CIGAF

Collections of Insect Gut Associated Fungi

CIGAF is an R Shiny app for exploring and visualizing over 90 years of insect gut-associated fungi collections.
Currently, CIGAF contains 3198 specimens, 289 species, 48 genera, 4 families, and 3 orders of insect-gut-associated fungi!

Choropleth Map of Fungal Specimens in the CIGAF database

Mouse over each country to see the associated number of specimens currently included in the CIGAF database.The darker the colour of a country, the greater the number of fungal specimens collected.
A specimen is defined here as the combination of an organisms species, location, and date of collection. I.e two species collected at the same location on different dates are two separate specimens



This site was made by Shal Chaudhary and currently curated by Bomin Kim in the Wang Lab for Fungal Genomics at the University of Toronto.


If you analyze data using this tool, please cite:

Shalini Chaudhary, Yibing Wu, Doug Strongman, Yan Wang. CIGAF—a database and interactive platform for insect-associated trichomycete fungi, Database, 2023, baad038, https://doi.org/10.1093/database/baad038






Collection Site Maps


In this section you can explore collected specimens by their collection site coordinates.

Only specimens with available collection site coordinates are included in this visualization. To view collections by country (which is more readily recorded) view the "Diversity" or "Species Range" tabs.



Map of Collected Fungal Specimens

Click on a marker to expand or view additional information. A specimen is defined here as the combination of an organism's species, location, and date of collection. I.e two species collected at the same location on different dates are two separate specimens.
Note: collection sites which appear to be in the water may have incorrect or imprecise coordinates recorded in their source publication. If this is not the case and an error has been made, please contact us.





Data Table of Collected Fungal Specimens

This data table reflects the data in the map above - i.e only entries that have associated coordinates. Additionally, if you have filtered the map to display a subset of fungi, that is also reflected here.

Choropleth Maps - Exploring Diversity


In this section you can explore species diversity by taxonomic level by generating a country level choropleth map.
Only entries with a recorded country of collection are included in this visualization.



Choropleth Map of Collections by Country at the Selected Taxonomic Level

Countries are coloured from light blue (lowest) to dark purple (highest) by the number of unique entries at the inputted taxonomic level.

The number of unique entries can be identified by mousing over the geographic region of interest, or by using the data table below.
To change the taxonomic level being represented (i.e specimen, species, genus, etc) select an option from the drop down menu

A specimen is defined here as the combination of an organisms species, location, and date of collection. I.e two species collected at the same location on different dates are two separate specimens



Data Table of Collections at the Selected Taxonomic Level

Choropleth Map - Exploring Range


In this section you can generate a country level range map using the drop down menus.
Note: You must select an Order before selecting a Family, and you must select a Family before selected a Genus etc.

Only entries with a recorded country of collection are included in this visualization.


Species Range Choropleth Map

Countries are coloured from light blue (lowest) to dark purple (highest) number of specimen collections of the selected species.
The number of specimens collected in each country can be identified by mousing over the geographic region of interest, or by using the data table below. A specimen is defined here as the combination of an organism's species, location, and date of collection. I.e two species collected at the same location on different dates are two separate specimens



Data table of the selected species

Ecoregions - Exploring Habitat Types



In this section you can generate a histogram of specimen counts for a taxonomic group of your choice by the ecoregion in which they were collected.
Use the x-axis drop down menue to select your prefered ecoregion descriptor. "Realm" is the least detailed habitat descriptor and "Eco_name" is the most detailed.

Note: Only entries with recorded coordinates are included in this visualization.

Ecoregion data was obtained from the 2017 Resolve Ecoregions and Biomes Map, available here. For more details, see

Dinerstein, E. et al., An Ecoregion-Based Approach to Protecting Half the Terrestrial Realm, BioScience, Volume 67, Issue 6, June 2017, Pages 534–545



Histogram of Collections by Ecoregion at the Selected Taxonomic Level

Countries are coloured only for aid in differentiating bars.
Data is ordered from highest count (left) to lowest count (right) by the number of unique specimens at the inputted taxonomic level.
The ecoregion and number of specimens can be identified by mousing over the bar of interest.
To change the taxonomic subset being represented select a group of interest from the drop down menues above.
A specimen is defined here as the combination of an organisms species, location, and date of collection. I.e two species collected at the same location on different dates are two separate specimens



Average Monthly Air Temperature in the Month and Year of Collection


In this section you can generate box plots of the minimum, maximum and average monthly temperature at the date (month + year) and location of collection for various subgroups of the collected fungi.

