ENV11115 Case Studies in Applied Ecology Assessment Questions

Published: 10 Dec, 2025

Category	Assignment	Subject	Education
University	Edinburgh Napier University (ENU)	Module Title	ENV11115 Case Studies in Applied Ecology

ENV11115 Case Studies in Applied Ecology ASSESSMENT INSTRUCTION SHEET

Patrick J. C. White (p.white@napier.ac.uk)

Answer as many of the following questions as you are able to. Present your answers in the form of a Word document. It must be very clear in your Word document which answer refers to which question (each question is uniquely numbered). Please read each question carefully and, where requested, show your working, R code or provide reasoning. For ease of marking, please present any R code or output in the font ‘Courier New’. Where a word limit is given, you must not exceed this (professional reports and articles regularly have strict word limits so this is a good habit to get into). Font size should not exceed size 11.

This assignment is subject to the University’s regulations. It is important that this assignment is carried out independently, it is not a group project and it cannot be completed with any assistance from other students. This would be treated as an issue of academic misconduct.

SECTION 1 – Studying highly mobile species

QUESTION 1.1 [marked out of 8]

Find a peer-reviewed article that describes a study of movement or space-use of a seabird species (or more than one) of your choice, based on telemetry/tagging.

Provide the reference for the study in APA style. Then, in 200 words or fewer, comment upon: the type of telemetry device used; its attachment method and mass relative to the animal; the method(s) used to study movements or space use of the species; the reason(s) for the study; any criticisms you may have regarding their practical or methodological approach; a brief statement about the main result(s) that the study revealed; any ethical considerations.

QUESTION 1.2 [marked out of 8]

Download the datasets ‘detections.csv’ and ‘porbegales.csv’ from Moodle. These are similar to thedata sets you used for the elasmobranchs case study tutorial.The ‘detections.csv’ is an acoustic telemetry data set for porbeagle sharks tagged around the Orkney Isles in the Scapa Flow area over a 2-year period (2018-2020). The ‘porbegales.csv’ file contains the relevant metadata for the tagged sharks: Date, Lat and Long (latitude and longitude in decimal degrees), sex (F = female, M = male), length (in cm), and Tag ID (unique to each animal).

Produce whatever figures and/or tables you feel suitable to demonstrate how porbeagle sharks use the Scapa Flow area and to present to managers. There should be an interpretation of the analysis to present what you found out, but you do not need to provide any information on the species.Provide figure and/or table captions that explain what the figures/tables represent and how to interpret them. You should refer to journal articles to see the types of captions that are provided in publishable-quality work. Marks will be awarded for both content and professionalism in presentation.

Please provide annotated R code for this answer. Annotations should be prefixed with the ‘#’symbol. Provide the code in the Courier New font.

QUESTION 1.3 [marked out of 5]

An MPA for porbeagle has been suggested in the Scapa Flow region; based on the analysis of the data, what information would you give managers for this idea? Justify your answer. If managers require additional advice on the movements of porbeagle sharks, what research methods would you suggest?

SECTION 2 – Analysing nest data

QUESTION 2.1 [marked out of 6]Use the dataset ‘DUNNOCK NEST DATA.csv’ which contains dunnock Prunella modularis nest data from lowland farmland in 1992 and 1993. In the dataframe there is a column called ‘success’ which indicates whether a nest was successful or not successful. There are also columns ‘observed.days’ which indicates the number of days each nest was observed for, and ‘success.days’ which indicates the number of days that each nest was successful for.If you were to estimate traditional/basic nest success, by what amount would you have over- estimated it, relative to estimating nest success using the daily survival rate method?

For this, assume the nest cycle duration of dunnocks is 32 days.

This question applies to the whole dataset. Explain your working.At the end of your answer, provide any annotated R code for your analysis. Annotations should beprefixed with the ‘#’ symbol. Provide the code in the Courier New font.

QUESTION 2.2 [marked out of 3]

Fill in an electronic nest record card based on the following description of a nest observation. There is a BLANK ELECTRONIC NEST RECORD CARD available on Moodle, which you can copy and paste into your answer document.On 24^th April 2022 you find a nest in ivy on a tall tree stump, but don’t yet know for sure which species it is. You hear, but don’t see a bird flutter away from the nest and on careful inspection you feel that the nest contains 3 warm eggs. You return on the 28^th April and a similar thing happens,

you hear a bird flutter away from the nest and see that the nest contains four eggs. On 1^st May you visit the nest but approach very cautiously and see there is a female greenfinch sitting on the nest. Based on the dates, you decide to leave the female to incubate, and return on the 6^th May. Again you hear a bird fly away from the nest and on careful inspection there are still four eggs in the nest. On visiting on the 10^th May, unfortunately, the nest is now empty, although in apparently good condition.

QUESTION 2.3 [marked out of 5]

Using the same format used in the DUNNOCK NEST DATA.csv file, extract the equivalent relevant data from the greenfinch nest record card from Question 2.2 and enter it in your answer sheet in the format of a small table similar to this one.

	year	observed.days	success.days	success

QUESTION 2.4 [marked out of 10]

For the dunnock data from Question 2.1, you have the following hypothesis: “daily survival probability is related to the year nests were recorded in”. ‘Year” can be treated as a categorical explanatory variable in this case. Test this hypothesis using the DUNNOCK NEST DATA.csv data and provide a full statement of results to answer this question.

