Literature course

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

This is a literature course on the book Evolution by Douglas J. Futuyma & Mark Kirkpatrick (Fourth Edition) during the first half of 2023. This write-up covers chapters 1 to 3 and is authored by Louis Addo (a Ph.D. student at KAU)

The historical background of Evolution Biology

Evolution in biology refers to the shift in the heritable traits of biological populations over successive generations. Charles Robert Darwin (English naturalist and biologist, Figure 1. left) and Alfred Russel Wallace (an English naturalist, explorer, geographer, anthropologist, biologist and illustrator, Figure 1. right) separately developed the theory of evolution by natural selection in the middle of the 19^th century, and it was extensively outlined in Darwin’s book On the Origin of Species. The hypotheses of evolution postulated that all living things share a common ancestor, and that natural selection acting on genetic variations is responsible for the changes in their populations over time. The theory of evolution became a scientific fact supported by other scientists in paleontology, genetics, and biochemistry. Prior to the postulation of the theory of evolution, the dominant worldview was that each species was uniquely created by God and had set characteristics. However, this worldview was challenged by the Enlightenment movement leading to the emergence of science. The foundation for evolutionary thought was laid by astronomers and geologists who postulated theories about the creation of stars, planets, and the earth including the changes the earth has gone through as well as its many extinct species. Unique to Darwin’s theory were its five components explaining concepts “descent with modification” and “natural selection”.

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The five distinct components of Darwin’s theory of evolution are natural selection which means that species characteristics change over time to meet changes in their environment, evolution which proposes that organisms change over time, gradualism which means that the differences between even fundamentally different organisms have evolved through intermediate forms rather than by large leaps, common descent which suggests that species diverged from shared progenitors and that species might be seen as one enormous family tree that represents ancestry, and finally population change which means that evolution occurs by changes in the proportions (frequencies) of different variant kinds of individuals within a population.

Most scientists acknowledged the historical truth of evolution through descent with modification from common ancestors by the 1870s, but natural selection, which drives evolution, was not widely accepted until around 60 years after The Origin of Species was published. Many ideas, including neo-Lamarckian, orthogenetic, and mutationist theories, were put out during this period.

In general, the idea of evolution is a scientific truth that explains how ancestors give rise to various descendants and how species change over time. Biologists generally agree with the theory, and while work is still being done in some areas, the fundamental ideas of evolutionary theory are well-supported.

The “Tree of Life” and phylogenetics

The concept of the Tree of Life was first proposed in Charles Darwin’s book On the Origin of Species and proposes that all species, alive and extinct, descended from a single ancestral form of life that existed billions of years ago. The history of the events by which species or other taxa have arisen from common ancestors is called phylogeny, which is often represented by a phylogenetic tree that shows the genealogical relationships among the taxa. Anagenesis, which is the evolutionary modification of a lineage’s (species’) physical characteristics, and cladogenesis, which is the division of a lineage into two or more descendant lineages, are the two main processes that contribute to the development of higher taxa. After cladogenesis, anagenesis causes each descendant lineage to diverge even farther from the others. The branching order and the length of the branch in the phylogenetic tree can show which species are more closely and less distantly related to one another.

Phylogenetic studies reveal the evolutionary relationships between organisms and gene sequences, often showing the pattern of separate and divergent lineages. However, sometimes branches of a phylogenetic tree rejoin, forming a network rather than just a branching tree. Hybrid speciation is one example of this, which is especially common in plants, where some species evolve from hybrid crosses between two different ancestors. Another example is horizontal gene transfer (HGT) where genes are passed among organisms, enabling them to adapt to changing circumstances.

