This post covers chapters 14 & 15 from Futuyma and Kirkpatrick’s book on Evolution (2018). The author of this post is Jeff Marker.

The Evolution of Genes and Genomes

One of the most common sources of evolutionary adaptation is the emergence of new genes. In eukaryotes, the most common mechanism for the emergence of new genes is by gene duplication, which occurs when there is an error in DNA replication. Gene duplication can result in the creation of a new gene copy, which can then evolve to acquire new functions or to specialize in one of the functions of the original gene. The result is a gene family, which is a set of loci that originated by gene duplication and that typically have related biochemical roles. Gene families can lead to the emergence of new biochemical pathways and new structures. For example, in humans, the amylase gene family has been duplicated and evolved to produce different amylase enzymes, allowing humans to digest a wide range of starches from different plants (Perry et al., 2007).

Whole genome duplication is much rarer than gene duplication, but is a key mechanism for the evolution of the genome in many groups of organisms, especially plants. Whole genome duplication can result in the doubling of the number of chromosomes in an organism, which can then allow for the emergence of new gene functions through the duplication and divergence of gene families. For example, the multiplication of complete sets of chromosomes that have occurred in the Brassicaceae family has resulted in the emergence of many new gene functions and the evolution of novel morphological traits (Bancroft et al., 2011).

Other mechanisms of gene emergence include exon shuffling and appearance of de novo genes. Exon shuffling is a process where coding regions (exons) from different genes are rearranged and recombined, creating new genes with unique functions. De novo genes originate from non-coding regions of the genome, evolving independently of existing genes. They contribute to biological functions and evolutionary innovation through mechanisms like mutation, selection, and gene duplication.

Another mechanism for the emergence of new genes is horizontal gene transfer (HGT), which involves the possession of genes from unrelated species (Figure 1). HGT is particularly common in prokaryotes, where it has enabled the rapid evolution of traits. For example, the spread of antibiotic-resistance genes among bacteria has been assisted by the HGT of plasmids carrying resistance genes (Davies and Davies, 2010).

In contrast to the previously mentioned methods of genome evolution that saw the creation of genes, chromosomal deletions can eliminate functioning genes contributing to both “good” and “bad” genomic outcomes. Natural selection can cause a deletion to increase in frequency if the deleted gene codes for a protein that increases the risk of infection. For example, a deletion in the CCR5 gene that codes for a cell surface protein used by the HIV virus to enter human cells has become fixed in some human populations.

The continuing evolution of genomes leads to a situation where some species end up with a very high number of genes. For example, the human genome consists of approximately 3 billion base pairs. However, only a small fraction of our genome is used to encode proteins and regulate gene expression. Estimates suggest that we only use about 2% of our genome to code for proteins or other gene products. The rest, termed “junk DNA,” includes regions with regulatory elements and non-functional remnants known as pseudogenes. Pseudogenes are genes that have lost their protein-coding ability through mutations. Their presence aligns with the neutral theory of molecular evolution proposed by Motoo Kimura. According to the neutral theory, the majority of genetic changes are caused by random genetic drift rather than selective pressure, resulting in non-functional sequences like pseudogenes. Understanding the significance and potential functions of these non-coding regions remains an active area of genomic research.

Evolution drives changes in gene expression patterns that can affect the survival of organisms ultimately leading to new traits and new species. Changes in gene expression occur through alterations in transcription factor binding sites, alternative splicing patterns, and epigenetic changes to DNA and histones. One example of the evolution of gene expression in insects is the wing pattern of Heliconius butterflies. Their diverse wing colors aid in reproduction and to signal to predators that they are unpalatable. Researchers found that changes in gene expression in the developmental pathway that produces the wing patterns of Heliconius butterflies have contributed to their diverse color patterns (Figure 2). The study showed that the expression of a transcription factor gene called optix, which is involved in forming the eyespot pattern on the wings, has evolved differently in different species of Heliconius butterflies (Martin et al., 2012).

Coding regions, gene expression, chromosome structure, and genome size are interconnected processes shaping an organism’s complex life. Changes in coding regions can lead to the emergence of new functional genes or alterations in protein structure. Concurrently, adjustments in gene expression patterns can drive phenotypic variation. Chromosome evolution plays a role in these processes, as rearrangements and other changes reshape the distribution of genes within a genome. Furthermore, changes in genome size can influence gene regulation, complexity, and the evolutionary trajectory of a species.

