Category Archives: Uncategorized

06/2/14

Simulating climates in growth chambers – Developing moisture regimes

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

In continental North-West America, summer heat is correlated with drought. To make our climates more realistic, we added drought treatments. The simplest way to do this is subject plants in a ‘dry treatment’ to drought cycles, with soil moisture content dropping to 25% relative to total saturation1, before plants are re-supplied with water and fertilizer. In the ‘wet’ treatment, soil moisture content is maintained above 65% relative to saturation. Wet and dry treatments receive the same amount of fertilizer2. In order to apply drought treatments consistently, we use boxes of 40×36 cm where 100 plants share the same soil volume (15.8 l). This circumvents the problem of larger plants being more drought-stressed, as can happen when using individual plant cones. The boxes are made from Coroplast, a plastic corrugated cardboard, which can easily be cut with an Exacto knife. This allows us to size the boxes exactly the way we want them, and optimally use the space in the growth chamber.

Plant box opened on the side with the plants tagged for root washing

Plant box opened on the side with the plants tagged for root washing

As with using individual containers, planting distance needs to be balanced against experiment duration, chosen climate and resulting expected plant size, unless mortality due to plant competition is desired. However, too low a plant density will result in very few and long drought cycles, smaller treatment effects, reduced opportunities to fertilize, and possibly malnutrition. If you need to separate the plants at the end of the experiment, check out this blog post to find out how we avoided the problem of the roots becoming too entangled.

Example of box weights for dry and wet treatments. The first column indicates the target maximum and minimum weights. All wet and all dry boxes are fertilized at the same time, hence individual box weights may differ slightly from the target

Example of box weights for dry and wet treatments. The first column indicates the target maximum and minimum weights. All wet and all dry boxes are fertilized at the same time, hence individual box weights may differ slightly from the target

Come back tomorrow to find out how I applied day length regimes or go back and see some of the other posts in the series.

1 This is a point we previously established for the given soil mix to correspond to a soil water potential of -1 MPa, the point at which permanent damage starts to occur.

2 That is, at the end of each drought cycle and in comparative amounts (topping up with water if needed).

06/1/14

Simulating climates in growth chambers – Developing temperature regimes

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

The choice of a point on the map representing your target climate is somewhat subjective, but there are reasons not to worry too much about this. Firstly, there is a similarity of patterns for locations in Western North America with continental climates, as indicated in the graph below. Secondly, we have always been more interested in the responses of genotypes relative to each other, rather than their absolute responses to the climate regimes. A third argument is that the averages affect plants far less than the extremes. Based on the monthly average temperatures obtained from ClimateBC for three chosen points on the map (indicated by *in the graph), a baseline curve was derived, and idealized curves can be derived by adding or subtracting a set number of degrees. The following graph shows how the (thick brown) baseline curve compares to several curves of real locations, as well as to the curve of weekly average temperatures (thin brown), which were obtained by interpolation.

Monthly average temperatures for seven locations in Western North America with continental climates, baseline curve for MAT 6 °C, and weekly averages interpolated from the baseline.

Monthly average temperatures for seven locations in Western North America with continental climates, baseline curve for MAT 6 °C, and weekly averages interpolated from the baseline.

On this weekly temperature average, we superimpose a daily variation. Initially, we chose a daily range between 12 and 15 °C, which is representative for the three chosen climate points between April 15 and October 15, the period we chose to represent one growing season. In the field, sites with a mean annual temperature (MAT) between 4 and 5°C produce optimal growth for lodgepole pine (Wang et al. 20061). Warmer climates result in decreased growth. However, a similar set of lodgepole pine populations grown in controlled climate chambers under temperature regimes from 1 to 13°C (MAT) reveal neither plant stress nor decreased growth in the warmest regimes. Likely, there was not enough ‘weather’ in our simulated climates. This makes intuitive sense if we think about representing a climate of MAT 6 by programming a constant 6°C: this is not realistic. Neither is it realistic to keep the daily average and range nearly constant. Plants adjust to the higher average temperatures by permanent modifications in their physiology and metabolism, and deal with deviations from the averages through plasticity. When the capacity to adapt using a plastic response is exceeded, survival is at stake and differences in the ability to cope are revealed. The capacity of a plant to respond to stress will depend on the background signal of past average temperatures and extremes. Yet significant plant mortality leads to loss of data, so we try to avoid it. This is the fine line we are skirting when trying to make temperature regimes ‘realistic’. The way the climate is perceived by the plant is more important than the absolute values of temperatures. Yet we want to evaluate stress levels in terms of factors that have relevance in the field.