Phylogenetic analysis is an effective method for determining how different traits in organisms have evolved through time. This approach shows that species have evolved from similar creatures since it is based on homologous traits that have descended from them. The majority of an organism’s traits are changed from traits that already existed in its ancestors and do not develop independently. Although they often have comparable genetic and developmental bases, homologous physical characteristics between species can vary more than the finished products. For instance, in the 1970s, scientists analyzed the protein amino acid sequences of pairs of animals that split from their common progenitors at various points in time. They created a molecular clock by plotting the matching DNA sequence discrepancies against predicted divergence periods and finding that the rise in differences increased linearly with time (Futuyma & Kirkpatrick 41). Assuming the genes in these lineages had developed at the same pace as those in the animals with fossil records, this permitted calculation of the period of divergence even for lineages lacking a fossil record. Yet, there is no one molecular clock and rates of sequence evolution vary among different types of organisms.

The analysis of the evolution of different organismal traits with phylogenetic analysis offers overwhelming proof of evolution. It is feasible to evaluate homologous traits that are descended from common ancestors since characteristics of organisms nearly invariably evolve from pre-existing aspects of their predecessors. However, a character may be shared by several species but not necessarily in the same character state. It can be challenging to determine if two species’ traits are homologous, but embryological research and anatomical correspondence of position and structure, are the two most often used methods for making this determination are often successful methods.

The concepts of Natural Selection and Adaptation

Changes in the environmental adaptation requirements of organisms trigger biological changes in their behavior and physical features to ensure their existence in the altered environment. Thus, altered environments can cause natural selection on the genetic variation in many characteristics of a species or population. For instance, soapberry beetles adapted to new food sources by changing the length of their beaks, and several insect and plant species have developed a resistance to heavy metals and chemical pesticides. Fish overfishing has also affected behavior and accelerated the onset of sexual maturity. The process by which individuals with advantageous traits have a better chance of surviving and reproducing than those without, resulting in the preservation of preferred variations and the rejection of harmful ones, is referred to as natural selection. Darwin first introduced this idea in “On the Origin of Species.” When various biological entities consistently vary in fitness, natural selection takes place. It is important to understand that evolution, which may also be brought about by other mechanisms like genetic drift, is not the same as natural selection. The environmental conditions that force natural selection on a species are determined by its traits. Certain species can create ecological niches for themselves by eliminating elements of their environment so that these no longer force natural selection. Natural selection can take place at several scales, including genes, cell types, individual organisms, populations, and species.

Selfish genes, which multiply in the genome whether they are advantageous to the organism or not, are an illustration of gene-level selection. Gene-level selection can conflict with individual selection and cause harm to organisms. Selection among individuals occurs at a higher level than selection among genes. Characteristics develop through individual selection; altruism can lower individual fitness but may develop through social selection; cooperation develops through kin selection. By varying the percentage of species throughout time, species selection modifies the diversity of biological traits. It has an impact on organism disparity but not adaptations. For instance, more asexual populations experience extinction than sexual groups.

Adaptation in biology refers to both the process by which organisms evolve over generations to improve survival and reproduction, and to a characteristic that evolved by natural selection. A trait must be developed and give greater fitness than the ancestral condition in order to qualify as an adaptation. A feature that unintentionally fulfills a new purpose is known as a preadaptation. For instance, parrots can eat fruits and seeds with the help of their strong, pointed beaks but, in case a new resource is presented, they can also use it to feed on that resource. Exaptation is the process of adapting a characteristic for use unrelated to the one for which it was originally selected. In birds that initially evolved feathers to keep warm, an example of an adaptation would be the use of feathers for mating displays or flying. Pre-adaptation is another name for an exaptation. Exaptations and preadaptations are common in the early stages of the evolution of new adaptations. To determine if a certain characteristic is an actual adaptation, scientists examine the available data. Species traits are not always adaptations or random characteristics but can be flawed and limited, such as in the case of mammals that are unable to evolve beneficial modifications in the number of vertebrae. The vast diversity of life is the result of natural selection, as varied habitats and other factors may force selection on different traits within a species.

The next blog will cover chapters 4 and 5 and will be authored by Samuel Shry.

References

Futuyma, D. J., & Kirkpatrick, M. (2017). Evolutionary. Evolution (Fourth ed.). pp. 3-76. Sunderland, Massachusetts: Sinauer Associates, Inc.