February 28, 2017
1st Wittkopp Lab Retreat
We enjoyed a break from the day-to-day realities in the lab to reflect on science and lab policies during our first Wittkopp Lab retreat in Lansing, MI. Invigorating discussions of diverse topics, brainstorming new project ideas, and lots of food, wine, and games made for a great couple days.
January 9, 2017
Remote First Paper Celebration
Congratulations to former lab member José Andrade López (now a PhD student at Stanford) for his first, first-authored paper, published in Molecular Ecology!! And Congratulations to former lab member Joseph Coolon (now Assistant Professor at Wesleyan) for earning senior authorship on this work and bringing it to completion with the help of some of the Coolon lab’s first lab members. Finally, a huge thank you to former lab member David Yuan (now a postdoc at Stanford) for keeping the Wittkopp lab first paper champagne traditional alive remotely by surprising José with a bottle and celebrating with him at Stanford. Cheers!
November 19th, 2016
FEMMES (Females Excelling More in Math Engineering and the Sciences) hosts an annual Saturday Science Capstone Event on the University of Michigan’s Ann Arbor campus, which is a free, daylong activity-filled event aimed at 4th to 6th grade girls. Our lab regularly contributes to an activity, this year Petra Vande Zande, Jade Diaz, Abby Lamb, Andrea Hodgins-Davis, and Alisha John all led a session on “DNA Detectives” where the girls learned about inheritance of genes, investigated slides vegetable DNA using a microscope, swabbed their own cheeks to visualize the components of a cell, and see DNA first hand with the Strawberry DNA experiment!
November 12th, 2016
Congrats to Jon, who was awarded 2nd place for his poster titled “Genetics of morphological and behavioral evolution between Drosophila elegans and D. gunungcola” at the Midwest Drosophila Conference in Monticello, IL!
October 17th, 2016
Abby Lamb received 2nd place for her (non-traditional and amazing) poster titled “Stronger together: how evolutionary insights enrich molecular, cellular and developmental biology” at the MCDB annual retreat at Eagle Crest in Ypsilanti, MI. Congrats Abby!
September 9th-11th, 2016
Trisha, Jon and Elizabeth attended the 32nd EEB Retreat at the UM Biological Station. We learned about fungi from members of the James Lab and Aquatic Species from Andrea Thomaz and Diarmaid O’Foighil on a few of the field trips. It was a wonderful way to reconnect with faculty and meet many incoming post-docs, Ph.D. and masters students!
July 14th, 2016
Bastille Day Journal Club on the patio!
Wang et al. 2016. Allele-Specific Transcriptome and Methylome Analysis Reveals Stable Inheritance and Cis–Regulation of DNA Methylation in Nasonia PloS Biology. Link
*Bintu et al. 2016. Dynamics of epigenetic regulation at the single-cell level. Science. Link
Good and Desai 2016. Evolution of mutation rates in rapidly adapting asexual populations. BioRxiV. Link
Lorberbaum et al. 2016. An ancient yet flexible cis–regulatory architecture allows localized Hedgehog tuning by patched/Ptch1. eLife. Link
Verfaillie et al. 2016. Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic. Genome Research. Link
Shin et al. 2016. Hierarchy within the mammary STAT5-driven Wap super-enhancer. Nature Genetics. Link
Panckey et al. 2014. Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid. PNAS. Link
Farley et al. 2016. Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers. PNAS. Link
*= Journal club choice
June 9th, 2016
Was a beautiful day on the patio at Silvio’s for Journal Club!
Alvarez et al. 2015. Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution? Molecular Ecology. Link
Knoppel et al. 2016. Compensating the Fitness Costs of Synonymous Mutations. MBE. Link
du Plessis et al. 2016. How good are statistical models at approximating complex ﬁtness landscapes? MBE. Link
Hauenschild et al. 2008. Evolutionary Plasticity of Polycomb/Trithorax Response Elements in Drosophila Species. PloS Biology. Link
He et al. 2016. The footprint of polygenic adaptation on stress-responsive cis-regulatory divergence in the Arabidopsis genus. MBE. Link
Huang et al. 2016. Spontaneous Mutations and the Origin and Maintenance of Quantitative Genetic Variation. eLife. Link
Kijimoto and Moczek 2016. Hedgehog signaling enables nutrition-responsive inhibition of an alternative morph in apolyphenic beetle. PNAS. Link
Agashe et al. 2016. Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium. MBE. Link
*McKenna et al. 2016. Whole organism lineage tracing by combinatorial and cumulative genome editing. Science. Link
Ebersole et al. 2016. Scientists’ Reputations Are Based on Getting It Right, Not Being Right. PloS Biology. Link
Ho and Smith 2016. Molecular evolution of anthocyanin pigmentation genes following losses of flower color. BMC. Link
Tamari and Barkai 2016. Natural Diversity in Pentose Fermentation Is Explained by Variations in Histone Deacetylases. Cell Reports. Link
van’t Hof et al. 2016. The industrial melanism mutation in British peppered moths is a transposable element. Nature Letters. Link
*= Journal club choice
May 9th, 2016
Hopefully we will finally get some patio weather for Journal Club this month… c’mon Spring!
Emera et al. 2016. Origin and evolution of developmental enhancers in the mammalian neocortex. PNAS. Link
Chuffart et al. 2016. Exploiting single-cell quantitative data to map genetic variants having probabilistic effects. bioRxiv. Link
Wang et al. 2016. The PSI–U1 snRNP interaction regulates male mating behavior in Drosophila. PNAS. Link
Mallarino, Linden et al. 2016. The role of isoforms in the evolution of cryptic coloration in Peromyscus mice. Molecular Ecology. Link
Harris et al. 2016. Localized epigenetic silencing of a damage-activated WNT enhancer limits regeneration in mature Drosophila imaginal discs. eLife. Link
Zhong et al. 2016. The effect of gene interactions on the long-term response to selection. Molecular Systems Biology. Link
Gerhart and Kirschner 2016. The theory of facilitated variation. PNAS. Link
Yao et al. 2015. Cis-regulatory architecture of a brain signaling center predates the origin of chordates. Nature Genetics. Link
*Li et al. 2016. RNA splicing is a primary link between genetic variation and disease. Science. Link
*= Journal club choice
April 12th, 2016
Great papers to choose from this month:
Mohammad et al. 2016. Ancient Anxiety Pathways Inﬂuence Drosophila Defense Behaviors. Current Biology. Link
Yassin et al. 2016. Recurrent specialization on a toxic fruit in an island Drosophila population. PNAS. Link
*Mack et al. 2016. Gene regulation and speciation in house mice. Genome Research. Link
Alcid and Tsukiyama 2016. Expansion of antisense lncRNA transcriptomes inbudding yeast species since the loss of RNAi. Nature Structural and Molecular Biology. Link
Yarrington et al. 2016. Nucleosomes Are Essential for Proper Regulation of a Multigated Promoter in Saccharomyces cerevisiae. Genetics. Link
Paixãoa and Barton 2016. The effect of gene interactions on the long-term response to selection. PNAS. Link
Handelsman et al. 2016. Entering Mentoring: A Seminar to Train a New Generation of Scientists. HHMI. Link STEM Adaptions Link Blog about mentoring info
Camino et al. 2015. The Evolutionary Origination and Diversification of a Dimorphic Gene Regulatory Network through Parallel Innovations in cis and trans. PloS Genetics. Link
Shearer et al. 2016. Seasonal cues induce phenotypic plasticity of Drosophila suzukii to enhance winter survival. BMC Ecology. Link
Svetec et al. 2016. The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster. PloS Genetics. Link
*= Journal club choice
March 7th, 2016
Lots of interesting options for Journal Club this month:
*McDonald et al. 2016. Sex speeds adaptation by altering the dynamics of molecular evolution. Nature Letters. Link
Plazcek et al. 2016. Translational control of nicotine-evoked synaptic potentiation in mice and neuronal responses in human smokers by eIF2a. eLife. Link
Huang et al. 2016. Translational control by eIF2a phosphorylation regulates vulnerability to the synaptic and behavioral effects of cocaine. eLife. Link
Bastide et al. 2014. Pigmentation in Drosophila melanogaster reaches its maximum in Ethiopia and correlates most strongly with ultra-violet radiation in sub-Saharan Africa. BMC Evolutionary Biology. Link
Yassin et al. 2016. Ancient balancing selection at tan underlies female colour dimorphism in Drosophila erecta. Nature Communications. Link
Eom et al. 2016. Long-distance communication by specialized cellular projections during pigment pattern development and evolution. eLife. Link
Levasseur et al. 2016. MIMIVIRE is a defence system in mimivirus that confers resistance to virophage. Nature. Link
Dudo & Besley 2016. Scientists’ Prioritization of Communication Objectives for Public Engagement. PloS One. Link
Linn et al. 2015. Undergraduate research experiences: Impacts and opportunities. Science. Link
Crocker et al. 2016. Quantitatively predictable control of Drosophila transcriptional enhancers in vivo with engineered transcription factors. Nature Genetics. Link
*= Journal club choice
February 25th, 2016
Congrats to EEB Ph.D. student (recently graduated, now a post-doc in the Thornton Lab at U Chicago) Brian Metzger on receiving the ProQuest Distinguished Dissertation Award for 2015. This award is given in recognition of the most exceptional scholarly work produced by doctoral students at the University of Michigan who completed their dissertations in 2015.
