Diversity of marine invertebrate is far greater than most people realize. In the Halanych lab, we are trying to understand how such extensive morphological variation came about by exploring questions on different time scales and with different types of genomic information. Combining a molecular systematic and/or genomic approach with information from organismal evolution has proved a powerful approach to study everything from the origin of major animal lineages to the recent biogeographic history of commercially important species.

2024

Warner, J.F., R.C. Range, J. Fenner, C. Ka, D.S. Waits, K. Boddy, K.T. David, A.R. Mahon, K. M. Halanych, 2024. Chromosomal-level genome assembly of the Antarctic sea urchin Sterechinus neumayeri, a model for Antarctic invertebrate biology. Genome Biology and Evolution, p.evae237.

Xu, B., L. Kong, J. Sin, J. Zhang, Y Zhang, H. Song, Q. Li, J. E. Uribe, K. M. Halanych, C. Cai, Y-W. Dong, S. Wang, Y. Li. 2024. Molluscan Systematics: historical perspective and the way ahead. Biological Reviews. doi: 10.1111/brv.13157

Zehnpfennig, J. R., M. P. Galaska, K. M. Halanych, A. R. Mahon. 2024. Single nucleotide polymorphism data reveals distinct geographic structuring in the Antarctic circumpolar sea spider Nymphon australe. Marine Biology. 2024:171-179.

Bogantes, V. E., K. Meiβner, D. S. Waits, K. M. Kocot, K. M. Halanych. 2024. Phylogenomic reconstruction influenced by assembly and annotation parameters:  Using whole genome data to unravel the relationships of Spionidae (Annelida). Zoologica Scripta. DOI: 10.1111/zsc.12676.

Yap-Chiongco, M. K., S. Pirro, R. M. Varney, H. Saito, K. M. Halanych, K. M. Kocot. 2024. Two draft genomes of enigmatic Solenogastres (Mollusca, Aplacophora) Epimenia babai and Neomenia megatrapezata. Faculty of 1000 13: 318.

Belato, F. A., B. Mello, C. J. Coates, K. M. Halanych, F. Brown, A. C. Morandini, J. de Moraes Leme, R. I. F. Trindade, E. M. Costa-Paiva. 2024. Divergence time estimates for the hypoxia-inducible factor-1 alpha (HIF1a) reveal an ancient emergence of animals in low-oxygen environments. Geobiology 22:e12577.

2023

Clark, M.S., J.I. Hoffman JI, L.S. Peck LS, L. Bargelloni L, D. Gande,  C. Havermans, B. Meyer, T. Patarnello, T. Phillips, K.R. Stoof-Leichsenring, D.L.J. Vendrami, A. Beck, G. Collins, M.W. Friedrich, K. M. Halanych, J.F. Masello, R. Nagel, K. Norén, C. Printzen, M.B. Ruiz, S. Wohlrab, B. Becker, K. Dumack, F. Ghaderiardakani, K. Glaser, S. Heesch, C. Held, U. Karsten, S. Kempf, M. Lucassen, A. Paijmans, K. Schimani, A. Wallberg, L.C. Wunder, T. Mock. 2023. Multi-omics for studying and understanding polar life. Nature Communications 14:7451

Aroh, O., M. Liles, K. M. Halanych. 2023. Genomic characterization of a novel, widely distributed Mycoplasma Species “Candidatus Mycoplasma mahonii” associated with the brittlestar Gorgonocephalus chilensis. PLOS One 18: e0290305.

David, K. T., K. M. Halanych. 2023. Unsupervised deep learning can identify protein functional groups from unaligned sequences. Genome Biology and Evolution 15: evad084.

Vandepas, L.E., M.G. Tassia, K. M. Halanych, C.T Amemiya. 2023. Unexpected distribution of chitin and chitin synthase across soft-bodied cnidarians. Biomolecules 13: 777.

Tassia, M. G., H. A. Hallowell, D. S. Waits, R. C. Range, C. J. Lowe, R. M. Graze, E. Hiltbolt-Schwartz, K. M. Halanych. 2023. Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity. Molecular Biology and Evolution 40:msad097.

