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Genetic evolution

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https://www.readbyqxmd.com/read/29679714/population-genetics-phylogenomics-and-hybrid-speciation-of-juglans-in-china-determined-from-whole-chloroplast-genomes-transcriptomes-and-genotyping-by-sequencing-gbs
#1
Peng Zhao, Hui-Juan Zhou, Daniel Potter, Yi-Heng Hu, Xiao-Jia Feng, Meng Dang, Li Feng, Saman Zulfiqar, Wen-Zhe Liu, Guifang Zhao, Keith Woeste
Genomic data are a powerful tool for elucidating the processes involved in the evolution and divergence of species. The speciation and phylogenetic relationships among Chinese Juglans remain unclear. Here, we used results from phylogenomic and population genetic analyses, transcriptomics, Genotyping-By-Sequencing (GBS), and whole chloroplast genomes (Cp genome) data to infer processes of lineage formation among the five native Chinese species of the walnut genus (Juglans, Juglandaceae), a widespread, economically important group...
April 18, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29679645/sequencing-of-pt5282-ctxm-p13190-kpc-and-p30860-nr-and-comparative-genomics-analysis-of-incx8-plasmids
#2
Haihong Fang, Jiao Feng, Yuanhong Xu, Ying Zhang, Zhe Zhan, Zhe Yin, Xiongbo Duan, Bo Gao, Yigang Tong, Jinglin Wang, Yanping Luo, Erhei Dai, Dongsheng Zhou
This study proposed a replicon-based scheme for typing IncX into nine separately clustering subgroups, including IncX1α, IncX1β and IncX2-8. The complete nucleotide sequences of three IncX8 plasmids, namely pT5282-CTXM and p30860-NR from Enterobacter cloacae and p13190-KPC from Klebsiella pneumoniae, were determined and compared with all the other two previously sequenced IncX8 plasmids pCAV1043-58 and pCAV1741-16. These five plasmids possessed conserved IncX8 backbones with limited genetic variations with respect to gene content and organization, and each of them carried one or three accessory modules that harbored resistance markers and metabolic gene clusters as well as transposons, insertion sequence (IS)-based transposition units and miniature inverted repeat transposable elements, indicating that the relatively small IncX8 backbones were able to integrate various foreign genetic contents...
April 18, 2018: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29679560/developmental-origin-and-morphogenesis-of-the-diaphragm-an-essential-mammalian-muscle
#3
Elizabeth M Sefton, Mirialys Gallardo, Gabrielle Kardon
The diaphragm is a mammalian skeletal muscle essential for respiration and for separating the thoracic and abdominal cavities. Development of the diaphragm requires the coordinated development of muscle, muscle connective tissue, tendon, nerves, and vasculature that derive from different embryonic sources. However, defects in diaphragm development are common and the cause of an often deadly birth defect, Congenital Diaphragmatic Hernia (CDH). Here we comprehensively describe the normal developmental origin and complex spatial-temporal relationship between the different developing tissues to form a functional diaphragm using a developmental series of mouse embryos genetically and immunofluorescently labeled and analyzed in whole mount...
April 18, 2018: Developmental Biology
https://www.readbyqxmd.com/read/29679096/protein-evolution-is-potentially-governed-by-protein-stability-directed-evolution-of-an-esterase-from-the-hyperthermophilic-archaeon-sulfolobus-tokodaii
#4
Ryo Kurahashi, Satoshi Sano, Kazufumi Takano
The study of evolution is important to understand biological phenomena. During evolutionary processes, genetic changes confer amino acid substitutions in proteins, resulting in new or improved functions. Unfortunately, most mutations destabilize proteins. Thus, protein stability is a significant factor in evolution; however, its role remains unclear. Here, we simply and directly explored the association between protein activity and stability in random mutant libraries to elucidate the role of protein stability in evolutionary processes...
