Review articles

Photosynthetic eukaryotes unite:

endosymbiosis connects the dots
Debashish Bhattacharya,* Hwan Su Yoon, and Jeremiah D. Hackett

Summary biology. The photosynthetic organelle, termed the plastid, is

The photosynthetic organelle of algae and plants (the found in forms as diverse as microscopic diatoms, giant kelps,
plastid) traces its origin to a primary endosymbiotic
toxic dinoflagellates, edible red algae, and land plants (see
event in which a previously non-photosynthetic protist
engulfed and enslaved a cyanobacterium. This eukaryote Table 1). A critical question is whether all photosynthetic forms
then gave rise to the red, green and glaucophyte algae. are united on a single branch of the tree of life or whether
However, many algal lineages, such as the chlorophyll plastids have been spread throughout the tree through
c-containing chromists, have a more complicated evolu- multiple independent lateral transfers. If the latter, then how
tionary history involving a secondary endosymbiotic
many lateral transfers are needed to explain extant algal
event, in which a protist engulfed an existing eukaryotic
alga (in this case, a red alga). Chromists such as diatoms lineages? Answers to these questions have been rapidly
and kelps then rose to great importance in aquatic accumulating recently and they provide surprising insights into
habitats. Another algal group, the dinoflagellates, has the course of eukaryotic evolution.
undergone tertiary (engulfment of a secondary plastid) It has now been clearly documented that plastids originate
and even quaternary endosymbioses. In this review, we
through endosymbiosis,(1 –6) whereby a single-celled protist
examine algal diversity and show endosymbiosis to be a
major force in algal evolution. This area of research has engulfs and retains a foreign photosynthetic cell (see Fig. 1).
advanced rapidly and long-standing issues such as the Over time, the foreign cell is reduced to a plastid and is
chromalveolate hypothesis and the extent of endosym- vertically transmitted to subsequent generations. Endosym-
biotic gene transfer have recently been clarified. biosis comes in three major types, primary, secondary and
BioEssays 26:50–60, 2004.
tertiary endosymbiosis. The first results from the engulfment of
ß 2003 Wiley Periodicals, Inc.
a photosynthetic prokaryote (cyanobacterium, Fig. 1A) and
Introduction gives rise to a plastid bound by two membranes (the inner,
Accounting for the remarkable diversity of photosynthetic 1st, and outer, 2nd, membranes of the cyanobacterium, see
protists (algae) remains an important challenge in evolutionary Ref. 7). The outer, phagosomal membrane of this primary
‘‘host’’ cell is lost. Primary endosymbiosis is believed to have
occurred once in evolution, giving rise to the proto-alga that is
the ultimate root of all plastids.(4) The plastid became fully
Department of Biological Sciences and Center for Comparative established in the proto-algal population and many genes of
Genomics, University of Iowa, Iowa City both photosynthetic and non-photosynthetic function were
Funding agency: This work was supported by grants by the National transferred to the nucleus of the primary host. The remarkable
Science Foundation. (NSF) awarded to D. B. (DEB 01-07754, MCB
achievement of these cells was to engineer a way of reintro-
01-10252, MCB 02-36631). J. D. H. was supported by an Institutional
NRSA (T 32 GM98629) from the National Institutes of Health and
ducing all the plastid proteins, whose genes were transferred
H. S. Y. was partially supported by the Post Doctoral Fellows Program to the nucleus and translated in the cytoplasm, back into
of the Korean Science and Engineering Foundation. the plastid compartment to express their function. The esta-
*Correspondence to: Debashish Bhattacharya, Department of Biolo- blishment of this protein import system after primary endo-
gical Sciences and Center for Comparative Genomics, University of
symbiosis required the evolution of a ‘‘transit’’ sequence
Iowa, 210 Biology Building, Iowa City, Iowa 52242-1324.
E-mail: [email protected]
(about 24–100 amino acids in length)(8) at their N termini. This
DOI 10.1002/bies.10376 extra sequence probably originated through mutations that
Published online in Wiley InterScience (www.interscience.wiley.com). extended the original open reading frame at the 50 terminus,
and the encoded proteins were selected for because of their
targeting capacity. Once the sequences encoding these
transit peptides were established in a few genes, then they
Abbreviations: COXII, mitochondrial cytochrome c oxidase subunit II;
gnd, 6-phosphogluconate dehydrogenase gene; GAPDH, glyceralde-
may have spread through exon shuffling into other photosyn-
hyde-3-phosphate dehydrogenase; Ma, millions of years ago; rRNA, thetic genes.(9,10) It appears that, once these unlikely events
ribosomal RNA. had occurred and the first algal populations were established,
the path was paved for the rise of photosynthetic eukaryotes.

