The need for a phylogeny driven genomic encyclopedia of eukaryotes #SMBEEuks
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This document discusses the need for a phylogeny-driven genomic encyclopedia of eukaryotes. It notes that current sources of information on sequenced eukaryotic genomes, such as Wikipedia and GOLD, are disorganized and lack phylogenetic context. The document then analyzes genomic data from the poorly studied protist Collodictyon using 18S and 28S ribosomal DNA sequencing and phylogenomic trees inferred from 124 genes. The analysis finds that Collodictyon is closely related to Diphylleia and occupies a very early divergence in the eukaryote tree of life, either alone or as the sister group to Malawimonas. This suggests Collodictyon represents an important new lineage for
![2010 PARFREY ET AL.—BROADLY SAMPLED TREE OF EUKARYOTIC LIFE 523
FIGURE 1. Most likely eukaryotic tree of life reconstructed using all 451 taxa and all 16 genes (SSU-rDNA plus 15 protein genes). Major
nodes in this topology are robust to analyses of subsets of taxa and genes, which include varying levels of missing data (Table 1). Clades in bold
are monophyletic in analyses with 2 or more members except in all:15 in which taxa represented by a single gene were sometimes misplaced.
Numbers in boxes represent support at key nodes in analyses with increasing amounts of missing data (10:16, 6:16, 4:16, and all:16 analyses; see
Table 1 for more details). Given uncertainties around the root of the eukaryotic tree of life (see text), we have chosen to draw the tree rooted with
the well-supported clade Opisthokonta. Dashed line indicates alternate branching pattern seen for Amoebozoa in other analyses. Long branches,
indicated by //, have been reduced by half. The 6 lineages labeled by * represent taxa that are misplaced, probably due to LBA, listed from
top to bottom with expected clade in parentheses. These are Protoopalina japonica (Stramenopiles), Aggregata octopiana (Apicomplexa), Mikrocytos
mackini (Haplosporidia), Centropyxis laevigata (Tubulinea), Marteilioides chungmuensis (unplaced), and Cochliopodium spiniferum (Amoebozoa).
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c The Author(s) 2010. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.
For Permissions, please email: journals.permissions@oxfordjournals.org
DOI:10.1093/sysbio/syq037
Advance Access publication on July 23, 2010
Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life
LAURA WEGENER PARFREY1
, JESSICA GRANT2
, YONAS I. TEKLE2,6
, ERICA LASEK-NESSELQUIST3,4
,
HILARY G. MORRISON3
, MITCHELL L. SOGIN3
, DAVID J. PATTERSON5
, AND LAURA A. KATZ1,2,∗
1Program in Organismic and Evolutionary Biology, University of Massachusetts, 611 North Pleasant Street, Amherst,
MA 01003, USA; 2Department of Biological Sciences, Smith College, 44 College Lane, Northampton, MA 01063, USA; 3Bay Paul Center for
Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA; 4Department of Ecology and
Evolutionary Biology, Brown University, 80 Waterman Street, Providence, RI 02912, USA; 5Biodiversity Informatics Group, Marine Biological
Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA; 6Present address: Department of Epidemiology and Public Health, Yale University School of
Medicine, New Haven, CT 06520, USA;
∗Correspondence to be sent to: Laura A. Katz, 44 College Lane, Northampton, MA 01003, USA; E-mail: lkatz@smith.edu.
Laura Wegener Parfrey and Jessica Grant have contributed equally to this work.
Received 30 September 2009; reviews returned 1 December 2009; accepted 25 May 2010
Associate Editor: C´ecile An´e
Abstract.—An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the
diversity of microbial and macroscopic (e.g., plants and animals) eukaryotes. Previous work has divided eukaryotic diver-
sity into a small number of high-level “supergroups,” many of which receive strong support in phylogenomic analyses.
However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due
to systematic phylogenetic error. Furthermore, the paucity of major eukaryotic lineages (19 or fewer) included in these
genomic studies may exaggerate systematic error and reduce power to evaluate hypotheses. Here, we use a taxon-rich
strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa
representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life.
The consistency across analyses with varying numbers of taxa (88–451) and levels of missing data (17–69%) supports the
accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes
or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these
analyses (e.g., SAR, Rhizaria, Excavata), whereas the proposed supergroup “Chromalveolata” is rejected. Furthermore, ex-
tensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene
transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary
relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxon-rich analy-
ses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support
(BS) in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data. [Excavata;
microbial eukaryotes; Rhizaria; supergroups; systematic error; taxon sampling.]
Perspectives on the structure of the eukaryotic tree
of life have shifted in the past decade as molecular
analyses provide hypotheses for relationships among
marks throughout to note groups where uncertaintie
remain. Moreover, it is difficult to evaluate the overal
stability of major clades of eukaryotes because phyloge
http://sysbio.oxfordjournals.org/content/59/5/518.full
Euks More Resolution
Monday, April 29, 13](https://image.slidesharecdn.com/smbetalk-130429102503-phpapp01/85/The-need-for-a-phylogeny-driven-genomic-encyclopedia-of-eukaryotes-SMBEEuks-11-320.jpg)
![Syst. Biol. 59(5):518–533, 2010
c The Author(s) 2010. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.
For Permissions, please email: journals.permissions@oxfordjournals.org
DOI:10.1093/sysbio/syq037
Advance Access publication on July 23, 2010
Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life
LAURA WEGENER PARFREY1
, JESSICA GRANT2
, YONAS I. TEKLE2,6
, ERICA LASEK-NESSELQUIST3,4
,
HILARY G. MORRISON3
, MITCHELL L. SOGIN3
, DAVID J. PATTERSON5
, AND LAURA A. KATZ1,2,∗
1Program in Organismic and Evolutionary Biology, University of Massachusetts, 611 North Pleasant Street, Amherst,
MA 01003, USA; 2Department of Biological Sciences, Smith College, 44 College Lane, Northampton, MA 01063, USA; 3Bay Paul Center for
Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA; 4Department of Ecology and
Evolutionary Biology, Brown University, 80 Waterman Street, Providence, RI 02912, USA; 5Biodiversity Informatics Group, Marine Biological
Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA; 6Present address: Department of Epidemiology and Public Health, Yale University School of
Medicine, New Haven, CT 06520, USA;
∗Correspondence to be sent to: Laura A. Katz, 44 College Lane, Northampton, MA 01003, USA; E-mail: lkatz@smith.edu.
Laura Wegener Parfrey and Jessica Grant have contributed equally to this work.
Received 30 September 2009; reviews returned 1 December 2009; accepted 25 May 2010
Associate Editor: C´ecile An´e
Abstract.—An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the
diversity of microbial and macroscopic (e.g., plants and animals) eukaryotes. Previous work has divided eukaryotic diver-
sity into a small number of high-level “supergroups,” many of which receive strong support in phylogenomic analyses.
However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due
to systematic phylogenetic error. Furthermore, the paucity of major eukaryotic lineages (19 or fewer) included in these
genomic studies may exaggerate systematic error and reduce power to evaluate hypotheses. Here, we use a taxon-rich
strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa
representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life.
The consistency across analyses with varying numbers of taxa (88–451) and levels of missing data (17–69%) supports the
accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes
or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these
analyses (e.g., SAR, Rhizaria, Excavata), whereas the proposed supergroup “Chromalveolata” is rejected. Furthermore, ex-
tensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene
transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary
relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxon-rich analy-
ses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support
(BS) in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data. [Excavata;
microbial eukaryotes; Rhizaria; supergroups; systematic error; taxon sampling.]
Perspectives on the structure of the eukaryotic tree
of life have shifted in the past decade as molecular
analyses provide hypotheses for relationships among
the approximately 75 robust lineages of eukaryotes.
These lineages are defined by ultrastructural identities
(Patterson 1999)—patterns of cellular and subcellular
organization revealed by electron microscopy—and are
strongly supported in molecular analyses (Parfrey et al.
