Halanych Kenneth M.

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Last Name
Halanych
First Name
Kenneth M.
ORCID
0000-0002-8658-9674

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  • Preprint
    Mitochondrial genomes of Clymenella torquata (Maldanidae) and Riftia pachyptila (Siboglinidae) : evidence for conserved gene order in Annelida
    ( 2004-10-04) Jennings, Robert M. ; Halanych, Kenneth M.
    Mitochondrial genomes are useful tools for inferring evolutionary history. However, many taxa are poorly represented by available data. Thus, to further understand the phylogenetic potential of complete mitochondrial genome sequence data in Annelida (segmented worms), we examined the complete mitochondrial sequence for Clymenella torquata (Maldanidae) and an estimated 80% of the sequence of Riftia pachyptila (Siboglinidae). These genomes have remarkably similar gene orders to previously published annelid genomes, suggesting that gene order is conserved across annelids. This result is interesting given the high variation seen in the closely related Mollusca and Brachiopoda. Phylogenetic analyses of DNA sequence, amino acid sequence and gene order all support the recent hypothesis that Sipuncula and Annelida are closely related. Our findings suggest that gene order data is of limited utility in annelids but that sequence data holds promise. Additionally, these genomes show AT bias (~66%) and codon usage biases, but have a typical gene complement for bilaterian mitochondrial genomes.
  • Article
    TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity
    (Oxford University Press, 2021-08-30) Tassia, Michael G. ; David, Kyle T. ; Townsend, James P. ; Halanych, Kenneth M.
    Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR’s NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt’s flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species.
  • Dataset
    Infauna counts from BoWLs moorings deployed and recovered from R/V Oceanus cruises OC1304A and OC1406B off the Coast of Oregon from 2013-2014 (BOWLS project)
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-01-14) Smith, Craig R. ; Halanych, Kenneth M.
    This dataset contains counts of infaunal organism Phyla from BOWLS moorings deployed in April of 2013 and recovered in June of 2014. Phyla sampled: Annelida, Arthropoda,Chordata, Cnidaria, Echinodermata, Kinorhynca, Mollusca, Nemertea, and Platyhelminthes. Also included are the mooring identifiers, substrate type (control, wood, whale-bone), latitude, longitude, depth, and deployment and recovery dates. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/724434
  • Preprint
    Seasonal occurrence of balanomorph barnacle nauplius larvae in the region of the Antarctic Peninsula
    ( 2010-03-01) Scheltema, Rudolf S. ; Scheltema, Amelie H. ; Williams, Isabelle P. ; Halanych, Kenneth M.
    Plankton samples taken along the west coast of the Antarctic Peninsula and in Bransfield Strait show widespread occurrence of Bathylasma corolliforme nauplius larvae during the austral spring, mid-October to the third week of December. During autumn, between the first week of May and early June there was a complete absence of balanomorph nauplii. This evidence shows periodicity in reproduction. There is a seemingly close correlation between the presence of these nauplii and the published data on phytoplankton biomass and seawater surface temperature.
  • Dataset
    Metadata associated with genomic and genetic data collected from organisms obtained on BOWLs landers, R/V Oceanus June 22-27, 2014 (BOWLS project)
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-01-14) Smith, Craig R. ; Halanych, Kenneth M.
    Metadata associated with genomic and genetic data collected from organisms obtained on BOWLs landers, R/V Oceanus June 22-27, 2014. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/662996
  • Article
    Summary of findings and research recommendations from the Gulf of Mexico Research Initiative
    (Oceanography Society, 2021-06-03) Wilson, Charles A. ; Feldman, Michael G. ; Carron, Michael J. ; Dannreuther, Nilde Maggie ; Farrington, John W. ; Halanych, Kenneth M. ; Petitt, Jennifer L. ; Rullkötter, Jürgen ; Sandifer, Paul ; Shaw, J. Kevin ; Shepherd, John G. ; Westerholm, David G. ; Yanoff, Callan J. ; Zimmermann, Leigh A.
    Following the Deepwater Horizon explosion and oil spill in 2010, the Gulf of Mexico Research Initiative (GoMRI) was established to improve society’s ability to understand, respond to, and mitigate the impacts of petroleum pollution and related stressors of the marine and coastal ecosystems. This article provides a high-level overview of the major outcomes of the scientific work undertaken by GoMRI. This i scientifically independent initiative, consisting of over 4,500 experts in academia, government, and industry, contributed to significant knowledge advances across the physical, chemical, geological, and biological oceanographic research fields, as well as in related technology, socioeconomics, human health, and oil spill response measures. For each of these fields, this paper outlines key advances and discoveries made by GoMRI-funded scientists (along with a few surprises), synthesizing their efforts in order to highlight lessons learned, future research needs, remaining gaps, and suggestions for the next generation of scientists.
  • Dataset
    Metadata describing mooring deployment and recovery from R/V Oceanus cruises OC1304A and OC1406B off the Coast of Oregon from 2013-2014 (BOWLS project)
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-01-14) Smith, Craig R. ; Halanych, Kenneth M.
    Metadata describing mooring deployment and recovery from R/V Oceanus cruises OC1304A and OC1406B off the Coast of Oregon from 2013-2014 (BOWLS project) For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/568713
  • Dataset
    Epifauna counts from BOWLS moorings deployed and recovered from R/V Oceanus cruises OC1304A and OC1406B off the Coast of Oregon from 2013-2014 (BOWLS project)
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-01-14) Smith, Craig R. ; Halanych, Kenneth M.
    This dataset contains counts of epifaunal organism Phyla from BOWLS moorings deployed in April of 2013 and recovered in June of 2014. Phyla sampled: Annelida, Arthropoda, Chaetognatha, Chordata, Cnidaria, Echinodermata, Kinorhynca, Mollusca, Nematoda, Nemertea, and Platyhelminthes. Also included are the mooring identifiers, substrate type (control, wood, whale-bone), latitude, longitude, depth, and deployment and recovery dates. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/676064