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.

 

2017 Project Titles

 


Biodiversity

Black Bear Evolutionary Ecology

Mentors: Dr. Rae Wynn-Grant and Dr. Mary Blair  (Center for Biodiversity and Conservation)

The black bear population in the Western Great Basin of Nevada is growing, but for more than 100 years they have been extirpated from most of their historic range.  In this project, the REU student will leverage ecological and geographic information from Dr. Wynn-Grant’s fieldwork on black bear habitat preferences and movement in the Western Great Basin as well as information from the Museum’s collections to build ecological niche models for black bear habitat suitability. The models will be used to compare ecological niches between unique evolutionary lineages of black bear and to determine whether one of these lineages might be likely to re-colonize their historic range in Nevada. Models will also explore the influence of human development on black bear habitat suitability at the urban-wildland interface (where human development meets forest areas). The results of this project will improve understanding about ecological niche evolution and breadth in black bear subspecies, and will help inform conservation management. (top)


Capturing visual data from Ornithological collections for systematic studies

  Mentors: Dr. Ana Luz Porzecanski and Dr. Felicity Arengo (Center for Biodiversity and Conservation)

Tinamous

Despite the tinamous (Palaeonathiformes: Tinamidae) being a crucial group for understanding basal divergences in the bird tree of life, the phylogeny of this Neotropical group of birds has received limited attention. Two recent studies produced phylogenies for the family using external and some internal morphology, and DNA sequences. The two hypotheses had some similarities but also several disagreements. In this project, the REU student will examine a selection of tinamou specimens in the AMNH ornithological collection to collect more detailed data on external morphology, test multiple methods of photographic data capture, and explore preliminary methods of annotation and data analysis. Mentors and REU student will also work closely with Dr. Sara Bertelli, in Argentina, on study design and data analysis approaches. (top)


Protein evolution and the origin of social behavior in insects

wasp

Mentors: Dr. Federico Lopez-Osorio and Dr. Jim Carpenter (Division of Invertebrate Zoology)

Sociality in insects represents a major evolutionary transition that involved worker individuals forgoing their reproduction and caring for the offspring of a reproductive queen caste. This division of labor has arisen independently in various insect groups, primarily in hymenopterans (ants, certain bees and wasps) and termites, therefore enabling the discovery of shared genomic changes associated with the transition from solitary to social living. Several hypotheses have been proposed to understand the origin of sociality in molecular terms. The protein evolution hypothesis, for example, suggests that rapid evolution of specific genes and new protein functions influenced the origin of social behavior. The goal of this project is to test the protein evolution hypothesis in a broad comparative framework using transcriptomic data from social insects. The REU student will be actively involved in retrieving and analyzing raw data from high-throughput sequencing platforms. The data analysis procedures will include quality control, transcriptome assembly, phylogenomic analysis, tests of positive selection, and sequence annotation. Throughout the process, the REU student will become familiar with writing shell, Python, and R scripts. Moreover, the REU student will learn how to create reproducible research reports using R Markdown and a project website using GitHub Pages. The results of this study will provide novel insights into the molecular basis of sociality and a background for studies on the genetics of social behavior in insects.  (top)


Mosquito

 Mosquito proboscis development and evolution

Mentors: Dr. Steve Davis and Dr. David Grimaldi (Division of Invertebrate Zoology)

Owing to their preponderance in nearly every terrestrial habitat, insects have evolved a vast diversity in mouthpart structure to accommodate a correspondingly tremendous breadth in diets and feeding styles. However, mouthpart structure and function have independently converged several times in disparate lineages which share similar feeding regimes. For example, insects which feed on nectar and/or blood (both vertebrate and invertebrate), such as various flies, moths, and butterflies, have converged on probosciform/stylet-like mouthparts for reaching into flowers and piercing thick epidermal tissues. Understanding the developmental nature by which these convergences have occurred can help inform processes in morphological evolution and relate genetic change to phenotypic change. Student projects will therefore include, but are not limited to, using developmental techniques (such as RNAi) to understand the formation of adult mosquito mouthparts and to relate changes in gene expression to anatomical modifications, as well as characterizing RNAi mouthpart phenotypes through electron microscopy (top)


gibbons

Understanding intraspecific variation within Gibbons and Siamang

Mentors: Dr. Lu Yao and Dr. Ross MacPhee (Division of Vertebrate Zoology)

