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"Evolutionary mechanisms"

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https://www.readbyqxmd.com/read/29327728/diverse-modes-of-clonal-evolution-in-hbv-related-hepatocellular-carcinoma-revealed-by-single-cell-genome-sequencing
#1
Meng Duan, Junfeng Hao, Sijia Cui, Daniel L Worthley, Shu Zhang, Zhichao Wang, Jieyi Shi, Longzi Liu, Xiaoying Wang, Aiwu Ke, Ya Cao, Ruibin Xi, Xiaoming Zhang, Jian Zhou, Jia Fan, Chong Li, Qiang Gao
Hepatocellular carcinoma (HCC) is a cancer of substantial morphologic, genetic and phenotypic diversity. Yet we do not understand the relationship between intratumor heterogeneity and the associated morphologic/histological characteristics of the tumor. Using single-cell whole-genome sequencing to profile 96 tumor cells (30-36 each) and 15 normal liver cells (5 each), collected from three male patients with HBV-associated HCC, we confirmed that copy number variations occur early in hepatocarcinogenesis but thereafter remain relatively stable throughout tumor progression...
January 12, 2018: Cell Research
https://www.readbyqxmd.com/read/29321524/phenotypic-divergence-despite-low-genetic-differentiation-in-house-sparrow-populations
#2
Shachar Ben Cohen, Roi Dor
Studying patterns of phenotypic variation among populations can shed light on the drivers of evolutionary processes. The house sparrow (Passer domesticus) is one of the world's most ubiquitous bird species, as well as a successful invader. We investigated phenotypic variation in house sparrow populations across a climatic gradient and in relation to a possible scenario of an invasion. We measured variation in morphological, coloration, and behavioral traits (exploratory behavior and neophobia) and compared it to the neutral genetic variation...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29284160/developmental-biology-the-stem-cell-of-biological-disciplines
#3
Scott F Gilbert
Developmental biology (including embryology) is proposed as "the stem cell of biological disciplines." Genetics, cell biology, oncology, immunology, evolutionary mechanisms, neurobiology, and systems biology each has its ancestry in developmental biology. Moreover, developmental biology continues to roll on, budding off more disciplines, while retaining its own identity. While its descendant disciplines differentiate into sciences with a restricted set of paradigms, examples, and techniques, developmental biology remains vigorous, pluripotent, and relatively undifferentiated...
December 2017: PLoS Biology
https://www.readbyqxmd.com/read/29246101/diversification-of-defensins-and-nlrs-in-arabidopsis-species-by-different-evolutionary-mechanisms
#4
Mariana Mondragón-Palomino, Remco Stam, Ajay John-Arputharaj, Thomas Dresselhaus
BACKGROUND: Genes encoding proteins underlying host-pathogen co-evolution and which are selected for new resistance specificities frequently are under positive selection, a process that maintains diversity. Here, we tested the contribution of natural selection, recombination and transcriptional divergence to the evolutionary diversification of the plant defensins superfamily in three Arabidopsis species. The intracellular NOD-like receptor (NLR) family was used for comparison because positive selection has been well documented in its members...
December 15, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29240975/macroecological-patterns-of-sexual-size-dimorphism-in-turtles-of-the-world
#5
Mickey Agha, Joshua R Ennen, A Justin Nowakowski, Jeffrey E Lovich, Sarah C Sweat, Brian D Todd
Sexual size dimorphism (SSD) is a well-documented phenomenon in both plants and animals; however, the ecological and evolutionary mechanisms that drive and maintain SSD patterns across geographic space at regional and global scales are understudied, especially for reptiles. Our goal was to examine geographic variation of turtle SSD and to explore ecological and environmental correlates using phylogenetic comparative methods. We use published body size data on 135 species from nine turtle families to examine how geographic patterns and the evolution of SSD are influenced by habitat specialization, climate (annual mean temperature and annual precipitation) and climate variability, latitude, or a combination of these predictor variables...