2006; Yoon et al. 2008). Most of these lineages now
fall within a small number of higher level clades, the
supergroups of eukaryotes (Simpson and Roger 2004;
Adl et al. 2005; Keeling et al. 2005). Several of these
clades—Opisthokonta, Rhizaria, and Amoebozoa—
marks throughout to note groups where uncertainties
remain. Moreover, it is difficult to evaluate the overall
stability of major clades of eukaryotes because phyloge-
nomic analyses have 19 or fewer of the major lineages
and hence do not sufficiently sample eukaryotic diver-
sity (Rodr´ıguez-Ezpeleta et al. 2007b; Burki et al. 2008;
Hampl et al. 2009), whereas taxon-rich analyses with
4 or fewer genes yield topologies with poor support at
deep nodes (Cavalier-Smith 2004; Parfrey et al. 2006;
Yoon et al. 2008).
Estimating the relationships of the major lineages
of eukaryotes is difficult because of both the ancient
age of eukaryotes (1.2–1.8 billion years; Knoll et al.
SYSTEMATIC BIOLOGY VOL. 59
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FIGURE 5. Summary of major findings—the evolutionary relation-
ships among major lineages of eukaryotes. Clades have been collapsed
into those that we view to be strongly supported. The many poly-
tomies represent uncertainties that remain.
FUNDING
This work was made possible by the US National
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Euks More Resolution but Simpler
Monday, April 29, 13](https://image.slidesharecdn.com/smbetalk-130429102503-phpapp01/85/The-need-for-a-phylogeny-driven-genomic-encyclopedia-of-eukaryotes-SMBEEuks-12-320.jpg)
The need for a phylogeny driven genomic encyclopedia of eukaryotes #SMBEEuks
- 1. The Need for a Phylogeny-Driven Genomic Encyclopedia of Eukaryotes Jonathan A. Eisen @phylogenomics University of California, Davis Talk for SMBE-EUKS Monday, April 29, 13
- 2. I: The Problem Monday, April 29, 13
- 3. Googling Sequenced Eukaryotic Genomes Monday, April 29, 13
- 4. Wikipedia On Sequenced Euks Monday, April 29, 13
- 5. More from Wikipedia Monday, April 29, 13
- 6. Better Source: GOLD http://www.genomesonline.org/cgi-bin/GOLD/index.cgi Monday, April 29, 13
- 7. GOLD by Taxonomy http://www.genomesonline.org/cgi-bin/GOLD/index.cgi Monday, April 29, 13
- 8. GOLD: Euks by Phylum Phylum Count Percent Korarchaeota 1 0 Nanoarchaeota 2 0 Thaumarchaeota 30 5 Crenarchaeota 142 25 Euryarchaeota 356 64 Unclassified 28 5 Phylum Count Percent Caldiserica 1 0 Nitrospinae 1 0 Crenarchaeota 2 0 Chrysiogenetes 2 0 Dictyoglomi 2 0 Fibrobacteres 2 0 Armatimonadetes 3 0 Elusimicrobia 3 0 Lentisphaerae 3 0 Poribacteria 4 0 Gemmatimonadetes 6 0 Thermodesulfobacteria 7 0 Ignavibacteria 8 0 Deferribacteres 10 0 Chlorobi 14 0 Synergistetes 21 0 Euryarchaeota 23 0 Nitrospirae 24 0 Aquificae 24 0 Acidobacteria 30 0 Verrucomicrobia 41 0 Planctomycetes 42 0 Thermotogae 50 0 Chloroflexi 51 0 Fusobacteria 80 0 Deinococcus-Thermus 92 0 Chlamydiae 207 1 Cyanobacteria 245 1 Tenericutes 251 1 Spirochaetes 472 2 Bacteroidetes 762 4 Actinobacteria 2,065 10 Firmicutes 5,342 26 Proteobacteria 10,088 50 Unclassified 17 0 Phylum Count Percent Phaeophyceae 1 0 Priapulida 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 Unclassified 704 13 Back to GOLD bution Percent 0 0 0 0 0 0 0 Eukaryotic Phylum Distribution Phylum Count Percent Phaeophyceae 1 0 Priapulida 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 18/18 Family: 30/29 Genus: 103/118 Species: 340/673 24/118 Family: 280/298 Genus: 1368/2106 Species: 6352/11424 0/1037 Family: 689/6689 Genus: 1170/54319 Species: 1769/218222 jects over number of the classified subdivisions of this phylogenetic group. http://www.genomesonline.org/cgi-bin/GOLD/index.cgi Monday, April 29, 13
- 9. GOLD: Euks by Phylum Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 Monday, April 29, 13
- 10. Euks More Resolution 0.2 Bodomorpha minima Lumbricus rubellus Diplophrys BOLA458 Chaunacanthida sp. Labyrinthuloides minuta Filamoeba nolandi Chlamydaster sterni RT7iin2 Phalansterium solitarium Euglena gracilis RT5iin20 BOLA383 Ulkenia profunda LEMD267 Ammonia sp. Oxymonas sp. DH148EKB1 Diplonema ambulator Minchinia teredinis Pavlova salina Glaucosphaera vacuolata Cyanoptyche gloeocystis OLI11305 Gromia oviformis Cryptosporidium parvum Breviata anathema Achlya bisexualis LEMD052 Phagomyxa odontellae Raphidiophrys ambigua Compsopogon coeruleus BOLA212 Colpodella pontica Uncultured eukaryote clone BOLA187 Jakoba libera RT5iin2 CS.E036 Acrosphaera sp. CR6A Acanthamoeba castellanii AT1.3 Saccharomyces cerevisiae OLI11150 Nuclearia simplex RA000412.136 TCS 2002 BOLA868 Allogromia sp. Monosiga brevicollis RT5iin4 Plasmodiophora brassicae RT5iin8 OLI51105 RA010412.17 BOLA515 OLI11032 RT 5iin25 AT4.11 Symphyacanthida RT5iin44 CS.E045 Urosporidium crescens Goniomonas truncata Gymnophrys cometa Podocoryne carnea OLI11066 Reclinomonas americana Reticulomyxa filosa RT8n7 Oxytricha nova AT4.50 C1.E027 Arthracanthida sp. RT1n14cul AT4.94 Telonema antarcticum OLI11025 LKM30 LKM48 Filobasidiella neoformans DH147EKD17 Mayorella sp. C2.E026 Bacillaria paxillifer Retortamonas sp. OLI11059 Malawimonas jakobiformis BOLA048 Streblomastix strix Guillardia theta Platyamoeba stenopodia DH148EKD18 Cafeteria roenbergensis Telonema subtilis RCC404.5 DH148EKD53 LKM74 Ciliophrys infusionum Scherffelia dubia Volvox carteri CS.R003 Trypanosoma cruzi BL010625.25 AT4.56 N-Por Jakoba incarcerata Sphaerozoum punctatum Uncultured eukaryote clone BOLA366 Lecythium sp. Acanthometra sp. Loxophyllum utriculare LKM101 Glaucocystis nostochinearum OLI11056 BAQA072 Apusomonas proboscidea Trimastix marina C3.E012 Helianthus annuus AT8.54 Ichthyobodo necator CS.E022 RA001219.10 RT5in38 Paravahlkampfia ustiana OLI11007 Telonema subtilis RCC358.7 Amastigomonas debruynei Emiliania huxleyi Leptomyxa reticulata Hartmannella vermiformis OLI11072 DH145EKD11 Noctiluca scintillans Cyanophora paradoxa Trimastix pyriformis Naegleria gruberi AT 4.96 Amoeba proteus Gonyaulax spinifera sp. 0.99/68 0.89/-0.40/- 0.87/- 0.88/- 0.88/- 0.84/- 0.78/59 0.66/61 0.55/- 0.89/- Collodictyon triciliatum Diphylleia rotans Uncultured Collodictyonidae partial 1.0/77 -/84 1.0/63 1.0/56 0.99/- 1.0/- 0.96/- 0.99/- 0.95/- 0.99/- 0.99/68 1.0/63 1.0/62 0.69/- 0.63/- 0.83/- 0.79/75 0.69/57 0.79/- 0.87/- 0.59/- 0.68/- 1.0/- 0.57/50 0.63/- 1.0/78 0.53/- SAR Excavata Diphyllatia Amoebozoa Opisthokonta 0.53/76 0.73/- 0.81/- 0.84/- -/- 0.63/- 0.79/- 0.81/- 0.70/- 0.98/- 1.0/74 0.51/- -/- -/- Haptophyta Telonemia Apusozoa Centrohelida Cryptophyta Rhodophyta Glaucophyta Viridiplantae FIG. 1. 18S rDNA phylogeny of the Diphyllatia species Collodictyon triciliatum (highlighted by black box) and Diphylleia rotans. The topology was reconstructed by MrBayes v3.1.2 under the GTR þ GAMMA þ I þ covarion model. Posterior probabilities (PP) and ML bootstrap supports (BP, inferred by RAxML v7.1.2 under GTR þ GAMMA þ I model) are shown at the nodes. Thick lines indicate PP . 0.90 and BP . 