Evolutionary clocks out of sync

Evolutionary time

It shouldn’t come as a surprise to anyone with a basic understanding of evolution that it is a temporal (and also spatial concept). Time is a fundamental aspect of the process of evolution by natural selection, and without it evolution wouldn’t exist. But time is also a fickle thing, and although it remains constant (let’s not delve into that issue here) not all things experience it in the same way.

Evolutionary clocks.jpg — Not all time is equal, but some are more equal than others?

Within the concept of evolution, time is the underlying factor which determines what we describe as ‘evolutionary rate’: that is, the speed by which evolution occurs. Typically, we might think of evolutionary rate as being very slow and gradual, accumulating over millennia as indescribably small or rare changes shape the characteristics of species or populations. But this isn’t always the case, and sometimes evolution can happen shockingly fast or with greater ease than we would expect. So, what drives this spurt of increased evolutionary rate? Can it be predicted? What factors are important in determining the overall evolutionary rate of a species?

Mutation vs. evolutionary rate

Before we delve further into that, a clarification is in order. You may have read previously on The G-CAT about mutation rate: that is, how frequently new mutations occur within the DNA of an organism. These are often reported in terms of mutations per thousands of base pairs per millions of years, indicating that mutations are not actually that common or frequent relative to the humungous size of the genome of most organisms. Mutation rates can be affected by a number of different biological aspects of the creature in question, as well as external influences such as radiation or chemicals (dubbed ‘mutagens’). Although this doesn’t usually result in superpowers (thanks for that mislead, comic books), chemical reactions between DNA and mutagenic compounds can lead to increased frequency of mutations occurring. This phenomenon explains the link between radiation and cancer, for example.

Evolutionary rate is not the exact same concept. Instead, evolutionary rate is described as the speed at which particular mutations become fixed within a population or species (i.e. all individuals of that group share the mutation). As you can imagine, not all mutations become fixed, or even stay within the gene pool for a long time (particularly if they relate to various negative traits such as congenital diseases or other low fitness traits). However, since mutation rates influence the speed at which new genetic variants appear in the gene pool, and may thus become targets of natural selection, they can lead to increased evolutionary rate.

Mutation and evolutionary rates — The difference between mutation and (molecular) evolutionary rate. New mutations appear in the genome via a variety of mechanisms: the frequency of these new alterations occurring is the mutation rate. However, most mutations are purged from the genome due to genetic drift or natural selection, leaving few survivors. From these, some mutations may become beneficial to the point of spreading throughout the entire population (or species). This is fixation, and the rate at which new alleles become fixed is called the evolutionary rate. In this example, the mutation rate is fairly high (5 mutations per ‘time’) but evolutionary rate is much lower (1 fixation per ‘time’).

Variation in evolutionary rates

You might expect that, given the broad universal nature of evolution as a process and the limitations of life, that evolutionary rates must be constrained and relatively constant across the tree of life. In fact, this assumption underpinned early ideas of a ‘strict molecular clock’, which attempted to determine how fast evolution (or mutations, depending on scale) occur to estimate times of divergence between species. As is always the case in science (particularly biological science), this is not true. Evolutionary rates vary widely across different taxonomic groups, species, and even across genes within a single genome. How does this happen? Is this because of differences in mutation rate?

Between species

Mutation rate is not the only factor that underpins the notion of evolutionary rate. Across the swathe of biota present today, there is considerable variation in evolutionary rates. A number of biological factors can drive this variance: first, is the notion that time (in terms of evolution) is not experienced the same way across all organisms. In fact, in most cases where we analyse evolutionary rate, we discuss the results in terms of generation times: that is, how fast evolution occurs per number of generations, not per unit time (like years).

Variation in generation times — Variations in generation times across various organisms. The y-axis demonstrates how many generations of the species occur over one year: given the huge disparity shown here, this is shown on a logarithmic scale. This ranges from the most rapidly reproducing (the bacterium E. coli) with a generation time of 20 minutes to the slowest reproducing (blue whales) with a generation time of ~30 years.