Grimes, C. J., K. Donnelly, C. Ka, N. Noor, A. R. Mahon, K. M. Halanych. 2023. Community structure across the Western Antarctic continental shelf and a latitudinal change in epibenthic faunal abundance assessed by photographic surveys. Frontiers in Marine Science. 10:1094283.

Brannock, P. M., A. Demopoulos, S. C. Landers, D. S. Waits, K. M. Halanych. 2023. Metabarcoding analysis of meiobenthic biodiversity along the Gulf of Mexico continental shelf. Estuarine, Coastal and Shelf Science 285:108303.

Coppo, G. C., F. S. Pais, T. O. Ferreira, K. M. Halanych, K. B. Donnelly, A. Carolina de A. Mazzuco, Angelo F. Bernardino. 2023. Transition of an estuarine benthic meiofauna assemblage 1.7 and 2.8 years after a mining disaster. Peer J 11:e14992.

Alves, P.R., K. M. Halanych, E. P. Silva, C. S. G. Santos. 2023. Nereididae (Annelida) phylogeny based on molecular data. Organisms, Diversity, Evolution https://doi.org/10.1007/s13127-023-00608-9.

Whalen, N. V., K. M. Halanych. 2023. Communications Arising - Available data support Ctenophora as the sister group to all other Metazoa. Nature Communications 14: 711.

2022

Zhang, N., Y. Li, K. M. Halanych, L. Kong, Q. Li. 2022. A comparative analysis of mitochondrial ORFs provides new insights on expansion of mitochondrial genome size in Arcidae. BMC Genomics 23:809.

Coats, C. J., F. A. Belato, K. M. Halanych, E. M. Costa-Paiva. 2022.Structure-function relationships of oxygen transport proteins in marine invertebrates enduring higher temperatures and deoxygenation. Biological Bulletin 243:134-148.

Zehnpfenning, J. R., R. M. Varney, K. M. Halanych, A. R. Mahon. 2022. Mitochondrial genomes provide insight into interfamilial relationships within Pycnogonida. Polar Biology 45:1513-1522, https://doi.org/10.1007/s00300-022-03085-6.

Li, Y., M. A. Altamia, J. R. Shipway, M. R. Brugler, A. F. Bernardino, T. L. De Brito, Z. Lin, F. A. da Silva Oliveira, P. Sumida, C. R. Smith, A. Trindade-Silva, K. M. Halanych, D. L. Distel. 2022. Contrasting modes of mitochondrial genome evolution in sister taxa of wood-eating marine bivalves (Teredinidae and Xylophagaidae). Genome Biology and Evolution 14: evac089.

Drábková, M., J. Zrzavý, K. M. Halanych, T. H. Oakley, L. L. Moroz, J. T. Cannon, A. Kuris, A. E. Garcia-Vedrenne, J. Štefka, E. A. Ellis, K. M. Kocot. 2022. Enigmatic ‘mesozoan’ phyla Dicyemida and Orthonectid (Lophotrochozoa): different views from different phylogenomic methods. Proceedings of the Royal Society B 289: 20220683.

Young, E.L., K. M. Halanych, D. J. Amon, I. Altamira, J. R. Voigt, N. D. Higgs, C. R. Smith. 2022. Community structure and biodiversity of organic-fall habitats on the deep Washington-Oregon margin, NE Pacific. Marine Ecological Progress Series 687: 23-42.

Costa-Paiva, E. B. Mello, B. S. Bezerra, C. Coates, K. M. Halanych, F. Brown, J. de Moraes Leme & R. I. F. Trindade. 2022. Molecular dating of the blood pigment hemocyanin provides new insight on the origin of animals. Geobiology. 20: 333-345. https://doi.org/10.1111/gbi.12481.

2021

Garber, A. I., J. R. Zehnpfennig, C. S. Sheik, M. W. Henson, G. A. Ramirez, A. R. Mahon, K. M. Halanych, D. R. Learman. 2021. Metagenomics of Antarctic marine sediment reveals potential for diverse chemolithoautotroph. mSphere 6:e00770-21.