50 BioEssays 26.1 BioEssays 26:50–60, ß 2003 Wiley Periodicals, Inc.

 15211878, 2004, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/bies.10376 by Universitat De Barcelona, Wiley Online Library on [22/10/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Review articles

Table 1. A list of the different types of algae and related protists, their classification, and key characteristics with
an emphasis on plastid features*
Plastid

Well - Known Tree of Life

Algal group # Species Origin Mem. Representatives Distinctive Features Classification

Red algae 5000–6000 Primary - CB 2 Porphyra, Gracilaria, Lack of flagellate stages, widely cultivated, used Plantae
(Rhodophyta) nori to make sushi, and source of agar and
carrageenan. (http://www.ucmp.berkeley.edu/
protista/rhodophyta.html)
Green algae/land plants >500,000 Primary - CB 2 Chlamydomonas, The green algae are common in intertidal regions Plantae
(Viridiplantae) flowering plants and are the sister to land plants that are
dominant in the terrestrial ecosystem. (http://
www.ucmp.berkeley.edu/
greenalgae/greenalgae.html)
Glaucophytes 13 Primary - CB 2 Cyanophora A small group of algae best known for their Plantae
(Glaucocystophyceae) primary plastid (cyanelle) that retains the
ancestral peptidiglycan wall of cyanobacterial
origin between its two plastid membranes.
(http://protist.i.hosei.ac.jp/taxonomy/Others/
Glaucophyta.html)
Cryptophytes 200 Secondary - RA 4 Guillardia Cold water-loving algae that retain the Chromista
(Cryptophyta) nucleomorph of the red algal secondary
endosymbiont. (http://www.uni-koeln.de/
math-nat-fak/botanik/bot1/Phylogenie-
Webseite/cryptophyta.html)
Haptophytes 500 Secondary - RA 4 Emiliania, Bloom-forming algae that can form coccolith Chromista
(Haptophyceae) coccolithophore scales that are a global carbon sink in oceans.
(http://www.soes.soton.ac.uk/staff/tt/)
Stramenopiles >10,000 Secondary - RA 4 Kelps, diatoms, A diverse group of both unicellular and Chromista
water molds, macroscopic protists that includes plastid-
downy mildews, containing (often called chromophyte algae)
late blight of potato and plastid-less forms (oomycetes) that have
presumably lost the organelle. (http://
www.ucmp.berkeley.edu/chromista/
chromista.html)
Dinoflagellates >4,000 Secondary - RA 3 Alexandrium, Predominantly unicellular algae that are often Alveolata
(Dinophyceae) Tertiary - HA* Karenia, mixotrophic and contain a diversity of different
Pfiesteria, red tide plastids. They cause harmful algal blooms
such as toxic red tides and are
a serious health threat (e.g., paralytic and
diarrhetic shellfish poisoning) in coastal
waters. (http://www.ucmp.berkeley.edu/
protista/dinoflagellata.html)
Apicomplexans >2,400 Secondary - RA* 4 Plasmodium, Non-photosynthetic, obligate intracellular Alveolata
(Apicomplexa) Toxoplasma, parasites that are causes of serious human
Cryptosporidium diseases such as malaria and toxoplasmosis.
Their remnant plastid (apicoplast) contains
a reduced (35 kb) genome. (http://www.ucmp.
berkeley.edu/protista/apicomplexa.html)
Ciliates (Ciliophora) >7,500 Loss — Paramecium, Plastid-less protists whose cell bodies are Alveolata
Tetrahymena covered with cilia, often fused together in rows
or tufts called cirri. The ciliate nucleus is
differentiated into macro- and micronuclei.
(http://www.ucmp.berkeley.edu/protista/
ciliata.html)
Chlorarachniophytes 6 Secondary - GA 4 Chlorarachnion Unicellular marine amoebae containing a green Cercozoa
(Chlorarachniophyceae) plastid. The plastid retains the remnant
nucleus (nucleomorph) of the green algal
secondary endosymbiont.
(http://tolweb.org/tree?group¼
Chlorarachniophytes&contgroup¼
The_Other_Protists)

