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Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
Parfrey smbe euk_2013_final
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Parfrey smbe euk_2013_final

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  • Microbes play essential roles in the biogeochemical cycles and nutrient cycling in addition to making up a huge portion of the biomass and biodiversity on our planet.
  • Still not right but maybe closer. Alternate: A phylogenetic framework for understanding the host associated eukaryotes, and other aspects of eukaryotic biology?
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    • 1. Laura Wegener ParfreyRob Knight, University of ColoradoHost-associated eukaryoticcommunities
    • 2. We live in a microbial worldEukaryotaArchaeaBacteriaDerived from Woese et al. 1990
    • 3. EukaryotaArchaeaBacteriaWoese et al. 1990
    • 4. versusHuman cells andgenesCells GenesProportionhumanModified from Hamady 2008Microbes are dominant closer to home as well
    • 5. They influence many aspects of our lives
    • 6. What about eukaryotes?Adl et al 2012
    • 7. Eukaryotic contribution to the human microbiome• Human health– Major source of morbidity and mortality• Ecology– predation, parasitism, competition
    • 8. What is a normal/healthy community?
    • 9. A phylogenetic framework providesthe context for understandingeukaryotic communities
    • 10. Perspectives on eukaryotic diversityWhittaker 1969
    • 11. StramenopilesApicomplexaDinoflagellatesCiliatesHaptophytesGreen algae (including plants)TelonemaCentroheliozoaRed algaeCryptomonads + KathablepharidsEuglenozoaHeterolobosea + JakobidsPreaxostylaMalawimonasFornicataParabasaliaEntamoebidaeMastigamoebidaeTubulineaThecamoebidaeAcanthamoebidaeFlabellineaEumycetozoaBreviataAncyromonasApusomonadsFungiMesomycetozoaAnimalsChoanoflagellatesGlaucocystophytesHaplosporidia, Plasmodiophora,Vampyrellids, GromiaForaminifera, Acantharea,Polycystineacore Cercozoa
    • 12. Patterson 1999, American Naturalist70 + lineages,predominatelymicrobialEukaryotic diversity as of 1999
    • 13. 70+ lineages of eukaryotesImages from O. Roger Anderson• Defined by ultrastructural identities– Characteristic patterns of subcellular organization• Lineages robust, confirmed by molecular data
    • 14. c Biology010oupled with a moderate number of genes has the power to r econstruct deep phylogenetict the support for major eukaryotic clades using taxon-rich analyses, including 88–451 taxaanalyzing data fr om up to 16 genes. These analyses reveal remarkable consistency in supportedg levels of missing data (17–69%). Several major gr oups are both stable and strongly supportedta), while the pr oposed supergroup “Chromalveolata” is rejected. This approach contrastsaucity of major eukaryotic lineages (19 or fewer). Images ar e of representative organisms andity of eukaryotic lineages. All images are from http:/ / www.mbl.edu/ microscope.and Codominant Multilocus Markersnig ...................................................................................... ......................................... 491essing Life-History Evolution in a Fr eshwater Fish Radiationhristopher P. Burridge, and Graham P. Wallis ............................................ .............. 504Yield a Well-Resolved Eukaryotic Tree of LifeYonas I. Tekle, Erica Lasek-Nesselquist, Hilary G. Morrison,and Laura A. Katz ..................................................................... .................................. 518c, and Relaxed Clock Methods in a Comparative Genomicsory of Soybean ( Glycine max).................................................................................................................. ................... 534ntinental Colonization Events during the Rapid): the Utility of AFLPs versus Mitochondrial andnt Excoffier, and Gerald Heckel.................................................................................... 548ee Estimation: Impact of Mutational and Coalescent Ef fects onng among Dif ferent Methodsubatko, and L. Lacey Knowles ............................................................. ....................... 573lanced Repr esentation of Phylogenetic Topologies....................................................................................... .............................................. 584ally Survive the Oligocene Dr owning of New Zealand?J. Lowe ....................................................................................... .................................. 594fects on Trait Variance in Clades........................................................................ ............................................................ 602uation of Comparative Data, 2nd edition............................................................................................... ..................................... 608Viruses...................................................................................... ............................................... 610tics and V icariances........................................................................................ ........................................... 612ed on behalf of the Society of Systematic Biologistshttp://systbiol.org/Volume59Number5,pp.491–614October2010oxfordSYSTEMATICBIOLOGYSystematic BiologyA JOURNAL OF THESociety of Systematic BiologistsOCTOBER 2010VOLUME 59NUMBER 5ONLINE ISSN 1076-836XPRINT ISSN 1063-5157
    • 15. Parfrey et al. 2010451 taxa:72 lineages – 53 withUltrastructuralidentities16 genes, includingribosomal DNA
    • 16. Current perspective of eukaryotic diversityImages from Micro*scope and Saldarriaga
    • 17. Does this perspective matter?
