4.3.1: Evolution of Genomes

The Evolution of Genomes

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Learning Objectives

• Identify how variations in the size and number of genes in different species can impact evolution;
• Explain the importance of genomic changes in an evolutionary context;
• Recognize the evolutionary implications of observed genome similarities between distant species.

Video

This 9-minute video provides an overview of how the genes and genome of a species can change over time to lead to different species. 
Questions after watching: How can a gene duplication event fuel evolution? Can you think of another example where something was duplicated and then repurposed by evolution?

Genetic Diversity 

Genetic variation is essential for a species to evolve in response to environmental change, including any variation in nucleotides, genes, chromosomes, or genomes of organisms. Each of these levels of genetic diversity adds to the capacity of a population to evolve. 

Variations in Number of Genes

DNA is contained in the chromosomes present within the cell; some chromosomes are contained within specific organelles in the cell (for example, the chromosomes of mitochondria and chloroplast). A gene is a discrete section of a chromosome that codes for one or more proteins. Each gene is a hereditary section of DNA that occupies a specific place on the chromosome and controls a particular characteristic of an organism. Genetic diversity at its most elementary level is represented by differences in the sequence of nucleotides (with one of the following bases: adenine, cytosine, guanine) that form DNA (deoxyribonucleic acid) within the cells of the organism.  During sexual reproduction, offspring inherit alleles from both parents. These inherited alleles might be slightly different, especially if there has been migration or hybridization of organisms. Also, when the offspring’s chromosomes are copied after fertilization, genes can be exchanged in a process called sexual recombination. Helpful or silent mutations and sexual recombination may allow the evolution of new characteristics.

Sometimes whole genes are duplicated, or deleted. This results in an organism having more or fewer copies of that gene than others. The effect on the phenotype may be to increase or decrease the gene product’s function (e.g., if the gene encoded a protein that makes pigment, and now the organism has two genes encoding pigment, the organism may now be twice as pigmented as its parents with only one copy of the gene). Natural selection may then select for or against organisms with this altered number of gene copies.

Sometimes there is no immediate effect of the gene duplication on phenotype. The additional copy of the gene may accumulate mutations without deleterious effects on the organism. These mutations will likely modify the gene product’s function if it is transcribed. In doing this, the gene may acquire slightly different abilities, such as the factor X blood clotting example the video above.

Mutation Rates

Mutation rates differ between species and even between different regions of the genome of a single species. Spontaneous mutations often occur which can cause various changes in the genome. Mutations can result in the addition or deletion of one or more nucleotide bases. A change in the code can result in a frameshift mutation which causes the entire code to be read in the wrong order and thus often results in a protein becoming non-functional. A mutation in a promoter region, enhancer region or a region coding for transcription factors can also result in either a loss of function or and upregulation or downregulation in transcription of that gene. Mutations are constantly occurring in an organism’s genome and can cause either a negative effect, positive effect or no effect at all.

Figure \(\PageIndex{1}\): Chromosomal Mutations: Chromosomal mutations over time can accumulate and promote diversity and evolution if a produced trait is favorable.

Transposable Elements

Transposable elements are regions of DNA that can be inserted into the genetic code through one of two mechanisms. These mechanisms work similarly to “cut-and-paste” and “copy-and-paste” functionalities in word processing programs. The “cut-and-paste” mechanism works by excising DNA from one place in the genome and inserting itself into another location in the code. The “copy-and-paste” mechanism works by making a genetic copy or copies of a specific region of DNA and inserting these copies elsewhere in the code. The most common transposable element in the human genome is the Alu sequence, which is present in the genome over one million times.

Pseudogenes

Often a result of spontaneous mutation, pseudogenes are dysfunctional genes derived from previously functional gene relatives. There are many mechanisms by which a functional gene can become a pseudogene including the deletion or insertion of one or multiple nucleotides. This can result in a shift of reading frame, causing the gene to longer code for the expected protein, a premature stop codon or a mutation in the promoter region. Often cited examples of pseudogenes within the human genome include the once functional olfactory gene families. Over time, many olfactory genes in the human genome became pseudogenes and were no longer able to produce functional proteins, explaining the poor sense of smell humans possess in comparison to their mammalian relatives.

