Friday Action Item: Support science teaching through Donors Choose

Posted on 25 Nov, 2016 by Jeremy Yoder


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

Posted on 23 Nov, 2016 by Kelle Freel

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

The road ahead

Posted on 22 Nov, 2016 by Jeremy Yoder

(Flickr: Allison Meier)

Since Election Day, people have been [posting](http://www.wnyc.org/story/mta-okay-subway-therapy-now/) their thoughts and fears about the future on the walls of the New York City subway. (Flickr: Allison Meier)


It’s been almost two weeks since we woke up to the reality that Donald Trump — the failed casino mogul, the virtuoso tax-dodger, the reality-show star, the self-described serial sexual assailant, the Ku Klux Klan endorsee and darling of white supremacists, and, yes, the short-fingered vulgarian — will be the next President of the United States. It was a shock on the night of November 8th, and it is no less disorienting a fortnight later. Every aspect of U.S. society as we’ve known it faces an uncertain future after Inauguration Day, and scientific research and education is at the top of that crowded list.
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Posted in citizen science, community, funding, NIH, NSF, politics, United States | 29 Comments

Fungi and the quest for old polyploids

Posted on 17 Nov, 2016 by Rob Denton

Polyploidy, that curious increase in a species’ number of genomes, is now a well recognized force in the evolutionary history of plants and animals. Those extra genomes are often much more than just extra: having a spare genome or four may help lineages radiate into unexplored niches and colonize harsh environments previously uninhabitable by parental species.
Importantly, transitions to polyploidy aren’t just a recent phenomenon. Ancient polyploidization events can be found across the eukaryotic tree of life, from the appearance of angiosperms to the origin of vertebrates:

Figure 1 from Campbell et al.

Figure 1 from Campbell et al. (2016) — starbursts indicate well-characterized (red), partially-supported (grey), and proposed (blue) instances of polyploidization among eukaryotes.


It doesn’t take long to see something weird about this annotated tree. What is up with Fungi? The fungal Kingdom is old and diverse, yet it displays a lack of ancient polyploidization events that are common across other eukaryotes. In a recent volume of The American Naturalist, Matthew Campbell and colleagues lay out the case for the missing ancient polyploids.
The authors focus on three hypotheses:
(1) Ancient fungal polyploids are actually rare (a.k.a. “The Null”)
For some interesting biological reason, maybe polyploidy just doesn’t happen that often in fungi. However, this is fairly straightforward to reject. Polyploidy is found in a wide swath of diverse fungi and can be initiated in the laboratory by crossing species. Additionally, chromosome-based sex determination — one of the major roadblocks for polyploidy in animals — doesn’t appear among fungi.
(2) Fungal polyploids don’t last for the evolutionary long haul.
One of the major talking points in the discussion on the evolutionary significance of polyploidy is the trend for most polyploid lineages to be relatively young. The higher extinction rate of polyploids might be overemphasized in fungi, making extant polyploids that emerged far in the past unlikely. The problem here is that polyploidy is often tied to asexuality in many taxa, and asexual reproduction is a more established cause for evolutionary dead ends. Currently recognized fungal polyploids, such as Saccharomyces yeasts, are in fact sexual polyploids, which suggests that fungi can produce sexual polyploid lineages similar to those seen in plants and animals.
(3) Ancient cases of polyploidization are hard to detect.
Finally, ancient fungal polyploids might be out there right now, happily stretching their little hyphae after a rain, but are just difficult for scientists to identify. Some of the most fundamental work recognizing plant/animal polyploids is via karyotyping, which is a mighty task when looking at the small, condensed, and membranous chromosomes of fungi. Modern approaches to identifying polyploidization use genomic signatures (synteny-based methods for example), but fungi also display significant genome restructuring over short time frames that could confound the search for ancient signals of polyploidization.
Saccharomyces cerevisiae, the stuff of bread, beer, and undergraduate microbiology midterms.

