Besnard, G.; Khadari, B.; Navascués, M.; Fernández-Mazuecos, M.; El Bakkali, B.; Arrigo, N.; Baali-Cherif, D.; Brunini-Bronzini de Caraffa, V.; Santoni, S.; Vargas, P.; Savolainen, V. 2013. The complex history of the olive tree: from Late Quaternary diversification of Mediterranean lineages to primary domestication in the northern Levant. Proceedings of the Royal Society B: Biological Sciences 280: 20122833.

Fernández-Mazuecos, M.; Blanco-Pastor, J.L.; Vargas, P. 2013. A phylogeny of toadflaxes (Linaria Mill.) based on nuclear ITS sequences: systematic and evolutionary consequences. International Journal of Plant Sciences 174(2): 234-249.

Fernández-Mazuecos, M.; Vargas, P. 2013. Congruence between distribution modelling and phylogeographical analyses reveals Quaternary survival of a toadflax species (Linaria elegans) in oceanic climate areas of a mountain ring range. New Phytologist 198(4): 1274-1289.

Guzmán, B.; Narbona, E; Vargas, P. 2013. Investigating reproductive incompatibility barriers in a Mediterranean rock-rose (Cistus ladanifer). Plant Biosystems. In Press

Alarcón, M.; Vargas, P.; Sáez, L.; Molero, J.;  Aldasoro, J. J. 2012. Genetic diversity of mountain plants: two migration episodes of Mediterranean Erodium (Geraniaceae). Molecular Phylogenetics and Evolution 63: 866-876.  

Blanco-Pastor, J.L.; Vargas, P.; Pfeil, B.E. 2012. Coalescent simulations reveal hybridization and incomplete lineage sorting in mediterranean Linaria. PLoS ONE 7 (6): e39089. 

Calviño-Cancela, M.; Escudero, M.; Rodríguez-Pérez, J.; Cano, E.; Vargas, P., Velo-Antón, G., Traveset, A. The role of seed dispersal, pollination and historical effects on genetic patterns of an insular plant that has lost its only seed disperser. Journal of Biogeography 39: 1996-2006.

Cires, E.; Cuesta, C.; Vargas, P.; Fernández Prieto, J.A. 2012. Unravelling the evolutionary history of the polyploid complex Ranunculus parnassiifolius (Ranunculaceae). Biological Journal of the Linnean Society 107: 477-493. 

Nogales, M.; Heleno, R.; Traveset, A.; Vargas, P. 2012 Evidence for overlooked mechanisms of long-distance seed dispersal to and between oceanic islands. The New Phytologist 194: 313-317.

Santos-Gally, R. Vargas, P.; Arroyo, J. 2012. Insights into Neogene Mediterranean biogeography based on phylogenetic relationships of mountain and lowland lineages of Narcissus (Amaryllidaceae). Journal of Biogeography 39: 782-798.

Vargas, P.; Heleno, R.; Traveset, A.; Nogales, M. 2012 Colonization of the Galápagos Islands by plants with no specific syndromes for long-distance dispersal: a new perspective. Ecography 35: 33-43. 

Amat, M.E.; Vargas, P.; Gómez, J.M. 2011. Pollen quality limitation in the Iberian critically endangered genus Pseudomisopates (Antirrhinaceae). Plant Ecology 212(6): 1069-1078. 

Balaguer, L.; Arroyo-García, R.; Jiménez, P.; Jiménez, M. D.; Villegas, L.; Cordero, I.; Rubio de Casas, R.; Fernández-Delgado, R.; Ron, M. E.; Manrique, E.; Vargas, P.; Cano, E.; Pueyo, J.J.; Aronson, J. 2011. Forest Restoration in a Fog Oasis: Genetic and Ecophysiological Evidence Indicates Need for Cultural Awareness in Constructing the Reference. PLoS ONE  6(8): e23004.

De Casas, R.R.; Vargas, P.; Pérez-Corona, E.; Manrique, E.; García-Verdugo, C.; Balaguer, L. 2011. Sun and shade leaves of Olea europaea respond differently to plant size, light availability and genetic variation. Functional Ecology 25: 802-812.

