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https://www.readbyqxmd.com/read/28209761/genetic-adaptation-of-the-schizothoracine-fishes-to-the-phased-uplifting-of-qinghai-tibetan-plateau
#1
Dongsheng Zhang, Mengchao Yu, Peng Hu, Sihua Peng, Yimeng Liu, Weiwen Li, Congcong Wang, Shunping He, Wanying Zhai, Qianghua Xu, Liangbiao Chen
Many species of Schizothoracine, a sub-family of Cyprinidae, are highly endemic to the Qinghai-Tibetan Plateau (QTP). To characterize the adaptive changes associated with the Schizothoracine expansion in high-altitudes, we sequenced tissue transcriptomes of two highland and two sub-highland Schizothoracines, and analyzed gene evolution patterns by comparing to lowland cyprinids. Phylogenetic tree reconstruction and divergence time estimation indicated that the common ancestor of Schizothoracine fishes lived around 32...
February 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28202767/genotype-specific-evolution-of-hepatitis-e-virus
#2
Adam B Brayne, Bethany L Dearlove, James S Lester, Sergei L Kosakovsky Pond, Simon D W Frost
Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis globally. HEV comprises four genotypes with different geographic distributions and host ranges. We utilise this natural case-control study for investigating the evolution of zoonotic viruses compared to single host viruses, using 244 near full length HEV genomes. Genome wide estimates of dN/dS located a region of overlapping reading frames, which is subject to positive selection in genotypes 3 and 4. The open reading frames (ORFs) involved have functions related to host-pathogen interaction, so genotype specific evolution of these regions may reflect their fitness...
February 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28166720/increased-rates-of-protein-evolution-and-asymmetric-deceleration-after-the-whole-genome-duplication-in-yeasts
#3
Diana Ascencio, Soledad Ochoa, Luis Delaye, Alexander DeLuna
BACKGROUND: Whole-genome duplication (WGD) events have shaped the genomes of eukaryotic organisms. Relaxed selection after duplication along with inherent functional constraints are thought to determine the fate of the paralogs and, ultimately, the evolution of gene function. Here, we investigated the rate of protein evolution (as measured by dN/dS ratios) before and after the WGD in the hemiascomycete yeasts, and the way in which changes in such rates relate to molecular and biological function...
February 6, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28159865/comparative-transcriptomics-of-malaria-mosquito-testes-function-evolution-and-linkage
#4
Bryan J Cassone, Raissa G G Kay, Matthew P Daugherty, Bradley J White
Testes-biased genes evolve rapidly and are important in the establishment, solidification, and maintenance of reproductive isolation between incipient species. The Anopheles gambiae complex, a group of at least eight isomorphic mosquito species endemic to Sub-Saharan Africa, is an excellent system to explore the evolution of testes-biased genes. Within this group, the testes are an important tissue in the diversification process since hybridization between species results in sterile hybrid males, but fully fertile females...
February 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28120868/evidence-for-positive-selection-and-recombination-hotspots-in-deformed-wing-virus-dwv
#5
A Dalmon, C Desbiez, M Coulon, M Thomasson, Y Le Conte, C Alaux, J Vallon, B Moury
Deformed wing virus (DWV) is considered one of the most damaging pests in honey bees since the spread of its vector, Varroa destructor. In this study, we sequenced the whole genomes of two virus isolates and studied the evolutionary forces that act on DWV genomes. The isolate from a Varroa-tolerant bee colony was characterized by three recombination breakpoints between DWV and the closely related Varroa destructor virus-1 (VDV-1), whereas the variant from the colony using conventional Varroa management was similar to the originally described DWV...
January 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28110273/shifting-balance-on-a-static-mutation-selection-landscape-a-novel-scenario-of-positive-selection
#6
Christopher T Jones, Noor Youssef, Edward Susko, Joseph P Bielawski
A version of the mechanistic mutation-selection (MutSel) model that accounts for temporal dynamics at a site is presented. This is used to show that the rate ratio dN/dS at a site can be transiently >1 even when fitness coefficients are fixed or the fitness landscape is static. This occurs whenever a site drifts away from its fitness peak and is then forced back by selection, a process reminiscent of shifting balance. Shifting balance is strongest when the substitution process is not dominated by selection or drift, but admits interplay between the two...
November 8, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28108586/fluctuating-selection-in-the-moran
#7
Antony M Dean, Clarence Lehman, Xiao Yi
Contrary to classical population genetics theory, experiments demonstrate that fluctuating selection can protect a haploid polymorphism in the absence of frequency dependent effects on fitness. Using forward simulations with the Moran model we confirm our analytical results showing that a fluctuating selection regime, with a mean selection coefficient of zero, promotes polymorphism. We find that increases in heterozygosity over neutral expectations are especially pronounced when fluctuations are rapid, mutation is weak, the population size is large and the variance in selection is big...