BioEssays 26.1 51
 15211878, 2004, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/bies.10376 by Universitat De Barcelona, Wiley Online Library on [22/10/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Review articles

Table 1. (Continued)
Plastid

Well - Known Tree of Life

Algal group # Species Origin Mem. Representatives Distinctive Features Classification

Euglenids >800 Secondary - GA 3 Euglena, Astasia Algae that are common in organic-rich Euglenozoa
(Euglenida) freshwater habitats. They contain a green
plastid of secondary endosymbiotic origin and
are known for their distinctive flowing
movement (metaboly) and cell surface
(pellicle). Euglenids are closely related to the
parasitic trypanosomes. (http://bio.rutgers.
edu/euglena/)

*Mem. is for the number of membranes surrounding plastids, CB is cyanobacterium, RA is red alga, GA is green alga, and HA is haptophyte alga. The taxonomic
classification of the algal groups follows NCBI (http://www.ncbi.nlm.nih.gov/), whereas the Tree of Life classifications indicates their position in the eukaryotic
tree and follows different authors (see text for details) - the groups shown in bold are the chromalveolates and share a single red algal secondary endosymbiont,
whereas the underlined groups may share a single green algal endosymbiont and are termed cabozoans. The asterisks indicate cases of possible plastid
replacements. The web sites are good sources for additional information and/or images of the different algae.

Recent phylogenetic analyses using nuclear and mitochon- (Table 1). The extra membranes, from inside out, are thought
drial loci(11–13) suggest that the proto-alga split into two to be the plasma membrane of the engulfed alga (3rd) and the
lineages. The first contains the glaucophyte algae, which failed phagosomal membrane of the host cell of the secondary
to rise to any great taxonomic importance,(14,15) whereas the plastid (4th).(25) The 4th membrane has presumably been lost
second gave rise to the highly successful red algae(16) and in some groups (e.g., euglenids and most dinoflagellates, see
their sister group the green algae(17) plus land plants.(18) below) and two retain a smoking gun of eukaryotic enslave-
These three lineages are classified as the Plantae (see ment, the remnant nucleus of the algal symbiont. This reduced
Table 1). Endosymbiosis left a sizeable mark on the Plantae genome, the nucleomorph, is found between the 2nd and 3rd
that goes well beyond the lateral transfer of photosynthetic plastid membranes in the periplastid space (the former
capacity. A recent analysis(19) of the complete Arabidopsis cytoplasm of the algal endosymbiont) and has been se-
nuclear genome suggests that up to 18% of this plant’s genes, quenced in a cryptophyte and a chlorarachniophyte (see
many of non-photosynthetic function (e.g., disease resistance, Fig. 1B). Phylogenies using nucleomorph genes reveal the
intracellular protein routing), originated from the cyanobacter- identity of the algal symbiont (red in cryptophytes and green
ium through endosymbiotic gene transfer. Endosymbiosis in chlorarachniophytes).(26–28) Interestingly, both reduced
had, therefore, a considerable influence in the early evolution genomes have converged on a similar size (551 kb for
of algae by significantly enriching their nuclear genomes with cryptophytes, 380 kb for chlorarachniophytes), set of retained
cyanobacterial, often duplicated genes. Selection could act genes, and a compact organization.(29,30)
on these divergent sequences to explore new functions(13,19) A final important marker of secondary endosymbiosis
or to replace existing host genes with those from the is the presence of an extended N terminus in nuclear-
endosymbiont.(20,21) encoded plastid proteins that encodes a bipartite targeting
sequence. The first extension is a signal sequence that
Secondary endosymbiosis and leads the plastid-bound proteins to the secretory pathway
the rise of algae via the endoplasmic reticulum-derived outer membrane of
Once the Plantae had been established (Fig. 1A), the stage these plastids, whereas the second sequence is the typical
was set for secondary endosymbiosis, whereby a protist transit peptide used to cross the inner two plastid mem-
engulfed an existing alga (Fig. 1B).(22,23) This type of branes.(8,25) Therefore, like primary endosymbiosis, second-
eukaryote–eukaryote endosymbiosis explains the vast ma- ary endosymbiosis also required at least one significant
jority of algal diversity. Secondary plastids are found in algae evolutionary innovation to make the process work: the
containing chlorophyll c (chromophytic algae)(24) and non- independent origin of a signal sequence that is N-terminal
green algal/plant forms containing chlorophyll b (euglenids of the existing transit peptide for each nuclear-encoded
and chlorarachniophytes), and are unambiguously identified plastid protein to ensure correct passage across the three to
by the presence of three or four bounding membranes four membranes.

