JS Modules: Evolutionary Genetics

Much as I did with my subjects last year, I'm going to do a quick recap of each of my JS modules so that I can remember where I learned things. It's probably not going to be very accessible to non-bio people because it's just a record-keeping post rather than an explanatory one, I'm afraid. I'm starting with Evolutionary Genetics, which involved 28 lectures over 5 weeks. It was divided into three sections:

Aoife McLysaght: Molecular & Genome Evolution

• Molecular vs morphological data
• Models of nucleotide substitution (Jukes-Cantor one-parameter, Kimura's two-parameter)
• Selectionist v neutral/mutationist theories
• Genetic drift & neutral theory
• The molecular clock (and things that perturb it) & functional constraint
• Measuring selecion via Ka/Ks
• Phylogenetics and its applications
• Exon/gene/segmental/chromosome/genome duplication (polyploidy)
• Orthology vs paralogy
• Patterns in the genome: GC bias and codon usage bias
• Tree of Life
• Concerted evolution via unequal crossing over and gene conversion
• Transposable Elements and their effects across domains of life e.g. hybrid dysgenesis in Drosophila

I liked this lecture series in general. I particularly enjoyed the bits on gene duplication, especially when I studied it in the textbook and read about cool things like subfunctionalisation allowing escape from adaptive conflict and avoiding segregational load caused by heterozygote advantage. A lot of it wasn't new to me but it usually went into significantly more detail than I'd seen before. I struggled with gene conversion because I don't actually understand some of the basics like meiosis as it turns out, but after watching some videos on it to understand the physical process I think I've mostly figured gene conversion out.

I really liked the empirical focus in this lecture series - we usually learned about things via the seminal experiments in the field and then went from there. A lot of my courses this year were like this, which was great.

Lecture series 2: Mutation

I am honestly not certain what this covered as I didn't go over it for the exam or write out the last two lectures on it, but roughly it was:

• Mutation rates
• Lesions vs mutations
• Types of mutation e.g. base change, indel, large-scale chromosomal mutations such as duplications/inversions/translocations/deletions
• Spontaneous and artificial causes of mutation e.g. DNA tautomerisation, reactive oxygen species
• Mutation repair
• Mutations in cancer

I did not like this course at all and thus did not study it. Firstly, it was very heavy on organic chemistry, which would be OK on its own but there were additional problems. Secondly, the lectures basically consisted of listing off things such as all the different causes of mutations or all the different types of mutations. It didn't feel like I was learning any sort of new intellectual framework or new skill, just learning a collection of things to memorise as if I was a med student. This might be because this lecturer also lectures in the med school. Thirdly, he sped through the lectures, still finished ten minutes late most of the time, and still asked us to go through stuff from his slides that he hadn't managed to get through on our own time. I think that's a pretty clear indication there was just too much on his slides and he shouldn't have tried to cram so much into four lectures. The lectures were also very dry, which honestly is fair enough, I've just been blessed to have basically all of my other lecturers this year lecture very engagingly.

Russell McLaughlin: Population Genetics

Loved this course! He and Aoife both lectured very well, but here there was the added bonus that I hadn't encountered many of these concepts before so they were new and exciting.

We covered or mentioned:

• what population genetics is and what it's used for
• assessing variability in population e.g. whole genome SNP-genotyping and sequencing (sanger/next gen)
• Hardy-Weinberg equilibrium
• genetic drift & the molecular clock
• inbreeding and effective population size
• linkage disequilibrium
• genome-wide association studies & Manhattan plots (I'm kinda mad I did the inbreeding question on the exam now, missed out on the chance to do a mean Manhattan plot and muse about the usefulness of GWAS data) 
• Correction for multiple testing
• Principal Component Analysis - though unfortunately we didn't go into the maths of it
• Population Stratification

This was a lot of fun. He's an engaging lecturer and has extremely fancy animated slides, plus it was really cool learning about new (to me) methods like GWAS and PCA. We covered correcting p-values for multiple testing but I already knew a fair bit about that from my summer research in Aoife's lab so that was chill.