S366: The exam

The exam - oh my!

So the exam comes around, as always a bit of a tense time. The exam consists of several sections.
The first section is 10 questions which comes in pairs. You have to answer 1 from each pair, plus two others. So 7 questions in total from 10, but narrowed down so you have to be able to focus on the topics within each pair.

Q1 concerns 5 statements, and you have to explain why each of them is false. From mutations to molecular clocks to the allometry of horses teeth.
Q2 picks pairs of definitions and you have to explain why they are related.
I did both of these in the end, despite not quite knowing what one of the terms was.

Q3 Is about area cladograms and vicariance. Two subjects that didn't stick with me, so I missed this out.
Q4 Is about mass extinctions and what can cause them. I attempted this one

Q5 Is about the neutral theory of evolution, and molecular clocks
Q6 Concerns the different type of selection, directional, stabilising and disruptive.
Both of these tried

Q7 is about birds and sexual selection, and life balance trade offs. I tried this one.
Q8 is about allopatric selection. I wished I could remember exactly what that was - on the day I wasn't certain enough to attempt it.

Q9 Is about chromosome counts and how breeding possibilities between near relatives such as horse and donkey. I tried this one
Q10 Is about morphological constraints and how they affect things - I think I skipped this one


The next section part 2 and mandatory, is usually a question on cladograms. You have to be able to draw one usually, and usually amend it. In this exam we had to draw the given one with state changes marked on it. Then redraw it in a different format, and see which version was more parsimonious. It concerned various birds and their ancestors. I found the cladograms easier to draw than I had on mocks for this one, although I messed up the definition of sister taxon, drawing a line parallel to its sister, rather than a branch. It became obvious when the two tree lengths were the same. After looking at it for a time, and checking all the transformation states twice, I spotted the branch and everything became better.

Part 3 is also mandatory and is to do with graphs and data associated with the breeding date of birds. You are then asked to relate these things to natural selection and say whats going on. Based on the results you found you then had to infer a few things about their histories.

Finally part 4 is about a paper that you are given before hand and have to read. Then the question asks various things about the paper, and the evolutionary concepts it relates to. The paper is one from Scientific American about the loss of hair in humans, the probable time it happened and the reasons behind it. I think this went ok - but its all a bit hazy now.

All in all, it wasn't a bad exam. I'm not sure I'll have done staggering well, but enough to pass I think. It was a fair test of the stuff learnt on the course, and seemed eminently achievable. I could have done better, I could have been better prepared for some of the questions - but that is always the case. In contrast to my other exam - this seemed like a breeze!

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S366: TMA-5

TMA 5 - the final one! Three questions - but as usual, big questions with lots of sub parts.

The first question covers quite a few basic definitions of evolution, and what causes genetic variation. You are presented with various scenarios and asked to hypothesis what is going on to give the resulting diversity. It also contains a part where a mutual relationship between plants and ants is considered, and the hybridisation of two species. Finally it finishes up with a bit on Bats and the genes that have probably changed to give them their ability with questions about these concepts.

Question 2 gives you a list of scenarios a) - k) and then a list of possible answers and asked to match them up. There is not necessarily a one to one relationship between questions and answers, and also there is the additional option of "none of the above" and you can insert your own answer into the question. Its reasonably tricky, as in some cases you could easily use more than one explanation for a given event. I got most of them right, with one or two exceptions, and some of my explanatory notes were a little off the mark.

Question 3 you are given a paper to read, in this case one about the origination of dogs in the new world. Did dogs come with the settlers that  had already been domesticated before, and then came across the bearing straits, or did they come over and domesticate wolves in the Americas? So lots of questions on the paper. Interpreting their cladograms, looking at the stats, trying to find out the conclusions and the supporting data.

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S366: The book - part 2

The rest of the book contains the following chapters:

Section K - Genetic drift: Evolution at random
This is one of the few random bits of evolution, where mutations and other characteristics which aren;t strongly selected for settle out at random. Like blue eyes/brown eyes. Eventually they would settle out just by chance.

Section L - Natural selection and adaptation

Section M - The genetical theory of natural selection
Onto the genetics and the cellular level of natural selection.

Section N - Evolution under domestication and its relevance to the origins of natural phenotypic traits.
This is about artificial selection and what changes and traits can be preserved.

Section O - Conflict and cooperation
Symbiotic relationships, predator prey and paracitism.

Section P - Species
The rise of species.

Section Q - Speciation
Different models of how species can come about - through isolation mostly, but also through other ways such as behavioural isolation

Section R - How to be fit: reproductive success
Looking into the metric that is fitness, and how to measure it.

Section S - Coevolution: evolving interactions among species
How one species can affect another in its evolution.

Section T - Evolution and development
The whole evo/devo debate. I regret not being able to quote ontology recapitulates phylogeny in my TMA's and exam.

Section U - Macroevolution: evolution above the species level
How big changes happen - mostly small changes and lots of time.

Section V- Contemporary evolution
All about recent changes to humans, domestication and so o.n.

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S366: TMA-4

TMA-4 - the project.