This should include a statement relative to the hypothesis, statistical evidence for that statement, and any effect sizes if required. At the end of your answer, provide any annotated R code for your analysis. Annotations should be prefixed with the ‘#’ symbol. Provide the code in the Courier New font.

QUESTION 2.5 [marked out of 3]

You intend to carry out a study to estimate the daily survival probability of tree pipits Anthus trivialis, a migrant species which winters in sub-Saharan Africa and the Indian subcontinent, and breeds across large parts of Eurasia.

What value(s) would be appropriate to use as a nest cycle duration for a population in the UK, so you could convert your daily survival probability estimate to a daily survival rate nest success estimate. Explain your reasoning.

QUESTION 2.6 [marked out of 3]

You carry out a study and estimate nest success using the daily survival rate method for a population of black redstarts Phoenicurus ochruros estimating that 21% of nests fail. Another study is carried out in a different region and published in a journal. You want to compare your estimate to theirs. They publish their estimate in the form of a daily survival probability of 0.989.

Assuming a nest cycle duration of 34 days for this species, is estimated nest success using the daily survival rate higher or lower in their study than in yours? Show your working.

SECTION 3 – Camera-trapping data extraction

QUESTION 3.1 [marked out of 7]
Watch the following camera-trap videos of otters camera-trapped in the UK. Please try to identify the sex and age-class of the otter(s) shown and give reasons based on characteristics you observe. Please provide your answer as a table with columns:

Clip; Sex/age class; Reasons. Include a Table caption. If you do not think there is sufficient information to assign a sex/age class, please say so but justify this.

There will be marks for accurate answers but also presentation and justifications given.

CLIP 1: Method(Ec)ology Lab

CLIP 2: V8 Rolling

SECTION 4 – Transferring analysis skills to different applied ecology scenarios

QUESTION 4.1 [marked out of 8]

A marine biologist is interested in the probability of coral bleaching in an area of coral reef. She dives to 10 fixed reef quadrats and records, in each plot, the number of corals (from a random selection of 20) that were bleached and the number of corals that were healthy. Below is the page from her notebook, where she recorded the data after the dive.

Estimate the probability of a coral being bleached based on her data, and provide a standard error of that estimate. At the end of your answer, provide any annotated R code for your analysis. Annotations should be prefixed with the ‘#’ symbol. Provide the code in the Courier New font.

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QUESTION 4.2 [marked out of 13]

The biologist returns and records the distance (in km) of each plot to the coastline. These are recorded for sites 1 to 10 respectively as: 3 km, 30 km, 37 km, 48 km, 20 km, 1 km, 84 m, 20 km, 8km and 20 km. She hypothesizes that the probability of bleaching will be related to the distance of the plot to the coastline. Test this hypothesis and produce a statement of results. Also produce an appropriate plot. As if you were presenting this in a scientific paper, provide a figure caption.. At the end of your answer, provide any annotated R code for your analysis. Annotations should be prefixed with the ‘#’ symbol. Provide the code in the Courier New font.

QUESTION 4.3 [marked out of 9]

An ecologist is investigating habitat selection patterns of smooth-coated otters Lutrogale perspicillata in Goa, India, where otters live in close proximity to fishing communities. He uses field signs to assess presence (1) or absence (0) of otters within 78 grid squares and also restimates mangrove cover for each square, using satellite imagery. Data are stored in the file “SMOOTH COATED OTTERS.csv”, with the variable otter presence/absence called “OTTER.SIGNS” and estimate mangrove cover called “EMC”. Test the hypothesis that “probability of presence of smooth coated otters is significantly positively related to estimated mangrove cover”, and produce an appropriate statement of results that addresses this hypothesis. Additionally, if the relationship is significant, provide an appropriate plot to visualise the hypothesised relationship, including standard errors for the best fit line. Write a caption for the figure that would be appropriate for presentation in a report or publication. At the end of your answer, provide any annotated R code for your analysis. Annotations should be prefixed with the ‘#’ symbol. Provide the code in the Courier New font.

QUESTION 4.4 [marked out of 12]

A research team are studying habitat use of flapper skates Duipturus intermedius in waters of Orkney, Scotland. They want to categorise seabed substrate so they can use this as a habitat variable, taking this by observing the sea floor on videos of Baited Underwater Remote Video (BRUVs), which are baited cameras lowered to the seafloor to study fish behaviour, diversity and abundance. Three research assistants are asked to classify the sediments as “rock”, “coarse”, “mixed” and “fine”. Initially, the researchers carry out an inter-observer reliability assessment on 15 videos to check consistency, each watching the videos independently and not sharing their data until the end. The data are below.

VIDEO	RESEARCHER 1	RESEARCHER 2	RESEARCHER 3
1	coarse	coarse	coarse
2	fine	fine	mixed
3	rock	rock	rock
4	coarse	coarse	coarse
5	fine	mixed	fine
6	mixed	mixed	NA (not sure so left blank
7	rock	rock	rock
8	rock	rock	rock
9	coarse	coarse	coarse
10	coarse	mixed	mixed
11	coarse	coarse	coarse
12	rock	rock	rock
13	fine	fine	fine
14	fine	fine	fine
15	fine	fine	fine

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