Storing and organizing photos on Flickr

As discussed in lab meeting last week, I created our lab Flickr site for storing and organizing photos. The site is here.
I think that the advantages of a site like this “in the cloud” are pretty obvious, and were articulated some time ago by Dan Ebert in this blog post, in which he encouraged us to create folders of photos on this blog. A few such folders currently exist, but the idea never really caught on as far as I can tell. I decided to use Flicker instead of this blog because of the sheer volume of photos that people routinely produce these days. I came back from my field work with 16 GB of photos, and I found the native WordPress photo organization tools to be cumbersome. It’s also not clear how much storage we have on this blog; on Flickr, we have up to 1 TB, so we’re pretty future-proof there.
In an effort to get the ball rolling, I went ahead and migrated the photos from this blog to our new Flicker site.
Here are the login details for the site:
User name: sunflower_photos
Password: sun flower head
I added most of my photos as individual folders that are labeled by my field collection number. In the meta-data for each folder, I mentioned who took the photo, and how to contact me for questions. I also added a folder for just “pretty photos” that I took this field season (photos of nice scenes, possibly for use in talks and cover photos, etc.).
If you have photos that you want to add, I recommend making your own folder (go to “You”, then scroll down to “Organize”) and adding them to that folder. Otherwise they go directly into the folder stream and it’s hard to tell who took them or where.
Right now, I believe that the default upload option is to keep the photos as “private” so that only we are able to see them. But I also made a few of them public so our Flickr site has a public face (and a pretty one, if you ask me).
For more thoughts on how to add and organize photos, see Dan Ebert’s blog post.
Anyway, I hope that this helps us organize our photos in a way that allows people to look at other people’s pics and also find cool pics when they need them.

Drill, dry, sieve

I wanted to let everyone know about some supplies and equipment that are new in the lab. During the 2015 field season, I bought a couple of things that are now part of the lab general use equipment and supplies. Here they are:

  1. Drill. We now have a nice, battery-powered drill that is really good for drilling things. The drill is in the hardware cupboard near the lab computer. It’s in an orange bag.
  2. Silica Gel. I returned from the field with more than 50 kg of used silica gel. It’s not pristine (was used to dry seeds), but great for field work. It’s stored in sealed, orange buckets in the Lab Extension in Biology (check the tall metal shelves).
  3. Seed Sieves. For processing seeds in Iowa, I bought some seed sieves. These are supposed to be the best ones for wild Helianthus, so if you are processing a lot of seeds, these might be of use. These are also now in the Lab Extension.

Happy drilling, drying, and sieving.

New germplasm from Dylan’s 2015 field work

As many of you know, I was tasked with collecting wild populations of Helianthus annuus, H. petiolaris, and H. argophyllus from across the geographic range of the species, for use in the abiotic stress adaptation project. Over a three month period, I drove more than 30,000 miles and collected at 145 Helianthus localities in 15 western states. I found a lot of really interesting plants, including what might be several new species. In future posts, I’ll talk some more about the trip, and what I found.

The seeds are now here. They are cleaned and packaged in individual envelopes numbered by population and mother plant. I cleaned the seeds in Ames, Iowa at the UDSA facility, so they are high quality, ready to go. All of the seeds are now part of the seed collection in our lab in the Biodiversity building. The new seeds have been added to the permanent database of seeds for the whole lab. But I also put a copy of my complete notes here. My notes give details about where the plants were collected, their ecology, etc. I’ll be putting printed data in the boxes with the seeds as well, just in case the zombie apocalypse arrives and these electronic data go dark. I also plan to post photos of each population I visited, but that’s down the line. For now, the seeds are here, so if you need to access any of them for a project, the data linked to this post should help you do that. If you happen to use any of these plants in a project, please note that voucher specimens were deposited in the herbarium at Indiana University (herbarium code: IU).

If you need to contact me about these seeds, and you have no idea who I am or where I am located, here is my “permanent” email address, which should also last for some time.

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Introducing Phoebanthus, Sibling to Sunflower

Before I left UBC to head to California, Rose and I got interested in looking closely at the nearest relatives of Sunflower. In particular, Rose was looking to obtain an “outgroup” for her analyses of cpDNA phylogeny in the sunflowers. We found out that the sister-genus to sunflower is a little plant called Phoebathus, which consists of just two species, one diploid and one tetraploid. Both of them are perennials that are endemic to Florida.

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Phoebanthus grandiflorus

After learning about the plant, I started looking for a way to get some samples. I learned very quickly that it’s basically not cultivated at all. So I contacted several naturalists from Florida who live near Phoebanthus country, and one of them (a gentleman named Wayne Matchett) volunteered to get us some tissue and seeds for the more common tetraploid species, Phoebanthus grandiflorus. It took a while for Wayne to locate a flowering population, and then to wait for the seed heads to mature (at my recommendation, he “bagged” the heads), but he finally managed to secure about 100 mature seeds, along with a sample of leaf tissue, both of which I am now in possession of.

