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https://www.readbyqxmd.com/read/28817696/phenotypic-and-molecular-characterization-of-sweet-sorghum-accessions-for-bioenergy-production
#1
Michele Jorge da Silva, Maria Marta Pastina, Vander Fillipe de Souza, Robert Eugene Schaffert, Pedro Crescêncio Souza Carneiro, Roberto Willians Noda, José Eustáquio de Souza Carneiro, Cynthia Maria Borges Damasceno, Rafael Augusto da Costa Parrella
Sweet sorghum [Sorghum bicolor (L.) Moench] is a type of cultivated sorghum characterized by the accumulation of high levels of sugar in the stems and high biomass accumulation, making this crop an important feedstock for bioenergy production. Sweet sorghum breeding programs that focus on bioenergy have two main goals: to improve quantity and quality of sugars in the juicy stem and to increase fresh biomass productivity. Genetic diversity studies are very important for the success of a breeding program, especially in the early stages, where understanding the genetic relationship between accessions is essential to identify superior parents for the development of improved breeding lines...
2017: PloS One
https://www.readbyqxmd.com/read/28812610/genome-wide-interrogation-advances-resolution-of-recalcitrant-groups-in-the-tree-of-life
#2
Dahiana Arcila, Guillermo Ortí, Richard Vari, Jonathan W Armbruster, Melanie L J Stiassny, Kyung D Ko, Mark H Sabaj, John Lundberg, Liam J Revell, Ricardo Betancur-R
Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051 loci from 225 species...
January 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28805766/-results-of-a-clinical-and-genealogical-analysis-of-pedigrees-of-children-with-cerebral-palsy-in-the-population-of-rostov-region
#3
V A Tupikov, T S Kolmakova, V B Shamik, M V Tupikov, N M Churilov
AIM: To perform clinical and genealogical pedigree analysis and determine the proportion of hereditary factors in the etiopathogenesis of cerebral palsy (CP) in children in the Rostov Region. MATERIAL AND METHODS: Pedigrees and the prevalence of CP, congenital malformations and other related diseases among relatives of I, II and III degrees of kinship of 229 probands with CP were studied. RESULTS AND CONCLUSION: The family concentration of the disease was detected in 15 (6...
2017: Zhurnal Nevrologii i Psikhiatrii Imeni S.S. Korsakova
https://www.readbyqxmd.com/read/28805044/nm%C3%AF-improved-re-implementation-of-nm-a-software-for-estimating-gene-dispersal-and-mating-patterns
#4
Igor J Chybicki
This paper introduces the NMπ computer program designed for estimation of plant mating system and seed and pollen dispersal kernels. NMπ is a re-implementation of the NM+ program and provides new features such as support for multi-core processors, explicit treatment of dioecy, the possibility of incorporating uniparentally cytoplasmic markers, the possibility of assessing assortative mating due to phenotypic similarity and inference about offspring genealogies. The probability model of parentage (the neighborhood model) accounts for missing data and genotyping errors, which can be estimated along with regular parameters of the mating system...
August 14, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28802020/investigating-the-diversity-of-effector-genes-in-the-banana-pathogen-fusarium-oxysporum-f-sp-cubense-reveals-evidence-of-horizontal-gene-transfer
#5
Elizabeth Czislowski, Sam Fraser-Smith, Manuel Zander, Wayne T O'Neill, Rachel A Meldrum, Lucy T T Tran-Nguyen, Jacqueline Batley, Elizabeth A B Aitken
It is hypothesised that the virulence of phytopathogenic fungi is mediated through the secretion of small effector proteins that interfere with the defence responses of the host plant. In Fusarium oxysporum, one family of effectors, the secreted in xylem (SIX) genes, have been identified. We sought to characterise the diversity and evolution of the SIX genes in the banana-infecting lineages of F. oxysporum f.sp. cubense (Foc). Whole-genome sequencing data was generated for the 23 genetic lineages of Foc, which were subsequently queried for the 14 known SIX genes (SIX1-SIX14)...
August 12, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28790994/insight-into-the-origin-and-evolution-of-the-vibrio-parahaemolyticus-pandemic-strain
#6
REVIEW
Romilio T Espejo, Katherine García, Nicolas Plaza
A strain of Vibrio parahaemolyticus that emerged in 1995 caused the first known pandemic involving this species. This strain comprises clonal autochthonous ocean-dwelling bacteria whose evolution has occurred in the ocean environment. The low sequence diversity in this population enabled the discovery of information on its origin and evolution that has been hidden in bacterial clones that have evolved over a long period. Multilocus sequencing and microarray analysis, together with phylogenetic analysis, of pandemic and pre-pandemic isolates has suggested that the founder clone was an O3:K6 non-pathogenic strain that initially acquired a toxRS/new region and subsequently acquired at least seven novel genomic islands...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28776400/book-review-chris-millard-a-history-of-self-harm-in-britain-a-genealogy-of-cutting-and-overdosing-millard-chris-a-history-of-self-harm-in-britain-a-genealogy-of-cutting-and-overdosing-palgrave-macmillan-houndmills-2015-ix-268-pp-9781137529626-free-ebook-9781137529619
#7
https://www.readbyqxmd.com/read/28776029/genome-wide-signatures-of-complex-introgression-and-adaptive-evolution-in-the-big-cats
#8
Henrique V Figueiró, Gang Li, Fernanda J Trindade, Juliana Assis, Fabiano Pais, Gabriel Fernandes, Sarah H D Santos, Graham M Hughes, Aleksey Komissarov, Agostinho Antunes, Cristine S Trinca, Maíra R Rodrigues, Tyler Linderoth, Ke Bi, Leandro Silveira, Fernando C C Azevedo, Daniel Kantek, Emiliano Ramalho, Ricardo A Brassaloti, Priscilla M S Villela, Adauto L V Nunes, Rodrigo H F Teixeira, Ronaldo G Morato, Damian Loska, Patricia Saragüeta, Toni Gabaldón, Emma C Teeling, Stephen J O'Brien, Rasmus Nielsen, Luiz L Coutinho, Guilherme Oliveira, William J Murphy, Eduardo Eizirik
The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes...
