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Genetic evolution

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https://www.readbyqxmd.com/read/29045840/clonal-heterogeneity-influences-the-fate-of-new-adaptive-mutations
#1
Ignacio Vázquez-García, Francisco Salinas, Jing Li, Andrej Fischer, Benjamin Barré, Johan Hallin, Anders Bergström, Elisa Alonso-Perez, Jonas Warringer, Ville Mustonen, Gianni Liti
The joint contribution of pre-existing and de novo genetic variation to clonal adaptation is poorly understood but essential to designing successful antimicrobial or cancer therapies. To address this, we evolve genetically diverse populations of budding yeast, S. cerevisiae, consisting of diploid cells with unique haplotype combinations. We study the asexual evolution of these populations under selective inhibition with chemotherapeutic drugs by time-resolved whole-genome sequencing and phenotyping. All populations undergo clonal expansions driven by de novo mutations but remain genetically and phenotypically diverse...
October 17, 2017: Cell Reports
https://www.readbyqxmd.com/read/29045724/effects-of-demographic-history-on-the-detection-of-recombination-hotspots-from-linkage-disequilibrium
#2
Amy L Dapper, Bret A Payseur
In some species, meiotic recombination is concentrated in small genomic regions. These "recombination hotspots" leave signatures in fine-scale patterns of linkage disequilibrium, raising the prospect that the genomic landscape of hotspots can be characterized from sequence variation. This approach has led to the inference that hotspots evolve rapidly in some species, but are conserved in others. Historic demographic events, such as population bottlenecks, are known to affect patterns of linkage disequilibrium across the genome, violating population genetic assumptions of this approach...
October 17, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29045669/genetic-decoupling-of-thermal-hardiness-across-metamorphosis-in-drosophila-melanogaster
#3
Philip J Freda, Jackson T Alex, Theodore J Morgan, Gregory J Ragland
As organisms age the environment fluctuates, exerting differential selection across ontogeny. In particular, highly seasonal environments expose life stages to often drastically different thermal environments. This developmental variation is particularly striking in organisms with complex life cycles, wherein life history stages also exhibit distinct morphologies, physiologies, and behaviors. Genes acting pleiotropically on thermal responses may produce genetic correlations across ontogeny, constraining the independent evolution of each life stage to their respective thermal environments...
October 16, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/29045649/understanding-evolutionary-impacts-of-seasonality-an-introduction-to-the-symposium
#4
Caroline M Williams, Gregory J Ragland, Gustavo Betini, Lauren B Buckley, Zachary A Cheviron, Kathleen Donohue, Joe Hereford, Murray M Humphries, Simeon Lisovski, Katie E Marshall, Paul S Schmidt, Kimberly S Sheldon, Øystein Varpe, Marcel E Visser
Seasonality is a critically important aspect of environmental variability, and strongly shapes all aspects of life for organisms living in highly seasonal environments. Seasonality has played a key role in generating biodiversity, and has driven the evolution of extreme physiological adaptations and behaviors such as migration and hibernation. Fluctuating selection pressures on survival and fecundity between summer and winter provide a complex selective landscape, which can be met by a combination of three outcomes of adaptive evolution: genetic polymorphism, phenotypic plasticity, and bet-hedging...
October 16, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/29045601/genomic-changes-associated-with-reproductive-and-migratory-ecotypes-in-sockeye-salmon-oncorhynchus-nerka
#5
Andrew J Veale, Michael A Russello
Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence...
October 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29045530/tracking-evolution-of-aromatase-inhibitor-resistance-with-circulating-tumour-dna-analysis-in-metastatic-breast-cancer
#6
Charlotte Fribbens, Isaac Garcia Murillas, Matthew Beaney, Sarah Hrebien, Ben O'Leary, Lucy Kilburn, Karen Howarth, Michael Epstein, Emma Green, Nitzan Rosenfeld, Alistair Ring, Stephen Johnston, Nicholas Turner
Background: Selection of resistance mutations may play a major role in the development of endocrine resistance. ESR1 mutations are rare in primary breast cancer but have high prevalence in patients treated with aromatase inhibitors (AI) for advanced breast cancer. We investigated the evolution of genetic resistance to first line AI therapy using sequential ctDNA sampling in patients with advanced breast cancer. Patients and Methods: 83 patients on first line AI therapy for metastatic breast cancer were enrolled in a prospective study...
October 4, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29044944/rapid-evolution-of-phenology-during-range-expansion-with-recent-climate-change
#7
Nicky Lustenhouwer, Rutger A Wilschut, Jennifer L Williams, Wim H van der Putten, Jonathan M Levine
Although climate warming is expected to make habitat beyond species' current cold range edge suitable for future colonization, this new habitat may present an array of biotic or abiotic conditions not experienced within the current range. Species' ability to shift their range with climate change may therefore depend on how populations evolve in response to such novel environmental conditions. However, due to the recent nature of thus far observed range expansions, the role of rapid adaptation during climate change migration is only beginning to be understood...