January 20, 2017: Genetics
https://www.readbyqxmd.com/read/28053111/evolutionary-interplay-between-structure-energy-and-epistasis-in-the-coat-protein-of-the-%C3%AF-x174-phage-family
#8
Rodrigo A F Redondo, Harold P de Vladar, Tomasz Włodarski, Jonathan P Bollback
Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28051058/purifying-selection-and-genetic-drift-shaped-pleistocene-evolution-of-the-mitochondrial-genome-in-an-endangered-australian-freshwater-fish
#9
A Pavlova, H M Gan, Y P Lee, C M Austin, D M Gilligan, M Lintermans, P Sunnucks
Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB)...
January 4, 2017: Heredity
https://www.readbyqxmd.com/read/28049516/genetic-clustering-and-polymorphism-of-the-merozoite-surface-protein-3-of-plasmodium-knowlesi-clinical-isolates-from-peninsular-malaysia
#10
Jeremy Ryan De Silva, Yee Ling Lau, Mun Yik Fong
BACKGROUND: The simian malaria parasite Plasmodium knowlesi has been reported to cause significant numbers of human infection in South East Asia. Its merozoite surface protein-3 (MSP3) is a protein that belongs to a multi-gene family of proteins first found in Plasmodium falciparum. Several studies have evaluated the potential of P. falciparum MSP3 as a potential vaccine candidate. However, to date no detailed studies have been carried out on P. knowlesi MSP3 gene (pkmsp3). The present study investigates the genetic diversity, and haplotypes groups of pkmsp3 in P...
January 3, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28024871/balancing-selection-on-allorecognition-genes-in-the-colonial-ascidian-botryllus-schlosseri
#11
Marie L Nydam, Emily E Stephenson, Claire E Waldman, Anthony W De Tomaso
Allorecognition is the capability of an organism to recognize its own or related tissues. The colonial ascidian Botryllus schlosseri, which comprises five genetically distinct and divergent species (Clades A-E), contains two adjacent genes that control allorecognition: fuhc(sec) and fuhc(tm). These genes have been characterized extensively in Clade A and are highly polymorphic. Using alleles from 10 populations across the range of Clade A, we investigated the type and strength of selection maintaining this variation...
December 24, 2016: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/27951521/virulence-in-newcastle-disease-virus-a-genotyping-and-molecular-evolution-spectrum-perspective
#12
Wentao Fan, Yang Wang, Shenghua Wang, Ziqiang Cheng, Huijun Guo, Xiaona Zhao, Jianzhu Liu
In our research, the molecular evolutions of NDV F and HN genes were analyzed. The phylogenetic analyses of NDV sequences indicated that NDV could be divided into two genotypes: Class I (lentogenic strains) and Class II (velogenic or mesogenic strains). Each genotype possesses high gene homology. Furthermore, the selected pressure analysis showed that the dN/dS of velogenic, mesogenic NDV strains F gene was significantly high and the ω(dN/dS) is 1.1725>1. These results imply that mutations in velogenic, mesogenic NDV F gene are favored by positive natural selection and it has acted to diversify NDV virulence at the nucleotide and amino acid level...
December 7, 2016: Research in Veterinary Science
https://www.readbyqxmd.com/read/27909914/association-of-snp-variants-of-mhc-class-ii-drb-gene-with-thermo-physiological-traits-in-tropical-goats
#13
Abdulmojeed Yakubu, Adebowale E Salako, Marcos De Donato, Sunday O Peters, Michael I Takeet, Mathew Wheto, Moses Okpeku, Ikhide G Imumorin
Host defense in vertebrates depend on many secreted regulatory proteins such as major histocompatibility complex (MHC) class II which provide important regulatory and effector functions of T cells. Gene polymorphism in the second exon of Capra-DRB gene in three major Nigerian goat breeds [West African Dwarf (WAD), Red Sokoto (RS), and Sahel (SH)] was analyzed by restriction fragment length polymorphisms (RFLP). Four restriction enzymes, BsaHI, AluI, HaeIII, and SacII, were utilized. The association between the polymorphic sites and some heat tolerance traits were also investigated in a total of 70 WAD, 90 RS, and 50 SH goats...
February 2017: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/27881098/genomic-determination-of-minimum-multi-locus-sequence-typing-schemas-to-represent-the-genomic-phylogeny-of-mycoplasma-hominis
#14
Aleksey Jironkin, Rebecca J Brown, Anthony Underwood, Victoria J Chalker, Owen B Spiller
BACKGROUND: Mycoplasma hominis is an opportunistic human pathogen, associated with clinically diverse disease. Currently, there is no standardised method for typing M. hominis, which would aid in understanding pathogen epidemiology and transmission. Due to availability and costs of whole genome sequencing and the challenges in obtaining adequate M. hominis DNA, the use of whole genome sequence analysis to provide clinical guidance is unpractical for this bacterial species as well as other fastidious organisms...