52 BioEssays 26.1
 15211878, 2004, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/bies.10376 by Universitat De Barcelona, Wiley Online Library on [22/10/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Review articles

Figure 1. Origins of plastids via A: primary, B:

secondary, and C: tertiary endosymbiosis. Gene
transfer from the endosymbiont to the host nucleus
is shown with the arrows and the colored chro-
mosomes. The mitochondrion has been omitted
from these figures. The remnant algal nucleus
(nucleomorph) in secondary and tertiary endosym-
bioses is shown. This genome has been lost in all
algae but the cryptophytes (member of the
chromalveolates) and chlorarachniophytes
(marked with asterisks).

The secondary plastids in brief hypothesis. Analysis of small subunit rRNA(44) and a combined
data set of EF-1a, actin, a-tubulin, and b-tubulin amino acid
The chromalveolate hypothesis sequences (that did not include haptophytes)(45) are consis-
The chromalveolates group was postulated primarily on the tent with a sister group relationship between two chromalveo-
basis of molecular phylogenetic analyses that unite particular late groups, the stramenopiles and alveolates. The limited
members of these morphologically disparate lineages,(32) taxon sampling and phylogenetic power of these data sets are
and the hypothesis that all taxa containing chlorophyll c a weakness that needs to be addressed in future studies. In
(i.e., a chromophytic plastid)(33,34) share a common origin. contrast, strong support for chromalveolate monophyly has
The alveolates share two characters that unambiguously come from analyses of plastid genes(43) and from the finding
unite them as a lineage, namely tubular mitochondrial cristae of a unique gene duplication shared by members of this
and sacs or alveoli under the plasma membrane. The assemblage.(42)
ecologically and economically important chromalveolates We have recently analyzed a concatenated data set of five
(see Table 1)(35) defines a broadly diverse group that includes plastid-encoded genes (5827 nt in total) from 36 taxonomically
the Chromista, comprising the cryptophyte,(36) haptophyte,(37) diverse members of the red and chromist algae. In this study,
and stramenopile(16) algae, and the Alveolata, comprising we addressed one cornerstone of the chromalveolate hypoth-
the parasitic apicomplexans,(38) the plastid-less ciliates,(39) esis that had not yet been adequately tested using multiple
and the dinoflagellate algae.(40) The chromalveolate plastid nuclear loci, the monophyly of the Chromista (see Table 1).(33)
is believed to have originated from a red algal secondary This group previously had little justification on morphologi-
endosymbiosis with the ensuing evolution of chlorophyll c2. cal(24) or phylogenetic grounds (nuclear and mitochondrial loci
The plastid was putatively lost in ciliates and parasitic/ do not resolve their positions)(4,11,13) for being united in a single
saprobic stramenopiles like oomycetes (e.g., the water mold lineage. They primarily share a four-membrane-bound chlor-
Achlya) and its genome reduced to a 35 kb DNA circle in the ophyll c-containing plastid that is located within the lumen of
apicomplexan plastid (the apicoplast).(41,42) Evidence in the rough endoplasmic reticulum. The haptophytes and
support of these ideas has been slow in coming but recent stramenopiles, however, share characters such as tubular
data now appear to have established the chromalveolates as a mitochondrial cristae, similar storage products, and fucox-
monophyletic entity.(42,43) anthin that suggest a specific relationship between these
Phylogenies of nuclear genes have until now, however, taxa.(24) The combined plastid gene tree (Fig. 2) appears to
only provided marginal support for the chromalveolate have settled the issue of chromist monophyly by providing

