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REU Biology Program

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Biology Research Experience for Undergraduates Program

 

About our Program

The Research Experience for Undergraduates Program in Systematics and Evolutionary Biology is funded by the National Science Foundation and has been in place for 24 years.  Our program brings approximately eight 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 $5000 traineeship stipend, as well as per diem costs for housing and meals, relocation expenses, and transportation subsidies. Housing is made available at nearby Columbia University.  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 U.S.  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.

 2018 Project Titles



Building a Tree of Life for the New Guinea Birds-of-Paradise

Cracraft Bio REU 2018 pic

Mentors: Dr. Joel Cracraft and Jessica McKay  (Division of Vertebrate Zoology, Department of Ornithology)

The birds-of-paradise (BOPs) of New Guinea represent one of the most spectacular adaptive radiations of any group of vertebrates.  Not only do they exhibit great diversity in body size and plumage adornments, they also exhibit spectacular differences in sexual displays.  Understanding the evolution of these phenotypic features depends on having a dense phylogenetic tree for all the taxonomic forms that diversified across the Australo-New Guinea region.  The REU student will be involved in collecting new genetic data, undertaking phylogenetic analysis, and inferring the history of the BOP phenotype as well as their biogeographic history of speciation.  The work will involve collecting genetic and phenotypic data that address broad patterns of relationships as well as fine-scale phylogeographic patterns across the New Guinea landscape.  Having some knowledge of birds and laboratory experience with DNA methods and analysis will be a plus.   (top)



Assessing the Suitability of Nano-Satellite Image data for Quantifying Habitat Change and Potential Impact for Distribution and Community Reassembly in Puerto Rico before and after Hurricane Maria

  Mentors: Dr. Ana Luz Porzecanski, Ned Horning and Peter Galante (Center for Biodiversity and Conservation)

Porzecanski Bio REU 2018

This project centers on investigating the usefulness of a new generation of satellites, known as nano-satellites, for quantifying habitat change. Sensors aboard nano-satellites provide high-frequency, optical imagery of the Earth surface but have limited resolution when compared with other commercially available sub-meter resolution imagery. In order to test the performance and usefulness of these data, we will compare estimates of habitat change for selected areas within Puerto Rico, before and after Hurricane Maria obtained from nano-satellites, and compare those with estimates obtained from more traditional satellite imagery, such as Landsat and commercially available high resolution imagery. The project will provide insights into the potential uses of nano-satellite data for conservation, will generate baseline information for continued monitoring of habitat change in Puerto Rican sites, and allow for preliminary investigation of impacts on the biodiversity and community reassembly in those sites. This project is best suited for students with basic skills in geographic information systems.   (top)



Degradation Products of Bird Eggshell Pigments

Norell Bio REU 2018

Mentor: Dr. Mark Norell (Division of Paleontology)

