My research focuses on evolutionary genomics in Lepidoptera, the moths and butterflies. I am particularly interested in the molecular evolution of sex chromosomes and reproductive traits. My work makes extensive use of next-generation sequencing data (i.e. Illumina) for measuring gene expression and genetic variation genome-wide. We also use shotgun proteomics to directly identify proteins found in complex biological samples, such as the saliva and also sperm of butterflies.
Basic computational data analysis for biologists using R
Biological research is becoming increasingly data-rich. Whether you are analyzing next-generation sequencing, ecological remote sensing, or citizen science contributions, standard tools like spreadsheet programs typically are inefficient or ineffective for achieving the desired outcomes with today's large-scale data sets. Often a far more efficient, powerful, and flexible approach is writing your own scripts to analyze and visualize your data. The aim of this course is to facilitate building a foundational skill set for computational data analysis using the statistical and graphical scripting language "R". This course assumes no prior experience with coding or scripting and only a very modest mastery of statistics.
Introductory Genetics (BIOL 350)
Why are related individuals more similar than unrelated individuals and what is the basis for heritable traits? From Mendel's discoveries of the patterns of genetic inheritance, to the study of transmissible hereditary factors, genetics is central to understanding the biological sciences. Topics to be covered include molecular genetics and genetic engineering, Mendelian genetics and mapping, the control of gene expression, cytogenetics, epigenetics and non-Mendelian genetics, and population and quantitative genetics. Examples will be taken from a wide variety of organisms, including viruses, bacteria, plants, fungi, insects, and humans. Genetics is both a body of knowledge encompassing genetic transmission and function, and an experimental approach to the study of biological processes. In addition to acquiring the necessary background knowledge in genetics, throughout the semester we will emphasize problem solving and the analysis of genetic data.
- Whittington, E., Karr, TL, Mongue, AJ, Dorus, S, and Walters, JR. 2019. Evolutionary proteomics reveals distinct patterns of complexity and divergence between lepidopteran sperm morphs. Genome Biology and Evolution 11(7): 1838-1846.
- Mongue, A.J, Hensen, ME., Gu, L., Sorenson, CE, and Walters, JR. 2019. Nonfertilizing sperm in Lepidoptera show little evidence for recurrent positive selection. Molecular Ecology 18(2): 205-14.
- Wan, F, Yin, C, Tang, R., (53 other co-authors), Xiong R., Walters, JR and Li, F. 2019. A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance. Nature Communications 10:4237, 1-14.
- Tan, WH., Acevedo, T. Harris, EV., Alcaide, TY, Walters, JR., Hunter, MD, Gerardo, NM, and deRoode, JC. 2019. Transcriptomics of monarch butterflies (Danaus plexippus) reveals that toxic host plants alter expression of detoxification genes and down-regulate a small number of immune genes. Molecular Ecology 7(5): 651-59.
- Li, F, Zhao X, Li M., He K, Huang, C. Zhou, Y. Li, Z., and Walters, JR. 2019. Insect genomes: Progress and challenges. Insect Molecular Biology, 120(7): 1077-20.
- Yin, C., Li, M., Hu, J., Lang, K., Chen, Q., Liu, J., Guo, D., He, K., Dong, Y., Luo, J., Song, Z., Walters, J.R., Zhang, W., Lin, F., and Chen, F. 2018. The genomic features of parasitism, polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum. BMC Genomics. 19: 420.
- Whittington E, Forsythe D, Borziak K, Karr T. L, and Walters J.R, Dorus S. 2017. Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera. BMC Genomics 18(1): 931.Mongue AJ, Nguyen P, Volenikova A, and Walters J. R. 2017. Neo-sex Chromosomes in the Monarch Butterfly, Danaus plexippus 7(10): 3281–3294.
- Mongue AJ, and Walters J. 2017. The Z chromosome is enriched for sperm proteins in two divergent species of Lepidoptera. Genome Sep:gen–0068
- Gu L, and Walters J.R. 2017. Evolution of Sex Chromosome Dosage Compensation in Animals: A Beautiful Theory, Undermined by Facts and Bedeviled by Details. Genome Biology and Evolution 9(9): 2461–2476.
