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https://www.readbyqxmd.com/read/29788493/how-the-central-american-seaway-and-an-ancient-northern-passage-affected-flatfish-diversification
#1
Lisa Byrne, François Chapleau, Stéphane Aris-Brosou
While the natural history of flatfish has been debated for decades, the mode of diversification of this biologically and economically important group has never been elucidated. To address this question, we assembled the largest molecular data set to date, covering > 300 species (out of ca. 800 extant), from 13 of the 14 known families over nine genes, and employed relaxed molecular clocks to uncover their patterns of diversification. As the fossil record of flatfish is contentious, we used sister species distributed on both sides of the American continent to calibrate clock models based on the closure of the Central American Seaway (CAS), and on their current species range...
May 21, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29787874/ancient-observation-of-spinal-cord-injury-the-case-of-the-assiryan-lion
#2
REVIEW
Gustavo J Luvizutto, Emerson G Siqueira, Pedro Tadao Hamamoto Filho, Viviane F Zétola, Marcos C Lange, Hélio A Theive, Luiz A Resende, Rodrigo Bazan
The description of paraplegia is considered a milestone in the history of neurology. The Egyptians provided excellent descriptions of spinal cord injuries, the Bible has several references to paraplegia, and, more recently, the pioneers of neurology described the classic syndromes related to spinal injuries and paraplegia. Here, we describe an ancient observation by the Assyrian people of paraplegia in an animal. In ancient Assyria, lion hunting was a ritualized activity conducted for political and religious purposes...
May 19, 2018: World Neurosurgery
https://www.readbyqxmd.com/read/29784781/c-4-sterol-demethylation-enzymes-distinguish-bacterial-and-eukaryotic-sterol-synthesis
#3
Alysha K Lee, Amy B Banta, Jeremy H Wei, David J Kiemle, Ju Feng, José-Luis Giner, Paula V Welander
Sterols are essential eukaryotic lipids that are required for a variety of physiological roles. The diagenetic products of sterol lipids, sterane hydrocarbons, are preserved in ancient sedimentary rocks and are utilized as geological biomarkers, indicating the presence of both eukaryotes and oxic environments throughout Earth's history. However, a few bacterial species are also known to produce sterols, bringing into question the significance of bacterial sterol synthesis for our interpretation of sterane biomarkers...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29773513/insights-in-the-history-of-pancreas-restoring-the-true-meaning-of-kallikreas
#4
REVIEW
Niki Papavramidou
BACKGROUND/PURPOSE: This paper investigates the history of pancreas in classical and late antiquity with the intent to correlate it to the modern medical knowledge. Furthermore, an attempt is made to understand the true meaning of the term "kallikreas". METHODS: Only primary textual sources are used in the transcription of ancient references of "pancreas" and/or "kallikreas". All of the references are analyzed and interpreted under a modern prism for better understanding the ancient anatomy proposed...
May 4, 2018: Pancreatology: Official Journal of the International Association of Pancreatology (IAP) ... [et Al.]
https://www.readbyqxmd.com/read/29755813/silicosis-in-turkey-is-it-an-endless-nightmare-or-is-there-still-hope
#5
REVIEW
Metin Akgün, Begüm Ergan
Silicosis is an ancient but still life-threatening occupational lung disease because of its incurable nature. Although its risks are known in many occupational settings and effective control strategies are well established, new cases, even epidemics, continue to occur in different sectors of Turkey. Before taking action, defining the magnitude of the problem is essential. In this concise review, we aimed to present the current situation of silicosis in Turkey. According to the data available to date, silicosis continues to be a major health problem in different sectors...
April 2018: Turkish Thoracic Journal
https://www.readbyqxmd.com/read/29747566/analysis-of-the-canid-y-chromosome-phylogeny-using-short-read-sequencing-data-reveals-the-presence-of-distinct-haplogroups-among-neolithic-european-dogs
#6
Matthew T Oetjens, Axel Martin, Krishna R Veeramah, Jeffrey M Kidd
BACKGROUND: Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochondrial analyses have revealed important insights into the evolutionary history of canids. Utilizing a recently published dog Y-chromosome reference, we analyzed Y-chromosome sequence across a diverse collection of canids and determined the Y haplogroup of three ancient European dogs...
