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Evolutionary Applications

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https://www.readbyqxmd.com/read/30026805/diversity-from-genes-to-ecosystems-a-unifying-framework-to-study-variation-across-biological-metrics-and-scales
#1
Oscar E Gaggiotti, Anne Chao, Pedro Peres-Neto, Chun-Huo Chiu, Christine Edwards, Marie-Josée Fortin, Lou Jost, Christopher M Richards, Kimberly A Selkoe
Biological diversity is a key concept in the life sciences and plays a fundamental role in many ecological and evolutionary processes. Although biodiversity is inherently a hierarchical concept covering different levels of organization (genes, population, species, ecological communities and ecosystems), a diversity index that behaves consistently across these different levels has so far been lacking, hindering the development of truly integrative biodiversity studies. To fill this important knowledge gap, we present a unifying framework for the measurement of biodiversity across hierarchical levels of organization...
August 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/30026804/relationship-between-effective-and-demographic-population-size-in-continuously-distributed-populations
#2
Jennifer C Pierson, Tabitha A Graves, Sam C Banks, Katherine C Kendall, David B Lindenmayer
Genetic monitoring of wild populations can offer insights into demographic and genetic information simultaneously. However, widespread application of genetic monitoring is hindered by large uncertainty in the estimation and interpretation of target metrics such as contemporary effective population size, N e . We used four long-term genetic and demographic studies (≥9 years) to evaluate the temporal stability of the relationship between N e and demographic population size ( N c ). These case studies focused on mammals that are continuously distributed, yet dispersal-limited within the spatial scale of the study...
August 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/30026803/disentangling-genetic-structure-for-genetic-monitoring-of-complex-populations
#3
Brook G Milligan, Frederick I Archer, Anne-Laure Ferchaud, Brian K Hand, Elizabeth M Kierepka, Robin S Waples
Genetic monitoring estimates temporal changes in population parameters from molecular marker information. Most populations are complex in structure and change through time by expanding or contracting their geographic range, becoming fragmented or coalescing, or increasing or decreasing density. Traditional approaches to genetic monitoring rely on quantifying temporal shifts of specific population metrics-heterozygosity, numbers of alleles, effective population size-or measures of geographic differentiation such as F ST ...
August 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/30026802/differentiation-measures-for-conservation-genetics
#4
Lou Jost, Frederick Archer, Sarah Flanagan, Oscar Gaggiotti, Sean Hoban, Emily Latch
We compare the two main classes of measures of population structure in genetics: (i) fixation measures such as F ST , G ST , and θ and (ii) allelic differentiation measures such as Jost's D and entropy differentiation. These two groups of measures quantify complementary aspects of population structure, which have no necessary relationship with each other. We focus especially on empirical aspects of population structure relevant to conservation analyses. At the empirical level, the first set of measures quantify nearness to fixation, while the second set of measures quantify relative degree of allelic differentiation...
August 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/30026801/multifaceted-dna-metabarcoding-validation-of-a-noninvasive-next-generation-approach-to-studying-bat-populations
#5
Joel F Swift, Richard F Lance, Xin Guan, Eric R Britzke, Denise L Lindsay, Christine E Edwards
As multiple species of bats are currently experiencing dramatic declines in populations due to white-nose syndrome (WNS) and other factors, conservation managers have an urgent need for data on the ecology and overall status of populations of once-common bat species. Standard approaches to obtain data on bat populations often involve capture and handling, requiring extensive expertise and unavoidably resulting in stress to the bats. New methods to rapidly obtain critical data are needed that minimize both the stress on bats and the spread of WNS...
August 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/30026800/genetic-and-genomic-monitoring-with-minimally-invasive-sampling-methods
#6
Emma L Carroll, Mike W Bruford, J Andrew DeWoody, Gregoire Leroy, Alan Strand, Lisette Waits, Jinliang Wang
The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations...
August 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/30026799/theory-practice-and-conservation-in-the-age-of-genomics-the-gal%C3%A3-pagos-giant-tortoise-as-a-case-study
#7
Stephen J Gaughran, Maud C Quinzin, Joshua M Miller, Ryan C Garrick, Danielle L Edwards, Michael A Russello, Nikos Poulakakis, Claudio Ciofi, Luciano B Beheregaray, Adalgisa Caccone
High-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in nonmodel species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of sampling design on estimating genetic differentiation among populations that represent three species of Galápagos giant tortoises ( Chelonoidis spp...
