LIFE324 Current Skills and Topics in Evolutionary Biology Semester 2 2023/24Statistics

Java Python School of Life Sciences

Coursework assessment for Assessment Cycle 1

(Semester 2, 2023/24)

LIFE324 Current Skills and Topics in Evolutionary Biology

Submission date: Monday 11^th March 2024 at 10:00

Maximum word count: 1000

Please read all instructions (general and specific) carefully! Please also make sure to familiarise yourself with the student guidance for written assessments (Canvas > OX-LIFE-Sciences-202223 > Assessment).

General instructions to students:

1. Word count

· The word count is a maximum (not plus/minus 10%). There is no minimum word count.

· Please refer to the specific instructions below regarding what is and what isn’t included in the maximum word count for this assignment.

· Penalties will be applied for exceeding the word count as follows:

o Up to 1% (e.g. up to 2020 for a 2000 word maximum) no penalty

o Up to 10% (e.g. between 2021 and 2200 words) 5 % penalty

o Up to 20% (e.g. between 2201 and 2400 words) 10 % penalty

o Etc. (i.e. 5% penalty for every 10% above word count)

· Enter your word count at the bottom of your submission

2. Submission

· Your work should be submitted via the submission link in your module area in Canvas

· Please make sure that you follow the guidance on ‘Submission procedures for assessed coursework’ which is published in the School Handbook on Canvas.

· Also refer to the School Handbook in relation to the penalties for Late Submission and possible exemptions.

· If you have any technical problems submitting to Canvas by the deadline, you must email your work to the module organiser (copying in [email protected] ) by the deadline, as evidence that you have submitted in time. You should then continue to attempt submitting via Canvas.

3. Academic Integrity

The University’s Academic Integrity policy and your annual Academic Integrity declaration

apply to this assessment. If necessary, the full range of penalties (Category A, B, C, D, and E)

will be available to examiners if they discover contraventions of the Academic Integrity

policy. You can consult the University’s Academic Integrity guide for students here:  

https://www.liverpool.ac.uk/media/livacuk/tqsd/code-of-practice-on-assessment/appendix_L_cop_assess_annex1.pdf  

Please note: Your answer should be written in your own words. Do not use any verbatim (word for word) quotes. Your assignment may not contain verbatim (copy-and-paste) material that you have submitted for another assessment, either on this or a different module.

Expectations: Concise scientific report on the convergence of diving capacity in aquatic mammals and its association with patterns in amino acid sequence of myoglobin. The report, which includes an annotated phylogenetic tree figure and a table, builds on the phylogenetic analyses that students have performed during a series of computer tutorials which are delivered in weeks 1 and 2.

Coursework Questi LIFE324 Current Skills and Topics in Evolutionary Biology Semester 2, 2023/24Statistics on:

‘To what extent are convergent phenotypes determined by the same mechanisms at the molecular level?’

Specific instructions:

You must write a scientific report dealing with this broad question, using your analysis of diving and myoglobin in mammals as the central case study. You are encouraged to expand the depth and/or breadth of your report by discussing, for example, other traits/molecular mechanisms in relation to an aquatic lifestyle. in vertebrates, or entirely different systems of your choice.

The text of the report should be 1000 (excluding references and legends) and include, one figure and one table. It should contain the following sections:

1. Title – you decide on the specific title

2. Introduction – including background, aims of the study and, if appropriate, explicit hypotheses

3. Methods

- indicate that you used the accepted tree (rather than the CO1 tree that you generated), citing Mirceta et al. 2013, Science 340, 1234192.

- summarise how you inferred where on the tree aquatic and semi-aquatic phenotypes evolved and the reconstruction of myoglobin charge-changing mutations.

4. Results

- Figure 1 (you can use a whole page for this). Some version of the tree on the last page of the Day 4 tutorial, showing ancestral myoglobin sequence reconstruction of charge-changing substitutions and associated net charge of ancestral and contemporary sequences, in the context of aquatic lifestyle. and diving capacity evolution.

- Table 1. Listing common and scientific species name, family and myoglobin accession number.

- compare myoglobin charge properties between (and within) the main groups, in both living species and their ancestors.

5. Discussion – some questions you might consider include:

General questions

- What is the link between myoglobin net surface charge, diving behaviour and fitness?

- To what extent is the convergent evolution of an aquatic lifestyle. supported by the same amino acid substitutions in myoglobin?

- How do the results of your study compare with literature findings?

- Limitations of your analysis?

Molecular, Biochemical, Genetic Aspects

- If a myoglobin net surface charge increase is advantageous, why do not all species (terrestrial ones included) show this?

- Can you speculate on what happened with myoglobin charge evolution in ruminants?

- Do you think a net charge decrease in myoglobin would have the same effect as an increase?

- Are there other examples where convergent phenotypes could be explained by similar molecular mechanisms?

- What could be the reason for widespread occurrence of convergent molecular evolution?

Evolutionary Physiology/Ecology

- Are there other convergent traits in the evolution of aquatic mammals?

- Do you think the pygmy hippo shared a semiaquatic common ancestor with cetaceans?

- What about the river otter; did it likely share a common semiaquatic ancestor with pinnipeds?

- Could you infer past semiaquatic phases in terrestrial mammal lineages using myoglobin charge reconstruction?

- Assuming similar body masses, who could dive longer, the last common ancestor of cetaceans or pinnipeds?

- Are there other examples where convergent phenotypes could be explained by similar molecular mechanisms?

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