Browsing FAS Scholarly Articles by Keyword "Evolutionary Biology"

Now showing items 1-20 of 50

    • The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum 

      Harcombe, William R.; Delaney, Nigel F.; Leiby, Nicholas; Klitgord, Niels; Marx, Christopher J. (Public Library of Science, 2013)
      The most powerful genome-scale framework to model metabolism, flux balance analysis (FBA), is an evolutionary optimality model. It hypothesizes selection upon a proposed optimality criterion in order to predict the set of ...

    • Abnormal Dosage of Ultraconserved Elements Is Highly Disfavored in Healthy Cells but Not Cancer Cells 

      McCole, Ruth B.; Fonseka, Chamith Y.; Koren, Amnon; Wu, C.-ting (Public Library of Science, 2014)
      Ultraconserved elements (UCEs) are strongly depleted from segmental duplications and copy number variations (CNVs) in the human genome, suggesting that deletion or duplication of a UCE can be deleterious to the mammalian ...

    • Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance 

      Ogbunugafor, C. Brandon; Wylie, C. Scott; Diakite, Ibrahim; Weinreich, Daniel M.; Hartl, Daniel L. (Public Library of Science, 2016)
      The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to ...

    • An Anatomical Description of a Miniaturized Acorn Worm (Hemichordata, Enteropneusta) with Asexual Reproduction by Paratomy 

      Worsaae, Katrine; Sterrer, Wolfgang; Kaul-Strehlow, Sabrina; Hay-Schmidt, Anders; Giribet, Gonzalo (Public Library of Science, 2012)
      The interstitial environment of marine sandy bottoms is a nutrient-rich, sheltered habitat whilst at the same time also often a turbulent, space-limited, and ecologically challenging environment dominated by meiofauna. The ...

    • Characterizing the Infection-Induced Transcriptome of Nasonia vitripennis Reveals a Preponderance of Taxonomically-Restricted Immune Genes 

      Sackton, Timothy B.; Werren, John H.; Clark, Andrew G. (Public Library of Science, 2013)
      The innate immune system in insects consists of a conserved core signaling network and rapidly diversifying effector and recognition components, often containing a high proportion of taxonomically-restricted genes. In the ...

    • A Comprehensive Reference Transcriptome Resource for the Common House Spider Parasteatoda tepidariorum 

      Posnien, Nico; Zeng, Victor; Schwager, Evelyn E.; Pechmann, Matthias; Hilbrant, Maarten; Keefe, Joseph D.; Damen, Wim G. M.; Prpic, Nikola-Michael; McGregor, Alistair P.; Extavour, Cassandra G. (Public Library of Science, 2014)
      Parasteatoda tepidariorum is an increasingly popular model for the study of spider development and the evolution of development more broadly. However, fully understanding the regulation and evolution of P. tepidariorum ...

    • Contrasting Patterns in Mammal–Bacteria Coevolution: Bartonella and Leptospira in Bats and Rodents 

      Lei, Bonnie R.; Olival, Kevin J. (Public Library of Science, 2014)
      Background: Emerging bacterial zoonoses in bats and rodents remain relatively understudied. We conduct the first comparative host–pathogen coevolutionary analyses of bacterial pathogens in these hosts, using Bartonella ...

    • Cooperation and the Fate of Microbial Societies 

      Allen, Benjamin Isaac; Nowak, Martin A. (Public Library of Science, 2013)
      Microorganisms have been cooperating with each other for billions of years: by sharing resources, communicating with each other, and joining together to form biofilms and other large structures. These cooperative behaviors ...

    • Dietary Variation and Evolution of Gene Copy Number among Dog Breeds 

      Reiter, Taylor; Jagoda, Evelyn; Capellini, Terence D. (Public Library of Science, 2016)
      Prolonged human interactions and artificial selection have influenced the genotypic and phenotypic diversity among dog breeds. Because humans and dogs occupy diverse habitats, ecological contexts have likely contributed ...

    • Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus 

      Tully, Damien C.; Ogilvie, Colin B.; Batorsky, Rebecca E.; Bean, David J.; Power, Karen A.; Ghebremichael, Musie; Bedard, Hunter E.; Gladden, Adrianne D.; Seese, Aaron M.; Amero, Molly A.; Lane, Kimberly; McGrath, Graham; Bazner, Suzane B.; Tinsley, Jake; Lennon, Niall J.; Henn, Matthew R.; Brumme, Zabrina L.; Norris, Philip J.; Rosenberg, Eric S.; Mayer, Kenneth H.; Jessen, Heiko; Kosakovsky Pond, Sergei L.; Walker, Bruce D.; Altfeld, Marcus; Carlson, Jonathan M.; Allen, Todd M. (Public Library of Science, 2016)
      Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the ...

    • Differential Haemoparasite Intensity between Black Sparrowhawk (Accipiter melanoleucus) Morphs Suggests an Adaptive Function for Polymorphism 

      Lei, Bonnie; Amar, Arjun; Koeslag, Ann; Gous, Tertius A.; Tate, Gareth J. (Public Library of Science, 2013)
      Recent research suggests that genes coding for melanin based colouration may have pleiotropic properties, in particular conveying raised immune function. Thus adaptive function of polymorphism may be associated with parasite ...

