PEER-REVIEWED ARTICLES

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72.

Colis-Torres A, Neri-Castro E, Strickland JL, Olvera-Rodríguez A, Borja M, Calvete J, Jones J, Parkinson CL, Bañuelos J, López de León J, et al. Intraspecific venom variation of Mexican west coast rattlesnakes (Crotalus Basiliscus) and its implications for antivenom production. Biochimie. 2021. doi:10.1016/j.biochi.2021.10.006

71.

Hofmann, E.P.; Rautsaw, R.M.; Mason, A.J.; Strickland, J.L.; Parkinson, C.L. Duvernoy’s Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes. Toxins 2021, 13, 336. https://doi.org/10.3390/toxins13050336

70.

Matthew L. Holding, Jason L. Strickland, Rhett M. Rautsaw, Erich P. Hofmann, Andrew J. Mason, Michael P. Hogan, Gunnar S. Nystrom, Schyler A. Ellsworth, Timothy J. Colston, Miguel Borja, Gamaliel Castañeda-Gaytán, Christoph I. Grünwald, Jason M. Jones, Luciana A. Freitas-de-Sousa, Vincent Louis Viala, Mark J. Margres, Erika Hingst-Zaher, Inácio L. M. Junqueira-de-Azevedo, Ana M. Moura-da-Silva, Felipe G. Grazziotin, H. Lisle Gibbs, Darin R. Rokyta, Christopher L. Parkinson. Phylogenetically diverse diets favor more complex venoms in North American pitvipers. Proceedings of the National Academy of Sciences, 2021; 118 (17): e2015579118 DOI: 10.1073/pnas.2015579118

69.

Pedro G Nachtigall, Rhett M Rautsaw, Schyler A Ellsworth, Andrew J Mason, Darin R Rokyta, Christopher L Parkinson, Inácio L M Junqueira-de-Azevedo, ToxCodAn: a new toxin annotator and guide to venom gland transcriptomics, Briefings in Bioinformatics, 2021;, bbab095, https://doi.org/10.1093/bib/bbab095

68.

Margres MJ, Rautsaw RM, Strickland JL, Mason AJ, Schramer TD, Hofmann EP, Stiers E, Ellsworth SA, Nystrom GS, Hogan MP, Bartlett DA, Colston TJ, Gilbert DM, Rokyta DR, Parkinson CL. 2021. The Tiger Rattlesnake genome reveals a complex genotype underlying a simple venom phenotype. Proceedings of the National Academy of Science. Jan 2021, 118 (4) e2014634118; DOI: 10.1073/pnas.2014634118

67.

Rautsaw RM, Schramer TD, Acuña R, Arick LN, DiMeo M, Mercier KP, Schrum M, Mason AJ, Margres MJ, Strickland JL, Parkinson CL. 2020. Genomic adaptations to salinity resist gene flow in the evolution of Floridian watersnakes. Molecular Biology and Evolution. DOI: 10.1093/molbev/msaa266

66.

Bayona-Serrano JD, Viala VL, Rautsaw RM, Schramer TD, Barros G. Nishiyama Junior MY, Sousa L, Moura-da-Silva AM, Parkinson CL, Grazziotin FG, Junqueira-de-Azevedo ILM. 2020. Metalloproteinase replacement and parallel structural simplification maintain venom phenotypes in diverse groups of rear-fanged snakes. Molecular Biology and Evolution. DOI: 10.1093/molbev/msaa192

65.

Reyes-Velasco J, Adams RH, Boissinot S, Parkinson CL, Campbell JA, Castoe TA, Smith EN. 2020. Genome-wide SNPs clarify lineage diversity confused by coloration in coralsnakes of the Micrurus diastema species complex (Serpentes: Elapidae). Molecular Phylogenetics and Evolution 147(106770). DOI: 10.1016/j.ympev.2020.106770

64.

Mason AJ, Margres MJ, Strickland JL, Rokyta DR, Sasa M, Parkinson CL. 2020. Trait differentiation and modular toxin expression in Palm-Pitvipers. BMC Genomics 1–20. DOI: 10.1186/s12864-020-6545-9

63.

