Category: Percy Hebert

Post 8: Tables and Graphs

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Figure 1: Boxplot showing median (thick line), interquartile range (box), variability (whiskers), and outliers of flower per plant measurements at each site.

Due to snow, I have changed my project and traveled several hours further afield to find sites that aren’t coated in a sheet of ice. As such, I am now investigating differences in average number of flowers on Achillea millefolium (commonly known as yarrow) at two sites near Abbotsford with different elevations.

Luckily for me, I am taking this course concurrently with statistics, and so I am becoming very comfortable with using R to analyze data and produce graphs. I decided that a boxplot was the best way to compare my data, due to the ease with which one can see the differences between the two categories in median and variability. Seeing the precise numbers of every sample is simply unnecessary.

The graph does show that Site B averages a higher number of flowers than Site A. Unfortunately, the graph also exposes that the differences are fairly slight and are not likely to be statistically significance (but maybe I’ll get lucky and they will be).

I feel like I could have used further observations to reduce the variability and be more confident that the differences aren’t chance, but unfortunately the snow shows no signs of melting and another four hour trip to Abbotsford is not particularly feasible, so I will have to settle for my poorly designed little experiment and hope to gain marks for pointing out how poorly designed it is.

Blog Post #6

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I have collected data from three locations along Dallas Road, Victoria at varying distances from the ocean. At each location, I took 10 replicates using a 0.3m x 0.3m quadrat and a 3m transect in order to count the number of red rose hips and black rose hips. I employed a systematic sampling method.  It has been a few weeks since my initial observations and the winter has been hard on the rose bush. In particular, the bush closed to the ocean, which I defined as 0m from the ocean, was completely dead.  However, the dead rose hips were still present on the bush and hadn’t fallen off yet, so this bush actually provided a great “control” bush that I can compare further bushes to.

 

At first, I was set on having 3 locations and taking all my samples from these bushes; however, I will need to find more locations along Dallas Road as the 3 locations will not provide enough replicates solely from themselves.

 

I did notice how much the survival of the rose hips varied on a temporal scale, even within just 2 weeks. This observation will not directly affect my hypothesis, but makes me wonder how the survival of the rose hips varies based on the season.

Post #5: Design Reflections

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I took my initial samples along Dallas Road and Beacon Hill Park (Victoria, BC) this week. The weather was sunny, 8°C and windy.  I used a 0.3m x 0.3m quadrat, systematic sampling strategy and counted the number of Nootka dead and alive rose hips at three locations along a gradient differing in distance from the ocean. When I arrived at the first site (an exposed bush along a coastal bluff near Dallas Road), I was surprised that nearly all the rose hips were dead. I observed that the coastal bluff had a higher proportion of red, alive hips earlier this month. It appears the winter has been hard on the Nootka Rose.

 

I was nervous that the other sites would also display a similar trend; however, the sites further from the ocean, an intermediate site called “deciduous forest” and the end range site called “Beacon Hill” did have some alive hips.

 

I came across a difficulty using my quadrat as I placed the quadrat on the top of the bush, and there would be hips present at different depths beneath the quadrat.  Therefore, I will have to define my sampling area as within the same plane as the quadrat.

 

As well, I will need to find more sites within each gradient for the final data.  There are not enough sample units from the single site I collected data from for the initial data.  I have confidence that there are other sites within each gradient where the Nootka Rose grows.

 

I will continue to collect data in the same manner; however, modify my definition of the quadrat region and search for additional sites within each gradient.  Redefining the area of the quadrat region will make the replicates more standardized. As well, collecting more data from additional sites will provide a more accurate measure.

This article is suitable to use for a reference ✔︎

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The article that I found is academic, peer-reviewed research material. The research was done following the flooding in 2005, when the macrophyte and water dynamics were changed by the influx of rainwater. Over a period of four months, samples of periphyton were collected bi-weekly from the Bow River at six different locations in the Southeast area of Calgary. The purpose of this study was to determine whether the Bow River water quality model (BRWQM) used by the City of Calgary was calibrated properly to detect dissolved oxygen and periphyton levels in the water. The BRWQM is an invaluable tool used to ascertain the quality of water that has been treated by the wastewater treatment plants.

