Live from #Evol2016 – Saturday June 18th

Posted on 17 Jun, 2016 by Melissa DeBiasse

The Molecular Ecologist team is all over this year’s Evolution meeting in Austin, Texas.
You can find all of the TME contributors on Twitter using the sidebar on the right or compiled in a handy Twitter list here. Follow along with all meeting news using the hashtag #Evol2016.
As part of our coverage of the meeting, we will be previewing presentations we’re excited about and recapping the highlights of each day here on the blog. To kick things off, here are some of the talks we’ve bookmarked for day 1 of the conference:
Jeremy 
Mark Margres: Quantity, not quality: rapid adaptation to local prey proceeds through venom- gene expression changes in rattlesnakes (11:15, Adaptation/genomics 2, MR9AB) — Fun natural history, rapid adaptation, genomics, species interactions. Heck, yes.

Naomi Pierce: Ant symbioses: from parasitism to mutualism (1:00, ASN Spotlight: Evolution of species interactions 1, Ballroom A) — of course I want to hear Naomi Pierce talk about ant symbioses. Unfortunately it’s during the session in which I’m presenting.

Moises Exposito-Alonso: The 1001 genomes of Arabidopsis thaliana reveal a deep climatic adaptation history driven by summer drought (1:00, Adaptation/genomics 3, MR9AB) — This is leading off my session, and it’s one I’d hate to have missed anyway. Looks like a lot of data, and I want to see how they use it.
Melissa
Sarah Barfield & Mikhail Matz: Genomics of local adaptation in corals (Acropora millepora) from the Great Barrier Reef (9:00am MR9AB) — The Matz Lab is based here in UT Austin and I’m looking forward to seeing some local science on marine inverts.

Laura Lagomarsino, Fabien Condamine, Andreas Mulch, Alexandre Antonelli, Charles Davis: The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae) (9:15am Ballroom A) — Laura recently accepted a TT job at LSU and she rocked her job talk so I’m sure her presentation here will impress.

David Plachetzki: Phylogenomics reveals an ancient metazoan sensory toolkit and a more recent chemosensitivity paradigm shift in the ancestor of protostomes (3:30pm MR10A) — As someone who works on sponges, I can’t resist a talk on metazoan evolution
 

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Greetings from Austin, with a look towards Evolution 2016.

Posted on 16 Jun, 2016 by Bryan McLean

As the yearly conference season approaches full swing, the minds of many evolution-oriented scientists turn, naturally, to Evolution. The Evolution conference is the annual conclave of three of the discipline’s foremost societies (American Society of Naturalists, Society for the Study of Evolution, Society of Systematic Biologists), and it routinely delivers a wealth of new information on advances across the diverse field of evolutionary biology. In this post, I provide a brief glance towards the start of Evolution 2016.
Austin, here we (evolutionary biologists) come!
Evolution 2016 convenes officially this week in Austin, Texas. Besides the bats, boots and bbq (each a draw in its own right), we expect the strong tradition of exciting evolutionary research to continue here. However, a number of preconference proceedings deserve equal attention. For example, the conference is kicking off informally this year with the Phylogenetics Symposium (16 June), sponsored by Society of Systematic Biologists (SSB). This most recent iteration of the symposium continues its focus on newer methods for phylogenetic inference under various evolutionary scenarios and with the use of genome-scale data.
SSB is also sponsoring the Phylogenomics Software School, which on Friday (17 June) will provide hands-on training for some of the software programs highlighted in Thursday’s Symposium. The School is actually one of several thematic workshops that day. For example, American Society of Naturalists is also sponsoring a Science Communication workshop focused on, well, you guessed it. (I’m attending, with dreams of emerging armed with a perfectly polished elevator pitch). In addition, on Friday afternoon, the Society for the Study of Evolution (SSE) is sponsoring a Diverse Careers workshop “to point young professionals towards the first steps of personal career exploration.”
To kick off Evolution 2016 in earnest, Carl Zimmer will speak RE: his 2016 Stephen Jay Gould prize from SSE. Zimmer’s contributions to public understanding of evolutionary science are extensive, and include a number of award-winning books and regular contributions to both New York Times and National Geographic. With the Gould prize, Zimmer joins venerable ranks of other great biologists and science writers. His talk will center on new insights into the evolution of humans as revealed using genomic data. This promises to be a great beginning to Evolution 2016.
Finally, be sure to check Molecular Ecologist throughout the conference for updates from Austin!

