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Evolutionary biology

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https://www.readbyqxmd.com/read/27923053/different-evolutionary-paths-to-complexity-for-small-and-large-populations-of-digital-organisms
#1
Thomas LaBar, Christoph Adami
A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes, this does not automatically imply that strong selection enhances the chance for the emergence of novel traits, that is, the origination of complexity. Population size is one parameter that alters the relative importance of adaptive and non-adaptive processes: as population size decreases, selection weakens and genetic drift grows in importance...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27921363/morphomechanics-and-developmental-constraints-in-the-evolution-of-ammonites-shell-form
#2
Alexander Erlich, Derek E Moulton, Alain Goriely, Regis Chirat
The idea that physical processes involved in biological development underlie morphogenetic rules and channel morphological evolution has been central to the rise of evolutionary developmental biology. Here, we explore this idea in the context of seashell morphogenesis. We show that a morphomechanical model predicts the effects of variations in shell shape on the ornamental pattern in ammonites, a now extinct group of cephalopods with external chambered shell. Our model shows that several seemingly unrelated characteristics of synchronous, ontogenetic, intraspecific, and evolutionary variations in ornamental patterns among various ammonite species may all be understood from the fact that the mechanical forces underlying the oscillatory behavior of the shell secreting system scale with the cross-sectional curvature of the shell aperture...
December 6, 2016: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/27921292/cranial-joint-histology-in-the-mallard-duck-anas-platyrhynchos-new-insights-on-avian-cranial-kinesis
#3
Alida M Bailleul, Lawrence M Witmer, Casey M Holliday
The evolution of avian cranial kinesis is a phenomenon in part responsible for the remarkable diversity of avian feeding adaptations observable today. Although osteological, developmental and behavioral features of the feeding system are frequently studied, comparatively little is known about cranial joint skeletal tissue composition and morphology from a microscopic perspective. These data are key to understanding the developmental, biomechanical and evolutionary underpinnings of kinesis. Therefore, here we investigated joint microstructure in juvenile and adult mallard ducks (Anas platyrhynchos; Anseriformes)...
December 6, 2016: Journal of Anatomy
https://www.readbyqxmd.com/read/27920762/artificial-intelligence-vs-statistical-modeling-and-optimization-of-continuous-bead-milling-process-for-bacterial-cell-lysis
#4
Shafiul Haque, Saif Khan, Mohd Wahid, Sajad A Dar, Nipunjot Soni, Raju K Mandal, Vineeta Singh, Dileep Tiwari, Mohtashim Lohani, Mohammed Y Areeshi, Thavendran Govender, Hendrik G Kruger, Arshad Jawed
For a commercially viable recombinant intracellular protein production process, efficient cell lysis and protein release is a major bottleneck. The recovery of recombinant protein, cholesterol oxidase (COD) was studied in a continuous bead milling process. A full factorial response surface methodology (RSM) design was employed and compared to artificial neural networks coupled with genetic algorithm (ANN-GA). Significant process variables, cell slurry feed rate (A), bead load (B), cell load (C), and run time (D), were investigated and optimized for maximizing COD recovery...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920384/antibiotic-resistance-in-the-wild-an-eco-evolutionary-perspective
#5
REVIEW
Teppo Hiltunen, Marko Virta, Anna-Liisa Laine
The legacy of the use and misuse of antibiotics in recent decades has left us with a global public health crisis: antibiotic-resistant bacteria are on the rise, making it harder to treat infections. At the same time, evolution of antibiotic resistance is probably the best-documented case of contemporary evolution. To date, research on antibiotic resistance has largely ignored the complexity of interactions that bacteria engage in. However, in natural populations, bacteria interact with other species; for example, competition and grazing are import interactions influencing bacterial population dynamics...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920381/harvest-induced-evolution-insights-from-aquatic-and-terrestrial-systems
#6
REVIEW
Anna Kuparinen, Marco Festa-Bianchet
Commercial and recreational harvests create selection pressures for fitness-related phenotypic traits that are partly under genetic control. Consequently, harvesting can drive evolution in targeted traits. However, the quantification of harvest-induced evolutionary life history and phenotypic changes is challenging, because both density-dependent feedback and environmental changes may also affect these changes through phenotypic plasticity. Here, we synthesize current knowledge and uncertainties on six key points: (i) whether or not harvest-induced evolution is happening, (ii) whether or not it is beneficial, (iii) how it shapes biological systems, (iv) how it could be avoided, (v) its importance relative to other drivers of phenotypic changes, and (vi) whether or not it should be explicitly accounted for in management...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920373/human-influences-on-evolution-and-the-ecological-and-societal-consequences
#7
Andrew P Hendry, Kiyoko M Gotanda, Erik I Svensson
Humans have dramatic, diverse and far-reaching influences on the evolution of other organisms. Numerous examples of this human-induced contemporary evolution have been reported in a number of 'contexts', including hunting, harvesting, fishing, agriculture, medicine, climate change, pollution, eutrophication, urbanization, habitat fragmentation, biological invasions and emerging/disappearing diseases. Although numerous papers, journal special issues and books have addressed each of these contexts individually, the time has come to consider them together and thereby seek important similarities and differences...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920057/acropora-digitifera-encodes-the-largest-known-family-of-fluorescent-proteins-that-has-persisted-during-the-evolution-of-acropora-species
#8
Shiho Takahashi-Kariyazono, Jun Gojobori, Yoko Satta, Kazuhiko Sakai, Yohey Terai
Fluorescent proteins (FPs) are well known and broadly used as bio-imaging markers in molecular biology research. Many FP genes were cloned from anthozoan species and it was suggested that multi-copies of these genes are present in their genomes. However, the full complement of FP genes in any single coral species remained unidentified. In this study, we analyzed the FP genes in two stony coral species. FP cDNA sequences from Acropora digitifera and Acropora tenuis revealed the presence of a multi-gene family with an unexpectedly large number of genes, separated into short-/middle-wavelength emission (S/MWE), middle-/long-wavelength emission (M/LWE), and chromoprotein (CP) clades...
