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"Evolutionary biology"

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https://www.readbyqxmd.com/read/28230247/digest-less-than-the-sum-of-its-parts-negative-epistasis-in-bacterial-swarming
#1
Sonia Singhal, Katrina van Raay
Understanding how mutations change phenotypes is vital to evolutionary biology. However, predicting evolutionary outcomes is complicated by the fact that a mutation's effect may depend on the individual's genetic background. Epistasis occurs when interactions among different genes or mutations result in phenotypes that differ from the sum of their parts. Uncovering epistasis usually involves genetic engineering of point mutations and then comparing the phenotypic effect of each mutation individually against its effect in combination with others (e...
February 23, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28228542/accelerated-simulation-of-evolutionary-trajectories-in-origin-fixation-models
#2
Ashley I Teufel, Claus O Wilke
We present an accelerated algorithm to forward-simulate origin-fixation models. Our algorithm requires, on average, only about two fitness evaluations per fixed mutation, whereas traditional algorithms require, per one fixed mutation, a number of fitness evaluations of the order of the effective population size, Ne Our accelerated algorithm yields the exact same steady state as the original algorithm but produces a different order of fixed mutations. By comparing several relevant evolutionary metrics, such as the distribution of fixed selection coefficients and the probability of reversion, we find that the two algorithms behave equivalently in many respects...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28211582/what-can-genome-wide-association-studies-tell-us-about-the-evolutionary-forces-maintaining-genetic-variation-for-quantitative-traits
#3
REVIEW
Emily B Josephs, John R Stinchcombe, Stephen I Wright
I. II. III. IV. V. References SUMMARY: Understanding the evolutionary forces that shape genetic variation within species has long been a goal of evolutionary biology. Integrating data for the genetic architecture of traits from genome-wide association mapping studies (GWAS) along with the development of new population genetic methods for identifying selection in sequence data may allow us to evaluate the roles of mutation-selection balance and balancing selection in shaping genetic variation at various scales...
February 17, 2017: New Phytologist
https://www.readbyqxmd.com/read/28202591/non-classical-phase-diagram-for-virus-bacterial-coevolution-mediated-by-clustered-regularly-interspaced-short-palindromic-repeats
#4
Pu Han, Michael W Deem
CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The condition for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work, we show an intriguing phase diagram of the virus extinction probability, which is more complex than that of the classical predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape recognition by CRISPR...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28186332/exploring-the-hidden-landscape-of-female-preferences-for-complex-signals
#5
Michael S Reichert, Jonas Finck, Bernhard Ronacher
A major challenge in evolutionary biology is explaining the origins of complex phenotypic diversity. In animal communication, complex signals may evolve from simpler signals because novel signal elements exploit pre-existing biases in receivers' sensory systems. Investigating the shape of female preference functions for novel signal characteristics is a powerful, but underutilized, method to describe the adaptive landscape potentially guiding complex signal evolution. We measured female preference functions for characteristics of acoustic appendages added to male calling songs in the grasshopper Chorthippus biguttulus, which naturally produces only simple songs...
February 10, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28186104/ancient-hybridization-fuels-rapid-cichlid-fish-adaptive-radiations
#6
Joana I Meier, David A Marques, Salome Mwaiko, Catherine E Wagner, Laurent Excoffier, Ole Seehausen
Understanding why some evolutionary lineages generate exceptionally high species diversity is an important goal in evolutionary biology. Haplochromine cichlid fishes of Africa's Lake Victoria region encompass >700 diverse species that all evolved in the last 150,000 years. How this 'Lake Victoria Region Superflock' could evolve on such rapid timescales is an enduring question. Here, we demonstrate that hybridization between two divergent lineages facilitated this process by providing genetic variation that subsequently became recombined and sorted into many new species...
