Profile photo of Dr. Fernando Alda
Dr. Fernando Alda
Assistant Professor
Biology, Geology & Environmental Science
Ph.D., University Complutense of Madrid (Spain)
  351A Holt

Alda Lab Website

Research Interests

I am an evolutionary biologist with a broad interest in understanding the mechanisms that generate biological diversity, and particularly in the relative roles of geological and ecological factors driving within and among species variation. My research focuses on patterns and processes controlling the evolution and diversity of—mostly but not only—freshwater fishes, which I study using a combination of fieldwork, phylogenomic systematics, population genetics and collections-based research tools that allow me to reach broad goals in ecology and evolution including: biogeography, speciation, and conservation.

Phylogenetics and Biogeography

Most of my recent work has focused on the systematics and historical biogeography of Neotropical freshwater fishes. Currently, my main interest is integrating the use of genomic markers from ultra conserved elements (UCEs) into large-scale phylogenetic analyses, and explore the best methods and strategies to analyze and recover consistent species trees estimates.

From a phylogeographical perspective, I am particularly interested on how the history of regional geological formation determines the tempo and mode of species colonization and expansion. 

Host-Parasite cospeciation

Parasitism is the most common life strategy yet the nature and diversity of host and parasite relationships remain highly unknown. I am interested in testing the factors shaping parasite species variation and distribution among and within fish host species. This approach allows me to test the relative roles of geography vs. ecological or evolutionary resemblance of the hosts in driving parasite diversification.

Conservation and Population Genetics

I want to understand how abiotic and biotic factors, including anthropogenic impacts, shape genetic diversity and structure at the population level, and how these are ultimately related to population viability in small and endangered populations.

I am also interested in reconstructing invasive species introduction histories, both to understand the effect of genetic diversity to species invasion potential. The ultimate goal of this research is to be applied to management plans of endangered species or with economic or ecological importance.


Alda F. 2018 (PI) Diversity and evolution of electric signals in Colombian weakly electric fishes (Gymnotiformes). NSF-Colciencias (Colombia): $12,000.

Alda F. 2013 (PI) Estimating diversity of Neotropical monogenean (Platyhelminthes) fish parasites, Consortium for the Barcode of Life and Smithsonian Institutio: $50,000.

Alda F. 2004 (co-PI) Population genetics of yellow legged gulls. Government of Basque Country (Spain) $6,000.


Alda F, Tagliacollo V, Bernt M, Waltz B, Ludt WB, Faircloth BC, Alfaro ME, Albert JS, Chakrabarty P (2018) Resolving deep nodes in an ancient radiation of Neotropical fishes in the presence of conflicting signals from incomplete lineage sorting. Systematic Biology syy085,

Faircloth BC, Alda F, Hoekzema K, Burns MD, Oliveira C, Albert JS, Melo BF, Ochoa LE, Roxo FF, Chakrabarty P, Sidlauskas BL, Alfaro ME (2018) A target enrichment bait set for studying relationships among ostariophysan fishes. bioRxiv 432583: doi:

Schönhuth S, Gagne RB, Alda F, Neely DA, Mayden RL, Blum MJ (2018) Phylogeography of the widespread Creek Chub Semotilus atromaculatus (Cypriniformes: Cyprinoidei). Journal of Fish Biology 93: 778-791.

Alda F, Adams AJ, Chakrabarty P, McMillan WO (2018) Mitogenomic divergence between three pairs of putative geminate fishes from Panama. Mitochondrial DNA Part B 3: 1-5.

Gagne RB, Sprehn CG, Alda F, McIntyre PB, Gilliam JF, Blum MJ (2018) Invasion pathways and genetic structure of a non-native parasite infecting a native stream fish in Hawai`i. Ecography 41: 528-539.

Burress ED, Alda F, Duarte A, Loureiro M, Armbruster JW, Chakrabarty P (2018) Phylogenomics of the pike cichlids (Cichlidae: Crenicichla) and the rapid ecological speciation of an incipient species flock. Journal of Evolutionary Biology 31: 14-30.

