@misc{hanson1961animal2,
    author = "Hanson, E. D",
    title = "Animal Diversity",
    year = "1961",
    howpublished = "Englewood Cliffs, New Jersey, Prentice- Hall, 116 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Hanson, E. D., 1961, Animal Diversity: Englewood Cliffs, New Jersey, Prentice- Hall, 116 p.}"
}

@techreport{brown1964the1,
    author = "Brown, J. L",
    title = "The evolution of diversity in avian territorial systems",
    year = "1964",
    howpublished = "Wilson Bulletin, v. 76, p. 160-169",
    note = "talkorigins\_source = {true}; raw\_reference = {Brown, J. L., 1964, The evolution of diversity in avian territorial systems: Wilson Bulletin, v. 76, p. 160-169.}"
}

@inproceedings{whittaker1969evolution6,
    author = "Whittaker, R. H",
    title = "Evolution of diversity in plant communities",
    year = "1969",
    booktitle = "Brookhaven Symposium on Biology, v. 22, p. 178-196",
    note = "talkorigins\_source = {true}; raw\_reference = {Whittaker, R. H., 1969, Evolution of diversity in plant communities: Brookhaven Symposium on Biology, v. 22, p. 178-196.}"
}

@article{doi1023071218190,
    author = "Whittaker, R. H.",
    title = "EVOLUTION AND MEASUREMENT OF SPECIES DIVERSITY",
    year = "1972",
    journal = "Taxon",
    abstract = "Summary Given a resource gradient (e.g. light intensity, prey size) in a community, species evolve to use different parts of this gradient; competition between them is thereby reduced. Species relationships in the community may be conceived in terms of a multidimensional coordinate system, the axes of which are the various resource gradients (and other aspects of species relationships to space, time, and one another in the community). This coordinate system defines a hyperspace, and the range of the space that a given species occupies is its niche hypervolume, as an abstract characterization of its intra‐community position, or niche. Species evolve toward difference in niche, and consequently toward difference in location of their hypervolumes in the niche hyperspace. Through evolutionary time additional species can fit into the community in niche hypervolumes different from those of other species, and the niche hyperspace can become increasingly complex. Its complexity relates to the community's richness in species, its alpha diversity. Species differ in the proportions of the niche hyperspace they are able to occupy and the share of the community's resources they utilize. The share of resources utilized is expressed in species' productivities, and when species are ranked by relative productivity (or some other measurement) from most to least important, importance‐value or dominance‐diversity curves are formed. Three types of curves may represent manners in which resources are divided among species: (a) niche pre‐emption with strong dominance, expressed in a geometric series, (b) random boundaries between niches, expressed in the MacArthur distribution, and (c) determination of relative importance by many factors, so that species form a frequency distribution on a logarithmic base of importance values, a lognormal distribution. The forms of importance‐value curves do not permit strong inference about resource division, but are of interest for their expression of species relationships and bearing on measurement of diversity.",
    url = "https://doi.org/10.2307/1218190",
    doi = "10.2307/1218190",
    openalex = "W2006690660",
    references = "doi1010160022519366900130, doi101038163688a0, doi101086282070, doi101086282106, doi101086282171, doi101086282286, doi101086282398, doi101086282400, doi101086282505, doi101086282687, doi101086282738, doi101111j1469185x1965tb00815x, doi101111j155856461960tb03057x, doi101111j155856461963tb03295x, doi101111j155856461964tb01674x, doi101111j155856461970tb01782x, doi101126science14235991575, doi101126science1473655250, doi101126science1643877262, doi1015159780691209418, doi1015159781400881376, doi1023071931976, doi1023071932254, doi1023071942268, doi1023071943577, doi1023072406825, doi1023072628, doi1023072989767, doi102307jctvx5wbbh, doi105962bhltitle4489, openalexw2418669733"
}

@article{raup1973stochastic4,
    author = "Raup, D. M. and Gould, S. J. and Schopf, T. J. M. and Simberloff, D. S",
    title = "Stochastic models of phylogeny and the evolution of diversity",
    year = "1973",
    journal = "Journal of Geology, v. 81, no. 5, p. 525-542",
    note = "talkorigins\_source = {true}; raw\_reference = {Raup, D. M., Gould, S. J., Schopf, T. J. M., and Simberloff, D. S., 1973, Stochastic models of phylogeny and the evolution of diversity: Journal of Geology, v. 81, no. 5, p. 525-542.}"
}