80%. Dashes ‘‘-’’ indicate PP , 0.5 or BP , 50%. A few long branches are shortened by 50% (/) or 75% (//). Zhao et al. · doi:10.1093/molbev/mss001 MBE 1560 byguestonApril28,2013http://mbe.oxfordjournals.org/Downloadedfrom Collodictyon—An Ancient Lineage in the Tree of Eukaryotes Sen Zhao, ,1 Fabien Burki, ,2 Jon Bra˚te,1 Patrick J. Keeling,2 Dag Klaveness,1 and Kamran Shalchian-Tabrizi*,1 1 Microbial Evolution Research Group, Department of Biology, University of Oslo, Oslo, Norway 2 Canadian Institute for Advanced Research, Botany Department, University of British Columbia, Vancouver, British Columbia, Canada These authors contributed equally to this work. *Corresponding author: E-mail: kamran@bio.uio.no. Associate editor: Herve´ Philippe Abstract The current consensus for the eukaryote tree of life consists of several large assemblages (supergroups) that are hypothesized to describe the existing diversity. Phylogenomic analyses have shed light on the evolutionary relationships within and between supergroups as well as placed newly sequenced enigmatic species close to known lineages. Yet, a few eukaryote species remain of unknown origin and could represent key evolutionary forms for inferring ancient genomic and cellular characteristics of eukaryotes. Here, we investigate the evolutionary origin of the poorly studied protist Collodictyon (subphylum Diphyllatia) by sequencing a cDNA library as well as the 18S and 28S ribosomal DNA (rDNA) genes. Phylogenomic trees inferred from 124 genes placed Collodictyon close to the bifurcation of the ‘‘unikont’’ and ‘‘bikont’’ groups, either alone or as sister to the potentially contentious excavate Malawimonas. Phylogenies based on rDNA genes confirmed that Collodictyon is closely related to another genus, Diphylleia, and revealed a very low diversity in environmental DNA samples. The early and distinct origin of Collodictyon suggests that it constitutes a new lineage in the global eukaryote phylogeny. Collodictyon shares cellular characteristics with Excavata and Amoebozoa, such as ventral feeding groove supported by microtubular structures and the ability to form thin and broad pseudopods. These may therefore be ancient morphological features among eukaryotes. Overall, this shows that Collodictyon is a key lineage to understand early eukaryote evolution. Key words: 18S and 28S rDNA, Collodictyon, Diphyllatia, tree of life, phylogenomics, cDNA, pyrosequencing. Introduction Over the last few years, molecular sequence data have ad- dressed some of the most intriguing questions about the eukaryote tree of life. Phylogenomic analyses have con- firmed the existence of several major eukaryote groups (supergroups) as well as shown various levels of evidences for the relationships among them (Burki et al. 2007; Parfrey et al. 2010). Recently, two new large assemblages, SAR (Stramenopila, Alveolata, and Rhizaria) and CCTH (Crypto- phyta, Centrohelida, Telonemia, and Haptophyta), were proposed to encompass a large fraction of the eukaryote diversity, together with the other supergroups Opisthokon- ta, Amoebozoa, Archaeplastida, and Excavata (Patron et al. 2007; Burki et al. 2009). Solid phylogenomic evidence and complex genome histories (Simpson and Roger 2004; Parfrey et al. 2006; Roger and Simpson 2009). Identification of sister lineages to these supergroups is crucial for resolving the eukaryote tree and understanding the early history of eukaryotes. If these key lineages exist, they may be found among the few species that harbor dis- tinct morphological features but are of unknown evolu- tionary origin in single-gene phylogenies (Patterson 1999; Shalchian-Tabrizi et al. 2006; Kim et al. 2011). Indications that such enigmatic species can be placed in the eukaryote tree come from recent phylogenomic analyses. For in- stance, Ministeria (Opisthokonta), Breviata (Amoebozoa) and Telonemia, Centroheliozoa, and Picobiliphyta have been shown to constitute deep lineages within their re- ResearcharticlebyguestonApril28,2013http://mbe.oxfordjournals.org/Downloadedfrom http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351787/ Monday, April 29, 13
- 11. 2010 PARFREY ET AL.—BROADLY SAMPLED TREE OF EUKARYOTIC LIFE 523 FIGURE 1. Most likely eukaryotic tree of life reconstructed using all 451 taxa and all 16 genes (SSU-rDNA plus 15 protein genes). Major nodes in this topology are robust to analyses of subsets of taxa and genes, which include varying levels of missing data (Table 1). Clades in bold are monophyletic in analyses with 2 or more members except in all:15 in which taxa represented by a single gene were sometimes misplaced. Numbers in boxes represent support at key nodes in analyses with increasing amounts of missing data (10:16, 6:16, 4:16, and all:16 analyses; see Table 1 for more details). Given uncertainties around the root of the eukaryotic tree of life (see text), we have chosen to draw the tree rooted with the well-supported clade Opisthokonta. Dashed line indicates alternate branching pattern seen for Amoebozoa in other analyses. Long branches, indicated by //, have been reduced by half. The 6 lineages labeled by * represent taxa that are misplaced, probably due to LBA, listed from top to bottom with expected clade in parentheses. These are Protoopalina japonica (Stramenopiles), Aggregata octopiana (Apicomplexa), Mikrocytos mackini (Haplosporidia), Centropyxis laevigata (Tubulinea), Marteilioides chungmuensis (unplaced), and Cochliopodium spiniferum (Amoebozoa). byguestonApril28,2013http://sysbio.oxfordjournals.org/Downloadedfrom Syst. Biol. 59(5):518–533, 2010 c The Author(s) 2010. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org DOI:10.1093/sysbio/syq037 Advance Access publication on July 23, 2010 Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life LAURA WEGENER PARFREY1 , JESSICA GRANT2 , YONAS I. TEKLE2,6 , ERICA LASEK-NESSELQUIST3,4 , HILARY G. MORRISON3 , MITCHELL L. SOGIN3 , DAVID J. PATTERSON5 , AND LAURA A. KATZ1,2,∗ 1Program in Organismic and Evolutionary Biology, University of Massachusetts, 611 North Pleasant Street, Amherst, MA 01003, USA; 2Department of Biological Sciences, Smith College, 44 College Lane, Northampton, MA 01063, USA; 3Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA; 4Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, RI 02912, USA; 5Biodiversity Informatics Group, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA; 6Present address: Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06520, USA; ∗Correspondence to be sent to: Laura A. Katz, 44 College Lane, Northampton, MA 01003, USA; E-mail: lkatz@smith.edu. Laura Wegener Parfrey and Jessica Grant have contributed equally to this work. Received 30 September 2009; reviews returned 1 December 2009; accepted 25 May 2010 Associate Editor: C´ecile An´e Abstract.—An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g., plants and animals) eukaryotes. Previous work has divided eukaryotic diver- sity into a small number of high-level “supergroups,” many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Furthermore, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduce power to evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life. The consistency across analyses with varying numbers of taxa (88–451) and levels of missing data (17–69%) supports the accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these analyses (e.g., SAR, Rhizaria, Excavata), whereas the proposed supergroup “Chromalveolata” is rejected. Furthermore, ex- tensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxon-rich analy- ses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support (BS) in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data. [Excavata; microbial eukaryotes; Rhizaria; supergroups; systematic error; taxon sampling.] Perspectives on the structure of the eukaryotic tree of life have shifted in the past decade as molecular analyses provide hypotheses for relationships among marks throughout to note groups where uncertaintie remain. Moreover, it is difficult to evaluate the overal stability of major clades of eukaryotes because phyloge http://sysbio.oxfordjournals.org/content/59/5/518.full Euks More Resolution Monday, April 29, 13
