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REU Biology Program

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Biology Research Experience for Undergraduates 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 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 $6000 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. Applications will be accepted from January 1-January 31, 2021.  For questions with application process, contact [email protected].

 

 2021 Project Titles 

Systematics and Evolution of Arachnids

Spider fights a scorpion.

Mentors: Ricardo Botero-Trujillo, Jairo Moreno-GonzalezPio Colmenares, 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.

 

Further exploration of the Sahelanthropus femur

Hammond Summer REU Photo

Mentors: Ashley Hammond (Division of Anthropology) and William Harcourt-Smith (CUNY, and Division of Paleontology)

For decades, bipedality has been considered the defining feature of the hominin lineage.  The earliest hominin fossils are always identified by paleoanthropologists based on adaptations for bipedality found in the skeleton and the cranium. Sahelanthropus tchadensis from Chad, dated to approximately 7 million years ago, has been considered the earliest hominin species based on features of the cranial base suggesting the species walked upright. This species has been known entirely from cranial evidence until recently, when a femoral shaft fragment was published (Machiarelli et al., 2020, Journal of Human Evolution).  This femoral shaft, attributed by the authors to Sahelanthropus, reportedly does not bear hallmarks of a bipedal femur.  This finding has a number of significant implications for early hominin evolution and our interpretations of the fossil record, including the possibility that (a) bipedality may not distinguish the earliest hominins or (b) that Sahelanthropus may not in fact be a hominin.

This project will further investigate the morphological affinities of this important femoral shaft from Chad.  The femur shaft was qualitatively and quantitatively compared to extant apes and humans, but it should be explored whether this fragmentary shaft can be fully excluded from other fossil taxa. The specific goal of this project is to test whether the femoral shaft from Chad can be excluded from large carnivores.  The REU intern will gain the following experiences: (1) learn how to use 3D imaging and processing software such as Image J, Avizo, Dragonfly, and VG Studio; (2) collect data from CT scans of extant African large carnivores housed in the AMNH collections (i.e., lions, leopards, hyenas, and wild dogs); (3) learn about femoral shaft shape and cross-sectional properties of extant apes, humans, and large African carnivores; (4) learn and conduct data analysis in R software; and (5) contribute to a research project on early hominin adaptations to bipedality.  Prior basic knowledge of human anatomy and osteology would be beneficial for successful completion of this internship.

 

Relating Insect Wing Sensilla to Flight Ability

Diagram illustrates the relation of insect wing sensilla to flight ability.
 

Mentors: Hollister Herhold (RGGS), Steve Davis and David Grimaldi (Division of Invertebrate Zoology)

With nearly one million described species, insects represent the largest arthropod lineage. The evolution of flight is believed to be one of the major reasons behind this diversity. Although most hexapods in the class Insecta possess wings (some having secondarily lost them), their flight abilities are variable. Flight performance is attributable to many things, such as certain wing modifications, e.g., reduction of the hind wings to halteres in Diptera, hardening of the fore wings to elytra in Coleoptera, etc., as well as variation in wing sensilla distribution.

This project aims to document the campaniform sensilla on the wings of various insect groups and compare their distribution to several aspects of flight ability, such as wing shape and wing beat frequency. In order to accomplish this work, dissections will be made of wings and imaged using light and scanning electron microscopy. Wing shape variation will be analyzed using morphometrics and live imaging will be done to determine wing beat frequency of selected taxa.

 

Exploring evolutionary links among wing anatomy, landing biomechanics, and roosting ecology in phyllostomid bats

Left: Bat in flight. Right: Bat skeleton.
 

Mentors: David Boerma and Nancy Simmons (Division of Vertebrate Zoology)

Animal anatomy (form), movement (function), and environment (ecology) change together over the course of evolution to shape the diversity of life. Each of these factors are individually important but learning how they are linked can shed light on what sparks the rapid appearance of new species, evolutionary periods called adaptive radiations. This research project takes advantage of the breathtaking diversity of bats to explore how form, function, and ecology were linked during bat evolution by examining it through the lens of the biomechanics of landing behavior. Of the over 1,400 living bat species, those belonging to the family Phyllostomidae (> 200 species) show the greatest diversity of roosting ecologies. In this project, we will use high-resolution micro Computed Tomography (µCT) scans to explore the extent to which the evolution of particular roosting habits (ecology) has been connected to the evolution of specific limb morphologies (form) and landing biomechanics (function) in phyllostomid bats. The REU student will be involved with all aspects of the project, including collecting and processing µCT scans, building and extracting measurements from digital bone models, and conducting phylogenetic analyses to test evolutionary hypotheses. The ideal student is patient, inquisitive, and enthusiastic, and might have prior experience with vertebrate anatomy (human anatomy counts), basic statistics, and coding in R and/or MATLAB. However, experience in these areas is not a requirement.

