The Plight of Heterozygotes and the Balanced Lethal System of Crested Newts

Heterozygotes have a tough time of it, because no matter how good they are they just can't breed true; heterozyte X heterozygote matings always produce 50% homozygotes. 



Worse, in assortative mating the proportion of heterozygotes will decrease very quickly (and the proportion of homozygotes increase), because the homozygotes will keep to themselves but the heterozygotes will keep producing homozygotes. I suppose in disassortative mating (mating with those different from you) between the two different homozgyotes you will get 100% heterozygotes as a result, but I'm not even sure who heterozygotes would mate with in that situation. I am assuming mating based on genotype (AA with AA, Aa with Aa, aa with aa), ignoring dominance effects that could have, for example, the AA be indistinguishable from the Aa. 

To illustrate assortative mating, I've drawn this (loosely based on a slide from Russell McLaughlin's Population Genetics lectures). To be generous to the heterozygotes, I've started it with 100% heterozygotes for this trait in the population, and you can see that the number of heterozygotes halves each time so it decreases very rapidly. 




Now in the next generation we have 25% of each homozygote, and they stay true and also each get a quarter of the heterozygotes from their parent generation, so they go up to 37.5% frequency. 

(This is all very basic stuff, but it's fun to draw.)

I did a quick Excel graph (I know, the shame, I'm sorry R/ggplot2). This is for one locus and assumes no dominance and complete assortative mating, i.e. individuals of one genotype will always mate with those of their same genotype. You can't see AA because it exactly tracks aa. You can see that the proportion of each homozygote nears (but never quite reaches, though I suppose it would in a non-infinite population) 50% as the proportion of heterozygotes approaches 0%. I hope this is correct but feel free to correct me if not.

This is just how the genetics works. But what if the genotype frequencies have different fitnesses? What if the heterozygote is by far the most fit? Sometimes, this can be resolved by duplicating the gene so that each paralog is one of the alleles, creating a state of permanent heterozygosity to escape the segregational load (Susumu Ohno did say in 1970 that this has risks though, by upsetting the dosage balance of genes, and points to the absence of a duplication of haemoglobin alleles in African populations despite their heterozygote advantage against malaria as evidence for this). 





But what if recombination isn't possible? Crested newts provide a remarkable example of this: 50% of their offspring fail to develop because only heterozygotes for chromosome 1 (1A/1B) are viable. Since only heterozygotes are viable, the parental population will be 100% 1A/1B so 50% of their offspring will be that too and all the 1A/1A and 1B/1B offspring will die. This occurs because 1A and 1B each have a different deleterious recessive allele fixed on a nonrecombining segment (I would reference Grossen et al's 2012 paper in The American Naturalist here, but essentially this entire section is based on that paper so). 

There are various models for how this maladaptive system could have occurred.

• Sims & Sessions: unequal genic exchange between two homologues of an autosomal pair made crossing over impossible in the region, and then inversions and repeat sequences accumulated. Each haplotype, 1A and 1B, would have a different duplication and deletion affecting something essential to embryonic development, and would show extremely strong negative frequency dependence (their fitness would decrease the more of them there were in the population, I think because if there are lots of them they're more likely to be found in a homozygote and thus their vehicle would die), and should die out. 
• Wallace et al: chromosome 1 used to be the sex chromosome, though that is now chromosome 4 (male-heterogametic XX/XY system). 1A and 1B used to be an AA/AB sex determining system, and so BB homozygotes are lethal because B accumulated deleterious mutations in the heterogametic form, I imagine because it was shielded by the A and thus could gain deleterious recessive mutations without selective pressure. The issues Grossen et al raise with this are (a) why are 1A/1A homozygotes lethal in the crested newt then? With an AA/AB system there would have been AAs (b) why the new XY system on chromosome 4 only operated in the formerly heterogametic sex (AB). I guess maybe (b) could be the only thing observed because only the AB survives, but if it's saying it only operates at all there then I don't know. 

Instead of these, Grossen et al propose that chromosomes 1A and 1B are forms of the nonrecombining Y chromosome from an ancestral XX/XY system. The Y would have been shielded and safe to develop deleterious recessive mutations such as deletions, and different deletions caused formation of different haplotypes. They discuss and simulate a whole bunch of different paths this could have taken, incorporating the ancestral XX/XY system and the fact that newt sex is partially determined by temperature (males are more likely to develop when it's warmer, females when it's colder - I had no idea of the mechanism behind this at first but apparently it can be related to differential temperature-regulation of genes and activity of enzymes).

Origin of Y haplotypes - the nonrecombining, degraded Y

Because the Y chromosome does not recombine (at least most of it doesn't - in humans the pseudoautosomal regions do), and because in the XX/XY system it's shielded from the effects of deleterious recessive mutations, it has strange evolutionary patterns. 

• Increased genetic drift - the Y chromosome has an effective population size of 1/4Ne (if you're counting Ne in alleles rather than individuals) because while autosomes are present in two copies in every organism, it is only present in half the individuals of the species and then only in one copy. (Similarly, the X chromosome has 3/4Ne)
• Selective sweeps and background selection - individual mutations don't really get tested because of the lack of recombination, so if the chromosome as a whole is good they'll stay, if not they'll go
• Muller's ratchet - again, no recombination, so deleterious mutations are not lost and there are far more deleterious mutations than positive ones so those build up. 

