What is going on with invasive knapweed? OR How I spent my PhD

Over the course of my PhD work (published here, and most recently here), I have found evidence for evolved differences in phenotype (in other words, in their morphology, development, phenology, stress responses) between native and invasive populations of diffuse knapweed. Why is that interesting? Well the invasive populations didn’t even exist until barely 100 years ago. And something about them has let them succeed and spread over vast areas of their new habitat. Perhaps what has made them so successful can be revealed by comparing the invasive diffuse knapweed populations to their closest relatives, the native diffuse knapweed populations.

Knapweed in the greenhouse, 2009.

How have we never talked about knapweed before???

Surely I’m not the only one that thinks of their study organism in terms of fictional criminal geniuses?

Wow, sorry folks, I’ve been slacking, and that whole PhD thing is a sorry excuse! Let me tell you a little natural history about a plant called diffuse knapweed (Centaurea diffusa), the  Dr. Moriarty to my Sherlock Holmes.

Nuts and Bolts: Examine invasiveness across phylogenetic tree

I had a nail. @rOpenSci had the hammer. Photo by Zorro.

The helpful folks over at rOpenSci have come up with exactly the tool I needed, exactly when I needed it.

Nuts and Bolts: Squishing columns together to get rid of NAs in R

Zipper picture from Wikimedia Commons, by Rabensteiner – Bearbeitet von Rainer Z

I found my self in a bit of a quandry. I had a data frame which contained many columns that needed to be squished together – each contained a few values, but mostly NAs, and none of the values were overlapping. They represented the same variable, but broken apart across several columns. I needed to condense several columns into one.

Nuts and Bolts: Extracting global climate and soil data in R

There are a few publicly available data sets that are useful for looking at the abiotic environments of specific locations.

A public dataset of global climate variables. From WorldClim.org.

Nuts and Bolts: Finding minima around a peak in R

So finding minima is apparently a really complex problem. But all I need is a consistent, non-subjective way to determine cut-offs around a peak. This is what I came up with, perhaps useful to you?

Nuts and Bolts: Modern maps of Eurasia in R

Maps are quite useful things, if you want to convey information about where in the world something happens. But, turns out, they are harder to make than I naively thought! But not that hard.

Introducing: Nuts and bolts

Nuts…

So, long time, no talk, gentle reader. That’s because I’ve been writing a paper (my first first-authored paper, if you must know) and I feel really guilty about extraneous writing activities, like somehow I am cheating on my paper. How can I justify reading up on a tasty tuber or invasive insect and crafting its story and biology into an intriguing knowledge nugget, when mountains of data await re-analysis for the billionth time, and co-authors deserve satisfaction? How indeed?

You wish you had germination this good!

Here’s a rough graph of germination rate from field collected seed of the invasive weed I work on, Centaurea diffusa (seen here). Each point represents a different maternal plant from 57 different populations, with native individuals in red and invasive individuals in black. I have collections that were up to 8 years old when I ran this trial, and no decrease in germination rate! That’s just silly! I’m sure it doesn’t hurt with the being invasive and all.