April 20, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29679020/comparative-genomics-provides-insights-into-the-lifestyle-and-reveals-functional-heterogeneity-of-dark-septate-endophytic-fungi
#5
Dániel G Knapp, Julianna B Németh, Kerrie Barry, Matthieu Hainaut, Bernard Henrissat, Jenifer Johnson, Alan Kuo, Joanne Hui Ping Lim, Anna Lipzen, Matt Nolan, Robin A Ohm, László Tamás, Igor V Grigoriev, Joseph W Spatafora, László G Nagy, Gábor M Kovács
Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29678979/observational-cross-sectional-study-of-nasal-staphylococcal-species-of-medical-students-of-diverse-geographical-origin-prior-to-healthcare-exposure-prevalence-of-scc-mec-fusc-fusb-and-the-arginine-catabolite-mobile-element-acme-in-the-absence-of-selective-antibiotic
#6
Paulo E Budri, Anna C Shore, David C Coleman, Peter M Kinnevey, Hilary Humpreys, Deirdre Fitzgerald-Hughes
OBJECTIVE: The aim of this study was to investigate co-located nasal Staphylococcus aureus and coagulase-negative staphylococci (CoNS) (mainly Staphylococcus epidermidis ), recovered from healthy medical students in their preclinical year, prior to exposure to the healthcare environment, for the carriage of genes and genetic elements common to both species and that may contribute to S. aureus and methicillin-resistant S. aureus (MRSA) evolution. DESIGN: Prospective observational cross-sectional study...
April 20, 2018: BMJ Open
https://www.readbyqxmd.com/read/29678917/genomic-inference-of-recombination-mediated-evolution-in-xanthomonas-euvesicatoria-and-x-perforans
#7
Mustafa O Jibrin, Neha Potnis, Sujan Timilsina, Gerald V Minsavage, Gary E Vallad, Pamela D Roberts, Jeffrey B Jones, Erica M Goss
Recombination is a major driver of evolution in bacterial populations because it can spread and combine independently evolved beneficial mutations. Recombinant lineages of plant bacterial pathogens are typically associated with colonization of novel hosts and emergence of new diseases. Here, we show that recombination between evolutionarily and phenotypically distinct plant pathogenic lineages generated recombinant lineages with unique combinations of pathogenicity and virulence factors. X. euvesicatoria ( Xe ) and X...
April 20, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29678149/comparative-mitochondrial-genomics-of-cryptophyte-algae-gene-shuffling-and-dynamic-mobile-genetic-elements
#8
Jong Im Kim, Hwan Su Yoon, Gangman Yi, Woongghi Shin, John M Archibald
BACKGROUND: Cryptophytes are an ecologically important group of algae comprised of phototrophic, heterotrophic and osmotrophic species. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin. Cryptophytes have a clear phylogenetic affinity to heterotrophic eukaryotes and possess four genomes: host-derived nuclear and mitochondrial genomes, and plastid and nucleomorph genomes of endosymbiotic origin. RESULTS: To gain insight into cryptophyte mitochondrial genome evolution, we sequenced the mitochondrial DNAs of five species and performed a comparative analysis of seven genomes from the following cryptophyte genera: Chroomonas, Cryptomonas, Hemiselmis, Proteomonas, Rhodomonas, Storeatula and Teleaulax...
April 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29677478/unfinished-business-evolution-of-the-mhc-and-the-adaptive-immune-system-of-jawed-vertebrates
#9
Jim Kaufman
The major histocompatibility complex (MHC) is a large genetic region with many genes, including the highly polymorphic classical class I and II genes that play crucial roles in adaptive as well as innate immune responses. The organization of the MHC varies enormously among jawed vertebrates, but class I and II genes have not been found in other animals. How did the MHC arise, and are there underlying principles that can help us to understand the evolution of the MHC? This review considers what it means to be an MHC and the potential importance of genome-wide duplication, gene linkage, and gene coevolution for the emergence and evolution of an adaptive immune system...
