Postdoctoral FellowHarvard University Department of Organismic
Evolutionary Biology & Dept. of Biology
Senior Research FellowUCLA Department of Ecology and Evolutionary Biology
Department of Organismic and Evolutionary Biology
26 Oxford Street
Department of Ecology and Evolutionary Biology
University of California, Los Angeles
The stunning phenotypic diversity observed both within and among rainforest species has long captured the imagination of non-scientists and scientists alike. Attempts to elucidate the causes of this diversity have led to not only major advances in evolutionary thought, but contentious debates that remain unresolved. And given an increasing awareness that evolutionary processes should be incorporated into conservation planning, this newfound knowledge will have practical consequences, as we struggle to preserve rainforest biodiversity in the face of ongoing threats from habitat destruction and global warming. Beyond whatever intrinsic value society may ascribe to them, tropical rainforests represent underappreciated resources as carbon sinks, regulators of local climate, and repositories of biological materials that may benefit human health and welfare. My research is motivated by my own fascination with rainforest biodiversity, and concerns for its future. In particular, I examine the mechanisms responsible for genetic and phenotypic variation within and between species, in reptiles, birds, and mammals, with a particular emphasis on African rainforest biota. Essential to my research is the integration of data from a variety of sources: reconstructions of historical distributions using museum records and statistical estimates of a species' environmental niche; assays of genomic variation; data on climate and vegetation collected from remote sensing; predictive statistical models that link genetic and landscape-level environmental variation; and measurements of phenotypic traits that impact survival and reproduction.
A complication to understanding diversification is the extent to which human impacts–e.g. climate change and habitat modification–may obscure or alter its signals. More importantly, anthropogenic change may short-circuit the formation of incipient species, reduce variation in fitness-related traits potentially important in adaptation to future environmental regimes, and generally lead to biodiversity loss. For these reasons, I also investigate the evolutionary consequences of anthropogenic environmental change.
Across all of the investigations I initiate and collaborate on, a large premium is placed on the appropriate use and integration of analytical methods across disciplines (e.g. remote sensing, population genetics, niche modeling). More recently, through my postdoctoral research and training in bioinformatics, I am actively involved in overcoming the challenges posed by the daunting amount of data produced by massively parallel sequencing technologies, particularly with respect to non-model organisms.
Savanna Snake Invasions into African Rainforest
Snake species adapted to African savanna have recently started to appear deep in the rainforest zone of Cameroon. Reported occurrences were proximal to disturbed habitats, suggesting the potential for a broader invasion from the adjacent savanna biome. Using species locality data obtained from country-wide reptile surveys by CAMHERP, a Cameroon-based NGO, and remote sensing data, I used ecological niche models to predict the relative roles of vegetation and climate on invasion potential in the rainforest zone for three snakes adapted to savanna and open, disturbed habitats: the night adder (Causus maculatus), the olympic lined snake (Dromophis lineatus), and the African house snake (Lamprophis fuliginosus). With these models, I determined that (i) rainforest habitats are typically unsuitable for these snakes, but that removal of rainforest vegetation has apparently created suitable habitats which these species can invade, (ii) that all three species were predicted across large areas of the rainforest zone, suggesting high invasion potential, and (iii) based upon projections of future climate from the CCM3 global circulation model, climate change will have heterogeneous effects on invasion potential (Freedman et al. 2009, Conservation Biology).
Genomic Signals of Diversification in an African Rainforest Skink
A fundamental question in evolutionary biology concerns the relative importance of genetic drift and natural selection in speciation, with the debate concerning how these evolutionary forces operate in rainforests being particularly contentious. As part of my dissertation, I analyzed an AFLP genome scan within a landscape genetics framework in order to test alternative diversification hypotheses for an African rainforest lizard, Trachylepis affinis (Freedman et al. 2010, Molecular Ecology). Neutral loci and outliers likely under selection were examined separately, and likely demographic influences of climate-mediated forest expansions and contractions on genetic differentiation were independently evaluated with ecological niche modeling and mitochondrial sequence variation. Results indicate natural selection along the rainforest-savanna gradient plays the dominant role in driving population divergence, and that it may be augmented by a synergy with climate cycles and concomitant spatial demography. Currently underway, I am conducting a follow-up study to examine gene flow between west and central African populations, and whether climate cycles have led to congruent demographic histories between the two regions.