November 23, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27872816/evidence-of-triple-mutant-pfdhps-isgnga-haplotype-in-plasmodium-falciparum-isolates-from-north-east-india-an-analysis-of-sulfadoxine-resistant-haplotype-selection
#15
Manuj K Das, Sumi Chetry, Mohan C Kalita, Prafulla Dutta
BACKGROUND: North-east region of India has consistent role in the spread of multi drug resistant Plasmodium (P.) falciparum to other parts of Southeast Asia. After rapid clinical treatment failure of Artemisinin based combination therapy-Sulphadoxine/Pyrimethamine (ACT-SP) chemoprophylaxis, Artemether-Lumefantrine (ACT-AL) combination therapy was introduced in the year 2012 in this region for the treatment of uncomplicated P. falciparum malaria. In a DNA sequencing based polymorphism analysis, seven codons of P...
December 2016: Genomics Data
https://www.readbyqxmd.com/read/27867038/comparative-mitogenomic-analysis-of-three-species-of-periwinkles-littorina-fabalis-l-obtusata-and-l-saxatilis
#16
João P Marques, Graciela Sotelo, Tomas Larsson, Kerstin Johannesson, Marina Panova, Rui Faria
The flat periwinkles, Littorina fabalis and L.obtusata, offer an interesting system for local adaptation and ecological speciation studies. In order to provide genomic resources for these species, we sequenced their mitogenomes together with that of the rough periwinkle L.saxatilis by means of next-generation sequencing technologies. The three mitogenomes present the typical repertoire of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a putative control region. Although the latter could not be fully recovered in flat periwinkles using short-reads due to a highly repetitive fragment, in L...
November 17, 2016: Marine Genomics
https://www.readbyqxmd.com/read/27857066/positive-and-strongly-relaxed-purifying-selection-drive-the-evolution-of-repeats-in-proteins
#17
Erez Persi, Yuri I Wolf, Eugene V Koonin
Protein repeats are considered hotspots of protein evolution, associated with acquisition of new functions and novel phenotypic traits, including disease. Paradoxically, however, repeats are often strongly conserved through long spans of evolution. To resolve this conundrum, it is necessary to directly compare paralogous (horizontal) evolution of repeats within proteins with their orthologous (vertical) evolution through speciation. Here we develop a rigorous methodology to identify highly periodic repeats with significant sequence similarity, for which evolutionary rates and selection (dN/dS) can be estimated, and systematically characterize their evolution...
November 18, 2016: Nature Communications
https://www.readbyqxmd.com/read/27846808/pinpointing-genes-underlying-annual-perennial-transitions-with-comparative-genomics
#18
Andrew J Heidel, Christiane Kiefer, George Coupland, Laura E Rose
BACKGROUND: Transitions between perennial and an annual life history occur often in plant lineages, but the genes that control whether a plant is an annual or perennial are largely unknown. To identify genes that confer differences between annuals and perennials we compared the gene content of four pairs of sister lineages (Arabidopsis thaliana/Arabidopsis lyrata, Arabis montbretiana/Arabis alpina, Arabis verna/Aubrieta parviflora and Draba nemorosa/Draba hispanica) in the Brassicaceae in which each pair contains one annual and one perennial, plus one extra annual species (Capsella rubella)...
November 15, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27822527/differential-functional-constraints-cause-strain-level-endemism-in-polynucleobacter-populations
#19
Naseer Sangwan, Iratxe Zarraonaindia, Jarrad T Hampton-Marcell, Herbert Ssegane, Tifani W Eshoo, Geeta Rijal, M Cristina Negri, Jack A Gilbert
The adaptation of bacterial lineages to local environmental conditions creates the potential for broader genotypic diversity within a species, which can enable a species to dominate across ecological gradients because of niche flexibility. The genus Polynucleobacter maintains both free-living and symbiotic ecotypes and maintains an apparently ubiquitous distribution in freshwater ecosystems. Subspecies-level resolution supplemented with metagenome-derived genotype analysis revealed that differential functional constraints, not geographic distance, produce and maintain strain-level genetic conservation in Polynucleobacter populations across three geographically proximal riverine environments...
May 2016: MSystems
https://www.readbyqxmd.com/read/27812410/evolution-of-genes-involved-in-feeding-preference-and-metabolic-processes-in-calliphoridae-diptera-calyptratae
#20
Gisele Antoniazzi Cardoso, Marco Antonio Tonus Marinho, Raquel Dietsche Monfardini, Ana Maria Lima de Azeredo Espin, Tatiana Teixeira Torres
BACKGROUND: The genotype-phenotype interactions among traits governing feeding preference are of fundamental importance to behavioral genetics and evolutionary biology. The genetic basis of behavioral traits has been explored in different taxa using different approaches. However, the complex nature of the genetic mechanisms undergirding behavior is poorly understood. Here, we present an evolutionary study of candidate genes related to parasitism in Calliphoridae (Diptera: Calyptratae)...
2016: PeerJ
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