Winter Quarter 2017
Lab meetings were Fridays from 9:30-11:00 in KIN 502
January 6: Katie
- Please take a moment to skim Active learning increases student performance in science, engineering, and mathematics . We are not going to discuss the paper in detail but I would like to use it as a jumping off point to discuss: the nature of science and being a scientist, biology education, retention in STEM, etc...
January 13: Hannah
January 20: Hannah
- Research Update
January 27: Peter
February 3: Sonia - paper for PRESS
February 10: BEACON Proposal Party
- Brian: N-Step Evolutionary Programs and Addiction to Niche Construction
- Hannah: Plasmid and host coevolution encourages the emergence of multi-drug resistance
- Peter: Pleiotropic effects of compensatory evolution in drug-resistant Escherichia coli
February 17: Katrina
February 24: Peter
- Feedback on fellowship proposal
March 3: Katrina
- Emulsion update
March 10: Carrie and Sonia
- Exit presentation on colicin stuff!
March 17: Peter
- Research Update
Fall Quarter 2016
Lab meetings are Fridays from 9:30-11:00 in KIN 502
September 30: Quarterly lab update
- Add a paper or two to the paper queue
- Lab duties updates
- EH&S survey
October 7: Research Update - Carrie
- Note: We will meet in PAA A042C instead of our usual room.
October 14: Paper Queue
- Hannah and Sylvie: Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities
October 21: Research Update - Mitch
October 28: Paper Queue
- Luis: Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria-phage system
November 4: Research Update - Brian
November 11: Canceled for Veterans Day
November 18: Paper Queue
- Brian and Peter: A competitive trade-off limits the selective advantage of increased antibiotic production
December 2: Research Update - Sonia
December 9: Canceled
|Paper||Total Votes||Num Votes|
|Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities||3.80||5|
|Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria-phage system||3.40||5|
|A competitive trade-off limits the selective advantage of increased antibiotic production||2.90||6|
|A Quick Introduction to Version Control with Git and GitHub||2.70||4|
|Evolution of parasitism and mutualism between filamentous phage M13 and Escherichia coli||1.30||4|
|Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations||1.30||3|
|Spatiotemporal microbial evolution on antibiotic landscapes||1.00||4|
|How Good Are Statistical Models at Approximating Complex Fitness Landscapes?||0.95||3|
|Evolution by flight and fight: diverse mechanisms of adaptation by actively motile microbes||0.85||3|
|Forecasting Epidemiological and Evolutionary Dynamics of Infectious Diseases||0.70||3|
|Biological invasions and host–parasite coevolution: different coevolutionary trajectories along separate parasite invasion fronts||0.50||1|
|The Ecology and Evolution of Microbial Competition||0.40||1|
|Laboratory Evolution of Microbial Interactions in Bacterial Biofilms||0.20||1|
|Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast||0.00||0|
|The fitness landscape of a tRNA gene||0.00||0|
|Rapid and widespread de novo evolution of kin discrimination||0.00||0|
Summer Quarter 2016
Lab meetings are Fridays from 10:00-11:30 in KIN 502
June 24: Lab meeting organization
- Beforehand: Add one or two papers to the paper list
- Are there any dates besides August 12th when we should not meet?
- 90-second updates
July 1: Paper
July 8: Research Updates
- Katrina: Host-Phage Interactions and the Evolution of Novel Unicorn Horns (or TBA)
July 15: Paper
- Hannah and Peter: "Rapid evolution of thermotolerance in the water flea Daphnia"
July 22: Research Updates
- Hannah: Plasmid addiction and all that Jazz
July 29: Paper
- Brian and Luis: "Frequency of antibiotic application drives rapid evolutionary adaptation of Escherichia coli persistence"
- Your assignment: submit 2-3 questions by Thursday at 8:47 pm here. They can be about the paper’s methods, its results, or an idea for extending this work in any system.
