This post covers chapters 4 & 5 from Futuyma & Kirkpatrick’s book on Evolution (2018). The author of this post is Sam Shry.

We are all special: mutation and variation

It is quite obvious to see variation among individuals, but how does this variation come about? Chapter 4 takes us on a journey through the evolutionary processes of mutations, variations, and how they are linked to inheritance.

We start off small with DNA (or RNA for some organisms), genetic material made up of base pairs that are the building blocks of all forms of life. DNA is carried by chromosomes, with one inherited from each parent in humans. Interestingly enough, the complexity of an individual has no correlation with the size of their genome (e.g. salamanders are more complex gnomically than humans). These chromosomes contain genes, which are the areas of a chromosome that perform a function. The chapter covers in-depth the processes in which a gene’s DNA is used to make proteins, via transcription, splicing, and translation, but that’s all a little dense for a blog. What is interesting to me is how only 2% of our genetic makeup is actually used for making proteins while the rest is just there as non-coding “stuff”. Even in our DNA we are hoarders…We find, however, that protein synthesis is the driver that creates variation in our appearance (phenotype) and genetic makeup (genotype) via inheritance. Inheritance is really just a locus or gene that is passed down to the next generation, but this locus varies in its DNA sequence, giving rise to alleles, a term given to locus variation in a population. The mixing of genes in sexually reproducing organisms causes variation in allele frequencies for a population. This mixing is done through segregation and recombination, where segregation selects one or two gene copies from a locus of each parent and recombination combines gene copies from each parent. Segregation is interesting in how the frequencies of genotypes and alleles change over time. We have developed a mathematical model (Hardy-Weinberg equilibrium) in order to understand how evolutionary forces affect populations. Similarly, with recombination, we have developed a model (linkage equilibrium) in order to study the effects of recombination rates in loci. Of course, the models do not represent reality, but give us a starting point that we can use to examine how evolution is occurring in a population and what factors are having the largest effects on which loci. We also have a large proportion of species reproducing asexually, using horizontal gene transfer to move DNA between individuals, which is particularly important to bacteria’s ability to evolve antibiotic resistance.

Even with all this inheritable mixing, most variation occurs from mutations. Mutations are errors, messed up DNA replication that is the ultimate source of genetic variation. See! It’s good to mess up sometimes! They can be small, dented my car screw-ups like point mutations, which only occur at a single DNA base, or they can be hot mess situations like whole genome duplications tetraploidy, where offspring can’t reproduce with their parental population, resulting in a whole new species with a single mutation. Each type of mutation can occur at a different rate and can cause different degrees of effect. Usually, there is a linear trend in genome size and mutation rate, which can affect almost every aspect of an organism. Mutations can affect both an individual’s traits as well as their fitness. Natural selection tries to drive mutation rates down, but ironically it is mutations that drive adaption and allow us to survive. We’ve been hyping up mutations, but most of them are bad, with natural selection “picking out” what mutations are favorable in an individual’s environment, or in other words, what works in an environment doesn’t die or at least has a chance to “get-it on” before dying. There are also a vast number of fields that delve into the inheritable, but non-genetic, cultural changes that can alter the physical behavior and learning of the offspring, but we steer clear of that in this book.

Just natural selection bro

In chapter 5 we can explain the genetic theory of natural selection as fundamental and simple, though Darwin may disagree as he wrecked himself trying to understand this “simple” concept till he died. It wasn’t till after his death that Mendelian genetics was fused with Darwinian selection theory. Of all organisms, the peppered moth is our shining example of documented evolution via natural selection, ironically adapting to survive our coal burning in the industrial revolution. After documenting this discovery we went straight to work figuring out how we could exploit this beautiful, natural process by developing the technique of industrial artificial selection; selecting the best traits of what we consume to make it taste, tastier.

