Difference between revisions of "David Hillis"

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[[File:HillisDH.jpg|thumb|right]]
 
[[File:HillisDH.jpg|thumb|right]]
  
===Co-Director of Workshop===
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===Time at workshop===
  
David Hillis will be present throughout the workshop.
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David Hillis will be present from July 20 to July 26.
  
  
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=== Lecture Materials ===
 
=== Lecture Materials ===
[http://www.doublehelixranch.com/WoodsHoleMole2014.pdf Introduction]
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[http://www.doublehelixranch.com/WoodsHoleMole2017.pptx.pdf Introduction]
  
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===Reading List===
  
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'''General Background on Phylogenetic Methods:'''
  
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Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pp. 407-514 in Molecular Systematics, 2nd. ed. (D. M. Hillis, B. K. Mable, and C. Moritz, eds.). Sinauer, Sunderland, Massachusetts.
  
Tree Set Visualization Paper
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'''Forensic Applications of Phylogenetic Analysis:'''
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Metzker, M. L., D. P. Mindell, X.-M. Liu, R. G. Ptak, R. A. Gibbs, and D. M. Hillis. 2002. Molecular evidence of HIV-1 transmission in a criminal case. Proc. National Academy Sciences USA 99:14292-14297.
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* [http://www.zo.utexas.edu/faculty/antisense/papers/Metzker_et_al.pdf HIV Forensics1]
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Scaduto, D. I., J. M. Brown, W. C. Haaland, D. J. Zwickl, D. M. Hillis, and M. L. Metzker. 2010. Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences. Proceedings of the National Academy of Sciences USA 107:21242-21247.
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* [http://www.zo.utexas.edu/faculty/antisense/papers/Scadutoetal2010PNAS.pdf Forensics2]
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'''The Effects of Taxon Sampling on Phylogenetic Analysis:'''
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Zwickl, D. J., and D. M. Hillis. 2002. Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology 51:588-598.
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* [http://www.zo.utexas.edu/faculty/antisense/papers/ZwicklandHillis.pdf Taxon Sampling1]
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Pollock, D. D., D. J. Zwickl, J. A. McGuire, and D. M. Hillis. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Systematic Biology 51:664-671.
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* [http://www.zo.utexas.edu/faculty/antisense/papers/Pollocketal.pdf Taxon Sampling2]
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Hedtke, S.M., T. Townsend, and D. M. Hillis. 2006.  Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Systematic Biology 55:522-529.
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* [http://www.zo.utexas.edu/faculty/antisense/papers/Hedtkeetal2006.pdf Taxon Sampling3]
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Heath, T. A., D. J. Zwickl, J. Kim, and D. M. Hillis. 2008. Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Systematic Biology 57: 160-166.
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* [http://www.zo.utexas.edu/faculty/antisense/papers/Heathetal2008.pdf Taxon Sampling4]
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Heath, T. A., S. M. Hedtke, and D. M. Hillis. 2008. Taxon sampling and the accuracy of phylogenetic analyses. Journal of Systematics and Evolution 46: 239-257.
 +
 
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* [http://www.zo.utexas.edu/faculty/antisense/papers/Heathetal2008JSE.pdf Taxon Sampling5]
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'''Performance Comparisons of Phylogenetic Methods:'''
 +
 
 +
Huelsenbeck, J. P., and D. M. Hillis.  1993.  Success of phylogenetic methods in the four-taxon case.  Syst. Biol. 42: 247-264.
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* [http://www.zo.utexas.edu/faculty/antisense/papers/HuelsenbeckHillis1993Four.pdf Performance1]
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Hillis, D. M., J. P. Huelsenbeck, and C. W. Cunningham.  1994.  Application and accuracy of molecular phylogenies.  Science 264:671-677.
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* [http://www.zo.utexas.edu/faculty/antisense/papers/Hillisetal1994.pdf Performance2]
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Hillis, D. M., J. P. Huelsenbeck, and D. L. Swofford.  1994.  Hobgoblin of Phylogenetics?  Nature 369:363-364.
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* [http://www.zo.utexas.edu/faculty/antisense/papers/HillisetalNature1994.pdf Performance3]
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Hillis, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.
 +
 
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* [http://www.zo.utexas.edu/faculty/antisense/papers/Hillis1996Nature.pdf Performance4]
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 +
'''Evolution of Sodium Channel Genes in Electric Fishes:'''
 +
 
 +
Zakon, H. H., Y. Lu, D. J. Zwickl, and D. M. Hillis. 2006. Sodium channel genes and the evolution of diversity in communication signals of electric fishes: Convergent molecular evolution. Proceedings of the National Academy of Sciences USA 103:3675-3680.
 +
 