October 16, 2017: Global Change Biology
https://www.readbyqxmd.com/read/29044885/heritability-and-social-brood-effects-on-personality-in-juvenile-and-adult-life-history-stages-in-a-wild-passerine
#8
Isabel S Winney, Julia Schroeder, Shinichi Nakagawa, Yu-Hsun Hsu, Mirre Jp Simons, Alfredo Sánchez-Tójar, Maria-Elena Mannarelli, Terry Burke
How has evolution led to the variation in behavioural phenotypes (personalities) in a population? Knowledge of whether personality is heritable, and to what degree it is influenced by the social environment, is crucial to understanding its evolutionary significance, yet few estimates are available from natural populations. We tracked three behavioural traits during different life-history stages in a pedigreed population of wild house sparrows. Using a quantitative genetic approach, we demonstrated heritability in adult exploration, and in nestling activity after accounting for fixed effects, but not in adult boldness...
October 17, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29044880/targeted-deep-sequencing-of-effusion-cytology-samples-is-feasible-informs-spatiotemporal-tumor-evolution-and-has-clinical-and-diagnostic-utility
#9
Jonas Leichsenring, Anna-Lena Volckmar, Martina Kirchner, Daniel Kazdal, Mark Kriegsmann, Fabian Stögbauer, Teresa Bockmayr, Frederick Klauschen, Felix J F Herth, Roland Penzel, Arne Warth, Peter Schirmacher, Volker Endris, Albrecht Stenzinger
During the course of disease, many cancer patients eventually present with metastatic disease including peritoneal or pleural spread. In this context, cytology specimens derived from ascites or pleural effusion may help to differentiate malignant from benign conditions and sometimes yield diagnosis of a malignancy. However, even when supported by immunohistochemistry, cytological interpretation can be challenging, especially if tumor cellularity is low. Here, we investigated whether targeted deep sequencing of formalin-fixed and paraffin embedded (FFPE) cytology specimens of cancer patients is feasible, and has diagnostic and clinical impact...
October 16, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29044796/social-traits-social-networks-and-evolutionary-biology
#10
David N Fisher, Andrew G McAdam
The social environment is both an important agent of selection for most organisms, and an emergent property of their interactions. As an aggregation of interactions among members of a population, the social environment is a product of many sets of relationships, and so can be represented as a network or matrix. Social network analysis in animals has focused on why these networks possess the structure they do, and whether individuals' network traits, representing some aspect of their social phenotype, relate to their fitness...
October 17, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29044782/phylogenomics-of-pike-cichlids-cichlidae-crenicichla-the-rapid-evolution-and-trophic-diversification-of-an-incipient-species-flock
#11
Edward D Burress, Fernando Alda, Alejandro Duarte, Marcelo Loureiro, Jonathan W Armbruster, Prosanta Chakrabarty
The rapid rise of phenotypic and ecological diversity in independent lake-dwelling groups of cichlids is emblematic of the East African Great Lakes. In this study, we show that similar ecologically-based diversification has occurred in pike cichlids (Crenicichla) throughout the Uruguay River drainage of South America. We collected genomic data from nearly 500 ultraconserved element (UCEs) loci and >260,000 base pairs across 33 species, to obtain a phylogenetic hypothesis for the major species-groups and to evaluate the relationships and genetic structure among five closely-related, endemic, co-occurring species (the Uruguay River species flock; URSF)...
October 17, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29044435/impact-of-clinical-parameters-in-the-intrahost-evolution-of-hiv-1-subtype-b-in-pediatric-patients-a-machine-learning-approach
#12
Patricia Rojas Sánchez, Alberto Cobos, Marisa Navaro, José Tomas Ramos, Israel Pagán, África Holguín
Determining the factors modulating the genetic diversity of HIV-1 populations is essential to understand viral evolution. This study analyzes the relative importance of clinical factors in the intrahost HIV-1 subtype B (HIV-1B) evolution and in the fixation of drug resistance mutations (DRM) during longitudinal pediatric HIV-1 infection. We recovered 162 partial HIV-1B pol sequences (from 3 to 24 per patient) from 24 perinatally infected patients from the Madrid Cohort of HIV-1 infected children and adolescents in a time interval ranging from 2...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29043615/molecular-genetic-characterization-of-mutagenesis-using-a-highly-sensitive-single-stranded-dna-reporter-system-in-budding-yeast
#13
Kin Chan
Mutations are permanent alterations to the coding content of DNA. They are starting material for the Darwinian evolution of species by natural selection, which has yielded an amazing diversity of life on Earth. Mutations can also be the fundamental basis of serious human maladies, most notably cancers. In this chapter, I describe a highly sensitive reporter system for the molecular genetic analysis of mutagenesis, featuring controlled generation of long stretches of single-stranded DNA in budding yeast cells...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043052/evolution-of-a-mating-preference-for-a-dual-utility-trait-used-in-intrasexual-competition-in-genetically-monogamous-populations
#14
Caitlin A Stern, Maria R Servedio
The selection pressures by which mating preferences for ornamental traits can evolve in genetically monogamous mating systems remain understudied. Empirical evidence from several taxa supports the prevalence of dual-utility traits, defined as traits used both as armaments in intersexual selection and ornaments in intrasexual selection, as well as the importance of intrasexual resource competition for the evolution of female ornamentation. Here, we study whether mating preferences for traits used in intrasexual resource competition can evolve under genetic monogamy...