@misc{sepkoski1981phanerozoic5,
    author = "Sepkoski, J. J. and Bambach, R. K. and Raup, D. M. and Valentine, J. W",
    title = "Phanerozoic marine diversity and the fossil record",
    year = "1981",
    howpublished = "Nature, v. 293, p. 435",
    note = "talkorigins\_source = {true}; raw\_reference = {Sepkoski, J. J., Bambach, R. K., Raup, D. M., and Valentine, J. W., 1981, Phanerozoic marine diversity and the fossil record: Nature, v. 293, p. 435.}"
}

@book{mayr1982the3,
    author = "Mayr, E",
    title = "The Growth of Biological Thought; Diversity, Evolution, and Inheritance",
    year = "1982",
    publisher = "Cambridge, Mass., Belknap Press of Harvard University Press, 974 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Mayr, E., 1982, The Growth of Biological Thought; Diversity, Evolution, and Inheritance: Cambridge, Mass., Belknap Press of Harvard University Press, 974 p.}"
}

@book{openalexw1550375751,
    author = "Mayr, Ernst",
    title = "The Growth of Biological Thought: Diversity, Evolution, and Inheritance",
    year = "1982",
    abstract = "1 Introduction: How to write history of biology Subjectivity and bias Why study the history of biology? 2 The place of biology in the sciences and its conceptual structure The nature of science Method in science The position of biology within the sciences How and why is biology different? Special characteristics of living organisms Reduction and biology Emergence The conceptual structure of biology A new philosophy of biology 3 The changing intellectual milieu of biology Antiquity The Christian world picture The Renaissance The discovery of diversity Biology in the Enlightenment The rise of science from the seventeenth to the nineteenth century Divisive developments in the nineteenth century Biology in the twentieth century Major periods in the history of biology Biology and philosophy Biology today PART I DIVERSITY OF LIFE 4 Macrotaxonomy, the science of classifying Aristotle The classification of plants by the ancients and the herbalists Downward classification by logical division Pre-Linnaean zoologists Carl Linnaeus Buffon A new start in animal classification Taxonomic characters Upward classification by empirical grouping Transition period (1758-1859) Hierarchical classifications 5 Grouping according to common ancestry The decline of macrotaxonomic research Numerical phenetics Cladistics The traditional or evolutionary methodology New taxonomic characters Facilitation of information retrieval The study of diversity 6 Microtaxonomy, the science of species Early species concepts The essentialist species concept The nominalistic species concept Darwin's species concept The rise of the biological species concept Applying the biological species concept to multidimensional species taxa The significance of species in biology PART II EVOLUTION 7 Origins without evolution The coming of evolutionism The French Enlightenment 8 Evolution before Darwin Lamarck Cuvier England Lyell and uniformitarianism Germany 9 Charles Darwin Darwin and evolution Alfred Russel Wallace The publication of the Origin 10 Darwin's evidence for evolution and common descent Common descent and the natural system Common descent and geographical distribution Morphology as evidence for evolution and common descent Embryology as evidence for evolution and common descent 11 The causation of evolution: natural selection The major components of the theory of natural selection The origin of the concept of natural selection The impact of the Darwinian revolution The resistance to natural selection Alternate evolutionary theories 12 Diversity and synthesis of evolutionary thought The growing split among the evolutionists Advances in evolutionary genetics Advances in evolutionary systematics The evolutionary synthesis 13 Post-synthesis developments Molecular biology Natural selection Unresolved issues in natural selection Modes of speciation Macroevolution The evolution of man Evolution in modern thought PART III VARIATION AND ITS INHERITANCE 14 Early theories and breeding experiments Theories of inheritance among the ancients Mendel's forerunners 15 Germ cells, vehicles of heredity The Schwann-Schleiden cell theory The meaning of sex and fertilization Chromosomes and their role 16 The nature of inheritance Darwin and variation August Weismann Hugo de Vries Gregor Mendel 17 The flowering of Mendelian genetics The rediscoverers of Mendel The classical period of Mendelian genetics The origin of new variation (mutation) The emergence of modern genetics The Sutton-Boveri chromosome theory Sex determination Morgan and the fly room Meiosis Morgan and the chromosome theory 18 Theories of the gene Competing theories of inheritance The Mendelian explanation of continuous variation 19 The chemical basis of inheritance The discovery of the double helix Genetics in modern thought 20 Epilogue: Toward a science of science Scientists and the scientific milieu The maturation of theories and concepts Impediments to the maturation of theories and concepts The sciences and the external milieu Progress in science Notes References Glossary Index",
    url = "https://openalex.org/W1550375751",
    openalex = "W1550375751"
}

