02/11/15

The last big push – wrapping up the phenotyping for AdapTree

One last experiment of the AdapTree project remained in the ground: the trial comparing natural and seed orchard seed lots. The roughly 6000 plants were kept for a third season to collect periodic height measurements for the pine, and cold hardiness data for the spruce. The spruce trees announced themselves ready for freeze testing by the end of August, so September was dedicated to needle chopping and conductivity measurements. Thousands of them. Three whole weeks. Those who stuck it out were by then thinking with fond memories of the days gone by when the AdapTree team was large and fresh. But we did it, and the resulting data were clean.

Fig 1: Pine heights, diameters, and harvesting for shoot dry mass

Fig. 1: Pine heights, diameters, data logging and harvesting for shoot dry mass

Nonetheless, it was the middle of October by the time we were performing the final height and diameter measurements on the pine, while simultaneously harvesting them for shoot dry weights. (Figure 1). Harvest time was preferred for diameter measurements because it gives us easy access to the stems. We had sun, we had fog, we had beautiful autumn days and we had rain. Now, we don’t exactly melt from a little rain. But shoving wet plants in wet paper bags which are marked with sticky labels of moderate stickiness is asking for trouble. And while the recording tablets are protected, raindrops beading on a screen are not ideal for visibility. So this became a long, drawn-out affair. Of course, we only take pictures on the nicest days!

Fig. 2: Gradual progress

The ideal team consisted of three people, so we organized our schedules, waited for the rain to stop, and gradually made progress (Figure 2). We finished the pine and thought we’d just continue at the same speed with the spruce. (Figure 3). Not so. While the spruce plants were much smaller than the pine, the stems were thick and asymmetric, with multiple roots spreading horizontally almost before touching the ground. Individual diameter measurements were not very repeatable, so multiple measurements were taken. Rather than taking turns at measuring, recording and bagging, for consistency’s sake all twelve blocks were measured by the same person. The repetitive bending over proved fatiguing.

Fig. 3 : Some large pine, and the first snowfall

If you wonder what I am holding up: it’s an old toothbrush, to clean the root collar of sand and mud before taking a diameter measurement.

Then we had frost and snow in November! And the frozen ground in combination with the frozen liverworts and moss did not make a good basis for reliable height measurements – who’d have thought frozen bryophytes could bring science to a halt? As the days got shorter and shorter, we completed the heights separately.

Fig. 4: Dry weights – so many!

In the meantime, shoot dry weights were measured in the lab, to keep the accumulating boxes of dried plants under control. (Figure 4). We didn’t finish before Christmas as planned, and Ian had to wait and wait for his data. With mild weather in the first week of January, we made one last big push, and the last spruce tree was cut on January 9 (Figure 5), with the last dry weights gathered two weeks later.

Fig. 5 : The last spruce tree is cut …

And now all the plants are gone and no more measurements can possibly be collected from them!!!

I am grateful to all those who helped out (you can see some of them in the pictures!), and for the hot tub in the swimming pool. Did I mention the guys who (re)built the raised beds in the first place (Figure 6) ? And the summer students who helped sowing, and the technicians and students who collected weekly height measurements (Figure 7) ?

Fig. 6 : Re-building the beds …

Fig. 7 : Sowing, observing, measuring, ...

Fig. 7 : Sowing, observing, DNA collection, measuring, …

09/24/14

Science storytelling

In August, I was privileged to attend a storytelling workshop with Denise Withers, as part of the genomics entrepreneurship program. Denise is convinced that every research proposal can be boiled down to a 3 minute sales pitch that your neighbor can understand, though it may take a lot of hard work. Denise spends her time coaching scientists and entrepreneurs to do just that.

These days, it isn’t enough to have excellent science in a proposal for funding or an evaluation report. Eventually, administrators and politicians also need to be convinced that we deserve to get a slice of their scarce financial resources. Research proposals increasingly need to demonstrate impact. This is some steps removed from direct project outputs, with all the risk and uncertainty involved, so scientists are understandably hesitant to ‘promise the moon’, while at the same time feeling the pressure to do just that. The funding agency may then appear be “playing Civilization”: starting at level 3 and investing 10 units in science should automatically result in reaching level 4. But real life is not like that, is it?