February 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28176798/anhedonia-to-music-and-mu-opioids-evidence-from-the-administration-of-naltrexone
#7
Adiel Mallik, Mona Lisa Chanda, Daniel J Levitin
Music's universality and its ability to deeply affect emotions suggest an evolutionary origin. Previous investigators have found that naltrexone (NTX), a μ-opioid antagonist, may induce reversible anhedonia, attenuating both positive and negative emotions. The neurochemical basis of musical experience is not well-understood, and the NTX-induced anhedonia hypothesis has not been tested with music. Accordingly, we administered NTX or placebo on two different days in a double-blind crossover study, and assessed participants' responses to music using both psychophysiological (objective) and behavioral (subjective) measures...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28160333/the-genomic-basis-of-eco-evolutionary-dynamics
#8
Alejandra Rodríguez-Verdugo, James Buckley, Jessica Stapley
Recent recognition that ecological and evolutionary processes can operate on similar time scales has led to a rapid increase in theoretical and empirical studies on eco-evolutionary dynamics. Progress in the fields of evolutionary biology, genomics, and ecology is greatly enhancing our understanding of rapid adaptive processes, the predictability of adaptation and the genetics of ecologically important traits. However, progress in these fields has proceeded largely independently of one another. In an attempt to better integrate these fields the center for 'Adaptation to a Changing Environment' organized a conference entitled 'The genomic basis of eco-evolutionary change' and brought together experts in ecological genomics and eco-evolutionary dynamics...
February 3, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28158373/special-issue-mathematical-and-computational-evolutionary-biology-2015
#9
David Bryant, Olivier Gascuel
No abstract text is available yet for this article.
January 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28157193/unraveling-the-evolutionary-dynamics-of-ancient-and-recent-polypoidization-events-in-avena-poaceae
#10
Qing Liu, Lei Lin, Xiangying Zhou, Paul M Peterson, Jun Wen
Understanding the diversification of polyploid crops in the circum-Mediterranean region is a challenging issue in evolutionary biology. Sequence data of three nuclear genes and three plastid DNA fragments from 109 accessions of Avena L. (Poaceae) and the outgroups were used for maximum likelihood and Bayesian analyses. The evolution of cultivated oat (Avena sativa L.) and its close relatives was inferred to have involved ancient allotetraploidy and subsequent recent allohexaploidy events. The crown ages of two infrageneric lineages (Avena sect...
February 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28149683/evolution-of-gremlin-2-in-cetartiodactyl-mammals-gene-loss-coincides-with-lack-of-upper-jaw-incisors-in-ruminants
#11
Juan C Opazo, Kattina Zavala, Paola Krall, Rodrigo A Arias
Understanding the processes that give rise to genomic variability in extant species is an active area of research within evolutionary biology. With the availability of whole genome sequences, it is possible to quantify different forms of variability such as variation in gene copy number, which has been described as an important source of genetic variability and in consequence of phenotypic variability. Most of the research on this topic has been focused on understanding the biological significance of gene duplication, and less attention has been given to the evolutionary role of gene loss...
2017: PeerJ
https://www.readbyqxmd.com/read/28148564/natural-selection-in-cancer-biology-from-molecular-snowflakes-to-trait-hallmarks
#12
REVIEW
Angelo Fortunato, Amy Boddy, Diego Mallo, Athena Aktipis, Carlo C Maley, John W Pepper
Evolution by natural selection is the conceptual foundation for nearly every branch of biology and increasingly also for biomedicine and medical research. In cancer biology, evolution explains how populations of cells in tumors change over time. It is a fundamental question whether this evolutionary process is driven primarily by natural selection and adaptation or by other evolutionary processes such as founder effects and drift. In cancer biology, as in organismal evolutionary biology, there is controversy about this question and also about the use of adaptation through natural selection as a guiding framework for research...
February 1, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28142282/trade-offs-between-plant-growth-and-defense-against-insect-herbivory-an-emerging-mechanistic-synthesis
#13
Tobias Züst, Anurag A Agrawal
Costs of defense are central to our understanding of interactions between organisms and their environment, and defensive phenotypes of plants have long been considered to be constrained by trade-offs that reflect the allocation of limiting resources. Recent advances in uncovering signal transduction networks have revealed that defense trade-offs are often the result of regulatory "decisions" by the plant, enabling it to fine-tune its phenotype in response to diverse environmental challenges. We place these results in the context of classic studies in ecology and evolutionary biology, and propose a unifying framework for growth-defense trade-offs as a means to study the plant's allocation of limiting resources...
