Grantee Spotlight: Stephanie Bogart

Stephanie Bogart was awarded a Leakey Foundation Research Grant during our spring 2015 cycle for her project entitled “Savanna chimpanzee ecology at MARS (Mount Assirik Research Site).”

Stephanie Bogart with a chimpanzee nest

Stephanie Bogart with a chimpanzee nest

At Mount Assirik Research Site (MARS) in Senegal’s Niokolo Koba National Park, a new long-term field study on savanna chimpanzees has begun with the aid of the Leakey Foundation. This site is directed by Leakey grantee Stephanie Bogart (University of Southern California) and her co-PI, Stacy Lindshield (Iowa State University). MARS will provide pertinent information on how chimpanzees adapt to a savanna environment. We know little about savanna chimpanzees compared to forested communities, and MARS will provide great insight on how they adapt to this different environment with a nine-month dry season and temperatures reaching over 100 degrees Fahrenheit. Previous research from the only habituated savanna chimpanzee site (Fongoli) indicates that these chimpanzees have unique behaviors specific to coping with a stressful environment with limited permanent water resources. Thus, using savanna chimpanzees as a referential model provides discussion of how similar environments may have played a role in human evolution in the Plio-Pleistocene. MARS is in a protected area with fewer disturbances from humans than Fongoli and will provide valuable data on predator presence and resource (food and water) availability. Numerous ecological methods are used to collect data, including data from six camera traps placed around the site. Finally, Stephanie and her team are initiating a habituation program with the Assirik chimpanzees to eventually provide comparative data on ecology and behavior. Establishing MARS will offer insights on behavioral ecology in a protected savanna habitat and future projects on gene flow, predator-prey interactions, and human impacts.

From the Field: Genevieve Housman

Genevieve Housman loading prepared samples onto DNA methylation arrays

Genevieve Housman was awarded a Leakey Foundation Research Grant during our fall 2015 cycle for her project entitled “Assessment of DNA methylation patterns in primate skeletal tissues.” In March we featured her work on our blog, which you can read by clicking here. Below she updates us on her progress.   

Genevieve Housman loading prepared samples onto DNA methylation arrays

Genevieve Housman loading prepared samples onto DNA methylation arrays

As I wrap up a significant portion of my data collection, I feel it’s time to send out some news from the field.

Being a molecular anthropologist, I don’t exactly have a “field site.” Rather, my work takes place in the clean, safe, and temperature controlled environments of laboratories. In particular, I have collected and processed data at both the Molecular Anthropology Laboratory at Arizona State University and the Genetics Department at the Texas Biomedical Research Institute (TxBiomed).

My research centers on understanding how epigenetic changes contribute to complex skeletal phenotypes in non-human primates. Specifically, I study how variations in DNA methylation patterns relate to variations in femur bone morphologies and the development of skeletal disorders such as osteoarthritis.

To do this, I collected morphological measurements and tissue samples from the femora of over 300 non-human primate specimens. These included mostly baboons, as well as chimpanzees, macaques, marmosets, and vervets. I did this initial collection at TxBiomed one year ago. It involved dissecting out previously necropsied and frozen limbs, collecting 29 linear measurements and 55 digital landmarks from each specimen, and sampling cartilage scrapings and drilled bone cores from each specimen. All together, these efforts produced over 25,000 morphological data points and over 500 tissue specimens.

My focus then shifted towards processing and extracting DNA from my tissue specimens so that they could be used in downstream efforts to collect DNA methylation data at a genome-wide level using an advanced probe-based array technology and at a gene-specific level using bisulfite sequencing methods.

Example of pulverized bone before undergoing DNA extraction

Example of pulverized bone before undergoing DNA extraction

First, I pulverized my bone and cartilage samples so that DNA could be more readily extracted from them. To avoid contamination, this process required a series of equipment cleaning steps in between each sample. Then, each sample was extracted using a phenol-chloroform protocol, and DNA concentrations were quantified.

With these steps completed, I just recently began my downstream genome-wide DNA methylation work. This summer I again travelled to TxBiomed, where I assembled and ran 160 of my DNA extractions on probe-based arrays. These arrays examine the DNA methylation levels of over 850,000 loci throughout the genome, and the data look good so far!

