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Evolutionary dynamics

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https://www.readbyqxmd.com/read/29691935/mitochondria-and-wolbachia-titers-are-positively-correlated-during-maternal-transmission
#1
Lucas P Henry, Irene L G Newton
Mothers provide their offspring with symbionts. Maternally transmitted, intracellular symbionts must disperse from mother to offspring with other cytoplasmic elements, like mitochondria. Here, we investigated how the intracellular symbiont Wolbachia interacts with mitochondria during maternal transmission. Mitochondria and Wolbachia may interact antagonistically and compete as each population tries to ensure its own evolutionary success. Alternatively, mitochondria and Wolbachia may cooperate as both benefit from ensuring the fitness of the mother...
April 25, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29689067/pathogenic-adaptations-of-colletotrichum-fungi-revealed-by-genome-wide-gene-family-evolutionary-analyses
#2
Xiaofei Liang, Bo Wang, Qiuyue Dong, Lingnan Li, Jeffrey A Rollins, Rong Zhang, Guangyu Sun
The fungal genus Colletotrichum contains hemibiotrophic phytopathogens being highly variable in host and tissue specificities. We sequenced a C. fructicola genome (1104-7) derived from an isolate of apple in China and compared it with the reference genome (Nara_gc5) derived from an isolate of strawberry in Japan. Mauve alignment and BlastN search identified 0.62 Mb lineage-specific (LS) genomic regions in 1104-7 with a length criterion of 10 kb. Genes located within LS regions evolved more dynamically, and a strongly elevated proportion of genes were closely related to non-Colletotrichum sequences...
2018: PloS One
https://www.readbyqxmd.com/read/29688481/neutral-theory-and-rapidly-evolving-viral-pathogens
#3
Simon D W Frost, Brittany Rife Magalis, Sergei L Kosakovsky Pond
The evolution of viral pathogens is shaped by strong selective forces that are exerted during jumps to new hosts, confrontations with host immune responses and antiviral drugs, and numerous other processes. However, while undeniably strong and frequent, adaptive evolution is largely confined to small parts of information-packed viral genomes, and the majority of observed variation is effectively neutral. The predictions and implications of the neutral theory have proven immensely useful in this context, with applications spanning understanding within-host population structure, tracing the origins and spread of viral pathogens, predicting evolutionary dynamics, and modeling the emergence of drug resistance...
April 24, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29687111/grain-boundary-phases-in-bcc-metals
#4
T Frolov, W Setyawan, R J Kurtz, J Marian, A R Oganov, R E Rudd, Q Zhu
We report a computational discovery of novel grain boundary structures and multiple grain boundary phases in elemental body-centered cubic (bcc) metals represented by tungsten, tantalum and molybdenum. While grain boundary structures created by the γ-surface method as a union of two perfect half crystals have been studied extensively, it is known that the method has limitations and does not always predict the correct ground states. Herein, we use a newly developed computational tool, based on evolutionary algorithms, to perform a grand-canonical search of high-angle symmetric tilt and twist boundaries, and we find new ground states and multiple phases that cannot be described using the conventional structural unit model...
April 24, 2018: Nanoscale
https://www.readbyqxmd.com/read/29686839/signatures-of-competition-and-strain-structure-within-the-major-blood-stage-antigen-of-plasmodium-falciparum-in-a-local-community-in-ghana
#5
Mary M Rorick, Yael Artzy-Randrup, Shazia Ruybal-Pesántez, Kathryn E Tiedje, Thomas S Rask, Abraham Oduro, Anita Ghansah, Kwadwo Koram, Karen P Day, Mercedes Pascual
The concept of niche partitioning has received considerable theoretical attention at the interface of ecology and evolution of infectious diseases. Strain theory postulates that pathogen populations can be structured into distinct nonoverlapping strains by frequency-dependent selection in response to intraspecific competition for host immune space. The malaria parasite Plasmodium falciparum presents an opportunity to investigate this phenomenon in nature, under conditions of high recombination rate and extensive antigenic diversity...
