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Evolutionary Applications

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https://www.readbyqxmd.com/read/28250813/modelling-the-evolution-of-hiv-1-virulence-in-response-to-imperfect-therapy-and-prophylaxis
#1
David R M Smith, Nicole Mideo
Average HIV-1 virulence appears to have evolved in different directions in different host populations since antiretroviral therapy first became available, and models predict that HIV drugs can select for either higher or lower virulence, depending on how treatment is administered. However, HIV virulence evolution in response to "leaky" therapy (treatment that imperfectly suppresses viral replication) and the use of preventive drugs (pre-exposure prophylaxis) has not been explored. Using adaptive dynamics, we show that higher virulence can evolve when antiretroviral therapy is imperfectly effective and that this evolution erodes some of the long-term clinical and epidemiological benefits of HIV treatment...
March 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28250812/a-genome-scan-for-selection-signatures-comparing-farmed-atlantic-salmon-with-two-wild-populations-testing-colocalization-among-outlier-markers-candidate-genes-and-quantitative-trait-loci-for-production-traits
#2
Lei Liu, Keng Pee Ang, J A K Elliott, Matthew Peter Kent, Sigbjørn Lien, Danielle MacDonald, Elizabeth Grace Boulding
Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset...
March 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28250811/the-other-96-can-neglected-sources-of-fitness-variation-offer-new-insights-into-adaptation-to-global-change
#3
Evatt Chirgwin, Dustin J Marshall, Carla M Sgrò, Keyne Monro
Mounting research considers whether populations may adapt to global change based on additive genetic variance in fitness. Yet selection acts on phenotypes, not additive genetic variance alone, meaning that persistence and evolutionary potential in the near term, at least, may be influenced by other sources of fitness variation, including nonadditive genetic and maternal environmental effects. The fitness consequences of these effects, and their environmental sensitivity, are largely unknown. Here, applying a quantitative genetic breeding design to an ecologically important marine tubeworm, we examined nonadditive genetic and maternal environmental effects on fitness (larval survival) across three thermal environments...
March 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28250810/managing-cryptic-biodiversity-fine-scale-intralacustrine-speciation-along-a-benthic-gradient-in-alpine-whitefish-coregonus-spp
#4
Alan G Hudson, Baenz Lundsgaard-Hansen, Kay Lucek, Pascal Vonlanthen, Ole Seehausen
Whitefish (Coregonus spp.) are an important catch for many freshwater fisheries, particularly in Switzerland. In support of this, supplemental stocking of whitefish species is carried out, despite lacking complete knowledge of the extent, distribution and origin of whitefish diversity in these lakes, potentially threatening local endemics via artificial gene flow. Here, we investigate phenotypic and genetic differentiation among coexisting whitefish species spawning along a depth gradient in a subalpine Swiss lake to better delineate intralacustrine whitefish biodiversity...
March 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28250809/genetic-admixture-and-heterosis-may-enhance-the-invasiveness-of-common-ragweed
#5
Min A Hahn, Loren H Rieseberg
Biological invasions are often associated with multiple introductions and genetic admixture of previously isolated populations. In addition to enhanced evolutionary potential through increased genetic variation, admixed genotypes may benefit from heterosis, which could contribute to their increased performance and invasiveness. To deepen our understanding of the mechanisms and management strategies for biological invasions, we experimentally studied whether intraspecific admixture causes heterosis in common ragweed (Ambrosia artemisiifolia) by comparing the performance of crosses (F1) between populations relative to crosses within these populations for each range (native, introduced) under different ecologically relevant conditions (control, drought, competition, simulated herbivory)...
March 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28250808/behavioural-responses-to-human-induced-change-why-fishing-should-not-be-ignored
#6
Beatriz Diaz Pauli, Andrew Sih
Change in behaviour is usually the first response to human-induced environmental change and key for determining whether a species adapts to environmental change or becomes maladapted. Thus, understanding the behavioural response to human-induced changes is crucial in the interplay between ecology, evolution, conservation and management. Yet the behavioural response to fishing activities has been largely ignored. We review studies contrasting how fish behaviour affects catch by passive (e.g., long lines, angling) versus active gears (e...
March 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28250807/the-darwin-cure-for-apiculture-natural-selection-and-managed-honeybee-health
#7
Peter Neumann, Tjeerd Blacquière
Recent major losses of managed honeybee, Apis mellifera, colonies at a global scale have resulted in a multitude of research efforts to identify the underlying mechanisms. Numerous factors acting singly and/or in combination have been identified, ranging from pathogens, over nutrition to pesticides. However, the role of apiculture in limiting natural selection has largely been ignored. This is unfortunate, because honeybees are more exposed to environmental stressors compared to other livestock and management can severely compromise bee health...
