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https://www.readbyqxmd.com/read/29668018/how-strong-was-the-bottleneck-associated-to-the-peopling-of-the-americas-new-insights-from-multilocus-sequence-data
#1
Nelson J R Fagundes, Alice Tagliani-Ribeiro, Rohina Rubicz, Larissa Tarskaia, Michael H Crawford, Francisco M Salzano, Sandro L Bonatto
In spite of many genetic studies that contributed for a deep knowledge about the peopling of the Americas, no consensus has emerged about important parameters such as the effective size of the Native Americans founder population. Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations...
2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29668017/phylogeographic-analyses-of-the-pampas-cat-leopardus-colocola-carnivora-felidae-reveal-a-complex-demographic-history
#2
Anelisie da Silva Santos, Tatiane Campos Trigo, Tadeu Gomes de Oliveira, Leandro Silveira, Eduardo Eizirik
The pampas cat is a small felid that occurs in open habitats throughout much of South America. Previous studies have revealed intriguing patterns of morphological differentiation and genetic structure among its populations, as well as molecular evidence for hybridization with the closely related L. tigrinus. Here we report phylogeographic analyses encompassing most of its distribution (focusing particularly on Brazilian specimens, which had been poorly sampled in previous studies), using a novel dataset comprising 2,143 bp of the mitogenome, along with previously reported mtDNA sequences...
2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29668016/genetic-and-ecological-niche-modeling-of-calydorea-crocoides-iridaceae-an-endemic-species-of-subtropical-highland-grasslands
#3
Juliana Lustosa Matos de Alencar, Eliane Kaltchuk-Santos, Juliana Fachinetto, Luana Olinda Tacuatiá, Eliana Regina Forni-Martins, Eudes Maria Stiehl-Alves, Tatiana Teixeira de Souza-Chies
Evolutionary analyses have been widely used for evaluation of genetic diversity of natural populations and correlate these data to the fitness of the species, especially in the case of threatened species. Calydorea crocoides occurs in a restricted area at altitudes from 800 to 1500 m in southern Brazil and is considered endangered. A study assessing genetic diversity, cytogenetic features and ecological niche was performed aiming to characterize C. crocoides by multidisciplinary approaches. Molecular data highlighted that most of the total variation (76%; p < 0...
2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29668011/effective-population-size-and-the-genetic-consequences-of-commercial-whaling-on-the-humpback-whales-megaptera-novaeangliae-from-southwestern-atlantic-ocean
#4
Ana Lúcia Cypriano-Souza, Tiago Ferraz da Silva, Márcia H Engel, Sandro L Bonatto
Genotypes of 10 microsatellite loci of 420 humpback whales from the Southwestern Atlantic Ocean population were used to estimate for the first time its contemporary effective (Ne) and census (Nc) population sizes and to test the genetic effect of commercial whaling. The results are in agreement with our previous studies that found high genetic diversity for this breeding population. Using an approximate Bayesian computation approach, the scenario of constant Ne was significantly supported over scenarios with moderate to strong size changes during the commercial whaling period...
2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29668009/ecological-drivers-of-plant-genetic-diversity-at-the-southern-edge-of-geographical-distributions-forestal-vines-in-a-temperate-region
#5
Michel J F Barros, José Alexandre F Diniz-Filho, Loreta B Freitas
The Tropical Niche Conservatism hypothesis is one of the most relevant theories to explain why tropical diversity is high, although the mechanisms underlying this hypothesis require further clarification. A possible research avenue to address the underlying mechanisms includes determining population-level processes associated with such a hypothesis, in particular by trying to identify how adaptation may occur in extreme niche conditions at the edges of species ranges. However, the determinants of molecular diversity at the edges of geographical distributions of tropical taxa are still poorly known...
2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29667458/sudden-unexpected-death-in-epilepsy-ongoing-challenges-in-finding-mechanisms-and-prevention
#6
Doungporn Ruthirago, Parunyou Julayanont, Amputch Karukote, Mohamed Shehabeldin, Kenneth Nugent
Patients with epilepsy have a significantly higher risk of death than the general population. Sudden unexpected death in epilepsy (SUDEP) is the leading cause of sudden death among patients with epilepsy. Despite on-going research, there are still deficits in our knowledge about the mechanisms, genetic factors, and prevention of SUDEP. Current evidence suggests that cardiac arrhythmias, respiratory dysfunction, and brainstem arousal system dysfunction are the major mechanisms of SUDEP, and animal models support the role of neurotransmitters, especially serotonin and adenosine, in pathophysiology of SUDEP...