@article{doi101093auk1002507,
    author = "Farner, Donald S.",
    title = "The growth of biological thought. Diversity, evolution, and inheritance",
    year = "1983",
    journal = "The Auk",
    url = "https://doi.org/10.1093/auk/100.2.507",
    doi = "10.1093/auk/100.2.507",
    openalex = "W2978851794"
}

@article{doi105860choice332720,
    author = "Rosenzweig, Michael L.",
    title = "Species diversity in space and time",
    year = "1996",
    journal = "Choice Reviews Online",
    abstract = "Preface 1. The road ahead 2. Patterns in space 3. Temporal patterns 4. Dimensionless patterns 5. Speciation 6. Extinction 7. Evolution of the relationship between habitat diversity and species diversity 8. Species-area curves in ecological time 9. Species-area curves in evolutionary time 10. Paleobiological patterns 11. Other patterns with dynamic roots 12. Energy flow and diversity 13. A hierarchical dynamic puzzle References Index.",
    url = "https://doi.org/10.5860/choice.33-2720",
    doi = "10.5860/choice.33-2720",
    openalex = "W2018204894"
}

@article{doi101126science2765313734,
    author = "Pace, Norman R.",
    title = "A Molecular View of Microbial Diversity and the Biosphere",
    year = "1997",
    journal = "Science",
    abstract = "Over three decades of molecular-phylogenetic studies, researchers have compiled an increasingly robust map of evolutionary diversification showing that the main diversity of life is microbial, distributed among three primary relatedness groups or domains: Archaea, Bacteria, and Eucarya. The general properties of representatives of the three domains indicate that the earliest life was based on inorganic nutrition and that photosynthesis and use of organic compounds for carbon and energy metabolism came comparatively later. The application of molecular-phylogenetic methods to study natural microbial ecosystems without the traditional requirement for cultivation has resulted in the discovery of many unexpected evolutionary lineages; members of some of these lineages are only distantly related to known organisms but are sufficiently abundant that they are likely to have impact on the chemistry of the biosphere.",
    url = "https://doi.org/10.1126/science.276.5313.734",
    doi = "10.1126/science.276.5313.734",
    openalex = "W2068687524",
    references = "doi101073pnas74115088, doi101073pnas87124576, doi101073pnas89125685, doi101126science202030, doi101128mr5122212711987"
}

@article{doi101073pnas0605127103,
    author = "Sogin, Mitchell L. and Morrison, Hilary G. and Huber, Julie A. and Welch, David B. Mark and Huse, Susan M. and Neal, Phillip R. and Arrieta, Jesús M. and Herndl, Gerhard J.",
    title = "Microbial diversity in the deep sea and the underexplored “rare biosphere”",
    year = "2006",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = {The evolution of marine microbes over billions of years predicts that the composition of microbial communities should be much greater than the published estimates of a few thousand distinct kinds of microbes per liter of seawater. By adopting a massively parallel tag sequencing strategy, we show that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment. A relatively small number of different populations dominate all samples, but thousands of low-abundance populations account for most of the observed phylogenetic diversity. This "rare biosphere" is very ancient and may represent a nearly inexhaustible source of genomic innovation. Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes.},
    url = "https://doi.org/10.1073/pnas.0605127103",
    doi = "10.1073/pnas.0605127103",
    openalex = "W2087671769",
    references = "doi101016s0168952500020242, doi101038nature03959, doi101073pnas89125685, doi101093nar25173389, doi101093nargkh073, doi101093nargkh293, doi101093nargkm864, doi101098rspb20022218, doi101128aem7112822882352005, doi101186147121055113, doi104319lo19802550943"
}

