the last 40 years of protistan evolution

1
Protistan diversity
the last 40 years of protistan evolution
David J. Patterson
dpatterson_at_mbl.edu
2
The gist was published as American Naturalist,
154 S96-S124
3
multigene / genomes
2005
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, CRYPTOPHYTES
• 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
7
MICROSCOPES Royal Mail Mint Stamps
8
multigene / genomes
2005
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
multigene / genomes
2005
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
An example of creating bits of the tree
enigmatic opalines large (1 mm.) flat
flagellates living in amphibia
17
Opalina
Karotomorpha
Proteromonas
18
Hairs link proteromonads to the chrysophytes
19
New insights include lineages that include algae
and protozoa 3 UIs in here
20
STRAMENOPILES
WITH STRAW HAIRS
Protsville
21
EUGLENOZOA
TWO FLAGELLA WITH PARAXONEMAL RODS Three
microtubular rootlets Cruciate extrusomes
KINETOPLASTIDS such as trypanosomes causes
sleeping sickness
EUGLENIDS such as Euglena
and diplonemids
22
The PROTISTS are getting fewer ...

• Acantharea Adriamonas Ancyromonas
  Alveolates Apusomonads Centrohelida
  Cercomonads Chlorarachnion Coelosporidium
  Colponema Copromyxids Cryothecomonas
  Cryptomonads Desmothoracids Dimorphids
  Diphylleia Discocelis Ebriids 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

23
multigene / genomes
2005
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
24
Small subunit (16S) rRNA 1250 - 2500 bases
Large subunit 28S, 5.8S and 5S rRNA
25
AACUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCAAAG AUUAGCCA
UGCAAGUGAAAUAUAUGCAUAUUUUAUAUGUAGAAACUGCGAACGGCUCA
UUAAAACAGUUAUAAUCUAXUUGACAUUUUAUUAUUAUAAGGAUAACUAC
GGAAAACGUGUAGCUAAUAACUUGCUUUAAGUGUUUUUACUUCUUGGAGU
AAUUAGCAUGUAUUGUUAAGCUUAUAAGAAAAAUUUUUAAUUAAAGCAAA
UUAUAACAAAGAAGUAACACAUAAUAUAUUUACUAUAUUUAGUGUGUACA
AUCGAGUUUCUGACCAUUCAGCUUUUCAUGUUAGGGUAUUGGCCUAACAU
GGCAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAAGAGGGAGCCC
UGAGAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGGGUAAAUUACCCA
AUUCUAAAUAAGAGGGUAGUGACAAGAAUAACAAUAUAAGGCCAAAUUUU
GGUUUUAUAUAAUUGGAAUGAUGGGAAUUUAAAACCUUCCCAAAAUCAAU
UGGAGGGCAAGUCUGGUGCCAGCAGCAGCCGCGGUAAUUCCAGCUCCAAU
AGCUAUAUUAAAAUUGUUGCAGUUAAAGCGUCGUAGUUGAACUUCAAGGG
UAUUAUUAUUUUAAGUAACUCACUUGCAGAAUCUUGGCUCCGCCUCGAUA
UCUUCAUGCCUUGUUGUAGGUUCUUUUAAUUACACCCUUUGAGACCCCAA
UGAUUUAUCACUGGGUUUU...16SRIBOSOMALRNASEQUENCEFROMS
ARCOCYSTISMURIS ...
Protsville
26
Bringing together UIs into larger clusters

• Robust high level taxonomic from molecular
  biology have NOT been numerous
• Not
• Stramenopiles
• Euglenozoa
• Myxozoa as Cnidaria
• Alveolates
• Pelobionts and entamoebae
• Microsporidia as fungi
• Opisthokonts (chytrids, choanoflagellates and
  descendent fungi and animals)
• And there are many new arrays in contemporary
  trees ..

trichomonads
27
ALVEOLATES
Ciliates
Dinoflagellates
Apicomplexa - malaria
heterotrophic flagellates Colpodella,
Perkinsus, Acrocoelus
28
Such as - cercozoa amoebozoa - excavates
29
Such as - plantae chromalveolates -
rhizaria There are 6-8 major groups being
promulgated
30
In ALL cases, the names have multiple
meanings Plantae green streptophytes to some
and to green and red and glaucophytes to
others Heterokonts a subset of chlorophyll a
and c containing algae to some, and
stramenopiles to others Radiolaria
polycystines, phaeodarea and acantharea to some
they are the polycystines, phaeodarea and
Sticholonche Cercozoa can be Cercozoa and core
cercozoa and are as unclear as the Archezoa were
31
If groups in this case the Archezoa - are
defined badly they are unstable and we do not
know what the name means
32
When there is a reference to Cercozoa, we dont
know what is referred to. Poor TAXONOMIC
practice. Molecular phylogeneticists need to
apply taxonomic standards Ideally, a name needs
to have a single meaning and this can be done
by reference to - circumscription (the
appearance - bad) - composition (ALL of the
content - unstable) - relationships (nodes and
sisters - contextual, unstable) - innovation
(synapomorphy - stramenopiles) Currently part of
molecular phylogeny of protists and this is not
good.
33
The gist was published as American Naturalist,
154 S96-S124
34
The genera are in here Within a conservative
superstructure