Uncommon Ground – Academics, biodiversity, genetics, & evolution

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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).

kent September 26, 2023 Uncategorized 0 Read more >

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.

kent September 13, 2023 Uncategorized 0 Read more >

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

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

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. ↩
The 925 symbol is discreetly placed against the cap, which you can see in one of the photos on The Pen Addict. ↩
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. ↩

kent August 8, 2022 Uncategorized 0 Read more >

Apple Care and Apple service are better than I thought

Apple service is better than I realized. I bought a new iPad Pro and Magic Keyboard last December, and I am a heavy user. I don’t use my Apple Pencil a lot, but my iPad is constantly with me on working days and on airplanes and on weekends when I catch up on my reading. And I use the Magic Keyboard a lot. In fact, I’m writing this entry (in Ulysses) on my iPad using my Magic Keyboard while waiting in a car dealership to have my engine battery replaced.

About a month and a half ago I lost one of the key caps. Since it’s a key I don’t use too often (the -/_ key) I didn’t think much about it. Then a couple of weeks ago two more key caps fell off and I noticed that a fourth was loose. Now I need a new keyboard.

So I went to a local Apple Store on Sunday expecting to buy a new Magic Keyboard. When I checked in the agent asked “Do you have Apple Care on the iPad? Did you buy the keyboard at the same time?” “Yes.” “Well, you may be covered by Apple Care. Go to the Genius Bar, and I’ll send a technician your way.” The technician arrived a few minutes later, confirmed my problem, checked on a few things, and reported that he’s ordering a replacement keyboard for me. It should arrive today or tomorrow.

Good service is less common than it should be. I was impressed and pleased. Your mileage may vary, but I’m glad that I bought Apple Care last December.

kent July 18, 2022 Personal 0 Read more >

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.

Abstract

Premise

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.

Methods

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.

Results

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.

Conclusions

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

kent January 4, 2022 Uncategorized 0 Read more >

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.

kent September 27, 2021 Population genetics, Uncategorized 0 Read more >

Genetic structure and clonal diversity in an important Chinese grass

Since you’re reading this blog, you must know that I don’t have a lot of time for research these days. My duties as Vice Provost for Graduate Education and Dean of The Graduate School at UConn take up most of my time. I do manage to contribute to some research, so long as other people do the real work and I contribute some ideas or some statistical analyses. Here’s another example of that.

Last fall I was asked about the old C++ program Hickory that I had written to facilitate analysis of Wright’s F-statistics with dominant markers. It was never terribly widely used, and it was difficult to maintain. I gave up about 10 years ago. In the meantime, I realized that there’s an easy way to rewrite Hickory using Stan. After being contacted, I finally bit the bullet and did the rewrite in a combination of Stan and R. I even mentioned the R/Stan implementation last September.

Yesterday, we posted a pre-print on bioRxiv that uses the new version of Hickory as one of a variety of analytical methods that provide some insight into the genetic structure of Leymus chinensis. Here’s the abstract and a link.

Genetic structure in patchy populations of a candidate foundation plant: a case study of Leymus chinensis (Poaceae) using genetic and clonal diversity

Jian Guo, Christina L. Richards, Kent E. Holsinger, Gordon A. Fox, Zhuo Zhang, Chan Zhou

doi: https://doi.org/10.1101/2021.06.12.448174

PREMISE 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 since they create and define ecological communities, contributing disproportionately to ecosystem function.

METHODS We examined the distribution of genetic diversity and clones, which we defined first as unique multi-locus genotypes (MLG), and then by grouping similar MLGs into multi-locus lineages (MLL). 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.

RESULTS Every ramet had a unique MLG. Almost all patches consisted of individuals belonging to a single MLL. 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.

CONCLUSIONS 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.

kent June 16, 2021 Botany, Population genetics 0 Read more >

The link between traits and performance in Protea

If you’re reading this, you probably know enough about me to know that my students and I have been working on Protea for the last 10-15 years. Today I am pleased to report that the most recent work, from Kristen Nolting’s PhD dissertation has appeared in Annals of Botany. The advance publication version appeared nearly a year ago, but the paper is officially out in a special issue focusing on intraspecific trait variation in plants. Here’s the abstract and a link.

