J. Alan Clark

Associate Professor

Social Innovation Collaboratory Alan Clark

Department of Biological Sciences
Fordham University
Larkin Hall 370
441 East Fordham Road
Bronx, NY 10458

Phone: 718-817-3678
Fax: 718-817-3645
Email: jaclark@fordham.edu


PhD Department of Biology, University of Washington, 2006
MS Natural Resource Policy, School of Natural Resources & Environment, University of Michigan, 1994
JD School of Law, University of Michigan, 1992
BA Religious Studies. Evangel College, 1981
BME Music Education. Evangel College, 1981

Research Interests

Taxonomy, mate choice, and conservation of the Little Blue Penguin
During a Faculty Fellowship/Sabbatical from May 2011 – January 2012, I began a new line of research focused on understanding the taxonomy and behavior of Little Blue Penguins in New Zealand. Although originally conceived of as a behavioral study, my initial research efforts have focused on using molecular techniques to sex and determine ancestry in a colony with two different types or “clades” of this species. We’re also exploring mate choice in this mixed colony. At present, we’re correlating morphological characters (e.g., head, bill, foot, and flipper length, as well as feather color and flipper color patterns) with clade and measures of reproductive success. In the future, we will examine the role of vocalizations in mate choice in this species. (See Dr. Clark's Research photos of Little Blue Penguins)

Night migration of birds and bats through New York City
Understanding how birds and bats assess and utilize increasingly large, brightly lit, and noisy cities as they travel through urban-rural corridors and encounter tall buildings, bridges, towers, and aircraft is essential to their conservation. However, little is known about how birds evaluate and navigate the resources available in and obstacles presented by urban landscapes during migration, which generally occurs at night and is confounded by ubiquitous, yet highly variable, light and noise pollution. My students are I are using acoustic recorders to record the vocalizations birds and bats make as they migrate and short-range radar to track movement patterns to examine how light and noise affect birds as they migrate through urban landscapes. Our radar studies at Fordham University and on Governor’s Island (in collaboration with New York City Audubon Society and the U.S. National Park Service). (See photos of Bird and Bat Migration in NYC)

Effects of a public art installation/light show on migrating birds in Philadelphia
Canadian-Mexican electronic artist Rafael Lozano-Hemmer created an art installation sponsored by Philadelphia’s Association for Public Art, the Open Air that used 24 powerful robotic searchlights placed along a ½ mile section of the Benjamin Franklin Parkway from September 20 to October 14, 2012. The lights were activated by anyone downloading an app to their phone and making a recording and used software to translate the intonation, frequency, amplitude, and quality of each voice recording into the movements of the Parkway’s searchlights. The 3D light formations in the night sky formed a canopy of light over the city and was visible for up to 10 miles. To monitor potential impacts of the light show on night-migrating birds, I used human observation, small-scale radar, and acoustic recordings of species-specific night flight calls.

Bog Turtle habitat
Students in my lab are exploring the effectiveness of habitat restoration projects as well as the habitat requirements of the federally-threatened Bog Turtle  in collaboration with Environmental Defense Fund and The Nature Conservancy. In addition, we're following gravid females to find their nest locations and then assessing nest-site microhabitat conditions that should inform conservation managers as they restore/protect Bog Turtle habitat. In addition to in field studies of Bog Turtle nesting ecology, we are exploring molecular techniques to answer questions relating to the breeding ecology of Bog Turtles. (See photos of Bog Turtle)

Song form and function in the Eastern Wood-pewee, a suboscine
Birds are a model for understanding human language development. But most bird song studies focus on oscine songbirds, which learn their songs, unlike suboscines, which generally do not require learning to produce species-appropriate song. We're studying this neglected taxon and have found that the two main call types of the suboscine Eastern Wood-pewee (the onomatopoeic “pee-ah-wee”  and “we-ooo”  calls) are indeed distinctive, though they appear to use their songs differently than do oscines. (See photos of Eastern Wood-pewee)

Sexual conflict and cooperation in two duetting tropical wrens
While complex songs  duetting is common in many wren species, the Stripe-throated and Stripe-breasted Wrens are outliers with a highly unusual second song type – a series of hoots. We're exploring the form and function of this second song type to better understand how socially monogamous pairs balance conflict and cooperation in these Central American species. (See photos of Tropical Wrens)

Urban green roofs
The development of green roofs in urban areas is expanding dramatically. We're studying both new and mature green roofs in New York City and are showing that green roofs are highly important to both migrating and breeding birds. (See photos of Urban Green Roofs, or video on Green Roofs)

Stress in urban migratory stopover sites
Recent studies show migrating birds that stopover in urban parks are able to acquire substantial fat reserves. We're supplementing those data by evaluating whether these urban stopover sites are also more stressful, by evaluating stress hormones. (See photos of Bird Banding and Lab Analysis)

Changes in avian tick density
We're replicating a 1984 study of avian tick density to explore how avian tick prevalence and diversity may have changed over the past 25 years, in addition to assessing avian ticks and the birds themselves as potential disease vectors.