Rautsaw RM, Hofmann EP, Margres MJ, Holding ML, Strickland JL, Mason AJ, Rokyta DR, Parkinson CL. 2019. Intraspecific sequence variation and gene expression contribute little to venom diversity in the Sidewinder Rattlesnake (Crotalus cerastes). Proceedings of the Royal Society B: Biological Sciences 286(1906). DOI: 10.1098/rspb.2019.0810

62.

Mason AJ, Grazziotin FG, Zaher H, Lemmon AR, Moriarty Lemmon E, Parkinson CL. 2019. Reticulate evolution in nuclear Middle America causes discordance in the phylogeny of palm‐pitvipers (Viperidae: Bothriechis). Journal of Biogeography. DOI: 10.1111/jbi.13542

61.

Strickland JL, Smith CF, Mason AJ, Schield DR, Borja M, Castañeda-Gaytán G, Spencer CL, Smith LL, Trápaga A, Bouzid NM, Campillo-García G, Flores-Villela OA, Antonio-Rangel D, Mackessy SP, Castoe TA, Rokyta DR, Parkinson CL. 2018. Evidence for divergent patterns of local selection driving venom variation in Mojave Rattlesnakes (Crotalus scutulatus). Scientific Reports 8: 17622.

60.

Borja M, Neri-Castro E, Pérez-Morales R, Strickland JL, Ponce-López R, Parkinson CL, Espinosa-Fematt J, Sáenz-Mata J, Flores-Martínez E, Alagón A, Castañeda-Gaytán Gamaliel. 2018. Ontogenetic change in the venom of Mexican Black-tailed Rattlesnakes (Crotalus molossus nigrescens). Toxins 10(12): 501. DOI: 10.3390/toxins10120501

59.

Hofmann EP†, Rautsaw RM†, Strickland JL, Holding ML, Hogan MP, Mason AJ, Rokyta DR, Parkinson CL. 2018. Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation. Scientific Reports 8: 15534. DOI:10.1038/s41598-018-33943-5

58.

Dahn HA, Strickland JL, Osorio A, Colston TJ, Parkinson CL. 2018. Hidden diversity within the depauperate genera of the snake tribe Lampropeltini (Serpentes, Colubridae). Molecular Phylogenetics and Evolution 129: 214-225. 

57.

Kalkvik HM, Stout IJ, Hoffman EA, Parkinson CL. 2018. Colonization and divergence: phylogeography and population genetics of the Atlantic coast beach mice. Systematics and Biodiversity. 

56.

Holding M, Margres M, Mason A, Parkinson C, Rokyta D. 2018. Evaluating the performance of de novo assembly methods for venom-gland transcriptomics. Toxins 10: 249. 

55.

Schield DR, Adams RH, Card DC, Corbin AB, Jezkova T, Hales NR, Meik JM, Perry BW, Spencer CL, Smith LL, García GC, Bouzid NM, Strickland JL, Parkinson CL, Borja M, Castañeda-Gaytán G, Bryson RW, Flores-Villela OA, Mackessy SP, Castoe TA. 2018. Cryptic genetic diversity, population structure, and gene flow in the Mojave rattlesnake (Crotalus scutulatus). Molecular Phylogenetics and Evolution.

54.

∞Strickland, J.L., A.J. Mason∞, D. Rokyta and C.L. Parkinson. 2018. Phenotypic variation in Mojave Rattlesnake (Crotalus scutulatus) venom is driven by four toxin families. Toxins 10 (4). doi:10.3390/toxins10040135 

53.

∞Lawrance, M.F., G. Muthukrishnan∞, J. Deichen∞, M. Deichen, J. Schaus, A.M. Cole, and C.L. Parkinson. 2018. Genetic Assessment of Staphylococcus aureus in an Underreported Locale: Ambulatory Care Clinic. Journal of Infection and Public Health 

52.

