L19 HGT in cooperation Flashcards
What is the central question of the lecture?
Does horizontal gene transfer (HGT) favor cooperation?
How is relatedness traditionally determined in kin selection theory?
By genetic similarity at cooperation loci, implying co-ancestry when genes are similar.
How does plasmid-mediated HGT complicate relatedness classifications?
It creates high relatedness at the plasmid level but low relatedness across the rest of the chromosome.
What rule from kin selection theory predicts when cooperation will evolve?
Hamilton’s rule, which weighs the cost to the actor against the benefit to recipients multiplied by relatedness.
What are bacterial public goods?
Molecules secreted at a cost to individuals that benefit the group, such as enzymes that break down nutrients or antibiotics.
What defines a cheating cell in bacterial cooperation?
A cell that stops producing public goods but still benefits from those secreted by others.
How are bacterial virulence factors related to cooperation?
Many virulence factors are public goods spread cooperatively, enabling host infection.
What is a plasmid?
A small, transferable DNA molecule in bacteria that can carry genes—often for cooperation—and spread between cells.
Through which structure do bacteria exchange plasmids?
Sex pili, which connect cells and facilitate plasmid transfer.
How can plasmid transfer affect relatedness in a bacterial population?
It generates localized regions of high relatedness at cooperative loci, even among otherwise unrelated cells.
How can reinfection of cheaters via HGT favor cooperation?
Plasmids carrying cooperation genes can transfer into cheaters, converting them back into cooperators.
How does increased relatedness at cooperative loci via plasmid transfer promote cooperation?
It raises the probability that cooperative genes benefit other carriers of the same plasmid.
What do mathematical models predict about HGT’s effect on cooperation?
HGT provides a transmission bonus (spreading cooperation genes) and increases local relatedness at cooperative loci.
What pattern is observed regarding extracellular protein genes on plasmids versus chromosomes?
Extracellular (public-good) genes are more commonly found on plasmids than on chromosomes.
What did the study of 21 E. coli genomes reveal about cooperative genes?
Plasmids carried a higher percentage of public-good genes, with identifiable hotspots for these genes.
What did analysis of 109,000 extracellular-protein genes across 5,000 genomes show?
Statistical tests confirmed plasmids generally harbor more cooperative genes than chromosomes.
Why can treating bacterial species as independent data points introduce bias?
Shared evolutionary history causes non-independence, violating assumptions of comparative analyses.
What happened when researchers accounted for phylogenetic non-independence across species?
They found no consistent pattern of plasmids carrying more cooperative genes than chromosomes.
How can researchers control for bias in genomic studies of cooperative genes?
By focusing on within-species comparisons rather than pooling all genomes together.
What distinguishes conjugative, non-conjugative, and intermediate plasmids?
Conjugative plasmids self-transfer; non-conjugative cannot transfer alone; intermediate plasmids hitchhike with conjugative ones.
What was the prediction about plasmid transmissibility and cooperative gene frequency?
That higher-transfer plasmids would carry more cooperative genes—but this correlation was not supported.
What did experimental analyses reveal about plasmid transfer rates and cooperation gene proportions?
Across most species, higher transfer rates did not correspond to more cooperative genes on plasmids.
Define horizontal gene transfer (HGT).
The movement of genes between organisms in the same generation, often via plasmids in bacteria.
Why do cheating cells pose a challenge to bacterial cooperation?
They exploit public goods without bearing production costs, undermining cooperative populations.
What is the SOCFinder tool designed to do?
Identify genes for complex cooperative traits beyond simple extracellular proteins, such as operons coding intracellular components that interact with non-protein molecules.
What limitation did previous methods for finding cooperative genes have?
They only considered simple extracellular proteins, potentially missing complex cooperative traits.
How many genomes were analyzed with SOCFinder in the recent paper?
4,600 bacterial genomes.
What key finding emerged when SOCFinder was applied?
Plasmids carried significantly fewer cooperative-trait genes than chromosomes.
Why is phylogeny important when comparing cooperative gene locations across species?
Shared ancestry means species data aren’t independent, so phylogeny controls for evolutionary non-independence.
