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https://www.readbyqxmd.com/read/28330913/reconciling-evidence-from-ancient-and-contemporary-genomes-a-major-source-for-the-european-neolithic-within-mediterranean-europe
#1
Joana B Pereira, Marta D Costa, Daniel Vieira, Maria Pala, Lisa Bamford, Nourdin Harich, Lotfi Cherni, Farida Alshamali, Jiři Hatina, Sergey Rychkov, Gheorghe Stefanescu, Turi King, Antonio Torroni, Pedro Soares, Luísa Pereira, Martin B Richards
Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic...
March 29, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28330205/dna-record-of-some-traditional-small-millet-landraces-in-india-and-nepal
#2
Subramanyam Ragupathy, Shanmughanandhan Dhivya, Kirit Patel, Abiran Sritharan, Kathirvelu Sambandan, Hom Gartaula, Ramalingam Sathishkumar, Kamal Khadka, Balasubramanian C Nirmala, A Nirmala Kumari, Steven G Newmaster
Despite the extensive use of small millet landraces as an important source of nutrition for people living in semi-arid regions, they are presently marginalized and their diversity and distribution are threatened at a global scale. Local farmers have developed ancient breeding programs entrenched in traditional knowledge (TK) that has sustained rural cultures for thousands of years. The convention on biological diversity seeks fair and equitable sharing of genetic resources arising from local knowledge and requires signatory nations to provide appropriate policy and legal framework to farmers' rights over plant genetic resources and associated TK...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28316883/middle-pleistocene-protein-sequences-from-the-rhinoceros-genus-stephanorhinus-and-the-phylogeny-of-extant-and-extinct-middle-late-pleistocene-rhinocerotidae
#3
Frido Welker, Geoff M Smith, Jarod M Hutson, Lutz Kindler, Alejandro Garcia-Moreno, Aritza Villaluenga, Elaine Turner, Sabine Gaudzinski-Windheuser
BACKGROUND: Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis)...
2017: PeerJ
https://www.readbyqxmd.com/read/28302420/a-cryptic-mitochondrial-dna-link-between-north-european-and-west-african-dogs
#4
Adeniyi C Adeola, Sheila C Ommeh, Jiao-Jiao Song, S Charles Olaogun, Oscar J Sanke, Ting-Ting Yin, Guo-Dong Wang, Shi-Fang Wu, Zhong-Yin Zhou, Jacqueline K Lichoti, Bernard R Agwanda, Philip M Dawuda, Robert W Murphy, Min-Sheng Peng, Ya-Ping Zhang
Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA (mtDNA) D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups (matrilines; clades): A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D...
November 24, 2016: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28300151/insights-into-early-pig-domestication-provided-by-ancient-dna-analysis
#5
Amke Caliebe, Almut Nebel, Cheryl Makarewicz, Michael Krawczak, Ben Krause-Kyora
Pigs (Sus scrofa) were first domesticated between 8,500 and 8,000 cal BC in the Near East, from where they were subsequently brought into Europe by agriculturalists. Soon after the arrival of the first domestic pigs in northern Europe (~4500 BC), farmers are thought to have started to incorporate local wild boars into their swine herds. This husbandry strategy ultimately resulted in the domestication of European wild boars. Here, we set out to provide a more precise geographic and temporal framework of the early management of suid populations in northern Europe, drawing upon mitochondrial DNA haplotype data from 116 Neolithic Sus specimens...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28286102/historical-gene-flow-and-profound-spatial-genetic-structure-among-golden-pheasant-populations-suggested-by-multi-locus-analysis
#6
Ke He, Hong-Yi Liu, Yun-Fa Ge, Shao-Ying Wu, Qiu-Hong Wan
Major histocompatibility complex (MHC) is a good marker system for geographical genetics since they are functional genes in the immune system that are likely to affect the fitness of the individual, and the survival and evolutionary potential of a population in a changing environment. Golden pheasant (Chrysolophus pictus) is a wild Phasianidae distributed in central and north China. In this study, we used a locus-specific genotyping technique for MHC IIB genes of golden pheasant. Combining with microsatellites (simple sequence repeat, SSR) and mitochondrial DNA (mtDNA) D-loop region, we investigated the demographic history and illuminate genetic structure of this bird in detail...
