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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.

2016 Project Titles


Slow Loris

A pygmy slow loris in Lam Dong Province, Vietnam, from our previous field season.

© Thạch Mai HoàngA

Slow Loris Evolution, Ecology and Conservation

Mentors: Dr. Mary Blair  (Center for Biodiversity and Conservation)

Slow lorises are small nocturnal primates threatened by the illegal wildlife trade in South and Southeast Asia. This project will utilize the Museum's collections to distinguish among unique evolutionary lineages of lorises using genetic information, morphological characters, and ecological preferences. The REU student will have the opportunity to extract, sequence, and analyze DNA from slow loris Museum specimens, and learn how to build ecological niche models from Museum specimen occurrence data. The results of the project will not only improve our understanding of the diversity and evolution of this poorly known group, it will also help to inform conservation management and enforcement of wildlife trade policies. (top)


The evolution of Sexual Size Dimorphism in Snakes

Mentors:  Dr. Frank Burbrink (Department of Herpetology, Division of Vertebrate Zoology)

Studies on sex-biased size dimorphism (SSD), where either males are larger than females or females are larger than males, can provide evidence of the major outcomes of evolution regarding morphology. Specifically, Rensch’s Rule indicates that within a clade, sexual size dimorphism is expressed more strongly in the larger species such that the difference in size between sexes increases generally when males are the larger sex. Variations in the pattern s of SSD can then provide evidence for three major processes that enhance biological variation: constraint, natural sexual or sexual selection. Rensch’s Rule has been tested in a number of vertebrates and invertebrates showing evidence for all three causes generating SSD. However, this has never been examined in snakes where SSD is commonly biased directionally for either sex. To understand the processes that generate SSD, we will record body size, sex and number of pre-caudal and caudal vertebrae across all species of natricine water snakes (n=226 species) using specimens from the herpetology collection at the AMNH. We will also generate a phylogeny using genomic-scale data. To address Rench’s Rule and understand the processes driving body size differences in these snakes, we will then use structural equation or phylogenetic linear mixed models modeling to examine allometry between male and female driven SSD in a phylogenetically corrected comparative context while accounting for ecology. This research will ultimately provide a better understanding about directionality and bias in SSD, how often it is generated, and if it evolves in parallel across the water snake tree of life.  (top)

Modern Birds

Unraveling the Rapid Radiation of Modern Birds

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

New phylogenomic studies agree that most major lineages of modern birds arose over a narrow window of time around 65-55 million years ago, following the Cretaceous-Paleocene asteroid extinction event. We are beginning to understand the phylogenetic relationships of these lineages using large datasets of molecular data, but we still have a poor understanding about the sequence of phenotypic changes that resulted in birds having their high diversity of size and shape. Nor do we understand when those phenotypes arose after the K-Pg extinction event. Therefore our lab is undertaking studies to synthesize previous morphological databases for birds and to improve character descriptions and taxonomic coverage. In doing this we are focusing attention of some of the very earliest lineages to branch off the avian tree of life. We are looking for an intern with an interest in vertebrate paleontology, morphology and evolution (especially of birds) to help us build this database, analyze phenotypic data, with the goal of reconstructing the steps in the evolution of modern birds. The intern will then integrate these data with available molecular data and the fossil record to help resolve the evolutionary history of major groups of birds. (top)

3D Imaging Carnivoran Mammals

3D Imaging and Shape Analyses of the Bony Labyrinth in Basal Carnivoran Mammals

Mentors: Dr. Camille Grohé and Dr. John J. Flynn (Division of Paleontology)

The bony labyrinth is an osseous structure surrounding the inner ear (soft tissues) in vertebrates; it is a primary cognitive organ responsible for hearing, perceiving movements and maintaining balance during locomotion. Its shape is influenced , as is that of the inner ear that it encloses, by both phylogeny (relationships between species) and ecology (head movements during locomotion). The goal of this project is to virtually reconstruct the bony labyrinths of fossil carnivoran mammal species by using Computed Tomography (CT) digital data of their skulls to analyze their shapes relative to previously analyzed extant and extinct taxa and existing phylogenies for the Carnivora and their nearest relatives. Previously analyzed representatives of major clades of extant Carnivora (including felids, hyenas, bears, canids, seals, weasels, raccoons, etc.) will be used as exemplars and comparators for this study, in which the REU intern will reconstruct and analyze the bony labyrinths of early fossil representatives of the broader Carnivoramorpha and Ferae mammal clades that include the diverse radiation of Carnivora. The REU student will learn fundamental concepts in 3D-imaging methods and comparative ear anatomy, will gain experience with 3D reconstruction software programs, and will apply geometric morphometric tools and multivariate statistical analyses to analyze the shape and evolutionary transformations of biological structures within a phylogenetic context. (top)