This results in long blocks of Y chromosome that are passed down as-is leading to a couple of Y haplotypes segregating in the population.  Some interesting examples of these haplotypes are mentioned in the Grossen et al paper, including a guppy species with at least 3 coexisting Y variants which code for 'different male coloration morphs and are thus possibly maintained by frequency-dependent selection occurring through female mate choice'. An experiment that mated sex-reversed (i.e. phenotypic not matching genetic sex) XY female guppies with XY males resulted in 25% YY offspring, which were viable as long as their Y haplotypes were different but show a lethal homozygous phenotype. I wonder do these guppies have a sexual selection or disassortative mating mechanism to avoid mating with a guppy with the same Y as them? Are there enough sex-reversed females for it to have evolved? I figure that for an XY female and XY male mating in a system with three Y haplotypes (assumed equal in frequency), for a given XY female there's a 1/3rd chance that her XY male mate has the same Y haplotype as her, which makes a 1/3*1/4  = 1/12 chance that a particular offspring with any XY male mate will be nonviable. 

Two examples of crosses between an XY male and XY female, the first where they have different Y haplotypes and the second where they don't and 25% of the offspring are nonviable.

The other example they give is of Rana rugosa, a type of wrinkled frog, which has a female-heterogametic ZW/ZZ system:

[D]ifferent populations have fixed different W haplotypes, so that WW individuals are viable when their two W chromosomes stem from different populations but not when they are from the same population...[E]ach haplotype has fixed one or more recessive lethal mutations (e.g., loss of function of some housekeeping genes)

So these Y haplotypes can arise. Once that happens, there's a set of steps they lay out to show how this balanced lethality could come about, which I have diagrammed to the best of my understanding below (they didn't phrase it like this set of states and events).

Top row is female, bottom male. Circled A, B and C refer to events while the A, B, C and D on top refer to states.

We start out in state A, with mm referring to a locus on chromosome 4 that will become important in state D, and X and Y referring to ancestral sex chromosomes that are now chromosome 1, with the Y having haplotypes A and B. (I'm now going to say 'X happened' for brevity but it really means 'the authors propose that X happened). 


In this state, there is no 50% offspring mortality, because Y chromosomes don't occur together - they either don't appear at all, as in the female, or they occur alongside an X, which compensates for any deleterious recessive mutations they carry. 

Event A is a climatic or range change that results in decreased temperature, so that - because newt sex is influenced by temperature, and colder temperatures are feminising - some XY newts are females (State B). These females can then mate with XY males as in the Punnett squares above to produce 50% lethal homozygotes (Ya/Ya or Yb/Yb) and 50% viable heterozygotes (Ya/Yb).  This increase in females produced an imbalanced sex ratio which created a selective advantage for an allele that could increase the number of males, i.e. a masculinising allele, to spread through the population. 

Aside box: Why is an imbalanced sex ratio a problem? 

According to Fisher, the reason most sexually reproducing species have a 1:1 sex ratio is because if the ratio is disturbed, the less common sex will be able to get more mates and thus have an advantage, and so if there's any allele that increases the proportion of that sex, it will be favoured by selection and thus more of the less common sex will be born (assuming it costs the same amount of energy to have either sex, which is not necessarily true e.g. males may need more feeding) until the sex ratio equalises. 

My issue with that is - how common are alleles that make an organism more likely to have offspring of a particular sex? This masculinising one in newts is the first I've heard of, but there may be many especially in quantitative temperature-controlled (fully or partially) systems. 

If the temperature gets even colder (Event B), even some YY newts will develop as females and so since there are enough females the X can be lost from the population by drift, resulting in a fully temperature-controlled sex determination process (State C), such as the YaYb newt developing as female if it's colder, or male if it's warmer. 

Event C was the mutation of a locus on chromosome 4 to a masculinising allele (M), which meant the sex-determination system was no longer (fully) temperature controlled but instead determined partly by the presence or absence of the M allele, with Ya and Yb (the two chromosome 1s), as in state C, not acting as sex chromosomes.

If the X had not been lost by drift, they could have evolved to the much better state (without the 50% segregational load) of MMXX/MMXY, but whenever X was eliminated before the appearance of M, this male-heterogametic mmYaYb/mMYaYb system with 50% segregational load was seen.

The authors explored several different paths in their simulations and also looked at the effect of environmental variability (e.g. if it was very cold but there was a lot of variation the temperature spikes gave chances to produce males and avoid extinction) and population size. The paths were:

• no masculinising mutation on chromosome 4 (i.e. no sex determining chromosomes other than chromosome 1's X/Y) - this meant travelling straight upwards on the diagram below as the temperature decreased.
• early-occurring masculinising mutation on chromosome 4 - in the simulations, this increased in frequency as the temperature dropped until fixation in the population, with first a female-heterogametic system at T = -4 (mMXX/MMXX), then full temperature controlled sex determination (TSD) at T = -6, with X often being fixed by drift in small populations. This presented a problem when temperatures decreased further to T = -8 because this skewed the sex ratio by creating more females as more MMXX newts developed into females, restoring selection for Y except at high environmental variance, where a few MMXX males would still be born and those would have an advantage because MMXY males mating with MMXY females produced some lethal MMYY homozygotes. If X was fixed and Y had been lost, then either the population would go extinct (small N) or survive with female-biased sex ratios.
• late-occurring masculinising mutation on chromosome 4: when mmXY (pale green) was still around, i.e. X had not been lost, M was fixed and the original male-heterogametic system was restored (MMXX/MMXY). However, if X had been lost, i.e. the mmYaYb TSD arrangement had been reached before the introduction of M, the YaYb segregational load system was fixed and a male-heterogametic system now based on the X chromosome emerged, with mmYaYb/mMYaYb (dark green female, blue male). That's the one we see today.

