Tag Archives: biodiversity


Friday SNPpets

This week I left the “call to action” tweet at the top–you can vote for GenBank every day in August. The cut is coming soon, so go vote again. In other news this week, a story about big data for assessing biodiversity across time and space. And a Big Photo. Whole-genome sequencing in primary care–not ready yet. #CRISPR ethics–not ready yet. Animal breeding, plant bioinformatics, and horizontal gene transfer round out the week.

SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…



Video Tip of the Week: iDigBio for access to historical specimens and more

idigbio_logoUsually for Thanksgiving week posting is light. In the past, we’ve all done turkey breeding and genomics, cranberry genome, and some people have included apples, potatoes, and more. But another key aspect of the holiday is to remember the past and thank those who came before. And as I was watching this video that crossed my desk, I was thinking about our really ancient ancestors and their companions on the planet. And those who have created and preserved specimens in museum collections documenting the planet’s history. Increasingly those things are being digitized when appropriate, and sometimes even sequenced now when possible.

Some people think of these types of things as “stamp collecting”. But I think we are going to find these resources increasingly valuable as more folks can access and explore them.

So I want to thank folks who have been collecting, curating, and documenting our planet and its species over the millennia. This week I highlight iDigBio and their specimen portal that will provide access to these important curated collections for researchers to take into the future.

This week’s video is only one of the presentations at their iDigBio Summit V. They have a great Vimeo channel with other talks, but this one on Digitized Data in Biodiversity Research caught my attention first. It talks about work in wrangling information in biodiversity, making it available for further work with tools and workflows. It’s a nice overview of the goals and umbrella of topics they are interested in. And also mentions PhyloJIVE, which can integrate phylogeny data and available specimens. That’s a very cool bridge, it seems to me.

iDigBio Summit V: Digitized Data in Biodiversity Research from iDigBio on Vimeo.

So as you are eating and drinking a diverse range of species over the next few days, thank evolution. And thank folks who have been monitoring biodiversity in the past, and moving the studies into the future, on this pale blue dot we share.

Quick links:

iDigBio Portal: https://www.idigbio.org/portal

PhyloJIVE: http://phylojive.acis.ufl.edu/PhyloJive


Nelson, G., Sweeney, P., Wallace, L., Rabeler, R., Allard, D., Brown, H., Carter, J., Denslow, M., Ellwood, E., Germain-Aubrey, C., Gilbert, E., Gillespie, E., Goertzen, L., Legler, B., Marchant, D., Marsico, T., Morris, A., Murrell, Z., Nazaire, M., Neefus, C., Oberreiter, S., Paul, D., Ruhfel, B., Sasek, T., Shaw, J., Soltis, P., Watson, K., Weeks, A., & Mast, A. (2015). Digitization Workflows for Flat Sheets and Packets of Plants, Algae, and Fungi Applications in Plant Sciences, 3 (9) DOI: 10.3732/apps.1500065

Nelson, G., Paul, D., Riccardi, G., & Mast, A. (2012). Five task clusters that enable efficient and effective digitization of biological collections ZooKeys, 209, 19-45 DOI: 10.3897/zookeys.209.3135

Jolley-Rogers, G., Varghese, T., Harvey, P., dos Remedios, N., & Miller, J. (2014). PhyloJIVE: Integrating biodiversity data with the Tree of Life Bioinformatics, 30 (9), 1308-1309 DOI: 10.1093/bioinformatics/btu024

Tip of the Week: uBIO federated taxonomic search

This week’s tip of the week introduces a thesaurus of biological names, called uBio.  http://www.ubio.org/ The uBio project aims to collect and organize biological names–historical and current–and make them available for searching or for use in other tools.  It also contains dozens of cool links to other tools and projects around taxonomy and biodiversity around the world. I found out about them from Trey’s recent Tip on the PhyloWidget tool–one of the links you can use after you build a phylogeny is to uBio.  This short movie focuses mostly on the basic search, and points to a few of the other related items.

A brief description of the project can be found at the project description at the Wood’s Hole Marine Biological Laboratory site:

The Main component of the uBio project is a Taxonomic Name Server that acts as a thesaurus. One Taxon can have many names and the same name can refer to many taxa; this project provides services to reconcile these differences. There are two component to this: NameBank, a repository of millions of recorded biological names, and ClassificationBank which stores multiple classifications and taxonomic concepts.

They collaborate with a huge range of projects, from natural history to biodiversity resources.  One of the available links included digitized access to the Nomenclator Zoologicus which is a descendant of Linnaeus’ Systema Naturae.

Check out uBio for some nifty taxonomic and biodiversity utilities. http://www.ubio.org

A Tree is Barcoded in Brooklyn

Figure 1 of the Plant Barcoding paperScrolling through some of my regular podcasts the other day I came across this tidbit about bioinformatics growing in New York (among other things, or course!):

Barcoding Plant DNA (I hope the embed of the audio file works, first time I’m trying that…)

It is a discussion with Dr. Damon Little, a curator of bioinformatics from the New York Botanical Garden.  The focus of the discussion is the recent publication of the CBOL Plant Working Group which has settled on the regions that will be used for barcoding plants.

