Friday, March 30, 2012

MSA Symposium on Fungal Diversity

As I noted in my last post, I will be attending the Mycological Society of America meeting at Yale this summer. At the meeting, I will be chairing a symposium that I put together, entitled Phylogenetic, Ecological, and Functional Diversity of Fungi. Financial support for the symposium will be provided by 454 Life Sciences, a Roche company. The symposium will have an introduction from a representative of 454, one of the major companies providing solutions for large-scale studies of diversity through metagenomics and related fields. After that, there will then be five talks on a variety of topics relating to fungal diversity. Abstracts for all of the talks in the symposium can be found here:

Here is the brief formal summary of the event:
"How do we best characterize fungal diversity? The speakers in this symposium will explore fungi in the environment from varied perspectives, examining the relationships and interactions between organisms. This symposium links various disciplines (e.g., systematics, ecology, genetics, metagenomics, metaproteomics) around the theme of studying environmental fungal diversity."

My own talk at the symposium will focus on a new pyrosequencing-based approach that I am using to obtain sequence data for studying the systematics of lichen-forming fungi. Here is the abstract:
"Lichen-forming fungi represent one of the most readily visible and publicly accessible groups of organisms studied by mycologists. Remarkably, despite their 'high profile' nature, many aspects of lichen biology and taxonomy remain poorly understood and critically understudied. These two factors converge noticeably in a highly speciose assemblage of lichens that are referred to as sterile asexually-reproducing crustose lichens, or more simply, 'sterile crusts.' These taxa do not represent a monophyletic group, but rather are treated together because they have all evolved to reproduce primarily through the dispersal of lichenized diaspores (specialized dispersal units that include the major constituents of the lichen microbiome). Species that employ this mode of reproduction have evolved in nearly all of the diverse lineages that comprise lichen-forming fungi. In an effort to overcome the taxonomic impasse in this group, we have developed a set of high-throughput procedures to test for correlations between molecular sequence data and non-molecular character data to phylogenetically place and phenotypically define a large number of species so that they can be formally described and subsequently integrated into conservation and management plans. This work includes using slower-evolving loci (e.g., mtSSU and nucLSU) to place many of the 'incertae sedis' lichen-forming fungi into a higher-level framework and testing species boundaries using the ITS fungal 'barcode' region."

Thanks to all of the speakers for agreeing to participate in the symposium and to all of the people at MSA and 454 who helped me to get this symposium together!

- Brendan

Saturday, March 10, 2012

A Modern, Integrated, High-Throughput Biodiversity Research Workflow

This summer I will be attending the Mycological Society of America (MSA) meeting at Yale.  I will be presenting a poster there that details the overall workflow for the research I am conducting at the New York Botanical Garden. You can find the abstract online here:

A modern, high-throughput workflow for biodiversity research integrating floristics, taxonomy, phylogeny, ecology and conservation

Brendan P Hodkinson* and James C Lendemer

Abstract: The field of Systematic Biology has increasingly become fragmented in recent years, with many scientists focusing in on a small number of methods or approaches for studying biodiversity and its origins. Here we present an integrated workflow for studying the many facets of biodiversity and systematics. This workflow is currently being used to conduct a large-scale inventory of lichens in the Mid-Atlantic Coastal Plain of the United States that includes the collection and analysis of ~35,000 new specimens. Using floristic habitat sampling (FHS), specimens representing the organismal group of interest are collected from individual sites throughout the study region, and are subsequently analyzed anatomically and chemically. Specimens that cannot be identified taxonomically with anatomical/chemical analyses alone are sequenced using a multi-locus 454-based approach. Sequences from the genes of interest (in our case, mtSSU, nucLSU and nucITS) are compared with publicly-available reference sequences to determine the phylogenetic affinities of species that remain either unnamed or 'incertae sedis.' All collections are databased rapidly using modular databasing software (KE EMu). Large-scale ecological analyses are performed on database-generated taxon lists by hijacking data management software originally designed for organizing and analyzing large molecular sequence data sets. Overall results are compiled and made available on the web in the form of, e.g., checklists (for regions, sub-regions and sites), detailed taxonomic treatments, molecular sequence alignments, phylogenetic trees, and specimen-based ecological data sets. Both through these online resources and workshops/forays for the public, information is disseminated for integration into conservation and management plans to preserve biodiversity for the future.

Please contact me if you'd like more specific information on this type of work.  I'm looking forward to putting together the poster and discussing it at the conference!


Thursday, March 1, 2012

Lichens of the Mid-Atlantic Coastal Plain

The National Science Foundation (NSF) recently granted me an award to study the lichen biodiversity of the Mid-Atlantic Coastal Plain (MACP) of North America. Here is a link to the official public abstract for the award:
[DEB-1145511; "Lichen biodiversity in the threatened Middle Atlantic Coastal Plain of North America: Improving classification, conservation, and communication;" PI: Brendan P. Hodkinson, Co-PI: James C. Lendemer, Co-PI: Richard C. Harris]

Although the focus of the project is a lichen diversity survey of the MACP, the project has many additional facets, including ecological hypothesis-testing (to obtain information relevant to pressing conservation issues), molecular phylogenetic work (to resolve species boundaries and place incertae sedis taxa), outreach (to grade-schoolers, undergraduates, graduate students, land managers, etc.), and the production of two major book-length taxonomic works. The taxonomic, floristic, and ecological research will be informed by the collections housed at the New York Botanical Garden's herbarium (NY; totaling ~1/4 of a million specimens) as well as 35,000 new specimens that we will collect from the study area as part of this project.

Here is the full text of the award abstract:

"Lichens are fungi with a unique lifestyle involving a semi-parasitic relationship with an alga and/or cyanobacterium. Although lichens are critical to maintaining healthy ecosystems on land, they remain chronically understudied. This project centers on a survey of lichen diversity in the environmentally threatened Middle Atlantic Coastal Plain of the United States and represents an efficient, comprehensive means of addressing a critical information gap for one of the least known and most environmentally sensitive organismal groups. The survey data will be used to resolve numerous problems related to conservation and ecology through a unique system that integrates newly written computer scripts and programs.

"The project will set conservation priorities in the region and will result in two book-length works on lichens. While preparing these treatments, the authors will depart from traditional approaches by using dynamic online resources to incorporate the insights of professionals and amateurs alike. The investigators will teach a series of courses, mentor a diverse cohort of high school and undergraduate students, and train a PhD student. Extensive interactions and collaborations with regional land managers and naturalists, including a three-day workshop led by the investigators, will ensure that this project has the maximum impact on conservation efforts."

As we make progress in the later stages of the project, we will update the NYBG Southeastern Coastal Plain Lichens website:
If you have any interest in Mid-Atlantic Coastal Plain lichens, please let me know and we can stay in touch!