    • 18. Example 1 – MitosisVazquez, Parfrey, Katz 2010Is this universal?
    • 19. Vazquez, Parfrey, Katz 2010
    • 20. Mitosis in EukaryotesVazquez, Parfrey, Katz 2010
    • 21. Integrating eukaryotes into microbialcommunity analyses
    • 22. Data analysis with QiimeOpen source, supported, and freely available (http://qiime.org)Caporaso et al. 2010 Nature Methods18S tutorial available (Tony Walters)
    • 23. Marker gene – ribosomal DNA• Ribosomal DNA is universally present• Sequenced for the broadest sample of taxa• Mix of conserved and variable regions• Target SSU-rDNA (18S)
    • 24. Tree of Silva eukaryotes• Tree: backbone defined by 2010eukaryotic tree + updates• Database: Silva 108 ribosomaldatabase. 97% representativesequences.
    • 25. Eukaryotic databaseSilva ribosomal databasehttp://www.arb-silva.de/
    • 26. Challenges of using Silva• Taxonomy based on NCBI• 20% listed as uncultured eukaryote• Not standardized for computational analyses
    • 27. • Collaboration between Silva ribosomal database(Pelin Yilmaz), ISOP systematics committee andothers with computational or taxonomic expertise.• Goal: revise classification– reflect phylogeny– Take advantage of phylogenetic information– Interface with computational tools• Implemented in Silva 111 releaseEukaryotic Taxonomy Working GroupPelin Yilmaz and Frank Oliver Glocknerhttp://www.arb-silva.de/projects/eukaryotic-taxonomy/
    • 28. Curated Silva tree
    • 29. Eukaryotic communities in human microbiome
    • 30. Who lives in the human gut?http://www.stanford.edu/group/parasites/ParaSites2009/NevinsANDLiu_Giardiasis/NevinsANDLiu_Giardiasis.htmFirst description of Giardia:“I have sometimes also seen tiny creatures moving very prettily…and their belly, which was flattish, furnished with sundry little paws…”-- van Leeuwenhoek 1681+ + =
    • 31. http://www.stanford.edu/group/parasites/ParaSites2009/NevinsANDLiu_Giardiasis/NevinsANDLiu_Giardiasis.htmEukaryotes in thehuman gut
    • 32. Eukaryotic parasites
    • 33. But not all are pathogenic• Commensals
    • 34. But not all are pathogenic• Commensals• Variation in pathogenicity even in parasites
    • 35. Eukaryotes are also beneficialDigestion of cellulose in termites and ruminants
    • 36. http://www.stanford.edu/group/parasites/ParaSites2009/NevinsANDLiu_Giardiasis/NevinsANDLiu_Giardiasis.htmWhat is a normal/healthycommunity?