The authors are all based out of the University of Calgary. Robinson is in the Geomatics Engineering department in the Schulich School of Engineering; Valeo, Chu and Iwanyshyn are in the Civil Engineering department in the Schulich School of Engineering; and Ryan is in the Geoscience department. This means that the article is an academic one, researched and written by experts. The acknowledgments section thanks the reviewers, as well as City of Calgary and the Natural Sciences and Engineering Research Council (NSERC) for funding the paper.

 

Reference Cited

Robinson KL, Valeo C, Ryan MC, Chu A, Iwanyshyn M. 2009. Modelling aquatic vegetation and dissolved oxygen after a flood event in the Bow River, Alberta, Canada. Canadian Journal of Civil Engineering [Internet]. [cited 2018 Feb 8]; 36(3), 492-503. Available from: http://www.nrcresearchpress.com/doi/full/10.1139/L08-126#.Wny4dmbMzOQ doi:10.1139/L08-126

Blog Post #2 — Cameron Purdy

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Academic Peer Reviewed Research Paper

Title:  Terminal Nerve GnRH3 Neurons Mediate Slow Avoidance of Carbon Dioxide in Larval Zebrafish

Source: Koide T, Yabuki Y, Yoshihara Y. Terminal nerve GnRH3 neurons mediate slow avoidance of carbon dioxide in larval zebrafish. Cell Reports, 2018 DOI: 10.1016/j.celrep.2018.01.019

Link: http://www.cell.com/cell-reports/pdf/S2211-1247(18)30036-6.pdf

 

The following paper is an Academic Peer Reviewed Research Paper for the following reasons:

a) The paper is written by experts in the field. Koide, Yabuki, and Yoshihara are all associated with the Laboratory for Neurobiology of Synapse in Japan. It was published in the journal “Cell Reports” which publishes high quality peer-reviewed material.

b) The paper contains a bibliography citing additional sources used as information. These sources are cited in text throughout the article. (Ex.  “This fast escape response is mediated by reticulospinal neurons, including the large, morphologically conspicuous Mauthner cells” (Gahtan et al., 2002; Liu and Fetcho, 1999; O’Malley et al., 1996).)

c) Acknowledgements thank two editors for their critical reading of the manuscript indicating that the paper had gone through the peer review process. This is further supported by the journal the article is posted in.

d) The paper is formatted as a research paper as it contains an introduction, results and discussion. The experimental methods were included within the results section. We can see that there are multiple intervention levels further leading us to believe that the paper is experimental in nature. *(See below)

(To examine what chemosensory signals affect behaviors of larval zebrafish, we applied various chemicals to the head of fish at 5 days post-fertilization).

Blog Post 1: Observations

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Blog Post #1: Initial Observations of Study Area

Cameron Purdy – T00028679

January 31, 2018

Address:  33844 King Rd, Abbotsford, BC, V2S7M7

Coordinates: 49.0291° N, 122.2854° W. ~40m above sea level

Weather: Light rain showers, ~ 4ºC.

Seasonality: Winter

Time: 3:20PM

Description of Study Area:

The area(s) I have decided to observe are two separate ecological islands on the University of the Fraser Valley campus. Prior to UFV being built, the location was comprised of mainly farmland. Historically, the Fraser River had a much larger footprint and had floodplains that covered much of Abbotsford including areas surrounding UFV. 

Location A is a temperate deciduous forest with area (A=440m²). It is bordered to the north by the Abbotsford Entertainment and Sports Center, and surrounded by parking lots to the east, west, and south. The general topography of the forest is flat, however there is a slight slope coming down from the parking lot on the east most side. The most prevalent vegetation found includes Convallaria majalis, Oemleria cerasiformis, Maianthemum racemosum, and Trientalis borealis. Additionally, tree canopy cover in this forest is quite dense and filters out much of the sunlight. Few species of birds could be seen flying amongst the trees. 

From left to right:

  1. Forest A looking north from the south. Parking lot can be seen to east with the slight slope leading down into the forest.
  2. Forest A looking north from south. Parking lot can be seen to west, Abbotsford Entertainment Center can be seen at the north end of forest.
  3. Forest A looking north from south. Proposed transect line through middle of forest.

 

Location B is also a temperate deciduous forest with area (A=540m²). It is bordered by buildings and a walkway to the west and south, and grass fields to the north and east. Centrally located in the forest is a small pond (A~200m²) that is surrounded by marshy wetlands. The general topography is relatively flat, with a slight slope on the east most side of the forest. The pond situated within the forest collects water that runs off the slope, and has a small stream that exits the forest to the south. The most prevalent vegetation found includes Rubus spectabilis, Rubus idaeus, Oemleria cerasiformis. The tree canopy cover in this forest is less dense than that of location A. While no wildlife was seen, frogs could be heard from the pond. 

