Experimental demonstration of thermal differences in mitochondrial metabolism between two finch subspecies
Hector Pacheco-Fuentes, Riccardo Ton, Ondi Crino, Federico Ferraccioli, Christine Cooper, Daniel M. Hooper, and Simon C. Griffith
In Review

Independent evolution of atypical sperm morphology in a passerine bird, the red-browed finch (Neochmia temporalis temporalis)
Melissah Rowe, Daniel M. Hooper, Antje Hoffgaard, Laura Hurley, Callum S. McDiarmid, Ioanna Pataraia, Jan T. Lifjeld, and Simon C. Griffith
In Revision - see preprint on BioRxiv here.

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
Accepted PLOS Genetics - see preprint on BioRxiv here.

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

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
*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

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
*Undergraduate student mentee

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

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. 2018.
DOI: 10.1111/ibi.12735

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

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

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

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

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

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

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

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

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

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

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

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)