 +
* [http://www.zo.utexas.edu/faculty/antisense/papers/Zakonetal2006.pdf Electric Fish1]
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Zakon, H. H., D. J. Zwickl, Y. Lu, and D. M. Hillis. 2008. Molecular evolution of communication signals in electric fish. Journal of Experimental Biology 211: 1814-1818.
 +
 
 +
* [http://www.zo.utexas.edu/faculty/antisense/papers/Zakonetal2008.pdf Electric Fish2]
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Zakon, H. H., M. C. Jost, D. J. Zwickl, Y. Lu, and D. M. Hillis. 2009. Molecular evolution of Na+ channels in teleost fishes. Integrative Biology 4:64-74.
 +
 
 +
* [http://www.zo.utexas.edu/faculty/antisense/papers/Zakonetal2009.pdf Electric Fish3]
 +
 
 +
'''Tree Set Visualization:'''
 +
 
 +
Hillis, D. M., T. Heath, and K. St. John. 2005. Analysis and visualization of tree space. Systematic Biology 54:471-482.
  
 
* [http://www.zo.utexas.edu/faculty/antisense/papers/Hillisetal2005TreeSpace.pdf Tree Space Paper]
 
* [http://www.zo.utexas.edu/faculty/antisense/papers/Hillisetal2005TreeSpace.pdf Tree Space Paper]

Latest revision as of 08:42, 21 July 2017

HillisDH.jpg

Time at workshop

David Hillis will be present from July 20 to July 26.


Institutional home page

Lecture Materials

Introduction

Reading List

General Background on Phylogenetic Methods:

Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pp. 407-514 in Molecular Systematics, 2nd. ed. (D. M. Hillis, B. K. Mable, and C. Moritz, eds.). Sinauer, Sunderland, Massachusetts.

Forensic Applications of Phylogenetic Analysis:

Metzker, M. L., D. P. Mindell, X.-M. Liu, R. G. Ptak, R. A. Gibbs, and D. M. Hillis. 2002. Molecular evidence of HIV-1 transmission in a criminal case. Proc. National Academy Sciences USA 99:14292-14297.

Scaduto, D. I., J. M. Brown, W. C. Haaland, D. J. Zwickl, D. M. Hillis, and M. L. Metzker. 2010. Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences. Proceedings of the National Academy of Sciences USA 107:21242-21247.

The Effects of Taxon Sampling on Phylogenetic Analysis:

Zwickl, D. J., and D. M. Hillis. 2002. Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology 51:588-598.

Pollock, D. D., D. J. Zwickl, J. A. McGuire, and D. M. Hillis. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Systematic Biology 51:664-671.

Hedtke, S.M., T. Townsend, and D. M. Hillis. 2006. Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Systematic Biology 55:522-529.

Heath, T. A., D. J. Zwickl, J. Kim, and D. M. Hillis. 2008. Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Systematic Biology 57: 160-166.

Heath, T. A., S. M. Hedtke, and D. M. Hillis. 2008. Taxon sampling and the accuracy of phylogenetic analyses. Journal of Systematics and Evolution 46: 239-257.

Performance Comparisons of Phylogenetic Methods:

Huelsenbeck, J. P., and D. M. Hillis. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42: 247-264.

Hillis, D. M., J. P. Huelsenbeck, and C. W. Cunningham. 1994. Application and accuracy of molecular phylogenies. Science 264:671-677.

Hillis, D. M., J. P. Huelsenbeck, and D. L. Swofford. 1994. Hobgoblin of Phylogenetics? Nature 369:363-364.

Hillis, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.

Evolution of Sodium Channel Genes in Electric Fishes:

Zakon, H. H., Y. Lu, D. J. Zwickl, and D. M. Hillis. 2006. Sodium channel genes and the evolution of diversity in communication signals of electric fishes: Convergent molecular evolution. Proceedings of the National Academy of Sciences USA 103:3675-3680.

Zakon, H. H., D. J. Zwickl, Y. Lu, and D. M. Hillis. 2008. Molecular evolution of communication signals in electric fish. Journal of Experimental Biology 211: 1814-1818.

Zakon, H. H., M. C. Jost, D. J. Zwickl, Y. Lu, and D. M. Hillis. 2009. Molecular evolution of Na+ channels in teleost fishes. Integrative Biology 4:64-74.

Tree Set Visualization:

Hillis, D. M., T. Heath, and K. St. John. 2005. Analysis and visualization of tree space. Systematic Biology 54:471-482.

Download most of my other papers as pdf's: