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evolutionary genetics

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https://www.readbyqxmd.com/read/29055159/genomics-of-natural-populations-evolutionary-forces-that-establish-and-maintain-gene-arrangements-in-drosophila-pseudoobscura
#1
Zachary L Fuller, Gwilym D Haynes, Stephen Richards, Stephen W Schaeffer
The evolution of complex traits in heterogeneous environments may shape the order of genes within chromosomes. Drosophila pseudoobscura has a rich gene arrangement polymorphism that allows one to test evolutionary genetic hypotheses about how chromosomal inversions are established in populations. D. pseudoobscura has >30 gene arrangements on a single chromosome that were generated through a series of overlapping inversion mutations with > 10 inversions with appreciable frequencies and wide geographic distributions...
October 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29055150/distinct-sources-of-gene-flow-produce-contrasting-population-genetic-dynamics-at-different-range-boundaries-of-a-choristoneura-budworm
#2
Gwylim S Blackburn, Bryan M T Brunet, Kevin Muirhead, Michel Cusson, Catherine Béliveau, Roger C Levesque, Lisa M Lumley, Felix A H Sperling
Populations are often exposed to multiple sources of gene flow, but accounts are lacking of the population genetic dynamics that result from these interactions or their effects on local evolution. Using a genomic clines framework applied to 1195 SNPs, we documented genome-wide, locus-specific patterns of introgression between Choristoneura occidentalis biennis spruce budworms and two ecologically divergent relatives, C. o. occidentalis and C. fumiferana, that it interacts with at alternate boundaries of its range...
October 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29054284/the-extended-evolutionary-synthesis-and-addiction-the-price-we-pay-for-adaptability
#3
Tanya Calvey
Humans are more likely to become addicted and to stay addicted than are other animals. This chapter is a neurobiological and molecular review of addiction and the cooccurring traits and psychiatric disorders from the perspective of the Extended Evolutionary Synthesis (EES). Addiction is an example of pleiotropy as many common haplotypes that are associated with individual differences in vulnerability to substance dependence express a variety of important brain-based phenotypes such as neuroadaptive processes...
2017: Progress in Brain Research
https://www.readbyqxmd.com/read/29054249/hiv-1-infected-t-cells-dynamics-and-prognosis-an-evolutionary-game-model
#4
Bahareh Khazaei, Javad Salimi Sartakhti, Mohammad Hossein Manshaei, Quanyan Zhu, Mehdi Sadeghi, Seyed Rasoul Mousavi
BACKGROUND AND OBJECTIVE: Understanding the dynamics of human immunodeficiency virus (HIV) is essential for depicting, developing, and investigating effective treatment strategies. HIV infects several types of immune cells, but its main target is to destroy helper T-cells. In the lymph nodes, the infected T-cells interact with each other and their environment to obtain more resources. According to infectivity and replicative capacity of T-cells in the HIV infection process, they can be divided into four phenotypes...
December 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/29053361/artificial-selection-to-increase-the-phenotypic-variance-in-gmax-fails
#5
Jacqueline L Sztepanacz, Mark W Blows
Stabilizing selection is important in evolutionary theories of the maintenance of genetic variance and has been invoked as the key process determining macroevolutionary patterns of trait evolution. However, manipulative evidence for the extent of stabilizing selection, particularly on multivariate traits, is lacking. We used artificial disruptive selection in Drosophila serrata as a tool to determine the relative strength of stabilizing selection experienced by multivariate trait combinations with contrasting levels of genetic and mutational variance...
November 2017: American Naturalist
https://www.readbyqxmd.com/read/29053360/habitat-association-predicts-genetic-diversity-and-population-divergence-in-amazonian-birds
#6
Michael G Harvey, Alexandre Aleixo, Camila C Ribas, Robb T Brumfield
The ecological traits of organisms may predict their genetic diversity and population genetic structure and mediate the action of evolutionary processes important for speciation and adaptation. Making these ecological-evolutionary links is difficult because it requires comparable genetic estimates from many species with differing ecologies. In Amazonian birds, habitat association is an important component of ecological diversity. Here, we examine the link between habitat association and genetic parameters using 20 pairs of closely related Amazonian bird species in which one member of the pair occurs primarily in forest edge and floodplains and the other occurs in upland forest interior...
November 2017: American Naturalist
https://www.readbyqxmd.com/read/29052958/whole-genome-re-sequencing-reveals-evolutionary-patterns-of-sacred-lotus-nelumbo-nucifera
#7
Longyu Huang, Mei Yang, Ling Li, Hui Li, Dong Yang, Tao Shi, Pingfang Yang
Sacred lotus (Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystem. As a foundation for exploring genomic variationand evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups (rhizome lotus, seed lotus and flower lotus),one wild temperate lotus subgroup (wild lotus), one tropical lotus group (Thai lotus) and outgroup (Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, weconfirmed that wild lotus and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus...
