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Ellen Baake, Fernando Cordero, Sebastian Hummel
We reconsider the deterministic haploid mutation-selection equation with two types. This is an ordinary differential equation that describes the type distribution (forward in time) in a population of infinite size. This paper establishes ancestral (random) structures inherent in this deterministic model. In a first step, we obtain a representation of the deterministic equation's solution (and, in particular, of its equilibria) in terms of an ancestral process called the killed ancestral selection graph. This representation allows one to understand the bifurcations related to the error threshold phenomenon from a genealogical point of view...
April 19, 2018: Journal of Mathematical Biology
Meenakshi Chatterjee, Murat Acar
Cells often respond to environmental stimuli by activating specific transcription factors. Upon exposure to glucose limitation stress, it is known that yeast Saccharomyces cerevisiae cells dephosphorylate the general stress response factor Msn2, leading to its nuclear localization, which in turn activates the expression of many genes. However, the precise dynamics of Msn2 nucleocytoplasmic translocations and whether they are inherited over multiple generations in a stress-dependent manner are not well understood...
April 2018: Science Advances
Gabriela Padilla-Jacobo, Horacio Cano-Camacho, Rigoberto López-Zavala, María E Cornejo-Pérez, María G Zavala-Páramo
BACKGROUND: The distribution of the wild turkey (Meleagris gallopavo) extends from Mexico to southeastern Canada and to the eastern and southern regions of the USA. Six subspecies have been described based on morphological characteristics and/or geographical variations in wild and domesticated populations. In this paper, based on DNA sequence data from the mitochondrial D-loop, we investigated the genetic diversity and structure, genealogical relationships, divergence time and demographic history of M...
April 17, 2018: Genetics, Selection, Evolution: GSE
Siobhán M Mattison, Edmond Seabright, Adam Z Reynolds, Jingzhe Bill Cao, Melissa J Brown, Marcus W Feldman
Adoption is sometimes considered paradoxical from an evolutionary perspective because the costs spent supporting an adopted child would be better spent on rearing one's own. Kin selection theory is commonly used to solve this paradox, because the adoption of closely related kin contributes to the inclusive fitness of the adoptive parent. In this paper, we perform a novel test of kin selection theory in the context of adoption by asking whether adopted daughters-in-law, who contribute directly (i.e. genealogically) to the perpetuation of their adoptive families' lineages, experience lower mortality than daughters adopted for other purposes in historical Taiwan...
March 2018: Royal Society Open Science
Andrew Melfi, Divakar Viswanath
The Kingman coalescent is a commonly used model in genetics, which is often justified with reference to the Wright-Fisher (WF) model. Current proofs of convergence of WF and other models to the Kingman coalescent assume a constant sample size. However, sample sizes have become quite large in human genetics. Therefore, we develop a convergence theory that allows the sample size to increase with population size. If the haploid population size is N and the sample size is N1∕3-ϵ , ϵ>0, we prove that Wright-Fisher genealogies involve at most a single binary merger in each generation with probability converging to 1 in the limit of large N...
April 12, 2018: Theoretical Population Biology
Alexandre A Lussier, Alon Keinan
No abstract text is available yet for this article.
April 13, 2018: Science
Simon R Evans, Dominique Waldvogel, Nina Vasiljevic, Erik Postma
Sexual reproduction is inherently interactive, especially in animal species such as humans that exhibit extended pair bonding. Yet we have little knowledge of the role of male characteristics and their evolutionary impact on reproductive behavioural phenotypes, to the extent that biologists typically consider component traits (e.g. reproductive timing) as female-specific. Based on extensive genealogical data detailing the life histories of 6435 human mothers born across four centuries of modern history, we use an animal modelling approach to estimate the indirect genetic effect of men on the reproductive phenotype of their partners...
April 11, 2018: Proceedings. Biological Sciences
Shamus R Carr, Wallace Akerley, Lisa Cannon-Albright
INTRODUCTION: Lung carcinogenesis is strongly influenced by environmental and heritable factors. The genetic contribution to the different histologies is unknown. METHODS: A population-based computerized genealogy resource linked to a statewide cancer registry of lung cancer cases (n=5408) was analyzed to evaluate the heritable contribution to lung cancer histology in smoking (n=1751) and non-smoking cases (n=818). Statistical methods were used to test for significant excess relatedness of lung cancer cases...