∞Martin SA, Rautsaw RM∞, Bolt MR, Parkinson CL, Seigel RA. 2018. Estimating the response of wildlife communities to coastal dune construction. Ocean & Coastal Management 161(1): 31-36.

51.

∞Rautsaw, R. M., S. A. Martin∞, K. Lanctot*, B. Vincent*, M. Rebecca Bolt, Richard A. Seigel, C. L. Parkinson. 2018 On the road again: Assessing the use of roadsides as wildlife corridors for Gopher Tortoises (Gopherus polyphemus). Journal of Herpetology 52 (2) 136-144 

50.

∞Rautsaw, R.M., S.A. Martin∞, B.A. Vincent*, K. Lanctot*, M.R. Bolt, R.A. Siegel, and C.L. Parkinson. 2018. Stopped dead in their tracks: The impact of railways on Testudine movement and behavior. Copeia 2018 (1) 135-143. 

49.

Borja, M. E. Neri-Castro, G. Castañeda-Gaytán, JL. Strickland, CL. Parkinson, J Castañeda-Gaytán, R. Ponce-López, B. Lomonte, A. Olvera-Rodríguez, A. Alagón, R. Pérez-Morales. 2018. Biological and proteolytic variation in the venom of Crotalus scutulatus scutulatus from Mexico. Toxins 10(1): doi:10.3390/toxins10010035 

48.

Saldarriaga-Córdoba M., C.L. Parkinson, J.M. Daza, W. Wüster, and M. Sasa. 2017. Phylogeography of the Central American lancehead Bothrops asper (SERPENTES: VIPERIDAE). Plos One 12(11) doi: 10.1371/journal.pone.0187969

47.

∞Martin, S.A., R.M. Rautsaw∞, F. Robb, M.R. Bolt, C.L. Parkinson, and R.A. Seigel. 2017. Set AHDriFT: Applying Game Cameras to Survey Herpetofauna and Small Mammals. Wildlife Society Bulletin doi: 10.1002/wsb.805 

46.

∞Lawrance, M.F., ∞Mercier, K.P., Solomon, J.A., L.J. Walters, and C.L. Parkinson. 2017. Apalachicola Bay oysters: does genetic differentiation explain subtidal and intertidal phenotypes? Florida Scientist. 80(4) 145-150. 

45.

∞Martin, S.A., R.M. Rautsaw∞, M.R. Bolt, C.L. Parkinson, and R.A. Seigel. 2017. Adapting Wildlife Management to Climate Change: Response of an Ecosystem Engineer to Dune Construction. Submitted to the Journal of Wildlife Management 80(6): 982-989. doi: 10.1002/jwmg.21275 

44.

∞Reece, J.S, A. Alansari, A. AlKindi, I. Mahmoud, A.Y, Al Kiyumi, A. Elshafie, H.M. Kalkvik∞, and C.L. Parkinson. 2016. The Loggerhead Turtles of Oman: Multilocus Evidence for Interoceanic Gene Flow with Atlantic Rookeries. Bulletin for the Florida Museum of Natural History 54(6): 104-117 

43.

Doan, T. M., A. J. Mason∞, T. A. Castoe, M. Sasa & C. L. Parkinson. 2016 A cryptic palm-pitviper species (Squamata: Viperidae: Bothriechis) from the Costa Rican highlands, with notes on the variation within B. nigroviridis. Zootaxa 4138 (2):271-290 DOI: 10.11646/zootaxa.4138.2.3 

42.

Streicher, J.W., McEntee, J.P., Drzich, L.C., Card, D.C., Schield, D.R., Smart, U., Parkinson, C.L., Jezkova, T., Smith, E.N., and T.A. Castoe. 2016. Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes. Evolution. 70:1435-1449. DOI: 10.1111/evo.12967 

41.

∞Strickland, J.L., *Carter, S., Kraus, F., and C.L. Parkinson. 2016 Snake evolution in Melanesia: origin of the Hydrophiinae (Serpentes, Elapidae), and the evolutionary history of the enigmatic New Guinean elapid Toxicocalamus. Zoological Journal of the Linnean Society. DOI: 10.1111/zoj.12423 

40.

