Identification of common freshwater diatoms of Britain …craticula.ncl.ac.uk/EADiatomKey/html/manual.pdf · Identification of common freshwater diatoms of Britain ... include characteristics

Identification of common freshwater diatoms of Britainand Ireland: An Interactive CD-ROMVersion 1.0

User’s Guide

Contents

1. Introduction 22. System requirements and installation 53. Overview of the CD-ROM 64. Use of lucid: tutorial 75. Help for the beginner: expert routes 126. Tips for more advanced users 147. Technical support 188. How Lucid works 189. References 2010.Acknowledgements 21

Diatom CD-ROM manual Version 1.0

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1. Introduction

1.1 General introductionThis CD-ROM is the third in a series of identification guides developed with fundingfrom the UK Environment Agency. Previous CD-ROMs covered the identification ofblue-green algae (Cyanobacteria) and green algae and this CD-ROM extends coverageto the freshwater diatoms. However, with over 2500 species of freshwater diatomsrecorded from Britain and Ireland and diatom taxonomy in a state of flux, acomprehensive guide would have been impossible to complete with the limitedfunding available. This key covers those taxa most likely to be encountered byEnvironment Agency staff and others involved in routine monitoring whilst stillincorporating enough functionality to permit the database to be expanded in the future.

1.2 What is Lucid?Lucid is a software tool developed by the Centre for Biological InformationTechnology (CBIT) at the University of Queensland, Australia that provides an expertsystem for developing and using interactive keys. The earliest keys were developed tohelp students identify insect orders; however, the idea was picked up by the Australianresearch organisation CSIRO and developed to provide user-friendly keys to helpthose involved in pest management programs. The first version of Lucid Professionalwent on sale in 1998 and since then a large number of keys have been developed usingthe software, and distributed either as CD-ROMs or via the internet.

Previous Lucid-based keys to freshwater algae include earlier keys in this series to theblue-green (Whitton et al. 2003) and green (Whitton et al. 2002) algae and keys toEuglenophyta (http://bio.rutgers.edu/euglena/).

Lucid allows the development of keys that are ‘multi-access’, rather than thetraditional ‘dichotomous’ keys with which most biologists will be familiar. The userof a dichotomous key addresses a series of questions each of which has twoalternative outcomes. Selecting the most appropriate outcome at each stage leads theuser to further questions that progressively narrows the number of possibleidentifications until only a single taxon is left. Crucially, the order of the questions isdetermined, in advance, by the key’s author. Whilst dichotomous keys can beimproved by end-user testing (Tilling, 1987) they are fundamentally inflexible andsituations often arise where important characters are visible to the user but do notfeature in the key until a relatively late stage. Occasionally, couplets are encounteredthat are unanswerable, for one reason or another (in the case of green algae such asOedogonium and the filamentous Zygnematales, the absence of reproductivestructures is often a handicap to accurate identification).

Multi-access keys differ from dichotomous keys in that there is no pre-ordained orderin which the user has to answer questions. The Lucid interface, for example, presentsusers with a series of characters, each of which has a number of possible states. Usersthen select those states that are most relevant to the specimen under scrutiny. Witheach selection, the list of possible taxa is filtered and taxa that do not possess the stateare removed. As more characters and states are included, so the list is whittled downuntil the user reaches a unique solution.


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1.3 Dvelopment of the diatom CD-ROMAt the time that the project was conceived, the primary reason for monitoring UKrivers using diatoms was to guide implementation of the UWWTD. This Directivefocussed attention on lowland, eutrophic rivers and, for this reason, the key has beendesigned to permit all diatoms collected from freshwaters in Britain and Ireland to beidentified to at least genus and for all the species and infraspecific taxa necessary touse the common trophic indices (Kelly, 1998; Coring et al., 1999; Rott et al., 1999) tobe distinguished as well. In effect, this will provide a core database plus one ‘module’(‘lowland rivers’) to which further ‘modules’ can be added in the future to increasefunctionality.

