Yale Community

Project Description:

Sidney I. Smith graduated from Yale in 1867 and was appointed Assistant in Zoology at the Sheffield Scientific School and later promoted to Professor of Comparative Anatomy. During his 39 years at Yale, Smith collaborated with Addison Verrill, Yale’s first Professor of Zoology and the Peabody Museum’s first Curator of Zoology. Smith, a carcinologist, authored more than 70 scientific papers and described over 100 new species of Crustacea.

The Division of Invertebrate Zoology houses thousands of type specimens that were the basis for new species descriptions. These specimens are rarely static and are often restudied in various ways; age never diminishes their value. As new species are described these historical specimens are vital as comparative material. A thorough review of Smith’s Brachyura (true crabs) types deposited in the Peabody Museum will shed light on these important specimens; the new metadata will be a valuable contribution to scientists seeking to compare potential new species with those previously described more than a hundred years ago.

Under the supervision of Daniel Drew, Museum Assistant II, the intern will research the taxonomic history of Smith’s Brachyura type specimens, representing approximately 30 species. With the goal of publishing an illustrated peer reviewed type catalog, the intern will review the relevant scientific literature, tracking the taxonomic changes of each species from the time it was described through its modern interpretation. They will gain an understanding of how to appropriately handle and examine specimens to confirm species identifications, while also learning taxonomic emphasized photography for publication. If time permits, it may be possible to review the Smith Brachyura type specimens in the holdings of the Smithsonian Institute’s Museum of Natural History and the Harvard University’s Museum of Comparative Zoology.

Suggested readings:

Coe, W.R. 1929. Biographical memoir of Sidney Irving Smith 1843-1926. National Academy of Sciences Biographical Memoirs 14: 5-16.

Prosser, S.W.J., et al. 2016. DNA barcodes from century-old type specimens using next-generation sequencing. Molecular Ecology Resources 16: 487-497.

Smith, S.I. 1869. Notes on new or little known species of American cancroid Crustacea. Proceedings of the Boston Society of Natural History 12: 274-289.

Advisor:
Daniel Drew (Museum Assistant II)

Length: 8 weeks

Stipend: $3,800

Project Description:

The way to an ancient person’s mind is through their stomach. In other words, what did people eat in the deep past? How did they acquire and prepare their food? And how can archaeologists accurately reconstruct events that happened thousands of years ago? Stone Age archaeological sites are often full of animal bones. Some are the discarded remains of animals that ancient hunters killed and ate. However, a “site” is also a convenient place on the landscape that provides shelter, and so it draws many inhabitants. Some bones found there may be the remains of carnivore meals from times when people were not around. Still others may simply be the remains of animals that lived at the site. In this project, interns will collect data from fossil and subfossil (near-fossil) animal bones from Stone Age archaeological sites from Malawi, in the Zambezian open woodland forests of southern-central Africa. In this unique ecozone, animals shared habitats where they are not typically found together in other parts of Africa. This makes the identification of species challenging, but it is still possible to collect other kinds of data. By analyzing the body sizes of animals represented by the bones and studying patterns in fragmentation and modification to the bone surfaces (e.g., if they were burned, cut, or bitten), it is possible to reconstruct which animals were hunted by people and which became mixed into the collection through natural processes. This project will involve collection and analysis of those data for sites dating between 30,000 years ago to the present, using a comparative osteological collection, light microscope, MS Access databases, and MS Excel.

Content warning: this study will take place within the Yale Paleoarchaeology Laboratory, which also stores human osteological remains and a plasticized teaching cadaver.

