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Dr Daniel Thomas staff profile picture

Contact details +6492136595

Dr Daniel Thomas PhD, BSc(Hons)

Senior Lecturer in Zoology and Ecology

Doctoral Supervisor
School of Natural Sciences

My research group studies modern and fossil bone to contributes new knowledge about the biology and origins of birds. We discover new species that explain the evolutionary history of penguins and reveal the deep time origins of taonga seabird species. Our investigations into the biology of penguins have led to the discovery of adaptations for foraging and visual communication. We specialise in using technologies and methods from ecology, chemistry, engineering and statistics in my biological analyses. For example, have recently developed a new method for analysing bone shape that is available freely as the R package morphoBlocks.

Professional

Contact details

  • Ph: DDL +64 9 2136595
    Location: 50.03, Building 50
    Campus: Albany

Qualifications

  • Doctor of Philosophy - University of Otago (2009)
  • Bachelor of Science (Honours) - University of Otago (2005)

Certifications and Registrations

  • Licence, Supervisor, Massey University

Prizes and Awards

  • Unlocking Curious Minds Funding - Ministry of Business, Innovation and Employment, New Zealand. (2017)
  • Catalyst: Seeding General grant - Royal Society of New Zealand (2017)

Research Expertise

Research Interests

370506 - Palaeontology (incl. palynology)
310401 - Animal systematics and taxonomy
310402 - Biogeography and phylogeography

Area of Expertise

Field of research codes
Biological Sciences (060000):
Earth Sciences (040000): Geology (040300): Palaeontology (incl. Palynology) (040308):
Vertebrate Biology (060809): Zoology (060800)

Keywords

3D scanning, birds, evolution, fossils, geometric morphometrics, museum collections research, systematics

Research Projects

Summary of Research Projects

Position Current Completed
Project Leader 0 9

Completed Projects

Project Title: Local taonga as the nexus for STEM introduction

Date Range: 2019 - 2019

Funding Body: Ministry of Business, Innovation and Employment

Project Team:

Project Title: O tatou tamariki, nga Kaitiaki Taiao. Our children, our environmental guardians (Unlocking Curious Minds)

Date Range: 2017 - 2017

Funding Body: Ministry of Business, Innovation and Employment

Project Team:

Research Outputs

Journal

Thomas, DB., Harmer, AMT., Giovanardi, S., Holvast, EJ., McGoverin, CM., & Tenenhaus, A. (2023). Constructing a multiple-part morphospace using a multiblock method. Methods in Ecology and Evolution. 14(1), 65-76
[Journal article]Authored by: Thomas, D.
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Holvast, EJ., & Thomas, DB. (2022). Taxonomic classification of seabird long bones using 3D shape: A method with wider potential in zooarchaeology. Journal of Archaeological Science: Reports. 45
[Journal article]Authored by: Thomas, D.
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Cole, TL., Zhou, C., Fang, M., Pan, H., Ksepka, DT., Fiddaman, SR., . . . Zhang, G. (2022). Genomic insights into the secondary aquatic transition of penguins. Nature Communications. 13(1)
[Journal article]Authored by: Thomas, D.
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Hadden, PW., Ober, WC., Gerneke, DA., Thomas, D., Scadeng, M., McGhee, CNJ., . . . Zhang, J. (2022). Micro-CT guided illustration of the head anatomy of penguins (Aves: Sphenisciformes: Spheniscidae). Journal of Morphology. 283(6), 827-851
[Journal article]Authored by: Thomas, D.
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1
Giovanardi, S., Ksepka, DT., & Thomas, DB. (2021). A giant Oligocene fossil penguin from the North Island of New Zealand. Journal of Vertebrate Paleontology. 41(3)
[Journal article]Authored by: Thomas, D.
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Tay, EJ., Barnsley, JE., Thomas, DB., & Gordon, KC. (2021). Elucidating the resonance Raman spectra of psittacofulvins. Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy. 262
[Journal article]Authored by: Thomas, D.
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1
Thomas, DB., Tennyson, AJD., Scofield, RP., Heath, TA., Pett, W., & Ksepka, DT. (2020). Ancient crested penguin constrains timing of recruitment into seabird hotspot: Penguin recruitment into seabird hotspot. Proceedings of the Royal Society B: Biological Sciences. 287(1932)
[Journal article]Authored by: Thomas, D.
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Harmer, A., & Thomas, D. (2019). pathtrackr: An r package for video tracking and analysing animal movement. Methods in Ecology and Evolution. 10(8), 1196-1202
[Journal article]Authored by: Thomas, D.
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Thomas, DB., Ksepka, DT., Holvast, EJ., Tennyson, AJD., & Scofield, P. (2020). Re-evaluating New Zealand’s endemic Pliocene penguin genus. New Zealand Journal of Geology and Geophysics. 63(3), 324-330
[Journal article]Authored by: Thomas, D.
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Cole, TL., Ksepka, DT., Mitchell, KJ., Tennyson, AJD., Thomas, DB., Pan, H., . . . Waters, JM. (2019). Mitogenomes uncover extinct penguin taxa and reveal island formation as a key driver of speciation. Molecular Biology and Evolution. 36(4), 784-797
[Journal article]Authored by: Thomas, D.
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Thomas, DB., & McGraw, KJ. (2018). Hidden carotenoids in the powder down of herons. Journal of Ornithology. 159(3), 785-792
[Journal article]Authored by: Thomas, D.
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3
Barnsley, JE., Tay, EJ., Gordon, KC., & Thomas, DB. (2018). Frequency dispersion reveals chromophore diversity and colour-tuning mechanism in parrot feathers. Royal Society Open Science. 5(7)
[Journal article]Authored by: Thomas, D.
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Thomas, DB., & Ksepka, DT. (2016). The Glen Murray fossil penguin from the North Island of New Zealand extends the geographic range of Kairuku. Journal of the Royal Society of New Zealand. 46(3-4), 200-213
[Journal article]Authored by: Thomas, D.
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2
Webb, WH., Brunton, DH., Aguirre, JD., Thomas, DB., Valcu, M., & Dale, J. (2016). Female song occurs in songbirds with more elaborate female coloration and reduced sexual dichromatism. Frontiers in Ecology and Evolution. 4(MAR)
[Journal article]Authored by: Aguirre-Davies, J., Dale, J., Thomas, D., Webb, W.
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Thomas, DB., Hiscox, JD., Dixon, BJ., & Potgieter, J. (2016). 3D scanning and printing skeletal tissues for anatomy education. Journal of Anatomy. 229(3), 473-481
[Journal article]Authored by: Potgieter, J., Thomas, D.
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Thomas, DB., & James, HF. (2016). Nondestructive Raman spectroscopy confirms carotenoid-pigmented plumage in the Pink-headed Duck. Auk. 133(2), 147-154
[Journal article]Authored by: Thomas, D.
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Thomas, DB., & McGoverin, CM. (2016). The analytical niche for Raman spectroscopy in biological pigment research. Spectroscopy Europe. 28(1), 6-9
[Journal article]Authored by: Thomas, D.
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Aguirre, JD., Bollard-Breen, B., Cameron, M., Constantine, R., Duffy, CAJ., Dunphy, B., . . . Wilson, R. (2016). Loved to pieces: Toward the sustainable management of the Waitematā Harbour and Hauraki Gulf. Regional Studies in Marine Science. 8, 220-233
[Journal article]Authored by: Aguirre-Davies, J., Liggins, L., Smith, A., Thomas, D.
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Thomas, DB., Hauber, ME., Hanley, D., Waterhouse, GIN., Fraser, S., & Gordon, KC. (2015). Analysing avian eggshell pigments with Raman spectroscopy. Journal of Experimental Biology. 218(17), 2670-2674
[Journal article]Authored by: Thomas, D.
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Thomas, DB. (2014). Ancient origins and multiple appearances of carotenoid-pigmented feathers in birds. Proceedings. Biological sciences / The Royal Society. 281(1788), 20140806
[Journal article]Authored by: Thomas, D.
