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https://www.readbyqxmd.com/read/28205612/dna-analysis-of-a-30-000-year-old-urocitellus-glacialis-from-northeastern-siberia-reveals-phylogenetic-relationships-between-ancient-and-present-day-arctic-ground-squirrels
#1
Marina Faerman, Gila Kahila Bar-Gal, Elisabetta Boaretto, Gennady G Boeskorov, Nikolai E Dokuchaev, Oleg A Ermakov, Fedor N Golenishchev, Stanislav V Gubin, Eugenia Mintz, Evgeniy Simonov, Vadim L Surin, Sergei V Titov, Oksana G Zanina, Nikolai A Formozov
In contrast to the abundant fossil record of arctic ground squirrels, Urocitellus parryii, from eastern Beringia, only a limited number of fossils is known from its western part. In 1946, unnamed GULAG prisoners discovered a nest with three mummified carcasses of arctic ground squirrels in the permafrost sediments of the El'ga river, Yakutia, Russia, that were later attributed to a new species, Citellus (Urocitellus) glacialis Vinogr. To verify this assignment and to explore phylogenetic relationships between ancient and present-day arctic ground squirrels, we performed (14)C dating and ancient DNA analyses of one of the El'ga mummies and four contemporaneous fossils from Duvanny Yar, northeastern Yakutia...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28201986/the-origin-of-chow-chows-in-the-light-of-the-east-asian-breeds
#2
Hechuan Yang, Guodong Wang, Meng Wang, Yaping Ma, Tingting Yin, Ruoxi Fan, Hong Wu, Li Zhong, David M Irwin, Weiwei Zhai, Yaping Zhang
BACKGROUND: East Asian dog breeds are one of the most ancient groups of dogs that radiated after the domestication of the dog and represent the most basal lineages of dog evolution. Among these, the Chow Chow is an ancient breed that embodies very distinct morphological and physiological features, such as sturdy build, dense coat, and blue/purple tongue. RESULTS: Using a Restricted site Associated DNA (RAD) sequencing approach, we sequenced the genomes of nine Chow Chows from China...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28188902/dental-pulp-as-a-source-of-low-contaminated-dna
#3
Michel Drancourt, Gérard Aboudharam, Olivier Croce, Fabrice Armougom, Catherine Robert, Didier Raoult
The in-laboratory contamination of the ancient samples hinders the result interpretation of the investigations in the field of paleomicrobiology. We had promoted the dental pulp as a sample that limits the risks of in-laboratory contamination of the ancient material. In this work, we measured the contamination of the dental pulp manipulated according to paleomicrobiology protocol, used as a source of a total DNA for metagenomics. First, total DNA extracted from two dog canines was sequenced using next generation sequencing...
February 8, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28187792/evolution-of-rna-and-dna-guided-antivirus-defense-systems-in-prokaryotes-and-eukaryotes-common-ancestry-vs-convergence
#4
REVIEW
Eugene V Koonin
: Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation...
February 10, 2017: Biology Direct
https://www.readbyqxmd.com/read/28187706/genome-data-on-the-extinct-bison-schoetensacki-establish-it-as-a-sister-species-of-the-extant-european-bison-bison-bonasus
#5
Pauline Palacio, Véronique Berthonaud, Claude Guérin, Josie Lambourdière, Frédéric Maksud, Michel Philippe, Delphine Plaire, Thomas Stafford, Marie-Claude Marsolier-Kergoat, Jean-Marc Elalouf
BACKGROUND: The European bison (Bison bonasus), now found in Europe and the Caucasus, has been proposed to originate either from the extinct steppe/extant American bison lineage or from the extinct Bison schoetensacki lineage. Bison schoetensacki remains are documented in Eurasian Middle Pleistocene sites, but their presence in Upper Pleistocene sites has been questioned. Despite extensive genetic studies carried out on the steppe and European bison, no remains from the fossil record morphologically identified as Bison schoetensacki has been analyzed up to now...
February 10, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28185987/real-time-pcr-strategy-for-the-identification-of-trypanosoma-cruzi-discrete-typing-units-directly-in-chronically-infected-human-blood
#6
Catalina Muñoz-San Martín, Werner Apt, Inés Zulantay
The protozoan Trypanosoma cruzi is the causative agent of Chagas disease, a major public health problem in Latin America. This parasite has a complex population structure comprised by six or seven major evolutionary lineages (discrete typing units or DTUs) TcI-TcVI and TcBat, some of which have apparently resulted from ancient hybridization events. Because of the existence of significant biological differences between these lineages, strain characterization methods have been essential to study T. cruzi in its different vectors and hosts...
February 6, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28185825/amazonian-waters-harbour-an-ancient-freshwater-ceratomyxa-lineage-cnidaria-myxosporea
#7
Suellen A Zatti, Stephen D Atkinson, Jerri L Bartholomew, Antônio A M Maia, Edson A Adriano
A new species of Ceratomyxa parasitizing the gall bladder of Cichla monoculus, an endemic cichlid fish from the Amazon basin in Brazil, is described using morphological and molecular data. In the bile, both immature and mature myxospores were found floating freely or inside elongated plasmodia: length 304 (196-402) μm and width 35.7 (18.3-55.1) μm. Mature spores were elongated and only slightly crescent-shaped in frontal view with a prominent sutural line between two valve cells, which had rounded ends. Measurements of formalin-fixed myxospores: length 6...
