Microbial drivers of animal diversity

The processes that govern the formation of intimate partnerships between animals and microbes are of fundamental importance to ecosystem function, evolution and human health. I explore these processes using novel comparative biology approaches that integrate quantitative genomics, phylogenetics, ecology and physiology. As a post-doc at the University of New Hampshire, I examine how microbial diversity drives evolution and ecological function of sponge and coral hosts.

Host-imposed selection on symbiont traits

Using squid as agents of natural selection in the lab, poor (squid-naive) strains of Vibrio evolved into competent symbionts which readily colonize available hosts. This novel approach to experimental evolution, in which the squid host provides the selective pressure on naive strains, also allows us to examine the trajectory of genomic changes occurring within the evolving symbiont. Using a highly integrative approach, I further dissected the molecular, physiological and immunological processes that facilitate host adaptation from the perspectives of both symbionts. Future work will exploit tools developed here to interrogate mechanisms through which early animals navigated interactions with microbes.

Evolution of gene expression in convergent symbioses

How does natural selection navigate pre-existing genomic constraints to ultimately produce similar phenotypic solutions? My research seeks to understand if the number of possible ‘molecular solutions’ for a favorable trait is as limited as the number of phenotypic solutions. Bioluminescence via luminous symbiotic bacteria has evolved multiple times. Using target species Euprymna and Uroteuthis in a comparative transcriptomic approach, my dissertation work indicates that expression profiles for genes required for the specialized organ housing these bacteria are as similar as the profiles between organs that share an evolutionary history (eyes, brain, etc.). In so doing, we can examine whether the pressure of natural selection influences genomic resourcefulness and causes the independent deployment of similar genetic pathways during the evolution of animal-bacteria symbiosis. I continue to investigate transcriptomic convergence in sponge-microbe symbioses.

Marine systematics

Occupying nearly every marine habitat, cephalopod molluscs are a diverse and ancient class whose sophisticated behavior, crypsis and communication are unrivaled among invertebrates. Formerly the dominant large predators of paleozoic seas, the success of this group has produced clades of stunning morphological varieties. Currently, we are developing new systematics approaches to assess phylogenetic relationships (and ties between divergence rates and key genomic and morphological features) of the beguiling cnidarian and poriferan phyla.

flora & fauna


Data links provided for relevant publications. Please check Google Scholar for updated pub list.


MP Lesser, B Mueller, MS Pankey, KJ Macartney, M Slattery, JM de Goeij. Depth–dependent detritus production in the sponge, Halisarca caerulea. Limnology and Oceanography, 9999: 1-17

MP Lesser, KM Morrow, M Sabrina Pankey. N2 Fixation, and The Relative Contribution of Fixed N, in Corals from Curaçao and Hawaii. Coral Reefs 38(6):1145-58.

M Slattery, MS Pankey, MP Lesser. Annual thermal stress increases a soft coral's susceptibility to bleaching. Scientific Reports 9, Article number: 8064 .

M Belcaid, G Casaburi, SJ McAnulty, H Schmidbaur, AM Suria, S Moriano-Gutierrez, MS Pankey, TH Oakley, N Kremer, EJ Koch, AJ Collins, H Nguyen, S Lek, I Goncharenko-Foster, P Minx, E Sodergren, G Weinstock, DS Rokhsar, MN McFall-Ngai, O Simakov, JS Foster, SV Nyholm. Symbiotic organs shaped by distinct modes of genome evolution in cephalopods. PNAS Jan 2019, 201817322; DOI: 10.1073/pnas.1817322116


VE Duback, MS Pankey, RI Thomas, TL Huyck, IM Mbarani, KR Bernier, GM Cook, CA O'Dowd, JM Newcomb, WH Watson. Localization and expression of putative circadian clock transcripts in the brain of the nudibranch Melibe leonina. Comp Biochem and Physiol Part A: Molecular & Integrative Physiology 228:52-59

GM Cook, AE Gruen, J Morris, MS Pankey, A Senatore, PS Katz, WH Watson, JM Newcomb. Sequences of circadian clock proteins in the nudibranch mollusks Hermissenda crassicornis, Melibe leonina, and Tritonia diomedea. Biological Bull. 234(3):207-218

E Kayal, B Bastian, MS Pankey, AH Ohdera, M Medina, DC Plachetzki, AG Collins, JF Ryan. Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits. BMC Evol Biol 18:68

KM Morrow, AR Tedford, MS Pankey, MP Lesser. A member of the Roseobacter clade, Octadecabacter sp., is the dominant symbiont in the brittle star Amphipholis squamata. FEMS Microbiol Ecol 94(1) doi: 10.1093/femsec/fiy030

MP Lesser, KM Morrow, MS Pankey, SHC Noonan. Diazotroph diversity and nitrogen fixation in the coral Stylophora pistillata from the Great Barrier Reef. ISME J Dec 8. doi: 10.1038/s41396-017-0008-6


JK Jarett, MD MacManes, KM Morrow, MS Pankey, MP Lesser. Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa. Scientific Reports 7, Article number: 16039. doi:10.1038/s41598-017-16371-9

E Kayal, B Bastian,MS Pankey, A Ohdera, M Medina, DC Plachetzki, A Collins, JF Ryan. Comprehensive phylogenomic analyses resolve cnidarian relationships and the origins of key organismal traits . Peer J Preprints

MS Pankey, RL Foxall, IM Ster, LA Perry, BM Schuster, RA Donner, M Coyle, VS Cooper, CA Whistler. Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria. eLife 2017;6:e24414 DOI: 10.7554/eLife.24414

