Browsing by Subject "adaptation"

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Ecological Opportunity In Adaptive Radiation Of Galapagos Endemic Land Snails
(2009-12) Parent, Christine E.; Crespi, Bernard J.; Parent, Christine E.
The classic evolutionary hypothesis of ecological opportunity proposes that both heterogeneity of resources and freedom from enemies promote phenotypic divergence as a response to increased niche availability. Although phenotypic divergence and speciation have often been inferred to be the primary consequences of the release from competition or predation that accompanies a shift to a new adaptive zone, increased phenotypic variation within species is expected to represent the first stage resulting from such a shift. Using measures of intraspecific morphological variation of 30 species of Galapagos endemic land snails in a phylogenetically controlled framework, we show that the number of local congeners and the number of local plant species are associated with lower and higher intraspecific phenotypic variation, respectively. In this clade, ecological opportunity thus explicitly links the role of competition from congeners and the heterogeneity of resources to the extent of intraspecific phenotypic divergence as adaptive radiation proceeds.
Identifying Structural Variation in Haploid Microbial Genomes from Short-Read Resequencing Data Using Breseq
(2014-11) Barrick, Jeffrey E.; Colburn, Geoffrey; Deatherage, Daniel E.; Traverse, Charles C.; Strand, Matthew D.; Borges, Jordan J.; Knoester, David B.; Reba, Aaron; Meyer, Austin G.; Barrick, Jeffrey E.; Colburn, Geoffrey; Deatherage, Daniel E.; Traverse, Charles C.; Strand, Matthew D.; Borges, Jordan J.; Reba, Aaron; Meyer, Austin G.
Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. Results: We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for similar to 25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation with modest read-depth coverage of the reference genome (>40-fold). Conclusions: Using breseq to predict structural variation should be useful for studies of microbial epidemiology, experimental evolution, synthetic biology, and genetics when a reference genome for a closely related strain is available. In these cases, breseq can discover mutations that may be responsible for important or unintended changes in genomes that might otherwise go undetected.
Interchangeable Punishments During Aversive Conditioning in Drosophila
(2013-11) Robinson, Brooks G.; Khurana, Sukant; Nguyen, Andrew; Chuang, Tammy; Young, Melvin; Yu, Jun; Hooten, Jeff; Atkinson, Nigel S.; Robinson, Brooks G.; Khurana, Sukant; Nguyen, Andrew; Chuang, Tammy; Young, Melvin; Yu, Jun; Hooten, Jeff; Atkinson, Nigel S.
Using Drosophila melanogaster larvae we asked whether distinct aversive stimuli have a common neural representation during associative learning. We tested the interchangeability of heat shock and electroshock punishments when used within a single olfactory associative conditioning experiment. We find that compared to animals trained with the repetitive use of a single punishment, the use of two alternating punishments results in similar associative learning. Additionally, the two punishments are shown to have different sensory origins. Therefore, while punishments are processed differently by the larvae of Drosophila melanogaster, the value of the stimulus is preserved.
Letter to Thurlow C. Nelson from H.B. Stenzel on 1943-02-08
(1943-02-08) Stenzel, H.B.
Me and Earl and the Adapted Girl: Learning to Write a Young Adult Adaptation
(2018) Zhang, Michelle
Since the late 2000s, the movie industry has experienced a boom in Young Adult (YA) book-tomovie adaptations, from the wildly popular Twilight series to romantic drama The Fault In Our Stars. Having been an avid YA literature reader throughout my teenaged years, I found myself consistently disappointed with the quality of these adaptations in the way they portrayed their source material, often feeling that the cinematic qualities of the adaptation weren’t on par with the literary. This frustration prompted me to wonder: How would I go about writing a YA adaptation? With this question in mind, I went on a personal discovery of what makes up my favorite literary genre and how I would adapt it into a film. To understand the contextual and analytical background of my question, I researched the state of the YA literature and movie industries, as well as looked at film theory on adaptations. I then analyzed a case of what I consider to be a good YA adaptation — Me and Earl and the Dying Girl, a 2012 novel by Jesse Andrews and a 2015 movie directed by Alfonso Gomez-Rejon — to understand what qualities in particular I find important to adaptation. In my final section, I put theory into practice by writing my own adapted screenplay based on Please Ignore Vera Dietz, a 2010 novel by A.S. King, going on to discuss the problems I faced, choices I made, and revelations I discovered in the writing process.
Paradise Staged: Milton'S Epic As Dramatic Text
(2019-05-01) Hanna, Austin; Rumrich, John
Paradise Lost is an epic poem, yet elements of Milton’s work are undeniably theatrical and are indebted more to the dramatic genre than the epic. Milton, in fact, first conceived the poem as a drama—tentatively titled Adam Unparadised—and at least one section of Satan’s Book IV soliloquy was evidently written with the stage in mind. These original theatrical designs are crucial to the process of (re-)contextualizing Paradise Lost, prompting us to look backward to the influence of Milton’s inherited dramatic tradition as well as forward to modern theatrical adaptation. Milton draws from Shakespearean drama in particular, oscillating generically from tragedy to history to romance and channeling some of Shakespeare’s most compelling villains in his famous portrayal of Satan. Last year, the Stratford Festival staged a new adaptation of Paradise Lost by Erin Shields to much acclaim; the play puts Milton in conversation with present-day political and social issues as well as simply demonstrating the dramatic potential of Milton’s source material. The implications of a dramatic consideration of Paradise Lost touch both stage and classroom. Milton deserves a place in Shakespearean and early modern theater companies’ repertoires. Correspondingly, performance and play should be employed as pedagogical tools, expanding the successful strategy of teaching Shakespeare’s plays through performance to less explicitly dramatic works. Paradise Lost gains much in the transition from page to stage, and the conceits of the dramatic form complement and reinforce the conflicts and ideas at the heart of Milton’s epic.
Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host
(PLoS ONE, 2011-01) Jerome, John P.; Bell, Julia A.; Plovanich-Jones, Anne E.; Barrick, Jeffrey E.; Brown, C. Titus; Mansfield, Linda S.
The genome of the food-borne pathogen Campylobacter jejuni contains multiple highly mutable sites, or contingency loci. It has been suggested that standing variation at these loci is a mechanism for rapid adaptation to a novel environment, but this phenomenon has not been shown experimentally. In previous work we showed that the virulence of C. jejuni NCTC11168 increased after serial passage through a C57BL/6 IL-10-/- mouse model of campylobacteriosis. Here we sought to determine the genetic basis of this adaptation during passage. Re-sequencing of the 1.64Mb genome to 200-500X coverage allowed us to define variation in 23 contingency loci to an unprecedented depth both before and after in vivo adaptation. Mutations in the mouse-adapted C. jejuni were largely restricted to the homopolymeric tracts of thirteen contingency loci. These changes cause significant alterations in open reading frames of genes in surface structure biosynthesis loci and in genes with only putative functions. Several loci with open reading frame changes also had altered transcript abundance. The increase in specific phases of contingency loci during in vivo passage of C. jejuni, coupled with the observed virulence increase and the lack of other types of genetic changes, is the first experimental evidence that these variable regions play a significant role in C. jejuni adaptation and virulence in a novel host.