Research
Research interests
Structural variation
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Balancing selection
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Genome evolution
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Conservation
Organisms look strikingly different as a result of mutation and selection. I am interested in how complex regions of the genome, which can now be more easily "seen" and investigated due to advances in long-read sequencing, evolve and contribute to phenotypic variation. I also aim to study the evolutionary forces contributing to the maintenance of functional variation within species (e.g. introgression and balancing selection) and their importance in different systems. Addressing these questions can increase our understanding of adaptive evolution and improve conservation practices.
To address questions relating to the origin and maintenance of functional variation, I take an interdisciplinary approach that integrates long-read sequencing, computational genomics, molecular biology, and field ecology. During my PhD, I've primarily worked with swordtail fish, but through side projects and collaborations, I've studied a variety of taxa including:
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
Origin and maintenance of phenotypic variation
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 ancestral variation, independent evolution, and introgression. I am also interested in testing if mechanisms of balancing selection are similar across shared phenotypic polymorphisms with distinct genetic architectures.
Balancing selection in swordtail 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.
Dodge et al. (2024) Current Biology [full text]
Structural variation and genome evolution
Advances in long-read sequencing technologies and assembly algorithms have demonstrated that structural variation is ubiquitous in genomes. For example, in humans SNPs represent less than 10% of variable bases between any two individuals. I am interested in how these dynamic regions evolve and how they contribute to functional differences between and within species.
Sex-chromosome diversity
Schumer Lab — Stanford University
Sex chromosomes represent some of the most dynamically evolving regions of genomes. Using ONT ultra-long sequencing, we assembled the first gapless, chromosome-level genome of a Poeciliid fish, X. nezahaulcoyotl, as well as 10 sex chromosomes from this species. We found a small sex-determining region, which was highly variable within Y chromosome haplotypes. We uncovered ampliconic gene copy number variation, differential accumulation of repetitive sequence, and presence of an oncogene (xmrk) liked to malignant melanoma. This work showcases how complete assembly of formerly intractable regions can shed light on their dynamic evolution. This study was led primarily by an undergraduate and myself, representing the first time I've taken on this supervisory role in analysis and writing.
Given et al. (submitted) [BioRxiv preprint]
Species 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 study 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 conservation program had been successful. 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]