@article{doi101111j14610248200701020x,
    author = "Mittelbach, Gary G. and Schemske, Douglas W. and Cornell, Howard V. and Allen, Andrew P. and Brown, J. Mark and Bush, Mark B. and Harrison, Susan and Hurlbert, Allen H. and Knowlton­, Nancy­ and Lessios, H. A. and McCain, Christy M. and McCune, Amy R. and McDade, Lucinda A. and McPeek, Mark A. and Near, Thomas J. and Price, Trevor D. and Ricklefs, Robert E. and Roy, Kaustuv and Sax, Dov F. and Schluter, Dolph and Sobel, James M. and Turelli, Michael",
    title = "Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography",
    year = "2007",
    journal = "Ecology Letters",
    abstract = "A latitudinal gradient in biodiversity has existed since before the time of the dinosaurs, yet how and why this gradient arose remains unresolved. Here we review two major hypotheses for the origin of the latitudinal diversity gradient. The time and area hypothesis holds that tropical climates are older and historically larger, allowing more opportunity for diversification. This hypothesis is supported by observations that temperate taxa are often younger than, and nested within, tropical taxa, and that diversity is positively correlated with the age and area of geographical regions. The diversification rate hypothesis holds that tropical regions diversify faster due to higher rates of speciation (caused by increased opportunities for the evolution of reproductive isolation, or faster molecular evolution, or the increased importance of biotic interactions), or due to lower extinction rates. There is phylogenetic evidence for higher rates of diversification in tropical clades, and palaeontological data demonstrate higher rates of origination for tropical taxa, but mixed evidence for latitudinal differences in extinction rates. Studies of latitudinal variation in incipient speciation also suggest faster speciation in the tropics. Distinguishing the roles of history, speciation and extinction in the origin of the latitudinal gradient represents a major challenge to future research.",
    url = "https://doi.org/10.1111/j.1461-0248.2007.01020.x",
    doi = "10.1111/j.1461-0248.2007.01020.x",
    openalex = "W2142834673",
    references = "doi101038217624a0, doi101086381004, doi101093aibsbulletin2214b, doi101093oso97801985052350010001, doi101098rstb20031393, doi101111j001438202006tb01143x, doi101111j155856461960tb03057x, doi101111j20060906759004272x, doi101126science1059412, doi101126science1130880, doi101126science2354785167, doi101146annurevecolsys34012103144032, doi101722611310, doi1023071435536, doi1023072485224, doi105860choice332720, doi105860choice435875, doi105962bhltitle46292, doi105962bhltitle59991, openalexw1840956397, openalexw2145250129, openalexw2989964553"
}

@article{doi101128aem0199606,
    author = "Lozupone, Catherine and Hamady, Micah and Kelley, Scott T. and Knight, Rob",
    title = "Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities",
    year = "2007",
    journal = "Applied and Environmental Microbiology",
    abstract = "The assessment of microbial diversity and distribution is a major concern in environmental microbiology. There are two general approaches for measuring community diversity: quantitative measures, which use the abundance of each taxon, and qualitative measures, which use only the presence/absence of data. Quantitative measures are ideally suited to revealing community differences that are due to changes in relative taxon abundance (e.g., when a particular set of taxa flourish because a limiting nutrient source becomes abundant). Qualitative measures are most informative when communities differ primarily by what can live in them (e.g., at high temperatures), in part because abundance information can obscure significant patterns of variation in which taxa are present. We illustrate these principles using two 16S rRNA-based surveys of microbial populations and two phylogenetic measures of community beta diversity: unweighted UniFrac, a qualitative measure, and weighted UniFrac, a new quantitative measure, which we have added to the UniFrac website (http://bmf.colorado.edu/unifrac). These studies considered the relative influences of mineral chemistry, temperature, and geography on microbial community composition in acidic thermal springs in Yellowstone National Park and the influences of obesity and kinship on microbial community composition in the mouse gut. We show that applying qualitative and quantitative measures to the same data set can lead to dramatically different conclusions about the main factors that structure microbial diversity and can provide insight into the nature of community differences. We also demonstrate that both weighted and unweighted UniFrac measurements are robust to the methods used to build the underlying phylogeny.",
    url = "https://doi.org/10.1128/aem.01996-06",
    doi = "10.1128/aem.01996-06",
    openalex = "W2145664556",
    references = "doi101038260204c0, doi101086321317, doi101093bioinformaticsbtg180, doi101146annurevecolsys33010802150448, doi1023071218190, doi105860choice421547, openalexw2032279931"
}

