Juan C. Martínez-Cruzado

Caribbean Research Institute

Juan C.  Martínez-Cruzado Title: Professor
Office: Department of Biology, University of Puerto Rico at Mayaguez.
Building: Mayaguez, Puerto Rico 00681-9000
Phone: (787) 340-3867


Dr. Juan C. Martínez-Cruzado was born in Pittsburgh, Pennsylvania in 1959 and raised in western Puerto Rico. He gained a B.Sc. degree in Biology from the University of Puerto Rico, Mayagüez Campus (UPRM), and a Ph.D. degree in Biology from Harvard University in 1988. His doctoral thesis, entitled “The organization and DNA sequence of the autosomal chorion gene cluster in Hawaiian Drosophila”, was honoured in the World Literature Bibliography List in the December, 1991 issue of Current Opinion in Genetics and Development. After a one-year postdoctoral experience in the same university, he joined the faculty of the UPRM Department of Biology. He is well known for his pioneering work on the Amerindian ancestry of most mitochondrial DNA molecules in the Puerto Rican population, and has becomes an advisor to the Smithsonian National Museum of the American Indian. Since 2009, Dr. Martínez-Cruzado has ventured in genomics projects. He is part of the 1000 Genomes Consortium and has published on admixture in Caribbean populations from a genomic standpoint. He has also co-founder of the Puerto Rican parrot genome project.

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Teaching Areas: Genetics, Genetics and Evolution of Human Population, Genomic Annotation in Eukaryotes, Eukaryotic Molecular Genetics

Research Interests:

Molecular evolutionary genetics and population genetics. Comparative genomics. Studies on pre-contact human migrations in the Circum-Caribbean region through ancient and modern DNA analyses.


Leung W., …Martínez-Cruzado JC, …Elgin SCR (1014 authors). (2015) Drosophila Muller F elements maintain a distinct set of genomic properties over 40 million years of evolution. G3 5(5): 719-740.

Lopatto D…Martínez-Cruzado JC…Elgin SCR (68 authors). (2014). A Central Support System Can Facilitate Implementation and Sustainability of a Classroom-Based Undergraduate Research Experience (CURE) in Genomics CBE-Life Sci Educ 13(4): 711-723.

Afanador, Y., Velez-Valentín, J., Valentín-de la Rosa, R., Martínez-Cruzado, J-C., vonHoldt, B., Oleksyk, T.K. Oleksyk. (2014) Isolation and characterization of microsatellite loci in the critically endangered Puerto Rican parrot (Amazona vittata). Conservation Genet Resour DOI 10.1007/s12686-014-0232-6.

Shaffer CD…Martínez-Cruzado JC,…Elgin SCR (83 authors) (2014) A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time. CBE Life Sci Educ 13:111-130.

Gravel, S., Zakharia, F., Moreno-Estrada, A., Byrnes, J.K., Muzzio, M., Rodriguez-Flores, J.L., Kenny, E.E., Gignoux, C.R., Maples, B.K., Guiblet, W., Dutil, J., Via, M., Sandoval, K., Bedoya, G., Oleksyk, T.K., Ruiz-Linares, A., Burchard, E.G., Martinez-Cruzado, J.C., Bustamante, C.D., The 1000 Genomes Consortium (2013) Reconstructing Native American migrations from whole-genome and whole-exom data. PLoS Genetics 9: e1004023.

Moreno-Estrada, A., Gravel, S., Zakharia, F., McCauley, J.L., Byrnes, J.K., Gignoux, C.R., Ortiz-Tello, P., Martinez, R.J., Hedges, D.J., Morris, R.W., Eng, C., Sandoval, K., Acevedo, S., Norman, P.J., Layrisse, Z., Parham, P., Martínez-Cruzado, J.C., Gonzalez-Burchard, E., Cuccaro, M.L., Martin, E.R. and Bustamante, C.D. (2013) Reconstructing the population genetic history of the Caribbean Basin. PLoS Genetics 9:e1003925.

Díaz-Lameiro, A., Oleksyk, T.K., Bird-Picó, F.J. and Martínez-Cruzado, J.C. (2013) Colonization of Islands in the Mona Passage by Endemic Dwarf Geckoes (genus Sphaerodactylus) Reconstructed with Mitochondrial Phylogeny. Ecol. Evol 3:4488-4500.

The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.

Oleksyk TK, Guiblet W, Pombert JF, Valentin R and Martinez-Cruzado JC (2012) Genomic data of the Puerto Rican Parrot (Amazona vittata) from a locally funded project. GigaScience 1:14.

Via, M., Gignoux, C.R., Roth, L., Fejerman, L., Galanter, J., Choudhry, S., Toro-Labrador, G., Viera-Vera, J., Oleksyk, T., Beckman, K., Ziv, E., Risch, N., Burchard, E.G. and Martínez-Cruzado, J.C. (2011) History shaped the geographic distribution of genomic admixture on the island of Puerto Rico. PLoS ONE 6: e16513.

