Selected papers
* Corresponding author. # Equal contribution.
Bat genomes illuminate adaptations to viral tolerance and disease resistance
Morales AE #, Dong Y #, Brown T, Baid K, Kontopoulos DG, Gonzalez V, Huang Z, Ahmed AW, Hilgers L, Winkler S, Hughes G, Li X, Kirilenko BM, Devanna P, Lama TM, Nissan Y, Pippel M, Dávalos LM, Vernes SC, Puechmaille SJ, Rossiter SJ, Yossi Y, Prescott JB, Kurth A, Ray DA, Lim BK, Myers E, Teeling EC, Banerjee A, Irving AT, Hiller M.
(2025) Nature, https://doi.org/10.1038/s41586-024-08471-0
Distinct Genes with Similar Functions Underlie Convergent Evolution in Myotis Bat Ecomorphs
Morales AE *, Burbrink FT, Segall M, Meza M, Munegowda C, Webala P, Patterson B, Thong VD, Ruedi M, Hiller M, Simmons NB.
(2024) Molecular Biology and Evolution, msae165. https://doi.org/10.1093/molbev/msae165
Comment on “Population genetics reveal Myotis keenii (Keen’s myotis) and Myotis evotis (long-eared myotis) to be a single species”
Morales AE *, Fenton MB, Carstens BC, Simmons NB.
(2021) Canadian Journal of Zoology, 99: 415–422. https://doi.org/10.1139/cjz-2020-0048
Diversification rates have no effect on the convergent evolution of foraging strategies in the most species-rich genus of bats, Myotis
Morales AE*, Ruedi M, Field K, Carstens BC
(2019) Evolution, 73:2263–2280. https://doi.org/10.1111/evo.13849
Evidence that Myotis lucifugus ‘subspecies’ are five non-sister species, despite gene flow
Morales AE*, Carstens BC
(2018) Systematic Biology, 67:756–769. https://doi.org/10.1093/sysbio/syy010
Speciation with gene flow in North American Myotis bats
Morales AE, Jackson N, Dewey T, O’Meara BC, Carstens BC
(2017) Systematic Biology, 66:440–452. https://doi.org/10.1093/sysbio/syx001
Space and environment predict skull variation and genetic structure in the cosmopolitan bat Tadarida brasiliensis
Morales AE*, De-la-Mora M, Piñero D
(2018) Journal of Biogeography, 45:1529–1540. https://doi.org/10.1111/jbi.13243
Environmental niche drives genetic and morphometric structure in a widespread bat
Morales AE*, Villalobos F, Velazco PM, Simmons NB, Piñero D
(2016) Journal of Biogeography, 43:1057–1068. https://doi.org/10.1111/jbi.12666
Preprints
–– Integrated genomics and transcriptomics reveal mechanisms of extreme dietary adaptation in vampire bats
Liu S, Freitas MB, Sartori SSR, Albertini M, Leushkin E, Alvarez van Tussenbroek I, Morales AE, Pippel M, Brown T, de Sousa AFR, de Paula RA, Patmanidis I, Jespers W, Hilgers L, Yi X, Bein B, Malovichko Y, Schell T, Greve C, Winkler S, Ben Hamadou A, Blumer M, Prange G, Hechavarria Cueria JC, Koessl M, Winter Y, Dilrosun S, Bechan SD, Engstrom MD, Jafferally D, Norman Z, Sornoza F, Dávalos LM, Lim B, Vernes S, Hiller M.
(2026) bioRxiv. Preprint; in review. https://doi.org/10.64898/2026.07.24.740446
All peer-reviewed papers
* Corresponding author. # Equal contribution.
