Best Of 2016: A year of visual communication

via GIPHY

2016 rang in with a new medium for us at SciColl: a video series! This year we jumped feet-first into video profiles of folks working with collections every day. We inquired about how they use collections, who they collaborate with, and how collections-based research is unlike any other. The stories are as diverse as the collections, and we’re looking forward to bringing you more in 2017!

• Interested in plants and how to study the tallest trees in the forest if you can’t get to canopy? Check out The Ultimate Identifier.
• Flies are everywhere, but these kinds of flies are often easier to find in collections than the field. Learn more in The Assassin (Flies) of Entomology.
• What do archaeology, wildlife management and conservation genomics have in common? Check out The Archaeogenomics Equation and learn how this interdisciplinary field got started.
• We also collaborated with our friends at Biodiversity Heritage Library to revamp one of their 2014 blog posts into a video: Monsters Are Real. Is it just us, or do these monsters seemingly come to life when animated with an appropriate soundtrack?

Looking for more? We always are, and compile the best from around the web on our YouTube Channel. Come see what we have in our playlists:

• #ScientificCollections
• #FoodSecurity
• #EnvironmentalChange

We look forward to a blog-filled 2017 and hope you’ll continue to join us!

Monsters are real

Have you ever considered where the myth of monsters originated? As it turns out, the link between science and the supernatural is smaller than you may think.

• Our friends at the Biodiversity Heritage Library rolled out a blog series on the matter in 2014. 
• Smithsonian Magazine also featured much of BHL's research in a compelling piece about five "real" sea monsters. 
• And most recently the magazine published a piece about a Renaissance-era sea monster that looked similar to a monk with scales. 

The Archaeogenomics Equation

What do you get when you mix archaeology, ecology, wildlife management, and conservation genomics? No, this isn’t a tagline similar to a duck-in-a-bar joke. What you have is an emerging field of studying called conservation archaeogenomics.

At the forefront of this work are Robert Fleischer and Jesús Maldonado, both of the Center for Conservation Genomics (CCG) at the Smithsonian Conservation Biology Institute and National Zoo. The purpose of archaeogenomics is to use genomic methods to learn how humans impacted the environment over time, and Fleischer and Maldonado use this information to make recommendations for conservation.

The Assassin (Flies) of Entomology

Editor's Note: This is the second in a series of videos we will release in 2016 about the use of scientific collections and DNA technology.

Torsten Dikow has traveled around the world to find the perfect fit. And he seems to have found it at the Smithsonian’s National Museum of Natural History (NMNH).

The Ultimate Identifier

Editor's Note: This is the first in a series of videos we will release in 2016 about the use of scientific collections and DNA technology.

When it comes to reliable plant identification in their work, Ida Lopez and Dr. Caroline Puente, of the Smithsonian’s National Museum of Natural History (NMNH) Plant DNA Barcoding Project, botany department, have a tool most associate with the retail world. But barcodes, in this case DNA barcodes, are creating many research opportunities in the scientific world in areas of ecology, evolution, conservation and more.

A DNA barcode, which is made up of approximately 600 base pairs of the species’ entire genome, can authentically identify down to the species level. A commonly used barcode marker in animals is the mitochondrial gene cytochrome oxidase 1 (CO1). This gene however does not successfully identify plant species.

“We knew that in animals the CO1 site was very indicative,” Lopez said. “Zoologists could just sequence this one site and tell exactly what type of animal it was.”

Because the CO1 gene has evolved slower in plants, it is not useful to identify plant species. So around 10 years ago, researchers, under the direction of John Kress, NMNH Department of Botany curator, began looking for candidate genes in plants. They found that they needed a combination of at least two chloroplast regions - rbcL and trnH-psbA - to create a workable plant DNA barcode. Today matK, another chloroplast gene, and a nuclear region – the Internal Transcribed Spacer (ITS) are added to insure success.

While researchers agree that fresh tissue is ideal for extracting DNA, Puente said that in cases where scientists can’t revisit a location to collect samples, museum collections, in this case botanical specimens, are invaluable.

“One of the big advantages of DNA barcoding is that we do not need a lot of tissue material” Puente said. “... You can barcode small organisms such as insects and bacteria - anything that has DNA even in limited amounts.”

A tissue sample just a little larger than a pencil eraser is enough for DNA extraction and barcoding. Lopez and Puente have specimens at their fingertips in the Department of Botany’s vast collection at NMNH. The collection holds 5 million specimens, with approximately 105,000 of those serving as type specimens.

To learn more about Lopez and Puente's work, visit The Plant DNA Barcode Project.


References
W. John Kress, Carlos García-Robledo, Maria Uriarte, and David L. Erickson (2014, November 19). DNA barcodes for ecology, evolution, and conservation. CellPress, vol 30 (1): 25-35. doi: 10.1016/j.tree.2014.10.008

What is DNA Barcoding? Barcode of Life. Retrieved from http://www.barcodeoflife.org/content/about/what-dna-barcoding 

W. John Kress, David L. Erickson. (2007, June 6) A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region. PLOSOne(6): e508. doi: 10.1371/journal.pone.0000508

Search the Department of Botany Collections. Smithsonian National Museum of Natural History. Retrieved from http://collections.nmnh.si.edu/search/botany/

Plant DNA Barcode Project. Smithsonian National Museum of Natural History. Retrieved from http://botany.si.edu/projects/DNAbarcode/

Glossary

type specimens
The representative for an animal or plant species, which acts as a reference point when a species is first named.