The award will be presented at a ceremony and reception from 2:00 to 4:00 pm on Tuesday, April 26, 2016 in the Assembly Hall on the fourth floor of the Rackham Building.
Can’t wait to for the reunion with the Wittkopp lab in April, we miss you!
February 19th, 2016
Congrats to Trisha for receiving one of this year’s Arthur F. Thurnau Professorships!
From Diarmaid O’Foighil, EEB Chair:
“Thurnau Professorships are highly prestigious and they honor tenured U-M faculty who make outstanding contributions to undergraduate education. The competition is rather stiff: Trisha‘s award doubles the EEB count. Until now, our only Thurnau Professor has been John Vandermeer who received his in 1994.”
*LSA article (4/6/16)
February 11th, 2016
New journal club articles this month, that share our diverse interests in the lab:
Li et al. 2016. A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity. PloS Genetics. Link
Aspiras et al. 2015. Melanocortin 4 receptor mutations contribute to the adaptation of cavefish to nutrient-poor conditions. PNAS. Link
Benoit et al. 2015. Unique features of a global human ectoparasite identiﬁed through sequencing of the bed bug genome. Nature Communications. Link
*Phadnis et al. 2015. An essential cell cycle regulation gene causes hybrid inviability in Drosophila. Science. Link
Imsland et al. 2016. Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses. Nature Genetics. Link
Lack et al. 2016. Decanalization of wing development accompanied the evolution of large wings in high-altitude Drosophila. PNAS. Link
Wallbank et al. 2016. Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling. PloS Genetics. Link
*= Journal club choice
January 6th, 2016
Happy New Year! The end of year push to publish resulted in some good papers for Journal Club:
Quandt et al. 2015. Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment. eLife Link
Hart et_al. 2015. Drosophila Chemoreceptors: A Molecular Interface Between the Chemical World and the Brain. Trends in Genetics. Link
Ashbrook et al. 2015. Genetic variation in offspring indirectly influences the quality of maternal behaviour in mice. eLife. Link
Lamichhaney et al. 2015. Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax). Nature Genetics. Link
Domcke et al. 2015. Competition between DNA methylation and transcription factors determines binding of NRF1. Nature Letters. Link
Peter and Koch 2015. When Debunking Scientific Myths Fails (and When It Does Not): The Backfire Effect in the Context of Journalistic Coverage and Immediate Judgments as Prevention Strategy. Science Communication. Link
Endler et al. 2015. Reconciling differences in Pool-GWAS between populations: a case study of 4 female abdominal pigmentation in Drosophila melanogaster. Genetics. Link
*Naranjo et al. 2015. Dissecting the Genetic Basis of a Complex cis–Regulatory Adaptation. PloS Genetics. Link
*= Journal club choice
December 4th, 2015
Another month, another bunch of papers to read!
Liu et al. 2015. Gene Essentiality Is a Quantitative Property Linked to Cellular Evolvability. Cell. Link
Hart et al. 2015. High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities. Cell. Link
Cinquin et al. 2015. Semi-permeable Diffusion Barriers Enhance Patterning Robustness in the C. elegans Germline. Cell. Link
*Fyon et al. 2015. Enhancer Runaway and the Evolution of Diploid Gene Expression. PloS Genetics. Link
Decety et al. 2015. The Negative Association between Religiousness and Children’s Altruism across the World. Current Biology. Link
Ling et al. 2015. Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution. PNAS. Link
Pool 2015. The Mosaic Ancestry of the Drosophila Genetic Reference Panel and the D. melanogaster Reference Genome Reveals a Network of Epistatic Fitness Interactions. MBE. Link
Chevereau et al. 2015. Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance. PloS Biology. Link
*= Journal club choice
November 11th, 2015
Papers of Interest to the lab:
Shannon et al. 2015. Genetic structure in village dogs reveals a Central Asian domestication origin. PNAS. Link
*Sigova et al. 2015. Transcription factor trapping by RNA ingene regulatory elements. Science. Link
Musser and Wagner 2015. Character Trees From Transcriptome Data: Origin and Individuation of Morphological Characters and the So-Called “Species Signal”. Journal of Experimental Biology. Link
Aakre et al. 2015. Evolving New Protein-Protein Interaction Speciﬁcity through Promiscuous Intermediates. Cell. Link
Huang et al. 2015. Genetic basis of transcriptome diversity in Drosophila melanogaster. PNAS. Link
Ming et al. 2015. The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics. Link
Yang et al. 2015. Functionally conserved enhancers with
divergent sequences in distant vertebrates. BMC Genomics. Link
Farley et al. 2015. Suboptimization of developmental enhancers. Science. Link
Rodríguez-Verdugo et al. 2015. First-step mutations during adaptation restore the expression of hundreds of genes. MBE. Link
*= Journal club choice
October 13th, 2015
Papers of Interest to the lab:
*Kaltenbach et al. 2015. Reverse evolution leads to genotypic incompatibility despite functional and active site convergence. eLife. Link
Bolstad et al. 2015. Complex constraints on allometry revealed by artificial selection on the wing of Drosophila melanogaster. PNAS. Link
Yao et al. 2015. A microRNA allele that emerged prior to apple domestication may underliefruit size evolution. The Plant Journal. Link
Shiao et al. 2015. Expression divergence of chemosensory genes between Drosophila sechellia and its sibling species and its implications for host shift. GBE. Link
Fox et al. 2015. An expanded regulatory network temporally controls Candida albicans bioﬁlm formation. Mol. Microbiol. Link
Villar et al. 2015. Enhancer Evolution across 20 Mammalian Species. Cell. Link
Monteiro et al. 2015. Differential Expression of Ecdysone Receptor Leads to Variation in Phenotypic Plasticity across Serial Homologs. PloS Genetics. Link
*= Journal club choice
September 12th, 2015
Many EEB’ers in the lab (Jennifer Lachowiec, Andrea Hodgins-Davis, Jon Massey, Trisha Wittkopp, and Fabien Duveau) gathered at Nordman Lake Lodge in Dexter, MI this weekend to take field trips to the Nan Weston Nature Preserve and Sharon Hollow, listen to various talks, including Trisha and Meg Duffy’s talk about work-life balance and time management strategies, and even get in on some night time banjo playing!
