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https://www.readbyqxmd.com/read/29675468/decline-of-genetic-diversity-in-ancient-domestic-stallions-in-europe
#1
Saskia Wutke, Edson Sandoval-Castellanos, Norbert Benecke, Hans-Jürgen Döhle, Susanne Friederich, Javier Gonzalez, Michael Hofreiter, Lembi Lõugas, Ola Magnell, Anna-Sapfo Malaspinas, Arturo Morales-Muñiz, Ludovic Orlando, Monika Reissmann, Alexandra Trinks, Arne Ludwig
Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages...
April 2018: Science Advances
https://www.readbyqxmd.com/read/29674573/ancient-dna-untangles-south-asian-roots
#2
Lizzie Wade
No abstract text is available yet for this article.
April 20, 2018: Science
https://www.readbyqxmd.com/read/29665884/factors-influencing-horizontal-gene-transfer-in-the-intestine
#3
Ximin Zeng, Jun Lin
Antibiotic resistance (AR) is ancient. Use of antibiotics is a selective driving force that enriches AR genes and promotes the emergence of resistant pathogens. It also has been widely accepted that horizontal gene transfer (HGT) occurs everywhere and plays a critical role in the transmission of AR genes among bacteria. However, our understanding of HGT processes primarily build on extensive in vitro studies; to date, there is still a significant knowledge gap regarding in situ HGT events as well as the factors that influence HGT in different ecological niches...
December 2017: Animal Health Research Reviews
https://www.readbyqxmd.com/read/29665771/evidence-for-late-pleistocene-origin-of-astyanax-mexicanus-cavefish
#4
Julien Fumey, Hélène Hinaux, Céline Noirot, Claude Thermes, Sylvie Rétaux, Didier Casane
BACKGROUND: Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to two main groups, the so-called "old" and "new" lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations. RESULTS: We reanalyzed the geographic distribution of mitochondrial and nuclear DNA polymorphisms and we found that these data do not support the existence of two cavefish lineages...
April 18, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29657119/reconciling-conflicting-phylogenies-in-the-origin-of-sweet-potato-and-dispersal-to-polynesia
#5
Pablo Muñoz-Rodríguez, Tom Carruthers, John R I Wood, Bethany R M Williams, Kevin Weitemier, Brent Kronmiller, David Ellis, Noelle L Anglin, Lucas Longway, Stephen A Harris, Mark D Rausher, Steven Kelly, Aaron Liston, Robert W Scotland
The sweet potato is one of the world's most widely consumed crops, yet its evolutionary history is poorly understood. In this paper, we present a comprehensive phylogenetic study of all species closely related to the sweet potato and address several questions pertaining to the sweet potato that remained unanswered. Our research combined genome skimming and target DNA capture to sequence whole chloroplasts and 605 single-copy nuclear regions from 199 specimens representing the sweet potato and all of its crop wild relatives (CWRs)...
April 7, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29656370/role-of-exosomes-in-human-retroviral-mediated-disorders
#6
REVIEW
Monique Anderson, Fatah Kashanchi, Steven Jacobson
Retroviruses comprise an ancient and varied group of viruses with the unique ability to integrate DNA from an RNA transcript into the genome, a subset of which are able to integrate in humans. The timing of these integrations during human history has dictated whether these viruses have remained exogenous and given rise to various human diseases or have become inseparable from the host genome (endogenous retroviruses). Given the ability of retroviruses to integrate into the host and subsequently co-opt host cellular process for viral propagation, retroviruses have been shown to be closely associated with several cellular processes including exosome formation...
April 14, 2018: Journal of Neuroimmune Pharmacology: the Official Journal of the Society on NeuroImmune Pharmacology
https://www.readbyqxmd.com/read/29642393/ancient-dna-from-giant-panda-ailuropoda-melanoleuca-of-south-western-china-reveals-genetic-diversity-loss-during-the-holocene
#7
Gui-Lian Sheng, Axel Barlow, Alan Cooper, Xin-Dong Hou, Xue-Ping Ji, Nina G Jablonski, Bo-Jian Zhong, Hong Liu, Lawrence J Flynn, Jun-Xia Yuan, Li-Rui Wang, Nikolas Basler, Michael V Westbury, Michael Hofreiter, Xu-Long Lai
The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations...
April 6, 2018: Genes
https://www.readbyqxmd.com/read/29626805/evaluation-of-the-precision-id-whole-mtdna-genome-panel-for-forensic-analyses
#8
Christina Strobl, Mayra Eduardoff, Magdalena M Bus, Marie Allen, Walther Parson
Mitochondrial DNA (mtDNA) amplification and Massively Parallel Sequencing (MPS) using an early access version of the Precision ID Whole MtDNA Genome Panel (Thermo Fisher Scientific) and the Ion Personal Genome Machine (PGM) were evaluated using 15 forensically relevant samples. Samples were selected to represent typical forensic specimens for mtDNA analysis including hairs, hair shafts, swabs and ancient solid tissue samples (bones and teeth) that were stored in the freezer for up to several years after having been typed with conventional Sanger-type Sequencing and Capillary Electrophoresis...