(24) Lassa virus circumvents macrophage and dendritic cell antiviral defences in its natural reservoir, the Natal multimammate mouse (Mastomys natalensis) Corrales N, Wozniak DM, Yordanova IA, Suder EL, Morales AE, Lander A, Hansen-Kant K, Hiller M, Prescott JB (2026) npj Viruses 4(1), 9. https://doi.org/10.1038/s44298-026-00177-6
(23) Proteomic signatures of SARS-CoV-2 susceptibility in Mexican free-tailed bats and their application to viral surveillance Becker DJ, Vicente-Santos A, Morales AE, Dyer KE, Olbrys BL, Lock LR, Smotherman MS, Vernes SC, Hiller M, Adams AM, Phinney BS, Frick WF, Hall JS (2025) Integrative and Comparative Biology, icaf148. https://doi.org/10.1093/icb/icaf148
(22) Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene programme in bat wing development Schindler M, Feregrino C, Aldrovandi S, Lo BW, Monaco AA, Ringel AR, Morales AE, Zehnder T, Behncke RY, Glaser J, Barclay A, Andrey G, Kragesteen BK, Hägerling R, Haas SA, Vingron M, Ulitsky I, Marti-Renom MA, Hechavarria J, Fasel N, Hiller M, Lupiáñez DG, Mundlos S, Real FM (2025) Nature Ecology and Evolution, https://www.nature.com/articles/s41559-025-02780-x
(21) Bat genomes illuminate adaptations to viral tolerance and disease resistance Morales AE #, Dong Y #, Brown T, Baid K, Kontopoulos DG, Gonzalez V, Huang Z, Ahmed AW, Hilgers L, Winkler S, Hughes G, Li X, Kirilenko BM, Devanna P, Lama TM, Nissan Y, Pippel M, Dávalos LM, Vernes SC, Puechmaille SJ, Rossiter SJ, Yossi Y, Prescott JB, Kurth A, Ray DA, Lim BK, Myers E, Teeling EC, Banerjee A, Irving AT, Hiller M. (2025) Nature, https://doi.org/10.1038/s41586-024-08471-0
(20) Distinct Genes with Similar Functions Underlie Convergent Evolution in Myotis Bat Ecomorphs Morales AE*, Burbrink FT, Segall M, Meza M, Munegowda C, Webala P, Patterson B, Thong VD, Ruedi M, Hiller M, Simmons NB. (2024) Molecular Biology and Evolution, msae165. https://doi.org/10.1093/molbev/msae165
(19) Where do they live? Predictive geographic distribution of Tadarida brasiliensis brasiliensis Amaral IS, Bandeira Pereira J, Vancine MH, Morales AE, Althoff SL, Gregorin R, Pereira MJR, Valiati VH, Rosa de Oliveira L (2023) Neotropical Biology and Conservation, 18(3):139-156. https://doi.org/10.3897/neotropical.18.e101390
(18) Bat pluripotent stem cells reveal unique entanglement between host and viruses Déjosez M, Marin A #, Hughes GM #, Morales AE #, Godoy-Parejo C, Gray J, Qin Y, Singh A, Xu H, Juste J, Ibáñez C, White KM, Rosales R, Francoeur NJ, Sebra RP, Alcock D, Puechmaille SJ, Pastusiak A, Frost DW, Hiller M, Young RA, Teeling EC, Garcia-Sastre A, Zwaka TP. (2023) Cell, 86(5):957–974.e28. https://doi.org/10.1016/j.cell.2023.01.011
(17) Integrating gene annotation with orthology inference at scale Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales AE, Ahmed AW, Kontopoulos DG, Hilgers L, Lindblad-Toh K, Karlsson EK, Zoonomia Consortium‡, Hiller M. (2023) Science, 380: eabn3107. https://doi.org/10.1126/science.abn3107
(16) The Pale Spear-nosed Bat – a neuromolecular and transgenic model for vocal learning Vernes SJ, Devanna P, Gareth JH, Alvarez van Tussenbroek I, Firzlaff U, Hagoort P, Hiller M, Hoeksema N, Hughes GM, Lavrichenko K, Mengede J, Morales AE, Wiesmann M. (2022) Annals of the New York Academy of Sciences, 1517(1):125–142. https://doi.org/10.1111/nyas.14884
(15) Gene losses in the common vampire bat genome illuminate molecular adaptations to blood feeding Blumer M, Brown T, Freitas MB, Destro AL, Oliveira JA, Morales AE, Schell T, Greve C, Pippel M, Jebb D, Hecker N, Ahmed A, Kirilenko B, Janke A, Lim B, Hiller M. (2022) Science Advances, 8(12):eabm6494. https://doi.org/10.1126/sciadv.abm6494
(14) Comment on “Population genetics reveal Myotis keenii (Keen’s myotis) and Myotis evotis (long-eared myotis) to be a single species” Morales AE*, Fenton MB, Carstens BC, Simmons NB. (2021) Canadian Journal of Zoology, 99: 415–422. https://doi.org/10.1139/cjz-2020-0048
(13) A new dichromatic species of Myotis (Chiroptera: Vespertilionidae) from the Nimba Mountains, Guinea Simmons NB, Flanders J, Fils EMB, Parker G, Suter JD, Bamba S, Douno M, Keita MK, Morales AE, Frick WF. (2021) American Museum Novitates, 3963: 1–40. https://digitallibrary.amnh.org/items/c50b2d12-30ba-40e5-8967-78b24a5bed2c Press coverage includes The New York Times!