Peterson AC, Ghersi BM, Alda F, Firth C, Frye MJ, Bai Y, Osikowicz LM, Riegel C, Lipkin WI, Kosoy MY, Blum MJ (2017) Rodent-borne Bartonella infections varies according to host species within and among cities. EcoHealth 14: 771-782.

Alda F, Adams AJ, McMillan WO, Chakrabarty P (2017) Complete mitochondrial genomes of three Neotropical sleeper gobies: Eleotris amblyopsis, Eleotris picta and Hemieleotris latifasciata Mitochondrial DNA Part B 2: 747-750.

Le Pendu J, Abrantes J, Bertagnoli S, Guitton JS, Le Gall-Reculé G, Lopes AM, Marchandeau S, Alda F, [+43 authors], Esteves PJ (2017) Proposal for a unified classification system and nomenclature of lagoviruses. Journal of General Virology 98: 1658-1666.

Moody KN, Gagne RB, Heim-Ballew H, Alda F, Hain EF, Lisi P, Walter RP, Higashi GR, Hogan JD, McIntyre PB, Gilliam JF, Blum MJ (2017) Invasion hotspots and ecological saturation of streams across the Hawaiian archipelago. Cybium 41: 137-156.

Chakrabarty P, Faircloth BC, Alda F, Ludt WB, McMahan CD, Near TJ, Dornburg A, Albert JS, Arroyave J, Stiassny MLJ, Sorenson L, Alfaro ME (2017) Phylogenomic systematics of Ostariophysan fishes: ultraconserved elements support the surprising non-monophyly of Characiformes. Systematic Biology 66: 881-895.

Rocha G, Alda F, Pagés A, Merchán T (2017) Experimental transmission of rabbit haemorrhagic disease virus (RHDV) from rabbit to wild mice (Mus spretus and Apodemus sylvaticus) under laboratory conditions. Infection, Genetics and Evolution 47: 94-98.

Picq S, Alda F, Bermingham E, Krahe R (2016) Drift-driven evolution of electric signals in a Neotropical knifefish. Evolution 70: 2134-2144.

Alda F, Gagne RB, Hogan JD, Walter R, Moody K, Zink F, McIntyre PB, Gilliam JF, Blum MJ (2016) Colonization and demographic expansion of freshwater fauna across the Hawaiian Archipelago. Journal of Evolutionary Biology 29: 2054-2069.

Strobel HM, Alda F, Sprehn CG, Blum MJ, Heins DC (2016) Geographic and host-mediated population genetic structure in a cestode parasite of three-spined stickleback. Biological Journal of the Linnean Society 119: 381-396.

Galván-Quesada S, Doadrio I, Alda F, Perdices A, Reina RG, García Varela M, Hernández N, Campos Mendoza A, Bermingham E, Domínguez-Domínguez O (2016) Molecular phylogeny and biogeography of the amphidromous fish genus Dormitator Gill 1861 (Teleostei: Eleotridae). PLoS ONE 11(4): e0153538.

Rossi Lafferriere NA, Antelo R, Alda F, Mårternsson D, Hailer F, Castroviejo-Fisher S, Ayarzagüena, Vilá C, Ginsberg JR, Castroviejo J, Doadrio I, Amato GD (2016) Multiple paternity in a reintroduced population of the Orinoco crocodile (Crocodylus intermedius) at the El Frío Biological Station, Venezuela. PLoS ONE 1(3): e0150245.

Glotzbecker GJ, Alda F, Broughton RE, Neely DA, Mayden RL, Blum MJ (2016) Geographic independence and phylogenetic diversity of red shiner introductions. Conservation Genetics 17: 795-809.

Calvo M*, Alda F*, Oliverio M, Templado J, Machordom A (2015) Suriving the Messinian Salinity Crisis: divergence patterns in the genus Dendropoma (Gastropoda: Vermetidae) in the Mediterranean Sea. Molecular Phylogenetics and Evolution 91: 17-26. *These authors contributed equally to this work.