@article{doi101196annals1419019,
    author = "Liu, Yuchen and Whitman, William B.",
    title = "Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea",
    year = "2008",
    journal = "Annals of the New York Academy of Sciences",
    abstract = "Although of limited metabolic diversity, methanogenic archaea or methanogens possess great phylogenetic and ecological diversity. Only three types of methanogenic pathways are known: CO(2)-reduction, methyl-group reduction, and the aceticlastic reaction. Cultured methanogens are grouped into five orders based upon their phylogeny and phenotypic properties. In addition, uncultured methanogens that may represent new orders are present in many environments. The ecology of methanogens highlights their complex interactions with other anaerobes and the physical and chemical factors controlling their function.",
    url = "https://doi.org/10.1196/annals.1419.019",
    doi = "10.1196/annals.1419.019",
    openalex = "W2014254156",
    references = "doi101016s0009254199000923, doi1073260003481911154487"
}

@article{doi101073pnas0903410106,
    author = "Simon, Marcelo Fragomeni and Grether, Rosaura and de Queiroz, Luciano Paganucci and Skema, Cynthia and Pennington, R. Toby and Hughes, Colin E.",
    title = "Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire",
    year = "2009",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "The relative importance of local ecological and larger-scale historical processes in causing differences in species richness across the globe remains keenly debated. To gain insight into these questions, we investigated the assembly of plant diversity in the Cerrado in South America, the world's most species-rich tropical savanna. Time-calibrated phylogenies suggest that Cerrado lineages started to diversify less than 10 Mya, with most lineages diversifying at 4 Mya or less, coinciding with the rise to dominance of flammable C4 grasses and expansion of the savanna biome worldwide. These plant phylogenies show that Cerrado lineages are strongly associated with adaptations to fire and have sister groups in largely fire-free nearby wet forest, seasonally dry forest, subtropical grassland, or wetland vegetation. These findings imply that the Cerrado formed in situ via recent and frequent adaptive shifts to resist fire, rather than via dispersal of lineages already adapted to fire. The location of the Cerrado surrounded by a diverse array of species-rich biomes, and the apparently modest adaptive barrier posed by fire, are likely to have contributed to its striking species richness. These findings add to growing evidence that the origins and historical assembly of species-rich biomes have been idiosyncratic, driven in large part by unique features of regional- and continental-scale geohistory and that different historical processes can lead to similar levels of modern species richness.",
    url = "https://doi.org/10.1073/pnas.0903410106",
    doi = "10.1073/pnas.0903410106",
    openalex = "W2151396518",
    references = "doi101073pnas0608361104, doi101146annurevecolsys110308120327, openalexw2611511275"
}

@article{doi101146annurevecolsys110308120327,
    author = "Pennington, R. Toby and Lavin, Matt and de Oliveira‐Filho, Ary Teixeira",
    title = "Woody Plant Diversity, Evolution, and Ecology in the Tropics: Perspectives from Seasonally Dry Tropical Forests",
    year = "2009",
    journal = "Annual Review of Ecology Evolution and Systematics",
    abstract = "This review suggests that the ecology and patchy global distribution of seasonally dry tropical forest (SDTF) has distinctively structured the evolutionary history and biogeography of woody plant groups that are confined to it. SDTFs have few widespread woody plant species causing high β-diversity between separate areas of forests. These separate areas contain geologically old, monophyletic clades of endemic plant species that often have geographically structured intraspecific genetic variation. These patterns of diversity, endemism, and phylogeny indicate a stable, dispersal-limited SDTF system. SDTF species tend to belong to larger clades confined to this vegetation, exemplifying phylogenetic niche conservatism, and we argue that this is evidence that the SDTF is a metacommunity (biome) for woody plant clades. That phylogenetic, population genetic, biogeographic, and community ecological patterns differ in woody plants from tropical rain forests and savannas suggests a hypothesis that broad ecological settings strongly influence plant diversification in the tropics.",
    url = "https://doi.org/10.1146/annurev.ecolsys.110308.120327",
    doi = "10.1146/annurev.ecolsys.110308.120327",
    openalex = "W2108333212",
    references = "doi101007978146121694015, doi101093oso97801985464120010001, doi101146annurevecolsys33010802150448, doi101146annurevecolsys37091305110035, doi1016410006356820010510933teotwa20co2, doi1018637jssv022i07, doi1018900012965820020831771tuntob20co2, doi1023073071998, doi1023073802723, doi1023073803199, doi105860choice295104"
}