Figure from Grossen et al (2012) showing the different paths and results at different temperatures. For example, the optimal path with no segregational load and fixed MM results in females being the red circle and males being purple in the diagram; the current system  is dark green and blue. Being below and to the left of the line indicates femaleness, with the opposite indicating maleness, so in the ancestral state at T = 0 almost all of the mmXX (yellow) newts will be female except for the few in the dotted circle that go past the dark black line, and similarly with the light green mmXY males. As the temperature increases, more and more of the mmXY and eventually mmYY newts will develop as female, e.g. at T = -6 the dotted line goes straight through the middle of the dark green mmYY circle, so about half of mmYYs will be male and half will be female, which would be a temperature-controlled sex determination (TSD) system (this TSD system would also occur at T -6 with the genotype MMXX). 

So there you go - a very complicated system and one whose answer is highly speculative, but interesting due to its gene-environment interplay.

References

1. Grossen et al (2012). The Balanced Lethal System of Crested Newts: A Ghost of Sex Chromosomes Past? The American Naturalist.

2. Charlesworth & Charlesworth (2000) The Degeneration of Y Chromosomes. Philosophical Transactions of the Royal Society London B. 

(No, these are not properly-formatted references. It's a blog post, these are elleloughranblogspot.ie house rules.)

Traits and Genetics of Domestic Cat Interspecies Hybrids: Savannah, Bengal, Chausie

I came across savannah cats in a Reddit post and thought they were fascinating, so did a bit of a dive into their characteristics and genetics. Unfortunately, there is a remarkable dearth of papers on them and I am very much not an expert, but I figured it'd be fun to look into it and try to make sense of what I can.

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Felidae are genetically very similar, and interbreed frequently with each other in the wild. Humans have also bred certain hybrid cats, especially the Savannah, Bengal and Chausie cats, to be domesticated housepets while keeping the exotic look of their wild ancestors.

Look at all those hybridisation events! (black and red lines). Image from a conference presentation at Tufts Canine and Feline Breeding and Genetics Conference by Dr. William Murphy. 

Savannah cat



Chausie cat







Bengal cat

Savannah

Chausie cat

Bengal

I'm going to mainly talk about savannah cats since those are the ones I'm most interested in. They're generally bred from a female domestic cat (often an Egyptian Mau, ocicat, bengal (another hybrid!) or a domestic shorthair) and a male serval to produce an F1 cat that is 50% serval. This can be backcrossed with a male serval to produce a cat that's 75% serval, but instead these cats are usually backcrossed with domestic cats like so:

Red means % serval in savannah cats of that generation

Until at least F4, the males are not fertile, but the females are fertile from F1 onwards, an example of Haldane's Rule: when in the F1 offspring of two different animal races one sex is absent, rare, or sterile, that sex is the heterozygous sex (heterogametic sex). It can get a bit messy around F5 because those fertile F5 males can now be bred with F1 or other generations of female savannahs, rather than breeding them with domestic cats (outcrossing), and this is now generally preferred to maintain breed type (though probably not great for their health...)

Interestingly, more late-generation male savannahs (F5, F6) seem to be sterile lately, which is suggested by the author of the Wikipedia article to be because of the higher percentage serval savannahs are usually made with lately (due to less outcrossing), or because of the Bengal cat DNA from the foundation of the breed. Both of these relate to a higher percentage of nondomestic cat DNA, which I think from the paper I just read by Davis et al 2015 (which I plan to use as an example in a later blog post about how I annotate papers) could be because sterility relates to the presence of nondomestic haplotypes on the X chromosome. 

Savannahs are known for being playful, intelligent, energetic, enjoying water, and leaping high, like on top of fridges. Both savannahs and Bengals are known to be vocal, with the savannah sometimes miaowing and sometimes chirping like a serval. However, several cat sanctuaries and organisation warn against buying hybrid cats because they can suddenly become aggressive on reaching maturity and 'unlearn domestication' and start peeing everywhere, leading to an excess of surrenders to shelters. Because it's random which 50% of the DNA comes from which parent, you can't know how wild the cat's temperament will remain. I do wonder - to get a bit science fictiony - if that could be controlled via a gene drive or some sort of manipulation of genomic imprinting so you can silence a certain category of genes (e.g. aggression) if they come from a particular parent (e.g. the wild one). Note: even if we could do that, I'm not saying we should. Just an interesting thought.

Genetics of Hybrid Cat Sterility

Davis et al 2015, in their paper Mechanisms Underlying Mammalian Hybrid Sterility in Two Feline Interspecies Models, looked for genes influencing male sterility in savannahs and bengals as compared to fertile hybrids and their parent species (domestic cats, servals, and asian leopard cats). They hypothesized (apparently this is from the Dobzhansky-Muller model, which I need to look up more about) that sterile hybrids would be enriched for SNP alleles from the wild species rather than the domestic one. I liked this study because not only did it do a GWAS, it also did expression level measurement via RNA-Seq to partially verify the GWAS hits, and sometimes also compared to results from mouse knockout studies. I won't go into all the details from it, but the major points I got from it were as follows.

