Just back from the 8th Latin American Congress of Mycology, in Medellin, Colombia, the city of never-ending springtime. This was a fantastic meeting, only marginally disrupted by (fairly mild) student protests (I gather they are concerned about tuition increases–I think I am with the students). There is great interest in basic taxonomy in South and Central America, which makes sense given the tremendous amount of undescribed biodiversity in these countries. Basidiomycete systematics was a particularly strong theme at the congress, with 55 posters on this subject alone! Here are a few photos of the city and the venue–more to come later, perhaps–and the poster titles from the basidiomycete taxonomy section (scroll down).
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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