 

Learning from the mouth parts: morphology, paleobiology and phylogeny of “living fossils” nautiloids

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Mentors: Amane Tajika and Neil H. Landman (Division of Paleontology)

Nautiloids are a group of externally shelled cephalopods, a relative of squids and octoposes. Their modern descendants Nautilus and Allonautilus are often called “living fossils” since they have retained a similar shell morphology over some hundred million years. A big question regarding nautiloid evolution is why nautiloids survived the mass extinction event at the end of the Cretaceous while ammonoids, which also possessed an external shell similar to nautiloids, went extinct. To answer this question, paleontologists studied these organisms over decades, which significantly increased our understanding of these mysterious animals. Nevertheless, the ultimate reason for the survival and extinction still remains under discussion. Jaw morphology is one of the most important characters that can provide useful information on the paleobiology and evolution of nautiloids and ammonoids; a comparative analysis focusing on the mandibular region provides a direct link between the morphology of fossilized specimens and the feeding habits of their modern-day representatives. The jaw morphology serves not only to reveal their feeding strategy but also to reconstruct their phylogeny. Thus, this trait needs to be studied in detail in a wider range of taxa from various geological times. This project involves detailed 3D reconstruction of undocumented upper jaws of latest Cretaceous nautiloids using CT-scans, which will contribute to a better understanding of the feeding strategy of nautilids right before the mass extinction event. The REU student working on this project will gain experience in 3-dimensionally reconstructing fossil CT-data and subsequent morphological analysis. This project may also include some field work to collect additional fossil material.

 

Macroevolutionary trends among Cretaceous cephalopods

Mentors: Christopher Whalen and Neil H. Landman (Division of Paleontology)

Cephalopods, such as squids and octopuses, are among the most complex and intelligent invertebrates, and are key components of global marine ecosystems and nutrient cycling. Ammonoids, belemnoids, and vampyropods (octopods and vampire squid) flourished in Mesozoic oceans, but their diversity was catastrophically reduced during the Cretaceous-Paleogene mass extinction; ammonoids and belemnoids went extinct. Vampyropods survived, but their higher-level diversity was greatly reduced. Conversely, decabrachians (squids and cuttlefish) seem to have been somewhat insignificant in Mesozoic oceans, but comprise a supermajority of extant cephalopod diversity. To reconstruct the macroevolutionary dynamics governing this transition, we need to understand the diversity trajectories of the various Late Cretaceous cephalopod taxa. Although cephalopods possess an excellent fossil record, most of the existing diversity-through-time analyses are inadequate or outdated. There is no comprehensive database of Mesozoic cephalopod occurrences that can be used as a basis for modern statistical analyses. Through examination of AMNH fossils and literature surveys, the student will assemble a new database that he or she can tailor to a variety of questions. The overall objective will be for the student to map genus-level cephalopod diversity trends throughout the Late Cretaceous (~100.5 – 66.0 Ma), and to use these data to interpret inter-clade dynamics. The student will also discover new insights into fossil belemnoid or ammonoid anatomy from microCT scans of previously unidentified or misidentified museum specimens. The project could involve fieldwork and visits to other nearby museums, such as the Yale Peabody. Given the literature component, the student will be able to produce results even if museum access is limited by the COVID-19 pandemic.

 

Lorisiform Evolution and Conservation: Museum Phylogenomics of Endangered Nocturnal Primates

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Photo credit: Luca Pozzi
Photo credit: Luca Pozzi

Mentors: Mary Blair (Center for Biodiversity and Conservation) and Luca Pozzi (University of Texas at San Antonio)

The lorisiforms are elusive nocturnal primates including lorises, galagos, pottos, and angwantibos. Many of these understudied primates are highly threatened with extinction due to illegal wildlife trade and habitat loss, while much remains to be understood about their evolution and phylogenetic relationships. A more comprehensive understanding of this poorly known group is highly likely to resolve knowledge gaps about the early history of primate evolution. This project will utilize the Museum's collections to produce genomic data for representatives of this understudied group, allowing unprecedented study of their evolutionary history, species diversity, and biogeography. If on-site web lab work becomes possible during the internship period, the REU student will have the opportunity to learn DNA extraction methods from Museum specimens and produce and analyze genomic datasets for lorisiforms. If on-site work is not possible, the REU student will focus on analysis of in-hand genomic data from lorisiform samples.

 

Evolutionary analysis of human language, culture, and whole genome sequences

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Mentor: Ward Wheeler (Division of Invertebrate Zoology)

The project will work to integrate databases of linguistic, cultural, and whole genome sequence information of Bantu-speaking peoples.  The goal is to test hypotheses of historical migration patterns in sub-saharan Africa 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.

