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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 25 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

(Applications Open January 2020)  

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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.

 2019 Project Titles

  • Computational analysis of language relationships: The Northwest Coast of Native North America
  • Systematics and Evolution of Arachnids
  • The unexplored bacterial diversity lurking in protist cell cultures
  • What shapes the heads of snakes?
  • Using machine-learning tools to identify traits that predict feeding strategies in insectivorous bats
  • The Path to Parasitism: Myxozoan Parasites of Amazonian Fishes
  • Structure and development of insect cuticular modifications
  • Testing “wireless mesh” networks for fine-scale movement studies of wildlife in Black Rock Forest
  • The Bees of NYC


Computational analysis of language relationships: The Northwest Coast of Native North America

map of language across west coast

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

The Northwest Coast is the second most diverse area of Native North America linguistically (after California). Numerous proposals have been made over the years about potential relationships among distinct languages, e.g. of Tlingit or Haida with "Na-dene" languages—but with no resolution. To date, these two remain "isolates" though with clear relationships to each other in some elements of vocabulary. Overall there are two recognized "families": Wakashan (Kwakwaka'wakw, Nuu-chah-nulth, Makah) and Salishan (multiple Coast Salish groups as well as some interior Salish-speakers), as well as a series of small linguistic entities—Tsimshian (Tsimshian proper, Gitxsan, Nisga'a), Haida, Heiltsuk, and Tlingit. All share what is generally regarded as a common culture in numerous practices, including economic adaptation, ritual, and instituted social hierarchy.  The data for this study come from a diversity of sources (e.g. PDFs, transcribed field notes, online public databases). The REU student will work on developing tools to compile Swadesh lists (and probably other vocabulary; species names, for example) in a common orthography. This will involve creating data scraping and encoding tools.  The compiled data will then be subjected to phylogenetic analysis using the phylogenetic analysis program POY (Wheeler et al., 2015) in a related fashion to a previous study concerning Uto-Aztecan and Bantu (Wheeler and Whiteley, 2015; Whiteley, Xue, and Wheeler 2018). The scientific problem concerns whether we can develop better measures of linguistic relatedness among these languages, and whether there are indicators of horizontal transfer linguistically (obviously, there are culturally), similar to another study relating to Pueblo languages in the Southwest. The REU student is expected to learn POY and some aspects of computational linguistics to apply to a concrete analytical problem. Wheeler, W. C., N. Lucaroni, L. Hong, L. M. Crowley, and A. Varón. 2015. POY version 5: Phylogenetic analysis using dynamic homologies under multiple optimality criteria. Cladistics 31:189-196. Wheeler, W. C. and P. M. Whiteley. 2015. Historical Linguistics as a Sequence Optimization Problem: Uto-Aztecan Language Evolution and Biogeography. Cladistics 31:113-125. 2018  Whiteley, M. Xue, and W.C. Wheeler, 2018, Revising the Bantu Tree. Cladistics. (Early view 8-31-2018).(top)



Systematics and Evolution of Arachnids

spider fighting scorpion

Mentors: Ricardo Botero-Trujillo, Pio Colmenares, Stephanie Loria, Lorenzo Prendini (Division of Invertebrate Zoology)

Arachnids, the second most diverse group of terrestrial animals, after insects, inhabit every terrestrial ecosystem and are tremendously important ecologically and economically, performing vital ecosystem services by keeping insect populations in check. Many arachnids are habitat specialists, extremely range-restricted and often micro-endemic to areas with particular geography, vegetation and climate. As such, arachnids are bioindicators of habitat degradation and climate change. Some of the most ancient arthropods, and the earliest to colonize land, were arachnids, e.g. scorpions, derived from aquatic ancestors that lived more than 425 million years ago. Different arachnid taxa have followed separate evolutionary paths, some hardly changing morphologically from fossil forms, whereas others are greatly modified. Many arachnids are increasingly threatened by habitat destruction and harvesting for the exotic pet trade, which taken together with their often low vagility and narrow geographic distributions, exacerbates their risk of extinction due to human activities. In a time of accelerating deforestation and global warming, arachnids offer an important window on our changing world. The task of inventorying arachnid diversity and distribution is a priority if steps towards their conservation are to be implemented. Improving baseline knowledge about arachnids, a primary aim of the AMNH arachnology lab, requires scholars curious and motivated to be involved in research projects in arachnid systematics and evolutionary biology. During the summer, students will undertake projects assessing the taxonomy and phylogeny of particular arachnid taxa (e.g. camel spiders, hooded tick spiders, scorpions, whip scorpions or whip spiders) involving (1) morphological examination, measurement, microscopy and imaging of arachnid specimens, (2) genomic DNA extraction and sequencing, and (3) mapping and GIS analysis of distributions. (top)



