THE LAST 35 YEARS

1
THE LAST 35 YEARS OF PROTISTAN EVOLUTION
David J. Patterson University of Sydney
Adjunct Scientist, Astrobiology Institute,
Marine Biological Laboratory, Woods Hole
paddy_at_mbl.edu
2
This talk was published last year American
Naturalist, 154 S96-S124
3
EVOLUTIONARY PROTISTOLOGY IN THE LAST 35 YEARS
APPROACHES IMPACTS
Comprehensive tree
2000
Protein gene sequences
1995
Skeletal trees
1990
Reconstruction begins
16S rRNA sequence data
1985
Scenarios
Rejection of traditional taxonomy
1980
Endosymbiotic origins of organelles
1975
Integrated protistology
More diversity recognized
1970
Electron microscopy
Traditional taxonomy
1965
4
Traditionally ..

• PROKARYOTES
• EUKARYOTES

• THE MACROBIAL TYPES
• ANIMALS
• PLANTS
• FUNGI

• AND THE MICROBIAL EUKARYOTES
• ALGAE REDS, BROWNS, GREENS, DIATOMS, EUGLENIDS,
  DINOFLAGELLATES, HETEROKONTS, CRYPTOS
• PROTOZOA CILIATES, AMOEBAE, FLAGELLATES,
  SPOROZOA
• SLIME MOULDS MYCETOZOA, ACRASIDS,
  DICTYOSTELIDS LABYRINTHULIDS

5
Traditionally .. 4 types of protozoa
amoebae flagellates ciliates
sporozoa
6
Otto Bütschli his view, 1880
Protozoa Class Sarkodina Class
Mastigophora Class Sporozoa Class Infusoria
Sporozoa
Infusoria
Mastigophora
Sarkodina
Protsville
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MICROSCOPES Royal Mail Mint Stamps
8
EVOLUTIONARY PROTISTOLOGY IN THE LAST 35 YEARS
APPROACHES IMPACTS
Comprehensive tree
2000
Protein gene sequences
1995
Skeletal trees
1990
Reconstruction begins
16S rRNA sequence data
1985
Scenarios
Rejection of traditional taxonomy
1980
Endosymbiotic origins of organelles
1975
Integrated protistology
More diversity recognized
1970
Electron microscopy
Traditional taxonomy
1965
9
The 1960s and the advent of good fixation
protocols for electron-microscopy
GLUTARALDEHYDE
10
Goniomonas
Electron microscopy provides more data
than light microscopy
11
Heliozoa
Centrohelids
Actinophryids
12
Ultrastructural features define robust groups of
protists

• Flagellum - structure and associations
• Flagellar rootlets
• Mitotic spindle characters
• Dividing nucleus
• Mitochondrial cristae
• Plastid structure bounding membranes
• External spines, scales, etc.
• Cytoskeletal materials
• Extrusomes, contractile vacuoles, ingestion
  organelles
• etc.

ultrastructural identity
13
How many groups have distinct ultrastructural
identities?
Algae 10 Amoebae 20 Slime Molds
6 Flagellates 39 Sporozoa 4 Ciliates
1 Animals 1 Plants 1 Fungi
1 TOTAL 82 RESIDUA - 320
genera
On this scale Animals 1, Plants 1 , Fungi
1 that is - the units are kingdoms. By the
1980s, there were about 80 kingdoms of protists
14
By the 1980s, the PROTISTS were ...

