- Arroyo J, Aparicio A, Albaladejo RG, Muñoz J, Braza R. (2008) Genetic structure and population differentiation of the Mediterranean pioneer spiny broom Calicotome villosa across the Strait of Gibraltar. Biological Journal of the Linnean Society. 93: 39-51.
- Garrido B, Hampe A, Marañón T & Arroyo J. (2003). Regional differences in land use affect population performance of the threatened insectivorous plant Drosophyllum lusitanicum (L.) Link. Diversity and Distributions. 9: 335-350.
- Hampe A & Arroyo J. (2002). Recruitment and regeneration of populations of an endangered South Iberian Tertiary relict tree. Biological Conservation. 107: 263-271
- Hampe A, Arroyo J, Jordano P, Petit RJ. (2003). Rangewide phylogeography of a bird-dispersed Eurasian shrub: contrasting Mediterranean and temperate glacial refugia. Molecular Ecology. 12: 3415-3426.
- Mejías JA, Arroyo J & Ojeda F. (2002). Reproductive ecology of Rhododendron ponticum (Ericaceae) in relict Mediterranean populations. Botanical Journal of the Linnean Society. 140: 297-311.
- Mejías JA, Arroyo J, Marañón T. (2007) Ecology and biogeography of plant communities associated with the post Plio-Pleistocene relict Rhododendron ponticum subsp. baeticum in southern Spain. Journal of Biogeography. 34: 456-472.
- Ojeda F, Marañón T & Arroyo J. (1996). Patterns of ecological, chorological and taxonomic diversity at both sides of the Strait of Gibraltar. Journal of Vegetation Science 7: 63-7
- Ojeda F, Simmons MT, Arroyo J, Marañón T & Cowling RM. (2001). Biodiversity patterns in South African fynbos and Mediterranean heathland. Journal of Vegetation Science. 12: 867-874.
- Rodríguez FJ, Arroyo J. (2008) Reconstructing the demise of Tethyan plants: climate-driven range dynamics of Laurus since the Pliocene. Global Ecology and Biogeography. DOI: 10.1111/j.1466-8238.2008.00410.x
- Rodríguez FJ, Pérez-Barrales R, Ojeda F, Vargas P, Arroyo J. (2008) The strait of Gibraltar as a melting pot for plant biodiversity. Quaternary Science Reviews.27: 2110-2117.
- Rodríguez-Sánchez, F, Guzmán B, Valido A, Vargas P, Arroyo J. (2009) Late Neogene history of the laurel tree (Laurus L., Lauraceae) based on phylogeographical analyses of Mediterranean and Macaronesian populations. Journal of Biogeography. 36: 1270-1281.