Gibbons and siamang (family Hylobatidae) are relatively understudied compared to other apes. They were the first to branch off in the adaptive radiation of apes, about 16-17 million years ago. The Hylobatidae taxon is unique in comparison to other extant ape taxa in that this group is particularly speciose. In fact, the family Hylobatidae currently contains 20 described species that fall within four genera: Hylobates, Hoolock, Nomascus, and Symphalangus. Although some species are relatively well known, so far no attempts have been made to sample widely within each species to understand intraspecific in addition to interspecific variation. This project will utilize the museum’s collections to analyze both size and morphological variation (body size, brain size, limb lengths, number of vertebrae, trunk length, 3D skull morphology) between and within extant hylobatid species. In this project, an REU student will collect and analyze linear measurements, volumetric measurements, and 3D landmarks from the specimens in the Museum’s mammalogy collections. The student will have the opportunity to gain experience in traditional anthropological measurement methods, 3D surface scanning techniques, 3D geometric morphometric tools, allometric scaling, and statistical analyses to understand inter- and intraspecific variation in gibbons and siamang.    (top)


bat fossil

  Putting Fossils in the Bat Family Tree

 Mentors: Dr. Nancy Simmons, (Department of Mammalogy, Division of Vertebrate Zoology)

Bats are the second most diverse group of mammals with nearly 1,400 extant species.  Distributed worldwide, bats fill a wide variety of ecological niches, have diverse roosting habits, and exhibit a remarkable array of dietary specializations ranging from insectivory to carnivory, frugivory, nectarivory, and even sanguinivory (blood feeding).  Modern molecular techniques have been used to construct a fairly robust phylogeny of extant bats, but controversies remain regarding relationships of some key fossils and time calibration of the tree remains problematic because many important fossils have not been explicitly included in phylogenetic analyses. This summer we will build on an existing database of morphological characters scored widely across extant bats to help alleviate these gaps by integrating more fossil data.  Working in the cloud-based software platform MorphoBank (http://morphobank.org), the intern this summer will help integrate additional morphological characters relevant for placing the fossil bat taxa, image and score fossils for phylogenetic analysis, and help to analyze these data in the context of previously published DNA data to build a more robust time-calibrated phylogeny for bats.  Our goals will include ongoing development of the phenomic database, integration of additional fossils, and testing previous hypotheses of relationships of fossil bat taxa to one another and to living lineages.  (top)


    

Declining or thriving? Unraveling the mass extinciton of ammonites at the Cretaceous-Paleogene (K-Pg) boundary

ammonites

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

Ammonites are externally shelled cephalopod molluscs related to modern squid and octopus, and among the most common fossil invertebrates in marine sedimentary deposits. Having dominated the oceans for over 300 million years, they finally went extinct 66 million years ago, during the famous Cretaceous-Paleogene (K-Pg) mass extinction event which also caused the demise of the non-avian dinosaurs. The details of this extinction are still the subject of intense debate; whether the primary cause was a sudden, catastrophic event such as an extraterrestrial bolide impact, or a slower decline in diversity over a longer timescale with sea level, climate changes or volcanism playing a role. The REU student will help examine new collections of ammonite fossils at the AMNH from K-Pg boundary sites along the Gulf Coast, USA. The overall aim is to look at the patterns of abundance and diversity of this group prior to the K-Pg extinction, in order to better test hypotheses as to the cause (and effect) of this event. Were ammonites declining or thriving prior to the mass extinction? This project would suit a student with some experience of, and interest in geology and paleontology, and may also involve the opportunity for fieldwork within the USA to collect additional material for analysis.


    

The Bloodsucker Proxy: Leveraging iDNA from leeches to monitor biodiversity in Cambodia

leech

Mentor: Dr. Mark Siddall and Michael Tessler Department of Invertebrate Zoology

Gathering knowledge on the abundance, dynamics and distributions of species is a fundamental challenges for conservation biology . In recent years, interest has grown in the application of environmental DNA as a non-invasive tool with which to obtain biodiversity information.  Terrestrial “jungle” leeches in the family (Haemadipsidae) retain blood in their digestive system for months after feeding. In contrast to invertebrates with high metabolism and short inter-meal intervals such as flies and mosquitoes, terrestrial leeches only feed few times annually, and to some extent possess the ability to retard the rate of DNA degradation. In 2015 we established new collections from Cambodia which allow determination both of vertebrate diversity in protected areas as well as assess resident bacteria and protozoon species carried by the leeches.  Already we have been able to confirm the integrity of iDNA from these specimens. This summer's REU intern will strategically apply a battery of PCR primers against many hundreds of isolates in order to characterize not only mammals, but ground bird, amphibian and saurischian DNA in the isolates as well as bacterial and protozoon parasites so as to form a more complete metagenomic picture.

 

2015 Biology REU Interns and their Research Projects