Snake Population Genomics & Adaptation
In certain instances, snakes can serve as ideal models for understanding adaptation. I am using genome-level data to investigate selection and adaptation in two independent systems.
(1) The invasive population of Burmese pythons in South Florida: Invasive species represent a promising model for analyzing the processes of evolution and adaptation on timescales that are tractable for study, and have been shown to demonstrate rapid evolutionary responses over short, ‘ecological’ timescales. I’m leveraging the well-known Burmese python (Python molurus bivittatus) invasion in Florida and am combining temporal population sampling (provided through collaboration with the USGS) and a known selective event (high mortality due to a freeze event in 2010) to understand how severe selection can lead to rapid adaptation. This work has been partially funded by a Rosemary Grant award from the Society for the Study of Evolution.
(2) Putatively independent evolution of insular dwarfism in Boa constrictor: Numerous species across the animal tree-of-life have evolved a dwarfed body size on islands, and some, including Boa constrictor, the focal species for this work, have evolved this radical morphology multiple times on multiple independent islands. The drastic variation between normal, large-sized mainland boas and their closely-related dwarfed island relatives suggests that a relatively small number of highly penetrant genetic variants in the B. constrictor genome may underlie island dwarfism, and that this system may therefore provide new insight into the genetics of body size in vertebrates. This project also leverages the replicated evolution of dwarf populations of Boa constrictor to investigate if repeated evolution of dwarfism is driven by shared or unique genes or functional pathways across multiple independently evolved dwarf island populations. This work was recently supported with an NSF Doctoral Dissertation Improvement Grant.
Vertebrate Genome Structure & Function
A good deal is already known about mammal and, more recently, bird genomes due to large initiatives. Unfortunately, less is known about the other major tetrapod clades, where only a few focal taxa are represented by complete genome sequences. In response to this shortcoming, I am involved with sample sequencing efforts that will shed preliminary light on genomic structure in these neglected groups.
(1) Squamate Reptiles: Existing work has shown that squamate reptiles, especially snakes, have remarkable genome size conservation, despite having quite variable repetitive element content. We have begun expanded genome sample sequencing using representative taxa from across Squamata to understand patterns of repetitive element composition and to estimate the rates of accumulation and turnover.
(2) Amphibians: Much like squamates, amphibians are also thought to have variable repetitive element composition, which is presumed based upon the order of magnitude variation in genome size across the clade, especially among salamanders. As a result, they have been almost entirely ignored in the modern genome sequencing era, with only the model frog Xenopus and, just recently, the Tibetan frog having complete genomes sequenced. Using economical sample sequencing, we aim to begin illuminating the composition of amphibian genomes.
Non-Model Species & Comparative Genomics
The advent of next-generation sequencing technologies has led to significant non-model species sequencing. I have been involved and continue to participate in producing whole-genome resources and using these resources to shed light on interesting topics in biology.
(1) Burmese python genome: The Burmese python was among the first snake and squamate genomes and provided great insight into the processes of adaptive protein evolution and to the patterns of differential gene expression underlying the extreme physiological remodeling in this species. This resource and the accompanying data have since been used to put forth a new model of venom gene evolution and to better understand intestinal remodeling following feeding.
(2) Guided assembly of two bird genomes: I led an effort that used low-coverage genome sequencing of two non-model birds (the Gunnison Sage Grouse and the Clark’s Nutcracker) to compare the power of de novo versus reference-guided (using the high-quality Chicken and Zebra Finch genomes) assembly techniques. Reference-guided assembly yielded higher-quality draft genomes, a finding that provides support for leveraging high-quality genomes to more efficiently and affordably construct non-model species draft genomes.
(3) Snake genomes: Multiple low-coverage draft snake genomes were used to test for positive protein evolution in the Burmese python genome paper, and since then I have helped improve them to various degrees with further sequencing data.
(4) Boa constrictor reference transcriptome: The boa constrictor genome was assembled as part of the Assemblathon2 initiative, producing an extremely high-quality reference genome. Unfortunately, this resource lacks annotation, and as part of my work on boa island dwarfism I have begun building a reference transcriptome that will be utilized in my work and by the broader scientific community.
Vertebrate Phylogenetics, Biogeography, & Evolution
I maintain active interests in vertebrate phylogenetics, biogeography, and evolution, focusing mostly on reptiles. As part of my work on adaptation in boa constrictors and Burmese pythons, I have initiated work to understand the relationships between populations across both species.