- Greenspan SE, Peloso P, Fuentes-González JA, Bletz M, Lyra ML, Machado IF, Martins RA, Medina D, Moura-Campos D, Neely WJ, Preuss J, Sturaro MJ, Vaz RI, Navas CA, Toledo LF, Tozetti AM, Vences M, Woodhams DC, Haddad CFB, Pienaar J, Becker CG. 2022. Low microbiome diversity in threatened amphibians from two biodiversity hotspots. Animal Microbiome 4 (69): 1-9.
- García-Cabello KN, Fuentes-González JA, Saleh-Subai N, Pienaar J, Zúñiga-Vega JJ. 2022. Increased superfetation precedes the evolution of advanced degrees of placentotrophy in viviparous fishes of the family Poeciliidae. Biology Letters 18(10): 20220173.
- Momeni S, Fuentes-González J, Pienaar J. 2022. How to culture limnoterrestrial heterotardigrades. Invertebrate Biology 141(1): e12360.
- Turberville C, Fuentes-González J, Rogers S, Pienaar J. 2021. Moss phyllid morphology varies systematically with substrate slope. Plant Ecology and Evolution 154(3): 419-431.
- Fuentes-G JA, Polly PD, Martins EP. 2020. A Bayesian extension of phylogenetic generalized least squares: Incorporating uncertainty in the comparative study of trait relationships and evolutionary rates. Evolution 74(2): 311-325.
- Gevedon O, Bolus H, Lye SH, Schmitz K, Fuentes-González J, Hatchell K, Bley L, Pienaar J, Loewen C, Chtarbanova S. 2019. In vivo forward genetic screen to identify novel neuroprotective genes in Drosophila melanogaster. Journal of Visualized Experiments 149: e59720.
- Fuentes-G JA, Martins EP. 2019. Using phylogenetic comparative methods to gain insight into the evolution of social complexity. Behavioral Ecology and Sociobiology 73: 3.
- Mendes FK, Fuentes-González JA, Schraiber JG, Hahn MW. 2018. A multispecies coalescent model for quantitative traits. eLife 7:e36482.
- Martins EP, Fuentes-G JA. 2018. Phylogenetic comparative methods and tests of macroevolutionary questions. In: Oxford Bibliographies in Evolutionary Biology. Ed. Karin Pfennig. New York: Oxford University Press.
- Zúñiga-Vega JJ, Fuentes-G JA, Zamora-Abrego JG, García-Vásquez UO, Nieto-Montes de Oca A, Martins EP. 2017. Evolutionary patterns in life-history traits of lizards of the genus Xenosaurus. Herpetological Journal 27: 346-360.
- Vergara D, Fuentes JA, Stoy KS, Lively CM. 2017. Evaluating shell variation across different populations of a freshwater snail. Molluscan Research 37(2): 120-132.
- Fuentes–González JA, Muñoz–Durán J. 2017. Comportamiento social y preferencias alimentarias en la evolución de los cánidos actuales. Revista Mexicana de Biodiversidad 88(1): 192-206.
- Polly PD, Fuentes-G J, Lawing AM, Bormet AK, Dundas RG. 2017. Clade sorting has a greater effect than local adaptation on ecometric patterns in Carnivora. Evolutionary Ecology Research 18: 61-95.
- Zúñiga-Vega JJ, Fuentes-G JA, Ossip-Drahos AG, Martins EP. 2016. Repeated evolution of viviparity in phrynosomatid lizards constrained interspecific diversification in some life-history traits. Biology Letters 12(11): 1-5.
- Fuentes-G JA, Housworth E, Weber A, Martins EP. 2016. Phylogenetic ANCOVA: Estimating changes in evolutionary rates as well as relationships between traits. The American Naturalist 188(6): 615-627.
- Gibson AK, Fuentes JA. 2015. A phylogenetic test of the Red Queen Hypothesis: Outcrossing and parasitism in the Nematode phylum. Evolution 69(2): 530-540.
- Fuentes JA, Zerda–Ordóñez E, Muñoz–Durán J. 2013. Vocal communication of White-footed tamarin (Saguinus leucopus) in the wild. Caldasia 35(1): 49-63.
- Ossip–Klein AG, Fuentes JA, Hews DK, Martins EP. 2013. Information content is more important than sensory system or physical distance in guiding the long-term evolutionary relationships between signaling modalities in Sceloporus lizards. Behavioral Ecology and Sociobiology 67(9): 1513-1522.
- Fuentes–González JA, Muñoz–Durán J. 2012. Filogenia de los cánidos actuales (Carnivora: Canidae) mediante análisis de congruencia de caracteres bajo parsimonia. Actualidades Biológicas 34(96): 85-102.
- Muñoz-Durán J, Fuentes JA. 2012. Evolución de la socialidad, estrategias alimentarias y anatomía cráneodental en la subfamilia Caninae. Acta Biológica Colombiana 17(1): 173-200.