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https://www.readbyqxmd.com/read/29351742/herv-w-group-evolutionary-history-in-non-human-primates-characterization-of-erv-w-orthologs-in-catarrhini-and-related-erv-groups-in-platyrrhini
#1
Nicole Grandi, Marta Cadeddu, Jonas Blomberg, Jens Mayer, Enzo Tramontano
BACKGROUND: The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology...
January 19, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29343863/genetic-analyses-favour-an-ancient-and-natural-origin-of-elephants-on-borneo
#2
Reeta Sharma, Benoit Goossens, Rasmus Heller, Rita Rasteiro, Nurzhafarina Othman, Michael W Bruford, Lounès Chikhi
The origin of the elephant on the island of Borneo remains elusive. Research has suggested two alternative hypotheses: the Bornean elephant stems either from a recent introduction in the 17th century or from an ancient colonization several hundreds of thousands years ago. Lack of elephant fossils has been interpreted as evidence for a very recent introduction, whereas mtDNA divergence from other Asian elephants has been argued to favor an ancient colonization. We investigated the demographic history of Bornean elephants using full-likelihood and approximate Bayesian computation analyses...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29334417/combining-allele-frequency-and-tree-based-approaches-improves-phylogeographic-inference-from-natural-history-collections
#3
M Ruffley, M L Smith, A Espíndola, B C Carstens, J Sullivan, D C Tank
Model selection approaches in phylogeography have allowed researchers to evaluate the support for competing demographic histories, which provides a mode of inference and a measure of uncertainty in understanding climatic and spatial influences on intraspecific diversity. Here, to rank all models in the comparison set, and determine what proportion of the total support the top-ranked model garners, we conduct model selection using two analytical approaches -allele frequency-based, implemented in fastsimcoal2, and gene tree-based, implemented in PHRAPL...
January 15, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29333704/asian-horses-deepen-the-msy-phylogeny
#4
S Felkel, C Vogl, D Rigler, V Jagannathan, T Leeb, R Fries, M Neuditschko, S Rieder, B Velie, G Lindgren, C-J Rubin, C Schlötterer, T Rattei, G Brem, B Wallner
Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46 Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds...
January 15, 2018: Animal Genetics
https://www.readbyqxmd.com/read/29333609/runs-of-homozygosity-reveal-genome-wide-autozygosity-in-italian-sheep-breeds
#5
S Mastrangelo, E Ciani, M T Sardina, G Sottile, F Pilla, B Portolano
The availability of dense single nucleotide polymorphism (SNP) assays allows for the determination of autozygous segments based on runs of consecutive homozygous genotypes (ROH). The aim of the present study was to investigate the occurrence and distribution of ROH in 21 Italian sheep breeds using medium-density SNP genotypes in order to characterize autozygosity and identify genomic regions that frequently appeared in ROH within individuals, namely ROH islands. After filtering, the final number of animals and SNPs retained for analyses were 502 and 46 277 respectively...
January 15, 2018: Animal Genetics
https://www.readbyqxmd.com/read/29332417/-concise-history-of-toxicology-from-empiric-knowledge-to-science
#6
Anna Tompa, Péter Balázs
Toxicology is a science of poisonings by xenobiotics and endogenous physiological changes. Its empiric roots may be traced back to the emerging of the human race because the most important pledge of our predecessors' survival was the differentiation between eatable and poisonous plants and animals. In the course of social evolution, there were three main fields of using poisons: 1) hunting and warfare, 2) to settle social tensions by avoiding military conflicts through hiding strategy of eliminating enemies by toxic substances, 3) medicines applied first as anti-poisons and later by introducing strong substances to defeat diseases, but paradoxically active euthanasia is also a part of the whole story...