April 26, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29676786/host-parasite-coevolution-can-promote-the-evolution-of-seed-banking-as-a-bet-hedging-strategy
#10
Mélissa Verin, Aurélien Tellier
Seed (egg) banking is a common bet-hedging strategy maximizing the fitness of organisms facing environmental unpredictability by the delayed emergence of offspring. Yet, this condition often requires fast and drastic stochastic shifts between good and bad years. We hypothesize that the host seed banking strategy can evolve in response to coevolution with parasites because the coevolutionary cycles promote a gradually changing environment over longer times than seed persistence. We study the evolution of host germination fraction as a quantitative trait using both pairwise competition and multiple mutant competition methods, while the germination locus can be genetically linked or unlinked with the host locus under coevolution...
April 20, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29676775/cross-sex-genetic-correlations-and-the-evolution-of-sex-specific-local-adaptation-insights-from-classical-trait-clines-in-drosophila-melanogaster
#11
Clémentine Lasne, Sandra B Hangartner, Tim Connallon, Carla M Sgrò
Natural selection varies widely among locations of a species' range, favouring population divergence and adaptation to local environmental conditions. Selection also differs between females and males, favouring the evolution of sexual dimorphism. Both forms of within-species evolutionary diversification are widely studied, though largely in isolation, and it remains unclear whether environmental variability typically generates similar or distinct patterns of selection on each sex. Studies of sex-specific local adaptation are also challenging because they must account for genetic correlations between female and male traits, which may lead to correlated patterns of trait divergence between sexes, whether or not local selection patterns are aligned or differ between the sexes...
April 20, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29676059/among-year-variation-in-selection-during-early-life-stages-and-the-genetic-basis-of-fitness-in-arabidopsis-thaliana
#12
Froukje M Postma, Jon Ågren
Incomplete information regarding both selection regimes and the genetic basis of fitness limits our understanding of adaptive evolution. Among-year variation in the genetic basis of fitness is rarely quantified, and estimates of selection are typically based on single components of fitness, thus potentially missing conflicting selection acting during other life-history stages. Here, we examined among-year variation in selection on a key life-history trait and the genetic basis of fitness covering the whole life cycle in the annual plant Arabidopsis thaliana...
April 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29675836/complex-multicellularity-in-fungi-evolutionary-convergence-single-origin-or-both
#13
László G Nagy, Gábor M Kovács, Krisztina Krizsán
Complex multicellularity represents the most advanced level of biological organization and it has evolved only a few times: in metazoans, green plants, brown and red algae and fungi. Compared to other lineages, the evolution of multicellularity in fungi follows different principles; both simple and complex multicellularity evolved via unique mechanisms not found in other lineages. Herein we review ecological, palaeontological, developmental and genomic aspects of complex multicellularity in fungi and discuss general principles of the evolution of complex multicellularity in light of its fungal manifestations...
April 19, 2018: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/29675466/parallel-evolution-of-batesian-mimicry-supergene-in-two-papilio-butterflies-p-polytes-and-p-memnon
#14
Takuro Iijima, Rei Kajitani, Shinya Komata, Chung-Ping Lin, Teiji Sota, Takehiko Itoh, Haruhiko Fujiwara
Batesian mimicry protects animals from predators when mimics resemble distasteful models. The female-limited Batesian mimicry in Papilio butterflies is controlled by a supergene locus switching mimetic and nonmimetic forms. In Papilio polytes , recent studies revealed that a highly diversified region (HDR) containing doublesex ( dsx -HDR) constitutes the supergene with dimorphic alleles and is likely maintained by a chromosomal inversion. In the closely related Papilio memnon , which exhibits a similar mimicry polymorphism, we performed whole-genome sequence analyses in 11 butterflies, which revealed a nearly identical dsx -HDR containing three genes ( dsx , Nach-like , and UXT ) with dimorphic sequences strictly associated with the mimetic/nonmimetic phenotypes...