September 9th, 2015
Rossi et al. 2015. Genetic compensation induced by deleterious mutations but not gene knockdowns. Nature. Link
Wolf, Silander and Nimwegen 2015. Expression noise facilitates the evolution
of gene regulation. eLife. Link
*Haber and Dworkin 2015. Dis-integrating the fly: A mutational perspective on phenotypic integration and covariation. BioRxIV. Link
Stankowski and Streisfeld et al. 2015. Introgressive hybridization facilitates adaptive divergence in a recent radiation of monkey flowers. Royal Proc. Soc. Link
Bordenstein and Theis 2015. Host Biology in Light of the Microbiome: TenPrinciples of Holobionts and Hologenomes. PLoS Biology. Link
Carroll 2015. Sharing Research Data and Intellectual Property Law: A Primer.
PLoS Biology. Link
Singh et al. 2015. Fruit flies diversify their offspring in response to parasite infection. Science. Link
Akbari et al. 2015. Safeguarding gene drive experiments in the laboratory. Science. Link
Hasegawa et al. 2015. Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development. PLoS Genetics. Link
Albertin et al. 2015. The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature. Link
*= Journal club choice
August 27th, 2015
A while ago we had an e-mail exchange going around the lab where Jen challenged all of us to attempt the Up Goer Five challenge of explaining our work using only the 1000 most common words.
Here are some of our attempts to explain our research (or thesis title) in the Wittkopp Lab:
I study how animals change over time. I do this by looking at how children are the same and different from their parents and how what is different between them can cause different types of animals to become different from each other. – Trisha
How time has changed the ways in which the complete set of plans in a cell is controlled. – Kraig
When there is a change in the directions that control how living things grow up, the way the whole living thing looks or acts can change. We don’t know how different kinds of changes in these directions can change the way things look or act. We don’t even really know how to read the directions yet. Does it take lots of changes in lots of steps in the directions, or can changing one really important step make a big change in a living thing? How do these changes work together as they build up over time? And how can studying these changes help us understand how living things came to be so different? – Abby
I study how changes in the color of animals cause changes in the way animals act and how the way animals act cause changes in animal color. –Jon
Understanding how and why animals (and humans) change the way they look over time remains a struggle. We know that in each cell there are directions controlling how each animal looks and acts and that these directions are passed from moms and dads to their children. We also know changes to these directions can lead to different animals looking and acting different from one another. To figure out which direction in the cell cause these changes to happen, we need to know which change out of all the changes between different animals is the reason they look or act different. To help answer the question of how animals change over time, I am studying two sister types of animal that look very different from one another (one is dark in color, one is light) and trying to find the change in cell directions making them different colors. –Alisha
August 21st, 2015
Wittkopp Lab’s 1st EEB Graduate student, Brian Metzger, defended his thesis today: “Disentangling the effects of mutation and selection on the evolution of gene expression”
August 6th, 2015
Wittkopp West Coast Reunion while attending the PanAm EvoDevo Conference in @ UC Berkeley.
Trisha Wittkopp, Katya Mack, Jonathan Gruber, Kerem & Gizem Gruber, Dave Yuan, Jose Andrade-Lopez.
Kerem Gruber (Homozygous Wittkopp Lab Baby) & Trisha
August 6th, 2015
Interesting recent papers our lab is reading this month:
Pinto et al. 2015. JAK/STAT and Hox Dynamic Interactions in an Organogenetic Gene Cascade. Plos Genetics. Link
Gao et al. 2015. Predominant contribution of cis-regulatory divergence in the evolution of mouse alternative splicing. Molecular Systems Biology. Link
Ma and O’Farrell 2015. Selections that isolate recombinant mitochondrial genomes in animals. eLife. Link
Schaefke et al. 2015. Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and S. paradoxus. GBE. Link
Lavista-Llanos et al. 2015. Dopamine drives Drosophila sechellia
adaptation to its toxic host. eLife. Link
*Vu et al. 2015. Natural Variation in Gene Expression Modulates the Severity of Mutant Phenotypes. Cell. Link
Sorrells et al. 2015. Intersecting transcription networks constrain gene regulatory evolution. Nature. Link
Xu et al. 2015. Combining protein and mrna quantification to decipher transcriptional regulation. Nature Methods. Link
Buenrostro et al. 2015. Single-cell chromatin accessibility reveals principlesof regulatory variation. Nature. Link
*= Journal club choice
July 7th, 2015
We’re chatting on a patio somewhere next week about this paper:
Crocker et al. 2015. Low Afﬁnity Binding Site Clusters Confer Hox Speciﬁcity and Regulatory Robustness. Cell. Link
Other notable papers this month:
Lubliner et al. 2015. Core promoter sequence in yeast is a major determinant of expression level. Genome Research. Link
Johnson et al. 2015. Genetic Changes to a Transcriptional Silencer Element Confers Phenotypic Diversity withinand between Drosophila Species. Plos Genetics. Link
Comeault et al. 2015. Selection on a Genetic Polymorphism Counteracts Ecological Speciation in a Stick Insect. Current Biology. Link
Markow 2015. The secret lives of Drosophila flies. eLife. Link
Anderson, McKeown and Thornton 2015. Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites. eLife. Link
Gitschier 2015. The Whole of a Scientific Career: An Interview with Oliver Smithies. pLoS Genetics. Link
Dixon et al. 2015. Genomic determinants of coral heat tolerance across latitudes. Science. Link
June 6th, 2015
The paper we chose to discuss this month at Journal Club:
Sunshine et al. 2015. The Fitness Consequences of Aneuploidy Are Driven by Condition-Dependent Gene Effects. PLoS Biology. Link
Other papers worth checking out:
Graur, Zheng and Azevedo 2015. An evolutionary classification of genomic function. Genome Biology and Evolution. Link
Koshikawa et al. 2015. Gain of cis-regulatory activities underlies novel domains of wingless gene expression in Drosophila. PNAS. Link
Sillero et al. 2015. Niche evolution and thermal adaptation in the temperate species
Lumley et al. 2015. Sexual selection protects against extinction. Nature. Link
Cook-Andersen and Wilkinson. 2015. Splicing does the two-step. Nature. Link
Hose et al 2015. Dosage compensation can buffer copy-number variation in wild yeast. eLIFE. Link
Kachroo et al. 2015. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Science. Link
June 5th, 2015
Congrats to Trisha on her John Dewey teaching award! #LSAvictors
May 16, 2015
Assistant Research Scientist, Joe Coolon and Post-doc, Andrea Hodgins-Davis, represented the Wittkopp lab at the Detroit Zoo today! As part of their Portal to the Public Fellowship, they both created hands-on tabletop activities aimed to demonstrate a key concept in their own research. If you missed them, come out on Saturday, May 30th 10:30-12:30!
