5-6 Forestry paper with graphs, due 4.15

The genecology and conservation genetics of Garry oak

FRST 210 – Forest Biology II

March 24th 2020

This project is designed to give you a better idea of how differences among populations from different provenances of trees reflect adaptation to their home climate in a common garden experiment. It will also demonstrate some of the principles that have been presented in lectures.

There are two major parts to the report you will write. The first will include an analysis of a provenance trial of Garry oak (Quercus garryana) growing at UBC. The second will be a discussion of your results, including a comparison of Garry oak with another species that you will be assigned (not all students will have the same species). A full individual report is due via Turnitin on Saturday, April 18th, by 11:59PM. Late reports will lose 10% per day.

REPORT PART I

INTRODUCTION

The Centre for Forest Conservation Genetics in the Department of Forest Sciences maintains a range-wide provenance trial of natural populations of Garry oak (Quercus garryana Douglas ex Hooker). This collection was established by a M.Sc. student studying conservation genetics in this species (Huebert 2009). He collected acorns from trees in thirteen natural populations throughout the species range, from central California to Vancouver Island (figure 1). This sampling included two taxonomic varieties, Quercus garryana var. garryana and Q. garryana var. semota (also known as var. breweri or var. fruticosa). Present throughout most of the species range, Q. garryana var. garryana grows as a medium-sized tree in well-drained valley bottoms with rich soils. In the southern portion of the range, Q. garryana var. semota grows as a short, multi-stemmed shrub in rocky soils and at high elevations. Climatic data were estimated for each of these provenances using ClimateWNA (Wang et al. 2012) and used to assess clinal variation in seedling growth. Seedlings were grown in a greenhouse for one year then sown into two common garden experiments, one of which was planted in Totem Field at UBC, and the other in Duncan, BC. You will collect and analyze data from the Totem Field experiment.

Table 1: Geographic, taxonomic, and climatic data for thirteen provenances of Quercus garryana.

Prov. Taxonomic variety Latitude Longitude Dist. from Vancouver

(km)

Mean annual temp. (°C)

Mean temp. of the

warmest month (°C)

Mean temp. of the

coldest month (°C)

Mean summer precip. (mm)

1 semota 35.87 -118.64 1544 12.3 22.2 4.6 57 2 semota 36.8 -119.09 1425 13.5 23.6 6.3 62 3 semota 39.1 -120.85 1145 14.1 24.1 5.9 86 4 semota 40.36 -122.94 990 12.1 22.4 3.5 78 5 semota 40.85 -122.03 940 15.0 25.3 5.8 159 6 garryana 41.85 -122.84 825 11.6 22.2 2.0 81 7 garryana 42.47 -122.62 757 10.6 20.2 2.1 133 8 garryana 45.01 -123.17 472 10.8 18.5 3.7 221 9 garryana 45.28 -121.35 465 8.7 18.7 -0.7 68

11 garryana 46.83 -123.01 271 10.4 17.7 3.6 214 13 garryana 48.79 -123.7 61 9.9 17.6 3.1 172 14 garryana 48.46 -123.4 89 10.0 16.4 4.2 139 15 garryana 49.73 -125.02 138 9.1 17.0 2.1 234

Figure 1: Species range of Quercus garryana, showing sampling locations of thirteen provenances planted in Vancouver, BC, in 2008.

MATERIALS

In the autumn of 2006, acorns were planted in individual containers with standard perennial potting soil. In 2007, the germinated seedlings were grown in a greenhouse at UBC for their first year. The climatic conditions in the greenhouse were very mild. Temperatures remained warm and the seedlings were well-watered. While in the greenhouse, the seedlings were measured for date of seedling emergence, height, circumference, and date of bud set.

One-year-old seedlings were planted into a common garden at Totem Field in 2008. The ground below the common garden was covered with landscape cloth to prevent weeds growing in the garden, and to insulate the soil over the winter. The common garden was established as a randomized complete block design, with all populations represented across twelve blocks, and with a ring of border trees around the experiment to control for extra light and soil availability at the edge of the experiment. Trees were planted 60 cm apart to prevent root competition and to ensure that all seedlings had adequate access to light. The experiment was watered as needed during the summer, but was not fertilized.