August 5: Research Updates
- Peter: deep mutational scanning and such
August 12: Canceled for BEACON Congress
August 26: Paper
- Ben: "Environmental changes bridge evolutionary valleys"
- Note: we will be meeting in PAA 049
September 2: Paper
- Luis: "Co-evolutionary dynamics between public good producers and cheats in the bacterium Pseudomonas aeruginosa"
September 9: Research Update
- #Hannah- She will give a practice talk that will feature the very latest data and story line of her project looking at how conjugative plasmids can persist in bacterial populations, despite their associated costs.
September 16: Paper
Spring Quarter 2016
Unless otherwise noted, lab meetings are on Fridays from 10:00-11:30 in PAA049.
If you are presenting, send information to the lab mailing list before Wednesday at noon.
April 1: Lab meeting organization
- Should we meet on May 20th, which is when the undergraduate research symposium is?
- Schedule research updates. For each research update week, we’ll have two presenters.
- Fill the research queue with new papers. Add one or two here.
- Each person will give a short update on their outgoing lab duty.
- Include: what you accomplished, what needs to be accomplished, and any other notes for the new person on that duty.
- Put links to related wiki pages or notes next to your former task on the lab duties page before lab meeting.
- If you won’t be in lab meeting, please send me a brief summary for the first part and make sure the wiki’s been updated.
April 8: Canceled: Evolution: Making Sense of Biology (MCB Symposium)
April 15: Canceled: EVO-WIBO 2016!
April 22: Research Update
- Hannah. TBA.
April 29: Paper:
- Katrina and Sonia: Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein.
May 6: Research Updates:
- Sylvie. TBA.
- Brian: THUMB Project Introduction and Status.
May 13: Guest:
- Kevin Gross from NC State
May 20: Canceled: Undergraduate Research Symposium
May 27: Paper:
June 3: Research Updates:
- Robin. TBA.
- Luis. Big Science Extravaganza: Evolving Tiny Stuff and Counting Things with Fancy Machines.
Winter Quarter 2016
Lab meeting consisting of research update, literature queue or queue-jumping.
When: Fridays, 10.00-11.30am. Where: Kincaid 502 (except Jan 8, PAA A049D)
Paper queue and lab meeting schedule: https://docs.google.com/spreadsheets/d/1vl4eHTq_lvFDvhNugp9W99ZkFGeaIR8asrsbal-VSyw/edit?usp=sharing
Jan 8: Hannah & Sylvie : Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids
Jan 15: research update ( Josh )
Jan 22: Luis & Katrina: Evolutionary Rationale for Phages as Complements of Antibiotics
Jan 29: Sylvie & Ben: Engineering microbiomes to improve plant and animal health
Feb 5: Sarah: The ecology of the microbiome: Networks, competition, and stability
Feb 12: research update ( Sarah & Katie )
Feb 19: Ben: Breaking evolutionary constraint with a tradeoff ratchet
Feb 26: Queue Jump ( Jake )
Mar 4: (GSS is all day)
Mar 11: research update ( Peter )
Mar 18: Robin: Single gene locus changes perturb complex microbial communities as much as apex predator loss
Fall Quarter 2015
Lab meeting consisting of research update, literature queue or queue-jumping.
Time: 11.00-12.20pm. Place: Kincaid A023D
Oct 2: Brian & Jake : Shape matters: lifecycle of cooperative patches promotes cooperation in bulky populations
Oct 9: research update (Hannah)
Oct 16: Katie & Robin : Evolutionary limits to cooperation in microbial communities
Oct 23: research update (Joya)
Oct 30: Sonia & _ : Multiple Fitness Peaks on the Adaptive Landscape Drive Adaptive Radiation in the Wild
Nov 6: research update (Sarah re: Oxford work)
Nov 13: Katrina & Katie : Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages
Nov 20: queue jump: Katrina & Ben: Background reading Additional reading to be posted Wed evening (Nov 18).
