Research
Research interests
Adaptation
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Hybridization
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Conservation
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Structural Variation
Organisms look vastly different as a result of mutation and selection. I want to understand the genetic underpinnings of phenotypic variation, particularly in challenging regions of the genome, which are now becoming accessible thanks to advances in long-read sequencing technologies. I also want to understand what kinds of forces maintain such variation (e.g. introgression and balancing selection) and the relative importance of these forces in different systems. Addressing these questions can increase our understanding of adaptive evolution and improve conservation practices.​
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To address questions at the intersection of adaptation, hybridization, and conservation, I take an interdisciplinary approach that integrates field ecology, molecular biology, and computational genomics. Systems I've used to understand study processes include:
Rockcress
Boechera stricta
Blue-tailed skink
Cryptoblepharus egeriae
Common sunflower
Helianthus annuus
Mountain swordtail
Xiphophorus nezahualcoyotl
Seep monkeyflower
Narrow-leaf coneflower
Lister's gecko
Mimulus guttatus
Echinacea angustifolia
Lepidodactylus listeri
Adaptation
Connecting genotypes to adaptive phenotypes is a central goal of my PhD research. I am particularly interested in the evolution of traits that are polymorphic across multiple species in a clade. I want to quantify the relative importance of standing variation, de novo mutations, and introgression as species adapt to different selective pressures. I am also interested in testing if mechanisms of balancing selection are similar across shared phenotypic polymorphisms.
Sexual mimicry in swortail fishes
Schumer Lab — Stanford University
The false gravid spot (FGS) is a striking example of a sexual mimicry polymorphism that is shared across 11 Xiphophorus species. Females and some males develop a visually similar melanic spot during puberty. In X. birchmanni, presence of this spot maps to a structural variant upstream of kitlga, a known pigmentation gene. The structurally complex FGS haplotype drives cis-regulatory increases of kitlga expression in specific tissues, which become pigmented as a result. Similar phenotypic frequencies, simulations, and genetic signatures suggest this polymorphism is maintained by balancing selection. Behavioral trials suggest FGS males experience less aggression (but also more courtship) from other males. We also found some females disdain the spot. Together, these factors may contribute to the maintenance of this sexual mimicry polymorphism in nature.
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Dodge et al. (2024) Current Biology [full text]
Hybridization
Once thought to be rare in nature, advances in genome sequencing have shown that hybridization is widespread across the tree of life. Gene flow between species can enable rapid adaptation, which can be especially important in this age of human-driven environmental change. I am curious about how structural features of genomes interact with ecological selection to control gene flow and shape the functional consequences of introgression, and use this information to improve species conservation in a changing world.
Evolution of hybrid incompatibilities
Schumer Lab — Stanford University
Coming soon...
Conservation
The world is losing diversity at an alarming rate, in many cases due to the introduction of invasive species. Recent advances in genomic sequencing technologies has made it possible to studying both declining native species populations as well as invasive species. Interestingly, hybridization often plays a central role in this story, as native and invasive species hybridize in many cases when they come in contact. I want to use genomic technologies to better understand threats to endangered native species, as well as identify the drivers of invasive species success.
Developing genomic resources for extinct-in-the-wild reptiles
Australasian Wildlife Genomics Group — University of Sydney
Two endemic reptiles from Australia, the Christmas Island blue-tailed skink (Cryptoblepharus egeriae) and Lister's gecko (Lepidodactylus listeri), went extinct in the wild over a decade ago and have been managed to maintain genetic diversity since. Despite this, we knew nothing about their genetics or if this program had worked. As a Fulbright Scholar at the University of Sydney, I assembled reference genomes for both species and analyzed them to understand their ancient and recent histories. These genomes will provide a resource for future genome resequencing studies in these species and for comparative studies in reptiles. They showcase the amount of information relevant to conservation that can be gained from sequencing a single individual of an extinct-in-the-wild species.
Dodge et al. (2023) Mol. Ecol. Resour. [full text]