years [MY]); and 2) genes that are frequently mutated in cancer and whose mutations are functionally important for the emergence of the cancer phenotype evolved within the past 1000 million years, and thus would exhibit an age distribution that is skewed to younger genes...
2017: PloS One
https://www.readbyqxmd.com/read/28434019/recent-developments-in-olive-olea-europaea-l-genetics-and-genomics-applications-in-taxonomy-varietal-identification-traceability-and-breeding
#3
REVIEW
L Sebastiani, M Busconi
The latest results in DNA markers application and genomic studies in olive. Olive (Olea europaea L.) is among the most ancient tree crops worldwide and the source of oil beneficial for human health. Despite this, few data on olive genetics are available in comparison with other cultivated plant species. Molecular information is mainly linked to molecular markers and their application to the study of DNA variation in the Olea europaea complex. In terms of genomic research, efforts have been made in sequencing, heralding the era of olive genomic...
April 22, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28423167/what-pre-columbian-mummies-could-teach-us-about-south-american-leishmaniases
#4
Denis Sereno, Mohammad Akhoundi, Franck Dorkeld, Bruno Oury, Hooman Momen, Pascale Perrin
A recent report on the taxonomic profile of the human gut microbiome in pre-Columbian mummies (Santiago-Rodriguez et al. 2016) gives for the first time evidence of the presence of Leishmania DNA (sequences similar to Leishmania donovani according to the authors) that can be reminiscent of visceral leishmaniasis during the pre-Columbian era. It is commonly assumed that Leishmania infantum, the etiological agent of American visceral leishmaniasis (AVL) was introduced into the New World by the Iberian conquest...
April 1, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28422985/revising-mtdna-haplotypes-of-the-ancient-hungarian-conquerors-with-next-generation-sequencing
#5
Endre Neparáczki, Klaudia Kocsy, Gábor Endre Tóth, Zoltán Maróti, Tibor Kalmár, Péter Bihari, István Nagy, György Pálfi, Erika Molnár, István Raskó, Tibor Török
As part of the effort to create a high resolution representative sequence database of the medieval Hungarian conquerors we have resequenced the entire mtDNA genome of 24 published ancient samples with Next Generation Sequencing, whose haplotypes had been previously determined with traditional PCR based methods. We show that PCR based methods are prone to erroneous haplotype or haplogroup determination due to ambiguous sequence reads, and many of the resequenced samples had been classified inaccurately. The SNaPshot method applied with published ancient DNA authenticity criteria is the most straightforward and cheapest PCR based approach for testing a large number of coding region SNP-s, which greatly facilitates correct haplogroup determination...
2017: PloS One
https://www.readbyqxmd.com/read/28422966/taming-the-late-quaternary-phylogeography-of-the-eurasiatic-wild-ass-through-ancient-and-modern-dna
#6
E Andrew Bennett, Sophie Champlot, Joris Peters, Benjamin S Arbuckle, Silvia Guimaraes, Mélanie Pruvost, Shirli Bar-David, Simon J M Davis, Mathieu Gautier, Petra Kaczensky, Ralph Kuehn, Marjan Mashkour, Arturo Morales-Muñiz, Erich Pucher, Jean-François Tournepiche, Hans-Peter Uerpmann, Adrian Bălăşescu, Mietje Germonpré, Can Y Gündem, Mahmoud-Reza Hemami, Pierre-Elie Moullé, Aliye Ötzan, Margarete Uerpmann, Chris Walzer, Thierry Grange, Eva-Maria Geigl
Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia...
2017: PloS One
https://www.readbyqxmd.com/read/28409264/a-study-of-the-bodrogk%C3%A3-z-population-in-north-eastern-hungary-by-y-chromosomal-haplotypes-and-haplogroups
#7
Horolma Pamjav, Á Fóthi, T Fehér, Erzsébet Fóthi
We have determined the distribution of Y chromosomal haplotypes and haplogroups in population samples from one of the most important areas in north-eastern Hungary from many villages in the Bodrogköz. The Bodrogköz region was chosen due to its isolated nature, because this area was a moorland encircled by the Tisza, Bodrog, and Latorca Rivers and inhabitants of this part of Hungary escaped from both Tatar and Ottoman invasions, which decimated the post-Hungarian Conquest populations in many parts of the country...
