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https://www.readbyqxmd.com/read/27903777/repeated-evolution-of-viviparity-in-phrynosomatid-lizards-constrained-interspecific-diversification-in-some-life-history-traits
#1
J Jaime Zúñiga-Vega, Jesualdo A Fuentes-G, Alison G Ossip-Drahos, Emília P Martins
In vertebrates, viviparity has evolved independently multiple times, apparently increasing morphological diversification and speciation rates as a consequence. We tested whether the evolution of viviparity has also increased diversification of life-history traits by estimating evolutionary rates of lizards from the North American family Phrynosomatidae. Using modern phylogenetic comparative methods, we compared these rates between oviparous and viviparous species, and found no support for this hypothesis. Instead, we found higher evolutionary rates for oviparous species in some life-history traits...
November 2016: Biology Letters
https://www.readbyqxmd.com/read/27886661/bacterial-diversity-shift-determined-by-different-diets-in-the-gut-of-the-spotted-wing-fly-drosophila-suzukii-is-primarily-reflected-on-acetic-acid-bacteria
#2
Violetta Vacchini, Elena Gonella, Elena Crotti, Erica M Prosdocimi, Fabio Mazzetto, Bessem Chouaia, Matteo Callegari, Francesca Mapelli, Mauro Mandrioli, Alberto Alma, Daniele Daffonchio
The pivotal role of diet in shaping gut microbiota has been evaluated in different animal models, including insects. Drosophila flies harbour an inconstant microbiota among which acetic acid bacteria (AAB) are important components. Here, we investigated the bacterial and AAB components of the invasive pest Drosophila suzukii microbiota, by studying the same insect population separately grown on fruit-based or non-fruit artificial diet. AAB were highly prevalent in the gut under both diets (90 and 92% infection rates with fruits and artificial diet, respectively)...
November 25, 2016: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/27886660/evaluation-of-the-safety-and-adjuvant-effect-of-a-detoxified-listeriolysin-o-mutant-on-the-humoral-response-to-dengue-virus-antigens
#3
K G Hernández-Flores, A L Calderón-Garcidueñas, G Mellado-Sánchez, R Ruiz-Ramos, L A Sánchez-Vargas, P Thomas-Dupont, I Y Izaguirre-Hernández, J Téllez-Sosa, J Martínez-Barnetche, L Wood, Y Paterson, L Cedillo-Barrón, O López-Franco, H Vivanco-Cid
Listeriolysin O (LLO) has been proposed as a potential carrier or adjuvant molecule in the vaccination field. However, the cytotoxic and pro-apoptotic effects of LLO are the major limitations for this purpose. Here, we have performed a preclinical safety evaluation and characterized a new potential adjuvant application for a non-cytolytic LLO mutant (dtLLO) to enhance and modulate the immune response against the envelope (E) protein from Dengue virus. In addition, we have studied the adjuvant effects of dtLLO on human immune cells and the role of membrane cholesterol for the binding and the pro-inflammatory property of the toxoid...
November 25, 2016: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/27873369/the-genetic-architecture-of-novel-trophic-specialists-higher-effect-sizes-are-associated-with-exceptional-oral-jaw-diversification-in-a-pupfish-adaptive-radiation
#4
Christopher H Martin, Priscilla A Erickson, Craig T Miller
The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining the origins of ecological novelty: a sympatric radiation of pupfishes endemic to San Salvador Island, Bahamas containing a large-jawed scale-eater and a short-jawed molluscivore with a skeletal nasal protrusion...
November 22, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27871818/oxidatively-generated-base-modifications-in-dna-not-only-carcinogenic-risk-factor-but-also-regulatory-mark
#5
Marco Seifermann, Bernd Epe
The generation of DNA modifications in cells is in most cases accidental and associated with detrimental consequences such as increased mutation rates and an elevated risk of malignant transformation. Accordingly, repair enzymes involved in the removal of the modifications have primarily a protective function. Among the well-established exceptions of this rule are 5-methylcytosine and uracil, which are generated in DNA enzymatically under controlled conditions and fulfill important regulatory functions in DNA as epigenetic marks and in antibody diversification, respectively...
