Halanych Publications

In Press

Galaska, M. T., C. J. Sands, S. R. Santos, A. R. Mahon, K. M. Halanych. In Press. Crossing the divide: Admixture across the Antarctic Polar Front revealed by the brittle star Astrotoma agassizii. Biological Bulletin.

Bernardino, A.F., Y. Li, C.R. Smith, K.M. Halanych. In Press. Multiple introns in a deep-sea Annelid mitochondrial genome. Scientific Reports.


Tassia, M. G., N. V. Whelan, K. M. Halanych .2017. Toll-like receptor pathway evolution in deuterostomes. Proc. Natl. Acad. Sci. USA Early Edition.

Anderson, F. E., B. W. Williams, K. M. Horn, C. Erséus , K. M. Halanych, Scott R. Santos, S. W. James. In Press. Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangean origin for earthworms. BMC Evolutionary Biology 17: 123.

Halanych, K. M., K. M. Kocot. 2017. Shellfish genomes. Nature Ecology and Evolution 1: 0142. News & Views.

Costa-Paiva, E. M., N. V. Whelan, D. S. Waits, S. R. Santos, C. G. Schrago and K. M. Halanych. 2017. Discovery and evolution of novel hemerythrin genes in annelid worms. BMC Evolutionary Biology 17:85.

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. Leib, and K. M. Halanych. 2017. Phylogenomics of Lophotrochozoa with consideration of systematic error. Systematic Biology 66:256-282.

Whelan, N. V., and K. M. Halanych. 2017. Who let the CAT out of the bag? Accurately dealing with substitution heterogeneity in phylogenomics. Systematic Biology 66:232-255.

Orélis-Ribeiro, R., K. M. Halanych, B. T. Dang, M. D. Bakenhaster, C. R. Arias, S. A. Bullard. 2017. Two new species of Elopicola (Digenea: Aporocotylidae) from Hawaiian ladyfish, Elops hawaiensis (South China Sea) and Atlantic tarpon, Megalops atlanticus (Gulf of Mexico) with a comment on monophyly of elopomorph blood flukes. Parasitology International 66 305-318.

Tanner A. R., D. Fuchs, Winkelmann I. E., Gilbert M. Thomas P., Pankey M. S., Ribeiro A. M., Kocot K. M., Halanych K. M., Oakley T. H., da Fonseca R. R., Pisani D. and Vinther J. 2017. Molecular clocks indicate diversification of coleoid cephalopods during the Mesozoic Marine Revolution. Proceedings of the Royal Society B. 284:20162818.

Li, Y., K. M. Kocot, N. V. Whelan, S. R. Santos, D. S. Waits, D. J. Thornhill, K. M. Halanych. 2017. Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods. Zoological Scripta 46: 200-213.

Galaska, M.P., C. J. Sands, S .R. Santos, A. R. Mahon , and K. M. Halanych. 2017. Geographic structure in the Southern Ocean circumpolar brittle star Ophionotus victoriae (Ophiuridae) revealed from mtDNA and single-nucleotide polymorphism data. Ecology & Evolution 7: 475-485.


Roberts, J. R., R. Orélis-Ribeiro, K. M. Halanych, C. R. Arias, S. A. Bullard. 2016. New species of Spirorchis MacCallum, 1918 (Digenea: Schistosomatoidea) and Spirorchis cf. scripta from chicken turtle, Deirochelys reticularia, (Emydidae), with an emendation and molecular phylogeny of Spirorchis. Folia Parasitologica 63: 041.

Stöger, I., K. M. Kocot, A. J. Poustka, N. G. Wilson, D. Ivanov, K. M. Halanych, M. Schrödl. 2016. Monoplacophoran mitochondrial genomes: convergent gene arrangements and little phylogenetic signal. BMC Evolutionary Biology 16: 274.

Tassia. M.G, J. Cannon, C. E. Konikoff, N. Shenkar, K. M. Halanych, and B. J Swalla. 2016. The Global Diversity of the Hemichordata. PLoS One 11: e0162564.

Roberts, J. R., R. Orelis-Ribeiro, B. T. Dang, K.M. Halanych, and S. A. Bullard. 2016. Blood flukes of Asiatic softshell turtles: revision of Coeuritrema Mehra 1933 (Digenea: Schistosomatoidea) and a new species infecting Chinese softshell turtles, Pelodiscus sinensis, (Trionychidae) from the Da Rang River, Vietnam. Folia Parasitologica 63: 031.

Benoit, D. S., L. Zimmermann, K. Fillingham, S.H. Sempier, N.M. Dannreuther, J.B. Ritchie, and K. M. Halanych. 2016. An Opportunity to Inform and Educate Through the Gulf of Mexico Research Initiative: Outreach Efforts Surrounding the Deepwater Horizon Oil Spill. Oceanography Magazine 29: 38-45.

Shepherd, J., D. Benoit, K. M. Halanych, M. Carron, R. Shaw, and C. Wilson. 2016. Introduction to the Special Issue: An Overview of the Gulf of Mexico Research Initiative. Oceanography Magazine 29: 26-32.