Evolution and Development

Evolutionary developmental biology (EDB) aims to integrate information from embryology, developmental genetics, and population genetics to understand how genes and changes in genes are expressed as phenotypes and changes in phenotypes. By understanding the mechanisms that produce phenotypes, we can better grasp how they evolve. Mutational changes in the genes that produce a developmental pathway may cause advantageous alterations in the phenotype, leading to the evolution of both the phenotype and its underlying genetic network.

Differences among species often result from changes in the relative developmental rates of different body parts or in the rates or durations of different life history stages, which are known as allometry and heterochrony. Some characteristics have evolved by heterotopy, where the expression occurs at a novel location on the body. For example, the inner ear bones of mammals were originally found as part of the jaw in distant common ancestors. These bones co-opted to function in the ear away from the jaw and helped mammals become more effective at hearing, aiding their survival and reproduction.

The vast diversity of multicellular eukaryotes is due to the diverse uses of a toolkit of genes and developmental pathways. Developmental pathways include signaling proteins, enhancers, transcription factors, and structural genes. Evolutionary changes in the regulatory connections among signaling pathways and transcription factors are believed to underlie much of the phenotypic diversity seen in nature. These regulatory networks coordinate the interactions among genes and other molecules to control gene expression. Regulatory networks govern biological processes and organism responses to environmental cues. One example of a gene regulatory network is that involved in the development of fruit flies. This network includes genes such as the Hox genes, which control the body segment identity, or where the different body segments are supposed to line up. The Hox genes regulate each other’s expression through a series of complex interactions, forming a network that ensures the proper patterning and differentiation of different body segments during development.

During evolution, genes and developmental pathways are often co-opted for new functions, a process that is probably responsible for the evolution of many new traits. This process results from evolutionary changes in functional connections between transcription factors and cis-regulatory elements. Modularity among body parts is achieved by patterning mechanisms whose regulation is often specific to certain structures, segments, and life history stages. Modularity helps different parts of the body develop divergent morphologies. Pleiotropic effects of genes that affect functionally interacting characteristics may evolve, resulting in the evolution of functional modules known as phenotypic integration. One example of phenotypic integration is the correlation between beak size and body size in birds. In many bird species, larger birds tend to have larger beaks, and smaller birds tend to have smaller beaks. This is an example of phenotypic integration because the size of the beak and the size of the body are functionally related traits that are influenced by overlapping sets of genes.

Genetic and developmental constraints can make some imaginable evolutionary changes unlikely. Based on changes in the expression of certain genes and developmental pathways in response to environmental signals, a single genotype may be expressed as an array of different phenotypes, known as the genotype’s norm of reaction. Reaction norms are genetically variable and can evolve by natural selection. If an environment varies, phenotypic plasticity may evolve. Conversely, selection for a constant phenotype can result in canalization. Genetic assimilation is the genetic fixation of one of the states of a phenotypically plastic character. It is not known how important genetic assimilation is in evolution, nor is it known if adaptation may occur first by a non-genetic phenotypic change that later becomes genetically fixed by natural selection.

The evolution of genes and genomes involves complex processes such as gene duplication, whole genome duplication, exon shuffling, de novo gene emergence, and horizontal gene transfer. These mechanisms contribute to the emergence of new functions and the huge amounts of genetic diversity we see in the world. Changes in gene expression patterns play a vital role in evolutionary adaptation and the development of new traits. Chromosome evolution and alterations in genome size further shape the evolutionary course of species. Understanding that these processes are firmly connected provides insights into the complexity and diversity of life forms that have evolved on our planet.

References

Bancroft, I., Morgan, C., Fraser, F., Higgins, J., Wells, R., Clissold, L., … & Trick, M. (2011). Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nature biotechnology, 29(8), 762-766.

Davies, J., & Davies, D. (2010). Origins and evolution of antibiotic resistance. Microbiology and molecular biology reviews, 74(3), 417-433.

Martin, A., Papa, R., Nadeau, N. J., Hill, R. I., Counterman, B. A., Halder, G., … & Reed, R. D. (2012). Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand. Proceedings of the National Academy of Sciences, 109(31), 12632-12637.

Perry, G. H., Dominy, N. J., Claw, K. G., Lee, A. S., Fiegler, H., Redon, R., … & Stone, A. C. (2007). Diet and the evolution of human amylase gene copy number variation. Nature genetics, 39(10), 1256-1260.

