Friday Action Item: Two weeks until we #MarchForScience

On Fridays while the current administration is in office we’re posting small, concrete things you can do to help make things better. Got a suggestion for an Action Item? E-mail us!

In just over three weeks, we’ll march for science. Whether you’ll be in Washington DC on Earth Day, or joining one of the hundreds of local events around the world, April 22 is our date to gather, in public, in support of science and its role in a free and healthy society.

We’ll have more detail about where TME contributors will be marching, but if you’re a molecular ecologist, there’s plenty of opportunity to highlight your expertise and find folks with similar interests. The Genetics Society of America is offering T-shirts just for the March, including one with a nice evolution-y slogan, and you have two days left to order for delivery by the 22nd. (Or consider repping TME?) Members of the American Society of Naturalists, the Society for Systematic Biology, and the Society for the Study of Evolution are also invited to take this survey to help meet up at individual marches, and to volunteer to organize activities around them.

We’ll see you in a fortnight — in Washington and worldwide.

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The N50 filtering problem

This is the second in a series of posts where we explain the N50 (Nx) metric, discuss the problems surrounding it, give solutions to those problems, and suggest an alternative N50 metric for transcriptome assemblies.

The problem with N50 (or Nx in general) is not the number itself but that it can be highly misleading when describing sequence assemblies. In an ideal world, the optimal genome assembly would consist of a few contigs representing entire chromosome sequences, leading to a high N50 value. In contrast, a poor assembly of low quality would instead consist of a massive number of tiny, fragmented contigs, leading to a low contig N50. This is the reason why people generally view larger N50 values as indicative measures of better assemblies. However, this is not always the case, and the N50 number can be manipulated in various ways, falsely giving the impression that the assembly is of higher quality than it is.

To illustrate how easy it is to increase one’s contig N50 value, we will borrow a filtering example from the great ACGT blog by Keith Bradnam (unfortunately no longer updated).

Imagine that you perform a de novo genome assembly and end up with the following contig distribution:

  • 5,000 contigs of 100 bp length
  • 100 contigs of 10 kbp
  • 10 contigs of 1 Mbp
  • 1 contig of 10 Mbp

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Like Turtles, Terrapin Research Moves a Little Slow

Marlee Hayes wrote this post as a final project for Stacy Krueger-Hadfield’s Science Communication course at the University of Alabama at Birmingham. Her primary interests focus on challenges in conservation and sustainability. Previously, she evaluated fitness of post-hatchling Diamondback terrapins (Malaclemys terrapin), a species of conservation concern in Alabama. She is currently a MS student at UAB studying nutrition and feed intake in the sea urchin Lytechinus variegatus. The sea urchin has potential for aquaculture and is also an aquatic model organism, often used to study embryonic development. She is part of a group at UAB developing sustainable sea urchin culture techniques.

What’s for dinner? Just 50 years ago, turtle soup might have been!

In North America, terrapin soup became a popular meal in restaurants and coastal households in the 1800s, which ultimately resulted in a significant decline in terrapin populations by the 1900s (Hart & Lee 2006).

Though many regions of the globe have prohbited turtle harvest, there are still areas where it is legal and other areas where poaching is a major concern. The legacy of turtle soup has left an indelible mark on turtle populations.

The diamondback terrapin Malaclemys terrapin is one of the few turtles that thrive in brackish water ecosystems along North American Atlantic and Gulf Coasts (Coleman et al. 2011). In addition to harvesting, the diamondback terrapin continues to face consequences of by-catch in crab (Coleman et al. 2011). Human colonization of coastal areas brings its own set of problems, bringing with it raccoons that often raid terrapin nests (Munscher et al. 2012). Furthermore, large amounts of trash accumulate along critical nesting grounds in estuaries and marshes, which may ultimately impede nesting female terrapins.

Due to declining populations, many conservation projects have been launched to aid the recovery of the diamondback terrapin. It is protected by legislatures in many states and is listed as “near threatened” status by the IUCN. In 2004, the Diamondback Terrapin Working Group was formed and academic institutions, such as The University of Alabama at Birmingham, continue recovery efforts. Though we know quite a bit about its biology, ecology, and conservation, we don’t know that much about population connectivity. Understanding population structure and gene flow will allow for strategic conservation plans best suited for different populations.

