Behavioral Genomics

Given rapid advances in genomic techniques we are now able to assay, at the whole genome level, gene expression level, genomic content and epigenetic state for a broad range of organisms not previously amenable to genetic/genomic techniques. Genetic systems that underlie sensory processing, emotion and motivation, neuronal development and plasticity are all essential for generating behaviors. By studying how these genetic programs vary between and within species we can begin to understand how they give rise to behavioral diversity.

Each topic will span two weeks. Student pairs will select a behavioral genomics paper that has been published in the last few years (no older than 3 years). They will select another, possibly older, paper that describes the behavior of interest.

Week 1: Discussion about the behavior paper. ~30 minutes
All students read the paper and discuss what types of questions could be asked with genomics, how they should be approached etc. Student presenters may use other sources and prepare some power point slides but this should be a discussion and focus on familiarization with the behavior and generating questions. Presenters will hand out a set of questions to be answered while reading the behavioral genomics paper for the following week.

Week 2: Discussion about the genomics paper. 60 – 90 minutes. Presenters will prepare power point of the figures possibly including some additional information related to methods or specifics of the behavior from the previous week. While students only turn in written answer for 4 question sets, all students are responsible for participating in discussion.

The student pair who presented the previous week will be responsible for snacks and the “who is who” presentation.

-- Students should expect to spend 4-6 hours outside of class each week that they are not presenting/leading and more time the weeks that they are presenting/leading.

-- Both papers should be sent to Suzy at least 1 week before the behavior discussion to be posted.

--Study Questions must be available 1 week before Genomics Discussion.

-- All students must turn in prepared answers for at least 4 topics to be evaluated by student presenters. (All students should be prepared to discuss on all topics!)

Instructor: Suzy Renn
Office Hours: by appointment renns@reed.edu
Website: http://www.reed.edu/biology/courses/BIO431S05_2017/Syllabus.html

Behavior Paper Genomics Paper
Brantley RK, Bass AH. 1994. Alternative Male Spawning Tactics and Acoustic-Signals in the Plainfin Midshipman Fish Porichthys-Notatus Girard (Teleostei, Batrachoididae). Ethology 96: 213-32 Feng NY, Fergus DJ, Bass AH. 2015. Neural transcriptome reveals molecular mechanisms for temporal control of vocalization across multiple timescales. Bmc Genomics 16
Diamond J. 2002. Evolution, consequences and future of plant and animal domestication. Nature 418: 700-07 Stanley & Kkulathenal (2016) Genomic signatures of domestication on neurogenetic genes in Drosophila melanogaster. BMC Evol Biol. 16:6
Eggert AK, Reinking M, Muller JK. 1998. Parental care improves offspring survival and growth in burying beetles. Animal Behaviour 55: 97-107 Parker DJ, Cunningham CB, Walling CA,. Stampe CE, Head ML, Roy-Zokan EM, McKinne EC, Ritchie M, & . Moore (2015) Transcriptomes of parents identify parenting strategies and sexual conflict in a subsocial beetle. Nature Comm 6:8449
Brenowitz EA, Margoliash D, Nordeen KW (1997) An Introduction to Birdsong and the Avian Song System J. Neurobiol. 33:495-500. Lin Y-C, Balakrishnan CN, Clayton DF. 2014. Functional genomic analysis and neuroanatomical localization of miR-2954, a song-responsive sex-linked microRNA in the zebra finch. Frontiers in Neuroscience 8
Patalano S, Hore TA, Reik W, Sumner S. 2012. Shifting behaviour: epigenetic reprogramming in eusocial insects. Current Opinion in Cell Biology 24: 367-73 Patalano S, Vlasova A, Wyatt C, Ewels P, Camara F, et al. 2015. Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies. Proceedings of the National Academy of Sciences of the United States of America 112: 13970-75
Yan H, Simola DF, Bonasio R, Liebig J, . Berger SL, and Reinberg D (2014) Eusocial insects as emerging models for behavioral epigenetic. Nature Rev Genet 15:677-688. Simola DF, Graham RJ, Brady CM, Enzmann BL, Desplan C, et al. 2016. Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus. Science (New York, N.Y.) 351: aac6633-aac33
Taborsky, Oliveira,& Brockman (2008) The evolution of alternative reproductive tactics: concepts and questions Partridge CG, MacManes MD, Knapp R, Neff BD (2016) Brain Transcriptional Profiles of Male Alternative Reproductive Tactics in 2 Bluegill Sunfish PLoSOne 11(12): e0167509
Hogan-Warburg, A.J. (1966) Social behaviour of the Ruff Philomachus pugnax (L.). Ardea 13:109–229. Lamichhaney et al (2015) Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax) Nature Reviews Genetics 48:84-88.
Scott, M.P. (1998) The ecology and behavior of burrying beetles. Annu. Rev. Entomol. 43:595–618 Cunningham et al (2015) The Genome and Methylome of a Beetle with Complex Social Behavior, Nicrophorus vespilloides (Coleoptera: Silphidae). Genome Biology & Evolution 7:3383–3396.
McGraw LA, and Young LJ (2010) The prairie vole: an emerging model organism for understanding the social brain Trends Neurosci. 33(2):103-9. Okhovat, M., Berrio, A., Wallace, G., Ophir, A.G. and Phelps, S.M. 2015. Sexual fidelity trade-offs promote regulatory variation in the prairie vole brain. Science 350:1371-1374.

Sapolsky (2005) The Influence of Social Hierarchy on Primate Health. Science 308:648-652.

 Snyder-Mackler, N., Sanz, J., Kohn, J.N., Brinkworth, J.F., Morrow, S., Shaver, A.O., Grenier, J., Pique-Regi, R., Johnson, Z.P., Wilson, M.E., Barreiro, L.B., and Tung, J. 2016. Social status alters immune regulation and response to infection in macaques. Science 354: 1041-1045.
Cameron, S.A., Mardulyn, P. (2001) Multiple Molecular Data Sets Suggest Independent Origins of Highly Eusocial Behavior in Bees (Hymenoptera:Apinae) Systematic Biology, 50:194-214.
(and find a simple review on genetic assimilation)
Jones, B.M., Kingwell, C.J., Wcislo, W.T., Robinson, G.E. (2017) Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality. Proc. R. Soc. B 284: 20162228

Reading Scientific papers is not easy. Take notes. Take your time. Go back and forth between sections. Question the statements. Interpret the data yourself. Look up terms you don't know. Record questions as they occur to you. Here is a template that may be useful in general.