Publications by authors named "Todd A Castoe"

85Publications

Physiological demands and signaling associated with snake venom production and storage illustrated by transcriptional analyses of venom glands.

Sci Rep 2020 Oct 22;10(1):18083. Epub 2020 Oct 22.

Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr., Arlington, TX, 76019, USA.

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http://dx.doi.org/10.1038/s41598-020-75048-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7582160PMC
October 2020

PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments.

Bioinformatics 2020 Oct 14. Epub 2020 Oct 14.

Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL.

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http://dx.doi.org/10.1093/bioinformatics/btaa884DOI Listing
October 2020

Microchromosomes exhibit distinct features of vertebrate chromosome structure and function with underappreciated ramifications for genome evolution.

Mol Biol Evol 2020 Sep 28. Epub 2020 Sep 28.

Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX, USA.

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http://dx.doi.org/10.1093/molbev/msaa253DOI Listing
September 2020

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic.

Nat Microbiol 2020 11 28;5(11):1408-1417. Epub 2020 Jul 28.

MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.

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http://dx.doi.org/10.1038/s41564-020-0771-4DOI Listing
November 2020

Genome-wide SNPs clarify lineage diversity confused by coloration in coralsnakes of the Micrurus diastema species complex (Serpentes: Elapidae).

Mol Phylogenet Evol 2020 06 18;147:106770. Epub 2020 Feb 18.

Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, 337 Life Science, Arlington, TX 76010, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ympev.2020.106770DOI Listing
June 2020

Geographic variation in morphology in the Mohave Rattlesnake (Crotalus scutulatus Kennicott 1861) (Serpentes: Viperidae): implications for species boundaries.

Zootaxa 2019 Oct 7;4683(1):zootaxa.4683.1.7. Epub 2019 Oct 7.

Department of Biological Sciences, Tarleton State University, 1333 W. Washington Street, Stephenville, Texas, 76402 USA..

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http://dx.doi.org/10.11646/zootaxa.4683.1.7DOI Listing
October 2019

Supergene validation: A model-based protocol for assessing the accuracy of non-model-based supergene methods.

MethodsX 2019 24;6:2181-2188. Epub 2019 Sep 24.

Department of Biology, The University of Texas at Arlington, Arlington, TX, 76019, USA.

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http://dx.doi.org/10.1016/j.mex.2019.09.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6812401PMC
September 2019

Probabilistic Species Tree Distances: Implementing the Multispecies Coalescent to Compare Species Trees Within the Same Model-Based Framework Used to Estimate Them.

Syst Biol 2020 01;69(1):194-207

Department of Biology, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, USA.

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http://dx.doi.org/10.1093/sysbio/syz031DOI Listing
January 2020

The transcriptome of the veiled chameleon (Chamaeleo calyptratus): A resource for studying the evolution and development of vertebrates.

Dev Dyn 2019 08 25;248(8):702-708. Epub 2019 Mar 25.

Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin.

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http://dx.doi.org/10.1002/dvdy.20DOI Listing
August 2019

Statistical binning leads to profound model violation due to gene tree error incurred by trying to avoid gene tree error.

Mol Phylogenet Evol 2019 05 18;134:164-171. Epub 2019 Feb 18.

Department of Biology, The University of Texas at Arlington, Arlington, TX 76019, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ympev.2019.02.012DOI Listing
May 2019

Evolution: Plasticity versus Selection, or Plasticity and Selection?

Curr Biol 2018 09;28(18):R1104-R1106

Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09609822183098
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http://dx.doi.org/10.1016/j.cub.2018.07.050DOI Listing
September 2018

Shifts in Selective Pressures on Snake Phototransduction Genes Associated with Photoreceptor Transmutation and Dim-Light Ancestry.

Mol Biol Evol 2018 06;35(6):1376-1389

Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1093/molbev/msy025DOI Listing
June 2018

Assessing the Impacts of Positive Selection on Coalescent-Based Species Tree Estimation and Species Delimitation.

Syst Biol 2018 11;67(6):1076-1090

Department of Biology, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, USA.

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http://dx.doi.org/10.1093/sysbio/syy034DOI Listing
November 2018

Plasticity and local adaptation explain lizard cold tolerance.

Mol Ecol 2018 05;27(9):2173-2175

Department of Biology, University of Texas at Arlington, Arlington, Texas.

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http://dx.doi.org/10.1111/mec.14575DOI Listing
May 2018

ThetaMater: Bayesian estimation of population size parameter θ from genomic data.

Bioinformatics 2018 03;34(6):1072-1073

Department of Biology, The University of Texas at Arlington, Arlington, TX 76019, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx733DOI Listing
March 2018

The Discovery of XY Sex Chromosomes in a Boa and Python.

Curr Biol 2017 Jul 6;27(14):2148-2153.e4. Epub 2017 Jul 6.

Department of Biological Science, The University of Tulsa, Tulsa, OK 74104, USA.