The experiment has been measured several times since its establishment. In 2008, all seedlings were measured for date of bud break, date of bud set, height, and circumference. A subset of trees were tested for frost resistance at this time. Five-year heights and circumferences were measured in 2012. In 2013, as part of a Forest Science student’s undergraduate thesis, genetic and morphological markers were used to determine that the five southernmost provenances (1 – 5) belong to the shrub variety, Q. garryana var. semota. The remaining provenances are the tree variety, Q. garryana var. garryana (Degner 2014). Ten-year height measurements were made by another undergraduate student in 2017.

This common garden was designed to measure small seedlings, but eventually the trees grew large enough to compete with one another for light and soil resources. To limit competitive effects, every other tree was thinned in 2015.

METHODS

Hypothesis development

First, you should develop two hypotheses regarding genetic variation in this species. You must use these hypotheses in your lab report. You will develop one hypothesis regarding growth pattern. Choose one provenance climatic variable from table 1 that you think will be strongly correlated with height in the common garden (for both 1st-year and 10th-year measurements). You might want to read about the genecology and climate adaptation of the second species you are assigned before developing your hypothesis. For this, hypothesize the direction you think this relationship will take e.g., “As provenance mean annual temperature increases, seedling and tree height in the common garden will decrease”. You will also develop a hypothesis regarding whether the growth form of the two varieties is under environmental or genetic control i.e., will the differences in number of stems and height observed in natural populations persist in the common garden? Remember that hypotheses don’t need to be correct, and it is not good science to change them after you analyze your data.

Table 2: Phenotypic data collected for a range-wide common garden of Quercus garryana established in Vancouver, BC, in 2007.

Phenotype Year collected Units Notes

Seedling height 2007 centimeters Measured in greenhouse Tree height 2017 centimeters May be approximate for tall trees. Tree circumference 2019 centimeters Basal circumference of the tallest stem Number of basal stems 2019 Number of stems

Measured near base of tree

Measurements

The trees were measured by FRST 210 students in 2019. For each tree, students measured the stem circumference and recorded the total number of basal stems. For circumference, trees were measured to the nearest mm at the lowest point of the stem without any prominent swelling from roots or branches, or at approximately 20cm above the ground if there was no section of the stem without these features. For trees with multiple stems, the circumference of the tallest stem was measured. The number of more-or-less vertical basal stems within the first 10 cm above the ground was counted for each tree. The TAs compiled the circumference and stem number data from all four lab sections, and calculated averages for each tree. These measurements were added to the 2007 and 2017 height data that we already have, and are posted on Canvas as an Excel spreadsheet for you to use in your analyses.

Analysis

You will test your hypotheses by analyzing data in the Excel file. You will need to use MS Excel or import the data table to another spreadsheet program to complete this lab. First, you will need to calculate provenance means for all phenotypic traits. Then you need to create a table that includes the provenance means for all of your phenotypic variables, as well as the climatic variable(s) used in your analyses. You will use this table to calculate statistics and generate the scatter plots described below. You will input these average measurements into the linear regression calculator that will be provided with your data to determine the statistical significance of your trends and to generate descriptive statistics for these trends (slope and R2 values). You will also input the individual measurements for 2017 height and 2019 number of stems into the t-test calculator to determine whether the varieties differ in either 2017 height or number of stems in 2019. When reporting your results, only include slope and R2 values for linear regressions if they are statistically significant (p<0.05), and only compare mean values between your varieties if the differences are significant (p < 0.05). We’ve included a primer on understanding statistics for those who have not yet completed FRST 231 or would like a refresher. I highly recommend that all students read this, even if you’ve already taken FRST 231 and feel comfortable with statistics. There will be an online tutorial available on Canvas for using Excel for this analysis.

Part I of your report

Introduction (Garry oak): 1 – 1.5 pages

Provide background knowledge for the study (e.g. genecology, common gardens, the ecology of Garry oak), as well as scientific justification and a purpose for this study and your hypotheses.

Material and Methods (Garry oak): 0.75 – 1 page

Describe the common garden experiment and how it was established. Explain how the data was gathered and how it was analysed. Only include information relevant to your paper.

Results (Garry oak): 0.75 – 1.5 pages, not including figures

Report the results of your data analyses and how they relate to your hypotheses. Anything that you made a figure for or performed a statistical analysis for should be reported in your results. Remember that results should be purely descriptive and quantitative.

(1) One table with climatic data for each provenance, as well as provenance averages for each of the four phenotypic traits.