Most of the candidate hybrid male sterility (HMS) loci show very little amino acid divergence between the domestic and wild cat species - the change seems to be in the regulatory regions

They found associations with male sterility for 5 SNPs in savannahs and 3 in Bengals. These included genes involved in the blood-testis barrier, a glutamate receptor, a Ser/Thr kinase and a transcription factor, as well as AKAP9 which anchors protein kinase A, and a DNA methylase that suggested epigenetic effects. There were two interesting links to cAMP, but that may just be because cAMP is involved in a lot. 

The major sterility issues were problems with the blood:testis barrier, with acrosomal (a sperm structure) development, and with transcriptional regulation.

While they say the X chromosome is important in this, they didn't get any statistically significant SNPs on the X chromosome from the GWAS (though they sure try to sneak it in with 'suggestive' and 'approached' significance!). They attribute this to low X SNP density on the array and/or the Large X Effect being especially polygenic due to the long divergence time between the parental species - something I imagine could be investigated using Chausie cats, since they have a divergence time about a third as long (~3 MYA).

Manhattan plots: too pretty for their own good.

Genes on the X chromosome were highly overexpressed compared to autosomal genes. The expression patterns were consistent across both hybrids (Bengals and savannahs). They tried to correct for spurious expression differences caused by different cellular composition in sterile vs fertile testes (specifically, sterile testes have fewer postmeiotic cells which could make it seem like postmeiotic genes were being expressed at a lower level when the expression level per cell was the same) using housekeeping genes, an issue I was introduced to recently via Kevin Mitchell's blog (post here). Sidenote: I really enjoy that blog - dude seems to know what he's talking about. Which is good, since he'll be my lecturer next semester.

Here are their graphs comparing the sterile hybrids' testis gene expression to fertile hybrids and parent species. What I gather from that is that in all six groups, more of the X chromosome genes are in the bins for being overexpressed compared to the other type (fertile hybrid, wild parent, domestic cat), whereas the autosomal genes aren't clustered around the left of the graph so aren't generally overexpressed. The consistency between Bengals and Savannahs suggests commonalities in the reason for sterility among the two breeds, and other similarities with mouse suggest it could go even further.

Ignore my blue writing, if only because it'll be explained in the paper-annotating post.

Questions*

• Why have cats diverged so little from each other?
• Why do Bengal males become fertile in earlier generations than savannahs?
• Haldane's Rule, and its various proposed answers that open up more questions...
• What are the implications of the relationship between HMS and copy number variation on the X chromosome?
• Why is it X chromosome blocks from the wild parent, rather than the domestic parent, that seem to induce sterility? Is it because these cats are usually more domestic than wild in ancestry? I'm not sure if this data includes 75% servals etc.
• Why are there so few studies in this area?? These cats are cool.
• WHY is the supplemental data in PDF? Please, whoever is responsible for this, whether it's the authors, the journal, or the flying spaghetti monster himself - just put it in a CSV. Thank you.

*some of these questions may well have an answer, but this is what popped into my head.


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Finally, have this. Because what's the point of science without a poorly-drawn sketch of a Savannah cat sitting on top of a fridge?

JS Modules: Genomics

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. Number two is Genomics, which involved 30 lectures over 5 weeks. It was divided into three sections, two lecture series and one computational:

Systems Biology

To be honest, I still couldn't tell you exactly what systems biology is and I don't think it can always be differentiated from reductionism, but basically I think it's looking at a complex biological system from the top down and modelling it quantitatively over time to understand the connections between its components, whereas reductionism would be understanding each individual component in turn and building up from there. This was all taught by Frank Wellmer and was cool. We covered:

• Systems biology vs reductionism
• Genomics & genome sequencing techniques (Agarose gel electrophoresis, PCR, Sanger dideoxy chain termination, next-gen, Oxford Nanopore)
• Structural genomics: Identifying genes, transcribed regions, and regulatory regions in a genome
• Comparative genomics: comparing genomes between individuals, populations, species and higher taxa
• Functional genomics: identifying functions of genes on a genome-wide scale.
• Transcriptomics: measuring expression of genes using techniques such as RNA-seq and microarrays to see for example whether a given gene is expressed differentially in different tissues, or when a cell is infected by a virus vs not.
• Proteomics: studying the full protein complement of an organism, techniques to do this such as mass-spec, SDS-PAGE gels and Mud-PIT and how they work, and why proteomics has fallen behind genomics
• Networks & gene regulation + techniques to study that (ChIP-seq)
• Genomics/transcriptomics in medicine e.g. breast cancer prognostics using differentially expressed marker genes as indicators of metastasis likelihood

A big takeaway from this was that the  human genome sequence, as with all genome sequences, simply gives us a list of ATGCTAGCTAGCTCs. The much harder task is to annotate that to figure out where the genes actually are (only 2% of the genome is coding DNA, though not all genes are coding - and how do you define a gene anyway?) and then what they do and how they're related to each other.

Molecular Genetics Techniques

This was taught in part by Frank and in part by Ursula Bond. With Frank, we covered the process of molecular cloning, including the enzymes involved and a bit on how they work (restriction endonucleases, ligases, recombinases, DNA polymerase for PCR, topoisomerases, kinases, phosphatases, DNA methylases), choosing a good cloning vector, ligating the vector with the insert (and avoiding vector religations using either double digestion or dephosphorylating the end of the vector, or using blue/white screening), transforming the host (usually bacteria - done with heat shock or electroporation), then after propagation isolating the plasmid using alkaline lysis. This was a very handy course because we physically did a lot of these things in our Molecular Genetics lab, so it was nice to cover it twice from different perspectives and helpful in the exam. 

