L19 HGT in cooperation

Question 1

What is the central question of the lecture?

Answer 1

Does horizontal gene transfer (HGT) favor cooperation?

Question 2

How is relatedness traditionally determined in kin selection theory?

Answer 2

By genetic similarity at cooperation loci, implying co-ancestry when genes are similar.

Question 3

How does plasmid-mediated HGT complicate relatedness classifications?

Answer 3

It creates high relatedness at the plasmid level but low relatedness across the rest of the chromosome.

Question 4

What rule from kin selection theory predicts when cooperation will evolve?

Answer 4

Hamilton’s rule, which weighs the cost to the actor against the benefit to recipients multiplied by relatedness.

Question 5

What are bacterial public goods?

Answer 5

Molecules secreted at a cost to individuals that benefit the group, such as enzymes that break down nutrients or antibiotics.

Question 6

What defines a cheating cell in bacterial cooperation?

Answer 6

A cell that stops producing public goods but still benefits from those secreted by others.

Question 7

How are bacterial virulence factors related to cooperation?

Answer 7

Many virulence factors are public goods spread cooperatively, enabling host infection.

Question 8

What is a plasmid?

Answer 8

A small, transferable DNA molecule in bacteria that can carry genes—often for cooperation—and spread between cells.

Question 9

Through which structure do bacteria exchange plasmids?

Answer 9

Sex pili, which connect cells and facilitate plasmid transfer.

Question 10

How can plasmid transfer affect relatedness in a bacterial population?

Answer 10

It generates localized regions of high relatedness at cooperative loci, even among otherwise unrelated cells.

Question 11

How can reinfection of cheaters via HGT favor cooperation?

Answer 11

Plasmids carrying cooperation genes can transfer into cheaters, converting them back into cooperators.

Question 12

How does increased relatedness at cooperative loci via plasmid transfer promote cooperation?

Answer 12

It raises the probability that cooperative genes benefit other carriers of the same plasmid.

Question 13

What do mathematical models predict about HGT’s effect on cooperation?

Answer 13

HGT provides a transmission bonus (spreading cooperation genes) and increases local relatedness at cooperative loci.

Question 14

What pattern is observed regarding extracellular protein genes on plasmids versus chromosomes?

Answer 14

Extracellular (public-good) genes are more commonly found on plasmids than on chromosomes.

Question 15

What did the study of 21 E. coli genomes reveal about cooperative genes?

Answer 15

Plasmids carried a higher percentage of public-good genes, with identifiable hotspots for these genes.

Question 16

What did analysis of 109,000 extracellular-protein genes across 5,000 genomes show?

Answer 16

Statistical tests confirmed plasmids generally harbor more cooperative genes than chromosomes.

Question 17

Why can treating bacterial species as independent data points introduce bias?

Answer 17

Shared evolutionary history causes non-independence, violating assumptions of comparative analyses.

Question 18

What happened when researchers accounted for phylogenetic non-independence across species?

Answer 18

They found no consistent pattern of plasmids carrying more cooperative genes than chromosomes.

Question 19

How can researchers control for bias in genomic studies of cooperative genes?

Answer 19

By focusing on within-species comparisons rather than pooling all genomes together.

Question 20

What distinguishes conjugative, non-conjugative, and intermediate plasmids?

Answer 20

Conjugative plasmids self-transfer; non-conjugative cannot transfer alone; intermediate plasmids hitchhike with conjugative ones.

Question 21

What was the prediction about plasmid transmissibility and cooperative gene frequency?

Answer 21

That higher-transfer plasmids would carry more cooperative genes—but this correlation was not supported.

Question 22

What did experimental analyses reveal about plasmid transfer rates and cooperation gene proportions?

Answer 22

Across most species, higher transfer rates did not correspond to more cooperative genes on plasmids.

Question 23

Define horizontal gene transfer (HGT).

Answer 23

The movement of genes between organisms in the same generation, often via plasmids in bacteria.

Question 24

Why do cheating cells pose a challenge to bacterial cooperation?

Answer 24

They exploit public goods without bearing production costs, undermining cooperative populations.

Question 25

What is the SOCFinder tool designed to do?

Answer 25

Identify genes for complex cooperative traits beyond simple extracellular proteins, such as operons coding intracellular components that interact with non-protein molecules.

Question 26

What limitation did previous methods for finding cooperative genes have?

Answer 26

They only considered simple extracellular proteins, potentially missing complex cooperative traits.

Question 27

How many genomes were analyzed with SOCFinder in the recent paper?

Answer 27

4,600 bacterial genomes.

Question 28

What key finding emerged when SOCFinder was applied?

Answer 28

Plasmids carried significantly fewer cooperative-trait genes than chromosomes.

Question 29

Why is phylogeny important when comparing cooperative gene locations across species?

Answer 29

Shared ancestry means species data aren’t independent, so phylogeny controls for evolutionary non-independence.