May 15th, 2015
Hopefully we will be chatting about this paper today on a patio:
Gantz and Bier 2015. The mutagenic chain reaction: A method for converting heterozygous to homozygous mutations. Science. Link
Other papers the lab has been checking out:
Conallon and Clark 2015. The distribution of fitness effects in an uncertain world. Evolution. Link
Ilardo et al. 2015. Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids. Science Reports. Link
Pelsy et al. 2015. Chromosome Replacement and Deletion Lead to Clonal Polymorphism of Berry Colorin Grapevine. PloS Genetics. Link
Ghanbarian and Hurst 2015. Neighboring Genes Show Correlated Evolution in Gene Expression. MBE. Link
Heers and Dial 2015. Wings versus legs in the avian bauplan: Development and evolution of alternative locomotor strategies. Evolution. Link
Dembeck et al 2015. Genetic Architecture of Abdominal Pigmentation in Drosophila melanogaster. PloS Genetics. Link
Weinberger et al. 2015. Ten Simple (Empirical) Rules for Writing Science. PloS Computational Biology. Link
Yoda et al. 2015. The transcription factor Apontic-like controls diverse colouration pattern in caterpillars. Nature Communications. Link
Sapiro et al. 2015. Cis Regulatory Effects on A-to-I RNA Editing in Related Drosophila Species. Cell Reports. Link
May 6th, 2015
Post-doc in the lab, Jen Lachowiec, collected sap from surrounding Ann Arbor maple trees and made home-made syrup to share with the lab. What better way to celebrate than with a pancake-fest! …It was phenomenal… we kind of wish it could happen every week…
May 4th, 2015
The EEB spring picnic was attended by many in the lab, including our very own EEB graduate student, Brian Metzger, who won the coveted best grad paper award given by the department for his Nature paper, “Selection on noise constraints variation in a eukaryotic promoter.”
April 27th, 2015
Congrats Jose on your thesis defense!! We are sad to see you go, but we know you will do great things at Stanford! Good luck with your Ph.D.!
April 22nd, 2015
Daayun presented her new poster at the UROP Symposium, great job to you and your mentor Andrea Hodgins-Davis!
April 15th, 2015
This month we chose to chat about the following paper:
Camino et al. 2015. The Evolutionary Origination and Diversification of a Dimorphic Gene Regulatory Network through Parallel Innovations in cis and trans. Plos Genetics. Link
A look into what else the lab is reading:
Nishikawa et al. 2015. A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly. Nature Genetics. Link
Bader et al. 2015. Negative feedback buffers effects of regulatory variants. Molecular Systems Biology. Link
Schmiedel et al. 2015. MicroRNA control of protein expression noise. Science. Link
Crowley et al. 2015. Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nature Genetics. Link
Dayan et al. 2015. Phenotypic Plasticity in Gene Expression Contributes to Divergence of Locally-Adapted Populations of Fundulus heteroclitus. Molecular Ecology. Link
Haasl and Payseur et al. 2014. Remarkable selective constraints on exonic dinucleotide repeats. Evolution. Link
Levy et al. 2015. Quantitative evolutionary dynamics using high-resolution lineage tracking. Nature. Link
Lamichhaney et al. 2015. Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature. Link
March 30th, 2015
Several Wittkopp lab members — Andrea Hodgins-Davis, Daayun Chung, Jose Andrade-Lopez, and Jon Massey — traveled to Bloomington, Indiana for the Midwest Ecology and Evolution Conference (MEEC).
March 16th, 2015
Congrats to Brian Metzger, Dave Yuan, Fabien Duveau, Jonathan Gruber and Trisha Wittkopp on their study, Selection on noise constrains variation in a eukaryotic promoter, which has just appeared in Nature and is also the subject of a press release by Jim Erickson: Consistency is the key to success in bread baking and biology.
Co-1st author Dave Yuan, who’s now in the Petrov lab at Stanford wrote a nice blog about it as well.
This is another nicely written article written on the Saccharomyces Genome Database.
March 11th, 2015
We are chatting about this interesting paper today:
Farhadifar et al. 2015. Scaling, Selection, and Evolutionary Dynamics of the Mitotic Spindle. Current Biology. Link
Other lab choices this month:
Selmecki et al. 2015. Polyploidy can drive rapid adaptation in yeast. Nature Letters. Link
Bauer et al. 2015. Essential gene disruptions reveal complex relationships between phenotypic robustness, pleiotropy, and fitness. Molecular Systems Biology. Link
O’Brown et al. 2015. A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA. eLife. Link
Yang et al. 2014. Comparative Transcriptome Analyses Reveal Core ParasitismGenes and Suggest Gene Duplication and Repurposing asSources of Structural Novelty. MBE. Link
Luo and Baker 2015. Constraints on the evolution of a doublesex target gene arising from doublesex’s pleiotropic deployment. PNAS. Link
Boyd et al. 2015. Human-Chimpanzee Differences in a FZD8 Enhancer Alter Cell-Cycle Dynamics in the Developing Neocortex. Current Biology. Link
Delsuc and Tilak. 2015. Naked But Not hairless: The Pitfalls of Analyses of Molecular Adaptation Based on Few Genome Sequence Comparisons. GBE. Link
Levy et al. 2015. Quantitative evolutionary dynamics using high-resolution lineage tracking. Nature. Link
February 11th, 2015
We discussed the following paper today:
Ratcliff et al. 2015. Origins of multicellular evolvability in snowflake yeast. Nature Communications. Link
Other cool papers this month:
Joseph et al. 2015. Genetic Variation in the Nuclear and Organellar Genomes Modulates Stochastic Variation in the Metabolome, Growth, and Defense. PloS Genetics. Link
Gutierrez-Arcelus et al. 2015. Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing. PloS Genetics. Link
Makunin et al. 2015 Genes on B chromosomes of vertebrates. Molecular Cytogenetics. Link
Kim and Velando 2015. Phenotypic Integration Between Anti-Predator Behaviour and Camouflage Pattern in Juvenile Sticklebacks. Evolution. Link
Oakeson et al. 2015. Genome Degeneration and Adaptation in a Nascent Stage of Symbiosis. GBE. Link
Foote et al. 2015. Convergent evolution of the genomes of marine mammals. Nature Genetics. Link
Maharjan et al. 2015. Simple phenotypic sweeps hide complex genetic changes in populations. GBE. Link
Cheatle Jarvella and Hinman 2015. Evolution of transcription factor function as a mechanism for changing metazoan developmental gene regulatory networks. EvoDevo. Link
Villar et al. 2015. Enhancer Evolution across 20 Mammalian Species. Cell. Link
Ahmed-Braimah and Sweigart 2015. A Single Gene Causes an Interspecific Difference in Pigmentation in Drosophila. BioRxiV. Link
January 12th, 2015
Happy New Year!
Today we will be discussing the following paper at Journal Club:
Lynch and Hagner 2015. Evolutionary meandering of intermolecular interactions along the drift barrier. PNAS. Link
Other papers of interest this month:
Bank et al. 2015. A Systematic Survey of an Intragenic Epistatic Landscape. MBE. Link
Ling et al. 2015. A new antibiotic kills pathogens without
detectable resistance. Nature. Link
Jones et al. 2014. Promoter architecture dictates cell-to-cell variability in gene expression. Science. Link
Xiong et al. 2015. The human splicing code reveals new insights into the genetic determinants of disease. Science. Link
Schiabor et al. 2014. Saccharomyces cerevisiae mitochondria are required for optimal attractiveness to Drosophila melanogaster. PlosOne. Link
Viersta et al. 2014. Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. Science. Link
Kristler et al. 2015. Genome-engineering with CRISPR-Cas9 in the mosquito Aedes aegypti. BioRxiv. Link
Paaby et al. 2014. A highly pleiotropic amino acid polymorphism in the Drosophila insulin receptor contributes to life-history adaptation. Evolution. Link
Wong et al. 2015. Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals. Genome Research. Link
Today we will be discussing the following paper:
McBride et al. 2014. Evolution of mosquito preference for
humans linked to an odorant receptor. Nature. Link Description: This group studied Aedes aegypti, a ”domestic” form of the mosquito to look at why it has evolved to specialize in biting humans. They found an odor response, which was linked to expression of the gene AaegOr4. It is an interesting example of a single gene contributing to behavioral change in the mosquito host preference.