February 7, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28177846/nuclear-dna-content-correlates-with-depth-body-size-and-diversification-rate-in-amphipod-crustaceans-from-ancient-lake-baikal-russia
#8
Nicholas W Jeffery, Lev Y Yampolsky, Ryan Gregory
Lake Baikal in Russia is a large, ancient lake that has been the site of a major radiation of amphipod crustaceans. Nearly 400 named species are known in this single lake, and it is thought that many more await description. The size and depth of Lake Baikal, in particular, may have contributed to the radiation of endemic amphipods by providing a large number of microhabitats for species to invade and subsequently experience reproductive isolation. Here we investigate the possibility that large-scale genomic changes have also accompanied diversification in these crustaceans...
November 14, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28173586/evolutionary-patterns-and-processes-lessons-from-ancient-dna
#9
Michela Leonardi, Pablo Librado, Clio Der Sarkissian, Mikkel Schubert, Ahmed H Alfarhan, Saleh A Alquraishi, Khaled A S Al-Rasheid, Cristina Gamba, Eske Willerslev, Ludovic Orlando
No abstract text is available yet for this article.
January 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28170092/quantifying-the-impact-of-%C3%A2%C2%B5ct-scanning-of-human-fossil-teeth-on-esr-age-results
#10
Mathieu Duval, Laura Martín-Francés
Fossil human teeth are nowadays systematically CT-scanned by palaeoanthropologists prior to any further analysis. It has been recently demonstrated that this noninvasive technique has, in most cases, virtually no influence on ancient DNA preservation. However, it may have nevertheless an impact on other techniques, like Electron Spin Resonance (ESR) dating, by artificially ageing the apparent age of the sample. To evaluate this impact, we µCT-scanned several modern enamel fragments following the standard analytical procedures employed by the Dental Anthropology Group at CENIEH, Spain, and then performed ESR dose reconstruction for each of them...
February 7, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28163008/the-information-capacity-of-the-genetic-code-is-the-natural-code-optimal
#11
Ercan E Kuruoglu, Peter F Arndt
We envision the molecular evolution process as an information transfer process and provide a quantitative measure for information preservation in terms of the channel capacity according to the channel coding theorem of Shannon. We calculate Information capacities of DNA on the nucleotide (for non-coding DNA) and amino acid (for coding DNA) level using various substitution models. We extend our results on coding DNA to a discussion about the optimality of the natural codon-amino acid code. We provide the results of an adaptive search algorithm in the code domain and demonstrate the existence of a large number of genetic codes with higher information capacity...
February 2, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28162894/the-neolithic-transition-in-the-baltic-was-not-driven-by-admixture-with-early-european-farmers
#12
Eppie R Jones, Gunita Zarina, Vyacheslav Moiseyev, Emma Lightfoot, Philip R Nigst, Andrea Manica, Ron Pinhasi, Daniel G Bradley
The Neolithic transition was a dynamic time in European prehistory of cultural, social, and technological change. Although this period has been well explored in central Europe using ancient nuclear DNA [1, 2], its genetic impact on northern and eastern parts of this continent has not been as extensively studied. To broaden our understanding of the Neolithic transition across Europe, we analyzed eight ancient genomes: six samples (four to ∼1- to 4-fold coverage) from a 3,500 year temporal transect (∼8,300-4,800 calibrated years before present) through the Baltic region dating from the Mesolithic to the Late Neolithic and two samples spanning the Mesolithic-Neolithic boundary from the Dnieper Rapids region of Ukraine...
January 27, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28160617/reinforcing-plant-evolutionary-genomics-using-ancient-dna
#13
REVIEW
Rafal M Gutaker, Hernán A Burbano
Improved understanding of ancient DNA (aDNA) biochemical properties coupled with application of next generation sequencing (NGS) methods enabled sequencing and authenticating genomes of historical samples. This advancement ignited a revolution in plant evolutionary genomics by allowing direct observations of past molecular diversity. Analyses of genomes sequenced from temporally distributed samples of Gossypium sp., Phytophthora infestans and Arabidopsis thaliana improved our understanding of the evolutionary rates and time scales at which genome remodeling takes place...
February 1, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28157193/unraveling-the-evolutionary-dynamics-of-ancient-and-recent-polypoidization-events-in-avena-poaceae
#14
Qing Liu, Lei Lin, Xiangying Zhou, Paul M Peterson, Jun Wen
Understanding the diversification of polyploid crops in the circum-Mediterranean region is a challenging issue in evolutionary biology. Sequence data of three nuclear genes and three plastid DNA fragments from 109 accessions of Avena L. (Poaceae) and the outgroups were used for maximum likelihood and Bayesian analyses. The evolution of cultivated oat (Avena sativa L.) and its close relatives was inferred to have involved ancient allotetraploidy and subsequent recent allohexaploidy events. The crown ages of two infrageneric lineages (Avena sect...