Birds are the only extant amniotes to have colored eggs. First described by Darwin, pigmented eggs have long been considered a synapomorphy for the avian crown group.  The myriad colors and patterns found on avian eggshell are caused by the deposition of two compounds during the last few hours of egg formation.  These tetrapyrrolic compounds named protoporphyrin and biliverdin have different chemical properties, and are thus incorporated into the eggshell in different ways: the hydrophobic protoporphyrin, a metabolic heme precursor, is responsible for brown coloration and is deposited within the outermost waxy cuticle of the eggshell.  In contrast, the hydrophilic biliverdin - a heme catabolite - imparts a blue coloration and is incorporated into, if not covalently bound to the proteinaceous eggshell scaffold.  Combinations of these two secondary metabolites account for the vast diversity of colors and patterns seen in avian eggshell.   Recently, biliverdin and protoporphyrin have been discovered in non-avian dinosaur eggshells.  I am involved on this continuing work and our group is about to submit a major paper on this topic of dinosaur egg color reconstruction. Proper reconstruction of dinosaur egg colors allows inferences on behavior and ecology of extinct animals and therefore offers a valuable bioindicator for paleobiologists.  However, reliable reconstruction of egg colors requires quantification of preserved pigments and taphonomic extrapolation of the original pigment amounts stored inside the eggshell. This could be done by inclusion of pigment breakdown products, but tetrapyrrole pigment taphonomy is yet completely unknown. To fill in this essential gap of knowledge, I propose a series of actualistic decay experiments to qualitatively and quantitatively understand the taphonomic trajectories of biliverdin and protoporphyrin, to identify and quantify pigment breakdown products in eggshells.   This project will take heavily pigmented eggshells from extant birds (emu, chicken, quail, duck) and subject them to a number of (photo)chemical treatments mimicking currently known degradation/fossilization pathways.  Considered environmental parameters are humidity, light, temperature and sediment conditions. I am targeting for hydrous and anhydrous pigment reactions, oxidative and reducing alterations, as well as photochemistry. In overall 18 calibrated maturation experiments (exposure to aqueous solutions at pH 1, 7, 9, each at 25, 60, 90, 120 °C; incubation with Fenton’s agent; autoxidation; incubation with sodium borohydride;  exposure to 250 nm, 365 nm UV, and polychromatic light) different types of pigment degradation products will be generated. Using Raman microspectroscopy point measurements and mapping (method of choice in modern biomedicine), unaltered eggshell pigments will be compared to the different maturation products, aiming for identification of pigment degradation products, reconstruction of pigment decay mechanisms, and quantification of reaction kinetics. I expect to find two major classes of pigment degradation products: One class comprises side chain peroxidation products, yielding a change from blue and reddish pigment color to a brown, heterogenous mixture of carbonyle-rich products, and another class including π-molecular orbital break down by macrocycle addition reactions, yielding visible-range colorless, non-alternating polyene products. The insights gained through this project will allow a significantly more accurate reconstruction of dinosaur egg colors based on inclusion of not only the preserved, unaltered pigment trace amounts, but also of pigment breakdown products. Accurate dinosaur egg color reconstruction will impact paleoecologists, science educators, and artists.   (top)



 Ammonites as Inhabitants of Ancient Methane Seep Environments

Witts Bio REU 2018

Mentors: Dr. James Witts and Dr. Neil Landman (Division of Paleontology)

Throughout their long geologic history, ammonoid cephalopods (ammonites) inhabited marine environments around the globe, and are justifiably appreciated as among the most famous invertebrate fossils. Recent discoveries indicate that ammonites were also inhabitants at cold methane seeps throughout the Paleozoic and Mesozoic. These unique ecosystems are the subject of increasing study in the modern ocean, but many question remains about fossil examples and their inhabitants. In this project, the REU student will study the ammonite fauna from Upper Cretaceous methane seep deposits from the last epicontinental sea that covered the interior of North America during the Campanian and Maastrichtian (84-66 million years ago) time periods. The student, relying on museum collections at the AMNH, will make detailed comparisons between the composition and distribution of the ammonite faunas at these methane seeps and at nearby age-equivalent non-seep sites. Such a comparison may reveal the role of ammonites in ancient methane seep ecosystems, as well as answer questions about the ecology and evolution of these charismatic fossils. This project will involve approximately 10 days of field work in South Dakota and Montana to collect fossil material for the study.   (top)



Molecular systematics and species delimitation of the clownfish sea anemones: are there really only 10 species?

Mentors: Dr. Estefania Rodriguez and Dr. Benjamin Titus (Division of Invertebrate Zoology)