Compilation of the key has involved a synthesis of existing, published material,combined with the development team’s own experience of the freshwater flora ofBritain and Ireland. The principal published sources consulted are: Hartley et al.(1986); Hustedt (1930; 1927-1966); Krammer and Lange-Bertalot (1986-1991) andPatrick and Reimer (1966; 1970). The nomenclature adopted in this CD-ROM broadlyfollows that of Round et al. (1990), along with some (but not all) of the more recentchanges. We believe that many of the taxonomic changes made at the genus andspecies level since 1990 need to be tested before they are accepted, particularly wherethe new genera are incompletely characterized (e.g. there is no information aboutchloroplasts and other characteristics of the living cell, life history, or sexualreproduction). We have therefore taken a rather conservative approach to recentchanges and have not followed all the changes in recent volumes of Diatoms ofEurope or Iconographia Diatomologica.

The classification adopted here should be adequate for the monitoring programmesthe CD-ROM is designed to assist. This classification will undoubtedly change andone of the benefits is that monitoring will become even more precise. A greatadvantage of the new tools such as Lucid is that change is easily accommodated,because the identification algorithm and the data matrix of characters are separate,whereas a traditional dichotomous key may be destroyed by a single taxonomicalteration.

However, this pragmatic approach carries the risk that taxa not included in the keywill be ‘shoehorned’ to fit one of the species that have been described in detail. Twoprecautions have been included in order to minimise this risk. First, some lesscommon taxa have been included where there is a risk of confusion with a morecommon taxon. For example, Synedra cyclopum is recorded in Hartley (1986)’schecklist but is not at all common in Britain or Ireland. It is possible that, as anaraphid lunate diatom, it might be confused with the more common Hannaea arcusunless the key draws attention to its existence. A few other species that might causesimilar problems have also been included.

Second, each genus has been included in the key alongside the common species. Therationale for this is to provide a category to cover all these less commonrepresentatives of each genus. If the list of ‘taxa remaining’ is reduced to a genusname, then users should refer first to the generic descriptions (which will includeimages of taxa not covered by species descriptions) but then also to more detailedtaxonomic literature. In many cases, the list of ‘taxa remaining’ will reduce to a


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species plus genus. This, again, is a clue to the user that more specialist literature isrequired in order to confirm an identification.

One additional novel feature of this key has been the inclusion of each valve of amonoraphid taxon as a distinct entity. Our experience is that questions aboutheterovalvy in dichotomous keys are often a source of confusion for beginners andinclusion of separate entries in the key for the raphe and rapheless valves, shouldmean that it is less likely that raphe valves of small Achnanthes and relatives areconfused with small Navicula spp. However, if the user knows a specimen to beheterovalvar (perhaps because raphe and rapheless valves are adjacent to one another)then it is possible to include this state. The ‘taxa remaining’ list should then reduce toa pair of names – e.g. Achnanthes conspicua RV and Achnanthes conspicua RLV,representing the two valves of the species in question. An implication of the use ofseparate entries for RV and RLV is that the number of taxa will often be misleading.

Finally, the nature of the multi-access key has meant that it has been possible toinclude characteristics of the live diatom cell alongside those associated with thecleaned valve. This gives users a much wider range of characteristics from which tochoose and should mean that the key is applicable to a wider range of situations thanwas the case with earlier keys. Many of the descriptions of live characteristics arederived from Cox (1996).

1.4 Images

Diatom frustules are transparent and colourless. Hence they become visible in thelight microscope only if there is a difference in refractive index (RI) between themand the material in which they are mounted, which is usually either water (for livingdiatoms), which has an RI less than diatom silica, or a special high RI diatommountant, such as Naphrax. If they are mounted in traditional mountants used formicroscopy, such as Canada balsam or Euparal, diatom frustules are almost invisible,because their refractive index is so close to that of the material surrounding them.

