Caught sweeping ‘cross the sea

 

Sea lice are regularly monitored and counted on fish at a salmon farm.  © cermaq.com

Sea lice are regularly monitored and counted on fish at a salmon farm. © cermaq.com

The salmon louse Lepeophtheirus salmonis is an ectoparasite linked to declines in wild salmonid populations as well as causing huge economic losses in salmon farms. Previous studies, using a variety of molecular markers, yielded conflicting results ranging from strong genetic differentiation among nearby farms to no structure across the entire North Atlantic.

Besnier et al. (2014) investigated the effects of anthropogenically-driven rapid evolution to pesticide resistance using a SNP-array. Emamectin benzoate, or EMB, is the most commonly-used pesticide to control L. salmonis in the Atlantic.

 [EMB] resistance developed at a single source, and rapidly spread across the Atlantic [within a decade] … and importantly demonstrates that alleles conveying resistance to pesticides may be quickly spread over very large areas in the marine environment.

From a management perspective, this study demonstrates the necessity of ocean-wide policies, rather than management at the regional level.

From a population genetic perspective, the seascape in which L. salmonis is evolving is extremely heterogeneous:

 with patches of high host density in salmon farms and coastal areas, and large areas of low host density in the offshore regions.

Thus, standard popgen protocols with which to investigate different evolutionary dynamics may be difficult to apply due to biased estimates in these sea louse population(s).

Finally, from an evolutionary perspective, the strong selective sweeps detected in this study strongly suggest that:

L. salmonis has a high capacity to spread new advantageous mutations across [ocean basins] in the time scale of just a few generations [max 11 years] … thus corroborating concerns that pesticide resistance can develop and rapidly spread over large areas on an ecological time-scale.

 

 

Besnier F, M Kent, R Skern-Mauritzen et al. (2014) Human-induced evolution caught-in action: SNP-array revels rapid amphi-atlantic spread of pesticide resistance in the salmon ectoparasite Lepeophtheirus salmonis. BMC Genomics 15: 937. http://www.biomedcentral.com/1471-2164/15/937

 

 

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Geophylogeny plots in R for Dummies

Amid basting my tofurky, here’s a follow-up to my previous post on quick-fix overlays of admixture plots on geographical maps in R. I recently discovered a wonderful R package called “phytools” from Liam Revell, which makes really neat phylogenetic trees (with several new functions added to the “ape” package). I highly recommend Liam’s blog which has a wealth of examples and hacks to make cool figures. “phytools” also has a function called “phylo.to.map” which lets you make some neat geophylogenies. I will use the same example from my previous post (you’ll need the same gps.data and admixprops.data files) to show you how. You will also need a NEWICK tree string for your phylogeny – I am assuming here that you have a population tree created using your method of choice. Importantly, the ID’s of your GIS coordinates for each locale (here described by the “ID” column) should be the same as the labels in your NEWICK string.

Eg. (3:0.6,(4:0.1,(1:0.03,2:0.03):0.08):0.5);

library(phytools)
library(plotrix)
phy<-"(3:0.6,(4:0.1,(1:0.03,2:0.03):0.08):0.5);"
tree<-read.newick(text=phy)
gps<-read.csv(“gps.data”,header=TRUE) #Read input files
admix<-read.csv(“admixprops.data”,header=TRUE)

Now you should have your tree, GPS coordinates, and admixture proportions read. To plot them all in one figure:

obj<-phylo.to.map(tree,gps[,2:3],
type="phylogram",database="state")
plot(obj,colors=c("blue","red"),ftype="i",
fsize=1.5,asp=1.2,split=c(0.5,0.5))
for (x in 1:nrow(gps)){ floating.pie(gps$Lon[x],gps$Lat[x],
c(admix$K1[x],admix$K2[x]),radius=admix$Num[x]/8,
col=c("red","blue") }

And tada!

usa-geophyloThere are a lot of way cooler tools that do the same thing, including GeoPhyloBuilder and GenGIS, but hey – if you can do it in four lines of code in R, why not? Happy Thanksgiving from all of us at The Molecular Ecologist! This year, like every year, I am very thankful for R.

