Research Interests
Rapidly diverging, species rich systems provide evolutionary biologists with powerful platforms in which fundamental biological questions can be investigated.  I have benefited from working on the two rapidly diverging extant lineages, East African cichlid fish and Hawaiian crickets.  Within each system I address core biological issues concerning the development and maintenance of biological diversity.  My primary research interest is in identifying the factors that contribute to the reproductive isolation of species at the behavioral, ecological and genetic levels.
Past Research
 
Working within these systems, I’ve had the opportunity to pursue many biological disciplines; ecology, development, neurobiology and behavior.  My current interest focuses on the genetics of speciation.  In both systems, one or more phenotypes have been identified which contribute to ongoing precopulatory reproductive isolation.  My work concerns identifying the genes which contribute to
these phenotypes, and hence, to the reproductive isolation of species.  It is through the identification and analysis of genes contributing to reproductive isolation that we can begin to understand the genetics of species divergence.
Within East African cichlids, my and others work has indicated that female choice of male coloration has contributed to the diversification of species.  By focusing on two closely related species with dramatically different color patterns, I have begun to dissect the genetic basis of male color patterns using both classical biometric methods and Quantitative Trait Loci mapping.
 
 
Patrick Danley
Ph.D. Advisor: Tom Kocher Hubbard Center For Genome Studies 
University of New Hampshire
Durham, NH 2001 Current Position Post-Doctoral Research Assistant Advisor: Kerry Shaw Department of Biology
University of Maryland
College Park MD 20742

Phone: (301) 405-8303
Fax: (301) 314-9358
Email: pdanley at umd.edu  Publications CV Links Malawi cichlids Malawi Tree of Life NCBI The Institute of Genome Research Gene Index Page Brought to you by the Letters N I H N S F Patrick Danley_files/danley%20vitae%202006.pdfhttp://hcgs.unh.edu/Staff/kocher/kochercv.htmlhttp://hcgs.unh.edu/Patrick Danley_files/danley%20vitae%202006_1.pdfhttp://www.life.umd.edu/biology/faculty/shaw/index.htmlhttp://www.life.umd.edu/biology/mailto:pdanley@umd.eduhttp://www.life.umd.edu/biology/shawlab/patrickdanley/EvolgenPublications.htmlPatrick Danley_files/danley%20vitae%202006_2.pdfhttp://malawicichlids.com/index.htmhttp://www.infoplease.com/ipa/A0107747.htmlhttp://tolweb.org/tree/http://www.ncbi.nih.gov/http://www.tigr.org/http://biocomp.dfci.harvard.edu/tgi/http://www.life.umd.edu/biology/shawlab/patrickdanley/pdf's/danley_vitae.pdfshapeimage_3_link_0shapeimage_3_link_1shapeimage_3_link_2shapeimage_3_link_3shapeimage_3_link_4shapeimage_3_link_5shapeimage_3_link_6shapeimage_3_link_8shapeimage_3_link_9shapeimage_3_link_10shapeimage_3_link_11shapeimage_3_link_12shapeimage_3_link_13shapeimage_3_link_14shapeimage_3_link_15
Current Research  Hawaiian crickets, like African cichlids, have diverged extensively and rapidly. Their divergence has been largely attributed to the diversification of pulse rates within the male song. However, my research has identified several additional time related phenotypes, including the timing of developmental events (Danley and Shaw 2005) and diel reproductive behavior (Danley et al. in prep), which have diverged and may contribute to reproductive isolation in this system. Chronobiological phenotypes, like the ones diverging in Laupala, are known to be associated via pleiotropy. For example, the gene governing circadian behavior in diverse set of taxa, Period, is also known to influence the timing of ecdysal events in nematodes (via its homologue lin-42) as well as song pulse rate in Drosophila. Using microarrays, I am currently examining patterns of gene expression related to both developmental events and male pulse rate. Genes which show correlated patterns of expression across developmental periods and between species of varying pulse rate will be identified as candidate genes. I will study the action of these candidate genes in order to examine how pleiotropy may have facilitated the rapid divergence of Laupala species.  Future Research Cichlid Speciation and Cricket Chronobiology The cichlids of Lake Malawi provide a fertile system in which to study the rapid divergence of phenotypic traits and the evolution of new species. My future work will continue to focus on a closely related species pair that differs in behavioral and physical characters that are believed to contribute to their divergence and persistence. Using resources made available through the Cichlid Genome Consortium, which include a genetic map of 550 microsatellites (with an average spacing of 3 cM), two BAC libraries (each with > 5x coverage), a 5x physical map, over 60, 000 EST, and five genomes, including that of my study species, shotgun sequenced at low coverage by the Joint Genome Institue, my immediate work will focus on identifying the genetic basis of a male color pattern and female mate preferences. Utilizing a wide array of cichlid genomic resources and comparative Evo-Devo techniques developed in zebrafish, my research will address both broad evolutionary questions and fundamental biomedical issues. Within Hawaiian crickets, I have identified several chronobiological phenotypes, such as the diel pattern of mating behavior and the differential timing of developmental events, which have diverged between closely related species. Using genomic resources I have developed, I will continue to examine how these chronobiological phenotypes have diverged at the molecular level. In particular, I propose to investigate how the modification of candidate gene expression patterns (see above) influence multiple chronobiological characters through the use of RNAi. http://www.sciencemag.org/cgi/content/full/286/5442/1141http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1266053http://biocomp.dfci.harvard.edu/tgi/shapeimage_4_link_0shapeimage_4_link_1
Publications
 
