C Phylogenetic Tree

    CPhylogenetic Tree

    A species is a unique group of organisms and is the first rung on the ladder of taxonomic classifications that stretches all the way up to the three domains of life: Bacteria, Archaea and Eukarya. How exactly a species is defined, though, is a surprisingly complicated question, especially for single-celled organisms. For most animals, species boundaries are defined by the infertility of offspring from matings across that boundary. This does not always work, though, and many species are defined by geographical, rather than reproductive, separation. For organisms that reproduce asexually, the boundaries are even more nebulous and often simply reflect a fairly arbitrary degree of difference, either morphological or genetic. Also, remember that bacteria and archaea frequently exchange genes, or larger stretches of DNA, through horizontal gene transfer (for a familiar example, think of the transfer of antibiotic resistance). This further blurs the lines between species. In an extreme view, perhaps we should think of environments less as collections of species than as pools of genes temporarily stored in a variety of containers. Still, despite its inexactness, taxonomic classification provides a useful way to trace biological traits so we can begin to answer questions like how the machines you see in this book may have evolved.

    This phylogenetic tree shows the relatedness of the species in this book. The length of the branches separating two species from their last common ancestor is proportional to the amount of time that they have been evolving separately. Keep in mind that individual species of Bacteria and Archaea can be as evolutionarily divergent from one another as they are from us. The deeper we go into the past, toward the center of the tree, the less accurate the predictions of relatedness become. The branch point between Bacteria/Archaea and Eukaryotes is particularly hazy, and a topic of lively debate. We’re still discovering new species, and even higher-order clades, and the computational tools we have to detect genetic relationships are improving, so this tree, too, will continue to evolve.

    Haloferax gibbonsii Brucella abortus Helicobacter pylori Methanoregula formicica Pseudoalteromonas luteoviolacea Asgard group Magnetospirillum magneticum Campylobacter jejuni Chrysiogenetes Deferribacteres Hydrogenovibrio crunogenus Porphyromonas gingivalis Sulfolobus solfataricus Myxococcus xanthus Lysobacter antibioticus Cupriavidus necator Archaea incertae sedis Pseudomonas flexibilis Methylomicrobium alcaliphilum Halohasta litchfieldiae Delftia acidovorans Caulobacter crescentus Candidatus Krumholzibacteriota Agrobacterium tumefaciens Listeria monocytogenes Mycoplasma genitalium Staphylococcus aureus Nitrospinae/Tectomicrobia group Tetrasphaera remsis Idiomarina loihiensis Borrelia burgdorferi Halothiobacillus neapolitanus Halobacterium salinarum Caldiserica/Cryosericota group unclassified Bacteria Prosthecobacter vanneervenii Salmonella typhimurium Candidatus Hydrothermarchaeota Shewanella oneidensis Dictyoglomi Bacillus subtilis Chloroflexi Thermotogae Haloquadratum walsbyi Verrucomicrobium spinosum Hyphomonas neptunium Sphingopyxis alaskensis Nitrospirae EUKARYOTES Fusobacteria Methyloprofundus sedimenti Azospirillum brasilense DPANN group Bdellovibrio bacteriovorus Proteus mirabilis Halomicrobium mukohataei Acetonema longum Thermodesulfobacteria Clostridium thermocellum Pseudomonas aeruginosa Coleospermum Acidobacteria Elusimicrobia Thiomonas intermedia Mycoplasma pneumoniae Methanospirillum hungatei Aquificae Rhodopseudomonas palustris Synergistetes Methanobacterium formicicum Escherichia coli Halorubrum litoreum Amoebophilus asiaticus Sporomusa acidovorans Coprothermobacterota Thermococcus kodakaraensis Haloarcula argentinensis Bacteroidetes JT5 Hylemonella gracilis Mycobacterium marinum Calditrichaeota Nitrosopumilus maritimus Gluconacetobacter hansenii Treponema primitia Legionella pneumophila unclassified Archaea environmental samples Prosthecobacter debontii Flavobacterium johnsoniae Sulfolobus acidocaldarius Simkania negevensis Helicobacter hepaticus Vibrio cholerae Bacteria incertae sedis BACTERIA ARCHAEA

    Staphylococcus aureus

    Mycoplasma genitalium


    1. 2.1 Membrane

    Listeria monocytogenes


    1. 2.2 Cell Wall

    Methanobacterium formicicum

    Prosthecobacter debontii

    Halomicrobium mukohataei

    Mycobacterium marinum

    Delftia acidovorans

    Methylomicrobium alcaliphilum

    Clostridium thermocellum

    Nitrosopumilus maritimus

    Methanospirillum hungatei

    Haloarcula argentinensis


    1. 2.9 DNA

    Simkania negevensis


    1. 3.1 Coccoid

    Brucella abortus


    1. 3.2 Rod: Variety

    Hylemonella gracilis

    Verrucomicrobium spinosum


    1. 3.6 Prosthecate

    Prosthecobacter vanneervenii

    Haloquadratum walsbyi


    1. 3.7 Square

    Rhodopseudomonas palustris

    Methyloprofundus sedimenti

    Thiomonas intermedia

    Lysobacter antibioticus

    Halorubrum litoreum

    Haloferax gibbonsii

    Halohasta litchfieldiae

    Hyphomonas neptunium

    Tetrasphaera remsis

    Idiomarina loihiensis

    Sphingopyxis alaskensis

    Sulfolobus acidocaldarius

    Pseudomonas flexibilis

    Proteus mirabilis

    Helicobacter hepaticus

    Treponema primitia

    Flavobacterium johnsoniae

    Mycoplasma pneumoniae

    Azospirillum brasilense

    Magnetospirillum magneticum


    1. 7.6 Magnetotaxis

    Sporomusa acidovorans

    Gluconacetobacter hansenii


    1. 9.2 Biofilm Matrix

    Legionella pneumophila

    Amoebophilus asiaticus

    Pseudoalteromonas luteoviolacea

    Porphyromonas gingivalis

    Bdellovibrio bacteriovorus / Escherichia coli

    Bacteroidetes JT5