Free-living nematodes of the Murray-Darling riversystem and coastal freshwaters of southeastern Australia
An interactive key to genera
Version 1.0 for MicrosoftWindows
User Manual
M Hodda, E Stewart-Reed, MJ Dallwitz, TA Paine and EJ Zurcher
CSIRO Entomology, Canberra, Australia
Contact address for the data in the key
M Hodda, CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601, Australia
Fax: +61 2 6246 4000
Email:
Contact address for DELTA software
DELTA, CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601, Australia
Fax: +61 2 6246 4000
Email: Internet:
Available from
CSIRO Publishing
150 Oxford St, PO Box 1139, Collingwood, Victoria 3066, Australia
Fax: +61 3 9662 7555
Email: Internet:
Licence
This licence entitles you to use the program Intkey only with the data and images in this package. You may also use later versions of the program with these data (but there is no guarantee that later versions will be compatible with the data).
The Commonwealth Scientific and Industrial Research Organisation shall not be liable for any loss, damages, or injury (including without limitation any loss of profit, indirect, consequential, or incidental loss, damage, or injury) arising from the use of the package.
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Contents
Introduction......
Interactive Identification and Information Retrieval......
Starting Intkey......
The Toolbar......
Introduction......
Identification and database query......
Select subsets of taxa......
Subsets of characters......
Information Retrieval......
Advanced mode......
Example of Identification......
Example of Information Retrieval......
More sophisticated use of Intkey......
Further Hints on Using Intkey......
Descriptions......
Contributions......
References......
Index......
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Free-living nematodes of the Murray-Darling riversystem and coastal freshwaters of southeastern Australia
Introduction
This package is generated from a DELTA database (Dallwitz 1980; Dallwitz, Paine, and Zurcher 1993 onwards). It comprises an interactive identification and information retrieval system using the program Intkey (Dallwitz, Paine, and Zurcher 1998), descriptions, illustrations, references, and other subsidiary material. It allows the identification of freshwater aquatic nematodes from southeastern Australia to generic level.
This is the first release of the package. The author welcomes constructive suggestions for improvements.
The database consists of a set of 212 items, which represent the juvenile or larval stage, the adult female, the adult male, and all life stages together from 53 taxa (mostly genera), each of which is coded for 422 characters with from 1 to 11 character states (usually 2 or 3), or a numerical measurement with an error. There are 9 additional text characters, which include a short statement on distribution, notes on general biology (habitat, feeding habits etc.), alternative group name(s) (synonymy), taxon images with their accompanying specimen data and systematic references pertaining to a particular taxon.
Most of the characters have been coded from preserved specimens, which have been processed by a standard method (see the 'introduction' button in the key under "Specimens"). In a few cases, however, character states were obtained from published information or theoretical considerations. In many nematode taxa certain stages, such as adult males, are extremely rare, and in some cases unknown. The fact that males were not found in the collections made for production of this key, does not, however, mean that they are never present and will never be found by users. For the taxa where adult males were not found, the most probable values according to the experience of the senior author, have been used.
This manual contains a longer version of the notes and help available within the electronic key. Once the key is operating, it will often be sufficient to refer to the help or information available electronically from within the program than to refer back to this document. If the help within the document is insufficient, then this document will hopefully contain the information required.
Interactive Identification and Information Retrieval
The interactive identification and information retrieval package uses the program Intkey (Dallwitz, Paine and Zurcher 1995 onwards; 1998). It provides convenient and flexible access to most of the information in the DELTA database.
Starting Intkey
Windows 95/98/NT
In Windows Explorer, double click on \Intkey.exe on the CD-ROM. (Depending on your Windows settings, the file name may be displayed without the ‘.exe’. The program icon is a red and black triangle.)
The Toolbar
As you move the cursor over each active toolbar button, a brief description of the function of the button is displayed. Some buttons are active only when an identification or query is in progress.
To get more information about the function of a toolbar button, first press the help button , which is on the right hand side of the toolbar. The cursor changes to ‘?’. Then click on any active button.
The buttons are colour coded.
GREEN buttons carry out an identification or interrogate the database.
RED buttons control the taxa which the key subsequently operates on.
YELLOW buttons control the character list which the key subsequently operates on.
CYAN (light blue) buttons display information: about the key, about the specimens or about nematodes generally. Note that the information generally depends on the currently selected character set (yellow buttons), except for the 'information' button, which will display any information or illustration of any taxa at any time.
Introduction
INTRODUCTION
This button allows you to display an introduction to the package. Included are a general introduction, the scope of the key, how to operate the key, scientific details of the scientific assumptions or philosophy, and acknowledgments.
