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https://www.readbyqxmd.com/read/28437587/relationship-type-affects-the-reliability-of-dispersal-distance-estimated-using-pedigree-inferences-in-partially-sampled-populations-a-case-study-involving-invasive-american-mink-in-scotland
#1
Y Melero, M K Oliver, X Lambin
Estimating dispersal - a key parameter for population ecology and management - is notoriously difficult. The use of pedigree assignments, aided by likelihood-based softwares, has become popular to estimate dispersal rate and distance. However, the partial sampling of populations may produce false assignments. Further, it is unknown how the accuracy of assignment is affected by the genealogical relationships of individuals and is reflected by software-derived assignment probabilities. Inspired by a project managing invasive American mink (Neovison vison), we estimated individual dispersal distances using inferred pairwise relationships of culled individuals...
April 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28433481/genetics-of-common-complex-diseases-a-view-from-iceland
#2
REVIEW
David O Arnar, Runolfur Palsson
In the past decade, large scale genotyping has led to discoveries of numerous sequence variants that confer increased risk of many common complex diseases. Interestingly, a substantial proportion of pioneering genetic work has originated from the small nation of Iceland and has been facilitated by an extensive genealogy database. We provide examples of relevant observations made so far in several major disease categories central to internal medicine practice. Some of these findings offer new mechanistic clues into the pathophysiology of common disorders and may suggest novel approaches in diagnosis and drug therapy...
April 19, 2017: European Journal of Internal Medicine
https://www.readbyqxmd.com/read/28415890/correction-to-deep-genealogical-analysis-of-a-large-cohort-of-participants-in-the-cartagene-project-quebec-canada
#3
(no author information available yet)
No abstract text is available yet for this article.
April 18, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/28410396/evolution-of-the-neuraminidase-gene-of-seasonal-influenza-a-and-b-viruses-in-thailand-between-2010-and-2015
#4
Nipaporn Tewawong, Preeyaporn Vichiwattana, Sumeth Korkong, Sirapa Klinfueng, Nungruthai Suntronwong, Thanunrat Thongmee, Apiradee Theamboonlers, Sompong Vongpunsawad, Yong Poovorawan
The neuraminidase inhibitors (NAIs) oseltamivir and zanamivir are commonly used for the treatment and control of influenza A and B virus infection. However, the emergence of new influenza virus strains with reduced susceptibility to NAIs may appear with the use of these antivirals or even naturally. We therefore screened the neuraminidase (NA) sequences of seasonal influenza virus A(H1N1), A(H1N1)pdm09, A(H3N2), and influenza B virus strains identified in Thailand for the presence of substitutions previously reported to reduce susceptibility to NAIs...
2017: PloS One
https://www.readbyqxmd.com/read/28397796/geographic-barriers-and-pleistocene-climate-change-shaped-patterns-of-genetic-variation-in-the-eastern-afromontane-biodiversity-hotspot
#5
Mario Mairal, Isabel Sanmartín, Alberto Herrero, Lisa Pokorny, Pablo Vargas, Juan J Aldasoro, Marisa Alarcón
The Eastern African Afromontane forest is getting increased attention in conservation studies because of its high endemicity levels and shrinking geographic distribution. Phylogeographic studies have found evidence of high levels of genetic variation structured across the Great Rift System. Here, we use the epiphytic plant species Canarina eminii to explore causal explanations for this pattern. Phylogeographic analyses were undertaken using plastid regions and AFLP fragments. Population genetic analyses, Statistical Parsimony, and Bayesian methods were used to infer genetic diversity, genealogical relationships, structure, gene flow barriers, and the spatiotemporal evolution of populations...
April 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28393289/practically-delineating-bacterial-species-with-genealogical-concordance
#6
Stephanus N Venter, Marike Palmer, Chrizelle W Beukes, Wai-Yin Chan, Giyoon Shin, Elritha van Zyl, Tarren Seale, Teresa A Coutinho, Emma T Steenkamp
Bacterial species are commonly defined by applying a set of predetermined criteria, including DNA-DNA hybridization values, 16S rRNA gene sequence similarity, phenotypic data as well as genome-based criteria such as average nucleotide identity or digital DNA-DNA hybridization. These criteria mostly allow for the delimitation of taxa that resemble typical bacterial species. Their application is often complicated when the objective is to delineate new species that are characterized by significant population-level diversity or recent speciation...
April 9, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28390909/deep-reticulation-and-incomplete-lineage-sorting-obscure-the-diploid-phylogeny-of-rain-lilies-and-allies-amaryllidaceae-tribe-hippeastreae
#7
Nicolás García, Ryan A Folk, Alan W Meerow, Srikar Chamala, Matthew A Gitzendanner, Renata Souza de Oliveira, Douglas E Soltis, Pamela S Soltis
Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups...