Dr. Ken Marion (left), Dr. Thane Wibbels (center), and Andy Coleman (right) from the University of Alabama at Birmingham working at their field site in Dauphin Island, AL. A crucial nesting marsh for the Mississippi diamondback terrapin is located on this barrier island. “The diamondback terrapin is a priority one species of high conservation in Alabama and is a crucial species for the salt marsh ecosystem,” states Dr. Thane Wibbels.

Recently, Petre et al. (2015) found a genetic pattern between populations on the east and west sides of Louisiana, which may stem from the differences in habitat. The southeastern region of Louisiana’s salt marshes offer a more open network of marshes as a result of habitat fragmentation. These terrapins were known to be historically harvested as well, but no evidence of bottlenecks was found. In comparison, the southwestern portions of Louisiana’s salt marshes are more isolated with barriers, such as beaches and dunes.

Drabeck et al. (2014) suggested that differing patterns of gene flow may be the result of migration patterns. It is rare for terrapins to migrate more than 10 kilometers to nesting grounds, but with the loss of nesting grounds due to anthropogenic and natural impacts, such as erosion and oil spills, individuals may need to migrate further. Thus, different management practices may be necessary in order to protect different types of populations.

Interestingly, recent studies have suggested Louisiana terrapins share more genetic similarities with East Coast populations than with closer Floridian populations. Louisiana terrapins showed the greatest similarity with Carolina populations, which may reflect a translocation in the 1900s for farming and harvesting. Similarly, Converse et al. (2015) suggested translocation into the Chesapeake Bay for farming and harvesting resulted in distinct patterns of genetic diversity.

Despite all the attention in the U.S., a population of terrapins was unnoticed in Bermuda until the early 2000s. Bermuda news reported the recently classified terrapin and the launch of the Diamondback Terrapin Project piloted by scientist, Mark Outerbridge. After their recognition, Parham et al. (2008) used radiocarbon dating of terrapin fossils and found were to be from approximately 1620 CE. Because the origins of the fossils predate human consumption of terrapin and almost predate human settlement of Bermuda, the authors suggest that the Bermuda terrapins are native species. Based on genetic patterns, the authors suggested that the terrapins arrived in Bermuda by way of the Gulf Stream, originating from the Carolinas.

We are starting to understand terrapin population dynamics, but population genetic tools are still sorely needed in order to protect these turtles. Researchers are better able to continue to protect and aid recovery of the many species, like the diamondback terrapin, that have been and continue to be at risk due to anthropogenic impacts.


Effects of By-Catch Reduction Devices (BRDs) on the Capture of the Diamondback Terrapin in Crab Pots in an Alabama Salt Marsh. Coleman, A.T., Wibbels, T., Marion, K., Nelson, D., & Dindo, J. 2011, The Journal of the Alabama Academy of Science.

The Diamondback Terrapin: The Biology, Ecology, Cultural History, and Conservation Status of an obligate Estuarine Turtle. Hart, K.M., & Lee, D.S. 32, s.l. : Studies in Avian Biology, 2006.

Decreased Nest Mortality for the Carolina Diamondback Terrapin (Malaclemys Terrapin Centrata) Following Removal of Raccoons (Procyon Lotor) From a Nesting Beach in Northern Florida. Munscher, Eric C., Kuhns, Emily H., Cox, Candace A., and Butler, Joseph A. Herpetological Conservation and Biology, 2012. Vol 7

Population genetics of the diamondback terrapin, Malaclemys terrapin, in Louisiana. Petre, Charlotte; Selman, W., Kreiser, B., Pearson, S. H.; Wiebe, J. J. Conservation Genetics, 2015, Vol. 16.

Analyses, The Status of Louisana’s Diamondback Terrapin (Malaclemys terrapin) Populations in the Wake of the Deepwater Horizon Oil Spill: Insights from Population Genetic and Contaminant. Drabeck, D. H., Chatfeild, M. W.H. and Richards-Zawacki, C, L. Journal of Herpteology, 2014, Vol. 48.

Spatiotemporal analysis of gene flow in Chesapeake Bay Diamondback Terrapins (Malaclemys terrapin). Converse, Paul E., Kuchta, Shawn R., Roosenburg, William M., Henry, Paula F.P., Haramis, G. Michael, King, Tim L. Molecular Ecology, 2015, Vol. 24.