Nov 27: Thanksgiving! (canceled)
Dec 4: research update (Peter)
Dec 11: lab goals (Katrina)
Summer 2015- Lab meeting
Research updates only. Place: Kin 502. Time: 9.00-10.30
- July 31: ( Katrina & Gordon updates )
- Aug 21: ( Brian & Luis )
- Sep 11: ( Jake & Sylvie )
Weekly goal (please update as you go along) can be updated on the spreadsheet here: https://docs.google.com/a/uw.edu/spreadsheets/d/1MHcCunzaAFxFIFswIkcuMm_EBOuog1PtYdLw3mdAgEY/edit?usp=sharing
Group name: HACK (Currently: Hannah, Amanda, Carrie, Katrina, Katie)
Mission: This group is for beginner programmers. We will work on learning R or Python. Totally ok if you've never opened up Python or R, as Carrie said it's "no scientist left behind".
Meeting day and time: Thursdays, 11:00 in KIN 502.
Group name: Tea with SQuEE (Brian and Katie, sometimes Luis)
Mission: Eco & Evo of QS journal club
Meeting day and time: Friday's usually around 4pm at a pub
Papers: SQuEE Zotero Group
Additional Discussion: #squee channel on Slack, also updated on Kerr Lab Meeting calendar (at least for summer)
Group name: Methods to our Madness
Mission: Introduce each other to a new tool (technique, device, software, etc.) at each meeting
Meeting day and time: First meeting Tuesday June 16 at 11:00. Meetings added to Kerr Lab Meeting calendar.
Discussion: #methods channel on Slack
Group name: Breakfast Club
Mission: To stay abreast of evidence-based pedagogy, focusing on higher ed STEM teaching.
Meeting day and time: Wed 8am, KIN 502
Contact Jake or Hannah for more information
Group name: Phage Club
Mission: Read and discuss papers related to bacteriophage evolution and ecology. Impromptu brainstorming sessions encouraged.
Meeting day and time: Thurs. 11am, but please note we sometimes reschedule (and sometimes meet off campus). The Phage Club reading list and schedule will be updated regularly, but please e-mail Katrina, Sonia, or Luis to confirm time and location of meeting, just in case we forget to update something.
Group name: pOP (aka plasmid group with Hannah and Sylvie)
Mission: Read and discuss papers related to plasmid eco/evo and horizontal gene transfer.
Meeting day and time: Fridays at 11am.
July 17- Frost & Koraimann (2010) Regulation of bacterial conjugation: balancing opportunity with adversity
July 2- Lau et al (2013) New quantitative methods for measuring plasmid loss rates reveal unexpected stability
June 26- Turner et al (2014) Antibiotic resistance correlates with transmission in plasmid evolution
June 19- San Millan et al (2014) Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids
Spring Quarter 2015
Revamped lab meeting.
Queues, queue-jumping, & research updates.
9-10:30 in KIN 502, unless otherwise noted.
- APR 3: Amanda & Hannah : Heterogeneity for IGF-II production maintained by public goods dynamics in neuroendocrine pancreatic cancer
- APR 10: Robin & Luis : Bacterial Adaptation Through Loss of Function
- APR 17: - cancelled for GSS -
- APR 24: research updates (Robin, Jake)
- MAY 1: Luis & Hannah : Evolution and emergence of infectious diseases in theoretical and real-world networks
- MAY 8: Kayla Peck (guest lab meeting host!)
- MAY 15: - cancelled for Mary Gates UGRS -
- MAY 22: Jake & Katie : Rapid evolution of a native species following invasion by a congener & Rate of language evolution is affected by population size
- MAY 29: research updates (Discussion of "Lab Duties" Ben)
- Brian & Jake : Shape matters: lifecycle of cooperative patches promotes cooperation in bulky populations
- Katie & Robin : Evolutionary limits to cooperation in microbial communities
- Sonia & _ : Multiple Fitness Peaks on the Adaptive Landscape Drive Adaptive Radiation in the Wild
- Katrina & Katie : The costs of evolving resistance in heterogeneous parasite environments
- Hannah & Sylvie : Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids
- Sylvie & _ :
- Peter & _ :
- Carrie & _ :
- Ben & Peter : The genetical theory of multilevel selection
- Amanda & _ :
- Robin & _ :
- Jake & _ :
- Peter & Ben's Games of life and death: antibiotic resistance and production through the lens of evolutionary game theory
- Ben's Life cycles, fitness decoupling and the evolution of multicellularity
- Character displacement and the evolution of niche complementarity in a model biofilm community - The paper focuses on the evolution of coexisting mutants within a population of Burkholderia cenocepacia and how their interactions affected productivity.
