Contacts Centre for Environmental Biology


PhD, Marie Curie Research Fellow
(October 2011-September 2014)


CBA research group(s):

Evolutionary Genetics (main)
Animal Diversity & Conservation

Personal webpage

Team webpage

Catarina Ginja

Main Research Interests

These include population and conservation genetics, phylogenetics and evolution of domesticated animal species.
My research work is related with the screening of several molecular markers (autosomal STRs and SNPs, Y-chromosomal and mtDNA sequence variation) in order to study the process of domestication and investigate the origins of domestic animals. The statistical analysis of genetic data across time and space in combination with phenotypic information can provide important clues about this matter.
I am also interested in applying novel technologies (high-throughput genomic sequencing and whole-genome SNPs genotyping) to refine and complement information available from other molecular markers to investigate phylogenetic relationships and detect selection signatures.
More recently, I have been developing research in the field of zoo-archaeogenetics by making use of ancient DNA methods to perform a phylochronological analysis of animal populations. By comparing this information with genetic data available for extant domestic animals it will be possible to determine more accurately their evolutionary trajectories and to detect fluctuations of genetic variability over time in association with human and/or environmental selection.
I have developed extensive research in these scientific fields, particularly on what concerns the study of the genetic diversity, population structure and origins of cattle. I have studied other domesticated species (dog, goat, sheep, pig and horse) as well as the wild ancestral species of two of our domesticated animals – aurochs (ancestor of cattle), and wolf (ancestor of the dog).
During my PhD research I described a number of novel SNP-STR haplotypes in the cattle Y-chromosome to investigate male-mediated gene flow; which resulted in the most comprehensive dataset of Y-chromosomal variation in cattle and in an international hallmark paper. I have accomplished an extensive genetic characterization of Portuguese native cattle by making use of multiple markers, and described the phylogenetic relationships between Iberian breeds and the Creole cattle from the Americas. These studies have generated significant information concerning the genetic composition of native breeds from peripheral European regions supportive of conservation programs aiming to preserve the genetic resources of farm animals.


Academic Qualifications

- 2009 – PhD in Animal Science (Zootechnical Engineering) – Animal Breeding and Genetics (Instituto Superior de Agronomia da Universidade Técnica de Lisboa and Veterinary Genetics Laboratory, University of California, Davis)

- 2002 – MSc in Animal Science – Animal Breeding and Genetics (Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal)

- 1998 – 5-year college graduation in Animal Science/Zootechnical Engineering (Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal)


Recent Publications

Gama L.T., Martinez A., Carolino M.I., Periati V.L., Bermejo J.V.D., Vicente A.P., Vega-Pla J., Cortés O., Sousa C.O. & the BIOPIG Consortium. 2013. Genetic structure, relationships and admixture with wild relatives in native pig breeds from Iberia and its islands. Genetics Selection Evolution 45:18.

Ginja C., Gama L.T., Cortes Ó., Delgado J.V., Dunner S., García D., Landi V., Martín-Burriel I., Martínez-Martínez A., Penedo M.C.T., Rodellar C.,Zaragoza P., Cañon J. & the BIOBOVIS Consortium. 2013. Analysis of conservation priorities of Iberoamerican cattle based on autosomal microsatellite markers. Genetics Selection Evolution 45:35.

Bonfiglio S., Ginja C., Gaetano A., Achilli A., Olivieri A., Colli L., Tesfaye K., Agha S.H., Gama L.T., Cattonaro F., Penedo M.C.T.,  Ajmone-Marsan P., Torroni A. & Ferretti L. 2012. Origin and Spread of Bos taurus: New Clues from Mitochondrial Genomes Belonging to Haplogroup T1. Plos One  7(6):e38601.

Davis S.J.M., Svensson E., Albarella U., Detry C.,Götherström A., Pires A.E. & Ginja C. 2012. Molecular and Osteometric Sexing Of Cattle Metacarpals: A Case Study From 15th Century AD Beja, Portugal. Journal of Archaeological Science 39(5):1445–1454.

Martínez A.M., Gama L.T., Cañón J., Ginja C., Delgado J.V., Dunner S., Landi V., Martín-Burriel I., Penedo M.C.T., Rodellar C., Vega-Pla J., Acosta A., Álvarez L.A., Camacho E., Cortés O., Marques J.R., Martínez R., Martínez R.D., Melucci L., Martínez-Velásquez G., Muñoz J.E., Postiglioni A., Quiroz J., Sponenberg P., Uffo O., Villalobos A., Zambrano D., Zaragoza P. 2012. Genetic Footprints of Iberian Cattle in America 500 Years after the Arrival of Columbus. Plos One 7(11):e49066.

Ribeiro M.N., Bruno-de-Sousa C., Martínez-Martínez A., Ginja C., Menezes M.P., Pimenta-Filho E.C., Delgado J.V. & Gama. L.T. 2012. Drift across the Atlantic: genetic differentiation and population structure in Brazilian and Portuguese native goat breeds. Journal of Animal Breeding and Genetic 129(1):79-87.

Bruno-de-Sousa C., Martinez A.M., Ginja C., Santos-Silva F., Carolino M.I., Delgado J.V. & Gama L.T. 2011. Genetic diversity and population structure in Portuguese goat breeds. Livestock Science 135(2):131-139.

Cañón J., García D., Delgado J.V., Dunner S., Gama L.T., Landi V., Martín-Burriel I., Martínez A., Penedo M.C.T., Rodellar C., Zaragoza P. & Ginja C. 2011. Relative breed contributions to neutral genetic diversity of a comprehensive representation of Iberian native cattle. Animal 5(9):1323–1334.