An extra problem affecting light microscopy of diatoms is diffraction. Many of thefeatures of diatom frustules – striations, pores, spines, etc – are very small,approaching the same dimensions as the wavelengths of visible light (c. 0.5 µm forblue-green light) and this means that diffraction is the major factor determiningwhether or not structures can be seen. This in turn means that microscopes must be ofgood quality and, perhaps even more importantly, they must be used well (e.g. seeBradbury 1984) if some of the fine details necessary for identification of diatoms areto be observed. A further peculiarity of ‘diffraction limited systems’ is that smallstructures, like pores or spines or the raphe system, appear in focus more than once, indifferent horizontal planes. For example, in a normal light microscope as one focusesthrough a specimen vertically, a feature may first appear in-focus dark against thebackground, then it will virtually disappear, and then it will appear in-focus again, butnow light against the background. Neither of the in-focus images is ‘correct’. Both areartifacts of diffraction at the interface between two transparent materials of differentrefractive index. In many ways, it seems more reasonable to choose the ‘white-spotfocus’ for small pores and the raphe slit, because these are immaterial features – theabsence of silica – whereas the ‘dark-spot focus’ seems more appropriate for solid


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structures like spines and warts. However, such choices are arbitrary and observerschoose on the basis of aesthetics and convention. So, for example, it is more commonto photograph most pennate diatoms with the striae (the lines of pores) and raphe in‘dark-spot focus’. However, Epithemia is usually photographed with the pores in‘white-spot focus’.

The images used on this CD-ROM derive from a variety of sources. The principalsources are two databases of images collected by the Royal Botanic Garden,Edinburgh as part of earlier EU-funded projects: EDDI (European Diatom DatabaseInitiative: http://craticula.ncl.ac.uk:8000/Eddi/jsp/index.jspref) and ADIAC(Automated Diatom Identification and Classification: du Buf & Bayer, 2002:http://www.ualg.pt/adiac/). Many of the taxa not represented in these databases werephotographed especially for this project from material collected in Britain and Irelandby the authors. Full details of the imaging systems are given in Bayer and Juggins(2002) and Bayer et al. (2001). Most of the images are valve views of cleanedspecimens, photographed using brightfield optics (rather than using phase contrast ordifferential interference contrast condensers). However, wherever possible, liveimages have been included, along with girdle views, macroscopic images (in the caseof large diatoms such as Didymosphenia) and scanning electron micrographs. Severalcolleagues around Europe and beyond have allowed the use of their images tosupplement our own collections. The origin of material from outside Britain andIreland is indicated in the figure legends.

2. System requirements and installation

2.1 Minimum SpecificationThe minimum specifications required to run Lucid version 2.2 on your computer are:

• Operating system: Windows 95/98/2000/NT (Service pack 6 or greater)/ME/XP

• Minimum RAM: 16 MB for Windows 95/98, 32 MB Windows NT/2000/ME/XP

• Recommended RAM: 32 MB for Windows 95/98, 64 MB WindowsNT/2000/ME/XP

• Hard Disk space: 52 MB plus additional hard disk space for Internet Explorer orMozilla (for HTML display)

• CD ROM: 2x speed. 4x speed or greater recommended.

• Monitor and Video card capable of displaying millions of colours.

• Either Internet Explorer 5.0 or greater or Mozilla Web Browser.


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An internet connection is not required for the key to freshwater diatoms; however, itwill enable you to download other keys via www.Lucidcentral.com. If you choose todo this, you will also need to ensure that you have sufficient hard disk space for thesekeys.

2.2 Installation1. Insert your CD into the CD drive on your computer.

2. Double click the setup.exe file on the CD.

3. Follow the setup prompts. During this stage of the setup you will have theopportunity to select the destination of the Player (Default: C:\program files\lucid)and the program group name.

4. Reboot your computer when the setup package is complete.

3. Overview of the CD-ROM1. Start Lucid by clicking on the desktop icon, or via the ‘start’ menu. This loads the

program and brings up the following screen:

All the features of the CD-ROM can be accessed from this screen.

To start the key itself, click anywhere on the diatom image.

Manual takes you to a pdf file containing this document.

Introduction to the diatom frustule provides an overview of the structure andbasic biology of the diatom cell.

Taxa takes you to the taxon descriptions, organised by Class.