April 4, 2018: Journal of Thoracic Oncology
Marie Doležálková-Kaštánková, Nicolas B M Pruvost, Jörg Plötner, Heinz-Ulrich Reyer, Karel Janko, Lukáš Choleva
BACKGROUND: Sexual parasites offer unique insights into the reproduction of unisexual and sexual populations. Because unisexuality is almost exclusively linked to the female sex, most studies addressed host-parasite dynamics in populations where sperm-dependent females dominate. Pelophylax water frogs from Central Europe include hybrids of both sexes, collectively named P. esculentus. They live syntopically with their parental species P. lessonae and/or P. ridibundus. Some hybrid lineages consist of all males providing a chance to understand the origin and perpetuation of a host-parasite (egg-dependent) system compared to sperm-dependent parthenogenesis...
April 2, 2018: Biology of Sex Differences
Ji Zhang, Yanwen Xiong, Lynn Rogers, Glen P Carter, Nigel French
Motivation: Large-scale whole-genome sequencing (WGS) dataset based studies are becoming increasingly common in pathogen surveillance and outbreak investigations. A highly discriminative and time-efficient bioinformatics tool is needed to transform large amounts of sequencing data into usable biological information. To replace the intuitive, yet inefficient, way of gene-by-gene allele calling algorithm, a new algorithm using genome-by-genome approach was developed. Results: Tests showed that the program equipped with the new algorithm achieved significant improvements in allele calling efficiency compared to a conventional gene-by-gene approach...
March 28, 2018: Bioinformatics
O V Paliychuk, L Z Polishchuk, Z I Rossokha, V F Chekhun
AIM: To develop a prognostic molecular genetic model for assessing the risk of development of benign and malignant tumors of female reproductive organs (FRO) in patients from cancer-affected families. PATIENTS AND METHODS: The work presents the data on a comprehensive clinical examination of 210 women (90 patients with FRO cancer with aggregation of tumor pathology in families, 65 patients with benign pathology of FRO from cancer-affected families, 55 women - control group of healthy women without family history of cancer)...
March 2018: Experimental Oncology
Michael C Campbell, Lunden T Smith, Jayla Harvey
Despite its critical role in the defense against microbial infection and tumor development, little is known about the range of nucleotide and haplotype variation at IFN-γ, or the evolutionary forces that have shaped patterns of diversity at this locus. To address this gap in knowledge, we examined sequence data from the IFN-γ gene in 1461 individuals from 15 worldwide populations. Our analyses uncovered novel patterns of variation in distinct African populations, including an excess of high frequency-derived alleles, unusually long haplotype structure surrounding the IFN-γ gene, and a "star-like" genealogy of African-specific haplotypes carrying variants previously associated with infectious disease...
March 29, 2018: Genes and Immunity
Miriam Baeta, Carolina Núñez, Patricia Villaescusa, Urko Ortueta, Nerea Ibarbia, Rene J Herrera, José Luis Blazquez-Caeiro, Juan José Builes, Susana Jiménez-Moreno, Begoña Martínez-Jarreta, Marian M de Pancorbo
Y-specific short tandem repeat (Y-STR) loci display different mutation rates and consequently are suitable for forensic, genealogical, and evolutionary studies that require different levels of timelines and resolution. Recent efforts have focused on implementing Rapidly Mutating (RM) Y-STRs to assess male specific profiles. However, due to their high mutation rate their use in kinship testing or in phylogenetic studies may be less reliable. In the present study, a novel Slowly Mutating Y-STR (SM) panel, including DYS388, DYS426, DYS461 (Y-GATA-A7...
March 20, 2018: Forensic Science International. Genetics
Evgeniya N Solovyeva, Vladimir S Lebedev, Evgeniy A Dunayev, Roman A Nazarov, Anna A Bannikova, Jing Che, Robert W Murphy, Nikolay A Poyarkov
We hypothesize the phylogenetic relationships of the agamid genus Phrynocephalus to assess how past environmental changes shaped the evolutionary and biogeographic history of these lizards and especially the impact of paleogeography and climatic factors. Phrynocephalus is one of the most diverse and taxonomically confusing lizard genera. As a key element of Palearctic deserts, it serves as a promising model for studies of historical biogeography and formation of arid habitats in Eurasia. We used 51 samples representing 33 of 40 recognized species of Phrynocephalus covering all major areas of the genus...