 

Posted in howto, phylogenetics, population genetics, R, software, STRUCTURE | Tagged , | Leave a comment

The big chief at Molecular Ecology Resources: Interviewing Shawn Narum

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What are the most exciting parts of doing science? The first look at results? The sheen of your publication finally in print? That initial foray out into the field?

What about the moment you figure out a way to make a good idea come to life?

If you’ve learned a new tool, a new technique, or new piece of software in the last few years, you likely ended up citing a paper from Molecular Ecology Resources (MER). The journal has undergone some big changes recently, and we asked its new Editor-in-Chief, Shawn Narum, to give us his perspective on the present and future of the journal.

Tell us about your work at the Columbia River Inter-Tribal Fish Commission (CRITFC)

I lead a research group involved in population and ecological genomics of multiple fish species in the Columbia River and Pacific Northwest USA.  We work at the interface of academic and applied research where genomic tools are utilized for long-term preservation of once abundant aquatic resources in this region.  In particular, species of Pacific salmon are a vital component of communities in the western USA ranging from California to Alaska and have sustained Native American tribes in the region for several centuries.  Salmon are keystone species in aquatic ecosystems in need of careful conservation, yet remain as some of the few remaining sources of wild caught food for human consumption.  Extensive research efforts have been underway for decades to better understand how to best conserve and manage this declining resource, and genomic tools have begun to contribute greatly.  Recent examples of our work include association mapping of important traits such as disease resistance (Campbell et al. 2014), testing for local adaptation in wild populations experiencing climate change (Narum et al. 2013), and evaluating fitness effects of supportive breeding (Hess et al. 2012).

This work has been a great match for me personally as I have always had a strong connection with aquatic systems and the fish that swim in them.  When I’m not at work, you can often find me on a river with my family and a fly rod in my hand.

Tip: Don't include any Big Fish stories in your cover letters.

Tip: Don’t include any Big Fish stories in your cover letters.

As Chief Editor of Molecular Ecology Resources (MER), can you describe the recent shifts that have taken place for the journal?

The primary focus of the journal is on the development of broad resources for the community of molecular ecologists.  The journal actually made this shift towards developing various types of resources several years ago as reflected by the change in the name in 2008, from Molecular Ecology Notes to Molecular Ecology Resources.  Instead of primer notes, we now publish a broad array of papers including computer programs, statistical and molecular advances, and extensive molecular resources.

Unfortunately, many people still associate MER with microsatellite primer notes, but we have not published a primer note in years!  However, this transition to broader resources has begun to take hold and has led to a dramatic increase in impact factor over the past few years, reaching 7.3 in 2012 and 5.6 in 2013.

Change in impact factor for MER

How has the drastic increase in impact factor over the last three years affected the journal?

This is obviously a positive direction for the journal, but also reflects how important the resources we publish are to the community of molecular ecologists.  Authors have begun to recognize that MER is a highly satisfying journal to publish their innovations that utilize spectacular advances in genomics technology in the last decade.  Contributions are increasing and have the editorial board scrambling at times, but overall we continue to maintain a relatively quick review process that averages a just over a month for original manuscripts.  Thus we are receiving some of the best resources that are being developed in our field.

What are some of the most exciting advances you’ve seen in the field since you’ve been Chief Editor? Any areas of research that you’re particularly excited about?

All things next-generation sequencing (NGS) have been stunning to observe and exciting to be involved with.  Just a few years ago, many of us working with non-model species found genome assemblies to be a distant dream, but here we are with so many genomes available including some of my favorite fish.  For many years, we’ve heard declarations of decreasing costs for genomics and I believe we are beginning to fully appreciate that in the field of molecular ecology.  There are abundant resources and tools now available for non-model species as NGS technology opens unlimited avenues of research.

I have particularly been excited about tools such as RAD-seq and RNA-seq to address compelling questions regarding ecological genomics and local adaptation. My lab has also just developed a protocol for amplicon sequencing called GT-seq (Genotyping-in-thousands by sequencing) that will dramatically reduce our costs and increase our ability to genotype large numbers of fish for our various projects.  The combination of tools that capitalize on NGS makes it a very exciting time, but the bioinformatics realm continues to be strained and will need to move forward very quickly.  I envision MER as a partner in helping advance and publish many bioinformatic tools.