 

Evolution of mammalian body shapes 

Illustration of the skeleton of a carnivoran species.
 

Mentor: Christopher Law and (Division of Paleontology)

Understanding the major patterns and adaptive significance of phenotypic variation is a central goal of evolutionary biology. In vertebrates, body shape diversity is one of the most prominent features of phenotypic variation that can lead to increased diversification, niche specialization, and innovations within a clade. However, biologists still lack a full understanding of the underlying morphological components that contribute to body shape diversity in mammals. Consequently, little is known about the morphology, ecology, and evolution of mammalian body shapes as well as the underlying traits that contribute to different body plans. This research will test hypotheses pertaining to the evolutionary connectivity of the cranial, axial, and appendicular components that contribute to body shape diversity, and the adaptive significance of body shapes. To accomplish these goals, this research will generate a database of mammalian body shapes using skeletal specimens held at the Burke museum and test the following hypotheses: H1) skeletal components contributing to body shape diversity in carnivorans are evolutionarily integrated, H2) the relationship between body shape and limb length in mammals follows a similar trend as ectothermic vertebrates, and H3) locomotor and dietary ecologies influence the evolution of carnivoran body shapes. The student will learn to (1) collect morphological data from osteological specimens, (2) conduct literature reviews, (3) perform statistical analyses using command-line approaches in R, and (4) interpret and present results.

 

Inferring horizontal gene transfers across the Tree of Life

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Mentors: Victor Sojo and Apurva Narechania (Comparative Genomics)

Horizontal gene transfer (HGT) is the acquisition of genes from sources outside the parent-offspring relationship. It is a pervasive phenomenon in prokaryotes, in which it plays a major role in the acquisition of drug resistance in pathogenic bacteria. HGT also occurs in eukaryotes, and it is believed to have been on continue to be crucial in the evolution of multiple lineages across the Tree of Life. The students will perform a thorough review of current methods for HGT inference, and develop new methods for the detection of gene transfers. The project will be bioinformatics-focused. The students will learn and make ample use of the Python programming language, as well as develop skills in phylogenetics and evolutionary biology.

 

Improving Low-Cost Technology to Monitor Fine-Scale Movement of Wildlife in Black Rock Forest

Eastern box turtle makes its way across ground covered with small rocks.

Mentors: Suzanne Macey and Ana Luz Porzecanski (Center for Biodiversity and Conservation)Christopher Raxworthy (Division of Vertebrate Zoology), and Matt Palmer (Columbia University)

Black Rock Forest, a living laboratory for field-based research approximately an hour north of NYC, is installing 20 self-powered “nodes” for a new “wireless mesh" network. These low-cost cutting-edge networks will provide researchers with real-time data from their existing environmental monitoring stations but can also provide an opportunity to work towards the network’s ability to accurately monitor fine-scale movements of animals. Leveraging new tracking technologies and preliminary research from the past two years, this project aims to 1) obtain a more complete field season of turtle movement and ecology data, 2) add temperature logging capabilities to "homemade" GPS backpacks, 3) make advancements towards automation of data retrieval from the backpacks to the wireless mesh network. This study will establish improved methodologies and understanding of using affordable GPS trackers in below tree canopy environments, and for finer scale spatial movements (where GPS position error becomes more important). These results will have interest to a broad range of ecologists. If conditions allow, the participating student would be based at Black Rock Forest for part of the internship and would acquire skills relating to field and data analysis methods used in wildlife movement ecology studies (previous knowledge of R and GIS software considered helpful).

 

Impacts of Climate Change for Avian Malaria

 

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Mentors: Johanna Harvey (Division of Invertebrate Zoology) and Susan Perkins (City College of New York).

Avian malaria parasites and associated haemosporidians are a group of vector-borne pathogens that are transmitted by a suite of distinct dipteran families. Avian malaria vectors have their own ecological constraints which affect their distributions and thereby limit the available host taxa. Despite the vast number of sequenced and morphologically identified haemosporidian pathogens, there remain many understudied geographic regions and avian host taxa that remain unsampled. In this project, we will examine mitochondrial DNA sequencing for a large diversity of passerines across numerous ecoregions. Students will be trained primarily in 1) genetic sequencing data analysis, focusing on phylogenetic and analysis of associated environmental data, 2) conducting of literature reviews. There is also potential for lab training 3) including DNA extraction and sequencing and 4) microscopy. Determining current pathogen distributions and constraints is needed in order to understand and best model the effects of future changes in distributions due to the effects of climate change.

 

Insect Evolution

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Mentor: Jessica Ware and Ware lab (Division of Invertebrate Zoology)

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, ancestral character states, and PCA/Hypervolume analysis. Additionally, you would learn how to model species distributions and test biogeographical hypotheses for a changing climate.