 
Kidd, M., P. D. Danley, and T. D. Kocher.  2006.  A direct assay of female choice in cichlid fishes: All eggs in one basket.  Journal of Fish Biology 68(2):373-384.
P. D. Danley and K. S. Shaw.  2005.  Differential developmental programs in two closely related Hawaiian crickets.  Annals of the Entomological Society of America 98 (2):219-226.
Sulikowski, J.A., J. Kneebone, S. Elzey, P. D.Danley, W. H. Howell and P.W.C Tsang. 2005.  Age and growth estimates of the thorny skate (Amblyraja radiata) in the western Gulf of Maine.  Fisheries Bulletin 103(1): 161-168.
Sulikowski, J.A., J. Kneebone, S. Elzey, P. D.Danley, W. H. Howell and P.W.C Tsang. 2005.  The reproductive cycle of the thorny skate (Amblyraja radiata) in the western Gulf of Maine. Fisheries Bulletin 103(3): 536-543.
Shaw, K. L., and P. D. Danley.  2003.  Behavioral genomics and the study of speciation at a porous species boundary.  Zoology 106:261-273.
Streelman, J. T. and P. D. Danley.  2003. The stages of vertebrate evolutionary radiation.  Trends in Ecology and Evolution 18 (3): 126-131.
Danley P. D., and T. D. Kocher.  2001.  Speciation in rapidly diverging systems: Lessons from Lake Malawi.  Molecular Ecology 10:1075-1086.
Markert, J. A., P. D. Danley, and M. E. Arnegard.  2001.  New markers for new species: Microsatellite loci and the East African cichlids.  Trends in Ecology and Evolution 16 (2): 100-107.
Danley, P. D., J. A. Markert, M. E. Arnegard, and T. D. Kocher.  2000.  Divergence with gene flow in the rock-dwelling cichlids of Lake Malawi.  Evolution 54 (5): 1725-1737.
Markert, J. A., M. E. Arnegard, P. D. Danley, T. D. Kocher.  1999. Biogeography and population genetics of the Lake Malawi cichlid Melanochromis auratus:  Habitat transience, philopatry and speciation.  Molecular Ecology 8:1013-1026.
Albertson, R. C., J. A. Markert, P. D. Danley, T. D. Kocher.  1999.  Phylogeny of a rapidly evolving clade: The cichlid fishes of Lake Malawi, East Africa. Proc. Natl. Acad. Sci.  USA 96: 5107-5010.
Arnegard, M. E., J. A. Markert, P. D. Danley, J. R. Stauffer, Jr., A. Ambali, T. D. Kocher.  1999.  Population structure and colour variation in the lithophilous cichlid Labeotropheus fuelleborni Ahl along a recently formed archipelago of rocky habitat patches in southern Lake Malawi.  Proc. R. Soc. Lond. B 266:119-130.
 
Non-Referred Publications:
Markert, J. A., M. E. Arnegard, P. D. Danley.  2001.  Interpopulation migration in Mbuna as inferred from DNA fingerprinting data in and around Lake Malawi National Park.  Prepared for The Malawi Ministry of Tourism, National Parks, and Wildlife.  
 
In Prep:
Danley, P.D., S. P. Mullen, F. Lui, V. Nene, J. Quackenbush and K. L. Shaw.  Submitted.  The cricket gene index: A neurological, behavioral, and evolutionary genetic resource.  BMC Genomics.
Danley, P. D., and T. D. Kocher.  Submitted.  Aggression and the diversification of Lake Malawi’s rock-dwelling cichlids. Environmental Biology of Fishes.
Danley, P. D., T. N. deCarvalho, D. J. Fergus, and K. L. Shaw.  Submitted.  Reproductive asynchrony and the divergence of Hawaiian crickets.  Ethology.
Danley, P. D., G. Perta, S. Salzberg, and K. L. Shaw.  On improving gene annotation: the need for non-model genomic resources.