    • 37. Eukaryotic communities in human microbiome• Hypothesis: Communities of microbial eukaryotesfollow the same diversity patterns as bacteria.– Shared diversity patterns: environmental factors stronger– Different: Biological differences (geneticarchitecture, size, population structure) more important
    • 38. Host-associated bacterial communitiesdistinct from environmental communitiesLey, Lozupone et al. 2008, Nature Reviews Microbiol
    • 39. Few bacterial lineages are host-associatedBacteria foundonly in theenvironmentBacteria found inhumans and otheranimal hostsLey et al 2006
    • 40. But these few are very successfulLey et al 2008; Image Wikipedia
    • 41. Parfrey, Walters, Knight 2011Vertebrate-associatedlineagesaccording toparasitological literatureBlastocystisCryptosporidiumBalantidiumTrichomonas,DientamoebaGiardiaEnteromonasChilomastixEntamoebaCandidaEnterocytozoonAscarisPneumocystis
    • 42. Parfrey, Walters, Knight 2011BlastocystisCryptosporidiumBalantidiumTrichomonas,DientamoebaGiardiaEnteromonasChilomastixEntamoebaCandidaEnterocytozoonAscarisPneumocystis
    • 43. Parfrey, Walters, Knight 2011BlastocystisCryptosporidiumBalantidiumTrichomonas,DientamoebaGiardiaEnteromonasChilomastixEntamoebaCandidaEnterocytozoonAscarisPneumocystis
    • 44. Comparison of eukaryotic communities:Dataset
    • 45. DatasetEnvironmentalSoil, water, lichen, air75 samples65017 readsHost-associatedFecal samples(mammals)Human skin51 samples25574 readsTotal:126 samples90591 reads4092 OTUs
    • 46. Comparison of eukaryotic communities:DatasetThe bacterial communities in thesesamples were also sequenced toenable direct comparison.
    • 47. Representative sequences placed in the eukaryotic tree• RAxML EPA placementalgorithm
    • 48. Alveolates4092 representativesequences within inSilva eukaryotic treeframework
    • 49. Host-AssociatedEnvironmental
    • 50. Beta diversity of host-associated vsenvironmental samples: EukaryotesSkin communitiesHost-AssociatedEnvironmentalParfrey et al. in prep
    • 51. Beta diversity of host-associated vsenvironmental samples: EukaryotesHost-AssociatedEnvironmentalProcrustes and mantel test: Significant correlation (p < .001), but a poor fit
    • 52. Beta diversity of host-associated vsenvironmental samplesProcrustes and mantel test: Significant correlation (p < .001), but a poor fit
    • 53. What factors account for differencebetween bacteria and eukaryotes?
    • 54. Taxa summaries bacteria:composition consistent across individualsHuman and other mammal fecal samplesRelativeabundanceoftaxaParfrey et al. in prep
    • 55. Taxa summaries eukaryotes:higher variabilityRelativeabundanceoftaxaHuman and other mammal fecal samplesParfrey et al. in prep
    • 56. Eukaryotic communities in thevertebrate gut• Eukaryote distribution is patchy• Few lineages of eukaryotes are host-associated• Same lineages found across vertebrate taxa (e.g.Blastocystis and Entamoeba)Parfrey et al 2011; Parfrey et al. in prep
    • 57. “Parasites” = normal?
    • 58. RelativeabundanceoftaxaHuman and other mammal fecal samplesParfrey et al. in prep“Parasites” = normal?Entamoeba
    • 59. http://www.stanford.edu/group/parasites/ParaSites2009/NevinsANDLiu_Giardiasis/NevinsANDLiu_Giardiasis.htmJust beginning to elucidate the normalhuman microbiome
    • 60. AcknowledgementsCollaborators:Valerie McKenzie (CU)Greg Caporaso (NAU)Jack Gilbert (Argonne)Maria Gloria Dominguez (NYU)Dan Lahr (USP)Tim Marques (USP)Orin Shanks (EPA)Rob Knight (CU)Knight Lab:Jessica MetcalfMatt GebertChris LauberSe Jin SongLaura Katz

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