In this TMA you have to write up two reports, in the style of a scientific paper. Its a little weird as there is a limit of 2500 words split how you like between the two papers. This is not too bad, as there is a lot of basic stuff to write about in the first paper, that you can then reference in the second. Calculations and meaning of variables etc.

I did mine on the computer project, which was the analysis of a virtual populations of the Adonis blue butterfly. It was a lot of analysis of data. Analysing virtual gels of DNA of the microsatellite markers. Then there were lots of calculations to see how related populations are, and what this might mean. This meant quite a lot of quality time with excel. The calculations aren't hard, but there are a lot of them, and its easy to get so of the steps the wrong way around.

Then there are references to find, and conclusions to write. I got a little confused about some of the statistical texts, not sure how to see if they were significant or not,  but in the end I did something that seemed to sort of read ok, and got not too bad a mark.

After many reads, I got a friend to also ready it, and based on comments I had, I went back and explained a lot more what the variables were and what they meant, which in turn made me understand them a lot better. So that was useful, but I did miss out a few key things in the report.

So - one TMA left.

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S366: TMA-3

The third TMA in this course. Three questions to answer - more conventional than TMA-2.

The first question has parts (a) - (h) and covers things from basic definitions of evolution, to matching up statements and definitions, interpreting graphs in evolutionary terms. designing experiments, working out F_ST numbers, molecular clocks and mutation effects. Phew! 40%

Question 2 is all about Hardy-Weinberger equilibriums and is just (a) - (f). It looks at a sample of mice in the wild and how closely it matches theoretical H-W models. 20%

Question 3 involves quite a lot of rather tedious measuring on a virtual experiment. It looks at the size of house sparrow bib markings and if they might give an advantage. (a) - (d) - some of them involving calculations, others speculating on how these markings might enhance or diminish an individuals prospects. It also looks at a variety of habitats and how this also changes the dynamics. 40%.

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S366: TMA-2

TMA 2

This is a bit of a weird one. Its one of 5 pieces of coursework for this course, but this only counts 5% towards the total of assessed work. You have to pick a sort of project thing to do that explores evolution a bit There are 4 projects on offer.

• Bird Predation Project -this is where you bake little bits of coloured pastry and look to see if there is selection of the bait favoured by the birds coming to feed on it in your garden.
  
• Conservation genetics project -Looking at two different species of tree or flower and making measurements.
  
• Hybridisation project -A computer based butterfly project, where you look at microsatellite information to see what populations of butterflies exhibit and how related they are.
  
• Snail shell project -collecting common garden snails and looking at the banding on them. This is an extension of the S170 work.

I chose the conservation genetics project, as I like computers and am fundamentally lazy!
Anyway - apparently this TMA is a forerunner for TMA-4 which counts for 30% of the marks, and requires you to write up two experiements for the project. So this TMA is for you to make mistakes in, and mess up calculations and graphs so it can be corrected.

I spent a long time on it though, far longer than the 5% justified. However I hope quite a lot of it will be reusable for the TMA4.

The TMA also has a proforma like thing where it tells you what data to put in, what calculations to make and what questions to answer, so it is fairly easy to tick all the boxes.

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S366: The book

As I've said, this course is a combination of two books. The text book that comes with it, and the companion text which tells you which bits to read. Sometimes this directs you to read a whole chapter, sometimes just bits and the companion text then has lots of text to read that replaces or supplements that in the text book. So what do we do in this course? Well here are the first few chapters. All labelled with letter of the alphabet.

Section A Evolutionary biology - this is an introduction to evolution. Where it stands, what its principles are, how secure it is etc. Sets the scene nicely.

Section B Adaptation - here we look at some examples of adaptation. It includes a DVD video on Adaptation in Svalbard reindeer. Some reindeer that are unique to a small island, which has influenced their evolution.

Section C The Tree of Life: classification and phylogeny. Lots of stuff on constructing cladograms, and phylogenetic analysis. Several exercises to do here, some stuff for TMA 1 too.

Section D Patterns of evolution - more on phylogeny, and a look at trends and adaptive radiation.

Section E Evolution in the fossil record - some examples including the origin of feathers and the ancestry of birds. A look at fossil trends, punctuated equilibrium, and this is where the brachipod stuff fits in.

Section F A history of life on Earth - From Earth’s earliest life, through evolution in the precambrian to evolution in the more recent eras.

Section G The geography of evolution - looking at geographical influences, barriers, climates, ecologies.

Section H The evolution of biodiversity - which looks at how to quantify taxonomic diversity, mass extinctions, and so on.

Section I The origin of genetic variation and Evolution of genes and genomes - here we look at genes and genomes, how mutations occur and the randomness of it. Also things like recombination, the origin of new genes and then some parts on the phylogenetic processes applied to genes.

Section J Variation - Distinguishing sources of phenotypic variation, some work on population genetics, molecular markers and qunatative traits. Some maths involved here.

So - thats about half the course.

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S366: TMA-1

So - time for the first TMA. Its quite a long way into the course, so you have a lot of time to devote to it if you want - or alternatively to ignore it!
So whats in this TMA?