April 18, 2018: International Journal of Neuroscience
https://www.readbyqxmd.com/read/29667373/heritability-estimates-from-genome-wide-relatedness-matrices-in-wild-populations-application-to-a-passerine-using-a-small-sample-size
#7
C Perrier, B Delahaie, A Charmantier
Genomic developments have empowered the investigation of heritability in wild populations directly from genome wide relatedness matrices (GRM). Such GRM based approaches can in particular be used to improve or substitute approaches based on social pedigree (PED-social). However, measuring heritability from GRM in the wild has not been widely applied yet, especially using small samples and in non-model species. Here, we estimated heritability for four quantitative traits (tarsus length, wing length, bill length and body mass), using PED-social, a pedigree corrected by genetic data (PED-corrected) and a GRM from a small sample (n = 494) of blue tits from natural populations in Corsica genotyped at nearly 50,000 filtered SNPs derived from RAD-seq...
April 17, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29667364/heritability-of-body-size-in-the-polar-bears-of-western-hudson-bay
#8
René M Malenfant, Corey S Davis, Evan S Richardson, Nicholas J Lunn, David W Coltman
Among polar bears (Ursus maritimus), fitness is dependent on body size through males' abilities to win mates, females' abilities to provide for their young, and all bears' abilities to survive increasingly longer fasting periods caused by climate change. In the Western Hudson Bay subpopulation (near Churchill, Manitoba, Canada), polar bears have declined in body size and condition, but nothing is known about the genetic underpinnings of body size variation, which may be subject to natural selection. Here, we combine a 4449-individual pedigree and an array of 5433 single-nucleotide polymorphisms (SNPs) to provide the first quantitative genetics study of polar bears...
April 18, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29667323/clades-a-classification-based-machine-learning-method-for-species-delimitation-from-population-genetic-data
#9
Jingwen Pei, Chong Chu, Xin Li, Bin Lu, Yufeng Wu
Species are considered to be the basic unit of ecological and evolutionary studies. Since multi-locus genomic data are increasingly available there has been considerable interests in the use of DNA sequence data to delimit species. In this paper, we show that machine learning can be used for species delimitation. Our method treats the species delimitation problem as a classification problem for identifying the category of a new observation on the basis of training data. Extensive simulation is first conducted over a broad range of evolutionary parameters for training purposes...
April 18, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29667198/alcohol-availability-and-onset-and-recurrence-of-alcohol-use-disorder-examination-in-a-longitudinal-cohort-with-co-sibling-analysis
#10
Katherine J Karriker-Jaffe, Henrik Ohlsson, Kenneth S Kendler, Won Kim Cook, Kristina Sundquist
BACKGROUND: Recent reviews of associations of alcohol availability with alcohol outcomes suggest findings are highly inconsistent and highlight a lack of longitudinal and causal evidence. Effect modification (moderation or statistical interaction), which could contribute to the inconsistent picture in the existing literature, has not been systematically assessed. We examined associations of alcohol availability with onset and recurrence of alcohol use disorder (AUD) using multi-level, longitudinal population data from Sweden and test hypothesized effect modifiers to identify groups for whom increased alcohol availability may be particularly risky...
April 18, 2018: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/29666902/effect-of-cyp2c19-ugt1a8-and-ugt2b7-on-valproic-acid-clearance-in-children-with-epilepsy-a-population-pharmacokinetic-model
#11
Shenghui Mei, Weixing Feng, Leting Zhu, Xingang Li, Yazhen Yu, Weili Yang, Baoqin Gao, Xiaojuan Wu, Fang Fang, Zhigang Zhao
PURPOSE: Valproic acid (VPA) is an important drug in seizure control with great inter-individual differences in metabolism and treatment effect. This study aims to identify the effects of genetic variants on VPA clearance in a population pharmacokinetic (popPK) model in children with epilepsy. METHODS: A total of 325 VPA plasma concentrations from 290 children with epilepsy were used to develop the popPK model by using the nonlinear mixed-effects modeling method...