What is key to evolution by natural selection is that the trait (phenotype) has to be good enough to allow individuals to make lots of offspring (absolute fitness) and that the trait is inherited by the offspring, which in turn causes the evolution of the species. Fitness is a combination of the probability of survival to maturity and the expected number of offspring the individual will have. If we think of a male bodybuilder, he may seem “fit” physically, but from an evolution standpoint his fitness is only measured in his survival to maturity and the number of offspring he produces, which could be a problem due to all the steroids…

If an allele has higher fitness after a mutation, this will cause a positive selection of that mutation in the population. One example of this is the adaption to drinking cow’s milk (lactase persistence) in Northern European populations. We can calculate a measurable selection strength score for these beneficial alleles (selection coefficient), which can then be compared with the genetic variation in the population to predict the rate of adaptation. The rate of adaptation can vary based on the organisms’ generation time (bacteria vs. humans) and the allele dominance (dominant, non-dominant, recessive). There can also be crappy mutations (deleterious) that decrease fitness and unfortunately due to their lousy recessive qualities and low frequency, selection can’t remove them easily. Just like gambling, mutations are subject to chance and can be removed from a population even if they are beneficial, such as via genetic drift.

There is also a mix of situations where natural selection has side effects, some of which are good and others not so good. Some of these genetic side effects are genetic correlations, allele hitchhiking, and trade-offs between alleles, all of which are a by-product of selection that can have serious effects on the population. For example, the Scottish soay sheep have an evolutionary trade-off in their population where a polymorphism at a single locus causes homozygous individuals to grow vestigial horns. These sad-looking horns make it harder with the ladies (decreasing mating success) but increase survival (no macho fights).

Just as natural selection can lead to new forms of variation, it can also preserve variation available in a population via balancing selection. This can occur when hard-core heterozygote alleles have higher fitness than the homozygotes (overdominance) and lead to polymorphic equilibrium, where both alleles are maintained in the population. Balancing selection can also occur with frequency–dependent selection, where the frequency of the alleles determines their fitness. Specialization can also balance polymorphism, either via niche specialization or space specialization. Just as yin and yang, genetic variation can also be destroyed by natural selection via under-dominance and positive-frequency-dependent selection. Almost nothing can escape time though, with alleles spreading to fixation in the population, with the deep, thought-provoking idea that “the outcome of evolution is determined by where the population begins” (page 125).

Where a population begins is important, because natural selection is continuously adapting species to the environment in which they live, making this coupling between species to the environment. Fitness can increase or decrease based on the organism’s mutations, but the same ebbs and flows in fitness can be the result of environmental changes too.

To measure the fitness of a population over time, mean fitness can be calculated and compared between populations. This theorem of natural selection mathematically demonstrates that populations evolve via natural selection in order to increase their average survival and reproduction through time. The measurable adaptive landscape is the balance between fitness selection, environmental gains, mutations, etc., and though the fundamental theorem doesn’t exactly apply to real-world situations sometimes (typical math), it acts as a guide to understanding approximately what the hell is going on in the population from an evolutionary point of view. Some instances where the math is way off is when selection is frequency dependent, which can lead to mean fitness decline of the population. The same can be said for competition within a population, where some individuals develop nasty traits that become dominant in the population, but then turn out to bring down the fitness of the group.

Most of the time though, these mutations, usually bad, are killed off (deleterious). Selection does an adequate job of “purifying” our DNA from these crap mutations, but the problem is they can reappear at almost the same rate, causing the numbers to balance out. What’s interesting is it doesn’t matter how crap the mutation is (strong or weak deleterious mutations), the population’s mean fitness still decreases by the same amount. It’s important to understand how this load of crap (mutation load) is spread throughout the genome in order to understand its effect on the mean population fitness. These deleterious mutations cause a lot of problems in humans a.k.a. death, but modern medicine has decreased and postponed these deaths, and individuals have lived long enough to reproduce, making a controversial discussion as to the future impact this will have on humans, but maybe concentrating on climate change and keeping us from catching on fire is a more pressing issue