Daniel F. Hughes, Ph.D.
Research
My research addresses questions about the ecology and evolution of organisms. My approach is to generate comparative data from the field and lab, using both modern and traditional techniques. Data sources for my research come from museum specimens, genomic DNA, brains, and field sites.
Demography
Biodiversity
Systematics
Phylogenetics
Behavior
Neurobiology
Evolution
I conduct investigations into the geographic distribution of genetic diversity to improve our understanding of the evolution of biodiversity. I use molecular data in combination with morphological measurements to test evolutionary hypotheses and document species diversity. This research is based on exploration and field work combined with modern molecular and bioinformatics toolkits. I have spent many months in the field collecting museum specimens and genetic material, which I use to discover new diversity and species-specific responses to evolutionary barriers. I also leverage phylogenetic comparative methods to reconstruct the evolutionary history of lineages and their traits. Ancestral trait reconstructions are caried out with stochastic character mapping and maximum likelihood approaches in an attempt to understand how traits evolved within and across lineages. I also address questions in comparative neurobiology by studying neural traits across species from micro- to macroscopic scales of analysis within the backdrop of their phylogenetic histories.
Systematics and Taxonomy
Hughes, D.F., M. Behangana, W. Lukwago, M. Menegon, J.M. Dehling, P. Wagner, C.R. Tilbury, T. South, C. Kusamba, and E. Greenbaum. 2024. Taxonomy of the Rhampholeon boulengeri complex (Sauria: Chamaeleonidae): Five new species from Central Africa’s Albertine Rift. Zootaxa 5458(4): 451–494.
Hughes, D.F., K.A. Tolley, W. Lukwago, M. Menegon, J.M. Dehling, J. Stipala, C.R. Tilbury, A.M. Khan, M. Behangana, C. Kusamba, and E. Greenbaum. 2018. Cryptic diversity in Rhampholeon boulengeri (Sauria: Chamaeleonidae), a pygmy chameleon from the Albertine Rift biodiversity hotspot. Molecular Phylogenetics and Evolution 122: 125–141.
Hughes, D.F., C. Kusamba, M. Behangana, and E. Greenbaum. 2017. Integrative taxonomy of the Central African forest chameleon, Kinyongia adolfifriderici (Sauria, Chamaeleonidae), reveals underestimated species diversity in the Albertine Rift. Zoological Journal of the Linnean Society 181: 400–438.
Comparative Phylogenetics
Blackburn, D.G., and D.F. Hughes. 2024. Phylogenetic analysis of viviparity, matrotrophy, and other reproductive patterns in chondrichthyan fishes. Biological Reviews 99(2024): 1314–1356.
Hughes, D.F., and D.G. Blackburn. 2020. Evolutionary origins of viviparity in Chamaeleonidae. Journal of Zoological Systematics and Evolutionary Research 58(1): 284–302.
Portillo, F., E.L. Stanley, W.R. Branch, W. Conradie, M.-O. Rödel, J. Penner, M.F. Barej, C. Kusamba, W.M. Muninga, M.M. Aristote, A.M. Bauer, J.-F. Trape, Z.T. Nagy, P. Carlino, O.S.G. Pauwels, M. Menegon, I. Ineich, M. Burger, T. Mazuch, K. Jackson, D.F. Hughes, M. Behangana, and E. Greenbaum. 2019. Evolutionary history of burrowing asps (Atractaspidinae) (Squamata: Lamprophiidae) with emphasis on fang evolution and prey selection. PLoS ONE 14(4): e0214889.
Neurobiology
Hughes, D.F., E.M. Walker, P.M. Gignac, A. Martinez, K. Negishi, C.S. Lieb, E. Greenbaum, and A.M. Khan. 2016. Rescuing perishable neuroanatomical information from a threatened Biodiversity Hotspot: Remote field methods for brain tissue preservation validated by cytoarchitectonic analysis, immunohistochemistry, and x‐ray microcomputed tomography. PLoS ONE 11(5): e0155824.
Ecology
I am interested in the factors that influence the ecology of organisms. I aim to understand the extent of variation in organisms, what processes generated the observed variation, and how the degree of variation can be used to decipher patterns and processes in ecology. I use repeated field observations in combination with historical records and phylogenies to study how populations have responded to change in the past and how they will cope with it in the future. Leveraging long-term field studies, genetic datasets, and specimens, I explore the fate of biodiversity in the face of global change. This research is based on a combination of measuring museum specimens, behavioral experiments, and mark-recapture methods of wild animals. This research is based upon reliable access to field sites and museum collections. I also study movement patterns, such as home ranges with radiotelemetry, which I integrate into studies of animal personality, thermal preferences, and habitat choices to understand how variation in behavior and relatedness can impact ecological decisions within and across populations. By examining variation in behavior and movements with known relationships, my work functionally links ecology with evolution and can elucidate mechanisms of personality.
Demography
Hughes, D.F., S. Dukuly, D.F. Becker, J. Scharosch, J.G. Otten, S. Wagner, and B.M. Reed. 2023. Copulation phenology of Ornate Box Turtles (Terrapene ornata). Journal of Herpetology 57(2): 246–253.
Meshaka, W.E., Jr., E. Wingert, J.D. Riedle, S. Boback, and D.F. Hughes. 2023. Demography of a painted turtle intergrade (Chrysemys picta picta X C. p. marginata) population from an altered wetland. The Herpetological Journal 33: 14–24.
Hughes, D.F., and D.B. Wylie. 2021. Reproductive ecology of Rhinophrynus dorsalis (Anura: Rhinophrynidae) in México. Journal of Herpetology 55(3): 298–309.
Biodiversity
Ahern, A.L., and D.F. Hughes. 2024. Citizen science initiatives document biodiversity at an urban lake. PeerJ 12: e17209.
Isingoma, J., E. Sande, R. Kityo, D.F. Hughes. 2023. Amphibian communities along a forest degradation gradient in an East African forest reserve. Ecological Informatics 75: 102021.
Lukwago, W., M. Behangana, E. Mwavu, and D.F. Hughes. 2020. Effects of selective timber harvest on amphibian species diversity in Budongo Forest Reserve, Uganda. Forest Ecology and Management 458: 117809.
Behavioral Ecology
Reed, B.M., K. Hobelman, A. Gauntt, M. Schwenka, A. Trautman, P. Wagner, S. Kim, C. Armstrong, S. Wagner, A. Weller, K. Brighton, S. Bloom, C. Nelson, F. Suboh, C. Kolthoff, S. Dukuly, R.J. Mercader, and D.F. Hughes. 2023. Spatiotemporal variation of behavior and repeatability in a long-lived turtle. Behavioral Ecology and Sociobiology 77: 88.