Other papers of interest this month:
Parker et al. 2014. The evolution of novelty in conserved genes; evidence of positive selection in the Drosophila fruitless gene is localised to alternatively spliced exons. Heredity. Link Description: In our lab, we often think about the contribution of cis-regulatory and trans-regulatory mutations to phenotypic evolution; however, we often don’t consider other potential mechanisms such as alternative splicing. These authors examine the gene fruitless in multiple species of Drosophila and look for signals of selection. They find that most of the gene is under purifying selection, but regions that are alternatively spliced showed evidence of positive selection. This suggests that alternative splicing may be a mechanism for phenotypic evolution that we and others should considered more often.
Bank et al. 2014. A Systematic Survey of an Intragenic Epistatic Landscape MBE. Link Description: The latest paper reporting the results of the EMPIRIC assay from the Bolon lab characterizing the distribution of fitness effects for HSP90. In this elegant paper, the group compares the spectrum of mutational effects in the wild type genetic background to the spectrum effects identified in a set of mutants one mutational step away from wild type. They find abundant epistasis between mutations and, with one intriguing exception, it is mostly negative epistasis. Interestingly, they find no evidence that moving the population off the optimal fitness peak increases the frequency of beneficial mutations. One beautiful thing about their system is that they can then use the HSP90 crystal structure to identify any structural/biochemical correlates of the patterns they observe across different mutations.
Lopez-Rios et al. 2014. Attenuated sensing of SHH by Ptch1
underlies evolution of bovine limbs. Nature. Link Description: This paper looks at the mechanisms underlying digit evolution in animals with hooves, who have lost their 1st, 2nd, and 5th digits since diverging from pentadactyl precursors. They show some really cool evidence that the derived digit morphology is a result of evolution in cis at a sonic hedgehog effector gene, patched. This causes a change in the sonic hedgehog signaling gradient, which appears to lead to loss of asymmetry. Overall, it is a pretty cool story of pinning down the genetic mechanisms underlying the evolution of a very noticeable morphological characteristic.
Marvig et al 2014. Convergent evolution and adaptation of Pseudomonasaeruginosa within patients with cystic fibrosis. Nature Genetics. Link Description: Host infection involves adaptation to a new and challenging environment for opportunistic pathogens, especially when the host is treated with antibiotics to fight the infection. To understand this adaptive process and improve therapeutic strategies, the authors sequenced the genomes of 474 clinical isolates of Pseudomonas aeruginosa sampled from young patients with cystic fibrosis. They identified 36 clone types and established the phylogenetic relationship within each clonal lineage. Interstingly, these lineages share many features with strains obtained from experimental evolution, such as pronounced convergent evolution, several occurences of hypermutability and evidence for contingent evolutionary trajectories (where mutations in specific pathways occured multiple times in the same order). Such predictability in pathogen evolution might help in the design of treatments targeting key adaptive processes.
Bewick and Dyer. 2014. Reinforcement shapes clines in female matediscrimination in Drosophila subquinaria. Evolution. Link Description: How does natural and sexual selection for premating isolation change between allopatric, sympatric, and interspecific populations? Bewick and Dyer associated patterns of genetic similarity and gene flow with behavioral mate discrimination between sympatric and allopatric Drosophila subquinaria populations and sympatric and allopatric populations of Drosophila recens. They found that conspecific D. subquinaria populations that were sympatric with D. recens (a species that shares a most recent common ancestor with D. subquinaria) were less likely to mate with each other than populations that were allopatric with D. recens. None of the D. recens populations were able to mate with heterospecific D. subquinaria populations if these two species were found in sympatry, but some D. recens populations that were allopatric to D. subquinaria were able to mate. The clines in behavioral discrimination within and between species, therefore, was found to be similar in shape. Bewick and Dyer find that the genetic basis for this observed clinal pattern of intraspecific and interspecific mate descrimination may be due to shared or linked loci.
Smith et al. 2014. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nature Genetics. Link Description: Might have read this before. Interesting paper of how to use synthetic promoters to investigate organization rule of gene regulation in promoter region. It is not directly relevant to our research, but a good understanding of this field might help predict fitness effect of mutations generated in future experiments.
Stergachis et al. 2014. Conservation of trans-acting circuitry
during mammalian regulatory evolution. Nature. Link Description: **This paper goes with the Vierstra 2014 Science paper and they are best read together.** Gene regulation is controlled by interactions between cis- and trans-regulatory elements. This paper uses DNase I footprinting in mouse to identify locations where cis-regulatory elements are bound by trans-regulatory factors and compares the results to similar data collected in humans. They find that while the vast majority of transcription factors have the same recognition sequence between species and the majority of regulatory regions are conserved, the underlying transcription-factor binding sites are not conserved. Next, they look at conservation of transcription factor to transcription factor networks, finding substantially more conservation than for the specific cis-regulatory elements. They conclude that selection on gene regulation acts primarily to conserve trans-regulatory interactions, allowing for divergence of cis-regulatory elements.
Vierstra et al. 2014. Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. Science. Link Description: Vierstra et al use DNaseI-seq accessibility to identify potentially regulatory sequences in multiple mouse tissues, including enhancers. They identify a set of shared DNaseI-hypersensitive (DHS) by comparing DHS in humans and mouse across about a dozen cell types/tissues. Within these shared DHS, the density of transcription factor binding site is maintained, but the specific positioning and composition of TFBS varies.They propose that cis changes are evolutionarily plastic in the presence of an invariant trans-regulatory environment.
November 6, 2014
Monday we will be discussing the following paper:
Buil et al. 2014. Transcriptome Sequencing Reveals Widespread Gene-Gene and Gene-Environment Interactions. BioRxiv. Link Description: A short and interesting paper– they sequenced a huge (by our standards) population of twins and looked for the genetic drivers of allele-specific expression. Surprisingly, they found that variation in cis plays a limited role– finding the rest better explained by widespread gene-gene and gene-environment interactions. They concluded that, roughly quoting, ”while allele-specific expression requires genetic variability in cis, the magnitude of the difference depends on trans genetic and environmental factors that interact with the cis regulatory variants.”
Other papers the lab found interesting this month:
Christiaens et al. 2014. The Fungal Aroma Gene ATF1 Promotes Dispersal of Yeast Cells through Insect Vectors. Cell Reports. Link Description: This is a very exciting piece of work comprehensively demonstrating the impact of expression of yeast gene ATF1 on Drosophila behavior with consequences for yeast dispersal. (See also, why beer tastes good.)
Hope and Dunham 2014. Ploidy-Regulated Variation in Bioﬁlm-Related Phenotypes in Natural Isolates of Saccharomyces cerevisiae. G3. Link Description: Using a new collection of natural isolates from yeast, this group characterizes 6 biofilm-related phenotypes and show a complex view of the impact of ploidy on biofilm phenotypes.
Sharon et al. 2014. Probing the effect of promoters on noise in gene expression using thousands of designed sequences. Genome Research. Link Description: A very cool paper using synthetic promoter to study expression noise. This is highly relevant to our work and might improve understanding of our data better. The authors use synthetic sequences before marker genes to study the relationship between mean expression level and expression noise and find out that thought mean might be the same, noise can vary a lot. They derive a kinetic model from the data and conclude target search of TFs along chromosome might be important for noise. The chromosome disfavouring sequences are also mentioned in the paper.
Lewis et al. 2014. Genetic Architecture of Ethanol-Responsive Transcriptome Variation in Saccharomyces cerevisiae Strains. Genetics. Link Description: Authors did QTL mapping of the ethanol response in 2 strains of yeast, focusing on a “hospot” loci that reveal some of the genetic architecture underlying natural variation in a stress response and shows new specifics about how yeast respond to ethanol stress.
