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SOLES_edited

Publications

Publications

2023

Dodge, T.O., Farquharson, K.A., Ford, C., Cavanagh, L., Schubert, K., Schumer, M., Belov, K., & Hogg, C.J. (2023). Genomes of two Extinct-in-the-Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights. Molecular Ecology Resources, 00: 1–17. doi: 10.1111/1755-0998.13780 [Full Article]

2022

Aguillon, S.M., Dodge, T.O., Preising, G.A., and Schumer, M. (2022) Introgression. Current Biology 32(16): 865-868. doi: 10.1016/j.cub.2022.07.004 [Full Article]

Langdon, Q.K., Powell, D.L., Kim, B., Banerjee, S.M., Payne, C.Y., Dodge, T.O., Moran, B., Fascinetto-Zago, P., and Schumer, M. (2022) Predictability and parallelism in the contemporary evolution of hybrid genomes. PLoS Genetics 18(1): e1009914. doi: 10.1371/journal.pgen.1009914 [Full Article]

Preprints

Dodge, T.O., Kim, B.Y, Baczenas, J.J., Banerjee, S.M., Gunn, T.R., Donny, A.E., Given, L.A., Rice, A.R., Haase Cox, S.K., Weinstein, M.L., Cross, R., Moran, B.M., Haber, K., Haghani, N.B., Machin Kairuz, J.A., Gellert, H.R., Du, K., Aguillon, S.M., Tudor, M.S., Gutiérrez-Rodríguez, C., Rios-Cardenas, O., Morris, M.R., Schartl, M., Powell, D.L., and Schumer, M. (in review) Complex structural variation and behavioral interactions underpin a balanced sexual mimicry polymorphism. bioRxiv. doi: 10.1101/2024.05.13.594052 [Preprint]

Du, K., Lu, Y., Garcia-Olazabal, M., Walter, R.B., Warren, W.C., Dodge, T.O., Schumer, M., Park, H., Meyer, A. and Schartl, M. (in review) Phylogenomics analyses of all species of swordtails (genus Xiphophorus) highlights hybridization precedes speciation. bioRxiv. doi: 10.1101/2023.12.30.573732 [Preprint]

Langdon, Q.K., Groh, J.S., Aguillon, S.M., Powell, D.L., Gunn, T.R., Payne, C.Y., Baczenas, J.J., Donny, A., Dodge, T.O., Du, K., Schartl, M., Ríos-Cárdenas, O., Gutierrez-Rodríguez, C, Morris, M., and Schumer, M. (in review). Genome evolution is surprisingly predictable after initial hybridization. bioRxiv. doi: 10.1101/2023.12.21.572897. [Preprint]

Preising, G.A., Gunn, T.R., Baczenas, J.J., Pollock, A., Powell, D.L, Dodge, T.O., Machin Kairuz, J.A., Savage, M.L., Lu, Y., Fitschen-Brown, M., Cummings, M., Thakur, S., Tobler, M., Ríos-Cardenas, O., Morris, M., and Schumer, M. (in review) Recurrent evolution of small body size and loss of the sword ornament in Northern Swordtail fish. bioRxiv. doi: 10.1101/2022.12.24.521833 [Preprint]

Grant Proposals

Determining the origin and maintenance of a sexual mimicry polymorphism in swordtail fish [PDF]
NSF GRFP  October, 2021
Awarded

Are the mechanisms underpinning the origin and maintenance of polymorphisms shared across a radiations of species similar or different? I proposed testing this question by studying a sexual mimicry phenotype, the false gravid spot (FGS), which is polymorphic in 11 Xiphophorus species. My first aim was to determine if the FGS originated multiple times independently, evolved as an ancestral polymorphism, or introgressed between species. My second aim was to establish if the behavioral mechanisms of selection favoring the FGS are consistent across Xiphophorus species, or if different mechanisms predominate, depending on sexual dimorphism of other traits. This research will help determine the genetic architecture of adaptive variation and the repeatability of evolutionary trajectories. I am using this research as a spring board to mentor undergraduate students at Stanford and other local colleges in the Bay Area, and will conduct outreach to students in classrooms.