If you aren’t familiar with barcoding efforts yet, you can check out Jennifer’s prior post with some background and great links.  Essentially a small snippet of DNA sequence is used to (hopefully) uniquely identify a given species.  This can be stored in a database–Dr. Little of the NY Botanical Garden refers to GenBank at NCBI, but there are other sites as well.  I was just reading about the web interface for barcoding called iBarcode.org for analyzing and managing this sort of data.

The Consortium for the Barcode Of Life Plant Working Group summary press release of this work can be found here.   The paper that describes the work is Open Access in PNAS here.  The paper describes the genes that had been candidates for the barcode, and the ones that were selected (rbcL + matK).  They described primer selection and sequencing results for the series they examined.  They evaluate which ones meet the barcoding standard criteria and provide the selections.  They use MUSCLE to examine the sequence alignments.

This is an excellent effort on many fronts.  Just assessing and cataloging biodiversity is useful itself, but this can also help to identify plants that are claimed to be used in food or medicine products to see if that is what’s really in there.  It can help combat poaching of protected species–for example, it can identify wood harvested that shouldn’t have been taken for lumber.

Glad to see this work moving forward and getting out in front of the public!

Related links

Podcast direct page: http://www.wnyc.org/shows/lopate/episodes/2009/07/29/segments/137623

NYBG: http://www.nybg.org/

Barcode blog: http://phe.rockefeller.edu/barcode/blog/

Scientific American article on the topic: http://www.scientificamerican.com/blog/60-second-science/post.cfm?id=botanists-agree-on-dna-barcode-for-2009-07-29

Consortium for the Barcode of Life (CBOL): http://www.barcoding.si.edu/

CBOL Plant Working Group (2009). A DNA barcode for land plants PNAS, 106 (31), 12794-12797 : 10.1073/pnas.0905845106

Singer, G., & Hajibabaei, M. (2009). iBarcode.org: web-based molecular biodiversity analysis BMC Bioinformatics, 10 (Suppl 6) DOI: 10.1186/1471-2105-10-S6-S14

Edgar, R. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Research, 32 (5), 1792-1797 DOI: 10.1093/nar/gkh340

BREAD: rising money for science?

I keep an eye on a lot of mailing lists.  Usually they are the ones for database or software resources in our field.  But I also keep an eye on some funding ones.  We aren’t always eligible, but it also helps us to get a sense of the directions that projects are going.

Yesterday I saw one that surprised me on several levels.  It is called BREAD funding.  BREAD stands for Basic Research to Enable Agricultural Development.  I found this one interesting because:

1. It is a joint project between NSF and The Gates Foundation.  Maybe there are other federal funding projects that involve private foundations like this.  But I haven’t seen them.

The National Science Foundation (NSF) and the Bill & Melinda Gates Foundation (BMGF) are partnering to support a new research program to be administered by NSF. The objective of the BREAD Program is to support innovative scientific research designed to address key constraints to smallholder agriculture in the developing world

2. It is giving money for plant genomics in agriculture.  Cool! Among the possible directions for the research:

  • New strategies for creating resistance to major diseases and pests that affect plants, animals or insects of agricultural importance, and that have major impact in broad regions of the developing world.

3. It actually uses the phrase “climate change” and calls it a threat.  And acknowledges several thing that I don’t think the last administration was serious about at all:

  • Novel approaches to using the genetic diversity of plants, microbes, or animals to enhance the ability of small-scale farmers to adapt to emerging threats of global climate change, emerging diseases, and the rising costs of energy.

Anyway, I’m delighted to see basic research on plants in agriculture in Africa and Asia getting some attention.  I was pleased when I heard Hillary Clinton refer to this recently, but I was waiting for someone to show me the money. And what do you know–they did.

This specific grant: http://www.nsf.gov/pubs/2009/nsf09566/nsf09566.htm?govDel=USNSF_25

More on the BREAD program: http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503285

Press release on the NSF + BMGF partnership:  http://www.eurekalert.org/pub_releases/2009-03/nsf-nsf033009.php

Tip of the Week: Bioversity resources

bioversity_movieI’ve been reading a lot more on biodiversity lately, and I was really pleased to come across the Bioversity International site to learn more about this topic. Not a standard sequence or algorithm type of bioinformatics resource, the site is a collection of biological information on  a wide range of topics and database resources that serve the needs of researchers interested in biodiversity.  It’s really refreshing to see species that aren’t just the model organisms (although I do still love the mods, of course!).  But cacao…mmmmm…..

But it is much more than just informative web pages.  There are databases of collections including germplasm and species databases, geographically organized information, and more.  There are training materials that faculty might want to use.  There’s even a terrific collection of images of biodiversity that may be useful for presentations.   Check out this brief (~3 min) introduction to the Bioversity International resources for more details.

Bioversity International site: http://www.bioversityinternational.org/

Hoarding Genomes (DNA, tissue, organisms)

plos imageBefore disasters people will often scour stores to hoard food and other essentials. We are now faced with changes in our global climate that are as bad, or worse, as our earlier worst case scenarios and a species die off that is unprecedented (Nature article, subscription required):

…biodiversity loss is accelerating globally. Some 12% of all bird species, 23% of mammals, 25% of conifers, 32% of amphibians and 52% of cycads are threatened with extinction1, and climate change alone might commit an additional 15 to 37% of extant species to premature extinction within the next 50 years.

So, we have begun to hoard.

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