May 10, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29747009/transoceanic-stepping-stones-between-cretaceous-waterfalls-the-enigmatic-biogeography-of-pantropical-oocyclus-cascade-beetles
#7
Emmanuel F A Toussaint, Andrew Short
Beetles have colonized freshwater habitats multiple times throughout their evolutionary history. Some of these aquatic lineages are associated exclusively with waterfall-like habitats, often with modified morphologies to cope with their unusual way of life. The historical biogeography of such cascade beetle lineages has been shown to strongly reflect ancient tectonic events. We focus on the pantropical genus Oocyclus of which species dwell in waterfalls and associated habitats. We infer the first molecular phylogeny of Oocyclus using a dataset of seven gene fragments...
May 7, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29746563/ancient-genomes-reveal-a-high-diversity-of-mycobacterium-leprae-in-medieval-europe
#8
Verena J Schuenemann, Charlotte Avanzi, Ben Krause-Kyora, Alexander Seitz, Alexander Herbig, Sarah Inskip, Marion Bonazzi, Ella Reiter, Christian Urban, Dorthe Dangvard Pedersen, G Michael Taylor, Pushpendra Singh, Graham R Stewart, Petr Velemínský, Jakub Likovsky, Antónia Marcsik, Erika Molnár, György Pálfi, Valentina Mariotti, Alessandro Riga, M Giovanna Belcastro, Jesper L Boldsen, Almut Nebel, Simon Mays, Helen D Donoghue, Sonia Zakrzewski, Andrej Benjak, Kay Nieselt, Stewart T Cole, Johannes Krause
Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe...
May 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29745896/neolithic-and-medieval-virus-genomes-reveal-complex-evolution-of-hepatitis-b
#9
Ben Krause-Kyora, Julian Susat, Felix M Key, Denise Kühnert, Esther Bosse, Alexander Immel, Christoph Rinne, Sabin-Christin Kornell, Diego Yepes, Sören Franzenburg, Henrike O Heyne, Thomas Meier, Sandra Lösch, Harald Meller, Susanne Friederich, Nicole Nicklisch, Kurt W Alt, Stefan Schreiber, Andreas Tholey, Alexander Herbig, Almut Nebel, Johannes Krause
The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genomes by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results show that HBV circulates in the European population for at least 7000 years...
May 10, 2018: ELife
https://www.readbyqxmd.com/read/29745247/mitochondrial-dna-phylogenetic-information-and-the-reconstruction-of-human-population-history-the-south-american-case
#10
María Bárbara Postillone, S Ivan Perez
Mitochondrial DNA (mtDNA) sequences are becoming increasingly important in the study of human population history. Here, we explore the differences in the amount of information of different mtDNA regions and their utility for the reconstruction of South American population history. We analyzed six data sets comprising 259 mtDNA sequences from South America: Complete mtDNA, Coding, Control, hypervariable region I (HVRI), Control plus cytochrome b (cytb), and cytb plus 12S plus 16S. The amount of information in each data set was estimated employing several site-by-site and haplotype-based statistics, distances among sequences, neighbor-joining trees, distances among the estimated trees, Bayesian skyline plots, and phylogenetic informativeness profiles...
July 2017: Human Biology
https://www.readbyqxmd.com/read/29745246/chaco-canyon-dig-unearths-ethical-concerns
#11
Katrina G Claw, Dorothy Lippert, Jessica Bardill, Anna Cordova, Keolu Fox, Joseph M Yracheta, Alyssa C Bader, Deborah A Bolnick, Ripan S Malhi, Kimberly TallBear, Nanibaa' A Garrison
The field of paleogenomics (the study of ancient genomes) is rapidly advancing, with more robust methods of isolating ancient DNA and increasing access to next-generation DNA sequencing technology. As these studies progress, many important ethical issues have emerged that should be considered when ancient Native American remains, whom we refer to as ancestors, are used in research. We highlight a 2017 article by Kennett et al., "Archaeogenomic evidence reveals prehistoric matrilineal dynasty," that brings to light several ethical issues that should be addressed in paleogenomics research...