Bagley JC, Alda F, Bermingham E, Breitman MF, van den Berghe E, Johnson JB (2015) Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of Neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae). PLoS ONE 10(4):e0121139.

Alda F, Doadrio I (2014) Spatial genetic structure across a hybrid zone between European rabbit subspecies. PeerJ 2: e582.

Picq S, Alda F, Krahe R, Bermingham E (2014) Miocene and Pliocene colonization of the Central American Isthmus by the weakly electric fish Brachyhypopomus occidentalis (Hypopomidae, Gymnotiformes). Journal of Biogeography 41: 1520-1532.

Alda F, Picq S, De León Reina LF, González R, Waltz H, Bermingham E, Krahe R (2013) First record of Gymnotus henni in Panama, phylogenetic position and electric signal characterization. Check List 9: 655-659.

Alda F*, Gonzalez MA*, Olea PP, Godinho R, Drovetski S (2013) Genetic diversity, structure and conservation of the endangered Cantabrian Capercaillie in a unique peripheral habitat. European Journal of Wildlife Research 59: 719-728. *These authors contributed equally to this work.

Alda F, Reina RG, Doadrio I, Bermingham E (2013) Phylogeny and biogeography of the Poecilia sphenops species complex (Actinopterygii, Poeciliidae) in Central America. Molecular Phylogenetics and Evolution 66: 1011-1026.

Alda F, Ruiz-López MJ, García FJ, Gompper ME, Eggert LS, García JT (2013) Genetic evidence for multiple introduction events of raccoons (Procyon lotor) in Spain. Biological Invasions 15: 687-698.

Alda F, García J, García JT, Suárez-Seoane S (2013) Local genetic structure on breeding grounds of a long-distance migrant passerine: the bluethroat (Luscinia svecica) in Spain. Journal of Heredity 104: 36-46.

Ornelas-García CP, Alda F , Díaz-Pardo E, Gutiérrez-Hernández A, Doadrio I (2012) Genetic diversity shaped by historical and recent factors in the live-bearing twoline skiffia Neotoca bilineata. Journal of Fish Biology 81: 1963-1984.

Cabezas P, Alda F, Macpherson E, Machordom A (2012) Genetic characterization of the endangered and endemic anchialine squat lobster Munidopsis polymorpha from Lanzarote (Canary Islands): management implications. ICES Journal of Marine Science 69: 1030-1037.

García JT, García FJ, Alda F, González JL, Aramburu MJ, Cortés Y, Prieto B, Pliego B, Pérez M, Herrera J, García-Román L (2012) Recent invasion and reproduction of the raccoon (Procyon lotor) in Spain. Biological Invasions 14: 1305-1310.

Calero-Riestra M, Alda F, Dávila JA, García JT (2012) Isolation and characterization of polymorphic microsatellites loci from the tawny pipit (Anthus campestris) and their utility in other steppe birds. European Journal of Wildlife Research 58: 379-383.

García JT, Alda F, Terraube J, Mougeot F, Sternalski A, Bretagnolle V, Arroyo B (2011) Demographic history, genetic structure and gene flow in a steppe-associated raptor species. BMC Evolutionary Biology 11: 333.

Rodríguez R, Ramírez O, Valdiosera C, García N, Alda F, Madurell-Malapeira J, Marmi J, Doadrio I, Willerslev E, Götherström A, Arsuaga JL, Thomas M, Lalueza-Fox C, Dalén L (2011) 50,000 years of genetic uniformity in the critically endangered Iberian lynx. Molecular Ecology 20: 3785-3795.

Merchán T, Rocha G, Alda F, Hidalgo S, Silva E, Thompson G, Pagés (2011) Detection of Rabbit Haemorrhagic Disease Virus (RHDV) in nonspecific vertebrate hosts sympatric to the European rabbit (Oryctolagus cuniculus). Infection, Genetics and Evolution 11: 1469-1474.