Science is characterized by the unexpected, so rather than a problem, this hurdle allows the characters to shine … if we tell the story well. Seeing the story in our research work requires zooming out from the detailed focus in which we spend our daily lives. Developing a logic model and a theory of change for the project are steps which can help us develop the overview. Doing it as a team may enhance mutual understanding of the various project activities, how they are connected, and any unstated assumptions. It can be built into the funding proposal to provide ongoing evaluation. And towards the projects’ end, we scientists turn into heroes having overcome insurmountable obstacles, to reach places where we perhaps didn’t expect to get to, and having changed the world just a little bit… And this, more than the 100 page report and the 10 papers, is what evaluators (and your neighbor) will remember. Although the 100 pages and the 10 papers are still needed.

Example: A story of the AdapTree Project in three minutes, based on logic models and theory of change.

Due to climate change, the seed sources being planted in our forest are becoming increasingly mismatched to the climates they will experience. This mismatch can be addressed by moving seed over the landscape where needed. This requires adjusting the rules of what can be planted where. However, we must first know which seed sources are best adapted to given sites, both now and in the future.

We reduced the scope of this problem to the two provinces of BC and AB and two important commercial species, interior spruce and lodgepole pine. However, we still can’t plant every seed source on every planting site and wait thirty years for the results. Instead, we looked at the underlying patterns of adaptation in the genome of these species.

Because of the enormous size of conifer genomes, we zoomed in on >25,000 candidate genes. These genes were then sequenced in 500 natural seedlots from all over to find genotypic variation at the base-pair level. The adaptive value was revealed by growing plants of the same seedlots in controlled environments simulating present and future climates.

We then developed a SNP chip to evaluate adaptive genetic potential in orchard seed lots, whose top quality seed is used by preference in tree planting. Using that, we can evaluate the ecological risks of moving seed sources over the landscape or ‘assisted migration’, including the status quo. This allows policy makers to update seed transfer guidelines as climate changes. A socio-economic research component ensures that stakeholders can make informed decisions regarding new strategies.

The main outcome of AdapTree is information about the adaptive potential of seed sources regarding present and near-future climates. The resulting impact, long-term, would be reduced plantation failures, increased forest productivity, and resilient forest-dependent communities. A short term outcome is the development of sampling and research methods that are transferable to other seed sources, species and climates.

07/29/14

Welcome to Beautiful Gavin Lake!

In early July, Tyler, Joanne, Ian, Sally, and I (the Aitken lab crew, a.k.a. the A-Team) were dispatched to the BC interior to liberate some pine and spruce tissue samples from the clutches of an army of berry-picking bear cubs.

The REAL A-Team.

The sneaky bear cubs defending their strawberry patch.

Our destination was the Gavin Lake Forest Education Society camp (http://gavinlakecamp.wordpress.com/), which, among other things, serves as basecamp for many UBC research teams working in the UBC Alex Fraser Research Forest (AFRF) and an annual group of 4th year Forestry students participating in the education-veiled debauchery known as “Fall Camp” (one recent cohort saunaed so hard the sauna roof caught on fire).

The cut block where the two field trials were planted.

Sampling the lodgepole pine seedlings.

Our elite squad of tissue wrangling researchers made the 8 hour trek north to collect lodegepole pine and interior spruce tissue samples from a field site in the AFRF. The field site was established on a recently harvested cut block in spring 2013, and contains two separate field trials, one of lodgepole pine (2200 seedlings) and one of interior spruce (3100 seedlings). These two field trials are medium-term (10 – 15 year) validation studies for our current common garden experiment at Totem field on the UBC Vancouver campus that are part of the AdapTree project. Such validation studies allow for an understanding of how translatable our results are from a seedling trial conducted outside of both of the species natural ranges, to more realistic scenarios of reforestation in the BC interior. In other words, it will tell us if coddled seedlings in raised beds, experiencing mild Vancouver weather accurately represent the seedlings out there in the wild trying to make it on their own. In OTHER other words, it will tell our graduate students if they wasted the last 5 years of their life. Just kidding, but only just.