Redak, C.A., A. S. Williams, J. T. Garner, K. M. Halanych, N. V. Whelan. 2021. Assessing genomic diversity, connectivity, and riverscape genetics hypotheses in the endangered Rough Hornsnail, Pleurocera foremani, following habitat disruption. Journal of Heredity 112: 635–645.

Tassia, M. G. , K. T. David, J. P. Townsend, K. M. Halanych. 2021. TIAMMAt: Leveraging biodiversity to revise protein domain models, evidence from innate immunity. Molecular Biology and Evolution 38:5806-5818.

Aroh, O., K. M. Halanych. 2021. Genome-wide characterization of LTR retrotransposons in the non-model deep-sea annelid Lamellibrachia luymesi. BMC Genomics 22 (1), 1-11.

Bogantes, V. E. M. J. Boyle, K. M. Halanych. 2021. New reports of Pseupodolydora (Annelida: Spionidae) from the East Coast of Florida, including the non-native species P. paucibranchiata. Biological Invasions 10.

Wilson, C. A., N. M. Dannreuther, J. W. Farrington, M. G. Feldman, K. M. Halanych, J. L. Pettit, J. Rullkötter, P. A. Sandifer, J. G. Shepherd, D. Westerholm, C. J. Yanoff, L. A. Zimmermann. 2021. Summary of Findings and Research Recommendations from the Gulf of Mexico Research Initiative. Oceanography 34:228-239.

Halanych, K. M., C. H. Ainsworth, E. E. Cordes, R. E. Dodge, M. Huettel, I.A. Mendelssohn, S. A. Murawski, C. B. Paris-Limouzy, P. T. Schwing, R. F. Shaw, T. Sutton. 2021. Effects of petroleum by-products and dispersants on ecosystems. Oceanography 34:152-163.

Halanych, K. M., D. Westerholm. 2021. Considerations for scientists getting involved in oil spill research. Oceanography 34:112-123.

Murawski, S. A., M. Grosell, C. Smith, T. Sutton, K. M. Halanych, R. Shaw, C. A. Wilson. 2021. Chapter 10: Impacts of Petroleum, Petroleum Components and Dispersants on Organisms and Populations. Oceanography 34:136-151

Weiman, S., S. B. Joye, J. E. Kostka, R. R. Colwell, K. M. Halanych. 2021. GoMRI insights into microbial genomics and hydrocarbon bioremediation response in marine ecosystems. Oceanography 34:124-135, https://www.jstor.org/stable/27020065

Galaska, M.P, D. S. Wethey, A. Arias, S. F. Dubois, K. M. Halanych, S. A. Woodin. 2021. The impact of aquaculture on the genetics and distribution of the onuphid annelid Diopatra biscayensis. Ecology and Evolution 11, 6184-6194.

David, K. T., K. M. Halanych. 2021. Spatial proximity between polyploids across South American frog genera. Journal of Biogeography 48(5), 991-1000.

K. M. Halanych, J.T. Cannon, J. Benito. 2021. Access Science

Ingels, J., R. B. Aronson, C. R. Smith, A. Baco, H. M. Bik, J. A. Blake, A. Brandt, M. Cape, D. Demaster, E. Dolan, E. Domack, S. Fire, H. Geisz, M. Gigliotti, H. Griffiths, K. M. Halanych, C. Havermans, F. Huettmann, S. Ishman, S. Kranz, A. Leventer, A. R. Mahon, J. McClintock, M. L. McCormick, B. G. Mitchell, A. Murray, L. Peck, A. Rogers, B. Shoplock, K. E. Smith, B. Steffel, M. R. Stukel, A. Sweetman, M. Taylor, A. R. Thurber, M. Truffer, A. van de Putte, A. Vanreusel, M. A. Zamora-Duran. 2021. Antarctic Ecosystem Responses following Ice Shelf Collapse and Iceberg Calving: Science Review and Future Research. WIRE’s Climate Change. 2021:e682.

2020

Li, Y., K. T. David, X.-X. Shen, J. L. Steenwyk, K. M. Halanych, A.Rokas. 2020. Feature Frequency Profile-based phylogenies are inaccurate. Proceedings of the National Academy of Sciences. On-line letter. https://doi.org/10.6084/m9.figshare.12543050.v1.