- 12. Syst. Biol. 59(5):518–533, 2010 c The Author(s) 2010. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org DOI:10.1093/sysbio/syq037 Advance Access publication on July 23, 2010 Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life LAURA WEGENER PARFREY1 , JESSICA GRANT2 , YONAS I. TEKLE2,6 , ERICA LASEK-NESSELQUIST3,4 , HILARY G. MORRISON3 , MITCHELL L. SOGIN3 , DAVID J. PATTERSON5 , AND LAURA A. KATZ1,2,∗ 1Program in Organismic and Evolutionary Biology, University of Massachusetts, 611 North Pleasant Street, Amherst, MA 01003, USA; 2Department of Biological Sciences, Smith College, 44 College Lane, Northampton, MA 01063, USA; 3Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA; 4Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, RI 02912, USA; 5Biodiversity Informatics Group, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA; 6Present address: Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06520, USA; ∗Correspondence to be sent to: Laura A. Katz, 44 College Lane, Northampton, MA 01003, USA; E-mail: lkatz@smith.edu. Laura Wegener Parfrey and Jessica Grant have contributed equally to this work. Received 30 September 2009; reviews returned 1 December 2009; accepted 25 May 2010 Associate Editor: C´ecile An´e Abstract.—An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g., plants and animals) eukaryotes. Previous work has divided eukaryotic diver- sity into a small number of high-level “supergroups,” many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Furthermore, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduce power to evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life. The consistency across analyses with varying numbers of taxa (88–451) and levels of missing data (17–69%) supports the accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these analyses (e.g., SAR, Rhizaria, Excavata), whereas the proposed supergroup “Chromalveolata” is rejected. Furthermore, ex- tensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxon-rich analy- ses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support (BS) in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data. [Excavata; microbial eukaryotes; Rhizaria; supergroups; systematic error; taxon sampling.] Perspectives on the structure of the eukaryotic tree of life have shifted in the past decade as molecular analyses provide hypotheses for relationships among the approximately 75 robust lineages of eukaryotes. These lineages are defined by ultrastructural identities (Patterson 1999)—patterns of cellular and subcellular organization revealed by electron microscopy—and are strongly supported in molecular analyses (Parfrey et al. 2006; Yoon et al. 2008). Most of these lineages now fall within a small number of higher level clades, the supergroups of eukaryotes (Simpson and Roger 2004; Adl et al. 2005; Keeling et al. 2005). Several of these clades—Opisthokonta, Rhizaria, and Amoebozoa— marks throughout to note groups where uncertainties remain. Moreover, it is difficult to evaluate the overall stability of major clades of eukaryotes because phyloge- nomic analyses have 19 or fewer of the major lineages and hence do not sufficiently sample eukaryotic diver- sity (Rodr´ıguez-Ezpeleta et al. 2007b; Burki et al. 2008; Hampl et al. 2009), whereas taxon-rich analyses with 4 or fewer genes yield topologies with poor support at deep nodes (Cavalier-Smith 2004; Parfrey et al. 2006; Yoon et al. 2008). Estimating the relationships of the major lineages of eukaryotes is difficult because of both the ancient age of eukaryotes (1.2–1.8 billion years; Knoll et al. SYSTEMATIC BIOLOGY VOL. 59 uded all lin- s additional study (Table rted, though ed: i) Cerco- Acantharea adiolarians), Plasmodio- Fig. 3; Bass a nematode- lid amoebae r to the plant e SSU-rDNA amoeba iso- as Arachnula nsistent with trastructural contaminant omastix strix 6). Excavata ause Malaw- of Excavata et al. 2009), avata mem- 2006; Simp- ests robustly not have a independent tephanopogon hin Heterolo- Yubuki and igmatic flag- inia anisocys- m this study on sampling nalyses pro- d representa- mbined with FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed into those that we view to be strongly supported. The many poly- tomies represent uncertainties that remain. FUNDING This work was made possible by the US National byguestonApril28,2013http://sysbio.oxfordjournals.org/Downloadedfrom http://sysbio.oxfordjournals.org/content/59/5/518.full Euks More Resolution but Simpler Monday, April 29, 13
- 13. Mapping GOLD to Tree Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed included all lin- a plus additional this study (Table esolved: i) Cerco- as radiolarians), and Plasmodio- Bass a nematode- pyrellid amoebae sister to the plant to an amoeba iso- Arachnula th ultrastructural hen contaminant ). Excavata Malaw- ), s Excavata mem- Simp- t an independent within Heterolo- er enigmatic flag- Soginia anisocys- Monday, April 29, 13
- 14. Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed included all lin- a plus additional this study (Table esolved: i) Cerco- as radiolarians), and Plasmodio- Bass a nematode- pyrellid amoebae sister to the plant to an amoeba iso- Arachnula th ultrastructural hen contaminant ). Excavata Malaw- ), s Excavata mem- Simp- t an independent within Heterolo- er enigmatic flag- Soginia anisocys- Mapping GOLD to Tree Monday, April 29, 13
- 15. Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed included all lin- a plus additional this study (Table esolved: i) Cerco- as radiolarians), and Plasmodio- Bass a nematode- pyrellid amoebae sister to the plant to an amoeba iso- Arachnula th ultrastructural hen contaminant ). Excavata Malaw- ), s Excavata mem- Simp- t an independent within Heterolo- er enigmatic flag- Soginia anisocys- Fungi 49% Mapping GOLD to Tree Monday, April 29, 13
- 16. Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed included all lin- a plus additional this study (Table esolved: i) Cerco- as radiolarians), and Plasmodio- Bass a nematode- pyrellid amoebae sister to the plant to an amoeba iso- Arachnula th ultrastructural hen contaminant ). Excavata Malaw- ), s Excavata mem- Simp- t an independent within Heterolo- er enigmatic flag- Soginia anisocys- Mapping GOLD to Tree Monday, April 29, 13
- 17. Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed included all lin- a plus additional this study (Table esolved: i) Cerco- as radiolarians), and Plasmodio- Bass a nematode- pyrellid amoebae sister to the plant to an amoeba iso- Arachnula th ultrastructural hen contaminant ). Excavata Malaw- ), s Excavata mem- Simp- t an independent within Heterolo- er enigmatic flag- Soginia anisocys- Mapping GOLD to Tree Monday, April 29, 13
- 18. Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed included all lin- a plus additional this study (Table esolved: i) Cerco- as radiolarians), and Plasmodio- Bass a nematode- pyrellid amoebae sister to the plant to an amoeba iso- Arachnula th ultrastructural hen contaminant ). Excavata Malaw- ), s Excavata mem- Simp- t an independent within Heterolo- er enigmatic flag- Soginia anisocys- Animals 26% Mapping GOLD to Tree Monday, April 29, 13
- 19. Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed included all lin- a plus additional this study (Table esolved: i) Cerco- as radiolarians), and Plasmodio- Bass a nematode- pyrellid amoebae sister to the plant to an amoeba iso- Arachnula th ultrastructural hen contaminant ). Excavata Malaw- ), s Excavata mem- Simp- t an independent within Heterolo- er enigmatic flag- Soginia anisocys- Mapping GOLD to Tree Monday, April 29, 13