July 2017: Human Biology
https://www.readbyqxmd.com/read/29743675/137-ancient-human-genomes-from-across-the-eurasian-steppes
#12
Peter de Barros Damgaard, Nina Marchi, Simon Rasmussen, Michaël Peyrot, Gabriel Renaud, Thorfinn Korneliussen, J Víctor Moreno-Mayar, Mikkel Winther Pedersen, Amy Goldberg, Emma Usmanova, Nurbol Baimukhanov, Valeriy Loman, Lotte Hedeager, Anders Gorm Pedersen, Kasper Nielsen, Gennady Afanasiev, Kunbolot Akmatov, Almaz Aldashev, Ashyk Alpaslan, Gabit Baimbetov, Vladimir I Bazaliiskii, Arman Beisenov, Bazartseren Boldbaatar, Bazartseren Boldgiv, Choduraa Dorzhu, Sturla Ellingvag, Diimaajav Erdenebaatar, Rana Dajani, Evgeniy Dmitriev, Valeriy Evdokimov, Karin M Frei, Andrey Gromov, Alexander Goryachev, Hakon Hakonarson, Tatyana Hegay, Zaruhi Khachatryan, Ruslan Khaskhanov, Egor Kitov, Alina Kolbina, Tabaldiev Kubatbek, Alexey Kukushkin, Igor Kukushkin, Nina Lau, Ashot Margaryan, Inga Merkyte, Ilya V Mertz, Viktor K Mertz, Enkhbayar Mijiddorj, Vyacheslav Moiyesev, Gulmira Mukhtarova, Bekmukhanbet Nurmukhanbetov, Z Orozbekova, Irina Panyushkina, Karol Pieta, Václav Smrčka, Irina Shevnina, Andrey Logvin, Karl-Göran Sjögren, Tereza Štolcová, Kadicha Tashbaeva, Alexander Tkachev, Turaly Tulegenov, Dmitriy Voyakin, Levon Yepiskoposyan, Sainbileg Undrakhbold, Victor Varfolomeev, Andrzej Weber, Nikolay Kradin, Morten E Allentoft, Ludovic Orlando, Rasmus Nielsen, Martin Sikora, Evelyne Heyer, Kristian Kristiansen, Eske Willerslev
For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scythian groups that dominated the Eurasian steppes throughout the Iron Age were highly structured, with diverse origins comprising Late Bronze Age herders, European farmers and southern Siberian hunter-gatherers...
May 9, 2018: Nature
https://www.readbyqxmd.com/read/29743267/overestimation-of-the-adaptive-substitution-rate-in-fluctuating-populations
#13
Marjolaine Rousselle, Maeva Mollion, Benoit Nabholz, Thomas Bataillon, Nicolas Galtier
Estimating the proportion of adaptive substitutions ( α ) is of primary importance to uncover the determinants of adaptation in comparative genomic studies. Several methods have been proposed to estimate α from patterns polymorphism and divergence in coding sequences. However, estimators of α can be biased when the underlying assumptions are not met. Here we focus on a potential source of bias, i.e. variation through time in the long-term population size ( N ) of the considered species. We show via simulations that ancient demographic fluctuations can generate severe overestimations of α , and this is irrespective of the recent population history...
May 2018: Biology Letters
https://www.readbyqxmd.com/read/29741686/african-genetic-diversity-provides-novel-insights-into-evolutionary-history-and-local-adaptations
#14
Ananyo Choudhury, Shaun Aron, Dhriti Sengupta, Scott Hazelhurst, Michèle Ramsay
Genetic variation and susceptibility to disease are shaped by human demographic history. We can now study the genomes of extant Africans and uncover traces of population migration, admixture, assimilation and selection by applying sophisticated computational algorithms. There are four major ethnolinguistic divisions among present day Africans: Hunter-gatherer populations in southern and central Africa; Nilo-Saharan speakers from north and northeast Africa; Afro-Asiatic speakers from east Africa; and Niger-Congo speakers who are the predominant ethnolinguistic group spread across most of sub-Saharan Africa...