Population structure in wild cats
In collaboration with the American Museum of Natural History and Panthera, students in my lab have evaluated population structure in Puma (Puma concolor) and the Asian Golden Cat (Catopuma temminckii) using genetic data obtained from scat samples. (See photos of Genetic Analysis of Scat Samples)

Management of wild Canada Geese
In collaboration with the Wildlife Conservation Society/Bronx Zoo, we’re investigating the effects of dummying eggs on mate and nest-site fidelity in Canada Geese (Branta canadensis).

Acoustic enrichment for captive colonial birds
In collaboration with the Wildlife Conservation Society/Bronx Zoo, we've developed a highly successful acoustic enrichment program from captive populations of colonial bird species that are underachieving in the avian romance department. In 2009 and 2010, we dramatically increased the reproductive success of the Zoo's Chilean and American Flamingo populations and were able to move up the date of first egg by an entire month - increasing chick survival chances. In 2010, we were successful in helping produce the first new endangered Northern Bald Ibis chicks in several years. This research was the academic journal Zoo Biology’s January 2102 featured cover story. (See photos of Acoustic Enrichment for Captive Colonial Birds)

With campuses in Manhattan and the Bronx, and with its Calder Biological Field Station in Westchester County, Fordham is ideally situated to explore ecological questions associated with the urban environment and the urban-rural corridor.

Selected Publications

Clark, J.A., J.C. Banks., & J.R. Waas. In press. Economical genotyping of little blue penguin (Eudyptula minor) clades from feather-based DNA. New Zealand Journal of Ecology 37: xx-xx.

Knafler, G.J., J.A. Clark, P.D. Boersma, & J.L. Bouzat. In press. MHC diversity and mate choice in the Magellanic penguin, Spheniscus magellanicus. Journal of Heredity.

Kane, O.J., M.M. Uhart, V. Rago, A.J. Pereda, J.R. Smith, A. Van Buren, J.A. Clark, & P.D. Boersma. 2012. Avian pox in Magellanic penguins. Journal of Wildlife Diseases 48:790-794.

Clark, J.A., A. Haseley, G. Van Genderen, M. Hofling, & N. Clum. 2012. Increasing breeding behaviors in a captive colony of Northern Bald Ibis through conspecific acoustic enrichment. Zoo Biology 31:71-81.

Clark, J.A. & J. Leung. 2011. Vocal distinctiveness and information coding in a suboscine with multiple song types: Eastern Wood-Pewee. Wilson Journal of Ornithology 123:835-840.

Macey, S. & J.A. Clark. 2011. Hudson/Housatonic Sub Unit Bog Turtle Nesting/Basking Habitat Monitoring Report. January 2011. Fordham University. 26 pp.

Clark, J.A. 2010. An Assessment of the UNEP Equator Initiative’s Internship Program: Supervisors. January 2010. Fordham University. 6 pp.

Clark, J.A. & B. Cerney. 2010. An Assessment of the UNEP Equator Initiative’s Internship Program. January 2010. Fordham University. 110 pp.

Higgins, A.D., S. Mitre, J.A. Clark, & B. Cerney. 2009. An Assessment of the UNEP Equator Initiative. December 2009. Fordham University. 59 pp.

Macey, S., Cure Dominguez, A., & J.A. Clark. 2009. Tracking 2009 Bog Turtle Locations at: [undisclosed locations] in New York. Final Report to the Environmental Defense Fund. December 2009. Fordham University. 86 pp.

Cure, A., S. Macey, & J.A. Clark. 2009. Tracking 2008 Bog Turtle Locations at: [undisclosed locations] in New York. Final Report to the Environmental Defense Fund. May 2009. Fordham University. 36 pp.

Clark, J.A., P.D. Boersma, & D.M. Olmsted. 2006. Name that tune: call discrimination and individual recognition in Magellanic penguins. Animal Behaviour 72:1141-1148.

Clark, J.A. & P.D. Boersma. 2006. Southern elephant seal Mirounga leonina kills Magellanic penguins Spheniscus magellanicus on land. Marine Mammal Science 22:21-25.

Clark, J.A. & R.M. May. 2002. Taxonomic bias in conservation research. Science 297:191-192.

Clark, J.A., J.M. Hoekstra, P.D. Boersma, & P. Kareiva. 2002. Improving U.S. Endangered Species Act recovery plans: key findings and recommendations of the SCB recovery plan project. Conservation Biology 16:1510-1519.

Clark, J.A. & E. Harvey. 2002. Assessing multi-species recovery plans under the Endangered Species Act. Ecological Applications 12:655-662.

Hoekstra, J.M., J.A. Clark, P.D. Boersma, W.F. Fagan, & P. Kareiva. 2002. A comprehensive review of Endangered Species Act recovery plans. Ecological Applications 12:630-640.

Campbell, S.P., J.A. Clark, L. Crampton, A.D. Guerry, L.R. Hatch, P.R. Hosseini, J.J. Lawler, & R.J. O’Connor. 2002. An assessment of monitoring efforts in endangered species recovery plans. Ecological Applications 12:674-681.

Boersma, P.D., P. Kareiva, W.F. Fagan, J.A. Clark, & J.M. Hoekstra. 2001. How good are endangered species recovery plans? BioScience 51:643.