Introduction of two alternating phases.

Introduction of two alternating phases.

In a second iteration of the lodgepole pine experiment designed to produce response curves, the daily sinusoidal pattern, identical for all MAT, was overlaid on the seasonal trend in two alternating phases: a 3-day warm phase with large temperature variation, mimicking sunny days, and a 4-day cool phase with smaller diurnal fluctuations to mimic cloudy days. The analog temperature chart on the side gives a visual impression of these two phases for MAT13. Both diurnal range (between 8 and 23 °C) and daily average temperature were manipulated to achieve this goal. Weekly averages of temperature and daily range were maintained at their respective baselines. The result was a more realistic absolute maximum temperature in August of 35.4°C for MAT07. This is very close to 35.2°C, which is the absolute maximum in August in Vernon North weather station between 2006 and 2012. Indeed, absolute maximum temperature was the criterion around which the ranges were developed.

Daily temperatures on day 3 and 4 of the week. Each day represents one of the two alternating phases (warm sunny days and cool cloudy days) introduced to render the growing regimes more realistic. Left: gradually increasing temperatures during spring. Right: gradually decreasing temperatures from July 15 onwards.

Daily temperatures on day 3 and 4 of the week. Each day represents one of the two alternating phases (warm sunny days and cool cloudy days) introduced to render the growing regimes more realistic. Left: gradually increasing temperatures during spring. Right: gradually decreasing temperatures from July 15 onwards.

Extreme events play a large role in the response of plants to present and future climates. The background trend determines the pre-conditioning of the plants, and therefore the response to the extreme event. Both trends and extreme events need to be simulated carefully, close to the level of tolerance, to reveal differences in population response determining which populations survive and which ones don’t. Next I’ll cover moisture regimes.

Wang, T., A. Hamann, A. Yanchuk, G. A. O’Neill and S. N. Aitken. 2006. Use of response functions in selecting lodgepole pine populations for future climates. Global Change Biology 12: 2404–2416.

06/1/14

Climate vs. Weather: the why and how of simulating climates in growth chambers

This is the first in a series of posts on simulating climates in growth chambers. See the end of this post for a full list of entries in this series.

Our lab group investigates genetic variation that is meaningful to local adaptation, with a focus on trees. This is especially important in the context of climate change: long-lived trees may become maladapted over time to the local climate. To what extent are trees locally adapted, and to what extent does plasticity enable them to deal with a variety of circumstances? Valuable information is provided by long-term “provenance trials” in the field and nursery-type “common gardens”, in which a collection of genotypes from various sources is grown in the same environment, or set of environments. The weather in such environments varies from year to year and is not under our control. Over a longer term, the impact of this varying weather is expected to average out and represent the local climate. Yet there will always be some extreme event, perhaps an unusually late spring frost, a summer heat wave, a prolonged drought, or perhaps a very wet rainy season, which affects growth and survival in field trials. And these extreme events have a large effect on ‘adaptation’ in the genetic sense: natural selection for fitness.

WHY ?

Wishing to free ourselves from the vagaries of weather and to test our plant materials in warmer environments than those presently available in the field, we arrive at the controlled climate chamber. There are many restrictions inherent in using growth chambers. They are expensive. Only a limited number of genotypes can be observed over a short period of time. And simulating realistic winters has so far eluded us. This method should be regarded as complementary to field trials, and not a substitute.