Brannock, P. M., A. C. Ortmann, A. G. Moss, and K. M. Halanych. 2016. Temporal and spatial variation in pelagic micro-eukaryotes assemblages in Mobile Bay and along the Alabama coast. Molecular Ecology 25: 3593–3604.

Brannock, P.M., L. Wang, A. C. Ortmann, D. S. Waits, and K. M. Halanych. 2016. Genetic assessment of meiobenthic community composition and spatial distribution in coastal sediments along northern Gulf of Mexico. Marine Environmental Research 119: 166-175.

Halanych, K. M. 2016. How our view of animal phylogeny was reshaped by molecular approaches: Lessons learned. Organisms, Diversity and Evolution 16: 319-328.

Waits, D. S., D. J. Thornhill, S. R. Santos, Y. Li, and K. M. Halanych. 2016. Evolution of Sulfur Binding in Hemoglobin in Siboglinidae (Annelida) with Special Reference to Bone Eating Worms, Osedax. Journal of Molecular Evolution 82: 219-229.

Halanych, K. M. 2016. Lophotrochozoa, Diversification of. In: Kilman, R.M. (ed.), Encyclopedia of Evolutionary Biology. 2: 405-408. Oxford: Academic Press.

Harder A. M., K. M. Halanych, A. R. Mahon. 2016. Diversity within the sea spider genus Pallenopsis (Pycnogonida: Chelicerata) in the Western Antarctic. Polar Biology 39: 677-688.

Learman, D. R., M. W. Henson, J. C. Thrash, B. Temperton, P. M. Brannock, S. R. Santos, A. R. Mahon, K. M. Halanych. 2016. Biogeochemical and microbial variation across 5500 km of Antarctic surface sediment implicates organic matter as a driver of benthic community structure. Frontiers in Microbiology 7:284. doi: 10.3389/fmicb.2016.00284.

Halanych, K. M., N. V. Whelan, K. M. Kocot, A. B. Kohn, L. L. Moroz. 2016. Miscues misplace sponges. Proceedings of the National Academy of Sciences. 113: E946-E947.— Online Letter.

Moroz, L. L., Halanych, K. M. 2016. A sisterly dispute: Methodological misconceptions. Nature 529: 286-287. News & Views Forum.

Kocot, K. M., N. W. Jeffery, K. Mulligan, K. M. Halanych, and T. R. Gregory. 2016. Genome size estimates for Aplacophora, Polyplacophora, and Scaphopoda: Small solenogasters and sizeable scaphopods. Journal of Molluscan Studies. 82: 216-219


D’Aniello S., J. Delroisse, A. Valero-Gracia A, E.K. Lowe, M. Byrne, J.T. Cannon, K. M. Halanych, M. R. Elphick, J. Mallefet , S. Kaul-Strehlow, C. J. Lowe, P. Flammang, J. Smith, E. Ullrich-Lüter, A. Wanninger, and M. I. Arnone. 2015. Opsin evolution in the Ambulacraria. Marine Genomics. 24: 177-183

Whelan, N. V., K. M. Kocot, K. M. Halanych. 2015. Employing phylogenomics to resolve basal animal phylogeny. Integrative and Comparative Biology. 55: 1084–1095.

Brannock, P. M., and K. M. Halanych. 2015. Meiofaunal community analysis by high-throughput sequencing: Comparison of extraction, quality filtering, and clustering methods. Marine Genomics. 23: 67-75.

Dietz, L., C. P. Arango, K. M. Halanych, A. M. Harder, C. Held, A. R. Mahon, C. Mayer, R. R. Melzer, G. Rouse, A. Weis, N. Wilson and F. Leese. 2015. Regional differentiation and extensive hybridisation between mitochondrial clades of the Southern Ocean giant sea spider Colossendeis megalonyx. Royal Society Open Science. 2: 100424.

Struck, T.H., A. Golombek, A.Weiger, F. A.Franke, W. Westheide, G. Purschke, C. Bleidorn, K. M. Halanych. In Press. Two routes to a safe haven – the evolution of interstitial annelids. Current Biology 25: 1993-1999.

Whelan, N. V., K. M. Kocot, L. L. Moroz, K. M. Halanych. 2015. Error, signal, and the placement of Ctenophora sister to all other animals. Proceedings of the National Academy of Sciences. 112: 5773-5778. www.pnas.org/cgi/doi/10.1073/pnas.1503453112.

Havird, J.C., K. M. Kocot, P. M. Brannock, J. T. Cannon, D. S. Waits, D. A. Weese, S. R. Santos, K. M. Halanych. 2015. Reconstruction of cyclooxygenase evolution in animals suggests variable, lineage-specific prostaglandin synthesis pathways. Journal of Molecular Evolution. 80: 193-208.