April 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28385666/optimal-point-process-filtering-and-estimation-of-the-coalescent-process
#8
Kris V Parag, Oliver G Pybus
The coalescent process is a widely used approach for inferring the demographic history of a population, from samples of its genetic diversity. Several parametric and non-parametric coalescent inference methods, involving Markov chain Monte Carlo, Gaussian processes, and other algorithms, already exist. However, these techniques are not always easy to adapt and apply, thus creating a need for alternative methodologies. We introduce the Bayesian Snyder filter as an easily implementable and flexible minimum mean square error estimator for parametric demographic functions on fixed genealogies...
April 3, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28379570/gene-tree-discordance-does-not-explain-away-the-temporal-decline-of-convergence-in-mammalian-protein-sequence-evolution
#9
Zhengting Zou, Jianzhi Zhang
Several authors reported lower frequencies of protein sequence convergence between more distantly related evolutionary lineages and attributed this trend to epistasis, which renders the acceptable amino acids at a site more different and convergence less likely in more divergent lineages. A recent primate study, however, suggested that this trend is at least partially and potentially entirely an artifact of gene tree discordance (GTD). Here we demonstrate in a genome-wide dataset from 17 mammals that the temporal trend remains (1) upon the control of the GTD level, (2) in genes whose genealogies are concordant with the species tree, and (3) for convergent changes, which are extremely unlikely to be caused by GTD...
April 3, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28371627/the-problem-of-choice-from-the-voluntary-way-to-affordable-care-act-health-insurance-exchanges
#10
Jessica Mulligan
This article takes a genealogical and ethnographic approach to the problem of choice, arguing that what choice means has been reworked several times since health insurance first figured prominently in national debates about health reform. Whereas voluntary choice of doctor and hospital used to be framed as an American right, contemporary choice rhetoric includes consumer choice of insurance plan. Understanding who has deployed choice rhetoric and to what ends helps explain how offering choices has become the common sense justification for defending and preserving the exclusionary health care system in the United States...
May 2017: Social Science & Medicine
https://www.readbyqxmd.com/read/28355314/ideology-science-and-people-in-am%C3%A3-lcar-cabral
#11
José Neves
The present article contributes to the debate on how historians and social scientists perceive and understand relations between ideology and science, which are often seen as realms belonging to rival kingdoms. Following an analysis and critical positioning vis-à-vis Cabralian studies, the text examines how scholars of Cabral have portrayed his agronomic activities. It then undertakes a genealogical analysis of the Cabralian concept of people and suggests that the emergence of this concept in Cabral's discourse derives from the intersection of the development of anti-colonial nationalist thought in the former Portuguese Empire and the development of agrarian studies in metropolitan Portugal...
March 23, 2017: História, Ciências, Saúde—Manguinhos
https://www.readbyqxmd.com/read/28351409/identification-of-a-novel-merozoite-surface-antigen-of-plasmodium-vivax-pvmsa180
#12
Fauzi Muh, Jin-Hee Han, Myat Htut Nyunt, Seong-Kyun Lee, Hye-Yoon Jeon, Kwon-Soo Ha, Won Sun Park, Seok-Ho Hong, Md Atique Ahmed, Sunghun Na, Eizo Takashima, Takafumi Tsuboi, Eun-Taek Han
BACKGROUND: Although a number of Plasmodium vivax proteins have been identified, few have been investigated as potential vaccine candidates. This study characterized the Plasmodium vivax merozoite surface antigen 180 (PvMSA180, PVX_094920), a novel P. vivax antigenic protein. METHODS: The target gene was amplified as four overlapping domains (D1, D2, D3 and D4) to enable expression of the recombinant protein using cell-free and bacterial expression systems. The recombinant PvMSA180 proteins were used in protein microarrays to evaluate the humoral immune response of 72 vivax-infected patients and 24 vivax-naïve individuals...
March 28, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28348829/monomorphic-genotypes-within-a-generalist-lineage-of-campylobacter-jejuni-show-signs-of-global-dispersion
#13
Ann-Katrin Llarena, Ji Zhang, Minna Vehkala, Niko Välimäki, Marjaana Hakkinen, Marja-Liisa Hänninen, Mati Roasto, Mihkel Mäesaar, Eduardo Taboada, Dillon Barker, Giuliano Garofolo, Cesare Cammà, Elisabetta Di Giannatale, Jukka Corander, Mirko Rossi
The decreased costs of genome sequencing have increased the capability to apply whole-genome sequencing to epidemiological surveillance of zoonotic Campylobacter jejuni. However, knowledge of the genetic diversity of this bacteria is vital for inferring relatedness between epidemiologically linked isolates and a necessary prerequisite for correct application of this methodology. To address this issue in C. jejuni we investigated the spatial and temporal signals in the genomes of a major clonal complex and generalist lineage, ST-45 CC, by analysing the population structure and genealogy as well as applying genome-wide association analysis of 340 isolates from across Europe collected over a wide time range...