Advisors:
Dr. Jessica Thompson (Assistant Professor of Anthropology)

The intern will also regularly interact with Dr. Gary Aronsen (Yale Biological Anthropology Laboratories Manager; YPM Curatorial Affiliate, Divisions of Vertebrate Zoology and Anthropology)

Outcomes:
Interns will gain firsthand experience with the major stages in the research process: acquisition of data, cleaning/quality checking of data, analysis, and presentation. They will understand how decisions made at the outset of research, such as what variables to collect and how to standardize them, affect the analyses they can do at later stages. They will learn how to manage basic relational databases, and how to perform basic analytical tests to understand patterns in their data. Interns will gain experience working with fossil and subfossil animal bones, learning how to organize and store them. They will become experienced in the collection of fossil bone data, but more crucially they will acquire transferrable skills about data collection, organization, and analysis that can be deployed in other contexts.

The collections the intern will work with are large and will take more time to work through them all than what is available in this internship. However, this project is designed as an informative subsample of available collections. It can therefore be presented on its own merits at professional conferences, with the intern as lead author. If the intern is the lead presenter, then they will do the majority of the analysis and design of the poster or podium talk, with ongoing support from Dr. Thompson and colleagues who are working on these collections. 

If the intern wishes to publish the data in any formal context, they should first consult with Dr. Thompson. It is anticipated that fragmentation data will, once completed, be published together with other analyses. At this time, which may be months to years after completion of the internship, the intern may contribute as a co-author. Authorship expectations are that the intern will contribute analysis and writing effort as well as the data they generate under this internship. At any time, the intern may freely present or talk about the results of their data collection in informal outreach or broader education contexts, and they will have perpetual access to all data they generate for subsequent educational uses (e.g. class projects). Dr. Thompson will also be available to write letters of recommendation as interns progress through their careers.

Connection to YPM Collections and Departmental/Divisional Goals:
As an Assistant Curator of Anthropology at the YPM, Dr. Thompson has led fieldwork to recover the objects the intern will study under this internship. The collections remain the property of the Government of Malawi, and are presently on temporary loan to the Yale Paleoarchaeology Laboratory. According to heritage regulations they must be returned to Malawi after analysis. Therefore, they will not become a part of the regular physical collections of the YPM. However, this is an issue that many researchers working with heritage objects or other “one of a kind” objects are currently facing, and the future of museum collections is likely to require a broader view of what constitutes a “collection”. Dr. Thompson is in the process of developing a plan with her colleagues in Malawi to generate digital collections of these objects that may be able to be formally accessioned into the YPM, including tabular data, images, and 3D scans.

Length: 8 weeks

Restrictions on timing:  

Dr. Thompson may take a research trip to Malawi during the summer of 2024, but these plans are flexible as they do not involve extended fieldwork. Therefore, Dr. Thompson can arrange to be unavailable either in June or August, leaving time for an 8-week internship between. This internship will need to take place at the same time as the other Yale Paleoarchaeology Laboratory internship.

Stipend: $3,800

Project Description:

How can archaeologists accurately reconstruct events that happened thousands of years ago? If you went through a Stone Age garbage heap you would find it is often full of snail shells. Some are the discarded remains of ancient meals. Others, however, might have been the debris from making ornaments meant for body decoration or trade. This practice leaves distinctive breakage patterns on the shells that are different from when they used them for other things, such as food. Shells may also simply be the remains of snails that lived naturally at the site. In this project, interns will tackle this problem by collecting data from fossil and subfossil (near-fossil) snail shells from Stone Age archaeological sites from Malawi, in the Zambezian open woodland forests of southern-central Africa. In this unique ecozone, ostriches inhabited extensive grasslands during the last Ice Age, but are not found after climates warmed and forests expanded around 11,5000 years ago. Because people had made ornaments from ostrich eggshells in the Ice Age, they had to adapt: they began to make ornaments out of snail shells instead. By analyzing the sizes, patterns of fragmentation, and modifications to the surfaces of ancient shells, it is possible to reconstruct how people used them in the past – or if the are only present at the site through natural processes. This project will involve collection and analysis of those data for sites dating between 30,000 years ago to the present, using a comparative shell collection, light microscope, MS Access databases, and MS Excel.

Content warning: this study will take place within the Yale Paleoarchaeology Laboratory, which also stores human osteological remains and a plasticized teaching cadaver.