∞Strickland, J.L., Parkinson, C.L., J.K. McCoy and L.K. Ammerman. (2014) Phylogeography of Agkistrodon piscivorus in Texas and throughout its range. Copeia 2014(4)639-649. 

39.

∞Muthukrishnan, G, ∞Lamers, R.P., Ellis*, A., Paramanandam∞, V., Tafur, S. Parkinson, C.L. and A.M. Cole. (2013) Longitudinal genetic analyses of Staphylococcus aureus nasal carriage dynamics in a diverse population. BMC Infectious Disease.13:221. doi:10.1186/1471-2334-13-221 

38.

∞Kalkvik, H.M., I.J. Stout, and C.L. Parkinson. (2012) Unraveling natural versus anthropogenic effects on genetic diversity within the southeastern beach mouse (Peromyscus polionotus niveiventris) Conservation Genetics 13:165. doi: 10.1007/s10592-012-0417-z

37.

∞Lamers, R.P., G. Muthukrishnan∞, T.A. Castoe, A.M. Cole, and C.L. Parkinson. (2012) Bayesian phylogenetics of Staphylococcus spp. based on DNA sequence concatenation and complex data partitioning. BMC Evolutionary Biology 2012. B12:171. doi:10.1186/1471-2148-12-171 

36.

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. (2012) 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. doi:10.1111/1755-0998.12000 

35.

∞Kalkvik, H.M., I.J. Stout, T.J. Doonan, and C.L. Parkinson. (2012) Investigating patterns and processes of lineage diversification: phylogeography and niche modeling of Peromyscus maniculatus species group. Ecography 35:54-64. DOI: 10.1111/j.1600-0587.2011.06994.x 

34.

∞Fenwick, A., H. W. Greene, and C.L. Parkinson. (2012) The Serpent and the Egg: Unidirectional Evolution of Reproductive Mode in Vipers? Journal of Zoological Systematics and Evolutionary Research: 50:59–66. doi: 10.1111/j.1439-0469.2011646.x 

33.

∞Lamers, R.P., J.W. Stinnett∞, G. Muthukrishnan∞, C.L. Parkinson, and A.M. Cole. (2011) Evolutionary Analyses of Staphylococcus aureus Identify Genetic Relationships Between Nasal Carriage and Clinical Isolates. Plos One 6(1): e16426. doi:10.1371/journal.pone16426 

32.

∞Daza, J.M., T.A. Castoe∞, and C.L. Parkinson. (2010) Using regional-scale comparative phylogeographic data to infer historical processes in Middle America. Ecography 33:343-354. doi: 10.1111/j.1600-0587.2010.06281. [өjoint primary authors] 

31.

∞Metzger, G.A., Kraus, F. Allison, A. and C. L. Parkinson. (2010) Uncovering cryptic diversity in Aspidomorphus (Serpentes: Elapidae): evidence from mitochondrial and nuclear markers. Molecular Phylogenetics and Evolution 54:405-416. 

30.

Castoe, T.A., A.P.J. de Koning, W. Gu, J.M. Daza∞, Z.J. Jiang, C.L. Parkinson, and D.D. Pollock. (2010) Dynamic nucleotide mutational gradients and control region usage in squamate reptile mitochondrial genomes. Cytogenetic and Genome Research.127:112-127. DOI: 10.1159/000295342 

29.

∞Daza, J.M., E.N. Smith, V. P. Páez and C.L. Parkinson. (2009) Complex evolution in the Neotropics: the origin and diversification of the widespread genus Leptodeira (Serpentes: Colubridae). Molecular Phylogenetics and Evolution 53:653–667. 

28.

∞Suazo, A.A., J.E. Fauth, J.D. Roth, C.L. Parkinson, and I.J.Stout. (2009) Responses of small rodents to habitat restoration and management for the endangered Florida Scrub-Jay. Biological Conservation 142:2322-2328. 

27.