@article{doi103109104092382011600437,
    author = "Hayes, Finbarr and Melderen, Laurence Van",
    title = "Toxins-antitoxins: diversity, evolution and function",
    year = "2011",
    journal = "Critical Reviews in Biochemistry and Molecular Biology",
    abstract = "Genes for toxin-antitoxin (TA) complexes are widespread in prokaryote genomes, and species frequently possess tens of plasmid and chromosomal TA loci. The complexes are categorized into three types based on genetic organization and mode of action. The toxins universally are proteins directed against specific intracellular targets, whereas the antitoxins are either proteins or small RNAs that neutralize the toxin or inhibit toxin synthesis. Within the three types of complex, there has been extensive evolutionary shuffling of toxin and antitoxin genes leading to considerable diversity in TA combinations. The intracellular targets of the protein toxins similarly are varied. Numerous toxins, many of which are sequence-specific endoribonucleases, dampen protein synthesis levels in response to a range of stress and nutritional stimuli. Key resources are conserved as a result ensuring the survival of individual cells and therefore the bacterial population. The toxin effects generally are transient and reversible permitting a set of dynamic, tunable responses that reflect environmental conditions. Moreover, by harboring multiple toxins that intercede in protein synthesis in response to different physiological cues, bacteria potentially sense an assortment of metabolic perturbations that are channeled through different TA complexes. Other toxins interfere with the action of topoisomersases, cell wall assembly, or cytoskeletal structures. TAs also play important roles in bacterial persistence, biofilm formation and multidrug tolerance, and have considerable potential both as new components of the genetic toolbox and as targets for novel antibacterial drugs.",
    url = "https://doi.org/10.3109/10409238.2011.600437",
    doi = "10.3109/10409238.2011.600437",
    openalex = "W2163406805",
    references = "doi101038nrmicro1147, doi101073pnas252529799, doi101073pnas83103116, doi101073pnas93126059, doi101093nargki201, doi101128jb15527687751983, doi101128jb18624817281802004, doi101128mmbr0002110, doi101146annurevmicro112408134306, doi101371journalpbio1000317"
}

@article{doi103389fmicb201100155,
    author = "Filloux, Alain",
    title = "Protein Secretion Systems in Pseudomonas aeruginosa: An Essay on Diversity, Evolution, and Function",
    year = "2011",
    journal = "Frontiers in Microbiology",
    abstract = "Protein secretion systems are molecular nanomachines used by Gram-negative bacteria to thrive within their environment. They are used to release enzymes that hydrolyze complex carbon sources into usable compounds, or to release proteins that capture essential ions such as iron. They are also used to colonize and survive within eukaryotic hosts, causing acute or chronic infections, subverting the host cell response and escaping the immune system. In this article, the opportunistic human pathogen Pseudomonas aeruginosa is used as a model to review the diversity of secretion systems that bacteria have evolved to achieve these goals. This diversity may result from a progressive transformation of cell envelope complexes that initially may not have been dedicated to secretion. The striking similarities between secretion systems and type IV pili, flagella, bacteriophage tail, or efflux pumps is a nice illustration of this evolution. Differences are also needed since various secretion configurations call for diversity. For example, some proteins are released in the extracellular medium while others are directly injected into the cytosol of eukaryotic cells. Some proteins are folded before being released and transit into the periplasm. Other proteins cross the whole cell envelope at once in an unfolded state. However, the secretion system requires conserved basic elements or features. For example, there is a need for an energy source or for an outer membrane channel. The structure of this review is thus quite unconventional. Instead of listing secretion types one after each other, it presents a melting pot of concepts indicating that secretion types are in constant evolution and use basic principles. In other words, emergence of new secretion systems could be predicted the way Mendeleïev had anticipated characteristics of yet unknown elements.",
    url = "https://doi.org/10.3389/fmicb.2011.00155",
    doi = "10.3389/fmicb.2011.00155",
    openalex = "W2166412853",
    references = "doi1010160022283685900464, doi10103835016007, doi10103835023079, doi101038358727a0, doi101038nprot20092, doi101038nrmicro1526, doi101073pnas0510322103, doi101126science1128393, doi101146annurevmicro56012302160938, doi101146annurevmicro58030603123811"
}