Advisors:
Dr. Jessica Thompson (Assistant Professor of Anthropology)

The intern will also regularly interact with Dr. Gary Aronsen (Yale Biological Anthropology Laboratories Manager; YPM Curatorial Affiliate, Divisions of Vertebrate Zoology and Anthropology)

Outcomes:
Interns will gain firsthand experience with the major stages in the research process: acquisition of data, cleaning/quality checking of data, analysis, and presentation. They will understand how decisions made at the outset of research, such as what variables to collect and how to standardize them, affect the analyses they can do at later stages. They will learn how to manage basic relational databases, and how to perform basic analytical tests to understand patterns in their data. Interns will gain experience working with fossil and subfossil animal bones, learning how to organize and store them. They will become experienced in the collection of fossil shell data, but more crucially they will acquire transferrable skills about data collection, organization, and analysis that can be deployed in other contexts.

The collections the intern will work with are large and will take more time to work through them all than what is available in this internship. However, this project is designed as an informative subsample of available collections. It can therefore be presented on its own merits at professional conferences, with the intern as lead author. If the intern is the lead presenter, then they will do the majority of the analysis and design of the poster or podium talk, with ongoing support from Dr. Thompson and colleagues who are working on these collections. 

If the intern wishes to publish the data in any formal context, they should first consult with Dr. Thompson. It is anticipated that fragmentation data will, once completed, be published together with other analyses. At this time, which may be months to years after completion of the internship, the intern may contribute as a co-author. Authorship expectations are that the intern will contribute analysis and writing effort as well as the data they generate under this internship. At any time, the intern may freely present or talk about the results of their data collection in informal outreach or broader education contexts, and they will have perpetual access to all data they generate for subsequent educational uses (e.g. class projects). Dr. Thompson will also be available to write letters of recommendation as interns progress through their careers.

Connection to YPM Collections and Departmental/Divisional Goals:
As an Assistant Curator of Anthropology at the YPM, Dr. Thompson has led fieldwork to recover the objects the intern will study under this internship. The collections remain the property of the Government of Malawi, and are presently on temporary loan to the Yale Paleoarchaeology Laboratory. According to heritage regulations they must be returned to Malawi after analysis. Therefore, they will not become a part of the regular physical collections of the YPM. However, this is an issue that many researchers working with heritage objects or other “one of a kind” objects are currently facing, and the future of museum collections is likely to require a broader view of what constitutes a “collection”. Dr. Thompson is in the process of developing a plan with her colleagues in Malawi to generate digital collections of these objects that may be able to be formally accessioned into the YPM, including tabular data, images, and 3D scans.

Length: 8 weeks

Restrictions on timing:  

Dr. Thompson may take a research trip to Malawi during the summer of 2024, but these plans are flexible as they do not involve extended fieldwork. Therefore, Dr. Thompson can arrange to be unavailable either in June or August, leaving time for an 8-week internship between. This internship will need to take place at the same time as the other Yale Paleoarchaeology Laboratory internship.

Stipend: $3,800

Project Description:

North America is a temperate biodiversity hotspot for freshwater fishes. Darters are small teleost fishes that are distributed throughout Eastern North America and are one of the most species rich groups with approximately 250 species. Within darters there is substantial variation in traits, such as body coloration, reproductive strategy, habitat preference, and diet. We aim to evaluate morphological evolution among species of darters using landmark morphometric techniques. This project will use specimens resulting from field work in the southeastern US and from the Peabody Museum. The morphological dataset will allow an understanding of the relationship between morphological evolution, speciation, and lineage diversification. The project involves work in the Near Lab housed in the ESC on campus, at least one field trip to Tennessee and Alabama, and in the Vertebrate Zoology collections of the Yale Peabody Museum.