- 20. Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed included all lin- a plus additional this study (Table esolved: i) Cerco- as radiolarians), and Plasmodio- Bass a nematode- pyrellid amoebae sister to the plant to an amoeba iso- Arachnula th ultrastructural hen contaminant ). Excavata Malaw- ), s Excavata mem- Simp- t an independent within Heterolo- er enigmatic flag- Soginia anisocys- Mapping GOLD to Tree Monday, April 29, 13
- 21. Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed included all lin- a plus additional this study (Table esolved: i) Cerco- as radiolarians), and Plasmodio- Bass a nematode- pyrellid amoebae sister to the plant to an amoeba iso- Arachnula th ultrastructural hen contaminant ). Excavata Malaw- ), s Excavata mem- Simp- t an independent within Heterolo- er enigmatic flag- Soginia anisocys- Green algae 19% Mapping GOLD to Tree Monday, April 29, 13
- 22. Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed included all lin- a plus additional this study (Table esolved: i) Cerco- as radiolarians), and Plasmodio- Bass a nematode- pyrellid amoebae sister to the plant to an amoeba iso- Arachnula th ultrastructural hen contaminant ). Excavata Malaw- ), s Excavata mem- Simp- t an independent within Heterolo- er enigmatic flag- Soginia anisocys- Mapping GOLD to Tree Monday, April 29, 13
- 23. Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed included all lin- a plus additional this study (Table esolved: i) Cerco- as radiolarians), and Plasmodio- Bass a nematode- pyrellid amoebae sister to the plant to an amoeba iso- Arachnula th ultrastructural hen contaminant ). Excavata Malaw- ), s Excavata mem- Simp- t an independent within Heterolo- er enigmatic flag- Soginia anisocys- Mapping GOLD to Tree Monday, April 29, 13
- 24. Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed included all lin- a plus additional this study (Table esolved: i) Cerco- as radiolarians), and Plasmodio- Bass a nematode- pyrellid amoebae sister to the plant to an amoeba iso- Arachnula th ultrastructural hen contaminant ). Excavata Malaw- ), s Excavata mem- Simp- t an independent within Heterolo- er enigmatic flag- Soginia anisocys- Apicomplexa 5% Mapping GOLD to Tree Monday, April 29, 13
- 25. Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed included all lin- a plus additional this study (Table esolved: i) Cerco- as radiolarians), and Plasmodio- Bass a nematode- pyrellid amoebae sister to the plant to an amoeba iso- Arachnula th ultrastructural hen contaminant ). Excavata Malaw- ), s Excavata mem- Simp- t an independent within Heterolo- er enigmatic flag- Soginia anisocys- A Very Biased Sampling Monday, April 29, 13
- 26. Solution to Biased Sampling? Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed included all lin- a plus additional this study (Table esolved: i) Cerco- as radiolarians), and Plasmodio- Bass a nematode- pyrellid amoebae sister to the plant to an amoeba iso- Arachnula th ultrastructural hen contaminant ). Excavata Malaw- ), s Excavata mem- Simp- t an independent within Heterolo- er enigmatic flag- Soginia anisocys- Monday, April 29, 13
- 27. Solution: Fill in the Tree Priapulida 1 0 Phaeophyceae 1 0 Rotifera 1 0 Hemichordata 1 0 Pinguiophyceae 1 0 Ctenophora 1 0 Bolidophyceae 1 0 Chaetognatha 1 0 Porifera 2 0 Xanthophyceae 2 0 Tardigrada 2 0 Euglenida 2 0 Chromerida 3 0 Placozoa 3 0 Glomeromycota 3 0 Cryptomycota 4 0 Blastocladiomycota 5 0 Echinodermata 6 0 Entomophthoromycota 9 0 Chytridiomycota 12 0 Neocallimastigomycota 12 0 Annelida 13 0 Eustigmatophyceae 13 0 Cnidaria 18 0 Bacillariophyta 21 0 Platyhelminthes 23 0 Mollusca 25 0 Microsporidia 31 1 Chlorophyta 77 1 Nematoda 110 2 Apicomplexa 264 5 Arthropoda 370 7 Chordata 626 12 Streptophyta 796 15 Basidiomycota 976 18 Ascomycota 1,251 23 530 SYSTEMATIC BIOLOGY VOL. 59 a 97-taxon data set of Rhizaria that included all lin- eages with previously published data plus additional multigene data for 12 taxa added for this study (Table S1). Three major clades are strongly supported, though the relationships among them are unresolved: i) Cerco- zoa, ii) Foraminifera plus Polycystinea and Acantharea (formerly classified with Phaeodarea as radiolarians), and (iii) the parasitic Haplosporidia and Plasmodio- phorida with Gromia and vampyrellids (Fig. 3; Bass et al. 2009). We show that Theratromyxa, a nematode- eating soil amoeba, is related to vampyrellid amoebae (Fig. 3; 100% BS), and together they are sister to the plant parasites plasmodiophorids (100% BS). The SSU-rDNA sequence for Theratromyxa is identical to an amoeba iso- lated from Siberia where it was identified as Arachnula impatiens (EU567294; Bass et al. 2009). The topology within the Excavata is consistent with previous hypotheses and clades with ultrastructural identities (Simpson 2003; Fig. 4), when contaminant EST data originally mislabeled as Streblomastix strix are excluded (Slamovits and Keeling 2006). Excavata is often polyphyletic in other analyses because Malaw- imonas branches outside the other clades of Excavata (Rodr´ıguez-Ezpeleta et al. 2007a; Hampl et al. 2009), whereas in analyses of fewer genes Excavata mem- bers fall into 2 or 3 clades (Parfrey et al. 2006; Simp- son et al. 2006). Although Malawimonas nests robustly within Excavata in our analyses, it does not have a stable sister group and may represent an independent lineage (Fig. 4). Our analyses confirm that Stephanopogon (unplaced in Patterson 1999) branches within Heterolo- bosea (Cavalier-Smith and Nikolaev 2008; Yubuki and Leander 2008) and suggests that another enigmatic flag- ellate, ATCC 50646 (tentatively named Soginia anisocys- tis) is a basal member of Heterolobosea. FIGURE 5. Summary of major findings—the evolutionary relation- ships among major lineages of eukaryotes. Clades have been collapsed SYSTEMATIC BIOLOGY included all lin- a plus additional this study (Table upported, though esolved: i) Cerco- a and Acantharea as radiolarians), and Plasmodio- lids (Fig. 3; Bass yxa, a nematode- pyrellid amoebae sister to the plant ). The SSU-rDNA to an amoeba iso- ified as Arachnula is consistent with th ultrastructural hen contaminant Streblomastix strix g 2006). Excavata s because Malaw- ades of Excavata ampl et al. 2009), s Excavata mem- et al. 2006; Simp- nas nests robustly does not have a t an independent hat Stephanopogon within Heterolo- 2008; Yubuki and er enigmatic flag- d Soginia anisocys- a. FI G U R E 5. Summary of major findings ships among major lineages of eukaryotes.Monday, April 29, 13
- 28. II: Filling in the Tree Example Monday, April 29, 13
- 29. Big Microbial Sequencing Projects • Coordinated, top-down efforts • Fungal Genome Initiative (Broad/Whitehead) • Gordon and Betty Moore Foundation Marine Microbial Genome Sequencing Project • Sanger Center Pathogen Sequencing Unit • NHGRI Human Gut Microbiome Project • NIH Human Microbiome Program • White paper or grant systems • NIAID Microbial Sequencing Centers • DOE/JGI Community Sequencing Program • DOE/JGI BER Sequencing Program • NSF/USDA Microbial Genome Sequencing • Covers lots of ground and biological diversity Monday, April 29, 13
- 30. As of 2002 Monday, April 29, 13
- 31. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 32. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 33. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 34. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 35. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 36. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled • Solution I: sequence more phyla • NSF-funded Tree of Life Project • A genome from each of eight phyla Eisen, Ward, Robb, Nelson, et al Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 37. Phylum Species selected Chrysiogenes Chrysiogenes arsenatis (GCA) Coprothermobacter Coprothermobacter proteolyticus (GCBP) Dictyoglomi Dictyoglomus thermophilum (GD T ) Thermodesulfobacteria Thermodesulfobacterium commune (GTC) Nitrospirae Thermodesulfovibrio yellowstonii (GTY) Thermomicrobia Thermomicrobium roseum (GTR ) Deferribacteres Geovibrio thiophilus (GGT) Synergistes Synergistes jonesii (GSJ) Organisms Selected Monday, April 29, 13