December 5, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27919924/gradual-vs-abrupt-reduction-of-carpels-in-syncarpous-gynoecia-a-case-study-from-polyscias-subg-arthrophyllum-araliaceae-apiales
#9
Polina V Karpunina, Alexei A Oskolski, Maxim S Nuraliev, Porter P Lowry, Galina V Degtjareva, Tahir H Samigullin, Carmen M Valiejo-Roman, Dmitry D Sokoloff
PREMISE OF THE STUDY: Revealing the relative roles of gradual and abrupt transformations of morphological characters is an important topic of evolutionary biology. Gynoecia apparently consisting of one carpel have evolved from pluricarpellate syncarpous gynoecia in several angiosperm clades. The process of reduction can involve intermediate stages, with one fertile and one or more sterile carpels (pseudomonomery). The possible origin of monomery directly via an abrupt change of gynoecium merism has been a matter of dispute...
December 5, 2016: American Journal of Botany
https://www.readbyqxmd.com/read/27919705/the-complete-mitochondrial-genome-of-thitarodes-sejilaensis-lepidoptera-hepialidae-a-host-insect-of-ophiocordyceps-sinensis-and-its-implication-in-taxonomic-revision-of-hepialusadopted-in-china
#10
Zhiwen Zou, Qiang Min, Shiyu Cheng, Tianrong Xin, Bin Xia
The mitochondrial genome is widely used for phylogenetic analyses and evolutionary biology. The complete mitochondrial genome of Thitarodes sejilaensis (Lepidoptera: Hepialidae) was sequenced and analyzed in this study. This mitogenome is a typical circular molecule of 15,290bp, with the gene content, orientation and order identical to other insects in the family Hepialidae. The genome nucleotide composition is heavily biased towards As and Ts, accounting for 80.87% of total nucleotide content. The major strand shows a positive AT-skew and negative GC-skew...
December 2, 2016: Gene
https://www.readbyqxmd.com/read/27917480/evolutionary-processes-and-its-environmental-correlates-in-the-cranial-morphology-of-western-chipmunks-tamias
#11
Ana Paula A Assis, Daniela M Rossoni, James L Patton, Gabriel Marroig
The importance of the environment in shaping phenotypic evolution lies at the core of evolutionary biology. Chipmunks of the genus Tamias (subgenus Neotamias) are part of a very recent radiation, occupying a wide range of environments with marked niche partitioning among species. One open question is if and how those differences in environments affected phenotypic evolution in this lineage. Herein we examine the relative importance of genetic drift versus natural selection in the origin of cranial diversity exhibited by clade members...
December 5, 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27915984/structure-function-and-evolution-of-clostridium-botulinum-c2-and-c3-toxins-insight-to-poultry-and-veterinary-vaccines
#12
P Chellapandi, A Prisilla
Clostridium botulinum group III strains are able to produce cytotoxins, C2 toxin and C3 exotoxin, along with botulinum neurotoxin types C and D. C2 toxin and C3 exotoxin produced from this organism are the most important members of bacterial ADP-ribosyltransferase superfamily. Both toxins have distinct pathophysiological functions in the avian and mammalian hosts. The members of this superfamily transfer an ADP-ribose moiety of NAD+ to specific eukaryotic target proteins. The present review describes the structure, function and evolution aspects of these toxins with a special emphasis to the development of veterinary vaccines...
December 1, 2016: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/27915074/evolutionary-stability-for-matrix-games-under-time-constraints
#13
József Garay, Villő Csiszár, Tamás F Móri
Game theory focuses on payoffs and typically ignores time constraints that play an important role in evolutionary processes where the repetition of games can depend on the strategies, too. We introduce a matrix game under time constraints, where each pairwise interaction has two consequences: both players receive a payoff and they cannot play the next game for a specified time duration. Thus our model is defined by two matrices: a payoff matrix and an average time duration matrix. Maynard Smith's concept of evolutionary stability is extended to this class of games...