Advisors:
Dr. Tom Near (Professor and Chair of Ecology and Evolutionary Biology; Bingham Oceanographic Curator of Ichthyology, Peabody Museum)

Julia Wood (Graduate Student of Ecology & Evolutionary Biology)

Length: 8 weeks

Stipend: $3,800

Project Description:

Horse Island is the largest of the Thimble Islands off Branford, CT. It was purchased by Yale in the early 1970s, prior to which the vegetation was controlled by landscaping – there was at one time half a dozen buildings, a tennis court, and a field maintained for picnicking. Since Yale’s acquisition, the island has been used for biological research and allowed to return to a “natural” state. Apart from clearing a small amount of land on the northeastern side of the island for the construction of a new research station, the island’s plant community has largely been left unmanaged.

In 1986, botanists Lauren Brown and Penelope Sharp published “The Vegetation of the Thimble Islands, Branford, Connecticut,” in which they described and catalogued the vegetation of each of the Thimble Islands, including Horse Island. Through their documentation, they described and mapped Horse Island’s vegetation 15 years after Yale’s purchase and made predictions as to what the island would look like if allowed to continue its recovery: “Now, sassafras trees about four feet tall have invaded and will probably soon close in and create an understory.” Shortly after, Brown developed a checklist of all the plant species on Horse Island (Brown, 1990). With Brown and Sharp’s well-timed documentation, Horse Island offers a unique opportunity to determine whether their predictions proved accurate by studying a successional island ecosystem.

In this project, a student researcher will assess how the plant community of Horse Island has changed since the 1986 and 1990 surveys using quantitative methods. The student will learn plant identification in the field and will collect identified specimens for the Peabody’s botany collection, the Yale University Herbarium. The student researcher will compare past and present vegetation to determine the degree of change using the Sorensen index and/or spatial analysis using digitized maps of the past and current species distribution. The student will be able to assess when new species were first discovered on Horse Island by comparing current species composition to specimens in the botany collection.

Advisors:
Dr. Natalie Mastick (Student Programs Postdoctoral Associate at the Peabody)

Dr. Patrick Sweeney (Collections Manager of Botany)

Outcomes:
This research could culminate in a short paper, possibly in the Peabody Bulletin, or a public talk.

Connection to YPM Collections and Departmental/Divisional Goals:
Horse Island is a YPM Natural Property, and it is one of the Peabody Student Program’s goals to increase student research initiatives on the island. Additionally, by collecting botanical specimens with the supervision of Patrick, the student would be contributing to the Peabody’s collections. These data will be useful for future student studies of Horse Island as the ecosystem continues to change.

Length: 8 weeks

Restrictions on timing:  

Natalie will be in New Haven all summer. Patrick will be away during July 21–27.

Stipend: $3,800

Project Description:

A recent study of the YPM orangutan (Pongo sp.) skeletal collection identified taxonomic diversity, age/sex variation, life history indicators, trauma, and ecological markers on bones and teeth.  In 2023, another orangutan individual was accessioned into the YPM VZ Division.  This individual has a complete skeleton as well as detailed records that (potentially) allow for correlations between life history events, growth, health, and other variables.

The intern will learn how to perform an inventory and assessment of skeletal and dental elements, apply life history theory and forensic techniques to identify and interpret individual variation, use metric data collection to support or falsify available taxonomic information, and learn to use radiography and other specialized tools to evaluate health, injury, and disease using medical and/or veterinary standards.  The resulting data will not only connect a single organism to applied conservation and management questions but also address broader issues such as dental development, taxonomic diversity, and the effects of captive versus wild conditions on morphology and phenotype.

Experience in osteology, primate ecology, zoology, or related fields is encouraged.  The goal of this project is to generate a publication in a peer reviewed journal (Bulletin of the Peabody Museum of Natural History), and possibly to present the results at a professional conference.  The project will follow the methods and techniques used in the publications below, allowing for both structured learning and relatively quick turnaround in publication.