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http://dx.doi.org/10.1016/j.cub.2017.06.010DOI Listing
July 2017

Contrasting gene expression programs correspond with predator-induced phenotypic plasticity within and across generations in Daphnia.

Mol Ecol 2017 Oct 10;26(19):5003-5015. Epub 2017 Jul 10.

Department of Biology, University of Texas at Arlington, Arlington, TX, USA.

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http://dx.doi.org/10.1111/mec.14213DOI Listing
October 2017

GppFst: genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data.

Bioinformatics 2017 05;33(9):1414-1415

Department of Biology, The University of Texas at Arlington, Arlington, TX 76019, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw795DOI Listing
May 2017

Targeted Capture of Complete Coding Regions across Divergent Species.

Genome Biol Evol 2017 Feb;9(2):398-414

Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/gbe/evx005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381602PMC
February 2017

Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia.

PLoS Negl Trop Dis 2017 01 20;11(1):e0005292. Epub 2017 Jan 20.

Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States of America.

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https://dx.plos.org/10.1371/journal.pntd.0005292
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http://dx.doi.org/10.1371/journal.pntd.0005292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5287463PMC
January 2017

A cryptic palm-pitviper species (Squamata: Viperidae: Bothriechis) from the Costa Rican highlands, with notes on the variation within B. nigroviridis.

Zootaxa 2016 Jul 15;4138(2):271-90. Epub 2016 Jul 15.

Department of Biology, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.; Email:

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http://dx.doi.org/10.11646/zootaxa.4138.2.3DOI Listing
July 2016

Historical Contingency in a Multigene Family Facilitates Adaptive Evolution of Toxin Resistance.

Curr Biol 2016 Jun 9;26(12):1616-1621. Epub 2016 Jun 9.

Department of Biology, University of Virginia, P.O. Box 400328, Charlottesville, VA 22904, USA; Mountain Lake Biological Station, University of Virginia, P.O. Box 400328, Charlottesville, VA 22904, USA.

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http://dx.doi.org/10.1016/j.cub.2016.04.056DOI Listing
June 2016

Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

Mol Phylogenet Evol 2016 09 27;102:104-16. Epub 2016 May 27.

Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ympev.2016.05.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894333PMC
September 2016

Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution.

Genome 2016 May 1;59(5):295-310. Epub 2016 Mar 1.

a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA.

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http://dx.doi.org/10.1139/gen-2015-0124DOI Listing
May 2016

Contrasting Patterns of Evolutionary Diversification in the Olfactory Repertoires of Reptile and Bird Genomes.

Genome Biol Evol 2016 Feb 9;8(3):470-80. Epub 2016 Feb 9.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biochemistry, Mississippi State University

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http://dx.doi.org/10.1093/gbe/evw013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4825420PMC
February 2016

Incipient speciation with biased gene flow between two lineages of the Western Diamondback Rattlesnake (Crotalus atrox).

Mol Phylogenet Evol 2015 Feb 19;83:213-23. Epub 2014 Dec 19.

Department of Biology & Amphibian and Reptile Diversity Research Center, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ympev.2014.12.006DOI Listing
February 2015

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Science 2014 Dec 11;346(6215):1254449. Epub 2014 Dec 11.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

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http://jarvislab.net/wp-content/uploads/2012/02/Green-et-al-
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http://www.sciencemag.org/cgi/doi/10.1126/science.1254449
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http://dx.doi.org/10.1126/science.1254449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873PMC
December 2014

Genetic consequences of postglacial range expansion in two codistributed rodents (genus Dipodomys) depend on ecology and genetic locus.

Mol Ecol 2015 Jan 13;24(1):83-97. Epub 2014 Dec 13.

School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA.

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http://dx.doi.org/10.1111/mec.13012DOI Listing
January 2015

Chinese alligator genome illustrates molecular adaptations.

Cell Res 2013 Nov 24;23(11):1254-5. Epub 2013 Sep 24.

Department of Biology, University of Texas Arlington, Arlington, TX 76010, USA.

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http://dx.doi.org/10.1038/cr.2013.134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817551PMC
November 2013

Phylogenetic relationships of the enigmatic longtailed rattlesnakes (Crotalus ericsmithi, C. lannomi, and C. stejnegeri).

Mol Phylogenet Evol 2013 Dec 2;69(3):524-34. Epub 2013 Aug 2.

Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, 337 Life Science, Arlington, TX 76010-0498, United States; Entorno Biotico A.C., Simon Bolivar #145, San Pablo, Colima, Colima 28000, Mexico.

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http://dx.doi.org/10.1016/j.ympev.2013.07.025DOI Listing
December 2013

Phylogenetics, likelihood, evolution and complexity.

Bioinformatics 2012 Nov 12;28(22):2989-90. Epub 2012 Sep 12.

Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3496332PMC
November 2012

Phylogenetic relationships among Staphylococcus species and refinement of cluster groups based on multilocus data.

