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Surveying Macrofungi of Yosemite
          & Pt Reyes
               Mochella sp nova
                                       Conocybe sp nova




 Tuber sp




            Mycena pura

                                  Agrocybe pediades
What is a macrofungus?
• Answer: a fungus that produces a
  macroscopically fruiting structure that can be
  seen (and sometimes identified) without a
  microscope.
Macrofungi can be very macro

     Boletus
     edulis




                     Kabir Peay
Or they can be just a few millimeters




Dasyscyphus nudipes
var. minor
Who is involved?
• Members of the amateur mushroom groups:
  Bay Area Mycological Society, Mycological
  Society of San Francisco, Sonoma Mycological
  Association, Santa Cruz Fungus Federation
• Members of the general public
• Professional mycologist, especially students
  and postdocs, from Berkeley, Davis, SF State,
  Humboldt State
David Arora, Norm Andresen, Fred Stevens, Mike Wood,Erin Blanchard , Christian
Schwarz, Debbie Viess, David Rust, and many others not pictured
Some of the “Amateurs” are amazing

              Cortinarius (>1000 described species)


                                  Dimitar Bojantchev
Galerina – an example of an LBM (little brown
mushroom) genus

                               Doug Smith
Mike Wood – the author of Mykoweb
The Berkeley crew: Jennifer Kerekes, Anthony Amend, Kabir Peay,
Nicole Hynson, Sir David Read, Nhu Nguyen, Todd Osmundsen Else Vellinga
Why do we want to survey the
   macrofungi of the National Parks?
• Surprising little is known about the mycoflora
  of North America
• The park contains some of the best and most
  easily accessible examples of native plant
  communities
• Fungi are crucial components of all terrestrial
  ecosystems
• Provides ground truth for ITS sequence data!
Example of the Pt Reyes Survey
     http://www.mykoweb.com/PtReyes/

• The survey was structured into five public
  “mycoblitzs”
• People from the MSSF, FFSC, BAMS, and SOMA
  provided most of the manpower for collecting and
  identifying.
• Collections were sequenced (ITS and sometimes
  RPB2)
We assigned people routes and zones to cover
Collection instructions were passed out:
Identification of the collections
• Collections were made and coarsely sorted on the Saturday of
  each foray, and then examined more closely, photographed
  and dried on the following Sunday.
• Collection tags from common species were saved and
  catalogued to provide distribution data
• Species that were new to the park list, or for which no
  permanent collections were previous made were saved.
• Sunday a smaller group at Berkeley sorted through the the
  latter collections, examined some with microscopes, selected
  those worth saving, and photographed and dried them.
Curation of collections
• Collection data were entered in a database
• Collections were accessioned into the UC
  Herbarium
• Data and images were be made web
  accessible
• Eventual goal is to sequence the ITS region
  from all of them, and RPB1 from all collections
Inocybe central
Peter Kennedy                     Kabir Peay
DNA sequences helped to sort out the difficult groups
Increase in number of recorded species
          with each mycoblitz at Pt. Reyes

600

500

400

300

200

100

  0
      0      1     2      3     4      5     6     7
Inverse Ranked Abundance Curve of Pt. Reyes fungal species
                 by number of collections
A different plan for Yosemite
• Fewer people (but many specialists)
• No “mycoblitzes”, but lots of small group
  collecting
• Voucher specimens with similar labeling and
  photographic conventions as at Pt. Reyes
• DNA sequences still a must
• Better internet coordination
The Mushroom Observer
           Nathan Wilsons cool tool


• Google “Mushroom Observer”
• Plug in “Yosemite” in the find widow
In 8 month we when from 39 pages to 63 pages of
15 collections/page
Google Doc: the non-public coordination interface
A small piece of the collections
spreadsheet on Google Docs
Some numbers from the first year’s survey
• >500 collections were made, 110 have been
  sequenced in one direction for the ITS region
• The collections included >130 species, and 111
  genera
• 90% of the species and 62% of the genera were new
  records for the Yosemite
• This more than doubled the number of species
  known from the park and increases the known
  genera by 88%
• When compared to Pt Reyes 62% of the species and
  47% of genera were unique to the park
• Several new species have been described
Time consuming issues
• Keeping up with curation of specimens
• Keeping up with the website
• Keeping up with sequence acquisition and
  dissemination
• Dealing with permits (especially from
  Yosemite!)
My Dream:
• Expand this effort to survey the continent
  with a goal of producing an North American
  mycoflora
• Use this is a platform for training both
  professions (grad students and postdocs), and
  the general public
• Find major funding for this

