I am an evolutionary ecologist broadly trained in behavioral and quantitative genetics. My work seeks to answer one of the biggest questions in biology, “How do organisms and communities of organisms respond to change?” I study how organisms respond and evolve to changes on both large and small scales. Much of my work seeks to understand the role that two particular processes, symbiosis, and horizontal gene transfer, have played in the evolution and ecological diversification of arthropods. Since arriving at Agnes Scott, my lab has also begun to explore the impact that changes associated with urbanization have on organisms and communities living in those spaces. We use large publicly available datasets and datasets from my lab to identify ecological changes in human-altered environments.
Symbiosis
Symbiosis is the ecologically close association of two organisms. It can range from a parasitic association, where one partner is harmed by the other, to a mutualist one, where both partners benefit. Often eukaryotes harbor symbiotic bacteria inside themselves. Symbionts can provide their hosts with essential traits that the host alone does not possess. For example, in the agricultural pest, the pea aphid, symbionts can allow their hosts to live on clover. This plant is usually toxic to aphids and survives at higher temperatures than aphids without symbionts. In my lab, we focus on how microbes affect the survival and fitness of their host, whether through influencing cannibalism in flour beetles or diet in honeybees.
I’ve published three peer-reviewed studies with undergraduate co-authors demonstrating some novel protective effects that symbiotic bacteria can provide for their insect hosts. This work highlights the often far-reaching effects that bacterial symbionts can have on their hosts, predators, and other ecological partners. Since Fall 2020, I have continued this work with my team of Agnes Scott undergraduate researchers. In the summer of 2021, Esther Okamoto ‘24 completed a summer research project focused on elucidating the microbiome’s influence on kin recognition, diet, and cannibalism in flour beetles. Esther has continued that work, expanding it to look at the generational effects of diet on the microbiome. She has also based her recent Goldwater grant application on her preliminary work in my lab.
Horizontal Gene Transfer
Horizontal gene transfer (HGT) is the movement of genes between often distantly related species without sex. For example, if a bacterium transfers a gene into a mosquito’s genome, it would have to do it through a mechanism other than sexual reproduction. That gene transfer from a bacterium to a mosquito would be an example of HGT. HGT can allow an organism to rapidly acquire new traits between bacterial species. It is currently unknown how common HGTs are and how they have affected their evolution in eukaryotes, such as mammals and insects. I am particularly interested in the role that HGTs play in allowing organisms to exploit new environments like host plants or diets.
I have continuously funded the work in my lab with federal grants since 2014. I have been the sole PI on all five of these highly competitive grants, which have allowed me and my undergraduate research students to conduct groundbreaking and novel research in the field of evolutionary ecology. Most recently, I was awarded a highly competitive NSF grant through the Division of Environmental Biology (DEB) to study HGT in arthropods (Award #2042735, $603,128). The goal of this project is to use three independent bioinformatic pipelines to identify HGTs and validate and characterize candidate HGTs in fifteen species of blood-feeding and herbivorous arthropods, including two species of ecologically and economically important mites which will have their transcriptomes (all their expressed genes) and genomes sequenced as part of this work. I am particularly interested in determining whether these HGTs played a role in acquiring similar phenotypic traits necessary for invading new ecological niches by distantly related arthropod species. I hypothesize that HGT has repeatedly allowed for the independent acquisition of similar new phenotypic traits in multiple distantly related arthropod species and has allowed for niche invasion and novel resource exploitation. In the reviews of my full proposal, a reviewer said that my project is “novel and tackles an exciting question at the forefront of evolutionary biology research.”
I have recently more formally combined my work on HGT and symbiosis in two NSF grants (an awarded NSF supplement and another invited pre-proposal). The NSF supplement allowed me to extend my work on HGT in the blow-fly P. sailia to identify the ecological factors that shape its gut microbiome. Protocalliphora sailia is a generalist bird parasite found in the nests of multiple bird species. At our field site in Boone, North Carolina, we collected blow-fly larvae from the nests of bluebirds and tree swallows. I am currently using both 16s meta DNA barcoding sequencing and meta-shotgun sequencing to identify the bacterial gut communities in P. sailia larvae collected from two different host bird species’ nests and to characterize the functions of these bacterial gut symbionts and the variation between host species. Fieldwork for the completion of this study has been temporarily delayed due to COVID. I worked this summer to re-establish a collaboration with faculty at Appalachia State University. I fully anticipate completing a large enough subset of the collections during the summer of 2023 to complete the sequencing needed for publication.
This extension of my HGT work to include the sequencing and characterization of symbionts has served as the basis for another very well-received NSF grant application, which expands my research to include comparisons of traits provided by HGT with those conferred by symbiotic bacteria. My preliminary research has found that, for several species, HGTs present in the arthropod host’s genome are missing from the genomes of their symbionts and that HGT genes are generally NOT transferred from the bacterial symbionts associated with the host species. The NSF review panel called my proposal “innovative, and its premise has the potential to redefine how we think about adaptation and acquisition of novel traits.” My future work will compare and contrast how these two processes, HGT and symbiosis, can allow eukaryotic organisms to acquire novel traits and how they may result in the convergent evolution of divergent species.
