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Evolutionary dynamics

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https://www.readbyqxmd.com/read/29040794/evaluating-the-peptide-structure-prediction-capabilities-of-a-purely-ab-initio-method
#1
M Amitay, M Goldstein
DEEPSAM is a relatively new global optimization algorithm aimed to predict the structure of bio-molecules from sequence, without any additional preliminary assumption. It is an evolutionary algorithm whose mutation operators are built by hybridizing the diffusion equation method, molecular dynamics simulated annealing, and a quasi-Newton local minimization method. The goal of this study was to evaluate the structure prediction capabilities of DEEPSAM by running it upon NMR structures of linear peptides (10-20 residues)...
October 13, 2017: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/29040605/negative-assortative-mating-in-the-white-throated-sparrow
#2
Philip W Hedrick, Elaina M Tuttle, Rusty A Gonser
Non-random mating based on phenotype has been observed in a number of organisms, but a very high proportion of these examples are of assortative mating. The strongest example of negative-assortative mating is for white-striped versus tan-striped crown in the white-throated sparrow, where about 98% of the observed pairings (mated pairs or social pairs) are between mates with different phenotypes and the correlation between mating types is -0.964. Although non-random mating has been explored theoretically for decades, these models have generally not focused on specific well-documented examples...
October 10, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036417/coprophagous-insects-and-the-ecology-of-infectious-diseases-of-wildlife
#3
Elizabeth Nichols, Viviana Alarcón, Shaun Forgie, Luis A Gomez-Puerta, Matthew S Jones
A diversity of macro- and microparasitic species exert strong influences on wildlife population density, community structure, and ecosystem functioning, all through their impacts on individual host fitness. Through consuming, manipulating, and relocating wildlife feces, over 7,000 species of coprophagous dung beetles interact with a staggering diversity of wildlife parasites with fecal-oral transmission in ways that both increase and decrease transmission. Here, we review the mechanisms by which dung beetles influence micro- and macroparasite transmission and outline a future research framework that integrates theory and empirical insights to advance our understanding of how these relationships may interact with ongoing environmental change drivers to further influence wildlife populations and community structure...
September 28, 2017: ILAR Journal
https://www.readbyqxmd.com/read/29036290/comparative-genomics-of-apomictic-root-knot-nematodes-hybridization-ploidy-and-dynamic-genome-change
#4
Amir Szitenberg, Laura Salazar-Jaramillo, Vivian C Blok, Dominik R Laetsch, Soumi Joseph, Valerie M Williamson, Mark L Blaxter, David H Lunt
The Root-Knot Nematodes (RKN; genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species, most of which are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture. While understanding the genomic basis for their variable success on different crops could benefit future agriculture, analyses of their genomes are challenging due to complex evolutionary histories that may incorporate hybridization, ploidy changes, and chromosomal fragmentation...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29034568/innovation-not-recovery-dynamic-redox-promotes-metazoan-radiations
#5
Rachel Wood, Douglas H Erwin
Environmental fluctuations in redox may reinforce rather than hinder evolutionary transitions, such that variability in near-surface oceanic oxygenation can promote morphological evolution and novelty. Modern, low-oxygen regions are heterogeneous and dynamic habitats that support low diversity and are inhabited by opportunistic and non-skeletal metazoans. We note that several major radiation episodes follow protracted or repeating intervals (>1 million years) of persistent and dynamic shallow marine redox (oceanic anoxic events)...
October 16, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/29033780/evolutionary-musicology-meets-embodied-cognition-biocultural-coevolution-and-the-enactive-origins-of-human-musicality
#6
REVIEW
Dylan van der Schyff, Andrea Schiavio
Despite evolutionary musicology's interdisciplinary nature, and the diverse methods it employs, the field has nevertheless tended to divide into two main positions. Some argue that music should be understood as a naturally selected adaptation, while others claim that music is a product of culture with little or no relevance for the survival of the species. We review these arguments, suggesting that while interesting and well-reasoned positions have been offered on both sides of the debate, the nature-or-culture (or adaptation vs...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/29033313/developing-a-model-for-cystic-fibrosis-sociomicrobiology-based-on-antibiotic-and-environmental-stress
#7
Susana Patrícia Lopes, Nuno Filipe Azevedo, Maria Olívia Pereira
Cystic fibrosis (CF) infections are invariably biofilm-mediated and polymicrobial, being safe to assume that a myriad of factors affects the sociomicrobiology within the CF infection site and modulate the CF community dynamics, by shaping their social activities, overall functions, virulence, ultimately affecting disease outcome. This work aimed to assess changes in the dynamics (particularly on the microbial composition) of dual-/three-species biofilms involving CF-classical (Pseudomonas aeruginosa) and unusual species (Inquilinus limosus and Dolosigranulum pigrum), according to variable oxygen conditions and antibiotic exposure...
