Assembling the Fungal Tree of Life

For questions and comments contact tkakumar@gmail.com




General guide




Database

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Users may view the list of the species in the Database with their taxonomic status.

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Note that some entries whose taxonomic placement is uncertain are lacking one or more classification levels. ‘Anamorph’ indicated in a separate field is provided for some species and denotes the anamorphic id when the teleomorphic id is unknown or uncertain.

Clicking on any of the taxon links from Phylum to Genus will list all the taxa below that classification level. Clicking on a species will call up that organism's page.

Structural and biochemical data available on a species is displayed on the species page. The cell type (e.g., diploid mycelium) of the organism for which the data is available is specified. This is followed by the characters and coded (0, 1, 2, …) character states (for a complete list of characters and character states, see Character list and Glossary page). Sources section provides data source (unpublished AFTOL data is indicated as "AFTOL data") and voucher details. Images are included for characters wherever possible provided blanket copyright permissions have been obtained from the concerned publishers.

Example from species page

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Character list and Glossary

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Character list provides information on the organization of structural and biochemical data (e.g., Nuclear Division, Septum/Pore Cap, Motile Cell, Sterol composition) into characters (e.g., uniperforate septa, multiperforate septa) and their states (e.g., absent, present). Septal characters are divided into the following five developmental stages:

  • Hyphae excluding ascogenous hyphae/ascus (e.g. vegetative hyphae, paraphyses)
  • Multiperforate septum (includes plasmodesmata)
  • Basidium
  • Ascogenous hyphae/ascus, immature
  • Ascogenous hyphae/ascus, mature

A single species may have data listed under one or more subgroup headings, e.g., having data entered for "Hyphae excluding ascogenous hyphae/ascus", "Ascogenous hyphae/ascus, immature", and "Ascogenous hyphae/ascus, mature".

Location/cell type: Information about the type of cell from which data was collected is indicated. An abbreviated 2-letter location code is used for the cell types, which also appear within NEXUS files appended to the taxon ids (e.g., "Tuber_species_AC"). The locations themselves can apply to more than one subgroup.

Location/cell type codes

2N
diploid mycelium
XN
mycelium of unknown nuclear status
ZO
zoospore
ME
meiosis
MI
mitosis
AH
ascogenous hyphae/ascus
1N
haploid mycelium
2N
diploid mycelium
AC
ascocarp -- nonascogenous hyphae or ascospore
AS
asexual spore
BC
basidiocarp
MN
multinucleate
NN
dikaryotic mycelium
RS
junction of rhizoid and sporangium
SC
sporocarp
SF
sporangiophore
ZF
zygophore



NEXUS

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Character state data of one or more species can be displayed as a functional NEXUS file by clicking the NEXUS button. NEXUS files can be generated by searches based on taxonomy or according to character(s) of interest (either individually or in combination). For a search, select the taxonomic rank(s) or character(s) from the pull down menus.

For a search based on selected taxonomy use the menu shown below:

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To restrict your search to include information from the character sets of interest, select from the following menu:

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For this search, you can select up to a combination of 3 character sets.

A search for species based on a specific character state from a chosen taxonomy is also possible using the pull down menu option shown in the excerpt below.

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Here you will be prompted to narrow down your selection based on the character state you choose.

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Once you have made your selections, choose the NEXUS format radio button and then click "search".

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This gives you NEXUS data with all cell types based on your search criteria.

The "click here to display NEXUS cell type refinement" button now allows you to further refine the data search and assemble a final NEXUS file ready to be downloaded. The box displayed under this option appears with taxa pulled up based on your selection criteria and has check/uncheck boxes next to its location/cell type code (see location/cell type information above) link, indicating that it has been selected for merging. Files are selected and unselected manually by clicking on the boxes.

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Once the desired NEXUS files have been chosen, click on the "Download refined NEXUS file" button. A window opens with the NEXUS file text of the merged data, which may be copied and pasted as needed.

Note that NEXUS entries of the same organism with different location codes (circled) are NOT MERGED into a single entry, but have separate entries.

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It is up to the user to create a single entry for analysis.

The "human-readable table" format gives you the option to view the list of species that possess the specified character and its attributes (as shown below).

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For Contributors

Data submission

Contributions to the AFTOL Structural and Biochemical Database (SBD) can be made by anyone who possesses primary or secondary data on ultrastructural and/or biochemical characters of true fungal species (Kingdom Fungi). The data can be from any published/unpublished source and the contributor need not always be the original generator of the data. In the data submission process, the contributor first enters the data on Excel files that are downloaded to his/her computer. Template Excel files for different characters (e.g., septal ultrastructure, nuclear division) used in the database are available for download from the site. Contributors should use these template files to enter new data. An example entry has been included in one Excel file (Hyphal Tip) for reference. Excel data files with new data are directly submitted to the AFTOL SBD administrator (tkakumar@gmail.com) by e-mail. An Excel file can contain data on one or more than one species. Separate Excel files should be used for each different character data. For more information on the characters and character states used in the database see the Character list and Glossary page.

Images/illustrations that support the data can also be sent to the administrator as attachments. Quality images need to be submitted. Images should be scanned at a high resolution (700-1200 dpi) and can be saved in TIFF or JPEG formats. JPEG is the preferred format. Source acknowledgements for images should be clearly given along with the submission e-mail. Legends for each image also should be provided. For published or unpublished images please indicate the copyright holders and what license they are subject to. The preferred licenses would be public domain, Creative Commons Attribution-Share Alike (see Flickr), or other open content license. We strongly encourage authors who wish their data to be made available to the scientific community to choose journals with appropriate scientific policies on reuse of images or retain copyright to their images.

Data review and accession number

Upon receipt of the submissions and initial review by the administrator, expert curators are assigned to review the submissions. AFTOL expert curators (specialists in various character data) review and decide on the suitability of the data and images. Once acceptance of the new character data from the expert curators is received, the administrator files the approved data, makes entries in the SBD and then makes the data publicly available on the database. The administrator can hold any unpublished data as requested until initial publication by the contributor/author. The contributor will be notified by e-mail about the acceptance and availability of the data on the SBD and will be given an SBD accession number for each Excel file submission. The accession numbers can be used during publication of new data in scientific literature. The accession numbers assigned for submissions will help track the data when later modifications are required.

Spreadsheets available:







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