Uncommon Ground


Drift simulation and binomial simulation uploaded

I’ve added both an HTML and an R notebook version of the simple drift simulation I showed in class so that you can play with it on your own if you don’t want to bother with the snazzier online version. I’ve also added a simulation you can play with to convince yourself that there’s no directional tendency for allele frequencies using sampling from a binomial distribution. Both are linked to from the lecture detail page.

By the way, I tried the snazzy online version that wasn’t updating properly, and it worked this time. As you can see below, when I set the population size to 1000, the allele frequencies change, but not nearly as much as when the population size is only 100 (or 10).

My time as Vice Provost and Dean is coming to an end

The very small number of people who read what I write here probably all know the news in the headline, but it’s now official. Provost Anne D’Alleva sent an overly nice email about my departure as Vice Provost for Graduate Education and Dean of The Graduate School at the end of this academic year. The exact date when I step down will depend on when my successor wants to start, but I anticipate that my last day as VP and Dean will be either 30 June 2024 or 31 July 2024.

On the off chance that you’re interested in what the Provost had to say about my departure, here’s the text of the email she sent to faculty, staff, and graduate students yesterday. (I’m still blushing.)

Dear Faculty, Staff and Graduate Students,

With mixed emotions, I write to inform you that Kent Holsinger, our esteemed Vice Provost for Graduate Education and Dean of The Graduate School, will be stepping down from his position at the end of this academic year. Kent’s departure marks the end of a remarkable 12-year tenure in this position.

Kent has been an integral part of our university community for over 38 years, and his contributions to graduate education and unwavering commitment to supporting students have left an indelible mark on our institution. Throughout his time as Vice Provost and Dean Kent has displayed exceptional leadership, fostering an environment of academic excellence and inclusivity.

Under Kent’s guidance, our graduate programs have flourished, reflecting his passion for advancing the academic and professional pursuits of our graduate students. His tireless efforts have resulted in innovative programs that empower our students to thrive in their chosen fields. Kent has played an important role in the development of entrepreneurial graduate programs and has spearheaded efforts to bring new graduate programs like Data Science to UConn.

One of Kent’s defining characteristics is his genuine dedication to supporting students. He has worked tirelessly to create resources and initiatives that enhance the graduate student experience, ensuring that they have access to the tools and opportunities needed for success. Many students have benefited from his mentorship, guidance, and advocacy, and his impact will be felt for years to come.

We will be organizing a special event to celebrate Kent’s accomplishments and contributions at the end of the year. In the coming weeks I will share plans for forming a committee to conduct an internal search for Kent’s successor.

Please join me in expressing our deepest gratitude to Kent for his remarkable service as Vice Provost and Dean of the Graduate School.

I couldn’t help myself. I bought a new fountain pen.

Waldmann Limited Edition Tango Imagination fountain pen
Waldmann Limited Edition Tango Imagination fountain pen

I couldn’t help myself. I received an email from Fahrney’s last Saturday with an ad for the Waldmann Limited Edition Tango Imagination Fountain Pen in Dark Teal with an 18K nib. It was a bit pricey, but the photo was spectacular. I don’t usually care about limited editions, but this happens to be limited to 200 pieces. I succumbed and ordered it later that day. It arrived via UPS last Wednesday.

It is even more beautiful in person than in the catalog photographs. The photograph doesn’t show how light dances on the engraving, making the body shimmer. Its color seems to change depending on the background. As Kimberly describes in a review on The Pen Addict,1 the body of the pen is 925 sterling silver.2 She reviews a version with an aquamarine finish rather than the dark teal that I have. Like hers, mine wrote beautifully out of the box. Unlike hers, mine is a limited edition, and if you look very carefully on the cap band, you’ll find not only “Waldmann” and “Made in Germany”, but “174/200”, meaning that my pen is number 174 out of the limited edition of 200.

Cap band of my Waldmann showing 174/200.
Cap band of my Waldmann showing 174/200.

