Phylogeny of the elves illustrates why we need to sample elf DNA immediately

Maybe not sister taxa, but these are definitely members of the same clade.

Last year for Christmas Eve, Dominic Evangelista reconstructed the evolutionary history of elves and elf-like fantasy creatures in a tour-de-force of nerd crossover. Seriously, go read that piece if you haven’t. It has an alternate abstract in Elvish.

As with all phylogenetic studies, which reconstruct the historical relationships among living and extinct species that share common ancestors, Evangelista’s goal is to understand those relationships. To do this, he recorded a long list of characteristics for each species in his elf-tree — how tall are they? are they stocky or slim? do they like music? He then used a program called Mesquite to identify a set of evolutionary relationships that minimized the number of times those traits would have had to change, which we call the most parsimonious evolutionary tree.

This analysis produces at least one big surprise: it concludes that the closest relatives of the elves working in Santa’s workshop isn’t another type of elves, but dwarves.

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I do not think it means what you think it means: "relic DNA" can obscure microbial diversity studies

Although microbes are small, they play an important part in both biogeochemical cycles in the ocean as well as on land. However, as they are not so easy to observe by eye, and in many cases can’t be cultured in the laboratory, sequencing-based methods are essential in the field of microbial ecology.
There are plenty of different sequencing approaches that might be implemented ranging from sequencing a single gene from an environmental DNA extract (or set of isolates, if you’re lucky enough to get them growing), to quantitative PCR, to metagenomics. As a recent article by Carini and colleagues points out, these tools have revolutionized how we understand microbiology, but the resulting data should be examined with caution.

Figure 1. Relic DNA inflates soil microbial diversity estimates. Carini et al., (2016)


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Artificial connectivity … have we overlooked the native range?

Invasive species are problematic throughout the world’s ecosystems, down even to their very name which incites heated debates. Every month, studies are published that describe the genetic structure and gene flow of non-native species in their introduced ranges. Often, these studies include native populations and try to trace the origin of an invasion. You’re in luck if there’s lots of structure in the native range as it increases the chances on stumbling onto patterns.
But, do we often think about the impacts of human activities on moving species around in their native ranges even before they get moved to a non-native range?
We know that human activities are responsible for altering patterns of dispersal and gene flow.We can guess that anthropogenic transport will eliminate IBD and substantially alter genetic composition regardless of whether a species is moving about in its native range or its non-native range. But, why don’t we look at these impacts more frequently in the native ranges of non-native species?
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Friday action item: Visit a local library

The Boston Public Library (Flickr: Little Koshka)


In the wake of the recent U.S. election, we’ve started these “Friday Action Item” posts with ideas about specific things you can do to support science — from calling Congress to helping crowd-fund a cool new research project. Got a suggestion for a future Action Item? E-mail and tell us all about it!
Among many other accomplishments, Benjamin Franklin — the American Founding Father who’s probably nearest and dearest to most scientists’ hearts — was instrumental in founding what was arguably the first public library in what would become the United States. Today libraries are one of the most remarkable commonplaces of U.S. society, publicly supported institutions that make information available to anyone, for free.
The library Franklin founded was closely tied to scientific work, including in its collection zoological and botanical specimens, fossils, and technical apparatus — and to this day, the libraries of public research universities provide access for anyone who wants to read new scientific publications. Some of my own first encounters with peer-reviewed “primary” scientific literature were in the stacks of libraries, browsing the bound back issues of research journals. As most journals have gone online, actually going into a physical library is probably pretty rare for most of us, but the subscriptions and servers that make digital publications available to us all have their roots in campus libraries.
So that’s your Friday action item: take some time this week to visit a publicly accessible library, on campus or off. Browse the shelves. (The Dewey Decimal code for Biology is 570; Genetics and Evolution are under 576, and Ecology is 577.) Pull something down, find a seat, and read for a bit. Chat up a librarian and ask if there’s any way you can be of service. Or just be a good, quiet library patron. Like a lot of public spaces, libraries need our civil, civic-minded solidarity now more than ever.

