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Evolutionary Applications

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https://www.readbyqxmd.com/read/28127396/environmental-and-anthropogenic-drivers-of-connectivity-patterns-a-basis-for-prioritizing-conservation-efforts-for-threatened-populations
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/28035235/ancestry-and-adaptive-evolution-of-anadromous-resident-and-adfluvial-rainbow-trout-oncorhynchus-mykiss-in-the-san-francisco-bay-area-application-of-adaptive-genomic-variation-to-conservation-in-a-highly-impacted-landscape
#13
Maeva Leitwein, John Carlos Garza, Devon E Pearse
The streams draining of into San Francisco Bay, California, have been impacted by habitat alteration for over 150 years, and roads, dams, water diversions, and other impediments now block the paths of many aquatic migratory species. These changes can affect the genetic structure of fish populations, as well as driving adaptive evolution to novel environmental conditions. Here, we determine the evolutionary relationships of San Francisco Bay Area steelhead/rainbow trout (Oncorhynchus mykiss) populations and show that (i) they are more closely related to native coastal steelhead than to the California Central Valley lineage, with no evidence of introgression by domesticated hatchery rainbow trout, (ii) populations above and below barriers within watersheds are each other's closest relatives, and (iii) adaptive genomic variation associated with migratory life-history traits in O...
January 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28035234/genetic-diversity-and-connectivity-within-mytilus-spp-in-the-subarctic-and-arctic
#14
Sofie Smedegaard Mathiesen, Jakob Thyrring, Jakob Hemmer-Hansen, Jørgen Berge, Alexey Sukhotin, Peter Leopold, Michaël Bekaert, Mikael Kristian Sejr, Einar Eg Nielsen
Climate changes in the Arctic are predicted to alter distributions of marine species. However, such changes are difficult to quantify because information on present species distribution and the genetic variation within species is lacking or poorly examined. Blue mussels, Mytilus spp., are ecosystem engineers in the coastal zone globally. To improve knowledge of distribution and genetic structure of the Mytilus edulis complex in the Arctic, we analyzed 81 SNPs in 534 Mytilus spp. individuals sampled at 13 sites to provide baseline data for distribution and genetic variation of Mytilus mussels in the European Arctic...
January 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28035233/varying-selection-differential-throughout-the-climatic-range-of-norway-spruce-in-central-europe
#15
Stefan Kapeller, Ulf Dieckmann, Silvio Schueler
Predicting species distribution changes in global warming requires an understanding of how climatic constraints shape the genetic variation of adaptive traits and force local adaptations. To understand the genetic capacity of Norway spruce populations in Central Europe, we analyzed the variation in tree heights at the juvenile stage in common garden experiments established from the species' warm-dry to cold-moist distribution limits. We report the following findings: First, 47% of the total tree height variation at trial sites is attributable to the tree populations irrespective of site climate...
January 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28035232/back-into-the-wild-apply-untapped-genetic-diversity-of-wild-relatives-for-crop-improvement
#16
REVIEW
Hengyou Zhang, Neha Mittal, Larry J Leamy, Oz Barazani, Bao-Hua Song
Deleterious effects of climate change and human activities, as well as diverse environmental stresses, present critical challenges to food production and the maintenance of natural diversity. These challenges may be met by the development of novel crop varieties with increased biotic or abiotic resistance that enables them to thrive in marginal lands. However, considering the diverse interactions between crops and environmental factors, it is surprising that evolutionary principles have been underexploited in addressing these food and environmental challenges...
January 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/27877207/sockeye-salmon-repatriation-leads-to-population-re-establishment-and-rapid-introgression-with-native-kokanee
#17
Andrew J Veale, Michael A Russello
Re-establishing salmonid populations to areas historically occupied has the substantial potential for conservation gains; however, such interventions also risk negatively impacting native resident stocks. Here, we assessed the success of the hatchery-assisted reintroduction of anadromous sockeye salmon (Oncorhynchus nerka) into Skaha Lake, British Columbia, Canada, and evaluated the genetic consequences for native kokanee, a freshwater-obligate ecotype, using single nucleotide polymorphism genotypic data collected from the reference samples of spawning Okanagan River sockeye and Skaha Lake kokanee presockeye reintroduction, along with annual trawl survey and angler-caught samples obtained over an eight-year period...
December 2016: Evolutionary Applications
https://www.readbyqxmd.com/read/27877206/genomic-signatures-among-oncorhynchus-nerka-ecotypes-to-inform-conservation-and-management-of-endangered-sockeye-salmon
#18
Krista M Nichols, Christine C Kozfkay, Shawn R Narum
Conservation of life history variation is an important consideration for many species with trade-offs in migratory characteristics. Many salmonid species exhibit both resident and migratory strategies that capitalize on benefits in freshwater and marine environments. In this study, we investigated genomic signatures for migratory life history in collections of resident and anadromous Oncorhynchus nerka (Kokanee and Sockeye Salmon, respectively) from two lake systems, using ~2,600 SNPs from restriction-site-associated DNA sequencing (RAD-seq)...
December 2016: Evolutionary Applications
https://www.readbyqxmd.com/read/27877205/spatial-patterns-of-immunogenetic-and-neutral-variation-underscore-the-conservation-value-of-small-isolated-american-badger-populations
#19
Yessica Rico, Danielle M Ethier, Christina M Davy, Josh Sayers, Richard D Weir, Bradley J Swanson, Joseph J Nocera, Christopher J Kyle
Small and isolated populations often exhibit low genetic diversity due to drift and inbreeding, but may simultaneously harbour adaptive variation. We investigate spatial distributions of immunogenetic variation in American badger subspecies (Taxidea taxus), as a proxy for evaluating their evolutionary potential across the northern extent of the species' range. We compared genetic structure of 20 microsatellites and the major histocompatibility complex (MHC DRB exon 2) to evaluate whether small, isolated populations show low adaptive polymorphism relative to large and well-connected populations...
December 2016: Evolutionary Applications
https://www.readbyqxmd.com/read/27877204/increases-in-the-mean-and-variability-of-thermal-regimes-result-in-differential-phenotypic-responses-among-genotypes-during-early-ontogenetic-stages-of-lake-sturgeon-acipenser-fulvescens
#20
Kari J Dammerman, Juan P Steibel, Kim T Scribner
Climate change is affecting thermal conditions worldwide. Understanding organismal responses associated with predicted changes are essential for predicting population persistence. Few studies have examined the effects of both increased mean and variance in temperature on organismal traits, particularly during early life stages. Using lake sturgeon (Acipenser fulvescens) from Black Lake, MI, we tested whether phenotypic variation differed among families reared in two constant (10 and 18°C) and two fluctuating-temperature treatments (10-19°C) representing temperatures experienced in the river and a simulated anthropogenic disturbance...
December 2016: Evolutionary Applications
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