Characters takes you to pages with descriptions of all the characters and statesused in the key to identify diatoms. Each page has images and/or text. There is


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no fixed format for these: in some cases, a picture alone was sufficient to conveythe meaning of a character or state whilst in other cases, pictures needed to besupplemented by text. We have used light micrographs wherever possible, so thatthe image is as close as possible to what you will see when identifying a diatom,but we have also used SEMs and diagrams, particularly to convey details of thefiner structure of the valve. Several of the characters have simple ‘present’ /’absent’ states. It is, however, not always easy to convey an absence convincinglyand sometimes only the ‘present’ state is illustrated.

Glossary explains the terms used in the key.

Environment provides background information on the indices and other sourcesof environmental data used on the taxa pages.

References lists all the bibliographic sources cited on the CD-ROM.

Credits acknowledges not just the team responsible for developing the CD-ROM,but also the many people who provided advice, allowed us use of their images orwho helped test the CD-ROM.

The Environment Agency and Lucid logos take you to the homepages of theorganisations that funded this key and developed the software.

4. Use of Lucid: tutorial2. Start Lucid by clicking on the desktop icon, or via the ‘start’ menu. This should

load the program and you should see the above screen.

3. Links on this page take you to the taxon database and other supporting information(see above). If you want to identify an unknown diatom then click anywhere onthe diatom image or on the key icon in the top left hand corner. This takes you tothe Lucid interface:


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The screen is divided into four quadrants. The upper two quadrants list the charactersand states, with those available on the left hand side and those selected by the user onthe right hand side. The lower two quadrants list the taxa, with those discarded on theleft hand side and those remaining on the right. At the start, all the states will be in thetop left hand quadrant and all the taxa in the bottom right hand quadrant.

4. Click on the top left hand quadrant (‘characters available’) and then scrollthrough the list of characters until you see ‘shape in valve view’. Click on thisand the four possible ‘states’ for this character will appear:

Circular

Elliptical or elongated

Triradiate

Multi-angled

5. Left click on ‘elliptical or elongated’ then, holding the left mouse button down,pull this state across to the top right hand quadrant. Then move to the nextcharacter (‘if elliptic or elongate, apical symmetry’) and the following statesshould appear:

Isopolar

Heteropolar

6. Left click on ‘heteropolar’ and, holding the left mouse button down, pull thisstate across to the top right hand quadrant. You should now have two states in thetop right hand quadrant. See what has happened to the taxa in the bottom twoquadrants:

As heteropolarity is a relatively rare condition in freshwater diatoms, most of thetaxa have been discarded as they do not fulfil either or both of the conditions thatyou have set, and you are left with a list of 41 taxa, belonging to 15 genera.


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7. You can now continue to scroll down the list and choose more characters in orderto complete the diagnosis. If you are a beginner, we recommend that you startusing the expert routes (see page 7). If you are not sure what is meant by aparticular character or state place the mouse over the purple button to the left ofthe character name and click. A screen will pop up with definitions andillustrations to help you:

Click the ‘close’ button in the top right hand corner of the pop-up box when youhave finished with these definitions and illustrations.

8. You can select more than one state for any character. For example, the character‘if isobilateral or sigmoid, valve shape’ has six possible states:

Lanceolate

Linear-elliptical

Linear-lanceolate

Linear

Rhombic

Elliptical

If you are unsure whether a particular diatom has a ‘lanceolate’ or a ‘linear-lanceolate’ outline, you should select both states so that only taxa to which neitherof these states applies are discarded.


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9. You might also decide to remove some of the taxa remaining. For example, youmight be confident that the heteropolar diatom that you are trying to identify is notAsterionella. If this is the case, click on the taxon and, holding the left mousebutton down, drag it to the ‘taxa discarded’ quadrant. If you change your mind,you can drag a taxon that you have discarded manually back to the ‘taxaremaining’ quadrant.

10. Once you have reduced the list of taxa substantially, you can use some of the moreadvanced facilities that can be found in Lucid. From the menu at the top of thescreen, select ‘Characters’ and then ‘Best options’:

This gives you three check boxes:

o Sort characters on BEST – this will sort all the characters in the top leftquadrant, placing the one that is most likely to reduce the number of taxaremaining at the top

o Find BEST character –this will not sort the characters but will, instead, takeyou to the character most likely to reduce the number of taxa remaining.

o Use numeric characters – this can be switched on or off, depending uponyour preference. If it is not checked, none of the numeric characters will beconsidered when Lucid sorts the characters.