Collaborative publications with undergraduates (in bold):

Walls, K., & Aronsen, G. P. (2023). Inventory and Assessment of the Pongo (Linnaeus, 1760) Skeletal Collection Housed at the Yale Peabody Museum. Bulletin of the Peabody Museum of Natural History, 64(2), 83-129.

McRae, R., & Aronsen, G. P. (2018). Inventory and assessment of the Gorilla gorilla (Savage, 1847) skeletal collection housed at the Yale Peabody Museum of Natural History. Bulletin of the Peabody Museum of Natural History, 59(2), 199-247.

Aronsen, G. P., & Kirkham, M. (2017). Inventory and assessment of the Pan troglodytes (Blumenbach, 1799) skeletal collection housed at the Yale Peabody Museum. Bulletin of the Peabody Museum of Natural History, 58(1), 209-259.

Advisors:

Professor Eric Sargis (YPM Curator of Vertebrate Paleontology and Vertebrate Zoology)

Dr. Gary P. Aronsen (Yale Biological Anthropology Laboratories Manager; YPM Curatorial Affiliate, Divisions of Vertebrate Zoology and Anthropology)

Length: 6 weeks

Stipend: $2,850

Project Description:

Preventive conservation is described as all the actions that can be taken to mitigate damage or deterioration on museum objects and specimens. In the case of the environmental conditions the objects are exposed to, there are three main agents of change that will affect their long-term preservation: light levels (visible and ultraviolet), relative humidity, and temperature. These agents will be accompanied by others. For example, the temperature and relative humidity conditions may welcome pests into the space, or they may trigger chemical reactions that generate contaminants inside the exhibit case.

The renovated galleries at the Yale Peabody Museum have new exhibit cases, new exposed windows, new heating and cooling systems, among other changes and therefore, the three main agents of change are still being assessed to determine what effect they may have on the collections on display. The participant will aid in data collection of the three main agents at different times of the day in different exhibit cases, to help the conservator understand which measures should be taken to mitigate such agents. In addition, the participant will compare the data with that from the environmental monitors placed in the exhibit galleries to inform whether those monitors are placed in the best places to understand the conditions of the rooms.

The data collection and interpretation, together with research on the agents of change and other observations in the exhibit galleries will aid in policies that will help preserve YPM collections into the future.

This project will utilize resources from Conservation at YPM.

Advisors:
Mariana Di Giacomo (Peabody Museum Conservator)

Outcomes:
the project will allow the Conservation team to learn about the environmental conditions in the renovated galleries, which will inform future exhibition recommendations. The work can result in an oral presentation or poster at a conference.

Connection to YPM Collections and Departmental/Divisional Goals:
the participant will work directly on the care and conservation of YPM collections, and the data retrieved will live in the museum’s database, informing future exhibitions.

Length: 8 weeks

Stipend: $3,800

Project Description:
Salamanders are exceptionally diverse in the habitats they occupy and their life history. These differences have allowed them to occupy different ecological niches and to utilize different feeding modes (e.g., suction feeding, tongue protrusion). These differences in feeding modes reflect adaptive shifts in cranial and hyobranchial morphology. The goal of this project will be to collect and analyze skeletal and musculature data and compare differences in morphology to better understand the evolution of salamander feeding systems.

The YPM intern will learn how to collect morphological data from museum specimens available at the YPM. Interns will have the opportunity to prepare specimens to be micro-CT scanned for 3-D visualization. Scanning will be conducted by Henry Camarillo, but the intern may observe and assist with the process. Interns will have the opportunity to post-process micro-CT scans and collect morphometric data from the salamander cranium and tongue skeleton. The intern will be trained to analyze the morphological data through statistical and evolutionary methods utilizing the R programming language. Specifically, the intern will combine data they collected with morphometric data previously collected by the Muñoz lab and learn how to do comparative evolutionary analyses between salamander species.

This project has the potential to lead to a continued undergraduate research position in the Fall semester, senior thesis project, presentation at conferences, and/or publication in peer-reviewed journals.

