Methods in Ecological Genomics Analysis workshops (MEGA 2015)

Ecological genomics is the new and extremely powerful way to address old-standing ecological and evolutionary questions. We endeavor to teach the methods that we have developed specifically for working with non-model organisms to students with limited or no genomics or bioinformatics experience. Two back-to-back workshops will take place at the Mote Tropical Research Laboratory, using reef-building corals as subjects for specific research projects. The projects are designed to yield novel publishable results, and we encourage students to continue collaborating on these projects after the course has ended. Students making significant contributions to data analysis and manuscript preparation will be offered authorship (see previous publications stemming from our workshops at Mote).

Click on these links to see syllabi and costs (costs include accommodation but not board):

Instructor-in-chief: Mikhail V. Matz (google scholar page)

Applications now open for the summer 2015 “Bioinformatics & Biodiversity” Undergraduate Workshop

Following on from a highly successful event last year, we’re very excited to announce the second annual “Bioinformatics & Biodiversity” Undergraduate Workshop at the University of New Hampshire, scheduled for July 27-30, 2015 in Durham, NH. Click here to download a PDF flyer – we encourage you to post and share this opportunity!


Microscopic eukaryotes (meiofauna e.g. nematode worms, copepods, protists, fungi, etc.) are some of the most abundant animals on Earth, but species within these groups are often overlooked by the general public and even many biologists. This NSF-sponsored workshop will explore the field of environmental DNA sequencing, including collection and analysis of data. Students will learn how high-throughput approaches (rRNA gene surveys, metagenomics) are being used to investigate the biodiversity of microbial eukaryotes and deepen our knowledge of ecosystem function. The workshop program will be a combination of lectures and practical exercises, where students will learn about traditional taxonomic approaches and also gain experience using the command line and bioinformatics tools to analyze environmental DNA datasets.

We welcome applications from undergraduates currently enrolled in any higher-educational institution in the USA.  All applicants are expected to have taken, at minimum, an introductory college-level course in Biology. Successful applicants will receive a stipend to cover all costs including travel.

To apply, e-mail the following materials to by Monday April 13, 2015:

  • Curriculum Vitae (including contact details for references)
  • Statement of interest (indicating biology courses taken and how attending the workshop would benefit your long-term career goals; maximum length 1 page)
  • Reference letters are recommended but not required

Frequently Asked Questions

Q. Can international/overseas students apply for this workshop? 

A.  No, unfortunately workshop application is restricted to students currently enrolled at US-based institutes (which includes international students attending US colleges). For future workshops we may extend the application process to students enrolled at overseas institutes (this will depend on the conditions of our funding). Thanks for your interest, and keep an eye on on the RCN website for future opportunities.

Q. For the CV (including references), exactly how many and what kind of references are preferred? 

A. One letter of recommendation can accompany the application (written by a professor or research supervisor) – this is optional, but may significantly increase the strength of your application. On your CV you can also list contact information for any additional professional references (up to three references); for example, you may want to list references relating to any relevant work experience or research projects.


NSF Dimensions of Biodiversity Funding Opportunity

[reposting an email from the American Society for Microbiology]

The National Science Foundation (NSF) has requested that ASM bring to the attention of interested members the following funding opportunity:

Dimensions of Biodiversity FY 2015
Full Proposal Deadline: April 9, 2015 (due by 5 p.m. proposer’s local time)

Synopsis of Program:

Despite centuries of discovery, most of our planet’s biodiversity remains unknown. The scale of the unknown diversity on Earth is especially troubling given the rapid and permanent loss of biodiversity across the globe. The goal of the Dimensions of Biodiversity campaign is to transform, by 2020, how we describe and understand the scope and role of life on Earth.

This campaign promotes novel integrative approaches to fill the most substantial gaps in our understanding of the diversity of life on Earth. It takes a broad view of biodiversity, and focuses on the intersection of genetic, phylogenetic, and functional dimensions of biodiversity. Successful proposals must integrate these three dimensions to understand interactions and feedbacks among them. While this focus complements several core programs in BIO and GEO, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, in novel ways, to understand their synergistic roles in critical ecological and evolutionary processes.

Award Information:      

  • Anticipated Type of Award: Standard Grant or Continuing Grant
  • Estimated Number of Awards: 8 to 12
  • Anticipated Funding Amount: $16,000,000 to $22,000,000

More Information:  

Matthew D. Kane, BIO/DEB: (703) 292-7186,

Ronald M. Atlas, Ph.D.
Chair, Public and Scientific Affairs Board

Joint Genome Institute – Metagenomics workshop & 10th Annual Meeting

Announcement from the Joint Genome Institute Mailing list:

February 9 – 13, 2015

The U.S. Department of Energy Joint Genome Institute is offering a five-day workshop on Microbial Genomics and Metagenomics (MGM). The MGM Workshop include seminars and extensive hands-on tutorials on how to use the IMG family of systems for comparative analysis of isolate genomes and metagenomes. Our goal is to provide you with training in microbial genomic and metagenomic analysis and demonstrate how the cutting-edge science and technology of DOE JGI can enhance your research. For more information and to register, click here. Attendance is limited, so act now!