2018: PeerJ
Yanjing Wang, Jinming Lu, G Andrew C Beattie, Md Rashidul Islam, Namgay Om, Hang Thi Dao, Liem Van Nguyen, Syed Muhammad Zaka, Jun Guo, Mingyi Tian, Xiaoling Deng, Shunyun Tan, Paul Holford, Yurong He, Yijing Cen
BACKGROUND: In insects, little is known about the coevolution between their primary endosymbionts and hosts at the intraspecific level, and this study has examined codiversification between the notorious agricultural pest Diaphorina citri and its P-endosymbiont, 'Candidatus Carsonella ruddii' at the population level. RESULTS: Maximum likelihood, haplotype network, principal components and Bayesian clustering identified three lineages for D. citri and its P-endosymbiont: a Western clade containing individuals from Pakistan, Bhutan (Phuentsholing), Vietnam (Son La), USA, Myanmar and China (Ruili, Yunnan); a Central clade, with accessions originating from Southwest China, Bhutan (Tsirang) and Bangladesh; and an Eastern clade containing individuals from Southeast Asian countries, and East and South China...
March 25, 2018: Pest Management Science
Frédéric Keck
Culling, vaccinating, and monitoring animals are the three main techniques used in contemporary veterinary public health to manage animal diseases that can be transmitted to humans. Each technique is underpinned by different ontological understandings of how microbes figure in relations between humans and animals. Therefore, animal diseases are not only a question for an applied anthropology but also involve the theoretical core of the discipline i.e., understanding how social causality emerges out of physical causality...
March 23, 2018: Medical Anthropology Quarterly
R A Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, Luay Nakhleh
Summary: The evolutionary histories of individual regions across a genomic alignment - called 'local genealogies' - can differ from each other, due to processes such as recombination. Elucidating and analyzing these local genealogies are important for a large number of inference tasks, including those pertaining to species phylogenies, evolutionary processes, and trait mapping. In this paper, we present a toolkit for automated local phylogenomic analyses, or ALPHA. The purpose of this toolkit is to provide a wide array of functionalities for automated inference of local genealogies as well as analyses based on these local genealogies...
March 19, 2018: Bioinformatics
Brian Tilston Smith, Robert W Bryson, William M Mauck, Jaime Chaves, Mark B Robbins, Alexandre Aleixo, John Klicka
The New World avian family Polioptilidae (gnatcatchers and gnatwrens) is distributed from Argentina to Canada and includes 15 species and more than 60 subspecies. No study to date has evaluated phylogenetic relationships within this family and the historical pattern of diversification within the group remains unknown. Moreover, species limits, particularly in widespread taxa that show geographic variation, remain unclear. In this study, we delimited species and estimated phylogenetic relationships using multilocus data for the entire family...
March 15, 2018: Molecular Phylogenetics and Evolution
Niloofar Vaghefi, Julie R Kikkert, Frank S Hay, Gavriela D Carver, Lori B Koenick, Melvin D Bolton, Linda E Hanson, Gary A Secor, Sarah J Pethybridge
The taxonomy and evolutionary species boundaries in a global collection of Cercospora isolates from Beta vulgaris was investigated based on sequences of six loci. Species boundaries were assessed using concatenated multi-locus phylogenies, Generalized Mixed Yule Coalescent (GMYC), Poisson Tree Processes (PTP), and Bayes factor delimitation (BFD) framework. Cercospora beticola was confirmed as the primary cause of Cercospora leaf spot (CLS) on B. vulgaris. Cercospora apii, C. cf. flagellaris, Cercospora sp...
April 2018: Fungal Biology
Md Atique Ahmed, Muh Fauzi, Eun-Taek Han
BACKGROUND: Human infections due to the monkey malaria parasite Plasmodium knowlesi is on the rise in most Southeast Asian countries specifically Malaysia. The C-terminal 19 kDa domain of PvMSP1P is a potential vaccine candidate, however, no study has been conducted in the orthologous gene of P. knowlesi. This study investigates level of polymorphisms, haplotypes and natural selection of full-length pkmsp1p in clinical samples from Malaysia. METHODS: A total of 36 full-length pkmsp1p sequences along with the reference H-strain and 40 C-terminal pkmsp1p sequences from clinical isolates of Malaysia were downloaded from published genomes...
March 14, 2018: Malaria Journal
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