November 18, 2016: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/27864882/diversification-of-the-kinetic-properties-of-yeast-nadp-glutamate-dehydrogenase-isozymes-proceeds-independently-of-their-evolutionary-origin
#6
Carlos Campero-Basaldua, Héctor Quezada, Lina Riego-Ruíz, Dariel Márquez, Erendira Rojas, James González, Mohammed El-Hafidi, Alicia González
In the yeast Saccharomyces cerevisiae, the ScGDH1 and ScGDH3 encoded glutamate dehydrogenases (NADP-GDHs) catalyze the synthesis of glutamate from ammonium and α-ketoglutarate (α-KG). Previous kinetic characterization showed that these enzymes displayed different allosteric properties and respectively high or low rate of α-KG utilization. Accordingly, the coordinated action of ScGdh1 and ScGdh3, regulated balanced α-KG utilization for glutamate biosynthesis under either fermentative or respiratory conditions, safeguarding energy provision...
November 19, 2016: MicrobiologyOpen
https://www.readbyqxmd.com/read/27862578/rapid-postglacial-diversification-and-long-term-stasis-within-the-songbird-genus-junco-phylogeographic-and-phylogenomic-evidence
#7
Guillermo Friis, Pau Aleixandre, Ricardo Rodríguez-Estrella, Adolfo G Navarro-Sigüenza, Borja Milá
Natural systems composed of closely-related taxa that vary in the degree of phenotypic divergence and geographic isolation, provide an opportunity to investigate the rate of phenotypic diversification and the relative roles of selection and drift in driving lineage formation. The genus Junco (Aves: Emberizidae) of North America includes parapatric northern forms that are markedly divergent in plumage pattern and color, in contrast to geographically isolated southern populations in remote areas that show moderate phenotypic divergence...
November 14, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27834665/genetic-bases-of-fungal-white-rot-wood-decay-predicted-by-phylogenomic-analysis-of-correlated-gene-phenotype-evolution
#8
László G Nagy, Robert Riley, Philip J Bergmann, Krisztina Krizsán, Francis M Martin, Igor V Grigoriev, Dan Cullen, David S Hibbett
Fungal decomposition of plant cell walls (PCW) is a complex process that has diverse industrial applications and huge impacts on the carbon cycle. White rot (WR) is a powerful mode of PCW decay in which lignin and carbohydrates are both degraded. Mechanistic studies of decay coupled with comparative genomic analyses have provided clues to the enzymatic components of WR systems and their evolutionary origins, but the complete suite of genes necessary for WR remains undetermined. Here, we use phylogenomic comparative methods, which we validate through simulations, to identify shifts in gene family diversification rates that are correlated with evolution of WR, using data from 62 fungal genomes...
November 10, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27834200/bats-primates-and-the-evolutionary-origins-and-diversification-of-mammalian-gammaherpesviruses
#9
Marina Escalera-Zamudio, Edith Rojas-Anaya, Sergios-Orestis Kolokotronis, Blanca Taboada, Elizabeth Loza-Rubio, Maria L Méndez-Ojeda, Carlos F Arias, Nikolaus Osterrieder, Alex D Greenwood
: Gammaherpesviruses (γHVs) are generally considered host specific and to have codiverged with their hosts over millions of years. This tenet is challenged here by broad-scale phylogenetic analysis of two viral genes using the largest sample of mammalian γHVs to date, integrating for the first time bat γHV sequences available from public repositories and newly generated viral sequences from two vampire bat species (Desmodus rotundus and Diphylla ecaudata). Bat and primate viruses frequently represented deep branches within the supported phylogenies and clustered among viruses from distantly related mammalian taxa...
November 8, 2016: MBio
https://www.readbyqxmd.com/read/27829352/short-tandem-repeats-segmental-duplications-gene-deletion-and-genomic-instability-in-a-rapidly-diversified-immune-gene-family
#10
Matan Oren, Megan A Barela Hudgell, Brian D'Allura, Jacob Agronin, Alexandra Gross, Daniele Podini, L Courtney Smith
BACKGROUND: Genomic regions with repetitive sequences are considered unstable and prone to swift DNA diversification processes. A highly diverse immune gene family of the sea urchin (Strongylocentrotus purpuratus), called Sp185/333, is composed of clustered genes with similar sequence as well as several types of repeats ranging in size from short tandem repeats (STRs) to large segmental duplications. This repetitive structure may have been the basis for the incorrect assembly of this gene family in the sea urchin genome sequence...