HOW ?

How does one go about programming a controlled climate chamber to achieve a set goal? Which temperatures, light intensities and day lengths do we program? From which data set do we derive relevant climate variables, which are those variables, what range do we wish to cover, and is the resulting program actually realistic?

Choosing a baseline data set

We use data from Canadian Climate Normals of 1961-1990, the earliest data set of sufficient coverage and detail.This represents the climate before significant warming occurred, and it is the climate we assume the trees have adapted to through natural selection.

Choosing relevant climate variable(s) and a range you wish to cover

In our first experiments we studied interior lodgepole pine (Pinus contorta ssp. latifolia) populations. For this species, mean annual temperature (MAT) of the seed source is the variable revealing the strongest patterns of correlation with growth (Wang et al. 2006). ClimateWNA (Wang et al. 2012) data were used to plot the map of MAT below.

Natural range of Pinus contorta in North America (insert, dark grey) and detail of climate conditions (MAT, °C) in the area of interest (British Columbia, excluding the milky-white overlay where the species does not occur). Three chosen locations with representative climates (black dots).

Natural range of Pinus contorta in North America (insert, dark grey) and detail of climate conditions (MAT, °C) in the area of interest (British Columbia, excluding the milky-white overlay where the species does not occur). Three chosen locations with representative climates (black dots).

Our range of interest was interior British Columbia (BC), MAT 1 to 10 °C, to fully capture the growth response functions derived from field data (Wang et al. 2006). The geographic range for ssp. latifolia does not incorporate any areas with MAT 10°C, so this warmer, future climate regime was created by extrapolation. No attempt was made to average the climate for all the points with the same MAT. Instead, three points were chosen on the map, with MAT close to 1, 4 and 7°C, which had weather stations nearby. Such proximity is not really required, since ClimateWNA also provides detail on average daily ranges, but is still useful to inform us about the absolute maximum temperature. Other species may require other approaches, depending on the climate variables that best explain their adaptation. Now that a target climate has been chosen, find out how I developed realistic temperature regimes, moisture regimes, and where you can find suitable photoperiod data. Over the next several days, we’ll be posting on simulating winter conditions, heat waves, stimulating germination and bud set. At the end of the story, you will be familiar with most of the methods we had to use for growing plants for our AdapTree project. If you have tried similar or even stranger things, let me know. I’m curious to find out!

Simulating climates in growth chambers

Note: entries in this list will become available as posts go live between June 1 and June 8

Wang, T., A. Hamann, A. Yanchuk, G. A. O’Neill and S. N. Aitken. 2006. Use of response functions in selecting lodgepole pine populations for future climates. Global Change Biology 12: 2404–2416. Wang, T., A. Hamann, D.L. Spittlehouse and T. Murdock. 2012. ClimateWNA – High-Resolution Spatial Climate Data for Western North America. Journal of Applied Meteorology and Climatology, 51: 16-29.

05/8/14

Oaks at the fringe

I was raised in the Rogue Valley of southern Oregon, in the heart of the Garry oak a.k.a Oregon white oak (Quercus garryana) species distribution. My early years were shaped by long afternoons spent wandering sere meadows, chasing lizards and snakes and tossing natural whiffle balls formed by Oregon oak gall wasps (Besbicus mirabilis), and always finding midday reprieve in the shade of mighty oaks. I hadn’t developed my current fascination with trees at that time, but my love for those forests was already engrained in me. If I’d been told then that I would move to another country and study a threatened tree that was considered a weed to farmers around my home, I surely would’ve called shenanigans. Yet here I am, many years later, with a much greater appreciation for the trees that surrounded me, doing just that.

Life amongst the oaks in Totem Field. Trees from high in the mountains of southern California down to the rocky shores of eastern Vancouver Island are planted side-by-side.

