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evolutionary genetics

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https://www.readbyqxmd.com/read/29244833/genomic-characterization-and-molecular-evolution-analysis-of-subtype-b-and-bf-recombinant-hiv-1-strains-among-argentinean-men-who-have-sex-with-men-reveal-a-complex-scenario
#1
Cintia G Cevallos, Leandro R Jones, Maria A Pando, Jean K Carr, Maria M Avila, Jorge Quarleri
Currently, data on HIV-1 circulating strains among men who have sex with men (MSM) in Argentina is scarce. In South America, the distribution and the prevalence of BF recombinants are dissimilar and exhibit an underappreciated heterogeneity of recombinant structures. Here, we studied for the first time the genetic diversity of HIV-1 BF recombinants and their evolution over time through in-depth phylogenetic analysis and multiple recombination detection methods involving 337 HIV-1 nucleotide sequences (25 near full-length (NFL) and 312 partial pol gene) obtained from Argentinean MSM...
2017: PloS One
https://www.readbyqxmd.com/read/29244566/the-price-equation-gradient-dynamics-and-continuous-trait-game-theory
#2
Jussi Lehtonen
A recent article convincingly nominated the Price equation as the fundamental theorem of evolution and used it as a foundation to derive several other theorems. A major section of evolutionary theory that was not addressed is that of game theory and gradient dynamics of continuous traits with frequency-dependent fitness. Deriving fundamental results in these fields under the unifying framework of the Price equation illuminates similarities and differences between approaches and allows a simple, unified view of game-theoretical and dynamic concepts...
January 2018: American Naturalist
https://www.readbyqxmd.com/read/29244562/learning-to-cooperate-the-evolution-of-social-rewards-in-repeated-interactions
#3
Slimane Dridi, Erol Akçay
Understanding the behavioral and psychological mechanisms underlying social behaviors is one of the major goals of social evolutionary theory. In particular, a persistent question about animal cooperation is to what extent it is supported by other-regarding preferences-the motivation to increase the welfare of others. In many situations, animals adjust their behaviors through learning by responding to the rewards they experience as a consequence of their actions. Therefore, we may ask whether learning in social situations can be driven by evolved other-regarding rewards...
January 2018: American Naturalist
https://www.readbyqxmd.com/read/29244558/loss-of-color-pigmentation-is-maintained-at-high-frequency-in-a-monkey-flower-population
#4
Alex D Twyford, Aaron M Caola, Pratibha Choudhary, Ramesh Raina, Jannice Friedman
Color polymorphisms have long been of evolutionary interest for their diverse roles, including mate choice, predator avoidance, and pollinator attraction. While color variation is often under strong selection, some taxa demonstrate unexpectedly high frequencies of presumed deleterious color forms. Here we show that a genetic variant underlying complete loss of anthocyanin pigmentation has risen to an unexpectedly high frequency of >0.2 in a natural population of the plant Mimulus guttatus. Decreased expression of MYB5 transcription factor is associated with unpigmented morphs...
January 2018: American Naturalist
https://www.readbyqxmd.com/read/29244555/theoretical-approaches-in-evolutionary-ecology-environmental-feedback-as-a-unifying-perspective
#5
Sébastien Lion
Evolutionary biology and ecology have a strong theoretical underpinning, and this has fostered a variety of modeling approaches. A major challenge of this theoretical work has been to unravel the tangled feedback loop between ecology and evolution. This has prompted the development of two main classes of models. While quantitative genetics models jointly consider the ecological and evolutionary dynamics of a focal population, a separation of timescales between ecology and evolution is assumed by evolutionary game theory, adaptive dynamics, and inclusive fitness theory...
January 2018: American Naturalist
https://www.readbyqxmd.com/read/29244009/inference-of-genetic-relatedness-between-viral-quasispecies-from-sequencing-data
#6
Olga Glebova, Sergey Knyazev, Andrew Melnyk, Alexander Artyomenko, Yury Khudyakov, Alex Zelikovsky, Pavel Skums
BACKGROUND: RNA viruses such as HCV and HIV mutate at extremely high rates, and as a result, they exist in infected hosts as populations of genetically related variants. Recent advances in sequencing technologies make possible to identify such populations at great depth. In particular, these technologies provide new opportunities for inference of relatedness between viral samples, identification of transmission clusters and sources of infection, which are crucial tasks for viral outbreaks investigations...