November 9, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27825385/neurogenomics-and-the-role-of-a-large-mutational-target-on-rapid-behavioral-change
#11
Craig E Stanley, Rob J Kulathinal
BACKGROUND: Behavior, while complex and dynamic, is among the most diverse, derived, and rapidly evolving traits in animals. The highly labile nature of heritable behavioral change is observed in such evolutionary phenomena as the emergence of converged behaviors in domesticated animals, the rapid evolution of preferences, and the routine development of ethological isolation between diverging populations and species. In fact, it is believed that nervous system development and its potential to evolve a seemingly infinite array of behavioral innovations played a major role in the successful diversification of metazoans, including our own human lineage...
November 8, 2016: Biology Direct
https://www.readbyqxmd.com/read/27822534/long-term-evolution-of-burkholderia-multivorans-during-a-chronic-cystic-fibrosis-infection-reveals-shifting-forces-of-selection
#12
Inês N Silva, Pedro M Santos, Mário R Santos, James E A Zlosnik, David P Speert, Sean W Buskirk, Eric L Bruger, Christopher M Waters, Vaughn S Cooper, Leonilde M Moreira
Burkholderia multivorans is an opportunistic pathogen capable of causing severe disease in patients with cystic fibrosis (CF). Patients may be chronically infected for years, during which the bacterial population evolves in response to unknown forces. Here we analyze the genomic and functional evolution of a B. multivorans infection that was sequentially sampled from a CF patient over 20 years. The population diversified into at least four primary, coexisting clades with distinct evolutionary dynamics. The average substitution rate was only 2...
May 2016: MSystems
https://www.readbyqxmd.com/read/27821704/speciation-with-gene-flow-in-north-american-myotis-bats
#13
Ariadna E Morales, Nathan D Jackson, Tanya A Dewey, Brian C O'Meara, Bryan C Carstens
Growing evidence supports the idea that species can diverge in the presence of gene flow. However, most methods of phylogeny estimation do not consider this process, despite the fact that ignoring gene flow is known to bias phylogenetic inference. Furthermore, studies that do consider divergence-with-gene-flow typically do so by estimating rates of gene flow using a isolation-with-migration model (IM), rather than evaluating scenarios of gene flow (such as divergence-with-gene flow or secondary contact) that represent very different types of diversification...
November 7, 2016: Systematic Biology
https://www.readbyqxmd.com/read/27821703/do-macrophylogenies-yield-stable-macroevolutionary-inferences-an-example-from-squamate-reptiles
#14
Pascal O Title, Daniel L Rabosky
Advances in the generation, retrieval and analysis of phylogenetic data have enabled researchers to create phylogenies that contain many thousands of taxa. These "macrophylogenies" - large trees that typically derive from megaphylogeny, supermatrix, or supertree approaches - provide researchers with an unprecedented ability to conduct evolutionary analyses across broad phylogenetic scales. Many studies have now used these phylogenies to explore the dynamics of speciation, extinction, and phenotypic evolution across large swaths of the tree of life...
November 7, 2016: Systematic Biology
https://www.readbyqxmd.com/read/27821148/understanding-pneumococcal-serotype-1-biology-through-population-genomic-analysis
#15
Chrispin Chaguza, Jennifer E Cornick, Simon R Harris, Cheryl P Andam, Laura Bricio-Moreno, Marie Yang, Feyruz Yalcin, Sani Ousmane, Shanil Govindpersad, Madikay Senghore, Chinelo Ebruke, Mignon Du Plessis, Anmol M Kiran, Gerd Pluschke, Betuel Sigauque, Lesley McGee, Keith P Klugman, Paul Turner, Jukka Corander, Julian Parkhill, Jean-Marc Collard, Martin Antonio, Anne von Gottberg, Robert S Heyderman, Neil French, Aras Kadioglu, William P Hanage, Dean B Everett, Stephen D Bentley
BACKGROUND: Pneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype 1 pneumococci particularly the endemic ST217 clone, causes majority of the pneumococcal disease burden. To understand the evolution of the virulent ST217 clone, we analysed ST217 whole genomes from isolates sampled from African and Asian countries. METHODS: We analysed 226 whole genome sequences from the ST217 lineage sampled from 9 African and 4 Asian countries...