Question 30

Why must we consider proportions rather than raw gene counts in plasmid vs. chromosome analysis?

Answer 30

Plasmid genomes are much smaller, so raw counts underrepresent their relative cooperative-gene load.

Question 31

In a typical bacterial genome example, how many cooperative genes are on the chromosome vs. plasmids?

Answer 31

Chromosome: 2,800 genes total with 87 cooperative; Plasmids: 280 genes total with 6 cooperative.

Question 32

How did new empirical data compare theory vs. reality for HGT-favored cooperation?

Answer 32

Data showed plasmids are not more likely to carry cooperative genes than chromosomes, contradicting earlier theory.

Question 33

What is the “transmission bonus” in HGT theory?

Answer 33

The benefit that any gene—cooperative or not—gets by spreading through plasmid transfer.

Question 34

What aspect of long-term cooperation maintenance did the original HGT theory overlook?

Answer 34

The loss of transmission advantage once plasmids reach fixation and the potential for cheating mutations.

Question 35

What happens to the transmission bonus after plasmid fixation in a population?

Answer 35

It vanishes, because nearly all cells already carry the plasmid.

Question 36

How can cheating mutations on a plasmid undermine cooperation?

Answer 36

A mutation that ceases cooperative function will spread unchecked once transfer stops at fixation.

Question 37

What is plasmid compatibility and why does it matter?

Answer 37

Some plasmids cannot coexist; a cheating plasmid may displace a cooperative one in the same cell, harming cooperation.

Question 38

What parameters did the new model of cooperation and plasmid behavior include?

Answer 38

Plasmid transfer rate (efficiency of spread) and plasmid loss rate (frequency lost during cell division).

Question 39

What is the model’s prediction for low plasmid transfer rates?

Answer 39

Plasmids fail to spread, so cooperation cannot establish.

Question 40

What is the model’s prediction for high plasmid transfer rates?

Answer 40

Initial spread of cooperation, followed by invasion of cheating plasmids that drive out cooperation.

Question 41

Under what condition can cooperation be maintained according to the model?

Answer 41

Intermediate plasmid loss rates allow enough reinfection to sustain cooperative plasmids without fixation.

Question 42

Why do plasmids not favor cooperation in the long term?

Answer 42

Fixation removes transmission benefits, and cheating mutations and incompatibilities undermine cooperation.

Question 43

How do plasmid fixation and cheating dynamics interact?

Answer 43

Fixed cooperative plasmids lose transfer advantage, allowing cheating plasmids to outcompete them.

Question 44

What role does plasmid loss play in cooperation dynamics?

Answer 44

Loss reintroduces transmission benefits, but too frequent loss prevents stable cooperation.

Question 45

What are selfish genetic elements?

Answer 45

Genes or elements that spread for their own benefit, often at the host’s or other genes’ expense.

Question 46

Why are plasmids considered selfish genetic elements?

Answer 46

They replicate and transfer independently, potentially imposing costs on the host genome.

Question 47

What is the “parliament of genes”?

Answer 47

The concept that genes within a genome compete for transmission, sometimes suppressing others that impose costs.

Question 48

What overall tension emerged between theory and empirical data on HGT and cooperation?

Answer 48

Theoretical predictions of HGT-favored cooperation were not supported by genomic and experimental evidence.

Question 49

Why doesn’t the transmission bonus ensure long-term cooperation?

Answer 49

Because it applies to all genes and disappears at fixation, offering no selective edge to cooperation specifically.

Question 50

How do plasmid loss and cheating mutations together hinder cooperation?

Answer 50

Loss rates that are too high prevent fixation, while cheating mutants exploit cooperative plasmids once transfer stops.

Question 51

Where are most complex cooperative traits found when using SOCFinder?

Answer 51

Predominantly on chromosomes rather than plasmids.

Question 52

What is the significance of the SOCFinder tool in cooperation studies?

Answer 52

It reveals that earlier methods underestimated chromosome-based cooperative traits, reversing prior trends.

Question 53

What does the updated evidence say about the role of plasmid transfer in spreading cooperation?

Answer 53

Plasmid transfer is not a reliable mechanism for promoting cooperation broadly across bacteria.

Question 54

Which genomic location now appears to harbor most cooperative traits?

Answer 54

The bacterial chromosome.

Question 55

How has our understanding of HGT and cooperation shifted?

Answer 55

From HGT-favored cooperation to recognizing that plasmid dynamics, loss, and cheating often prevent long-term cooperation.

Question 56

Why are plasmid loss rates critical for cooperative stability?

Answer 56

They balance reinfection with the need to keep plasmids common without allowing fixation to remove transfer advantages.

Question 57

How do selfish gene dynamics on plasmids affect the rest of the bacterial genome?

Answer 57

They can provoke chromosomal suppressors and reduce overall host benefits from plasmid-borne cooperation.