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Back from South Africa - #dimensionsZA

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Protea canaliculata at Teeberg in the Swartberg Pass, South Africa
Photograph by Kent Holsinger
Click on the image for a high-resolution image in a new window.

I left Capetown about 8:00pm last Thursday (2:00pm EDT), and I arrived back in Hartford just before 7:00pm EDT on Friday (1:00am Saturday in Capetown, 29 hours after I left). The flight was long, but uneventful.

My personal bag and, more importantly, the duffle with DNA samples arrived with me. The trip was a great success.

The focus of this trip was to collect samples in a hybrid zone between Protea punctata and Protea venusta at Blesberg and to collect additional samples of both species in areas of Swartberg Pass where they are not known to be hybridizing.

Nora will use the samples to unravel the dynamics of this hybrid zone. She left dataloggers in place at Blesberg to record temperature and humidity for the next year. She'll use the results from analysis of RAD SNPs (more on that in a moment) to develop a hybrid index, look at performance of individuals along the steep environmental gradient, and relate individual performance to traits. In addition, she collected seed for half-sib families which she'll use for paternity analysis to determine whether there are asymmetries in gene exchange and to identify the causes of any asymmetry she detects.

The hybrid zone is also of great interest for the Dimensions of Biodiversity project. Justin will use RAD sequencing to identify a large number of polymorphic SNPs. We'll use those SNPs as markers in a genome-wide association study to dissect the genetic basis of traits that distinguish these two very different species.

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Protea venusta at Blesberg, ca. 20km east of Klaarstoom, South Africa
Photograph by Kent Holsinger
Click on the image for a high-resolution image in a new window.

Nora and Jane did remarkable work in getting all of the samples. Notice I said "Nora and Jane did remarkable work." I bagged out on a lot of it. I made it down the slope at Blesberg on the first day of work there. That's a Protea venusta in the foreground about 2/3 of the way to the bottom. What the photograph doesn't show is that the only way to where we were when I took it was down the cliffs in the background. We were about 200m below the top when I took the photo. The other thing the photo doesn't show is that it had rained heavily the day before so that the rocks and restios were slick.

On the first day of work at Blesberg, I know that I slowed things down, because I'm not as sure on my feet as Nora and Jane. On the second day, I started down again and was making progress slowly. But as I was clambering down a particularly steep pitch about 150m from the top my legs started to give out. It wasn't just that I was moving slowly. I was afraid that if I descended any further, I wasn't going to make it back to the top. I asked Nora and Jane to go on without me. I climbed back to the top by myself -- slowly -- and waited for them to return.

For the next two days I didn't even try to make the descent and help. I collected some samples of Protea montana and looked for more than the single individual of Protea pruinosa -- without success. But Nora and Jane made the trip quicker every day, even though the conditions got worse.

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Nora (on the left) and Jane (on the right) heading down from the top of Blesberg on one of those days where I wimped out and stayed on top.
Photograph by Kent Holsinger
Click on the image for a high-resolution image in a new window.

At least it didn't snow while we -- they -- were working on Blesberg. A few days later we were working in Swartberg Pass. I made the (short) steep hike to Waboomsberg without a hitch. It was cold and windy, but the trail was dry. We quickly found the 20 individuals of Protea venusta we went for and returned to the pass. Then I even managed to remember where the Protea venusta population in the pass was better than Jane. I was pretty proud of myself about that.

The next day, we were planning a longer, 14km hike to Oliewensberg (7km each way), but we passed a policeman on our way up to the pass, and when we arrived at Teeberg, we decided to turn around. The road was covered with ice and snow. I'm sure our 4x4 would have made it, but we were 200m or so below the summit, and the hiking conditions would have been even worse.

We left Prince Albert the next morning making contingency plans, since we didn't think the snow would have melted and we didn't expect to be able to collect samples. To our surprise, the drive to the summit was pretty easy, so we started up the path. At first, the going wasn't bad, occasional patches of snow, but the trail was mostly bare, although it was a bit wet.