Li, Y., K.M. Kocot, C. Schander, S.R. Santos, D. J. Thornhill, and K.M. Halanych. In Press. Mitogenomics reveals phylogeny and dramatic size variations of control regions in the deep-sea family Siboglinidae (Annelida). Molecular Phylogeny and Evolution. 85: 221-229.

Halanych, K.M. 2015. The ctenophore lineage is older then sponges? That cannot be right! Or can it? Journal of Experimental Biology 218: 592-597.


Whelan, N. V., K. M. Kocot, S. R. Santos, and K. M. Halanych. 2014. Nemertean toxin genes revealed through transcriptome sequencing. Genome Biology and Evolution 6:3314-3325.

Cannon, J.T., K. 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: 2827-2832.

Halanych, K.M., and A. R. Mahon. 2014. Discovering diversity with high-throughput approaches: Introduction to a virtual symposium in The Biological Bulletin. Biological Bulletin 227: 91-92.

Brannock, P. M., D. S. Waits , J. Sharma , K. M. Halanych. 2014. High-throughput sequencing characterization of intertidal meiofaunal communities in northern Gulf of Mexico (Dauphin Island and Mobile Bay, Alabama). Biological Bulletin 227 161-174.

Halanych, K.M., and K.M. Kocot. 2014. Repurposed transcriptomic data facilitate discovery of innate immunity Toll-Like Receptor (TLRs) genes across Lophotrochozoa. Biological Bulletin 227 201-209.

Orélis-Ribeiro, R., C.R. Arias, K.M. Halanych, T.H. Cribb, and S.A. Bullard. 2014. Chapter One - Diversity and ancestry of flatworms infecting blood of non-tetrapod craniates (“fishes”). Advances in Parasitology. 85:1-64.

Brix, S.,K. MeiBner, B. Stransky, K.M. Halanych, R.M. Jennings, K.M. Kocot, J. Svavarsson. 2014. Preface: The IceAGE project – a follow up of BIOICE. Polish Polar Research. 35: 141-150.

Cowart, D.A., K.M. Halanych, S.W. Shaeffer, C.R. Fisher. 2014. Depth-dependent gene flow in Gulf of Mexico cold seep Lamellibrachia tubeworms. Hydrobiologica 736:139-154.

Moroz, L.L, K. 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. Ptytsyn, 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, A. B. Kohn. 2014. The Ctenophore Genome and the Emergence of Neural Systems. Nature 510: 109-114. doi:10.1038/nature13400.

Weigert, A., C. Helm, M. Meyer, B. Nickel, D. Arendt, B. Hausdorf, S. R. Santos, K. M. Halanych, G. Purschke, C. Bleidorn, T. H. Struck. 2014. Illuminating the base of the annelid tree using transcriptomics. Molecular Biology and Evolution 31: 1391-1401.

Zanol. J., K.M. Halanych, K. Fauchald. 2014. Reconciling taxonomy and phylogeny in the bristleworm family Eunicidae (polychaete, Annelida). Zoo. Scripta 43:79-100.


Cannon, J.T., B.J. Swalla, and K.M. Halanych. 2013. Hemichordate molecular phylogeny reveals a novel cold-water clade of harrimaniid acorn worms. Biological Bulletin 225:194-204.

Halanych, K.M., J.T. Cannon, A.R. Mahon, B.J. Swalla, C.R. Smith. 2013. Tubicolous acorn worms from Antarctica. Nature Communications DOI://10.1038/ncomms3738.

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. 9:429-435.

Halanych, K.M., E. T. Vodoti, P. Sundberg and T. G. Dahlgren. 2013. Phylogeography of the horse mussel Modiolus modiolus. Journal Marine Biological Association of the United Kingdom 93: 1857-1869.

Kocot, K.M., , K.M. Halanych, and P.J. Krug. 2013. Phylogenomics supports Panpulmonata: Resolving key evolutionary steps in a major radiation of gastropod molluscs. Mol. Phylogenet. Evol. 69:764-771.

Kaiser, S., S. N. Brandão, S. Brix, D. K.A. Barnes, D. A. Bowden, N. Brenke, J. Ingels, F. Leese, S. Schiaparelli, C. P. Arango, R. Badhe, N. Bax, M. Blazewicz-Paszkowycz, A. Brandt, A. I. Catarino, B. David, C. De Ridder, P. Dubois, K. E. Ellingsen, Ad. G. Glover, H. J. Griffiths, J. Gutt, K. M. Halanych, C. Havermans, C. Held, D. Janussen, A. Lörz, D. A. Pearce, B. Pierrat, T. Riehl, A. Rose, C. J. Sands, A. Soler-Membrives, M. Schüller, J. M. Strugnell, A. Vanreusel, G. Veit-Köhler, N. G. Wilson and M. Yasuhara. 2013. Pattern, process and vulnerability of Antarctic and Southern Ocean benthos - a decadal leap in knowledge and understanding. Marine Biology. 160: 2295-2317.

