Materials to Supplement the Publications

of George F. Estabrook

Will, To download the original photos for my EPA paper, click the blue filename. ERAgfefigs

Download suplmental materials for a cited publication by clicking on the blue word that follows the citation. You will receive an archive of files. Double click on the archive's icon to extract the files in the archive. Frequently, an archive will contain an exectutable computer program application file with extention ---.EXE for a program described in the cited publication. In another file with the same name but with the extention ---.DOC will be the user's instruction document, which explains what the application does and how to use it. The archive will typically also contain a file of example data, and a file of results produced by the application when it analyses the example data. The archive may also contain a file of data whose analysis was reported in the cited publication.

Unless otherwise noted, application programs will run in a WINDOWS operating environment. To run the application put a copy of its ---.EXE file and the data file you intend to analyize with it in a folder/directory. Then double click the ---.EXE file's icon. Then press ALT+Enter and follow the instructions on the screen and in the user;s document. You are advised to print and read the user's document first.

Please message me at ESTABROOK@UMICH.EDU if you have difficulties, questions or comments.

Estabrook, G.F., G.R. Smith and T.E. Dowling 2007. Body Mass and Temperture Influence Rates of Mitochondrial Evolution in North American Cyprinid Fishes. Evolution 61(5):1176-1187 ECERFODM Program ECERFODM reads a phylogenetic tree structure table in which amount of evolutionary change along each phyletic line segment has been specified, together with body mass and thermal regime for each modern taxon. Thermal regime is described by the average maximum ambient temperature during June, July and August, and the average number of frost free days per year. ECERFODM uses the formula of Gilooly et al 2005 PNAS to estimate metabolic rate for each taxon. Then for every specified pair of taxa ECERFODM compares amount of evolutionary change in each from its most recent common ancestor with the estimated metabolic rate of each to identify monotonic pairs in which the one with the most evolutionary change has the fastest metabolic rate. The realized significance of the number of monotonic pairs is estimated by simulation. Other statistics and their significances are also calculated. Example data files include the data reported in the cited publication.

Rissech, Carme, George Estabrook et al. 2006. Using the Acetabulum to Estimate Age at Death of Adult Males. Journal of Forensic Science 51(2):213-229 IDADE2 Program IDADE2 estimates the age at death of human skeletal remains, based on the valuse of seven variables measured for a reference collection of human skeletal remains of known age at death. The variables are explicitly described in the cited publication. Example data files include values measured for the large reference collection in teh Anthropology Museum of the University of Coimbra.

METASIG (for DOS) (META SIGnificance) In the context of vascular plant families in North America north of Mexico (or other context) METASIG calculates the Meta-Significance of numbers of families (or other clasificatory units) among families of a given size (or other quality) with significantly many or few species chosen for medicinal use by Native American traditions (or that have some other property of interest). METASIG was used by Moerman, D.E. and G.F, Estabrook. 2003 Journal of Ethnopharmacology. 87:51-59. METASIG also runs in WINDOWS in text mode only. Updated Sept 2003.

STRATCOM (for DOS) (STRATigraphic COMpatibility) analyses Qualitative Taxonomic Characters (QTC's) for Evolutionary Units (EU's) represented by fossils or other artifacts recovered from strata presumed to indicate the relative time spans when the respective EU's were extant. Reveals incompatibilities among QTC's and stratigraphy. Described in Estabrook G.F. and F.R. McMorris 2006. Systematics and Biodiversity 4(2). Updated Dec 2005.

PHENCON2 (for DOS) (PHENetics with CONfidence, version 2) is a descendant of PHENCON (see below). PHENCON2 accepts large datasets and uses heuristic algorithms to speed up processing time, but incorporate a number of additional powers for multivariate analyses, including choice of scaling factors, and computational analogs of 1-way and simultaneous ANOVA, correlations, and cluster analyses. Stutz, A.J. and G.F. Estabrook 2004 Archeological Science 31:1643-1658 describe an a application to the analysis of neolithic stone tool kits. Updated Dec 2005.

MEAWILK (for DOS) (MEAcham and WILKinson criteria) evaluates support from character data for hypothesized monophyletic groups, using criteria published by Meacham 1994. Syst. Bot. 19:506, and by Wilkinson 1998. Syst. Biol.47:673; A MEAWILK aplication is reported by Frohlich, M and G.F. Estabrook 2000. Mol. Biol. Evol. 17(12):1914-1925. Also available for WINDOWS. Updated Dec 2005.

ACTUS2 (for DOS) (Analysis of Contingency Tables Using Simulation) is intended for use with sparse contingency tables, as a guide for the interpretation of individual table entries. Estabrook, C.B. and G.F. Estabrook 1989 Historical Methods 82:5-8; Estabrook, G.F. 2002. Historical Methods 35(1):21-31. Also available for WINDOWS. Updated Dec 2005

ADQUARC (for DOS) (Assessment of Data QUAlity by Random Compatibility) tests each pair of qualitative characters for potential compatibility. For each character, the number of other characters with which it is potentially compatible is a random variable under the probability model that all permutations of Evolutionary Units among the states of a character are equally likely. For each character, the realized significances of the observed number of other characters potentially compatibile with it is estimated by simulation. Day, W.H.E., G.F. Estabrook & F.R.McMorris 1998. Systematic Biology 47:604-616 Updated June 1999.