Belato, F. A., C. J. Coates, K. M. Halanych, R. E. Weber, E. M. Costa-Paiva. 2020. Evolutionary history of the globin gene family in annelids. Genome Biology and Evolution 12:1719-1733.

Kong, L., K. M. Kocot, Y. Yang, L. Qi, Q. Li, K. M. Halanych. 2020. Mitogenomics reveals phylogenetic relationships of Arcoida (Mollusca, Bivalvia) and multiple independent expansions in mitochondrial genome size. Molecular Phylogenetics and Evolution 150:106857.

Erséus, C., B. W. Williams, K. M. Horn, K. M. Halanych, S. R. Santos, S. W. James, M. C. des Châtelliers, F. E. Anderson. 2020. Phylogenomic analyses reveal a Paleozoic radiation and support a fresh water origin for clitellate annelids. Zoologica Scripta49:614-640.

Zhou. Y., Y. Li, H. Cheng, K. M. Halanych, C. Wang. 2020. The mitochondrial genome of the bone-eating worm Osedax rubiplumus (Annelida, Siboglinidae). Mitochondrial DNA Part B: Resources 5:2267-2268.

Townsend, J.P., M. G. Tassia, A. Damian-Serrano, N. V. Whelan, K. M. Halanych, A. M. Sweeney. 2020. A mesopelagic ctenophore representing a new family, with notes on family-level taxonomy in Ctenophora: Vampyroctena delmarvensis gen. nov. sp. nov (Vampyroctenidae, fam. nov.). Marine Biodiversity 50:34.

Alves, P. R., K. M. Halanych, C. S. G. Santos. 2020. The phylogeny of Nereididae (Annelida) based on mitochondrial genomes. Zoologica Scripta 49: 366–378.

David, K. T., J. R. Oaks, K. M. Halanych. 2020. Patterns of Gene Evolution Following Duplications and Speciations in Vertebrates. PeerJ 8:e8813

Bogantes, V. E., N. V. Whelan, K. Webster, A. R. Mahon, K. M. Halanych. 2020. Unrecognized diversity of a scale worm, Polyeunoa laevis (Annelida: Polynoidae), that feeds on soft coral. Zoologica Scripta 49:236-249.

Kocot, K.M., A. J. Poustka, I. Stöger, K. M. Halanych, M. Schrödl. 2020. New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships. Scientific Reports 10:101.

Garey, J.B., C.B. Cameron, K.M. Halanych, J.A. Servin, J.A. Lake. 2020. Deuterostomia. Pp.607-610. In Ed. K. de Queiroz, P. D. Cantino, J. A. Gauthier, Phylonyms, A Companion to the PhyloCode, 1st Edition. CRC Press.

Lake, J.A., K.M. Halanych, M.C. Rivera, J.A. Servin, J.R. Garey. 2020. Ecdysozoa. Pp. 555-556. In Ed. K. de Queiroz, P. D. Cantino, J. A. Gauthier, Phylonyms, A Companion to the PhyloCode, 1st Edition. CRC Press.

Halanych, K.M., J.R. Garey, J.A. Servin, J.A. Lake. 2020. Lophotrochozoa. Pp. 485-488. In Ed. K. de Queiroz, P. D. Cantino, J. A. Gauthier, Phylonyms, A Companion to the PhyloCode, 1st Edition. CRC Press.

Garey, J.R., K.M. Halanych, J.A. Servin, J.A. Lake. 2020. Protostomia. Pp. 479-483. In Ed. K. de Queiroz, P. D. Cantino, J. A. Gauthier, Phylonyms, A Companion to the PhyloCode, 1st Edition. CRC Press.

Lake, J.A., J.R. Garey, J.A. Servin, K.M. Halanych. 2020. Bilateria. Pp. 475-477. In Ed. K. de Queiroz, P. D. Cantino, J. A. Gauthier, Phylonyms, A Companion to the PhyloCode, 1st Edition. CRC Press.

Garey, J.A., K.M. Halanych. 2020. Metazoa. Pp. 418-419. In Ed. K. de Queiroz, P. D. Cantino, J. A. Gauthier, Phylonyms, A Companion to the PhyloCode, 1st Edition. CRC Press.