- Evolutionary limits to cooperation in microbial communities - K.Foz and group use a model to look at microbial cooperation between different strains and species.
- Alternating Antibiotic Treatments Constrain Evolutionary Paths to Multidrug Resistance - Using experimental evolution and whole-genome sequencing, we find that alternating drugs slows the rate of increase in resistance compared with single-drug treatments, by constraining resistance mutations with trade-offs in resistance to a second drug.
- The Time Scale of Evolutionary Innovation - But here we ask a different question, which is concerned with the much longer time scale of evolutionary trajectories: how long does it take for a population exploring a fitness landscape to find target sequences that encode new biological functions?
- Importance of Positioning for Microbial Evolution - Microbes commonly form dense communities that are central to many diseases and bioremediation. Here we demonstrate a simple and general principle of living in dense communities: microbes will commonly compete to reach nutrients at the community edge, akin to plants competing for light. Our work suggests that positioning is a major basis for evolutionary competition in dense microbial communities.
- Biogeographic Patterns in Ocean Microbes Emerge in a Neutral Agent-Based Model - A key question in ecology and evolution is the relative role of natural selection and neutral evolution in producing biogeographic patterns. We quantify the role of neutral processes...The emergent patterns are substantial and suggest that microbes evolve faster than ocean currents can disperse them.
- Epistatically Interacting Substitutions Are Enriched during Adaptive Protein Evolution - Mutations can fix during evolution for two reasons: they can be beneficial and fix for adaptive reasons, or they can be neutral or deleterious and fix solely by chance. Most studies focus on adaptation, where the evolving population is increasing in fitness due to a new selection pressure. Such studies have found an important evolutionary role for epistasis, the phenomenon where the effect of one mutation depends on another mutation. But adaptation only accounts for a fraction of overall evolutionary change. Here we investigate whether epistasis is as common during non-adaptive as adaptive evolution by comparing the same protein from human (under constant adaptive pressure) and swine influenza (under less adaptive pressure).
- More bang for your buck: Quorum-sensing capabilities improve the efficacy of suicidal altruism - We use digital evolution (a form of experimental evolution that uses self-replicating computer programs as organisms) to investigate the effects of enabling altruistic organisms to communicate via quorum sensing. We found that quorum-sensing altruists killed a greater number of competitors per explosion, winning competitions against non-communicative altruists.
- Global epistasis makes adaptation predictable despite sequence-level stochasticity - Epistatic interactions between mutations can make evolutionary trajectories contingent on the chance occurrence of initial mutations. We used experimental evolution in Saccharomyces cerevisiae to quantify this contingency, finding differences in adaptability among 64 closely related genotypes. Despite these differences, sequencing of 104 evolved clones showed that initial genotype did not constrain future mutational trajectories. Instead, reconstructed combinations of mutations revealed a pattern of diminishing-returns epistasis: Beneficial mutations have consistently smaller effects in fitter backgrounds. Taken together, these results show that beneficial mutations affecting a variety of biological processes are globally coupled; they interact strongly, but only through their combined effect on fitness. As a consequence, fitness evolution follows a predictable trajectory even though sequence-level adaptation is stochastic.