November 30, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27914918/epigenetic-game-theory-how-to-compute-the-epigenetic-control-of-maternal-to-zygotic-transition
#14
REVIEW
Qian Wang, Kirk Gosik, Sujuan Xing, Libo Jiang, Lidan Sun, Vernon M Chinchilli, Rongling Wu
Epigenetic reprogramming is thought to play a critical role in maintaining the normal development of embryos. How the methylation state of paternal and maternal genomes regulates embryogenesis depends on the interaction and coordination of the gametes of two sexes. While there is abundant research in exploring the epigenetic interactions of sperms and oocytes, a knowledge gap exists in the mechanistic quantitation of these interactions and their impact on embryo development. This review aims at formulating a modeling framework to address this gap through the integration and synthesis of evolutionary game theory and the latest discoveries of the epigenetic control of embryo development by next-generation sequencing...
November 9, 2016: Physics of Life Reviews
https://www.readbyqxmd.com/read/27914620/gene-regulation-and-speciation
#15
REVIEW
Katya L Mack, Michael W Nachman
Understanding the genetic architecture of speciation is a major goal in evolutionary biology. Hybrid dysfunction is thought to arise most commonly through negative interactions between alleles at two or more loci. Divergence between interacting regulatory elements that affect gene expression (i.e., regulatory divergence) may be a common route for these negative interactions to arise. We review here how regulatory divergence between species can result in hybrid dysfunction, including recent theoretical support for this model...
November 30, 2016: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27914460/possible-mechanisms-of-acquisition-of-herpesvirus-virokines
#16
E A Gorshkova, E S Shilov
The genomes of certain types of human and primate herpesviruses contain functional homologs of important host cytokines (IL-6, IL-17, and IL-10), or so-called virokines. Virokines can interact with immune cell receptors, transmit a signal to them, and thus switch the type of immune response that facilitates viral infection development. In this work, we have summarized possible ways of virokine origin and proposed an evolutionary scenario of virokine acquisition with involvement of retroviral coinfection of the host...
November 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27914049/modeling-binding-affinity-of-pathological-mutations-for-computational-protein-design
#17
Miguel Romero-Durana, Chiara Pallara, Fabian Glaser, Juan Fernández-Recio
An important aspect of protein functionality is the formation of specific complexes with other proteins, which are involved in the majority of biological processes. The functional characterization of such interactions at molecular level is necessary, not only to understand biological and pathological phenomena but also to design improved, or even new interfaces, or to develop new therapeutic approaches. X-ray crystallography and NMR spectroscopy have increased the number of 3D protein complex structures deposited in the Protein Data Bank (PDB)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913843/molecular-evolution-in-historical-perspective
#18
Edna Suárez-Díaz
In the 1960s, advances in protein chemistry and molecular genetics provided new means for the study of biological evolution. Amino acid sequencing, nucleic acid hybridization, zone gel electrophoresis, and immunochemistry were some of the experimental techniques that brought about new perspectives to the study of the patterns and mechanisms of evolution. New concepts, such as the molecular evolutionary clock, and the discovery of unexpected molecular phenomena, like the presence of repetitive sequences in eukaryotic genomes, eventually led to the realization that evolution might occur at a different pace at the organismic and the molecular levels, and according to different mechanisms...
December 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27913680/new-nuclear-and-perinuclear-functions-of-formins
#19
REVIEW
Tadamoto Isogai, Metello Innocenti
Formin family proteins (formins) represent an evolutionary conserved protein family encoded in the genome of a wide range of eukaryotes. Formins are hallmarked by a formin homology 1 (FH1) domain juxtaposed to an FH2 domain whereby they control actin and microtubule dynamics. Not surprisingly, formins are best known as key regulators of the cytoskeleton in a variety of morphogenetic processes. However, mounting evidence implicates several formins in the assembly and organization of actin within and around the nucleus...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27912247/molecular-evolution-in-insect-societies-an-eco-evo-devo-synthesis
#20
Amy L Toth, Sandra M Rehan
The evolution of eusociality is a perennial issue in evolutionary biology, and genomic advances have fueled steadily growing interest in the genetic changes underlying social evolution. Along with a recent flurry of research on comparative and evolutionary genomics in different eusocial insect groups (bees, ants, wasps, and termites), several mechanistic explanations have emerged to describe the molecular evolution of eusociality from solitary behavior. These include solitary physiological ground plans, genetic toolkits of deeply conserved genes, evolutionary changes in protein-coding genes, cis regulation, and the structure of gene networks, epigenetics, and novel genes...
November 28, 2016: Annual Review of Entomology
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