Delgado J.V., Martínez A., Acosta A., Alvarez L., Armstrong E., Camacho E., Cañon J., Cortés O., Dunner S., Landi V., Marques J.R., Martin-Burriel I., Martínez O.R., Martínez R.D., Melluci L., Muñoz J.E., Penedo M.C.T., Postiglioni A., Qiroz J., Rodellar C., Sponenberg P., Uffo O., Ulloa-Arvizu R., Vega-Pla J.L., Villalobos A., Zambrano D., Zaragoza P., Gama L.T. & Ginja C. 2011. Genetic characterization of Latin-American Creole cattle using microsatellite markers. Animal Genetics 43(1):2-10.

Edwards C.J., Ginja C., Kantanen J., Pérez-Pardal L., Tresset A., Stock F., European Cattle Genetic Diversity Consortium, Gama L.T., Penedo M.C.T., Bradley D.G., Lenstra J.A. & Nijman I.J. 2011. Dual origins of dairy cattle farming - Evidence from a comprehensive survey of European Y-chromosomal variation. Plos One 6(1):e15922.

Martín-Burriel I., Rodellar C., Cañón J., Cortés O., Dunner S., Landi V., Martínez Martínez A., Gama L.T., Ginja C., Penedo M.C.T., Sanz A., Zaragoza P & Delgado Bermejo J.V. 2011. Diversity of Iberian cattle Genetic diversity, structure and breed relationships in Iberian cattle. Journal of Animal Science 89(4):893-906.

Perez-Pardal L., Ginja C., Royo L.J., A lvarez I., Fernandez I., del Valle A., Traore A., Ponce de Leon F.A., Beja-Pereira A., Penedo M.C.T. & Goyache F. 2011. Genetic structure of the bovine Y-specific microsatellite UMN0103 reflects the genetic history of the species. Animal Genetics 42(5):566-567.

Ginja C., Penedo M.C.T., Sobral M.F., Matos J., Borges C., Neves D., Rangel-Figueiredo T. & Cravador A. 2010. Molecular genetic analysis of a cattle population for recovery of the highly threatened Algarvia breed. Genetics Selection Evolution 42(1):18.

Bastos-Silveira C., Luís C., Ginja C., Gama T. & Oom M.M. 2009. Genetic variation of BoLA and non-BoLA microsatellite loci in Portuguese cattle breeds. Animal Genetics 40:101-105.

Pires A.E., Amorim I.R., Ginja C., Gomes M., Godinho I., Simões F., Oom M.M., Petrucci-Fonseca F., Matos J. & Bruford M.W. 2009. Molecular structure in peripheral dog breeds: Portuguese native breeds as a case study. Animal Genetics 40:383-392.

Ginja C., Melucci L., Quiroz J., Martínez López R., Revidatti M.A., Martínez-Martínez A., Delgado J.V., Penedo M.C.T. & Gama L.T. 2009. Origins and genetic diversity of New World Creole cattle: inferences from mitochondrial and Y chromosome polymorphisms. Animal Genetics 41:128-141.

Ginja C., Gama L.T. & Penedo M.C.T. 2009. Analysis of STR markers reveals high genetic structure in Portuguese native cattle. Journal of Heredity 100(2):148-157.

Ginja C., Gama L.T. & Penedo M.C.T. 2009. Y chromosome haplotype analysis in Portuguese cattle breeds using SNPs and STRs. Journal of Heredity 100(2):148-157.

Fernandes C.A., Ginja C., Pereira I., Tenreiro R., Bruford M.W. & Santos-Reis M. 2008. Species-specific mitochondrial DNA markers for identification of non-invasive samples from sympatric carnivores in the Iberian Peninsula. Conservation Genetics 9:681-690.

Vicente A.A., Carolino M.I., Sousa M.C.O., Ginja C., Silva F.S., Martínez A.M., Vega-Pla J.L., Carolino N. & Gama L.T. 2008. Genetic diversity in native and commercial breeds of pigs in Portugal assessed by microsatellites. Journal of Animal Science 86:2496-2507.


Ongoing projects

  • PTDC/HIS-ARQ/120183/2010 – Researcher (March 2012-2015), “HDI - Horse Domestication in Iberia – What else is there to be known?” (€101,160). PI C. Luis, CBA/FCUL, Lisboa, PT.

  • BIOBOVIS Consortium ( – Researcher, “study of Iberoamerican cattle biodiversity in the framework of a scientific network - Red Conbiand” (since 2004), INRB, PT; Univ. Cordoba, SP; and several Latin American Institutions.

  • PTDC/HIS-ARQ/100225/2008 – Researcher (February 2010-2013), “Tracing back animal domestication in Iberia: Clues from zooarchaeology and DNA analysis” (€102,000). PI A. E. Pires, CBA/FCUL and Instituto Nacional de Recursos Biológicos, Lisboa, PT.


Other Information

  • Membership: International Society for Animal Genetics (ISAG); Sociedade Portuguesa de Recursos Genéticos Animais (SPREGA);

  • International collaborations: M.C.T. Penedo, VGL/UCDavis, CA, USA; C. Hänni, Palgene/ENS-IGFL, FR; E. Svensson, Victorian AgriBiosciences Centre, AUS; A. Götherström, EBC/ Uppsala Univ., SE; J.A. Lenstra, Utrecht Univ., NL; A. Martínez-Martínez, Univ. Cordoba, ES; C. Fernández Rodríguez, Univ. León, ES;

  • Reviewer for: Animal Genetics, PlosONE, Livestock Science, Archivos Zootecnia, Biology Letters, Journal of Animal Breeding and Genetics, Journal of Heredity