March 29, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29618319/nquire-a-statistical-framework-for-ploidy-estimation-using-next-generation-sequencing
#9
Clemens L Weiß, Marina Pais, Liliana M Cano, Sophien Kamoun, Hernán A Burbano
BACKGROUND: Intraspecific variation in ploidy occurs in a wide range of species including pathogenic and nonpathogenic eukaryotes such as yeasts and oomycetes. Ploidy can be inferred indirectly - without measuring DNA content - from experiments using next-generation sequencing (NGS). We present nQuire, a statistical framework that distinguishes between diploids, triploids and tetraploids using NGS. The command-line tool models the distribution of base frequencies at variable sites using a Gaussian Mixture Model, and uses maximum likelihood to select the most plausible ploidy model...
April 4, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29610337/human-bony-labyrinth-is-an-indicator-of-population-history-and-dispersal-from-africa
#10
Marcia S Ponce de León, Toetik Koesbardiati, John David Weissmann, Marco Milella, Carlos S Reyna-Blanco, Gen Suwa, Osamu Kondo, Anna-Sapfo Malaspinas, Tim D White, Christoph P E Zollikofer
The dispersal of modern humans from Africa is now well documented with genetic data that track population history, as well as gene flow between populations. Phenetic skeletal data, such as cranial and pelvic morphologies, also exhibit a dispersal-from-Africa signal, which, however, tends to be blurred by the effects of local adaptation and in vivo phenotypic plasticity, and that is often deteriorated by postmortem damage to skeletal remains. These complexities raise the question of which skeletal structures most effectively track neutral population history...
April 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29609050/poisoning-histories-in-the-italian-renaissance-the-case-of-pico-della-mirandola-and-angelo-poliziano
#11
Gianni Gallello, Elisabetta Cilli, Fulvio Bartoli, Massimo Andretta, Lucio Calcagnile, Agustin Pastor, Miguel de la Guardia, Patrizia Serventi, Alberto Marino, Stefano Benazzi, Giorgio Gruppioni
Giovanni Pico della Mirandola and Angelo Poliziano were two of the most important humanists of the Italian Renaissance. They died suddenly in 1494 and their deaths have been for centuries a subject of debate. The exhumation of their remains offered the opportunity to study the cause of their death through a multidisciplinary research project. Anthropological analyses, together with documentary evidences, radiocarbon dating and ancient DNA analysis supported the identification of the remains attributed to Pico...
March 28, 2018: Journal of Forensic and Legal Medicine
https://www.readbyqxmd.com/read/29607928/mechanisms-of-the-ph-and-oxygen-dependent-oxidation-activities-of-artesunate
#12
Katsunori Tsuda, Licht Miyamoto, Shuichi Hamano, Yuri Morimoto, Yumi Kangawa, Chika Fukue, Yoko Kagawa, Yuya Horinouchi, Wenting Xu, Yasumasa Ikeda, Toshiaki Tamaki, Koichiro Tsuchiya
Artemisinin was discovered in 1971 as a constituent of the wormwood genus plant (Artemisia annua). This plant has been used as an herbal medicine to treat malaria since ancient times. The compound artemisinin has a sesquiterpene lactone bearing a peroxide group that offers its biological activity. In addition to anti-malarial activity, artemisinin derivatives have been reported to exert antitumor activity in cancer cells, and have attracted attention as potential anti-cancer drugs. Mechanisms that might explain the antitumor activities of artemisinin derivatives reportedly induction of apoptosis, angiogenesis inhibitory effects, inhibition of hypoxia-inducible factor-1α (HIF-1α) activation, and direct DNA injury...
2018: Biological & Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/29607481/ancient-dna-reveals-temporal-population-structure-within-the-south-central-andes-area
#13
M Gabriela Russo, Fanny Mendisco, Sergio A Avena, Cristian M Crespo, Valeria Arencibia, Cristina B Dejean, Verónica Seldes
OBJECTIVES: The main aim of this work was to contribute to the knowledge of pre-Hispanic genetic variation and population structure among the South-central Andes Area by studying individuals from Quebrada de Humahuaca, North-western (NW) Argentina. MATERIALS AND METHODS: We analyzed 15 autosomal STRs in 19 individuals from several archaeological sites in Quebrada de Humahuaca, belonging to the Regional Developments Period (900-1430 AD). Compiling autosomal, mitochondrial, and Y-chromosome data, we evaluated population structure and differentiation among eight South-central Andean groups from the current territories of NW Argentina and Peru...