- Gu L, Walters, J.R, and Knipple D.C. 2017. Conserved patterns of sex chromosome dosage compensation in the Lepidoptera (WZ/ZZ): insights from a moth neo-Z chromosome. Genome Biology and Evolution 9(3): 802–816.
- Walters, J. R., et al. (Manudca sexta genome consortium). 2016. Multifaceted biological insights from a draft genome sequence of a lepidopteran insect, Manduca sexta. Insect Biochemistry and Molecular Biology 76: 118-147.
- Walters JR, Hardcastle TJ, and Jiggins CD. 2015. Sex chromosome dosage compensation in Heliconius butterflies: global yet still incomplete? Genome Biology & Evolution, 7, 2545–2559.
- Karr, TL and Walters JR. 2015. Panning for sperm gold: Isolation and purification of apyrene and eupyrene sperm from lepidopterans. Insect Biochemistry and Molecular Biology, 63, 152–158.
- Harpel D, Cullen DA, Ott SR, Jiggins CD, Walters JR. 2015. Pollen feeding proteomics: salivary proteins of the passion flower butterfly, Heliconius melpomene. Insect Biochemistry and Molecular Biology, 63:7-13.
- Whittington E, Zhao Q, Borziak K, Walters JR, and Dorus S. 2015. Characterisation of the Manduca sexta sperm proteome: Genetic novelty underlying sperm composition in Lepidoptera. Insect biochemistry and molecular biology. 62:183-193.
- Martin SH, Dasmahapatra KK, Nadeau NN, Salazar C, Walters JR, Blaxter M, Manica A, Mallet J, and Jiggins CD. 2013. Genome-wide evidence for speciation with gene flow in Heliconius butterflies. Genome Research 23, 1817–1828.
- Briscoe AD, Munos AM, Kozak KM, Walters JR, Yuan F, Jamie GA, Martin, SH, Jacuin-Joly E, & Jiggins CD. 2013. Female behaviour drives expression and evolution of gustatory receptors in butterflies. PLoS Genetics, 9, e1003620.
- Heliconius Genome Consortium*. 2012 . Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature, 487, 94–98. (*Dasmahapatra & Walters, co-first authors)
- Walters JR, Stafford C, Hardcastle, TJ & Jiggins CD. 2012. Evaluating female remating rates in light of spermatophore degradation in Heliconius butterflies: pupal‐mating monandry versus adult‐mating polyandry. Ecological Entomology, 37, 257–268.
- Walters JR & Hardcastle TJ. 2011. Getting a full dose? Reconsidering sex chromosome dosage compensation in the silkworm, Bombyx mori. Genome Biology and Evolution, 3, 491–504.
- Walters, JR & Harrison RG. 2011. Decoupling of rapid and adaptive evolution among seminal fluid proteins in heliconius butterflies with divergent mating systems. Evolution, 65, 2855–2871.
- Walters JR & Harrison RG. 2010. Combined EST and proteomic analysis identifies rapidly evolving seminal fluid proteins in Heliconius butterflies. Mol Biol Evol. 27 (9):2000-13.
- Maroja LM, Andres JA, Walters JR, & Harrison RG. 2009. Multiple barriers to gene exchange in a field cricket hybrid zone. Biological Journal of the Linnean Society 97:2 390-402.
- Walters JR & Harrison RG. 2008. EST analysis of male accessory glands from Heliconius butterflies with divergent mating systems. BMC genomics, 9: 593.
- Papa R, Morrison CM, Walters JR, Counterman BA, Chen R, Halder G, Roberts L, Kapan DD, Jiggins CD, Reed RD, McMillan WO. 2008. Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies. BMC Genomics 9: 345.
- Wright TF, Johns PM, Walters JR, Lerner AP, Swallow JG and Wilkinson GS. 2004. Microsatellite variation among divergent populations of stalk-eyed flies, genus Cyrtodiopsis. Genetical Research 84(1) 27-40.
- Graustein A, Gaspar JM, Walters JR, Palopoli MF. 2002. Levels of DNA polymorphism vary with mating system in the nematode genus Caenorhabditis. Genetics. 161 (1) 99-107.