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| Domínguez JC, Alda F, Calero-Riestra M, et al. (2023) Genetic footprints of a rapid and large-scale range expansion: the case of cyclic common vole in Spain. Heredity |
| Elías DJ, McMahan CD, Alda F, et al. (2023) Phylogenomics of trans-Andean tetras of the genus Hyphessobrycon Durbin 1908 (Stethaprioninae: Characidae) and colonization patterns of Middle America. Plos One. 18: e0279924 |
| Hart PB, Arnold RJ, Alda F, et al. (2022) Evolutionary relationships of anglerfishes (Lophiiformes) reconstructed using ultraconserved elements. Molecular Phylogenetics and Evolution. 171: 107459 |
| Alda F, Ludt WB, Elías DJ, et al. (2021) Comparing ultraconserved elements and exons for phylogenomic analyses of Middle American cichlids: when data agree to disagree. Genome Biology and Evolution |
| Rossi NA, Menchaca-Rodriguez A, Antelo R, et al. (2020) High levels of population genetic differentiation in the American crocodile (Crocodylus acutus). Plos One. 15: e0235288 |
| Faircloth BC, Alda F, Hoekzema K, et al. (2020) A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes Copeia. 108: 47 |
| García JT, Domínguez‐Villaseñor J, Alda F, et al. (2020) A complex scenario of glacial survival in Mediterranean and continental refugia of a temperate continental vole species (Microtus arvalis) in Europe Journal of Zoological Systematics and Evolutionary Research. 58: 459-474 |
| Alda F, Tagliacollo VA, Bernt MJ, et al. (2018) Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting. Systematic Biology |
| Schönhuth S, Gagne RB, Alda F, et al. (2018) Phylogeography of the widespread creek chub Semotilus atromaculatus (Cypriniformes: Leuciscidae). Journal of Fish Biology |
| Alda F, Adams AJ, McMillan WO, et al. (2017) Complete mitochondrial genomes of three Neotropical sleeper gobies: , and (Gobiiformes: Eleotridae). Mitochondrial Dna. Part B, Resources. 2: 747-750 |