May 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29741623/a-short-history-of-nearly-every-sense-the-evolutionary-history-of-vertebrate-sensory-cell-types
#15
Gerhard Schlosser
Evolving from filter feeding chordate ancestors, vertebrates adopted a more active life style. These ecological and behavioral changes went along with an elaboration of the vertebrate head including novel complex paired sense organs such as the eyes, inner ears and olfactory epithelia. However, the photoreceptors, mechanoreceptors and chemoreceptors used in these sense organs have a long evolutionary history and homologous cell types can be recognized in many other bilaterians or even cnidarians. After briefly introducing some of the major sensory cell types found in vertebrates, this review summarizes the phylogenetic distribution of sensory cell types in metazoans and presents a scenario for the evolutionary history of various sensory cell types involving several cell type diversification and fusion events...
May 8, 2018: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/29740326/using-ssr-hrm-to-identify-closely-related-species-in-herbal-medicine-products-a-case-study-on-licorice
#16
Jingjian Li, Chao Xiong, Xia He, Zhaocen Lu, Xin Zhang, Xiaoyang Chen, Wei Sun
Traditional herbal medicines have played important roles in the ways of life of people around the world since ancient times. Despite the advanced medical technology of the modern world, herbal medicines are still used as popular alternatives to synthetic drugs. Due to the increasing demand for herbal medicines, plant species identification has become an important tool to prevent substitution and adulteration. Here we propose a method for biological assessment of the quality of prescribed species in the Chinese Pharmacopoeia by use of high resolution melting (HRM) analysis of microsatellite loci...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29738726/human-genetics-busy-subway-networks-in-remote-oceania
#17
Anders Bergström, Chris Tyler-Smith
Ancient human DNA from the Oceanian islands of Vanuatu reveals a surprisingly complex history of human settlement, featuring almost complete replacement shortly after initial colonisation, followed by mixing and a puzzling disconnect between genetic ancestry and language.
May 7, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29732264/algorithms-and-strategies-in-short-read-shotgun-metagenomic-reconstruction-of-plant-communities
#18
Robert S Harbert
Premise of the Study: DNA may be preserved for thousands of years in very cold or dry environments, and plant tissue fragments and pollen trapped in soils and shallow aquatic sediments are well suited for the molecular characterization of past floras. However, one obstacle in this area of study is the limiting bias in the bioinformatic classification of short fragments of degraded DNA from the large, complex genomes of plants. Methods: To establish one possible baseline protocol for the rapid classification of short-read shotgun metagenomic data for reconstructing plant communities, the read classification programs Kraken, Centrifuge, and MegaBLAST were tested on simulated and ancient data with classification against a reference database targeting plants...
March 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29728043/-discussion-on-exploitation-of-foreign-traditional-chinese-medicine-resources-based-on-the-belt-and-road
#19
Xiao-Bo Zhang, Dong-Mei Lyu, Lu-Qi Huang, Meng Li, Lan-Ping Guo, Hua-Sheng Peng
At the beginning of the ancient "Silk Road", traditional Chinese medicine resources (TCM resources) have long been integrated into it, and it was once the "important part" of the ancient "Silk Road" in Chinese history, benefited from this, the political connections was strengthened, the economic and trade was developed, and Chinese medicine culture was spread. Before Qing Dynasty, people took out the "silk" and brought back "herbs" on the "Silk Road", which enriched China's medicinal resources...
April 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29725100/sporophytes-of-polysporangiate-land-plants-from-the-early-silurian-period-may-have-been-photosynthetically-autonomous
#20
Milan Libertín, Jiří Kvaček, Jiří Bek, Viktor Žárský, Petr Štorch
The colonization of land by vascular plants is an extremely important phase in Earth's life history. This key evolutionary process is thought to have begun during the Middle Cambrian 1 period and culminated in the Silurian/Early Devonian period (interval about 509-393 million years ago (Ma)), and is documented primarily by microfossils (that is, by dispersed spores, phytodebris including fragments of algae, tissues, sporangia and cuticles), tubes and rare megafossils 2 . A newly recognized fossil cooksonioid plant with in situ spores from the Barrandian area, Czech Republic, is of the highest importance because it represents extremely ancient megafossil evidence of land plant diploid generation: sporophytes (~432 Ma)...
May 2018: Nature Plants
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