Publications

 

 

Under Revision

  Kalkvik, H.M., I.J. Stout, E.A. Hoffman, and C.L. Parkinson. Colonization and Divergence: Phylogeography and population genetics of the Atlantic Coast beach mice.
     

Under Revision

  Fenwick, A., K.M. Diamond, T.J. Laduc, and C.L. Parkinson. Combined morphological and molecular evidence evaluates species relationships among rattlesnakes, Crotalus and Sistrurus (Serpentes: Viperidae). Zootaxa.
     

2017

  Reece, J.S, A. Alansari, H.M. Kalkvik, A. Alkindi, I. Mahmoud, A.Y. Al Kiyumi, A.E. Elshafie, M.P. Jensen, and C.L. Parkinson. A survey of the genetic diversity of the Loggerhead and Green Sea Turtles of the Sultanate of Oman. Bulletin for the Florida Museum of Natural History 54(6): 104-117
     
 2016pdf-icon-copy-min   Doan, T.M., A.J. Mason, T.A. Castoe, M. Sasa, C.L. Parkinson. A cryptic palm-pitviper species (Squamata: Viperidae: Bothriechis) from the Costa Rican highlands, with notes on the variation within B. nigroviridisZootaxa.
     
2016pdf-icon-copy-min   Streicher, J.W., J.P. McEntee, L.C. Drzich, D.C. Card, D.R. Schield, U. Smart, C.L. Parkinson, T. Jezkova, E.N. Smith, T.A. Castoe. Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes. Evolution.
     
2016pdf-icon-copy-min   Strickland, J.L., S. Carter, F. Kraus, C.L. Parkinson. Snake evolution in Melanesia: origin of Hydrophiinae (Serpentes, Elapidae), and the evolutionary history of the enigmatic New Guinean elapid Toxicocalamus. Zoological Journal of the Linnean Society.
     

2014

  Strickland, J.L., C.L. Parkinson, J.K. McCoy and L.K. Ammerman. Phylogeography of Agkistrodon piscivorus in Texas and throughout its range. Copeia
     

2013

  Muthukrishnan, G., Lamers, R.P., Ellis, A., Paramanandam, V., Tafur, S. Parkinson, C.L. and A.M. Cole. Longitudinal genetic analyses of Staphylococcus aureus nasal carriage dynamics in a diverse population. BMC Infectious Disease 13:221. 
     

2012

  Kalkvik, H.M., I.J. Stout, and C.L. Parkinson. Unraveling natural versus anthropogenic effects on genetic diversity within the southeastern beach mouse (Peromyscus polionotus niveiventris). Conservation Genetics 13:1653-1664.  
     

2012

  Lamers, R.P., G. Muthukrishnan, T.A. Castoe, S. Tafur, A.M. Cole, and C.L. Parkinson. Phylogenetic relationships among Staphylococcus species and refinemeent of cluster groups based on multilocus data. BMC Evolutionary Biology 12:171. 
     

2012

  Castoe, T.A., J.W. Streicher, J.M. Meik, M.J. Ingrasci, A.W. Poole, A.P.J. de Koning, J.A. Campbell, C.L. Parkinson, E.N. Smith, and D.D. Pollock. Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related species. Molecular Ecology Resources 12:1105-1113. 
     

2012

  Fenwick, A. , H. W. Greene, and C.L. Parkinson. The Serpent and the Egg: Unidirectional evolution of reproductive mode in vipers? Journal of Zoological Systematics and Evolutionary Research 50:59-66. 
     

2012

  Kalkvik, H.M., I.J. Stout, T.J. Doonan, and C.L. Parkinson. Investigating niche and lineage diversification in widely distributed taxa: phylogeography and ecological niche modeling of the Peromyscus maniculatus species group. Ecography 34:1-11. 
     

2011

  Lamers, R.P. , J.W. Stinnett, G. Muthukrishnan, C.L. Parkinson, and A.M. Cole. Evolutionary analyses of Staphylococcus aureus identify genetic relationships between nasal carriage and clinical isolates. Plos One 6(1): e16426. 
     

2010

 

Daza, J.M.* , T.A. Castoe*, and C.L. Parkinson. Using regional comparative phylogeographic data from snake lineages to infer historical processes in Middle America. Ecography.  

[*These authors contributed equally and should be considered joint primary authors]

     

2010

  Metzger, G.A., F. Kraus, A. Allison, and C. L. Parkinson . Uncovering cryptic diversity in Aspidomorphus (Serpentes: Elapidae): evidence from mitochondrial and nuclear markers.  Molecular Phylogenetics and Evolution 54(2):405-416. 
     