Identification and database query
START OR CONTINUE AN IDENTIFICATION, USING BEST CHARACTERS
To identify a specimen proceed as follows.
- Press the button. The program displays a list of characters, with the best ones near the top. Click on a character, and press ‘OK’.
- The program displays a list of character states, or a box for entering values such as lengths. If there is an illustration for the character, it will be automatically displayed. Click on the state, or enter the value that applies to the specimen, and press ‘OK’. If you are not sure of the correct state or value, do not guess. Instead, click on more than one state, enter a range of values, or press ‘Cancel’ and try another character.
- Repeat from step 2 until only one taxon remains.
This button is also used to resume the identification process if you have interrupted it for some reason (for example, to view the images of the remaining taxa, or to set the error tolerance).
This button does not reset the taxa remaining in an identification. To start a new identification, press the 'reset' button (6 to the right) before pressing this button.
DISPLAY THE DIFFERENCES BETWEEN TAXA
This button displays the differences between selected remaining taxa in terms of the characters selected using the YELLOW buttons. Best used when only a few taxa remain in an identification. There must be at least two taxa remaining to use this button.
DISPLAY THE DIFFERENCES BETWEEN THE SPECIMEN AND THE REMAINING TAXA
Use after the message "No taxa remaining" to display the differences between the closest of the taxa selected and the attributes of the specimen which have been entered in an identification. A number in parentheses preceding the name of a remaining taxon in an identification indicates the number of differences between the specimen and the taxon. This button can be used to find the characters in which these differences occurred. If you reach a correct identification after making errors (or if there were errors in the data), you can find what those errors were by pressing this button.
DISPLAY THE CHARACTERS OF THE SPECIMEN
This button displays the characters of the specimen which have been entered or changed. Use where an identification requires many characters or changes. Note that this button only presents characters that have been entered. For descriptions of specimens in terms of other characters, use the GREEN button to the left or the CYAN buttons.
CHANGE PREVIOUSLY ENTERED INFORMATION ABOUT THE SPECIMEN BEING IDENTIFIED
This button allows you to change previously entered information about the specimen being identified. Press this button if, at any stage, you think you have made a mistake and want to correct it.
SET THE ERROR TOLERANCE
This button allows you to set the 'error tolerance' for an identification. A taxon will remain under consideration until the number of differences between it and the specimen is greater than the error tolerance. You should increase the current value by 1 if you are aware that you have made a mistake in an identification (because the illustration or description of the remaining taxon does not correspond to your specimen), but you do not know what the mistake is. This also allows a correct identification when there are errors in the database, and provides a way to increase your confidence in an identification even when no error is apparent.
The error tolerance will be increased automatically by 1 - that is allowing 1 additional mistake in the character states entered - if an there are no taxa left.
RESET READY TO START AN IDENTIFICATION
This button clears any information entered in previous identifications or queries, and sets parameters suitable for identification. Note that the characters and taxa included are NOT changed by this button, but must be changed explicitly using YELLOW or RED buttons.
FIND TAXA HAVING SPECIFIED ATTRIBUTES
This button finds those taxa having a specified attribute or combination of attributes. The characters can be selected from the list of characters currently chosen using YELLOW buttons, and are listed in no particular order. Use to select taxa from the currently selected set with particular attributes that are known, rather than have the program select the best characters for identification.Do not use this button to start a new identification.
Note that this button selects taxa which have the character state(s) entered (positive selection), rather than eliminating taxa which have different character state(s) (negative elimination). Under this button, taxa with no value recorded for a character will not be selected, whereas under the 'identify' button, taxa with no value recorded for a character will be retained because they cannot be eliminated.
RESET FOR A NEW QUERY
This button clears any information entered in previous identifications or queries, and sets parameters suitable for information retrieval. Note that the characters and taxa included are NOT changed by this button, but must be changed explicitly using YELLOW or RED buttons. Note that this button only resets program and does not start a query. Use the button immediately to the left to carry out a query. This button does not reset for an identification.
Select subsets of taxa
Note that resetting to start a new identification or query does not cancel the selection of a subset of taxa.
INCLUDE ALL STAGES OF ALL NEMATODES
This button sets the program to include any single nematode specimen or series of specimens of the same life stage or gender. This is the default. Subsequent commands will operate on this set of nematodes.
INCLUDE POPULATION DATA, RATHER THAN SINGLE SPECIMEN DATA
This button allows you to operate the key using data on populations for each taxon. Subsequent buttons or commands will operate on this dataset only. This button should only be used if confident that the different stages are definitely the same taxon, for example from a culture started with a single adult female.
