Tree-for-All hackathon series: Taxon sampling, part 1 

Originally posted on OPEN TREE OF LIFE:

Sampling taxa with Python and Perl scripts

This continues a series of posts featuring results from the recent “Tree-for-all” hackathon (Sept 15 to 19, 2014, U. Mich Ann Arbor) aimed at leveraging data resources of the Open Tree of Life project.  To read the whole series, go to the Introduction page.

More specifically, this is the first of two posts addressing the outputs of the “Sampling taxa” team, consisting of Nicky Nicolson (Kew Gardens), Kayce Bell (U. New Mexico), Andréa Matsunaga (U. Florida), Dilrini De Silva (U. Oxford), Jonathan Rees (OpenTree) and Arlin Stoltzfus (NIST).[1]

The “taxon sampling” idea

Although users seeking a tree may have a predetermined set of species in mind, often the user is focused on taxon T without having a prior list of species. For instance, the typical user interested in a tree of mammals does not really want the full tree of > 5000 known species of mammals, but some subset…

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BIOL 254/354 Molecular Systematics and Evolution. Spring 2015

Phylogenetic trees, the branching diagrams that represent historical relationships among genes, genomes and species, are used in virtually all biological disciplines, including epidemiology, comparative genomics, molecular genetics, ecology, and evolutionary biology. For example, the tree below shows a dated phylogeny of the Ebola virus, which provides clues to the geographic origins of the current outbreak. The ability to understand and interpret phylogenetic trees is an essential skill for all biologists.

Molecular Systematics and Evolution will be a practical, hands-on course in phylogenetic methods. Topics to be discussed include evolution of genes and genomes, methods for estimating evolutionary relationships using molecular data, and applications of molecular data to general problems in biology (e.g., diversification of gene families, historical biogeography, molecular clock dating, and character evolution). The course will include lectures, student-led discussions, laboratory projects using computer-based applications, and presentations.

Prerequisites: BIOL 101 and 102

Meeting time and place: Friday 1:25-4:25, Lasry rm 355

Enrollment cap: 12

For more information, please contact the instructors: David Hibbett and Romina Gazis

Why Do We Need Big Trees, Anyway?

Originally posted on OPEN TREE OF LIFE:

An explicit goal of the Open Tree of Life is to create a single phylogenetic tree that encompasses all living (and some extinct) biodiversity on earth. A question some may have, especially non-scientists, is why do we need a tree like that, and what would we do with it? You can’t even see it all at once, right? The answer to this question, of course, is that with bigger and more resolved trees we can answer evolutionary questions on scales not previously possible.

Currently, postdocs from the labs of Doug Soltis (Univ. of Florida) and Stephen Smith (Univ. of Michigan) are collaborating on several projects within the plant world that leverage the power of big trees. Cody Hinchliff, a postdoc in the Smith lab, recently presented some of these findings during a standing room only presentation at the Botanical Society of America conference in Boise, Idaho, employing a tree with…

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MassMyco 2014

The second biennial MassMyco meeting was held Saturday at Harvard Forest. As before, this was a wonderful, friendly meeting with a remarkably diverse range of topics presented, including: maternal effects in fungi, mechanisms of manganese oxide formation by ascomycetes, canker disease of jackfruit in Bangladesh, effects of nitrogen deposition on fungal communities and decomposition rates, arboreal amoeba-trapping discomycetes, and lots more. This is a great meeting for undergraduates, such as Sam Kovaka and Sara Waldman from Clark, who presented posters on their summer projects (photos below–more here).

The New England mycology scene is getting stronger, with a number of recent hires at local universities. Speakers at this year’s MassMyco included Jenny Talbot, who  just joined the faculty at Boston University, Ben Wolfe, who is a new professor at Tufts, and Kevin Drees, who was representing Jeff Foster’s new lab at the University of New Hampshire (not to mention our new colleague John Gibbons, who was not at the meeting but has just joined the faculty at Clark). It will be exciting to hear from these groups and others at the third MassMyco in 2016.