January 2018: Orvosi Hetilap
https://www.readbyqxmd.com/read/29323793/atmospheric-nitrogen-deposition-on-petals-enhances-seed-quality-of-the-forest-herb-anemone-nemorosa
#7
Pieter De Frenne, Haben Blondeel, Jörg Brunet, Maria Mercedes Caron, Olivier Chabrerie, Mathias Cougnon, Sara A O Cousins, Guillaume Decocq, Martin Diekmann, Bente J Graae, Mick E Hanley, Thilo Heinken, Martin Hermy, Annette Kolb, Jonathan Lenoir, Jaan Liira, Anna Orczewska, Anna Shevtsova, Thomas Vanneste, Kris Verheyen
Elevated atmospheric input of nitrogen (N) is currently affecting plant biodiversity and ecosystem functioning. The growth and survival of numerous plant species is known to respond strongly to N fertilization. Yet, few studies have assessed the effects of N deposition on seed quality and reproductive performance, which is an important life-history stage of plants. Here we address this knowledge gap by assessing the effects of atmospheric N deposition on seed quality of the ancient forest herb Anemone nemorosa using two complementary approaches...
January 11, 2018: Plant Biology
https://www.readbyqxmd.com/read/29323299/rotation-in-c-ii-emitting-gas-in-two-galaxies-at-a-redshift-of-6-8
#8
Renske Smit, Rychard J Bouwens, Stefano Carniani, Pascal A Oesch, Ivo Labbé, Garth D Illingworth, Paul van der Werf, Larry D Bradley, Valentino Gonzalez, Jacqueline A Hodge, Benne W Holwerda, Roberto Maiolino, Wei Zheng
The earliest galaxies are thought to have emerged during the first billion years of cosmic history, initiating the ionization of the neutral hydrogen that pervaded the Universe at this time. Studying this 'epoch of reionization' involves looking for the spectral signatures of ancient galaxies that are, owing to the expansion of the Universe, now very distant from Earth and therefore exhibit large redshifts. However, finding these spectral fingerprints is challenging. One spectral characteristic of ancient and distant galaxies is strong hydrogen-emission lines (known as Lyman-α lines), but the neutral intergalactic medium that was present early in the epoch of reionization scatters such Lyman-α photons...
January 10, 2018: Nature
https://www.readbyqxmd.com/read/29321891/population-genetic-structure-of-the-endemic-rosewoods-dalbergia-cochinchinensis-and-d-%C3%A2-oliveri-at-a-regional-scale-reflects-the-indochinese-landscape-and-life-history-traits
#9
Ida Hartvig, Thea So, Suchitra Changtragoon, Hoa Thi Tran, Somsanith Bouamanivong, Ida Theilade, Erik Dahl Kjær, Lene Rostgaard Nielsen
Indochina is a biodiversity hot spot and harbors a high number of endemic species, most of which are poorly studied. This study explores the genetic structure and reproductive system of the threatened endemic timber species Dalbergia cochinchinensis and Dalbergia oliveri using microsatellite data from populations across Indochina and relates it to landscape characteristics and life-history traits. We found that the major water bodies in the region, Mekong and Tonle Sap, represented barriers to gene flow and that higher levels of genetic diversity were found in populations in the center of the distribution area, particularly in Cambodia...
January 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29320518/increased-mitochondrial-dna-diversity-in-ancient-columbia-river-basin-chinook-salmon-oncorhynchus-tshawytscha
#10
Bobbi M Johnson, Brian M Kemp, Gary H Thorgaard
The Columbia River and its tributaries provide essential spawning and rearing habitat for many salmonid species, including Chinook salmon (Oncorhynchus tshawytscha). Chinook salmon were historically abundant throughout the basin and Native Americans in the region relied heavily on these fish for thousands of years. Following the arrival of Europeans in the 1800s, salmon in the basin experienced broad declines linked to overfishing, water diversion projects, habitat destruction, connectivity reduction, introgression with hatchery-origin fish, and hydropower development...