BMC Evol Biol 2012 Sep 6;12:171. Epub 2012 Sep 6.

Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, 4000 Central Florida Boulevard, Orlando, FL 32816, USA.

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http://dx.doi.org/10.1186/1471-2148-12-171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464590PMC
September 2012

Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development.

Open Biol 2012 Apr;2(4):120054

Population Biology and Conservation Biology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 75236 Uppsala, Sweden.

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http://dx.doi.org/10.1098/rsob.120054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376728PMC
April 2012

Repetitive elements may comprise over two-thirds of the human genome.

PLoS Genet 2011 Dec 1;7(12):e1002384. Epub 2011 Dec 1.

Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, USA.

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http://dx.doi.org/10.1371/journal.pgen.1002384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228813PMC
December 2011

Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions.

PLoS One 2011 1;6(11):e26105. Epub 2011 Nov 1.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0026105PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3206046PMC
March 2012

A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus).

BMC Res Notes 2011 Aug 25;4:310. Epub 2011 Aug 25.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045 USA.

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http://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0
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http://dx.doi.org/10.1186/1756-0500-4-310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173347PMC
August 2011

Adaptive molecular convergence: Molecular evolution versus molecular phylogenetics.

Commun Integr Biol 2010 Jan;3(1):67-9

Department of Biochemistry and Molecular Genetics; University of Colorado School of Medicine; Aurora, CO USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881246PMC
http://dx.doi.org/10.4161/cib.3.1.10174DOI Listing
January 2010

Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing.

Appl Environ Microbiol 2010 Jun 23;76(12):3863-8. Epub 2010 Apr 23.

Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA.

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http://aem.asm.org/cgi/doi/10.1128/AEM.02585-09
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http://dx.doi.org/10.1128/AEM.02585-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2893486PMC
June 2010

Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence.

Mol Ecol Resour 2010 Mar 30;10(2):341-7. Epub 2009 Jul 30.

Consortium for Comparative Genomics, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA Department of Biology & Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX 76019, USA.

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http://doi.wiley.com/10.1111/j.1755-0998.2009.02750.x
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http://dx.doi.org/10.1111/j.1755-0998.2009.02750.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172459PMC
March 2010

Evidence for an ancient adaptive episode of convergent molecular evolution.

Proc Natl Acad Sci U S A 2009 Jun 28;106(22):8986-91. Epub 2009 Apr 28.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1073/pnas.0900233106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690048PMC
June 2009

Identification of repeat structure in large genomes using repeat probability clouds.

Anal Biochem 2008 Sep 20;380(1):77-83. Epub 2008 May 20.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1016/j.ab.2008.05.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2533575PMC
September 2008

Adaptive evolution and functional redesign of core metabolic proteins in snakes.

PLoS One 2008 May 21;3(5):e2201. Epub 2008 May 21.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002201PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2376058PMC
May 2008

Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region.

BMC Evol Biol 2007 Jul 26;7:123. Epub 2007 Jul 26.

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA, USA.

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http://dx.doi.org/10.1186/1471-2148-7-123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950710PMC
July 2007

A novel group of type I polyketide synthases (PKS) in animals and the complex phylogenomics of PKSs.

Gene 2007 May 17;392(1-2):47-58. Epub 2006 Nov 17.

Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816-2368, USA.

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http://dx.doi.org/10.1016/j.gene.2006.11.005DOI Listing
May 2007

Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): A perspective on North American desert biogeography.

Mol Phylogenet Evol 2007 Jan 18;42(1):193-212. Epub 2006 Jul 18.

Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816-2368, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S105579030600271
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http://dx.doi.org/10.1016/j.ympev.2006.07.002DOI Listing
January 2007

Bayesian mixed models and the phylogeny of pitvipers (Viperidae: Serpentes).

Mol Phylogenet Evol 2006 Apr 28;39(1):91-110. Epub 2006 Feb 28.

Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816-2368, USA.

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http://dx.doi.org/10.1016/j.ympev.2005.12.014DOI Listing
April 2006

Modeling nucleotide evolution at the mesoscale: the phylogeny of the neotropical pitvipers of the Porthidium group (viperidae: crotalinae).

Mol Phylogenet Evol 2005 Dec 15;37(3):881-98. Epub 2005 Jul 15.

Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816-2368, USA.

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http://dx.doi.org/10.1016/j.ympev.2005.05.013DOI Listing
December 2005

Data partitions and complex models in Bayesian analysis: the phylogeny of Gymnophthalmid lizards.

Syst Biol 2004 Jun;53(3):448-69

Department of Biology, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2368, USA.

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http://dx.doi.org/10.1080/10635150490445797DOI Listing
June 2004

Sciurid phylogeny and the paraphyly of Holarctic ground squirrels (Spermophilus).

Mol Phylogenet Evol 2004 Jun;31(3):1015-30

Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816-2368, USA.

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http://dx.doi.org/10.1016/j.ympev.2003.09.015DOI Listing
June 2004