@article{doi101371journalpgen1002784,
    author = "Loper, Joyce E. and Hassan, Karl A. and Mavrodi, Dmitri V. and Davis, Edward W. and Lim, Chee Kent and Shaffer, Brenda T. and Elbourne, Liam D. H. and Stockwell, Virginia O. and Hartney, Sierra L. and Breakwell, Katy and Henkels, Marcella D. and Tetu, Sasha G. and Rangel, Lorena I. and Kidarsa, Teresa A. and Wilson, N. L. and van de Mortel, Judith E. and Song, Chunxu and Blumhagen, Rachel Z. and Radune, Diana and Hostetler, Jessica B. and Brinkac, Lauren and Durkin, A. Scott and Kluepfel, Daniel A. and Wechter, W. Patrick and Anderson, Anne J. and Kim, Young Cheol and Pierson, Leland S. and Pierson, Elizabeth A. and Lindow, Steven E. and Kobayashi, Donald Y. and Raaijmakers, Jos M. and Weller, David M. and Thomashow, Linda S. and Allen, Andrew E. and Paulsen, Ian T.",
    title = "Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions",
    year = "2012",
    journal = "PLoS Genetics",
    abstract = "We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54\% of the pan-genome of the genus as a whole, and a core genome representing only 45-52\% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire.",
    url = "https://doi.org/10.1371/journal.pgen.1002784",
    doi = "10.1371/journal.pgen.1002784",
    openalex = "W2055455922",
    references = "doi103389fmicb201100155"
}

@article{doi101371journalpone0089543,
    author = "Rabosky, Daniel L.",
    title = "Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees",
    year = "2014",
    journal = "PLoS ONE",
    abstract = "A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.",
    url = "https://doi.org/10.1371/journal.pone.0089543",
    doi = "10.1371/journal.pone.0089543",
    openalex = "W2042449834",
    references = "doi10100797814612066756, doi101017s0094837300005972, doi101038nature05634, doi101038nature11631, doi10106311699114, doi101093bioinformaticsbtm538, doi101093biomet57197, doi101093biomet824711, doi101111j14610248200701020x, doi101126science2354785167, doi101186147121481393"
}

@article{doi101098rstb20150290,
    author = "Mylonakis, Eleftherios and Podsiadłowski, Lars and Muhammed, Maged and Vilcinskas, Andreas",
    title = "Diversity, evolution and medical applications of insect antimicrobial peptides",
    year = "2016",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "Antimicrobial peptides (AMPs) are short proteins with antimicrobial activity. A large portion of known AMPs originate from insects, and the number and diversity of these molecules in different species varies considerably. Insect AMPs represent a potential source of alternative antibiotics to address the limitation of current antibiotics, which has been caused by the emergence and spread of multidrug-resistant pathogens. To get more insight into AMPs, we investigated the diversity and evolution of insect AMPs by mapping their phylogenetic distribution, allowing us to predict the evolutionary origins of selected AMP families and to identify evolutionarily conserved and taxon-specific families. Furthermore, we highlight the use of the nematode Caenorhabditis elegans as a whole-animal model in high-throughput screening methods to identify AMPs with efficacy against human pathogens, including Acinetobacter baumanii and methicillin-resistant Staphylococcus aureus We also discuss the potential medical applications of AMPs, including their use as alternatives for conventional antibiotics in ectopic therapies, their combined use with antibiotics to restore the susceptibility of multidrug-resistant pathogens, and their use as templates for the rational design of peptidomimetic drugs that overcome the disadvantages of therapeutic peptides.The article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'.",
    url = "https://doi.org/10.1098/rstb.2015.0290",
    doi = "10.1098/rstb.2015.0290",
    openalex = "W2346044263",
    references = "doi101016jdrudis200910009, doi101016s1473309913703189, doi101038292246a0, doi101038nbt1267, doi101038nrmicro1098, doi101086533452, doi101086651263, doi101111j0105289620040124x, doi101126science1257570, doi101371journalpcbi1002195"
}

@article{doi101186s1305901610042,
    author = "Daniell, Henry and Lin, Choun‐Sea and Yu, Ming and Chang, Wan‐Jung",
    title = "Chloroplast genomes: diversity, evolution, and applications in genetic engineering",
    year = "2016",
    journal = "Genome biology",
    abstract = "Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.",
    url = "https://doi.org/10.1186/s13059-016-1004-2",
    doi = "10.1186/s13059-016-1004-2",
    openalex = "W2475158195",
    references = "doi101002j146020751986tb04464x, doi101007bf02464880, doi101038nature06856, doi101038ng740, doi101038nmeth2474, doi101038nrg1271, doi101038nrmicro3050, doi101073pnas0709121104, doi101126science1162986, doi103732ajb921142"
}