2018: PloS One
https://www.readbyqxmd.com/read/29318984/a-brief-history-of-shigella
#11
Keith A Lampel, Samuel B Formal, Anthony T Maurelli
The history of Shigella, the causative agent of bacillary dysentery, is a long and fascinating one. This brief historical account starts with descriptions of the disease and its impact on human health from ancient time to the present. Our story of the bacterium starts just before the identification of the dysentery bacillus by Kiyoshi Shiga in 1898 and follows the scientific discoveries and principal scientists who contributed to the elucidation of Shigella pathogenesis in the first 100 years. Over the past century, Shigella has proved to be an outstanding model of an invasive bacterial pathogen and has served as a paradigm for the study of other bacterial pathogens...
January 2018: EcoSal Plus
https://www.readbyqxmd.com/read/29317314/phi-in-physiology-psychology-and-biomechanics-the-golden-ratio-between-myth-and-science
#12
REVIEW
Marco Iosa, Giovanni Morone, Stefano Paolucci
In recent years, there has been a renewed interest in the use of the so-called golden ratio (Phi, ϕ), an irrational number with fractal properties, used in artworks since V century BC. and now for modelling complex biological structures and functions. This number, in fact, recursively pops-up in human history, from Ancient Greeks to Renaissance, and to contemporary scientific studies. Nevertheless, recent scientific results often fall between two extremes: those of a priori sceptic researchers accusing the artificial emergence of ϕ in many studies, and those of researchers that find a mystic meaning in the presence of ϕ in human physiology...
January 6, 2018: Bio Systems
https://www.readbyqxmd.com/read/29302050/demographic-analysis-of-cyanobacteria-based-on-the-mutation-rates-estimated-from-an-ancient-ice-core
#13
Takahiro Segawa, Nozomu Takeuchi, Koji Fujita, Vladimir B Aizen, Eske Willerslev, Takahiro Yonezawa
Despite the crucial role of cyanobacteria in various ecosystems, little is known about their evolutionary histories, especially microevolutionary dynamics, because of the lack of knowledge regarding their mutation rates. Here we directly estimated cyanobacterial mutation rates based on ancient DNA analyses of ice core samples collected from Kyrgyz Republic that dates back to ~12,500 cal years before present. We successfully sequenced the 16S rRNA and 16S-23S internal transcribed spacer (ITS) region. Two cyanobacterial operational taxonomic units (OTUs) were detected from the ancient ice core samples, and these OTUs are shared with those from the modern glacier surface...
January 5, 2018: Heredity
https://www.readbyqxmd.com/read/29299966/ancient-dna-investigation-of-a-medieval-german-cemetery-confirms-long-term-stability-of-ccr5-%C3%AE-32-allele-frequencies-in-central-europe
#14
Abigail Bouwman, Natallia Shved, Gülfirde Akgül, Frank Rühli, Christina Warinner
The CCR5-Δ32 mutation present in European populations is among the most prominently debated cases of recent positive selection in humans. This allele, a 32-bp deletion that renders the T-cell CCR5 receptor nonfunctional, has important epidemiological and public health significance, as homozygous carriers are resistant to several HIV strains. However, although the function of this allele in preventing HIV infection is now well described, its human evolutionary origin is poorly understood. Initial attempts to determine the emergence of the CCR5-Δ32 allele pointed to selection during the 14th-century Black Death pandemic; however, subsequent analyses suggest that the allele rose in frequency more than 5,000 years ago, possibly through drift...
April 2017: Human Biology
https://www.readbyqxmd.com/read/29299965/the-multiple-histories-of-western-asia-perspectives-from-ancient-and-modern-genomes
#15
Recep Ozgur Taskent, Omer Gokcumen
Western Asia lies at the heart of the Old World, in the midst of Africa, Asia, and Europe. As such, this region has been populated and repopulated by myriad peoples, starting with the first migrants from Africa. All evidence points to Western Asia for the beginnings of sedentary life, and indeed, first the villages and later the cities of this land remain as archaeological wonders, revealing complex histories of multiple peoples and their interactions. With the wondrous breakthroughs in genomic studies, we now have the power to look at these histories with a truly quantitative lens...