    • The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth 

      Parr, Cynthia S.; Wilson, Nathan; Leary, Patrick; Schulz, Katja S.; Lans, Kristen; Walley, Lisa; Hammock, Jennifer A.; Goddard, Anthony; Rice, Jeremy; Studer, Marie; Holmes, Jeffrey T. G.; Corrigan, Jr., Robert J. (Pensoft Publishers, 2014)
      Abstract The Encyclopedia of Life (EOL, http://eol.org) aims to provide unprecedented global access to a broad range of information about life on Earth. It currently contains 3.5 million distinct pages for taxa and provides ...

    • Evidence for a Trade-Off Strategy in Stone Oak (Lithocarpus) Seeds between Physical and Chemical Defense Highlights Fiber as an Important Antifeedant 

      Chen, Xi; Cannon, Charles H.; Conklin-Brittain, Nancy Lou (Public Library of Science, 2012)
      Trees in the beech or oak family (Fagaceae) have a mutualistic relationship with scatter-hoarding rodents. Rodents obtain nutrients and energy by consuming seeds, while providing seed dispersal for the tree by allowing ...

    • Evolution after Introduction of a Novel Metabolic Pathway Consistently Leads to Restoration of Wild-Type Physiology 

      Carroll, Sean; Marx, Christopher J (Public Library of Science, 2013)
      Organisms cope with physiological stressors through acclimatizing mechanisms in the short-term and adaptive mechanisms over evolutionary timescales. During adaptation to an environmental or genetic perturbation, beneficial ...

    • The Evolution of Cell-to-Cell Communication in a Sporulating Bacterium 

      van Gestel, Jordi; Nowak, Martin A.; Tarnita, Corina (Public Library of Science, 2012)
      Traditionally microorganisms were considered to be autonomous organisms that could be studied in isolation. However, over the last decades cell-to-cell communication has been found to be ubiquitous. By secreting molecular ...

    • The Evolution of Quorum Sensing as a Mechanism to Infer Kinship 

      Schluter, Jonas; Schoech, Armin P.; Foster, Kevin R.; Mitri, Sara (Public Library of Science, 2016)
      Bacteria regulate many phenotypes via quorum sensing systems. Quorum sensing is typically thought to evolve because the regulated cooperative phenotypes are only beneficial at certain cell densities. However, quorum sensing ...

    • Female Behaviour Drives Expression and Evolution of Gustatory Receptors in Butterflies 

      Briscoe, Adriana D.; Macias-Muñoz, Aide; Kozak, Krzysztof M.; Walters, James R.; Yuan, Furong; Jamie, Gabriel A.; Martin, Simon H.; Dasmahapatra, Kanchon K.; Ferguson, Laura C.; Mallet, James; Jacquin-Joly, Emmanuelle; Jiggins, Chris D. (Public Library of Science, 2013)
      Secondary plant compounds are strong deterrents of insect oviposition and feeding, but may also be attractants for specialist herbivores. These insect-plant interactions are mediated by insect gustatory receptors (Grs) and ...

    • The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima 

      Chipman, Ariel D.; Ferrier, David E. K.; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S. T.; Schröder, Reinhard; Torres-Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C.; Alonso, Claudio R.; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C. J.; Blankenburg, Kerstin P.; Brites, Daniela; Capella-Gutiérrez, Salvador; Coyle, Marcus; Dearden, Peter K.; Du Pasquier, Louis; Duncan, Elizabeth J.; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D.; Extavour, Cassandra G.; Francisco, Liezl; Gabaldón, Toni; Gillis, William J.; Goodwin-Horn, Elizabeth A.; Green, Jack E.; Griffiths-Jones, Sam; Grimmelikhuijzen, Cornelis J. P.; Gubbala, Sai; Guigó, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H. L.; Hunn, Julia P.; Hunnekuhl, Vera S.; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N.; Jiggins, Francis M.; Jones, Tamsin E.; Kaiser, Tobias S.; Kalra, Divya; Kenny, Nathan J.; Korchina, Viktoriya; Kovar, Christie L.; Kraus, F. Bernhard; Lapraz, François; Lee, Sandra L.; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Robert; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N.; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J.; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling-Ling; Putman, Nicholas H.; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C.; Robertson, Helen E.; Robertson, Hugh M.; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sánchez-Gracia, Alejandro; Scherer, Steven E.; Schurko, Andrew M.; Siggens, Kenneth W.; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J.; Tessmar-Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M.; Willis, Judith H.; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M.; Worley, Kim C.; Gibbs, Richard A.; Akam, Michael; Richards, Stephen (Public Library of Science, 2014)
      Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda ...

    • Fossil Mice and Rats Show Isotopic Evidence of Niche Partitioning and Change in Dental Ecomorphology Related to Dietary Shift in Late Miocene of Pakistan 

      Kimura, Yuri; Jacobs, Louis L.; Cerling, Thure E.; Uno, Kevin T.; Ferguson, Kurt M.; Flynn, Lawrence J.; Patnaik, Rajeev (Public Library of Science, 2013)
      Stable carbon isotope analysis in tooth enamel is a well-established approach to infer C3 and C4 dietary composition in fossil mammals. The bulk of past work has been conducted on large herbivorous mammals. One important ...

    • FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations 

      Chubiz, Lon M; Lee, Ming-Chun; Delaney, Nigel Francis; Marx, Christopher J (Public Library of Science, 2012)
      Understanding evolutionary dynamics within microbial populations requires the ability to accurately follow allele frequencies through time. Here we present a rapid, cost-effective method (FREQ-Seq) that leverages Illumina ...