I am excited to continue my work identifying and characterizing HGT in phylogenetically diverse groups of arthropods and to begin expanding that work to more formally analyze how both HGT and symbionts can provide organisms with new phenotypic traits, though apparently not the same traits at the same time. In December of 2021, I applied for and received an $8,000 funding assistance award from Dovetail Genomics (Cantata Bio) to help fund the de novo sequencing, assembly, and annotation of the genome and transcriptome of the generalist mite Amblyseius swirskii. Dovetail’s cutting-edge sequencing and annotation technology (HiFi PacBio de novo Assembly + Proximity Ligation Library + Deep Sequencing + HiRise Scaffolding) will produce an accurately annotated, publishable genome assembly while also allowing me to identify and sequence any symbiotic bacteria associated with this species. I also plan on sequencing this mite’s microbiome using 16s metagenomic sequencing. Additionally, I am hopeful that I will be able to collect enough field collections of the chigger mite (Trombicula alfreddugesi) to allow for further collaboration with Dovetail Genomics to complete the de novo sequencing, assembly, and annotation of both the chigger mite’s genome and transcriptome (this is again after several years of COVID-related delays). Due to the funding award and extensive collaboration with Dovetail Genomics, the resulting sequencing data will be accessible to Agnes Scott undergraduate researchers for extensive downstream analyses, including HGT, symbiont, and microbiome analyses. This work will result in several publications with undergraduate co-authors. In Spring 2021, three lab members presented their work in my lab during Agnes Scott’s Spring undergraduate research conference SpARC during a panel I hosted focused on identifying novel HGT in arthropods using newly developed bioinformatic and phylogenetic methods.
Urbanization
Urbanization creates a heterogeneous landscape that is a mosaic of habitats and features. How does this near-continuous process of converting, degrading, and fragmenting natural habitats affect the organisms and the communities they form? Does it create novel communities completely unlike those found there previously, or do core functions and species remain within the community groups? Answering these large-scale questions often requires large amounts of data and the skills to wrangle and utilize these large datasets. Luckily, in recent years a move towards open access and community science based research projects have made these kinds of data much more accessible to the public. I have also worked intensively with students at Agnes Scott to develop the data science skills necessary to translate the data into something meaningful, thereby allowing us to begin exploring the impacts of urbanization on biodiversity and biological communities.
Overall, my research seeks to understand how novel traits arise in organisms and the ecological effects of these new traits. My interest in the ecological impacts of new evolutionary traits has resulted in several complementary projects that combine my ecology knowledge with my interest and passion for open science resources and publicly available big data. Since starting at Agnes Scott, I have begun several projects which use my computational skills to look at the impacts of urbanization on biological communities and community composition, including how the environment can affect the gut and honey microbiomes of rural and urban honey bees. This urban/rural honey bee microbiome manuscript is currently being completed in collaboration with former post-doctoral research fellow Erica Harris. She recently joined the Agnes Scott faculty as an assistant professor in graduate studies.
I have recently begun working on another manuscript with Agnes Scott undergraduate Sage Pasquale C’24 that uses data collected by amateur bird watchers through the citizen science project eBird to understand how bird biodiversity and bird communities are affected by urbanization, particularly by a systemically racist mortgage lending practice known as redlining. Eighty years ago, the federal Home Owners’ Loan Corporation created “Residential Security” maps for over 100 major American cities. These maps graded neighborhoods on an A-D scale, with “A” neighborhoods being desirable for investment and “D” neighborhoods being deemed hazardous. This redlining practice denied the minority residents in these “hazardous” areas access to capital investment. While outlawed in the 1970s, the long-term impacts of redlining can be seen across urban areas in the US today. For this project, we are asking how differences in urban development due to redlining affect bird biodiversity. We used birdwatching community science data collected by Project eBird to analyze bird counts from locations within urban counties that have been historically redlined. Our analyses focused on major metropolitan cities in the Atlantic Flyway between 1990 and 2020. We used R to download, clean, and analyze raw citizen science data to measure overall bird biodiversity, measured by species richness and the Shannon’s Diversity Index. Using ArcGIS to overlay historical redlining maps, we analyzed the relationship between the redlining grades and the recent patterns in bird diversity. We compiled much of this data during a one-day Science Sprint held in April 2022, in which ASC students learned and used R and GIS to clean up and analyze the bird and redlining data for a single city and year. We then compiled data from all the completed cities to better understand the large-scale regional effects of redlining on biodiversity.
Since joining the faculty at Agnes Scott College, I have worked to more fully utilize open data sources for developing undergraduate research skills. These resources, and the coding tools necessary to manage them, allow students to move beyond the menial tasks and endless troubleshooting that are often a large portion of undergraduate research at PUIs. Using, at least in part, open data that has already been collected allows students to explore more fully all of the research components, including data analysis, question, hypothesis, and prediction development, and most importantly, the storytelling that is crucial to good science communication. This inclusion of large, open-access data, including NEON, iDigBio, GBIF, and eBird, has allowed me to focus on cultivating data science, programming, and management skills with my research students and to more fully open my lab and my research to students from more backgrounds and interests. These projects have provided multiple funding and research opportunities for undergraduate biology, environmental science, and mathematics research students. I have worked extensively with underrepresented undergraduate researchers throughout my career. I look forward to continuing these kinds of student-driven evolutionary ecology projects at the same undergraduate research institution where my own research path started.