What words of advice can you give for those scientists looking to publish in MER?

Great potential remains for new innovations in molecular techniques with NGS platforms and advancement of bioinformatics tools. Resources that are developed specifically for one lab or study species could have the potential to be adopted more broadly in the scientific community.  I encourage graduate students and post-docs to develop their resources to reach a larger audience and consider MER as an outlet for that work.

Not only does MER have a strong impact factor, but we have recently implemented more ways to promote the best innovations that we publish through highlighting articles as ‘From the Cover’ articles and providing accompanying ‘Perspectives’.  We want to help get the word out about all the innovative resources that are being developed.

Literature Cited

Campbell N.R., K. Overturf, R. Towner & S. R. Narum (2014). Association Mapping of Disease Resistance Traits in Rainbow Trout Using RAD Sequencing, G3, DOI: http://dx.doi.org/10.1534/g3.114.014621

Hess M.A., Jason L. Vogel, Jeff J. Stephenson, Doug D. Nelson & Shawn R. Narum (2012). Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon, Molecular Ecology, 21 (21) 5236-5250. DOI: http://dx.doi.org/10.1111/mec.12046

Narum S.R., Kevin A. Meyer, Michael R. Miller & Ronald W. Hardy (2013). Thermal adaptation and acclimation of ectotherms from differing aquatic climates, Molecular Ecology, 22 (11) 3090-3097. DOI: http://dx.doi.org/10.1111/mec.12240

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Consuming raw or undercooked frogs may increase your risk of getting a rare tapeworm in your brain

Don’t eat me, bro. (photo from Wikipedia)

A 50-year-old UK resident had been living with an unwelcome visitor for the past 4 years and it was such a headache. Surgeons from Addenbrooke’s Hospital in Cambridge removed the tapeworm during a biopsy after noticing a small circular lesion migrating across his brain in a series of MRIs taken across the years:

Image from New Scientist / Nagui Antoun

The tapeworm turned out to be an rare find:Spirometra erinaceieuropaei. It is typically found in the intestines of their definitive hosts – cats and dogs. However, this time, it was found in what is known as an “aberrant host” – a dead-end for the tapeworm. But before it dies off, it can cause some issues in the aberrant host, such as seizures, headaches, and memory loss.

Fortunately for us, researchers at the Wellcome Trust Sanger Institute did what we all wanted to do: sequence it’s genome! What they found was pretty cool:

The 1.26Gb draft genome of S. erinaceieuropaei is currently the largest reported for any flatworm.

That’s a gigantic tapeworm genome. It’s 10x the size of any published tapeworm genome and over 1/3 the size of the human genome. The scientists went on to try and figure out why it didn’t die when the patient received antibiotics:

Through investigation of β-tubulin genes, we predict that S. erinaceieuropaeilarvae are insensitive to the tapeworm drug albendazole.

Fortunately, for us they also found targets for other known tapeworm drugs, which means that next time they might be able to stop the worm in its tracks… in your brain.

Bennett et al. (2014). The genome of the sparganosis tapewormSpirometra erinaceieuropaei isolated fromthe biopsy of a migrating brain lesion. Genome Biology. 15:510. doi:10.1186/s13059-014-0510-3

Posted in genomics, medicine, phylogenetics | Tagged , , | 1 Comment

All in the family: hierarchical social and genetic structure in the Old World monkey Theropithecus gelada

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A group of gelada monkeys (Theropithecus gelada). Photo by Noah Snyder-Mackler

Complex, multi-level animal societies have evolved convergently across many taxa but we know little about the mechanisms behind their formation and their associated fitness benefits. In their Molecular Ecology paper published online last week, Snyder-Mackler et al. addressed these questions using genetic data and behavioral observations to compare relatedness among individuals and hierarchical social structure in the gelada (Theropithecus gelada), an Old World monkey endemic to the highlands of Ethiopia.