July 2017: Science Advances
https://www.readbyqxmd.com/read/28771477/deconstructing-isolation-by-distance-the-genomic-consequences-of-limited-dispersal
#9
Stepfanie M Aguillon, John W Fitzpatrick, Reed Bowman, Stephan J Schoech, Andrew G Clark, Graham Coop, Nancy Chen
Geographically limited dispersal can shape genetic population structure and result in a correlation between genetic and geographic distance, commonly called isolation-by-distance. Despite the prevalence of isolation-by-distance in nature, to date few studies have empirically demonstrated the processes that generate this pattern, largely because few populations have direct measures of individual dispersal and pedigree information. Intensive, long-term demographic studies and exhaustive genomic surveys in the Florida Scrub-Jay (Aphelocoma coerulescens) provide an excellent opportunity to investigate the influence of dispersal on genetic structure...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28768476/pan-genome-and-phylogeny-of-bacillus-cereus-sensu-lato
#10
Adam L Bazinet
BACKGROUND: Bacillus cereus sensu lato (s. l.) is an ecologically diverse bacterial group of medical and agricultural significance. In this study, I use publicly available genomes and novel bioinformatic workflows to characterize the B. cereus s. l. pan-genome and perform the largest phylogenetic and population genetic analyses of this group to date in terms of the number of genes and taxa included. With these fundamental data in hand, I identify genes associated with particular phenotypic traits (i...
August 2, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28757490/the-philosophical-genealogy-of-taylor-s-social-imaginaries-a-complex-history-of-ideas-and-predecessors
#11
Guido M Vanheeswijck
The deepest sources of Charles Taylor's use of the concept "social imaginaries" are often related to political philosophy or social anthropology (Anderson, Castoriadis). The purpose of this article is to show that they also form part of Taylor's struggle to overcome the epistemological construal in modern philosophy and culture. Taylor locates the concept "social imaginaries" in the Kantian tradition, identifying their role to that of transcendental schemes. However, there remains a central difference between Kant's transcendental schemes and Taylor's social imaginaries...
2017: Journal of the History of Ideas
https://www.readbyqxmd.com/read/28752599/on-the-independent-gene-trees-assumption-in-phylogenomic-studies
#12
W Bryan Jennings
Multilocus coalescent methods for inferring species trees or historical demographic parameters typically require the assumption that gene trees for sampled SNPs or DNA sequence loci are conditionally independent given their species tree. In practice, researchers have used different criteria to delimit "independent loci." One criterion identifies sampled loci as being independent of each other if they undergo Mendelian independent assortment (IA criterion). O'Neill et al. (2013, Molecular Ecology, 22, 111-129) used this approach in their phylogeographic study of North American tiger salamander species complex...
July 28, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28750851/genealogical-patterns-and-cryptic-diversity-in-an-aposematic-toad-from-nw-argentina
#13
Rute B Clemente-Carvalho, Marcos Vaira, Laura E King, Daria Koscinski, Maria I Bonansea, Stephen C Lougheed
The Yungas Redbelly Toad, Melanophryniscus rubriventris, is patchily distributed in Argentina, confined to the upland portion (1000 to 2000 meters above sea level) of the montane forests of northern and central regions of Salta, and in central-eastern and south-eastern Jujuy. This species is known for its striking aposematic color variation across its geographic distribution, and was once treated as a complex of three subspecies based on distinctive color patterns. Here we assess the geographical genetic variation within M...
July 24, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28742445/becoming-lesbian-monique-wittig-s-queer-trans-feminism
#14
Kevin Henderson
Inspired by Lynne Huffer's queer feminist genealogy, this article explores queer-trans-feminism as a project that would bring together queer, feminist, and transgender theory and politics into a shared critical lineage. I suggest that Monique Wittig is a neglected thinker who could re-enliven connections and debates within queer, feminist, and trans theory and politics. Utilizing recent historiographies of queer and feminist theory, I imagine what it would mean to hold on to the figure of the lesbian as a figure for queer-trans-feminist politics rather than render the lesbian anachronistic...