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Citizen mycology

  • 1. Surveying Macrofungi of Yosemite & Pt Reyes Mochella sp nova Conocybe sp nova Tuber sp Mycena pura Agrocybe pediades
  • 2. What is a macrofungus? • Answer: a fungus that produces a macroscopically fruiting structure that can be seen (and sometimes identified) without a microscope.
  • 3. Macrofungi can be very macro Boletus edulis Kabir Peay
  • 4. Or they can be just a few millimeters Dasyscyphus nudipes var. minor
  • 5. Who is involved? • Members of the amateur mushroom groups: Bay Area Mycological Society, Mycological Society of San Francisco, Sonoma Mycological Association, Santa Cruz Fungus Federation • Members of the general public • Professional mycologist, especially students and postdocs, from Berkeley, Davis, SF State, Humboldt State
  • 6. David Arora, Norm Andresen, Fred Stevens, Mike Wood,Erin Blanchard , Christian Schwarz, Debbie Viess, David Rust, and many others not pictured
  • 7. Some of the “Amateurs” are amazing Cortinarius (>1000 described species) Dimitar Bojantchev
  • 8. Galerina – an example of an LBM (little brown mushroom) genus Doug Smith
  • 9. Mike Wood – the author of Mykoweb
  • 10. The Berkeley crew: Jennifer Kerekes, Anthony Amend, Kabir Peay, Nicole Hynson, Sir David Read, Nhu Nguyen, Todd Osmundsen Else Vellinga
  • 11. Why do we want to survey the macrofungi of the National Parks? • Surprising little is known about the mycoflora of North America • The park contains some of the best and most easily accessible examples of native plant communities • Fungi are crucial components of all terrestrial ecosystems • Provides ground truth for ITS sequence data!
  • 12. Example of the Pt Reyes Survey http://www.mykoweb.com/PtReyes/ • The survey was structured into five public “mycoblitzs” • People from the MSSF, FFSC, BAMS, and SOMA provided most of the manpower for collecting and identifying. • Collections were sequenced (ITS and sometimes RPB2)
  • 13. We assigned people routes and zones to cover
  • 15. Identification of the collections • Collections were made and coarsely sorted on the Saturday of each foray, and then examined more closely, photographed and dried on the following Sunday. • Collection tags from common species were saved and catalogued to provide distribution data • Species that were new to the park list, or for which no permanent collections were previous made were saved. • Sunday a smaller group at Berkeley sorted through the the latter collections, examined some with microscopes, selected those worth saving, and photographed and dried them.
  • 16. Curation of collections • Collection data were entered in a database • Collections were accessioned into the UC Herbarium • Data and images were be made web accessible • Eventual goal is to sequence the ITS region from all of them, and RPB1 from all collections
  • 18. DNA sequences helped to sort out the difficult groups
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  • 22. Increase in number of recorded species with each mycoblitz at Pt. Reyes 600 500 400 300 200 100 0 0 1 2 3 4 5 6 7
  • 23. Inverse Ranked Abundance Curve of Pt. Reyes fungal species by number of collections
  • 24. A different plan for Yosemite • Fewer people (but many specialists) • No “mycoblitzes”, but lots of small group collecting • Voucher specimens with similar labeling and photographic conventions as at Pt. Reyes • DNA sequences still a must • Better internet coordination
  • 25. The Mushroom Observer Nathan Wilsons cool tool • Google “Mushroom Observer” • Plug in “Yosemite” in the find widow
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  • 27. In 8 month we when from 39 pages to 63 pages of 15 collections/page
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  • 35. Google Doc: the non-public coordination interface
  • 36. A small piece of the collections spreadsheet on Google Docs
  • 37. Some numbers from the first year’s survey • >500 collections were made, 110 have been sequenced in one direction for the ITS region • The collections included >130 species, and 111 genera • 90% of the species and 62% of the genera were new records for the Yosemite • This more than doubled the number of species known from the park and increases the known genera by 88% • When compared to Pt Reyes 62% of the species and 47% of genera were unique to the park • Several new species have been described
  • 38. Time consuming issues • Keeping up with curation of specimens • Keeping up with the website • Keeping up with sequence acquisition and dissemination • Dealing with permits (especially from Yosemite!)
  • 39. My Dream: • Expand this effort to survey the continent with a goal of producing an North American mycoflora • Use this is a platform for training both professions (grad students and postdocs), and the general public • Find major funding for this