Uncommon Ground

Uncommon Ground

Author Archive: kent

Lecture notes in population genetics – final version from Spring 2017

I’ve finally had time to clean and post the final version of lecture notes from my graduate course in population genetics last spring. The individual lectures have been since I revised them for class, meaning that the last set of them was available in late April. You will find links to the individual lecture notes at http://darwin.eeb.uconn.edu/uncommon-ground/eeb348/notes/. If you’re interested in a particular topic in population genetics and I have a lecture that covers the topic, that’s probably where you’ll want to go.

If you want a single-volume reference to population genetics (including some old notes that I no longer maintain), you’ll find a PDF (5.89MB, 322 pages) at Figshare (doi: 10.6084/m9.figshare.100687.v2). If you want to print the PDF, I recommend that you print it on a double-sided printer. You can then put the pages in a binder and flip through them as if it were a bound book.

If you use LaTeX (and you’re a glutton for punishment), the LaTeX source and EPS files (for figures) is available in a Github repository (https://kholsinger.github.io/Lecture-Notes-in-Population-Genetics/).

These notes are released under a Creative Commons Attribution-ShareAlike license (http://creativecommons.org/licenses/by-sa/4.0/). I hope you find them useful. If you find errors in them, please let me know.

August 7, 2017 Population genetics 0 Read more >

Doctoral Dissertation Improvement Grants – RIP

The National Science Foundation released this Dear Colleague letter yesterday:

June 6, 2017

Dear Colleague:

With this Dear Colleague Letter, the Directorate for Biological Sciences (BIO) is notifying members of the research communities . served by the Division of Integrative Organismal Systems (IOS) and the Division of Environmental Biology (DEB) to changes to the Doctoral Dissertation Improvement Grant (DDIG) Program.

Following a process of internal review and discussion regarding available resources, both the DEB and IOS Divisions will no longer accept DDIG proposals. This difficult decision was necessitated because of increasing workload and changes in Division priorities. This change is consistent with decisions made by other programs in BIO, which have not participated in the DDIG competition for more than a decade. This decision does not affect DDIGs that are already awarded.

We recognize that the independent research that was encouraged by the DDIGs has been an important aspect of training the next generation of scientists; we hope that this culture will continue. BIO continues to support graduate student participation in PI-led research across the entire spectrum of topics supported by its programs. Proposals for conferences are encouraged to include support for graduate and postdoctoral trainee travel and attendance. Further, NSF continues to support graduate research through the Graduate Research Fellowship Program (GRFP) and the NSF Research Traineeship Program (NRT).

Please see the Frequently Asked Questions (FAQs) (NSF 17-095) related to this DCL for more information.

If you have any questions pertaining to graduate student support under existing awards or future grant proposals, please contact the cognizant program director in the relevant Division.

James L. Olds
Assistant Director
Directorate for Biological Sciences

I hesitate to second-guess my colleagues at NSF. I know many of the program officers in the Biological Sciences Directorate and especially those in the Division of Environmental Biology. I know that they reached this decision because they believe that NSF can more effectively support research in life sciences by redirecting resources currently used to support Doctoral Dissertation Improvement Grants to other purposes, and I am confident their evaluation included an assessment of the impact on training of the next generation of life scientists. I also agree with many comments I’ve seen that DDIGs provide a great return on investment, at least in terms of the quality and quantity of research (and training) done with DDIG support. But I also know from conversations with current and former NSF officials that the there are large costs in time and money associated with reviewing DDIGs. I don’t have access to the data I would need to make a fair evaluation of the costs and benefits of the program, so I have no choice but to trust the judgment of my NSF colleagues.

Still, it saddens me to see this program go away. It has been an important part of PhD training in environmental biology for decades.

June 7, 2017 Science funding 0 Read more >

Discussing privilege in environmental conservation

I last taught my graduate course in conservation biology in Fall 2015. Holly Brown, my teaching assistant in the course, had to fill in for me a couple of times because of commitments that took me out of town. She designed a creative and powerful exercise for one of the times I was out of town. In written evaluations of the course, almost every student reported that it was eye opening and, quite possibly, the most useful exercise in the course. What was this creative and powerful exercise? Holly’s version of a privilege walk. If you don’t know what that is or you want to know how she used a privilege walk in the context of conservation or both, it’s your lucky day. A paper describing the exercise recently appeared in Conservation Biology. Here’s the citation and a link.