- Pervasive domestication of defective prophages by bacteria - Several molecular systems with important adaptive roles have originated from the domestication of integrated phages (prophages). However, the evolutionary mechanisms and extent of prophage domestication remain poorly understood. In this work, we detected several hundred prophages originating from common integration events and described their dynamics of degradation within their hosts. Surprisingly, we observed strong conservation of the sequence of most vertically inherited prophages, including selection for genes encoding phage-specific functions. These results suggest pervasive domestication of parasites by the bacterial hosts. Because prophages account for a large fraction of bacterial genomes, phage domestication may drive bacterial adaptation.
- Engineering microbial consortia: a new frontier in synthetic biology - Microbial consortia are ubiquitous in nature and are implicated in processes of great importance to humans, from environmental remediation and wastewater treatment to assistance in food digestion. Synthetic biologists are honing their ability to program the behavior of individual microbial populations, forcing the microbes to focus on specific applications, such as the production of drugs and fuels. Given that microbial consortia can perform even more complicated tasks and endure more changeable environments than monocultures can, they represent an important new frontier for synthetic biology. Here, we review recent efforts to engineer synthetic microbial consortia, and we suggest future applications.
- Epistasis between adaptive mutations in hemoglobin - Two populations of deer mice – high and low elevation – differ in hemoglobin by 12aa in three clusters. Mix ‘n match of these three clusters show epistasis in O2-binding ability.
- Social punishment of dishonest signallers - Paper wasp facial patterning is a signal of aggression. Signal can be manipulated with paint, trait with hormones. Four groups with ~20 pairs each: control, added paint (signal more aggression), added hormone (actually more aggressive), added both. Fig 2 shows that "added paint" group received more aggressive acts than any other. This implies social punishment when signal is higher than trait.
- Adaptive valley crossing & recombination - Models genome structure as 4 loci: “abcd”. Uses two recombination rates, one within a “gene” (between a & b, between c & d) and another between “genes” (between b & c). With sufficiently many valley-crossings needed (e.g., 50 genes with xy local peak and XY global peak), asex gets trapped on an occasional local peak, but sex allows all global peaks thanks to recombination (Fig1).
- Multiple Fitness Peaks on the Adaptive Landscape Drive Adaptive Radiation in the Wild. - The authors experimentally measure a fitness landscape in populations of wild pupfishes. They relate their findings to the populations' adaptive radiations and their tendency towards ecological generalism.
- Explaining microbial genomic diversity in light of evolutionary ecology. - Review paper that suggests that much of microbial genetic diversity is due to social and ecological interactions. Population structure, niches, social cheating, quorum sensing are all talked about in this nicely written and easy to follow paper.
- The winnowing: establishing the squid–vibrio symbiosis. - Really fun review paper that covers everything you wanted to know about the squid-vibrio symbiosis.
- Genetic information transfer promotes cooperation in bacteria. -Talks about how horizontal gene transfer can favor cooperation. Authors compare structured and well-mixed environments to better understand the prevalence of cooperative genes on mobile elements.
- A shift from magnitude to sign epistasis during adaptive evolution of a bacterial social trait.- Authors look at how epistatic interactions evolve in real time in specific biological systems. They characterize how the epistatic fitness relationship between a social gene and an adapting genome changes radically over a short evolutionary time frame in the social bacterium Myxococcus xanthus.
- Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Population- Authors demonstrate a coupling between population dynamics and the evolutionary dynamics of a “social” microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene.
- The evolution of plasmid-carried antibiotic resistance
- Niche engineering demonstrates a latent capacity for fungal-algal mutualism
Winter Quarter 2014
This quarter is the first of a revamped lab meeting, in which we have a paper queue (with pilot & copilot), queue-jumping for emergent lab fun, and once-a-month research updates. We are meeting 9-10:30, in KIN 502.
