People in the Cooley Lab

Arielle Cooley. I am a broadly trained evolutionary biologist, primarily interested in the evolution of phenotypic diversity. My goal is to connect cellular, molecular and genomic processes to organismal variation in phenotype and fitness.

My research background includes a post doc in Patricia Wittkopp's lab, where I focused on two closely related fruit fly species that differ in body color. My ongoing research interest, initiated as a graduate student in John Willis' lab, involves floral diversification in a group of South American wildflowers in the "monkeyflower" genus Mimulus. I am pursuing this work at Whitman College as well as teaching Genetics; Evolution & Development; and Plant Physiology.

Current Lab Members

Dan Thomas, Ph.D. Dan joined the lab in April 2018 and is working on a variety of genomic and transgenic projects. One experiment is to compare petal transcriptomes of wild-type M. l. variegatus to those of M. l. variegatus transformed with RNAi against candidate petal-anthocyanin activating gene Myb5, in order to determine whether Myb5 was successfully down-regulated; whether its regulatory targets (the anthocyanin biosynthetic enzymes) are in turn down-regulated; and whether any other Myb genes show off-target reductions in expression as a result of the RNAi.

Melia Matthews '20. To explore how complexity can arise from inter-genomic interactions, Melia is advancing our genetic mapping of the floral color patterning seen in the F1 and F2 hybrids of the two apparently solid-colored species M. l. variegatus and M. cupreus. She is photographing petals, extracting DNA for Illumina sequencing, and trying out a new digital image analysis pipeline created by Dr. Doug Hundley of the Whitman College mathematics department. The image analysis method will be used to quantify aspects of hybrid color patterning that are too complex for simple measurement.


Jonah Rodewald '19. Jonah is launching gene expression work in our least-studied species, M. naiandinus. In both M. naiandinus and M. cupreus, genomic region pla1 activates petal anthocyanins, but we don't know whether the two species independently invented the idea (two separate mutations in the same region) or whether a single ancestral mutation has been shared between the species. We hope to discover this, in part by comparing the genes responsible for petal anthocyanin in M. naiandinus versus M. cupreus.


Ashley Person '19. Ashley is completing and testing RNAi constructs to knock down candidate petal anthocyanin genes Myb2b and Myb3a in the orange-flowered species M. cupreus, to determine whether either of these genes is necessary for the recent gain of petal anthocyanins in M. cupreus. She is also building a transgene to express Myb5 from the purple-flowered M. l. variegatus at high levels in species that lack petal anthocyanin, to determine whether the variegatus allele of Myb5 is sufficient to activate petal anthocyanin.


 

Graduates

Johanna AuJohanna Au '19. Johanna helped build RNAi constructs to silence two genes, Myb2b and and Myb3a, that are our top candidates for causing the evolutionary gain of petal anthocyanin pigmentation in the orange-flowered Mimulus cupreus. She used a Gateway strategy, in which fragments of each gene are directionally cloned into the pENTR entry vector and then recombined in to a destination vector that will be used for transformation.

Jessie FriedmanJessie Friedman '18. A recently-constructed Mimulus cupreus transcriptome provided coding sequence for petal pigment candidate genes Myb2b and Myb3a. To fully evaluate the functions of these genes, however, we need to know their upstream regulatory sequences so that we can build transgenic constructs driven by the native promoter of each gene. Jessie leveraged existing genomic resources to design primers to "fish out" promoter sequence from M. cupreus.

Kuenzang OmKuenzang Om '18. Kuenzang used transgenics to functionally test the role of candidate gene Myb5 in petal lobe anthocyanin (PLA) pigmentation. In this photo she is transforming the purple-flowered M. l. variegatus with an RNAi construct to silence Myb5. She found that the resulting transgenic offspring had white flowers, indicating that Myb5 is indeed necessary for the recently-evolved trait of PLA in M. l. variegatus.


ErinErin Minus '18. Erin continued the work of Aaron Williams '17, using digital image analysis in ArcGIS to quantify spatially complex pigment patterns in an F2 hybrid population derived from an M. cupreus x M. l. variegatus cross. You can see the ArcGIS program running in the background of this photo. Erin will compare phenotypes she obtains to the genotypes from our first sequenced individuals (96 F2 plants) in order to genetically map some of the traits.


Taylor WilkeTaylor Wilke '18. Taylor used the same F2 population as Erin to investigate a different trait, yellow carotenoid pigment. When Mimulus cupreus gained petal anthocyanin, it kept its carotenoids; the combination of the two pigments are what creates its orange color. Mimulus l. variegatus, in contrast, gained anthocyanin but lost floral carotenoids. Carotenoid abundance segregates in our F2 mapping population. Suprisingly little is known about the genetics of carotenoid regulation, and we hope to discover some of the genes involved over the course of this mapping project.

Rachel EguiaRachel Eguia '17. Rachel worked on building transgenes to test the function of candidate pigmentation gene Myb5. The eventual goal is to silence Myb5 in plants that have petal anthocyanin pigmentation, and activate Myb5 in plants that lack petal anthocyanin pigmentation, in order to test the hypothesis that Myb5 is both necessary and sufficient for the recent gain of petal anthocyanins in the purple-flowered Mimulus luteus var. variegatus.