- 38. Monday, April 29, 13
- 39. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled • Still highly biased in terms of the tree • NSF-funded Tree of Life Project • A genome from each of eight phyla Eisen & Ward, PIs Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 40. Major Lineages of Actinobacteria 2.5.1 Acidimicrobidae 2.5.1.1 Unclassified 2.5.1.2 "Microthrixineae 2.5.1.3 Acidimicrobineae 2.5.1.4 BD2-10 2.5.1.5 EB1017 2.5.2 Actinobacteridae 2.5.2.1 Unclassified 2.5.2.10 Ellin306/WR160 2.5.2.11 Ellin5012 2.5.2.12 Ellin5034 2.5.2.13 Frankineae 2.5.2.14 Glycomyces 2.5.2.15 Intrasporangiaceae 2.5.2.16 Kineosporiaceae 2.5.2.17 Microbacteriaceae 2.5.2.18 Micrococcaceae 2.5.2.19 Micromonosporaceae 2.5.2.2 Actinomyces 2.5.2.20 Propionibacterineae 2.5.2.21 Pseudonocardiaceae 2.5.2.22 Streptomycineae 2.5.2.23 Streptosporangineae 2.5.2.3 Actinomycineae 2.5.2.4 Actinosynnemataceae 2.5.2.5 Bifidobacteriaceae 2.5.2.6 Brevibacteriaceae 2.5.2.7 Cellulomonadaceae 2.5.2.8 Corynebacterineae 2.5.2.9 Dermabacteraceae 2.5.3 Coriobacteridae 2.5.3.1 Unclassified 2.5.3.2 Atopobiales 2.5.3.3 Coriobacteriales 2.5.3.4 Eggerthellales 2.5.4 OPB41 2.5.5 PK1 2.5.6 Rubrobacteridae 2.5.6.1 Unclassified 2.5.6.2 "Thermoleiphilaceae 2.5.6.3 MC47 2.5.6.4 Rubrobacteraceae 2.5 Actinobacteria 2.5.1 Acidimicrobidae 2.5.1.1 Unclassified 2.5.1.2 "Microthrixineae 2.5.1.3 Acidimicrobineae 2.5.1.3.1 Unclassified 2.5.1.3.2 Acidimicrobiaceae 2.5.1.4 BD2-10 2.5.1.5 EB1017 2.5.2 Actinobacteridae 2.5.2.1 Unclassified 2.5.2.10 Ellin306/WR160 2.5.2.11 Ellin5012 2.5.2.12 Ellin5034 2.5.2.13 Frankineae 2.5.2.13.1 Unclassified 2.5.2.13.2 Acidothermaceae 2.5.2.13.3 Ellin6090 2.5.2.13.4 Frankiaceae 2.5.2.13.5 Geodermatophilaceae 2.5.2.13.6 Microsphaeraceae 2.5.2.13.7 Sporichthyaceae 2.5.2.14 Glycomyces 2.5.2.15 Intrasporangiaceae 2.5.2.15.1 Unclassified 2.5.2.15.2 Dermacoccus 2.5.2.15.3 Intrasporangiaceae 2.5.2.16 Kineosporiaceae 2.5.2.17 Microbacteriaceae 2.5.2.17.1 Unclassified 2.5.2.17.2 Agrococcus 2.5.2.17.3 Agromyces 2.5.2.18 Micrococcaceae 2.5.2.19 Micromonosporaceae 2.5.2.2 Actinomyces 2.5.2.20 Propionibacterineae 2.5.2.20.1 Unclassified 2.5.2.20.2 Kribbella 2.5.2.20.3 Nocardioidaceae 2.5.2.20.4 Propionibacteriaceae 2.5.2.21 Pseudonocardiaceae 2.5.2.22 Streptomycineae 2.5.2.22.1 Unclassified 2.5.2.22.2 Kitasatospora 2.5.2.22.3 Streptacidiphilus 2.5.2.23 Streptosporangineae 2.5.2.23.1 Unclassified 2.5.2.23.2 Ellin5129 2.5.2.23.3 Nocardiopsaceae 2.5.2.23.4 Streptosporangiaceae 2.5.2.23.5 Thermomonosporaceae 2.5.2.3 Actinomycineae 2.5.2.4 Actinosynnemataceae 2.5.2.5 Bifidobacteriaceae 2.5.2.6 Brevibacteriaceae 2.5.2.7 Cellulomonadaceae 2.5.2.8 Corynebacterineae 2.5.2.8.1 Unclassified 2.5.2.8.2 Corynebacteriaceae 2.5.2.8.3 Dietziaceae 2.5.2.8.4 Gordoniaceae 2.5.2.8.5 Mycobacteriaceae 2.5.2.8.6 Rhodococcus 2.5.2.8.7 Rhodococcus 2.5.2.8.8 Rhodococcus 2.5.2.9 Dermabacteraceae 2.5.2.9.1 Unclassified 2.5.2.9.2 Brachybacterium 2.5.2.9.3 Dermabacter 2.5.3 Coriobacteridae 2.5.3.1 Unclassified 2.5.3.2 Atopobiales 2.5.3.3 Coriobacteriales 2.5.3.4 Eggerthellales 2.5.4 OPB41 2.5.5 PK1 2.5.6 Rubrobacteridae 2.5.6.1 Unclassified 2.5.6.2 "Thermoleiphilaceae 2.5.6.2.1 Unclassified 2.5.6.2.2 Conexibacter 2.5.6.2.3 XGE514 2.5.6.3 MC47 2.5.6.4 Rubrobacteraceae Monday, April 29, 13
- 41. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled • Same trend in Archaea • NSF-funded Tree of Life Project • A genome from each of eight phyla Eisen & Ward, PIs Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 42. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled • Same trend in Eukaryotes • NSF-funded Tree of Life Project • A genome from each of eight phyla Eisen & Ward, PIs Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 43. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled • Same trend in Viruses • NSF-funded Tree of Life Project • A genome from each of eight phyla Eisen & Ward, PIs Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 44. • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled • Solution: Really Fill in the Trees Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 45. Filling in the Tree Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Monday, April 29, 13
- 46. Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Filling in the Tree Monday, April 29, 13
- 47. Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Filling in the Tree Monday, April 29, 13
- 48. Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Filling in the Tree Monday, April 29, 13
- 49. Lots of Plants, Animals, Fungi Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Monday, April 29, 13
- 50. Exclude Plants, Animals, Fungi Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Monday, April 29, 13
- 51. A Genomic Encyclopedia of Microbes (GEM) Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Monday, April 29, 13
- 52. Just Say No to Eukaryotes Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Monday, April 29, 13
- 53. GEBA: A Genomic Encyclopedia of Bacteria and Archaea Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Monday, April 29, 13
- 54. GEBA Monday, April 29, 13
- 55. GEBA Pilot Project: Components • Project overview (Phil Hugenholtz, Nikos Kyrpides, Jonathan Eisen, Eddy Rubin, Jim Bristow) • Project management (David Bruce, Eileen Dalin, Lynne Goodwin) • Culture collection and DNA prep (DSMZ, Hans-Peter Klenk) • Sequencing and closure (Eileen Dalin, Susan Lucas, Alla Lapidus, Mat Nolan, Alex Copeland, Cliff Han, Feng Chen, Jan-Fang Cheng) • Annotation and data release (Nikos Kyrpides, Victor Markowitz, et al) • Analysis (Dongying Wu, Kostas Mavrommatis, Martin Wu, Victor Kunin, Neil Rawlings, Ian Paulsen, Patrick Chain, Patrik D’Haeseleer, Sean Hooper, Iain Anderson, Amrita Pati, Natalia N. Ivanova, Athanasios Lykidis, Adam Zemla) • Adopt a microbe education project (Cheryl Kerfeld) • Outreach (David Gilbert) • $$$ (DOE, Eddy Rubin, Jim Bristow) Monday, April 29, 13
- 56. rRNA Tree of Life FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Monday, April 29, 13
- 57. rRNA Tree of BA FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Monday, April 29, 13
- 58. GreenGenes Monday, April 29, 13
- 59. Monday, April 29, 13
- 60. DSMZ Monday, April 29, 13
- 61. Monday, April 29, 13
- 62. GEBA Pilot Project Overview • Identify major branches in rRNA tree for which no genomes are available • Identify those with a cultured representative in DSMZ • DSMZ grew > 200 of these and prepped DNA • Sequence and finish 200+ • Annotate, analyze, release data • Assess benefits of tree guided sequencing • 1st paper Wu et al in Nature Dec 2009 Monday, April 29, 13
- 63. GEBA Pilot Target List 0 5 10 15 20 25 30 35 B: Actinobacteria (H igh G C) B: Am inanaerobia B: Aquificae B: Bacteroidetes B: Chloroflexi B: D eferribacteres B: D eferribacteres B: D einococci B: D elta Proteobacteria B: Epsilon Proteobacteria B: Firm icutes B: Fusobacteria B: G am m a Proteobacteria B: G em m atim onadetes B: H aloanaerobiales B: Planctom ycetes B: Spirochaetes B: Therm odesulfobacteria B: Therm odesulfobia B: Therm ovenabulae A: H alobacteria A: Archaeoglobi A: M ethanobacteria A: M ethanom icrobia A: Therm ococci A: Therm oprotei Phyla #ofGenomes GEBA Initial Target List Monday, April 29, 13
- 64. Assess Benefits of GEBA • All genomes have some value • But what, if any, is the benefit of tree- guided sequencing over other selection methods • Lessons for other large scale microbial genome projects? Monday, April 29, 13