BioEssays 26.1 53
 15211878, 2004, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/bies.10376 by Universitat De Barcelona, Wiley Online Library on [22/10/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Review articles

Figure 2. Phylogenetic relationships of red algal and

chromist plastids inferred from a minimum evolution (ME)
analysis of the combined DNA sequences of 16S rRNA,
psaA, psbA, rbcL, and tufA (5827 nt). The general time
reversible model(79) with estimations of nucleotide fre-
quencies, the proportion of invariant sites that are unable
to accept substitutions, and the shape parameter of
the gamma distribution to accommodate rate variations
across sites (GTR þ I þ G [gtr] model) was used in this
analysis. Results of a ME-gtr bootstrap analysis (2000
replicates) are shown above the branches. The thick
branches are of significant evolutionary importance and
all have >95% posterior probability in a Bayesian analysis
of the DNA data (for details, see Yoon et al.).(43) This
tree is rooted on the branch leading to the glauco-
phyte sequence. The branch lengths are proportional to
the number of substitutions per site (see scale in figure).
The asterisk marks the branch where the chromist plastid
originated through a red algal secondary endosymbiosis
(ca. 1260 Ma).(43)

strong support for three important ideas: (1) as previously enolase gene in cryptophytes is consistent with this idea.(20)
suggested,(46) the chromist plastids are all of red algal origin, Verification of the early divergence of the cryptophytes will
(2) chromist plastids share a monophyletic origin and, by have to wait, however, until alveolate plastid sequences are
extension, so do the host cells containing these plastids, and included in the analysis shown in Fig. 2. This analysis could
(3) the basal position of the cryptophytes in the Chromista have two likely outcomes: (1) alveolate photosynthetic genes
suggests that retention of the red algal nucleomorph in the of red algal origin diverge from the branch uniting all chromists
periplastid space, the presence of phycobilin pigments, and (as expected ¼ 2 losses of flattened cristae, or (2) they diverge
the storage of photosynthates as starch (all are absent in on the branch uniting the haptophytes and stramenopiles (¼ 1
haptophytes and stramenopiles) are ancestral endosymbiont loss). Such target genes are most likely to be found in the
characters that were likely lost after the divergence of the nucleus of dinoflagellates because the non-photosynthetic
cryptophytes (see character evolution model in Fig. 3). apicomplexans and ciliates may not have maintained these
Furthermore, in contrast to the haptophytes and strame- coding regions.
nopiles that have tubular mitochondrial cristae, the crypto- Another important result from the Yoon et al.(43) study was
phytes have flattened cristae, suggesting that this was the the dating of the chromist secondary endosymbiotic event.
ancestral condition in the Chromista. The alveolates, however, Usage of two red algal fossil constraint dates and a molecular
contain tubular cristae and are presumably sister to the chro- clock method that does not assume a uniform mutation rate in
mists (Fig. 3). If flattened cristae was ancestral in the different lineages suggests that the earliest date (asterisk in
chromalveolates, then this character was lost twice, once in Fig. 2) for the origin of the chromist plastid is 1260
30 million
the common ancestor of alveolates and once after the years ago (Ma).(43) The endosymbiosis marks, therefore, the
divergence of the cryptophytes in the Chromista (see Fig. 3). birth of the chromist algae. This date is substantially earlier
A more parsimonious explanation for the cristae data would than some estimates (e.g., 850 Ma)(31) but agrees well with the
emerge if the cryptophytes were to branch at the base of the fossil record, which shows the appearance of a diversity of
chromalveolates and the chromists would become paraphy- algae and protists near the Mesoproterozoic/Neoproterozoic
letic. Analysis of an endosymbiotic replacement involving the boundary about 1000 Ma.(47,48) A recent analysis of the