Fernández-Mazuecos, M., Vargas, P. 2011. Historical isolation versus recent long-distance connections between Europe and Africa in bifid toadflaxes (Linaria sect. Versicolores) PLoS ONE, 6 (7): e22234. doi:10.1371/journal.pone.0022234

Fernández-Mazuecos, M.; Vargas, P. 2011. Genetically depauperate in the continent but rich in oceanic islands: Cistus monspeliensis (Cistaceae) in the canary islands PLoS ONE 6 (2): e17172

Guzmán, B.; Narbona, E.; Vargas, P. 2011. Similar reproductive success of the two petal colour polymorphisms of Cistus ladanifer (Cistaceae). Plant Biosystems 145: 931-937.

Heleno, R.; Blake, S.; Jaramillo, P.; Traveset, A.; Vargas, P.; Nogales, M. 2011. Frugivory and seed dispersal in the Galápagos: what is the state of the art? Integrative Zoology 6: 88-106.

Rumeu, B.; Caujapé-Castells, J.; Blanco-Pastor, J.L.; Jaén-Molina, R.; Nogales, M.; Elias, R.B.; Vargas, P. 2011. The colonization history of Juniperus brevifolia (Cupressaceae) in the Azores islands. PLoS ONE 6 (11): e27697

Valente, L.; Savolainen, V.; Manning, J.C.; Goldblatt, P.; Vargas, P. 2011. Explaining disparities in species richness between Mediterranean floristic regions: a case study in Gladiolus (Iridaceae). Global Ecology and Biogeography 20:881-892.

Valente, L.M.; Savolainen V.; Vargas, P. 2010. Unparalleled rates of species diversification in Europe. Proceedings of the Royal Society B published online before print January 27, 2010, (doi:10.1098/rspb.2009.2163)
http://rspb.royalsocietypublishing.org/content/early/2010/01/22/rspb.2009.2163.short?rss=1

Vargas, P.; Carrió, E.; Guzmán, B.; Amat, E.; Güemes, J. (2009) A geographical pattern of Antirrhinum (Scrophulariaceae) speciation since the Pliocene based on plastid and nuclear DNA polymorphisms. J. Biogeogr. 36, 1297–1312.

De Casas, R.R.; Cano, E.; Balaguer, L.; Pérez-Corona, E.; Manrique, E.; García-Verdugo, C. et al. 2007. Taxonomic identity of Quercus coccifera L. in the Iberian peninsula is maintained in spite of widespread hybridisation, as revealed by morphological, ISSR and ITS sequence data. Flora: Morphology, Distribution, Functional Ecology of Plants, 202 (6), 488-499.

Guzmán, B.; Vargas, P. 2005. Systematics, character evolution, and biogeography of Cistus L. (Cistaceae) based on ITS, trnL-trnF, and matK sequences. Molecular Phylogenetics and Evolution 37(2): 644-660. 

Hess, J.; Kadereit, J.; Vargas, P. 2000. The colonization history of Olea europaea L. in Macaronesia based on internal transcribed spacer 1 (ITS-1) sequences, randomly amplified polymorphic DNAs (RAPD), and inter-simple sequence repeats (ISSR). Molecular Ecology 9: 857-868.

Balao, F.; Valente, L.M.; Vargas, P.; Herrera, J.; Talavera, S. 2010 Radiative evolution of polyploid races of the Iberian carnation Dianthus broteri (Caryophyllaceae). The New Phytologist 187: 542-551.

Bastida, J.M.; Alcántara, J.M.; Rey, P.J.; Vargas, P.; Herrera, C.M. 2010 Extended phylogeny of Aquilegia: the biogeographical and ecological patterns of two simultaneous but contrasting radiations. Plant systematic and Evolution 284:171–185.

Carrió, E.; Forrest, A.D.; Güemes, J.; Vargas, P. 2010 Evaluating species nonmonophyly as a trait affecting genetic diversity: a case study in three endangered species of Antirrhinum L. (Scrophulariaceae). Plant Systematics and Evolution 288: 43-58.

Escudero, M.; Valcárcel, V.; Vargas, P.; Luceño, M. 2010 Bipolar disjunctions in Carex: Long distance dispersal, vicariance, or parallel evolution? Flora 205: 118–127.

Escudero, M.; Vargas, P.; Arens, P.; Ouborg, N.J.; Luceño, M. 2010 The east-west-north colonization history of the Mediterranean and Europe by the coastal plant Carex extensa (Cyperaceae). Molecular Ecology 19: 352-370.

