Members of my lab are currently working on several research projects. Our principle field site is in Costa Rica, but I collaborate with researchers working at field sites around the world. Our main areas of research are:



Through their senses, animals interface with the environment to find food, select mates, and avoid predators. The interrelationships among diet, activity pattern and the senses are central to hypotheses of primate origins and adaptive radiation (e.g., the “nocturnal visual predation” hypothesis), and shape the ecological niches of extant species. Through the integration of observational fieldwork, molecular ecology, metagenomics, stable isotope analysis and computer models of animal vision, we seek to understand the adaptive complexes of primates, including humans, using an innovative and multidisciplinary approach. Our research centers around: 1) intra- and interspecific color vision variation in primates and other mammals with functional and phylogenetic relevance to primate origins and adaptive radiation (treeshrews, fruit bats, opossums); 2) variation within and between species in diet and use of sensory behaviors (e.g. touch, sniff, lick) while foraging, with the goal of linking behavioral variation to sensory genotypes; and 3) the visual, olfactory, gustatory and mechanical cues of food quality, with the goal of identifying important cues that shape the sensory systems of consumers.

Current Collaborators: Shoji Kawamura (University of Tokyo), Nathanial Dominy (Dartmouth College), Konstans Wells (University of Ulm) and Brooke Crowley (University of Cincinnati) 




Above: Mutwa man in Bwindi Impenetrable Forest National Park, Uganda.

Photo credit: PJ  Perry


The genetic basis of human sensory ecology remains poorly understood. Humans are unique among catarrhine primates in possessing frequent red-green color vision deficiencies, but the extent to which this reflects genetic drift versus selective advantage is unknown. Another common narrative in the literature on human sensation is that we have poor olfactory abilities compared to other primates. However, there is growing recognition that human olfaction is much better than previously believed and plays important roles in diet and reproduction. Available studies on the genes underlying color vision (opsins) and the chemical senses - olfactory receptor (OR) and taste receptor (TR) genes - reveal substantial variation between populations, with associated differences in sensory abilities, suggesting that human sensory phenotypes are plastic and responsive to local environments. Thus, a more important role of natural selection, versus neutral processes, in shaping sensory function may be operating in societies that search for resources. We are currently undertaking a collaborative, genomic-scale project on sensory variation among different human populations, including rainforest hunter-gatherers and agriculturalists in Uganda and the Philippines using targeted genomic sequencing.  This work will robustly explore the links among foraging strategies and local environments in human sensory ecology, and shed light on the variables shaping sensory variation in hominin evolution.


Current Colaborators: Nathanial Dominy (Dartmouth College), George (PJ) Perry (Penn State University), Carrie Veilleux (University of Texas at Austin), and Richard Bankoff (Penn State University)




Recent research on the human microbiome has demonstrated a strong effect of diet, environment and health on the gut microbiota, raising the possibility that this relationship extends to other primates. However, little is known about how changing environments, accompanied by pronounced dietary shifts, affects the microbiome and shapes digestive adaptations. Ongoing advances in massive parallel sequencing are continually increasing our ability to ask refined, detailed question of wild populations. We are conducting a fecal metagenomic study spanning the seasonal transitions in Santa Rosa, Costa Rica to identify the taxonomic composition and functional genomes of the resident intestinal microbiota of capuchin monkeys and reveal how shifts in climate and diet impact these symbiotic organisms. We are additionally assembling a gemone reference for white-faced capuchin monkeys that will assist in this project and be broadly useful in comparative primate genomics. Together, this information will reveal how omnivorous primates manage the varied digestive challenges of their eclectic diet, and adapt to the profound seasonal shifts in food availability.


Current Collaborators: Gautam Dantas (Washington University in St. Louis), Wes Warren (The Genome Institute), Mike Montague (University of Pennsylvania), and Shoji Kawamura (University of Tokyo).



Genetic chimerism is a product of habitual twinning (more than 85% of the time) in callitrichids, which are diminutive Neotropical primates commonly refered to as marmosets and tamarins. Callitrichine twins are typically fraternal, and each embryo is therefore distinguishable from the other based on its genetics. Early in their development however, the outermost layer of both embryos begins to fuse, which results in a shared blood flow between them. As the blood supply intermingles, a few cells slough off from one embryo and attach to the other in some cases. In other animals, this can cause deleterious side effects, from infertility to birth defects that result in one fetus dying, but in callitrichids, remarkably, the new cells are often accepted. These cells then become a part of the embryo, despite having originated from the sibling, and twin infants are successfully born that are basically genetic combinations of each other - a phenomenon refered to as chimerism. The significance of this increased genetic relatedness is still subject to much debate, but we believe that it could have strong ties to the cooperative breeding systems of these primates, where alloparents provide infant care, in addition to biological parents. In order to assess this phenomenon in a wild population of primates, we have collected genetic samples from ~150 callitrichids over the last 5 years from a variety of tissues obtained through a capture-and-release program (the most invasive of which is a blood sample). We are currently screening multiple microsatellite markers against each tissue type of each individual to assess levels of chimerism across tissue types in each animal. These data, in conjunction with detailed life histories will allow us to shed light on the possible benefits of maintaining genetic chimerism in a cooperatively breeding primate society. 


Current Collaborators: Tony DiFiore (University of Texas at Austin) and Gideon Erkenswick Watsa (University of Missouri-St. Louis)



Computer models of animal vision allow humans to explore how our primate visual system and diurnal activity pattern bias an understanding of how other animals use vision to find food and other important tasks. In a collaboration involving psychologists, computer programmers, neuroscientists and field biologists, we use novel psychophysical experiments and custom-built software and that simulates, for human observers, how digital images might appear to animals with different color vision and spatial vision from ourselves. This approach takes advantage of human communicative abilities to treat topics not possible through observation of non-human primates and other animals. Past work has simulated images of different primate foods, taken in on-site in tropical forests using color-calibrated methods, for monkeys with different types of color vision. 

Watch an example of Monkey Vision Software from Amanda Melin on Vimeo.

We have recently expanded our scope and are currently assessing the conspicuousness of zebra stripes to humans, lions, hyaenas and zebras under daylight, twilight, and nocturnal conditions to address a debate that goes back to Darwin as to the costs and benefits of zebra stripes. 

Left: A human's view of a group of Plain's zebra in daylight; Right: A lion's view of the same animals after sunset

Current Collaborators: Donald Kline (University of Calgary), Tim Caro (University of California, Davis), and Chihiro Hiramatsu (Kyushu University)