October 20, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/29052539/engineering-diagnostic-and-therapeutic-gut-bacteria
#8
Brian P Landry, Jeffrey J Tabor
Genetically engineered bacteria have the potential to diagnose and treat a wide range of diseases linked to the gastrointestinal tract, or gut. Such engineered microbes will be less expensive and invasive than current diagnostics and more effective and safe than current therapeutics. Recent advances in synthetic biology have dramatically improved the reliability with which bacteria can be engineered with the sensors, genetic circuits, and output (actuator) genes necessary for diagnostic and therapeutic functions...
October 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/29052405/-its2-sequence-analysis-and-identification-of-medicinal-artemisia-plants
#9
Yao-Yao Ren, Nan-Ping Jiang, Rui-Ying Liu, Liang-Ke Song, Rui Tan, Jian Gu
Artemisia hedinii occupies an important position in the Tibetan medicine. Plants in Artemisia vary a lot and are widely distributed in the Qinghai-Tibet Plateau, many plants in Artemisia look similar, making traditional identification methods laborious. In this article, ITS2 sequences were used as DNA barcoding to identify four kinds of confusable Tibetan medicine plants in Artemisia, aiming to establish a rapid and accurate identification methods. Twenty-one samples in Artemisia were collected from the Qinghai-Tibet Plateau, ITS2 sequence PCR amplification and sequencing were conducted after the extraction of DNA...
April 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29052182/profiling-developmentally-and-environmentally-controlled-chromatin-reprogramming
#10
Clara Bourbousse, Moussa Benhamed, Fredy Barneche
Dynamic reshuffling of the chromatin landscape is a recurrent theme orchestrated in many, if not all, plant developmental transitions and adaptive responses. Spatiotemporal variations of the chromatin properties on regulatory genes and on structural genomic elements trigger the establishment of distinct transcriptional contexts, which in some instances can epigenetically be inherited. Studies on plant cell plasticity during the differentiation of stem cells, including gametogenesis, or the specialization of vegetative cells in various organs, as well as the investigation of allele-specific gene regulation have long been impaired by technical challenges in generating specific chromatin profiles in complex or hardly accessible cell populations...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29051748/retrotransposon-domestication-and-control-in-dictyostelium-discoideum
#11
REVIEW
Marek Malicki, Maro Iliopoulou, Christian Hammann
Transposable elements, identified in all eukaryotes, are mobile genetic units that can change their genomic position. Transposons usually employ an excision and reintegration mechanism, by which they change position, but not copy number. In contrast, retrotransposons amplify via RNA intermediates, increasing their genomic copy number. Hence, they represent a particular threat to the structural and informational integrity of the invaded genome. The social amoeba Dictyostelium discoideum, model organism of the evolutionary Amoebozoa supergroup, features a haploid, gene-dense genome that offers limited space for damage-free transposition...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29051394/evolution-on-rugged-adaptive-landscapes
#12
Uri Obolski, Yoav Ram, Lilach Hadany
Adaptive landscapes represent a mapping between genotype and fitness. Rugged adaptive landscapes contain two or more adaptive peaks: allele combinations with higher fitness than any of their neighbors on the genetic space. How would a population evolve on such rugged landscapes? Evolutionary biologists have struggled with this question since it was first introduced in the 1930's by Sewall Wright. Discoveries in the fields of genetics and biochemistry inspired various mathematical models of adaptive landscapes...
October 20, 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/29050795/evolutionary-trade-off-between-secondary-sexual-traits-and-ejaculates
#13
REVIEW
Leigh W Simmons, Stefan Lüpold, John L Fitzpatrick
Recent theoretical models predict that the evolutionary diversification of the weapons and ornaments of pre-mating sexual selection should be influenced by trade-offs with male expenditure on ejaculates. However, the patterns of association between secondary sexual traits and ejaculate expenditure are frequently inconsistent in their support of this prediction. We show why consideration of additional life-history, ecological, and mating-system variables is crucial for the interpretation of associations between secondary sexual traits and ejaculate production...
October 16, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/29050794/genomic-quantitative-genetics-to-study-evolution-in-the-wild
#14
REVIEW
Phillip Gienapp, Simone Fior, Frédéric Guillaume, Jesse R Lasky, Victoria L Sork, Katalin Csilléry
Quantitative genetic theory provides a means of estimating the evolutionary potential of natural populations. However, this approach was previously only feasible in systems where the genetic relatedness between individuals could be inferred from pedigrees or experimental crosses. The genomic revolution opened up the possibility of obtaining the realized proportion of genome shared among individuals in natural populations of virtually any species, which could promise (more) accurate estimates of quantitative genetic parameters in virtually any species...