September 28, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/29032843/the-evo-demo-implications-of-condition-dependent-mortality
#8
REVIEW
Victor Ronget, Michael Garratt, Jean-François Lemaître, Jean-Michel Gaillard
Animals in the wild die from a variety of different mortality sources, including predation, disease, and starvation. Different mortality sources selectively remove individuals with different body condition in different ways, and this variation in the condition dependence of mortality has evolutionary and demographic implications. Subsequent population dynamics are influenced by the strength of condition-dependent mortality during specific periods, with population growth impacted in different ways in short- versus long-lived species...
October 9, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/29031517/promotion-of-cooperation-in-evolutionary-game-dynamics-with-local-information
#9
Xuesong Liu, Qiuhui Pan, Mingfeng He
In this paper, we propose a strategy-updating rule driven by local information, which is called Local process. Unlike the standard Moran process, the Local process does not require global information about the strategic environment. By analyzing the dynamical behavior of the system, we explore how the local information influences the fixation of cooperation in two-player evolutionary games. Under weak selection, the decreasing local information leads to an increase of the fixation probability when natural selection does not favor cooperation replacing defection...
October 12, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29030214/fisher-s-fundamental-theorem-of-natural-selection-dynamic-sufficiency-and-the-necessity-of-higher-moments
#10
Matthijs van Veelen
The "average effects" of alleles in Fisher's Fundamental Theorem of Natural Selection are meant to capture what having an allele does to fitness. These average effects however are generally not constant, because the way they are determined implies that they may depend on the composition of the current population. This can easily be mistaken for dynamic insufficiency. In a recent paper by [Smerlak, M. and A. Youssef, 2017: Limiting fitness distributions in evolutionary dynamics. Journal of Theoretical Biology, 416, 68-80...
October 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29029264/a-general-model-for-estimating-macroevolutionary-landscapes
#11
Florian C Boucher, Vincent Démery, Elena Conti, Luke J Harmon, Josef Uyeda
The evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein-Uhlenbeck process, plus some of their extensions. Here we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios like directional trends, disruptive selection, or macroevolutionary landscapes with multiple peaks...
September 22, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029198/different-genomic-changes-underlie-adaptive-evolution-in-populations-of-contrasting-history
#12
S G Seabra, I Fragata, M A Antunes, G S Faria, M A Santos, V C Sousa, P Simões, M Matos
Experimental evolution is a powerful tool to understand the adaptive potential of populations under environmental change. Here, we study the importance of the historical genetic background in the outcome of evolution at the genome-wide level. Using the natural clinal variation of Drosophila subobscura, we sampled populations from two contrasting latitudes (Adraga, Portugal and Groningen, Netherlands) and introduced them in a new common environment in the laboratory. We characterized the genome-wide temporal changes underlying the evolutionary dynamics of these populations, which had previously shown fast convergence at the phenotypic level, but not at chromosomal inversion frequencies...
September 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29029188/an-analysis-of-the-epidemic-of-kpc-producing-klebsiella-pneumoniae-convergence-of-two-evolutionary-mechanisms-creates-the-perfect-storm
#13
Laura J Rojas, George M Weinstock, Elsa De La Cadena, Lorena Diaz, Rafael Rios, Blake M Hanson, Joseph S Brown, Purva Vats, Daniel S Phillips, Hoan Nguyen, Kristine M Hujer, Adriana Correa, Mark D Adams, Federico Perez, Erica Sodergren, Apurva Narechania, Paul J Planet, Maria V Villegas, Robert A Bonomo, Cesar A Arias
Background: Carbapenem resistance is a critical health care challenge worldwide. Particularly concerning is the widespread dissemination of Klebsiella pneumoniae carbapenemase (KPC). K. pneumoniae harboring blaKPC (KPC-Kpn) is endemic in many areas including United States, where the epidemic was primarily mediated by the clonal dissemination of Kpn ST258. We postulated that the spread of blaKPC in other regions occurs by different and more complex mechanisms. To test this, we investigated the evolution and dynamics of spread of KPC-Kpn in Colombia, where KPC became rapidly endemic after emerging in 2005...
September 27, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29028886/analysis-of-protein-targets-in-pathogen-host-interaction-in-infectious-diseases-a-case-study-on-plasmodium-falciparum-and-homo-sapiens-interaction-network
#14
Sovan Saha, Kaustav Sengupta, Piyali Chatterjee, Subhadip Basu, Mita Nasipuri
Infection and disease progression is the outcome of protein interactions between pathogen and host. Pathogen, the role player of Infection, is becoming a severe threat to life as because of its adaptability toward drugs and evolutionary dynamism in nature. Identifying protein targets by analyzing protein interactions between host and pathogen is the key point. Proteins with higher degree and possessing some topologically significant graph theoretical measures are found to be drug targets. On the other hand, exceptional nodes may be involved in infection mechanism because of some pathway process and biologically unknown factors...