2009

  Castoe, T.A., W. Gu, A.P.J. de Koning, J.M. Daza, Z.J. Jiang, C.L. Parkinson , and D.D. Pollock. Dynamic nucleotide mutation gradients and control region usage in squamate reptile mitochondrial genomes. Cytogenetic and Genome Research. 
     

2009

  Daza, J.M. , E.N. Smith, V. P. Páez and C.L. Parkinson. Complex evolution in the Neotropics: the origin and diversification of the widespread genus Leptodeira (Serpentes: Colubridae).  Molecular Phylogenetics and Evolution 53(3):653–667 
     

2009

  Manjerovic, M. B., J. M. Waterman, E. A Hoffman, C. L. Parkinson. Characterization of nine microsatellite loci in the Cape ground squirrel, Xerus inauris , and their cross-utility in other species. Molecular Ecology Resources.
     

2009

  Suazo, A.A., J.E. Fauth, J.D. Roth, C.L, Parkinson, and I.J.Stout. Responses of small rodents to habitat restoration and management for the imperiled Florida Scrub-Jay. Biological Conservation 142(10): 2322-2328. 
     

2009

 

Castoe, T.A.,*, A.P.J. de Koning*, H-M Kim, W. Gu, B.P. Noonan, G. Naylor, Z.J. Jiang, C.L. Parkinson, and D.D.Pollock. Evidence for an ancient adaptive episode of convergent molecular evolution. Proceedings of the National Academy of Sciences U. S. A. 106(22): 8986-8991.  

[*These authors contributed equally and should be considered joint primary authors] 

See Commentary by Scott Edwards

     

2009

 

Fenwick, A., R.L. Gutberlet, J.A. Evans, and C.L. Parkinson. Morphological and molecular evidence for phylogeny and classification of South American pitvipers, genera BothropsBothriopsis, and Bothrocophias (Serpentes: Viperidae).  Zoological Journal of the Linnean Society 156: 617–640.  

Supporting Material 

     

2009

 

Featured Cover Issue:

*Castoe, T.A., *Daza, J.M., Smith, E.N. Sasa, M.M., Kuch, U., Campbell, J.A., Chippindale, P.T. and C.L. Parkinson. Comparative phylogeography of pitvipers suggests a consensus of ancient middle American highland biogeography. Journal of Biogeography 36:88-103 

[*These authors contributed equally and should be considered joint primary authors] 

     

2007

  Castoe, T.A., E.N. Smith, R.M. Brown, and C.L. Parkinson. Higher-level phylogeny of Asian and American coralsnakes, their placement within the Elapidae (Squamata), and the systematic affinities of the enigmatic Asian coralsnake Hemibungarus calligasterZoological Journal of the Linnean Society 151:809-831. 
     

2007

 

Jiang, Z. / Castoe, T.A., C.C. Austin, F.T. Burbrink, M.D. Herron, J.A. McGuire, C.L. Parkinson, and D.D. Pollock. Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region. BMC-Evolutionary Biology. 

[*These authors contributed equally and should be considered joint primary authors] 

     

2007

  Degner, J.F., I.J. Stout, J.D. Roth, and C. L. Parkinson. Population genetics and conservation of the threatened southeastern beach mouse (Peromyscus polionotus niveiventris): Subspecies and evolutionary units. Conservation Genetics 8:1441–1452.
     

2007

  Castoe, T.A., C.L. Spencer, and C. L. Parkinson. Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): A perspective on North American desert biogeography. Molecular Phylogenetics and Evolution 42:193-212. 
     

2006

  Castoe, T.A., C.L. Parkinson. Bayesian mixed models and the phylogeny of pitvipers (Viperidae: Serpentes). Molecular Phylogenetics and Evolution 39:91-110. 
     

2006

  Reece, J.S., L.M. Ehrhart, C.L. Parkinson. Mixed stock analysis of juvenile loggerheads (Caretta caretta) in the Indian River Lagoon, Florida: Implications for conservation planning. Conservation Genetics 7:345-352. 
     

2005

  Parkinson, C.L. JP Mower, Y-L Qiu, AJ Shirk, K Song, ND Young, CW dePamphilis and JD Palmer. Multiple Major Increases and Decreases in Mitochondrial Substitution Rates in the Plant Family Geraniaceae. BMC Evolutionary Biology 5:73.  
     

2005 

  Castoe, T.A., M.M. Sasa, and C.L. Parkinson. Modeling nucleotide evolution at the mesoscale: The phylogeny of the Neotropical pitvipers of the Porthidium group (Viperidae). Molecular Phylogenetics and Evolution 37:881-898. 
     

2005

  Wiens, J.J., , J.W. Fetzner, C.L. Parkinson, and T.W. Reeder. Hylid frog phylogeny and sampling strategies for speciose clades. Systematic Biology 54(5):719–748. 
     

