18.4D: Gene duplications and divergence (2023)

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    learning goals
    • Explain the mechanisms of gene duplication and divergence

    gene copy

    Gene duplication is the process of copying a region of DNA that codes for a gene. Gene duplication can occur as a result of recombination error or through a retrotransposition event. Duplicated genes are often immune to the selection pressures under which the genes normally exist. This can lead to a large number of mutations accumulating in the duplicated genetic code. This can render the gene inoperable or, in some cases, provide some benefit to the organism. There are several mechanisms by which gene duplication can occur.


    Duplications can arise from unequal crossings that occur during meiosis between misaligned homologous chromosomes. The product of this recombination is a duplication at the point of exchange and a mutual deletion. Ectopic recombination is typically caused by sequence similarity at the duplicate breakpoints that form direct repeats. Repetitive genetic elements, such as transposable elements, provide a source of repetitive DNA that can facilitate recombination and are often found at replication breakpoints in plants and mammals.

    18.4D: Gene duplications and divergence (2)

    Scrolling during playback

    Replication slippage is an error in DNA replication that can lead to duplication of short genetic sequences. During replication, DNA polymerase begins to copy the DNA, and at some point during the replication process, the polymerase detaches from the DNA and replication stops. When the polymerase reattaches to the DNA strand, it reorients the replication strand to the wrong position, otherwise it copies the same segment more than once. Playback slippage is also often facilitated by repeated sequences, but requires few bases of similarity.

    Recursive Permutation

    During cell invasion by a replicating retroelement, or retrovirus, viral proteins replicate their genome by reverse transcription of RNA into DNA. When viral proteins bind abnormally to cellular mRNA, they can reverse transcribe gene copies to generate retrogenes. Retrogenes usually lack the intronic sequence and often contain poly A sequences that are also integrated into the genome. Many retrogenes exhibit changes in gene regulation compared to their parental gene sequences, sometimes resulting in new functions.


    Aneuploidy occurs when the failure of a single chromosome results in an abnormal number of chromosomes. Aneuploidy is often harmful and regularly leads to spontaneous abortion in mammals. Some aneuploid individuals are viable. For example, trisomy 21 leads to Down syndrome in humans, but it is not fatal. Aneuploidy often alters the gene dose in ways that adversely affect the organism and is therefore unlikely to spread in populations.

    Gene duplication as an evolutionary event

    Gene duplications are an important source of genetic innovation that can lead to evolutionary innovation. Duplication creates genetic redundancy, and if one copy of a gene develops a mutation that affects its original function, the other copy can act as a "backup" and continue to function properly. Duplicate genes therefore accumulate mutations faster than a functioning single-copy gene across generations of organisms, and it is possible for one of the two copies to evolve a new and different function. This is an example of neofunctionalization.

    Gene duplication is believed to play an important role in evolution. This position has been held by members of the scientific community for over 100 years. It has been argued that gene duplication is the most important evolutionary force since the emergence of the universal common ancestor.

    Another possible fate of duplicated genes is that both copies have equal opportunity to accumulate degenerative mutations as long as any defects are filled in by the other copy. This leads to a neutral model of "hypofunctionality" in which the functionality of the original gene is distributed between the two copies. Neither gene can be lost, as both now perform important, non-redundant functions, but ultimately neither is able to acquire new functions. Hypofunction can occur through neutral processes in which mutations accumulate with no harmful or beneficial effects. However, in some cases it can become under-functioning with clear adaptive benefits. When an ancestral gene is pleiotropic and performs two functions, often neither of these two functions can be altered without affecting the other function. In this way, splitting the ancestral functions into two separate genes may allow for adaptive specialization of subfunctions, thereby providing an adaptive advantage.


    Genetic divergence is the process by which two or more populations of an ancestral species accumulate independent genetic changes over time, often after the populations have been reproductively isolated for a period of time. In some cases, subpopulations living in ecologically distinct regional settings may exhibit genetic variances from the rest of the population, particularly when a population's range is very large. Genetic differences between different populations can include silent mutations (which do not affect the phenotype) or lead to significant morphological and/or physiological changes. Genetic divergence will always be associated with reproductive isolation, either due to new adaptations through selection and/or genetic drift, and is the main mechanism behind speciation.