Intraspecific trait variation influences physiological performance and fitness in the South Africa shrub genus Protea (Proteaceae)
Kristen M Nolting, Rachel Prunier, Guy F Midgley, Kent E Holsinger
Background and Aims
Global plant trait datasets commonly identify trait relationships that are interpreted to reflect fundamental trade-offs associated with plant strategies, but often these trait relationships are not identified when evaluating them at smaller taxonomic and spatial scales. In this study we evaluate trait relationships measured on individual plants for five widespread Protea species in South Africa to determine whether broad-scale patterns of structural trait (e.g. leaf area) and physiological trait (e.g. photosynthetic rates) relationships can be detected within natural populations, and if these traits are themselves related to plant fitness.
Methods
We evaluated the variance structure (i.e. the proportional intraspecific trait variation relative to among-species variation) for nine structural traits and six physiological traits measured in wild populations. We used a multivariate path model to evaluate the relationships between structural traits and physiological traits, and the relationship between these traits and plant size and reproductive effort.
Key Results
While intraspecific trait variation is relatively low for structural traits, it accounts for between 50 and 100 % of the variation in physiological traits. Furthermore, we identified few trait associations between any one structural trait and physiological trait, but multivariate regressions revealed clear associations between combinations of structural traits and physiological performance (R² = 0.37–0.64), and almost all traits had detectable associations with plant fitness.
Conclusions
Intraspecific variation in structural traits leads to predictable differences in individual-level physiological performance in a multivariate framework, even though the relationship of any particular structural trait to physiological performance may be weak or undetectable. Furthermore, intraspecific variation in both structural and physiological traits leads to differences in plant size and fitness. These results demonstrate the importance of considering measurements of multivariate phenotypes on individual plants when evaluating trait relationships and how trait variation influences predictions of ecological and evolutionary outcomes.
Annals of Botany 127:519–531; 2021 https://doi.org/10.1093/aob/mcaa060

kent April 20, 2021 Botany, EcologyProtea 0 Read more >

UConn Reads 2021 – Truth, Democracy, & Climate Change (the video)

Two weeks ago on the afternoon of March 25th, the UConn Humanities Institute hosted a panel discussion on Truth, Democracy, & Climate Change. Tom Bontly (Philosophy) moderated the panel, which included two distinguished philosophers, Elizabeth Anderson (University of Michigan) and Lee McIntyre (Boston University). For some reason, Tom also asked me to participate. After introductions and brief remarks, we had a lively discussion about why some people do not accept the evidence for human-caused climate change. Elizabeth mentioned, for example, Dan Kahan‘s idea that there are “conflict entrepreneurs” who purposely promote disinformation, not because it necessarily promotes the cause they appear to be supporting, but because they profit from the conflict in other ways. If you couldn’t join us on the 25th and you’re interested in learning more, you’re in luck. Like nearly every other seminar, meeting, or and panel in the last year, this one was held virtually. It was also recorded, and the edited video (with captions) is now available on YouTube.

kent April 5, 2021 Climate change, Science policy 0 Read more >

A Call to Action: Marshaling Science for Society – AIBS President and Past-Presidents

Greg Anderson, Gene Likens, and I are Past Presidents of the American Institute of Biological Sciences, an organization representing nearly 120 scientific societies, museums, botanical gardens, and universities (including the Department of Ecology & Evolutionary Biology at UConn). We joined Charles Fenster, current President of AIBS, and 20 of our fellow Past Presidents in writing A call to action: marshaling science for society, which appeared in BioScience today. Here are the first and the concluding paragraphs of what we wrote:

As the current and past presidents of the American Institute of Biological Sciences (AIBS), we find the assault by politicians and special interest groups on the use of scientific knowledge to guide public policy decision-making alarming and dangerous. The marginalization of scientific information in decision-making has significant negative effects on our public health and safety, our environmental sustainability, and our general well-being. We need not look further than the disruption and deaths that have resulted in many countries, including the United States, from failing to use scientific evidence in making decisions on how to control the COVID-19 pandemic.

…

The progress of science over the centuries has led to our deep understanding of natural phenomena. We must find ways to benefit from that understanding as we move into the future. Let us join together to insist on acting logically and rationally in a world so plagued by self-centered short-term goals and the false information that they all too often generate.

If you’d prefer a podcast version, here’s the link: http://bioscience-talks.aibs.org/science-leaders-issue-clarion-call-for-evidence-based-policy. Twenty-four organizations have endorsed the statement. You can see them here: https://aibs.wufoo.com/reports/aibs-past-and-current-presidents-viewpoint/.

I hope you’ll take time to read the call or listen to the podcast. If you belong to a society that has not yet endorsed the viewpoint, I encourage you to ask leaders of your society to sign on.

kent December 8, 2020 Science policy 0 Read more >