Advisors:
Dr. Martha Muñoz (Assistant Professor of Ecology & Evolutionary Biology; Assistant Curator of Vertebrate Zoology, Yale Peabody Museum of Natural History)
Henry Camarillo (Graduate Student of Ecology & Evolutionary Biology)

Outcomes:
The intern will be encouraged to publish a peer-reviewed paper in a scientific journal. In addition, the intern will have the opportunity to present work at the 2024 northeast regional and/or national meeting of the Society for Integrative and Comparative Biology (SICB 2025 in Atlanta, GA).

Connection to YPM Collections and Departmental/Divisional Goals:
This work will directly use specimens available in the Vertebrate Zoology (Herpetology) collections, with supervision and assistance of Sr. Collection Manger, Greg Watkins-Colwell. In addition, scan data will be uploaded to the Peabody Museum Collection Management System and eventually made available to online public outlets, which helps other researchers access data from natural history museums.

Length: 8 weeks

Stipend: $3,800

Project Description:
This project aims to contribute many new records from the archives of the Yale Peabody Museum’s archives and collections of the various curatorial divisions to Yale’s new cross-collections discovery portal, LUX (https://lux.collections.yale.edu/). New records for inclusion in LUX may include historical photographs, data registers, ledgers, catalogs, card files, slides, and more that illuminate relationships between the objects in the Peabody’s collections and their broader contexts in cultural heritage and natural history by linking objects, works, people, places, concepts, and events. These primary source materials contribute understanding for global change research, biodiversity information sciences, ecology and evolution, and much more.

To prepare data for inclusion in LUX, interns will need to familiarize themselves with many component modules of the YPM→LUX data pipeline. These processes will include 1) digitization; 2) ingestion into the YPM collections database, EMu; 3) identification of classes and types of information to be contributed; 4) extraction of relevant data using human transcription or optical character recognition (OCR) which are then improved and cleaned using semi- to fully-automated routines for data quality improvement; 5) transformed into useful data by validation processes and mapping to standard schemas and ontologies; and finally, 6) load the final data into the permanent repositories of the Peabody Museum.

New approaches to augment this data processing pipeline utilizing AI tools will be the primary research focus for this internship as a pilot for broader incorporation and use with the Yale Peabody Museum. The intern will produce a suitability analysis of various computational tools for parsing data into linked open data, including a diagnosis of novel computer vision and artificial intelligence models for data classification. The format of this internship will consist of an exploration of the existing Peabody digitization pipeline (week 1-2), using available data reconciliation services to link discrete data objects (e.g. WikiData Query Service and Bionomia, weeks 3-4), landscape survey of novel AI-powered workflows for data parsing (weeks 5-6), and finally, preparation of a report/presentation outlining the utility of existing tools and emerging technologies for harmonizing museum data as linked open data (week 7-8). The final presentation should be prepared as if it were to be presented at a professional meeting (SPNHC/TDWG 2024), though if the intern wishes, primary authorship and presentation at this meeting could be arranged.

This process of turning paper records, handwritten information, and other non-machine actionable content into linked open data will greatly augment the discoverability and research-readiness that has been collected over several hundred years and is now ready to be shared with the public, research, and teaching communities around the world…not just those with the means to visit Yale’s collections in person.

Advisor:
Gary Motz (Yale Peabody Museum, Head of Computer Systems)

Outcomes:
The project will evaluate mechanisms for producing linked open data using existing tools and emerging technologies as they may be applicable for the harmonization of digitized data from the Yale Peabody Museum’s collections and incorporation into LUX. The final report should be prepared as a presentation following the format and submission guidelines of the upcoming SPNHC/TDWG professional societies meeting in the fall (https://www.tdwg.org/conferences/2024/ - SPNHC is the Society for the Preservation of Natural History Collections and TDWG is the international data standards organization, Biodiversity Information Standards, formerly known as the Taxonomic Databases Working Group).

Length: 8 weeks

Stipend: $3,800