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The Fourth Reviewer: Pre-print reviews, parental monikers, and points for student participation

Posted on 14 Jun, 2016 by Jeremy Yoder
(Flickr: Heather Smithers)
In this one case, it would be acceptable to call the parents “old coots.” (Flickr: Heather Smithers)

Tim Vines is an evolutionary ecologist who found his calling in the process of peer review. He was Managing Editor of Molecular Ecology from 2008 to 2015, launched The Molecular Ecologist in 2010, and he’s now the founder and Managing Editor of Axios Review. Here, Tim is The Fourth Reviewer, taking on your questions about peer review and publishing. Got a question for the Fourth Reviewer? Send us an e-mail!

Say I post a paper to a pre-print server, and one of my preferred reviewers comments on it. Can I still name them as preferred reviewers when I submit the paper? Or do I actually need to list them as reviewers with conflicts, now that they’ve given me feedback directly?

If your preferred reviewer only pointed out a typo, ignore the below and list them as a preferred reviewer for the journal. If they’ve given more extensive feedback, the most appropriate course of action is to thank them in the acknowledgements for “providing feedback on an earlier version” or something like that. The journal will probably end up excluding them as a reviewer – they’ve already had their say on the paper – but at least they’re getting credit for their contribution.

You can still add them as a preferred reviewer if you like, but putting forward people who are likely to give a positive set of comments typically raises eyebrows at the journal. It’s far better to name people that you think are well placed to give an objective assessment of this version of the paper.

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#Evol2016: See you in Austin!

Posted on 13 Jun, 2016 by Jeremy Yoder

Downtown Austin, Texas. (Flickr: Norm Lanier)

Downtown Austin, Texas. (Flickr: Norm Lanier)


We’re a few days out from Evolution 2016, the biggest conference of a North American evolutionary biologist’s year. It’s the joint annual meeting of the American Society of Naturalists, the Society of Systematic Biologists, and the Society for the Study of Evolution — it’s also home base for our parent journal, Molecular Ecology, which will be holding its annual editorial meeting Friday, the day before regular conference sessions start. The Molecular Ecologist will be well-represented, with contributors presenting their work every day of the meeting — see the schedule below to find out what to prioritize and/or avoid. Many of us will also be joining the tweeted conference under #Evol2016; you can find our all handles in the sidebar, or follow that hashtag.
Finally, we’d like to invite readers to join us for a meet up during the afternoon coffee break on Monday, the 20th. (We’ll announce more specific details closer to, via Twitter.) It’ll be a chance to say hi and to thank you for your page-views — and we’ll hold a drawing for some TME swag.
Hope to see you there!
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New insight into the genetic basis of industrial melanism

Posted on 9 Jun, 2016 by Reid Brennan

The evolution of coloration in peppered moths during the industrial revolution is one of the most well known examples of natural selection in action. Part of the appeal of the system is the apparent simplicity. The once-abundant light colored morph (typica) dominated in the early 1800’s. However, by 1900 nearly all individuals were black (carbonaria). As early as 1896 it was hypothesized that this drastic change in coloration was driven by an increase of soot produced from the smoke stacks of factories built in the 1800s. It was thought that predation by birds resulted in high mortality in the typica morphs, which would stand out on black, sooty backgrounds. Predation on white typica morphs would then increase the proportion of carbonaria morphs that could match the color of their background and… poof! Evolution.

© wikipedia

Examples of carbonaria (left) and typica (right) morphs. © wikipedia


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Microbes are going to infinity and beyond! Monitoring community changes on a simulated space station

Posted on 8 Jun, 2016 by Kelle Freel

As we’ve discussed previously here, understanding microbes in the natural and built environment around us, has implications related to human health and disease. It has turned out to be pretty tricky to clarify what is going on with our most constant companions, even though we all know the truth is out there.

Figure 1. Mayer et al., 2016


 

ALF! image courtsey of google commons.


Other studies have found that increasing confinement, and maintaining closed off spaces leads to an increase in opportunistic pathogens as well as other closely human-related genera and pose a risk to human health. Additional research conducted in hospitals also found (maybe as you might guess?) that regulating air ventilation impacted microbial community composition as well.It has been shown that the human immune system isn’t quite as efficient as it could be when we are confined to tiny spaces and sent up in space. As we move into that big black abyss above us, we have to take into account the microbes that we bring with us and think about how these communities trapped with us on enclosed space stations might affect the health of astronauts, as well as any ALFs (Alien Life Forms) we run into.
Figure 2. Mayer et al., 2016

Figure 2. Mayer et al., 2016


A recent study in Microbiome by Mayer and colleagues, has presented data collected from an “inflatable lunar/Mars analogous habitat (ILMAH)” that was manned by three graduate students (who maybe drew the short straws for who gets to do what for the study?) for up to 30 days. The study was undertaken in part to see if the students would have some kind of mental breakdowns or flip out after being confined to a small space with two other people. Even though, hard to see…the microbial community is…the researchers involved also decided to study changes in the microbial community associated with the crew living in ILMAH.
The group monitored certain locations in the ILMAH before and during the ‘mission’ using a variety of sequencing techniques and looking at both the microbes that could be cultured as well as those that could not. They found that, as time went on, more cultivable and viable bacteria were found. Additionally, statistically significant larger populations of Actinobacteria and Firmicutes were observed at the end of the mission in comparison. Maybe it’s not a big surprise, but the study also concluded that humans are the source of ‘contamination’ on the pseudo space station.

Figure 4. Mayer et al., 2016


This is an interesting foray into the world of microbes in space. In the future, I’m sure more studies will follow, in attempts to both regulate human health on space crafts as well as avoid potential contamination that we might bring to other planets (or moons!). To read more about different space / microbe related stuff, check out this page by Jonathan Eisen, pretty interesting! Hopefully, in the future, studies focused on unraveling the complex microbial world that thrives in our built environment will help us live long and prosper.

References

Mayer, Teresa, Adriana Blachowicz, Alexander J. Probst, Parag Vaishampayan, Aleksandra Checinska, Tiffany Swarmer, Pablo de Leon, and Kasthuri Venkateswaran. “Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation.” Microbiome 4, no. 1 (2016): 1. DOI: 10.1186/s40168-016-0167-0

La Duc MT, Kern RG, Venkateswaran K. Microbial monitoring of spacecraft and associated environments. Microb Ecol. 2004;47:150–8.

Pierson D, Botkin D, Bruce R, Castro V, Smith M, Oubre C, et al. Microbial monitoring of the International Space Station. In: Moldenhauer J, editor. Environmental Monitoring: A Comprehensive Handbook. River Grove: DHI Publishing, LLC; 2012.

Venkateswaran K, La Duc MT, Horneck G. Microbial existence in controlled habitats and their resistance to space conditions. Microbes Environ. 2014;29(3):243–9.

Kembel SW, Jones E, Kline J, Northcutt D, Stenson J, Womack AM, et al. Architectural design influences the diversity and structure of the built environment microbiome. ISME J. 2012;6(8):1469–79.

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Mitogenomes from extinct New Zealand wrens shed light on the oldest songbird lineage

Posted on 7 Jun, 2016 by Ethan Linck

The order Passeriformes, commonly known as “perching birds” or “songbirds,” contains over half of all known avian species. Sister to all other Passeriformes are the acanthisittid wrens, a small and enigmatic family of New Zealand endemics. Though their providential phylogenetic position makes them an important taxon for understanding avian diversification more broadly, research efforts have been hindered by the family’s other notable attribute: a sad history of extinction.

A female rifleman (Acanthisitta chloris), South Island, New Zealand. Photo credit digitialtrails.


You’re probably at least passingly familiar with the wrens’ woes because of the the well-known story of the Stephens Island Wren, Traversia lyalli, apocryphally eliminated within a decade of its discovery by a single cat named Tibble. This tragedy is emblematic of the family’s broader decline, with five of seven known acanthisittid wrens becoming extinct since the arrival of humans in New Zealand. And because these extinctions occurred prior to modern tissue collection practices, previous phylogenetic studies have largely relied on morphological characters — data that proved insufficient to resolve many relationships.
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New World snakes are "mimics until proven otherwise"

Posted on 6 Jun, 2016 by Rob Denton

Henry Walter Bates spent more than a decade living in the Amazon, having the sort of adventures that inspired generations of naturalists. His most famous and lasting contributions to natural history are his foundational descriptions of mimicry among species. The type of mimicry that carries his name, Batesian Mimicry, involves a harmful species (the model) and a species that copies the appearance of the model while not actually sharing the harmful phenotype (the mimic). In vertebrates, the primary examples of this type of mimicry are brightly-banded snakes that mimic venomous species:

Dramatization of Henry Walter Bates thinking about mimicry in snakes. I'm not saying this actually happened this way.