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Thomas, DB., Nascimbene, PC., Dove, CJ., Grimaldi, DA., & James, HF. (2014). Seeking carotenoid pigments in amber-preserved fossil feathers. Scientific Reports. 4
[Journal article]Authored by: Thomas, D.
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Canoville, A., Thomas, DB., & Chinsamy, A. (2014). Insights into the habitat of Middle Permian pareiasaurs (Parareptilia) from preliminary isotopic analyses. Lethaia. 47(2), 266-274
[Journal article]Authored by: Thomas, D.
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France, CAM., Thomas, DB., Doney, CR., & Madden, O. (2014). FT-Raman spectroscopy as a method for screening collagen diagenesis in bone. Journal of Archaeological Science. 42(1), 346-355
[Journal article]Authored by: Thomas, D.
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Thomas, DB., McGraw, KJ., James, HF., & Madden, O. (2014). Non-destructive descriptions of carotenoids in feathers using Raman spectroscopy. Analytical Methods. 6(5), 1301-1308
[Journal article]Authored by: Thomas, D.
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Thomas, DB., & Ksepka, DT. (2013). A history of shifting fortunes for African penguins. Zoological Journal of the Linnean Society. 168(1), 207-219
[Journal article]Authored by: Thomas, D.
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Thomas, DB., McGoverin, CM., McGraw, KJ., James, HF., & Madden, O. (2013). Vibrational spectroscopic analyses of unique yellow feather pigments (spheniscins) in penguins. Journal of the Royal Society Interface. 10(83)
[Journal article]Authored by: Thomas, D.
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Thomas, DB., Fordyce, RE., & Gordon, KC. (2013). Evidence for a krill-rich diet from non-destructive analyses of penguin bone. Journal of Avian Biology. 44(2), 203-207
[Journal article]Authored by: Thomas, D.
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Ksepka, DT., & Thomas, DB. (2012). Multiple cenozoic invasions of Africa by penguins (Aves, Sphenisciformes). Proceedings of the Royal Society B: Biological Sciences. 279(1730), 1027-1032
[Journal article]Authored by: Thomas, D.
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24
Chinsamy, A., Tunogllf, C., & Thomas, DB. (2012). Dental microstructure and geochemistry of Mosasaurus hoffmanni (Squamata: Mosasauridae) from the Late Cretaceous of Turkey. Bulletin de la Societe Geologique de France. 183(2), 85-92
[Journal article]Authored by: Thomas, D.
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Thomas, DB., Chinsamy, A., Conard, NJ., & Kandel, AW. (2012). Chemical investigation of mineralisation categories used to assess taphonomy. Palaeogeography, Palaeoclimatology, Palaeoecology. 361-362, 104-110
[Journal article]Authored by: Thomas, D.
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Chinsamy, A., Thomas, DB., Tumarkin-Deratzian, AR., & Fiorillo, AR. (2012). Hadrosaurs Were Perennial Polar Residents. Anatomical Record. 295(4), 610-614
[Journal article]Authored by: Thomas, D.
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Thomas, DB., & Fordyce, RE. (2012). Biological Plasticity in Penguin Heat-Retention Structures. Anatomical Record. 295(2), 249-256
[Journal article]Authored by: Thomas, D.
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Fukuda, K., Thomas, DB., Frew, RD., & Fordyce, RE. (2012). Antarctic glaciation recorded in Early Miocene New Zealand foraminifera. Marine Micropaleontology. 92-93, 52-60
[Journal article]Authored by: Thomas, D.
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Thomas, DB., McGoverin, CM., Chinsamy, A., & Manley, M. (2011). Near infrared analysis of fossil bone from the Western Cape of South Africa. Journal of Near Infrared Spectroscopy. 19(3), 151-159
[Journal article]Authored by: Thomas, D.
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Thomas, DB., & Chinsamy, A. (2011). Chemometric analysis of EDXRF measurements from fossil bone. X-Ray Spectrometry. 40(6), 441-445
[Journal article]Authored by: Thomas, D.
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Thomas, DB., Ksepka, DT., & Fordyce, RE. (2011). Penguin heat-retention structures evolved in a greenhouse Earth. Biology Letters. 7(3), 461-464
[Journal article]Authored by: Thomas, D.
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Thomas, DB., McGoverin, CM., Fordyce, RE., Frew, RD., & Gordon, KC. (2011). Raman spectroscopy of fossil bioapatite - A proxy for diagenetic alteration of the oxygen isotope composition. Palaeogeography, Palaeoclimatology, Palaeoecology. 310(1-2), 62-70
[Journal article]Authored by: Thomas, D.
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Fordyce, RE., & Thomas, DB. (2011). Kaiika maxwelli, a new early eocene archaic penguin (Sphenisciformes, Aves) from Waihao Valley, South Canterbury, New Zealand. New Zealand Journal of Geology and Geophysics. 54(1), 43-51
[Journal article]Authored by: Thomas, D.
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Thomas, DB., & Schallenberg, M. (2008). Benthic shear stress gradient defines three mutually exclusive modes of non-biological internal nutrient loading in shallow lakes. Hydrobiologia. 610(1), 1-11
[Journal article]Authored by: Thomas, D.
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Thomas, DB., & Fordyce, RE. (2007). The heterothermic loophole exploited by penguins. Australian Journal of Zoology. 55(5), 317-321
[Journal article]Authored by: Thomas, D.
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Thomas, DB., Fordyce, RE., Frew, RD., & Gordon, KC. (2007). A rapid, non-destructive method of detecting diagenetic alteration in fossil bone using Raman spectroscopy. Journal of Raman Spectroscopy. 38(12), 1533-1537
[Journal article]Authored by: Thomas, D.
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Book