Janosik, A.M., and K.M. Halanych,. 2013. Seeing stars: a molecular and morphological investigation of the evolutionary history of Odontasteridae (Asteroidea) with description of a new species from the Galapagos Islands. Marine Biology.160:821-841.

Halanych, K.M. 2013. Evolution and Embryology: A brief synopsis of how developmental biology has played into evolutionary theory. Pp 157-174, In Eds .J. Bradley and J. Lamar, Charles Darwin, A Celebration of His Life and Legacy. Alabama Press.


Thornhill, D. J., T. H. Struck, B. Ebbe, R. W. Lee, G. F. Mendoza, L. A. Levin, K. M. Halanych. 2012. Adaptive Radiation in Extremophilic Dorvilleids: Diversification of a Single Colonizer or Multiple Independent Lineages? Ecology & Evolution. 2(8): 1958–1970.

Bik, H. M., K. M. Halanych, J. Sharma, W. K. Thomas. 2012. Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill. PlosOne 7: e38550.

Kohn, A. B., M. R. Citarella , K. M. Kocot , Y. V. Bobkova, K. M. Halanych, Leonid L. Moroz. 2012. Rapid evolution of the compact and unusual mitochondrial genome in the ctenophore, Pleurobrachia bachei. Mol. Phylogenet. Evol. 63:203-207.

Halanych, K.M., J.T. Cannon, J.Benito. 2012. Pterobranchia. Pp. 586-587. In McGraw Hill, Editors, McGraw Hill Encyclopedia of Science & Technology, 11th Edition. Vol 14. McGraw Hill Publishers.


Zhong, M., B. Hansen, M. Nesnidal, A. Golombek, K. M.Halanych, T.H. Struck. 2011. Escaping the symplesiomorphy trap: A multigene phylogenetic analysis for terebelliform annelids. BMC Evolutionary Biology 11:369.

Oyarzun, F.X., A.R. Mahon, B.J. Swalla, and K.M. Halanych. 2011. Phylogeography and reproductive variation of the poecilogonous polychaete Boccardia proboscidea (Annelida: Spionidae) along the West Coast of North America. Evolution and Development 13:489-503.

Kocot, K.M., J.T. Cannon, C Todt, M.R. Citarella, A.B. Kohn, A Meyer, S.R. Santos, C. Schander, L. L. Moroz, B. Leib, and K.M. Halanych. 2011. Phylogenomics reveals deep molluscan relationships. Nature 477:452-456.

Janosik, A.M., A.R. Mahon, and K.M. Halanych. 2011. Evolutionary history of Southern Ocean seastar species across the Drake Passage, and the discovery of 2 species of Odontaster (Odontasteridae; Asteroidea). Polar Biology 34: 575-586.

Hilário, A., M. Capa, T. G. Dahlgren, K. M. Halanych, C. T.S. Little, D. J. Thornhill, C. Verna, A. G. Glover. 2011. New perspectives on the ecology and evolution of siboglinid tubeworms. Plos One 6: e16309


Paul, C., K.M. Halanych, R. Tiedemann, C. Bleidorn. In Press. Molecules reject an opheliid affinity for Travisia (Annelida). Systematics and Biodiversity 8: 507-512.

Kocot, K.M., J.T. Cannon, K.M. Halanych. 2010. Elucidating animal phylogeny: advances in knowledge and forthcoming challenges. PP. 16-35. In Ed, R. DeSalle, B. Sheirwater, Key Transitions. CRC Press Baco Raton, FL.

Janosik, A.M., K.M. Halanych. 2010. Unrecognized Antarctic biodiversity: a case study with Odontaster (Odontasteridae; Asteroidea). Journal of Integrative and Comparative Biology 50: 981-992.

Scheltema, R.S., A.H. Scheltema, I.P. Williams, K.M. Halanych. 2010. Seasonal occurrence of balanomorph barnacle nauplius larvae in the region of the Antarctic Peninsula. J. Exp. Mar. Biol. Ecol. 392: 125-128. doi:10.1016/j.jembe.2010.04.016

Hunter, R.L. K.M. Halanych. 2010. Phylogeography of the Antarctic planktotrophic brittle star Ophionotus victoriae reveals genetic structure inconsistent with early life history. Marine Biology. 157:1693–1704. doi: 10.1007/s00227-010-1446-0.

Schander, C., H.T. Rapp, K.M. Halanych, J.A. Kongsrud, J.A. Sneli, J.-A. 2010. An exceptional case of symbiosis or commensalism from a North-east Atlantic wood-fall. Journal of the Marine Biological Association Biodiversity Records. 3: e43

Zanol, J., K.M. Halanych, T.H. Struck, K. Fauchald. 2010. Phylogeny of the bristle worm family Eunicidae (Eunicida, Annelida) and the phylogenetic utility of noncongruent 16S, COI and 18S in combined analyses. Mol. Phylogen. Evol. 55: 660-676.

Struck T.H., and K.M. Halanych. 2010. Phylogenetic position of holopelagic Typhloscolecidae and Lopadorhynchidae as within Phyllodocidae (Phyllodocida, Annelida) revealed by 18S and 28S rDNA data. Zoological Scripta. 39: 269-275.