@article{doi101038ismej2017122,
    author = "Adam, Panagiotis S. and Borrel, Guillaume and Brochier‐Armanet, Céline and Gribaldo, Simonetta",
    title = "The growing tree of Archaea: new perspectives on their diversity, evolution and ecology",
    year = "2017",
    journal = "The ISME Journal",
    abstract = "The Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial diversity. Abundant in soils, ocean sediments and the water column, they have crucial roles in processes mediating global carbon and nutrient fluxes. Moreover, they represent an important component of the human microbiome, where their role in health and disease is still unclear. The development of culture-independent sequencing techniques has provided unprecedented access to genomic data from a large number of so far inaccessible archaeal lineages. This is revolutionizing our view of the diversity and metabolic potential of the Archaea in a wide variety of environments, an important step toward understanding their ecological role. The archaeal tree is being rapidly filled up with new branches constituting phyla, classes and orders, generating novel challenges for high-rank systematics, and providing key information for dissecting the origin of this domain, the evolutionary trajectories that have shaped its current diversity, and its relationships with Bacteria and Eukarya. The present picture is that of a huge diversity of the Archaea, which we are only starting to explore.",
    url = "https://doi.org/10.1038/ismej.2017.122",
    doi = "10.1038/ismej.2017.122",
    openalex = "W2743255823",
    references = "doi101038nature12352, doi101038nature14447, doi101038nature14486, doi101038nature21031, doi101038nmicrobiol201648, doi101038nrmicro1852, doi101038nrmicro1931, doi101038nrmicro3330, doi101073pnas87124576, doi101073pnas89125685"
}

@article{doi101073pnas1706756114,
    author = "Cardoso, Domingos and Särkinen, Tiina and Alexander, Sara N. and Amorim, André M. and Bittrich, Volker and Celis, Marcela and Daly, Douglas C. and Fiaschi, Pedro and Funk, Vicki A. and Giacomin, Leandro Lacerda and Goldenberg, Renato and Heiden, Gustavo and Iganci, João Ricardo Vieira and Kelloff, Carol L. and Knapp, Sandra and de Lima, Haroldo Cavalcante and Machado, Anderson Ferreira Pinto and dos Santos, Rubens Manoel and de Mello‐Silva, Renato and Michelangeli, Fabián A. and Mitchell, John D. and Moonlight, Peter W. and de Moraes, Pedro Luís Rodrigues and Mori, Scott A. and Nunes, Teonildes Sacramento and Pennington, Terry D. and Pirani, José Rubens and Prance, Ghillean Τ. and de Queiroz, Luciano Paganucci and Rapini, Alessandro and Riina, Ricarda and Rincon, Carlos Alberto Vargas and Roque, Nádia and Shimizu, Gustavo Hiroaki and Sobral, Marcos and Stehmann, João Renato and Stevens, W. D. and Taylor, Charlotte M. and Trovó, Marcelo and van den Berg, Cássio and van der Werff, Henk and Viana, Pedro Lage and Zartman, Charles E. and Forzza, Rafaela Campostrini",
    title = "Amazon plant diversity revealed by a taxonomically verified species list",
    year = "2017",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.",
    url = "https://doi.org/10.1073/pnas.1706756114",
    doi = "10.1073/pnas.1706756114",
    openalex = "W2754397646",
    references = "doi101146annurevecolsys110308120327"
}

@article{doi101038s415640200715z,
    author = "Baker, Brett J. and Anda, Valerie De and Seitz, Kiley W. and Dombrowski, Nina and Santoro, Alyson E. and Lloyd, Karen G.",
    title = "Diversity, ecology and evolution of Archaea",
    year = "2020",
    journal = "Nature Microbiology",
    url = "https://doi.org/10.1038/s41564-020-0715-z",
    doi = "10.1038/s41564-020-0715-z",
    openalex = "W3022704487",
    references = "doi101038ismej2017122, doi101038nature03911, doi101038nature04983, doi101038nature21031, doi101038nbt4229, doi101038nmeth3103, doi101038s41467018074180, doi101073pnas74115088, doi101073pnas87124576, doi101073pnas89125685, doi101093bioinformaticsbts174, doi101111j13652958201107635x, doi101126science1093857, doi101126science2765313734"
}