Funnily enough, even though Frank warned us this lecture series would be dry, I found it very interesting because he took a really inquiry-based approach so we could figure stuff out on the fly in class. I was proud that I figured out why restriction enzymes recognise palindromic sequences (because they have to make double-stranded breaks so recognise the same sequence on both strands, and then we learned that that's because they're usually homodimers). It felt like we were being treated as 'real trainee scientists' because he'd go through how to troubleshoot a restriction digest not working, or show an example of an origin of replication and then ask how we could increase copy number. I loved the problem-solving approach.

Bond's section was about producing recombinant proteins such as insulin in different hosts including bacteria, yeast, and mammalian cell culture. It was all about the choices you have to make when you want to pump out a protein: which host, promoter, expression vector, selectable markers, affinity tags for purification, secretion pathway, etc., do you use. She also gave a lecture on how to produce monoclonal antibodies and their therapeutic uses. 

While I didn't focus on her material for the exam because the slides weren't very informative and there was a fair bit of information to memorise such as antibody names, it was actually quite an interesting course and I loved the strategy aspect of it and the modular way you can build up an expression system. 

It was much more engineering than science, and even covered the whole workflow from designing the expression vector through scaling up production through product formulation to trials, marketing and sales. 

I loved the bits about controlling the expression of the recombinant protein - for example, if you're using yeast, you can attach a promoter behind the gene you want to express that is suppressed by glucose, so that once the yeast have grown a ton and used up all the glucose, they'll suddenly switch on the gene and produce loads of the product at once. It's a choice - you might alternatively want a constitutive promoter that'll just produce the protein steadily. 

An example of the modular combinations you can do so you can both positively and negatively control expression is:

 

• have gene to make T7 virus RNA polymerase, put under the control of the lac promoter so that it's IPTG-inducible
• have plasmid carrying lysozyme gene because lysozyme protein inhibits T7 RNA pol, under a rhamnose-repressible promoter
• have plasmid with the protein you want to express under a promoter bound by T7 RNA pol so that in the presence of IPTG and absence of rhamnose, your protein will be produced.

Bioinformatics

This was the computational third and was not at all what I'd been expecting. Honestly I thought I'd know most of it because I'd spent my summer doing research using bioinformatics, but this had no coding at all whereas that was basically all I'd done. Turns out there are tons of resources I didn't know about that would've been very helpful! We covered PubMed, the literature database (did you know you can link out directly from there to datasets? Gamechanger. Also, it has fancy searching), nucleotide and protein databases, sequence similarity searching and BLAST, pairwise and multiple sequence alignment, personal genomics, and Ensembl and UCSC genome browsers.

Bizarrely, until recently this part was also assessed in the normal exam, meaning you'd have to do things like 'discuss the four types of BLAST program' or 'design an alignment matrix for these two sequences using the pam250 whatever' on paper in an exam, which, oof. Thankfully we did it via a test so we could actually be tested on it in the way we'd use these skills IRL, like the question would say 'Do a BLAST search to find out X' and we'd do that. I got 84% on the test which is decent.

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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.

Autistic Environmentalist Heroes

The environment needs heroes, and so does the autistic rights cause. Here are some inspiring autistic environmentalists who manage to be heroes for both.

These people are brilliant environmental advocates not despite their autism, but as well as or sometimes because of it. Autistic people, particularly given appropriate supports and assisted with co-occurring conditions, can be a powerful force for good in the world. 

They may be blunt, abrasive, obsessive and/or awkward, but the flipside of that is their directness, passion and devotion to a cause. It's neurodiversity: we need both autistic and allistic people in the world, and to support everyone to get the best out of both.

Even when autistic people are positively represented in the media - which is quite rare - it's usually as academic boffins. And while I am one of those, I want to highlight some autistic activists, because autistic people are not automatically shut off from the world - we can experience it, care about it, and some of us are changing it. 

Greta Thunberg

Greta is a fifteen-year-old Swedish climate activist known for striking outside the Swedish parliament on Fridays to demand climate action and adherence to the Paris goals in what she calls the 'Skolstrejk för klimatet' (School strike for climate), inspiring people around the world to join her. She was also involved in the Rise for Climate protest outside the European Parliament in Brussels and supports Extinction Rebellion. 

From her world-famous speech at the COP24 UN climate conference:

'You only speak of green eternal economic growth because you are too scared of being unpopular. You only talk about moving forward with the same bad ideas that got us into this mess, even when the only sensible thing to do is pull the emergency brake. You are not mature enough to tell it like it is. Even that burden you leave to us children. [...]

The year 2078, I will celebrate my 75th birthday. If I have children, maybe they will spend that day with me. Maybe they will ask me about you. Maybe they will ask why you didn’t do anything while there still was time to act. You say you love your children above all else, and yet you are stealing their future in front of their very eyes [...]

We have not come here to beg world leaders to care. You have ignored us in the past, and you will ignore us again. We have run out of excuses, and we are running out of time. We have come here to let you know that change is coming, whether you like it or not.'

Despite Sweden's reputation for progressiveness, she says they are too short-sighted when it comes to climate issues and aims to force the government to pay more attention to the future and look past 2050 when she, and I, will only be middle-aged. 