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Uncovering the origin and movement of serpentine-adapted alleles in monkeyflowers [PDF]
NSF GRFP  October, 2019

Honorable Mention

What is the relative importance of standing variation, de novo mutations, and introgression in generating the adaptive variation that allows plants to colonize harsh environments? In my NSF GRFP, I proposed using four monkeyflower species, which have evolved tolerance to serpentine soils, to identify sources of adaptive variation and the repeatability of evolutionary trajectories. My first aim was to identify the genetic basis of serpentine-tolerance, using a combination of GWA approaches and ancestry distortion QTL mapping. My second aim was to characterize origin timing and subsequent movement of alleles contributing to serpentine tolerance among these species using haplotype length comparisons and tests for introgression. This research has implications for serpentine species conservation and crop breeding in an increasingly harsh world. I planned to engage communities local to serpentine soils by providing well-rounded, interdisciplinary research experiences to community college students and by creating evolutionary biology lessons for high school students using the monkeyflower species found in their own backyards.

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Mimulus guttatus

Poster Presentations

The genetic architecture of a female mimicry trait in male swordtail fish
Society for Molecular Biology & Evolution (SMBEv2021)
Presented virtually — July, 2021
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Alternative reproductive strategies are common across the tree of life and often involve female mimicry. Despite their importance as an evolutionary strategy, little is known about the genetic basis of these phenotypes. In swordtail (Xiphophorus) fish, the false gravid spot (FGS) is a female mimicry trait that evolved over ~3 million years ago and segregates at intermediate frequency within multiple species. Using a genome-wide association study, we show that the FGS phenotype in X. birchmanni is almost entirely explained by variation in a 50 kb region upstream of Kit ligand (Kitlg), a well-described pigmentation gene. By quantifying allele specific expression in hybrids, we find cis-acting regulatory changes are responsible for a 3-fold increase in Kitlg expression in FGS individuals. This regulatory region is structurally complex, containing deletions, inversions, and repetitive sequences. Phylogenetic evidence suggests that this Kitlg regulatory region has also introgressed between species, potentially explaining the FGS’s unusual distribution. The FGS is polymorphic in nearly all Xiphophorus species in which it is found, and simulations implicate balancing selection as a likely cause of its maintenance. Disentangling the evolutionary tradeoffs that result in the maintenance of this female mimicry trait is an exciting direction for future work.

Little cost of reproduction in the long-lived perennial, Echinacea angustifolia
Midwest Ecology and Evolution Conference (MEEC)
Terre Haute, Indiana — April, 2019
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Pollen limitation is widespread in tallgrass prairies, which is causing decreased fitness of prairie plants. However, ecological theory suggests that if reproduction is costly, current pollen limitation might allow prairie plants to display higher fitness and growth in the future, at which time pollen might become non-limiting. To understand cost of reproduction in plants, I used generalized linear models to compare present survival and growth of plants in pollen addition, pollen exclusion, and open pollination treatments in Echinacea angustifolia. I found that past pollen limitation did not lead to increased future growth or fitness of E. angustifolia. There was some evidence that control plants experienced slightly increased growth and survival, which could hint that current methods of bagging flowers are detrimental. The finding that past pollen limitation did not increase future growth or fitness  suggests that these plants do not experience large costs of seed production. This finding confirms that perennial prairie plants are in a dire situation because present pollen limitation will not provide future benefit. Current land and pollinator conservation must therefore be a priority.

Mammalian herbivores differentially affect light availability and species richness in restored prairies
Carleton College Summer Research Symposium
Northfield, Minnesota — October, 2017
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Herbivore distribution and abundance are changing as a result of human-driven environmental change, which can affect the structure of prairie restorations. However, which herbivores (or combinations of herbivores) affect restored prairie communities is unknown. Using community composition data collected from herbivore exclosures, I compared species richness between different exclosures in restored prairies of different ages. I found that deer presence generally increased species richness, particularly the abundance of forbs, which greatly contribute to tallgrass prairie diversity. Deer, but not other herbivores, increased light availability at the soil level, which is a known mechanism to increase species diversity in prairies. Therefore, I propose that deer abundance should be managed with their impacts on prairie plant diversity in mind. 

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