April 17, 2018: European Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/29666883/snp-based-pool-genotyping-and-haplotype-analysis-accelerate-fine-mapping-of-the-wheat-genomic-region-containing-stripe-rust-resistance-gene-yr26
#12
Jianhui Wu, Qingdong Zeng, Qilin Wang, Shengjie Liu, Shizhou Yu, Jingmei Mu, Shuo Huang, Hanan Sela, Assaf Distelfeld, Lili Huang, Dejun Han, Zhensheng Kang
NGS-assisted super pooling emerging as powerful tool to accelerate gene mapping and haplotype association analysis within target region uncovering specific linkage SNPs or alleles for marker-assisted gene pyramiding. Conventional gene mapping methods to identify genes associated with important agronomic traits require significant amounts of financial support and time. Here, a single nucleotide polymorphism (SNP)-based mapping approach, RNA-Seq and SNP array assisted super pooling analysis, was used for rapid mining of a candidate genomic region for stripe rust resistance gene Yr26 that has been widely used in wheat breeding programs in China...
April 17, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29666773/estimating-intraspecific-genetic-diversity-from-community-dna-metabarcoding-data
#13
Vasco Elbrecht, Ecaterina Edith Vamos, Dirk Steinke, Florian Leese
Background: DNA metabarcoding is used to generate species composition data for entire communities. However, sequencing errors in high-throughput sequencing instruments are fairly common, usually requiring reads to be clustered into operational taxonomic units (OTUs), losing information on intraspecific diversity in the process. While Cytochrome c oxidase subunit I (COI) haplotype information is limited in resolving intraspecific diversity it is nevertheless often useful e.g. in a phylogeographic context, helping to formulate hypotheses on taxon distribution and dispersal...
2018: PeerJ
https://www.readbyqxmd.com/read/29666556/maturity-onset-diabetes-of-the-young-due-to-hnf1a-variants-in-croatia
#14
Tamara Pavić, Agata Juszczak, Edita Pape Medvidović, Carla Burrows, Mario Šekerija, Amanda J Bennett, Jadranka Ćuća Knežević, Anna L Gloyn, Gordan Lauc, Mark I McCarthy, Olga Gornik, Katharine R Owen
Introduction: Maturity onset diabetes of the young due to HNF1A mutations (HNF1A-MODY) is the most frequent form of monogenic diabetes in adults. It is often misdiagnosed as type 1 or type 2 diabetes, but establishing genetic diagnosis is important, as treatment differs from the common types of diabetes. HNF1A-MODY has not been investigated in Croatia before due to limited access to genetic testing. In this study we aimed to describe the characteristics of young adults diagnosed with diabetes before the age of 45 years, who have rare HNF1A allele variants, and estimate the prevalence of HNF1A-MODY in Croatia...
June 15, 2018: Biochemia Medica: časopis Hrvatskoga Društva Medicinskih Biokemičara
https://www.readbyqxmd.com/read/29666450/novel-hla-class-i-associations-with-hiv-1-control-in-a-unique-genetically-admixed-population
#15
Humberto Valenzuela-Ponce, Selma Alva-Hernández, Daniela Garrido-Rodríguez, Maribel Soto-Nava, Thalía García-Téllez, Tania Escamilla-Gómez, Claudia García-Morales, Verónica Sonia Quiroz-Morales, Daniela Tapia-Trejo, Silvia Del Arenal-Sánchez, Francisco-Javier Prado-Galbarro, Ramón Hernández-Juan, Edna Rodríguez-Aguirre, Akio Murakami-Ogasawara, Carlos Mejía-Villatoro, Ingrid Y Escobar-Urias, Rodolfo Pinzón-Meza, Juan Miguel Pascale, Yamitzel Zaldivar, Guillermo Porras-Cortés, Carlos Quant-Durán, Ivette Lorenzana, Rita I Meza, Elsa Y Palou, Marvin Manzanero, Rolando A Cedillos, Carmen Aláez, Mark A Brockman, P Richard Harrigan, Chanson J Brumme, Zabrina L Brumme, Santiago Ávila-Ríos, Gustavo Reyes-Terán
Associations between HLA class I alleles and HIV progression in populations exhibiting Amerindian and Caucasian genetic admixture remain understudied. Using univariable and multivariable analyses we evaluated HLA associations with five HIV clinical parameters in 3,213 HIV clade B-infected, ART-naïve individuals from Mexico and Central America (MEX/CAM cohort). A Canadian cohort (HOMER, n = 1622) was used for comparison. As expected, HLA allele frequencies in MEX/CAM and HOMER differed markedly. In MEX/CAM, 13 HLA-A, 24 HLA-B, and 14 HLA-C alleles were significantly associated with at least one clinical parameter...