Mahon, A.R., D.J. Thornhill, J.L. Norenburg, K.M. Halanych. 2010. DNA discovers missing Antarctic nemerteans and exposes a decades-old cold case of asymmetric inventory. Polar Biology 33: 193-202.

Berke, S.K., A.R. Mahon, F.P. Lima, K.M. Halanych, D.S. Wethey, and S.A Woodin. 2010. Ecological consequences of range shifts and species diversity in marine ecosystem engineers: patterns and predictions for European coastal habitats. Global Ecology and Biogeography 19: 223 -232.


Halanych, K.M., Goertzen, L.R. 2009. Grand challenges in organismal biology: The need to develop both theory and resources. Integrative and Comparative Biology 49: 475-479.

Bleidorn, C., Podsiadlowski, L., Zhong, M., Eeckhaut, I., Hartmann, S., Halanych, K. M., Tiedemann, R. On the phylogenetic position of Myzostomida: Can 77 genes get it wrong? BMC Evolutionary Biology 9:150 PDF

Simon, C.A., D.J.Thornhill, K.M. Halanych. 2009. Genetic similarity between Boccardia proboscidea from Western North American and cultured abalone, Haliotis midae, in South Africa. Aquaculture 294:18-24. PDF

Cannon, J.T., A.L. Rychel, H. Eccleston, K.M. Halanych, and B.J. Swalla. 2009. Molecular Phylogeny of Hemichordata.  Molecular Phylogenetics and Evolution 5: 17-24. PDF

Wilson, N.G., M Schrödl, and K.M. Halanych. 2009. Ocean barriers and glaciation: explosive radiation of Pleistocene lineages in the Antarctic sea slug Doris kerguelenensis (Mollusca, Nudibranchia). Molecular Ecology 18: 965–984. PDF

Mahon, A. R., H. K. Mahon, D. M. Dauer, and K. M. Halanych. 2009. Discrete genetic boundaries of three Streblospio (Spionidae, Annelida) species and the status of S. shrubsolii. Marine Biology Research 5: 172-178. PDF

Jennings, R. M., T. M. Shank, L. S. Mullineaux, and K. M. Halanych. 2009. Assessment of the Cape Cod phylogeographic break using the bamboo worm Clymenella torquata reveals the role of regional water masses in dispersal. Journal of Heredity 100:86-96. PDF

Halanych, K.M., and E. Borda. 2009. Chapter 1: Developing Models for Lophotrochozoan and Annelid Biology. Pp. 3-12, In Shain, D. H., Ed., Annelids as Model Systems in the Biological Sciences. John Wiley & Son.

Thornhill, D. J., T. G. Dahlgren, K. M. Halanych. 2009. Chapter 13: The evolution and ecology of Ophryotrocha (Dorvilleidae, Eunicida). Pp. 242-256 In Shain, D. H., Ed., Annelids as Model Systems in the Biological Sciences. John Wiley & Son.


Thornhill, D. J., A. R. Mahon, J. L. Norenburg, and K. M. Halanych. 2008. Open-ocean barriers to dispersal: a test case with the Antarctic Polar Front and the ribbon worm Parborlasia corrugatus (Lineidae: Nemertea). Molecular Ecology. 17: 5104-5177. PDF

Janosik, A. M., A. R. Mahon, R. S. Scheltema, and K. M. Halanych. 2008. Life history of the Antarctic sea star Labidiaster annulatus (Asteroidea: Labidiasteridae) revealed by DNA barcoding. Antarctic Science 20: 563-564. PDF

Thornhill, D.J., K.T. Fielman, S.R.Santos, and K.M. Halanych. 2008. Siboglinid-bacteria endosymbiosis: A model system for studying symbiotic mechanisms. Communicative & Integrative Biology 1: 163 – 166. PDF

Mahon, A. R, C. P. Arango, and K. M. Halanych. 2008. Genetic diversity of Nymphon (Arthropoda: Pycnogonida: Nymphonidae) along the Antarctic Peninsula with a focus on Nymphon austral. Marine Biology 155: 315-323. PDF

Struck, T.H., M. P. Nesnidal, G. Purschke, and K. M. Halanych. 2008. Detecting Possibly Saturated Positions in 18S and 28S Sequences and their Influence on Phylogenetic Reconstruction of Annelida (Lophotrochozoa). Molecular Phylogenetics and Evolution. 48: 628-645. PDF

Zhong, M., T. H. Struck, K. M. Halanych. 2008. Three mitochondrial genomes of Terebelliformia (Annelida) worms and duplication of the methionine tRNA. Gene 416: 11-21. PDF

Thornhill, D. J., A. A. Wiley, A. L. Campbell, F. F. Bartol, A. Teske, K. M. Halanych. 2008. Endosymbionts of Siboglinum fiordicum and the phylogeny of Siboglinidae (Annelida) endosymbionts. Biological Bulletin. 214:135-144. PDF

Haszprunar, G., C. Schander, and K. M. Halanych. 2008. Origin and relationships of higher molluscan taxa: From fossils and species to genes and molecules. Pp19-32,  In D.R. Lindberg and W.F. Ponder. Phylogeny and Evolution of the Mollusca, University of California Press.