February 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28134350/the-identification-of-a-1916-irish-rebel-new-approach-for-estimating-relatedness-from-low-coverage-homozygous-genomes
#15
Daniel Fernandes, Kendra Sirak, Mario Novak, John A Finarelli, John Byrne, Edward Connolly, Jeanette E L Carlsson, Edmondo Ferretti, Ron Pinhasi, Jens Carlsson
Thomas Kent was an Irish rebel who was executed by British forces in the aftermath of the Easter Rising armed insurrection of 1916 and buried in a shallow grave on Cork prison's grounds. In 2015, ninety-nine years after his death, a state funeral was offered to his living family to honor his role in the struggle for Irish independence. However, inaccuracies in record keeping did not allow the bodily remains that supposedly belonged to Kent to be identified with absolute certainty. Using a novel approach based on homozygous single nucleotide polymorphisms, we identified these remains to be those of Kent by comparing his genetic data to that of two known living relatives...
January 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28129388/comparing-ancient-dna-preservation-in-petrous-bone-and-tooth-cementum
#16
Henrik B Hansen, Peter B Damgaard, Ashot Margaryan, Jesper Stenderup, Niels Lynnerup, Eske Willerslev, Morten E Allentoft
Large-scale genomic analyses of ancient human populations have become feasible partly due to refined sampling methods. The inner part of petrous bones and the cementum layer in teeth roots are currently recognized as the best substrates for such research. We present a comparative analysis of DNA preservation in these two substrates obtained from the same human skulls, across a range of different ages and preservation environments. Both substrates display significantly higher endogenous DNA content (average of 16...
2017: PloS One
https://www.readbyqxmd.com/read/28119419/single-stranded-dna-library-preparation-from-highly-degraded-dna-using-t4-dna-ligase
#17
Marie-Theres Gansauge, Tobias Gerber, Isabelle Glocke, Petra Korlević, Laurin Lippik, Sarah Nagel, Lara Maria Riehl, Anna Schmidt, Matthias Meyer
DNA library preparation for high-throughput sequencing of genomic DNA usually involves ligation of adapters to double-stranded DNA fragments. However, for highly degraded DNA, especially ancient DNA, library preparation has been found to be more efficient if each of the two DNA strands are converted into library molecules separately. We present a new method for single-stranded library preparation, ssDNA2.0, which is based on single-stranded DNA ligation with T4 DNA ligase utilizing a splinter oligonucleotide with a stretch of random bases hybridized to a 3' biotinylated donor oligonucleotide...
January 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28119108/sex-biased-secondary-contact-obscures-ancient-speciation-onto-relictual-host-trees-in-central-california-moths-syndemis-tortricidae
#18
Daniel Rubinoff, Michael San Jose, Jerry A Powell
The tortricid moth genus Syndemis has ten described species, with two polyphagous species in Europe and North America respectively. We sequenced five nuclear and four mitochondrial genes for Syndemis samples across both continents and discovered unexpected, extensive diversification restricted to California. DNA evidence supports five new, undescribed, species endemic to California, while the rest of North America and Europe have only one species each. Further, the nuclear genes are less variable and yield contrasting phylogenetic signal compared to mitochondrial DNA for basal relationships between taxa across the genus...
January 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28114894/evolutional-dynamics-of-45s-and-5s-ribosomal-dna-in-ancient-allohexaploid-atropa-belladonna
#19
Roman A Volkov, Irina I Panchuk, Nikolai V Borisjuk, Marta Hosiawa-Baranska, Jolanta Maluszynska, Vera Hemleben
BACKGROUND: Polyploid hybrids represent a rich natural resource to study molecular evolution of plant genes and genomes. Here, we applied a combination of karyological and molecular methods to investigate chromosomal structure, molecular organization and evolution of ribosomal DNA (rDNA) in nightshade, Atropa belladonna (fam. Solanaceae), one of the oldest known allohexaploids among flowering plants. Because of their abundance and specific molecular organization (evolutionarily conserved coding regions linked to variable intergenic spacers, IGS), 45S and 5S rDNA are widely used in plant taxonomic and evolutionary studies...
January 23, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28111950/expansion-for-the-brachylophosaurus-canadensis-collagen-i-sequence-and-additional-evidence-of-the-preservation-of-cretaceous-protein
#20
Elena R Schroeter, Caroline J DeHart, Timothy P Cleland, Wenxia Zheng, Paul M Thomas, Neil L Kelleher, Marshall Bern, Mary H Schweitzer
Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these results remain controversial. For proteomic data derived from extinct Mesozoic organisms to reach their greatest potential for investigating questions of phylogeny and paleobiology, it must be shown that peptide sequences can be reliably and reproducibly obtained from fossils and that fragmentary sequences for ancient proteins can be increasingly expanded...
February 3, 2017: Journal of Proteome Research
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