Department of Biological Sciences

• Invertebrate taxonomy & systematics
• Genomics
• Phylogenetics
• Biomineralization

1. Sun, J., R. Li, C. Chen, J.D. Sigwart, and K.M. Kocot, 2021. Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes. Philosophical Transactions of the Royal Society B 376: 1825.
2. Davis-Berg, E.C. and K.M. Kocot. 2021. Innovation in teaching and learning invertebrate zoology in remote and online classrooms. Invertebrate Biology: e12329.
3. Cobo, M.C.* and K.M. Kocot. 2021. On the diversity of abyssal Dondersiidae (Mollusca, Aplacophora) with the description of a new genus, seven new species, and a review of the family. Zootaxa 4933(1): 63-97.
4. Varney, R.M.*, D.I. Speiser, C. McDougall, B.M. Degnan, and K.M. Kocot. 2021. The iron responsive genome of the chiton Acanthopleura granulata (Mollusca, Aculifera). Genome Biology and Evolution 13(1): evaa263.
5. Varney, R.M.*, B. Brenzinger, M.A.E. Malaquias, C.P. Meyer, M. Schrödl, and K.M. Kocot. 2021. Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics. BMC Evolutionary Biology 21:6.
6. Ramírez-Guerrero, G.M., K.M. Kocot, and C.B. Cameron. 2020. Zooid morphology and molecular phylogeny of the graptolite Rhabdopleura annulata (Hemichordata, Pterobranchia) from Heron Island, Australia. Canadian Journal of Zoology 98(12):844-849.
7. Kong, L., Y. Li, K.M. Kocot, Y. Yang, L. Qi, Q. Li, and K.M. Halanych. 2020. Mitogenomics reveals phylogenetic relationships of Arcoida (Mollusca, Bivalvia) and multiple independent expansions and contractions in mitochondrial genome size. Molecular Phylogenetics and Evolution 150:106857.
8. Cobo, M.C.* and M. Kocot. 2020. Micromenia amphiatlantica sp. nov.: First solenogaster (Mollusca, Aplacophora) with an amphi-Atlantic distribution and insight into abyssal solenogaster diversity. Deep Sea Research Part I.
9. Kocot, K.M., A.J. Poustka, I. Stöger, K.M. Halanych, and M. Schrödl. 2020. New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships. Scientific Reports 10:101.
10. Laumer, C.E., R. Fernández, S. Lemer, D. Combosch, M. Kocot, A. Riesgo, S.C.S. Andrade, W. Sterrer, M.V. Sørensen, and G. Giribet. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proceedings of the Royal Society B: Biological Sciences 286: 20190831.
11. Varney, R.M.*, P. Funch, M. Kocot, and M.V. Sørensen. 2019. A new species of Echinoderes (Cyclorhagida: Echinoderidae) from the San Juan Islands, Washington State, USA, and insights into the kinorhynch transcriptome. Zoologischer Anzeiger 282: 52-63.
12. Smythe, A.B., O. Holovachov, and M. Kocot. 2019. Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny. BMC Evolutionary Biology 19:121.
13. Sogabe, S., W. L. Hatleberg, M. Kocot, T. E. Say, D. Stoupin, K. Roper, S. Fernandez-Valverde, S. M. Degnan, and B. M. Degnan. 2019. Pluripotency and the origin of animal multicellularity. Nature. 570: 519-522.
14. Kocot, K.M., C. Todt, N.T. Mikkelsen, and K.M. Halanych. 2019. Phylogenomics of Aplacophora (Mollusca, Aculifera) and a solenogaster without a foot. Proceedings of the Royal Society B: Biological Sciences 286(1902):20190115.
15. Mikkelsen, N.T., C. Todt, M. Kocot, K.M. Halanych, and E. Willassen. 2018. Molecular phylogeny of Caudofoveata (Mollusca) challenges traditional views. Molecular Phylogenetics and Evolution 132: 138-150.
16. Galaska, M.P., Y. Li, M. Kocot, A.R. Mahon, and K.M. Halanych. 2019. Conservation of mitochondrial genome arrangements in brittle stars (Echinodermata, Ophiuroidea). Molecular Phylogenetics and Evolution 130:115-120.
17. Li, Y., M. Kocot, M.G. Tassia, J.T. Cannon, M. Bernt, and K.M. Halanych. 2018. Mitogenomics reveals a novel genetic code in Hemichordata. Genome Biology and Evolution evy254.
18. Pabst, E.A.* and M. Kocot. 2018. Phylogenomics confirms monophyly of Nudipleura (Gastropoda: Heterobranchia). Journal of Molluscan Studies 84(3): 259–265.
19. Mikkelsen, N.T., M. Kocot, and K.M. Halanych. 2018. Mitogenomics reveals phylogenetic relationships of caudofoveate aplacophoran molluscs. Molecular Phylogenetics and Evolution. 127: 429-436.
20. Rodriguez, J., T.P. Jones, P. Sierwald, P.E. Marek, W.A. Shear, M.S. Brewer, M. Kocot, and J.E. Bond. 2018. Step-wise evolution of complex chemical defenses in millipedes: a phylogenomic approach. Scientific Reports 8: 3209.
