. Author manuscript; available in PMC: 2021 Nov 30.

Published in final edited form as: Nat Ecol Evol. 2021 Jan 28;5(4):419–430. doi: 10.1038/s41559-020-01384-x

Table 1. Maybe not explaining cooperation.

Discoveries about the genetic architecture and mechanisms underlying cooperation in microorganisms have led to a number of novel explanations for cooperation being suggested. However, there is a lack of evidence that these mechanisms provide explanations for cooperation. In some cases, the suggested explanations arise from over-interpretation of short-term evolutionary dynamics, and / or from implicitly assuming that the genetic architecture cannot evolve (mixing proximate and ultimate explanations of behaviour). Cooperation is usually more parsimoniously explained by standard explanations, such as kin selection.

Suggested Explanation for Cooperation	Potential problems
A pleiotropic link between cooperation and a trait with a large personal (private) benefit (metabolic constraint / coregulation)^196–202. The idea here is that if cooperation is lost, then the directly beneficial trait would also be lost, and that the direct benefit could outweigh the cost of cooperation. Similar arguments have been made for ‘hormonal pleiotropy’ in social insects²⁰³.	Pleiotropic links can favour any trait, and not preferentially cooperation. If the genetic architecture is not fixed, individuals could evolve to perform the directly beneficial trait, and not cooperate. The role of kin selection had already been established in these species, and so explaining cooperation was not a problem²⁰⁴. Causality can also go in both directions – in cases where some cooperation is favoured, pleiotropy can be selected to reduce cheat build up.
The down-regulation of cooperation at certain times (metabolic prudence or facultative cooperation)^202,205.	Individuals will be selected to reduce their level of cooperation when the benefit is lower or cost is greater (Insight 4). However, this is not an answer to ‘why cooperate?’ - a mechanism such as kin selection is still required to explain when cooperation is carried out. The role of kin selection had already been established, and so explaining cooperation was not a problem.
The regulation of cooperation by quorum sensing in bacteria²⁰².	Quorum sensing restricts cooperation to times when it appears to be more cost effective. An explanation is still required for why cooperate at those times. The role of kin selection had already been established, and so explaining cooperation was not a problem.
Genes for cooperation could hitch hike with mutations that are advantageous in a new environment (‘adaptive race’)^206,207.	This hypothesis doesn’t favour cooperation per se, as cheats could also hitch hike²⁰⁷. Furthermore, any effects are only transient, as competition between cheats and cooperators can still take place within populations of locally adapted genomes.
Cooperation is favoured at greenbeard genes, which can identify copies of themselves in other individuals, and preferentially help those individuals^208,209.	There are genes that have the properties of greenbeards. However, it is not clear if it is the greenbeard effect per se (linkage) that is favouring cooperation^210,211. Cooperation may have been favoured anyway, due to kin selection, with the greenbeard affect just a mechanistic byproduct.
Horizontal gene transfer can increase relatedness for cooperative genes by ‘reinfecting cheats’^212–214.	If there are cheat plasmids, that don’t cooperate, then horizontal gene transfer doesn’t necessarily favour cooperation²¹⁵. While there is some evidence from E. coli that cooperative genes are more likely to be found on mobile elements²¹³, there are alternative explanations²¹⁶.