- JAN 9: planning meeting | 11:30 - 12:30
- JAN 16: GNH manuscript | 11 - 12:30 in BEACON
- JAN 23: planning meeting, Amanda's Mary Gates |11 - 12:30 in BEACON
- JAN 30: Luis's Coevolution drives the emergence of complex traits and promotes evolvability
- FEB 6: Sylvie's The demographic determinants of human microbiome health
- FEB 13: Peter & Katie : Testing the Role of Genetic Background in Parallel Evolution Using the Comparative Experimental Evolution of Antibiotic Resistance
- FEB 20: research updates (Luis, Brian)
- FEB 27: Carrie & Sonia : Epistatically Interacting Substitutions Are Enriched during Adaptive Protein Evolution
- MAR 6: Ben (& You?) : Quantitative evolutionary dynamics using high-resolution lineage tracking
- MAR 13: research updates (Carrie, Sylvie)
- MAR 20: Sylvie
Fall Quarter 2014
This quarter we are doing a pairwise journal club of current papers, with once a month research updates. We are meeting 11-12, in the BEACON space.
- OCT 3: Epistasis between adaptive mutations in hemoglobin (Jake & Carrie)
- OCT 10: Genetic information transfer promotes cooperation in bacteria. (Katie & Hannah)
- OCT 17: - [ cancelled - many folks absent ] -
- OCT 24: Fukushima’s Biological Impacts: The Case of the Pale Grass Blue Butterfly (Sonia & Jake)
- OCT 31: research updates | meeting till 12:30pm (Carrie, PRESS)
- NOV 7: Alternating Antibiotic Treatments Constrain Evolutionary Paths to Multidrug Resistance (Katrina & Brian)
- NOV 14: - [ cancelled - many folks absent ] -
- NOV 21: research updates | meeting till 12:30pm (SDAc, Brian, Peter, Jake [bumped])
- NOV 28: - [ thanksgiving ] -
- DEC 5: Niche engineering demonstrates a latent capacity for fungal-algal mutualism (Sylvie & Katie)
Summer Quarter 2014
This quarter we are working through Sex & Death (Sterelny & Griffiths 1999), which is an intro to the philosophy of biology. We are meeting 10-11, in KIN 502.
- JUN 20: Chapters 1, 2: Intro & The Received View - Ben
- JUN 27: Chapter 3: Gene's Eye View - Jake
- JUL 4: enjoy your BBQ
- JUL 11: Chapters 4, 5: Organism Strikes Back & Developmental Alternative - Sylvie
- JUL 18: Chapters 6, 7: Mendel and Molecules & Reductionism - Hannah
- JUL 25: Chapter 8: Organisms, Groups, and Superorganisms - Sarah
- AUG 1: Chapter 9: Species - Katrina
- AUG 8: research updates
- AUG 15: no lab meeting this week
- AUG 22: Chapter 10: Adaptation, Perfection, Function - Sonia
- AUG 29: Chapter 11: Adaptation, Ecology, and the Environment - Brian & Katie
- SEPT 5: Chapter 12: Life on Earth: The Big Picture - Luis
Spring Quarter 2014
This quarter we are doing a pairwise journal club of classic papers, with once a month research updates. We are meeting 10-11, in KIN 502.
- APR 4: Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species (PDF Δ) - Sarah & Hannah
- APR 11: Tragedy of the Commons (Hardin 1968) - Jake & Hannah
- APR 18: Nothing in Biology Makes Sense Except in the Light of Evolution Δ (Dobzhansky 1973) (transcription) - Brian and Sylvie
- APR 25: research updates | meeting till 11:30am
- MAY 2: An Experimental Study of Interaction Between Genetic Drift & Natural Selection (Dobzhansky 1957) - Jake and Carrie
- MAY 9: The logic of animal conflict (Maynard Smith & Price, 1973) Δ Katrina & Peter
- MAY 16: Sylvie research update
- MAY 23: research updates | meeting till 11:30am
- MAY 30: figuring out next quarter
- JUN 6: The Evolution of Reciprocal Altruism (Trivers 1971) - Sylvie & Katie
(papers submitted but not chosen this quarter)
- A Strategy of Win-Stay, Lose-Shift That Outperforms Tit-for-Tat in the Prisoner’s Dilemma (Nowak 1993)
- The Small World Problem (Milgram 1967)
- Developmental Plasticity of Species Differences (West-Eberhard 2005)
- The Prophage and I (Lwoff 1966)
- Evolutionary Rate at the Molecular Level (Kimura 1968)
- Evolutionary Games & Spatial Chaos (Nowak & May 1992)
- Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms (Woese & Fox 1977)
- The Origin & Behavior of Mutable Loci in Maize (McClintock 19xx)
- Is Wright’s Shifting Balance Process Important in Evolution? (Coyne 1999)
- Harold & the Purple Crayon (Johnson 1955)
Winter Quarter 2014
This quarter we are doing a pairwise journal club (2 "hosts" per week!), with once a month research updates. We are meeting 10:30-11:30, in basement room A023D.