Geladas form complex, hierarchical societies. At the lowest level, ‘units’ consist of one dominant male gelada, up to 5 subordinate males, and one to 12 female geladas. The social structure of geladas is dynamic such that units may fission (i.e. split) into two daughter units or two units may fuse. Says Snyder-Mackler,

The majority of the fissions have happened during a takeover event. That is, when new males enter the unit and de-throne the old leader male. The fission events need some catalyst for the fission to take place, potentially because the females need to have a leader male to join up with when they split from their unit – this is probably easier when a takeover happens.

At the next level up is the ‘team,’ an aggregation of two or more units that associate with each other at least 90% of the time, although not all units form teams. Above the level of the team is the ‘band,’ a group of units that spend 50%-90% of their time together, and finally, at the highest level of hierarchical structure is the ‘community,’ a set units with overlapping home ranges that spend at least 50% of their time together. Unattached males form groups loosely associated with bands (i.e. the bachelors).

Diagram courtesy of Noah Snyder-Mackler

Diagram courtesy of Noah Snyder-Mackler

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Posted in community, Molecular Ecology, the journal, primates, societal structure | Leave a comment

They’ll let anything through peer review these days

… where “they” are the hordes of bogus pay-to-publish journals that seem to be spamming every .edu email address (especially those connected to corresponding authors in real journals) with invitations to submit. Submission spam from the International Journal of Advanced Computer Technology apparently pushed computer scientists David Mazières and Eddie Kohler to the breaking point, because they submitted a “manuscript” with text, title, abstract, section headers, and two figures consisting entirely of the words “Get me off your fucking mailing list.”

Screen Shot 2014-11-21 at 10.44.14

Mazières and Kohler (in press), Figure 1.

And the journal accepted the manuscript.

Mazières and Kohler received a typeset copy of their submission, with a an alleged peer reviewer’s report [PDF] rating it “Accepted.” (The form includes a “Strongly Accepted” option, so you know this wasn’t a complete cakewalk.) All the coauthors had to do for publication to proceed was to wire in payment for the publication charges.

Scholarly Open Access has the full story, including links to the typeset manuscript and acceptance message. This is far from the first time someone has shamed a pay-to-publish journal or conference by submitting a nonsensical paper, but it’s got to be the most ridiculous example of the genre.

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The latest gadget for the molecular ecologist’s toolkit

Designing a sampling scheme to collect an organism of interest for a population genetic/genomic study can be fraught with difficulty. How best to sample? Randomly? Or, along a grid? How many individuals to sample? Thirty? Or, perhaps, the sample size employed in a recently published study on a similar organism?

This can be even more challenging if your pet organism(s) has a complex life cycle, whether that be a transition through different hosts (i.e., parasites), or the alternation of free-living phases which differ in ploidy (e.g., mosses or seaweeds). For example, the intertidal distribution of the red seaweed Gracilaria gracilis is much more discrete and, therefore, more survey-able than that of a co-occurring red, Chondrus crispus.

Discrete individuals of Gracilaria gracilis (left) in which it was easier to map individuals within a tide pool.  A more dense distribution of Chondrus crispus (right) in which a grid sampling approach was employed. © SA Krueger-Hadfield

Discrete individuals of Gracilaria gracilis (left) in which it was easier to map individuals within a tide pool. A more dense distribution of Chondrus crispus (right, along with other seaweeds) in which a grid sampling approach was employed. © SA Krueger-Hadfield

However, both are haploid-diploid, complicating a sampling strategy, let alone subsequent popgen analyses which are not, yet, equipped to deal with haploid-diploids in a straight forward manner. Nevertheless, the mating system of the haploid-diploid red seaweed G. gracilis is allogamous, whereas inbreeding (specifically, inter-gametophytic selfing, see Klekowski 1969) dominates in C. crispus (Engel et al. 1999, Engel et al. 2004, Krueger-Hadfield et al. 2013, Krueger-Hadfield et al., in press). Thus, how best to sample, in order to investigate a chosen hypothesis? Sampling every single seaweed isn’t possible, logistically and financially. Even more complicated, how to sample over a distributional range to address broader questions about gene flow?