    Genetic drift or allelic drift is the change in the frequency of a gene variant (allele) in a population based on random sampling. The alleles of the offspring are a sample of those of the parents, and luck plays a role in deciding whether a given individual survives and reproduces. The allele frequency of a population is the proportion of copies of a gene that share a particular shape. Genetic drift can cause gene variants to disappear entirely, thereby reducing genetic variation. When there are few copies of an allele, the effect of genetic drift is greater, and when there are many copies, the effect is less. These changes in gene frequency can contribute to the divergence.

    Divergent evolution usually results from the dispersal of the same species into different and isolated environments, preventing gene flow between different populations and allowing differential fixation of traits through genetic drift and natural selection. Divergent evolution can also be applied to molecular biology traits. This could apply to a signaling pathway in two or more organisms or cell types. This can apply to genes and proteins, such as nucleotide sequences or protein sequences derived from two or more homologous genes. It can be said that both rational genes (resulting from a speciation event) and irrational genes (resulting from gene duplication in a population) undergo different development.

    Central points

    • Ectopic recombination occurs when there is a missense junction and the product of that recombination is a duplication at the site of substitution and a reciprocal deletion.
    • Gene duplications do not always lead to harmful mutations. They can contribute to divergent evolution, which leads to the development of genetic differences between groups and the eventual emergence of new species.
    • Replication slippage can occur when DNA replication goes wrong, creating duplications of short genetic sequences.
    • Retrotranspositions occur when a retrovirus copies its genome by reverse transcribing RNA into DNA, abnormally binds to cellular mRNA, and reverse transcribes gene copies to create retrogenes.
    • Aneuploidy can occur when even a single chromosome is missing, resulting in an abnormal number of chromosomes.
    • Genetic divergence can arise through mechanisms such as genetic drift, which contribute to the accumulation of independent genetic changes from two or more populations descended from a common ancestor.

    Basic concept

    • irrational: have a similar structure, indicating divergence from a common ancestral gene
    • non-deterioration: failure of chromosome pairs to properly separate during meiosis
    • retrogen: a DNA gene copied from RNA by reverse transcription
    • genetic aberration: a general shift in allelic distribution in an isolated population due to random fluctuations in the frequency of individual gene alleles


    How are gene duplications related to divergence? ›

    Gene duplications do not always result in detrimental mutations; they can contribute to divergent evolution, which causes genetic differences between groups to develop and eventually form new species.

    What causes genetic divergence? ›

    Genetic diversity is reliant on the heritable variation within and between populations of organisms. New genetic variation arises in individuals by gene and chromosome mutations, and in organisms with sexual reproduction it can be spread through the population by recombination.

    What is the DDC model of gene duplication concerned with? ›

    The duplication-degeneration-complementation model, which involves no positive selection, stipulates a higher retention rate of duplicate genes in a small population than in a large one. This model has been accepted by many evolutionists.

    Are gene duplications rare? ›

    The rates of gene duplication in these model species are estimated at between 0.2% and 2% per gene per million years (5, 6).

    What is the most common cause for gene duplication? ›

    Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage.

    What is an example of gene divergence? ›

    For example, 10% of the original population has blue eyes and 90% has brown eyes. By chance, 10 individuals are separated from the original population. If this small group has 80% blue eyes and 20% brown eyes, then their offspring would be more likely to have the allele for the blue eyes.

    What is an example of a gene duplication in humans? ›

    Duplication. The type IA form of Charcot-Marie-Tooth disease is an example of an inherited human genetic disease that's caused by a gene duplication. Individuals with Charcot-Marie-Tooth disease have damage to their peripheral nerves, resulting in muscle weakness.

    What is the meaning of genetic divergence? ›

    Genetic divergence has been a hot topic in plant breeding in recent decades, and still is. It should be understood as the divergence of the gene pool of a population from the gene pools of other populations, which can be due to mutation, genetic drift and selection.

    What does divergence lead to? ›

    Thus, divergent selection eventually leads to speciation over an evolutionary time period (Rundle and Nosil 2005). Divergent evolution is mandatory to achieve best chances of survival in changing environment.

    How does genetic drift lead to divergence? ›

    Genetic drift thus removes genetic variation within demes but leads to differentiation among demes, completely through random changes in allele frequencies.

    How does gene flow affect divergence? ›

    Gene Flow Can Cause a High Variance in Divergence among Loci

    Genes that are linked to those under disruptive selection may not experience any gene exchange, whereas other unlinked genes may experience substantial gene flow.

    What is functional divergence of duplicated genes? ›

    Functional divergence can occur by neofunctionalization (a gene copy acquires a new function) or by subfunctionalization (the copies retain different subsets of the functionality of the ancestral gene; Force et al., 1999).


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