September 23, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29026650/accurate-quantification-of-within-and-between-host-hbv-evolutionary-rates-requires-explicit-transmission-chain-modelling
#15
Bram Vrancken, Marc A Suchard, Philippe Lemey
Analyses of virus evolution in known transmission chains have the potential to elucidate the impact of transmission dynamics on the viral evolutionary rate and its difference within and between hosts. Lin et al. (2015, Journal of Virology, 89/7: 3512-22) recently investigated the evolutionary history of hepatitis B virus in a transmission chain and postulated that the 'colonization-adaptation-transmission' model can explain the differential impact of transmission on synonymous and non-synonymous substitution rates...
July 2017: Virus Evolution
https://www.readbyqxmd.com/read/29024107/multi-speed-genome-diploidization-and-diversification-after-an-ancient-allopolyploidization
#16
Terezie Mandáková, Milan Pouch, Klára Harmanová, Shing Hei Zhan, Itay Mayrose, Martin A Lysak
Hybridization and genome doubling (allopolyploidy) have led to evolutionary novelties as well as to the origin of new clades and species. Despite the importance of allopolyploidization, the dynamics of post-polyploid diploidization (PPD) at the genome level has been only sparsely studied. The Microlepidieae (MICR) is a crucifer tribe of 17 genera and c. 56 species endemic to Australia and New Zealand. Our phylogenetic and cytogenomic analyses revealed that MICR originated via an inter-tribal hybridization between ancestors of Crucihimalayeae (n = 8; maternal genome) and Smelowskieae (n = 7; paternal genome), both native to the Northern Hemisphere...
October 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29023368/the-evolutionary-history-and-spatiotemporal-dynamics-of-the-nc-lineage-of-citrus-tristeza-virus
#17
María José Benítez-Galeano, Matías Castells, Rodney Colina
Citrus tristeza virus (CTV) is a major pathogen affecting citrus trees worldwide. However, few studies have focused on CTV's evolutionary history and geographic behavior. CTV is locally dispersed by an aphid vector and long distance dispersion due to transportation of contaminated material. With the aim to delve deeper into the CTV-NC (New Clade) genotype evolution, we estimated an evolution rate of 1.19 × 10(-3) subs/site/year and the most common recent ancestor in 1977. Furthermore, the place of origin of the genotype was in the United States, and a great expansion of the population was observed in Uruguay...
October 12, 2017: Viruses
https://www.readbyqxmd.com/read/29021524/ecogenomics-of-virophages-and-their-giant-virus-hosts-assessed-through-time-series-metagenomics
#18
Simon Roux, Leong-Keat Chan, Rob Egan, Rex R Malmstrom, Katherine D McMahon, Matthew B Sullivan
Virophages are small viruses that co-infect eukaryotic cells alongside giant viruses (Mimiviridae) and hijack their machinery to replicate. While two types of virophages have been isolated, their genomic diversity and ecology remain largely unknown. Here we use time series metagenomics to identify and study the dynamics of 25 uncultivated virophage populations, 17 of which represented by complete or near-complete genomes, in two North American freshwater lakes. Taxonomic analysis suggests that these freshwater virophages represent at least three new candidate genera...
October 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/28994707/why-human-papillomavirus-acute-infections-matter
#19
REVIEW
Samuel Alizon, Carmen Lía Murall, Ignacio G Bravo
Most infections by human papillomaviruses (HPVs) are `acute', that is non-persistent. Yet, for HPVs, as for many other oncoviruses, there is a striking gap between our detailed understanding of chronic infections and our limited data on the early stages of infection. Here we argue that studying HPV acute infections is necessary and timely. Focusing on early interactions will help explain why certain infections are cleared while others become chronic or latent. From a molecular perspective, descriptions of immune effectors and pro-inflammatory pathways during the initial stages of infections have the potential to lead to novel treatments or to improved handling algorithms...
October 10, 2017: Viruses
https://www.readbyqxmd.com/read/28992625/b-chromosome-variants-of-the-grasshopper-xyleus-discoideus-angulatus-are-potentially-derived-from-pericentromeric-dna
#20
Andrezza C S Bernardino, Diogo C Cabral-de-Mello, Carolina B Machado, Octavio M Palacios-Gimenez, Neide Santos, Vilma Loreto
B chromosomes, extra elements present in the karyotypes of some eukaryote species, have been described in the grasshopper Xyleus discoideus angulatus. Although some studies have proposed an autosomal origin of the B chromosome in X. d. angulatus, little is known about its repetitive DNA composition and evolutionary dynamics. The aim of the present work was to shed light on the B chromosome evolution in X. d. angulatus by cytogenetic analysis of 27 populations from Pernambuco and Ceará states (Brazil). The frequency of B chromosomes in the different populations was determined, and chromosome measurements and fluorescence in situ hybridization (FISH) with C0t-DNA and telomeric and B chromosome sequences were performed in cells from B-carrying individuals...
October 10, 2017: Cytogenetic and Genome Research
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