Investigating the Evolution of Neotropical Freshwater Fishes
Where do we work?
My lab's research program relies heavily on fieldwork that aims to 1) explore previously unknown regions of the Neotropics, 2) discover undetected biodiversity, 3) collect ecological and phenotypic data for our evolutionary studies and 4) document poorly known Neotropical fish diversity and promote its conservation. Most of our fieldwork is concentrated in South America, where recently we have worked with colleagues in Guyana, Brazil, Suriname, Trinidad and Tobago, Ecuador, Venezuela and Bolivia. In recent years we have concentrated large part of our fieldwork in the Guiana Shield (Guyana and Suriname). We are exploring remote river basins, assessing the conservation status of fish species, and studying the links between phylogeny, historical biogeography and community assembly.
Molecular phylogenetics of cichlids and other Neotropical fishes
We use molecular and morphological datasets to generate phylogenetic hypotheses of cichlid relationships and times of divergence. Current projects include the use of hundreds of coding DNA sequences to reconstruct the phylogeny of Neotropical cichlids (subfamily Cichlinae) and some of its constituent clades. In collaboration with colleagues and former lab members, our work also involves phylogenetic analyses of other Neotropical fishes such as armoured catfishes (Loricariidae) and some characiformes.
Recent publications in Neotropical fish phylogenetics
Argolo, LA, IP Azevedo Campos, H López-Fernández, H Batalha-Filho, PRA de Mello Affonso. 2024. Effects of past riverine connectivity on the population structure and species distribution of ‘Geophagus’ brasiliensis (Cichlidae) complex in a Neotropical hotspot. Freshwater Biology (In press)
Astudillo-Clavijo, V., M.L. J. Stiassny, Z. Musilová, W. Salzburger & H. López-Fernández. 2023. Exon-based phylogenomics and the relationships of African cichlids: tackling the challenges of reconstructing phylogenies with nested rapid radiations. Systematic Biology doi.org/10.1093/sysbio/syac051
Varella, HR, SO Kullander, NA Menezes, C Oliveira, H López-Fernández. 2023. Revision of the generic classification of pike cichlids using an integrative phylogenetic approach (Cichlidae: Geophagini: Crenicichlina). Zoological Journal of the Linnean Society 198: 982-1034. doi: 10.1111/ecog.06798
Kolmann, M.A., Hughes, L.C., Hernandez, L.P., Sabaj, M., H. López-Fernández, & G. Ortí. 2020. Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how convergent diets obfuscate traditional morphological taxonomy. Systematic Biology syaa065. doi.org/10.1093/sysbio/syaa065
L. Araujo Argolo, H. López-Fernández, H. Batalha-Filho & P.R.A.M Affonso. 2020. Unraveling the systematics and evolution of the ‘Geophagus’ brasiliensis (Cichliformes: Cichlidae) species complex. Molecular Phylogenetics and Evolution 150:106855. doi.org/10.1016/j.ympev.2020.106855
Ilves, KL, Torti, D. & H. López-Fernández. 2018. Exon-based phylogenomics strengthens the phylogeny of Neotropical cichlids and identifies remaining conflicting clades (Cichlomorphae: Cichlidae: Cichlinae). Molecular Phylogenetics and Evolution 118:232-243.
Comparative biology and Macroevolution of Neotropical cichlids
We use phylogeny-based comparative methods to analyze the patterns and rates of evolution of lineages and phenotypes of Neotropical cichlids. Comparative methods provide tools for two broad types of evolutionary inference: 1) establishing evolutionary correlations among characters (e.g. morphology, diet and habitat use) while accounting for lack of statistical independence due to common ancestry, and 2) fitting various models of evolution to describe the patterns and infer the processes that originated the observed diversity. Both approaches use models of evolution, but while the former corrects for phylogeny, the latter uses phylogenetic patterns to test hypotheses about the evolutionary process.
Recent publications in macroevolution of Neotropical cichlids
Astudillo-ClavijoP, V, T. MankisU, H. VarellaP, H López-Fernández. 2024. Historical field records reveal habitat as an ecological correlate of locomotor phenotypic diversity in the radiation of Neotropical Geophagini fishes. The American Naturalist (In press).
Astudillo-ClavijoP, V, T. MankisU, H López-Fernández. 2024. Opening the museum’s vault: historical field records preserve reliable ecological data. The American Naturalist 203:305-322. doi.org/10.1086/728422
Arbour, J, F. Rumpp & H. López-Fernández. 2024. Organismal form constrains the evolution of complex lever systems in Neotropical cichlid four-bar linkages. Anatomical Record (In press).