- JAN 10: planning meeting (4th floor hall)
- JAN 17: Bacterioicins as alternate antimicrobials? Δ - Carrie & Amanda
- JAN 24: research updates | meet at 10am
- JAN 31: The Niche Construction Perspective: A Critical Appraisal (PDF Δ) - Brian & Sarah
- FEB 7: slime molds farming bacteria - Brock_2011 - Katrina & Chase
- FEB 14: fitness trajectories in LTEE lines - Wiser_2013 - Sonia & Katie
- FEB 21: research updates | meet at 10am
- FEB 28: Reducing educational achievement gaps via self-affirmation - (Cohen_2006 Δ) Hannah & Carrie
- MAR 7: selection on mtDNA - Innocenti_2011, summary - Jake & Peter
- MAR 14: Biology Graduate Student Symposium
- MAR 21: research updates | meet at 10am
- MAR 28: no journal club
(papers submitted but not chosen this quarter)
- Cost-free honest signaling - Lachmann_2001
- Social punishment of dishonest signalers - Tibbets_2010
- Amino acid trend since LUCA - Jordan 2005
- Fitness landscape of a wild fish population - Martin & Wainwright 2013
- Mediation of genomic conflict in viruses - Sachs & Bull 2005
- Sequence expansion of the protein universe - Povolotskaya & Kondrashov 2010
- Does "aesthetics" mean something outside the human realm? - Prum 2013
- Gene duplication and the adaptive evolution of a classic genetic switch - Hittinger and Carroll 2007
- Designing and engineering evolutionary robust genetic circuits - Sleight et al 2010
- Increased water stress strengthens ant/tree/scale insect mutualism - Pringle et al. 2013
- Incipient speciation by divergent adaptation and antagonistic epistasis - Dettman et al. 2007
Fall Quarter 2013
This quarter we are having a journal club, with special guest Ben Skyping in from sabbatical once a month for research updates. We are meeting 11:30-12:30, in HCK 312.
- OCT 4: The Decay of Unused Traits - Paper, Review (Jake)
- OCT 11: Research updates with Ben
- OCT 18: no journal club, but there's a topical defense at 11am in 123 Marine Sciences
- OCT 25: Brian - paper
- NOV 1: Evolutionary Reversals of Antibiotic Resistance (Peter)
- NOV 8: Research updates with Ben
- NOV 15: Genome Dynamics during Experimental Evolution Review (Hannah)
- NOV 22: Carrie Take 1 test
- NOV 29: Thanksgiving
- DEC 6: Darwinian Individuals (Katrina)
- DEC 13: Research updates with Ben
Summer Quarter 2013
This quarter we are going to be reviewing basic computational skills (using the shell, using the wiki, basic programing using python and R, data analysis, figure generation, using cloud computing, object-oriented concepts, etc.).
- 21 JUN: Orientation (wiki introduction, basic shell, downloading software)
- 28 JUN: Reading, writing, using and manipulating CSV files using Python, R, and Excel
- 05 JUL: Python basics (basic data types [integers, floats, strings], lists, conditionals, loops)
- 12 JUL: More Python basics (functions, dictionaries, sets)
- Make sure you understand the tutorials from last week.
