Sexual selection: Fruit first, signals second
Daniel M. Hooper
Current Biology, 2026.
DOI:10.1016/j.cub.2026.05.007 & Hooper 2026 PDF
Dispatch article on: Genomic and physiological changes in a sexually selected and frugivorous bird radiation

Recent divergence and microgeographic genetic structure in an endangered Australian songbird: the southern black-throated finch
Daniel M. Hooper, Kelsie A. Lopez, Bronwyn G. Butcher, Irby J. Lovette, and Simon C. Griffith
Ecology and Evolution, 2025.
DOI:10.1002/ece3.72313 & Hooper et al 2025 PDF

Independent evolution of atypical sperm morphology in a passerine bird
Melissah Rowe, Daniel M. Hooper, Antje Hoffgaard, Laura Hurley, Callum S. McDiarmid, Ioanna Pataraia, Jan T. Lifjeld, and Simon C. Griffith
Journal of Evolutionary Biology, 2025.
DOI:10.1093/jeb/voaf087 & Rowe et al 2025 PDF

Experimental demonstration of functional divergence in mitochondrial metabolism between two finch subspecies subjected to a thermal challenge
Hector Pacheco-Fuentes, Riccardo Ton, Ondi Crino, Federico Ferraccioli, Christine Cooper, Daniel M. Hooper, and Simon C. Griffith
Journal of Evolutionary Biology, 2025.
DOI:10.1093/jeb/voaf070 & Pacheco-Fuentes et al 2025 PDF

Germline mutation rates and fine-scale recombination parameters in zebra finch
Djivan Prentout, Daria Bykova, Carla Hoge, Daniel M. Hooper, Callum S. McDiarmid, Felix Wu, Simon C. Griffith, Marc de Manuel, and Molly Przeworski
PLOS Genetics, 2025.
DOI:10.1371/journal.pgen.1011661 & Prentout et al 2025 PDF

Spread of yellow-bill-color alleles favored by selection in the long-tailed finch hybrid system
Daniel M. Hooper, Callum S. McDiarmid, Matthew J. Powers, Nicholas M. Justyn, Marek Kuċka, Nathan S. Hart, Geoffrey E. Hill, Peter Andolfatto, Yingguang Frank Chan, and Simon C. Griffith
Current Biology, 2024.
DOI:10.1016/j.cub.2024.10.019 & Hooper et al 2024 PDF

Mitonuclear interactions impact aerobic metabolism and may explain mitonuclear discordance in young, naturally hybridizing bird lineages
Callum S. McDiarmid, Daniel M. Hooper*, Antoine Stier, and Simon C. Griffith
Molecular Ecology, 33: 1-16. 2024.
DOI:10.1111/mec.17374 & McDiarmid et al 2024 PDF
*Corresponding author

Experimentally testing mate preference in an avian system with unidirectional bill colour introgression
Callum S. McDiarmid, Fiona Finch, Marianne Peso, Erica van Rooij, Daniel M. Hooper, Melissah Rowe, and Simon C. Griffith
Ecology and Evolution, 13: 1-15. 2023.
DOI:10.1002/ece3.9812 & McDiarmid et al 2023 PDF

Evaluating evidence of mitonuclear incompatibilities with the sex chromosomes in an avian hybrid zone
Kelsie A. Lopez*, Callum S. McDiarmid, Simon C. Griffith, Irby J. Lovette, and Daniel M. Hooper
Evolution, 75: 1395-1414. 2021.
DOI: 10.1111/evo.14243 & Lopez et al 2021 PDF
*Undergraduate student mentee

Taxonomy of cryptic species in the Cyornis rubeculoides complex in the Indian Subcontinent
Ashutosh Singh, Sandeep K. Gupta, Per Alström, Dhananjai Mohan, Daniel M. Hooper, Ramani S. Kumar,
Dinesh Bhatt, Pratap Singh, and Trevor D. Price
IBIS, 162: 924-935. 2020.
DOI: 10.1111/ibi.12735 & Singh et al 2020 PDF

Sex chromosome inversions enforce reproductive isolation across an avian hybrid zone
Daniel M. Hooper, Simon C. Griffith, and Trevor D. Price
Molecular Ecology, 28: 1246-1262. 2019.
Special Issue: The role of genomic structural variants in adaptation and diversification
DOI: 10.1111/mec.14874 & Hooper et al 2019 PDF

Chromosomal inversion differences correlate with range overlap in passerine birds
Daniel M. Hooper and Trevor D. Price
Nature Ecology and Evolution, 1: 1526-1534. 2017.
DOI:10.1038/s41559-017-0284-6 & Hooper and Price 2017 PDF

Two new genera of songbirds represent endemic radiations from the Shola Sky Islands of the Western Ghats, India
V. V. Robin, C. K. Vishnudas, Pooja Gupta, Frank E. Rheindt, Daniel M. Hooper, Uma Ramakrishnan, and Sushma Reddy
BMC Evolutionary Biology, 17: 31. 2017.
DOI:https://doi.org/10.1186/s12862-017-0882-6 & Robin et al 2017 PDF

Geographical variation in bill colour in the Long-tailed Finch: Evidence for a narrow zone of admixture between sub-species
Simon C. Griffith and Daniel M. Hooper
Emu - Austral Ornithology, 117. 2017.
DOI:https://doi.org/10.1080/01584197.2016.1277763 & Griffith and Hooper 2017 PDF

The Rusty-tailed Flycatcher (Muscicapa ruficauda; Aves: Muscicapidae) is a member of the genus Ficedula
Daniel M. Hooper, Urban Olsson, and Per Alström
Molecular Phylogenetics and Evolution, 102: 56-61. 2016.
DOI:10.1016/j.ympev.2016.05.036 & Hooper et al 2016 PDF

The potential role of parapatric and alloparapatric divergence in Junco speciation
Trevor D. Price and Daniel M. Hooper. 
Snowbird: Integrative Biology and Evolutionary Diversity in the Junco (Ellen D. Ketterson and Jonathan W. Atwell, eds.). University of Chicago Press. 2016.