Cridland et al. 2014. Gene Expression Variation in Drosophila melanogaster Due to Rare Transposable Element Insertion Alleles of Large Effect. Genetics. Link Description: While many recent studies have focused on the effects of different types of mutation and their role in changes in gene regulation, this manuscript highlights a recognized but understudied mechanism of regulatory divergence, transposon movements.
Santos et al. 2014. The evolution of cichlid ﬁsh egg-spots is linked with a cis-regulatory change. Nature Communications. Link Description: Over the last few million years, ~1500 species of African cichlids have evolved a diverse array of colored spots on the anal fins of males. Here, the authors link this trait to novel expression patters of the b paralog of the fl2 gene, which contains a transposable element insertion in a cis-regulatory element specifically in lineages that display these novel spots. I think this is really cool, tying gene duplication, subfunctionalization, jumping genes, and gene expression evolution together into one story underlying a novel trait.
Lee et al. 2014. Unifying Genetic Canalization, Genetic Constraint, and Genotype-by-Environment Interaction: QTL by Genomic Background by Environment Interaction of Flowering Time in Boechera stricta Plos Genetics. Link Description: This group studies genetic canalization by detecting QTL covariance of phenological traits in 6 different environments in Boechera stricta (close relative of Arabidopsis).
Angert et al. 2014. Phenotypic constraints and community structure: Linking trade-offs within and among species. Evolution. Link Description: The paper looks at quantitative genetics of relative growth rate and water-use efficiency traits in distantly related desert plants to compare the phenotypic constrains within and between species. They find two limitations, genetic variation and negative trait correlation, acting on a community that prevents high relative growth rate and high water-use efficiency phenotypes in that population.
Lin et al. 2014. Genomic analyses provide insights into the history of tomato breeding. Nature Genetics. Link Description: Domestication of various plants and animals has had a significant impact not only on the human population that mediates the process, but also on the species being domesticated. Many of these effects are effectively cataloged in the genomes of domesticated species. By examining genomic sequences from 360 tomatoes, including domestic, wild, and hybrids, Lin et al. were able to examine the phylogenetic relationships among their sequenced samples. They detected and explored signals of selection, which gives insight into the selective pressures and molecular mechanisms that produced today’s tomato crops.
Yamamoto and Seto 2014. Dopamine Dynamics and Signaling in Drosophila: An Overview of Genes, Drugs and Behavioral Paradigms. Exp. Anim. Link Description: In the melanin pigmentation pathway in Drosophila, tan and ebony catalyze opposing reactions leading to the formation of dark and light pigments, respectively. At the biochemical level, these reactions convert dopamine to N-beta-alanyldopamine (tan) or NBAD to dopamine (ebony). Since dopamine is also a neurotransmitter, it follows that changes in tan and/or ebony function may impact behavior or other neurological function in addition to impacting cuticle pigmentation. In this review, Yamamoto and Seto provide an overview of dopamine signaling in Drosophila, which may provide a unique outlook on tan and ebony – two genes that contribute to the pigmentation difference seen between D. americana and D. novamexicana.
Wood et al. 2014. Defining the role of common variation in the genomic and biological architecture of adult human height. Nature Genetics. Link Description: Wood et al. identified a large number of gene sets and biological pathways associated with human height by sampling over 250,000 individuals. They identified 697 variants that together explain more than 20% of variance in human height. They highlight their results as evidence that increasing sample sizes in GWAS studies leads to identifying SNPs in enriched, previously associated regions of the genome instead of associating SNPs distributed at random across the entire genome as previously suggested. SNPs in genes associated with musculoskeletal development were among the genomic regions with the highest significance levels. Wood et al. (2014) illustrates the power of quantitative genetic research today.
Peterson et al. 2014. Reputation and impact in academic careers. PNAS. Link Description: Paper citation patterns are reflect by the ”reputation” of the central author…at least in the first years after publication.
October 30, 2014
Rich Lusk, a post-doctoral fellow in our lab, is getting some press for his recent paper – Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data – including a Michigan News release that is currently on the U-M Gateway as well as an article in The Scientist.
October 12, 2014
Monday we will be discussing the following paper:
Pougach et al. 2014. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. Link Description: Changes in gene regulation are important contributors to evolutionary change. Prior research has focused primarily on the role of cis-regulatory differences in mediating these changes. Four recent papers (Baker et al. 2013; Sayou et al. 2014, Pougach et al. 2014, McKeown et al. 2014) explore the mechanistic basis of differences in gene regulation in a more complete manner by determining the trans-regulatory changes required to rewire a transcriptional network. While there are many similarities in the questions addressed, the approaches vary widely. Surprisingly, clear differences in the evolutionary paths exist. For example, gene duplication seems to be important (Baker, Pougach, McKeown), but not required (Sayou). Likewise, three studies suggest that promiscuity in the ancestral state is crucial (Baker, Pougach, Sayou), but no evidence of this exists in the fourth (McKeown). In two instances, sub-functionalization of the regulatory network from a previously promiscuous ancestor occurred (Baker, Pougach), while the other cases suggest neo-functionalization (Sayou, McKeown). However, in both cases of neo-functionalization, data suggests that a permissive intermediate state was required. Thus, in all instances evolution proceeded through a path where ancestral function was retained. Finally, while all studies suggest that the number of cis-regulatory changes is small (<3), details are only known for a couple (Pougach, Sayou) and the exact path couldn’t be determined in all cases. Taken together, these studies provide mechanistic paths for evolution to modify gene regulatory networks and show how novel patterns can arise in a step-by-step manner.
Take a look at the others chosen to be of interest in the lab:
Lack et al. 2014. The Drosophila Genome Nexus: a population genomic resource of 605 Drosophila melanogaster genomes, including 197 genomes from a single ancestral range population. BioRxiv. Link Description: Authors have assembled a great population genetic resource– >600 aligned genomes, including ~200 from a single population.
Bravo et al. 2014. Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae). Evolution. Link Description: This paper looks at morphometrics and the natural history of Myrmotherula (antwrens) to investigate phenotypic similarities, specifically the evolution of similar patterning, in distantly related species. The researchers discuss the mechanisms of phylogenetic inch conversion and convergent evolution contributing to ecomorphological evolution in the genus.
Shakhmantsir et al. 2014. Regulation of Cuticle Pigmentation in Drosophila by the Nutrient Sensing Insulin and TOR Signaling Pathways. Developmental Dynamics. Link Description: After demonstrating that flies reared on 10% nutrition show reduced abdominal pigmentation, the authors employ a series of of genetic manipulations, which together suggest that Drosophila melanogaster pigmentation is responsive to nutrient conditions through insulin signaling and TOR signaling. They speculate that this nutrient-mediated modulation of pigmentation suggests a high metabolic cost of melanization, which may lead to selection for plasticity in nutrient-scarce conditions.
Zahn et al. 2014. The genetics of monarch butterfly migration and warning colouration. Nature. Link Description: Despite the popularity of the monarch butterfly migration and recent declines in the phenomenon being staggering enough to make mainstream media news, relatively little is known about the genetic basis of this and other iconic phenotype of the species. These authors sequence the genomes of 101 monarch butterflies (Danaud plexippus) to explore the genetic basis of migration and wing pigmentation phenotypes, as well as the evolutionary forces that have shaped those phenotypes.