Anderson, S.A.S., H. López-Fernández, J.T. Weir. 2023. Ecology and the origin of non-ephemeral species The American Naturalist 201: 000-000. doi.org/10.1086/723763
Weller, H., H. López-Fernández, C.D. McMahan & E.L. Brainerd. 2022. Relaxed feeding constraints facilitate the evolution of mouthbrooding in Neotropical cichlids. The American Naturalist 199(6)E197-E210.
López-Fernández H. 2021 Neotropical riverine cichlids: adaptive radiation and macroevolution at continental scales In: ME Abate & DLG Noakes (Eds.) The Behavior, Ecology and Evolution of Cichlid Fishes: A Modern Synthesis. Springer Academic (In press).
Hauser, F.E., Ilves, K.L, R.K. Schott, E. Alvi, H. López-Fernández, Chang. B. 2021. Evolution, inactivation, and loss of short wavelength-sensitive opsin genes during the diversification of Neotropical cichlids. Molecular Ecology 30:1688-1703. doi: 10.1111/mec.15838
Arbour, J.H., C.G. Montaña, K.O. Winemiller, A.A. Pease, M. Soria-Barreto, J.L. Cochran-Biederman & H. López-Fernández. 2020. Repeated adaptive shifts towards predatory diets affect functional diversity in Neotropical cichlids. Biological Journal of the Linnean Society 129:844-861. Doi: 10.1093/biolinnean/blaa001
Biodiversity discovery and conservation of Neotropical freshwater fishes
Taxonomic discovery and clarifying the patterns of distribution of species play a fundamental role in understanding the origin of biodiversity and ensuring its preservation. To understand the evolutionary processes that originated some of the most diverse fish assemblages on the planet we must recognize that unknown diversity represents both lost information and lost opportunity. Biodiversity discovery is also essential for biodiversity conservation. In my lab, we place high value in taxonomic and exploratory work as a foundation for our research. It is also a primary goal of our work to promote the conservation of the diverse freshwater fish fauna of the Neotropics.
Recent publications in biodiversity discovery and conservation
Varella, H.R., S.O. Kullander, N.A. Menezes, C. Oliveira & H. López-Fernández. 2023. Revision of the generic classification of pike cichlids using an integrative phylogenetic approach (Cichlidae: Geophagini: Crenicichlina). Zoological Journal of the Linnean Society (In press)
Borstein, S.R., O. Lucanus, K. Gajapersad, R.A. Singer, J. Mol, H. López-Fernández. 2022. Fish diversity of the upper Tapanahony River, Suriname. Miscellaneous Publications of the University of Michigan Museum of Zoology211:1-19. dx.doi.org/10.7302/4816
Taphorn, D.C., E. Liverpool, N.K. Lujan, C. do Nascimento, D.D. Hemraj, W.G.R. Crampton, M. Kolmann, J.P. Fontenelle, L.S. de Souza, D.C. Werneke, M. Ram, D.D. Bloom, B.L. Sidlauskas, E. Holm, J.G. Lundberg, M.H. Sabaj, C. Bernard, J.W. Armbruster & H. López-Fernández. 2022. Annotated checklist of the primarily freshwater fishes of Guyana. Proceedings of the Academy of Natural Sciences of Philadelphia 168: 1-95
Mark H. Sabaj, López-Fernández, H., Willis. S.C., Hemraj, D.D., Taphorn, D.C. & Winemiller, K.O. 2020. Cichla cataractae (Cichliformes: Cichlidae), new species of peacock bass from the Essequibo Basin, Guyana and Venezuela. Proceedings of the Academy of Natural Sciences of Philadelphia 167:69-86
Andrade, M.C., H. López-Fernández & E. A. Liverpool. 2019. New Myloplus from the Essequibo River basin, Guyana (Characiformes: Serrasalmidae), with discussion of the taxonomic status of Myleus pacu. Neotropical Ichthyology 17(4):e190026.
Leveraging museum extended specimens and historical data to study biodiversity
Natural history collections are as important for my lab's research as fieldwork, phylogenies, or comparative methods. The uses of natural history collections are often not those intended by their original collectors. While collections of specimens have long supported and recorded taxonomy, biodiversity discovery, and natural history, many modern uses of collections were largely unimagined even a few years ago. Advances in knowledge and technology have introduced new uses for “old” collections, spanning genome-wide sequencing, habitat modelling, ecosystem ecology, and revealing the impacts of global climate change. These advances also have changed the nature of what we collect, how we curate it, and how collections are accessed and studied at a global scale. We, and many other researchers studying biodiversity, rely heavily on "extended specimens" – those for which we can cross-reference ecological, geographic, genomic, and other data — to generate datasets for our evolutionary and ecological studies. Studying extended specimens led us to adopt or develop new methods of data collection or analysis of museum holdings.