Once again it became clear that I was going to slow Nora and Jane down, but since we had plenty of time, and I was only slowing them down a little, we kept going. At about kilometer 3, though, things changed. The going got very steep, which would have been fine had the trail been clear. Unfortunately, it was covered in 10-15cm of heavy, wet snow. I was climbing through it -- very, very slowly. Nora and Jane waited for me at the top of an intermediate summit, and just before I got there, I looked at my watch. We'd come about 3.5km in an hour, and we had another 3.5km to go -- under worse conditions. This time I could have made it, but I was moving so slowly because of my unsteadiness, it would have taken us another couple of hours to get to where we needed to sample. And once I arrived, I wouldn't have been able to help. I told them to go on without me, and I went back to the summit and waited in the car.

In the end, Nora and Jane got a lot of really good samples. We even picked up several taxa for the trait-environment analysis in Dimensions that we hadn't sampled before. So it was a very successful trip. At the same time, I began to wonder about my future in South Africa during the flight home.

Nora needs someone dependable, i.e. someone other than me, to help her when she goes back next year. We've collected samples and trait data from all of the taxa it's reasonable to imagine we can get for our trait-environment analyses. Jane doesn't need me as a field assistant for her polymorphism work. I can't think of a good reason that anyone should spend good money to get me to South Africa next year.

I don't like thinking this, but I have to wonder whether 2013 may have been my swan song.

Looking forward

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In April, I gave the banquet address at the Centennial Celebration of the California Botanical Society. Tomorrow I'll share a brief report on my time in South Africa. Until then you're welcome to watch this presentation -- if you have 40 minutes to waste.


Off to Africa - #dimensionsZA

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I leave from Bradley International for Capetown a little after 4:00pm this afternoon. My student, Nora, will be traveling with me, and we will meet Jane, my former post-doc,1 in Heathrow some time on Monday.2

We'll spend a few days in Capetown checking on things in the garden, meeting with collaborators, and taking care of a few last-minute logistics. On Friday, we'll exchange our rental car for a 4x4 and head off for El Yolo One, not too far from Klaarstroom. We'll be there until the following Friday, when we'll move to Acacia Cottage in Prince Albert. We'll return to Capetown on the following Wednesday, and I'll leave for Connecticut the following day. Nora and Jane will stay for another week to do some work in the garden.3

My Internet access will be limited (or non-existent), except while I'm in Capetown. I may make a post or two after we arrive and one when we get back to Capetown, but don't be surprised if you don't hear anything from me for the intervening two weeks. If for some reason you just can't live without updates,4 you can follow me on Twitter (@keholsinger) or search on the #dimensionsZA hashtag. I may be able to check in using my iPhone a bit more often.5

Photos from Dimensions 2012

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Protea rubripilosaFinally, six months after returning from South Africa, I am starting to process the photos I took while I was there. It will take me awhile to finish all of them. I've only posted ones from the first two days of fieldwork. That leaves about 25 days of photos to go. But if you're interested in seeing them, I'll be putting them all on Flickr. Just head over there for the South Africa 2012 collection. More sets will be added over the next week or two.1

APPS goes live!

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I am pleased to be part of a new open-access journal published by the Botanical Society of America. As Theresa Culley says in the lead editorial from Volume 1, Number 1:

Authors and readers can expect the same high level of scientific and editorial expertise in APPS as they have consistently seen in the American Journal of Botany, which celebrates 100 years of publication in 2014. Like the American Journal of Botany, APPS is a publication of the Botanical Society of America, a not-for-profit membership society that is driven by the mission of promoting botany. APPS will help further that mission by fostering communication within the botanical community, and by encouraging the forward movement of the plant sciences through the sharing of newly developed tools and protocols. For example, this issue includes articles by Samarakoon et al. (2013) featuring a new method for PCR amplification of recalcitrant DNA, a paper by Morawetz (2013) that presents a technique to effectively clear plant tissue for subsequent examination, and an article by Roschanski et al. (2013) that introduces a protocol for the annotation of transcriptome sequence data and the identification of candidate genes. We anticipate the research in this new journal to have great influence over the current and future direction of the field.
I'm especially pleased to be part of this journal not only because it is open access, but also because it involves two of my favorite organizations, the Botanical Society of America and BioOne. Please head over to the APPS site and check it out. And while you're there, please check out some of the other great journals from not-for-profit publishers for which BioOne provides on-line access.