December 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29243868/genetic-diversity-of-small-populations-not-always-doom-and-gloom
#7
Dylan J Fraser
Is a key theory of evolutionary and conservation biology-that loss of genetic diversity can be predicted from population size-on shaky ground? In the face of increasing human-induced species depletion and habitat fragmentation, this question and the study of genetic diversity in small populations are paramount to understanding the limits of species' responses to environmental change and to providing remedies to endangered species conservation. Few empirical studies have investigated to what degree some small populations might be buffered against losses of genetic diversity...
December 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29243391/bayesian-molecular-dating-opening-up-the-black-box
#8
Lindell Bromham, Sebastián Duchêne, Xia Hua, Andrew M Ritchie, David A Duchêne, Simon Y W Ho
Molecular dating analyses allow evolutionary timescales to be estimated from genetic data, offering an unprecedented capacity for investigating the evolutionary past of all species. These methods require us to make assumptions about the relationship between genetic change and evolutionary time, often referred to as a 'molecular clock'. Although initially regarded with scepticism, molecular dating has now been adopted in many areas of biology. This broad uptake has been due partly to the development of Bayesian methods that allow complex aspects of molecular evolution, such as variation in rates of change across lineages, to be taken into account...
December 15, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/29243070/extensive-evolution-analysis-of-the-global-chikungunya-virus-strains-revealed-the-origination-of-chikv-epidemics-in-pakistan-in-2016
#9
Junming Shi, Zhengyuan Su, Zhaojun Fan, Jun Wang, Siqing Liu, Bo Zhang, Hongping Wei, Shoukat Jehan, Nadia Jamil, Shu Shen, Fei Deng
Chikungunya virus (CHIKV) is a mosquito-borne virus that causes epidemics widely in the world especially in the tropical and subtropical regions. Phylogenetic analysis has found that the CHIKV lineages were associated with the spatial and temporal distributions, which were related to the virus adaption to the major mosquito species and their distributions. In this study, we reported the complete genome sequences of eight CHIKV isolates from the outbreak in Pakistan last year. Then we reviewed the evolutionary history using extensive phylogenetic analysis, analyzed lineagespecific substitutions in viral proteins, and characterized the spreading pathway of CHIKV strains including the Pakistani strains...
December 11, 2017: Virologica Sinica
https://www.readbyqxmd.com/read/29242625/regulation-of-hyperoxia-induced-social-behaviour-in-pristionchus-pacificus-nematodes-requires-a-novel-cilia-mediated-environmental-input
#10
Eduardo Moreno, Bogdan Sieriebriennikov, Hanh Witte, Christian Rödelsperger, James W Lightfoot, Ralf J Sommer
Social behaviours are frequently utilised for defence and stress avoidance in nature. Both Caenorhabditis elegans and Pristionchus pacificus nematodes display social behaviours including clumping and bordering, to avoid hyperoxic stress conditions. Additionally, both species show natural variation in social behaviours with "social" and "solitary" strains. While the single solitary C. elegans N2 strain has evolved under laboratory domestication due to a gain-of-function mutation in the neuropeptide receptor gene npr-1, P...
December 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29241941/finding-evolutionary-processes-hidden-in-cryptic-species
#11
REVIEW
Torsten H Struck, Jeffrey L Feder, Mika Bendiksby, Siri Birkeland, José Cerca, Vladimir I Gusarov, Sonja Kistenich, Karl-Henrik Larsson, Lee Hsiang Liow, Michael D Nowak, Brita Stedje, Lutz Bachmann, Dimitar Dimitrov
Cryptic species could represent a substantial fraction of biodiversity. However, inconsistent definitions and taxonomic treatment of cryptic species prevent informed estimates of their contribution to biodiversity and impede our understanding of their evolutionary and ecological significance. We propose a conceptual framework that recognizes cryptic species based on their low levels of phenotypic (morphological) disparity relative to their degree of genetic differentiation and divergence times as compared with non-cryptic species...