March 7, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28273082/ancient-dna-reveals-late-pleistocene-existence-of-ostriches-in-indian-sub-continent
#7
Sonal Jain, Niraj Rai, Giriraj Kumar, Parul Aggarwal Pruthi, Kumarasamy Thangaraj, Sunil Bajpai, Vikas Pruthi
Ancient DNA (aDNA) analysis of extinct ratite species is of considerable interest as it provides important insights into their origin, evolution, paleogeographical distribution and vicariant speciation in congruence with continental drift theory. In this study, DNA hotspots were detected in fossilized eggshell fragments of ratites (dated ≥25000 years B.P. by radiocarbon dating) using confocal laser scanning microscopy (CLSM). DNA was isolated from five eggshell fragments and a 43 base pair (bp) sequence of a 16S rRNA mitochondrial-conserved region was successfully amplified and sequenced from one of the samples...
2017: PloS One
https://www.readbyqxmd.com/read/28273061/neanderthal-behaviour-diet-and-disease-inferred-from-ancient-dna-in-dental-calculus
#8
Laura S Weyrich, Sebastian Duchene, Julien Soubrier, Luis Arriola, Bastien Llamas, James Breen, Alan G Morris, Kurt W Alt, David Caramelli, Veit Dresely, Milly Farrell, Andrew G Farrer, Michael Francken, Neville Gully, Wolfgang Haak, Karen Hardy, Katerina Harvati, Petra Held, Edward C Holmes, John Kaidonis, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Patrick Semal, Arkadiusz Soltysiak, Grant Townsend, Donatella Usai, Joachim Wahl, Daniel H Huson, Keith Dobney, Alan Cooper
Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment...
March 8, 2017: Nature
https://www.readbyqxmd.com/read/28272540/ancient-mitochondrial-lineages-support-the-prehistoric-maternal-root-of-basques-in-northern-iberian-peninsula
#9
Leire Palencia-Madrid, Sergio Cardoso, Christine Keyser, Juan Carlos López-Quintana, Amagoia Guenaga-Lizasu, Marian M de Pancorbo
The Basque population inhabits the Franco-Cantabrian region in southwest Europe where Palaeolithic human groups took refuge during the Last Glacial Maximum. Basques have been an isolated population, largely considered as one of the most ancient European populations and it is possible that they maintained some pre-Neolithic genetic characteristics. This work shows the results of mitochondrial DNA analysis of seven ancient human remains from the Cave of Santimamiñe in the Basque Country dated from Mesolithic to the Late Roman period...
March 8, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28266657/diverse-origin-of-mitochondrial-lineages-in-iron-age-black-sea-scythians
#10
Anna Juras, Maja Krzewińska, Alexey G Nikitin, Edvard Ehler, Maciej Chyleński, Sylwia Łukasik, Marta Krenz-Niedbała, Vitaly Sinika, Janusz Piontek, Svetlana Ivanova, Miroslawa Dabert, Anders Götherström
Scythians were nomadic and semi-nomadic people that ruled the Eurasian steppe during much of the first millennium BCE. While having been extensively studied by archaeology, very little is known about their genetic identity. To fill this gap, we analyzed ancient mitochondrial DNA (mtDNA) from Scythians of the North Pontic Region (NPR) and successfully retrieved 19 whole mtDNA genomes. We have identified three potential mtDNA lineage ancestries of the NPR Scythians tracing back to hunter-gatherer and nomadic populations of east and west Eurasia as well as the Neolithic farming expansion into Europe...
March 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28265503/neogene-paleogeography-provides-context-for-understanding-the-origin-and-spatial-distribution-of-cryptic-diversity-in-a-widespread-balkan-freshwater-amphipod
#11
Michał Grabowski, Tomasz Mamos, Karolina Bącela-Spychalska, Tomasz Rewicz, Remi A Wattier
BACKGROUND: The Balkans are a major worldwide biodiversity and endemism hotspot. Among the freshwater biota, amphipods are known for their high cryptic diversity. However, little is known about the temporal and paleogeographic aspects of their evolutionary history. We used paleogeography as a framework for understanding the onset of diversification in Gammarus roeselii: (1) we hypothesised that, given the high number of isolated waterbodies in the Balkans, the species is characterised by high level of cryptic diversity, even on a local scale; (2) the long geological history of the region might promote pre-Pleistocene divergence between lineages; (3) given that G...