October 16, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/29050554/natural-variation-and-genetics-of-photoperiodism-in-wyeomyia-smithii
#15
William E Bradshaw, Christina M Holzapfel
Seasonal change in the temperate and polar regions of Earth determines how the world looks around us and, in fact, how we live our day-to-day lives. For biological organisms, seasonal change typically involves complex physiological and metabolic reorganization, the majority of which is regulated by photoperiodism. Photoperiodism is the ability of animals and plants to use day length or night length, resulting in life-historical transformations, including seasonal development, migration, reproduction, and dormancy...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29048547/perspectives-on-integrating-genetic-and-physical-explanations-of-evolution-and-development-an-introduction-to-the-symposium
#16
Alan C Love, Thomas A Stewart, Gunter P Wagner, Stuart A Newman
In the 20th century, genetic explanatory approaches became dominant in both developmental and evolutionary biological research. By contrast, physical approaches, which appeal to properties such as mechanical forces, were largely relegated to the margins, despite important advances in modeling. Recently, there have been renewed attempts to find balanced viewpoints that integrate both biological physics and molecular genetics into explanations of developmental and evolutionary phenomena. Here we introduce the 2017 SICB symposium "Physical and Genetic Mechanisms for Evolutionary Novelty" that was dedicated to exploring empirical cases where both biological physics and developmental genetic considerations are crucial...
October 17, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/29046688/global-analysis-of-small-rna-dynamics-during-seed-development-of-picea-glauca-and-arabidopsis-thaliana-populations-reveals-insights-on-their-evolutionary-trajectories
#17
Yang Liu, Yousry A El-Kassaby
While DNA methylation carries genetic signals and is instrumental in the evolution of organismal complexity, small RNAs (sRNAs), ~18-24 ribonucleotide (nt) sequences, are crucial mediators of methylation as well as gene silencing. However, scant study deals with sRNA evolution via featuring their expression dynamics coupled with species of different evolutionary time. Here we report an atlas of sRNAs and microRNAs (miRNAs, single-stranded sRNAs) produced over time at seed-set of two major spermatophytes represented by populations of Picea glauca and Arabidopsis thaliana with different seed-set duration...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29046578/a-sex-linked-supergene-controls-sperm-morphology-and-swimming-speed-in-a-songbird
#18
Kang-Wook Kim, Clair Bennison, Nicola Hemmings, Lola Brookes, Laura L Hurley, Simon C Griffith, Terry Burke, Tim R Birkhead, Jon Slate
Sperm competition is an important selective force in many organisms. As a result, sperm have evolved to be among the most diverse cells in the animal kingdom. However, the relationship between sperm morphology, sperm motility and fertilization success is only partially understood. The extent to which between-male variation is heritable is largely unknown, and remarkably few studies have investigated the genetic architecture of sperm traits, especially sperm morphology. Here we use high-density genotyping and gene expression profiling to explore the considerable sperm trait variation that exists in the zebra finch Taeniopygia guttata...
August 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/29046567/molecular-signatures-of-fossil-leaves-provide-unexpected-new-evidence-for-extinct-plant-relationships
#19
Vivi Vajda, Milda Pucetaite, Stephen McLoughlin, Anders Engdahl, Jimmy Heimdal, Per Uvdal
Gene sequences form the primary basis for understanding the relationships among extant plant groups, but genetic data are unavailable from fossils to evaluate the affinities of extinct taxa. Here we show that geothermally resistant fossil cuticles of seed-bearing plants, analysed with Fourier transform infrared (FTIR) spectroscopy and hierarchical cluster analysis (HCA), retain biomolecular suites that consistently distinguish major taxa even after experiencing different diagenetic histories. Our results reveal that similarities between the cuticular biochemical signatures of major plant groups (extant and fossil) are mostly consistent with recent phylogenetic hypotheses based on molecular and morphological data...
August 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/29046555/mother-s-curse-neutralizes-natural-selection-against-a-human-genetic-disease-over-three-centuries
#20
Emmanuel Milot, Claudia Moreau, Alain Gagnon, Alan A Cohen, Bernard Brais, Damian Labuda
According to evolutionary theory, mitochondria could be poisoned gifts that mothers transmit to their sons. This is because mutations harmful to males are expected to accumulate in the mitochondrial genome, the so-called 'mother's curse'. However, the contribution of the mother's curse to the mutation load in nature remains largely unknown and hard to predict, because compensatory mechanisms could impede the spread of deleterious mitochondria. Here we provide evidence for the mother's curse in action over 290 years in a human population...
September 2017: Nature ecology & evolution
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