April 13, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28408977/mitogenomes-of-giant-skipper-butterflies-reveal-an-ancient-split-between-deep-and-shallow-root-feeders
#8
Jing Zhang, Qian Cong, Xiao-Ling Fan, Rongjiang Wang, Min Wang, Nick V Grishin
Background: Giant-Skipper butterflies from the genus Megathymus are North American endemics. These large and thick-bodied Skippers resemble moths and are unique in their life cycles. Grub-like at the later stages of development, caterpillars of these species feed and live inside yucca roots. Adults do not feed and are mostly local, not straying far from the patches of yucca plants. Methods: Pieces of muscle were dissected from the thorax of specimens and genomic DNA was extracted (also from the abdomen of a specimen collected nearly 60 years ago)...
2017: F1000Research
https://www.readbyqxmd.com/read/28408382/extending-the-spectrum-of-dna-sequences-retrieved-from-ancient-bones-and-teeth
#9
Isabelle Glocke, Matthias Meyer
The number of DNA fragments surviving in ancient bones and teeth is known to decrease with fragment length. Recent genetic analyses of Middle Pleistocene remains have shown that the recovery of extremely short fragments can prove critical for successful retrieval of sequence information from particularly degraded ancient biological material. Current sample preparation techniques, however, are not optimized to recover DNA sequences from fragments shorter than approximately 35 base pairs (bp). Here we show that much shorter DNA fragments are present in ancient skeletal remains but lost during DNA extraction...
April 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28402470/proper-authentication-of-ancient-dna-is-essential-yes-but-so-are-undogmatic-approaches
#10
Gary A Toranzos, Tasha M Santiago-Rodriguez, Raul J Cano, Gino Fornaciari
No abstract text is available yet for this article.
April 11, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28396504/joint-estimation-of-relatedness-coefficients-and-allele-frequencies-from-ancient-samples
#11
Christoph Theunert, Fernando Racimo, Montgomery Slatkin
We develop and test a method to address whether DNA samples sequenced from a group of fossil hominin bone or teeth fragments originate from the same individual or from closely related individuals. Our method assumes low amounts of retrievable DNA, significant levels of sequencing error and contamination from one or more present-day humans. We develop and implement a maximum likelihood method that estimates levels of contamination, sequencing error rates and pairwise relatedness coefficients in a set of individuals...
April 10, 2017: Genetics
https://www.readbyqxmd.com/read/28394451/ancient-dna-analysis-identifies-marine-mollusc-shells-as-new-metagenomic-archives-of-the-past
#12
Clio Der Sarkissian, Vianney Pichereau, Catherine Dupont, Peter C Ilsøe, Mickael Perrigault, Paul Butler, Laurent Chauvaud, Jón Eiríksson, James Scourse, Christine Paillard, Ludovic Orlando
Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity, and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories...
April 10, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28392981/improving-ancient-dna-genome-assembly
#13
Alexander Seitz, Kay Nieselt
Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used. However, because of inherent problems with ancient DNA, its de novo assembly is highly complicated. In order to tackle the diversity in the length of the input reads, we propose a two-layer approach, where multiple assemblies are generated in the first layer, which are then combined in the second layer...
2017: PeerJ
https://www.readbyqxmd.com/read/28391476/comparative-assessment-of-genetic-diversity-in-sesamum-indicum-l-using-rapd-and-ssr-markers
#14
Aejaz Ahmad Dar, Sushma Mudigunda, Pramod Kumar Mittal, Neelakantan Arumugam
Sesame (Sesamum indicum L.) is an ancient oilseed crop known for its nutty seeds and high-quality edible oil. It is an unexplored crop with a great economic potential. The present study deals with assessment of genetic diversity in the crop. Twenty two RAPD and 18 SSR primers were used for analysis of the 47 different sesame accessions grown in different agroclimatic zones of India. A total of 256 bands were obtained with RAPD primers, of which 191 were polymorphic. SSR primers gave 64 DNA bands, of which all of were polymorphic...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28390909/deep-reticulation-and-incomplete-lineage-sorting-obscure-the-diploid-phylogeny-of-rain-lilies-and-allies-amaryllidaceae-tribe-hippeastreae
#15
Nicolás García, Ryan A Folk, Alan W Meerow, Srikar Chamala, Matthew A Gitzendanner, Renata Souza de Oliveira, Douglas E Soltis, Pamela S Soltis
Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups...