December 11, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/29241296/evolving-aptamers-with-unnatural-base-pairs
#12
Michiko Kimoto, Ken-Ichiro Matsunaga, Ichiro Hirao
A novel technology, genetic alphabet expansion, has rapidly advanced through the successful creation of unnatural base pairs that function as a third base pair in replication. Recently, genetic alphabet expansion has been applied to some practical areas. Among them, the application to DNA aptamer generation is a good example of the broad utility of this technology. A hydrophobic unnatural base pair, Ds-Px, which exhibits high fidelity in replication as a third base pair, has been applied to an evolutionary engineering method called SELEX (Systematic Evolution of Ligands by EXponential enrichment) to generate DNA aptamers that bind to targets...
December 14, 2017: Current Protocols in Chemical Biology
https://www.readbyqxmd.com/read/29241022/evolution-as-an-ecosystem-process-insights-from-genomics
#13
Blake Matthews, Rebecca J Best, Philine G D Feulner, Anita Narwani, Romana Limberger
Evolution is a fundamental ecosystem process. The study of genomic variation of organisms can not only improve our understanding of evolutionary processes, but also of contemporary and future ecosystem dynamics. We argue that integrative research between the fields of genomics and ecosystem ecology could generate new insights. Specifically, studies of biodiversity and ecosystem functioning, evolutionary rescue, and eco-evolutionary dynamics could all benefit from information about variation in genome structure and the genetic architecture of traits, whereas genomic studies could benefit from information about the ecological context of evolutionary dynamics...
December 14, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29240932/homogenization-of-populations-in-the-wildflower-texas-bluebonnet-lupinus-texensis
#14
Kathryn G Turner, Daisie I Huang, Quentin C B Cronk, Loren H Rieseberg
Wildflower seeds are routinely spread along highways and thoroughfares throughout North America as part of federal beautification policy, but the genetic effect of the introduction of these cultivated populations on wild populations of the same species is unknown. Interbreeding may occur between these seeded and wild populations, resulting in several possible outcomes. Here we sample 187 individuals in 12 matched pairs of neighboring wild and seeded populations of the Texas bluebonnet (Lupinus texensis), a species popular in commercially available wildflower seed mixes used by both the Texas Department of Transportation and the public...
December 12, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29240929/the-genome-and-adult-somatic-transcriptome-of-the-mormyrid-electric-fish-paramormyrops-kingsleyae
#15
Jason R Gallant, Mauricio Losilla, Chad Tomlinson, Wesley C Warren
Several studies have begun to elucidate the genetic and developmental processes underlying major vertebrate traits. Few of these traits have evolved repeatedly in vertebrates, preventing the analysis of molecular mechanisms underlying these traits comparatively. Electric organs have evolved multiple times among vertebrates, presenting a unique opportunity to understand the degree of constraint and repeatability of the evolutionary processes underlying novel vertebrate traits. As there is now a completed genome sequence representing south american electric eels, we were motivated to obtain genomic sequence from a linage that independently evolved electric organs to facilitate future comparative analyses of the evolution and development of electric organs...
December 12, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29240811/whole-genome-analyses-of-human-adenovirus-type-55-emerged-in-tibet-sichuan-and-yunnan-in-china-in-2016
#16
Wenbo Wang, Yuan Liu, Yifan Zhou, Liangqi Gu, Lin Zhang, Xuelian Zhang, Maomao Chen, Ziying Zou, Wei Qiu, Xiaobing Hu, Quanshui Fan
Three outbreaks of acute respiratory disease occurred at military camps in 2016 at Tibet, Sichuan and Yunnan province, China. The pathogen induced these three outbreaks were all confirmed as HAdV-55 by genotype-specific PCR. The outbreak in Tibet was the first report that HAdV-55 occurred in the high altitude (HA, above sea level 3658 m). This study aims to determine the gene variation and evolution characteristics of these viral strains. Three strains of adenoviruses, LS89/Tibet/2016 (GenBank accession no...