This is an important distinction as most heritable mutations occur during the jump from one generation (parent) to the next (offspring). Similarly, the frequency of variants within the gene pool is related to how many offspring a parent produces and survive (as the primary measure of ‘fitness’). The incredibly fast generation time of viruses, for example, explains their capacity to evolve rapid resistance to treatments and the prevention of a cold ‘cure’.

Similar traits which control the life cycle of an organism, dubbed ‘life history traits’, also have significant impacts on evolutionary rates. For example, metabolic rates have been shown to play an important role in natural mutation rates, with higher metabolic rates leading to more frequent mutations due to the increased production of mutagenic chemicals during respiration. In this sense, we would expect faster reproducing organisms with higher metabolic rates, such as rodents compared to larger-bodied mammals, to have similarly higher evolutionary rates.

Between genes or markers

However, even trying to estimate evolutionary rate for all genes in a single species has been shown to be folly. Individual genes or genetic markers show variable evolutionary and mutation rates within the same individuals. This is because the process of natural selection places constraints of variable strength on different parts of the genome. Say we have a single chromosome from an animal: it contains a number of different genes, which directly code for functional proteins, and intragenic elements (which we can consider ‘junk’). Mutations which occur in the middle of genes will have an impact on how the resultant protein is expressed: if this mutation is beneficial, the new protein may help the organism (by conferring better heat tolerance, as an example). If this mutation is deleterious, it may ‘break’ the structure of the protein, causing it to become useless for its intended function.

Naturally, some proteins are very specifically shaped for their function, and even small changes in their structure may completely prevent them from working in a critical way. As a result, mutations that occur in these genes may very rarely be passed on (if the host dies immediately, or is too weak to reproduce). Thus, the genes appear genetically conserved and will evolve very slowly.

These barriers are unlikely to exist, or at least be significantly weaker, on parts of the genome which don’t code for functional traits or are a little more flexible in their ability to function. It is at these sections of DNA that many more mutations can accumulate, sometimes leading to higher evolutionary rates. This aspect of mitochondrial DNA, for example, solidified it as the marker of choice for studying evolutionary history for a long time (and still to this day is frequently used).

Variation across genome.jpg — Variation in evolutionary rates across the genome of a single organism. This diagram shows various sections of the genome on the left, with acquire mutations (stars; centre). For those mutations in protein-coding parts of the genes (second bottom row), this results in a change in protein structure. Because the structure of protein is critical to its function, many mutations that alter the protein shape are maladaptive and do not become fixed (crosses). However, rarely, some may be beneficial, leading to evolution (ticks). Within non-coding segments (bottom row), mutations do not confer any changes in the shape and thus don’t face the same constraints: most mutations are likely to pass on to future generations. At an even more complex level, individual genes themselves may vary depending on how critical their function is (top row), with some genes under more tight mutational constraints than others.

Between mutation types

Even more specifically than gene, particular mutation types may occur at varying rates. Chemically speaking, some alterations to nucleotides (the letters that make up the DNA) are ‘easier’ than others, leading certain transitions to occur more frequently. This is based on the chemical shape of the molecules and how alterations to these structures can influence the stability and nature of the DNA. Thus, particular mutations (in terms of which nucleotides change to which other) do not always occur at the same rate.

Transition vs transversion rates.jpg — Particular mutations may also be more frequent than others, an important factor in phylogenetic studies. In this diagram, the size and colours of the arrows demonstrate how common moving from one state to another is, with large green arrows more frequent transitions than small red arrows.

A clock that is always ticking

All of these factors combined (and likely many others) affect the rate at which evolution occurs for any given population, species or broader taxonomic group. Since nature is not a perfectly controlled experiment, variations in these traits can shift evolutionary rates throughout the tree of life and over time. Assuming that evolution is a predictable constant, and not a constantly fluctuating force, is an underestimation of the complexity of nature.

Sometimes it might feel like the evolutionary clock has stopped on the human race: that we’ve reached our ‘peak’ and can’t evolve any more. But evolution is still occurring in modern humans, and even if its not as fast as some other species on Earth, the clock has always been ticking for us. The real question is whether our own evolution can tick faster than the pressure of the world we’ve changed so much: not just for us, but for all life on Earth.