Rodriguez Bio REU 2018

The clownfish-sea anemone symbiosis is an icon of tropical coral reefs of the Indo-West Pacific and one of the most recognizable symbiotic relationships on the planet. There are 30 described species of clownfishes, which have adaptively radiated to live with sea anemones, but only 10 nominal species of host anemones. Why have the host anemones not undergone a radiation similar to the clownfishes? Given the co-dependent nature of the mutualism, their broad geographic and ecological distribution, extensive phenotypic variation, and that all 10 host species are only described morphologically, we hypothesize that there is undescribed cryptic species-level diversity within the host anemones. Using high-throughput sequencing (e.g. RADseq, transcriptomics), molecular species delimitation, and a comparative phylogeographic framework, we will search for cryptic species and reconstruct the evolutionary histories of the two most common sea anemone host species from the tropical Indo-West Pacific (IWP) oceans: the bubble-tip anemone Entacmaea quadricolor and leathery anemone Heteractis crispa. Samples obtained from throughout the IWP will be used to search for cryptic species and test for signatures of diversification via allopatry and ecological speciation. Much of our understanding of this symbiosis, and by extension, the fundamental evolutionary and ecological theory that has been derived using these relationships as model study systems, is centered on the assumption that we have full knowledge of the interacting species. However, no molecular or genomic research exists that focuses on population level questions of tropical sea anemone species worldwide. If hidden species-level diversity exists in the host anemones, it has the potential to transform our understanding of this important mutualism, and marine symbioses more broadly. Further, the charismatic nature of the symbiosis and its cinematic popularization have made it among the most heavily sought after organisms in the ornamental aquarium trade. these data will have important conservation implications and will directly support management of the ornamental aquarium trade; an economically important industry worth hundreds of millions of dollars each year. REU students involved in this project will participate primarily on genomic aspects of this research focused on our ecological speciation hypotheses. Specifically, whether water depth and reef zone promotes species-level divergence. For example, the bubble-tip anemone E. quadricolor is known to produce extensive aggregations of asexual clones on shallow reef crests, while found as large solitary individuals at depth.   (top)



  Language Evolution

 Mentors: Dr. Ward Wheeler (Division of Invertebrate Zoology) and Dr. Peter Whiteley (Division of Anthropology)

Wheeler Bio REU 2018

Human language undergoes historical change akin to biological evolution. The changes in language over time can reflect cultural change, population migration, and technology development and transfer among other phenomena. The phylogenetic analysis of linguistic systems can offer clues to the means and modes of human cultural change. The REU student will work with Curators Peter Whiteley and Ward Wheeler to construct and analyze Indo-European word lists. These lists will be collected and transcribed into a common symbolic representation (IPA) and used to construct an evolutionary tree of Indo-European languages.   (top)



Madagascar Biodiversity and Leech iDNA

Mentors: Dr. Mark Siddall, Evon Hekalla and Mai Fahmy (Division of Invertebrate Zoology)

Siddall Bio REU 2018

Recently a remote forest was discovered in the central part of Madagascar south of Ihosy; a patch of forest undisturbed and protected from fires and human influence by steep cliffs. Estimating abundance and distribution of vertebrate species is a challenge for conservation. In addition to needs regarding uncharacterized diversity, the conservation of even well-studied mammal taxa is best understood only in relation to temporal and spatial variability as measured by repeated sampling. Whereas we often rely heavily on camera-trapping and non-invasive (e.g., scat) sourced genomics, these are heavily biased toward large mammals, and necessarily miss the majority of vertebrate biodiversity in protected areas: small mammals, reptiles, amphibians, birds. We are part of an international team developing, assessing and ground-truthing new methodological breakthroughs in species monitoring; making data collection easier, more efficient, and lowering the impact on target species. The use of iDNA (residual host DNA of invertebrate ectoparasites), especially leeches, allows for the massive, rapid, inexpensive biodiversity monitoring of forests (where the terrestrial leech families Haemadipsidae and Xerobdellidae reside). To date, our research has evaluated the relative efficacy both of Sanger sequencing (individual leeches) and next-gen (pooled spatiotemporal sets) from each of Bangladesh, Cambodia, Southern China, and PN Ranomafana Madagascar. This summer’s undergraduate intern in our lab will work with hundreds of leeches collected from that recently discovered forest in Madagascar. Laboratory work will include DNA Isolation and genomic sequencing efforts (traditional and next-gen) both to identify the resident leech species as well what animals those leeches most recently fed upon.



Pugilistic Flycatchers: Wing spurs in the bird family Tyrannidae

Mentors: Dr. Brian Smith and Dr. Glenn Seeholzer, (Divison of Vertebrate Zoology, Dept. of Ornithology)

Smith Bio REU 2018 pic
Smith Bio REU 2018 pic 2

Wing spurs are a poorly known but exceedingly interesting feature of avian external anatomy present in only a few groups of large birds. Wing spurs are generally bony, large, sharp, and used for fighting or defense in a similar way to the antlers of deer or antelope. While prevalent in some large bodied bird families, wing spurs are almost unheard of in small songbirds except in the family Tyrannidae (Tyrant Flycatchers). Anecdotal observations of bony protuberances on tyrannid wings suggests a fascinating and completely unknown world of combat among these small flycatchers. Prominent wing spurs are present in the genus Myiarchus as well as other genera. The size of the spurs is sexually dimorphic and on some species, quite prominent. However, basic information on the morphological characteristics, phylogenetic distribution, and use of the spurs of Tyrant Flycatchers are completely lacking. This project will entail a systemic survey of specimens of Tyrannidae at the American Museum of Natural History (AMNH) to determine the phylogenetic distribution of wing spurs. Morphometric analysis of these spurs will be done with digital photo morphometrics and computed tomography (CT) scans using the state of the art spectroscopy facilities at the AMNH. The student working on this project will learn digital morphometrics, CT imaging, and morphometric and phylogenetic analyses in the computer program R. The interested student should be motivated, organized, self-sufficient, and eager to learn how to code.

(top) Wing spurs of the Southern Screamer (Chauna torquata) and (bottom) the Dusky-capped Flycatcher (Myiarchus tuberculifer).


Environmental DNA for Determining Recreational Impacts

Mentors: Dr. Michael Tessler, Dr. Mercer Brugler, and Dr. Rob DeSalle  (Sackler Institute for Comparative Genomics)

Tessler Bio REU Project 2018

Natural areas are increasingly threatened, yet these spaces are increasingly popular for human recreational activities. Hikers, climbers, and mountain bikers may have a strong vested interest in protecting these spaces to continue their pursuits, but there are few data indicating how they should interact with their environments. Little is known about the impacts of these sports on biota. This lack of data likely stems from impact studies being time consuming and requiring specialized knowledge. However, it recently has become clear that environmental DNA (eDNA) approaches can propel studies like this forward at an extraordinary pace. This approach is possible because genomic fragments surround us and the surfaces we encounter. By sequencing this DNA, we can rapidly and confidently determine the organisms inhabiting a space. This could include a toad hopping along, the bacteria growing amongst the leaves covering the toad’s path, and countless other macro and microscopic organisms living and passing through such a space. The REU will conduct field surveys in preserved areas and then use eDNA to compare the organisms (i.e., plant, animals, fungi, protists, and bacteria) found in locations with and without recreation occurring (e.g., hiking trails, and possibly climbing areas). This will provide a much needed eDNA account of the potential impacts caused through recreational activities.



Reconstructing Plant Communities from Ancient and Environmental DNA

Mentors: Dr. Robert Harbert  (Sackler Institute for Comparative Genomics - Bioniformatics)

Harbert Bio REu 2018 pic

Trace amounts of DNA can be extracted and sequenced using modern sequencing technology from highly degraded samples. This includes very old (i.e., sub-fossil, permafrost, and museum or herbarium specimens) and environmental samples (i.e., soil, water). Recently DNA has been extracted from packrat (Neotoma spp.) midden fossils from the Late Quaternary (<50,000 years old) of North America.  Historically these fossil deposits have recorded a high quality paleoecological history in the form of plant macrofossils embedded in the midden matrix, but the potential of ancient DNA (aDNA) analysis to expand on these studies is significant. The REU student will be actively involved in the isolation and analysis of aDNA samples from packrat midden macrofossils and control (known mixtures) samples. The data produced will be analyzed using bioinformatic software to provide taxonomic classifications for short-read metagenomic sequence data. The REU student will become familiar with basic bioinformatics tools for handling genomic data and working on the AMNH high-performance compute cluster. The REU student will gain experience programing in bash, Python, and R and using Git to manage and publish project code. Prior programming experience will NOT be required.

  

2015 Biology REU Interns and their Research Projects