April 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29666375/association-and-cis-mqtl-analysis-of-variants-in-chrna3-a5-chrna7-chrnb2-and-chrnb4-in-relation-to-nicotine-dependence-in-a-chinese-han-population
#16
Qiang Liu, Haijun Han, Maiqiu Wang, Yinghao Yao, Li Wen, Keran Jiang, Yunlong Ma, Rongli Fan, Jiali Chen, Kunkai Su, Zhongli Yang, Wenyan Cui, Wenji Yuan, Xianzhong Jiang, Jingjing Li, Thomas J Payne, Jundong Wang, Ming D Li
Nicotine dependence (ND) is a worldwide health problem. Numerous genetic studies have demonstrated a significant association of variants in nicotinic acetylcholine receptors (nAChRs) with smoking behaviors. However, most of these studies enrolled only subjects of European or African ancestry. In addition, although an increasing body of evidence implies a causal connection of single-nucleotide polymorphisms (SNPs) and epigenetic regulation of gene expression, few studies of this issue have been reported. In this study, we performed both association and interaction analysis for 67 SNPs in CHRNA3-A5, CHRNA7, CHRNB2, and CHRNB4 with ND in a Chinese Han population (N = 5055)...
April 18, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29666349/genetic-disease-in-india-and-the-west-compared-provisional-analysis-of-population-dynamics
#17
Nicholas Mitchison, Timothy Mitchison
The Indian Genetic Disease Database (IGDD) and Online Mendelian Inheritance in Man (OMIM) survey human populations that have different climate histories. Comparison of the two shows an outstanding difference in the relative frequency of recessive disease genes. Several of the diseases mediated at least in part by recessive gene mutations in India are not so mediated in the Western populations covered by OMIM, or are so mediated to a lesser extent. This we attribute to climate history, where population fall leading to inbreeding in the last ice age appears to have reduced the frequency of recessive disease genes in the Western world...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29666346/genetic-heterogeneity-in-van-der-woude-syndrome-identification-of-nol4-and-irf6-haplotype-from-the-noncoding-region-as-candidates-in-two-families
#18
Priyanka Kumari Kumari, Akhtar Ali, Subodh Kumar Singh, Amit Chaurasia, Rajiva Raman
Van der Woude syndrome (VWS) shows an autosomal dominant pattern of inheritance with two known candidate genes, IRF6 and GRHL3. In this study, by employing genome-wide linkage analyses on two VWS affected families, we report the cosegregation of an intronic rare variant in NOL4 in one family, and a haplotype consisting of three variants in the noncoding region of IRF6 (introns 1, 8 and 3'UTR) in the other family. Using mouse, as well as human embryos as a model, we demonstrate the expression of NOL4 in the lip and palate primordia during their development...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29666344/comparative-mapping-of-quantitative-trait-loci-for-tassel-related-traits-of-maize-in-f-2-3-and-ril-populations
#19
Qiang Yi, Yinghong Liu, Xiangge Zhang, Xianbin Hou, Junjie Zhang, Hanmei Liu, Yufeng Hu, Guowu Yu, Yubi Huang
Tassel architecture is an important trait in maize breeding and hybrid seed production. In this study, we investigated total tassel length (TTL) and tassel branch number (TBN) in 266 F2:3 families across six environments and in 301 recombinant inbred lines (RILs) across three environments, where all the plants were derived from a cross between 08-641 and Ye478. We compared the genetic architecture of the two traits across two generations through combined analysis. In total, 27 quantitative trait loci (QTLs) (15 in F2:3 ; 16 in RIL), two QTL × environment interactions (both in F2:3 ), 11 pairs of epistatic interactions (seven in F2:3 ; four in RIL) and four stable QTLs in both the F2:3 and RILs were detected...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29666343/interleukin-gene-polymorphisms-and-susceptibility-to-hiv-1-infection-a-meta-analysis
#20
Chrissa G Tsiara, Georgios K Nikolopoulos, Niki L Dimou, Katerina G Pantavou, Pantelis G Bagos, Benedicta Mensah, Michael Talias, Georgia G Braliou, Dimitra Paraskeva, Stefanos Bonovas, Angelos Hatzakis
Some subjects are repeatedly exposed to human immunodeficiency virus (HIV), yet they remain uninfected. This suggests the existence of host-resistance mechanisms. The current study synthesizes the evidence regarding the association between interleukin (IL) gene polymorphisms and HIV susceptibility. Medline, Scopus and the Web of Science databases were systematically searched, and a meta-analysis of case-control studies was conducted. Univariate and bivariate methods were used. The literature search identified 42 eligible studies involving 15,727 subjects...
March 2018: Journal of Genetics
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