December 14, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29237885/haldane-s-view-of-natural-selection
#6
Veena Rao
Among many things, J. B. S. Haldane is known for demonstrating how the principle of natural selection can be used to build a mathematical, and in particular quantitative, theory of evolution. However, to the end, he remained open to the idea of other evolutionary mechanisms. In his late writings, he repeatedly drew attention to situations in which natural selection did not operate, was hemmed in by constraints, or worked in a surprising manner. In this respect Haldane stands out among the architects of the Modern Synthesis...
November 2017: Journal of Genetics
https://www.readbyqxmd.com/read/29237058/evolution-and-function-of-the-populus-sabath-family-reveal-that-a-single-amino-acid-change-results-in-a-substrate-switch
#7
Xue-Min Han, Qi Yang, Yan-Jing Liu, Zhi-Ling Yang, Xiao-Ru Wang, Qing-Yin Zeng, Hai-Ling Yang
Evolutionary mechanisms of substrate specificities of enzyme families remain poorly understood. Plant SABATH methyltransferases catalyse methylation of the carboxyl group of various low molecular weight metabolites. Investigation into the functional diversification of the SABATH family in plants could shed light on the evolution of substrate specificities in this enzyme family. Zhao et al. identified 28 SABATH genes from the Populus trichocarpa genome. In this study, we re-annotated the Populus SABATH gene family, and performed molecular evolution, gene expression, and biochemical analyses of this large gene family...
December 11, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29234041/evolution-of-a-flipped-pathway-creates-metabolic-innovation-in-tomato-trichomes-through-bahd-enzyme-promiscuity
#8
Pengxiang Fan, Abigail M Miller, Xiaoxiao Liu, A Daniel Jones, Robert L Last
Plants produce hundreds of thousands of structurally diverse specialized metabolites via multistep biosynthetic networks, including compounds of ecological and therapeutic importance. These pathways are restricted to specific plant groups, and are excellent systems for understanding metabolic evolution. Tomato and other plants in the nightshade family synthesize protective acylated sugars in the tip cells of glandular trichomes on stems and leaves. We describe a metabolic innovation in wild tomato species that contributes to acylsucrose structural diversity...
December 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29218340/coexisting-properties-of-thermostability-and-ultraviolet-radiation-resistance-in-the-main-s-layer-complex-of-deinococcus-radiodurans
#9
Domenica Farci, Chavdar Slavov, Dario Piano
Deinococcus radiodurans is well known for its unusual resistance to different environmental stresses. Recently, we have described a novel complex composed of the surface (S)-layer protein DR_2577 and the carotenoid deinoxanthin. We also showed a role of this complex in the UV resistance under desiccation. Both these properties, UV and desiccation resistance, suggest a selective pressure generated by Sun irradiation. In order to confirm this hypothesis we checked whether this S-layer Deinoxanthin Binding Complex (SDBC) has features of thermo-resistance, a property also expected in proteins evolved under solar irradiative pressure...
December 8, 2017: Photochemical & Photobiological Sciences
https://www.readbyqxmd.com/read/29208647/cell-type-transcriptomes-of-the-multicellular-green-alga-volvox-carteri%C3%A2-yield-insights-into-the-evolutionary-origins-of-germ-and-somatic-differentiation-programs
#10
Gavriel Y Matt, James G Umen
Germ-soma differentiation is a hallmark of complex multicellular organisms, yet its origins are not well understood. Volvox carteri is a simple multicellular green alga that has recently evolved a simple germ-soma dichotomy with only two cell types: large germ cells called gonidia and small terminally differentiated somatic cells. Here, we provide a comprehensive characterization of the gonidial and somatic transcriptomes of Volvox to uncover fundamental differences between the molecular and metabolic programming of these cell types...
