Lecture 4: Bacterial Genome Evolution Flashcards
Pangenome Fluidity
describes how much a species’ genetic makeup can change and adapt, with the lifestyle and environmental pressures playing a major role in this variability.
High fluidity: A species with high fluidity has a more dynamic gene pool, meaning its genetic makeup can vary widely between individuals or populations. This can be due to factors like horizontal gene transfer, mutations, or adaptation to different environments.
Low fluidity: A species with low fluidity has a more stable and conserved gene pool. Its genetic makeup is relatively consistent across individuals or populations, with fewer changes over time.
Pangenome fluidity is influenced by the lifestyle of the species.
Example, bacteria that can exchange genes easily with others (like through horizontal gene transfer) tend to have higher fluidity, while species with more stable, isolated populations (like certain mammals) might show lower fluidity.
Pangenome
The total gene repretoire of a species, containing bothe core genes shared by all strains and accessory genes unique to some.
Pangenome size is driven by the interaction of genetic mechanisms (HGT, mutation, and gene duplication), population size, and environmental complexity, with species in diverse and variable environments tending to have larger, more open pangenomes.
In an open pangenome, the core genome is small, with many genes not shared by all individuals, while the accessory genome is large, containing genes present in some but not all individuals. This allows for greater genetic diversity through horizontal gene transfer or mutations.
In a closed pangenome, the core genome is large, with most individuals sharing a similar set of essential genes, while the accessory genome is smaller, indicating a more stable, conserved genetic structure with less variation.
Example Open: Species that live in diverse environments, such as soil bacteria, often have open pangenomes due to frequent Horizontal Gene Transfer (HGT) and the need for diverse metabolic functions.
Example Closed: Organisms like obligate symbionts (e.g., Buchnera aphidicola) often have closed pangenomes because they have lost many genes and live in highly stable environments where new gene acquisition is rare.
Balance GD and NS
is influenced by population size.
In small populations, genetic drift is more powerful, allowing random chance to dominate, which can lead to the fixation of deleterious mutations and loss of beneficial ones, regardless of their fitness effects.
In large populations, natural selection is more effective, favoring the fixation of beneficial mutations and purging deleterious ones. Overall, genetic drift introduces randomness in allele frequencies, while natural selection drives the process of adaptive evolution, with their relative influence determined by the population size
Phylogeny
refers to the evolutionary history and relationships among species or other taxa. It is often represented as a phylogenetic tree, which shows how species or groups of organisms are related based on shared characteristics or genetic data.
Phylogenetic studies can help answer questions about how different species evolved over time and how they are interconnected
Horizontal Gene Transfer (HGT)
a significant factor in the evolution of bacterial genomes, particularly in species with large effective population sizes. It facilitates the exchange of genes across different organisms, contributing to genome expansion, especially in complex environments with high species diversity
transformation, where bacteria take up free DNA from their environment; transduction, where viruses transfer bacterial DNA between cells; and conjugation, where DNA is transferred directly between bacteria through physical contact via a pilus.
These processes allow bacteria to rapidly acquire new genetic traits, such as antibiotic resistance or virulence factors (mostly through Conjugation). HGT plays a crucial role in bacterial evolution and adaptation to changing environments.
The chance of incorporating (HGT) a gene from a more distant species is lower the more distant.
Amount of HGT is also affected by location. HGT between species on my hand is more likely than between species on my hand and my face.
How can genomes get larger
Genome size can increase through several mechanisms, often driven by environmental pressures and the complexity of an organism’s habitat.
In general, species living in more complex or variable environments tend to have larger genomes because they require a broader set of genes to adapt to diverse conditions. In general, genome size increases through mechanisms like gene duplication, HGT, and mobile elements, and habitats that are complex and variable tend to promote larger genomes, while stable, specialized environments drive genome reduction.
The Black Queen Hypothesis
is an evolutionary theory explaining how certain organisms can lose genes and become dependent on others in their environment to perform essential functions, conserving energy and resources.
Key Concept: Named after the card game “Hearts,” where the goal is to avoid the Black Queen card, BQH suggests organisms “shed” costly genes when they can rely on others to perform those functions, avoiding the energetic cost.