Fernández Mazuecos, M.; Vargas, P. 2010. Ecological rather than geographical isolation dominates Quaternary formation of Mediterranean Cistus species. Molecular Ecology 19, 1381–1395

Fiz-Palacios, O.; Vargas, P.; Vila, R.; Papadopulos, A.S.T.; Aldasoro, J.J. 2010. The uneven phylogeny and biogeography of Erodium (Geraniaceae): radiations in the Mediterranean and recent recurrent intercontinental colonization. Annals of Botany 106: 871–884, doi:10.1093/aob/mcq184, www.aob.oxfordjournals.org

García-Verdugo C.; Forrest A.D.; Fay M.F.; Vargas P. 2010. The relevance of gene flow in metapopulation dynamics of an oceanic island endemic, Olea europaea subsp guanchica.  Evolution 64: 3525-3536.

García-Verdugo, C.; Forrest, A. D.; Fay, M. F.; Balaguer, L..; Vargas, P. 2010 Parallel evolution of insular Olea europaea subspecies based on geographical structuring of plastid DNA variation and phenotypic similarity in leaf traits. Botanical Journal of the Linnean Society 162: 54–63.

Guzmán, B.; Vargas, P. 2010. Unexpected synchronous differentiation in Mediterranean and Canarian Cistus. Perspectives in plant ecology, evolution and systematics 12:163-174. 

Martín-Bravo, S.; Valcárcel, V.; Vargas, P.; Luceño, M. 2010 Geographical speciation related to Pleistocene range shifts in the western Mediterranean mountains (Reseda sect. Glaucoreseda, Resedaceae). Taxon 59: 466-482.

Martínez, J.; Vargas, P.; Luceño, M.; Cuadrado, A. 2010 Evolution of Iris subgenus Xiphium base don chromosome numbers, FISH of nrDNA (5S, 45S) and trnL-trnF sequence analysis. Plant Systematics and Evolution 289: 223-235.

Narbona, E.; Guzmán, B.; Arroyo, J.; Vargas, P. 2010 Why are fruits of Cistus ladanifer (Cistaceae) so variable?: a multi-level study across its geographical range. Perspectives in Plant Ecology, Evolution and Systematics (aceptado). 12: 305–315.

Valcárcel, V.; Vargas, P. (2010) Quantitative morphology and species delimitation under the General Lineage Concept: Hedera L. (Araliaceae) case. American Journal of Botany (aceptado). 97: 1555-1573.

Vargas, P.; Ornosa, C.; Ortiz-Sánchez, F.J.; Arroyo, J. 2010 Is the occluded corolla of Antirrhinum bee-specialized? Journal of Natural History, 44: 23, 1427 - 1443.

Besnard, G.; Rubio de Casas, R.; Christin, P.A.; Vargas, P. 2009. Phylogenetics of Olea (Oleaceae) based on plastid and nuclear ribosomal DNA sequences: Tertiary climatic shifts and lineage differentiation times. Annals of Botany 104: 143-160.

Dixon, C J.; Schönswetter, P.; Vargas, P.; Ertl, S.; Schneeweiss, G.M. 2009. Bayesian hypothesis testing supports long-distance Pleistocene migrations in a European high mountain plant (Androsace vitaliana, Primulaceae)  Molecular Phylogenetics and Evolution 53: 580-591.

Escudero, M.; Valcárcel, V.; Vargas, P.; Luceño, M. 2009. Significance of ecological vicariance and long-distance dispersal in the diversification of Carex sect. Spirostachyae (Cyperaceae). American Journal of Botany 96 (11): 2100-2114

Ferrero, V.; Arroyo, J.; Vargas, P.; Thompson, J. D.; Navarro, L. 2009. Evolutionary transitions of style polymorphisms in Lithodora (Boraginaceae). Perspectives in Plant Ecology, Evolution and Systematics 11: 111-125.

García-Maroto, F.; Mañas-Fernández, A.; Garrido-Cárdenas, J.A.; López-Alonso, D.; Guil-Guerrero, J.L.; Guzmán, B.; Vargas, P. 2009. Delta6-desaturase sequence evidence for explosive Pliocene radiations within the adaptive radiation of Macaronesian Echium (Boraginaceae).Molecular Phylogenetics and Evolution 52, 563-574.

Guzmán, B.; Lledó, M.D.; Vargas, P. 2009. Adaptive radiation in Mediterranean Cistus (Cistaceae). PlosOne 4: e6362.

Guzmán, B.; Vargas, P. 2009. Historical biogeography and character evolution of Cistaceae (Malvales) based onanalysis of plastid rbcL and trnL-trnF sequences. Organisms, diversity and evolution 9: 83-99.