August 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/30026798/next-generation-metrics-for-monitoring-genetic-erosion-within-populations-of-conservation-concern
#8
REVIEW
Gregoire Leroy, Emma L Carroll, Mike W Bruford, J Andrew DeWoody, Allan Strand, Lisette Waits, Jinliang Wang
Genetic erosion is a major threat to biodiversity because it can reduce fitness and ultimately contribute to the extinction of populations. Here, we explore the use of quantitative metrics to detect and monitor genetic erosion. Monitoring systems should not only characterize the mechanisms and drivers of genetic erosion (inbreeding, genetic drift, demographic instability, population fragmentation, introgressive hybridization, selection) but also its consequences (inbreeding and outbreeding depression, emergence of large-effect detrimental alleles, maladaptation and loss of adaptability)...
August 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/30026797/impact-of-supplementation-on-deleterious-mutation-distribution-in-an-exploited-salmonid
#9
Anne-Laure Ferchaud, Martin Laporte, Charles Perrier, Louis Bernatchez
Deleterious mutations have important implications for the evolutionary trajectories of populations. While several studies recently investigated the dynamics of deleterious mutations in wild populations, no study has yet explored the fate of deleterious mutations in a context of populations managed by supplementation. Here, based on a dataset of nine wild and 15 supplemented Lake Trout populations genotyped at 4,982 single nucleotide polymorphisms (SNP)s by means of genotype by sequencing (GBS), we explored the effect of supplementation on the frequency of putatively deleterious variants...
August 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/30026796/guidelines-for-planning-genomic-assessment-and-monitoring-of-locally-adaptive-variation-to-inform-species-conservation
#10
REVIEW
Sarah P Flanagan, Brenna R Forester, Emily K Latch, Sally N Aitken, Sean Hoban
Identifying and monitoring locally adaptive genetic variation can have direct utility for conserving species at risk, especially when management may include actions such as translocations for restoration, genetic rescue, or assisted gene flow. However, genomic studies of local adaptation require careful planning to be successful, and in some cases may not be a worthwhile use of resources. Here, we offer an adaptive management framework to help conservation biologists and managers decide when genomics is likely to be effective in detecting local adaptation, and how to plan assessment and monitoring of adaptive variation to address conservation objectives...
August 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/30026795/next-generation-conservation-genetics-and-biodiversity-monitoring
#11
Margaret E Hunter, Sean M Hoban, Michael W Bruford, Gernot Segelbacher, Louis Bernatchez
This special issue of Evolutionary Applications consists of 10 publications investigating the use of next-generation tools and techniques in population genetic analyses and biodiversity assessment. The special issue stems from a 2016 Next Generation Genetic Monitoring Workshop, hosted by the National Institute for Mathematical and Biological Synthesis (NIMBioS) in Tennessee, USA. The improved accessibility of next-generation sequencing platforms has allowed molecular ecologists to rapidly produce large amounts of data...
August 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/29928306/modeling-fitness-changes-in-wild-atlantic-salmon-populations-faced-by-spawning-intrusion-of-domesticated-escapees
#12
Marco Castellani, Mikko Heino, John Gilbey, Hitoshi Araki, Terje Svåsand, Kevin A Glover
Genetic interaction between domesticated escapees and wild conspecifics represents a persistent challenge to an environmentally sustainable Atlantic salmon aquaculture industry. We used a recently developed eco-genetic model (IBSEM) to investigate potential changes in a wild salmon population subject to spawning intrusion from domesticated escapees. At low intrusion levels (5%-10% escapees), phenotypic and demographic characteristics of the recipient wild population only displayed weak changes over 50 years and only at high intrusion levels (30%-50% escapees) were clear changes visible in this period...
July 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/29928305/a-mosaic-of-phenotypic-variation-in-giant-ragweed-ambrosia-trifida-local-and-continental-scale-patterns-in-a-range-expanding-agricultural-weed
#13
Stephen M Hovick, Andrea McArdle, S Kent Harrison, Emilie E Regnier
Spatial patterns of trait variation across a species' range have implications for population success and evolutionary change potential, particularly in range-expanding and weedy species that encounter distinct selective pressures at large and small spatial scales simultaneously. We investigated intraspecific trait variation in a common garden experiment with giant ragweed ( Ambrosia trifida ), a highly variable agricultural weed with an expanding geographic range and broad ecological amplitude. Our study included paired populations from agricultural and natural riparian habitats in each of seven regions ranging east to west from the core of the species' distribution in central Ohio to southeastern Minnesota, which is nearer the current invasion front...
July 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/29928304/stepping-stones-to-isolation-impacts-of-a-changing-climate-on-the-connectivity-of-fragmented-fish-populations
#14
Emma F Young, Niklas Tysklind, Michael P Meredith, Mark de Bruyn, Mark Belchier, Eugene J Murphy, Gary R Carvalho
In the marine environment, understanding the biophysical mechanisms that drive variability in larval dispersal and population connectivity is essential for estimating the potential impacts of climate change on the resilience and genetic structure of populations. Species whose populations are small, isolated and discontinuous in distribution will differ fundamentally in their response and resilience to environmental stress, compared with species that are broadly distributed, abundant and frequently exchange conspecifics...