Dorothy Tang and Sara Waldman with Sara's poster on relationships of Stiptophyllum.

Dorothy Tang and Sara Waldman with Sara’s poster on relationships of Stiptophyllum.

Sam Kovaka, with a poster describing research at the Joint Genome Institute.

Sam Kovaka, with a poster describing research at the Joint Genome Institute.

Alicia presenting research on the magnificent and diverse Gomphales

Alicia presenting research on the magnificent and diverse Gomphales




BMC foray at the Upton State Forest

BMClogoOn Sunday, Sept. 21, the Boston Mycological Club held a foray at the Upton State Forest, where we were hosted by the Friends of the Upton State Forest. The weather has been dry but we still found a lot of mushrooms. As the finds came in, we distributed them on two tables; on one the fungi were arranged according to macromorphology (agarics, polypores, etc), as usual; on the second table the fungi were divided according to nutritional modes. A preliminary, partial checklist is at the bottom of this post.

Bill Taylor (FUSF) introduced the history of the property before everyone went collecting. Photo by Marcella Stasa

Bill Taylor (FUSF) introduced the history of the property before everyone went collecting. Photo by Marcella Stasa

Some of the mushrooms. Photo by Mary Beauchamp.

Some of the fungi that resulted from an hour and half of collecting by the group. Photo by Mary Beauchamp.

Sorting by form. Photo by Marcella Stasa.

Sorting by form. Photo by Marcella Stasa.

Sorting by ecology. Photo by Marcella Stasa.

Sorting by ecology. Photo by Marcella Stasa.

Some fungi are hard to categorize. Photo by Marcella Stasa.

Some fungi are hard to categorize. Photo by Marcella Stasa.

Preliminary (and incomplete) checklist of finds:


  • Bisporella citrina
  • Chlorociboria aeruginascens
  • Chlorosplenium chlora
  • Coccomyces tumidum
  • Dasyscyphus virgineus
  • Hyalorbilia sp.
  • Hypocrea sp.
  • Rhytisma sp. on leaves of Ilex verticillata
  • Rosellinia subiculata


  • Daedalea quercina
  • Exidia recisa
  • Ganoderma applanatum
  • Piptoporus betulinus
  • Postia fragilis
  • Scleroderma citrina
  • Steccherinum ochraceum
  • Stereum complicatum
  • Stereum ostrea
  • Tapinella atrotomentosa
  • Tomentella sp.
  • Trametes versicolor
  • Tremella mesenterica
  • Trichaptum biforme
  • Tyromyces chioneus

A push for fungal phylogenies in the Open Tree of Life

Originally posted on OPEN TREE OF LIFE:

Screen Shot 2014-09-15 at 1.16.35 PMThe summer of 2014 was a busy one for the mycology group in the Open Tree of Life. Postdoctoral Fellow Romina Gazis gave presentations on the Open Tree of Life at the Annual Meeting of the Mycological Society of America (June 8-12, East Lansing, Michigan) and the International Mycological Congress (Aug. 3-8, Bangkok, Thailand). You can download the IMC presentation here.

Meanwhile, back in Worcester, we continued to compile published phylogenetic trees for incorporation into the Open Tree database. Our goal is to create a synthetic tree that represents, as closely as possible, our current understanding of the broad outlines of fungal phylogenetic relationships, based on molecular studies and taxonomy in Index Fungorum and other sources. We plan to use the tree as the centerpiece of a revision of “higher level” fungal taxonomy, updating a study that we published with seventy coauthors way back in 20071.

Dr. Romina Gazis is a postdoc at Clark University. Dr. Gazis specializes in systematics of endophytes, including symbionts of rubber trees (Hevea brasiliensis) and the newly-described class Xylonomycetes, and also works on phylogenies for the Open Tree of Life project. Dr. Romina…

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