The unexplored bacterial diversity lurking in protist cell cultures

glowing microbes

Mentor: Sally Warring & Eunsoo Kim (Division of Invertebrate Zoology)

 Our lab works on microbial eukaryotes collected from oceans all over the world. We maintain the organisms in mono-eukaryote cultures in the laboratory. These cultures contain many bacterial species, some which came from the water the eukaryote species was isolated from, others from the lab itself. When we sequence and assemble genomes of the eukaryotic microbes, a byproduct is the assembled genomes of many of these bacteria. Usually, we throw these genomes out as junk, but they are actually a fantastic resource and we are interested in exploring the bacterial diversity among our cultures with the hope of identifying species (some potentially novel) and understanding their abundance, distribution, population dynamics, and origin.  This project is bioinformatics heavy and would involve mining eukaryotic genome assemblies to extract full-length bacterial genomes. These genomes would need to be assessed for completeness and annotated using typical genomics tools, and the species identified using phylogenomic methods. We would also explore the species distribution, abundance, and population genetics of each bacterial species, and attempt to identify where each species may have originated (ocean or lab contamination).(top)



 What shapes the heads of snakes?

Mentor: Marion Segall (Division of Vertebrate Zoology, Dept of Herpetology)

snake skull and teeth

Snakes are fascinating creatures; despite their lack of limbs, they have invaded all kinds of habitats, from deserts to cold climates, from trees to oceans or burrows. Snakes display a wide variety of ecological and behavioral habits, yet, they mostly rely on their head to survive. We try to understand the relationship between the shape of different elements of the head of snakes (from external shape to bony structures and soft-tissues), their ecology and the different functions of the head. In other words, we use the head of snakes to understand the link between ecology, morphology and behavior. We use microscopic computed tomography (μCT) to get a 3D model of the bony structures. Then, we use 3D geometric morphometrics and we run statistical analysis in a phylogenetic framework, using the R environment, to answer our questions. The student will be involved in every part of the research project, from data acquisition (CT scanning and bibliography) to analysis. Our goal is to give the student an overview of a researcher’s work. The student will have to work with collection specimens and is going to be involved in the life of the lab and with other member of the AMNH staff. Thus, we expect the student to be respectful, organized, patient and meticulous.(top)



Using machine-learning tools to identify traits that predict feeding strategies in insectivorous bats

Mentors: Nancy Simmons and Ariadna Morales (Division of Vertebrate Zoology, Department of Mammalogy)

bat in flight

Bats represent over 20% of the species diversity of living mammals and have colonized nearly all terrestrial ecosystems, providing extraordinary examples of adaptive radiations and morphological convergence. Adaptive radiations occur when a group diversifies into a wide variety of phenotypes as a response to different environments and ecological opportunities. However, evolutionary radiations can also occur in situations that constrain morphological evolution and promote convergence, where multiple species evolve traits in parallel in response to similar environments. One prominent example is found in the bat genus Myotis. We aim to understand what traits are linked to the convergent phenotypes and foraging strategies of this diverse group of bats by integrating morphological data and machine-learning tools. The REU student will participate in collecting morphological data and will learn machine-learning tools to assess what traits are important to predict feeding and foraging strategies in bats of the genus Myotis. The student will acquire a strong background in convergent evolution, statistical and coding tools, and evolution of bats. Having a basic knowledge of vertebrate morphology, statistics, and basic coding experience would be a plus, but is not required. (top)