54 BioEssays 26.1
 15211878, 2004, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/bies.10376 by Universitat De Barcelona, Wiley Online Library on [22/10/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Review articles

Figure 3. Proposed evolutionary tree of the chromalveolates showing the origin and loss of important (mostly plastid) characters. The
evidence for chromist plastid monophyly is described in Yoon et al.(43) The timing of the tertiary endosymbiosis that gave rise to the
haptophyte-type plastid in either the pre-dinoflagellate(66,80) or only in fucoxanthin-containing taxa(69) remains an open question (large filled
circle with a cross). The possible green algal endosymbiosis in the common ancestor of apicomplexans and dinoflagellates (large open
circle with a cross) is based on Funes et al.,(21,76) Kohler et al.,(75) and our preliminary results (see text for details). Gain or loss of character
states is shown with the slashes across the branches. The branches with broken lines at the origin represent uncertainty about the position of
these taxa in the host tree, whereas the small filled circles with dashes or the wavy line inside represent plastid loss and plastid degeneration,
respectively. pRER is the plastid rough endoplasmic reticulum.

Earth’s geochemical record, in particular with respect to chromalveolates such as green algae/land plants and red
the levels of the oxygen and nitrogen that are critical to algal algae. These latter taxa have not undergone the gene
growth, is consistent with the known eukaryotic fossil duplication–replacement event.(42) These findings all point
record(49) and our molecular dating results. Furthermore, a to a critical event in evolution, a single red algal secondary
subsequent analysis (H.S.Y., J.D.H., and D.B. unpublished endosymbiosis that gave birth to common ancestor of a super-
data) using a six plastid gene data set that includes green assemblage, the chromalveolates. The endosymbiotic event is
algae and land plants to incorporate additional robust fossil ancient (ca. 1200 Ma) and the host cell of the secondary plastid
constraints in the gene phylogeny (e.g., origin of land plants has diverged extensively during this long period of evolution.
and the monocot–dicot split) substantiates the findings of It is a testimony to the power of modern molecular evolu-
Yoon et al.(43) tionary methods and the slow evolutionary rate of many plastid
Now that Chromista monophyly appears to be established, genes that we are able to look back so far in evolutionary time
what evidence is there to include them in the chromalveolates? and still detect the signal of shared ancestry (see Fig. 2).
The strongest evidence comes from phylogenetic analyses The major insights into eukaryotic evolution that come from
that show a specific phylogenetic relationship between the the finding of chromalveolate monophyly are:
nuclear-encoded plastid-targeted glyceraldehyde-3-phos-
phate dehydrogenase (GAPDH) gene in the cryptophytes * secondary plastid loss is common (e.g., in plastid-less
and stramenopiles (chromists) on one hand and the apicom- stramenopiles such as oomycetes, in ciliates, and in some
plexans and dinoflagellates (alveolates) on the other.(42) dinoflagellates).(42,50) In support of this idea, Andersson
Importantly, this gene appears to have originated through a and Roger(51) have recently found a 6-phosphogluconate
unique duplication of the existing cytosolic gene in these taxa, dehydrogenase (gnd) gene of cyanobacterial (i.e., plastid)
and the subsequent replacement of the original plastid- origin in the parasitic stramenopile, Phytophthora infes-
targeted sequence (of cyanobacterial origin) by the gene dup- tans. This suggests that Phytophthora was likely once
licate. This unusual shared derived character unites the photosynthetic because its gnd gene is closely related to
studied chromalveolates and, as corroboration, the phyloge- the homologue in photosynthetic members of this lineage.
nies show the plastid-targeted genes to be phylogenetically * Chromalveolates share a homologous plastid protein
distinct from the homolog of cyanobacterial origin in non- import system that evolved once in their common ancestor.