Alda F, Sastre P, de la Cruz-Cardiel PJ, Doadrio I (2011) Population genetics of the endangered Cantabrian capercaillie in northern Spain. Animal Conservation 14: 249-260.

Alda F, Gaitero T, Suárez M, Merchán T, Rocha G, Doadrio I (2010) Evolutionary history of the rabbit haemorrhagic disease virus in the Iberian Peninsula and western Europe. BMC Evolutionary Biology 10: 347

Pedraza-Lara C, Alda F, Carranza S, Doadrio (2010) Mitochondrial DNA structure of the Iberian populations of white-clawed crayfish, Austropotamobius italicus italicus (Faxon, 1914). Molecular Phylogenetics and Evolution 57: 327-342.

Alda F, Gaitero T, Suárez M, Doadrio I (2009) Molecular characterization and recent evolution of Myxoma Virus in Spain. Archives of Virology 154: 1659-1670.

Alda F, Inogés J, Alcaraz L, Aranda A, Oria J, Doadrio I (2008) Looking for the Iberian Lynx (Lynx pardinus) in Central Spain: a needle in a haystack? Animal Conservation 11: 297-305.

Domínguez-Domínguez O, Alda F, Pérez-Ponce de León G, García-Garitagoitia JL, Doadrio I (2008) Evolutionary history of the endangered fish Zoogoneticus quitzeoensis (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear data. BMC Evolutionary Biology 8: 161.

Domínguez-Domínguez O, Boto L, Alda F, Pérez-Ponce de León G, Doadrio I (2007) Human impacts on drainages of the Mesa Central, Mexico, and its genetic effects on the endangered fish Zoogoneticus quitzeoensis. Conservation Biology 21: 168–180.

Alda F, Rey I, Doadrio I (2007) An improved method of extracting degraded DNA samples from birds and other species. Ardeola 54: 331-334.

Books/Book Chapters

Agudín S, Alda F, El Khadir N, Fernández M, García F, Martínez M, Moreno-Opo R, Muñoz J, Oria J, San Miguel A, Barrio S (2015) Actuaciones para el fomento del conejo de monte [Actions to enhance wild rabbit populations] (coord. Guil F) Real Federación Española de Caza- Fundación CBD-Hábitat, Madrid. 2nd Edition.

Agudín S, Alda F, El Khadir N, Fernández M, García F, Martínez M, Moreno-Opo R, Muñoz J, Oria J, San Miguel A, Barrio S (2009) Actuaciones para el fomento del conejo de monte [Actions to enhance wild rabbit populations] (coord. Guil F) Real Federación Española de Caza- Fundación CBD-Hábitat, Madrid.

Alda F, Gaitero T, Alcaraz L, Zardoya R, Doadrio I, Suárez M (2007) Coevolución de los virus de la mixomatosis y de la enfermedad hemorrágica con el conejo (Oryctolagus cuniculus L., 1758) en la Península Ibérica [Coevolution of myxomatosis and rabbit haemorrhagic disease virus and the wild rabbit in the Iberian Peninsula]. In: La investigación en los Parques Nacionales [Research in the National Parks] (Eds. Ramírez L, Asensio B), pp. 281-291. Ministerio de Medio Ambiente, Madrid.

Alda F, Doadrio I, Hernández M, Muñoz J, Silvestre F (2006) Gestión genética e inmunológica para el manejo de las traslocaciones y reintroducciones de conejo (Oryctolagus cuniculus L., 1758) en España [Genetic and immunological management of wild rabbit translocations and reintroductions in Spain]. In: Manual para la gestión del hábitat del lince ibérico (Lynx pardinus Temminck) y de su presa principal, el conejo de monte (Oryctolagus cuniculus L.) [Handbook of habitat management for the Iberian lynx and its main prey, the wild rabbit] (ed. San Miguel A), pp. 217-241. Fundación CBD-Habitat, Madrid.