Recent publications in museums data and biodiversity studies
Astudillo-ClavijoP, V, T. MankisU, H López-Fernández. 2024. Opening the museum’s vault: historical field records preserve reliable ecological data. The American Naturalist 203:305-322. doi.org/10.1086/728422
MW Nachman, EJ Beckman, RCK Bowie, C Cicero, CJ Conroy, R Dudley, TB Hayes, MS Koo, EA Lacey, CH Martin, JA McGuire, JL Patton, CL Spencer, RD Tarvin, MH Wake, IJ Wang, A Achmadi, ST Álvarez-Castañeda, MJ Andersen, J Arroyave, CC Austin, FK Barker, LN Barrow, GF Barrowclough, J Bates, AM Bauer, KC Bell, RC Bell, AW Bronson, RM Brown, FT Burbrink, KJ Burns, CD Cadena, DC Cannatella, TA Castoe, P Chakrabarty, JP Colella, JA Cook, JL Cracraft, DR Davis, AR Davis Rabosky, G D'Elía, JP Dumbacher, JL Dunnum, SV Edwards, JA Esselstyn, J Faivovich, J Fjeldså, OA Flores-Villela, K Ford, J Fuchs, MK Fujita, JM Good, E Greenbaum, HW Greene, S Hackett, A Hamidy, J Hanken, T Haryoko, MTR Hawkins, LR Heaney, DM Hillis, BD Hollingsworth, AD Hornsby, PA Hosner, M Irham, S Jansa, RA Jiménez, L Joseph, JJ Kirchman, TJ LaDuc, AD Leaché, EP Lessa, H López-Fernández, NA Mason, J McCormack, CD McMahan, RG Moyle, RA Ojeda, LE Olson, CK Onn, LR Parenti, G Parra-Olea, BD Patterson, GB Pauly, SE Pavan, AT Peterson, S Poe, DL Rabosky, CJ Raxworthy, S Reddy, A Rico-Guevara, A Riyanto, LA Rocha, SR Ron, SM Rovito, KC Rowe, J Rowley, S Ruane, D Salazar-Valenzuela, AJ Shultz, B Sidlauskas, DS Sikes, NB Simmons, MLJ Stiassny, JW Streicher, BL Stuart, AP Summers, JJ Tavera Vargas, P Teta, CW Thompson, RM Timm, O Torres-Carvajal, G Voelker, RS Voss, K Winker, C Witt, EA Wommack, RM Zin. 2023. Specimen collection is essential for modern science. PLoS Biology 21(11): e3002318 doi.org/10.1371/journal.pbio.3002318
Turner, TR, H Bart, F McCormick, A Besser, R Bowes, K Capps, E DeArmon, C Dillman, K Driscoll, A Dugger, G Hamilton, P Harris, D Hendrickson, J Hoffman, J Knouft, R Lepak, H López-Fernández, CG Montaña, S Newsome, A Pease, WL Smith, C Taylor, R Welicky. 2023. Long-term ecological research in freshwaters enabled by regional biodiversity collections, stable isotope analysis, and environmental informatics. Bioscience biad039. doi.org/10.1093/biosci/biad039
King, KBS, HC Giacomini, K Wehrly, H López-Fernández, AK Thomer, KM Alofs. 2023. Using historical fish catch data to evaluate predicted changes in relative abundance in response to a warming climate. Ecography 8: e06798. doi: 10.1111/ecog.06798
Kolmann, M, R Nagesan, J Andrews, PS Borstein, R Tinoco Figueroa, R Singer, M Friedman, H López-Fernández. 2023. DiceCT for Fishes: Recommendations for pairing iodine contrast agents with μCT to visualize soft tissues in fishes. Journal of Fish Biology 102:893–903. doi.org/10.1111/jfb.15320
Johnson, KR, IFP Owens & the Global Collection Group (154 authors who lead 73 Natural History museums in 28 countries, including H López-Fernández). 2023. A global approach for natural history museum collections – Integration of the world’s natural history collections can provide a resource for decision-makers. Science 379:1192-1194. Featured in The New York Times, Michigan News, among others.