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Some of the seeds that Wayne got

I guess that I became obsessed with this plant because it is such an underdog compared to Helianthus. While Helianthus is a weedy, widespread, diverse, and dominant genus that has more or less conquered North America as well as the human race, the sibling genus to sunflower amounts to just two species, both of them found in what is probably the cushiest, least stringent environment in all of North America: Florida (sorry, Chris).

In any case, I’m going to apply for a permit to bring the seeds and tissue to UBC when I visit in a month or so. I might also try to keep some here in California and try growing it here to see how it performs. In addition to providing a nice outgroup for phylogenetic analyses, it might be cool to do other comparisons between the vivacious head-turner that is Helianathus, and its runty little sister genus, Phoebanthus.

In the meantime, here are some of Wayne’s photos:

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Photographs of Helianthus annuus

Over the weekend, I took some photos of the H. annuus that are growing out at Totem Park, including some of Emily, Brook, and Greg’s plants. They are just such photogenic plants, I could not resist. I uploaded a complete set of hi-res .jpg files to the blog server, and they are presented above in the gallery. These are massive, but they are .jpg, so that means they are lossy. If you want to use these for printing, let me know and I can send you the raw files, from which you can make .tif files that are as good as film negatives.

If anyone else has plants flowering that they would like pictures of, let me know! I’d love to get a nice set together for the lab.

Extracting point data from vector and raster maps (for free)

I recently wrote a post on my research blog all about using free GIS software to extract point data from vector and raster maps. I won’t repeat it here, but this is the upshot:

One of the most powerful uses of GIS technology is to sample and analyze data from GIS data layers. For instance, if you have a set of GPS coordinates for a species of plant from Utah, and you want to find out what range of climate types the plant grows in, you can use digital raster layers for climate (high and low temperature, rainfall, etc.) to extract estimates for the conditions that your plants experience at the locations where you sampled it. Then, you can use that data for many purposes: reconstruct it on a phylogenetic tree, test for divergence in climate regime among populations, test for associations among variable (for instance among soil and climate). Really, anything.

Let me know if you have any questions! I’m happy to help people get this going for specific data sets.

Silica gel: God’s gift to botanists

Another Rieseberg lab member was asking me this week about preserving plant tissues on silica gel for later DNA extraction, and this got me to thinking about the general idea. I thought I would make a post about it, since it’s a useful technique, even in the genomic age. A lot of you already know all about this, so apologies for preaching to the choir.

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The miracle of silica gel

I put an extensive post on my own Research Blog, but here is the gist of it:

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Herbarium Vouchers

In a recent lab meeting, the issue of herbarium vouchering came up, and a spirited discussion ensued. Inspired by what I heard there, and by some discussions with the manager of the UBC Herbarium, I decided to create a post on the how and why of herbarium vouchering. I put the complete version of this on my own research blog, accessible here. Here, I mostly wanted to summarize the idea, and try to convince everyone in the lab that vouchering is really important.

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Momma’s CTAB

Like a few other people in the lab, I’ve been struggling with DNA extractions of late. I’ve tried several methods, including the “columnless” method that a few people are using. But I was having pretty spotty luck. Then, during a bout of methodological soul-searching, I also tried a CTAB protocol that used to be my go-to method. It failed me a few weeks ago, but in a second trial last week, it delivered the goods: loads of very pure, high molecular weight DNA. It might not work for all plants, and there do appear to be situations in which it is not the best option, but if anyone wants to get back to down-home, from-scratch extraction, the way momma used to do it, then give this one a try:

Please note: the results below are for Streptanthus (the plant I’m studying; Brassicaceae); I’m trying it for some Asteraceae right now, and will update the post once I have results.

Momma’s DNA Isolation via CTAB

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More on Hydroponics

This post is intended to give a few more details on the hydroponics rigs that I constructed, and am currently testing with Greg O. I built these rigs in collaboration with John Gourlay (jgourlay@mail.ubc.ca), who is a technician in the Botany Department workshop (room 1363; directly underneath the room that houses the growth chambers). John was able to create these rigs in less than a day after I described them to him, so if you’re thinking of starting a hydroponics project, you should consider having him do the work for you. He charges a small amount, and does the work very quickly. He’s also a very nice guy.

The rigs are based on a design that is pretty common in the world of hydroponics. The version described below is similar to one developed at Duke University by Jessica Selby and Kevin Wright (John Willis Lab). The idea is to suspend the roots of the plant in a nutrient solution, and provide oxygen to the roots via bubblers. As Greg says, the method requires development. However, it appears to work well for sunflowers (not so much for my plants). Anyway, here is the basic process of constructing the rigs.

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