This post covers chapters 12 & 13 from Futuyma and Kirkpatrick’s book on Evolution (2018). The author of this post is Jacqueline Hoppenreijs.

In blog 4, we briefly touched upon one of the advantages of dispersal: it decreases competition for resources with your nearest and dearest. Residency can have multiple outcomes that vary from extremely cooperative, via neutral, to extremely violent.

Cooperation and conflict

When two individuals coexist, one can help the other (“cooperate”) through altruism or mutualism, or do the opposite (“conflict”). Altruism is probably the most renowned example of these interactions, and indicates that one individual sacrifices something to another’s benefit. In the case of mutualism, there are only winners: everyone benefits. Conflict can consist of direct harm, but also indirect actions such as cheating. That’s not to say that a plant and a bee are sitting down for a game of Monopoly, but it might look like pollinators that are not doing their job by bypassing a plant’s anthers and stealing the nectar (Figure 1).

Figure 1. Pollinators robbing plants of their nectar instead of taking the front door and take some pollen with them.

Now, it is tempting to think that those that cheat will win from the others, because they get more resources with less effort, and might thus be able to withstand selection pressure better. But wouldn’t populations come to consist exclusively of cheaters and then collapse? Not quite, so there must be another mechanism at work. That mechanism is not group selection, which was a popular hypothesis until the 1960s and assumed that selection pressure didn’t work on the individual but on the level above. There is, however, a bunch of other mechanisms through which evolution has resulted in cooperation rather than conflict.

A well-known example of non-family cooperation is to find safety or success in numbers. This behaviour can directly increase the chance of not-being-eaten, or increase the chance of catching a prey. Other types of cooperation take more time to pay off, or only work as such because the individuals involved interact repeatedly. The latter means that actions are reciprocal, as opposed to one-off selfish behaviour. This might look like individuals copying each other’s behaviour or copying their own, previous behaviour until that’s not rewarding anymore. A series of cooperative interactions can also change if a helping individual decides to punish a cheater for being selfish. Or even worse, when one individual damages another at a cost for itself! All of this changes when family enters the game. Now, there’s not just profit for yourself and increased direct fitness to be gained, but you can gain by helping others survive. Why? Because they’re likely to be carrying the genes you carry, which means there’s an indirect fitness advantage to be gained! Kin selection like this is advantageous if the relatedness and benefit for the recipient outweigh the costs of the helping individual.

Conflict within family, on the other hand, can take some really extreme forms. That starts at the parental level: we’ve heard about male-male competition in blog five, but males can go as far as to harm the female they’re mating with (called sexually antagonistic competition) in order to increase their own reproductive success. The female praying mantis’ sexual cannibalism barely makes up for all the suffering her sisters go through. A less deadly form of parental conflict is the distribution of parental care to the offspring, which takes time and energy from either or both parents.

Moving onto the next generation, we see that there are parents that kill other individual’s offspring or even their own, which is called infanticide. The former makes sense in that they are making space for their own genes in the population by removing another individual’s genes, and the latter might make sense if there’s resource limitations. The same reasoning might apply when siblings compete for the same resource, which is called siblicide. This touches upon the conflict that exists between parents and their offspring. While one or few offspring are usually selfish as they profit most when they themselves survive, it’s in the interest of the parent to produce as many successful offspring as possible.

After so much dysfunctional family dynamics, we’re moving to animals that have taken family relationships to a whole other level: eusocial animals, such as many bees and termites. Here, we see the positive side of kin selection, in that infertile offspring all increase their indirect fitness by taking care of their mother, the nest, or helping rear their (half) siblings. There’s a, for lack of better words, negative side, too. To keep the relatedness with reproductively successful offspring high, eusocial animals don’t hesitate to disadvantage some family members that are not as related to them as others.