2017: PeerJ
https://www.readbyqxmd.com/read/28265086/polyphosphate-granule-biogenesis-is-temporally-and-functionally-tied-to-cell-cycle-exit-during-starvation-in-pseudomonas-aeruginosa
#12
Lisa R Racki, Elitza I Tocheva, Michael G Dieterle, Meaghan C Sullivan, Grant J Jensen, Dianne K Newman
Polyphosphate (polyP) granule biogenesis is an ancient and ubiquitous starvation response in bacteria. Although the ability to make polyP is important for survival during quiescence and resistance to diverse environmental stresses, granule genesis is poorly understood. Using quantitative microscopy at high spatial and temporal resolution, we show that granule genesis in Pseudomonas aeruginosa is tightly organized under nitrogen starvation. Following nucleation as many microgranules throughout the nucleoid, polyP granules consolidate and become transiently spatially organized during cell cycle exit...
March 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28260210/the-study-of-human-y-chromosome-variation-through-ancient-dna
#13
REVIEW
Toomas Kivisild
High throughput sequencing methods have completely transformed the study of human Y chromosome variation by offering a genome-scale view on genetic variation retrieved from ancient human remains in context of a growing number of high coverage whole Y chromosome sequence data from living populations from across the world. The ancient Y chromosome sequences are providing us the first exciting glimpses into the past variation of male-specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from patterns of genetic variation in living populations...
March 4, 2017: Human Genetics
https://www.readbyqxmd.com/read/28254675/from-ancient-herb-to-modern-drug-artemisia-annua-and-artemisinin-for-cancer-therapy
#14
REVIEW
Thomas Efferth
Artemisia annua L. is used throughout Asia and Africa as tea and press juice to treat malaria and related symptomes (fever, chills). Its active ingredient, artemisinin (ARS), has been developed as antimalarial drug and is used worldwide. Interestingly, the bioactivity is not restricted to malaria treatment. We and others found that ARS-type drugs also reveal anticancer in vitro and in vivo. In this review, we give a systematic overview of the literature published over the past two decades until the end of 2016...
February 28, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/28253255/excess-of-genomic-defects-in-a-woolly-mammoth-on-wrangel-island
#15
Rebekah L Rogers, Montgomery Slatkin
Woolly mammoths (Mammuthus primigenius) populated Siberia, Beringia, and North America during the Pleistocene and early Holocene. Recent breakthroughs in ancient DNA sequencing have allowed for complete genome sequencing for two specimens of woolly mammoths (Palkopoulou et al. 2015). One mammoth specimen is from a mainland population 45,000 years ago when mammoths were plentiful. The second, a 4300 yr old specimen, is derived from an isolated population on Wrangel island where mammoths subsisted with small effective population size more than 43-fold lower than previous populations...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28216890/evaluate-the-antigenotoxicity-and-anticancer-role-of-%C3%AE-sitosterol-by-determining-oxidative-dna-damage-and-the-expression-of-phosphorylated-mitogen-activated-protein-kinases-c-fos-c-jun-and-endothelial-growth-factor-receptor
#16
Ramalingam Sharmila, Ganapathy Sindhu
BACKGROUND: Plant sterols are the major source of micronutrients and have not shown any obvious side effects in human. β-sitosterol is one of the most prevalent phytosterols which have been recorded in ancient medicinal history for its use in the treatment of many chronic diseases, especially cancer. The modulations of mitogen-activated protein kinases' (MAPKs') play a crucial role in the development of human renal cell carcinoma. OBJECTIVE: The aim of the current study is to evaluate the antigenotoxic and anticancer role of β-sitosterol against renal carcinogen...
January 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/28212874/multilocus-phylogeny-of-alligator-lizards-elgaria-anguidae-testing-mtdna-introgression-as-the-source-of-discordant-molecular-phylogenetic-hypotheses
#17
Dean H Leavitt, Angela B Marion, Bradford D Hollingsworth, Tod W Reeder
The increased availability of nuclear DNA sequence data has led to a better appreciation of the role and frequency of introgressive hybridization and subsequent mitochondrial capture in misleading phylogenetic hypotheses based on mtDNA sequence data alone. Relationships among members of the alligator lizard genus Elgaria have been addressed with morphology, allozyme and mtDNA sequence data with discordant results. In this study, we use seven nuclear loci (total of 5.9kb) and ∼3kb of mtDNA to infer the phylogenetic relationships among Elgaria species and test whether the discordance among previous phylogenetic hypotheses is due to introgression and mtDNA capture...
February 16, 2017: Molecular Phylogenetics and Evolution
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
#18
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
#19
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
#20
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
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