bis2c: lecture 10 extras on "new view of the tree of life" paper

Hug et al 2016

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Hug et al. 2016 Tree of Life

92 Bacterial Phyla25 Archaeal Phyla5 Eukaryotic Supergroups

Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48

Laura Hug U. Waterloo

Jill Banfield UC Berkeley

http://dx.doi.org/10.1038/nmicrobiol.2016.48

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Hug et al 2016Hug et al. 2016 Bacteria



Taxa Covered in Textbook

!3Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48


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Hug et al 2016Phyla Never Grown in the Lab



Hug et al 2016

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Hug et al. 2016 Archaea and Eukaryotes



Hug et al 2016

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Hug et al. 2016 Archaea Phyla Never Grown in the Lab



Major Groups by Evolutionary Distance

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The Dark Matter of Biology

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0.2

Korarchaeota

DiapherotritesNanohaloarchaeota

Unclassified archaea Pacearchaeota

Woesearchaeota, Nanoarchaeota

Woesearchaeota

AltiarchaealesZ7ME43

Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria

Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata

ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa

CrenarchaeotaCrenarchaeota

Thorarchaeota Lokiarchaeota

YNPFFA

Thaumarchaeota Thaumarchaeota

Cyanobacteria, Melainabacteria

Dojkabacteria WS6 CPR3

Katanobacteria WWE3 Katanobacteria WWE3

Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria

Microgenomates Microgenomates Curtissbacteria Microgenomates Daviesbacteria

Microgenomates Levybacteria

Microgenomates Woesebacteria Microgenomates Amesbacteria

Microgenomates Shapirobacteria Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria

Microgenomates Gottesmanbacteria

KAZAN CPR2, Saccharibacteria TM7

Berkelbacteria

Berkelbacteria

Berkelbacteria Berkelbacteria

CPR Uncultured unclassified bacteria Peregrinibacteria

Peregrinibacteria

Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2

SM2F11Parcubacteria

Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria

Parcubacteria

ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria

Parcubacteria Moranbacteria

ParcubacteriaParcubacteria Yanofskybacteria

Deinococcus-Thermus Aquificae, Calescamantes EM19

Caldiserica, Dictyoglomi Thermotogae

Omnitrophica Omnitrophica

Spirochaetes Spirochaetes

Hydrogenedentes NKB19 Deltaproteobacteria

Epsilonproteobacteria TM6

Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot.

NC10, Rokubacteria, Aminicenantes, Acidobacteria

Planctomycetes Chlamydiae

Lentisphaerae Verrucomicrobia

Verrucomicrobia

RBX-1 WOR-1

Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes

Uncultured bacteria (CP RIF32)

Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres

Cloacamonetes

Atribacteria (OP9) BRC1, Poribacteria

Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06

ElusimicrobiaUncultured bacteria


Aigarchaeota, Cand. Caldiarchaeum subterraneum

Unclassified archaea

Parcubacteria

Candidate Phyla Radiation



Caldiserica, Dictyoglomiq ,q ,

ThermotogaeA ifi C


pp

Spirochaetes SpirochaetesS i h t


H d d t N

Epsilonproteobacteriab

TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres

Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria

D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey

LentisphaeraeC a yd Ch

Verrucomicrobia Verrucomicrobia

pp

RBX-1 WOR-1


Uncultured bacteria (CP RIF32), y g, y g


Cloacamonetes


( )Latescibacteria WS3

Gemmatimonadetes, WOR-3, TA06b M


Uncultured bacteria (CP RIF1)O h




MicrogenomatesMicrogenomates Curtissbacteria

ggMicrogenomates Daviesbacteria

gg


Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i

Microgenomates ShapirobacteriaMi t W bMi t

Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i

Microgenomates Gottesmanbacteriat R i b t i

g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria

Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a

ParcubacteriaParcubacteria

Parcubacteria

Parcubacteria AbscAbs

Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria

ggParcubacteriaParcubacteria Moranbacteria


P b i




Pacearchaeota


Woesearchaeota


Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43

Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,

Aciduliprofundum, Thermoplasmatagg

Uncultured Thermoplasmatap ,p ,

Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA

Cand. Caldiarchaeum subterraneum

C b t i M l i b t i

Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa

Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3

Bootstrap ≥ 85% 85% > Bootstrap ≥ 50%


Figure 2 | A reformatted view of the tree in Fig. 1 in which each major lineage represents the same amount of evolutionary distance. The threshold forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups to have special taxonomic status. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives(red dots) are apparent from this analysis. Bootstrap support values are indicated by circles on nodes—black for support of 85% and above, grey for supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat in Supplementary Dataset 2.

NATURE MICROBIOLOGY DOI: 10.1038/NMICROBIOL.2016.48 LETTERS

NATURE MICROBIOLOGY | www.nature.com/naturemicrobiology 3

© 2016 Macmillan Publishers Limited. All rights reserved

0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







bis2c: lecture 10 extras on "new view of the tree of life" paper

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