TaxoBiodiv2

This program is provided without any explicit or implicit warranty of correct functioning. It has
been developed as part of a university-based research program. If, however, you should encounter
problems with this program, the author will be happy to help solve them. Researchers may use this
program for scientific purposes, but the source code remains the property of Robert Poulin, Sylvain Gaillard and David Mouillot. Users of
the program may refer to the paper:

Poulin R. & Mouillot D. (2003) Parasite specialisation from a phylogenetic perspective: a new index of host specificity. Parasitology. 126(5): 473-480.
Poulin R. & Mouillot D. (2004) Combining phylogenetic and ecological information into a new index of host specificity. Journal of Parasitology. Submitted

The following papers are using Taxobiodiv2

Poulin R. & Mouillot D. (2003) Host introductions and the geography of parasite taxonomic diversity. Journal of Biogeography. 30(6): 837-845.
Luque J.L., Mouillot D. & Poulin R. (2004) Parasite biodiversity and its determinants in coastal marine teleost fishes of Brazil. Parasitology. In Press
Poulin R. & Mouillot D. (2004) The evolution of taxonomic diversity in parasite assemblages of mammalian hosts. Evolutionary Ecology. In Press
Poulin R. & Mouillot D. The relationship between specialization and local abundance: the case of helminth parasites of birds. Oecologia. Submitted
Krasnov B.R., Poulin R., Shenbrot G.I., Mouillot D. & Khokhlova I.S. Host specificity and geographic range in haematophagous ectoparasites. Oikos. Submitted
Krasnov B.R., Poulin R., Shenbrot G.I., Mouillot D. & Khokhlova I.S. Ectoparasitic jacks-of-all-trades: relationship between abundance and host specificity in fleas (Siphonaptera) parasitic on small mammals. American Naturalist. Submitted
Krasnov B.R., Mouillot D., Shenbrot G.I., Khokhlova I.S. & Poulin R. Geographical variation in host specificity of fleas (Siphonaptera): the influence of phylogeny and local environmental conditions. Ecography. Submitted



This program was initially developed to estimate original indices of Warwick & Clarke and Clarke & Warwick:

Clarke KR, Warwick RM (1998) A taxonomic distinctness index and its statistical properties. J Appl Ecol 35: 523-531
Clarke KR, Warwick RM (1999) The taxonomic distinctness measure of biodiversity: weighting of step lengths between hierarchical levels. Mar Ecol Prog Ser 184: 21-29
Clarke KR, Warwick RM (2001) A further biodiversity index applicable to species lists: variation in taxonomic distinctness. Mar Ecol Prog Ser 216: 265-278
Warwick RM, Clarke KR (1995) New 'biodiversity' measures reveal a decrease in taxonomic distinctness with increasing stress. Mar Ecol Prog Ser 129: 301-305
Warwick RM, Clarke KR (1998) Taxonomic distinctness and environmental assessment. J Appl Ecol 35: 532-543
Warwick RM, Clarke KR (2001) Practical measures of marine biodiversity based on relatedness of species. Oceanogr Mar Biol Annu Rev 39: 207-231



For parasitological studies you need only Std*, Std and VarStd indices. Three steps to estimate these indices:



1 Open the file containing the sample data
	This file must be a txt file with a phylum in each column from the species to the commun highest phylum to all the species
	! Don't forget to remove the last blank line in the txt file before using TaxiBiodiv
2 Check or uncheck the two options near the open button
	- if you have column names in your txt file check otherwise uncheck
	- you can consider you have no abundance for your data (prevalence) -> if you uncheck the two first indices disapear
3 Launch the estimates, results are in the lower case. The journal accumulates all the results from one session.
4 When you have calculated the indices for all your files you can save the journal in a text file


!!!! Becarefull. The last colomn contains abundance which are prevalence. The prevalence is usually a percentage but for our software you must give a integer.
Thus the prevalence has to be in /10000. For example a prevalence of 1 or 100% will be noted 10000 and a prevalence of 0.1 or 10% will be noted 1000 in the file. Examples are given in this package.



Five files are given with this package
The first one "Philon-agu" is to compute Std and VarStd, indices without prevalence
The four others are the examples provided by Poulin & Mouillot in their article (Journal of Parasitology). The last colomn contains prevalence.