Fossil Chelicerates

Cuticle Structure and Fluorescence in Living and Fossil Chelicerates

Mentors: Dr. James Lamsdell and Dr. Melanie Hopkins (Division of Paleontology), Dr. Lorenzo Prendini (Division of Invertebrate Zoology)

Several groups of chelicerates, most notable scorpions, fluoresce under ultraviolet (UV) light.  For this project, we will use scanning electron microscopy (SEM) to compare the cuticle structure in different groups that fluoresce to different degrees. We will then identify extinct taxa that are good candidates for exhibiting cuticle fluorescence, and then test these predictions by comparing exceptionally preserved cuticle from the fossil record to our findings from living chelicerates.  (top)


Species Limits in Malaria Parasites

Mentors: Dr. Susan Perkins (Division of Invertebrate Zoology)  and Spencer Galen (Richard Gilder Graduate School)

Malaria, an important disease of humans, is caused by protozoan parasites that are part of the family Haemosporida. Related parasites use birds, lizards, and other vertebrates as their hosts. Efforts to understand and describe their diversity have largely focused on using sequences from a single mitochondrial gene, and while they have uncovered many new potential lineages of malaria parasites, more comprehensive analyses with multiple genes are needed to effectively delineate species. This project will involve molecular systematics on a variety of malaria parasites in order to better understand species boundaries, host use, and other evolutionary patterns.  (top)


  What Explains Speciation and Extinction Dynamics of Primates in Deep  Time?

 Mentors: Dr. James Herrera (Postdoctoral Fellow) and Dr. Nancy Simmons (Curator), Department of Mammalogy, Division of Vertebrate Zoology

The pace of evolution, measured by the rate of speciation and extinction, is affected by both intrinsic biological traits and environmental variables. Evidence from life history traits suggests that traits related to fast reproduction, including short gestation periods and large litter size, are related to higher speciation rates , while traits related to slow life histories are related to low speciation and higher extinction rates. Environment may shape evolutionary potential at the molecular level, as evidenced by higher speciation rates in tropical than temperate environments, seemingly because high temperatures induce higher genetic mutation rates thus promoting speciation . In contrast, abrupt changes in paleo-environments linked to mass extinction events have reshaped patterns of biodiversity multiple times in life’s history. Testing the relative roles of traits and environment on evolutionary dynamics is best done in the framework of the evolutionary tree (the phylogeny). In this project, an REU student will compare and contrast the relative roles of inherited biological traits and external environments affecting speciation and extinction dynamics in Primates, the mammalian clade to which humans belong.  Primates have a fossil record that extends back 65 million years, and the drivers of evolutionary change in this group have been the source of considerable scientific controversy. The student will create a database of life history traits for primates from primary literature sources, and will assist in defining clear criteria for evaluating the quality of data sources critically. The student will compile this database in the online data archive MorphoBank, a phenotypic counterpart to the GenBank database for genetic data. Environmental data for the Cenozoic, including global temperature estimates and precise solar insolation estimates, will be drawn from the literature and used to contrast the effects of environment on diversification with the effects of biological traits. The student will be trained in statistical approaches and will learn to write their own statistics codes for the open-source R statistical environment. Training will emphasize broad applicability of statistical methods to test hypotheses, compare alternative models, and answer research questions. Specifically, the student will be trained in maximum-likelihood and Bayesian statistical techniques for estimating the rates of speciation and extinction from phylogenetic trees. The student will learn and execute regression techniques that have broad applicability in a range of sciences. Emphasis will be on critical thinking and evaluating the research question, the data at hand, and finding the right tools to address a diversity of problems.    (top)



Shipworm Endosymbionts

Mentor: Dr. Mark Siddall (Curator) Department of Invertebrate Zoology

Wood-eating animals (xylotrphic) are enabled by highly specific microbial symbionts.  In the best-studied system, termites, the break down of cellulose into short-chain fatty acids is facilitated by a complex microbiome consisting of bacteria, archaea and protists, with the latter often being enabled by their own endosymbiotic “endomicrobiota”. Less well studied, are the obligately xylotrophic shipworm mollusks in the family Teredinidae. Remarkably few microbes are found in the shipworm stomach. Instead bacteria in the  gamma-3 subdivision of the Proteobacteria, Teredinibacter species, are found principally in the gill tissues of shipworm where they not only facilitate the breakdown of lignocellulose, but also engage in dinitrogen fixation and in contributing essential amino acids to the molluscan host. Transmission of the essential microbiome across generations is ensured vertically through spawned eggs, a mode likely to manifest phylogeentically as strict co-divergence. This project would see a summer intern apply DNA isolation methods to access the microbiome of a variety of shipworm speciemens collected globally.  Each would then be assessed for resident species of bacteria using PCR, DNA sequencing, and would be prepped for eventual next-generation amplicon DNA sequencing. 


2015 Biology REU Interns and their Research Projects 


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