The advantage of Sort characters on BEST is that you then have a list of the mostuseful characters at the top of the screen from which to choose. If you Find BESTcharacter, then you may find that this is something that you cannot see on yourspecimen (for example, it might ask for the number of chloroplasts, which is nothelpful if you are using cleaned material.

Having set your preferences using BEST options, click on Characters – BEST toactivate the feature.

The next option down on the pull-down menu is Native order which resorts thecharacters back into their original order.


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11. An alternative to using the BEST character is to use the feature below BEST onthe Characters toolbar. This is called ‘Bingo’ and clicking on this will produce apop-up box which will list the features most likely to result in a unique diagnosis:

12. If you want to see what any of the taxa remaining actually look like, or read adetailed description, click on the green button to the left of the name. This willtake you to a ‘factsheet’ which includes images and descriptions:

You can return to Lucid from either by closing the window (click on the ‘close’ buttonin the top right corner) or by clicking on Lucid on the task bar at the bottom of thescreen. Alternatively, you use ‘previous taxon’ and ‘next taxon’ in the menu bar toscroll through the factsheets of all the remaining taxa.


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13. Once you have completed your diagnosis, you can restart the key by clicking onthe blue restart button at the top left hand side of the screen.

14. Note that all monoraphid taxa have two entries in the key, corresponding to theraphe valve (RV) and rapheless valve (RLV) respectively. If you select anattribute that is visible on just one valve (the raphe, for example), then the entryfor the RLV will move to the taxa discarded quadrant. However, dependingupon the characters and states chosen, you may find that the list of taxa remainingincludes both entries, e.g.

Achnanthes conspicua RV

Achnanthes conspicua RLV

15. It is also possible that you will get to a final list of taxa that includes a species plusa genus:

Gomphonema minutum

Gomphonema

As the key does not contain all representatives of many genera, we have includedthe genus in the key so that users are not tempted to ‘shoehorn’ all specimens intothose species in the key. In a situation such as this, you should first consult thedescription of Gomphonema minutum and, if your specimen does not correspond,consult a more detailed flora.

5. Help for the beginner: expert routesThis Lucid key has 129 characters from which the user can choose. Each of thesecharacters has at least two and up to eight states, presenting beginners with 386 statesfrom which to choose. Lucid has a facility called ‘expert routes’ which is, in effect, aguide to those characters that are most likely to be useful to a beginner. Access thisfeature via the key tab on the menu bar:


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If you select the route for diatoms in valve view, you will be taken to the firstcharacter that you should use:

This is shape in valve view. Select the appropriate state and you will be taken to thenext character, and so on. There are ten characters in this expert route; however, youdo not have to complete all of these. If you decide to use a character that is not onroute, select it and you will be asked to confirm that you wish to terminate the expertroute.


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You can then continue using Lucid in the conventional mode described earlier.

6. Tips for more advanced usersOnce you have grasped the basic principles of the Lucid interface, you can start to useother facilities within the software. Some are described below. Others are describedin the Help files, accessed via the toolbar. Selecting ‘contents’ takes you to the mainindex, from where detailed instructions on using Lucid can be accessed:

1. You have already been introduced to the best and bingo features on the charactertab. Another useful feature on this tab is ‘sets’. Clicking on this opens a drop-down menu with seven options:

All

Central, axial and hyaline areas


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Live characters

Other features

Raphe characters

Size and shape

Striae characters

The characters used in the key have been placed in three groups and this optionallows only those relevant to the user’s circumstances to be displayed. When facedwith a live diatom, for example, it is useful to have options for ‘live characters’and ‘size and shape’, but the other sets may be less relevant. Checking these twoboxes and leaving the others unchecked will present you with a shorter list ofcharacters to scroll through. Similarly, when trying to identify a cleaned valve,‘live characters’ can be left unchecked, whilst ‘central, axial and hyalineareas’, ‘raphe characters’, ‘striae characters’ and ‘other features’ should bechecked. Alternatively, you can select ‘all’ (the default) to have the whole rangeof characters displayed.