April 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29686235/tritrophic-phenological-match-mismatch-in-space-and-time
#6
Malcolm D Burgess, Ken W Smith, Karl L Evans, Dave Leech, James W Pearce-Higgins, Claire J Branston, Kevin Briggs, John R Clark, Chris R du Feu, Kate Lewthwaite, Ruedi G Nager, Ben C Sheldon, Jeremy A Smith, Robin C Whytock, Stephen G Willis, Albert B Phillimore
Increasing temperatures associated with climate change may generate phenological mismatches that disrupt previously synchronous trophic interactions. Most work on mismatch has focused on temporal trends, whereas spatial variation in the degree of trophic synchrony has largely been neglected, even though the degree to which mismatch varies in space has implications for meso-scale population dynamics and evolution. Here we quantify latitudinal trends in phenological mismatch, using phenological data on an oak-caterpillar-bird system from across the UK...
April 23, 2018: Nature Ecology & Evolution
https://www.readbyqxmd.com/read/29686074/sporadic-sampling-not-climatic-forcing-drives-observed-early-hominin-diversity
#7
Simon J Maxwell, Philip J Hopley, Paul Upchurch, Christophe Soligo
The role of climate change in the origin and diversification of early hominins is hotly debated. Most accounts of early hominin evolution link observed fluctuations in species diversity to directional shifts in climate or periods of intense climatic instability. None of these hypotheses, however, have tested whether observed diversity patterns are distorted by variation in the quality of the hominin fossil record. Here, we present a detailed examination of early hominin diversity dynamics, including both taxic and phylogenetically corrected diversity estimates...
April 23, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29686068/recurrent-structural-variation-clustered-sites-of-selection-and-disease-risk-for-the-complement-factor-h-cfh-gene-family
#8
Stuart Cantsilieris, Bradley J Nelson, John Huddleston, Carl Baker, Lana Harshman, Kelsi Penewit, Katherine M Munson, Melanie Sorensen, AnneMarie E Welch, Vy Dang, Felix Grassmann, Andrea J Richardson, Robyn H Guymer, Tina A Graves-Lindsay, Richard K Wilson, Bernhard H F Weber, Paul N Baird, Rando Allikmets, Evan E Eichler
Structural variation and single-nucleotide variation of the complement factor H ( CFH ) gene family underlie several complex genetic diseases, including age-related macular degeneration (AMD) and atypical hemolytic uremic syndrome (AHUS). To understand its diversity and evolution, we performed high-quality sequencing of this ∼360-kbp locus in six primate lineages, including multiple human haplotypes. Comparative sequence analyses reveal two distinct periods of gene duplication leading to the emergence of four CFH -related ( CFHR ) gene paralogs ( CFHR2 and CFHR4 ∼25-35 Mya and CFHR1 and CFHR3 ∼7-13 Mya)...
April 23, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29685580/can-multilayer-networks-advance-animal-behavior-research
#9
Matthew J Silk, Kelly R Finn, Mason A Porter, Noa Pinter-Wollman
Interactions among individual animals - and between these individuals and their environment - yield complex, multifaceted systems. The development of multilayer network analysis offers a promising new approach for studying animal social behavior and its relation to eco-evolutionary dynamics.
April 20, 2018: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/29684140/ultra-fast-global-homology-detection-with-discrete-cosine-transform-and-dynamic-time-warping
#10
Daniele Raimondi, Gabriele Orlando, Yves Moreau, Wim F Vranken
Motivation: Evolutionary information is crucial for the annotation of proteins in bioinformatics. The amount of retrieved homologs often correlates with the quality of predicted protein annotations related to structure or function. With a growing amount of sequences available, fast and reliable methods for homology detection are essential, as they have a direct impact on predicted protein annotations. Results: We developed a discriminative, alignment-free algorithm for homology detection with quasi-linear complexity, enabling theoretically much faster homology searches...