Only entries with recorded coordinates, a nearby weather station, and data associated with the user selected parameter are included in this visualization.
Each specimen meeting these requirements contributes one data point. A specimen is defined here as the combination of an organisms species, location, and date of collection. I.e two species collected at the same location on different dates are two separate specimens. Weather information for this visualization was obtained from www.worldclim.org

Box Plots of Average Monthly Collection Site Air Temperature ( C )

Hover over a box or data point to see additional details. Use the drop down menu to change the X axis or measurement value to your variable of interest. All temperature measures are in degrees Celsius and are the average for the month in which the sample was collected.





Data Table of Average Monthly Collection Site Air Temp

Average Monthly Precipitation in the Month and Year of Collection


In this section you can generate boxplots and beeswarm plots of the minimum, maximum and average monthly precipitation at the date (month + year) and location of collection for various subgroups of fungi.

Only entries with recorded coordinates, a nearby weather station, and data associated with the user selected parameter are included in this visualization.
Each specimen meeting these requirements contributes one datapoint. A specimen is defined here as the combination of an organism’s species, location, and date of collection. I.e two species collected at the same location on different dates are two separate specimens. Weather information for this visualization was obtained from www.worldclim.org

Box Plots of Average Monthly Collection Site Precipitation at Time of Collection

Hover over a box to see additional details. Use the drop down menus to change the X axis to investigate your variable of interest. All precipitation measures are the recorded average precipitation levels in mm for the month in which the sample was collected.





Data Table of Average Monthly Collection Site Preciptitation

Publications Through Time


In this section you can explore the collections published over time.
Select a start and end year below. Year inputs are inclusive.
Only peer-reviewed entries with a recorded year of publication are included in this visualization.

Each specimen meeting these requirements contributes one datapoint. A specimen is defined here as the combination of an organism’s species, location, and date of collection. I.e two species collected at the same location on different dates are two separate specimens.



Histogram of Collections by Year of Publication

to

Hover over a column to see Specimen Count. A specimen is defined here as the combination of an organism's species, location, and date of collection. I.e two species collected at the same location on different dates are two separate specimens.










Map of Collections Published Within the User Selected Time Frame








Data Table of Collections Published Within the User Selected Time Frame

Collections Through Time


In this section you can explore fungal collections over time.
Select a date resolution, as well as a start and end date below. Year and Month inputs are inclusive.

Only entries with a date recorded to the user selected date resolution are included in this visualization.
Note: The # entries with at least the year recorded > # entries with at least the year and month recorded > # of entries with the year, month, and day recorded.
Therefore, a lower date resolution will have more data included (i.e year will return more datapoints than year-month).




User Options

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Histogram of Collections Over Time

Hover over a column to see Specimen Count. A specimen is defined here as the combination of an organism's species, location, and date of collection. I.e two species collected at the same location on different dates are two separate specimens.






Map of Collections Within the User Selected Time Frame





Data Table of Collections Within the User Selected Time Frame

Taxonomy Exploration


In this section you can explore a hierarchical taxonomy tree of the collected fungi.
Node colour is proportional to the number of unique entries in each node, with red having the most entries and green having the fewest compared to other nodes at the same level.

Click on a node to expand.

To generate a link to the external Lucid Server Key description and photos, select a species level node then click on the “Link” in the box below.
Taxonomy information is updated regularly from the GBIF database.

Link out to Lucid Server - Select a species to activate


Hierarchical Taxonomy Tree of Insect-Gut Associated Fungi in the CIGAF Database

Insect Host Family


In this section you can visualize a heat plot and stacked bar graphs of the insect host family associated with the fungi.
Only entries for with associated host information are included in this visualization.
For the stacked bar graphs, the taxonomic level of the fungi (x axis) can be selected from the drop down menu.
This page may be slow to load. Please be patient.


Hover over a point to see additional details. The heatmap is coloured by percent of specimens of a given fungal genes which are associated with each host. A specimen is defined here as the combination of an organism's species, location, and date of collection. I.e two species collected at the same location on different dates are two separate specimens. The row colours on the right hand side indicate fungal family and order. Mouse over to see their values.







Hover over a column to see additional details. The Bar plot on the left shows stacked raw fungal specimen counts with each associated host for a user defined x axis. The plot on the right shows the proportion (from 0 to 1) of associated insect host family for the user defined X axis category. A specimen is defined here as the combination of an organism's species, location, and date of collection. I.e two species collected at the same location on different dates are two separate specimens.



Downloadable Data Table


In this section you can subset and search the CIGAF dataset.
You can also download the complete CIGAF dataset as a csv.
If you cannot find the data you are looking for, please contact us.




Download

Contact


Please send an email to Dr. Yan Wang at yanxw.wang@utoronto.ca for comments, questions, or concerns.


New collections of insect-gut associated fungi can be submitted to the CIGAF database using this Specimen Submission Form to submit your collection data.

For large collection submissions, please contact Dr. Yan Wang.


If you identify any errors in the dataset, please fill out this google form, being sure to include the CIGAF ID(s) of the data in question and a description of the error.


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