I am currently working on statistically comparing these DNA methylation patterns across my different species and with respect to my skeletal phenoypes, and I will begin my gene-specific data collection soon. Hopefully, I’ll have exciting results to share with everyone at the upcoming meetings this year!

Grantee Spotlight: Mathew Fox

Eastern edge of the Hanzhong Basin in the Southern Qinling Mountains. This area is rich in Paleolithic sites believed to associated with H. erectus occupations, some may date to 1.2 - 1.5 Ma.

Mathew Fox, PhD candidate from the University of Arizona, was awarded a Leakey Foundation Research Grant during our spring 2016 cycle for his project entitled “Paleoenvironments of Homo erectus occupations in the Luonan Basin, China.”

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Dr. Wang Shejiang of the Chinese Academy of Science’s Institute for Vertebrate Paleontology and Paleoanthropology explaining the location of sites in the basin

Many researchers consider one of the most pressing concerns in paleoanthropological research is the reconstruction of Homo erectus dispersals Out-of-Africa and the colonization of the Eurasian continent approximately 1.8 million years ago (Ma). Scientists also argue that the reconstruction of the ancient climates associated with early hominin occupations in Eurasia helps us understand the development of unique Paleolithic traditions and local adaptations.

Driving up into the Qinling Mountains of Central China for initial archaeological surveys in the summer 2015

Driving up into the Qinling Mountains of Central China for initial archaeological surveys in the summer 2015

Our research aims to investigate the ancient climates and ecosystems associated with some of the earliest Homo erectus occupations in central China, which appears to represent an important epicenter of hominin activity for over a million years. Located in the Qinling Mountains of central China, the Luonan and Hanzhong Basins contain some of the earliest Paleolithic sites in Eastern Eurasia dating to approximately 1.2 Ma. As a consequence, these areas are considered extremely important in understanding when our ancestors reached the interior of Asia and what sort of local adaptions they developed. Since climates and ecosystems in the region are intimately tied to variations in the East Asian Monsoon, this research is specifically concerned with the examination of how monsoonal variability may have affected Homo erectus environments and Paleolithic traditions. Through the use of isotopic geochemistry and quantitative soil and sediment characterizations, this interdisciplinary research aims to develop vegetation histories and a paleoenvironmental framework that will help explain the conditions associated with some of Asia’s earliest hominin colonists.

Eastern edge of the Hanzhong Basin in the Southern Qinling Mountains. This area is rich in Paleolithic sites believed to associated with H. erectus occupations, some may date to 1.2 - 1.5 Ma.

Eastern edge of the Hanzhong Basin in the Southern Qinling Mountains. This area is rich in Paleolithic sites believed to associated with H. erectus occupations, some may date to 1.2 – 1.5 Ma.

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Temple located at the Longgangsi Site in the Qinling Mountains. This beautiful complex is used to store archaeological and research material excavated from this Middle Pleistocene site.

Grantee Spotlight: Rebecca Miller

Site view

Rebecca Miller (University of Liege) was awarded a Leakey Foundation Research Grant for her project entitled “The Middle-Upper Paleolithic transition at Trou Al’Wesse (Belgium).” This is her second grant from The Leakey Foundation. You can read more about her 2015 season at this site by clicking here.

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Rebecca Miller

The replacement of Neandertals by modern humans during the Middle-Upper Paleolithic transition has been a longstanding debate with principal arguments focusing on either interspecific human competition or climatic driven environment change. Recently, dates ~36,000 uncal BP obtained from Spy Cave suggest that Neandertals persisted until relatively late in the area. Given that the earliest UP dates in Belgium are 34-33,000 uncal BP, Neandertals and modern humans may have been broadly contemporary. The terrace of the cave site of Trou Al’Wesse in Belgium has a largely unexcavated stratified sequence in units 17 to 15 (MIS 3-2) with Late Mousterian human occupations in unit 17 and Aurignacian in unit 15. It thus offers a good opportunity to obtain detailed behavioral, climatic and paleoenvironmental data for the MP-UP transition and to assess the degree to which climatic oscillations might have affected the presence of hominids in Northwest Europe. This project will ideally contribute to clarifying the timing of the end of the Neandertal occupation and the arrival of anatomically modern humans, changes in climatic and environmental context that affected human presence, and behavioral responses and adaptations to climate and environmental change across the transition