April 19, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29684025/first-cases-of-european-bat-lyssavirus-type-1-in-iberian-serotine-bats-implications-for-the-molecular-epidemiology-of-bat-rabies-in-europe
#11
Patricia Mingo-Casas, Virginia Sandonís, Elena Obón, José M Berciano, Sonia Vázquez-Morón, Javier Juste, Juan E Echevarría
Previous studies have shown that EBLV-1 strains exclusively hosted by Eptesicus isabellinus bats in the Iberian Peninsula cluster in a specific monophyletic group that is related to the EBLV-1b lineage found in the rest of Europe. More recently, enhanced passive surveillance has allowed the detection of the first EBLV-1 strains associated to Eptesicus serotinus south of the Pyrenees. The aim of this study is the reconstruction of the EBLV-1 phylogeny and phylodynamics in the Iberian Peninsula in the context of the European continent...
April 23, 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29683424/stochastic-processes-constrain-the-within-and-between-host-evolution-of-influenza-virus
#12
John T McCrone, Robert J Woods, Emily T Martin, Ryan E Malosh, Arnold S Monto, Adam S Lauring
The evolutionary dynamics of influenza virus ultimately derive from processes that take place within and between infected individuals. Here we define influenza virus dynamics in human hosts through sequencing of 249 specimens from 200 individuals collected over 6290 person-seasons of observation. Because these viruses were collected from individuals in a prospective community-based cohort, they are broadly representative of natural infections with seasonal viruses. Consistent with a neutral model of evolution, sequence data from 49 serially sampled individuals illustrated the dynamic turnover of synonymous and nonsynonymous single nucleotide variants and provided little evidence for positive selection of antigenic variants...
April 23, 2018: ELife
https://www.readbyqxmd.com/read/29681898/the-versatile-mutational-resistome-of-pseudomonas-aeruginosa
#13
REVIEW
Carla López-Causapé, Gabriel Cabot, Ester Del Barrio-Tofiño, Antonio Oliver
One of the most striking features of Pseudomonas aeruginosa is its outstanding capacity for developing antimicrobial resistance to nearly all available antipseudomonal agents through the selection of chromosomal mutations, leading to the failure of the treatment of severe hospital-acquired or chronic infections. Recent whole-genome sequencing (WGS) data obtained from in vitro assays on the evolution of antibiotic resistance, in vivo monitoring of antimicrobial resistance development, analysis of sequential cystic fibrosis isolates, and characterization of widespread epidemic high-risk clones have provided new insights into the evolutionary dynamics and mechanisms of P...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29679784/a-swinging-seesaw-as-a-novel-model-mechanism-for-time-dependent-hormesis-under-dose-dependent-stimulatory-and-inhibitory-effects-a-case-study-on-the-toxicity-of-antibacterial-chemicals-to-aliivibrio-fischeri
#14
Haoyu Sun, Edward J Calabrese, Min Zheng, Dali Wang, Yongzheng Pan, Zhifen Lin, Ying Liu
Hormesis occurs frequently in broadly ranging biological areas (e.g. plant biology, microbiology, biogerontology), toxicology, pharmacology and medicine. While numerous mechanisms (e.g. receptor and pathway mediated pathway responses) account for stimulatory and inhibitory features of hormetic dose responses, the vast majority emphasizes the inclusion of many doses but only one timepoint or use of a single optimized dose that is assessed over a broad range of timepoints. In this paper, a toxicity study was designed using a large number of properly spaced doses with responses determined over a large number of timepoints, which could help us reveal the underlying mechanism of hormesis...