Burns, KJ., McGraw, KJ., Shultz, AJ., Stoddard, MC., & Thomas, DB. (2017). Advanced methods for studying pigments and coloration using avian specimens. In The Extended Specimen: Emerging Frontiers in Collections-Based Ornithological Research. (pp. 23 - 57).
[Chapter]Authored by: Thomas, D.
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Conference

Harmer, AMT., & Thomas, DB.pathtrackr: An r package for video tracking and analysing animal movement.
[Conference Oral Presentation]Authored by: Thomas, D.
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Chandler, L., Qian, J., Wu, O., & Thomas, DB. (2014). Novel 1064 dispersive confocal Raman microscope for pigment identification at sub-micron spatial scales. , SCIX Conference 2014
[Conference Abstract]Authored by: Thomas, D.
Thomas, DB., & Ksepka, DT. (2014). The Glen Murray penguin, an Oligocene giant from the North Island. , Geosciences 2014 Conference
[Conference Abstract]Authored by: Thomas, D.
Thomas, DB., James, HF., & McGraw, KJ. (2013). Non-destructive, in situ analysis of avian plumage pigments using Raman spectroscopy.. , Joint meeting of American Ornithologists’ Union and Cooper Ornithological Society
[Conference Abstract]Authored by: Thomas, D.
Thomas, DB., McGraw, KJ., McGoverin, CM., & James, HF. (2013). Vibrational spectroscopic analyses of unique yellow feather pigments (spheniscins) in penguins.. , Joint meeting of American Ornithologists’ Union and Cooper Ornithological Society.
[Conference Abstract]Authored by: Thomas, D.

