REU Biology Program
Biology Research Experience for Undergraduates
The Research Experience for Undergraduates Program in Systematics and Evolutionary Biology is funded by the National Science Foundation and has been in place for 30 years. Our program brings approximately ten students to the American Museum of Natural History in New York City each summer for a ten-week experience working with our curators, faculty, and post-doctoral fellows.
Research projects span diverse fields of comparative biology including paleontology, genomics, population biology, conservation biology, and phylogenetics and taxonomy. Students have access to the Museum's immense natural history collections as well as state-of-the-art equipment for advanced imaging (CT scanner, SEM, TEM) and genomics (Sanger and pyrosequencing platforms).
Students receive a $6,000 traineeship stipend, as well as per diem costs for housing and meals, relocation expenses, and transportation subsidies. Pending COVID pandemic conditions, and assuming the program is held onsite at AMNH, housing at nearby Columbia University is made available. In addition to conducting original research projects throughout the summer, students also participate in formal instruction in systematics and evolution, and receive training in ethics, networking, communication, and other career-building skills.
Who Should Apply
All students in the program must be U.S. citizens, U.S. nationals or permanent residents of the United States. Students must be entering or continuing in an Associates or Baccalaureate degree program following their summer internship. As part of the National Science Foundation's commitment to broadening participation in STEM fields, we especially encourage students who come from community colleges, undergraduate-only institutions, and minority-serving institutions to apply. For questions with application process, contact [email protected].
Application Deadline: January 31st, 2023
Accepting Applications between January 1-31, 2023
For assistance with application process, contact [email protected]
2023 Biology Project Titles
Evolutionary analysis of language, culture, and genomic data of Amerind peoples
Mentors: Ward Wheeler
The project will work to integrate databases of linguistic, cultural, and genome sequence information of Amerind peoples. The goal is to test hypotheses of historical migration patters in the Americas and whether these different sorts of information have followed the same or different routes. The summer researcher will be using software tools developed at AMNH within a computational approach to create a unified view into this chapter of human history.
Evaluating evidence of mitonuclear coevolution in Estrildid finches
Mentors: Daniel Hooper and Brian Smith
Mitochondria are essential partners in the lives of bilaterian animals, they generate the energy required for nearly all cellular activities. Accomplishing this critical task requires direct interaction between the 13 proteins encoded on the mitochondrial (mt) genome and ~150 encoded on the nuclear (N) genome. This close working relationship is rife with opportunity for conflict. The mt genome has a mutation rate over an order of magnitude greater than that of the N genome and so mt genes tend to evolve much more rapidly than N genes. While a high mutation rate may facilitate rapid adaptive change, most mutations are thought to be at least somewhat deleterious. A critically under-tested hypothesis is that mitochondria remain functional despite their high mutation rate due in large part to compensatory mutations in the N genes that directly interact with mt gene products (i.e., N-mt genes). Another active question in evolutionary biology today is whether the arms-race like conflict between N and mt genomes within lineages results in N-mt incompatibilities between lineages This would occur when the mt genome of one species is forced to interact with the N genome of another (e.g., via hybridization). The REU student will be involved in evaluating evidence of coevolution between mitochondrial and nuclear genes involved in cellular respiration within a family of songbirds known as the estrildid finches (Estrildidae). The student will use available whole genome sequence data from ~30 estrildid finch species to infer phylogenetic relationships for the group, extract and align protein-coding sequences for mt and N genes, quantify synonymous and non-synonymous substitutions and polymorphisms, evaluate differential rates of evolution for mt, N-mt, N non-N-mt genes; and use protein modeling to examine evidence of both inter-molecular (between proteins) and intra-molecular (within protein) epistasis. The student will learn computationally biology and bioinformatics skills related to analyzing genomic sequence data. Prior experience with computational biology and bioinformatics (UNIX, R, etc.) would be beneficial but is not required.
Evolution of dragonflies and damselflies
Mentors: Lacie Newton and Jessica Ware
The insect order comprising dragonflies and damselflies, Odonata, contains ~6000 species with a multitude of different morphological traits, ecological traits, and geographic ranges. Variation in these traits make odonates ideal systems to investigate various biological questions, specifically evolutionary relationships, character evolution and adaptation, and biogeographical hypotheses. This project focuses on using the untapped potential of historical museum specimens for gathering not only morphological/ecological data but also molecular data to answer ecological and evolutionary questions. We will extract DNA from museum specimens of odonate taxa, generate libraries with an anchored hybrid enrichment protocol for sequencing, and then process and analyze sequence data. This subgenomic data, in conjunction with morphological and ecological data, will be used to answer questions regarding evolutionary relationships and biogeographical hypotheses within odonate taxa and what factors may have influenced diversification within this group (e.g., character evolution related to color and flight behavior).
Insect Evolution
Mentors: Jessica Ware
Insects are a diverse group of organisms with extreme variation among taxa. In our lab, we primarily study the evolutionary history of the termites, dragonflies and damselflies. In this project, you would work with us on genomic and morphological data analyses to answer broader questions about flight, biogeography and species distribution. In particular, you would learn comparative geometric morphometrics in order to infer niche differences, code ancestral character states, and optionally can do SEM analyses. Additionally, you would learn how to model species distributions and test biogeographical hypotheses for a changing climate.
