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Trait evolution

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https://www.readbyqxmd.com/read/29679020/comparative-genomics-provides-insights-into-the-lifestyle-and-reveals-functional-heterogeneity-of-dark-septate-endophytic-fungi
#1
Dániel G Knapp, Julianna B Németh, Kerrie Barry, Matthieu Hainaut, Bernard Henrissat, Jenifer Johnson, Alan Kuo, Joanne Hui Ping Lim, Anna Lipzen, Matt Nolan, Robin A Ohm, László Tamás, Igor V Grigoriev, Joseph W Spatafora, László G Nagy, Gábor M Kovács
Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29676927/woodpeckers-and-diamonds-some-aspects-of-evolutionary-convergence-in-astrobiology
#2
Milan M Ćirković
Jared Diamond's argument against extraterrestrial intelligence from evolutionary contingency is subjected to critical scrutiny. As with the earlier arguments of George Gaylord Simpson, it contains critical loopholes that lead to its unraveling. From the point of view of the contemporary debates about biological evolution, perhaps the most contentious aspect of such arguments is their atemporal and gradualist usage of the space of all possible biological forms (morphospace). Such usage enables the translation of the adaptive value of a trait into the probability of its evolving...
April 20, 2018: Astrobiology
https://www.readbyqxmd.com/read/29676786/host-parasite-coevolution-can-promote-the-evolution-of-seed-banking-as-a-bet-hedging-strategy
#3
Mélissa Verin, Aurélien Tellier
Seed (egg) banking is a common bet-hedging strategy maximizing the fitness of organisms facing environmental unpredictability by the delayed emergence of offspring. Yet, this condition often requires fast and drastic stochastic shifts between good and bad years. We hypothesize that the host seed banking strategy can evolve in response to coevolution with parasites because the coevolutionary cycles promote a gradually changing environment over longer times than seed persistence. We study the evolution of host germination fraction as a quantitative trait using both pairwise competition and multiple mutant competition methods, while the germination locus can be genetically linked or unlinked with the host locus under coevolution...
April 20, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29676775/cross-sex-genetic-correlations-and-the-evolution-of-sex-specific-local-adaptation-insights-from-classical-trait-clines-in-drosophila-melanogaster
#4
Clémentine Lasne, Sandra B Hangartner, Tim Connallon, Carla M Sgrò
Natural selection varies widely among locations of a species' range, favouring population divergence and adaptation to local environmental conditions. Selection also differs between females and males, favouring the evolution of sexual dimorphism. Both forms of within-species evolutionary diversification are widely studied, though largely in isolation, and it remains unclear whether environmental variability typically generates similar or distinct patterns of selection on each sex. Studies of sex-specific local adaptation are also challenging because they must account for genetic correlations between female and male traits, which may lead to correlated patterns of trait divergence between sexes, whether or not local selection patterns are aligned or differ between the sexes...
April 20, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29676059/among-year-variation-in-selection-during-early-life-stages-and-the-genetic-basis-of-fitness-in-arabidopsis-thaliana
#5
Froukje M Postma, Jon Ågren
Incomplete information regarding both selection regimes and the genetic basis of fitness limits our understanding of adaptive evolution. Among-year variation in the genetic basis of fitness is rarely quantified, and estimates of selection are typically based on single components of fitness, thus potentially missing conflicting selection acting during other life-history stages. Here, we examined among-year variation in selection on a key life-history trait and the genetic basis of fitness covering the whole life cycle in the annual plant Arabidopsis thaliana...
April 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29675137/variation-in-chromosome-number-and-breeding-systems-implications-for-diversification-in-pachycereus-pringlei-cactaceae
#6
Carina Gutiérrez-Flores, José L León-de la Luz, Francisco J García-De León, J Hugo Cota-Sánchez
Polyploidy, the possession of more than two sets of chromosomes, is a major biological process affecting plant evolution and diversification. In the Cactaceae, genome doubling has also been associated with reproductive isolation, changes in breeding systems, colonization ability, and speciation. Pachycereus pringlei (S. Watson, 1885) Britton & Rose, 1909, is a columnar cactus that has long drawn the attention of ecologists, geneticists, and systematists due to its wide distribution range and remarkable assortment of breeding systems in the Mexican Sonoran Desert and the Baja California Peninsula (BCP)...
2018: Comparative Cytogenetics
https://www.readbyqxmd.com/read/29673327/assessing-the-benefits-of-horizontal-gene-transfer-by-laboratory-evolution-and-genome-sequencing
#7
Hoi Yee Chu, Kathleen Sprouffske, Andreas Wagner
BACKGROUND: Recombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits. In prokaryotes, it often takes the form of horizontal gene transfer from a donor to a recipient bacterium. While such transfer is widespread in natural communities, its immediate fitness benefits are usually unknown. We asked whether any such benefits depend on the environment, and on the identity of donor and recipient strains. To this end, we adapted Escherichia coli to two novel carbon sources over several hundred generations of laboratory evolution, exposing evolving populations to various DNA donors...