Guzmán, B.; Vargas, P. 2009. Long distance colonisation by the Mediterranean Cistus ladanifer (Cistaceae) despite the absence of special dispersal mechanisms. Journal of Biogeography 36: 954-968.

Martínez Rodríguez, P;. Vargas, P.; Carine, M.; Jury, S. 2009. Iris rutherfordii Mart. Rodr., P. Vargas, Carine & Jury (iridaceae, Iris subgen. Xiphium (Mill.) Spach), a new species from Morocco. Candollea 64: 127-132.

Rodríguez, J.M.; Vargas Gómez, P.; Carine, M.; Jury, S. (2009). Iris rutherfordii Mart. Rodr., P. Vargas, Carine & Jury (Iridaceae, Iris subgen. Xiphium (Mill.) Spach), a new species from Morocco. Candollea, 64 (1): 127-132.

Rodríguez-García, 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.

Rodríguez-Sánchez, F.; Guzmán, B.; 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.

Rubio de Casas, R.; Vargas, P.; Pérez-Corona, E.; Cano, E.; Manrique, E.; García-Verdugo, C.; Balaguer, L. (2009) Variation in sclerophylly among Iberian populations of Quercus cocifera L. is associated with genetic differentiation across contrasting environments. Plant Biology 11: 464-472.

Besnard, G.; Garcia-Verdugo, C.; Rubio de Casas, R.; Treier, U.A.; Galland, N.; Vargas, P. 2008 Polyploidy in the olive complex (Olea europaea): evidence from flow cytometry and nuclear microsatellite analyses. Annals of Botany 101: 25-30.

Escudero, M.; Valcárcel, V.; Vargas, P.; Luceño, M. 2008 Evolution in Carex L. sect. Spirostachyae (Cyperaceae): a molecular and cytogenetic approach. Organism, Diversity and Evolution 7: 271-291.

Escudero, M.; Vargas, P.; Valcárcel, V.; Luceño, M. 2008. Strait of Gibraltar: an effective gene-flow barrier for wind-pollinated Carex helodes (Cyperaceae) as revealed by DNA sequences, AFLP, and cytogenetic variation. American Journal of Botany 95:745-755.

Fiz, O.; Vargas, P.; Alarcón, M.; Aedo, C.; García, J.L.; Aldasoro, J.J. 2008. Phylogeny and historical biogeography of geraniaceae in relation to climate changes and pollination ecology. Systematic Botany, 33 (2): 326-342.

Rodríguez Sánchez, F.; 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: 2100-2017.

Vargas, P.; García, B. 2008. Plant endemics to Sierra de Gredos (central Spain): taxonomic, distributional, and evolutionary aspects. Anales del Jardín Botánico de Madrid 65(2):353-366.

Vargas, P.; Manrique, E. 2008. La botánica española en el contexto de la biología evolutiva: análisis histórico, productividad y financiación. E-volución 3(1): 37-49.

Besnard, G.; de Casas, R.R.; Vargas, P. 2007. Plastid and nuclear DNA polymorphism reveals historical processes of isolation and reticulation in the olive tree complex (Olea europaea). Journal of Biogeography 34 (4): 736-752.

Martín-Bravo, S.; Meimberg H.; Luceño, M.; Märkl, W.; Valcárcel, V.; Bräuchler, C.; Vargas, P.; Heubl, G. 2007. Molecular systematics and biogeography of Resedaceae based on ITS and trnL-F sequences. Molecular Phylogenetics and Evolution 44(3): 1105-1120.

Rubio de Casas, R.; Cano, E.; Balaguer, L.; Pérez-Corona, E.; Manrique, E.; García-Verdugo, C.; Vargas, P. 2007. Taxonomic identity of Quercus coccifera L. in the Iberian Peninsula is maintained in spite of widespread hybridisation, as revealed by morphological, ISSR and ITS sequence data. Flora 202: 488-499.

Rubio de Casas, R.; Vargas, P.; Pérez-Corona, E.; Manrique, E.; Quintana, J.R.; García-Verdugo, C. et al. 2007. Field patterns of leaf plasticity in adults of the long-lived evergreen Quercus coccifera. Annals of Botany, 100 (2), 325-334.

Vargas, P. (2007). Are Macaronesian islands refugia of relict plant lineages?: a molecular survey. In: Phylogeography in Southern European Refugia: evolutionary perspectives on the origins and conservation of European biodiversity, Eds. Weiss, S. J. & Ferrand, N. Kluwer Academic Publishers, Dordrecht, Holanda.

