Category Archives: blogrolling

The Molecular Ecologist: Is Homo sapiens a model organism?

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New York City Photo by Bikoy.

Over at The Molecular Ecologist, guest contributor Jacob Tennessan suggests that for those of us who study the genetics of natural populations, the ultimate “model organism” may be … us.

Thus, the field of human population genetics has always been a step or two ahead of the molecular ecology of wildlife. Common techniques like mitochondrial- or microsatellite-based phylogeography analyses were pioneered with data from humans. Research into human molecular ecology has yielded countless fascinating stories that provide a baseline for what to expect when examining other taxa. Some are well-known textbook examples, like the sickle-cell hemoglobin balanced polymorphism that conveys resistance to malaria, or the human global diaspora reflected in sequence diversity that traces back to “mitochondrial Eve” and “Y-chromosome Adam.”

Does that make Homo sapiens a “model organism” in the same sense as fruitflies and Caenorhabditis elegans, or more of a proving ground for new molecular methods? Go read the whole thing, and tell us what you think in the comments.◼

Nothing in Biology Makes Sense: On the origins of bacon

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Pig Photo by mgabelmann.

Over at Nothing in Biology Makes Sense! Noah Reid takes a look at a new study of the recent evolutionary history of pigs:

Domestic pigs are in the family Suidae, which includes the babirusas, warthogs, the endangered pygmy hog (whose generic name is, Porcula, seems a likely candidate for America’s next tragic children’s cereal) and the domestic pig’s close relatives in the genus Sus. Depending on where you draw the lines, there are around 7 species in Sus. With the exception of the wild boar (Sus scrofa) their natural ranges are restricted to Southeast Asia west of Wallace’s Line.

Because domestic pigs are prone to going feral and getting, um, re-familiarized with their wild relatives, unravelling their history using genetic data is tricky business. To see what the new study found, go read the whole thing.◼

The Molecular Ecologist: Interview with Loren Rieseberg

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Sunflower (closely) Photo by ToOb.

This week at The Molecular Ecologist, we’re kicking off a new interview series, “People Behind the Science,” by John Stanton-Geddes. The inaugural interview is with Loren Rieseberg, the Chief Editor of Molecular Ecology and an expert in the evolutionary consequences of hybridization between species.

When I arrived at Washington State University (WSU) in the fall of 1984 to begin my PhD, my advisor, Doug Soltis, handed me a copy of Verne Grant’s Plant Speciation and told me to find a problem. I was especially intrigued by Grant’s discussion of the potential role of hybridization in adaptation and speciation.

The interview ranges from Rieseberg’s philosophy for Molecular Ecology to which one paper (out of over 300 he’s authored!) that he wishes more people would read. So go read the whole thing.◼

Nothing in Biology Makes Sense: Can we separate reproductive isolation and species formation?

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fork in the road Photo by dkwonsh.

This week at Nothing in Biology Makes Sense! Noah Reid takes a look at a study that attempts to disentangle the effects of reproductive isolation between species and the rate at which new species are formed. Why would you want to do that? So you can tell whether the former causes the latter!

RI [reproductive isolation] is often thought to be important in diversification because some theory predicts that even low levels of intermating between populations can prevent divergence from occurring and because hybridization between divergent populations can cause them to homogenize, or cause one population to become extinct. If these factors commonly prevent speciation or cause incipient species to go extinct, one might expect a positive correlation between the rate of evolution of RI and DR [species diversification]. This paper is the first test of this prediction.

But, of course, a lot of biologists would say that the evolution of reproductive isolation is the evolution of a new species … so things get a bit complicated. Go read the whole thing, and see what you think.◼

Nothing in Biology Makes Sense: Your dinner, or your life?

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2010 076 Masai Mara b 24 Photo by ngari.norway.

Over at Nothing in Biology Makes Sense!, I’ve written about a new study that tries to disentangle conflicting sources of natural selection to determine whether big herbivores like antelope, zebras, and ostriches have evolved to run because they’re always running away from predators.

An antelope’s frame is under more demands than evading cheetahs—it also needs to travel long distances to follow food availability with the shifting rainy season. In fact, the North American fossil record suggests that big herbivores on that continent evolved long legs for distance running millions of years before there were predators able to chase after them. And then again, not all predators run their prey down; lions, for instance, prefer to pounce from ambush.