Speaking to Masha Gessen for the New York Times, Greta said that her autism allows her to see the world from a different perspective and that she has a special interest, which is very common in people on the autism spectrum. It helps her stick to the same topic for hours, or years - in this case, climate change. In the same New York Times profile, she shares some traits that are very relatable as an autistic person, including her general avoidance of new foods and her anger when things are wrong and refusal to stay silent. I commend her for not hiding her autism but sharing it without apology, and hopefully contributing to a better public image of it as something not to be vilified or eradicated, but accommodated and even celebrated for its good parts as part of human diversity.

Dara McAnulty

Dara is a fourteen-year-old naturalist living in Fermanagh, Northern Ireland. He's originally from Belfast but struggled with the noise and busyness of the city until his family moved to Fermanagh and he could appreciate the quiet and get out in nature. I've followed his Twitter for a while now and found it a great way to keep up to date with naturalist causes - it's how I found out about the People's Walk for Wildlife, organised by Chris Packham. He recently won a Young Animal Hero of the Year Award among other honours, and has raised awareness of the plight of the hen harrier as well as raising money to tag raptors to help with science and conservation. He blogs at youngfermanaghnaturalist.wordpress.com and is currently working on a book due out in 2020 called Diary of a Young Naturalist.

He writes beautifully on his blog - take his post about the People's Walk for Wildlife for example - including poetry, and knowledgeably confronted the Tory government on their anti-environment policies during a visit to Parliament Buildings, a time when it would be easy to be awed into silence.

It's great to see him explain how his deep interest in and love for nature helped him connect with people when that hadn't really worked before, and how in turn that connection strengthened his advocacy; it illustrates the vital importance of special interests for autistic people and how they're both a source of joy and a means of connection. He has also spoken on his blog about having to push through his anxiety to do many of the things he has achieved. Anxiety can be a nightmare that massively amplifies the difficulty of tasks, and it's important for people to share their stories of getting through it to remind us that it can be done, and that advocacy is not just for the loudest, most confident people but for everyone with the passion, drive and compassion to stand up for what they believe in and make the world a better place.

He's also an advocate for youth, saying of his generation: 

We're not lost, we just haven't been found.

Chris Packham 

Chris is a naturalist, TV presenter, author and trained zoologist, who has been presenting TV programmes including The Really Wild Show and BBC's Springwatch for decades. He has also won a episode of Celebrity Mastermind with the Battle of Rorke's Drift between the British and the Zulu as his specialist subject. He has presented shows on all sorts of topics in recent years, from the cognition of animals to media representation of autism. He has also been involved with about a dozen nature and wildlife trusts, and is an Ambassador for the National Autistic Society. 

He has run into trouble for his outspokenness against barbaric practises such as fox hunting and other animal mistreatment, and against the misallocation of conservation funds for charismatic megafauna such as the giant panda to the detriment of other species. While these comments did raise calls for his sacking from pro-bloodsports groups, this openness and need to stand up for what is right is one of the reasons I have included him on this list, and a valuable autistic trait.

_________________________________________________________________________

Review: November 2018

LAB REPORTS

Spent large portions of the month tearing my hair out (figuratively) over writing two lab reports that made up a whole module worth 5 credits. It took so long to figure out how to do the particular kind of bloody error bars I needed, and then to figure out gel labelling, and then printing double-sided and making sure the arrows to the gels showed up in the printout, but eventually I got it done, printed, bound and handed in on time, which was a relief. 

PRISON PROJECT

I had done the bulk of this in October but finished off my prison essay quantitative paper on the topic of 'The Relationship Between Public Opinion and Prison Policy in Europe' in November and submitted it on Dec 1st, though the lecturer didn't email a confirmation or anything so I really hope it went through. I'm quite proud of it - I used data from the European Social Survey and SPACE I (European Prisons Report) to look at links between prison sentence lengths, prison conditions measured by space per prisoner, and public opinion on sentencing, conditions and crime.

DATA HANDLING

The bulk of my data handling module (one third each Python, ChIP-seq which is mostly command line use, and statistics) took place during November. I really enjoyed Python, quite enjoyed stats and do not (because I still have to do the project for it) like ChIP-seq, even though I'm familiar with the command line - it's the biological interpretation that's the issue for me.

JS CAREERS TALK

Someone from the TCD careers service came and gave us a talk about internships we could do over the summer on 5th November. Some of it was a bit annoying, like when she asked why people might not be on LinkedIn and didn't understand when I said because LinkedIn shows little respect for data privacy, but overall she did go through a lot of different opportunities. I am very glad I already have two internships sorted for next summer, because so many of these required seeking something outside the country.

GENSOC PUB QUIZ

The genetics society held a fun pub quiz on the 7th that loads of us (undergrads and postgrads and the odd lecturer) went to and really enjoyed. We did come fifth last but I didn't care - I got the very last answer, which I was unsure about (which of Jennifer Doudna and Feng Zhang got the CRISPR patent or something), right, and had a lot of fun during the music round listening to some NOW 74 classics.

LAIDLAW LEADERSHIP DAY

On November 10th, the Laidlaw scholars went to a coworking space near Trinity to do a leadership day. We first heard a panel discussion from someone who works for the Green Party, who was cool, a guy who works in VR/AR, and a filmmaker. We then did a session with Linda Doyle, who's the Dean of Research at Trinity. It was frustrating but quite good - we had to describe our research using only the 1000 most common words, which is basically impossible, and do a postcard symbolising the possible impact of our research. I felt like that was kind of silly because some research is just because it's valuable for humans to expand our knowledge, but I did think of an interesting thing about my codon usage bias research re the importance of understanding why our genome - with all its weird patterns of codon and GC bias, the transposons, duplications, etc - functions the way it does before we try to mess with it with gene editing that could have pleiotropic effects. 