  The Path to Parasitism: Myxozoan Parasites of Amazonian Fishes

Mentors: Kalani Williams and Mark Siddall (Division of Invertebrate Zoology)

micro parasite

The Arapiuns River, black with tannins, and the clearwater Tapajós River meet the Amazon near Santarém, Brazil. Here, in a span of about 10 miles, three wildly different aquatic habitats converge. While all three are home to various freshwater fishes, skates, and rays, these aquatic vertebrates may be host to different parasites across these different ecosystems. In particular, we’re interested in the varying diversity of myxozoan infections. Myxozoans are microscopic obligately parasitic cnidarians (sister to jellyfish), composed of just a few cells with a fish/annelid two-host life-cycle. In their fish hosts, myxozoans can cause a myriad of pathologies, including whirling disease, a condition sufficiently severe to reportedly have caused a 90% population loss in farmed rainbow trout. The goal of this project is to determine the identity of these myxozoan parasites, compare their diversity across the three ecosystems, and (eventually) to further investigate how their genome has changed to accommodate a parasitic life style.  Finding a 10 um parasite in a piece of fish gill is like finding a needle in a haystack. We are currently designing primers to maximize myxozoan amplification from DNA isolations and minimize off-target amplification of fish DNA. The REU student will be involved in DNA isolations of fish gills and next-generation amplicon sequencing. Additionally, the intern will apply bioinformatics to separate host from parasite reads, determine the identity of the myxozoans, compare the myxozoan diversity across sites.(top)



Structure and development of insect cuticular modifications

Mentors: Steve Davis and David Grimaldi (Department of Invertebrate Zoology)

insect cuticle

Arthropods constitute a vast radiation of life and are characterized by their hardened exoskeleton. With nearly one million described species, insects represent the largest arthropod lineage that are not only remarkable in their species diversity but also in their rich assortment of physical features and cuticular modifications. Current research is aimed at exploring and describing various components of this extraordinary morphological diversity, as well as understanding the development of some of these features. Student project topics may include, but are not limited to, studying the development of anti-wetting modifications of the collembolan (springtail) cuticle, scale (similar to butterfly scales) formation in basal and derived insect lineages, and the formation of needle-like stylets from insect appendages (such as with female ovipositors). Techniques that will be utilized include RNA interference (RNAi) and confocal and electron microscopy

 



Testing “wireless mesh” networks for fine-scale movement studies of wildlife in Black Rock Forest

Mentors: Suzanne Macey (AMNH-Center for Biodiversity and Conservation), Matt Palmer (Department of Ecology, Evolution and Environmental Biology, Columbia University), Christopher Raxworthy (AMNH-Herpetology) and Ana Luz Porzecanski (AMNH-CBC)

turtle closeup

The approach of low-cost yet cutting-edge “wireless mesh” networks that bring internet connectivity to areas with minimal broadband infrastructure can also be used to help scientists more accurately retrieve data from remote locations. Black Rock Forest, a 3,800+ acre living laboratory for field-based research approximately an hour north of NYC, has recently installed 20 self-powered “nodes” for their new mesh network. This network will provide researchers with real-time data from their existing environmental monitoring stations, but can also provide an opportunity to test the network’s ability to accurately monitor fine-scale movements of animals. In this project, our goal is to monitor the movements of understudied and often rare terrestrial animals (such as Eastern Box Turtles) at Black Rock Forest via the network and VHF receivers and transmitters. Together with a group of mentors, the REU student will be co-leading a pilot field research to survey, trap, deploy receivers at nodes, attach transmitters to animals, and analyze data to monitor movements of selected species of terrestrial reptiles or small-bodied mammals via the wireless network. The participating student will be based at Black Rock for part of the internship and acquire skills relating to field and data analysis methods involved in movement ecology and demographic studies of wildlife. Having field experience and basic knowledge of statistics and coding experience would be beneficial, but not required.

  



The Bees of New York City

bee on leaf

Mentors: Dr. Jerome G. Rozen, Sarah Kornbluth, Corey Smith (Division of Invertebrate Zoology)
New York is host to over 400 species of wild bees, nearly all of which play a vital role in our vegetable gardens, urban farms, and wild greenspaces. Understanding the geographical ranges, habitats and flight season of our native bees can provide a baseline knowledge we can use to monitor the health of our native bee populations and subsequently work to conserve the environment that provides the resources they need. The REU student will be responsible for processing a portion of the insect specimens collected over a period of five years from the Javits Center’s green roof, learning proper specimen preparation techniques and be instructed in insect identification methods. Duties will also include assisting in a survey of Green-Wood Cemetery, one of Brooklyn’s largest green spaces, where instruction in both net and pan trap collection techniques will be utilized to examine the bee community. The project will serve to provide further data to the ongoing survey of New York’s bees, and give insight into the changing bee biota of the city and the role of intentional greenspaces in promoting pollinator health.