Ayroles et al. 2014. Behavioral individuality reveals genetic control of phenotypic variability BiorXiv. Link Description: Most efforts to identify genes underlying a trait use the trait’s mean value. Here, Ayroles et al, instead map variance in the trait fly handedness using GWAS. They are able to validate a candidate gene with several approaches and trace one of its functions to the fly brain
Zid et al. 2014. Promoter sequences direct cytoplasmic localizationand translation of mRNAs during starvation in yeast. Nature. Link Description: In this paper, based on the study of a few genes whose transcription is increased upon glucose starvation in yeast, the authors showed that promoters do not only regulate gene expression at the transcriptional level, but can also affect translation efficiency and mRNA subcellular localization. They used chimaeric promoters and imaging of mRNA in individual cells to identify specific promoter elements involved in transcript localization.
Chandler, Eisen and Kopp 2012. Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts Applied and Environmental Microbiology. Link Description: In this paper from a few years back, Chandler, Eisen, and Kopp characterize the yeast diversity in Drosophila gut communities, with a focus on Ascomycetes. They find that relatively few taxa make up most of the diversity they uncover and that host diet is a stronger predictor of yeast community than host species identity.
Yeh and True 2014. The genetic architecture of coordinately evolving male wing pigmentation and courtship behavior in Drosophila elegans and D. gunungcola. G3. Link Description: Yeh and True map QTLs for courtship and pigmentation divergence between D. elegans and D. gunungcola. For both quantitative traits, they map multiple QTLs and it looks like one of these overlap for wing display behavior. This overlapping QTL includes the gene yellow (and several more). They suggest that future studies should include fine-scale mapping with the aid of CRISPR and automated behavioral monitoring technology.
Gire et al. 2014. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science. Link Description: A large group of researchers sequence genomes of 78 patients in Sierra Leone to ~2000x coverage, elucidating the Ebola virus origin and transmission during this years outbreak. Interesting to see how they traced the rapid evolution and the mutations in individuals causing new viral lineages.
Garrigan et al. 2014. Genome diversity and divergence in Drosophila mauritiana: multiple signatures of faster X evolution. Genome Biology and Evolution. Link
October 5, 2014
Congrats Trisha on your Faculty Recognition Award!
Trisha Wittkopp is included among the 26 UM faculty honorees listed in the latest University Record*. Her Faculty Recognition Award is given to faculty early in their careers who have demonstrated substantive contributions to the university through achievements in scholarly research and/or creative endeavors; excellence as a teacher, adviser and mentor; and distinguished participation in service activities of the university. * http://record.umich.edu/articles/faculty-members-honored-scholarship-service
September 8, 2014
Trisha, Brian, Jon, and Andrea all attended the EEB Retreat this weekend at the UM Biological Station and had a blast chatting, hiking and attending workshops!
September 5, 2014
Monday we will be discussing the following paper:
Szamecz et al. 2014. The Genomic Landscape of Compensatory Evolution. Plos Biology. Link Description: This group argues that despite core processes being well conserved, and while gene loss may initially be deleterious, organisms can recover fitness by the accumulation of compensatory mutations elsewhere in the genome.
Take a peek at the others chosen to be of interest in the lab:
Kebschull and Zador 2014. Sources of PCR-induced distortions in high-throughput sequencing datasets. BioRxiv. Link Description: The authors investigate sources of PCR bias in high-throughput sequencing data, finding that libraries prepared from dilute samples may be at particular risk to PCR stochasticity.
Burke, Liti, Long. 2014. Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae. MBE. Link Description: This paper represents another yeast evolution experiment imposing selection in a laboratory environment and then sequencing the final populations to identify the mutations that fixed. The wrinkle in this case is that the authors started from a genetically variable population and alternated between sexual and asexual growth. By allowing for outcrossing and starting from a large pool of standing genetic variation, the authors show that adaptations were largely drawn from standing genetic variation rather than new mutations. They also show that selection on this standing genetic variation results in greater repeatability across replicates, including adaptation involving the same variants, than in prior work studying de novo mutations. They use these observations to emphasize the importance of maximizing replication in evolutionary experiments of sexual organisms.
Lasky et al. 2014. Natural Variation in Abiotic Stress Responsive Gene Expression and Local Adaptation to Climate in Arabidopsis thaliana. MBE. Link Description: The authors look at changes in gene expression, comparing genes with consistent response to stress to genes with genetically variable response to stress, and how these expression differences affect fitness and adaptation in natural populations of Arabidopsis. They show that different processes act on genes with conserved versus genetically variable stress responses and conclude that cis-regulatory evolution and environmental plasticity in response to stress may drive adaptation. This paper is interesting because it investigates the mechanism that link polymorphism to fitness variation along climatic gradients.
Bastide et al. 2014. Pigmentation in Drosophila melanogaster reaches its maximum in Ethiopia and correlates most strongly with ultra-violet radiation in sub-Saharan Africa. BMC. Link Description: The authors compare sub-Saharan D. melanogaster pigmentation across latitudinal and altitudinal clines as well as within individual animals (between thoracic and abdominal landmarks). I find this approach interesting, since modular regulation of pigmentation genes could presumably allow pigmentation in different body segments to respond independently to selective pressures
Wang et al. 2014. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics. Link Description: Authors found out several loci that show convergent evolution under independent resources of artificial selection for two rice species.
Ghavi-Helm et al. 2014. Enhancer loops appear stable during development and are associated with paused polymerase. Nature Letters. Link Description: In this paper, the authors use 4C-seq (chromosome conformation capture sequencing) to characterize the topology of genomic interactions for a set of 100 D. melanogaster enhancers at two time points during embryogenesis and in two embryonic tissues. They show that most enhancers interact with several genomic regions at long range (>50kb) and these interactions tend to be very stable across tissues and time and are associated with paused RNA polymerase (measured using GRO-seq). Overall, the results suggest that chromatin is organized in 3D hubs from which the expression of distant genes can be co-regulated.
Parts et al. 2014. Heritability and genetic basis of protein level variation in an outbred population. Genome Research. Link
Albert et al. 2014. Genetics of single-cell protein abundance variation in large yeast populations. Nature Letters. Link Description: Changes in gene expression are important for evolution and there is a rapidly growing catalog of known expression QTLs (eQTLs). However, eQTLs are often detected by their effects on mRNA levels and not by their effects on protein levels. Disconcertingly, several recent studies suggest only a weak correlation between mRNA level and protein level for any specific gene, suggesting that many known eQTLs may largely be biologically irrelevant and that changes in mRNA level may often be unimportant. One of the concerns with this comparison, however, is the vastly different quality levels of mRNA abundance and protein abundance data; protein abundance measurements primarily rely on mass spectrometry data, which is more difficult to collect and analyze than the typical RNA-seq experiments used to measure mRNA abundance. These two papers take an alternative approach to estimating protein abundance using fluorescently tagged proteins. Using a cross between two yeast strains, they identify protein QTLs (pQTLs) and look at their overlap with previously identified eQTLs in this same cross. Overall, the results suggest that in fact, many pQTLs are eQTLs and that poor quality protein abundance data is likely the culprit for the low correlation between mRNA and protein abundance reported in previous studies. In addition to these results, the authors also identify a number of highly pleiotropic, trans-acting, pQTLs that dominate the total number of pQTL effects, suggesting that, at least within species, pleiotropic mutations may not be always removed by natural selection and instead, may actually play important roles in gene expression evolution.
Ryan et al. 2014. Selection of chromosomal DNA libraries using a multiplex CRISPR System in Saccharomyces cerevisiae. BioRxIV. Link Description: Using newly optimized CRISPR-Cas9 technologies, this group discusses a new multiplex system to accelerate selection experiments in yeast.