We’ve seen that conflict can exist between individuals because they want to increase their direct or indirect fitness. It also exists within individuals, for example when alleles kill off other alleles during meiosis, leading to segregation distortion, or in the form of transposons, bits of DNA that keep replicating themselves within a genome. Conflicts between mitochondrial and nuclear DNA, which are spread via the maternal line and both parents respectively, also occur widely. It’s in the mitochondrion’s interest to increase female production also when it comes at a cost to male production, so the nuclear DNA has to jump into an arms race to try and undo any changes that might disadvantage male reproduction. The previously mentioned concept of group selection shouldn’t get dismissed entirely, as there are examples of traits evolving in groups that are not necessarily advantageous for its individuals. Groups of individuals with such benevolent traits survive better than groups without them. Benevolence doesn’t always mean pure altruism, by the way: lower production of toxins by plants (Wilson, 1987) and “less-deadliness” of pathogens are well-described examples, too. Especially pathogens want to be careful: they’ll want to spread as much as they can, but there’s little use in killing off the entire host population since that means they’re doomed themselves. Units that depend on vertical transmission, that is reproduction as opposed to horizontal transmission/infection, profit from making their host as successful as possible. Not so surprising then, that they are the driving forces behind some of the major transitions that our planet has seen. The adoption of mitochondria and cyanobacteria have led to successful single-cell organisms. Some of these have, through mechanisms similar to kin and group selection, been able to transform to what we know as multicellular organisms today.

Interactions among species

Neither single-cell nor multicellular organisms exist in a vacuum or only interact with organisms of their own kind. Species interactions are variable over time, in how much species depend on each other and in its effect on the respective participants of the interaction. Examples include a specific insect and plant needing each other a few weeks per year for food and pollination respectively, to a parasite that spends its entire life in its host and depends on it for all its food and the dispersal of its offspring. Close associations are called symbiosis and species that are very attuned to each other, such as corals and zooxanthellae (Stanley & Swart, 1995), are said to be co-evolved. This means that they have undergone reciprocal genetic change because they’ve exercised selection on each other.

Not all of these interactions are positive; becoming the host to a parasite or a prey to a predator usually doesn’t bode well for an individual or a population. Both the enemy and the victim in these relationships need to evolve fast enough and in such a way that they can outperform the other; this can turn into an evolutionary arms race if both are under selection for the same trait. Co-evolution doesn’t have to be unidirectional, as enemy and victim can follow each other to increase and decrease trait values over time.

There are multiple strategies for escaping or outperforming enemies and becoming successful in this arms race. Many are visual-based: by displaying warning signals of being dangerous (aposematism) or mimicking a dangerous species (mimicry). If you’re not a dangerous species yourself (Batesian mimicry), you disadvantage the actually dangerous species by teaching enemies that risks are low. Being dangerous yourself and mimicking a dangerous colleague (Müllerian mimicry), on the other hand, reinforces the defence mechanism. Other strategies can be olfactory or taste-based, such as in plants that produce chemical compounds to protect themselves from herbivory. Throughout history, such successful adjustments have often been seen to lead to quick radiation and many new species with that adjustment, both on the enemy and the victim side. Whether a parasite can successfully infect its victim, can depend on whether the victim can recognise and resist (gene-for-gene model), or whether the parasite matches the victim’s genetic profile (matching allele model). Parasites and pathogens have been shown to adapt relatively quickly to their victims, which means that the above-mentioned shift towards benevolence doesn’t always take place. This depends, amongst others, on the genetic diversity on both the enemy- and victim-side and the way in which the parasite or pathogen is transmitted and received. The latter can be as simple as the difference between vertical and horizontal transmission, but can also have to do with the life cycle of host, pathogen and potential intermediate hosts. In the case of malaria, for example, humans and mosquitoes are hosts of most Plasmodium species, which is complicated as a life cycle in itself. There seems to be at least one Plasmodium species, however, that has found another intermediate host in macaque monkeys, complicating the transmission process further (Centers for Disease Control and Prevention, 2020).

Moving on to the sunnier side of life, there are also a lot of species interactions from which one or both species profit. This mutual exploitation, can, just as with the cheating family or population members that we saw earlier, go awry when one of the participants starts cheating the other. That can lead to immediate sanctions being taken (e.g. lower rewards for the cheater) but can also continue to exist because cheating happens relatively little or there are non-cheaters to compensate potential losses. Even here, one could speak of an arms race where both participants exploit the other as much as they can, and increasingly over time.

Not all species interactions are one-on-one, or as close as some of the previously-mentioned examples. Very often, species interact simply because they use the same space or other resources. If there are limited resources, however, this may lead to competition. One consequence of competition might be that one or more species is driven to extinction. This principle, and the related “Diversity Paradox”, have been the topic of many studies (Simha et al., 2022). A second consequence is the selection-by-lack-of-resources that can cause divergence of resource use and may lead to the evolution of new species. If species that overlap in their use of resources co-occur, they might each display more or different resource-use compared to when they occur alone. This is called ecological release, but shifts to interference competition when one of the species starts to affect its competitor to keep it from using the resource in question. If this is done by a species not native to the area, one can speak of invasive alien species (Figure 2).

