in

The rates of global bacterial and archaeal dispersal

  • 1.

    Kruckeberg AR, Rabinowitz D. Biological aspects of endemism in higher plants. Annu Rev Ecol Syst. 1985;16:447–79.

    Article 

    Google Scholar 

  • 2.

    Ceballos G, Brown JH. Global patterns of mammalian diversity, endemism, and endangerment. Conserv Biol. 1995;9:559–68.

    Article 

    Google Scholar 

  • 3.

    Mueller GM, Schmit JP, Leacock PR, Buyck B, Cifuentes J, Desjardin DE, et al. Global diversity and distribution of macrofungi. Biodivers Conserv. 2007;16:37–48.

    Article 

    Google Scholar 

  • 4.

    Prideaux GJ, Warburton NM. An osteology-based appraisal of the phylogeny and evolution of kangaroos and wallabies (macropodidae: Marsupialia). Zool J Linn Soc. 2010;159:954–87.

    Article 

    Google Scholar 

  • 5.

    Finlay BJ, Clarke KJ. Ubiquitous dispersal of microbial species. Nature. 1999;400:828.

    CAS 
    Article 

    Google Scholar 

  • 6.

    Whitaker RJ, Grogan DW, Taylor JW. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science. 2003;301:976–978.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 7.

    Whitfield J. Is everything everywhere? Science. 2005;310:960–61.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 8.

    Boenigk J, Pfandl K, Garstecki T, Harms H, Novarino G, Chatzinotas A. Evidence for geographic isolation and signs of endemism within a protistan morphospecies. Appl Environ Microbiol. 2006;72:5159–64.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 9.

    DeWit R, Bouvier T. ‘Everything is everywhere, but, the environment selects’; what did Baas Becking and Beijerinck really say? Environ Microbiol. 2006;8:755–8.

    Article 

    Google Scholar 

  • 10.

    van der Gast CJ. Microbial biogeography: the end of the ubiquitous dispersal hypothesis? Environ Microbiol. 2015;17:544–6.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 11.

    Whittaker KA, Rynearson TA. Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow. Proc Natl Acad Sci USA. 2017;114:2651–56.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 12.

    Louca S, Shih PM, Pennell MW, Fischer WW, Parfrey LW, Doebeli M. Bacterial diversification through geological time. Nat Ecol Evol. 2018;2:1458–67.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 13.

    Martiny JBH, Bohannan BJ, Brown JH, Colwell RK, Fuhrman JA, Green JL, et al. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol. 2006;4:102–12.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 14.

    Martiny JBH, Eisen JA, Penn K, Allison SD, Horner-Devine MC. Drivers of bacterial β-diversity depend on spatial scale. Proc Natl Acad Sci USA. 2011;108:7850–54.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 15.

    Jungblut AD, Lovejoy C, Vincent WF. Global distribution of cyanobacterial ecotypes in the cold biosphere. ISME J. 2010;4:191–202.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 16.

    Gibbons SM, Caporaso JG, Pirrung M, Field D, Knight R, Gilbert JA. Evidence for a persistent microbial seed bank throughout the global ocean. Proc Natl Acad Sci USA. 2013;110:4651–55.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 17.

    Ramirez KS, Leff JW, Barberán A, Bates ST, Betley J, Crowther TW, et al. Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally. Proc R Soc Lond B Biol Sci. 2014;281:20141988.

  • 18.

    Gonnella G, Böhnke S, Indenbirken D, Garbe-Schönberg D, Seifert R, Mertens C, et al. Endemic hydrothermal vent species identified in the open ocean seed bank. Nat Microbiol. 2016;1:16086 EP.

    Article 
    CAS 

    Google Scholar 

  • 19.

    Louca S, Mazel F, Doebeli M, Parfrey WL. A census-based estimate of Earth’s bacterial and archaeal diversity. PLoS Biol. 2019;17:e3000106.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 20.

    Ochman H, Wilson A. Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J Mol Evol. 1987;26:74–86.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 21.

    Kuo CH, Ochman H. Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biol Direct. 2009;4:35–35.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 22.

    Roberts MS, Cohan FM. Recombination and migration rates in natural populations of Bacillus subtilis and Bacillus mojavensis. Evolution. 1995;49:1081–94.

    PubMed 
    Article 

    Google Scholar 

  • 23.

    van Gremberghe I, Leliaert F, Mergeay J, Vanormelingen P, Van der Gucht K, Debeer AE, et al. Lack of phylogeographic structure in the freshwater cyanobacterium Microcystis aeruginosa suggests global dispersal. PLoS ONE. 2011;6:e19561.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 24.