Armbruster, W.S.; Perez-Barrales, R.; Arroyo, J.; Edwards, M.E.; Vargas, P. 2006. Three-dimensional reciprocity of floral morphs in wild flax (Linum suffruticosum): a new twist on heterostyly. New Phytologist 171 (3): 581-590.

De Casas, R.R.; Besnard, G.; Schonswetter, P.; Balaguer, L.; Vargas, P. 2006. Extensive gene flow blurs phylogeographic but not phylogenetic signal in Olea europaea L. Theoretical and Applied Genetics 113 (4): 575-583.

Fiz, O.; Vargas, P.; Alarcón, M.; Aldasoro, J.J. 2006. Phylogenetic Relationships and Evolution in Erodium (Geraniaceae) based on trnL-trnF Sequences. Systematic Botany, 31: 739-763.

Rubio, R.; Besnard, G.; Schönswetter, P.; Balaguer, L.; Vargas, P. 2006. Extensive gene flow blurs phylogeographic but not phylogenetic signal in Olea europaea L. Theoretical Applied Genetics 113: 575 - 583.

Valcarcel, V; Vargas, P.; Nieto Feliner, G. 2006. Phylogenetic and phylogeographic analysis of the westerm Mediterranean Arenaria section Plinthine (Caryophyllaceae) based on nuclear, plastid and morphological markers. Taxon 55 (2): 297-312.

Vargas, P. (2004). Jardín Botánico de Madrid: un paseo guiado (editor científico). Ibersaf, Madrid, 300 pp.

Aedo, C.; Vargas, P. 2003. Seseli L. In: Nieto Feliner, G., S. L. Jury & A. Herrero (eds.), Flora iberica 10: 202-215.CSIC, Madrid.

Vargas, P. (2003). Athamanta L. In: Nieto Feliner, G., S. L. Jury & A. Herrero (eds.), Flora iberica 10: 228-232.CSIC, Madrid.

Vargas, P. (2003). Sanicula L. In: Nieto Feliner, G., S. L. Jury & A. Herrero (eds.), Flora iberica 10: 30-32.CSIC, Madrid.

Vargas, P. (2003). Molecular evidence for multiple diversification patterns of alpine plants in Mediterranean Europe. Taxon 52(3): 463-476. 

Aldasoro, J. J.; Navarro, C.; Vargas, P.; Sáez, L.; Aedo, C. 2002. California, a new genus of Geraniaceae endemic to the southwest of North America. Anales Jard. Bot. Madrid 59(2): 209-216.

Fiz, O.; Valcárcel, V.; Vargas, P. 2002. Phylogenetic position of Mediterranean Astereaeand character evolution of daisies (Bellis, Asteraceae) inferredfrom nrDNA ITS sequences. Molecular Phylogenetics and Evolution 25:157-171. 

Aldasoro, J.J.; Navarro, C.; Vargas, P.; Aedo, C. 2001. Anatomy, morphology, and cladistic analysis of Monsonia L. (Geraniaceae). Anales Jard. Bot. Madrid 59: 75-100. 

Fiz, O.; Valcárcel, V.; Martínez, J.; Vargas, P.; Güemes, J. 2000.  Antirrhinum siculum Mill. (Scrophulariaceae) in Morocco: a new record for Africa. Anales Jard. Bot. Madrid 58(2):  362-363.

Vargas, P. & Kadereit, J.(2001). Molecular fingerprinting ISSR (Inter-Simple Sequence Repeats)evidence for a wild status of Olea europaea L. (Oleaceae) in the Eurosiberian North of the Iberian Peninsula. Flora 196(3): 142-152.

Vargas, P. (2001).Phylogenetic and evolutionary insights in the Saxifraga pentadactylis complex (Saxifragaceae): variation of nrITS sequences.  Nordic Journalof Botany 21: 75-82.

Esteban, J.; Martínez-Castro, I.; Vargas, P.; Sanz, J. 1999. Chemosystematic study on leaf volatile compounds of Saxifraga L. Series Ceratophyllae (Saxifragaceae). Biochemical Systematics and Ecology 27: 255-268.

Vargas, P., Morton, C. M. & Jury, S. L. (1999). Biogeographic patterns in Mediterranean and Macaronesian species of Saxifraga (Saxifragaceae) inferred from phylogenetic analyses of ITS sequences. American Journal of Botany 86(5): 724-734.