From left to right:

  1. Forest B looking north from south. Open grass field can be seen to east, ground slopes downward towards the west.
  2. Forest B looking north-east from south-west. Pond and marshy surrounding areas seen.
  3. Forest B looking south-west from north-east. Proposed transect line through middle of forest.

Follow up Questions: 

1) What leads to the difference in vegetation among the two forests. How could they have a significantly different prevalence of plant species when they are located so close to each other?

2) While we know the vegetation differs between the two sample forests. How does the fauna differ between the two. Is there a higher prevalence of specific invertebrates in one forest over the other?

3) What are the differences in soil composition? If there are differences, could these in fact be linked to the the prevalence of specific flora and fauna in their respective forests.

Post 1 – Initial Observations

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The area that I have chosen to study is a field that runs along the Bow River in the South of Calgary, Alberta. The Pine Creek Wastewater Treatment Plant is located here. The green space next to it, and which runs a long ways along the Bow River, is used by dog walkers (of which I am one) and some owners as an offleash area for dogs to run in. It is not designated as an offleash area by the City of Calgary. The region of the pathway that I walk runs approximately 6 km total, and is on a ridge slightly above the Bow River. A more accurate distance measurement must be made. The Northern stretch of path is more heavily wooded, with many plants growing around the path and on the hills that border the West side of the path. There is a smaller, secondary path that wanders down towards the river and then back up to the meet the main pathway. Walking South from the parking lots, the path is at a higher elevation from the river, and a steep rocky embankment makes it harder to access the river. Northeast of the parking lots there is a main access point to the river.

 

I go to this area at least once a day during the week with my dogs, but it wasn’t until the end of January that I brought my journal along with me. There are still many natural elements in the park, and more possible subjects to explore than I initially thought, as I had previously only thought about the dogs I was walking. There are many different species of plants, and I have observed ducks, hawks, deer, and coyotes in the area.

 

I brought my field journal with me on January 30, 2018 at 1030 hours. The weather was excellent that day: sunny and 7℃ with only about 1 cm of snow still on the ground. This is quite warm for the end of January, but was thanks in part to a Chinook blowing in.

 

Three questions that came to mind were:

  • Are there species of plants that are found only along the river, and not in areas that are farther removed from the river?
  • There are many wolf-willows (Elaeagnus commutate) along the pathways. The ones that are nearest the path are under 3’ tall, while the ones that are along the secondary pathway are well over 6’. Is this due to the proximity, either distance or elevation, from the river?
  • Are the plants on the islands in the middle of the river the same as those along the pathway that I walk, or are they different? Is this due to lack of human activity, or increased presence of wildlife?

Post #4

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Systematic, random and haphazard sampling techniques were compared in the virtual forest tutorial.

Systematic had the fastest estimated sampling time (12 hours and 7 minutes). Haphazard sampling was second fastest (12 hours 34 minutes) and random was the slowest (12 hours and 42 minutes).

The percent error is summarized in table 1. Systematic and haphazard produced similar percent error values for the two most common species (eastern hemlock and red maple).  Systematic sampling produced errors of 7.3% for eastern hemlock 15.6% for red maple. Random sampling yielded percent error of 1.57% for eastern hemlock and 51% for red maple.

White pine and striped maple were the least common. However, no method sampled either of these trees. The next least common were yellow birch and chestnut oak. Haphazard yielded the smallest percent error (4.3% for yellow birch and 5.13% for chestnut oak). Systematic was second best (14.8% for yellow birch and 15% for chestnut oak). Random had the highest percent error (33.9% for yellow birch and 61.5.0% for chestnut oak).

It appeared that systematic sampling became more slightly more inaccurate as species abundance decreases. Haphazard sampling was more stable, however it randomly had a very high error for sweet birch. Random produced the smallest error in entire tutorial for the most common species (eastern hemlock 1.57%), but produced more inaccurate results for all other less abundant species.

