Diverse modes of ecoevolutionary dynamics in communities of antibioticproducing microorganisms


 Ashley Fisher
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1 In the formt provided y the uthors nd unedited. ULEMENTAY INFOMATION VOLUME: 1 ATICLE NUMBE: 0189 iverse modes of ecoevolutionry dynmics in communities of ntiioticproducing microorgnisms Klin Vetsigin upplementry Figures undnce muttions%off time%steps High%muttion%rte c upplementry Figure 1. emonstrtion of ecologicl nd evolutionry stility. () Ecologicl stility ws scertined y turning off muttions nd oserving tht strin undnce over time reches (sttisticl) stedy stte. () The dynmics ws continued for 20,000 ecologicl cycles t 5 times the previous muttion rte (verge of 50 muttions per popultion per cycle). While, s expected, dditionl lmost neutrl strin diversity ccumulted within the ecotypes, the 5 ecotype motif remined stle, indicting evolutionry stility. (c) Invsiility mps for representtives of the two types of 5 strin E motifs (lrge circles). Invders with rndom phenotypes were introduced t 0.1%. Blck dots indicte filed invsions. Green indictes n ecotype specific selective sweep tht preserved the motif. No instnces of invders cusing community collpse were found. ee Methods for prmeters used. NATUE ECOLOGY & EVOLUTION OI: /s
2 ε =#0##(20%#5)strin) ε =#10 )4# (22%#5)strin) ε =#4 10 )4 (26%#5)strin) = = = = = = = = = C C =#4 10 ) C 0 C C =#8 10 )5 C =# ) C C C C C C C C C upplementry Figure 2. The frction of communities reching 5 strin evolutionry stle motifs s function of prmeters. Five prmeters relted to the costs of ntiiotic, production, degrdtion nd resistnce were systemticlly vried: e,, C, C, nd C 0. For ech prmeter set 6 replic simultions were performed. After 20,000 ecologicl cycles, muttions were turned off for 10,000 cycles or until stle stte ws reched. The trjectories were nlyzed to ensure tht the ecologicl diversity is stle nd not due to long persisting nerly neutrl vrints. The frction of simultions reching diverse sttes tht persisted for t lest 8,000 cycles during the eco evolutionry dynmics nd then remined stle fter turning off muttions ws clculted nd visulized s indicted y the colorr. For smll numer of prmeter comintions, not ll 6 simultions completed successfully. ee Methods for the vlues of the prmeters tht were kept fixed. NATUE ECOLOGY & EVOLUTION OI: /s
3 10 0 Aundnce Aundnce upplementry Figure 3. The evolutionry stle sttes could exhiit fixed point or limit cycle ttrctors for their ecologicl dynmics. Two evolutionry stle sttes were propgted without muttions in simultions with lrge popultion size. () The ecologicl dynmics reches n pprent stle fixed point. () The ecologicl dynmics reches n oscilltory stte. ee Methods for prmeters used. NATUE ECOLOGY & EVOLUTION OI: /s
4 undnce upplementry Figure 4. Intermittency with very long periods of qusi stility nd very rief periods of rpid strin turnover. A simultion result is presented in severl different wys. (Top) hown re lineges ove 0.1% undnce s function of time using the color scheme nd projection of phenotypes from Fig. 4. (Bottom) Aundnce over time for different lineges. (ight) hown re the loctions of ll phenotypes tht ever reched 0.1% undnce. oint size increses with mximl undnce. For prmeters, see Methods. NATUE ECOLOGY & EVOLUTION OI: /s
5 t = 5000 time%until%collpse% upplementry Figure 5. Invsiility mp of n evolutionry qusi stle stte. () We investigted the evolutionry stility of the qusi stle stte from cycle 5000 of simultion exhiiting intermittency. () The evolutionry stility of the ecologiclly stle 5 strin community (rown circles) ws proed y introducing mutnts with different phenotypes t 0.1% undnce. Blck dots indicte filed invsions. ed dots indicte ecotype specific selective sweeps tht do not led to community collpse. ots with other colors correspond to invsions cusing community collpse, with the time till extinction of t lest two strins indicted y the color ccording to the colorr. The two phenotypic regions in which invders led to community collpse re mgnified. Both of these regions re smll, close to existing strins, nd cn e reched y single muttion (rown rrows). Becuse they re close to existing strins their selection coefficients re tiny. The region mgnified t the ottom corresponds to muttions tht cn only e reched y glol (gin of function, ) muttions, which mkes this region hrder to discover. ee Methods for prmeters used. NATUE ECOLOGY & EVOLUTION OI: /s
6 lossoffunction muttions only undnce lossoffunction muttions only upplementry Figure 6. Other types of communities supported through loss of function muttions. () hown re two simultions leding to persistent communities tht re ecologiclly unstle. The communities re propgted for 20,000 ecologicl cycles, fter which muttions re turned off except for loss of function muttions. hown re the phenotypes of strins ove 0.1% reltive undnce s function of the numer of ecologicl cycles. henotypes re colored ccording to the 16 possile comintions of for two ntiiotics s detiled on Fig. 4. The phenotypes of the strins prticipting in the motif re show to the right. Lrger squres indicte higher mximum undnce. Thinner orders indicte smller mplitude fluctutions. (, ottom) hown is the oscilltory dynmics underlying the coexistence. The (drk green), (drk lue), (light pstel green), (light green) persist t high undnce while,,, nd, nd stins fluctute wildly ut re regenerted through loss of function muttions. ee Methods for prmeters used. NATUE ECOLOGY & EVOLUTION OI: /s
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