QUARTET2 (for DOS) Calculates measures of difference between pairs of ancestor-descendant relations (evolutionary trees) based on subtrees of 4 Evolutionary Units. Estabrook G.F. 1992 Systematic Biology 43:449-459

HYWIN (for DOS) suggests hybrid origins for some specimens (together with possible parent specimens) based on data and other criteria provided by the user. Estabrook, G.F. et al. 1996 TAXON 45:647-662 Also available for WINDOWS.

CONPHEN (for DOS) creates evolutionary classifications, constrained so that all classes are convex on a specified ancestor-descendant tree, and otherwise constructed in accordance with any of several phenetic clustering methods. Estabrook, G.F. 1986 Systematic Zoology 35:560-570 Also available for WINDOWS. Updated 1988.

DIVDEN (for DOS) generates, using computationally intense means, realized significances of observed diversity measures and abundances, predicted by the hypothesis that the species identities of observed individuals occur independently and in accordance with probabilities proportional to specified species frequencies. Estabrook, G.F. & D. Goldberg 1998. Journal of Ecology 86:983-988. Also available for WINDOWS.

PHENCON (for DOS) (PHEnetics with CONfidence.) Accepts quantitative specimen by character matrix, and exhaustively determines the partition of specimens (into a specified number of classes) that maximizes a given criterion. Then simulates 1000 data sets by permuting the character values. A maximal partition is determined as above for each simulated data set, and the number of simulated data sets for which the value of the maximized criterion exceeds that of the original data (divided by 1000) is a realized significance of the partition of the data. Julius, M.L. et al. 1997. J. Phycology 33:1049-1054. See PHENCON2 (above), a heuristic version of PHENCON for larger (>24) numbers of specimens for which an exhaustive search for optimal classifications would take too long. With some possible loss of precision it guesses very good if not optimal clasifications in much less time, which makes its use feesible with larger numbers of specimens. In some cases, this possible loss of precision has minimal impact on accuracy.

THERRAD3 (for DOS) (Testing Hypotheses of Evolutionary Rate by Resampling Available Data) For measured and dated fossils, time before present and measurement values are used to determine evolutionary rates. These can then be compared between times periods or places to test hypotheses of rate equality. The method is a computationally intense analog of classical analysis of covariance. Kitchell, J.A. et al. 1987. Paleobiology 13:272-285.

WINDOWS Programs

Each of the following programs consists of an executable file '---.EXE', a document file '---.DOC', an example data file '---.DAT', sometimes other related files, and an INSTALL.EXE file to run to install the program as a WINDOWS application. These files have been compressed together into a single, self extracting '---.EXE' file for you to download. 'Click' on the blue filename to download it to your hard disk. To extract the files first move the downloaded file to the directory where you intend to keep the program, then select Run from the File menu to run the downloaded file, which on its execution will create, in the same directory, the files described above. Then, again Select Run from the File menu to run INSTALL.EXE from this same directory. On its execution it will install an icon and prepare the application for execution.

ACTUS2 (for WINDOWS 95/NT) (Analysis of Contingency Tables Using Simulation) is intended for use with sparse contingency tables, as a guide for the interpretation of individual table entries. Estabrook, C.B. and G.F. Estabrook 1989 Historical Methods 82:5-8; Estabrook, G.F. in review Historical Methods. Updated Feb 2000

HYWIN (for WINDOWS 3.1) suggests hybrid origins for some specimens (together with possible parent specimens) based on data and other criteria provided by the user.

CONPHEN (for WINDOWS 3.1) creates evolutionary classifications, constrained so that all classes are convex on a specified ancestor-descendant tree, and otherwise constructed in accordance with any of several phenetic clustering methods. Estabrook, G.F. 1986 Systematic Zoology 35:560-570

DIVDEN (for WINDOWS 3.1) or DIVDEN (for WINDOWS 95/NT) generates, using computationally intense means, realized significances of observed diversity measures and abundances, predicted by the hypothesis that the species identities of observed individuals occur independently and in accordance with probabilities proportional to specified species frequencies. Estabrook, G.F. & D. Goldberg 1998. 86:

PROGRAMS OF INTEREST BY OTHER AUTHORS

SECANT (for WINDOWS 95/NT) by Ben Salisbury combines all the powers of CLINCH by Kent Fiala (1984) with the additional powers described in Salisbury (1999), TAXON 48:755, to take advantage of the speed, space, and convenience of modern PCs running WINDOWS. It analyses cladistic characters for logical phylogenetic consistency and reveals ancestor decendant relationships determined by maximal subsets of mutually consistent cladistic characters. Estabrook, G.F. 1997 DIMACS Series in Descrete Math 37:1-28; Estabrook, G.F., Strauch J.G. and Fiala, K.L. 1977. Systematic Zoology 26:269-276

OTHER DOCUMENTS

Frohlich and Estabrook MBE suplement for PC Frohlich and Estabrook MBE suplement for MAC Data set and MEAWILK output, for the study of the relationship of flowering plants to other seed plants, reported in Frohlich and Estabrook, Molec. Biol. Evol. accepted June 2000. Updated June 2000