Mariana Vargas

Computer files of the making of the M. Appl. Sc. thesis "Effect of a Free-Living Stage on Host-Parasite Coevolution: a Phylogenetic study in New Zealand"
Lincoln University 
November 2005

Appendix VI: 
Edited DNA sequences
Sequences (Se-Al files)
Inside "Odontacarus COI" folder:
OdontacarusCOInames 
Inside "OdontacarusITS2" folder:
ITS2names
Non-edited sequences (before editing)
Inside folders named:
Non-editedCOIsequences
Non-editedITS2sequences

Appendix VII: Pairwise COI distances 
Inside "Odontacarus COI" folder:
COIdistances.xls (Excel file)
COIdistances (tab-delimited PAUP* file)

Appendix VIII: Pairwise ITS2 distances 
Inside "OdontacarusITS2" folder:
ITS2distances.xls(Excel file)
ITS.distances (tab-delimited PAUP* file)

Tree files (not mentioned in the Contents section but present in the attached CD for future reference)
COI Tree-Building (PAUP* and Modeltest files)
Inside "Odontacarus COI" folder:
Nexus files: COI28Oct.nex, COINOV.nex
NJ tree: COINJNov.tre
NJ bootstrap: COINJBootNov.tre
COI sequences with repeats on different dates: COIrepeats.nex
Parsimony trees: COIPARSSPR.tre, COIPARSNNI.tre, COIPARSTBR.tre
Parsimony bootstrap: COIPARSNNIBoot.tre
Modeltest model selection and commands: COIModeltest.out
Maximum likelihood trees: COINOVML.tree
Maximum likelihood bootstrap: COINOVMLBoot.tre
Bayesian Nexus file: COI28Oct_Bayes.nex
Bayesian tree: COIBayes.tre

ITS2 Tree-Building(PAUP* and Modeltest files)
Inside "OdontacarusITS2" folder:
Nexus files: ITS28Oct.nex
NJ tree: ITS28OctNJ.tre
NJ bootstrap: ITS28OctNJBoot.tre
Parsimony tree: ITSPars4Nov.tre
Parsimony bootstrap: ITSPars4NovBoot.tre
Modeltest model selection and commands: ITSModeltest.out
Maximum likelihood tree: ITS2ML.tre
Maximum likelihood bootstrap: ITS28OctMLBoot.tre
Bayesian Nexus file: ITSBayes.nex
Bayesian tree: ITS_Bayes.tre

Photos of Odontacarus and Ophionyssus (Rob Cruickshank)
Dorsal view: "Odontacarus to left"
Ventral view: "Ophionyssus to right"

Skink data (from Hickson et al. 2001)
In folder named "skinks"
12Ssequences: skink12S
NJ tree: skinksNJ.tre
NJ bootstrap: skinksNJBoot.tre
Parsimony tree: skinksPars.tre
Parsimony bootstrap: skinksparsboot
Skink distance matrix: skink.tab.distances, skink distances.xls

Ophionyssus
In folder named "Ophionyssus":
Edited COI sequences: Ophionyssus COI
In folder named "non-edited ophionyssus COI":
All ophionyssus COI sequences before editing

Thesis text in full: Vargas2006.pdf