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"Evolutionary mechanisms"

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https://www.readbyqxmd.com/read/27920798/evolutionary-and-functional-features-of-copy-number-variation-in-the-cattle-genome
#1
Brittney N Keel, Amanda K Lindholm-Perry, Warren M Snelling
Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27909020/the-design-and-transformation-of-biofundamentals-a-nonsurvey-introductory-evolutionary-and-molecular-biology-course
#2
Michael W Klymkowsky, Jeremy D Rentsch, Emina Begovic, Melanie M Cooper
Many introductory biology courses amount to superficial surveys of disconnected topics. Often, foundational observations and the concepts derived from them and students' ability to use these ideas appropriately are overlooked, leading to unrealistic expectations and unrecognized learning obstacles. The result can be a focus on memorization at the expense of the development of a meaningful framework within which to consider biological phenomena. About a decade ago, we began a reconsideration of what an introductory course should present to students and the skills they need to master...
2016: CBE Life Sciences Education
https://www.readbyqxmd.com/read/27878094/host-mediated-shift-in-the-cold-tolerance-of-an-invasive-insect
#3
Amy C Morey, Robert C Venette, Erica C Nystrom Santacruz, Laurel A Mosca, W D Hutchison
While many insects cannot survive the formation of ice within their bodies, a few species can. On the evolutionary continuum from freeze-intolerant (i.e., freeze-avoidant) to freeze-tolerant insects, intermediates likely exist that can withstand some ice formation, but not enough to be considered fully freeze tolerant. Theory suggests that freeze tolerance should be favored over freeze avoidance among individuals that have low relative fitness before exposure to cold. For phytophagous insects, numerous studies have shown that host (or nutrition) can affect fitness and cold-tolerance strategy, respectively, but no research has investigated whether changes in fitness caused by different hosts of polyphagous species could lead to systematic changes in cold-tolerance strategy...
November 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/27856734/control-of-hoxd-gene-transcription-in-the-mammary-bud-by-hijacking-a-preexisting-regulatory-landscape
#4
Ruben Schep, Anamaria Necsulea, Eddie Rodríguez-Carballo, Isabel Guerreiro, Guillaume Andrey, Thi Hanh Nguyen Huynh, Virginie Marcet, Jozsef Zákány, Denis Duboule, Leonardo Beccari
Vertebrate Hox genes encode transcription factors operating during the development of multiple organs and structures. However, the evolutionary mechanism underlying this remarkable pleiotropy remains to be fully understood. Here, we show that Hoxd8 and Hoxd9, two genes of the HoxD complex, are transcribed during mammary bud (MB) development. However, unlike in other developmental contexts, their coexpression does not rely on the same regulatory mechanism. Hoxd8 is regulated by the combined activity of closely located sequences and the most distant telomeric gene desert...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27851751/environmental-predictors-of-diversity-in-recent-planktonic-foraminifera-as-recorded-in-marine-sediments
#5
Isabel S Fenton, Paul N Pearson, Tom Dunkley Jones, Andy Purvis
Global diversity patterns are thought to result from a combination of environmental and historical factors. This study tests the set of ecological and evolutionary hypotheses proposed to explain the global variation in present-day coretop diversity in the macroperforate planktonic foraminifera, a clade with an exceptional fossil record. Within this group, marine surface sediment assemblages are thought to represent an accurate, although centennial to millennial time-averaged, representation of recent diversity patterns...
2016: PloS One
https://www.readbyqxmd.com/read/27836984/recurrent-innovation-at-genes-required-for-telomere-integrity-in-drosophila
#6
Yuh Chwen G Lee, Courtney Leek, Mia T Levine
Telomeres are nucleoprotein complexes at the ends of linear chromosomes. These specialized structures ensure genome integrity and faithful chromosome inheritance. Recurrent addition of repetitive, telomere-specific DNA elements to chromosome ends combats end-attrition, while specialized telomere-associated proteins protect naked, double-stranded chromosome ends from promiscuous repair into end-to-end fusions. Although telomere length homeostasis and end-protection are ubiquitous across eukaryotes, there is sporadic but building evidence that the molecular machinery supporting these essential processes evolves rapidly...
November 11, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27834144/evolutionary-considerations-on-the-emerging-subculture-of-the-e-psychonauts-and-the-novel-psychoactive-substances-a-comeback-to-the-shamanism
#7
Laura Orsolini, Paul St John-Smith, Daniel McQueen, Duccio Papanti, John Corkery, Fabrizio Schifano
BACKGROUND: Evolutionary research on drug abuse has hitherto been restricted to proximate studies, considering aetiology, mechanism, and ontogeny. However, in order to explain the recent emergency of a new behavioral pattern (e.g. 'the e-psychonaut style') of novel psychoactive substances' (NPS) intake, a complementary evolutionary model may be needed. OBJECTIVE: A range of evolutionary interpretations on the 'psychonaut style' and the recent emergency of NPS was here considered...
November 11, 2016: Current Neuropharmacology
https://www.readbyqxmd.com/read/27830770/lineage-diversification-homo-and-heterologous-reassortment-and-recombination-shape-the-evolution-of-chicken-orthoreoviruses
#8
Szilvia L Farkas, Szilvia Marton, Eszter Dandár, Renáta Kugler, Bence Gál, Ferenc Jakab, Ádám Bálint, Sándor Kecskeméti, Krisztián Bányai
The near complete genome sequences of ten field avian orthoreovirus (ARV) strains collected from young chicken between 2002 and 2011 in Hungary have been determined in order to explore the genetic diversity and evolutionary mechanisms affecting ARVs in this region. Sequence analyses and phylogenetic calculations revealed similar geographic distribution and distinct evolution in case of eight studied strains that were closely related to the recently described Hungarian strain T1781. The remaining two strains showed the highest similarity with the US origin AVS-B...
November 10, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27794577/sex-reversal-in-reptiles-reproductive-oddity-or-powerful-driver-of-evolutionary-change
#9
Clare E Holleley, Stephen D Sarre, Denis O'Meally, Arthur Georges
Is sex a product of genes, the environment, or both? In this review, we describe the diversity of sex-determining mechanisms in reptiles, with a focus on systems that display gene-environment interactions. We summarise the field and laboratory-based evidence for the occurrence of environmental sex reversal in reptiles and ask whether this is a widespread evolutionary mechanism affecting the evolution of sex chromosomes and speciation in vertebrates. Sex determination systems exist across a continuum of genetic and environmental influences, blurring the lines between what was once considered a strict dichotomy between genetic sex determination and temperature-dependent sex determination...
October 29, 2016: Sexual Development: Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation
https://www.readbyqxmd.com/read/27793265/trichomoniasis-immunity-and-the-involvement-of-the-purinergic-signaling
#10
REVIEW
Camila Braz Menezes, Tiana Tasca
Innate and adaptive immunity play a significant role in trichomoniasis, the most common non-viral sexually transmitted disease worldwide. In the urogenital tract, innate immunity is accomplished by a defense physical barrier constituted by epithelial cells, mucus, and acidic pH. During infection, immune cells, antimicrobial peptides, cytokines, chemokines, and adaptive immunity evolve in the reproductive tract, and a proinflammatory response is generated to eliminate the invading extracellular pathogen Trichomonas vaginalis...
August 2016: Biomedical Journal
https://www.readbyqxmd.com/read/27775080/substitution-rate-and-natural-selection-in-parvovirus-b19
#11
Gorana G Stamenković, Valentina S Ćirković, Marina M Šiljić, Jelena V Blagojević, Aleksandra M Knežević, Ivana D Joksić, Maja P Stanojević
The aim of this study was to estimate substitution rate and imprints of natural selection on parvovirus B19 genotype 1. Studied datasets included 137 near complete coding B19 genomes (positions 665 to 4851) for phylogenetic and substitution rate analysis and 146 and 214 partial genomes for selection analyses in open reading frames ORF1 and ORF2, respectively, collected 1973-2012 and including 9 newly sequenced isolates from Serbia. Phylogenetic clustering assigned majority of studied isolates to G1A. Nucleotide substitution rate for total coding DNA was 1...
October 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27775042/male-food-defence-as-a-by-product-of-intersexual-cooperation-in-a-non-human-primate
#12
T Jean M Arseneau-Robar, Eliane Müller, Anouk L Taucher, Carel P van Schaik, Erik P Willems
Males in a number of group-living species fight in intergroup conflicts to defend access to food resources, a seemingly paradoxical behaviour, given that this resource does not usually limit male fitness directly. We investigated the mechanism(s) driving apparent male food defence in wild vervet monkeys (Chlorocebus aethiops pygerythrus) by testing the effect that female resource access, and female audience size and activity had on the response of focal males during simulated intergroup encounters. Males do not appear to defend food to increase the reproductive success of female group members because their response was not influenced by the presence of provisioning boxes that only females could access...
October 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27771735/the-orthologs-of-hla-dq-and-dp-genes-display-abundant-levels-of-variability-in-macaque-species
#13
Nel Otting, Marit K H van der Wiel, Nanine de Groot, Annemiek J M de Vos-Rouweler, Natasja G de Groot, Gaby G M Doxiadis, Roger W Wiseman, David H O'Connor, Ronald E Bontrop
The human major histocompatibility complex (MHC) region encodes three types of class II molecules designated HLA-DR, -DQ, and -DP. Both the HLA-DQ and -DP gene region comprise a duplicated tandem of A and B genes, whereas in macaques, only one set of genes is present per region. A substantial sequencing project on the DQ and DP genes in various macaque populations resulted in the detection of previously 304 unreported full-length alleles. Phylogenetic studies showed that humans and macaques share trans-species lineages for the DQA1 and DQB1 genes, whereas the DPA1 and DPB1 lineages in macaques appear to be species-specific...
October 22, 2016: Immunogenetics
https://www.readbyqxmd.com/read/27739447/a-paradoxical-evolutionary-mechanism-in-stochastically-switching-environments
#14
Kang Hao Cheong, Zong Xuan Tan, Neng-Gang Xie, Michael C Jones
Organisms with environmental sensors that guide survival are considered more likely to be favored by natural selection if they possess more accurate sensors. In this paper, we develop a theoretical model which shows that under certain conditions of environmental stochasticity, selection actually favors sensors of lower accuracy. An analogy between this counter-intuitive phenomenon and the well-known Parrondo's paradox is suggested.