The difference between operating on population data and single specimen data is that data from all stages can be used for identification. This is an advantage in several characters are available that are meaningless for individual specimens. For example, the presence or absence of males can be used as an identifying character (but see the proviso above).
A disadvantage with this option with the key at present is that some data, for example the Morphometric index a, refers to all life stages and both genders so that the range for population data is much greater than for each stage or gender separately, and so the discriminating power of many quantitative characters is lower for population data. Total body lengths, however, are coded separately for each stage and both genders, so can be used without loss of discriminating power.
INCLUDE FRESHWATER AQUATIC NEMATODES ONLY
This button sets the program to operate on freshwater aquatic nematodes only.
INCLUDE SPECIES OF THE GENUS PRATYLENCHUS ONLY
This button sets the program to operate on species of the genus Pratylenchus only.
INCLUDE A USER-DEFINED SUBSET OF THE TAXA
This button allows you to choose any set of taxa for subsequent commands to operate on. Select a pre-defined group of taxa from the dialogue box displayed or click LIST for a full list of all taxa.
Subsets of characters
Note that resetting to start a new identification or query does not cancel selection of a subset of characters. The set of characters used affects the results of most other buttons, and can be changed at any time.
USE ALL CHARACTERS AVAILABLE
This button removes all restrictions on characters and is the default. Many characters are suitable only for people familiar with nematode anatomy and systematics and with good laboratory and microscopy facilities.
USE CHARACTERS SUITABLE FOR INTERMEDIATE USERS
This button restricts characters to those suitable for people moderately familiar with nematode anatomy and systematics.
USE CHARACTERS SUITABLE FOR INEXPERIENCED USERS
This button restricts characters to those suitable for people unfamiliar with nematode anatomy and systematics.
SELECT QUALITATIVE CHARACTERS ONLY
This button allows the use of qualitative characters only, that is, characters which are a choice between alternatives requiring no measurements of length, diameter etc.
SELECT QUANTITATIVE CHARACTERS ONLY
This button allows the use of quantitative characters only, that is, characters requiring a measurement of length, diameter etc rather than a choice between alternatives. A microscope with graticule or camera lucida is normally required.
SELECT CHARACTERS WHICH CAN BE VIEWED WITHOUT COMPOUND MICROSCOPE
This button restricts the choice of characters to those which can be seen at magnifications of 100x or less. If a compound microscope is not available, this option may be useful, but may not lead to identification of a single taxon.
SELECT CHARACTERS FOR WHICH A COMPOUND MICROSCOPE MAY BE NEEDED
This button allows all characters to be available, including those which can be seen only at magnifications of 1000x (generally corresponding to oil immersion objectives on a compound microscope). If a compound microscope is not available, choose the button immediately to the left, which will restrict the character set to those visible at lower magnifications, but may not lead to identification of a single taxon.
USE STRICTLY TAXONOMIC CHARACTERS ONLY
This button selects the strictly taxonomic set of characters for subsequent commands to operate on. This set of characters are the characters on which taxa are defined, so, by definition, they should lead to a correct identification irrespective of geographical and other limitations on the key. Use if you are outside the defined area for the key.
These characters are generally suitable for experienced users with good microscopic equipment.
USE A SUBSET OF CHARACTERS FROM A PARTICULAR PART OF THE BODY
This button allows you to proceed with an identification by selecting a subset of the characters. Choose a region of the body from which to draw characters.
Information Retrieval
DISPLAY ILLUSTRATIONS OF SELECTED REMAINING TAXA
This button displays illustrations of any or all remaining taxa. It should be used to confirm (or reject) an identification. Images of a taxon are automatically displayed at the completion of an identification, and can be displayed at any time by pressing this button. Any other images can be displayed using the ‘Subject’ or ‘Control’ menus in the image window. (These menus are only available if there is more than one image of a taxon or more than one taxon remaining.) To display illustrations of any taxon (including those rejected or specifically excluded), use the CYAN INFORMATION button. Note that images of several taxa can be selected, and images displayed sequentially or simultaneously by using the 'Control' menu in the image window.
DISPLAY DESCRIPTIONS OF SELECTED REMAINING TAXA USING THE CURRENT CHARACTER SET
This button displays descriptions of any taxon or taxa which remain in an identification or query in terms of the current character set. To display a complete description, use the YELLOW 'all characters' button before pressing this button.
GENERATE DIAGNOSTIC DESCRIPTIONS OF SELECTED REMAINING TAXA