Evolution of diversity explains the impact of pre-adaptation of a focal species on the structure of a natural microbial community

Hairston NG Jr, Ellner SP, Geber MA, Yoshida T, Fox JA. Rapid evolution and the convergence of ecological and evolutionary time. Ecol Lett. 2005;8:1114–27.

Google Scholar 

Ellner SP, Geber MA, Hairston NG Jr. Does rapid evolution matter? Measuring the rate of contemporary evolution and its impacts on ecological dynamics. Ecol Lett. 2011;14:603–14.

PubMed  Google Scholar 

Gómez P, Paterson S, De Meester L, Liu X, Lenzi L, Sharma MD, et al. Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community. Nat Commun. 2016;7:12453.

PubMed  PubMed Central  Google Scholar 

Buckling A, Craig Maclean R, Brockhurst MA, Colegrave N. The beagle in a bottle. Nature. 2009;457:824–9.

CAS  PubMed  Google Scholar 

Gómez P, Buckling A. Real-time microbial adaptive diversification in soil. Ecol Lett. 2013;16:650–5.

PubMed  Google Scholar 

Lawrence D, Fiegna F, Behrends V, Bundy JG, Phillimore AB, Bell T, et al. Species interactions alter evolutionary responses to a novel environment. PLoS Biol. 2012;10:e1001330.

CAS  PubMed  PubMed Central  Google Scholar 

Lankau RA. Rapid evolutionary change and the coexistence of species. Annu Rev Ecol Evol Syst. 2011;42:335–54.

Google Scholar 

Pantel JH, Duvivier C, Meester LD. Rapid local adaptation mediates zooplankton community assembly in experimental mesocosms. Ecol Lett. 2015;18:992–1000.

PubMed  Google Scholar 

Hart SP, Turcotte MM, Levine JM. Effects of rapid evolution on species coexistence. Proc Natl Acad Sci. 2019;116:2112–7.

CAS  PubMed  Google Scholar 

Rainey PB, Travisano M. Adaptive radiation in a heterogeneous environment. Nature. 1998;394:69.

CAS  PubMed  Google Scholar 

Hughes AR, Inouye BD, Johnson MT, Underwood N, Vellend M. Ecological consequences of genetic diversity. Ecol Lett. 2008;11:609–23.

PubMed  Google Scholar 

Bolnick DI, Amarasekare P, Araújo MS, Bürger R, Levine JM, Novak M, et al. Why intraspecific trait variation matters in community ecology. Trends Ecol evolution. 2011;26:183–92.

Google Scholar 

Violle C, Enquist BJ, McGill BJ, Jiang LIN, Albert CH, Hulshof C, et al. The return of the variance: intraspecific variability in community ecology. Trends Ecol Evol. 2012;27:244–52.

PubMed  Google Scholar 

Bolnick DI, Ingram T, Stutz WE, Snowberg LK, Lau OL, Paull JS. Ecological release from interspecific competition leads to decoupled changes in population and individual niche width. Proc R Soc B Biol Sci. 2010;277:1789–97.

Google Scholar 

Bailey SF, Dettman JR, Rainey PB, Kassen R. Competition both drives and impedes diversification in a model adaptive radiation. Proc R Soc B Biol Sci. 2013;280:20131253.

Google Scholar 

Jousset A, Eisenhauer N, Merker M, Mouquet N, Scheu S. High functional diversity stimulates diversification in experimental microbial communities. Sci Adv. 2016;2:e1600124.

PubMed  PubMed Central  Google Scholar 

Schluter D. Experimental evidence that competition promotes divergence in adaptive radiation. Science. 1994;266:798–801.

CAS  PubMed  Google Scholar 

Ellis CN, Traverse CC, Mayo-Smith L, Buskirk SW, Cooper VS. Character displacement and the evolution of niche complementarity in a model biofilm community. Evolution. 2015;69:283–93.

PubMed  PubMed Central  Google Scholar 

Zee PC, Fukami T. Priority effects are weakened by a short, but not long, history of sympatric evolution. Proc R Soc B Biol Sci. 2018;285:20171722.

Google Scholar 

Schluter D. Ecological character displacement in adaptive radiation. Am Nat. 2000;156:S4–S16.

Google Scholar 

Urban MC, De Meester L. Community monopolization: local adaptation enhances priority effects in an evolving metacommunity. Proc R Soc B Biol Sci. 2009;276:4129–38.