2. The advantages of sorting characters using best were described above. The powerof this facility, however, increases considerably if used in conjunction withanother option on the character tab: prune redundants. Start the key and selectbest, as described above. You will see that the first character is now ‘centralarea, shape’, which has eight options:

Diamond shaped

Butterfly shaped

Rectangular

Transverse elliptical

Longitudinal elliptical

Rounded

Narrow (like axial area)

No central area

Assume, for the sake of this example, that you cannot see a central area and selectthe final option. 278 taxa are discarded and 112 are left. In doing this, however, anumber of the characters have also become redundant because all the taxa thatpossess these characters are now in the taxa discarded quadrant. So if you nowclick on prune redundants, the number of characters will reduce from 129 to111.

Sorting on best again brings a different character to the top, as the software hasreanalysed the taxa remaining and found a new order that reflects the taxa


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remaining. Note that element spacing - stria density is now at the top of the list.Enter the value 17 here, and a further 73 taxa are discarded, leaving just 39 taxaremaining.

3. Once again, sort on best again and see how the characters are reorganised. Thetop of the list is now raphe slit position, followed by valve breadth. Remember,you don’t have to choose the character at the very top of the list and if you entereda valve breadth of 4 µm, for example, you will shorten the list again, leaving just19 taxa.

4. Now select the taxa tab from the menu bar. There are a number of useful featureshere, particularly when you have narrowed down the list of taxa remaining.

o Similarities / differences opens a box that allows you to see how the taxaremaining differ from one another. Select a character from the top pane and thelower pane will then show how all taxa are scored for that character.


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o If you highlight any taxon in the taxa remaining quadrant and then select mostsimilar from the taxa tab you will see all other taxa in the database organised in alist from the most similar down to the least similar. This is done purely onstatistical, rather than taxonomic criteria, so is not a particularly useful feature.

o If you select a taxon and choose the diagnose option, then a box will appeartelling you which character-states are unique to this taxon. This may well beuseful when you have only a limited list although inclusion of broad genericcategories may mean that many taxa appear to have no uniquely diagnostic states.

o Selecting a taxon and clicking Describe simply opens a box that lists all thecharacters and how they are scored for this taxon.


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7. SupportFor questions or problems about the operation of the Lucid software, please look firstat the Help pages, accessed via the tool bar.

If these do not answer your question, look at the ‘frequently asked questions’ pageson www.lucidcentral.com/support

If you have a question about other aspects of this key, please send an e-mail [email protected] and we will respond as quickly as possible.

8. How Lucid worksThe Lucid software makes use of a matrix of information, with each row of the matrixrepresenting a taxon and each column representing one state for a particular character.Each cell of the matrix therefore represents the condition of a unique character-statecombination in a particular taxon.

There are six possible codes for each matrix position: 0, 1, 2, 3, 4 or 5, with thefollowing significance:

0 FALSE This state does not occur in this taxon.1 TRUE This state is normally present in this taxon.2 Unknown The condition of this state is not known for

this taxon.3 Rarely TRUE This state is found for this taxon, but not

commonly.4 Often recorded as TRUE,

but only bymisinterpretation

This state is FALSE for this taxon, butinexperienced users are likely to record it asTRUE.


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5 Occasionally recorded asTRUE, but only bymisinterpretation

This state is FALSE for this taxon, butinexperienced users might possibly record itas TRUE.

When one or more character-states is moved to the character state chosen quadrant,Lucid can work in one of two modes: Filter or Match modes. In Filter mode it willsort through all the taxa and retain only those that match all the states that have beenchosen, with the other taxa appearing in the ‘taxa discarded’ window. In Match modeno taxa are discarded, but instead all taxa are ranked in the taxa remaining window bya percentage probability, depending upon the number of states with an exact match.So a taxon that appears with ‘100%’ beside it matches all the states chosen, while onewith ‘80%’ will have a number of states for which there are not an exact match. Bydefault, Lucid is set to Filter mode but you can easily toggle between Filter andMatch modes via the Key menu on the taskbar:

Taxa remaining are listed according to their probability of being correct. This meansthat taxon that has the most TRUE states will be at the top of the list, whilst thosewith one or more states that are ‘Rarely present’ will occur further down.

