Research
Research interests
Adaptation
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Hybridization
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Conservation
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Structural Variation
Mutation and selection have profoundly shaped how organisms survive and reproduce, and organisms look vastly different as a result. I want to understand the genetic underpinnings of this variation, particularly in challenging regions of the genome, which thanks advances in long-read sequencing technology, are just becoming accessible. 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. Such questions are important to understand evolution and improve conservation practices.
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. I am working to map the genetic architecture of this and other pigmentation traits in Xiphophorus and to identify if key genes are involved in multiple pigmentation patterns. My goal is to determine if the genetic basis of pigmentation patterns are shared across distantly related Xiphophorus species or if the traits have originated multiple times independently. If the genetic basis is shared, I seek to understand if the trait arose ancestrally or if later introgression has driven its phylogenetic distribution.
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]