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Figure 1

The importance of this site (Figure 1) is due to a) its geographic location on a tributary south of the Meuse and thus relatively isolated from the concentration of other Belgian Paleolithic sites in the eastern and western parts of the Meuse Basin, b) evidence of repeated human occupation during the Mousterian, Aurignacian, Mesolithic and Neolithic periods and c) the presence of a relatively complete stratigraphy from Marine Isotope Stage (MIS) 3 onwards (the terrace fronting the cave has a stratigraphic sequence spanning the period > 45,000 to 4,000 uncal BP) with which to study climate variability and environmental change associated with hominid activity.

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Figure 2

During the 2015 field season, funded by The Leakey Foundation, excavation was conducted in the L-M 4-10 rows in the middle of the zone containing units 17 and 16 (Figure 2). An interdisciplinary approach was applied to record the sedimentary context during excavation, analyze the geological data, lithic and faunal data, reconstruct the chronological framework for the Neandertal occupations and ultimately, the climatic and environmental context. This approach is based on microstratigraphic, taphonomic and spatial analyses to reconstruct site formation processes and evaluate the depositional context, analysis of the lithic assemblages (technology, typology, taphonomy, raw materials), analysis of the faunal assemblages to study behavioral aspects (prey choice, processing, bone tool production) and reconstruct environment and climate phases. Dating of the sequence using OSL and AMS is in progress to propose a chronology for human presence/absence and climatic and environmental change for the ca. 50,000-30,000 BP period covered.

We are all very pleased with the results of the 2015 season, and even more so that The Leakey Foundation has now funded a second season to continue the excavation of these units within the overall 5×4 m area containing this sequence. Alongside the ongoing lithic, faunal and geological analyses, additional analyses supported by the 2016 Leakey grant include near infrared spectroscopy to detect and evaluate collagen content in bone for sample selection prior to AMS dating, pollen analysis for paleoenvironmental reconstruction and LA-ICP-MS analysis in an exploratory study to source the lithic raw materials exploited at Trou Al’Wesse.

Site view

Site view

Click here to read more about her team’s 2015 season at this site.

Video: The Secret Lives of Female Chimpanzees

A mother and baby chimpanzee. Photo by Kevin Langergraber.

Did you miss this summer’s speaker series event in Chicago? Well we have the full video right here!

On August 17, The Leakey Foundation in partnership with the Chicago Council of Science and Technology (C2ST) presented “The Secret Lives of Female Chimpanzees” with guest speaker Melissa Emery Thompson. We were honored to have Dr. Robert Martin from the Field Museum of Natural History and the University of Chicago introduce both organizations. Janice Bell Kaye, advisor to The Leakey Foundation, gave a warm welcome to Dr. Thompson.

Here is a short introduction to the talk

Female apes are easily overshadowed by their larger, more boisterous male counterparts. Thus, the nature of female social relationships has been shrouded in mystery. The subtlety of social behavior in female chimpanzees belies a complex set of strategies that allow them to navigate the costs and benefits of group life. By combining decades of behavioral research with innovative non-invasive approaches, Dr. Emery Thompson and her colleagues at the Kibale Chimpanzee Project have uncovered fascinating details about the secret lives of female chimpanzees. She will discuss how females negotiate rivalries to obtain the resources they need to reproduce, the chaotic, and sometimes violent, nature of sexual relationships with males, and the unexpected ways these relationships change with age. Along the way, you will learn about the challenges and rewards of studying this fascinating species in the wild.

Enjoy the video!

About Melissa Emery Thompson

Melissa Emery Thompson, Ph.D., is an assistant professor of anthropology at the University of New Mexico. She received her PhD in biological anthropology from Harvard in 2005. She has studied chimpanzee behavior and biology for eighteen years and serves on the board of directors of the Kibale Chimpanzee Project, one of the longest-running continuous field studies of great apes. While Dr. Emery Thompson is broadly interested in social behavior, her expertise is in developing and applying non-invasive methodologies for monitoring health and reproductive function in wild primates (and humans!). The Leakey Foundation has played an important role in supporting this research.

Interested in attending one of our upcoming events? Click here to visit our events page.