April 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28389681/-adna-research-from-a%C3%A2-historical-perspective
#16
Elsbeth Bösl
aDNA studies are a cooperative field of research with a broad range of applications including evolutionary biology, genetics, anthropology and archaeology. Scientists are using ancient molecules as source material for historical questions. Colleagues from the humanities are observing this with both interest and concern because aDNA research is affecting academic identities and both concepts of history and historiography. aDNA research developed in a way that can be described as a Hype Cycle (Chackie Fenn)...
April 7, 2017: NTM
https://www.readbyqxmd.com/read/28386123/eastern-mediterranean-mobility-in-the-bronze-and-early-iron-ages-inferences-from-ancient-dna-of-pigs-and-cattle
#17
Meirav Meiri, Philipp W Stockhammer, Nimrod Marom, Guy Bar-Oz, Lidar Sapir-Hen, Peggy Morgenstern, Stella Macheridis, Baruch Rosen, Dorothée Huchon, Joseph Maran, Israel Finkelstein
The Late Bronze of the Eastern Mediterranean (1550-1150 BCE) was a period of strong commercial relations and great prosperity, which ended in collapse and migration of groups to the Levant. Here we aim at studying the translocation of cattle and pigs during this period. We sequenced the first ancient mitochondrial and Y chromosome DNA of cattle from Greece and Israel and compared the results with morphometric analysis of the metacarpal in cattle. We also increased previous ancient pig DNA datasets from Israel and extracted the first mitochondrial DNA for samples from Greece...
April 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28385621/combination-of-morphological-and-molecular-markers-for-the-characterization-of-ancient-native-olive-accessions-in-central-eastern-tunisia
#18
Ibtissem Laaribi, Hassouna Gouta, Mouna Mezghani Ayachi, Foued Labidi, Messaoud Mars
Increasing olive germplasm erosion in the coastline of Tunisia has required an imperious conservation of the traditional genotypes before an ultimate disappearance. This region has been relatively neglected in the literature sources of olive identification. In this context, a prospection effort and a preliminary selection of olive accessions belonging to Central-Eastern Tunisia was carried out. Twenty-seven ancient olive accessions were studied by combining molecular and morphological data in order to fingerprint them, and to evaluate their relationships with classical cultivars...
April 3, 2017: Comptes Rendus Biologies
https://www.readbyqxmd.com/read/28384042/comparison-of-suitability-of-the-most-common-ancient-dna-quantification-methods
#19
Kristýna Brzobohatá, Eva Drozdová, Jiří Smutný, Tomáš Zeman, Radoslav Beňuš
AIMS: Ancient DNA (aDNA) extracted from historical bones is damaged and fragmented into short segments, present in low quantity, and usually copurified with microbial DNA. A wide range of DNA quantification methods are available. The aim of this study was to compare the five most common DNA quantification methods for aDNA. MATERIALS AND METHODS: Quantification methods were tested on DNA extracted from skeletal material originating from an early medieval burial site...
April 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28383827/adp-ribosylation-new-facets-of-an-ancient-modification
#20
REVIEW
Luca Palazzo, Andreja Mikoč, Ivan Ahel
Rapid response to environmental changes is achieved by uni- and multicellular organisms through a series of molecular events, often involving modification of macromolecules, including proteins, nucleic acids and lipids. Amongst these, ADP-ribosylation is of emerging interest because of its ability to modify different macromolecules in the cells, and its association with many key biological processes, such as DNA-damage repair, DNA replication, transcription, cell division, signal transduction, stress and infection responses, microbial pathogenicity and aging...
April 6, 2017: FEBS Journal
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