∞Manjerovic, M. B., J. M. Waterman, E. A Hoffman, and C. L. Parkinson. (2009) Characterization of nine microsatellite loci in the Cape ground squirrel, Xerus inauris, and their cross-utility in other species. Molecular Ecology Resources 9:1375-1379.

26.

∞Fenwick, A., R.L. Gutberlet, J.A. Evans*, and C.L. Parkinson. (2009) Morphological and molecular evidence for phylogeny and classification of South American pitvipers, genera Bothrops, Bothriopsis, and Bothrocophias (Serpentes: Viperidae). Zoological Journal of the Linnean Society 159:617-640. 

25.

Castoe,T.A, A. P. Jason de Koning, H-M. Kim, W. Gu, B. Noonan, G. Naylor , Z. Jiang, C.L. Parkinson, and D. Pollock. (2009) Evidence for an ancient adaptive episode of convergent molecular evolution. Proceedings of the National Academy of Sciences 106:8986-8991 Cover Feature- Faculty of 1000 

 

PNAS Commentary: Edwards, S. 2009. Natural selection and phylogenetic analysis. Proceedings of the National Academy of Sciences USA 106: 8799-8800. 

 

See Related: Castoe, T.A., A.P.J. de Koning, H.M. Kim, W. Gu, B.P. Noonan, Z.J. Jiang, C.L. Parkinson, and D.D. Pollock. 2008. An ancient adaptive episode of convergent molecular evolution misleads phylogenetic inference. Nature Precedings, npre.2008.2123.1 

24.

∞Castoe, T.A., J.M. Daza, E.N. Smith, M.M. Sasa, U. Kuch, J.A. Campbell, P.T. Chippindale, and C.L. Parkinson. (2009) Comparative Phylogeography of Pitvipers Suggests a Consensus of Ancient Middle American Highland Biogeography. Journal of Biogeography 36: 88–103. Note: Featured Cover of the Journal Article. 

23.

∞Castoe, T.A., E.N. Smith, R.M. Brown, and C.L. Parkinson. (2007) Higher-level phylogeny of Asian and American coralsnakes, their placement within the Elapidae (Squamata), and the systematic affinities of the enigmatic Asian coralsnake Hemibungarus calligaster. Zoological Journal of the Linnean Society 151:809-831 

22.

∞Degner, J.F., I.J. Stout, J.D. Roth, and C. L. Parkinson. (2007) Population Genetics and Conservation of the Threatened Southeastern Beach Mouse (Peromyscus polionotus niveiventris): Subspecies and Evolutionary Units. Conservation Genetics 8:1441–1452. 

21.

∞Jiang Z., T.A. Castoe∞, M.D. Herron∞, F. Burbrink, C. Austin, J. McGuire, C. L. Parkinson, and D.D. Pollock. (2007) Comparative Mitochondrial Genomics of Snakes and Genetic Consequences of the Duplicate Control Region. BMC Evolutionary Biology 7:123. 

20.

∞Castoe, T.A., C.L. Spencer, and C. L. Parkinson. (2007) Phylogeographic Structure and Historical Demography of the Western Diamondback Rattlesnake (Crotalus atrox): a Perspective on North American Desert Biogeography. Molecular Phylogenetics and Evolution. 43:193-212. 

19.

∞Castoe, T.A., and C.L. Parkinson. (2006) Bayesian Mixed Models and the Phylogeny of Pitvipers (Viperidae: Serpentes). Molecular Phylogenetics and Evolution 39:91–110. 

18.

∞Reece, J.S., L.M. Ehrhart, C.L. Parkinson. (2006) Mixed Stock Analysis of Juvenile Loggerhead Turtles in the Indian River Lagoon and Implications for Marine Turtle Conservation Planning. Conservation Genetics 7:345-352. 

17.

Parkinson, C.L. J.P. Mower∞, Y-L. Qiu, A.J. Shirk∞, K. Song, N.D. Young, C.W. de Pamphilis and J.D. Palmer. (2005) Multiple Major Increases and Decreases in Mitochondrial Substitution Rates in the Plant Family Geraniaceae. BMC Evolutionary Biology 5:73 

16.