August 10, 2014
Take a peek into the papers our lab finds interesting this month, which are possible Journal club candidates for further discussion:
Oz et al. 2014. Strength of Selection Pressure Is an Important Parameter Contributing to the Complexity of Antibiotic Resistance Evolution. MBE. Link Description: This E. coli article is a little outside our usual sphere as a study about prokaryotic phenotypes, but I was intrigued because the authors ask how evolving populations under selection for growth in the presence of one antibiotic influences their ability to survive other antibiotics. Put another way, how does selecting for high fitness in one area of the population’s reaction norm influence phenotypes expressed in other environments? A very basic question we don’t know the answer to in the context of an important and ongoing public health crisis. Unsurprisingly, the answer is ”it depends.” Adaptation to different classes of antibiotics provided varying levels of cross-protection depending on the specific pathways targeted, and in one case a tradeoff. More generally, the authors highlight differences in the rate of evolution between conditions varying in the strength of selection imposed—strongly selected populations acquired more mutations overall.
Hayward et al. 2014 Natural Selection on Individual Variation in Tolerance of Gastrointestinal Nematode Infection. PlosBio. Link. Description: The authors use a sheep model to estimate individual tolerance to impact from parasites. They find out that there are positive phenotypic selections on tolerance, and the variation observed in samples doesn’t have a additive genetic background, which is interesting.
Trombetta et al. 2014. Inter- and Intraspecies Phylogenetic Analyses Reveal ExtensiveX–Y Gene Conversion in the Evolution of Gametologous Sequences of Human Sex Chromosomes. MBE. Link. Description: The paper supports the idea that gene conversion on the X-Y chromosomes is present and that the male-specific region on the Y chromosome may be a result of genetic information from the X-chromosome even though it was believed that the male region was genetically independent of the X.
Buser et al. 2014. Niche construction initiates the evolution of mutualistic interactions. Ecology Letters. Link. Description: The authors suggest that niche construction might be a mechanism in the evolution of mutualisms. They study the symbiotic relationship between D. simulans and S. cerevisiae, which are of course, two species studied in our lab. The authors state that Drosophila benefit from yeast-infest fruit, and aimed to determine how the yeast were affected by this relationship. They claim that yeast niche modification provides evidence of a mutualistic interaction.
Chen et al. 2014. Dissection of a Ciona regulatory element reveals complexity of cross-species enhancer activity. Developmental Biology. Link. Description: Conserved Non-coding Elements (CNEs) are hypothesized to be under evolutionary constraint due to their specific clusters of transcription factor binding sites. In some cases, Cis Regulatory Modules (CRMs) can drive similar expression patterns to orthologous genes in cross-species transgenesis experiments, even when primary sequence conservation is insufficient to identify the element as a CNE. The authors dissect one such CRM, associated with the Ciona intestinalis ßγ-crystallin (ßγ-cry) gene to determine whether the TF-binding sites within the CRE have conserved function across taxa. This CRM had previously been shown to drive expression in vertebrate embryos in a pattern similar to the orthologous vertebrate ßγ-cry gene, despite great evolutionary distance. By constructing gene regulatory network models and comparing the function of selectively mutated reporter transgenes in both C. intestinalis and zebrafish, they show that the binding motifs necessary for expression in C. intestinalis are not required for expression in zebrafish. This suggests conservation of CRM function across taxa may be more complex than simple conservation of individual candidate TF-binding sites.
Sharon et al. 2014. Probing the effect of promoters on noise in gene expression using thousands of designed sequences. Genome Research. Link. Description: The authors use an elegant method that they developed 2 years ago to isolate the effects on mean expression and noise of different promoter properties (using a collection of 6500 designed promoters driving YFP expression in yeast). With this method, they can characterize the distribution of activity for all promoters at the same time. Although they recognize the current limitations of the approach, their results strongly suggest that different promoters features can affect the mean independant component of noise in different ways. For instance, nucleosome disfavoring sequences tend to increase mean and decrease noise, while increasing the number of Gcn4 transcription factor binding sites can increase both mean and noise.
Kryazhimskiy et al. 2014. Global epistasis makes adaptation predictable despite sequence-level stochasticity. Science. Link. Description: This paper uses experimental evolution in yeast to test to what extent prior adaptation to an environment determine the direction of further adaptation. Surprisingly, they find that genetically similar lines do not adapt in the same manner and suggest that this is caused by a large number of epistatic interactions. Even more surprisingly, however, is that the specific epistatic interactions appear to be largely irrelevant as the amount of adaptation in a line can predict nearly its entire future adaptive potential, mostly irrespective of its genotype. Hence, the authors conclude that while the individual course of adaptation is likely unpredictable, the end result may be very clear. They suggest that this is caused by a large degree of negative epistatic interactions for fitness, and not the particular mechanism by which the adaptation takes place.
Arnold et al. 2014 Quantitative genome-wide enhancer activity mapsfor five Drosophila species show functional enhancerconservation and turnover during cis-regulatory evolution. Nature Genetics. Link. Description: These authors use STARR-seq (Self-Transcribing Active Regulatory Region sequencing) to measure enhancer activity of 5 different Drosophila species (D. melanogaster, D. yakuba, D. ananassae, D. pseudoobscura, and D. willistoni). They do so in the common trans-regulatory environment of D. melanogaster S2 cells. Their findings suggest that a substantial amount of enhancer activity is conserved. Surprisingly, they also identify a large number of activity gains (rather than losses) between closely related Drosophila species.
Kao et al. 2014. Postmating reproductive barriers contribute to the incipient sexual isolation of US and Caribbean Drosophila melanogaster. BioRxiv. Link Description: Premating reproductive barriers do not fully explain the degree of isolation between two strains of melanogaster– one from the SE United States and one from the Caribbean– so the authors investigated a variety of postmating barrier mechanisms (e.g. remating, hatchability, etc). They found that more than one mechanism contributes, including differences in female lifespan after mating with genetically similar or different strains.
Noor, Myers, and Millman. 2014. Genetics and Evolution: An iOS Application to Supplement Introductory Courses in Transmission and Evolutionary Genetics. G3. Link Description: Noor (Duke) has developed with collaborators an iOS app that helps teach Evolution and Genetics. It involves everything from heritability to genetic cross mapping to ”Allele Freak” that tracks and graphs the fate of alleles over multiple generations based on relative fitness, genetic drift etc. It’s a free download on iTunes and seems like an awesome way to generate practice problems for high school and intro college students. Might be cool to check out how it works!
August 1, 2014
Kraig Stevenson, a Bioinformatics student in our lab, defended his thesis today! He is jumping right into a career as a Data Scientist at Trinity Health here in Michigan. We are sad to see him go, but happy for him in the next chapter of his life!
July 22nd, 2014
Have you heard about REBUILD?
Here at the University of Michigan, we like acronyms. REBUILD = Researching Evidence Based Undergraduate Instructional and Learning Developments
Dr. Wittkopp is actively taking a part in the development of new STEM (science, technology, engineering or math) courses, which will greatly benefit undergraduates by immersing them in active and engaged learning in the classrooms.
REBUILD will help institutionalize evidence-based instruction as the new normal.
Check out the website for more info!
May 10th, 2014
Our lovely undergraduates Cassi Kirkland, Natasha Sood, and Emily Roberts recently gave posters at the UROP Spring Symposium. Great Job Ladies!!
Emily Roberts also traveled to Boston for Scientista’s Symposium in early Spring 2014 to talk about her early experiments in D. sechellia larval preference
November 2013, Cinncinati Undergraduate Research Conference
Tiffany Brooks, a visiting undergraduate in our lab, presented at the CUR Conference.
April 2013 UROP Posters
Cassi Kirkland and Natasha Sood presented posters at this year’s UROP Spring Symposium