March 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28250806/cancer-a-disease-at-the-crossroads-of-trade-offs
#8
Camille Jacqueline, Peter A Biro, Christa Beckmann, Anders Pape Moller, François Renaud, Gabriele Sorci, Aurélie Tasiemski, Beata Ujvari, Frédéric Thomas
Central to evolutionary theory is the idea that living organisms face phenotypic and/or genetic trade-offs when allocating resources to competing life-history demands, such as growth, survival, and reproduction. These trade-offs are increasingly considered to be crucial to further our understanding of cancer. First, evidences suggest that neoplastic cells, as any living entities subject to natural selection, are governed by trade-offs such as between survival and proliferation. Second, selection might also have shaped trade-offs at the organismal level, especially regarding protective mechanisms against cancer...
March 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28127396/environmental-and-anthropogenic-drivers-of-connectivity-patterns-a-basis-for-prioritizing-conservation-efforts-for-threatened-populations
#9
Chrysoula Gubili, Stefano Mariani, Byron V Weckworth, Paul Galpern, Allan D McDevitt, Mark Hebblewhite, Barry Nickel, Marco Musiani
Ecosystem fragmentation and habitat loss have been the focus of landscape management due to restrictions on contemporary connectivity and dispersal of populations. Here, we used an individual approach to determine the drivers of genetic differentiation in caribou of the Canadian Rockies. We modelled the effects of isolation by distance, landscape resistance and predation risk and evaluated the consequences of individual migratory behaviour (seasonally migratory vs. sedentary) on gene flow in this threatened species...
February 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28127395/the-industrialization-of-farming-may-be-driving-virulence-evolution
#10
Carly Rozins, Troy Day
Farming practices have changed dramatically over the years. The industrialization of farming has provided parasites with an abundance of hosts and is thought to have influenced parasite evolution. For example, the parasite that causes the highly contagious poultry disease, Marek's disease, has evolved over the past 60 years into a highly virulent pathogen. It is assumed that the industrialization of the industry and vaccination have selected for more virulent strains of the virus. Here, with the use of an impulsive differential equation model, we investigate how modern broiler farm practices could independently lead to virulence evolution...
February 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28127394/crop-to-wild-gene-flow-and-its-fitness-consequences-for-a-wild-fruit-tree-towards-a-comprehensive-conservation-strategy-of-the-wild-apple-in-europe
#11
Alice Feurtey, Amandine Cornille, Jacqui A Shykoff, Alodie Snirc, Tatiana Giraud
Crop-to-wild gene flow can reduce the fitness and genetic integrity of wild species. Malus sylvestris, the European crab-apple fruit tree in particular, is threatened by the disappearance of its habitat and by gene flow from its domesticated relative, Malus domestica. With the aims of evaluating threats for M. sylvestris and of formulating recommendations for its conservation, we studied here, using microsatellite markers and growth experiments: (i) hybridization rates in seeds and trees from a French forest and in seeds used for replanting crab apples in agrosystems and in forests, (ii) the impact of the level of M...
February 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28127393/resistance-to-bacillus-thuringiensis-toxin-cry2ab-and-survival-on-single-toxin-and-pyramided-cotton-in-cotton-bollworm-from-china
#12
Laipan Liu, Meijing Gao, Song Yang, Shaoyan Liu, Yidong Wu, Yves Carrière, Yihua Yang
Evolution of Helicoverpa armigera resistance to Bacillus thuringiensis (Bt) cotton producing Cry1Ac is progressing in northern China, and replacement of Cry1Ac cotton by pyramided Bt cotton has been considered to counter such resistance. Here, we investigated four of the eight conditions underlying success of the refuge strategy for delaying resistance to Cry1Ac+Cry2Ab cotton, a pyramid that has been used extensively against H. armigera outside China. Laboratory bioassays of a Cry2Ab-selected strain (An2Ab) and a related unselected strain (An) reveal that resistance to Cry2Ab (130-fold) was nearly dominant, autosomally inherited, and controlled by more than one locus...
February 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28127392/bacterial-competition-and-quorum-sensing-signalling-shape-the-eco-evolutionary-outcomes-of-model-in-vitro-phage-therapy
#13
Rachel Mumford, Ville-Petri Friman
The rapid rise of antibiotic resistance has renewed interest in phage therapy - the use of bacteria-specific viruses (phages) to treat bacterial infections. Even though phages are often pathogen-specific, little is known about the efficiency and eco-evolutionary outcomes of phage therapy in polymicrobial infections. We studied this experimentally by exposing both quorum-sensing (QS) signalling PAO1 and QS-deficient lasR Pseudomonas aeruginosa genotypes (differing in their ability to signal intraspecifically) to lytic PT7 phage in the presence and absence of two bacterial competitors: Staphylococcus aureus and Stenotrophomonas maltophilia-two bacteria commonly associated with P...
February 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28127391/effective-number-of-breeders-from-sibship-reconstruction-empirical-evaluations-using-hatchery-steelhead
#14
Michael W Ackerman, Brian K Hand, Ryan K Waples, Gordon Luikart, Robin S Waples, Craig A Steele, Brittany A Garner, Jesse McCane, Matthew R Campbell
Effective population size (Ne ) is among the most important metrics in evolutionary biology. In natural populations, it is often difficult to collect adequate demographic data to calculate Ne directly. Consequently, genetic methods to estimate Ne have been developed. Two Ne estimators based on sibship reconstruction using multilocus genotype data have been developed in recent years: sibship assignment and parentage analysis without parents. In this study, we evaluated the accuracy of sibship reconstruction using a large empirical dataset from five hatchery steelhead populations with known pedigrees and using 95 single nucleotide polymorphism (SNP) markers...