Figure 2. Competition for light and space in a Swedish riparian zone by the American Skunk-cabbage (Lysichiton americanus). Photo by Owe Nilsson.

Whether friends or foes, newcomers and the species that already were in a certain place together form an ecological community. The local environment and its inhabitants impose a “filter” on the species that occur in a larger area to decide which of them manage to live in a certain spot. The mechanisms of competition can lead to evolutionary divergence, whereas the environmental filtering can lead to evolutionary convergence. That’s why we often see functionally similar, but taxonomically different species communities in ecologically similar, but geographically different areas. Uniting community ecology and evolutionary biology helps us discern these patterns and the eco-evolutionary past and present.

References

Centers for Disease Control and Prevention. (2020). Malaria. (DPDx – Laboratory Identification of Parasites of Public Health Concern). https://www.cdc.gov/dpdx/malaria/index.html

Futuyma, D., & Kirkpatrick, M. (2018). Evolution (4th ed.). Oxford University Press.

Simha, A., Pardo-De la Hoz, C. J., & Carley, L. N. (2022). Moving beyond the “Diversity Paradox”: The Limitations of Competition-Based Frameworks in Understanding Species Diversity. American Naturalist, 200(1), 89–100. https://doi.org/10.1086/720002

Stanley, G. D., & Swart, P. K. (1995). Evolution of the Coral-Zooxanthenllae Symbiosis During the Triassic: A Geochemical Approach. In Paleobiology (Vol. 21, Issue 2, pp. 179–199).

Wilson, J. B. (1987). Group selection in plant populations. Theoretical and Applied Genetics, 74(4), 493–502. https://doi.org/10.1007/BF00289828

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This post covers chapters 8 & 9 from Futuyma and Kirkpatrick’s book on Evolution (2018). The author of this post is Jacqueline Hoppenreijs.

Evolution in space

Variation in phenotypic traits can reflect variation in environmental factors on a global scale, such as temperature, or on a local scale, such as nutrient or toxicant concentrations. When this phenotypic variation looks like a smooth transition or gradient, we call it a cline. Such ecological variation is a consequence of the selection pressure’s spatial variation and can be seen between and within species, leading to specific patterns of phenotypic traits. An example of such a pattern between species is the occurrence of hairs and cuticles in drought-adjusted plants, that help them retain small amounts of water that they have managed to get a hold of (De Micco & Aronne, 2012). A within-species example is the variation in root depth and structure in individuals of one species that are grown in drier circumstances than others (Lenssen et al., 2004).

Trait patterns are further shaped by exchange between populations of the same species, a process called gene flow that happens through dispersal. Dispersal is different from migration in that it means that an organism ventures out to explore new grounds (or waters) and that it leads to exchange or introduction of genes. Dispersal can be passive (e.g. a seed falls into the water and ends up on a riverbank elsewhere), or active (e.g. an animal starts looking for a more suitable living environment if it runs out of food). There are also forms that could be seen as intermediate, such as plants (Figure 1) that disguise themselves to convince someone else to fix their dispersal for them!

Dispersal can be a bit of a pain, as it requires energy (even if it’s only the effort of growing your seeds in the form of poop) and can be dangerous. It can have big advantages though: by dispersing, you get the opportunity to find a more suitable spot to live and you simultaneously decrease the day-to-day competition with your family members in the place where you all are from. You’re also more likely to reproduce with an individual from a different population, thus decreasing the risk of inbreeding.

So, it’s clear that dispersal can be very profitable, and leads to exchange of genes between populations or establishment of new populations. Gene flow can be measured in multiple ways, that are applicable in discrete (think: migration rate between islands) or continuous (think: migration variance throughout a vast forest) environments, or both. This can be your typical mark-recapture set-up, but more and more often genetics-based methods are used. There are many ways to go about this, but one straightforward approach is to assess genetic difference between populations using their allele frequencies, a variable that then can be combined with the populations’ physical distance to give an idea of gene flow history. Things become less straightforward when there’s local selection involved, that favours one allele over the other and thus (partially) undoes the effect of gene flow. Which of the two processes predominates depends on both local selection and migration rate/variance. If local selection were the dominant process, different populations would have different alleles that fit their environment, and if gene flow were the dominant process, populations would have the exact same allele, also called gene swamping. The two processes often keep each other in somewhat of a balance, and understanding them can help trace past events and processes, and predict future developments (e.g. Love et al., 2023).