Hunter, R. L. and K. M. Halanych. 2008 . Evaluating connectivity in the brooding brittle star Astrotoma agassizii across the Drake Passage in the Southern Ocean. J. Hered. 99:137-148. PDF

Vallès, Y., K. M. Halanych, and J. L. Boore. 2008 . Group II introns break new boundaries: Presence in an animal genome. Plos One 3: e1488 (6 pages). PDF


Halanych, K. M., L. N. Cox, T. H. Struck. 2007. A brief review of holopelagic annelids. Int. Comp. Biol. 47:872-879. PDF

Matus, D. Q., K. M. Halanych, M. Q. Martindale. 2007. The Hox complement of a pelagic chaetognath, Flaccisagitta enflata: Insights into metazoan phylogeny. Int. Comp. Biol. 47:854-864. PDF

Wilson, N.G., R.L. Belcher , S.J. Lockhart, K.M. Halanych. 2007. Absence of panmixia in the Antarctic ‘circumpolar’ crinoid Promachocrinus kerguelensis Carpenter, 1888. Mar. Biol. 152: 895-904. PDF

Lilly, E. L., K. M. Halanych, and D. M. Anderson. 2007. Species boundaries and global biogeography of the “A. tamarense” complex of the dinoflagellate genus Alexandrium. Journal of Phycology 43: 1329-1338. PDF

Serrano L., K. M. Halanych, R. P. Henry. 2007. Salinity-stimulated changes in expression and activity of two carbonic anhydrase isoforms in the blue crab, Callinectes sapidus. J. Exp. Biol. 210:2320-2332. PDF

Bleidorn, C. I. Eeckhaut, L. Podsiadlowski, N. Schult, D. McHugh, K. M. Halanych, M. C. Milinkovitch, R. Tiedemann. 2007. Mitochondrial genome and nuclear sequence data support Mystomida as part of the annelid radiation. Mol. Biol. Evol. 24: 1690-1701. PDF

Struck, T.H., N. Schult, T. Kusen, E. Hickman, C. Bleidorn, D. McHugh, and K.M. Halanych. 2007. Annelid phylogeny and origins of Sipuncula and Echiura. BioMed Central: Evol. Biol. 7: 57. PDF

Shank T.M. and K.M. Halanych . 2007 . Extensive genetic structure among hydrothermal vent populations: evidence from AFLP fingerprinting of vestimentiferan tubeworms ( Riftia pachyptila ) along the East Pacific Rise. Marine Ecology 28 :25-35. PDF


Lutz, R. A., A. G. Collins, E. R. Annis, A. J. Reed, K. Bennett, K. M. Halanych, and R. C. Vrijenhoek . 2006. Stauromedusan populations inhabiting deep-sea hydrothermal vents along the southern East Pacific Rise. Cahiers de Biologie Marine 47 :409-414. PDF

Matus D. Q., R. R. Copley, C. W. Dunn,   A. Hejnol, H. Eccleston, H., K. M. Halanych , M. Q. Martindale, M. J. Telford. 2006. Broad taxon and gene sampling indicate that chaetognaths are protostomes. Current Biology 16 : R575-576 PDF

Halanych, K. M., and A. M. Janosik. 2006. The state of annelid phylogenetics. Int. Comp. Biol. 46: 533-543. PDF

Passamaneck, Y., and K. M. Halanych. 2006. Lophotrochozoan phylogeny assessed with LSU and SSU data: Evidence of Lophophorate Polyphyly. Molecular Phylogeny and Evolution. 40: 20-28. PDF

Govindarajan , A. F., F. Boero, and K. M. Halanych . 2006. Phylogenetic analysis with multiple markers indicates repeated loss of the adult medusa stage in Campanulariidae (Hydrozoa, Cnidaria) . Molecular Phylogenetics and Evolution. 38: 820-834. PDF

Struck, T. H., G. Purschke, and K. M. Halanych. 2006. Phylogeny of Eunicida (Annelida) and Exploring Data Congruence using a Partition Addition Bootstrap Alteration (PABA) approach. Systematic Biology. 55: 1-20.  PDF


Struck, T. H., K. M. Halanych and G. Purschke. 2005. Dinophilidae (Annelida) is not a progenetic Eunicida; Evidence from 18S and 28S rDNA. Molecular Phylogenetics and Evolution 37: 619-623. PDF

Struck, T. H., G. Purschke and K. M. Halanych. 2005. A scaleless scale worm: Molecular evidence for the phylogenetic placement of Pisione remota (Pisionidae, Annelida). Marine Biology Research 1: 243-253. PDF