Tiny fossil reptiles from Jurassic Scotland
Mentors: Roger Benson
Mesozoic reptiles include dinosaurs, alongside others such as early lizards, crocodylian-relatives and turtles, as well as entirely extinct groups. Smaller-bodied species in particular are poorly-known. This project will focus on small-bodied reptiles (estimated snout-vent lengths of 5-30 cm) from the Middle Jurassic of Isle of Skye, Scotland, which has yielded a well-preserved assemblage of tiny fossil reptiles, many of which have yet to be studied. The student will work with high resolution CT scans, doing digital segmentation to make 3D bones. They will do comparative anatomical study to determine the identity of the fossil specimens, including whether they represent new or existing species, and what other taxa they are related to. They may also do phylogenetic analysis, to determine the speciifc evolutionary relationships and implications of the new fossils. The project will provide experience in reptile anatomy, working with 3D data, taxonomic and phylogenetic research.
Mining Museums for DNA
Mentors: Alexander Salis, with Chris Raxworthy and Brian Smith
Natural History Museums have massive potential to yield genetic information about past populations and extinct species. Typical museum specimens (e.g., skins, skeletons, and fluid-preserved specimens) have long been considered poor sources of genetic material but are now being recognized as an unrivalled source of historical DNA (hDNA) for studying changes to biodiversity over the last 200 years. The uptake of fluid-preserved specimens in genetic research has been much slower, despite representing millions of museum specimens worldwide. This slower uptake is due to the difficulty in extracting endogenous DNA from fluid-preserved specimens, especially those fixed in formalin. This project focuses on using the vast herpetology and ornithology collections at the AMNH to identify the damage patterns of hDNA from specimens of different preservation types, specifically formalin-fixed specimens, and explore the utility of hDNA in phylogenetic inference and biodiversity analyses. The REU student will be involved in various aspects of the project but will be focused on processing sequencing data, analyzing damage patterns of hDNA, and performing phylogenetic analyses. Prior experience in analyzing sequence data would be beneficial.
Nudibranch morphological evolution and the theft of cnidarian stinging organelles
Mentors: Jessica Goodheart
Most gastropod molluscs (snails and slugs) possess a hard, calcified shell that among other functions serves as a refuge to protect them from predators. However, there has been a reduction or complete loss of this shell in multiple groups of marine gastropods, including a group of brightly colored sea slugs called nudibranchs (Nudibranchia). In the absence of a protective shell, these slug groups have evolved a diverse array of alternative defense mechanisms, including the use of stinging organelles (called nematocysts) acquired from their cnidarian prey (including anemones, hydroids, and jellyfish). The slugs house and mature these stinging organelles using a single, critical structure called the cnidosac. However, little is known about the evolution of this structure or how these organs evolved to recognize, acquire, and mature the stolen cnidarian nematocysts. This proposal seeks to characterize the different tissues of the cnidosac and the cell types that compose them to better understand the functioning of the sac and how this structure evolved within nudibranchs. To reach the proposed objectives, the student will use micro-computed tomography (micro-CT) techniques (including segmentation) in combination with histological data to distinguish between different tissues and describe their morphology across species.
Discovering the power of hidden collection's data
Mentors: Estefania Rodriguez
For two centuries, America has amassed an unparalleled collection of specimens from exploring the world's oceans, contributing to a library of biodiversity that captures the state of life in the ocean - year after year, decade after decade. The broadest evolutionary scope of those collections is in the marine invertebrates, animals without backbones - sea stars, corals, worms, jellyfish, crabs, and thousands of other animals. That library of preserved marine invertebrates is our essential guide to the diversity of ocean life across the globe, and these institutional collections also act as a time machine, letting us use the past to understand how our present will become the future. But there is a problem - vast numbers of these specimens are essentially invisible outside of a tiny community of museum specialists. The only record of these specimens' existence is on labels enclosed in the jars with the preserved animals or in paper logbooks on a shelf. These specimens will remain nearly undiscoverable on museum shelves until their core descriptive information is made digitally available: What was the species composition of marine communities 50 or 100 years ago? When and where did invasive species arrive, and what species disappeared from habitats they used to occupy? Can community diversity be reconstructed in part by database harvesting? Our core objective is to assemble a robust, extended, vouchered resource on marine invertebrate biodiversity to power research and education in systematics, ecology, oceanography, and other disciplines. These data will allow researchers to address diverse problems on global patterns of diversity and distribution, climate-driven range shifts, reconstruction of historical community structure, and biodiversity synthesis.
REU students involved in this project will participate in collection data digitalization of alcohol-preserved marine specimens, which will be used to show the power of uncovering data. Students will be introduced to basic concepts of databasing, georeferencing, specimen photography and other collection-based workflows. They will be able to make coarse inventories of marine invertebrate ecosystems, visualizations of collection holdings at the AMNH, reconstruction of former invertebrate marine communities, comparisons of former and current communities, etc. showing the applicability of uncovering museum collection data.