BioEssays 26.1 55
 15211878, 2004, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/bies.10376 by Universitat De Barcelona, Wiley Online Library on [22/10/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Review articles

* Chlorophyll c2 appears to have evolved only once in the nucleomorph sequences has established the green algal
common ancestor of the chromalveolates. Phylogenetic origin of the secondary plastid in chlorarachniophytes.(27,28)
analysis of chlorophyll a/b and chlorophyll a/c light harvest- A recent analysis of cDNAs from the chloroarachniophyte
ing complex proteins supports this idea showing that the Bigelowiella natans indicates that a large number of plastid
chlorophyll a/c-binding proteins in chromists (and dino- genes in this species were transferred from the green algal
flagellates) form a monophyletic group that traces its origin endosymbiont to the host nucleus. More remarkably, about
to a red algal-like ancestor.(46) 21% of the photosynthetic genes were derived from lateral
transfers involving non-green sources such as red or strame-
nopile algae.(61) These results underline the importance
Given these impressive data, one may be led to believe that
of endosymbiosis to facilitating intergenome gene transfer
the story of chromalveolate evolution has been convincingly
and suggest that mixotrophic species such as Bigelowiella
solved. This is not, however, entirely the case as the section
(and dinoflagellates, see below) may be particularly adept at
on dinoflagellates below will explain. But first, we will review
scavenging genes from different prey. In contrast, taxa such as
current knowledge about the secondary plastids of green algal
the green alga Chlamydomonas reinhardtii, which is auto-
origin.
trophic and for which the complete nuclear genome is known,
do not show evidence of lateral transfer of photosynthetic
The green secondary plastids genes from different sources (i.e., all are derived from the
Secondary endosymbiosis also gave rise to the chlorophyll original cyanobacterial primary endosymbiont).(61)
b-containing plant-like plastid in distinctly non-plant-like taxa, What still remains to be determined with regard to green
the euglenids(52) and the chlorarachniophytes. The Euglenida algal secondary plastids is whether chlorarachniophytes and
are sister to the Kinetoplastida (which includes the parasitic euglenids share the same green algal endosymbiont in a
trypanosomatids), and together form the Euglenozoa. The common ancestor. The available nuclear and plastid gene
presence of a three-membrane green plastid in photosynthetic data do not support this hypothesis,(62–64) although the high
euglenids and the absence of a plastid in the trypanosomes divergence rate and base composition bias of chlorarachnio-
had previously suggested that the algal secondary endosym- phyte and euglenid sequences leaves open the possibility of
biosis occurred at the base of the euglenid lineage and that Cercozoa–Euglenozoa monophyly (together the Cabozoa
trypanosomatids ancestrally lacked a plastid. The remarkable [Table 1]).(35) If true, this latter scenario would reduce the
finding of plant-like genes in trypanosomatids now suggest, number of secondary endosymbioses involving a chlorophyll
however, that all Euglenozoa may have at one time been b-containing endosymbiont to one, render secondary plastid
photosynthetic and that kinetoplastids lost their photosynthe- loss a widespread force in eukaryotic evolution, and place
tic organelle secondarily.(53) The footprint of the secondary algae near the root of much of the tree of life.
endosymbiosis in the trypanosomatids is metabolic enzymes
localized in specialized peroxisomes (glycosomes [not derived The dinoflagellates and
from plastids]) that trace their origin to the green alga through their tertiary endosymbioses
endosymbiotic gene transfer. This story underlines the As if the genomic gymnastics described above were not
surprising ancestral distribution of photosynthesis in eukar- enough, nature has devised yet another way of distributing
yotes and suggests that plastids may have been more plastids among eukaryotes, tertiary endosymbiosis. This pro-
widespread than we imagine. The distribution of these cess entails the engulfment of an alga with a secondary plastid
organelles has been decimated by secondary losses due (Fig. 1C). Tertiary endosymbiosis has, until now, been limited
often to the evolution of a parasitic or saprobic life-style (i.e., to the dinoflagellates and, in this group, involves the replace-
trypanosomatids were presumably once free-living algae),(54) ment of the existing red algal secondary plastid (shared with
a theme that was repeated in the chromalveolates. the chromists)(50,64–66) with another of secondary origin (so-
The second group of non-green algal protists that contain called tertiary plastid replacement). The putative ancestral
chlorophyll b is the chlorarachniophytes. These are amoebo- (and most common) plastid in this group is bound by three
flagellate members of the protist assemblage Cercozoa(55) membranes, contains chlorophyll c2 and the unique accessory
that includes euglyphids, formanifera, and plasmodiophorid pigment peridinin as the main carotenoid. The peridinin plastid
plant pathogens.(56–58) This broad array of protists contains does not, however, contain a typical genome because its
two photosynthetic groups, the chlorarachniophytes with genes have been reduced to single- or two-gene minicir-
their chlorophyll b-containing secondary plastid and the filose cles.(65,67,68) Until now, only 15 plastid protein genes have
amoeba, Paulinella chromatophora, with its cyanelle that been found in peridinin dinoflagellates, leaving in question the
superficially resembles the plastids of glaucophytes.(59,60) location of the sequences that encode the remaining
Whereas the origin of the Paulinella cyanelle still needs to be components of the photosynthetic apparatus. Although it has
resolved, the phylogenetic evidence based on plastid and been presumed that the minicircle genes trace their origin to