Aaron WilliamsAaron Williams '17. Crossing a plant with solid purple flowers (M. l. variegatus) to a plant with solid orange flowers (M. cupreus) yields a hybrid with complex patterns of red blotches overlaid on a cream background. Little is known about the developmental regulation of "speckliness," and it is difficult to measure using traditional means. Aaron helped develop a digital image analysis approach for extracting quantitative trait values from the complex spatial variation seen in an F2 hybrid population.

Anne VonadaAnne Vonada '17. The recent gain of petal anthocyanins in the orange-flowered M. cupreus is controlled by a single locus that we call pla1. This region of the genome is unlinked to Myb5 (the top candidate in M. l. variegatus), but it does contain numerous Myb transcription factors that are similarly good candidates for activating petal pigmentation in M. cupreus. Anne Vonada used genomics, transcriptomics, and RT-PCR to evaluate candidate genes at pla1, and was able to narrow down the list from six genes to two: Myb2b and Myb3a.

JessicaJessica Palacios '16. Previous work in the luteus complex of Mimulus has utilized a single inbred line as the representative of the species. But just how representative is that line? Jessica launched an exploration of the wider range of diversity within several species, which revealed consistent trends as well as important differences between our inbred lines and a panel of wild-collected accessions.


JeremyJeremy Nolan '16. Jeremy is interested in the physiological consequences of environmental pollution. He modified a plant incubator to serve as a CO2 chamber, in order to test the effects of elevated CO2 on plant growth and photosynthesis across a diverse collection of Mimulus accessions from Chile.



Allison EggertAllison Eggert '16. The luteus group of Mimulus is tetraploid, and contains two "homeologous" (duplicate) copies of the Myb5 gene. Myb5a is tightly linked to the gain of petal pigmentation in M. l. variegatus, while Myb5b is unlinked. Surprisingly, they are 100% identical from start codon through 3'UTR. Divergence in the 5'UTR allowed Allison to design homeolog-specific primers. She found that Myb5a has high expression in anthocyanin-pigmented petals, while Myb5b has uniformly low expression across tissues and species.

Kimmy Stanton prepares to transform MimulusKimberly Stanton. Kimmy, a Reed College ('14) graduate, worked as a technician in the Cooley lab before going on to graduate school in evolutionary biology at Duke University. She developed a transcriptome-supported approach to identifying qPCR reference genes for Mimulus, and worked towards transgenic transformation in M. cupreus. Here, Kimmy prepares plants for a vacuum infiltration to drive Agrobacteria into the floral bud tissue, as part of plant transformation. (Photo Credit: Larry North)

PhilipPhilip Cheng '15. Philip used quantitative RT-PCR to measure expression patterns of candidate pigmentation genes Myb4 and Myb5 in M. l. luteus and M. l. variegatus. Here he is setting up a run on the qPCR machine. Philip discovered that Myb4 has almost no expression in leaf, petal, or nectar guide tissue; in contrast, Myb5 expression is high in anthocyanin-pigmented tissues. This strongly supports Myb5 as the causal gene for pigment gain in M. l. variegatus.

MarijkeMarijke Wijnen '15. Celine's research revealed an anthocyanin-producing stress response following an (unplanned!) heat wave that imposed both heat and drought. Marijke followed up on this work, using controlled treatments to disentangle the effects of these two environmental stressors. She found that drought, but not heat, induced vegetative anthocyanin pigments. Interestingly, the heat treatment resulted in an increased proportion of deformed flowers - possibly a Heat Shock Protein effect..? Here she measures photosynthesis in the greenhouse.

Celine in the greenhouseCeline Valentin '14. Celine found that the yellow-flowered M. l. luteus and the orange-flowered, more anthocyanin-rich M. cupreus responded differently to an intense week-long heat wave: the former produced significantly more vegetative anthocyanin pigments. Such environmentally-induced vegetative anthocyanins are considered a sign of plant stress. M. l. luteus therefore appears to have been more stressed during the heat wave. We hypothesize that M. cupreus, in contrast, may be "pre-protected" by its higher constitutive levels of anthocyanin pigments.


Photo of Leah and JanaeLeah Mohtes-Chan '14 (left) and Janae Edelson '14 (right). Leah and Janae launched the molecular lab - Step 1, unpack a LOT of boxes! They extracted DNA from M. l. luteus and prepared it for genomic sequencing at Duke University, which led to the sequencing of the first ever Chilean Mimulus genome. They also used semi-quantitative RT-PCR to discover that two tandemly duplicated candidate pigmentation genes, Myb4 and Myb5, have diverged in function: Myb5 is expressed in both petal and leaf tissue, while Myb4 is not.

Photo of SageSage Stutsman '13. Founding member of the Cooley lab, Sage planted and tended the very first monkeyflower population at Whitman. She is especially interested in hydroponics and developed a hydroponics system to study the effects of different nutrient treatments on plant growth and development.