To find out whether gazelles are running for their lives, or running for dinner, go read the whole thing.◼

The Molecular Ecologist: Mutation rates shaped by population dynamics

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Polio virus (picornavirus) Photo by Sanofi Pasteur.

Over at The Molecular Ecologist, I have a new post up discussing an interesting new modeling paper. It suggests that, for some viruses, variation in the rate of evolutionary change may be driven not by selection imposed by their hosts, but by the dynamics of the viral population within, and spreading among, host individuals.

Viruses based on RNA, as opposed to DNA, generally have very high mutation rates—in part because the process of replicating RNA is more error-prone than DNA replication. But there’s also tremendous variation in the substitution rate between different RNA viruses, even between populations of closely related viruses.

To find out how simple population dynamics could shape this wide variation in substitution rates, go read the whole thing.◼

Nothing in Biology Makes Sense: For species delimitation, size matters

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Shewanella Scanning electron micrograph of Shewanella putrefaciens. Photo by EMSL.

This week at Nothing in Biology Makes Sense!, Sarah Hird explains a new theoretical study proposing that species concepts are hard to define for microorganisms not because just because they reproduce asexually and trade genetic code like playing cards … but simply because they’re small and numerous.

Specifically, the product of mutation rate and carrying capacity (uK) needs to be below a certain threshold for species to form. This is because there needs to be a small amount of variation relative to the amount of niche space available or no clear “best” type will emerge that can outcompete all the other types quickly enough to become established. If mutation rate is high, there are too many available types. If carrying capacity is high, there is no way to limit who’s there at all. Many other things are happening with this paper, but their big conclusion, put plainly, is that if there is too much variation, differentiation cannot occur.

If that sounds as freaky to you as it does to me, you’ll want to go read the whole thing.◼

The Molecular Ecologist: Got code? Share and enjoy!

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Fall 2011 Student Hackathon Coding Coding is better when done together. Photo by hackNY.

Over at the Molecular Ecologist, Kim Gilbert announces a new initiative, the Molecular Ecologist code snippet repository. It’ll be a place to put bits of useful code that wouldn’t warrant their own publication as a package or program, but would still be helpful to other biologists:

Do you have a script you regularly run to convert between data formats? A quick and easy way to run a certain analysis? Making a common figure for a given type of data? If you’re willing to share your code, we’ll put it online for public access with credit to your name.

To find out how to submit your snippets, go read the whole thing.◼

The Molecular Ecologist: Making heatmaps in R

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Image by Arianne Albert via The Molecular Ecologist.

Over at the Molecular Ecologist, guest contributor Arianne Albert walks through how to make heatmap figures in R.

Heatmaps are incredibly useful for the visual display of microarray data or data from high-trhoughput sequencing studies such as microbiome analysis. Basically, they are false colour images where cells in the matrix with high relative values are coloured differently from those with low relative values. Heatmaps can range from very simple blocks of colour with lists along 2 sides, or they can include information about hierarchical clustering, and/or values of other covariates of interest. Fortunately, R provides lots of options for constructing and annotating heatmaps.

I’ve personally used heatmap graphics for visualizing population structure in a sample, or linkage disequilibrium along a stretch of genetic sequence, but I haven’t done anything very complex. Arianne’s examples use a data set that’s freely available on Dryad, and she includes a lot of step-by-step detail to build up complex figures—if you’re going to be visualizing some microarrary results or metagenomics data any time soon, you should read the whole thing, and probably bookmark it.◼

The Molecular Ecologist: Domesticated genes answer the call of the wild

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Soay sheep on Hirta, St Kilda, with Cleits Wild Soay sheep, in an assortment of colors. Photo by Commonorgarden.

This week at the Molecular Ecologist, I’m discussing a new study from the blog’s parent publication, Molecular Ecology, which traces the origins of gene variants in a wild population of Soay sheep … back to domestic sheep.

The Soay sheep haven’t been completely isolated from other breeds. In recent centuries, they shared the Saint Kilda islands with humans, who kept domesticated sheep—providing several hundred years of opportunity for what geneticists call “an admixture event,” and everyone else calls “sex,” between the Soay breed and those domesticated sheep.

To learn how the study’s authors pinpointed the origin of the domestic genes variants, and how those variants have fared in the wild sheep, go read the whole thing.◼