October 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28341209/a-non-zero-variance-of-tajima-s-estimator-for-two-sequences-even-for-infinitely-many-unlinked-loci
#14
Léandra King, John Wakeley, Shai Carmi
The population-scaled mutation rate, θ, is informative on the effective population size and is thus widely used in population genetics. We show that for two sequences and n unlinked loci, the variance of Tajima's estimator (θˆ), which is the average number of pairwise differences, does not vanish even as n→∞. The non-zero variance of θˆ results from a (weak) correlation between coalescence times even at unlinked loci, which, in turn, is due to the underlying fixed pedigree shared by gene genealogies at all loci...
March 21, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28338786/recombination-mediated-host-adaptation-by-avian-staphylococcus-aureus
#15
Susan Murray, Ben Pascoe, Guillaume Méric, Leonardos Mageiros, Koji Yahara, Matthew D Hitchings, Yasmin Friedmann, Thomas S Wilkinson, Fraser J Gormley, Dietrich Mack, James E Bray, Sarah Lamble, Rory Bowden, Keith A Jolley, Martin C J Maiden, Sarah Wendlandt, Stefan Schwarz, Jukka Corander, J Ross Fitzgerald, Samuel K Sheppard
Staphylococcus aureus are globally disseminated among farmed chickens causing skeletal muscle infections, dermatitis, and septicaemia. The emergence of poultry-associated lineages has involved zoonotic transmission from humans to chickens but questions remain about the specific adaptations that promote proliferation of chicken pathogens. We characterized genetic variation in a population of genome-sequenced S. aureus isolates of poultry and human origin. Genealogical analysis identified a dominant poultry-associated sequence cluster within the CC5 clonal complex...
April 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28334237/dna-compass-a-secure-client-side-site-for-navigating-personal-genetic-information
#16
Charles Curnin, Assaf Gordon, Yaniv Erlich
Motivation: Millions of individuals have access to raw genomic data using direct-to-consumer companies. The advent of large-scale sequencing projects, such as the Precision Medicine Initiative, will further increase the number of individuals with access to their own genomic information. However, querying genomic data requires a computer terminal and computational skill to analyze the data - an impediment for the general public. Results: DNA Compass is a website designed to empower the public by enabling simple navigation of personal genomic data...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28325067/deep-genealogical-analysis-of-a-large-cohort-of-participants-in-the-cartagene-project-quebec-canada
#17
Marc Tremblay, Gabrielle Rouleau
BACKGROUND: Genealogical analysis helps to better understand the genetic structure of populations. The population of Quebec (Canada) often serves as a model for this type of analysis, having one of the world's most complete genealogical databases. AIM: The main objective of this study was to reconstruct, analyse and compare the ascending genealogies of participants to CARTaGENE, a project that aims at building a database on various aspects of public health. SUBJECTS AND METHODS: In total, 5110 genealogies from four Quebec regions were reconstructed...
March 21, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/28317545/phylogeny-and-pathogenicity-of-lasiodiplodia-species-associated-with-dieback-of-mango-in-peru
#18
Edgar Rodríguez-Gálvez, Pakita Guerrero, Carla Barradas, Pedro W Crous, Artur Alves
Mango, which is an important tropical fruit crop in the region of Piura (Peru), is known to be prone to a range of diseases caused by Lasiodiplodia spp. The aim of this study was to evaluate the incidence and prevalence of mango dieback in the region of Piura, and to identify the species of Lasiodiplodia associated with the disease and evaluate their pathogenicity towards mango. Mango dieback was present in all orchards surveyed but incidence varied with location. Identification of fungal isolates was based on morphological and cultural characteristics as well as sequence data of the rDNA internal transcribed spacer region (ITS) and translation elongation factor 1-alpha gene (tef1-α)...
April 2017: Fungal Biology
https://www.readbyqxmd.com/read/28317541/mating-type-genes-in-the-genus-neofusicoccum-mating-strategies-and-usefulness-in-species-delimitation
#19
Anabela Lopes, Alan J L Phillips, Artur Alves
The genus Neofusicoccum includes species with wide geographical and plant host distribution, some of them of economic importance. The genus currently comprises 27 species that are difficult to identify based on morphological features alone. Thus, species differentiation is based on phylogenetic species recognition using multigene genealogies. In this study, we characterised the mating type genes of Neofusicoccum species. Specific primers were designed to amplify and sequence MAT genes in several species and a PCR-based mating type diagnostic assay was developed...
April 2017: Fungal Biology
https://www.readbyqxmd.com/read/28285392/a-consensus-method-for-ancestral-recombination-graphs
#20
Mary K Kuhner, Jon Yamato
We propose a consensus method for ancestral recombination graphs (ARGs) that generates a single ARG representing commonalities among a cloud of ARGs defined for the same genomic region and set of taxa. Our method, which we call "threshold consensus," treats a genomic location as a potential recombination breakpoint only if the number of ARGs in the cloud possessing a breakpoint at that location exceeds a chosen threshold. The estimate is further refined by ignoring recombinations that do not change the local tree topologies, as well as collapsing breakpoint locations separated only by invariant sites...
March 11, 2017: Journal of Molecular Evolution
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