Why must we consider proportions rather than raw gene counts in plasmid vs. chromosome analysis?
Plasmid genomes are much smaller, so raw counts underrepresent their relative cooperative-gene load.
In a typical bacterial genome example, how many cooperative genes are on the chromosome vs. plasmids?
Chromosome: 2,800 genes total with 87 cooperative; Plasmids: 280 genes total with 6 cooperative.
How did new empirical data compare theory vs. reality for HGT-favored cooperation?
Data showed plasmids are not more likely to carry cooperative genes than chromosomes, contradicting earlier theory.
What is the “transmission bonus” in HGT theory?
The benefit that any gene—cooperative or not—gets by spreading through plasmid transfer.
What aspect of long-term cooperation maintenance did the original HGT theory overlook?
The loss of transmission advantage once plasmids reach fixation and the potential for cheating mutations.
What happens to the transmission bonus after plasmid fixation in a population?
It vanishes, because nearly all cells already carry the plasmid.
How can cheating mutations on a plasmid undermine cooperation?
A mutation that ceases cooperative function will spread unchecked once transfer stops at fixation.
What is plasmid compatibility and why does it matter?
Some plasmids cannot coexist; a cheating plasmid may displace a cooperative one in the same cell, harming cooperation.
What parameters did the new model of cooperation and plasmid behavior include?
Plasmid transfer rate (efficiency of spread) and plasmid loss rate (frequency lost during cell division).
What is the model’s prediction for low plasmid transfer rates?
Plasmids fail to spread, so cooperation cannot establish.
What is the model’s prediction for high plasmid transfer rates?
Initial spread of cooperation, followed by invasion of cheating plasmids that drive out cooperation.
Under what condition can cooperation be maintained according to the model?
Intermediate plasmid loss rates allow enough reinfection to sustain cooperative plasmids without fixation.
Why do plasmids not favor cooperation in the long term?
Fixation removes transmission benefits, and cheating mutations and incompatibilities undermine cooperation.
How do plasmid fixation and cheating dynamics interact?
Fixed cooperative plasmids lose transfer advantage, allowing cheating plasmids to outcompete them.
What role does plasmid loss play in cooperation dynamics?
Loss reintroduces transmission benefits, but too frequent loss prevents stable cooperation.
What are selfish genetic elements?
Genes or elements that spread for their own benefit, often at the host’s or other genes’ expense.
Why are plasmids considered selfish genetic elements?
They replicate and transfer independently, potentially imposing costs on the host genome.
What is the “parliament of genes”?
The concept that genes within a genome compete for transmission, sometimes suppressing others that impose costs.
What overall tension emerged between theory and empirical data on HGT and cooperation?
Theoretical predictions of HGT-favored cooperation were not supported by genomic and experimental evidence.
Why doesn’t the transmission bonus ensure long-term cooperation?
Because it applies to all genes and disappears at fixation, offering no selective edge to cooperation specifically.
How do plasmid loss and cheating mutations together hinder cooperation?
Loss rates that are too high prevent fixation, while cheating mutants exploit cooperative plasmids once transfer stops.
Where are most complex cooperative traits found when using SOCFinder?
Predominantly on chromosomes rather than plasmids.
What is the significance of the SOCFinder tool in cooperation studies?
It reveals that earlier methods underestimated chromosome-based cooperative traits, reversing prior trends.
What does the updated evidence say about the role of plasmid transfer in spreading cooperation?
Plasmid transfer is not a reliable mechanism for promoting cooperation broadly across bacteria.
Which genomic location now appears to harbor most cooperative traits?
The bacterial chromosome.
How has our understanding of HGT and cooperation shifted?
From HGT-favored cooperation to recognizing that plasmid dynamics, loss, and cheating often prevent long-term cooperation.
Why are plasmid loss rates critical for cooperative stability?
They balance reinfection with the need to keep plasmids common without allowing fixation to remove transfer advantages.
How do selfish gene dynamics on plasmids affect the rest of the bacterial genome?
They can provoke chromosomal suppressors and reduce overall host benefits from plasmid-borne cooperation.