Effects of Deforestation on Adaptive Diversity in an African Rainforest Bird
A fundamental principle revealed from both theoretical and empirical investigations is that the potential for diversification along an ecological gradient is strongly influenced by its slope. An important question is whether the reduction in slope of the rainforest-savanna gradient produced by deforestation—that converts rainforest to open, savanna-like habitat—has altered evolutionary dynamics and reduced adaptive diversity along the gradient. I investigated this possibility in my dissertation by comparing patterns of variation in morphological traits related to fitness in a songbird, Andropadus virens, between heavily deforested (West Africa) and less deforested (Central Africa) rainforests. Combined analysis of satellite-based tree cover measurements, contemporary bird samples and museums specimens collected prior to extensive deforestation demonstrated that the gradient had been made shallower in West Africa due to deforestation, and that selection for savanna-like phenotypes in deforested areas had caused a loss of adaptive phenotypic variation in West African populations along the rainforest-savanna gradient (Freedman et al. 2010, PLoS ONE). Ecological signatures of deforestation in Central Africa suggest that ongoing deforestation there may eventually produce an equivalent loss of adaptive diversity. The practical consequences are that, if variants capable of persisting under novel future environmental regimes are pushed to low frequency as a result of deforestation, lowered fitness may increase extinction risk for populations and perhaps even species.
Genome Sequencing and Comparative Genomics
My postdoctoral research represents both a substantial retraining in bioinformatics and an application of high throughput sequencing to dissect the genetic basis of rapid phenotypic evolution that has occurred during the domestication of dogs from wild canid ancestors. This project falls within my broader interest in the genetic basis of rapid phenotypic change. I am leading up a large collaborative effort to sequence 5 novel canid genomes–2 gray wolves, 1 golden jackal, and 2 divergent dog breeds (Basenji and Dingo)–as well as the Boxer from which the original draft genome sequence was generated, all to ~20x coverage. This project presents an interesting set of challenges, including the integration of data across diverse sequencing platforms, optimizing read mapping for samples that vary widely in their divergence from the reference genome, and integrating sequencing error rates into evolutionary analyses. The sequence of the golden jackal, a closely related outgroup to dogs and wolves, will permit us to assign observed wolf-dog divergences to the dog or wolf lineage, and in turn allow us to identify changes unique to the dog lineage that may have had important roles in the domestication process. The Basenji and Dingo will allow us to investigate the emergence of “modern” breeds and to identify changes that occurred early in dog domestication.
University of California, Los Angeles CA
Ph.D., Department of Ecology and Evolutionary Biology, 2009
University of Florida, Gainesville, FL
M.S., Department of Wildlife Ecology & Conservation, May 2000
University of Massachusetts, Amherst, MA
B.S., Environmental Science, Biology concentration, May 1995
The George Washington University, Washington, D.C.
B.A., Philosophy, May 1991
- NSF Postdoctoral Fellowship in Bioinformatics, 2010-2011
- UCLA/Department of Ecology and Evolutionary Biology Research Fellowship, 2009
- Environmental Protection Agency STAR Fellowship, 2006-2009
- UCLA/Biology Department Research Fellowship, Summer 2006
- UCLA/Biology Department Research Fellowship, Fall 2005
- Fulbright Fellowship for research in Cameroon, 2004-2005
- UCLA/Biology Department Research Fellowship, 2003
- UCLA Non-Resident Tuition Fellowship, 2002-2003
- Jennings Memorial Wildlife Ecology & Conservation Scholarship, 1998
- In Press A.H. Freedman, I. Gronau, R.M. Schweizer, E. Han, D. Ortega-Del Vecchyo, P. Silva, M. Galaverni, Z. Fan, P. Marx, B. Lorente-Galdos, H. Beale, O. Ramirez, F. Hormozdiari, C. Alkan, C. Vilà, K. Squire, E. Geffen, J. Kusak, A. R. Boyko, H. Parker, C. Lee, V. Tadigotla, A. Siepel, C.D. Bustamante, T. Harkins, S.F. Nelson, E.A. Ostrander , T. Marques-Bonet, R.K. Wayne, and J. Novembre. Genome sequencing highlights genes under selection and the dynamic early history of dogs. In Press: PLoS Genetics.