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Humans, selection, evolution and ecological timescales … a potent cocktail

It’s been awhile since I last was able to write for TME. But, finally, I’ve stolen away some time to write about a recent study in Ecology Letters that I couldn’t put down once I started reading it. Yes, it’s about mating systems which should be no surprise to regular readers of TME, but if the semester wasn’t over, I’d require my Science Communication students to read it as an incredible example of science and storytelling. I digress momentarily to a blog post I read awhile back at about the same time I accepted a role as a regular contributor at TME. I’ve tried to take the  “think like a fiction author” to heart in writing for TME and peer-reviewed papers alike. As a result, I’m always on the look out for papers that are compellingly written.
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Friday action item: Support the ACLU


In the wake of the recent U.S. election, we’ve started these “Friday Action Item” posts with ideas about specific things you can do to support science — from calling Congress to helping crowd-fund a cool new research project. Got a suggestion for a future Action Item? E-mail and tell us all about it!
The United States Constitution guarantees rights that are foundational to an open, democratic, free society — including freedom of speech and freedom from government-mandated religion, which are essential conditions for scientific inquiry. The Constitution’s guarantees alone don’t protect those rights, though. That task falls to organizations that take legal action to hold government at all levels accountable to the Constitution, and the premier organization taking on that responsibility is the American Civil Liberties Union. The ACLU promotes civic literacy, advocates for constitutional protections, and provides legal support for citizens facing government restrictions on speech, religious practice (or non-practice), and scientific inquiry, among many other issues. Remember the lawsuit against anti-evolution teaching in Dover, Pennsylvania, back in 2005? That was the ACLU, still fighting the fight that they started with the Scopes “Monkey” trial eighty years earlier.
So that’s your action item this week: become one of those famous card-carrying members, and if you can, kick in a few bucks beyond your membership dues.

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When the going gets hot the dinoflagellates (sometimes) get going, how viruses might affect coral symbionts

Corals represent more than meets the eye, they host intricate and interesting communities composed of dinoflagellates (also referred to as zooxanthellae), and a suite of microbes that include bacteria, archaea, fungi, protists, and viruses. One such dinoflagellate that often shares a symbiotic relationship with coral is Symbiodinium.

Image courtesy of wikicommons

Image courtesy of wikimedia commons


These algal symbionts are essential to overall reef function and are present in incredible numbers, a healthy coral reef could harbor more than 1010 algal symbionts per meter squared (!!!). These organisms are essential and understanding their role and unique relationship to coral is important, as it can be screwed up by heat stress, ultimately leading to bleaching (eg. when Symbiodinum cells get the heck out of Dodge and the coral then looks completely white).
Simbiodinium fitti. Image: Todd C. LaJeunesse, Penn State University

Simbiodinium fitti. Image: Todd C. LaJeunesse, Penn State University


However, the mechanism triggered by heat stress that leads to bleaching isn’t completely understood. While it was previously suggested that viruses might somehow play a part in such events, a recent short communication published last week in the ISME Journal presented interesting evidence from Levin and colleagues that it is likely that viral infections lead to thermal sensitivity in Symbiodinium and, ultimately, bleaching.
 
In a previous study, two Symbiodinium populations were cultured from Acropora tenuis at two sites on the Great Barrier Reef. The population from South Molle (SM) Island was thermosensitive and didn’t grow well at 32ºC, while the “thermotolerant” population from Magnetic Island (MI) was cool as a sea cucumber at this elevated temperature. Replicates of both populations (SM and MI) were then maintained at 27ºC or 32ºC and the transcriptomes (sequences of all of the mRNA extracted from the population) were obtained.

Our study exemplifies how RNA-Seq can be used to gain valuable insight into resident viruses.

Levin and colleagues found that only in the thermosensitive population (SM) were incredibly high expression levels of a new RNA virus observed at 27ºC, while at 32ºC anti-viral transcripts increased. At the same time, there was basically no change in the low level of virus RNA expressed in the thermotolerant MI population.

 
 
Thus, we conclude TR74740|c13_g1_i1 to be the RNA genome of a novel +ssRNAV, making this the first discovered genome of any virus infecting Symbiodinium

This study is cool because it presents the FIRST genome of a Symbiodinium virus, and provides a possible explanation for thermal sensitivity in coral symbionts that can lead to bleaching events. Understanding the intricate relationships that underlie coral reef function is important as we deal with climate change and attempt to protect such incredibly essential, not to mention beautiful, ecosystems.
References
Baker, A.C., 2003. Flexibility and specificity in coral-algal symbiosis: diversity, ecology, and biogeography of Symbiodinium. Annual Review of Ecology, Evolution, and Systematics, pp.661-689.
Levin, R.A., Voolstra, C.R., Weynberg, K.D. and van Oppen, M.J.H., 2016. Evidence for a role of viruses in the thermal sensitivity of coral photosymbionts. The ISME Journal.