January 30, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28133841/incipient-speciation-driven-by-hypertrophied-lips-in-midas-cichlids-fish
#14
Gonzalo Machado-Schiaffino, Andreas F Kautt, Julian Torres-Dowdall, Lukas Baumgarten, Frederico Henning, Axel Meyer
Sympatric speciation has been debated in evolutionary biology for decades. Although it has gained in acceptance recently, still only a handful of empirical examples are seen as valid (e.g. crater lake cichlids). In this study, we disentangle the role of hypertrophied lips in the repeated adaptive radiations of Nicaraguan crater lake cichlid fish. We assessed the role of disruptive selection and assortative mating during the early stages of divergence and found a functional trade-off in feeding behavior between thick- and thin-lipped ecotypes suggesting that this trait is a target of disruptive selection...
January 30, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28127391/effective-number-of-breeders-from-sibship-reconstruction-empirical-evaluations-using-hatchery-steelhead
#15
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/28126409/who-should-pick-the-winners-of-climate-change
#16
REVIEW
Michael S Webster, Madhavi A Colton, Emily S Darling, Jonathan Armstrong, Malin L Pinsky, Nancy Knowlton, Daniel E Schindler
Many conservation strategies identify a narrow subset of genotypes, species, or geographic locations that are predicted to be favored under different scenarios of future climate change. However, a focus on predicted winners, which might not prove to be correct, risks undervaluing the balance of biological diversity from which climate-change winners could otherwise emerge. Drawing on ecology, evolutionary biology, and portfolio theory, we propose a conservation approach designed to promote adaptation that is less dependent on uncertain predictions about the identity of winners and losers...
January 23, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/28123116/the-first-organ-based-free-ontology-for-arthropods-ontology-of-arthropod-circulatory-systems-oarcs-and-its-integration-into-a-novel-formalization-scheme-for-morphological-descriptions
#17
Christian S Wirkner, Torben Göpel, Jens Runge, Jonas Keiler, Bastian-Jesper Klussmann-Fricke, Katarina Huckstorf, Stephan Scholz, Istvan Mikó, Matt Yoder, Stefan Richter
Morphology, the oldest discipline in the biosciences, is currently experiencing a renaissance in the field of comparative phenomics. However, morphological/phenotypic research still suffers on various levels from a lack of standards. This shortcoming, first highlighted as the "linguistic problem of morphology", concerns the usage of terminology but also the need for formalization of morphological descriptions themselves, something of paramount importance not only to the field of morphology but also when it comes to the use of phenotypic data in systematics and evolutionary biology...
January 25, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28121383/digest-on-the-independence-of-aging-pathologies
#18
Jennifer N Lohr
Aging is a complex phenotype, and the future of our understanding its nature and pathology requires an interdisciplinary approach. Evolutionary biology and theory starting with Fisher, Medawar, Williams and Hamilton provided a solid base for the understanding of how and why aging evolves, based on a decreasing selection pressure with age (Charlesworth 2000). Further theoretical models by Charlesworth and others in the 1990s then generated a deeper understanding of aging as well as solid predictions that could be tested empirically...
January 25, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28121018/dynamics-of-molecular-evolution-in-rna-virus-populations-depend-on-sudden-versus-gradual-environmental-change
#19
Valerie J Morley, Paul E Turner
Understanding the dynamics of molecular adaptation is a fundamental goal of evolutionary biology. While adaptation to constant environments has been well characterized, the effects of environmental complexity remain seldom studied. One simple but understudied factor is the rate of environmental change. Here we used experimental evolution with RNA viruses to investigate whether evolutionary dynamics varied based on the rate of environmental turnover. We used whole-genome next-generation sequencing to characterize evolutionary dynamics in virus populations adapting to a sudden versus gradual shift onto a novel host cell type...
January 25, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28115607/common-foundations-of-optimal-control-across-the-sciences-evidence-of-a-free-lunch
#20
Benjamin Russell, Herschel Rabitz
A common goal in the sciences is optimization of an objective function by selecting control variables such that a desired outcome is achieved. This scenario can be expressed in terms of a control landscape of an objective considered as a function of the control variables. At the most basic level, it is known that the vast majority of quantum control landscapes possess no traps, whose presence would hinder reaching the objective. This paper reviews and extends the quantum control landscape assessment, presenting evidence that the same highly favourable landscape features exist in many other domains of science...
March 6, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
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