October 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29043027/genetic-diversity-and-sex-bias-dispersal-of-plateau-pika-in-tibetan-plateau
#15
Liangzhi Zhang, Jiapeng Qu, Kexin Li, Wenjing Li, Min Yang, Yanming Zhang
Dispersal is an important aspect in organism's life history which could influence the rate and outcome of evolution of organism. Plateau pika is the keystone species in community of grasslands in Tibetan Plateau. In this study, we combine genetic and field data to character the population genetic pattern and dispersal dynamics in plateau pika (Ochotona curzoniae). Totally, 1,352 individual samples were collected, and 10 microsatellite loci were analyzed. Results revealed that plateau pika possessed high genetic diversity and inbreeding coefficient in a fine-scale population...
October 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29043008/ancestors-dietary-patterns-and-environments-could-drive-positive-selection-in-genes-involved-in-micronutrient-metabolism-the-case-of-cofactor-transporters
#16
Silvia Parolo, Sébastien Lacroix, Jim Kaput, Marie-Pier Scott-Boyer
BACKGROUND: During evolution, humans colonized different ecological niches and adopted a variety of subsistence strategies that gave rise to diverse selective pressures acting across the genome. Environmentally induced selection of vitamin, mineral, or other cofactor transporters could influence micronutrient-requiring molecular reactions and contribute to inter-individual variability in response to foods and nutritional interventions. METHODS: A comprehensive list of genes coding for transporters of cofactors or their precursors was built using data mining procedures from the HGDP dataset and then explored to detect evidence of positive genetic selection...
2017: Genes & Nutrition
https://www.readbyqxmd.com/read/29042606/population-genomics-of-wolbachia-and-mtdna-in-drosophila-simulans-from-california
#17
Sarah Signor
Wolbachia pipientis is an intracellular endosymbiont infecting many arthropods and filarial nematodes. Little is known about the short-term evolution of Wolbachia or its interaction with its host. Wolbachia is maternally inherited, resulting in co-inheritance of mitochondrial organelles such as mtDNA. Here I explore the evolution of Wolbachia, and the relationship between Wolbachia and mtDNA, using a large inbred panel of Drosophila simulans. I compare this to the only other large population genomic Wolbachia dataset from D...
October 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29042504/unintended-laboratory-driven-evolution-reveals-genetic-requirements-for-biofilm-formation-by-desulfovibrio-vulgaris-hildenborough
#18
Kara B De León, Grant M Zane, Valentine V Trotter, Gregory P Krantz, Adam P Arkin, Gareth P Butland, Peter J Walian, Matthew W Fields, Judy D Wall
Biofilms of sulfate-reducing bacteria (SRB) are of particular interest as members of this group are culprits in corrosion of industrial metal and concrete pipelines as well as being key players in subsurface metal cycling. Yet the mechanism of biofilm formation by these bacteria has not been determined. Here we show that two supposedly identical wild-type cultures of the SRB Desulfovibrio vulgaris Hildenborough maintained in different laboratories have diverged in biofilm formation. From genome resequencing and subsequent mutant analyses, we discovered that a single nucleotide change within DVU1017, the ABC transporter of a type I secretion system (T1SS), was sufficient to eliminate biofilm formation in D...
October 17, 2017: MBio
https://www.readbyqxmd.com/read/29042494/insights-from-the-genome-sequence-of-mycobacterium-lepraemurium-massive-gene-decay-and-reductive-evolution
#19
Andrej Benjak, Tanvi P Honap, Charlotte Avanzi, Enrique Becerril-Villanueva, Iris Estrada-García, Oscar Rojas-Espinosa, Anne C Stone, Stewart T Cole
Mycobacterium lepraemurium is the causative agent of murine leprosy, a chronic, granulomatous disease similar to human leprosy. Due to the similar clinical manifestations of human and murine leprosy and the difficulty of growing both bacilli axenically, Mycobacterium leprae and M. lepraemurium were once thought to be closely related, although it was later suggested that M. lepraemurium might be related to Mycobacterium avium In this study, the complete genome of M. lepraemurium was sequenced using a combination of PacBio and Illumina sequencing...
October 17, 2017: MBio
https://www.readbyqxmd.com/read/29042403/plastic-transcriptomes-stabilize-immunity-to-pathogen-diversity-the-jasmonic-acid-and-salicylic-acid-networks-within-the-arabidopsis-botrytis-pathosystem
#20
Wei Zhang, Jason A Corwin, Daniel Copeland, Julie Feusier, Robert Eshbaugh, Fang Chen, Susanna Atwell, Daniel J Kliebenstein
To respond to pathogen attack, selection and associated evolution has led to the creation of plant immune system that are a highly effective and inducible defense system. Central to this system are the plant defense hormones jasmonic acid (JA) and salicylic acid (SA) and crosstalk between the two, which may play an important role in defense responses to specific pathogens or even genotypes. Here, we used the Arabidopsis-B. cinerea pathosystem to test how the host's defense system functions against genetic variation in a pathogen...
October 17, 2017: Plant Cell
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