 

Table 1. Percent error produced by systematic, random and haphazard sampling in a virtual forest tutorial

System Random Haphazard
Species Actual Density Data Density Error (%) Data Error

(%)

 Data Error (%)
Eastern Hemlock 469.9 504.2 7.3 462.5 1.57 550 17.0
Sweet Birch 117.5 112.5 4.3 141.7 20.6 183.3 56.0
Yellow Birch 108.9 104.2 4.3 145.8 33.9 125 14.8
Chestnut Oak 87.5 66.7 23.8 33.3 61.5 75 14.3
Red Maple 118.9 137.5 15.6 58.3 51 125 5.1
Striped Maple 17.5 0 N/A 0 N/A 0 N/A
White Pine 8.4 0 N/A 0 N/A 0 N/A

 

 

 

Post #3: Ongoing observations

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Date of observations: January 18 2018

Time: 11:00am

Location: Dallas Road pathway and Beacon Hill Park

Weather: Partly cloudy with light rain.  Medium wind coming from the SE (11km/h)

Temperature: 7C

 

I continued to make observations at Beacon Hill Park. Today, I opted to observe the environmental gradient between the exposed coastal bluff across from Beacon Hill, across Dallas Road and a sheltered Garry Oak ecosystem on the front face of Beacon Hill.  The gradient changes slightly in elevation as the distance from the ocean increases.

 

Today, I noted the change in appearance of the Nootka rose bush.  There were noticeably more dead, brown rose hips on the bushes closer to the ocean, then in a more protected area of Beacon Hill. This pattern prompted me to consider the Nootka rose bush for my research project.

 

Along the gradient, I choose 3 locations to observe the Nootka rose bush.  At the first location, Coastal Bluff (CB), the rose bush contained almost all dead, brown rose hips.  There were no other trees. It was the most exposed to wind. Some low-lying grasses were present.

 

The second location, Deciduous forest (DF), was between the Coastal bluff and Dallas Road.  There were substantially more red rose hips, in comparison to CB.  The rose bushes were more protected by large, deciduous trees and less wind was felt.

 

The third location, halfway up the front face of Beacon Hill (BH), was the most protected from the wind.  The elevation increased, and then plateaued. I found another patch of Nootka rose bush growing alongside Garry Oaks within a small depression. Almost all the rose hip berries were red.

 

I am curious about the relationship between the distance from the ocean and the Nootka rose bush.

 

Hypothesis: The number of red, living rose hips on the Nootka rose bush is determined by the distance it is from the ocean.

 

Prediction: Rose bushes further from the ocean should increase in the number of red rose hips on the Nootka rose bush, in comparison to brown, dead rose hips.

 

Response variable: The ratio of living, red rose hips to dead, brown rose hips

 

Explanatory variable: distance from the ocean

 

Figure 1. Page 1 from field journal
Figure 2. Page 2 of field journal
Figure 3. Topographical profile of environmental gradient

Post 2: Sources of Scientific Information

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The article I found, “Paleoecology and fire history of garry oak ecosystems in Canada: implications for conservation and environmental management”, is an academic, peer-reviewed research material.

 

It can be found at the following link:

 

https://link-springer-com.ezproxy.tru.ca/content/pdf/10.1007%2Fs10531-015-0880-1.pdf

 

I first determined whether the source is academic or non-academic by considering the following criteria:

 

  • was the material written by an expert?
  • Are there in-text citations?
  • Is there a bibliography?

 

The authors, Pellatt, McCoy and Mathewes are all experts in their field.  Pellatt is the Protected Areas Establishment and Conservation Directorate at Parks Canada. McCoy and Mathewes are both scientists at Simon Fraser University, in the Department of Biological Science.  There are in-text citations and a bibliography. Therefore, the source is academic.

 

The next criteria separate peer-reviewed academic sources, from non peer-reviewed academic sources.  A peer-reviewed academic source has been reviewed by at least 1-4 reviewers.  The article has been reviewed by 2 anonymous reviewers.  Therefore, the article is a peer-reviewed academic source.

 

The final criteria distinguishes peer-reviewed source research from peer-reviewed source reviews.  Peer-reviewed academic research material contains a methods and results section. Pellatt et al (2015) contains a methods or results section. Therefore, it is an academic, peer-reviewed research material.

 

Pellatt, M. G., McCoy, M. M., & Mathewes, R. W. (2015). Paleoecology and fire history of Garry oak ecosystems in Canada: implications for conservation and environmental management. Biodiversity and Conservation, 24(7), 1621-1639. doi:10.1007/s10531-015-0880-1