November 8, 2016: BMC Infectious Diseases
https://www.readbyqxmd.com/read/27810169/conservatism-and-variability-of-gene-expression-profiles-among-homeologous-transcription-factors-in-xenopus-laevis
#16
Minoru Watanabe, Yuuri Yasuoka, Shuuji Mawaribuchi, Aya Kuretani, Michihiko Ito, Mariko Kondo, Haruki Ochi, Hajime Ogino, Akimasa Fukui, Masanori Taira, Tsutomu Kinoshita
Xenopus laevis has an allotetraploid genome of 3.1Gb, in contrast to the diploid genome of a closely related species, Xenopus tropicalis. Here, we identified 412 genes (189 homeolog pairs, one homeologous gene cluster pair, and 28 singletons) encoding transcription factors (TFs) in the X. laevis genome by comparing them with their orthologs from X. tropicalis. Those genes include the homeobox gene family (Mix/Bix, Lhx, Nkx, Paired, POU, and Vent), Sox, Fox, Pax, Dmrt, Hes, GATA, T-box, and some clock genes...
October 31, 2016: Developmental Biology
https://www.readbyqxmd.com/read/27807262/non-reef-environments-impact-the-diversification-of-extant-jacks-remoras-and-allies-carangoidei-percomorpha
#17
Bruno Frédérich, Giuseppe Marramà, Giorgio Carnevale, Francesco Santini
Various factors may impact the processes of diversification of a clade. In the marine realm, it has been shown that coral reef environments have promoted diversification in various fish groups. With the exception of requiem sharks, all the groups showing a higher level of diversity in reefs than in non-reef habitats have diets based predominantly on plankton, algae or benthic invertebrates. Here we explore the pattern of diversification of carangoid fishes, a clade that includes numerous piscivorous species (e...
November 16, 2016: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/27804966/a-comparative-study-on-karyotypic-diversification-rate-in-mammals
#18
P A Martinez, U P Jacobina, R V Fernandes, C Brito, C Penone, T F Amado, C R Fonseca, C J Bidau
Chromosomal rearrangements have a relevant role in organismic evolution. However, little is known about the mechanisms that lead different phylogenetic clades to have different chromosomal rearrangement rates. Here, we investigate the causes behind the wide karyotypic diversity exhibited by mammals. In particular, we analyzed the role of metabolic, reproductive, biogeographic and genomic characteristics on the rates of macro- and microstructural karyotypic diversification (rKD) using comparative phylogenetic methods...
November 2, 2016: Heredity
https://www.readbyqxmd.com/read/27801910/trade-offs-between-microbiome-diversity-and-productivity-in-a-stratified-microbial-mat
#19
Hans C Bernstein, Colin Brislawn, Ryan S Renslow, Karl Dana, Beau Morton, Stephen R Lindemann, Hyun-Seob Song, Erhan Atci, Haluk Beyenal, James K Fredrickson, Janet K Jansson, James J Moran
Productivity is a major determinant of ecosystem diversity. Microbial ecosystems are the most diverse on the planet yet very few relationships between diversity and productivity have been reported as compared with macro-ecological studies. Here we evaluated the spatial relationships of productivity and microbiome diversity in a laboratory-cultivated photosynthetic mat. The goal was to determine how spatial diversification of microorganisms drives localized carbon and energy acquisition rates. We measured sub-millimeter depth profiles of net primary productivity and gross oxygenic photosynthesis in the context of the localized microenvironment and community structure, and observed negative correlations between species richness and productivity within the energy-replete, photic zone...
November 1, 2016: ISME Journal
https://www.readbyqxmd.com/read/27799532/intraspecific-genetic-variation-in-hosts-affects-regulation-of-obligate-heritable-symbionts
#20
Rebecca A Chong, Nancy A Moran
Symbiotic relationships promote biological diversification by unlocking new ecological niches. Over evolutionary time, hosts and symbionts often enter intimate and permanent relationships, which must be maintained and regulated for both lineages to persist. Many insect species harbor obligate, heritable symbiotic bacteria that provision essential nutrients and enable hosts to exploit niches that would otherwise be unavailable. Hosts must regulate symbiont population sizes, but optimal regulation may be affected by the need to respond to the ongoing evolution of symbionts, which experience high levels of genetic drift and potential selection for selfish traits...
October 31, 2016: Proceedings of the National Academy of Sciences of the United States of America
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