21. Kocot, K.M., Tassia, M.G., Halanych, K.M. and Swalla, B.J., 2018. Phylogenomics offers resolution of major tunicate relationships. Molecular Phylogenetics and Evolution 121: 166-173.
22. Kersken, D., M. Kocot, D. Janussen, T. Schell, M. Pfenninger, and P.M. Arbizu. 2018. First insights into the phylogeny of deep-sea glass sponges (Hexactinellida) from polymetallic nodule fields in the Clarion-Clipperton Fracture Zone (CCFZ), northeastern Pacific. Hydrobiologia 108: 101-112.
23. Whelan, N.V., M. Kocot, T. P. Moroz, K. Mukherjee, P. Williams, G. Paulay, L. L. Moroz and K. M. Halanych. 2017. Ctenophore relationships and their placement as the sister group to all other animals. Nature Ecology & Evolution 1(11): 1737.
24. Marlow, J., Borrelli, C., Jungbluth, S.P., Hoffman, C., Marlow, J., Girguis, P.R., and the AT36 Team. 2017. Opinion: Telepresence is a potentially transformative tool for field science. Proceedings of the National Academy of Sciences 114: 4841-4844.
25. Hall, M.R., M. Kocot, K.W. Baughman, S.L. Fernandez-Valverde, M.E.A. Gauthier, W.L. Hatleberg, A. Krishnan, C. McDougall, C.A. Motti, E. Shoguchi, T. Wang, X. Xiang, M. Zhao, U. Bose, C. Shinzato, K. Hisata, M. Fujie, M. Kanda, S.F. Cummins, N. Satoh, S.M. Degnan, and B.M. Degnan. 2017. The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest. Nature 544: 231-234.
26. Halanych, K.M. and M. Kocot. 2017. Genome evolution: Shellfish genes. Nature Ecology and Evolution 1:0142.
27. Voolstra, C.R., GIGA Community of Scientists, G. Wörheide, and J.V. Lopez. 2017. Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA). Invertebrate Systematics, 31(1): 1-7.
28. Tanner, A.R., D. Fuchs, I.E. Winkelmann, M.T.P. Gilbert, M.S. Pankey, A.M. Ribeiro, M. Kocot, K.M. Halanych, T.H. Oakley, R.R. da Fonesca, D. Pisani, J. Vinther. 2017. Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution. Proceedings of the Royal Society B: Biological Sciences 284: 20162818.
29. Stöger, I., Kocot, K.M., Poustka, A.J., Wilson, N.G., Ivanov, D., Halanych, K.M., and Schrödl, M. 2017. Monoplacophoran mitochondrial genomes: convergent gene arrangements and little phylogenetic signal. BMC Evolutionary Biology 16:274.
30. Kocot K.M., T.H. Struck, J. Merkel, D.S. Waits, C. Todt, P.M. Brannock, D.A. Weese, J.T. Cannon, L.L. Moroz, B. Lieb, and K.M. Halanych. 2017. Phylogenomics of Lophotrochozoa with consideration of systematic error. Systematic Biology 66(2): 256-282.
31. Li, Y., M. Kocot, N.V. Whelan, S.R. Santos, D.S. Waits, D.J. Thornhill, and K.M. Halanych. 2016. Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods. Zoologica Scripta 46(2): 200–213.
32. Kocot, K.M., F. Aguilera, C. McDougall, D.J. Jackson, and B.M. Degnan. 2016. Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization. Frontiers in Zoology 13(1): 1.
33. Garrison, N.L., J. Rodriguez, I. Agnarsson, J.A. Coddington, C.E. Griswold, C.A Hamilton, M. Hedin, M. Kocot, J.M. Ledford, and J.E. Bond. 2016. Spider phylogenomics: untangling the Spider Tree of Life. PeerJ 4:e1719.
34. Halanych, K. M., N.V. Whelan, M. Kocot, A.B. Kohn, and L. L. Moroz. 2016. Miscues misplace sponges. Proceedings of the National Academy of Sciences, 201525332.
35. Kocot, K.M. On 20 years of Lophotrochozoa. Organisms Diversity and Evolution, 16: 329-343.
36. Whelan, N.V., M. Kocot, L.L. Moroz, and K.M. Halanych. 2015. Employing phylogenomics to resolve basal animal phylogeny. Integrative and Comparative Biology 55(6): 1084-1095.
37. Whelan, N.V., M. Kocot, L.L. Moroz, and K.M. Halanych. 2015. Error, signal, and the placement of Ctenophora sister to all other animals. Proceedings of the National Academy of Sciences 112(18): 5773-5778.
38. Havird, J.C., M. Kocot, P.M. Brannock, J.T. Cannon, D.S. Waits, D.A. Weese, S.R. Santos, and K.M. Halanych. 2015. Reconstruction of cyclooxygenase evolution in animals suggests variable, lineage-specific duplications, and homologs with low sequence identity. Journal of Molecular Evolution 80(3-4): 1-16.