AR Tanner, D Fuchs, IE Winkelmann, MTP Gilbert, MS Pankey, ÂM Ribeiro, KM Kocot, KM Halanych, TH Oakley, RR da Fonseca, D Pisani, J Vinther. Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution. Proc. R. Soc. B 284 (1850) DOI: 10.1098/rspb.2016.2818

MW Kelly, MS Pankey, MB DeBiasse, DC Plachetzki. Adaptation to heat stress reduces phenotypic and transcriptional plasticity in a marine copepod. Functional Ecology 31 (2), 398-406 DOI: 10.1111/1365-2435.12725


MD Ramirez, AN Pairett, MS Pankey, JM Serb, DI Speiser, AJ Swafford, TH Oakley. The last common ancestor of most bilaterian animals possessed at least nine opsins. Genome Biol Evol 8 (12): 3640-3652. DOI: 10.1093/gbe/evw248


EI Jones, ME Afkhami, E Akçay, JL Bronstein, R Bshary, ME Frederickson, KD Heath, JD Hoeksema, JH Ness, MS Pankey, SS Porter, JL Sachs, K Scharnagl, ML Friesen. Cheaters must prosper: reconciling theoretical and empirical perspectives on cheating in mutualism. Ecology Letters 18 (11) DOI: 10.1111/ele.12507

MA Alexandrou, BJ Cardinale, JD Hall, CF Delwiche, K Fritschie, A Narwani, PA Venail, B Bentlage, MS Pankey, TH Oakley. Evolutionary relatedness does not predict competition and co-occurrence in natural or experimental communities of green algae. Proc Biol Sci 282 (1799) DOI: 10.1098/rspb.2014.1745


DI Speiser, MS Pankey, AK Zaharoff, BA Battelle, HD Bracken-Grissom, JW Breinholt, SM Bybee, TW Cronin, A Garm, AR Lindgren, NH Patel, ML Porter, ME Protas, AS Rivera, JM Serb, KS Zigler, KA Crandall, TH Oakley. Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. BMC Bioinformatics201415:350 DOI: 10.1186/s12859-014-0350-x

MS Pankey, VN Minin, GC Imholte, MA Suchard, TH Oakley. Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid. Proc Nat Acad Sci 111 (44) DOI: 10.1073/pnas.1416574111

FE Anderson, A Bergman , SH Cheng, MS Pankey, T Valinassab. 2014. Lights out: the evolution of bacterial bioluminescence in Loliginidae. Hydrobiologia 725(1): 189-203

SM Peyer, MS Pankey, TH Oakley, and MJ McFall-Ngai. 2014. Eye-specification genes in the bacterial light organ of the bobtail squid Euprymna scolopes, and their expression in response to symbiont cues. Mechanisms of development 131: 111-126

DC Plachetzki, MS Pankey, BR Johnson, EJ Ronne, A Kopp, RK Grosberg. Gene co-expression modules underlying polymorphic and monomorphic zooids in the colonial hydrozoan, Hydractinia symbiolongicarpus. Integr Comp Biol 54 (2) DOI: 10.1093/icb/icu080

TH Oakley, MA Alexandrou, R Ngo, MS Pankey, CKC Churchill, W Chen, KB Lopker. 2014. Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system. BMC Bioinformatics 15:230 DOI 10.1186/1471-2105-15-230


M Myers, MS Pankey, JP Wares. 2013. Genealogical approaches to the temporal origins of the Central American Gap. International Journal of Tropical Biology and Conservation Vol. 61 (1): 75-88


AR Lindgren*, MS Pankey*, FG Hochberg, TH Oakley. 2012. A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment. BMC Evolutionary Biology 12:129 *Authors contributed equally.


D Ramirez, DI Speiser, MS Pankey, TH Oakley. 2011. Understanding the dermal light sense in the context of integrative photoreceptor cell biology. Visual Neuroscience 28, 265-279.


MS Pankey, H Sunada, T Horikoshi, M Sakakibara. 2010. Cyclic nucleotide-gated channels are involved in phototransduction of dermal photoreceptors in Lymnaea stagnalisJournal of Comparative Physiology B 180(8), 1205-11.

AS Rivera, MS Pankey,  DC Plachetzki, C Villacorta, AE Syme, JM Serb, AR Omilian, TH Oakley. 2010. Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach. BMC Evolutionary Biology 10, 123.


MS Pankey and TH Oakley. 2009. “Evolution of animal eyes”. In: Grzimek’s Animal Life Encyclopedia: Evolution. M. Hutchins, Ed. Gale Cenage Learning, Detroit.

JP Wares, MS Pankey, F Pitombo, L Gomez-Daglio, Y Achituv. 2009. A ‘shallow phylogeny’ of shallow barnacles (Chthamalus). PLoS ONE 4(5): e5567.


TH Oakley and MS Pankey. 2008. Opening the Black Box: The Genetic and Biochemical Basis of Eye Evolution. Evolution: Education and Outreach 4(1) 390-402.

MS Pankey and JP Wares. 2008. Overdominant maintenance of diversity in the sea star Pisaster ochraceous. Journal of Evolutionary Biology 22(1) 80-87.


CDG Harley, MS Pankey, JP Wares, MJ Wonham, RK Grosberg. 2006. Color polymorphism and genetic structure in the sea star Pisaster ochraceus. Biological Bulletin 211 (3): 248-262.