July 25, 2017: Journal of Lesbian Studies
https://www.readbyqxmd.com/read/28742271/genetic-genealogy-approach-reveals-low-rate-of-extrapair-paternity-in-historical-dutch-populations
#15
Maarten H D Larmuseau, Sofie Claerhout, Leen Gruyters, Kelly Nivelle, Michiel Vandenbosch, Anke Peeters, Pieter van den Berg, Tom Wenseleers, Ronny Decorte
OBJECTIVE: Evolutionary theory has shown that seeking out extrapair paternity (EPP) can be a viable reproductive strategy for both sexes in pair-bonded species, also in humans. As yet, estimates of the contemporary or historical EPP rate in human population are still rare. In the present study, we estimated the historical EPP rate in the Dutch population over the last 400 years and compared the rate with those obtained for other human populations to determine the evolutionary, cultural, and socio-demographic factors that influence human cuckoldry behavior...
July 25, 2017: American Journal of Human Biology: the Official Journal of the Human Biology Council
https://www.readbyqxmd.com/read/28739658/benchmarking-relatedness-inference-methods-with-genome-wide-data-from-thousands-of-relatives
#16
Monica D Ramstetter, Thomas Dyer, Donna M Lehman, Joanne E Curran, Ravindranath Duggirala, John Blangero, Jason G Mezey, Amy L Williams
Inferring relatedness from genomic data is an essential component of genetic association studies, population genetics, forensics, and genealogy. While numerous methods exist for inferring relatedness, thorough evaluation of these approaches in real data has been lacking. Here, we report an assessment of 12 state-of-the-art pairwise relatedness inference methods using a dataset with 2,485 individuals contained in several large pedigrees that span up to six generations. We find that all methods have high accuracy (~92% - 99%) when detecting first and second degree relationships, but their accuracy dwindles to less than 43% for seventh degree relationships...
July 24, 2017: Genetics
https://www.readbyqxmd.com/read/28734863/significant-linkage-evidence-for-interstitial-cystitis-painful-bladder-syndrome-on-chromosome-3
#17
Kristina Allen-Brady, Kerry Rowe, Melissa Cessna, Sara Lenherr, Peggy Norton
PURPOSE: Interstitial cystitis/painful bladder syndrome (IC/PBS) is a chronic pelvic pain condition with unknown etiology. We hypothesized that related IC/PBS cases were more likely to have a genetic etiology. The purpose of this study was to perform a genetic linkage analysis. MATERIALS AND METHODS: IC/PBS cases were identified using diagnostic codes linked to a population-based genealogy resource (Utah Population Database) and electronic medical records. For this analysis, 13 high-risk pedigrees (defined as having a statistical excess number of IC/PBS cases among descendants compared to matched hospital population rates) were used...
July 19, 2017: Journal of Urology
https://www.readbyqxmd.com/read/28731872/bleeding-risk-assessment-in-hemophilia-a-carriers-from-dakar-senegal
#18
Moussa Seck, Blaise F Faye, Abibatou Sall, Diariétou Sy, Sokhna A Touré, Nata Dieng, Youssou B Guéye, Macoura Gadji, Awa O Touré, Cathérine Costa, Dominique Lasne, Chantal Rothschild, Saliou Diop
: Hemophilia A carriers have an abnormal X chromosome with a molecular abnormality of FVIII gene. These carriers, long considered to be free of bleeding risk, could have the same symptoms as mild hemophiliacs. This study aim to assess bleeding risk of hemophilia A carriers monitored at the Clinical Hematology of Dakar. This is a prospective study of a period of 6 months including 22 hemophilia A carriers aged between 8 and 48 years. Hemophilia carriers were recruited using the genealogical tree of hemophiliacs followed in the service...
July 20, 2017: Blood Coagulation & Fibrinolysis: An International Journal in Haemostasis and Thrombosis
https://www.readbyqxmd.com/read/28725387/origins-of-two-hemiclonal-hybrids-among-three-hexagrammos-species-teleostei-hexagrammidae-genetic-diversification-through-host-switching
#19
Hiroyuki Munehara, Miho Horita, Motoko R Kimura-Kawaguchi, Aya Yamazaki
Two natural, hemiclonal hybrid strains were discovered in three Hexagrammos species. The natural hybrids, all of which were females that produced haploid eggs containing only the Hexagrammos octogrammus genome (maternal ancestor; hereafter Hoc), generated F1 hybrid-type offspring by fertilization with haploid sperm of Hexagrammos agrammus or Hexagrammos otakii (paternal species; Hag and Hot, respectively). This study was performed to clarify the extent of diversification between the two hybrids and the maternal ancestor...
October 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28709926/an-efficient-algorithm-for-generating-the-internal-branches-of-a-kingman-coalescent
#20
M Reppell, S Zöllner
Coalescent simulations are a widely used approach for simulating sample genealogies, but can become computationally burdensome in large samples. Methods exist to analytically calculate a sample's expected frequency spectrum without simulating full genealogies. However, statistics that rely on the distribution of the length of internal coalescent branches, such as the probability that two mutations of equal size arose on the same genealogical branch, have previously required full coalescent simulations to estimate...
July 11, 2017: Theoretical Population Biology
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