Lilly, E. L.,  K. M. Halanych, and D. M. Anderson. 2005. Phylogeny, biogeography, and species boundaries within the Alexandrium minutum group. Harmful Algae 4:1004-1020. PDF

Burnette, A. B., T. H. Struck, and K. M. Halanych. 2005. Holopelagic Poeobius meseres (Poeobiidae, Annelida) is derived from within benthic Flabelligerid worms. Biological Bulletin. 208: 213-220. PDF

Jennings, R. M. and K.M. Halanych. 2005. Mitochondial genomes of Clymenella torquata (Maldanidae) and Rifta pachyprila (Siboglinidae): Evidence for conserved gene order in Annelida. Molecular Biology and Evolution 22: 210-222. PDF

Govindarajan A. F., K. M. Halanych, C. W. Cunningham. 2005. Mitochondrial evolution and phylogeography in the Hydrozoan Obelia geniculata (Cnidaria). Marine Biology 146:231-222. PDF

Halanych, K. M. 2005. Molecular phylogeny of siboglinid annelids (a.k.a. pogonophorans): A review. Hydrobiologia 535: 27-307. PDF


Halanych, K. M. 2004. The new view of animal phylogeny. Annual Reviews of Ecology and Systematics. 35: 229-256. PDF , Figures Link

Passamaneck, Y. J., and K. M. Halanych. 2004. Evidence from Hox genes that bryozoans are lophotrochozoans. Evolution and Development 6: 275-281. PDF

Passamaneck, Y. J., C. Schander, and K. M. Halanych. 2004. Investigation of Molluscan Phylogeny Using Large-Subunit and Small-Subunit Nuclear rRNA Sequences. Molecular Phylogenetics and Evolution. 32: 25-38. PDF

Hunt, H. L., A. Metaxas, R. M. Jennings, K. M. Halanych , L. S. Mullineaux. 2004. Testing biological control of colonization by vestimentiferan tubeworms at deep-sea hydrothermal vents (East Pacific Rise, 9 ° 50'N) Deep-Sea Research I 51: 225-234. PDF

Ottens-Wainright, P.,   K. M. Halanych , J. R. Eberhard, R. I. Burke, J. W. Wiley, R. S. Gnam, and X. G. Aquilera. 2004. Independent Geographic Origins of the genus Amazona in the West Indies. Journal of Caribbean Ornithology. 17: 23-49. PDF


Schander, C. and K. M. Halanych . 2003. DNA, PCR and formalized animal tissue - a short review and protocols. Organisms, Diversity & Evolution 3: 195-203. PDF

Weinberg, J. R., T. G. Dahlgren, N. Trowbridge, and K. M. Halanych . 2003. Genetic differences within and between species of Deep-Sea Crabs (Chaceon) from the North Atlantic Ocean. Biological Bulletin 204: 318-326. PDF

Schulze, A. and K. M. Halanych. 2003. Siboglinid evolution shaped by habitat preference and sulfide tolerance. Hydrobiologia 496: 199-205. PDF

Schander, C., K. M. Halanych, T. G. Dahlgren, and P. Sundberg. 2003. Test of the monophyly of Odostomiinae and Turbonilliinae (Gastropoda, Heterobranchia, Pyramidellidae) based on 16S mtDNA sequences. Zoological Scripta 32: 243-254. PDF


Halanych, K. M., T. G. Dahlgren, D. McHugh. 2002. Unsegmented Annelids? Possible origins of four Lophotrochozoan worm taxa. Integrative and Comparative Biology 42: 678–684. PDF

Weinberg, J. R., T. Dahlgren, and K. M. Halanych. 2002. Influence of rising sea temperature on commercial clam populations along the east coast of the USA. American Fisheries Society Symposium 32: 131-140.

Dahlgren, T. G., Åkesson, B., Schander, C., Halanych, K. M., and Sundberg, P. 2001. Molecular phylogeny of the model annelid Ophryotrocha. Biological Bulletin 201: 193-203. PDF


Halanych, K.M., Feldman, R.A., and R.C. Vrijenhoek. 2001. Molecular evidence that Sclerolinum brattstromi is closely related to vestimentiferans, not frenulate pogonophorans (Siboglinidae, Annelida). Biological Bulletin 201: 65-75. PDF

19. Halanych, K. M., and Y. Passamaneck. 2001. A brief review of metazoan phylogeny and future prospects in Hox-research. American Zoologist 41: 629-639. PDF


Dahlgren, T. G., J. R. Weinberg, K.M. Halanych. 2000. Phylogeography of the Ocean Quahog (Arctica islandica): influences of paleoclimate on genetic diversity and species range. Marine Biology 137: 487-495. PDF


Halanych, K.M. 1999. Metazoan phylogeny and the shifting comparative framework. In Roubos, Wendelaar Bonga, Vaudry & De Loof, (Eds.), Recent Developments in Comparative Endocrinology and Neurobiology. Pp. 3-7.