    Papke RT, Ramsing NB, Bateson MM, Ward DM. Geographical isolation in hot spring cyanobacteria. Environ Microbiol. 2003;5:650–9.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 25.

    Hongmei J, Aitchison JC, Lacap DC, Peerapornpisal Y, Sompong U, Pointing SB. Community phylogenetic analysis of moderately thermophilic cyanobacterial mats from China, the Philippines and Thailand. Extremophiles. 2005;9:325–32.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 26.

    Miller SR, Castenholz RW, Pedersen D. Phylogeography of the thermophilic cyanobacterium Mastigocladus laminosus. Appl Environ Microbiol. 2007;73:4751–59.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 27.

    Takacs-Vesbach C, Mitchell K, Jackson-Weaver O, Reysenbach AL. Volcanic calderas delineate biogeographic provinces among Yellowstone thermophiles. Environ Microbiol. 2008;10:1681–89.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 28.

    Reno ML, Held NL, Fields CJ, Burke PV, Whitaker RJ. Biogeography of the Sulfolobus islandicus pan-genome. Proc Natl Acad Sci USA. 2009;106:8605–10.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 29.

    Bahl J, Lau MCY, Smith GJD, Vijaykrishna D, Cary SC, Lacap DC, et al. Ancient origins determine global biogeography of hot and cold desert cyanobacteria. Nat Commun. 2011;2:163.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 30.

    Anderson RE, Kouris A, Seward CH, Campbell KM, Whitaker RJ. Structured populations of Sulfolobus acidocaldarius with susceptibility to mobile genetic elements. Genome Biol Evol. 2017;9:1699–710.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 31.

    Podar PT, Yang Z, Björnsdóttir SH, Podar M. Comparative analysis of microbial diversity across temperature gradients in hot springs from Yellowstone and Iceland. Front Microbiol. 2020;11:1625.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 32.

    Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. Genbank. Nucleic Acids Res. 2015;44:D67–D72.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 33.

    Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA. 2005;102:2567–72.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 34.

    Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014;64:346–51.

    CAS 
    Article 

    Google Scholar 

  • 35.

    Olm MR, Crits-Christoph A, Diamond S, Lavy A, Carnevali PBM, Banfield JF. Consistent metagenome-derived metrics verify and delineate bacterial species boundaries. mSystems. 2020;5:e00731-19.

  • 36.

    Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:5114.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 37.

    Shapiro BJ. What microbial population genomics has taught us about speciation. In: Polz MF, Rajora OP, editors. Population Genomics: Microorganisms. Cham, Switzerland: Springer International Publishing; 2019. p. 31–47.

  • 38.

    Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996–1004.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 39.

    Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2020;36:1925–27.

    CAS 

    Google Scholar 

  • 40.

    Felsenstein J. Phylogenies and the comparative method. Am Nat. 1985;125:1–15.

    Article 

    Google Scholar 

  • 41.

    Louca S. Phylogeographic estimation and simulation of global diffusive dispersal. Syst Biol. 2021;70:340–59.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 42.

    Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet. 2013;45:1176–82.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 43.

    Denef VJ, Banfield JF. In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids. Science. 2012;336:462–6.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 44.

    Bouckaert R, Cartwright R. Phylogeography by diffusion on a sphere: whole world phylogeography. PeerJ. 2016;4:e2406.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 45.

    Brillinger DR. A particle migrating randomly on a sphere. In: Selected Works of David Brillinger. Cham, Switzerland: Springer; 2012. p. 73–87.

  • 46.

    Ghosh A, Samuel J, Sinha SA. “Gaussian” for diffusion on the sphere. Europhys Lett. 2012;98:30003.

    Article 
    CAS 

    Google Scholar 

  • 47.

    Castenholz RW. The biogeography of hot spring algae through enrichment cultures. SIL Commun. 1978;21:296–315. 1953-1996

    Google Scholar 

  • 48.

    Valentine DL. Adaptations to energy stress dictate the ecology and evolution of the archaea. Nat Rev Micro. 2007;5:316–23.

    CAS 
    Article 

    Google Scholar 

  • 49.

    Louca S, Parfrey LW, Doebeli M. Decoupling function and taxonomy in the global ocean microbiome. Science. 2016;353:1272–77.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 50.