Finally, we had a three-hour session on resilience which was not good at all - the speaker kept getting science wrong, like saying things are passed down via 'gene cells' and - to the amusement of the med scholars - drawing a heartbeat trace wrong, as well as lots more pseudoscience and faux-deepness and saying things like 'failure doesn't exist' when, in the context of our lives within a college environment with rigid failure rules, it very much does. He also said you can't say someone is an angry (or anything else) person, just a person who gets angry sometimes, and the poor guy was argued with a lot about that. I know maybe the science terms nitpicking sounds petty, but I wouldn't do that if I was happy with the rest of the talk, and sadly I was not. The rest of the day was good though, and it was cool to see the other scholars again.

J1 RESEARCH INTERNSHIP

Aoife put me in touch with Emilia, a scientist at Brown University doing cool work in computational genetics, which was exactly what I was looking for, and Emilia and I had a Skype call in mid-November to start sorting out details. I am very excited that I'll get to do a project on the population genetics of the X chromosome. I am less excited about figuring out when to go, my flights, and the visa, but it must be done.

FUNERAL

My grandfather died and I went back to go to his funeral. It was sad and got me thinking a lot about death and the pointlessness of it. It was nice to have a family reunion, though.

BIOINFORMATICS EXAM GRADE

I got my bioinformatics exam grade back on 19th November (the lecturer kindly emailed it to me - I didn't want to walk over to the noticeboard because I'd hurt my foot) and I got 84%, which isn't amazing but is pretty solid.

PYTHON EXAM

On 27th November, I had my Python exam, which was worth 33% of a 5 credit module. It went well and was pretty fun - I like that I get to code for credit. While I only found this out in December, I got 97% in it. 

CHRISTMAS COMMONS

I had been looking forward to bringing my dad and his partner to the much-hyped Christmas Commons to show them how fancy it is, but Dad was sick so I brought some friends instead and still had quite a nice time so I'm glad they could join me.

STUDY

Obviously, I spent a lot of time studying as exam week started on December 10th. Because my more lecture-heavy modules Evolution and Genomics had finished in October, it was easier to keep up with writing up lectures and study, so I was quite happy about that. 

Review: October 2018

Why yes, it is indeed halfway into November as I write this. C'est la vie. Most of what I remember from October is just studying and working on assignments, but it turns out a fair few other things happened too.

This post is pretty thrown together because god I have so much to do for college jesus and I just want to have a record of what was up in my life each month. [misc religious terms]

Inktober

I did Inktober for the first time in October. The idea is to draw a different ink drawing every day following the prompts in order to develop good drawing habits. I totally ignored the 'ink' requirement and sometimes ignored the prompts, but I did draw every single day so that's cool. I'm writing a post specifically about Inktober at the moment so you can see the drawings.

Yesterday, instead of doing the day's #inktober2018 prompt, and in response to the Kavanaugh farce, I did this.

The scream of silenced survivors. pic.twitter.com/XDVQfv8noF

— Elle Loughran (@frizzyroselle) October 6, 2018

Schrodinger 'What is Life' Conference Mini-Symposium
We had the mini-symposium for the student rapporteurs to make speeches on our learnings from the conference. I did mine on Nick Lane's bioenergetics speech and waxed lyrical about connections, communion and equilibria very hippyishly...but with facts. It was a grand evening and we all got little medals and our essays on the website. The winning speeches were really good.

Halls
I moved into Halls finally! You're given it for free as a Scholar but originally I turned it down...until my housemates left and we couldn't afford to keep paying double rent. I emailed around 9th October and by the next day they had sorted me out a room! It had apparently been empty the whole time. It was a lot of stress off my back to no longer worry about rent.

Evolutionary Genetics
We had a lot of really cool lectures from Russell McLaughlin on population genetics and really not cool ones from another lecturer who I won't name on mutations. 

Eukaryotic Molecular Biology
Lectures on various aspects of eukaryotic transcriptional and translational control (meh) and control of the cell cycle (cool).

Genomics
Lectures on functional, comparative and structural genomics as well as molecular biology techniques like cloning genes and making monoclonal antibodies. 

Literature Review

One of our modules this semester is to write a 7000 word literature review. I got the top choice, Mitochondrial dysfunction and neurodegenerative disease, and met my lit review supervisor Jane Farrar on the 31st. It's pretty intimidating and I need to figure out how to narrow it down, but hopefully it'll be fun once I've done that. And it's due at the end of January so I can focus on my other assignments and exams first.

Extremely intimidated by this Lit Review I've to do on mitochondrial dysfunction and neurodegenerative disease (and by college in general tbh) but I finally read that recommended paper and made notes on my lovely whiteboard. So that's a start. pic.twitter.com/vilnhOGLdV

— Elle Loughran (@frizzyroselle) October 29, 2018

Reading Week

We had midterm break so I visited my family and saw my dad, siblings, nana and my aunt over from America, and then Leon's family. Also, the election happened.

Election

I voted for 1. Michael D 2. Liadh Ni Riada and for Yes in the Blasphemy referendum, and the vote went the way I wanted pretty much as expected. So that was grand. Also, there are so many referenda!