Shank, T.M., M.B. Black, K.M. Halanych, R.A. Lutz, and R.C. Vrijenhoek. 1999. Miocene radiation of deep-sea hydrothermal vent shrimp (Caridea: Bresiliidae): evidence from mitochondrial Cytochrome Oxidase subunit I. Molecular Phylogenetics and Evolution. 13: 244-254. PDF

Halanych, K.M., J.R. Demboski, B.J. van Vuuren, D.R. Klein, and J.A. Cook. 1999. Cytochrome b phylogeny of North American hares and jackrabbits (Lepus, Lagomorpha) and the effects of mutational saturation in outgroup taxa. Molecular Phylogenetics and Evolution. 11: 213-221. PDF

Halanych, K.M., and T.J. Robinson. 1999. Multiple substitutions affect the phylogenetic utility of cytochrome b and 12S rDNA data: Examining a rapid radiation in leporid (Lagomorpha) evolution. Journal of Molecular Evolution. 48: 369-379. PDF


Halanych, K.M., R.A. Lutz, and R.C. Vrijenhoek. 1998. Evolutionary origins and age of vestimentiferan tube worms. Cahiers de Biologie Marine 39: 355-358. PDF

Halanych, K. M. 1998. Considerations for reconstructing metazoan history: Signal, resolution, and hypothesis testing. American Zoologist. 38: 929-941.

Halanych, K.M. 1998. Lagomorphs misplaced by more data and fewer taxa. Systematic Biology 47: 138-146. PDF


Black, M.B., K.M. Halanych, P.A.Y. Maas, W. R. Hoeh, J. Hashimoto, D. Desbruyères, R.A. Lutz, and R.C. Vrijenhoek. 1997. Molecular systematics of vestimentiferan tubeworms from hydrothermal vents and cold-water seeps. Marine Biology 130: 141-149. PDF

Halanych, K.M., and T.J. Robinson. 1997. Phylogenetic relationships of cottontails (Sylvilagus, Lagomorpha): Congruence of 12S rRNA and cytogenetic data. Molecular Phylogenetics and Evolution 7: 294-302. PDF


Halanych, K.M. 1996. Testing hypotheses of chaetognath origins; long branches revealed by 18S rDNA. Systematic Biology 45: 223-246. (cover). PDF

Robinson, T.J., A.D. Bastos, K.M. Halanych, and B. Herzig. 1996. Mitochondrial DNA sequence relationships of the extinct blue antelope, Hippotragus leucophaeus. Naturwissenschaften 83: 178-182. 

Halanych, K.M. 1996. Convergence in the feeding apparatuses of lophophorates and pterobranch hemichordates revealed by 18S rDNA. Biological Bulletin 190: 1-5. PDF


Halanych, K.M., J. Bachelor, A.M. Aquinaldo, S. Liva, D.M. Hillis, and J.A. Lake. 1995. 18S rDNA evidence that the lophophorates are protostome animals. Science 267: 1641-1643. (cover). PDF

Halanych, K.M. 1995. The phylogenetic position of the pterobranch hemichordates based on 18S rDNA sequence data. Molecular Phylogenetics and Evolution 4: 72-76. PDF


Halanych, K.M. 1993. Suspension feeding and the lophophore-like apparatus of the pterobranch hemichordate Rhabdopleura normani. Biological Bulletin 185: 417-427.


Halanych, K.M. 1991. 5S ribosomal RNA sequence inappropriate for phylogenetic reconstruction. Molecular Biology and Evolution 8: 249-253. PDF


Browne, R.A. and K.M. Halanych. 1989. Competition between sexual and parthenogenetic Artemia: A reevaluation. Crustaceana 57: 57-71.

Other Scientific Comments:

Halanych, K. M., 2004. Book Review- Texts: Brusca & Brusca (2003) Invertebrates Second edition and Ruppert, Fox & Barnes (2003) Invertebrate Zoology, Seventh edition. Systematic Biology. 53 :662-664. PDF

Halanych, K.M., M. Tieger, G. D. O'Mullan, R. A. Lutz, and R. C. Vrijenhoek. 1999. Brief description of biological communities at 7oS on the Eastern Pacific Rise. InterRidge 8: 23-27. (gray lit.).

Eernisse, D. J. and K. M. Halanych. 1999. Tree of Life Metazoan Home page. http://Ag.Arizona.Edu/tree/eukaryotes/animals/animals.html

McHugh, D. and K.M. Halanych. 1998. Evolutionary relationships of metazoan phyla: Advances, problems, and approaches. American Zoologist. 38: 813-817. (Introduction to symposium).

Halanych, K.M., J. Bachelor, A.M. Aquinaldo, S. Liva, D.M. Hillis, and J.A. Lake. 1996. Lophophorate phylogeny. Science 272:283. (Technical comment related to publication #5.)

Halanych, K.M., J. Bachelor, A.M. Aquinaldo, S. Liva, D.M. Hillis, and J.A. Lake. 1995. 18S rDNA from Lophophorates. Science 270: 1852. (Technical comment related to publication #5.)