February 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28127390/weird-genotypes-don-t-discard-them-transmissible-cancer-could-be-an-explanation
#15
Florentine Riquet, Alexis Simon, Nicolas Bierne
Genetic chimerism is rarely considered in the analysis of population genetics data, because assumed to be an exceptionally rare, mostly benign, developmental accident. An unappreciated source of chimerism is transmissible cancer, when malignant cells have become independent parasites and can infect other individuals. Parasitic cancers were thought to be rare exceptions, only reported in dogs (Murgia et al., Cell, 2006, 126, 477; Rebbeck et al., Evolution, 2009, 63, 2340), Tasmanian devils (Pearse and Swift, Nature, 2006, 439, 549; Pye et al...
February 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28127389/understanding-and-monitoring-the-consequences-of-human-impacts-on-intraspecific-variation
#16
REVIEW
Makiko Mimura, Tetsukazu Yahara, Daniel P Faith, Ella Vázquez-Domínguez, Robert I Colautti, Hitoshi Araki, Firouzeh Javadi, Juan Núñez-Farfán, Akira S Mori, Shiliang Zhou, Peter M Hollingsworth, Linda E Neaves, Yuya Fukano, Gideon F Smith, Yo-Ichiro Sato, Hidenori Tachida, Andrew P Hendry
Intraspecific variation is a major component of biodiversity, yet it has received relatively little attention from governmental and nongovernmental organizations, especially with regard to conservation plans and the management of wild species. This omission is ill-advised because phenotypic and genetic variations within and among populations can have dramatic effects on ecological and evolutionary processes, including responses to environmental change, the maintenance of species diversity, and ecological stability and resilience...
February 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28035239/identifying-patterns-of-dispersal-connectivity-and-selection-in-the-sea-scallop-placopecten-magellanicus-using-radseq-derived-snps
#17
Mallory Van Wyngaarden, Paul V R Snelgrove, Claudio DiBacco, Lorraine C Hamilton, Naiara Rodríguez-Ezpeleta, Nicholas W Jeffery, Ryan R E Stanley, Ian R Bradbury
Understanding patterns of dispersal and connectivity among marine populations can directly inform fisheries conservation and management. Advances in high-throughput sequencing offer new opportunities for estimating marine connectivity. We used restriction-site-associated DNA sequencing to examine dispersal and realized connectivity in the sea scallop Placopecten magellanicus, an economically important marine bivalve. Based on 245 individuals sampled rangewide at 12 locations from Newfoundland to the Mid-Atlantic Bight, we identified and genotyped 7163 single nucleotide polymorphisms; 112 (1...
January 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28035238/manipulating-virulence-factor-availability-can-have-complex-consequences-for-infections
#18
Michael Weigert, Adin Ross-Gillespie, Anne Leinweber, Gabriella Pessi, Sam P Brown, Rolf Kümmerli
Given the rise of bacterial resistance against antibiotics, we urgently need alternative strategies to fight infections. Some propose we should disarm rather than kill bacteria, through targeted disruption of their virulence factors. It is assumed that this approach (i) induces weak selection for resistance because it should only minimally impact bacterial fitness, and (ii) is specific, only interfering with the virulence factor in question. Given that pathogenicity emerges from complex interactions between pathogens, hosts and their environment, such assumptions may be unrealistic...
January 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28035237/geographic-extent-of-introgression-in-sebastes%C3%A2-mentella-and-its-effect-on-genetic-population-structure
#19
Atal Saha, Torild Johansen, Rasmus Hedeholm, Einar E Nielsen, Jon-Ivar Westgaard, Lorenz Hauser, Benjamin Planque, Steven X Cadrin, Jesper Boje
Genetic population structure is often used to identify management units in exploited species, but the extent of genetic differentiation may be inflated by geographic variation in the level of hybridization between species. We identify the genetic population structure of Sebastes mentella and investigate possible introgression within the genus by analyzing 13 microsatellites in 2,562 redfish specimens sampled throughout the North Atlantic. The data support an historical divergence between the "shallow" and "deep" groups, beyond the Irminger Sea where they were described previously...
January 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28035236/evolution-informed-modeling-improves-outcome-prediction-for-cancers
#20
Li Liu, Yung Chang, Tao Yang, David P Noren, Byron Long, Steven Kornblau, Amina Qutub, Jieping Ye
Despite wide applications of high-throughput biotechnologies in cancer research, many biomarkers discovered by exploring large-scale omics data do not provide satisfactory performance when used to predict cancer treatment outcomes. This problem is partly due to the overlooking of functional implications of molecular markers. Here, we present a novel computational method that uses evolutionary conservation as prior knowledge to discover bona fide biomarkers. Evolutionary selection at the molecular level is nature's test on functional consequences of genetic elements...
January 2017: Evolutionary Applications
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