July 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/29928303/harvesting-changes-mating-behaviour-in-european-lobster
#15
Tonje K Sørdalen, Kim T Halvorsen, Hugo B Harrison, Charlie D Ellis, Leif Asbjørn Vøllestad, Halvor Knutsen, Even Moland, Esben M Olsen
Removing individuals from a wild population can affect the availability of prospective mates and the outcome of competitive interactions, with subsequent effects on mating patterns and sexual selection. Consequently, the rate of harvest-induced evolution is predicted to be strongly dependent on the strength and dynamics of sexual selection, yet there is limited empirical knowledge on the interplay between selective harvesting and the mating systems of exploited species. In this study, we used genetic parentage assignment to compare mating patterns of the highly valued and overexploited European lobster ( Homarus gammarus ) in a designated lobster reserve and nearby fished area in southern Norway...
July 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/29928302/influence-of-intergenotypic-competition-on-multigenerational-persistence-of-abiotic-stress-resistance-transgenes-in-populations-of-arabidopsis-thaliana
#16
Patrick J Bigelow, Wayne Loescher, James F Hancock, Rebecca Grumet
Reducing crop losses due to abiotic stresses is a major target of agricultural biotechnology that will increase with climate change and global population growth. Concerns, however, have been raised about potential ecological impacts if transgenes become established in wild populations and cause increased competitiveness of weedy or invasive species. Potential risks will be a function of transgene movement, population sizes, and fitness effects on the recipient population. While key components influencing gene flow have been extensively investigated, there have been few studies on factors subsequent to transgene movement that can influence persistence and competitiveness...
July 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/29928301/the-mycoparasitic-fungus-clonostachys-rosea-responds-with-both-common-and-specific-gene-expression-during-interspecific-interactions-with-fungal-prey
#17
Kristiina Nygren, Mukesh Dubey, Antonio Zapparata, Mudassir Iqbal, Georgios D Tzelepis, Mikael Brandström Durling, Dan Funck Jensen, Magnus Karlsson
Clonostachys rosea is a necrotrophic mycoparasitic fungus, used for biological control of plant pathogenic fungi. A better understanding of the underlying mechanisms resulting in successful biocontrol is important for knowledge-based improvements of the application and use of biocontrol in agricultural production systems. Transcriptomic analyses revealed that C. rosea responded with both common and specific gene expression during interactions with the fungal prey species Botrytis cinerea and Fusarium graminearum ...
July 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/29928300/genotyping-by-sequencing-of-genome-wide-microsatellite-loci-reveals-fine-scale-harvest-composition-in-a-coastal-atlantic-salmon-fishery
#18
Ian R Bradbury, Brendan F Wringe, Beth Watson, Ian Paterson, John Horne, Robert Beiko, Sarah J Lehnert, Marie Clément, Eric C Anderson, Nicholas W Jeffery, Steven Duffy, Emma Sylvester, Martha Robertson, Paul Bentzen
Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools, allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here, we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3...
July 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/29928299/transgenerational-interactions-between-pesticide-exposure-and-warming-in-a-vector-mosquito
#19
Tam T Tran, Lizanne Janssens, Khuong V Dinh, Robby Stoks
While transgenerational plasticity may buffer ectotherms to warming and pesticides separately, it remains unknown how combined exposure to warming and pesticides in the parental generation shapes the vulnerability to these stressors in the offspring. We studied the transgenerational effects of single and combined exposure to warming (4°C increase) and the pesticide chlorpyrifos on life-history traits of the vector mosquito Culex pipiens . Parental exposure to a single stressor, either warming or the pesticide, had negative effects on the offspring: parental exposure to both warming and the pesticide resulted in an overall lower offspring survival, and a delayed offspring metamorphosis...
July 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/29928298/optimization-and-performance-testing-of-a-sequence-processing-pipeline-applied-to-detection-of-nonindigenous-species
#20
Ryan Scott, Aibin Zhan, Emily A Brown, Frédéric J J Chain, Melania E Cristescu, Robin Gras, Hugh J MacIsaac
Genetic taxonomic assignment can be more sensitive than morphological taxonomic assignment, particularly for small, cryptic or rare species. Sequence processing is essential to taxonomic assignment, but can also produce errors because optimal parameters are not known a priori. Here, we explored how sequence processing parameters influence taxonomic assignment of 18S sequences from bulk zooplankton samples produced by 454 pyrosequencing. We optimized a sequence processing pipeline for two common research goals, estimation of species richness and early detection of aquatic invasive species (AIS), and then tested most optimal models' performances through simulations...
July 2018: Evolutionary Applications
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