My research focuses on explanation, causation, and individuality, predominantly in the areas of evolutionary biology, ecology, and medicine. I have interrelated projects which involve trying to understand and characterize the various explanatory patterns and strategies used by researchers in the life sciences, and the corresponding features of causal reasoning employed in these domains. My goal is to contribute to an account of explanation that better reflects the multifaceted nature of scientific explanation in practice. In a related set of projects, I seek to uncover and clarify connections between biological individuality, symbiosis, and the complexity and diversity of life. I have started to expand this work by looking at changing notions of health and the environment in the face of recent advances in microbiome research. My overall research program is largely interdisciplinary in nature, both through drawing on my background in biology and philosophy, and through collaboration with other scientists and philosophers.

Academic Publications

21) “Trojan Horses and Black Queens (2019) Causal Core Explanations in Microbiome Research.” Skillings, D. Biology & Philosophy.

20) O'Malley, MA, and Skillings DJ (2018) Methodological strategies in microbiome research and their explanatory implications. Perspectives on Science. 26(2): 239-265.

19) Skillings, DJ and K Hooks (2018) Microbiomes and Holobionts. Encyclopedia of Ecology, 2nd Edition. Elsevier. 

18) Crandall ED, Toonen RJ, ToBo Laboratory, Skillings DJ and Selkoe KA (2018) A Coalescent Sampler Successfully Detects Biologically Meaningful Population Structure Overlooked by F-Statistics. Evolutionary Applications. 

17) Skillings, DJ (2016) Holobionts and the Ecology of Organisms - Multi-Species Communities or Integrated Individuals? Biology & Philosophy. 31: 875. 

16) Skillings, DJ (2015) Mechanistic Explanation of Biological Processes. Philosophy of Science 82: 1139-1151.​

15) Selkoe KA, Gaggiotti OE, Treml EA, Wren JLK, Donovan MK, Andrews KA, Baums I, Bird CE, Bolick H, Bowen B, Coleman R, Craig MT, Daly-Engel TS, DiBattista JD, Eble J, Fernandez-Silva I, Franklin EC, Gaither MR, Iacchei M, Rocha LA, Skillings D, Santos SR, Timmers M, Wedding L, Williams GJ, Whitney NM, Toonen RJ (2016) The DNA of Coral Reef Biodiversity: Predicting and Protecting Genetic Diversity of Reef Assemblages.Proc. R. Soc. B. 283:20160354.

14) Kaleonani, KC Hurley, Molly A. Timmers, L. Scott Godwin, Joshua M. Copus, Derek. J. Skillings, Robert J. Toonen (2015) An assessment of shallow and mesophotic reef brachyuran crab assemblages on the south shore of Oahu, Hawaii. Coral Reefs. DOI: 10.1007 / s00338-015-1382-z

13) KA Selkoe, OE Gaggiotti, K. Andrews, MA Bernal, C. Bird, H. Bolick, I. Baums, R. Coleman, GT Concepcion, MT Craig, JD DiBattista, J. Eble, I. Fernandez-Silva, Mr. R. Gaither, Mr. Iacchei, NR Polato, MA Rivera, LA Rocha, D. Skillings, Timmers M., Z. Szabo, BW Bowen, RJ Toonen (2014)  Emerging Patterns of Population Genetics Structure for a Coral Reef Community. Molecular Ecology . DOI: 10.1111 / mec.12804.

12) Skillings, DJ, CE Bird, and RJ Toonen (2014) Comparative population structure of two edible Indo-Pacific coral reef sea cucumbers (Echinodermata: Holothuroidea). Bulletin of Marine Science . 90 (1). DOI: 10.5343 / bms.2013.1001.

11) Bowen, BW, Rocha, LA, Bird, CJ, Skillings, DS, Eble, JA, DiBattista, JD, Craig, MT, and RJ Toonen (2013) The Origins Of Tropical Marine Biodiversity. Trends in Ecology and Evolution .
10) DiBattista, JD, Berumen, ML, Gaither, MR, Rocha, LA, Eble, JA, Choat, JH, Craig, MT, Skillings, DJ and Bowen BW. (2013)  After continents divide: Comparative phylogeography of reef fishes from the Red Sea and Indian Ocean . Journal of Biogeography . 

9) Timmers, MA, Bird C, Skillings D, Smouse P, Toonen R (2012).  There's no place like this: Crown-of-thorns outbreaks in the Central Pacific are regionally derived and independent events . PLoS ONE .7 (2). 

8) Bird, CE, I. Fernandez, D. Skillings, & R. Toonen (2012)  Sympatric speciation in the post "Modern Synthesis" era of evolutionary biology . Evolutionary Biology . 39: 158-180.

7) Stat, M., A. Baker, D. Bourne, A. Correa, Z. Forsman, M. Huggett, X. Pochon, D. Skillings, C. Starger, R. Toonen, M. van Oppen, & R Gates (2012). Molecular delineation of species in the coral holobiont  Advances in Marine Biology . 

6) Toonen, RJ, K. Andrews, I. Baums, C. Bird, G. Concepcion, T. Daly-Engel, J. Eble, A. Faucci, M. Gaither, M. Iacchei, J. Puritz, J. Schultz, D. Skillings, Timmers & B. Bowen (2011) Defining boundaries for ecosystem-based management: A multispecies case study of marine connectivity across the Hawaiian Archipelago . Journal of Marine Biology. ID # 460173, 13 pp. 

5) Skillings, DJ, CE Bird, & RJ Toonen (2011)  Gateways to Hawai'i: genetic population structure of the tropical sea cucumber Holothuria atra . Journal of Marine Biology , ID # 783030, 16 pp. 

4) Toonen, RJ, CE Bird, J. Eble, A. Faucci, G. Concepcion, K. Andrews, D. Skillings, M. Iacchei, I. Baums, and BW Bowen. (2010) Where have all the larvae gone? Patterns of connectivity in the Hawaiian Archipelago . in Diving for Science.Proceedings of the American Academy of Underwater Science In: NW Pollock (ed). Diving for Science 2010. Proceedings of the 29th American Academy of Underwater Sciences Symposium . Dauphin Island, AL: AAUS.

3) Skillings, DJ, and RJ Toonen (2010)  It's just a flesh wound: no lethal sampling for conservation genetics studies . in Diving for Science. Proceedings of the American Academy of Underwater Science In: NW Pollock (ed). Diving for Science 2010. Proceedings of the 29th American Academy of Underwater Sciences Symposium . Dauphin Island, AL: AAUS.

2) Kittinger, JN, DJ Skillings, KL Carvalho, LLN Reeve, Hutchinson M, Cullison K, Shackeroff J, Chow M, Lemus J (2009) Reconciling ecosystem-based management and focal resource conservation in the Papahanaumokuakea Marine National Monument . Marine Sanctuaries Conservation Series ONMS-09-04 . NOAA, Office of National Marine Sanctuaries

1) Skillings, D. (2008)  Laboratory culture of the soft-coral  Carijoa riisei . Journal of Young Investigators . 15: 8.


Popular Media

"What constitutes an individual organism in nature?" Aeon Magazine. Oct, 2017.


"I, holobiont. Are you and your microbes a community or a single entity?" Aeon Magazine. September, 2018.   


​Book Reviews

Adrian Currie’s Rock, Bone, and Ruin: An Optimist’s Guide to the Historical Sciences.    Notre Dame Philosophical Reviews. (2018).

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