April 2017: Human Biology
https://www.readbyqxmd.com/read/29298933/diversity-and-disparity-of-sparassodonts-metatheria-reveal-non-analogue-nature-of-ancient-south-american-mammalian-carnivore-guilds
#16
Darin A Croft, Russell K Engelman, Tatiana Dolgushina, Gina Wesley
This study investigates whether terrestrial mammalian carnivore guilds of ancient South America, which developed in relative isolation, were similar to those of other continents. We do so through analyses of clade diversification, ecomorphology and guild structure in the Sparassodonta, metatherians that were the predominant mammalian carnivores of pre-Pleistocene South America. Body mass and 16 characters of the dentition are used to quantify morphological diversity (disparity) in sparassodonts and to compare them to extant marsupial and placental carnivores and extinct North American carnivoramorphans...
January 10, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29297395/between-lake-baikal-and-the-baltic-sea-genomic-history-of-the-gateway-to-europe
#17
Petr Triska, Nikolay Chekanov, Vadim Stepanov, Elza K Khusnutdinova, Ganesh Prasad Arun Kumar, Vita Akhmetova, Konstantin Babalyan, Eugenia Boulygina, Vladimir Kharkov, Marina Gubina, Irina Khidiyatova, Irina Khitrinskaya, Ekaterina E Khrameeva, Rita Khusainova, Natalia Konovalova, Sergey Litvinov, Andrey Marusin, Alexandr M Mazur, Valery Puzyrev, Dinara Ivanoshchuk, Maria Spiridonova, Anton Teslyuk, Svetlana Tsygankova, Martin Triska, Natalya Trofimova, Edward Vajda, Oleg Balanovsky, Ancha Baranova, Konstantin Skryabin, Tatiana V Tatarinova, Egor Prokhortchouk
BACKGROUND: The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic-speaking migrants as well as eastward by Europeans. Unfortunately, the material records of history of this region are not dense enough to reconstruct details of population history. These considerations stimulate growing interest to obtain a genetic picture of the demographic history of migrations and admixture in Northern Eurasia...
December 28, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29289355/quantifying-temporal-genomic-erosion-in-endangered-species
#18
REVIEW
David Díez-Del-Molino, Fatima Sánchez-Barreiro, Ian Barnes, M Thomas P Gilbert, Love Dalén
Many species have undergone dramatic population size declines over the past centuries. Although stochastic genetic processes during and after such declines are thought to elevate the risk of extinction, comparative analyses of genomic data from several endangered species suggest little concordance between genome-wide diversity and current population sizes. This is likely because species-specific life-history traits and ancient bottlenecks overshadow the genetic effect of recent demographic declines. Therefore, we advocate that temporal sampling of genomic data provides a more accurate approach to quantify genetic threats in endangered species...
December 27, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/29288555/the-focused-history-and-physical-circa-100-bce
#19
Katherine D van Schaik
When modern physicians reflect on 'ancient medicine' or 'Greek medicine,' they typically think of Hippocrates and Galen. Few know of the raging, centuries-long intellectual debates among physicians about what exactly mattered in the treatment of illness, or about a group of physicians whose pattern-based, systematized approach to health and disease was a forerunner of how today's emergency medicine physicians evaluate and treat their patients.Methodist physicians (c. 100 BCE to 500 CE, active mostly in Rome but present throughout the Mediterranean world) were named after their "method" of healing...
December 30, 2017: Academic Emergency Medicine: Official Journal of the Society for Academic Emergency Medicine
https://www.readbyqxmd.com/read/29285971/leveraging-multiple-populations-across-time-helps-define-accurate-models-of-human-evolution-a-reanalysis-of-the-lactase-persistence-adaptation
#20
Chenling Xu Antelope, Davide Marnetto, Fergal Casey, Emilia Huerta-Sanchez
Access to a geographically diverse set of modern human samples from the present time and from ancient remains, combined with archaic hominin samples, provides an unprecedented level of resolution to study both human history and adaptation. The amount and quality of ancient human data continue to improve and enable tracking the trajectory of genetic variation over time. These data have the potential to help us redefine or generate new hypotheses of how human evolution occurred and to revise previous conjectures...
January 2017: Human Biology
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