April 2018: Science Advances
https://www.readbyqxmd.com/read/29675137/variation-in-chromosome-number-and-breeding-systems-implications-for-diversification-in-pachycereus-pringlei-cactaceae
#15
Carina Gutiérrez-Flores, José L León-de la Luz, Francisco J García-De León, J Hugo Cota-Sánchez
Polyploidy, the possession of more than two sets of chromosomes, is a major biological process affecting plant evolution and diversification. In the Cactaceae, genome doubling has also been associated with reproductive isolation, changes in breeding systems, colonization ability, and speciation. Pachycereus pringlei (S. Watson, 1885) Britton & Rose, 1909, is a columnar cactus that has long drawn the attention of ecologists, geneticists, and systematists due to its wide distribution range and remarkable assortment of breeding systems in the Mexican Sonoran Desert and the Baja California Peninsula (BCP)...
2018: Comparative Cytogenetics
https://www.readbyqxmd.com/read/29674709/known-and-novel-roles-of-the-met-oncogene-in-cancer-a-coherent-approach-to-targeted-therapy
#16
REVIEW
Paolo M Comoglio, Livio Trusolino, Carla Boccaccio
The MET oncogene encodes an unconventional receptor tyrosine kinase with pleiotropic functions: it initiates and sustains neoplastic transformation when genetically altered ('oncogene addiction') and fosters cancer cell survival and tumour dissemination when transcriptionally activated in the context of an adaptive response to adverse microenvironmental conditions ('oncogene expedience'). Moreover, MET is an intrinsic modulator of the self-renewal and clonogenic ability of cancer stem cells ('oncogene inherence')...
April 19, 2018: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/29674434/natural-selection-interacts-with-recombination-to-shape-the-evolution-of-hybrid-genomes
#17
Molly Schumer, Chenling Xu, Daniel L Powell, Arun Durvasula, Laurits Skov, Chris Holland, John C Blazier, Sriram Sankararaman, Peter Andolfatto, Gil G Rosenthal, Molly Przeworski
To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the "minor" parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human and archaic admixture...
April 19, 2018: Science
https://www.readbyqxmd.com/read/29674422/a-perspective-on-the-evolving-story-of-psma-biology-and-psma-based-imaging-and-endoradiotherapeutic-strategies
#18
Denise S O'Keefe, Dean J Bacich, Steve S Huang, Warren D Heston
We will review the evolution of knowledge of the biology of Prostate-Specific Membrane Antigen (PSMA) and how the translation to therapy has also developed. The usual key to discovery is a realistic model for experimentation and hypothesis testing. This is especially true for the prostate where the human prostate differs significantly from that of other often used species for research models. We will emphasize the genetic characterization of PSMA, The nature of the PSMA protein and its role as a carboxypeptidase, with differing important substrates and products in different tissues...
April 19, 2018: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/29673330/modular-assembly-of-transposable-element-arrays-by-microsatellite-targeting-in-the-guayule-and-rice-genomes
#19
José A Valdes Franco, Yi Wang, Naxin Huo, Grisel Ponciano, Howard A Colvin, Colleen M McMahan, Yong Q Gu, William R Belknap
BACKGROUND: Guayule (Parthenium argentatum A. Gray) is a rubber-producing desert shrub native to Mexico and the United States. Guayule represents an alternative to Hevea brasiliensis as a source for commercial natural rubber. The efficient application of modern molecular/genetic tools to guayule improvement requires characterization of its genome. RESULTS: The 1.6 Gb guayule genome was sequenced, assembled and annotated. The final 1.5 Gb assembly, while fragmented (N50  = 22 kb), maps > 95% of the shotgun reads and is essentially complete...
April 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29673327/assessing-the-benefits-of-horizontal-gene-transfer-by-laboratory-evolution-and-genome-sequencing
#20
Hoi Yee Chu, Kathleen Sprouffske, Andreas Wagner
BACKGROUND: Recombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits. In prokaryotes, it often takes the form of horizontal gene transfer from a donor to a recipient bacterium. While such transfer is widespread in natural communities, its immediate fitness benefits are usually unknown. We asked whether any such benefits depend on the environment, and on the identity of donor and recipient strains. To this end, we adapted Escherichia coli to two novel carbon sources over several hundred generations of laboratory evolution, exposing evolving populations to various DNA donors...
April 19, 2018: BMC Evolutionary Biology
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