Dramatization of Henry Walter Bates thinking about mimicry in snakes. I’m not saying it actually happened this way, but yeah, it probably did.


However, the mimicry among New World snakes has turned out to not be as clear-cut of a case of Batesian Mimicry as first thought. Venomous coral snakes and the multitude of brightly-banded species that are putative mimics break a couple of key assumptions about mimicry that have been well supported in other examples of mimics. First, snake mimics can occur way outside the geographic range of the model species. Second, the model species are not necessarily more abundant than the mimics.
A new paper in Nature Communications led by Alison Davis Rabosky uses distributional, phenotypic, and phylogenetic data to take a fresh look at these key assumptions.
While there are mimic species that are allopatric to venomous coral snakes, once distributional information in adjusted based on total snake richness and phylogenetic non-independence, coral snake presence is a strong predictor for the number of mimetic species. Additionally, the 19 independent origins of mimetic coloration occur after the temporal/spatial overlap with coral snakes, meaning that in general, the mimicry has not appeared before the model appears in time or space.
Figure 1 from Rabosky et al. (2016) describing the spatial distribution of mimic and model New World snakes

Figure 1 from Rabosky et al. (2016) describing the spatial distribution of mimic and model New World snakes


Interestingly, the authors identify high rates for the gain or loss of brightly-banded coloration in mimics, even in geographic locations with the highest richness of model species. Both the loss of mimetic condition and the instances of this loss happening within stable regions of the model species’ range are unique to New World snakes. The loss of mimetic coloration is extremely rare in other Batesian systems within butterflies, hoverflies, and spiders.
So what makes snake mimics special? The answer is still out there, but the authors suggest several alternatives including less predation pressure on allopatric snake mimics, drastic range shifts among mimics and their models, or a unique genomic architecture for these alleles. Regardless of these losses and gains of mimetic coloration, this paper provides strong evidence that the phenotypic variation in the putative snake mimics is driven by the presence of coral snakes, or as the authors put it:

We propose that future research is best served by a working hypothesis in which as New World RBB [Red-Black Banded] snake species are considered mimics until proven otherwise..”

 
Cited
Rabosky, A. R. D., Cox, C. L., Rabosky, D. L., Title, P. O., Holmes, I. A., Feldman, A., & McGuire, J. A. (2016). Coral snakes predict the evolution of mimicry across New World snakes. Nature communications, 7. doi:10.1038/ncomms11484

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10 simple rules for designing a scientific poster

Posted on 3 Jun, 2016 by Katie Everson
conference season is coming

Conference season is upon us! Around the world, thousands of scientists face a daunting task: designing a scientific poster.

It should be sleek, yet informative; eye-catching, yet professional; and most of all it should attract the attention of your future advisors and collaborators who keep making trips to the beer and wine counter.

Here are some tips and tricks to make this perilous labor a little easier:

1) Follow the rules

I’m not sure why I have to say this but: read the instructions to presenters. Too often I see posters that are larger than their provided boards and spill onto their neighbors’ posters. #rude

2) Step away from the computer

In the early planning stages of your poster, use a pen and paper to sketch things out. Having an established storyboard will help when you move your ideas to the computer.

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Personal narrative of a journey from zoos to academia

Posted on 2 Jun, 2016 by Stacy Krueger-Hadfield
The American Theater in downtown Charleston, SC. (photo credit: SA Krueger-Hadfield)
The American Theater in downtown Charleston, SC. (photo credit: SA Krueger-Hadfield)

The Molecular Ecologist receives a small commission for purchases made on Bookshop.org via links from this post.

Back in February, the South Carolina Aquarium and The Center for Humans and Nature hosted the finale in the Holland Lifelong Learning series of “Why do zoos and aquariums matter?” in Charleston.

I’ll admit, at first, the main reason I wanted to attend was to see Dr. Sylvia Earle in person and hear her speak.

Dr. Sylvia Earle speaking about her life’s work and the importance of zoos and aquaria for the next generation. © SA Krueger-Hadfield
Dr. Sylvia Earle speaking about her life’s work and the importance of zoos and aquaria for the next generation. © SA Krueger-Hadfield

My parents had given me Earle’s book Sea Change when I was 9 or 10. I remember flipping through the pages long before I actually could read it and understand it. I think they bought it on a tidepooling expedition up the central coast of California on our way to the Monterey Bay Aquarium. Those trips were a driving force behind “wanting to be a marine biologist when I grew up.”

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