(12) Diversification rates have no effect on the convergent evolution of foraging strategies in the most species-rich genus of bats, Myotis Morales AE*, Ruedi M, Field K, Carstens BC (2019) Evolution, 73:2263–2280. https://doi.org/10.1111/evo.13849
(11) Phylogeography, population structure, gene flow and species delimitation in Rockhopper penguins (Eudyptes chrysocome and Eudyptes moseleyi) Mays H, Oehler D, Morrison K, Morales AE, Lycans A, …, Weakley L. (2019) Journal of Heredity. esz051. https://doi.org/10.1093/jhered/esz051
(10) Genome-specific histories of introgression into a polyploid unisexual salamander lineage as revealed using ultraconserved genetic elements Denton RD, Morales AE, Gibbs HL (2018) Evolution, 72:1689–1700. https://doi.org/10.1111/evo.13528
(9) A global analysis of bats using automated comparative phylogeography uncovers a surprising impact of Pleistocene glaciation Carstens BC, Morales AE, Field K, Pelletier TA (2018) Journal of Biogeography, 45:1795–1805. https://doi.org/10.1111/jbi.13382
(8) Space and environment predict skull variation and genetic structure in the cosmopolitan bat Tadarida brasiliensis Morales AE*, De-la-Mora M, Piñero D (2018) Journal of Biogeography, 45:1529–1540. https://doi.org/10.1111/jbi.13243
(7)Evidence that Myotis lucifugus ‘subspecies’ are five non-sister species, despite gene flow Morales AE*, Carstens BC (2018) Systematic Biology, 67:756–769. https://doi.org/10.1093/sysbio/syy010
(6) Objective choice of phylogeographic models Carstens BC, Morales AE, Jackson N, O’Meara BC (2017) Molecular Phylogenetics and Evolution, 116:136–140. https://doi.org/10.1016/j.ympev.2017.08.018
(5) PHRAPL: Phylogeographic Inference using Approximate likelihoods Jackson N, Morales AE, Carstens BC, O’Meara BC (2017) Systematic Biology, 66:1045–1053. https://doi.org/10.1093/sysbio/syx001
(4) Species delimitation with gene flow Jackson N, Carstens BC, Morales AE, O’Meara BC (2017) Systematic Biology, 66:799–812. https://doi.org/10.1093/sysbio/syw100
(3) Speciation with gene flow in North American Myotis bats Morales AE, Jackson N, Dewey T, O’Meara BC, Carstens BC (2017) Systematic Biology, 66:440–452. https://doi.org/10.1093/sysbio/syx001
(2) Environmental niche drives genetic and morphometric structure in a widespread bat Morales AE*, Villalobos F, Velazco PM, Simmons NB, Piñero D (2016) Journal of Biogeography, 43:1057–1068. https://doi.org/10.1111/jbi.12666
(1) The evolution of phylogeographic datasets Garrick RC, Bonatelli IAS, Hyseni C, Morales AE, Pelletier TA, Perez MF, Rice E, Satler JD, Symula RE, Thomé MTC, Carstens BC (2015) Molecular Ecology, 24:1164–1171. https://doi.org/10.1111/mec.13108
Chapters in books
Vasquez Lobo A, Morales Garcia AE (2014) Microsatélites. In: Herramientas moleculares aplicadas en ecología (eds. Cornejo Romero A, Serrato Díaz A, Rendón Aguilar B, Rocha Munive MG), pp. 75–100. INECC-SEMARNAT, Mexico. ISBN: 978-607-8246-72-4
Databases & Software
–– BatLit – The Bat Literature Project. Contributor and co-author of an international initiative developing an open, versioned, multilingual, and citable digital archive of bat research literature and bibliographic metadata. The resource provides open access to more than 20,000 publications supporting bat taxonomy, ecology, and conservation. Resource available at: https://batlit.org/ Versioned dataset: https://doi.org/10.5281/zenodo.20287843
–– Demographic model selection (R package): PHRAPL (phylogeographic model selection using approximated likelihood). Part of developer team in collaboration with Brian O’Meara, Nathan Jackson, Bryan Carstens at University Tennessee, in Knoxville and the Ohio State University in Columbus, USA. Code available at: https://github.com/bomeara/phrapl, user manual: https://github.com/ariadnamorales/phrapl-manual.
–– Genome annotation tool (python-based) – TOGA: Tool to infer Orthologs from Genome Alignments. Part of the developer team at Michael Hiller’s research group at the Senckenberg Museum of Natural History, Centre for Translational Biodiversity Genomics & Goethe University in Frankfurt am Main, Germany. Code available at: https://github.com/hillerlab/TOGA.