- You might find it helpful to go through our notes from last week. Try to solve the problems listed there: we will spend the first few minutes of next week sharing solutions.
- Connect to this link, and read the tutorials for "Functions" and "Dictionaries" (under the section "Learn the Basics"), as well as "Sets" (under the section "Advanced Tutorials") and try your hand at the exercises.
- Download the code for our meeting here and the colony counts to analyze here.
- 16 JUL: Object-oriented programming in Python (classes, objects, and inheritance)
- 02 AUG: Program design in Python (writing clear and reusable code; constructing libraries)
- 09 AUG: Special libraries in Python (NumPy, MatPlotLib, NetworkX, etc.)
- 23 AUG: Using the cloud (running Python)
- 30 AUG: Introduction to R (basic data types, conditionals, loops, functions, libraries)
- 06 SEP: Analyzing data and making figures (R/Python)
- Tradeoff data from class (csv)
- 20 SEP: Special topics (testing code, regular expressions, etc.)
Spring Quarter, 2013
This quarter we are reading the primary literature. We are discussing the following papers:
- April 5 Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space
- April 12 Does experimental evolution reflect patterns in natural populations?
- April 19 Improved use of a public good selects for the evolution of undifferentiated multicellularity & Experimental evolution of multicellularity using microbial pseudo-organisms
- April 26 Evolution of Stress Response in the Face of Unreliable Environmental Signals
- May 3 Public good dynamics drive evolution of iron acquisition strategies
- May 10 Social evolution in micro-organisms and a Trojan horse approach to medical intervention strategies
- May 17 Canceled
- May 24 Topological Signatures of Species Interactions in Metabolic Networks
- May 31 Evolutionary change during experimental ocean acidification
- June 6 Cause and Effect in Biology Revisited: Is Mayr's Proximate-Ultimate Dichotomy Still Useful?
Winter Quarter, 2013
This quarter we are giving progress reports on the various on-going projects in the lab as well as discussing one paper in each lab meeting.
Sign-up to present at lab meeting
Note: Remember that this is a public page. Do not attach published works, only links. Password-protected uploads are can be put here.
Fall Quarter, 2012
This quarter we are giving progress reports on the various on-going projects in the lab.
Sept 28: Lab Orientation (meet in the lab), SQuEE, and Brian Connelly
Sign-up to present at a lab meeting
Sign-up for one-on-one meetings
Spring Quarter, 2012
This quarter we are reading Robustness and Evolvability in Living Systems by Andreas Wagner.
March 30th: Chapters 1 & 2 (Josh)
April 6th: Chapters 3 & 4 (Jake)
April 13: Chapters 5 & 6 (Carrie)
April 20: Chapters 7 & 8 (OPEN)
April 27: Chapters 9 & 10 (Ben)
May 4th: Chapters 11 & 12 (OPEN)
May 11th: Chapters 13 & 14 (Peter)
May 25th: Chapters 15 & 16 (Sonia)
June 1st: Chapters 17 & 18 (Frazer)
June 8th: Chapters 19 & 20 & Epilogue (Katie)
Winter Quarter, 2012
This quarter we are reading Only A Theory: Evolution and the Battle for America's Soul. Please sign up for a week and link to an supplemental material paper.
Jan 13th: Chapter 1 and Wiki Tutorial (Josh Nahum)
Jan 20th: Cancelled due to weather
Jan 27th: Chapter 2 & 3 and The Evolutionary Origin of Complex Features (Ben Kerr)
Feb 3rd: Chapter 4 and A Draft Sequence of the Neandertal Genome (Neem)
Feb 10th: Chapter 5 and Oxygen and the Evolution of Complex Life (Sonia)
Feb 17th: Chapter 6 (Carrie)
Feb 24th: Cancelled
Mar 2nd: Chapter 7 (Peter)
Mar 9th: Chapter 8 and Using Avida-ED for Teaching and Learning About Evolution in Undergraduate Introductory Biology Courses (Josh Nahum)