Exon Shuffling

Exon shuffling is a mechanism by which new genes are created. This can occur when two or more exons from different genes are combined together or when exons are duplicated. Exon shuffling results in new genes by altering the current intron-exon structure. This can occur by any of the following processes: transposon mediated shuffling, sexual recombination or illegitimate recombination. Exon shuffling may introduce new genes into the genome that can be either selected against and deleted or selectively favored and conserved.

Genome Reduction and Gene Loss

Many species exhibit genome reduction when subsets of their genes are not needed anymore. This typically happens when organisms adapt to a parasitic life style, e.g. when their nutrients are supplied by a host. As a consequence, they lose the genes need to produce these nutrients. In many cases, there are both free living and parasitic species that can be compared and their lost genes identified. Good examples are the genomes of Mycobacterium tuberculosis and Mycobacterium leprae, the latter of which has a dramatically reduced genome. Another beautiful example are endosymbiont species. For instance, Polynucleobacter necessarius was first described as a cytoplasmic endosymbiont of the ciliate Euplotes aediculatus. The latter species dies soon after being cured of the endosymbiont. In the few cases in which P. necessarius is not present, a different and rarer bacterium apparently supplies the same function. No attempt to grow symbiotic P. necessarius outside their hosts has yet been successful, strongly suggesting that the relationship is obligate for both partners. Yet, closely related free-living relatives of P. necessarius have been identified. The endosymbionts have a significantly reduced genome when compared to their free-living relatives (1.56 Mbp vs. 2.16 Mbp).

Variations in Number of Chromosomes

Many organisms are diploid, having two sets of chromosomes, and therefore two copies (called alleles) of each gene. However, some organisms can be haploid, triploid, or tetraploid (having one, three, or four sets of chromosomes respectively). Within any single organism, there may be variation between the two (or more) alleles for each gene. This variation is introduced either through mutation of one of the alleles or as a result of recombination during sexual reproduction.

During replication events, there can be mutations that involve whole chromosomes or whole chunks of chromosomes. Some mutations duplicate a whole chromosome (a whole stretch of DNA with many genes); some may delete a large portion. Some rearrange chromosomes, keeping all of the DNA information but putting it in different places in the genome. It turns out that in some instances, the location matters because it contains sites that initiate and control transcription. In bacteria, this can matter because one transcription factor can control the transcription of many genes in a row.

Changes in chromosome number or structure can affect many genes at the same time. Like changes in individual genes, this can result in some immediate effects because of the change in the number of genes producing the gene products (proteins). Or there can be little to no immediate effect, but the extra copy gives rise to “spare copies” that are free to mutate and acquire new abilities and functions.

Variation in Genome Size 

A genome is the total genetic information of a cell or organism. The evolution of the genome is characterized by the accumulation of changes. Analysis of genomes and their changes in sequence or size over time involves various fields.  

Genome size is usually measured in base pairs (or bases in single-stranded DNA or RNA). Different species can have different numbers of genes within the entire DNA or genome of the organism. Gene number is the main factor influencing the size of the prokaryotic genome. However, a greater total number of genes might not correspond with greater complexity in the phenotype (behavior, structure, or function) of eukaryotes.

For example, the predicted size of the human genome is not much larger than the genomes of some invertebrates and is far smaller than some species of ferns. However, in humans, more proteins are encoded per gene than in other species. In eukaryotic organisms, this is an observed paradox: the number of genes that make up the genome does not correlate with genome size. In other words, the genome size is much larger than would be expected given the total number of protein-coding genes.

Larger amounts of genetic information may allow for more variation in the overall genome, conferring additional adaptability to environmental change. It may also play a role in speciation. On the other hand, longer genomes take more energy and time to duplicate, so there is an evolutionary trade-off. 