April 1, 2018: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/29607044/ancient-pathogen-dna-in-human-teeth-and-petrous-bones
#14
Ashot Margaryan, Henrik B Hansen, Simon Rasmussen, Martin Sikora, Vyacheslav Moiseyev, Alexandr Khoklov, Andrey Epimakhov, Levon Yepiskoposyan, Aivar Kriiska, Liivi Varul, Lehti Saag, Niels Lynnerup, Eske Willerslev, Morten E Allentoft
Recent ancient DNA (aDNA) studies of human pathogens have provided invaluable insights into their evolutionary history and prevalence in space and time. Most of these studies were based on DNA extracted from teeth or postcranial bones. In contrast, no pathogen DNA has been reported from the petrous bone which has become the most desired skeletal element in ancient DNA research due to its high endogenous DNA content. To compare the potential for pathogenic aDNA retrieval from teeth and petrous bones, we sampled these elements from five ancient skeletons, previously shown to be carrying Yersinia pestis ...
March 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29606093/dna-methylation-variability-among-individuals-is-related-to-cpgs-cluster-density-and-evolutionary-signatures
#15
Domenico Palumbo, Ornella Affinito, Antonella Monticelli, Sergio Cocozza
BACKGROUND: In recent years, epigenetics has gained a central role in the understanding of the process of natural selection. It is now clear how environmental impacts on the methylome could promote methylation variability with direct effects on disease etiology as well as phenotypic and genotypic variations in evolutionary processes. To identify possible factors influencing inter-individual methylation variability, we studied methylation values standard deviation of 166 healthy individuals searching for possible associations with genomic features and evolutionary signatures...
April 2, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29603124/comparison-of-two-ancient-dna-extraction-protocols-for-skeletal-remains-from-tropical-environments
#16
Maria A Nieves-Colón, Andrew T Ozga, William J Pestle, Andrea Cucina, Vera Tiesler, Travis W Stanton, Anne C Stone
OBJECTIVES: The tropics harbor a large part of the world's biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semi-tropical sites in Tanzania, Mexico, and Puerto Rico (N = 12). MATERIALS AND METHODS: All samples were extracted twice, built into double-stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500...
March 30, 2018: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/29602784/stable-isotope-probing-of-microbial-iron-reduction-in-chocolate-pots-hot-spring-yellowstone-national-park
#17
Nathaniel W Fortney, Shaomei He, Ajinkya Kulkarni, Michael W Friedrich, Charlotte Holz, Eric S Boyd, Eric E Roden
Chocolate Pots hot springs (CP) is a circumneutral pH, Fe-rich geothermal feature located in Yellowstone National Park. Previous Fe(III)-reducing enrichment culture studies with CP sediments identified close relatives of known dissimilatory Fe(III)-reducing bacterial (FeRB) taxa, including Geobacter and Melioribacter However, the abundance and activity of such organisms in the native microbial community is unknown. Here we used stable isotope probing experiments combined with 16S rRNA gene amplicon and shotgun metagenomic sequencing to gain an understanding of the in situ Fe(III)-reducing microbial community at CP...
March 30, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29601845/the-evolution-distribution-and-diversity-of-endogenous-circoviral-elements-in-vertebrate-genomes
#18
Tristan P W Dennis, William Marciel de Souza, Soledad Marsile-Medun, Joshua B Singer, Sam J Wilson, Robert J Gifford
Circoviruses (family Circoviridae) are small, non-enveloped viruses that have short, single-stranded DNA genomes. Circovirus sequences are frequently recovered in metagenomic investigations, indicating that these viruses are widespread, yet they remain relatively poorly understood. Endogenous circoviral elements (CVe) are DNA sequences derived from circoviruses that occur in vertebrate genomes. CVe are a useful source of information about the biology and evolution of circoviruses. In this study, we screened 362 vertebrate genome assemblies in silico to generate a catalog of CVe loci...
March 27, 2018: Virus Research
https://www.readbyqxmd.com/read/29599177/teleost-fish-specific-preferential-retention-of-pigmentation-gene-containing-families-after-whole-genome-duplications-in-vertebrates
#19
Thibault Lorin, Frédéric G Brunet, Vincent Laudet, Jean-Nicolas Volff
Vertebrate pigmentation is a highly diverse trait mainly determined by neural crest cell derivatives. It has been suggested that two rounds (1R/2R) of whole-genome duplications (WGDs) at the basis of vertebrates allowed changes in gene regulation associated with neural crest evolution. Subsequently, the teleost fish lineage experienced other WGDs, including the teleost-specific Ts3R before teleost radiation and the more recent Ss4R at the basis of salmonids. As the teleost lineage harbors the highest number of pigment cell types and pigmentation diversity in vertebrates, WGDs might have contributed to the evolution and diversification of the pigmentation gene repertoire in teleosts...
March 29, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29595802/divided-by-dna-the-uneasy-relationship-between-archaeology-and-ancient-genomics
#20
Ewen Callaway
No abstract text is available yet for this article.
March 29, 2018: Nature
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