Life as an evolutionary biologist is complicated enough with just these two processes going on, but there’s another one that comes into play: genetic drift. This process, that we heard about in blog 3 , is another source of genetic variation and it can be pretty complicated to find out whether it’s this or local adaptation (or both) that cause genetic and phenotypic differences between populations. Mapping of entire genomes makes it possible to look for differences between them, and can offer a solution to this problem. A comparison between the genetic variance in neutral and “under selection” regions in two or more different populations, gives you information on both. As the neutral regions will have a certain amount of variance that’s not a consequence of the environment favouring one allele over the other, this variance is most likely the consequence of genetic drift. The variance in the “under selection” region minus the variance in the neutral regions is than likely to be the result of local adaptation. It’s as simple as that!

Understanding local adaptations in the context of dispersal to new areas can open a whole new can of worms/research questions. One might wonder how other species in the region have adapted to their environment in the past and are now dealing with a new species entering the stage. Ecological research often has a competition-for-resources angle (Simha et al., 2022), but could for example also focus on niche construction (Laland et al., 2016). It’s thus virtually impossible that the entrance of a new species in an area will go unnoticed by the already present species. Researching this, however, requires somewhat of an understanding of how species are defined and come to be, which is our next topic.

Species and speciation

As we know now, species can adapt to new places that they disperse to, and to new circumstances that they’re confronted with. This can ultimately lead to the formation of one or more new species, also called speciation. Before understanding that process, it can be helpful to look at its results: how do we define species as different from each other? The answer is that this is almost always is arbitrary, and the approach can be simple: “they look different”. It gets a bit more complicated with “they can successfully reproduce”, also called the Biological Species Concept (BSC), or quite complicated with the approach “they are the smallest set of organisms that has the same ancestor” which is one of the versions of the Phylogenetic Species Concept (PSC). Why do I write “one of the versions”, you ask? That’s because there’s hardly ever a clear line to draw in biology: think of organisms that don’t sexually reproduce, or different species that hybridise with each other! Besides that, our knowledge and technology keep developing, which means that these concepts are still and probably always will be under debate (see for example Wheeler & Platnick, 2000).

While it’s easy to understand why spatially separated individuals of a species don’t get their genes flowing, there’s a bunch of less well-known mechanisms that prevent gene flow without geographical barriers. These are called Reproductive Isolating Barriers (RIBs), lead to speciation and can be divided in three main categories: pre-mating, pre-zygotic and post-zygotic barriers. Pre-mating RIBs mean that the male and female gamete never get to meet, for example because of a temporal mismatch or because the owners don’t recognise each other’s courting signals. For mating to turn into reproduction, we need a zygote to be formed. If there’s a pre-zygotic barrier such as a mismatch in physique or unsuccessful fertilisation, that means yet another barrier. If all this works and we have a hybrid zygote, it might simply not be able to survive in the environment that its parent organisms are well-adjusted to. Or it might have high mortality in no matter which environment, or is unable to produce offspring, all meaning we have a post-zygotic problem. Post-zygotic barriers are often caused by mismatches between the genes of the respective parents and are often found on the site of the heterogametic sex, i.e. the counterparts of humans that have XY instead of XX chromosomes. Different forms of reproductive isolation (RI) aren’t equally important, don’t necessarily occur equally fast in time and affect each other. These complications mean that experiments and technology in the lab and the field are incredibly important for our understanding of what’s (been) going on.

If we take a step back, we can at least say that evolutionary biologists have a pretty good understanding of what might be happening in individuals and their populations, and what processes and mechanisms can lead to the origination of a new species. There are several causes that can drive the processes that lead to speciation:

• Ecological: two populations of one species adapt to different environments through natural selection;
• Genetic conflict: a certain allele becomes very abundant but has negative effects on fertility, and another mutation, that repairs these effects, is incompatible with the “original” genetical set-up;
• Sexual selection: sex A prefers certain visual, audio or other traits in sex B over other trait expressions, leading to certain varieties of certain traits always reproducing with each other instead of with other varieties in the species;
• Reinforcement of RI: hybrids of two populations have lower survival or fertility meaning that they’ll be less successful reproducing than individuals from the two populations within themselves;
• Polyploidy: genome-duplication can result in a new species within one generation when tetraploid individuals are unable to reproduce successfully with individuals from the original, diploid populations;
• Hybrid speciation: the hybrid(s) of two “parent” species become genetically incompatible with them;
• Genetic drift: a population that becomes fixed for a chromosomal rearrangement, a consequence of genetic drift, may no longer be compatible with the rest of the species.

