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

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

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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Posted in birds, evolution, mutation, natural history, phylogenetics | Tagged , | Leave a comment

Still ruffling feathers after all these years: Darwin’s finches and a molecular view of adaptive radiation

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 , , | Leave a comment

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

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

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

Gene expression shows how a plant and its mutualists are better together

Medicago truncatula, in its model-organism habitat. (Flickr: Jeremy Yoder)

Medicago truncatula in its model-organism habitat. (Flickr: Jeremy Yoder)

No living thing is an island, and many of the encounters between living things that happen every day are not antagonistic or even indifferent, but mutually beneficial. Two such mutualisms that could be among the most important on the planet are the relationships plants have with nitrogen-fixing bacteria and mycorrhizal fungi. Rhizobial bacteria convert nitrogen from the biologically inaccessible form that makes up a large fraction of the atmosphere to a chemical compound plants can use to build amino acids; mycorrhizal fungi collect rare soil nutrients and water from sources a plant can’t access, like leaf litter. Many plants allow either rhizobia or mycorrhizae — or both — to colonize their roots, and feed them sugar in exchange for the nutrients they provide.

The possiblity of hosting both these relatively simple mutualists opens up interesting options — do they help each other, or compete for their hosts’ favor? How does a plant juggle both bacteria and fungus? One such plant is Medicago truncatula or barrel medick, a small, weedy relative of alfalfa that grows really well in greenhouses, and has become a “model species” for studying mutualism. A recent paper in Molecular Ecology examines how the “tripartite” relationship affects the activity of genes in the host plant.

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Posted in microbiology, next generation sequencing, plants, RNAseq | Tagged , , | Leave a comment

Conifer convergence

Convergent local adaptation is typically studied within a species or between closely related species. In these cases, it is perhaps not unexpected to observe parallel evolution due to common genetic variation, constraints, etc. Convergence between species is somewhat less studied, especially when complex polygenic traits are considered. Are similar genes required for different species to adapt to similar environments? That is, is adaptation genetically constrained?

To address this question (link to paper), Sam Yeaman and colleagues involved with the AdapTree project focused on two tree species from western North America, lodgepole pine and interior spruce. These species are about 140 million years diverged but occupy similar environmental clines and consist of locally adapted populations throughout their ranges.

It is known that these species show local adaptation to their environment, but are the underlying genetic adaptations convergent? To address this, the authors grew > 1100 individuals from 250 populations across the range of both species in a greenhouse. These individuals were phenotyped for 17 climate related traits. They were genotyped for > 1 million SNPs in 23,000 genes and genotype-phenotype and genotype-environment associations (for 22 environmental variables) were conducted. These associations identified outliers, and the authors looked at specific genes, identifying which had the highest proportion of their total SNPs as outliers. They then looked for signals of adaptation in the orthologs of these outliers in the other species.

For a false discovery rate (FDR) of 0.05, 47 genes showed evidence for convergence. That is, about 10-18% of locally adapted genes are evolving convergently (depending on the FDR used). I really don’t have a sense about whether this is high or low… if anyone has thoughts, please weigh in. Another interesting finding is that duplicated genes were more likely to show convergence than unduplicated genes (see figure). This pattern may be explained by a relaxation of selective constraint following duplication.

f3-large

Candidate genes with signatures of convergent local adaptation. From Yeaman et al., 2016

I like this study for a number of reasons. First, the authors are explicitly looking for convergence in distantly related species. This allows them to address the degree of convergence in adaptive evolution in species that should share no standing genetic variation. Second, they asked this question in regard to complex physiological traits. This is nice because many previous examples of convergence between species have been found in relatively simple traits (I’m looking at you, MC1R). Now, we just need other people to perform similar studies so we can figure out if these rates of convergence are consistent across taxa and phenotypes.

References:

Yeaman, Sam, Kathryn A. Hodgins, Katie E. Lotterhos, Haktan Suren, Simon Nadeau, Jon C. Degner, Kristin A. Nurkowski et al. “Convergent local adaptation to climate in distantly related conifers.” Science 353, no. 6306 (2016): 1431-1433. DOI: 10.1126/science.aaf7812

Posted in adaptation, association genetics, genomics, plants, selection, Uncategorized | Tagged , , | 1 Comment