1. Evolutionary ecology of human rainforest hunter-gatherers

Batwa elder in Bwindi Impenetrable Forest National Park, Uganda

Rainforests are incredibly challenging habitats for human hunter-gatherers. They are food limited, structurally dense, extremely hot and humid, and harbor a large number and diversity of parasitic and infectious disease pathogens. Rainforest hunter-gatherers in Africa, Southeast Asia, and South America share a number of cultural and physical traits hypothesized to represent convergent adaptations to this environment. Small body size, or the ‘pygmy’ phenotype, is one captivating example.

The long-term goal of this project is to build a comprehensive picture of rainforest hunter-gatherer evolutionary ecology. One approach is to identify signatures of natural selection in the genomes of both African and Southeast Asian rainforest hunter-gatherers and then link those signatures to adaptive phenotypes. We are also performing experiments with cryopreserved cell lines (including induced pluripotent stem cells, iPSCs) to study genome-wide growth hormone and immune system response differences between hunter-gatherers and agriculturalists in relevant cell types. In addition to evolutionary and functional genomics, this project also involves ecological experiments at a field site in Uganda (we have also done some work in Malaysia and the Philippines). This research is funded by a grant from the National Institutes of Health.

See publications: Perry & Verdu 2017  |  Bankoff & Perry 2016  |  Fagny et al. 2015  |  Perry et al. 2014  |  Perry & Dominy 2009


2. human effects on non-human evolution, including parasite co-evolution

There is a frontier of insight on human evolution to be obtained through studies of non-human, non-domesticated species whose evolution has been affected by our behavior and biology. Our lab is investigating these processes at both the broader ecosystem scale -- for example on the long-term evolutionary effects of human selective hunting pressures on the body sizes of terrestrial and marine animals -- and with respect to parasite-human co-evolution. That is, because many of our parasites flourish only under very specific human behaviors and habitats, are wholly dependent on us, and have evolved with us for thousands or millions of years, we can study when and how we first acquired those parasites, under which environmental and cultural conditions we are the most susceptible, and how the parasites have evolved and adapted to us and we in response to them to develop new insights into human evolutionary history.

Benefits of this approach include the ability to study many aspects of human evolution not accessible via our own genomes of the fossil or archaeological records, the opportunity to perform functional experiments with some of the non-human organisms, and (for parasites) potential health-related benefits to society. At present, our lab has ongoing and developing projects on the phenotypic and evolutionary genomic effects of human behavior in lemurs (see below), lizards, conch, lice, and tapeworms. The tapeworm project is nearest completion. Tapeworms have a lifecycle that is dependent on our consumption of meat, and tapeworm cysts become non-viable when heated sufficiently. Thus, the evolutionary history and biology of human tapeworms are intertwined with critical aspects of human evolution related to the origins of meat eating and food cooking as regular hominin behaviors. The initial stages of this research are funded by a grant from the Wenner-Gren Foundation.

See publications: Sullivan et al. 2017  |  Federman et al. 2016  |  Kistler et al. 2015  |  Perry 2014


3. Madagascar Human-environment interaction & lemur evolutionary ecology

Golden-crowned sifaka (Propithecus tattersalli), Daraina, Madagascar

Madagascar’s 100 or so extant lemur species are widely known for their incredible phenotypic and behavioral diversity. Yet, only several thousand years ago lemur diversity was considerably greater. For example, from skeletal remains, we know of at least 17 now-extinct species that lived as recently as 500 years ago. These species are often called the “subfossil” lemurs, as the bones are unmineralized. Each subfossil species was larger than any extant lemur, some substantially so -- up to the size of a male gorilla! Humans arrived to Madagascar within the past several thousand year, and thereafter may have contributed to the extinction of the subfossil lemurs through habitat changes and hunting activities. This phenomenon continues; more than 70% of extant lemurs are considered endangered or critically endangered due to continuing deforestation and hunting.

While humans arrived relatively recently to Madagascar, there is large uncertainty over the actual date. Also, while modern Malagasy have mixed Southeast Asian and mainland African ancestry, the order in which various people arrived is unknown, as is the pace of subsequent population expansions. All of this information is important for reconstructing the history of anthropogenic impacts on the island’s biodivdersity, as (for example) each human group arrived with different technologies and land-use practices. To study these processes, we are using high-resolution population genomic methods to reconstruct the recent demographic histories of both the Malagasy people and various lemur species, to then compare these results to each other and to paleoclimate data. We are also working to characterize signatures of recent natural selection in extant lemurs that could reflect adaptations to human habitat disturbance or hunting pressures. Finally, we are testing multiple hypotheses about longer-timescale lemur evolutionary ecology, for example with paleogenomic-based inferences about extinct subfossil lemur behavioral ecology (e.g., taste and visual perception). These projects are currently funded by grants from the National Science Foundation.

See publications: Thompson et al. 2016  |  Bankoff et al. 2015  |  Kistler et al. 2015  |  Hodgson et al. 2014  |  Perry et al. 2013