- 65. Lessons from GEBA Monday, April 29, 13
- 66. Lesson 1: rRNA PD IDs novel lineages From Wu et al. 2009 Nature 462, 1056-1060 Monday, April 29, 13
- 67. Concatenated Marker PD From Wu et al. 2009 Nature 462, 1056-1060 Monday, April 29, 13
- 68. Lesson 2: rRNA Tree is not perfect Badger et al. 2005 Int J System Evol Microbiol 55: 1021-1026. 16s WGT, 23S Monday, April 29, 13
- 69. How Pick Novel Lineages for Euks? • Molecular • rRNA PD? • Conserved markers by PCR? • EST shotgun? • Other data for phylogeny Monday, April 29, 13
- 70. Lesson 3: Improves annotation • Took 56 GEBA genomes and compared results vs. 56 randomly sampled new genomes • Better definition of protein family sequence “patterns” • Greatly improves “comparative” and “evolutionary” based predictions • Conversion of hypothetical into conserved hypotheticals • Linking distantly related members of protein families • Improved non-homology prediction Monday, April 29, 13
- 71. Annotation for Euks? Monday, April 29, 13
- 72. Lesson 4 : Metadata Important Monday, April 29, 13
- 73. Lesson 5: Project management critical • Tracking samples and status • Getting permissions • Shipping samples • Contacting collaborators • Data archiving and submission • Communicating with core facilities • and more Monday, April 29, 13
- 74. Lesson 6: Culture Collections Needed Monday, April 29, 13
- 75. Lesson 7: Data Publications Monday, April 29, 13
- 76. Lesson 8: Diversity Discovery • Phylogeny-driven genome selection helps discover new genetic diversity Monday, April 29, 13
- 77. Protein Family Rarefaction • Take data set of multiple complete genomes • Identify all protein families using MCL • Plot # of genomes vs. # of protein families Monday, April 29, 13
- 78. Wu et al. 2009 Nature 462, 1056-1060 Monday, April 29, 13
- 79. Wu et al. 2009 Nature 462, 1056-1060 Monday, April 29, 13
- 80. Wu et al. 2009 Nature 462, 1056-1060 Monday, April 29, 13
- 81. Wu et al. 2009 Nature 462, 1056-1060 Monday, April 29, 13
- 82. Wu et al. 2009 Nature 462, 1056-1060 Monday, April 29, 13
- 83. Synapomorphies exist Wu et al. 2009 Nature 462, 1056-1060 Monday, April 29, 13
- 84. True for Euks? Monday, April 29, 13
- 85. Lesson 9: Improves metagenomics Monday, April 29, 13
- 86. Phylotyping 0 0.125 0.250 0.375 0.500 Alphaproteobacteria Betaproteobacteria G am m aproteobacteria Epsilonproteobacteria Deltaproteobacteria C yanobacteriaFirm icutesActinobacteriaC hlorobi C FB C hloroflexiSpirochaetesFusobacteria Deinococcus-Therm us Euryarchaeota C renarchaeota Sargasso Phylotypes Weighted%ofClones Major Phylogenetic Group EFG EFTu HSP70 RecA RpoB rRNA Venter et al., Science 304: 66-74. 2004 GEBA Project improves metagenomic analysis Monday, April 29, 13
- 87. Eukaryotic Metagenomics? Monday, April 29, 13
- 88. GEBA Zoom Monday, April 29, 13
- 89. GEBA Now • 300+ genomes • Rich sampling of major groups of cultured organisms • Zoomed in sampling of haloarchaea, cyanobacteria and more Monday, April 29, 13
- 91. Haloarchaeal GEBA-like Lynch EA, Langille MGI, Darling A, Wilbanks EG, Haltiner C, et al. (2012) Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux. PLoS ONE 7(7): e41389. doi:10.1371/journal.pone.0041389 Monday, April 29, 13
- 92. 88 Plan: Sequence multiple Root Nodule Bacteria (RNBs) across the planet. Pilot: 100 RNBs. Alpha RNB Bradyrhizobium Mesorhizobium Rhizobium Beta RNB Sinorhizobium Cupriavidis Burkholderia Balneimonas-like Devosia Ochrobactrum Phyllobacterium Azorhizobium Allorhizobium Goal: • Understand BioGeographical effects on species evolution and understand host-specificity. Rationale: • N2 fixation by legume pastures and crops provides 65% of the N currently utilized in agricultural production. • Contributes 25 to 90 million metric tones N pa. • Symbioses save $US 6-10 billion annually on N fertilizer. • Grain and animal production enhanced by fixed nitrogen supplied by the symbiosis. Nikos Kyrpides GEBA RNB Monday, April 29, 13
- 93. But ... Monday, April 29, 13
- 94. Phylotyping 0 0.125 0.250 0.375 0.500 Alphaproteobacteria Betaproteobacteria G am m aproteobacteria Epsilonproteobacteria Deltaproteobacteria C yanobacteriaFirm icutesActinobacteriaC hlorobi C FB C hloroflexiSpirochaetesFusobacteria Deinococcus-Therm us Euryarchaeota C renarchaeota Sargasso Phylotypes Weighted%ofClones Major Phylogenetic Group EFG EFTu HSP70 RecA RpoB rRNA Venter et al., Science 304: 66-74. 2004 GEBA Project improves metagenomic analysis Monday, April 29, 13
- 95. Phylotyping 0 0.125 0.250 0.375 0.500 Alphaproteobacteria Betaproteobacteria G am m aproteobacteria Epsilonproteobacteria Deltaproteobacteria C yanobacteriaFirm icutesActinobacteriaC hlorobi C FB C hloroflexiSpirochaetesFusobacteria Deinococcus-Therm us Euryarchaeota C renarchaeota Sargasso Phylotypes Weighted%ofClones Major Phylogenetic Group EFG EFTu HSP70 RecA RpoB rRNA But not a lot Venter et al., Science 304: 66-74. 2004 Monday, April 29, 13
- 96. Phylogenomics Future 1 • Need to adapt genomic and metagenomic methods to make better use of data Monday, April 29, 13
- 97. Improving Metagenomic Analysis • Methods • More automation • Better phylogenetic methods for short reads and large data sets • Improved tools for using distantly related genomes in metagenomic analysis • Data sets • Rebuild protein family models • New phylogenetic markers • Need better reference phylogenies, including HGT • More simulations Monday, April 29, 13
- 98. Kembel Correction Kembel, Wu, Eisen, Green. In press. PLoS Computational Biology. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance Monday, April 29, 13
- 99. alignment used to build the profile, resulting in a multiple sequence alignment of full-length reference sequences and metagenomic reads. The final step of the alignment process is a PD versus PID clustering, 2) to explore overlap betw clusters and recognized taxonomic designations, and the accuracy of PhylOTU clusters from shotgun re Figure 1. PhylOTU Workflow. Computational processes are represented as squares and databases are represented as cylinders in workflow of PhylOTU. See Results section for details. doi:10.1371/journal.pcbi.1001061.g001 Finding Meta Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS. (2011) PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data. PLoS Comput Biol 7(1): e1001061. doi:10.1371/journal.pcbi.1001061 PhylOTU Monday, April 29, 13
- 100. Phylosift/ pplacer Aaron Darling, Guillaume Jospin, Holly Bik, Erik Matsen, Eric Lowe, and others Monday, April 29, 13
- 101. Kembel Combiner typically used as a qualitative measure because duplicate s quences are usually removed from the tree. However, the test may be used in a semiquantitative manner if all clone even those with identical or near-identical sequences, are i cluded in the tree (13). Here we describe a quantitative version of UniFrac that w call “weighted UniFrac.” We show that weighted UniFrac b haves similarly to the FST test in situations where both a FIG. 1. Calculation of the unweighted and the weighted UniFr measures. Squares and circles represent sequences from two differe environments. (a) In unweighted UniFrac, the distance between t circle and square communities is calculated as the fraction of t branch length that has descendants from either the square or the circ environment (black) but not both (gray). (b) In weighted UniFra branch lengths are weighted by the relative abundance of sequences the square and circle communities; square sequences are weight twice as much as circle sequences because there are twice as many tot circle sequences in the data set. The width of branches is proportion to the degree to which each branch is weighted in the calculations, an gray branches have no weight. Branches 1 and 2 have heavy weigh since the descendants are biased toward the square and circles, respe tively. Branch 3 contributes no value since it has an equal contributio from circle and square sequences after normalization. Kembel SW, Eisen JA, Pollard KS, Green JL (2011) The Phylogenetic Diversity of Metagenomes. PLoS ONE 6(8): e23214. doi:10.1371/journal.pone.0023214 Monday, April 29, 13