2017: PloS One
https://www.readbyqxmd.com/read/29240755/integrating-transcriptomics-and-metabolomics-to-characterize-the-regulation-of-epa-biosynthesis-in-response-to-cold-stress-in-seaweed-bangia-fuscopurpurea
#17
Min Cao, Dongmei Wang, Yunxiang Mao, Fanna Kong, Guiqi Bi, Qikun Xing, Zhen Weng
Bangia fuscopurpurea is a traditional mariculture crop having high nutritional value, eicosapntemacnioc acid (EPA) production, and protein content. As an intertidal species, it can tolerate drastic changes in abiotic factors such as temperature, hydration, and light radiation; however, genomic information on the evolutionary aspect and mechanism of EPA enrichment in B. fuscopurpurea and the role of EPA in cold tolerance in this species remain elusive. We conducted transcriptome profile analysis in B. fuscopurpurea to investigate the biological functions of genes associated with resistance to various environment factors...
2017: PloS One
https://www.readbyqxmd.com/read/29240241/okur-chung-neurodevelopmental-syndrome-eight-additional-cases-with-implications-on-phenotype-and-genotype-expansion
#18
A T G Chiu, S L C Pei, C C Y Mak, G K C Leung, M H C Yu, S L Lee, M Vreeburg, R Pfundt, I van der Burgt, T Kleefstra, T M-T Frederic, S Nambot, L Faivre, A-L Bruel, M Rossi, B Isidor, S Küry, B Cogne, T Besnard, M Willems, M R F Reijnders, B H Y Chung
Okur-Chung syndrome is a neurodevelopmental condition attributed to germline CSNK2A1 pathogenic missense variants. We present eight unreported subjects with the above syndrome, who have recognizable dysmorphism, varying degrees of developmental delay and multisystem involvement. Together with six previously reported cases, we present a case series of seven female and seven male subjects, highlighting the recognizable facial features of the syndrome (microcephaly, hypertelorism, epicanthic fold, ptosis, arched eyebrows, low set ears, ear fold abnormality, broad nasal bridge and round face) as well as frequently occurring clinical features including neurodevelopmental delay (93%), gastrointestinal (57%), musculoskeletal (57%) and immunological (43%) abnormalities...
December 14, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29238556/reliable-effective-number-of-breeders-adult-census-size-ratios-in-seasonal-breeding-species-opportunity-for-integrative-demographic-inferences-based-on-capture-mark-recapture-data-and-multilocus-genotypes
#19
Gregorio Sánchez-Montes, Jinliang Wang, Arturo H Ariño, José Luis Vizmanos, Iñigo Martínez-Solano
The ratio of the effective number of breeders (Nb) to the adult census size (Na), Nb/Na, approximates the departure from the standard capacity of a population to maintain genetic diversity in one reproductive season. This information is relevant for assessing population status, understanding evolutionary processes operating at local scales, and unraveling how life-history traits affect these processes. However, our knowledge on Nb/Na ratios in nature is limited because estimation of both parameters is challenging...
December 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29238551/genetic-differentiation-and-spatiotemporal-history-of-diploidy-and-tetraploidy-of-clintonia-udensis
#20
Juan He, Shengnan Wang, Jia Li, Zelu Fan, Xin Liu, Yiling Wang
Polyploidy is an important factor shaping the geographic range of a species. Clintonia udensis (Clintonia) is a primary perennial herb widely distributed in China with two karyotypic characteristics-diploid and tetraploid and thereby used to understand the ploidy and distribution. This study unraveled the patterns of genetic variation and spatiotemporal history among the cytotypes of C. udensis using simple sequence repeat or microsatellites. The results showed that the diploids and tetraploids showed the medium level of genetic differentiation; tetraploid was slightly lower than diploid in genetic diversity; recurrent polyploidization seems to have opened new possibilities for the local genotype; the spatiotemporal history of C...
December 2017: Ecology and Evolution
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