Until recently, my study of oaks took me no further than a short walk from my office, where a common garden spanning the species range had been established in 2006 by Colin Huebert, a former MS student of the Aitken lab. It was here that I first began nurturing a fascination with this species. I observed tremendous variation in growth, form, and phenology. Everything from shrubby, hairy, and spindly varieties from California to stout and stately forms from Washington and British Columbia could be found. Sharp-lobed leaves 3cm in length to deeply-sinused and rounded 15cm leaves could be compared on trees adjacent to one another. Although studying the population genetics of this species has been rewarding, I missed seeing these beautiful trees in their natural state.

Over the last couple of weeks I’ve had the pleasure of organising and executing a week of field collections: a whirlwind tour through four populations scattered across southern British Columbia at the absolute margins of the range of Garry oak. Of all the ecosystems to do field work in, rollicking oak meadows –free of the carpet burweed (Soliva sessilis) and poison oak (Toxicodendron diversilobum) characteristic of the familiar meadows in southern Oregon– must rank among the most hospitable.

Sampling locations.

Years of living in southern Oregon and the Willamette Valley (where Garry oaks reach their largest sizes) had given me much experience with oak savannahs in the core of the species range. However, my experience at the periphery was very limited. Here, little remains of the once-vast meadows maintained and cultivated by the First Nations. What oaks are left tend to be relegated to craggy bluffs or marginal lands with slightly deeper soils. As with so many dry ecosystems, the spectacular native flora has been largely replaced by exotic grasses and shrubs. Despite all this, the meadows still retain a majestic sense of place and awe upon entry.

I wasn’t sure what to expect from any of these sites as the only one I’d visited beforehand was Sumas Mountain (the location of the oaks there was not well-marked and I wanted to make sure they were worth sampling at all). Bright and early on the morning of 28 April, Sean King and I left Vancouver expecting poor weather and receiving nothing but blue skies and a gentle breeze. Despite how temperamental weather can be at this time of year, we were fortunate enough to hardly face a drop of water that didn’t come from our drinking supply.

Characteristic B.C. Q. garryana meadow. Twin Lichen Meadow, Crow’s Nest Ecological Research Area, Salt Spring Island.

The first stop on our trip was the Crow’s Nest Ecological Research Area on Salt Spring Island. This site was quite literally a walk in the park, complete with a road going most of the way through, with well maintained and signed trails beyond that. It was here we encountered the largest oak on our trip by far (pictured), as well as some staggeringly large Douglas-fir (Pseudotsuga menziesii) veterans. In addition to having the largest oaks, this was perhaps the most expansive of the areas we sampled. We collected samples from trees across five separate meadows and bluffs.

Huggin’ it out with a massive oak in Crow’s Nest’s Spring Meadow.

After a “long, hard day” of sampling, we headed back to Vancouver Island and drove/ferried to our camp site in Fillongley Park on Denman Island. The next morning we hitched a ferry over to the irresistibly-charming Hornby Island, and made our way to Helliwell Park. Dense conifer forests, lush with waist-high salal (Gaultheria shallon) and towering salmonberry (Rubus spectabilis) quickly faded into breathtaking wind-swept bluffs. Bald eagles (Haliaeetus leucocephalus) were commonplace and we were fortunate enough to catch glimpse of a massive golden eagle (Aquila chrysaetos). We sampled a small grove within the park and then headed just outside it to the High Salal Public Trail, where the major grove was located. Although still heavily invaded, this meadow had the most-intact flora of any site we found, with abundant blue camas (Camassia quamash), shortspur seablush (Plectritis congesta), and spring-gold (Lomatium utriculatum). We finished our sampling with plenty of time to hit rush-hour traffic on our way back into Vancouver. Yay!

Gorgeous blue camas (Camassia quamash) in Helliwell Provincial Park, Hornby Island

Sean King with bags upon bags of buds. High Salal Public Trail, Hornby Island

 

 

 

 

 

 

 

After a day of rest, we were at it again. This time, our goal was to sample two extremely isolated populations in the Fraser Valley, 52 and 128 km from the next-nearest oaks in Bellingham, Washington. The origins of these populations are unknown, although speculation abounds. Hypotheses range from rare dispersals within the crops of mourning doves (Zenaida macroura) or band-tailed pigeons (Patagioenas fasciata), to intentional plantings by First Nations, to the final relics from a broader distribution in times past. Either way they’re certainly oddities and I was very excited to visit them firsthand.

