VIII Latin American Congress of Mycology

CLAM logo copyJust 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).

Our venue, the Politécnico Colombiano Jaime Isaza Cadavid

Our venue, the Politécnico Colombiano Jaime Isaza Cadavid

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When the weather is always perfect, walls and windows are optional.

Parque del Poblado, just up the hill from the university

Parque del Poblado, just up the hill from the university

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Ricardo Drechsler Santos with Lentinus crinitus at the Parque Arví

Ricardo Drechsler Santos with Lentinus crinitus at the Parque Arví

with Amanita

At Parque Arvi, with Amanita muscaria under Pinus.

lunch at Parque Arvi

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Disappearing Trees

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.

Intersection of Main St. and Loudon St. in 2007 from www.google.com/maps

Intersection of Main St. and Loudon St. in 2007 from http://www.google.com/maps

2011 from www.google.com/maps

2011. Before this tree died, it produced a massive fruiting of oyster mushrooms, Pleurotus ostreatus. from http://www.google.com/maps

2014. Before this tree died, it produced a massive fruiting of Pleurotus ostreatus.

2014.

St. Peter's Church, across from Clark's main campus, 2007, from www.google.com/maps

St. Peter’s Church, across from Clark’s main campus, in 2007, from http://www.google.com/maps

2014.

2014.

2007. The dominant feature of the Kresge Quadrangle on Clark's main campus is the trio of Fagus sylvatica trees. Note the shapes of the crowns in this and the next image. From www.google.com/maps

2007. The dominant feature of the Kresge Quadrangle on Clark’s main campus is the trio of Fagus sylvatica trees (center). Note the shapes of the crowns in this and the next image, and compare to the image from 2014. From http://www.google.com/maps

October 28, 2014. The tree nearest the road is dying; it is losing its leaves before the other two trees (look at upper left portion of crown). All three trees were heavily pruned since the previous photos.

October 28, 2014. The tree nearest the road is dying; it is losing its leaves before the other two trees (look at upper left portion of crown). All three trees were heavily pruned (“limbed up”) since the previous photos.

2014.

2014. The tree in the foreground is in bad shape. The photos below are all of this one tree.

2014. The trunk is becoming decorticated. The vascular cambium, the thin layer under the "bark" that allows for continued growth of the trunk, is dying.

2014. The trunk is becoming decorticated. The vascular cambium, the thin layer under the “bark” that allows for continued growth of the trunk, is dying.

2014. A decorticated section of the trunk.

2014. A decorticated section of the trunk.

2014. Stereoid fungal fruiting bodies (reproductive structures).

2014. Stereoid fungal fruiting bodies (reproductive structures).

2014. Oyster mushroom, Pleurotus ostreatus (the same species that was fruiting on the Loudon St. tree). This is a vigorous "white rot" wood decayer.

2014. Oyster mushroom, Pleurotus ostreatus (the same species that was fruiting on the Loudon St. tree). This is a vigorous “white rot” wood decayer.

2014. This tremelloid fungus may actually be a parasite of the fungi that are attaching this Fagus tree, not a pathogen or decayer of the tree itself.

2014. This tremelloid fungus may actually be a parasite of the fungi that are attaching this Fagus tree, not a pathogen or decayer of the tree itself.

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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