Genomic approaches to understanding population divergence and speciation in birds
David P.L. Toews, Leonardo Campagna, Scott A. Taylor, Christopher N. Balakrishnan, Daniel T. Baldassarre, Petra E. Deane-Coe, Michael G. Harvey, Daniel M. Hooper, Darren E. Irwin, Caroline D. Judy, Nicholas A. Mason, John E. McCormack, Kevin G. McCracken, Carl H. Oliveros, Rebecca J. Safran, Elizabeth S. Scordato, Katherine F. Stryjewski, Anna Tigano, J. Albert Uy, and Benjamin M. Winger
The Auk, 133 (1): 13-30. 2016.
DOI:http://dx.doi.org/10.1642/AUK-15-51.1 & Toews et al 2016 PDF

Stable recombination hotspots in birds
Sonal Singhal, Ellen M. Leffler, Keerthi Sannareddy, Isaac Turner, Oliver Venn, Daniel M. Hooper, Alva I. Strand, Qiye Li, Brian Raney, Christopher N. Balakrishnan, Simon C. Griffith, Gil McVean, Molly Przeworski
Science,  350 (6263): 928-932. 2015.
DOI:10.1126/science.aad0843 & Singhal and Leffler et al 2015 PDF & see also Michael Lichten’s Commentary in the same issue.

Rates of karyotypic evolution in Estrildid finches differ between island and continental clades
Daniel M. Hooper and Trevor D. Price
Evolution, 69 (4): 890-903. 2015.
DOI:10.1111/evo.12633 & Hooper and Price 2015 PDF

Niche filling slows the diversification of Himalayan songbirds
Trevor D. Price, Daniel M. Hooper, Caitlyn D. Buchanan, Ulf S. Johansson, D. Thomas Tietze, Per Alström, Urban Olsson, Mousumi Ghosh-Harihar, Farah Ishtiaq, Sandeep K. Gupta, Jochen Martens, Bettina Harr, Pratap Singh, Dhananjai Mohan
Nature, 509 (7499): 222-225. 2014.
DOI:10.1038/nature13272 & Price et al 2014 PDF

Discovery of a relict lineage and monotypic family of passerine birds
Per Alström, Daniel M. Hooper, Yang Liu, Urban Olsson, Dhananjai Mohan, Magnus Gelang, Hung Le Manh, Jian Zhao, Fumin Lei, Trevor D. Price
Biology Letters, 10 (3): 20131067. 2014.
DOI:10.1098/rsbl.2013.1067 & Alström et al 2014 PDF

Ecological limits on diversification of the Himalayan core Corvoidea
Jonathan D. Kennedy, Jason T. Weir, Daniel M. Hooper, D. Thomas Tietze, Jochen Martens, Trevor D. Price
Evolution, 66 (8): 2599-2613. 2012.
DOI:10.1111/j.1558-5646.2012.01618.x & Kennedy et al 2012 PDF

Determinants of northerly range limits along the Himalayan bird diversity gradient
Trevor D. Price, Dhananjai Mohan, D. Thomas Tietze, Daniel M. Hooper, David L. Orme, Pamela C. Rasmussen
The American Naturalist, 178 (S1): S97-S108. 2011.
DOI:10.1086/661926 & Price et al 2011 PDF

Fellowships, Awards & Funding

• Australian Research Council Discovery Grant (ARC; 2023-2025): “Mitonuclear incompatibility, speciation, and the Z sex chromosome.”

• Research Initiatives in Science & Engineering Postdoctoral Fellowship - Columbia University (2019-2021): “A new and comprehensive approach to studying speciation via hybrid dysfunction.”

• Australian Research Council Discovery Grant (ARC; 2017-2021): “Hybridising long-tails to examine Large-Z effects and chromosome inversions.”

• Edward W. Rose Postdoctoral Fellowship - Cornell Lab of Ornithology (2017-2019)

• National Science Foundation (NSF) Doctoral Dissertation Improvement Grant (DDIG; 2016): “Chromosome inversions and reproductive isolation in an avian hybrid zone.”

• National Geographic Society Young Explorers Grant (2013): “The genomics of reproductive isolation in an avian hybrid zone: chromosomal rearrangements and the long-tailed finch (Poephila acuticauda sp.).”

• Henry Hinds Fund for Graduate Student Research in Evolutionary Biology (2012, 2013): “Comparative genomic analyses of chromosomal rearrangements in avian evolution: rate variation across the Estrildid finches (Estrildidae).”

• American Ornithologists' Union (AOU) Hesse Student Research Award (2012): “Chromosomal inversions and the incipient speciation of juncos (genus Junco).”

• National Science Foundation (NSF) Graduate Research Fellowship Program (GRFP; 2012)

• 'Outstanding Graduating Senior' Award from the Department of Evolution and Ecology, University of California, Davis (2010)