- 102. NMF in MetagenomesCharacterizing the niche-space distributions of components Sites North American East Coast_GS005_Embayment North American East Coast_GS002_Coastal North American East Coast_GS003_Coastal North American East Coast_GS007_Coastal North American East Coast_GS004_Coastal North American East Coast_GS013_Coastal North American East Coast_GS008_Coastal North American East Coast_GS011_Estuary North American East Coast_GS009_Coastal Eastern Tropical Pacific_GS021_Coastal North American East Coast_GS006_Estuary North American East Coast_GS014_Coastal Polynesia Archipelagos_GS051_Coral Reef Atoll Galapagos Islands_GS036_Coastal Galapagos Islands_GS028_Coastal Indian Ocean_GS117a_Coastal sample Galapagos Islands_GS031_Coastal upwelling Galapagos Islands_GS029_Coastal Galapagos Islands_GS030_Warm Seep Galapagos Islands_GS035_Coastal Sargasso Sea_GS001c_Open Ocean Eastern Tropical Pacific_GS022_Open Ocean Galapagos Islands_GS027_Coastal Indian Ocean_GS149_Harbor Indian Ocean_GS123_Open Ocean Caribbean Sea_GS016_Coastal Sea Indian Ocean_GS148_Fringing Reef Indian Ocean_GS113_Open Ocean Indian Ocean_GS112a_Open Ocean Caribbean Sea_GS017_Open Ocean Indian Ocean_GS121_Open Ocean Indian Ocean_GS122a_Open Ocean Galapagos Islands_GS034_Coastal Caribbean Sea_GS018_Open Ocean Indian Ocean_GS108a_Lagoon Reef Indian Ocean_GS110a_Open Ocean Eastern Tropical Pacific_GS023_Open Ocean Indian Ocean_GS114_Open Ocean Caribbean Sea_GS019_Coastal Caribbean Sea_GS015_Coastal Indian Ocean_GS119_Open Ocean Galapagos Islands_GS026_Open Ocean Polynesia Archipelagos_GS049_Coastal Indian Ocean_GS120_Open Ocean Polynesia Archipelagos_GS048a_Coral Reef Component 1 Component 2 Component 3 Component 4 Component 5 0.1 0.2 0.3 0.4 0.5 0.6 0.2 0.4 0.6 0.8 1.0 Salinity SampleDepth Chlorophyll Temperature Insolation WaterDepth General High M edium Low NA High M edium Low NA Water depth >4000m 2000!4000m 900!2000m 100!200m 20!100m 0!20m >4000m 2000!4000m 900!2000m 100!200m 20!100m 0!20m (a) (b) (c) Figure 3: a) Niche-space distributions for our five components (HT ); b) the site- similarity matrix ( ˆHT ˆH); c) environmental variables for the sites. The matrices are aligned so that the same row corresponds to the same site in each matrix. Sites are ordered by applying spectral reordering to the similarity matrix (see Materials and Methods). Rows are aligned across the three matrices. Functional biogeography of ocean microbes revealed through non-negative matrix factorization Jiang et al. In press PLoS One. Comes out 9/18. w/ Weitz, Dushoff, Langille, Neches, Levin, etc Monday, April 29, 13
- 103. More Markers Phylogenetic group Genome Number Gene Number Maker Candidates Archaea 62 145415 106 Actinobacteria 63 267783 136 Alphaproteobacteria 94 347287 121 Betaproteobacteria 56 266362 311 Gammaproteobacteria 126 483632 118 Deltaproteobacteria 25 102115 206 Epislonproteobacteria 18 33416 455 Bacteriodes 25 71531 286 Chlamydae 13 13823 560 Chloroflexi 10 33577 323 Cyanobacteria 36 124080 590 Firmicutes 106 312309 87 Spirochaetes 18 38832 176 Thermi 5 14160 974 Thermotogae 9 17037 684 Monday, April 29, 13
- 104. Better Reference Tree Morgan et al. submitted Monday, April 29, 13
- 105. Sifting Families Representative Genomes Extract Protein Annotation All v. All BLAST Homology Clustering (MCL) SFams Align & Build HMMs HMMs Screen for Homologs New Genomes Extract Protein Annotation Figure 1 Sharpton et al. submitted A B C Monday, April 29, 13
- 106. Zorro - Automated Masking cetoTrueTree 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 200 400 800 1600 3200 DistancetoTrueTree Sequence Length 200 no masking zorro gblocks Wu M, Chatterji S, Eisen JA (2012) Accounting For Alignment Uncertainty in Phylogenomics. PLoS ONE 7(1): e30288. doi:10.1371/journal.pone. 0030288 Monday, April 29, 13
- 107. Phylogenomics Future 2 • We have still only scratched the surface of microbial diversity Monday, April 29, 13
- 108. rRNA Tree of Life Figure from Barton, Eisen et al. “Evolution”, CSHL Press. 2007. Based on tree from Pace 1997 Science 276:734-740 Archaea Eukaryotes Bacteria Monday, April 29, 13
- 109. PD: Genomes From Wu et al. 2009 Nature 462, 1056-1060 Monday, April 29, 13
- 110. PD: Genomes + GEBA From Wu et al. 2009 Nature 462, 1056-1060 Monday, April 29, 13
- 111. PD: Isolates From Wu et al. 2009 Nature 462, 1056-1060 Monday, April 29, 13
- 112. PD: All From Wu et al. 2009 Nature 462, 1056-1060 Monday, April 29, 13
- 113. Uncultured Lineages: Methods • Get into culture • Enrichment cultures • If abundant in low diversity ecosystems • Flow sorting • Microbeads • Microfluidic sorting • Single cell amplification Monday, April 29, 13
- 114. 110 Number of SAGs from Candidate Phyla OD1 OP11 OP3 SAR406 Site A: Hydrothermal vent 4 1 - - Site B: Gold Mine 6 13 2 - Site C: Tropical gyres (Mesopelagic) - - - 2 Site D: Tropical gyres (Photic zone) 1 - - - Sample collections at 4 additional sites are underway. Phil Hugenholtz GEBA Uncultured Monday, April 29, 13
- 115. Uncultured Eukaryotes? Monday, April 29, 13
- 116. Phylogenomics Future 3 • Need Experiments from Across the Tree of Life too Monday, April 29, 13
- 117. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 118. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria • Experimental studies are mostly from three phyla As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 119. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria • Experimental studies are mostly from three phyla • Some studies in other phyla As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 120. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled • Same trend in Eukaryotes As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 121. Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled • Same trend in Viruses As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 122. 0.1 Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter Tree based on Hugenholtz (2002) with some modifications. Need experimental studies from across the tree too Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 123. 0.1 Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter Tree based on Hugenholtz (2002) with some modifications. Adopt a Microbe Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003 Monday, April 29, 13
- 124. What Next? Monday, April 29, 13
- 125. Acknowledgements • GEBA: • $$: DOE-JGI, DSMZ • Eddy Rubin, Phil Hugenholtz, Hans-Peter Klenk, Nikos Kyrpides, Tanya Woyke, Dongying Wu, Aaron Darling, Jenna Lang • GEBA Cyanobacteria • $$: DOE-JGI • Cheryl Kerfeld, Dongying Wu, Patrick Shih • Haloarchaea • $$$ NSF • Marc Facciotti, Aaron Darling, Erin Lynch, • iSEEM: • $$: GBMF • Katie Pollard, Jessica Green, Martin Wu, Steven Kembel, Tom Sharpton, Morgan Langille, Guillaume Jospin, Dongying Wu, • aTOL • $$: NSF • Naomi Ward, Jonathan Badger, Frank Robb, Martin Wu, Dongying Wu • Others (not mentioned in detail) • $$: NSF, NIH, DOE, GBMF, DARPA, Sloan • Frank Robb, Craig Venter, Doug Rusch, Shibu Yooseph, Nancy Moran, Colleen Cavanaugh, Josh Weitz • EisenLab: Srijak Bhatnagar, Russell Neches, Lizzy Wilbanks, Holly Bik Monday, April 29, 13