October 14, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27726774/emerging-foodborne-and-agriculture-related-viruses
#15
David H Kingsley
Viruses rapidly evolve and can emerge in unpredictable ways. Transmission pathways by which foodborne viruses may enter human populations and evolutionary mechanisms by which viruses can become virulent are discussed in this chapter. A majority of viruses emerge from zoonotic animal reservoirs, often by adapting and infecting intermediate hosts, such as domestic animals and livestock. Viruses that are known foodborne threats include hepatitis E virus, tick-borne encephalitis virus, enteroviruses, adenovirus, and astroviruses, among others...
August 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/27721820/genome-wide-gene-genome-dosage-imbalance-regulates-gene-expressions-in-synthetic-brassica-napus-and-derivatives-ac-aac-cca-ccaa
#16
Chen Tan, Qi Pan, Cheng Cui, Yi Xiang, Xianhong Ge, Zaiyun Li
Gene/genome dosage balance is an essential evolutionary mechanism for organisms to ensure a normal function, but the underlying causes of dosage-imbalance regulation remain poorly understood. Herein, the serial Brassica hybrids/polyploids (AC, AAC, CCA, CCAA) with different copies of A and C subgenomes from the same two parents of Brassica rapa and Brassica oleracea were synthesized to investigate the effects of genome dosages on gene expressions and interactions by using RNA-Seq. The expression changes of A- and C-subgenome genes were consistent with dosage alterations...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27718282/into-the-andes-multiple-independent-colonizations-drive-montane-diversity-in-the-neotropical-clearwing-butterflies-godyridina
#17
Nicolas Chazot, Keith R Willmott, Fabien L Condamine, Donna Lisa De-Silva, André V L Freitas, Gerardo Lamas, Hélène Morlon, Carlos E Giraldo, Chris D Jiggins, Mathieu Joron, James Mallet, Sandra Uribe, Marianne Elias
Understanding why species richness peaks along the Andes is a fundamental question in the study of Neotropical biodiversity. Several biogeographic and diversification scenarios have been proposed in the literature, but there is confusion about the processes underlying each scenario, and assessing their relative contribution is not straightforward. Here, we propose to refine these scenarios into a framework which evaluates four evolutionary mechanisms: higher speciation rate in the Andes, lower extinction rates in the Andes, older colonization times and higher colonization rates of the Andes from adjacent areas...
November 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27696900/gene-flow-recombination-and-positive-selection-in-stenotrophomonas-maltophilia-mechanisms-underlying-the-diversity-of-the-widespread-opportunistic-pathogen
#18
Dong Yu, Zhiqiu Yin, Beiping Li, Yuan Jin, Hongguang Ren, Jing Zhou, Wei Zhou, Long Liang, Junjie Yue
Stenotrophomonas maltophilia is a global multidrug-resistant human opportunistic pathogen in clinical environments. Stenotrophomonas maltophilia is also ubiquitous in aqueous environments, soil, and plants. Various molecular typing methods have revealed that S. maltophilia exhibits high levels of phenotypic and genotypic diversity. However, information regarding the genomic diversity within S. maltophilia and the corresponding genetic mechanisms resulting in said diversity remain scarce. The genome sequences of 17 S...
August 6, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/27690225/ongoing-resolution-of-duplicate-gene-functions-shapes-the-diversification-of-a-metabolic-network
#19
Meihua Christina Kuang, Paul D Hutchins, Jason D Russell, Joshua J Coon, Chris Todd Hittinger
The evolutionary mechanisms leading to duplicate gene retention are well understood, but the long-term impacts of paralog differentiation on the regulation of metabolism remain underappreciated. Here we experimentally dissect the functions of two pairs of ancient paralogs of the GALactose sugar utilization network in two yeast species. We show that the Saccharomyces uvarum network is more active, even as over-induction is prevented by a second co-repressor that the model yeast Saccharomyces cerevisiae lacks...
September 30, 2016: ELife
https://www.readbyqxmd.com/read/27686787/evolution-and-phylogenetic-application-of-the-mc1r-gene-in-the-cobitoidea-teleostei-cypriniformes
#20
Qiong-Ying Tang, Li-Xia Shi, Fei Liu, Dan Yu, Huan-Zhang Liu
Fish of the superfamily Cobitoidea sensu stricto (namely loaches) exhibit extremely high diversity of color patterns, but so far little is known about their evolutionary mechanism. Melanocortin 1 receptor gene (MC1R) plays an important role during the synthesis of melanin and formation of animal body color patterns. In this study, we amplified and sequenced the partial MC1R gene for 44 loach individuals representing 31 species of four families. Phylogenetic analyses yielded a topology congruent with previous studies using multiple nuclear loci, showing that each of the four families was monophyletic with sister relationships of Botiidae+ (Cobitidae+(Balitoridae+Nemacheilidae))...
September 18, 2016: Dong Wu Xue Yan Jiu, Zoological Research
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