March 24 – 26, 2015

The DOE Joint Genome Institute’s 10th Annual Genomics of Energy & Environment Meeting registration is open.  See the current roster of speakers and register now for the March 24-26, 2015 event. Check out and register for the workshops too.

Once you’ve registered, please submit poster abstracts (from which short talks will be selected). Guidance for abstracts and posters can be found here.

Wrap-up post – “Ecometagenomics” Symposium at BES/SFE meeting

Thanks to everyone who attended our Symposium at the Joint British/French Ecological Society Meeting last week in Lille, France –  “Accelerating ecology and biodiversity research via ecometagenomics: species, communities and environmental DNA”. A collection of Tweets from this session is now available here on Storify.

We had a great turnout for the meeting session, followed by a hugely successful wine & cheese social sponsored in conjunction with the BES Plants, Soils, and Ecosystems Special Interest Group. And of course we managed to find plenty of holiday cheer walking around the streets of Lille!

2014-12-10 19.45.00

Simon, Dorota, Holly and Serita (left to right), on their way to the wine & cheese social!


Moore Foundation EOI call – Marine Microeukaryotes as Experimental Model Systems

Request for Expressions of Interest: Increasing the Potential of Marine Microeukaryotes as Experimental Model Systems through the Development of Genetic Tools

The Marine Microbiology Initiative (MMI) at the Gordon and Betty Moore Foundation aims to enable scientists to uncover the principles that govern the interactions among microbes and that influence nutrient flow in the marine environment. MMI is targeting closing gaps in and supporting the advancement of experimental model systems in microbial oceanography to enable new ways to uncover fundamental biological mechanisms.

We are soliciting expressions of interest (EOIs) for early-stage research projects to develop methods to genetically manipulate marine microeukaryotes as a first step in breaking current bottlenecks in the advancement of experimental model systems. MMI has two primary foci for this expression of interest:

  1. Development of genetic tools for diatoms. Diatoms are key players in the world’s oceans, generating ~20% of the world’s organic carbon, and a strong community of researchers is in place suggesting broad use of successfully developed methods. We are specifically interested in projects to develop reverse and/or forward genetics.
  2. Screening laboratory-scale culture collections for transformable marine microeukaryotes.
    MMI will also consider projects to develop genetic tools and methods with other microeukaryotes that show promise for expanding the way the field can test hypotheses. If your idea does not fit category 1 or 2 above, please contact us prior to submitting your EOI.

MMI encourages EOIs from “inter-organismal” teams of researchers – i.e., complementary groups that have experience in a well-established model system and with a microeukaryote that is not currently genetically tractable – whose collaborative effort will bring innovative approaches to the field.

MMI invites you to send an expression of interest via email that briefly outlines a research project (one paragraph or less), using the following template:

  1. The lead researcher’s name, institution, and expertise.
  2. Indication of focus on genetic tools for diatoms (category 1 above) or laboratory culture screening for
    transformability (category 2 above).
  3. For category 1, the name of the organism(s); or, for category 2, the taxonomic group(s) to be screened.
  4. A methodological or technical challenge that is hindering the development of a genetically
    manipulable marine microeukaryotic system that is ripe for solving and how you would address this
    challenge (3-5 sentences).
  5. The research team that would tackle this challenge, and why each team member’s expertise is relevant
    (one sentence per team member; please include institutional affiliations).

The opportunities that best align with MMI’s strategies and goals will be invited to submit proposals. MMI has allocated $7–10M to support this effort and anticipates making multiple, 2–3 year awards beginning in mid- 2015.

Please submit your EOI by Tuesday January 6, 2015 to Samantha Forde at

NSF Genealogy of Life (GoLife) – 2015 call for proposals

NSF has once again issued its RFP for the Genealogy of Life (GoLife) program. Full proposal deadline is March 25, 2015.

Program Synopsis (from NSF website): 

Comprehensive understanding of life and how and why it changes over time depends on knowledge of the phylogeny (evolutionary relationships) of living and extinct organisms. The goals of the Genealogy of Life (GoLife) program are to resolve the phylogenetic history of all life’s diverse forms and to integrate this genealogical architecture with underlying organismal and environmental data.