Brown, H.M., A. Kamath, and M. Rubega.  2017.  Facilitating discussions about privilege among future conservation practitioners. Conservation Biology 31:727-730.  doi: 10.1111/cobi.12810

May 19, 2017 Conservation biology 0 Read more >

Causes of genetic differentiation in Protea repens

American Journal of Botany Volume 104, Number 5. May 2017.

Protea repens is the most widespread member of the genus. It was one of the focal species in our recently completed Dimensions of Biodiversity project. Part of the project involved genotyping-by-sequencing analyses of 663 individuals from 19 populations spanning most of the geographical range of the species. We summarize results of those analyses in a paper that just appeared in advance of the May issue (cover photo featured above) of the American Journal of Botany. Here’s the abstract. You’ll find the citation and a link at the bottom.

PREMISE OF THE STUDY: The Cape Floristic Region (CFR) of South Africa is renowned for its botanical diversity, but the evolutionary origins of this diversity remain controversial. Both neutral and adaptive processes have been implicated in driving diversification, but population-level studies of plants in the CFR are rare. Here, we investigate the limits to gene flow and potential environmental drivers of selection in Protea repens L. (Proteaceae L.), a widespread CFR species.
METHODS: We sampled 19 populations across the range of P. repens and used genotyping by sequencing to identify 2066 polymorphic loci in 663 individuals. We used a Bayesian FST outlier analysis to identify single-nucleotide polymorphisms (SNPs) marking genomic regions that may be under selection; we used those SNPs to identify potential drivers of selection and excluded them from analyses of gene flow and genetic structure.
RESULTS: A pattern of isolation by distance suggested limited gene flow between nearby populations. The populations of P. repens fell naturally into two or three groupings, which corresponded to an east-west split. Differences in rainfall seasonality contributed to diversification in highly divergent loci, as do barriers to gene flow that have been identified in other species.
CONCLUSIONS: The strong pattern of isolation by distance is in contrast to the findings in the only other widespread species in the CFR that has been similarly studied, while the effects of rainfall seasonality are consistent with well-known patterns. Assessing the generality of these results will require investigations of other CFR species.

Prunier, R., M. Akman, C.T. Kremer, N. Aitken, A. Chuah, J. Borevitz, and K. E. Holsinger. Isolation by distance and isolation by environment contribute to population differentiation in Protea repens (Proteaceae L.), a widespread South African species. American Journal of Botany doi: 10.3732/ajb.1600232 

May 17, 2017 Botany, Population genetics 0 Read more >

This is cool (if you’re a typography nerd)

A portion of the fontmap of Google Fonts generated by a designer from Ideo (http://fontmap.ideo.com)

Kevin Ho, software design lead at Ideo, created a fascinating tool to explore the 750+ typefaces available on Google Fonts. I’m not a designer,1 and I use only a small number of fonts,2 so I don’t need this tool, but I’ve been fascinated by printing and typography for several decades. I can’t stop playing with this fontmap, and I had to share the fun. There’s a nice article at Fast Company describing the project and how Ho used two open source algorithms to create it. Maybe future versions of Word will provide a fontmap to explore choices instead of vertical lists.
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May 15, 2017 Personal 0 Read more >

2017 Graduate Commencement Ceremonies @UConn

The University of Connecticut celebrated its 138th Commencement exercises last weekend.1 The Graduate School now confers so many degrees that we have two ceremonies, a ceremony for recipients of master’s degrees on Saturday afternoon and a ceremony for recipients of doctoral degrees on Monday evening. Stuart Rothenburg, who received his

Stuart Rothenburg, who received his PhD in Political Science from UConn, addressed the graduating class at the master’s ceremony. If you’d like to see his remarks, follow the link below, click on “Graduate School Ceremony: Masters Candidates, May 6, 2017”, and then click on “Commencement Address” at the left.