- O. Thalmann, B. Shapiro, P. Cui, V.J. Schuenemann, S.K. Sawyer, D.L. Greenfield, M.B. Germonpré, M.V. Sablin, F. López-Giráldez, H. Napierala, H-P. Uerpmann, D. M. Loponte, A.A. Acosta, L. Giemsch, R.W. Schmitz, B. Worthington, J. E. Buikstra, A. Druzhkova, A.S. Graphodatsky, N.D. Ovodov, N. Wahlberg, A.H. Freedman, R.M. Schweizer, K-P Koepfli, J.A. Leonard, M. Meyer, J. Krause, S. Pääbo, R.E. Green and R.K. Wayne. Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. 2013: Science 342:871-874.
- H.A. Thomassen, A.H. Freedman, D.M. Brown, W. Buermann, and D.K. Jacobs. Seasonal timing of rainfall sustains reproductive isolation in East African giraffes. 2013: PLoS ONE 8:e77191.
- T.B. Smith, H.A. Thomassen, A.H. Freedman, R.N.M. Sehgal. W. Buermann, S. Saatchi, J. Pollinger, B. Milá, D. Pires, G. Valkiunas, and R.K. Wayne. Patterns of divergence in the olive sunbird Cyanomitra olivacea (Aves:Nectariniidae) across the African rainforest-savanna ecotone. Biological Jounal of the Linnean Society 103:821-835.
- A.H. Freedman, W. Buermann, E.T.A. Mitchard, R.S. DeFries, and T.B. Smith. 2010. Human impacts flatten rainforest-savanna gradient and reduce adaptive diversity. PLoS ONE 5:1-9. *Selected by Faculty of 1000
- A.H. Freedman, H.A. Thomassen, W. Buermann, and T.B. Smith. 2010. Genomic signals of adaptive diversification in a rainforest lizard. Molecular Ecology 19:3773-3788 .
- H. Thomassen, Z. Cheviron, A.H. Freedman, R. Harrigan, R.K. Wayne, and T.B. Smith. 2010. Spatial modeling and landscape-level approaches for visualizing intra-specific variation. Molecular Ecology 19: 3532-3548 .
- K. M. Pease, A.H. Freedman, J. Pollinger, W. Buermann, and R.K. Wayne. 2009. Landscape genetic structure of Calfornia mule deer (Odocoileus hemionus): the role of contemporary ecological and historical factors. Molecular Ecology 18:1848-1862.
- A.H. Freedman, W. Buermann, M. Lebreton, L. Chirio, and T.B. Smith. 2009. Modeling the effects of anthropogenic habitat change on savanna snake invasions into African rainforest. Conservation Biology 23:81-92.
- D.W. Funk, L.E. Noel, and A.H. Freedman. 2004. Environmental gradients, plant distribution and species richness in Arctic salt marsh near Prudhoe Bay, Alaska. Wetlands Ecology and Management 12:215-233.
- Freedman, A.H., K.M. Portier, and M.E. Sunquist. 2003. Life history analysis for black bears (Ursus americanus) in a changing demographic landscape. Ecological Modelling 167:47-64.
- Hamilton, A.M., A.H. Freedman, and R. Franz. 2002. Influence of deer feeders, habitat, and sensory cues on predation rates on artificial turtle nests. American Midland Naturalist 147:123-134.