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Chandler, L., Qian, J., Wu, O., & Thomas, DB. (2013). Novel 1064 nm dispersive Raman spectrometer and Raman microscope for non-invasive pigment analysis.. , 7th International Conference on the application of Raman spectroscopy in Art and Archaeology Ljubljana, Slovenia: Institute for the Protection of Cultural Heritage of Slovenia
[Conference Abstract]Authored by: Thomas, D.
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Thomas, DB., James, HF., Carrano, MT., & Madden, O. (2012). SEARCHING FOR EVIDENCE OF FOSSIL FEATHER COLOR WITH SPECTROSCOPY. In JOURNAL OF VERTEBRATE PALEONTOLOGY Vol. 32 (pp. 183 - 184). , 72nd Annual Meeting of the Society-of-Vertebrate-Paleontology: TAYLOR & FRANCIS INC
[Conference Abstract]Authored by: Thomas, D.
Thomas, DB., McGoverin, CM., & Chinsamy, A. (2011). Near Infrared Spectroscopy of fossil antelope bone from South Africa. , 15th International Conference on Near Infrared Spectroscopy
[Conference Abstract]Authored by: Thomas, D.
Ksepka, D., & Thomas, D. (2011). EVIDENCE FOR MULTIPLE CENOZOIC INVASIONS OF AFRICA BY PENGUINS (AVES, SPHENISCIFORMES). In JOURNAL OF VERTEBRATE PALEONTOLOGY Vol. 31 (pp. 139 - 139). : SOC VERTEBRATE PALEONTOLOGY
[Conference Abstract]Authored by: Thomas, D.
Thomas, D., Brink, J., & Chinsamy-Turan, A. (2011). CHEMICAL EVIDENCE DEMONSTRATES A THERMAL SPRING DEPOSITIONAL ENVIRONMENT FOR THE FLORISBAD HOMININE SKULL. In JOURNAL OF VERTEBRATE PALEONTOLOGY Vol. 31 (pp. 204 - 204). : SOC VERTEBRATE PALEONTOLOGY
[Conference Abstract]Authored by: Thomas, D.
Thomas, DB. (2010). Evolution of heat retention in penguins. , 70th Society of Vertebrate Paleontology Annual Meeting: Pittsburgh PA, USA
[Conference Abstract]Authored by: Thomas, D.
Fox-Dobbs, K., Thomas, DB., & Koch, P. (2010). Paleoenvironmental and paleoecological interpretations of isotopic records derived from Eastern Beringian caribou antlers. , 70th Society of Vertebrate Paleontology Annual Meeting
[Conference Abstract]Authored by: Thomas, D.
Chinsamy, A., Tumarkin-Deratzian, A., Thomas, DB., & Fiorillo, A. (2010). The bone microstructure of the polar hadrosaurs from the North Slope of Alaska. Oral presentation.. , 70th Society of Vertebrate Paleontology Annual Meeting
[Conference Abstract]Authored by: Thomas, D.
Thomas, DB., Chinsamy, A., McGoverin, CM., & Manley, M. (2010). Fossil preservation at Swartklip 1 and Elandsfontein Main. , Langebaanweg 2010, changing landscapes and biotas of the Cape West Coast.
[Conference Abstract]Authored by: Thomas, D.
Thomas, DB., McGoverin, CM., Fordyce, RE., Frew, RD., & Gordon, KC. (2009). Analytical quality of fossil bone established using Raman spectroscopy. , Climatic and Biotic Events of the Paleogene Conference
[Conference Abstract]Authored by: Thomas, D.
Thomas, D., Gordon, K., Fordyce, RE., & Frew, R. (2008). RAMAN SPECTROSCOPY OF FOSSIL AND SYNTHETIC APATITES TRACKS DIAGENETIC ALTERATION IN FOSSIL BONE USED FOR ISOTOPE STUDIES. In JOURNAL OF VERTEBRATE PALEONTOLOGY Vol. 28 (pp. 151A - 152A). , 68th Annual Meeting of the Society-of-Vertebrate-Paleontology: SOC VERTEBRATE PALEONTOLOGY
[Conference Abstract]Authored by: Thomas, D.
Thomas, DB., Fordyce, RE., & Frew, RD. (2007). Oxygen isotopic evidence for the evolution of the humeral plexus. , Sixth International Penguin Conference
[Conference Abstract]Authored by: Thomas, D.
Thomas, DB., Fordyce, RE., & Frew, RD. (2007). Preliminary findings from an investigation into the origin of penguin wing regional heterothermy. , Fifth Conference on the Secondary Adaptations of Tetrapods to Life in Water,
[Conference Abstract]Authored by: Thomas, D.