Google Scholar 

De Meester L, Vanoverbeke J, Kilsdonk LJ, Urban MC. Evolving perspectives on monopolization and priority effects. Trends Ecol Evol. 2016;31:136–46.

PubMed  Google Scholar 

Luján AM, Gómez P, Buckling A. Siderophore cooperation of the bacterium Pseudomonas fluorescens in soil. Biol Lett. 2015;11:20140934.

PubMed  PubMed Central  Google Scholar 

O’Brien S, Hesse E, Luján A, Hodgson DJ, Gardner A, Buckling A. No effect of intraspecific relatedness on public goods cooperation in a complex community. Evolution. 2018;72:1165–73.

PubMed  PubMed Central  Google Scholar 

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10–12.

Google Scholar 

Li H Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:13033997 2013.

Garrison E, Marth G Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:12073907 2012.

Garrison E Vcflib: A C++ library for parsing and manipulating VCF files. GitHub https://www.githubcom/ekg/vcflib 2012.

Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000Research 2016;5:1492.

Maidak BL, Cole JR, Lilburn TG, Parker CT Jr, Saxman PR, Stredwick JM, et al. The RDP (ribosomal database project) continues. Nucleic Acids Res. 2000;28:173–4.

CAS  PubMed  PubMed Central  Google Scholar 

Schliep KP. phangorn: phylogenetic analysis in R. Bioinformatics. 2010;27:592–3.

PubMed  PubMed Central  Google Scholar 

Hall AR, Colegrave N. How does resource supply affect evolutionary diversification? Proc R Soc B Biol Sci. 2006;274:73–78.

Google Scholar 

Venail PA, MacLean RC, Bouvier T, Brockhurst MA, Hochberg ME, Mouquet N. Diversity and productivity peak at intermediate dispersal rate in evolving metacommunities. Nature. 2008;452:210.

CAS  PubMed  Google Scholar 

Robertson A. Experimental design on the measurement of heritabilities and genetic correlations: biometrical genetics. Biometrics. 1959;15:219–26.

Google Scholar 

Barrett RD, MacLean RC, Bell G. Experimental evolution of pseudomonas fluorescens in simple and complex environments. Am Naturalist. 2005;166:470–80.

Google Scholar 

Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B (Methodol). 1995;57:289–300.

Google Scholar 

Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. UniFrac: an effective distance metric for microbial community comparison. ISME J. 2011;5:169–72.

PubMed  Google Scholar 

McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.

CAS  PubMed  PubMed Central  Google Scholar 

Oksanen J, Kindt R, Legendre P, O’Hara B, Stevens MHH, Oksanen MJ, et al. The vegan package. Community Ecol Package. 2007;10:631–7.

Google Scholar 

Paradis E, Schliep K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics. 2019;35:526–8.

CAS  PubMed  Google Scholar 

Cailliez F. The analytical solution of the additive constant problem. Psychometrika. 1983;48:305–8.

Google Scholar 

Love M, Anders S, Huber W. Differential analysis of count data–the DESeq2 package. Genome Biol. 2014;15:10–1186.

Google Scholar 

McMurdie PJ, Holmes S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS computational Biol. 2014;10:e1003531.

Google Scholar 

Jombart T, Balloux F, Dray S. Adephylo: new tools for investigating the phylogenetic signal in biological traits. Bioinformatics. 2010;26:1907–9.

CAS  PubMed  Google Scholar 

Lenth R Emmeans: Estimated marginal means, aka least-squares means. R Package Version 2018; 1.

R Core Team. R: A language and environment for statistical computing. 2013.

Wickham H ggplot2: elegant graphics for data analysis. 2016. Springer.

Vellend M. The consequences of genetic diversity in competitive communities. Ecology. 2006;87:304–11.

PubMed  Google Scholar 

Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF. Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science. 2008;320:1081–5.

CAS  PubMed  Google Scholar 

Narwani A, Alexandrou MA, Herrin J, Vouaux A, Zhou C, Oakley TH, et al. Common ancestry is a poor predictor of competitive traits in freshwater green algae. PLoS ONE. 2015;10:e0137085.

PubMed  PubMed Central  Google Scholar 

Buckling A, Kassen R, Bell G, Rainey PB. Disturbance and diversity in experimental microcosms. Nature. 2000;408:961.

CAS  PubMed  Google Scholar 

Castledine M, Buckling A, Padfield D. A shared coevolutionary history does not alter the outcome of coalescence in experimental populations of Pseudomonas fluorescens. J Evol Biol. 2019;32:58–65.

CAS  PubMed  Google Scholar