April 19, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29672994/constraints-on-the-evolution-of-phenotypic-plasticity-in-the-clonal-plant-hydrocotyle-vulgaris
#8
Mozhu Wang, Xiangqi Bu, Lin Li, Bi-Cheng Dong, Hong-Li Li, Fei-Hai Yu
The evolution of phenotypic plasticity of plant traits may be constrained by costs and limits. However, the precise constraints are still unclear for many traits under different ecological contexts. In a greenhouse experiment, we grew ramets of 12 genotypes of a clonal plant Hydrocotyle vulgaris under the control (full light and no flood), shade, and flood conditions, and tested the potential costs and limits of plasticity in 13 morphological and physiological traits in response to light availability and flood variation...
April 19, 2018: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29672525/comparative-genomic-and-transcriptomic-analysis-of-selected-fatty-acid-biosynthesis-genes-and-cnl-disease-resistance-genes-in-oil-palm
#9
Rozana Rosli, Nadzirah Amiruddin, Mohd Amin Ab Halim, Pek-Lan Chan, Kuang-Lim Chan, Norazah Azizi, Priscilla E Morris, Eng-Ti Leslie Low, Meilina Ong-Abdullah, Ravigadevi Sambanthamurthi, Rajinder Singh, Denis J Murphy
Comparative genomics and transcriptomic analyses were performed on two agronomically important groups of genes from oil palm versus other major crop species and the model organism, Arabidopsis thaliana. The first analysis was of two gene families with key roles in regulation of oil quality and in particular the accumulation of oleic acid, namely stearoyl ACP desaturases (SAD) and acyl-acyl carrier protein (ACP) thioesterases (FAT). In both cases, these were found to be large gene families with complex expression profiles across a wide range of tissue types and developmental stages...
2018: PloS One
https://www.readbyqxmd.com/read/29669901/biased-generalization-of-salient-traits-drives-the-evolution-of-warning-signals
#10
Gabriella Gamberale-Stille, Baharan Kazemi, Alexandra Balogh, Olof Leimar
The importance of receiver biases in shaping the evolution of many signalling systems is widely acknowledged. Here, we show that receiver bias can explain which traits evolve to become warning signals. For warning coloration, a generalization bias for a signalling trait can result from predators learning to discriminate unprofitable from profitable prey. However, because the colour patterns of prey are complex traits with multiple components, it is crucial to understand which of the many aspects of prey appearance evolve into signals...
April 25, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29669899/conserved-but-flexible-modularity-in-the-zebrafish-skull-implications-for-craniofacial-evolvability
#11
Kevin J Parsons, Young H Son, Amelie Crespel, Davide Thambithurai, Shaun Killen, Matthew P Harris, R Craig Albertson
Morphological variation is the outward manifestation of development and provides fodder for adaptive evolution. Because of this contingency, evolution is often thought to be biased by developmental processes and functional interactions among structures, which are statistically detectable through forms of covariance among traits. This can take the form of substructures of integrated traits, termed modules, which together comprise patterns of variational modularity. While modularity is essential to an understanding of evolutionary potential, biologists currently have little understanding of its genetic basis and its temporal dynamics over generations...
April 25, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29669895/thermal-niche-evolution-across-replicated-anolis-lizard-adaptive-radiations
#12
Alex R Gunderson, D Luke Mahler, Manuel Leal
Elucidating how ecological and evolutionary mechanisms interact to produce and maintain biodiversity is a fundamental problem in evolutionary ecology. Here, we focus on how physiological evolution affects performance and species coexistence along the thermal niche axis in replicated radiations of Anolis lizards best known for resource partitioning based on morphological divergence. We find repeated divergence in thermal physiology within these radiations, and that this divergence significantly affects performance within natural thermal environments...
April 25, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29668959/whole-genome-sequences-of-89-chinese-sheep-suggest-role-of-rxfp2-in-the-development-of-unique-horn-phenotype-as-response-to-semi-feralization
#13
Zhangyuan Pan, Shengdi Li, Qiuyue Liu, Zhen Wang, Zhengkui Zhou, Ran Di, Benpeng Miao, Wenping Hu, Xiangyu Wang, Xiaoxiang Hu, Ze Xu, Dongkai Wei, Xiaoyun He, Liyun Yuan, Xiaofei Guo, Benmeng Liang, Ruichao Wang, Xiaoyu Li, Xiaohan Cao, Xinlong Dong, Qing Xia, Hongcai Shi, Geng Hao, Jean Yang, Cuicheng Luosang, Yiqiang Zhao, Mei Jin, Yingjie Zhang, Shenjin Lv, Fukuan Li, Guohui Ding, Mingxing Chu, Yixue Li
Background: Animal domestication has been extensively studied, but the process of feralization remains poorly understood. Results: Here, we performed whole-genome sequencing of 99 sheep and identified a primary genetic divergence between 2 heterogeneous populations in the Tibetan Plateau, including 1 semi-feral lineage. Selective sweep and candidate gene analysis revealed local adaptations of these sheep associated with sensory perception, muscle strength, eating habit, mating process, and aggressive behavior...