The screen above also shows other features on the Key menu that can affect theoutcome of a determination.

Retain uncertainties will treat states coded as 2 (unknown or uncertain) as TRUE,and will retain taxa with these values in the list of taxa remaining. This is the defaultoption, but users can toggle it on and off.

Allow misidentifications will treat states coded as 4 or 5 (TRUE bymisinterpretation) as TRUE and will retain these in the list of taxa remaining. Again,this is the default option and it can be easily toggled on or off.

The menu item error tolerance can be useful firstly because the team that producedthe key are human and fallible (even though we have tested and retested the keyseveral times) and secondly because you, the user, might make mistakes when you usethe key. The default setting for error tolerance is ‘0’; however, if you set it to ‘1’,then you are allowed to make one ‘mistake’ (or to disagree with the development


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team, depending upon your point of view) before a taxon is moved to the ‘taxadiscarded’ window. So if you select nine states, then the taxa remaining will includethose that match eight or nine of these, and only those that have more than onemismatch will be discarded.

9. ReferencesBayer, M.M., Droop, S.J.M. & Mann, D.G. (2001): Digital microscopy in

microscopical research, with special reference to microalgae. - PhycologicalResearch 49: 263-274.

Bayer, M.M. & Juggins, S. (2002): ADIAC imaging techniques and databases. - In: duBuf, H. & Bayer, M.M. (eds) Automated Diatom Identification: 55-73. WorldScientific Press, Singapore.

Bradbury, S. (1984): An introduction to the optical microscope. Oxford UniversityPress, Oxford.

Coring, E., Schneider, S., Hamm, A. & Hofmann, G. (1999): DurchgehendesTrophiesystem auf der Grundlage der Trophieindikaation mit Kieselalgen. –Deutscher Verband für Wasserwirtschaft und Kulturbau e.V., Koblenz.

Cox, E.J. (1996): Identification of Freshwater Diatoms from Live Material. -Chapman & Hall, London.

du Buf, H. & Bayer, M.M. (Eds) (2002): Automated Diatom Identification. - WorldScientific Press, Singapore.

Hartley, B. (1986): A check-list of the freshwater, brackish and marine diatoms of theBritish Isles and adjoining coastal waters. - J. Mar. Biol. Ass. U.K. 66: 531-610.

Hartley, B., Barber, H.G. & Carter, J.R. (1996): An Atlas of British Diatoms. -Biopress, Bristol.

Hustedt, F. (1927-1966): Kryptogamen-Flora von Deutschland, Österreich und derSchweiz Band VII Die Kieselalgen. - Leipzig: Akademische Verlagsgesellschaft.

Hustedt, F. (1930): Die Süsswasserflora Deutschlands, Österreichs und der Schweiz10: Bacillariophyta (Diatomeae) – Fischer, Jena.

Kelly, M.G. (1998): Use of the trophic diatom index to monitor eutrophication inrivers. - Wat. Res. 32: 236-242.

Krammer, K. & Lange-Bertalot, H. (1986-1991): Die Süsswasserflora vonMitteleuropa 2: Bacillariophyceae. - Gustav Fischer-Verlag, Stuttgart. 4 volumes.

Patrick, R. & Reimer, C.W. (1966): The Diatoms of the United States Exclusive ofAlaska and Hawaii. Volume 1: Fragilariaceae, Eunotiaceae, Achnanthaceae,Naviculaceae. - Academy of Natural Sciences, Philadelphia:

Patrick, R. & Reimer, C.W. (1975): The Diatoms of the United States Exclusive ofAlaska and Hawaii. Volume 2 Part 1: Entomoneidaceae, Cymbellaceae,Gomphonemaceae, Epithemiaceae. Academy of Natural Sciences, Philadelphia:


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Rott, E., Pipp, E., Pfister, P., van Dam, H., Ortler, K., Binder, N. & Pall, K. (1999):Indikationslisten für Aufwuchsalgen in Österreichischen Fliessgewassern. Teil 2:Trophieindikation. - Bundesministerium für Land- und Forstwirtschaft, Wien,Austria.