Introduced delicacy or native species? A natural origin of Bermudian terrapins supported by fossil and genetic data. Parham JF, Outerbridge ME, Stuart BL, Wingate DB, Erlenkeuser H, Papenfuss TJ. Introduced delicacy or native species? Biology Letters. 2008;4(2):216-219. doi:10.1098/rsbl.2007.0599.

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Nominations solicited for the 2017 Molecular Ecology Prize

Terry Burke, recipient of the 2009 Molecular Ecology Prize, and the Molecular Ecology Prize Selection Committee are now requesting nominations for the 2017 Prize, which recognizes contributions to the field of molecular ecology. The official announcement follows:

Nominations for the Molecular Ecology Prize

I am soliciting nominations for the annual Molecular Ecology Prize.

The field of molecular ecology is young and inherently interdisciplinary. As a consequence, research in molecular ecology is not currently represented by a single scientific society, so there is no body that actively promotes the discipline or celebrates its pioneers. The editorial board of the journal Molecular Ecology therefore created the Molecular Ecology Prize in order to fill this void and recognise significant contributions to this area of research. The prize selection committee is independent of the journal and its editorial board.

The prize will go to an outstanding scientist who has made significant contributions to Molecular Ecology. These contributions would mostly be scientific, but the door is open for other kinds of contributions that were crucial to the development of the field. The previous winners are: Godfrey Hewitt, John Avise, Pierre Taberlet, Harry Smith, Terry Burke, Josephine Pemberton, Deborah Charlesworth, Craig Moritz, Laurent Excoffier, Johanna Schmitt, Fred Allendorf and Louis Bernatchez.

Please send your nomination with a short supporting statement (no more than 250 words – longer submissions will not be accepted) directly to me by Friday 28 April 2017.

With thanks on behalf of the Molecular Ecology Prize Selection Committee

Terry Burke

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Friday Action Item: Cuts to funding even sooner than we thought

(Flickr: Kai Von Chang)

On Fridays while the current administration is in office we’re posting small, concrete things you can do to help make things better. Got a suggestion for an Action Item? E-mail us!

You’re already all too familiar with the cuts to science funding proposed in the Trump Administration’s budget outline for the next fiscal year — billions less for science by EPA and NIH. This week, we learned the administration wants to cut research and education funding basically right now. Congress needs to pass a budget resolution to fund the Federal government for the rest of the current fiscal year, and the administration has already been, um, rearranging spending priorities

The $18 billion in total cuts from discretionary spending bills is reportedly offsetting the $30 billion in supplementary increases in defense spending and spending on the border wall with Mexico. (Though it’s not entirely clear that the wall will be part of the supplemental defense budget.)

Yeah. Congress should probably hear what you think about this, wouldn’t you say?

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A sponge and its symbionts, using genomics to unravel complex relationships

Modified Figure 1 of Hentschel et al., 2012. Diverse marine sponges.

The ocean is full of interesting organisms and even more fascinating (as well as difficult to tease apart) are the interactions among them. From deep sea giant tube worms, to the adorable bobtail squid, symbioses have a central role, and sponges are no exception. In a recent article by Moitinho-Silva and colleagues in ISME, they used genomic sequence data to unravel the interactions between the marine sponge Cymbastela concentrica and its symbiotic microbes.

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What’s N50?

This is the first in a series of posts where we explain the N50 (Nx) metric, discuss the problems surrounding it, give solutions to those problems, and suggest an alternative N50 metric for transcriptome assemblies.

Most genome assembly papers include the N50 statistics these days. This measure is often being used to describe the ”completeness” of a genome assembly (and sometimes other assemblies). But what it essentially does, is telling you some information about the distribution of contig lengths.

Many people struggle initially to grasp the concept of N50, but we like to picture it like this. Imagine that you line up all the contigs in your assembly in the order of their sequence lengths (Fig. 1a). You have the longest contig first, then the second longest, and so on with the shortest ones in the end. Then you start adding up the lengths of all contigs from the beginning, so you take the longest contig + the second longest + the third longest and so on — all the way until you’ve reached the number that is making up 50% of your total assembly length. That length of the contig that you stopped counting at, this will be your N50 number (Fig. 1b).

1a. Contigs, sorted according to their lengths.

1b. Calculation of N50 using sorted contigs.

Fig. 1. Example of calculating N50 for a set of seven contigs. Here N50 equals 60 kbp.

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