The cut block, now 18 months after being clear cut, was home to three black bear families that passed their time munching on the sea of wild strawberries that have since recolonized the site. They were very considerate creatures, always maintain a healthy I’m-not-going-to-eat-you distance. We also saw several deer around the site. This little guy was particularly handsome.

Handsome Jack.

Mama and baby eating all the strawberries.

Seeing as the designated UBC research cabin had already been commandeered by another crack squad of UBC researchers, we were upgraded to the lakeside Prime Ministorial cabin, which was very nice, as you can see here. During our free time in the evening we took advantage of our gorgeous surroundings by swimming, canoeing, and hiking around the lake. I must admit, aside from the mild inconvenience of having to wake up at 7:00 in the morning, it felt like more of a vacation than work.

Work is so HARD sometimes.

Our humble lodgings. Sally shows us how to assemble a ‘Glory Bowl’.

06/8/14

Simulating climates in growth chambers – The AdapTree project

This post is part of the series Simulating Climates in Growth Chambers.

The AdapTree project evaluates the genetic and phenoptyic variation of two commercially important conifers in western Canada, interior spruce (Picea glauca, P. engelmannii, and their natural hybrids) and lodgepole pine (Pinus contorta). More than 580 seed sources were grown under controlled climate conditions to quantify genetic diversity and geographic structure for adaptive traits such as phenology, frost hardiness, seedling growth, and response to drought and heat. Concurrently, sequence capture and resequencing of much of the exome for ~600 individuals of each species reveals genetic variation, some of which is associated with this adaptation. Around 5,000 additional individuals per species growing in various other controlled climate regimes and outdoor common gardens will then be genotyped using a cheaper SNP array. All of these markers will be tested for a potential role in local adaptation to climate through 1) association with climate-relevant phenotypes; and 2) gene-environment correlations. The SNPs with evidence of local adaptation will then be used to evaluate the suitability of populations to future climates. Field-based validation studies have been established to confirm the genomic results.

Location of the target simulated climates on a map.

To bring out the differences in adaptive characteristics of populations from all over British Columbia and Alberta, three temperature regimes were developed to represent four different climates with mean annual temperatures (MAT) of 1, 6 and 11 °C (all well watered), as well as an MAT 11 dry climate.
Realistic climates were needed to yield realistic bud break and bud set data in growth chambers. The photoperiod regime was identical for all plants and day length corresponds to that at 54.5°N at the relevant time of the season. Time constraints on the project necessitated germination modification and growing season compaction to reach the desired plant sizes quickly for all experiments. Not all experiments could be grown under fully controlled conditions, and some of the plants grown in the greenhouse were out of sync with nature yet needed to be planted outdoors in the following season. Their blackout regime gave us trouble, since covering them up to keep light out caused conditions ideal for fungal growth. During the second growing season, simulated drought was applied in cycles to the MAT11 dry treatment. Half of the plants in MAT11 wet and half of the plants in MAT11 dry were also subjected to a heat wave in the middle of summer. Plants were well-watered and chlorophyll fluorescence was measured to evaluate plant stress as a consequence of the heat wave. Carbon isotope composition was used to evaluate plant response to drought integrated over the growing season. At the end of the second growing season, cold hardiness measurements required us to simulate real winter, and not just a chilling period. The night frost pre-treatments were successful and good cold hardiness data were obtained. After this, the plants could be destructively sampled for dry weights. This required washing the soil off the roots. Thanks to our foresight in using plant cones during the first season (see root washing) we were able to separate the roots even for the largest (MAT 6 and 11) plants and after two seasons of growth.

Further information about the AdapTree project can be found on the website.

