For once, the trees I am writing about are actual trees (rather than phylogenetic trees). Or rather, were actual trees. Recent years have not been kind to the trees of Clark’s campus and the surrounding neighborhood. Storms, fungi, pests, and campus improvements have all taken a toll. In this post, I focus on the European copper beech, Fagus sylvatica, a magnificent, smooth-barked tree with striking purple leaves and a spreading crown. Mature specimens lend an air of grandeur to the landscape. Here, with the aid of archived images from Google maps, I document two sites near Clark that have lost trees recently, and one site on campus with three large trees, one of which is dying.
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).
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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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
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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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.
On 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.
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