Round, F.E., Crawford, R.M. & Mann, D.G. (1990): The Diatoms: Biology andMorphology of the Genera. Cambridge University Press, Cambridge.

Tilling, S.M. (1987): Education and taxonomy: the role of the Field Studies Counciland AIDGAP. Biol. J. Linn. Soc.32: 87-96.

Whitton, B.A, Balbi, D.M, John, D.M., Ellwood, N.T.W. York P.V. & Donaldson, A.(2002): Freshwater Green Algae of the British Isles: An Interactive Key to theCommoner Genera and Species. School of Biological and Biomedical Sciences,University of Durham, Durham DH1 3LE, ISBN 0-9538842-3-6.

Whitton, B.A., Balbi, D.M. and Donaldson, A. (2003): Blue-Green Algae of theBritish Isles: Interactive Key to the Species. School of Biological and BiomedicalSciences, University of Durham, Durham DH1 3LE, UK

10. Acknowledgements

Development team

Helen Bennion (ECRC-ENSIS) centric diatomsEileen Cox (Natural History Museum) raphid diatomsBen Goldsmith (ECRC-ENSIS) raphid diatomsJane Jamieson (Environment Agency) project managementSteve Juggins (University of Newcastle) computingMartyn Kelly (Bowburn Consultancy) araphid and monoraphid diatoms,

project managementDavid Mann (Royal Botanic Garden,Edinburgh)

raphid diatoms, photography

Richard Telford (University of Newcastle) computing

OthersSpecial thanks to Brian Whitton for sharing experience gained during thedevelopment of two previous CD-ROMs for the Environment Agency and to MichaBayer, who took many of the images in the ADIAC database that were used for thisproject. Thanks, too, to Nigel Dobyn for help with illustrations.

Other people who have allowed use of their images or have lent material forphotography:Don Charles (Academy of Natural Sciences, Pittsburgh, USA)Bernie ni Chathàin (KMM, Ireland)Keith Clarke (Norfolk, UK)Richard Crawford (Alfred Wegener Institute, Bremen, Germany)Luc Ector (Public Research Center-Gabriel Lippman, Luxembourg)Friedel Hinz (Alfred Wegener Institute, Bremen, Germany)


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Joachim Hürlimann (AquaPlus, Switzerland)Plaman Ivanov (University of Sofia, Bulgaria)Viv Jones (ECRC, University College, London)Lydia King (University of Lancaster, UK)Jan Krokowski (Scottish Environment Protection Agency)Ralf Nötzel (Germany)Aloisie Poulíčková (Palacký University, Olomouc, Czech Republic)Derek Stevens (Dorset, UK)Jonathan Taylor (North-West University, South Africa)Morgan Vis (Ohio University, USA)Marian Yallop (University of Bristol, UK)

Every effort has been made to contact copyright holders of photographs and otherimages. Any copyright holders we have been unable to reach or to whom inaccurateacknowledgement has been made are invited to contact the development team:[email protected].

Testers and reviewers include: Chris Adams (Environment Agency)Nigel CameronJan Krokowski (Scottish Environment Protection Agency)Andrew Haigh (Environment Agency)Phil Harding (Environment Agency)Julie Gething (Environment Agency Wales)Jane Jamieson (Environment Agency)Michael Thomas (Environment Agency)Nicki Wiltshire (Environment Agency Wales)Marian Yallop (University of Bristol)Aleksandra Zgrundo (University of Gdansk, Poland)

Funding for the development of this key came from the Environment Agency (R&DProject E1D (01) 02: Development of an interactive CD-ROM for the identification offreshwater diatoms of the British Isles). However, the project also relied heavily onimages gathered during two EU-funded projects:

ADIAC (Automatic Diatom Identification And Classification) funded by theEuropean Marine Science and Technology (MAST) programme.

EDDI (European Diatom Database Initiative) funded by the EU Framework IVprogramme.


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Documents

Identification of common freshwater diatoms of Britain …craticula.ncl.ac.uk/EADiatomKey/html/manual.pdf · Identification of common freshwater diatoms of Britain ... include characteristics