April 10, 2018: Chemosphere
https://www.readbyqxmd.com/read/29678149/comparative-mitochondrial-genomics-of-cryptophyte-algae-gene-shuffling-and-dynamic-mobile-genetic-elements
#15
Jong Im Kim, Hwan Su Yoon, Gangman Yi, Woongghi Shin, John M Archibald
BACKGROUND: Cryptophytes are an ecologically important group of algae comprised of phototrophic, heterotrophic and osmotrophic species. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin. Cryptophytes have a clear phylogenetic affinity to heterotrophic eukaryotes and possess four genomes: host-derived nuclear and mitochondrial genomes, and plastid and nucleomorph genomes of endosymbiotic origin. RESULTS: To gain insight into cryptophyte mitochondrial genome evolution, we sequenced the mitochondrial DNAs of five species and performed a comparative analysis of seven genomes from the following cryptophyte genera: Chroomonas, Cryptomonas, Hemiselmis, Proteomonas, Rhodomonas, Storeatula and Teleaulax...
April 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29677667/co-evolutionary-dynamics-of-the-human-environment-system-in-the-heihe-river-basin-in-the-past-2000years
#16
Zhixiang Lu, Yongping Wei, Qi Feng, Jiali Xie, Honglang Xiao, Guodong Cheng
There is limited quantitative understanding of interactions between human and environmental systems over the millennial scale. We aim to reveal the co-evolutionary dynamics of the human-environment system in a river basin by simulating the water use and net primary production (NPP) allocation for human and environmental systems over the last 2000years in Heihe River basin (HRB) in northwest China. We partition the catchment total evapotranspiration (ET) into ET for human and environmental systems with a social-hydrological framework and estimate the NPP for human and environmental systems using the Box-Lieth model, then classify the co-evolutionary processes of the human-environment system into distinct phases using the rate of changes of NPP over time, and discover the trade-offs or synergies relationships between them based on the elasticity of change of the NPP for humans to the change of NPP for environment...
April 17, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29675652/an-alternative-formulation-for-a-distributed-delayed-logistic-equation
#17
Chiu-Ju Lin, Lin Wang, Gail S K Wolkowicz
We study an alternative single species logistic distributed delay differential equation (DDE) with decay-consistent delay in growth. Population oscillation is rarely observed in nature, in contrast to the outcomes of the classical logistic DDE. In the alternative discrete delay model proposed by Arino et al. (J Theor Biol 241(1):109-119, 2006), oscillatory behavior is excluded. This study adapts their idea of the decay-consistent delay and generalizes their model. We establish a threshold for survival and extinction: In the former case, it is confirmed using Lyapunov functionals that the population approaches the delay modified carrying capacity; in the later case the extinction is proved by the fluctuation lemma...
April 19, 2018: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/29670598/contribution-of-mobile-group-ii-introns-to-sinorhizobium-meliloti-genome-evolution
#18
REVIEW
Nicolás Toro, Francisco Martínez-Abarca, María D Molina-Sánchez, Fernando M García-Rodríguez, Rafael Nisa-Martínez
Mobile group II introns are ribozymes and retroelements that probably originate from bacteria. Sinorhizobium meliloti , the nitrogen-fixing endosymbiont of legumes of genus Medicago , harbors a large number of these retroelements. One of these elements, RmInt1, has been particularly successful at colonizing this multipartite genome. Many studies have improved our understanding of RmInt1 and phylogenetically related group II introns, their mobility mechanisms, spread and dynamics within S. meliloti and closely related species...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29669899/conserved-but-flexible-modularity-in-the-zebrafish-skull-implications-for-craniofacial-evolvability
#19
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/29668379/predictability-force-and-anti-resonance-in-complex-object-control
#20
Pauline Maurice, Neville Hogan, Dagmar Sternad
Manipulation of complex objects as in tool use is ubiquitous and has given humans an evolutionary advantage. This study examined the strategies humans choose when manipulating an object with underactuated internal dynamics, such as a cup of coffee. The object's dynamics renders the temporal evolution complex, possibly even chaotic, and difficult to predict. A cart-and-pendulum model, loosely mimicking coffee sloshing in a cup, was implemented in a virtual environment with a haptic interface. Participants rhythmically manipulated the virtual cup containing a rolling ball; they could choose the oscillation frequency, while the amplitude was prescribed...
April 18, 2018: Journal of Neurophysiology
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