2005

  Herron, M.D., J.M. Waterman, and C.L. Parkinson. Phylogeny and historical biogeography of African ground squirrels: the role of climate change in the evolution of Xerus. Molecular Ecology 14:2773-2788.
     


2005 

  Mulvaney, A., T.A. Castoe, K.G. Ashton, K.L. Krysko, and C.L. Parkinson. Evidence of population genetic structure within the Florida worm lizard, Rhineura floridana (Amphisbaenia: Rhineuridae). Journal of Herpetology 39:118-124. 
     

2005 

  Reece, J.S., T.A. Castoe, and C.L. Parkinson. Historical perspectives on population genetics and conservation of three marine turtle species. Conservation Genetics 6:235-251.
     

2004

  Castoe, T.A. , T.M. Doan, and C.L. Parkinson. Data partitions and complex models in Bayesian analysis: the phylogeny of gymnophthalmid lizards. Systematic Biology 53(3):448-469.
     

2004

  Herrmann, H.W, T. Ziegler, A. Malhotra, R. Thorpe, and C.L. Parkinson. Redescription and systematics of Trimeresurus cornutus (Serpentes: Viperidae) based on morphology and molecular data. Herpetologica. 60(2): 211-221. 
     

2004

  Herron, M.D., T.A. Castoe, C.L. Parkinson. Sciurid phylogeny and the paraphyly of Holarctic ground squirrels (Spermophilus). Molecular Phylogenetics and Evolution 31: 1015-1030.
     

2003

  Castoe, T.A., P. Chippindale, J. Campbell, L. K. Ammerman, and C. L. Parkinson. Molecular systematics of the Middle American jumping pitvipers (Genus Atropoides) and phylogeography of the Atropoides nummifer complex. Herpetologica 49:421-432.
     

2003

  Daniell, H. and C. L. Parkinson. Jumping genes and containment. Nature Biotechnology 21: 374-375.
     

2002

  Parkinson, C.L., P. Chippindale, and J. Campbell. Multigene phylogenetic analysis of pitvipers, with comments on their biogeography. In Biology of the Vipers (Ed by GW Schuett, M Höggren, ME Douglas, and HW Greene). Eagle Mountain Publishing, LC. Eagle Mountain, Utah.
     

2000

  Nickrent, D.L., C.L. Parkinson, J.D. Palmer, and R.J. Duff. Multigene phylogeny of land plants with special reference to Bryophytes and the earliest land plants. Molecular Biology Evolution 17(12): 1885-1895.
     

2000

  Palmer, J.D., K.L. Adams, Y. Cho, C.L. Parkinson, Y.-L. Qiu and K. Song. Dynamic evolution of plant mitochondrial genomes: Mobile genes and introns, and highly variable mutation rates. Proceedings of the National Academy of Sciences U. S. A. 97(13):6960-6966.
     

2000

  Parkinson, C.L., K.R. Zamudio, and H.W. Greene. Phylogeography of the pitviper clade Agkistrodon: historical ecology, species status, and conservation of the cantils. Molecular Ecology 9:411-420. 
     

2000

  Chaw, S-M., C.L. Parkinson, Y.Cheng, T.M. Vincent, and J.D. Palmer. Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant Gymnosperms and origin of Gnetales from conifers. Proceedings of the National Academy of Sciences U.S.A. 97(8):4086-4091.
     

2000

 

Featured Cover Issue

Parkinson C.L., K.L. Adams, and J.D. Palmer. Multigene analyses identify the three earliest lineages of extant flowering plants. Current Biology 9(24):1485-1488. 

     

1999

  Parkinson, C.L. Molecular systematics and biogeographical history of pitvipers as determined by mitochondrial ribosomal DNA sequences. Copeia 1999(3): 576-586. 
     

1998

  Adams, K.L., K. Song, Y.-L. Qiu, A. Shirk, Y. Cho, C.L. Parkinson, and J.D. Palmer. Evolution of flowering plant mitochondrial genomes: Gene content, gene transfer to the nucleus, and highly accelerated mutation rates. Pages 13-18 in Plant Mitochondria: From Gene to Function (I.M. Moller, P. Gardestrom, K. Glimeliusand E. Glaser eds.) Backhuys Publishers, Leiden, The Netherlands.
     

1997

  Parkinson, C.L., S.M. Moody, and J.E. Ahlquist. Phylogenetic relationships of the "Agkistrodon Complex" based on mitochondrial DNA sequence data. Pages 63-78 in Venomous Snakes: Ecology, Evolution and Snakebite (R.S. Thorpe, W. Wüster and A. Malhotra, eds.) The Zoological Society of London, Clarendon Press, Oxford.