• Acantharea Actinophryids Adriamonas
  Ancyromonas Apicomplexa Apusomonads
  Caecitellus Carpediemonas Centrohelida
  Cercomonads Chlorarachnion Choanoflagellates
  Chytrids Ciliophora Coelosporidium
  Colponema Copromyxids Cryothecomonas
  Cryptomonads Cyanophorids Desmothoracids
  Dimorphids Dinoflagellates Diphylleia
  Diplomonads Diplonema Discocelis Ebriids
  Ellobiopsiids Entamoebidae Euglenida
  Fonticula Glaucosphaera Gloeochaete
  Granuloreticulosa Gymnosphaerida Haplosporids
  Haptophytes Hedraiophrys Heterolobosea
  Histiona Hypermastigids Jakoba
  Kathablepharidae Kinetoplastida Komokiacea
  Leucodictyon Luffisphaera Microsporidia
  Ministeria Myxomycetes Nephridiophaga
  Nucleariidae Oxymonads Paramyxea Pelobionts
  Phaeodarea Phalansterium pkx
  Plasmodiophorids Polycystinea Protostelids
  Pseudodendromonads Pseudospora Ramicristates
  Reclinomonas Red algae Retortamonads
  Spironemidae Spongomonads Stephanopogon
  Sticholonche Stramenopiles Telonema
  Thaumatomonads Trichomonads Trimastix
  Vampyrellids Viridaeplantae Xenophyophores
  
• PLUS 300 UNDERSTUDIED GENERA PLUS CRYPTIC TAXA

15
EVOLUTIONARY PROTISTOLOGY IN THE LAST 35 YEARS
APPROACHES IMPACTS
Comprehensive tree
2000
Protein gene sequences
1995
Skeletal trees
1990
Reconstruction begins
16S rRNA sequence data
1985
Scenarios
Rejection of traditional taxonomy
1980
Endosymbiotic origins of organelles
1975
Integrated protistology
More diversity recognized
1970
Electron microscopy
Traditional taxonomy
1965
16
Endosymbiosis and the evolution of
eukaryotes from Merschkovsky 1910 .
17
The Serial Endosymbiosis Theory is an easy idea
to test .
18
EVOLUTIONARY PROTISTOLOGY IN THE LAST 35 YEARS
APPROACHES IMPACTS
Comprehensive tree
2000
Protein gene sequences
1995
Skeletal trees
1990
Reconstruction begins
16S rRNA sequence data
1985
Scenarios
Rejection of traditional taxonomy
1980
Endosymbiotic origins of organelles
1975
Integrated protistology
More diversity recognized
1970
Electron microscopy
Traditional taxonomy
1965
19
A phylogenetic problems - what is the
relationship of 1, 2 and 3. We have to find out
which pair of 1, 2 and 3 are more closely related
to each other than they are to the third
1 2 3
We depict ignorance as an unresolved polytomies
and understanding as dichotomies
20
An example of creating bits of the tree
enigmatic opalines large (1 mm.) flat
flagellates living in amphibia
21
Opalina
Karotomorpha
Proteromonas
22
Hairs link proteromonads to the chrysophytes
23
Identifying a lineage leading from algae
to protozoa grouping 3 ultrastructural
identities
24
STRAMENOPILES
WITH STRAW HAIRS
Protsville
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The PROTISTS are getting fewer ...

• Acantharea Adriamonas Ancyromonas
  Alveolates Apusomonads Centrohelida
  Cercomonads Chlorarachnion Coelosporidium
  Colponema Copromyxids Cryothecomonas
  Cryptomonads Desmothoracids Dimorphids
  Diphylleia Discocelis Ebriids
  Ellobiopsiids Euglenozoa Excavates
  Fonticula Glaucophytes Granuloreticulosa
  Gymnosphaerida Haplosporids Haptophytes
  Hedraiophrys Kathablepharids Komokiacea
  Leucodictyon Luffisphaera Ministeria
  Nephridiophaga Nucleariidae Opisthokonts
  Oxymonads Parabasalids Paramyxea
  Pelobionts Phaeodarea Phalansterium
  Plasmodiophorids Polycystinea Pseudospora
  Ramicristates Red algae Spironemidae
  Spongomonads Stephanopogon Sticholonche
  Stramenopiles Telonema Thaumatomonads
  Vampyrellids Viridaeplantae Xenophyophores
  