Application: Common in microbial communities, where species depend on others for essential functions, promoting cooperation, diversity, and evolutionary efficiency.
example, in marine environments, some bacteria have lost the ability to detoxify reactive oxygen species (like hydrogen peroxide) because other bacteria in the community produce catalase, an enzyme that breaks down these toxins. The bacteria that lost the gene for catalase benefit from this “leaky” (shared) function without paying the energy cost to produce it themselves. In this case they hold the Black Queen.
Streamlining hypothesis
Certain organisms, particularly microorganisms like bacteria, reduce the size of their genomes over time by eliminating non-essential genes. This process leads to more efficient use of resources, especially in nutrient-poor or stable environments where having a smaller genome can be advantageous. This hypothesis helps explain why some free-living bacteria and many obligate symbionts (which are “obligated” to live inside host organisms) have very small genomes.
Mullers Ratchet
describes the accumulation of deleterious (harmfull) mutations due to genetic drift, leading to a decline in fitness over time. . This mechanism is a key driver of genome reduction.
Over time, the accumulation of fixed deleterious mutations in small populations leads to reduced fitness and often gene loss due to factors like:
⦁ Muller’s ratchet: The irreversible accumulation of harmful mutations in asexual or small populations, as beneficial mutations are outnumbered or lost.
Bottleneck
refers to an event where a population’s size is drastically reduced for at least one generation, leading to a significant loss of genetic diversity. This reduction can occur due to natural disasters, disease, habitat destruction, or other catastrophic events.
- Drastic Reduction in Population Size so only a subset of the original genetic diversity survives.
- Amplified Genetic Drift: In the small surviving population, random changes in allele frequencies (genetic drift) become much stronger. Some alleles may disappear entirely (loss of genetic diversity), while others may become fixed by chance.
- Reduced Genetic Diversity: After the bottleneck, the population has less genetic variation, making it more vulnerable to future challenges, such as disease or environmental changes.
- Increased Risk of Fixation of Deleterious Mutations: Similar to small populations in general, deleterious mutations are more likely to become fixed due to stronger genetic drift.
- Founder Effect (if the bottleneck leads to colonization of a new area): If a small group of survivors, of the bottleneck event, establishes a new population elsewhere, the genetic diversity of the new population reflects that of the “founders” rather than the original population.
- Bottlenecks can have long-term evolutionary impacts, reducing the ability of a population to adapt to new environments.
- They may also lead to inbreeding, increasing the chance of harmful recessive traits becoming widespread.
Example:
* Cheetahs: Modern cheetah populations have undergone bottlenecks, leading to extreme genetic similarity among individuals. This makes them more susceptible to diseases and reduces their adaptability.
Founder Effect
This occurs when a small group of individuals establishes a new population. The new population is often genetically different from the original population because it is based on only a small subset of the original gene pool.
As a result, the genetic diversity of the new population is limited to the genes carried by the founders. This can lead to the new population having different allele frequencies and potentially lacking genetic variation present in the original population.
Example: If a few birds from a large population fly to a new island and start a new colony, their genetic diversity will be much smaller than the original population’s, as they only carry a small sample of the overall genetic variation.
Genetic Drift
is the random fluctuation of allele frequencies due to chance events.
⦁ In smaller populations, random changes have a greater impact because fewer individuals mean less genetic diversity and weaker “buffering” against these random changes.
-> Examples of Genetic Drift are Founder Effect and Bottleneck as is totaly random
Natural Selection
the process by which certain traits become more common in a population over time due to the advantages they provide in survival and reproduction.
atural selection leads to populations that are better adapted to their environments, shaping the genetic makeup of species over generations. It is one of the key drivers of evolutionary change.
Symbiotic Relationship Aphids and Buchnera
Vertical transmission ensures the symbiotic relationship between aphids and Buchnera aphidicola, with the bacteria providing essential nutrients like amino acids that the aphid cannot obtain from its phloem sap diet. The bacteria are passed directly from mother to offspring through oocytes, residing in specialized cells called bacteriocytes.