In case you were wondering

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What happens to branches as a tree grows.

Artist Giuseppe Penone carefully removes the rings of growth to reveal the 'sapling within'. By carving out the inside of a tree trunk and leaving the knots in place, they eventually emerge as tiny limbs.


Hat tip: Jeannette Whitton

Trees

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Hermann Hesse

Hermann Hesse (Photo credit: Wikipedia)

Maria Popova (@brainpicker) points us to a marvelous passage from Herman Hesse's Bäume: Betrachtungen und Gedichte (Trees: Reflections and Poems). Here's a bit of the passage. Head over to Brain Pickings for the rest.

Trees are sanctuaries. Whoever knows how to speak to them, whoever knows how to listen to them, can learn the truth. They do not preach learning and precepts, they preach, undeterred by particulars, the ancient law of life.
I am still learning to speak to trees and to listen to them. I have not learned the truth.

Developmental plasticity in Protea

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Jane and I have been working on this paper for a long time, and I'm delighted that it's finally appeared. I'm also delighted that it's available freely through PLoS One (http://dx.plos.org/10.1371/journal.pone.0052035).

That's a figure illustrating the times at which we made comparisons of leaf traits: (1) leaves in the same developmental cohort and in summer or winter of the same year and (2) leaves in different developmental cohorts during the same season of the year. Click on the image for a full-size pop-up. Here's the title and abstract:

Developmental Plasticity in Protea as an Evolutionary Response to Environmental Clines in the Cape Floristic Region

Jane E. Carlson¤, Kent E. Holsinger*

Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, United States of America

Abstract Top

Local adaptation along steep environmental gradients likely contributes to plant diversity in the Cape Region of South Africa, yet existing analyses of trait divergence are limited to static measurements of functional traits rather than trajectories of individual development. We explore whether five taxa of evergreen shrubs (Protea section Exsertae) differ in their developmental trajectories and capacity for plasticity using two environmentally-distinct common gardens in South Africa. We measured seedlings in the summer-dry season and winter-wet season of each of two consecutive years to characterize ontogeny and plasticity within years, as same-age leaf cohorts mature, and between years, i.e., from leaf one cohort to the next. We compared patterns of development between gardens to assess whether trait trajectories are programmed versus plastic and examined whether developmental differences covaried with characteristics of a seedling's home environment. We detected plasticity in developmental trajectories for leaf area, stomatal size, stomatal pore index, and to a limited extent specific leaf area, but not for stomatal density. We showed that the species growing in the harshest environments exhibits both the smallest increase in leaf area between years and the least change in SLA and photosynthetic rates as leaves age within years. These results show that within this clade, species have diverged in developmental trajectories and plasticity as well as in mean trait values. Some of these differences may be associated with adaptation to cold and drought stress within an environmentally-complex region.


International Lesser Known Pollinator Appreciation Day

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Michael Whitehead (@DrSway) points out that today is International Lesser Known Pollinator Appreciation Day. And in honor of that celebration, here's a YouTube video featuring the Bug Chicks and the Fly Guys.



From the text on the YouTube page:

The Bug Chicks (Kristie Reddick and Jessica Honaker) designate a new holiday called International Lesser Known Pollinator Appreciation Day. To celebrate, they wrote an anthem and invited The Fly Guys, a barbershop quartet, to sing it for them. This was a freebie video they made for Pollinator Live, a national webcast from the US Forest Service.

Plants are cool

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Chris Martine (@MartineBotany) has released the next in his video series Plants are cool, too!1 In this edition, he visits my home state to look at plant fossils. Enjoy!


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