• PLUS 300 UNDERSTUDIED GENERA PLUS CRYPTIC TAXA

26
EVOLUTIONARY PROTISTOLOGY IN THE LAST 35 YEARS
APPROACHES IMPACTS
Comprehensive tree
2000
Protein gene sequences
1995
Skeletal trees
1990
Reconstruction begins
16S rRNA sequence data
1985
Scenarios
Rejection of traditional taxonomy
1980
Endosymbiotic origins of organelles
1975
Integrated protistology
More diversity recognized
1970
Electron microscopy
Traditional taxonomy
1965
27
Small subunit (16S) rRNA 1250 - 2500 bases
Large subunit 28S, 5.8S and 5S rRNA
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AACUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCAAAG AUUAGCCA
UGCAAGUGAAAUAUAUGCAUAUUUUAUAUGUAGAAACUGCGAACGGCUCA
UUAAAACAGUUAUAAUCUAXUUGACAUUUUAUUAUUAUAAGGAUAACUAC
GGAAAACGUGUAGCUAAUAACUUGCUUUAAGUGUUUUUACUUCUUGGAGU
AAUUAGCAUGUAUUGUUAAGCUUAUAAGAAAAAUUUUUAAUUAAAGCAAA
UUAUAACAAAGAAGUAACACAUAAUAUAUUUACUAUAUUUAGUGUGUACA
AUCGAGUUUCUGACCAUUCAGCUUUUCAUGUUAGGGUAUUGGCCUAACAU
GGCAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAAGAGGGAGCCC
UGAGAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGGGUAAAUUACCCA
AUUCUAAAUAAGAGGGUAGUGACAAGAAUAACAAUAUAAGGCCAAAUUUU
GGUUUUAUAUAAUUGGAAUGAUGGGAAUUUAAAACCUUCCCAAAAUCAAU
UGGAGGGCAAGUCUGGUGCCAGCAGCAGCCGCGGUAAUUCCAGCUCCAAU
AGCUAUAUUAAAAUUGUUGCAGUUAAAGCGUCGUAGUUGAACUUCAAGGG
UAUUAUUAUUUUAAGUAACUCACUUGCAGAAUCUUGGCUCCGCCUCGAUA
UCUUCAUGCCUUGUUGUAGGUUCUUUUAAUUACACCCUUUGAGACCCCAA
UGAUUUAUCACUGGGUUUU...16SRIBOSOMALRNASEQUENCEFROMS
ARCOCYSTISMURIS ...
Protsville
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Giving universal trees of life
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A typical cell has endoplasmic
reticulum nuclei mitochondria dictyosomes micr
otubular cytoskeleton microfilamentous
cytoskeleton mitosis meiosis
secretory vesicles lysosomes
Wolfe
Protsville
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Microsporidia
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Leading to 1990s models of the evolution of the
eukaryotic cell
Early evolution was of amitochondriate eukaryotes
At a time when there was little free
oxygen? Might more ancient amitochondriate
protists still exist? And where would we find
them?
33
Thiobios The anoxic zone under the surface of
mud
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Free-living amitochondriate flagellates
retortamonads
Trimastix
trichomonads
Carpediemonas
pelobionts
diplomonads
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such as Mastigamoeba schizophrenia
pelobionts
Pelobionts Pelomyxa Mastigina
Mastigamoeba Mastigella Phreatamoeba
36
Mastigamoeba schizophrenia Pelobionts have
flagella one microtubular root
endoplasmic reticulum nuclei no Golgi
apparatus no mitochondria no plastids no
fibrous cytoskeleton
37
Flagellar idiosyncrasies in pelobionts might
indicate that they represent the first of the
flagellated eukaryotes