Prison Project 
I did a lot of the work on my project for my broad curriculum module on prison systems. My project is a quantitative research project using publicly available data from the European Social Survey and SPACE I report on prisons to assess the relationship between public opinion and prison policy (including sentencing and conditions). 

Bioinformatics Exam
First exam of the year, making up 33% of a 5 credit module was in Bioinformatics and went OK but not perfectly. I found out in November that I got 84% on it so not ideal but not terrible.

Laidlaw  Video Event
There was a showing of the videos each Laidlaw scholar had to submit about our experience in the program so far. It was a pretty fun night and it was cool that my supervisor Aoife came. 


Travel Scholarship - US/Ireland Programme
I found out that I officially got the top marks last year out of the people who got into Genetics and so I got one of the US/Ireland scholarships to do a J1 in a lab in America next summer and started organising that, again with lots of help from Aoife.


Hobbies
Some swimming and knitting, though it is very hard to find time and energy for them a lot of the time. Do chats at Commons count? I don't think I read very much unfortunately, and haven't in November either. Damn college stress.

Duolingo
I hit a 100 day streak of French on Duolingo.

Halloween
Leon and I kept up our Halloween tradition by playing a new board game together, this one one that we had actually helped support on Kickstarter called Pocket Pharma! 

Review: September 2018

Yoooo it's been a busy month, and I'm writing this on the 10th of October because the busyness has continued.

FRESHERS WEEK: College started back up, with Freshers' Week on the 3rd, 2-3 weeks earlier than last year. I was super busy in Freshers' Week with about 40 hours of volunteering between helping out the Science Course Office for orientation, and (wo)manning the stands for Netsoc and Physoc, as well as two and a half days devoted to attending and volunteering at the Schrodinger at 75: What is Life? conference.

SCHRODINGER CONFERENCE: I was a student rapporteur at the Schrodinger at 75 conference, so basically I volunteered at a nice poetry-reading and Long-Room-touring event the night before and then attended the two days of the conference. I found the first day wasn't great on the whole (though there were some good speakers), but the second day was amazing. I was also to shadow a speaker and then do a presentation on their talk a month later, but I'll save that for the October post.

RENTING HELL: Ended up paying double rent this month because we're too far away to easily find housemates, which was a nightmare. In the October post we shall see that thankfully that seems to be turning out okay in the end but it was certainly not pleasant.

GENETICS:  I've been loving my course so far. Currently I have four modules running:

- Evolutionary Genetics (6 lectures per week for 5 weeks) - love (well, the Molecular Evolution and Population Genetics submodules. We had 4 lectures on Mutations and those sucked.)
- Genomics (6 lectures per week for 5 weeks) - like a lot (very inquiry-based, at least with the main lecturer, and a third of it is bioinformatics which is computer-based.)
- Eukaryotic Molecular Genetics (3 lectures a week for 10 weeks) - find boring except the Cell Cycle lectures which are very cool. I think it's because a lot of the other stuff is like 'here are the steps in this process' whereas I like things that say 'here's the evidence, here's what was drawn from it' and generally proceed in an inquiry-based way.
- Molecular Genetics Lab (2 labs a week) - hard work and tiring but quite interesting and valuable. And I love the lab director/lecturer/whatever.
- The Prison System (2 lectures a week for 10 weeks) - this is my Broad Curriculum module and it's actually very interesting and thought-provoking. I didn't realise there was so much scholarship in this area. I do have one big complaint though; for my end-of-term report I'm trying to do a quantitative project so WHY IS THERE NOT QUANTITATIVE DATA ON PRISON CONDITIONS ANYWHERE? 

I did find the workload difficult in September - things were piling up much faster than I could properly study them, and the content seemed to have taken a definite jump from last year, and started rapidly covering  and far exceeding all the extra learning I did for Schols.

On the other hand, I'm experiencing this weird feeling of being back in school again because I'm asking/answering too many questions and having to try restrain myself, which kinda sucks. I'm OK with not answering questions but I don't like it when lecturers draw attention to it because I don't want to be singled out like that.

I'm in a new class this year since we've just specialised, so I'm just gradually getting to know everyone and they seem pretty cool. It's been difficult figuring out how to spend time socialising while also getting some work done - in first year I socialised but didn't study, in second year I studied all the time but didn't socialise, and so now in third year I'm trying to strike a balance between the two. I went to Anastasija's party, the first party I'd been to in ages since I didn't go out at all last year as far as I recall, and it was pretty fun.

LAIDLAW: Early enough in September I had to meet one of the Laidlaw co-ordinators to talk about my progress and give feedback. I was nervous because I thought I had to have this whole personal development plan done, but it was fine and Orla is great and we had a nice, productive chat. 

I also had to make a video summarising my development over the summer by October 1st, which was a bit of a pain to make.

SOCIETIES: Apart from Freshers' Week, I've been involved as a committee member in Physoc and Netsoc, and as an ordinary member in KnitSoc, which is cool because I'm actually making (slow) progress in learning how to knit! Woooo.

READING: I read Mistborn Book 3 (disappointing end to an amazing trilogy), the Mistborn 3.5 novella, A Crack in Creation by Jennifer Doudna and Sam Sternberg (book about CRISPR), and started reading a book about the secret life of trees but have been paused for ages just because I haven't been reading even though it's quite good.

LEON: Went to Mooch regularly etc, which was great.

In summary, I was very busy on an everyday level settling into 3rd year of college and getting to know my new class in September.