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Friday Action Item: Get involved with a scientific society


In the wake of the recent U.S. election, we at *The Molecular Ecologist wanted to better use the site to help organize our community’s support for scientific inquiry and science education under an administration that may be quite unfriendly to them. One small thing we thought we could do is highlight “action items” every week. Look for these “Friday Action Item” posts for ideas about specific things you can do to support science — from calling Congress to helping crowd-fund a cool new research project. Got a suggestion for a future Action Item? E-mail and tell us all about it!*
This week’s action item: get involved with a scientific society. Even in the days of science blogs (ahem) and preprints, scientific societies are the glue that holds together communities of experts on topics as broad as all of science, or as narrow as a single taxon. Societies provide research and travel funds for graduate students and early career scientists, organize training and conferences, and generally help us be, well, social. In many cases, they’re also advocates for scientific work in their respective fields — lobbying (yep) government for research support, and offering expertise where it connects to specific policy.
Probably most of our readers are members of at least one society — good fits for molecular ecologists can include the hyper-generalist American Association for the Advancement of Science, or more societies more focused on ecology, evolution and genetics, like

(These are, obviously, a list drawn from the TME team’s personal interests … please feel free to nominate some more in the comments!)
If you’re a member of any societies, your action item for the week is to find out how to be more useful to that society, and do that. Maybe just take the time to vote in the leadership election instead of letting reminder e-mails pile up. (Hey, it’s a chance to vote on something where every candidate has the necessary expertise.) Maybe add your name to the list of potential volunteers for conference organizing or governance work. Maybe donate a membership to a graduate student who needs an extra push, or has more urgent priorities for their TA stipend.
If you’re not a member of a society, then your action item for the week is to pick one and join it. You’ll probably earn discounted, or free, publication fees in a journal relevant to your interests and preferential rates for at least one conference you should be attending anyway — and you’ll be supporting the broader scientific effort of your closest colleagues.

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Friday Action Item: Support science teaching through Donors Choose


In the wake of the recent U.S. election, we at *The Molecular Ecologist wanted to better use the site to help organize our community’s support for scientific inquiry and science education under an administration that may be quite unfriendly to them. One small thing we thought we could do is highlight “action items” every week. Look for these “Friday Action Item” posts for ideas about specific things you can do to support science — from calling Congress to helping crowd-fund a cool new research project. Got a suggestion for a future Action Item? E-mail and tell us all about it!*
Public school classrooms are the point of entry into science for the vast majority of children in the United States, yet public schools are dramatically variable in the resources they have to offer. This is in large part because nationwide, public education is supported by local property taxes, which converts economic inequality into inequality of opportunity. One small way to help fix this is provided by Donors Choose, a kind of Kickstarter for classroom supplies. The Donors Choose website lets K-12 teachers propose projects, activities, or supply purchases with set budgets, and lets donors choose which to support — you can search proposals by subject matter, grade level, supply type, geography, and economic need. Here’s a few examples that are particularly apt for molecular ecologists:

Many of the proposed project budgets are heartbreakingly modest, and some have donation matching offers from Donors Choose sponsors — a donation of $20 can make a big difference. So that’s your Action Item this week: help fund science education at the earliest stage.

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Diving into chilly California waters, understanding genomic differentiation and the role of gene transfer in marine cyanophages

At this point, it’s clear: microbes are everywhere, there are a lot of them, and they are important. In fact, they are more abundant, more diverse and older than any other organism we have on this planet. In particular, cyanobacteria are pretty amazing, and contribute to the majority of the oxygen we breathe (2 of every 3 breaths).
Gregory et al., (2016) Figure 1.The most abundant marine cyanobacteria are Synechococcus and Prochlorococcus, the main representatives of oceanic phytoplankton, which contribute to about half of the world’s primary production. The forces driving population structure and ecotype differentiation in Synechococcus and Prochlorococcus are diverse (including light, temperature, nutrients) as well as cyanophages.
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Posted in Coevolution, evolution, genomics, horizontal gene transfer, microbiology, population genetics | Tagged , , | Leave a comment