38
But, when the first pelobionts were sequenced
...
39
EVOLUTIONARY PROTISTOLOGY IN THE LAST 35 YEARS
APPROACHES IMPACTS
Comprehensive tree
2000
Protein gene sequences
1995
Skeletal trees
1990
Reconstruction begins
16S rRNA sequence data
1985
Scenarios
Rejection of traditional taxonomy
1980
Endosymbiotic origins of organelles
1975
Integrated protistology
More diversity recognized
1970
Electron microscopy
Traditional taxonomy
1965
40
Molecular trees do not agree with each other
in the tubulin trees microsporidia go with
fungi amitochondriate organisms are dispersed
trichomonads
Suggesting that our earlier confidence in the 16S
trees was not justified
41
EVOLUTIONARY PROTISTOLOGY IN THE LAST 35 YEARS
APPROACHES IMPACTS
Comprehensive tree
2000
Protein gene sequences
1995
Skeletal trees
1990
Reconstruction begins
16S rRNA sequence data
1985
Scenarios
Rejection of traditional taxonomy
1980
Endosymbiotic origins of organelles
1975
Integrated protistology
More diversity recognized
1970
Electron microscopy
Traditional taxonomy
1965
42
EVOLUTIONARY PROTISTOLOGY IN THE LAST 35 YEARS
APPROACHES IMPACTS
Comprehensive tree
Protein gene sequences
1995
Skeletal trees
1990
Reconstruction begins
16S rRNA sequence data
1985
Scenarios
Rejection of traditional taxonomy
1980
Endosymbiotic origins of organelles
1975
Integrated protistology
More diversity recognized
1970
Electron microscopy
Traditional taxonomy
1965
43
(No Transcript)
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A more extensive analysis of 16S ribosomal RNA
genes confirms that pelobionts are not primitive
but related to slime moulds and entamoebae
Saccharomyces
opisthokonts - animals and fungi
Pneumocystis
Diaphanoeca
Euglypha
Apusomonas
Acanthamoeba
Chlamydomonas
green algae and land plants
Zea
Porphyra umbilicalis
red algae
Porphyra minia
Labyrinthuloides
stramenopiles
Thalassonema
Paramecium
Oxytricha
alveolates - ciliates dinoflagellates and
apicomplexa
Prorocentrum
Toxoplasma
Trimastix

Mastigamoeba invertens
Hartmannella
Bodo
Naegleria
Dictyostelium
mycetozoan slime moulds
Physarum
Mastigamoeba balamuthi
Mastigella commutans
pelobionts - well almost all of them
Mastigamoeba sp.
Mastigamoeba simplex
Endolimax nana
Entamoeba gingivalis
entamoebae
Entamoeba histolytica
Entamoeba coli
Trepomonas
Trichomonas
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Focussing and (taxonomically) intensifying the
analysis - the sister group of the
pelobionts are the entamoebae
Hyperamoeba
slime moulds
Physarum
Entamoeba gingivalus
Entamoeba histolytica
Entamoeba coli
entamoebae
Endolimax nana
Mastigamoeba simplex
Mastigamoeba sp.
pelobionts
Mastigamoeba balamuthi
Mastigella commutans
ramicristate amoebae
Hartmannella vermiformis

Mastigamoeba invertens
Oxytricha
46
Focussing and (taxonomically) intensifying the
analysisthe sister group to the pelobionts are
entamoebaeleading to models of character
innovation
tubular mitochondrial cristae
47
faster technologies more taxa genomics
Comprehensive tree
200?
2000
Protein gene sequences
1995
Skeletal trees
1990
Reconstruction begins
16S rRNA sequence data
1985
Scenarios
Rejection of traditional taxonomy
1980
Endosymbiotic origins of organelles
1975
Integrated protistology
More diversity recognized
1970
Electron microscopy
Traditional taxonomy
1965
48
CONCLUSIONS

• A tree will be assembled with ultrastructural and
  molecular data

• Early confidence was misplaced

STATUS Structural insights seem robust, but
there are conflicts between molecular trees to be
resolved.

• Disputes among molecular trees will be resolved
  in part by better taxonomic sampling, and by the
  benefits of accelerated technologies

• PROSPECT The universal tree will probably be
  assembled from the tips of the branches in, and
  probably within the next decade

49
(No Transcript)
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CONCLUSIONS

• A tree will be assembled with ultrastructural and
  molecular data
• Early confidence was misplaced
• STATUS Structural insights seem robust, but
  there are conflicts between molecular trees to be
  resolved.
• Disputes among molecular trees will be resolved
  in part by better taxonomic sampling, and by the
  benefits of accelerated technologies
• PROSPECT The universal tree will probably be
  assembled from the tips of the branches in, and
  probably within the next decade