April 1, 2018: GigaScience
https://www.readbyqxmd.com/read/29668109/coevolution-of-virulence-and-immunosuppression-in-multiple-infections
#14
Tsukushi Kamiya, Nicole Mideo, Samuel Alizon
Many components of host-parasite interactions have been shown to affect the way virulence (i.e., parasite-induced harm to the host) evolves. However, coevolution of multiple parasite traits is often neglected. We explore how an immunosuppressive mechanism of parasites affects and coevolves with virulence through multiple infections. Applying the adaptive dynamics framework to epidemiological models with coinfection, we show that immunosuppression is a double-edgedsword for the evolution of virulence. On one hand, it amplifies the adaptive benefit of virulence by increasing the abundance of coinfections through epidemiological feedbacks...
April 18, 2018: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29666427/consistent-differences-in-fitness-traits-across-multiple-generations-of-olympia-oysters
#15
Katherine E Silliman, Tynan K Bowyer, Steven B Roberts
Adaptive evolution and plasticity are two mechanisms that facilitate phenotypic differences between populations living in different environments. Understanding which mechanism underlies variation in fitness-related traits is a crucial step in designing conservation and restoration management strategies for taxa at risk from anthropogenic stressors. Olympia oysters (Ostrea lurida) have received considerable attention with regard to restoration, however there is limited information on adaptive population structure...
April 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29665035/challenges-of-comprehensive-taxon-sampling-in-comparative-biology-wrestling-with-rosids
#16
Ryan A Folk, Miao Sun, Pamela S Soltis, Stephen A Smith, Douglas E Soltis, Robert P Guralnick
Using phylogenetic approaches to test hypotheses on a large scale, in terms of both species sampling and associated species traits and occurrence data-and doing this with rigor despite all the attendant challenges-is critical for addressing many broad questions in evolution and ecology. However, application of such approaches to empirical systems is hampered by a lingering series of theoretical and practical bottlenecks. The community is still wrestling with the challenges of how to develop species-level, comprehensively sampled phylogenies and associated geographic and phenotypic resources that enable global-scale analyses...
April 17, 2018: American Journal of Botany
https://www.readbyqxmd.com/read/29661983/the-evolution-of-cpg-density-and-lifespan-in-conserved-primate-and-mammalian-promoters
#17
Adam T McLain, Christopher Faulk
Gene promoters are evolutionarily conserved across holozoans and enriched in CpG sites, the target for DNA methylation. As animals age, the epigenetic pattern of DNA methylation degrades, with highly methylated CpG sites gradually becoming demethylated while CpG islands increase in methylation. Across vertebrates, aging is a trait that varies among species. We used this variation to determine whether promoter CpG density correlates with species' maximum lifespan. Human promoter sequences were used to identify conserved regions in 131 mammals and a subset of 28 primate genomes...
April 14, 2018: Aging
https://www.readbyqxmd.com/read/29661172/mth1-deficiency-selectively-increases-non-cytotoxic-oxidative-dna-damage-in-lung-cancer-cells-more-bad-news-than-good
#18
Hussein H K Abbas, Kheloud M H Alhamoudi, Mark D Evans, George D D Jones, Steven S Foster
BACKGROUND: Targeted therapies are based on exploiting cancer-cell-specific genetic features or phenotypic traits to selectively kill cancer cells while leaving normal cells unaffected. Oxidative stress is a cancer hallmark phenotype. Given that free nucleotide pools are particularly vulnerable to oxidation, the nucleotide pool sanitising enzyme, MTH1, is potentially conditionally essential in cancer cells. However, findings from previous MTH1 studies have been contradictory, meaning the relevance of MTH1 in cancer is still to be determined...
April 16, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29660937/personality-modulates-the-efficacy-of-art-intervention-on-chronic-pain-in-a-population-of-patients-with-alzheimer-s-disease
#19
Isabelle Rouch, Elodie Pongan, Yohana Leveque, Barbara Tillmann, Béatrice Trombert, Jean Claude Getenet, Nicolas Auguste, Pierre Krolak-Salmon, Bernard Laurent, Jean-Michel Dorey
BACKGROUND: Alzheimer's disease (AD) mainly occurs in elderly individuals. Comorbidities and chronic pain are frequent in this population. Previous studies revealed that personality modulates both chronic pain (CP) andADoccurrence and evolution. Moreover, as pain treatments can induce side-effects, non-drugs treatments, such as art interventions, are interesting alternative therapies for decreasing CP in these patients. OBJECTIVE: Our aim was to assess the potential role of personality traits on art intervention efficacy for reducing CP in a population of patients with mild AD...
April 11, 2018: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/29659993/neutral-theory-and-phenotypic-evolution
#20
Jianzhi Zhang
Although the neutral theory of molecular evolution was proposed to explain DNA and protein sequence evolution, in principle it could also explain phenotypic evolution. Nevertheless, overall, phenotypes should be less likely than genotypes to evolve neutrally. I propose that, when phenotypic traits are stratified according to a hierarchy of biological organization, the fraction of evolutionary changes in phenotype that are adaptive rises with the phenotypic level considered. Consistently, molecular traits are frequently found to evolve neutrally whereas a large, random set of organismal traits were recently reported to vary largely adaptively...
April 5, 2018: Molecular Biology and Evolution
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