Table 2.

Studies reporting evolution of symbioses towards the parasitism end of the continuum

Transitiona	Host	Symbiont	Association	Condition	Mechanism and evidenceb	Approach	Refs
M → M (−)	Legume (Ensifer medicae)	Rhizobia	Nitrogen-fixing	Host choice blocked	Cheater strains favoured	Experimental	229
M → M (−)	Legume (Trifolium spp.)	Rhizobia	Nitrogen-fixing	Elevated nitrogen	Reduced cooperation under high nitrogen	Experimental	230
M → P	Vertebrate spp.	Coxiella burnetii	Intracellular parasite	Host shift	HGT of virulence-associated genes suggested	Phylogenetic	30
M → P	Jelly fish (Cassiopea xamachana)	Alga (Symbiodinium microadriaticum)	Photosynthate provisioning	HT only	Greater proliferation in host and dispersal rates	Experimental	109
M → P	Plant spp.	Agrobacterium spp.	Plant parasite	NA	HGT of virulence loci	Phylogenetic	29,231
M → P	Plant spp.	Pseudomonas syringae	Plant parasite	NA	HGT of hopZ T3SS effectors	Phylogenetic	29,79
M → P	Escherichia coli	M13 phage	Growth benefit	Host background	Parasitic when shifted to host ancestor	Experimental	228
M → P	E. coli	F1 phage	Parasitic phage	HT allowed	Antagonistic variants favoured	Experimental	217
C → P	Pill bug (Armadillidium vulgare)	Wolbachia (wVulC)	VT endosymbiont	HT only	Titre increased in non-germline-associated tissue	Experimental	110
C → P	In vitro immune envrionment	E. coli	Commensal strain	Macrophage pressure	Heightened macrophage evasion and delayed phagosome maturation, via TE insertion	Experimental	232
C → P	Arabidopsis thaliana	Pseudomonas fluorescens species complex	Rhizophere associated	NA	Gain of putative pathogenicity island	Comparative genomics, phylogenetic	39
C → P	Plant spp.	Rhodococcus spp.	Plant associated	NA	Gain of virulence plasmid (pFID188), host growth inhibition	Experimental, comparative genomics, phylogenetic	58
P → P (+)	Plant spp.	Xanthomonadaceae spp.	Phytopathogen	NA	Gain of hydrolase gene (cbsA); localized parasite become systemic	Comparative genomics, phylogenetic	54
P → P (+)	Barley (Hordeum vulgare)	Barley stripe mosaic virus	Plant parasite	HT only	Increased virulence, independent of titre	Experimental	111
P → P (+)	House finch (Haemorhous mexicanus)	Mycoplasma gallisepticum	Emerging parasite	Adaptation to novel host	Linear increase in virulence since shift	Natural sampling	83
P → P (+)	Mouse (Mus musculus)	Cryptococcus neoformans	Opportunistic parasite	Serial passage	Increased expression of iron reductase and host mortality	Experimental	233
P → P (+)	Amoebae (Acanthamoeba sp.)	Parachlamydia acanthamoebae	Obligate intracellular symbiont	HT only	Enhanced infectivity and virulence, T3SS upregulated	Experimental	46
P → P (+)	Mammal spp.	Yersinia pestis	Enteric parasite	NA	HGT of plasmids (pMT1 and pPCP1), increased transmissibility by fleas and virulence to mammals	Genomic	65

(−), reduced; (+), elevated (for example, P → P (+) indicates transition towards increased parasitism); C, commensalism; HGT, horizontal gene transfer; HT, horizontal transmission; M, mutualism; NA, specific drivers of transition unaccounted for owing to timescale; P, parasitism; T3SS, type III secretion system; TE, transposable element; VT, vertical transmission. ^aTransitions involve increased virulence or reduced benefit of the symbiotic relationship to hosts over time. ^bGeneral evidence to support the inferred transition, including the molecular mechanism if known.