December 5, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29191718/-how-nationality-influences-opinion-darwinism-and-palaeontology-in-france-1859-1914
#11
Claudine Cohen
This paper discusses the "non-reception" of Darwin's works and concepts in French palaeontology and palaeoanthropology between 1859 and 1914. Indeed, this integration was difficult, biased and belated, for ideological, intellectual and epistemological reasons: Clémence Royer's biased 1862 translation of Darwin's Origin of Species pulled its ideas toward "social darwinism", making them less attractive to the natural sciences. - French nationalism and the authority of religion, which imposed Cuvier's thinking until late into the century - the dominance of Lamarckian and neo-Lamarckian transformism in France, both in biology and in paleontology, which proposed the notion of orthogenetic laws and environmental determinations, and refused darwinian evolutionary mechanisms - obstacles inherent to the application of Darwin's concepts to palaeontology, namely the impossibility to identify evolutionary mechanisms through the fossil record, which was stressed by Darwin himself and underlined in turn by 19th century French palaeontologists...
November 27, 2017: Studies in History and Philosophy of Biological and Biomedical Sciences
https://www.readbyqxmd.com/read/29178946/a-putative-causal-relationship-between-genetically-determined-female-body-shape-and-posttraumatic-stress-disorder
#12
Renato Polimanti, Ananda B Amstadter, Murray B Stein, Lynn M Almli, Dewleen G Baker, Laura J Bierut, Bekh Bradley, Lindsay A Farrer, Eric O Johnson, Anthony King, Henry R Kranzler, Adam X Maihofer, John P Rice, Andrea L Roberts, Nancy L Saccone, Hongyu Zhao, Israel Liberzon, Kerry J Ressler, Caroline M Nievergelt, Karestan C Koenen, Joel Gelernter
BACKGROUND: The nature and underlying mechanisms of the observed increased vulnerability to posttraumatic stress disorder (PTSD) in women are unclear. METHODS: We investigated the genetic overlap of PTSD with anthropometric traits and reproductive behaviors and functions in women. The analysis was conducted using female-specific summary statistics from large genome-wide association studies (GWAS) and a cohort of 3577 European American women (966 PTSD cases and 2611 trauma-exposed controls)...
November 27, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29166155/drivers-of-diversification-in-individual-life-courses
#13
Raisa Hernández-Pacheco, Ulrich K Steiner
Heterogeneity in life courses among individuals of a population influences the speed of adaptive evolutionary processes, but it is less clear how biotic and abiotic environmental fluctuations influence such heterogeneity. We investigate principal drivers of variability in sequence of stages during an individual's life in a stage-structured population. We quantify heterogeneity by measuring population entropy of a Markov chain, which computes the rate of diversification of individual life courses. Using individual data of a primate population, we show that density regulates the stage composition of the population but that its entropy and the generating moments of heterogeneity are independent of density...
December 2017: American Naturalist
https://www.readbyqxmd.com/read/29166127/bat-biology-genomes-and-the-bat1k-project-to-generate-chromosome-level-genomes-for-all-living-bat-species
#14
Emma Teeling, Sonja Vernes, Liliana M Davalos, David A Ray, M Thomas P Gilbert, Eugene Myers, Bat K Consortium
Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene...
November 20, 2017: Annual Review of Animal Biosciences
https://www.readbyqxmd.com/read/29165806/host-preference-and-network-properties-in-biotrophic-plant-fungal-associations
#15
Sergei Põlme, Mohammad Bahram, Hans Jacquemyn, Peter Kennedy, Petr Kohout, Mari Moora, Jane Oja, Maarja Öpik, Lorenzo Pecoraro, Leho Tedersoo
Analytical methods can offer insights into the structure of biological networks, but mechanisms that determine the structure of these networks remain unclear. We conducted a synthesis based on 111 previously published datasets to assess a range of ecological and evolutionary mechanisms that may influence the plant-associated fungal interaction networks. We calculated the relative host effect on fungal community composition and compared nestedness and modularity among different mycorrhizal types and endophytic fungal guilds...