This is the first new fountain pen I’ve purchased in about 3 years. It’s so beautiful my initial thought was that I’d use it only for writing in my journal. But it writes so smoothly I’ve decided instead that I’m going to use it as my daily pen, but I am going to be very careful with it. Instead of putting it in a shirt or coat pocket when I leave for a meeting, I’ll carry it in a pen case that protects it from bumps or scratches. I’ve only had it a few days, but i can already tell that it’s going to be one of my favorites, along with my Namiki Falcon, my blue carbonesque Namiki Vanishing Point, and my Pelikan Souveran M400.3

  1. Yes, there are blogs about pens. There are people who are even more fanatic about fountain pens than I am. In fact, in the world of fountain pens, I would be seen as uninvolved – if anyone knew about me. I’ve never been to a pen show. I use primarily Aurora Black ink, with Brilliant Red Pelican for titles in my daily notebook, and Aurora Blue for signatures. Serious pen lovers not only have many more pens than I do, they have a large collection of inks that they’ve swabbed on tester cards to keep track of what they have in their collection.
  2. The 925 symbol is discreetly placed against the cap, which you can see in one of the photos on The Pen Addict.
  3. That’s right. Those are my favorites. I have at least a dozen more, including a couple of Pelikans, an S.T. DuPont, a Cross, a Parker, a Waterman or two, a Rotring (fountain pen and mechanical pencil), and several others.

Genetic structure and clonal diversity in Leymus chinensis

There’s a small chance you’ll remember that about six months ago I posted about a pre-print on which I am co-author. I’m pleased to report that the paper was published in the December issue of the American Journal of Botany. If you follow me on Twitter, you may have seen me retweet a couple of times about this already, but I thought I’d make a post here. It’s been a long time since I posted anything, and I hope to get back into the habit of writing something every week or two. Here’s the abstract and link in case you’re interested.



The distribution of genetic diversity on the landscape has critical ecological and evolutionary implications. This may be especially the case on a local scale for foundation plant species because they create and define ecological communities, contributing disproportionately to ecosystem function.


We examined the distribution of genetic diversity and clones, which we defined first as unique multilocus genotypes (MLG), and then by grouping similar MLGs into multilocus lineages. We used 186 markers from inter-simple sequence repeats (ISSR) across 358 ramets from 13 patches of the foundation grass Leymus chinensis. We examined the relationship between genetic and clonal diversities, their variation with patch size, and the effect of the number of markers used to evaluate genetic diversity and structure in this species.


Every ramet had a unique MLG. Almost all patches consisted of individuals belonging to a single multilocus lineages. We confirmed this with a clustering algorithm to group related genotypes. The predominance of a single lineage within each patch could be the result of the accumulation of somatic mutations, limited dispersal, some sexual reproduction with partners mainly restricted to the same patch, or a combination of all three.


We found strong genetic structure among patches of L. chinensis. Consistent with previous work on the species, the clustering of similar genotypes within patches suggests that clonal reproduction combined with somatic mutation, limited dispersal, and some degree of sexual reproduction among neighbors causes individuals within a patch to be more closely related than among patches.

doi: https://doi.org/10.1002/ajb2.1771

Sharing a new version of my genetic drift simulation

You may be aware that I wrote a series of applications in RShiny several years ago to illustrate some principles of population genetics. I just finished revising the genetic drift application. If you’ve used it in the past, you’ll know that it would get hung up when you tried to simulate a long time series or a lot of populations. After some digging around, I realized that the problem isn’t with running the simulation or with collecting the results. It’s with converting the results to a form that allows the simulation to unfold over time.

As a result, this version allows you to turn the animation off. Now you can run long time series with lots of populations (where “lots” equals “up to 10”). You won’t see the results played as a movie, but you’ll see them displayed very quickly. As you’ll see from the first link above, all of the source code is available on Github. If you find any of these applications useful, you’ll want to take a look at the Google Doc that Katie Lotterhos put together and announced on Twitter last January. It includes screenshots and links to applications written by CJ Battey, Graham Coop, and Chris Muir.