39. Li, Y., M. Kocot, S.R. Santos, D.J. Thornhill, and K.M. Halanych. 2015. Mitogenomics reveals phylogeny and dramatic size variations of control regions in the deep-sea family Siboglinidae (Annelida). Molecular Phylogenetics and Evolution 85: 221-229.
40. Kocot, K.M. and C. Todt. 2014. Three new species of meiofaunal solenogasters (Mollusca, Aplacophora) from Friday Harbor, WA, USA. Journal of Natural History 48: 3007-3031.
41. Whelan, N.V. M. Kocot, S.R. Santos, and K.M. Halanych. 2014. Nemertean toxin genes revealed through transcriptome sequencing. Genome Biology and Evolution 6(12):3314-3325.
42. Cannon, J.T., M. Kocot, D.S. Waits, D.A. Weese, B.J. Swalla, S.R. Santos, and K.M. Halanych. 2014. Phylogenomic Resolution of the hemichordate and echinoderm clade. Current Biology 24(23): 2827-2832.
43. Halanych, K.M. and M. Kocot. 2014. Repurposed transcriptomes facilitate discovery of innate immunity Toll-Like Receptor (TRLs) genes across Lophotrochozoa. Biological Bulletin 227.2: 201-209.
44. Todt, C. and M. Kocot. 2014. New records for Proneomenia sluiteri (Mollusca: Solenogastres) from Iceland and description of a new species, the brooding Proneomenia custodiens n. sp. Polish Journal of Polar Research 35(2): 291-310.
45. Brix, S., K. Meißner, B. Stransky, K.M. Halanych, R. Jennings, Kocot, and J. Svavarsson. 2014. The idea of the IceAGE project – a follow up of BIOICE. Polish Journal of Polar Research 35(2): 141-150.
46. Moroz, L.L., M. Kocot, M.R. Citarella, S. Dosung, T.P. Norekian, I.S. Povolotskaya, A.P. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, D. Reshetov, A. Ptitsyn, K. Mukherjee, T.P. Moroz, E. Dabe, F. Yu, V.V. Kapitonov, J. Jurka, Y. Bobkov, J.J. Swore, D.O. Girardo, R. Bruders, C.E. Mills, V.V. Solovyev, J. Rast, B. J. Swalla, F.A. Kondrashov, J.V. Sweedler, E.I. Rogaev, K.M. Halanych, and A.B. Kohn. 2014. The genome of the ctenophore and the emergence of nervous systems. Nature 510: 109-114.
47. Doty, K.E., A.M. Betzelberger, M. Kocot, and M.E. Cook. 2014. Immunofluorescence localization of the tubulin cytoskeleton during cell division and cell growth in members of the coleochaetales. Journal of Phycology 50(4): 624-639.
48. Kocot, K.M., M.R. Citarella, L.L. Moroz, and K.M. Halanych. 2013. PhyloTreePruner: a phylogenetic tree-based approach for selection of orthologous sequences for phylogenomics. Evolutionary Bioinformatics 2013(9): 429-435.
49. Kocot, K.M., K.M. Halanych, and P.J. Krug. 2013. Phylogenomics supports the Panpulmonata hypothesis: Resolving key steps in the evolutionary radiation of gastropod molluscs. Molecular Phylogenetics and Evolution 69(3): 764-771.
50. Kocot, K.M. Recent advances and unanswered questions in deep molluscan phylogenetics. American Malacological Bulletin 31(1): 1-14.
51. Scheltema, A.M., C. Schander, and M. Kocot. 2012. Hard and soft anatomy in two genera of Dondersiidae (Mollusca, Aplacophora, Solenogastres). Biological Bulletin 222: 233-269.
52. Kohn, A.B., M.R. Citarella, M. Kocot, Y.V. Bobkova, K.M. Halanych, and Leonid L Moroz. 2012. Rapid evolution of the compact and unusual mitochondrial genome in the ctenophore, Pleurobrachia bachei. Molecular Phylogenetics and Evolution 63: 203-207.
53. Pierce, S.K., X. Fang, J.A. Schwartz, X. Jiang W. Zhao, N.E. Curtis, M. Kocot, B. Yang, and J. Wang. 2011. Transcriptomic evidence for the expression of horizontally transferred algal nuclear genes in the photosynthetic sea slug, Elysia chlorotica. Molecular Biology and Evolution 29(6): 1545-1556.
54. Kocot, M., J.T. Cannon, C. Todt, A.B. Kohn, M.R. Citarella, A. Meyer, C. Schander, S.R. Santos, L.L. Moroz, B. Lieb, and K.M. Halanych. 2011. Phylogenomics reveals deep molluscan relationships. Nature 477: 452-456.
55. Kocot, K.M. and S.R. Santos. 2009. Secondary structural modeling of the second internal transcribed spacer (ITS2) from Pfiesteria-like dinoflagellates (Dinophyceae). Harmful Algae 8(3):441-446.
56. Jannot, J.E., J. Brinton, M. Kocot, O. Akman, and S.A. Juliano. 2009. Ontogenetic mechanisms underlying a geographic size cline in a grasshopper, Romalea microptera. Annals of the Entomological Society of America 102(3) 467-475.

*Kocot lab student or postdoc