Saccharomyces cerevisiae, the polyploid origin of bread, beer, and undergraduate microbiology midterms.


Given what we know about Fungi, hypothesis 3 is the most likely explanation for the lack of ancient fungal polyploids. Campbell et al. go on to provide a succinct review of the current genomic methods to evaluate polyploidization and their applicability to fungal biology, including Ks calculations, gene/species tree concepts, and the identification of conserved gene clusters in fungi.
Together, this perspective piece is a call to action for genomics and polyploid researchers: there is polyploid treasure somewhere in the fungal kingdom, now go find it.
 
Cited
Campbell, M. A., Ganley, A. R., Gabaldón, T., & Cox, M. P. (2016). The Case of the Missing Ancient Fungal Polyploids. The American Naturalist, 188(6), DOI: 10.1086/688763

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The importance of culturing the uncultured, delving into the microbial consortia in the human gut

Posted on 15 Nov, 2016 by Kelle Freel

Rappe (2013). Figure 1. Direct sequencing and cultivation efforts are both integral aspects of molecular ecology.

Rappe (2013). Figure 1. Direct sequencing and cultivation efforts are both integral aspects of molecular ecology.


The molecular side of ecology has grown by leaps and bounds in recent decades. The review we covered not too long ago, did a nice job of summarizing many key aspects highlighting the importance of this relatively new molecular view of the world. In particular, fancy high throughput sequencing has allowed us to explore the difficult to visualize world of microbes – we can identify things that are there without actually growing cultures in the laboratory.
It wasn’t until the mid 80’s that microbial diversity was examined using molecular tools, and eventually standard methods were developed for identification of bacterial isolates (namely, often sequencing the 16S rRNA gene). Metagenomics has been a game changer: from allowing us to explore the bacteria in a drop of seawater to identifying the key players affecting human health. In fact, once we were able to sequence environmental samples, we realized that only a small fraction of what is out there has been grown in a laboratory. Often the microbes that aren’t cultured are referred to as the “uncultivated microbial majority”.
Marine microbial ecology has benefitted greatly from all of the metagenomics, transcriptomics and (generally) genomics-based studies. Many of the most abundant microbes that play major roles in biogeochemical cycling worldwide are difficult to obtain in culture. It wasn’t until relatively recently that specific high throughput culturing approaches were applied to isolate some of the most abundant lineages inhabiting the oceans. However, this challenge is not unique to environmental microbiology and also must be considered when studying systems such as the human gut.
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Posted in community ecology, genomics, medicine, metagenomics, microbiology | Tagged , , | 2 Comments

There are more microbes than meet the eye: exploring the genomic diversity in an aquifer

Posted on 8 Nov, 2016 by Kelle Freel

First: it’s Tuesday, November 8th, 2016 – before you even think about putting your feet up and reading this post, I hope you’ve managed to wrangle yourself one of those highly prized “I voted” stickers.
Now, on to more microbial matters! Under all the dirt we build our houses on, is a whole lot of carbon. This carbon is involved in a variety of biogeochemical cycles, e.g. cycles that involve important elements (like carbon, nitrogen, sulfur and hydrogen), that are driven by biological, geological, and chemical forces. Studies exploring the terrestrial subsurface, not to mention those attempting to take a crack at what’s going on in the oceanic deep subsurface, have just begun to get a glimpse at the diversity of the microbes involved in the bio portion of those cycles. 
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Posted in bioinformatics, community ecology, metagenomics, microbiology, next generation sequencing | Tagged , , | 1 Comment

At the molecular level, there's more than one way to fly higher

Posted on 3 Nov, 2016 by Jeremy Yoder

The Andean hillstar (Oreotrochilus estella) (Flickr: Tor Egil Høgsås)

The Andean hillstar, Oreotrochilus estella. (Flickr: Tor Egil Høgsås)