Martínez-Cruzado JC (2010) The history of Amerindian mitochondrial DNA lineages in Puerto Rico, In: Island shores, distant pasts: archaeological and biological approaches to the Pre-Columbian settlement of the Caribbean, (Fitzpatrick SM, Ross A.H, eds), University Press of Florida, Gainesville, Florida, U.S.A.

Díaz-Matallana M, Martínez-Cruzado JC (2010) Estudios sobre ADN mitocondrial sugieren un linaje predominante en la Cordillera Oriental de Colombia y un vínculo suramericano para los Arcaicos de Puerto Rico. Universitas Medica 51: 241-272.

Santory-Jorge AO, Avilés LA, Martínez-Cruzado JC, Ramírez D (2008) The Paradox of the Puerto Rican Race: The Interplay of Racism and Nationalism under U.S. Colonialism. In: Grant-Thomas A, Orfield G (eds) Twenty-First Century Color Lines: Multiracial Change in Contemporary America. Temple University Press, Philadelphia, Pennsylvania, U.S.A.

Choudhry, S., Burchard, E.G., Borrell, L.N., Tang, H., Gómez, I., Navqi, M., Nazario, S., Torres, A., Casal, J., Martínez-Cruzado, J.C., Ziv, E., Ávila, P.C., Rodríguez-Cintrón, W. and Risch, N.J. (2006) Ancestry-environment interactions and asthma risk among Puerto Ricans. Am J Respir Crit Care Med 174: 1088-1093.

Martínez-Cruzado, J.C., Toro-Labrador, G., Viera-Vera, J., Rivera-Vega, M.Y., Startek, J., Latorre-Esteves, M., Román-Colón, A., Rivera-Torres, R., Navarro-Millán, I.Y., Gómez-Sánchez, E., Caro-González, H. and Valencia-Rivera, P. (2005). Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis. Am. J. Phys. Anthropol. 128: 131-155.

Toro-Labrador, G., Wever, O.R. and Martínez-Cruzado, J.C. (2003). Mitochondrial DNA analysis in Aruba: strong maternal ancestry of closely related Amerinds and implications for the peopling of northwestern Venezuela. Carib. J. Sci. 39: 11-22.

Martínez-Cruzado, J.C., Toro-Labrador, G., Ho-Fung, V., Estévez-Montero, M., Lobaina-Manzanet, A., Padovani-Claudio, D.A., Sánchez-Cruz, H., Ortiz-Bermúdez, P. and Sánchez-Crespo, A. (2001). Mitochondrial DNA analysis reveals substantial Native American ancestry in Puerto Rico. Hum. Biol. 73: 491-511.

Johnson, E., Miklas, P.N., Stavely, J.R. and Martínez-Cruzado, J.C. (1995). Coupling and repulsion RAPD markers for marker-assisted selection of a rust resistance gene in common bean. Theor. Appl. Gen. 90: 659-664.

Romano, C.P., Martínez-Cruzado, J.C. and Kafatos, F.C. (1991). The Relative Importance of Transcriptional and Post Transcriptional Regulation of Drosophila Chorion Gene Expression During Oogenesis. Dev. Genetics 12: 196-205.

Martínez-Cruzado, J.C. (1990). Evolution of the Autosomal Chorion Cluster in Drosophila. IV. The Hawaiian Drosophila: Rapid Protein Evolution and Constancy in the Rate of DNA Divergence. J. Mol. Evol. 31: 402-423.

Swimmer, C., Fenerjian, M.G., Martínez-Cruzado, J.C. and Kafatos, F.C. (1990). Evolution of the Autosomal Chorion Cluster in Drosophila. III. Comparison of the s18 gene in Evolutionarily Distant Species and Heterospecific Control of Chorion Gene Amplification. J. Mol. Biol. 215: 225-235.

Fenerjian, M.G., Martínez-Cruzado, J.C., Swimmer, C., King, D. and Kafatos, F.C. (1989). Evolution of the Autosomal Chorion Cluster in Drosophila. III. Chorion Gene Expression and Sequence Comparisons of the s16 and s19 genes in evolutionarily distant species. J. Mol. Evol. 29: 108-125.

Martínez-Cruzado, J.C., Swimmer, C., Fenerjian, M.G. and Kafatos, F.C. (1988). Evolution of the Autosomal Chorion Locus in Drosophila. I. General organization of the locus and sequence comparisons of genes s15 and s19 in evolutionarily distant species. Genetics 119: 663-677.

Keith, T.P., Brooks, L.D., Lewontin, R.C., Martínez-Cruzado, J.C. and Rigby, D.L. (1985). Nearly identical distributions of xanthine dehydrogenase in two populations of Drosophila pseudoobscura. Mol. Biol. Evol. 2: 206-