    Smith DJ, Jaffe DA, Birmele MN, Griffin DW, Schuerger AC, Hee J, et al. Free tropospheric transport of microorganisms from Asia to North America. Micro Ecol. 2012;64:973–85.

    CAS 
    Article 

    Google Scholar 

  • 51.

    Pagel M. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc R Soc Lond B Biol Sci. 1994;255:37–45.

    Article 

    Google Scholar 

  • 52.

    Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci USA. 1998;95:6578–83.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 53.

    Anderson D. The regulation of fishing and related activities in exclusive economic zones. In: Modern Law Sea, Publications on Ocean Development, vol. 59, chap. 11. Leiden, The Netherlands: Brill Nijhoff; 2008. p. 209–27.

  • 54.

    Bullock JM, Clarke RT. Long distance seed dispersal by wind: measuring and modelling the tail of the curve. Oecologia. 2000;124:506–21.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 55.

    Brynjarsdóttir J, O’Hagan A. Learning about physical parameters: the importance of model discrepancy. Inverse Probl. 2014;30:114007.

    Article 

    Google Scholar 

  • 56.

    Bell T. Experimental tests of the bacterial distance-decay relationship. ISME J. 2010;4:1357–65.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 57.

    Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 2010;11:119.

    Article 
    CAS 

    Google Scholar 

  • 58.

    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2014;25:1043–55.

    Article 
    CAS 

    Google Scholar 

  • 59.

    Chambat F, Valette B. Mean radius, mass, and inertia for reference Earth models. Phys Earth Planet Inter. 2001;124:237–53.

    Article 

    Google Scholar 

  • 60.

    Data NS, (SEDAC) AC Gridded Population of the World, Version 4 (GPW v4): Population Density, Revision 11. Tech. rep., Palisades, NY: Center for International Earth Science Information Network – CIESIN – Columbia University. 2018. Accessed November 23, 2020.

  • 61.

    Price MN, Dehal PS, Arkin AP. FastTree 2: approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5:e9490.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 62.

    Britton T, Anderson CL, Jacquet D, Lundqvist S, Bremer K. Estimating divergence times in large phylogenetic trees. Syst Biol. 2007;56:741–52.

    PubMed 
    Article 

    Google Scholar 

  • 63.

    Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, et al. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains bacteria and archaea. Nat Commun. 2019;10:5477.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 64.

    Perrin F. Étude mathématique du movement brownien de rotation. In: Annales scientifiques del’École Normale Supérieure, vol. 45. Paris, France: Elsevier; with 1928. p. 1–51.

  • 65.

    Louca S, Doebeli M. Efficient comparative phylogenetics on large trees. Bioinformatics. 2018;34:1053–55.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 66.

    Bloomquist EW, Lemey P, Suchard MA. Three roads diverged? routes to phylogeographic inference. Trends Ecol Evol. 2010;25:626–32.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 67.

    Lemey P, Rambaut A, Welch JJ, Suchard MA. Phylogeography takes a relaxed random walk in continuous space and time. Mol Biol Evol. 2010;27:1877–85.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 68.

    Faria NR, Suchard MA, Rambaut A, Lemey P. Toward a quantitative understanding of viral phylogeography. Curr Opin Virol. 2011;1:423–9.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 69.

    Faria NR, Suchard MA, Abecasis A, Sousa JD, Ndembi N, Bonfim I, et al. Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon. Infect Genet Evol. 2012;12:453–60.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 70.

    Lange K. Diffusion processes. In: Applied Probability, chap. 11. New York, NY: Springer New York; 2010. p. 269–95.

  • 71.

    Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, et al. Mash: fast genome and metagenome distance estimation using minhash. Genome Biol. 2016;17:132.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 72.

    Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell 2019;176:649–62.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 73.

    Criscuolo A, Gascuel O. Fast NJ-like algorithms to deal with incomplete distance matrices. BMC Bioinforma. 2008;9:166.

    Article 
    CAS 

    Google Scholar 

  • 74.

    Paradis E, Claude J, Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics. 2004;20:289–90.

  • 75.

    Kinene T, Wainaina J, Maina S, Boykin LM, Kliman RM. Methods for rooting trees, vol. 3. Oxford: Academic Press; 2016. p. 489–93.

  • 76.

    van Rossum G. Python tutorial. Tech. Rep. CS-R9526, Amsterdam: Centrum voor Wiskunde en Informatica (CWI); 1995.


  • Source: Ecology - nature.com

    MIT.nano receives American Institute of Architects’s Top Ten Award for sustainable design

    Push to make supply chains more sustainable continues to gain momentum