Alvin, Simon and Theodosius Dobzhansky*

You know the type. Big, brown eyes. Cute, little nose. Long, striped tail.

Tamias amoenus canicaudus, Steptoe Butte, WA, photo: Noah M Reid

Tamias amoenus canicaudus, Steptoe Butte, WA, photo: Noah M Reid

Chipmunks are adorable and one of the more easily viewed yet still kind of exotic North American mammals (in my opinion). I worked on red-tailed chipmunks for my Master’s degree at the University of Idaho with Jack Sullivan. Sullivan (et al.) just published a review of all the chipmunk research that’s taken place in his lab over the past 10 years or so. Central to the review is the concept of divergence with gene flow (DGF), but let’s start with some back story.

Figure 1: This is what a rapid radiation looks like. These are the ranges for the 23 western chipmunks.

Figure 1: This is what a rapid radiation looks like. These are the ranges for 21 of the western chipmunks.

A chipmunk is a type of squirrel. There is one species of chipmunk in Asia (Tamias sibiricus), one in eastern North America (T. striatus) and 23 (!!) in western North America – the western chipmunks represent a rapid radiation (Figure 1). All 23 species look somewhere between similar and identical to one another with the exception of a single morphological character – their bacula (or os penis or penis bone). The baculum is the way systematists have been reliably identifying chipmunks for many years – there is substantial differentiation between species but little  within a species (see Figure 2). Because bacula were so good at defining species and because of the – er – nature of the bone, it was long thought that these variations represented a “lock and key” mechanism of reproductive isolation. In other words, hybridization between species was thought to be rare since only the right combination of lock and key would unlock a baby.

Figure 2. Phylogenetic relationship and bacular morphology for western chipmunks (figure from Sullivan Lab)

And that’s where the story gets interesting. Hybridization within the western chipmunks appears to be a relatively frequent activity. In fact, 16% of the 1871 chipmunks with genetic data from the Sullivan lab have introgressed DNA. Mitochondrial DNA is a particularly useful marker for detecting hybridization in this system: since it is an organelle we all inherit from our mothers, even a single hybridization event can have major consequences. The yellow-pine chipmunk is an excellent example of this.

Yellow-pine chipmunks (Tamias amoenus) are widespread and contain many subspecies. While doing a comparative phylogeography study, the Sullivan lab discovered that one particular subspecies, T. a. canicaudus, had a mitochondrial genome that was most closely related to the red-tailed chipmunk (T. ruficaudus), instead of the other yellow-pine subspecies. Additional data show that the T. a. canicaudus nuclear genome is in fact most similar to other yellow-pines – it’s just that the mitochondria is of red-tailed origin. What’s more is that at another contact zone between yellow-pines and red-taileds is another instance of mitochondrial funny business: again, red-tailed mitochondria are found in yellow-pine chipmunks. Big deal, right? YES! Because red-tailed and yellow-pine chipmunks are relatively distantly related (see Fig. 2) – the fact that they have exchanged any genetic material is contradictory to some speciation models that require total isolation for species to form.

This is just one example of how leaky species boundaries can be in western chipmunks – so lets get back to divergence with gene flow. DGF says that some portions of the genome can be exchanged at some points in the divergence process while other portions cannot. Given time and very low levels of hybridization, the areas of the genome that cannot be mixed (or are “species” specific) get larger. Eventually, only very small portions of the genome can be exchanged and then finally – no exchange can occur. It has been posited that ANY amount of hybridization would erase any isolation that had accumulated and return the hybridizing populations back to a single homogeneous group. Chipmunks demonstrate that may not be the case: apparently some amount of gene flow is acceptable during the speciation process. (There are several more equally compelling examples in the paper – available here.)

I wish you all should come upon a chipmunk sometime soon. And I hope that when it happens,  you wonder about its genome. But until then, my final wish is that Star Wars Chipmunk makes your day just a little better (with more photos here):

*To be honest, Theodosius Dobzhansky doesn’t have much to do with this post (other than general evolutionary biology). I guess Alvin and Simon don’t either (other than their general chipmunk-ness)…

**Can’t get enough chipmunk? Heredity podcast also covered the paper.


Sullivan J., Demboski J.R., Bell K.C., Hird S., Sarver B., Reid N. & Good J.M. (2014). Divergence with gene flow within the recent chipmunk radiation (Tamias), Heredity, DOI:

2 comments on “Alvin, Simon and Theodosius Dobzhansky*

  1. […] to pick. Chipmunk hybrids more common than penis bones suggest, as Sarah Hird […]

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