I addressed the graduating class at the doctoral ceremony on behalf of Elizabeth Jockusch, this year’s winner of the Edward C. Marth Award for Mentorship, and Takiyah Harper-Shipman was our student speaker. If you’d like to see my remarks, follow the link below, click on “Graduate School Ceremony: Doctoral Candidates, May 8, 2017”,  and then click on “Welcome Remarks” at the left. After a brief welcome from Interim Provost Jeremy Teitelbaum, you’ll see me. If you’d like to see Takiyah’s remarks, click on “Commencement Address” instead. If for some reason you’d like to read my remarks, keep scrolling down (or click through if you’re on the home page).

University of Connecticut Commencement Ceremonies 2017 (from Total Webcasting)

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May 10, 2017 Academics, Public remarks, UConn 0 Read more >

Happy Birthday Sir David Attenborough

Wildscreen’s photograph of David Attenborough at ARKive’s launch in Bristol, England © May 2003 You are free: to share – to copy, distribute and transmit the work to remix – to adapt the work

Today is Sir David Attenborough’s 91st birthday. If you follow me on Twitter or read this blog, you don’t need me to tell you who he is, but just as a reminder, here is some of his biography from IMDb:

Born 8 May 1926, the younger brother of actor Lord Richard Attenborough. He never expressed a wish to act and, instead, studied Natural Sciences at Cambridge University, graduating in 1947, the year he began his two years National Service in the Royal Navy. In 1952, he joined BBC Television at Alexandra Palace and, in 1954, began his famous “Zoo Quest” series. When not “Zoo Questing”, he presented political broadcasts, archaeological quizzes, short stories, gardening and religious programmes. 1964 saw the start of BBC2, Britain’s third TV channel, with Michael Peacock as its Controller. A year later, Peacock was promoted to BBC1 and Attenborough became Controller of BBC2. As such, he was responsible for the introduction of colour television into Britain, and also for bringing Monty Python’s Flying Circus (1969) to the world. In 1969, he was appointed Director of Programmes with editorial responsibility for both the BBC’s television networks. Eight years behind a desk was too much for him, and he resigned in 1973 to return to programme making. First came “Eastwards with Attenborough”, a natural history series set in South East Asia, then “The Tribal Eye”, examining tribal art. In 1979, he wrote and presented all 13 parts of Life on Earth (1979) (then the most ambitious series ever produced by the BBC Natural History Unit). This became a trilogy, with The Living Planet (1984) and The Trials of Life (1990).

I knew about Life on Earth, The Living Planet, and The Trials of Life (obviously). I didn’t know that he’d introduced color TV to Britain and that he was responsible for “brining Monty Python’s Flying Circus to the world. What an amazing set of accomplishments. His contributions are simply astounding.

More at Wikipedia and Biography

May 8, 2017 Biology 0 Read more >

Science, doubt, and the need for action

From Merchants of Doubt, by Naomi Oreskes and Erik M. Conway:

All scientific work is incomplete—whether it be observational or experimental. All scientific work is liable to be upset or modified by advancing knowledge. That does not confer upon us a freedom to ignore the knowledge we already have, to postpone action that it appears to demand at a given time. Who knows, asks Robert Browning, but the world may end tonight? True, but on available evidence most of us make ready to commute on the 8:30 next day.

…

“A demand for scientific proof is always a formula for inaction and delay, and usually the first reaction of the guilty. The proper basis for such decisions is, of course, quite simply that which is reasonable in the circumstances.” Or as Bill Nierenberg put it in a candid moment, “You just know in your heart that you can’t throw 25 million tons a year of sulfates into the Northeast and not expect some … consequences.”

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May 5, 2017 Environment 0 Read more >

A thought on science and public policy

From Merchants of Doubt, by Naomi Oreskes and Erik M. Conway:

if science is about studying the world as it actually is—rather than as we wish it to be—then science will always have the potential to unsettle the status quo. As an independent source of authority and knowledge, science has always had the capacity to challenge ruling powers’ ability to control people by controlling their beliefs. Indeed, it has the power to challenge anyone who wishes to preserve, protect, or defend the status quo.

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May 1, 2017 Environment 0 Read more >