November 22, 2017: New Phytologist
https://www.readbyqxmd.com/read/29153656/tune-to-touch-affective-touch-enhances-learning-of-face-identity-in-4-month-old-infants
#16
Letizia Della Longa, Teodora Gliga, Teresa Farroni
Touch provides more than sensory input for discrimination of what is on the skin. From early in development it has a rewarding and motivational value, which may reflect an evolutionary mechanism that promotes learning and affiliative bonding. In the present study we investigated whether affective touch helps infants tune to social signals, such as faces. Four-month-old infants were habituated to an individual face with averted gaze, which typically does not engage infants to the same extent as direct gaze does...
November 11, 2017: Developmental Cognitive Neuroscience
https://www.readbyqxmd.com/read/29152178/the-genetics-of-phenotypic-plasticity-xv-genetic-assimilation-the-baldwin-effect-and-evolutionary-rescue
#17
Samuel M Scheiner, Michael Barfield, Robert D Holt
We used an individual-based simulation model to examine the role of phenotypic plasticity on persistence and adaptation to two patterns of environmental variation, a single, abrupt step change and continual, linear change. Our model tested the assumptions and predictions of the theory of genetic assimilation, explored the evolutionary dynamics of the Baldwin effect, and provided expectations for the evolutionary response to climate change. We found that genetic assimilation as originally postulated is not likely to occur because the replacement of plasticity by fixed genetic effects takes much longer than the environment is likely to remain stable...
November 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29151883/speciation-history-of-a-species-complex-of-primulina-eburnea-gesneriaceae-from-limestone-karsts-of-southern-china-a-biodiversity-hot-spot
#18
Jing Wang, Bin Ai, Hanghui Kong, Ming Kang
Limestone karsts in southern China are characterized by high edaphic and topographic heterogeneity and host high levels of species richness and endemism. However, the evolutionary mechanisms for generating such biodiversity remain poorly understood. Here, we performed species delimitation, population genetic analyses, simulations of gene flow and analyses of floral morphological traits to infer the geographic history of speciation in a species complex of Primulina eburnea from limestone karsts of southern China...
October 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/29142125/emergence-of-double-and-triple-gene-reassortant-g1p-8-rotaviruses-possessing-a-ds-1-like-backbone-post-rotavirus-vaccine-introduction-in-malawi
#19
Khuzwayo C Jere, Chrispin Chaguza, Naor Bar-Zeev, Jenna Lowe, Chikondi Peno, Benjamin Kumwenda, Osamu Nakagomi, Jacqueline E Tate, Umesh D Parashar, Robert S Heyderman, Neil French, Nigel A Cunliffe, Iturriza-Gomara Miren
To combat the high burden of rotavirus gastroenteritis, multiple African countries have introduced rotavirus vaccines into their childhood immunisation programmes. Malawi incorporated a G1P[8] rotavirus vaccine (Rotarix™) into its immunisation schedule in 2012. Utilising a surveillance platform of hospitalised rotavirus gastroenteritis cases, we examined the phylodynamics of G1P[8] rotavirus strains that circulated in Malawi before (1998 - 2012) and after (2013 - 2014) vaccine introduction. Analysis of whole genomes obtained through next generation sequencing revealed that all randomly-selected pre-vaccine G1P[8] strains sequenced (n=32) possessed a Wa-like genetic constellation, whereas post-vaccine G1P[8] strains (n=18) had a DS-1-like constellation...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29134627/the-evolution-of-genital-shape-variation-in-female-cetaceans
#20
Dara N Orbach, Brandon Hedrick, Bernd Würsig, Sarah L Mesnick, Patricia Lr Brennan
Male genital diversification is likely the result of sexual selection. Female genital diversification may also result from sexual selection, although it is less well studied and understood. Female genitalia are complex among whales, dolphins, and porpoises, especially compared to other vertebrates. The evolutionary factors affecting the diversity of vaginal complexity could include ontogeny, allometry, phylogeny, sexual selection, and natural selection. We quantified shape variation in female genitalia using 2-D geometric morphometric analysis, and validated the application of this method to study soft tissues...
November 14, 2017: Evolution; International Journal of Organic Evolution
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