Well - first thing to say is its big! Its 12 pages long, and for 3 questions thats quite a lot.

The first question is all about phylogenies.
First you have to identify a range of features in a sample, preparatory to doing an analysis on it.
Next you have to look the cladogram of these species and pick out some features in it.
Then you have to indicate the most parsimonious transitions on the diagram, which means finding the transition points for the 10 different features being considered.
Then there is more commentary required on the shape of the cladogram, and what this says for the inter-relatedness of the species.
The next step is to input the characteristics into a program, and perform your own cladogramatic analysis.

The next question is about statistical analysis - and it brings in the home kit.
A while lot of work is required to analyse some given data, and relate it to the data you have worked out from the home kit. There is a log of statistical manipulation required here. None of it is hard, but one figure feeds into the next, and its easy to make a mistake - subtract rather than add, or pick the wrong figure to divide by.
A couple of graphs have to be drawn or amended, and then commentary has to be made on the results and what they show of the species and now they are related. Whether their growth patterns are similar. You also have to make some predictions on what this might mean if you found new samples.

Finally question 3, which is 10% of this, is a SWOT analysis of each of the potential projects that need to be undertaken for the next TMA. It also includes a risk analysis section, which I struggle to take seriously, but complete through gritted teeth!

The course team reckoned 5 hours to complete the TMA, I wouldn't like to think how long I spent on it though.

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S366: The brachiopods measure up

So - with the arrival of the practical kit, and the appropriate part of the course reached. Its time to do some practical stuff. So here we are - presented with 30 plaster casts of various brachiopods, all from the same era.

My task is to measure them with the supplied calipers. They are accurate to about 0.1 mm although I suspect most of the error measurements comes from how you actually attempt the measurement. For each of the 30, I have to measure and record the length, width and thickness of them. Now you might think this is simple enough, and I suppose it is, until that is you offer up the first sample to the jaws of the vernier calipers. Width is perhaps the easiest, as there is really only one width, and the only trick is making sure the sample is perpendicular to the jaws to get a true reading. Length is next easiest, but you have to do it in the right orientation otherwise off axis sticky out bits tend to make it seem longer than it is. Thickness is more tricky, as the thickest bit on one side is not opposite the thickest bit on the other. Therefore you have to make sure the "seam" is appropriately flat to the jaws and you haven't got the whole thing crooked.

All simple enough really, but rather than sitting down at a table in a good light with sharpened pencil and pad, I find myself sliding into the event sitting on a settee with the TV on (Horizon) and dispensing with the pencil altogether and recording straight into excel. Is laziness ever a virtue I wonder? Its certainly much easier to read my writing back afterwards, so maybe it is. I'd planned the well lit desk I think, but just somehow drifted into the first measurement, oh well...

With the results recorded there is now a whole heap of stats to apply to the numbers to see if there is a correlation at all, if there is a relationship between the three dimensions, and then finally how they compare with some brachipods from a slightly different era. The calculations are not hard really - as either excel or a supplied program can do them, but they are fiddly. There are quite a number of them, and its quite easy to divide one number by the wrong one at some point which means the final answers are way out of line. It takes another night, and a fresh look at the calculations to have any confidence that the chain of about 20 results really do end up with something sensible. I mean, does -6.2 sound about right to you?

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S366: Evolution - first steps.

Well two things have happened since the original S366 materials arrived.

I've started working through the course, which involves quite a lot of cladograms and phylogenies. Making by hand, by computer and so on.

I find the course difficult to get to grips with in some ways, but this is mostly the way it is constructed. There is the very solid book Evolution by Futuyma, at 540 odd pages, but then there is the commentary on it written by the course team at over 300 pages that directs you which pages to read. So its read 2 pages of the course guide, which tells you to read 4 pages of Futuyma, and then run a program to generate a cladogram, or maybe watch a DVD.

I like to get stuck into the reading and absorb stuff, but the chopping and changing of books I find a bit disruptive. I mean they are big and heavy enough you can't just balance them somewhere while you flip to a page in the other. So I'm running a 3 bookmark system - one the place in the course guide where I'm at, another in Futuyma and another at the back of the course guide where the answers to the inline questions are.

The second was the exciting arrival of the practical kit. This comprises of a lot of fossils casts and some vernier callipers to allow you to measure them.

That at least looks fun. Though I suspect when it comes down to it, there will be a fair bit of tedious work involved.

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S366: Evolution - arrival

Well guess what arrived just now! I checked the site only yesterday, and it said it wasn't scheduled to start being delivered until next month, but here it is - and a heavy box full it is too!

So - what do you get in this box?

• Text book - Evolution by Futuyma - which accounts for most of the weight!
• A companion book to the text book
• A bookmark with some handy diagrams on
• An introduction and guide to the course
• A practical booklet
• A TMA form - hoping these are eTMAs.
• A DVD pack
• Checklist and Welcome note

Its quite a tome is old Futuyma, I don't know how much of it we'll have to read!

Anyway - something to do over the holidays, as if Christmas, kids parties and stuff weren't enough.

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