(2) Two bar plots showing comparisons between the two taxonomic varieties. Include error bars with +/- standard deviation. Include p-values either in your figure or in the figure caption.

1. Mean number of stems in 2019 2. Mean height in 2017

(2) Two additional scatter plots based on your hypotheses. Include p-values either in your figure or in the figure caption. Include a regression line (also known as a trend line) and R2 value only if your regression is significant.

1. Provenance mean height in 2007 vs. your provenance climate variable 2. Provenance mean height in 2017 vs. your provenance climate variable

Part II of your report

Discussion (Garry oak and a second species): 3-5 pages

Your discussion should include ~one paragraph addressing five of the questions (please number the paragraphs accordingly for our marking ease):

Answer all 4 of the following questions:

1. Do your results support your hypotheses for growth (height in 2007 and 2017? Address each of these independently and provide biological explanations for any trends you observe.

2. Do the two Garry oak varieties differ in height or number of stems? How does this relate to your hypothesis regarding whether variety differences are under genetic or environmental control? How might these differences be relevant to the adaptation of these plants? Could you selectively breed var. semota to have a tree form like var. garryana?

3. Are the phenotypic clines for growth traits in var. garryana similar to those for the other species you were assigned? Are the same climatic variables correlated with provenance growth in the same direction in both species?

4. How much is mean annual temperature predicted to warm by the 2080s compared to the baseline climate normal period of 1961-1990 under either a moderate climate change scenario (RCP 4.5) or a severe scenario (RCP 8.5) for the northernmost provenance of var. garryana in this experiment? How does this compare with the amount of warming predicted for the northernmost provenance of the other species you were assigned? Use the software ClimateNA (http://www.climatewna.com/) by entering the latitude and longitude of a provenance to estimate warming (you don’t need the elevation). A tutorial will be posted on how to use this software, and what settings to use.

Answer 1 of the following 2 questions:

5. How would you use information from the provenance trial in a restoration plan for Garry oak ecosystems on Vancouver Island, given predicted amounts of climate change (i.e., new temperature and/or precipitation regime)?

6. How would you recommend the genetic diversity of Garry oak in British Columbia best be conserved? Is Garry oak more or less of a conservation concern than the other species you were assigned?

References: For full marks, you need to cite at least eight separate scientific publications, ideally scientific journal articles. You should cite at least three in your introduction and at least five in your discussion. You may use any established reference style (e.g. APA, MLA, Vancouver) as long as you are consistent throughout. References should only be from peer-reviewed scientific journals or government publications, and must be properly cited and referenced. In addition to the above sources, you may cite the published chapter on genecology from the Encyclopedia of Forest Sciences posted in the lecture notes (Aitken 2004), Colin Huebert’s unpublished MSc thesis (Huebert 2009), and Jon Degner’s unpublished undergraduate thesis (Degner 2014). Be sure to consult the “How to write a lab report” handout as you write your report. Do not cite any lecture notes. There will be a short online tutorial on using the UBC Library and Web of Science or Google Scholar to find peer- reviewed scientific publications relevant to your report.

Formatting: Your report should be double-spaced in 11-point font with 2.5cm margins on all sides. Any deviations in formatting to circumvent page limits will receive penalties. Without figures, your report should be a total of 4.5-7 pages. If you can’t fit your sections into the allotted page limits, it means you need to write more concisely. Figures may be as large as you’d like, but please do not make them smaller than 1/3 of a page.

GRADING

Introduction - 15 pts

Materials and methods - 10 pts

Results - 10 pts

Table and Graphs - 15 pts

Discussion – 40 pts

References – 10 pts

Total: 100 pts

References

Aitken, S. N. "Genecology and adaptation of forest trees." Encyclopedia of Forest Sciences (2004): 197-204. Degner, J. C. (2014). Using a genotyping-by-sequencing (GBS) approach to elucidate population structure in Garry

Oak (Quercus garryana) (Undergraduate thesis, University of British Columbia). Huebert, C. A. (2009). The ecological and conservation genetics of Garry oak (Quercus garryana Dougl. ex

Hook) (Master’s thesis, University of British Columbia). Wang, T., Hamann, A., Spittlehouse, D. L., and Murdock, T. Q. (2012). ClimateWNA—high-resolution spatial climate

data for western North America. Journal of Applied Meteorology and Climatology, 51(1): 16-29.