08/27/13

Lodgepole pining

Another summer is drawing to a close and another school year starting, meaning that a few of us have wrapped up some successful field seasons! I spent a good chunk of my summer travelling across BC and the Yukon collecting lodgepole pine needles for DNA samples in my project looking at the genetic basis of local adaptation to climate, a ground-truth of the main AdapTree project. I’ve returned with 2,585 trees sampled from 122 different provenances grown across 16 different test sites I visited, as set up by the BC Ministry of Forests in the Illingworth provenance trial as well as a smaller provenance trial set up in the Yukon Territory.

I just want to share a few photos and fun stories to give a feel of what my field season was like, but first I have to acknowledge a lot of very great people. I had a lot of help along the way, and these are the people to whom I owe many thanks! First off, Sally, Ian, and Kristin, head of and in the Aitken lab, for all the help given in terms of advice for the field, getting gear together, and letting me borrow gear, supplies, and a great 4WD field truck. Second, to Nick Ukrainetz and Vicky Berger with the BC Ministry of Forests for their immense amount of help providing me detailed information on all of the provenance trial sites I visited, teaching me good safety practices for driving on logging roads, and providing me with a VHF transceiver. Third, a huge nod to my advisor Mike Whitlock for all of his support in making these collecting trips possible and imparting knowledge over the phone of what to do when we were being swarmed and chased for >20km by what we thought were angry bees in the woods. Fourth, to Anne Berland, graduate student at the University of Victoria for joining us in the field, not only being great company, but also an excellent navigator to finding our sites and to letting me borrow a second pruning pole from their lab. As well as to Stilianos Louca, UBC grad student, who without having been in a car accident in the Yukon (no one hurt) I would not have been able to visit test sites in the Yukon for sampling and received his help in exchange for helping on the long drive back to Vancouver. And lastly and also most greatly to my two amazing field assistants for my main sampling trip: Evan Cronmiller and Warren Neuvonen, UBC undergraduates, who endured hot days, cold nights, hard ground, tall trees, biting insects, scratching branches, swarming flies, long drives, slingshot fatigue, and in the face of it all remained happy, friendly, energetic, hard-working, and continued to keep me laughing and smiling on our whole trip. I really could not have done it without all of these people and have the good fortune of being able to now spend my fall semester extracting DNA from all of my samples.

So, on to the fun stuff. What is it like to sample lodgepole pine for 3 weeks in the woods?

First off, you see lots of trees, and lots of logging roads.

You drive around a lot, and often it is hard to find a site (the sites were established in 1974, so just under 40 years old!), but sometimes it is actually quite easy!

And you encounter many logging trucks along the way.

The loggers would often talk to us on the radio, curious about what we were doing in our truck way out in the middle of nowhere.

Short tree from a provenance in Yellowstone

The trees can be very tall, or they may be very short. We clearly could see effects of local adaptation going on in the field.

Holding a 40-year-old tree.

We used slingshots to sample the unreachable branches on the tallest trees. By the end of the trip, it was no problem to shoot a tree and get a branch to fall in one shot. The slingshots got so much use that we had to buy replacement straps halfway through the trip. But we sometimes resorted to extreme measures to sample when trees were too sparse for the slingshot.

Warren and Evan became pros.

These included throwing the pole to reach a just-out-of-reach branch or climbing a tree.

We had a lot of really, really buggy days where the incessant buzz in your ears almost makes you go mad.

But you manage to find your peaceful and pretty moments.

And enjoy some amazing campsites, like this one on the Bluewater River in the Canadian Rockies.

We often got covered in pollen, walking out of the woods with yellow boots and pants.

And I spent a lot of time each evening filling my samples with silica gel to dry them out for the long trip back to the lab.

And in the end, I even was able to see the Yukon and sample there!

Stilian with the pruning pole

So thanks again to everyone for all of the help and making this a productive and memorable summer. Stay tuned in the future for the results of my project!

The Modern Forest

Does my forest look good in these genes?

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