Parallel adaptation is coming into its own lately, as we’re increasingly able to examine the molecular changes underlying similar adaptations in distantly related species. A fundamental prediction of evolutionary theory is that species coping with the same environment should converge on similar solutions — a canonical example is the evolution of wings in the ancestors of modern birds and in bats. A corrollary is that the more distant the relationship between converging species, the more likely they are to use different means to get to the same place. Birds and bats are both tetrapods, and though their wings are different in a number of ways, they are formed from some of the same bones. Flying insects, however, had to “find” an entirely different developmental basis for their wings.
Recently on this very blog we covered a study that showed how deep the commonalities of convergent evolution can be, identifying 47 genes shared between pine and spruce that underlie adaptation to winter cold in both lodgepole pine and interior spruce, despite the fact that these species shared a common ancestor about 140 million years ago. Another paper recently published in the same journal, Science, takes an even more fine-grained look at a different convergent adaptation, and finds that, at the most basic level, more differences than commonalities.
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Still ruffling feathers after all these years: Darwin's finches and a molecular view of adaptive radiation

Posted on 31 Oct, 2016 by Kelle Freel

One of the many lovely things about molecular ecology is its ability to shine new light on old stories. The well-known case of Darwin’s finches is a classic example of adaptive radiation. These finches demonstrate a clear instance where over time, one species diversified into several that are adapted to different environments, or more specifically, food sources. In a nutshell (or maybe I should say seed), “Darwin’s finches” include 14 species that descended from those that first colonized the Galapagos about 2 million years ago, all with distinct beak shapes and sizes that allow them to eat different foods.
finches
In the most recent cover article from Molecular Ecology, Chaves and colleagues dig deep into the morphological and genomic variation among three sympatric Geospiza species found in El Garrapatero on Isla Santa Cruz in the Galapagos. While genome-wide association studies (GWAS) are popular in many model systems, the authors state that these three species represent the finest branches on the evolutionary tree, suggesting that the “genomic architecture of their adaptive traits should reflect the variation actively shaping – and being shaped by – natural selection”. Basically, these birds are diverging and adapting before our very eyes, and present a good opportunity to study evolution in action.
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Posted in adaptation, association genetics, evolution, genomics, Molecular Ecology, the journal, population genetics, RNAseq, selection, speciation | Tagged , , | 2 Comments

Making ecology “count”: a review of the why and how of molecular ecology  

Posted on 25 Oct, 2016 by Kelle Freel

It’s likely that everyone has been asked by either a friend or family member “What do you do?” Which, depending on what level of detail you shoot for, might be relatively straight forward. The follow-up question, however, can be a little trixie: “Why??”
A recent review by Creer and colleagues gives a nice broad overview of molecular ecology, defines key terms, and highlights the main advances that new technology has afforded the field. From sampling to sequencing, this article briefly covers landmark moments that have laid the foundation for the advancement of molecular ecology and emphasizes the future potential of continuing to link traditional ecological approaches with sequence-based techniques.
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Posted in bioinformatics, community, community ecology, metagenomics | Tagged , , , | 1 Comment

Video Tutorial: editing R plots in Adobe Illustrator

Posted on 20 Oct, 2016 by Katie Everson

Adobe Illustrator is a powerful tool for creating and editing figures; unfortunately, it’s also really intimidating. So today at The Molecular Ecologist we’re trying something a little different: a screen-capture video tutorial about using Adobe Illustrator to enhance and edit plots that you make in R.
If you want to follow along with the full 13.75 minute tutorial, you can download the example PDF plots by clicking these links: Phylogeny and Scatterplot.
Video contents:
0:10-1:25: Saving plots to PDF in R
1:25-8:07: Editing a phylogeny
8:07-10:27: Editing a scatterplot
10:27-13:45: Combining and finalizing the figures

This video barely scratches the surface of what you can do with Adobe Illustrator, but hopefully it helps you get started. Happy Illustrating!

Posted in howto, R | Tagged , , , , , , , , | 3 Comments