Chocolate lillies (Fritillaria affinis), an unexpected treat to find amongst the oaks of Yale.

Sean admiring the scenic Fraser River from our sampling site in the Garry Oak Ecological Reserve, Yale, B.C.

Once we’d arrived in Yale, we checked in with the local First Nations and were fortunate enough to catch a boat ride out and back from Chief Doug Hansen. Although we hadn’t brought a map of the grove’s location along the river, a short trip upstream revealed some oaks set high on sheer cliffs along the river’s eastern shore. We pulled into a rocky alcove and began scrambling up the boulders and into the forest. The flora at the Yale stand was particularly curious. Plants typically associated with coastal oak meadows such as chocolate lily (Fritillaria affinis) were found side-by-side with interior species like calypso orchid (Calypso bulbosa). The oaks were healthier and more abundant than I’d expected, often sporting a thick coat of mosses and lichens. However, there were many large oaks that had established away from the rocky cliffs and were facing encroachment by Douglas-firs, suggesting that fire may have played a role in establishing and/or maintaining this grove in the past. This site was the most pristine of any of the sites we visited, with only a few patches of exotic grasses. The dense Douglas-fir forest with moss-and-herb floor, air thick and sweet, opening up into oaken glades and cliffs, gave the site a very mystical feel. There is some evidence that this site was once a First Nations burial ground; the uniqueness of the site would certainly lend itself well to sacred purposes.

Peeking out at the Fraser Valley from behind some of the larger oaks at the Sumas Mountain site.

As soon as we were back ashore we set out for Sumas Mountain outside of Chilliwack. As I was familiar with this site, I knew we would be in for some genuine work getting to the trees. The site is some way up a brutally steep slope, with plenty of Himalayan and trailing blackberry (Rubus discolor and R. ursinus, respectively) and stinging nettle (Urtica dioica) along the way. I had the forethought to bring gloves and pants this time around. Despite the scrapes and stings incurred on our way up to the site, the view and the landscape were well worth it.

Large cliffs and boulders overlook the Fraser Valley with some seemingly out-of-place oaks nestled on exposed rock spurs or in sunny patches amongst a matrix of mature Douglas-firs. There are still perhaps fifty mature trees at the site spread atop and below a complex network of sharp granite escarpments, with myriad saplings lining the cliff edges, though the landowners had told me the oaks were more numerous when the farm was established some seventy years ago. Fire scars on some of the veteran conifers and the presence of large oaks among a fairly even cohort of bigleaf maple (Acer macrophyllum) and Douglas-fir makes me think that this grove may have established after a fire some time ago, with only the largest oaks still remaining amongst the fast-growing conifers and the remainder isolated to the driest and shallowest soils on spurs and cliffs.

Sampling an oak atop an isolated spur on Sumas Mountain.

Once we were back down the mountain and assured ourselves we were free of ticks, we got back on the road just in time for rush hour (again). Drenched in sweat and dirt, we were all smiles as we drove back to Vancouver at a crawling pace.

These outings have given me a wonderful perspective of Garry oak at its most marginal, eking out an existence in the face of human development and encroachment from competing vegetation. At every site, it was apparent that fire probably played a role in maintaining the meadows historically, and their persistence in an era of fire suppression is questionable. Some of the rockiest sites will probably persist for some time, but the deeper-soiled meadows are already shrinking and will certainly continue to do so without human intervention.

The samples I’ve collected on these trips will hopefully provide some insight into genetic diversity and gene flow at the absolute outskirts of the species range of Garry oak, far from other trees. Evidence of high levels of gene flow even at great distance in other areas of the species range suggests that, despite extreme physical isolation, perhaps these populations are staying healthy and viable with help from friends in far-away places.