Genomic Similarities Between Distant Species

Genetic distance refers to the genetic divergence between species or between populations within a species. Smaller genetic distances indicate that the populations have more similar genes, which indicates they are closely related; they have a recent common ancestor, or recent interbreeding has taken place. Genetic distance is useful in reconstructing the history of populations. For example, evidence from genetic distance suggests that humans arrived in America about 30,000 years ago. By examining the difference between allele frequencies between the populations, genetic distance can estimate how long ago the two populations were together.

Phylogenetic Relationships

Phylogeny describes the relationships of an organism, such as the relationship with its ancestors and the species it is most closely related. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different. The use of advanced genomic analysis has allowed us to establish phylogenetic trees, which map the relationship between species at a genetic and molecular level. The ability to use these technologies has established previously unknown relationships and has contributed to a more complex evolutionary history. These technologies have established genomic similarities between distant species by establishing genetic distances. In addition, the mechanisms by which genomic similarities between distant species occur can include horizontal gene transfer.

Figure \(\PageIndex{1}\): Tree of Life: Diagrammatic representation of the divergence of modern taxonomic groups from their common ancestor. This shows the genomic similarities that can exist between distant species based on their relationship with this ancestor.

Horizontal Gene Transfer

Horizontal gene transfer (HGT), also known as lateral gene transfer, is the transfer of genes between unrelated species. Genes have been shown to be passed between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to the understanding of phylogenetic relationships. The various ways that HGT occurs in prokaryotes is important to understanding phylogenies. Although at present, HGT is not viewed as important to eukaryotic evolution, HGT does occur in this domain as well. Finally, as an example of the ultimate gene transfer, theories of genome fusion between symbiotic or endosymbiotic organisms have been proposed to explain an event of great importance—the evolution of the first eukaryotic cell, without which humans could not have come into existence.

The mechanism of HGT has been shown to be quite common in the prokaryotic domains of Bacteria and Archaea, significantly changing the way their evolution is viewed. The majority of evolutionary models, such as in the endosymbiont theory, propose that eukaryotes descended from multiple prokaryotes, which makes HGT all the more important to understanding the phylogenetic relationships of all extant and extinct species. These gene transfers between species are the major mechanism whereby bacteria acquire resistance to antibiotics. Classically, this type of transfer has been thought to occur by three different mechanisms: transformation, transduction and conjugation.

Although it is easy to see how prokaryotes exchange genetic material by HGT, it was initially thought that this process was absent in eukaryotes, followed by the idea that the gene transfers between multicellular eukaryotes should be more difficult. In spite of this fact, HGT between distantly related organisms has been demonstrated in several eukaryotic species.

In animals, a particularly interesting example of HGT occurs within the aphid species. Aphids are insects that vary in color based on carotenoid content. Carotenoids are pigments made by a variety of plants, fungi, and microbes, and they serve a variety of functions in animals, who obtain these chemicals from their food. Humans require carotenoids to synthesize vitamin A, and we obtain them by eating orange fruits and vegetables: carrots, apricots, mangoes, and sweet potatoes. On the other hand, aphids have acquired the ability to make the carotenoids on their own. According to DNA analysis, this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food.

Figure \(\PageIndex{1}\): Horizontal Gene Transfer in Animals: (a) Red aphids get their color from red carotenoid pigment. Genes necessary to make this pigment are present in certain fungi, and scientists speculate that aphids acquired these genes through HGT after consuming fungi for food. If genes for making carotenoids are inactivated by mutation, the aphids revert back to (b) their green color. Red coloration makes the aphids a lot more conspicuous to predators, but evidence suggests that red aphids are more resistant to insecticides than green ones. Thus, red aphids may be more fit to survive in some environments than green ones.

Video

In this 8-minute video, evidence of human evolution in the human genome is demonstrated. 
Question after watching: What are three lines of evidence from the human genome of our evolutionary past?