The ultimate vision of this program is an open access, comprehensive Genealogy of Life that will provide the comparative framework necessary for testing questions in systematics, evolutionary biology, ecology, and other fields. Strategic integration of this genealogy of life with data layers from genomic, phenotypic, spatial, ecological and temporal data will produce an extensive synthesis of biodiversity and evolutionary sciences. The resulting knowledge infrastructure will enable synthetic research on biological dynamics throughout the history of life on Earth, within current ecosystems, and for predictive modeling of the future evolution of life.

Projects submitted to this program should emphasize increased efficiency in contributing to a complete Genealogy of Life and strategic integration of various types of organismal and environmental data with phylogenies.

This program also seeks to broadly train next generation, integrative phylogenetic biologists, creating the human resource infrastructure and workforce needed to tackle emerging research questions in comparative biology. Projects should train students for diverse careers by exposing them to the multidisciplinary areas of research within the proposal.

Detailed Program Description (from NSF website):

The Genealogy of Life program has four main goals: 1) Taxonomic completeness — containing all described species of a given clade, including those lineages that are extinct, 2) Data completeness —including diverse underlying data layers (e.g., digitized images, specimen collection information, environmental and habitat data, geographic and stratigraphic distributions, genomic and phenomic data, developmental data and ontologies), 3) Dynamic and open structure — allowing the automatic incorporation of new data and taxa, and mechanisms for accessibility to the broad scientific and non-scientific communities, and 4) Training of the next generation of phylogenetic biologists –– integrative training in diverse fields across comparative evolutionary biology. Successful projects will describe how research and training activities will achieve these four overarching goals.

All successful proposals will have the goal of massively increasing the taxonomic and character data space that contributes to making our understanding of life’s genealogy as thorough as possible. When preparing a GoLife proposal, proposers are required to justify the need for phylogenetic analysis on their chosen taxonomic group of study and their approach to advancing data inclusiveness. Taxonomic completeness, as described above in Goal 1, will likely be group-dependent. For example, work on clades that include a rich fossil record should include the fossil taxa in the proposed research. Completeness for other clades will likely be defined differently.

Proposals should focus on poorly sampled clades or data layers within the Genealogy of Life where new data will have a profound impact on new understanding of the pattern of life’s evolution. In accordance with Goal 2 above, justification of data layers to be added is expected to be strategic and to enable future hypothesis-based research. Chosen data layers are likely to be clade-specific. For example, some vertebrate, invertebrate and plant clades will enable approaches that add substantial phenotypic, geochronological, environmental, spatial, and other types of data layers; some prokaryotic clades will enable approaches that add metabolic pathway, genomic and environmental data layers. GoLife proposals should outline the specific types of novel, hypothesis-driven research that would be enabled by the specific phylogenetic and data layer choices that are proposed.

For this year’s solicitation, along with the generation of new phylogenetic data and phylogenetic analyses, GoLife research projects must integrate at least two different data types. Proposals that do not integrate at least two data layers will be returned without review.

Examples of data layers (not an exhaustive list) that could be integrated in GoLife proposals include:

  • a) Genomic/Phylogenomic sequence data
  • b) Genotype-phenotype linkage and mapping
  • c) Morphological data
  • d) Fossil data
  • e) Geochronological data
  • f) Developmental data
  • g) Ontologies
  • h) Geospatial data
  • i) Environmental data
  • j) Digitized voucher specimens
  • k) Encyclopedia of Life webpages
  • l) Behavioral data
  • m) Physiological data
  • n) Metabolic pathways

Length and size of award will depend upon the number and size of the data sets to be added to the Genealogy of Life. Priority will be given to those proposals that provide: 1) the most substantial increase in volume of tree space added, and/or 2) the most significant increase in annotated organismal and environmental data layers. The phylogenetic scope of a GoLife proposal should vastly exceed that of a typical Phylogenetic Systematics core program proposal. Given advances in the field, the size and scope of GoLife proposals should also vastly exceed that of AToL projects.

GoLife projects should leverage existing infrastructure when possible, to avoid redundancy in tools available for comparative biology. Examples of existing infrastructure that GoLife projects could build upon, or access digital data from, include iDigBio, Genbank, Open Tree of Life, etc.

Projects that largely repeat or replicate existing work will not be funded. Additional examples of projects that will not be considered by this program include: 1) projects that only use a single data type (e.g. genomic/phylogenomic or morphological), 2) projects that consist of species surveys, inventories, or descriptions (e.g., Biodiversity: Discovery and Analysis projects), 3) projects that are focused on revisionary systematics (e.g. Advancing Revisionary and Taxonomy and Systematics projects), 4) projects that aim to test a particular hypothesis related to the evolution of a particular group (e.g., Phylogenetic Systematics projects), and 5) projects that are solely focused on the development of new methods or technologies without the generation of substantial amounts of new phylogenetic data. Research proposals that do not focus on poorly sampled clades or data layers within the Genealogy of Life should be submitted to other relevant NSF programs.