Wiens, J.J., J.W. Fetzner, C.L. Parkinson, and T.W. Reeder. (2005) Hylid Frog Phylogeny and Sampling Strategies for Speciose Clades. Systematic Biology. 54:719–748. 

15.

∞Castoe, T.A., M.M. Sasa, and C.L. Parkinson. (2005) Modeling Nucleotide Evolution at the Mesoscale: The Phylogeny of the Neotropical Pitvipers of the Porthidium Group (Viperidae). Molecular Phylogenetics and Evolution 37:881-898. 

14.

∞Herron, M.D., J.M. Waterman, and C.L. Parkinson. (2005) Phylogeny and Historical Biogeography of African Ground Squirrels: The Role of Climate Change in the Evolution of Xerus. Molecular Ecology 14:2773-2788. 

13.

*Mulvaney, A., T.A. Castoe∞, K.G. Ashton, K.L. Krysko, and C.L. Parkinson. (2005) Population Genetic Structure within the Florida Worm Lizard, Rhineura floridana (Amphisbaenia: Rhineuridae): Biogeographic, Taxonomic, and Conservation Implications. Journal of Herpetology. 39:118-124. 

12.

∞Reece, J.S., T.A. Castoe∞, and C.L. Parkinson. (2005) Historical Perspectives on Population Genetics and Conservation of Three Marine Turtle Species. Conservation Genetics 6: 235-251. 

11.

∞Castoe, T.A., T.M. Doan, and C.L. Parkinson. (2004) Data Partitions and Complex Models in Bayesian Analysis: The Phylogeny of Gymnophthalmid Lizards. Systematic Biology. 53: 448-469. 

10.

∞Herron, M.D., T.A. Castoe∞, and C.L. Parkinson. (2004) Sciurid Phylogeny and the Paraphyly of Holarctic Ground Squirrels (Spermophilus). Molecular Phylogenetics and Evolution. 31: 1015-1030. 

9.

Herrmann, H.W, T. Ziegler, A. Malhotra, R. Thorpe, and C.L. Parkinson. (2004) Redescription and Systematics of Trimeresurus cornutus (Serpentes: Viperidae) Based on Morphology and Molecular data. Herpetologica 60: 211–221. 

8.

∞Castoe, T.A., P. Chippindale, J. Campbell, L. K. Ammerman, and C. L. Parkinson. (2003) Evolutionary Relationships of the Middle American Jumping Pitvipers (Genus Atropoides) and Phylogeography of the Atropoides nummifer complex. Herpetologica. 49:421-432. 

7.

Daniell, H. and C. L. Parkinson. (2003) Jumping Genes and Containment. Nature Biotechnology 21: 374-375. 

6.

Nickrent, D.L., C.L. Parkinson, J.D. Palmer, and R.J. Duff. (2000) Multigene Phylogeny of Land Plants with Special Reference to Bryophytes and the Earliest Land Plants. Molecular Biology and Evolution 17: 1885-1895. 

5.

Palmer, J.D., K.L. Adams, Y. Cho, C.L. Parkinson, Y.-L. Qiu and K. Song. (2000) 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. 97:6960-6966. 

4.

Parkinson, C.L., K.R. Zamudio, and H.W. Greene. (2000) Phylogeography of the Pitviper Clade Agkistrodon: Historical Ecology, Species Status, and Conservation of the Cantils. Molecular Ecology 9:411-420

3.

Chaw, S-M., C.L. Parkinson, Y. Cheng, T.M. Vincent*, and J.D. Palmer. (2000) 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. 97:4086-4091. 

2.

Parkinson C.L., K.L. Adams, and J.D. Palmer. (1999) Multigene Analyses Identify the Three Earliest Lineages of Extant Flowering Plants. Current Biology 9:1485-1488. Note: Featured Cover of the Journal Article. 

1.

Parkinson, C.L. (1999) The Molecular Systematics and Biogeography of the Subfamily Crotalinae as Determined by mtDNA Sequences. Copeia 1999 pp. 576-586.