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Posted in genomics, methods, Molecular Ecology, the journal, natural history, pedigree, population genetics, software | 1 Comment

#EntSoc14, a quick review

I have had a wonderful time at my first big bug conference – the annual meeting of the Entomological Society of America, at the Oregon Convention Center in Portland. Amid secretive (or not so secretive) break-out sessions to Voodoo Doughnuts, the meeting has been abuzz with several interesting symposia and posters, vastly covering (a) invasive species and their control, (b) human mediated biological control, (c) anthropological effects on habitat modifications, (d) bacterial symbionts and pathogens, (e) phylogeography and population genetics of native and non-native species, (f) insects as disease vectors, (f) ecological and genetic mechanisms of phenotypic variation in mobility, wing patterns, pheromone diversity, homing behavior, eusociality, to name a few.

Darwinilus sedaris

Darwinilus sedaris, only known sample of the species to be collected by Charles Darwin in 1832, in display at #EntSoc14. Image courtesy: Entomology Today -http://entomologytoday.org/2014/11/16/charles-darwins-rove-beetle-imaged-on-site-in-portland-or/

Here were my top three topic-picks for Molecular Ecology enthusiasts from #EntSoc14!

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Posted in conferences, genomics, phylogenetics, population genetics | Tagged , , , | 1 Comment

New faces: Karen James

New contributor Karen James

New contributor Karen James

Recently we’ve been pleased to welcome a big group of new contributors to the blog. By way of introduction, I asked each of them to answer a few quick questions about him- or herself. —Jeremy

Who are you? Where are you? I’m a staff scientist and member of faculty at a the MDI Biological Laboratory. I live in Bar Harbor, Maine, but I travel a fair amount for science and for fun. I postdoc’d at the Natural History Museum in London from 2003-2010 so I also have a lot of friends and former colleagues back there.

What do you study? I did my PhD in genetics, and my postdoc in molecular systematics, evolution, and biodiversity. Now I combine DNA-assisted species identification (DNA barcoding and related techniques) with citizen science to increase the scope and scale of environmental research, conservation, restoration, and management. I am working to develop the Acadia National Park region as a sort of model for exploring this combination. Considering the venue here, I think it’s important that I explain that I am not an ecologist, but I collaborate with ecologists!

What do you do when you’re not studying it? I love hiking, skiing, and biking in my backyard, that is, Acadia National Park. I’m on social media a lot – Twitter mainly (@kejames). I put a lot of effort into improving things for women and underrepresented minorities in science.

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Growing the evolutionary relationship between green algae and salamanders

Spotted Salamander (Ambystoma maculatum) egg mass. Photo by Rob Denton

Spotted Salamander (Ambystoma maculatum) egg mass. Photo by Rob Denton

The presence of  green algae within the developing egg masses of amphibians has been recognized since the early 1900s, but only recently have researchers discovered that the these algae (termed “Oophila”) persist in animal tissues far after leaving the egg. The allure of an unexpected mutualism between an alga and a vertebrate animal (a solar salamander!) is undeniable for both scientists and science journalists, but many authors pump the brakes on coevolutionary explanations until more is understood about the relationship between algae and amphibians at a wider taxonomic level.

Eunsoo Kim and colleagues provide a new perspective on this evolutionary relationship in a new publication appearing in PLOS ONE. Kim and colleagues sampled algal DNA from eggs of four different amphibian species across North America, showing not only a single clade of amphibian-egg algae, but also a partial species-specificity among those algal groups.

We designate this group as the ‘Oophila’ clade, within which the symbiotic algae are further divided into four distinct subclades. Phylogenies of the host amphibians and their algal symbionts are only partially congruent, suggesting that host-switching and co-speciation both play roles in their associations.

These results are another important and encouraging step in fully explaining the beginnings and extent of algal/amphibian symbiosis, while laying the groundwork for some fascinating questions concerning how amphibians allow for this strange association during their development.

Kim E., Lin Y., Kerney R. & Blumenberg L. (2014). Phylogenetic Analysis of Algal Symbionts Associated with Four North American Amphibian Egg Masses, PLOS ONE, 9 (11) e108915. DOI: http://dx.doi.org/10.1371/journal.pone.0108915

Posted in Coevolution, phylogenetics, speciation | Tagged , , , | Leave a comment