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Other

Harmer, AMT., & Thomas, DB. (2017). pathtrackr: An R package for video tracking and analysing animal movement.
[Other]Authored by: Thomas, D.

Teaching and Supervision

Teaching Statement

Teaching Contributions

199103 Animals and the Environment (Lecturer, Offering Coordinator)

199212 Vertebrate Zoology (Lecturer, Course Coordinator)

199330 Ornithology (Lecturer)

Courses Coordinated

Contact Supervisor

Graduate Supervision Statement

Examples of recent student topics:

  • Simone Giovanardi (PhD, Massey University). “The Shape of Penguins in Four Dimensions”.
  • Emma Holvast (MSc, Massey University). “Taxonomic Predictions of Seabird Identity using 3D Bone Shape”.
  • Nathan Michael (PhD, University of Akron). “The Influence of Diet and Foraging Behavior on Carotenoid Ornaments in the Brown Booby (Sula leucogaster)”.
  • Kaya Cooper (MSc, Massey University). “Ten Years After Pest Eradication: Little Penguins (Eudyptyla minor) at Tāwharanui Regional Park”.

Examples of potential student topics:

  • Theseus’ Shipwright: Identifying Variation in Evolutionary Rates Within a Skeleton (suits MSc or PhD).
  • History Repeating? Using Pliocene Fossils to Gain Insight into the Next Warm World Fauna (suits PhD).
  • Mātauranga Māori and the Fossil Record: Developing a Best Practice Guide for Paleontological Research in Aotearoa (suits MSc or PhD).
  • Low Cost, Large Sample Size Analysis of Tiny Bones for Exploring Important Sources of Shape Variation (suits MSc).
  • Developing Capability in 21st Century Natural History (topics including Advanced Statistical Methods, 3D Scanning and Printing, Shape Analysis) (suits undergraduate research student or can contribute to MSc).


Dr Daniel Thomas is available for Masters and Doctorial supervision.

Summary of Doctoral Supervision

Position Current Completed
Main Supervisor 0 1
Co-supervisor 0 1

Completed Doctoral Supervision

Main Supervisor of:

  • 2022 - Simone Giovanardi - Doctor of Philosophy
    The Shape of Penguins in Four Dimensions Assessing macroevolutionary shifts in a constructional morphology framework

Co-supervisor of:

  • 2020 - Wesley Webb - Doctor of Philosophy
    New horizons for female birdsong: evolution, culture and analysis tools

Media and Links

Media

  • 30 May 2014 - Online
    Smithsonian Science: Carotenoids in feathers
    http://smithsonianscience.org/2014/05/feather-pigments/
  • 28 Nov 2015 - Radio
    Fossil find reveals new giant penguin
    Radio New Zealand interview
  • 28 Nov 2014 - Newspaper
    Ancient penguin was a giant of NZ birdlife
    New Zealand Herald interview
  • 22 Apr 2013 - Online
    Smithsonian Science: Yellow Penguin Feathers
    http://smithsonianscience.org/2013/04/yellow-pigment-in-penguin-feathers-is-chemically-distinct-spectoscopic-studies-show/
  • 11 Sep 2014 - Newspaper
    Rare penguin fossil gets 3D scanning treatment
    Waikato Times interview

Other Links

  • Fauna Tookit - A portal to 3D digitised models of bird bones from museum collections.