The latter, speciation through genetic drift, occurs especially in small or highly-fluctuating populations. It is an important pillar under the founder effect: the start of a new population by a few individuals. If these few individuals have undergone changes due to genetic drift and get isolated from the rest of the population, they can come to form a new species if their genetic make-up is incompatible with the population of origin. This can be especially interesting at the edges of species ranges (Figure 2a), and there are descriptions of how this process can occur multiple times in a row, leading to a “wave” of changes through mutation (Figure 2b). If this leads to allele frequencies becoming relatively and unexpectedly high, this is called genetic “surfing” (Excoffier et al., 2009).

Figure 2. Allele frequencies a) during range expansion and b) during serial range expansion events. Derived from (Peischl et al., 2016).

While the founder effect is not fully understood or 100% supported by the literature, it’s clear that the geographical aspect that underlies it plays a role in many speciation events. If gene flow is completely blocked off by a geographical barrier, we speak of allopatric speciation. Note that the degree of geographic isolation depends on a geographic barrier, not on geographic distance, and that the degree to which it is an actual barrier also depends on the dispersal capacities of the species in question. Barriers can have their source in the environment, e.g. a new river divides two grasslands in two, or in a species itself, e.g. a few individuals manage to leave the mainland to start a population on an uninhabited island. Both can lead to allopatric speciation, but neither of these two processes has to be irreversible, as the river can fall dry again or the island species might expand their range to the mainland. In both situations, the populations of the mainland and the island can become sympatric. In such cases, we speak of secondary contact between the populations where, depending on the degree of reproductive isolation, gene flow is possible.

Sympatric speciation and the intermediate process, parapatric speciation, still have some gene flow going on. The former doesn’t depend on geographical barriers, but can depend on factors such as timing (e.g. flowering plants), local variation (e.g. soil characteristics) and behaviour (e.g. mating preferences). Sympatric speciation can reinforce itself if the allele in question is associated to another specific allele on another gene, which is rare but can occur when there’s a trait variety that works on both ecological divergence and reproductive isolation. Called a speciation trait, this trait can for example cause individuals with a specific feeding preference to only reproduce with each other. Other non-random mating patterns can lead to parapatric speciation. This leads to subpopulations continuing to interbreed with each other while getting more reproductively isolated from each other.

While the patterns of speciation are not easily understood and mapping them can become easier in collaboration with fields such as paleoarchaeology and geology, there is a lot of variation within the genome that’s left to be unravelled. The omics side of evolutionary biology can further the understanding of linkage equilibria, self-reinforcing processes and speciation genes and regions, to be able to understand what has happened in the past. Given the current pace of ecosystem degradation and destruction, we need this understanding of evolution to predict and, where possible, adapt to the future.

References

De Micco, V., & Aronne, G. (2012). Morpho-Anatomical Traits for Plant Adaptation to Drought. In R. Aroca (Ed.), Plant Responses to Drought Stress (pp. 37–61). Springer. https://doi.org/10.1007/978-3-642-32653-0_2

Excoffier, L., Foll, M., & Petit, R. J. (2009). Genetic consequences of range expansions. Annual Review of Ecology, Evolution, and Systematics, 40, 481–501. https://doi.org/10.1146/annurev.ecolsys.39.110707.173414

Futuyma, D., & Kirkpatrick, M. (2018). Evolution (4th ed.). Oxford University Press.

Laland, K., Matthews, B., & Feldman, M. W. (2016). An introduction to niche construction theory. Evolutionary Ecology, 30(2), 191–202. https://doi.org/10.1007/s10682-016-9821-z

Lenssen, J. P. M., Van Kleunen, M., Fischer, M., & De Kroon, H. (2004). Local adaptation of the clonal plant Ranunculus reptans to flooding along a small-scale gradient. Journal of Ecology, 92(4), 696–706. https://doi.org/10.1111/j.0022-0477.2004.00895.x

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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.