56 BioEssays 26.1
 15211878, 2004, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/bies.10376 by Universitat De Barcelona, Wiley Online Library on [22/10/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Review articles

the red algal secondary endosymbiosis in the chromalveol- identify the missing dinoflagellate plastid genes as compo-
ate ancestor(65), it is also possible that these sequences may nents of the Alexandrium nuclear genome. Preliminary data
have multiple origins from different endosymbiotic events from the Alexandrium cDNA data set have in fact confirmed the
(see below). presence of many plastid genes in the nucleus of this dino-
Given the ancestral origin of the red algal secondary flagellate (J.D.H., H.S.Y., and D.B. unpublished results).
plastid in dinoflagellates, tertiary replacement has been used
to explain the plastid in taxa such as Karenia spp. and Conclusions
Karlodinium micrum that contain chlorophylls c1 þ c2 and 190 - Endosymbiosis has created a plethora of photosynthetic
hexanoyloxy-fucoxanthin and/or 190 -butanoyloxy-fucoxanthin eukaryotes that have significantly shaped the Earth’s history.
but lack peridinin, similar to the haptophyte algae.(66,69) The known fossil record and our molecular dating analysis
Tertiary endosymbiosis also would account for plastid origin suggest that photosynthetic eukaryotes have been around for
in other dinoflagellates such as Dinophysis spp. (cryptophyte well over a billion years. The super-assemblage, chromalveo-
origin),(70) Peridinium foliaceum (stramenopile origin),(71) and lates, appears to be a monophyletic group and the ancient red
Lepidodinium viride (green algal origin).(72) Give these algal secondary endosymbiosis that we have recently de-
complex series of events, understanding the impact of scribed(43) and the GAPDH duplication found by Fast et al.(42)
endosymbiosis on dinoflagellate evolution will require a unite them as a cohesive lineage. The analysis of multi-gene
genomics approach. In this regard, we are currently generat- nuclear and mitochondrial data sets that accommodate a
ing a data set of up to 10,000 unique 30 reads from normalized broad taxonomic sampling should verify this hypothesis in the
and subtracted cDNA libraries of the toxic dinoflagellate coming years.(74) The present state of knowledge regarding
Alexandrium tamarense. These data will help us quantify the plastid and host relationships among algae is summarized in
genomic contribution of multiple endosymbioses to dinofla- Fig. 4. The plastid sequence data have significantly added to
gellate evolution and, as we and others(73) predict, likely our understanding of the algal tree of life both within lineages

Figure 4. Present understanding of the phylogenetic relationships of algae. The host relationships that have resulted from analyses of
nuclear or mitochondrial loci are shown with the black line. The branches with broken lines represent uncertainty about the position of these
taxa in the host tree. Phylogenetic relationships inferred from plastid gene comparisons are shown with the colored lines: red for the red algal
secondary endosymbiosis in chromalveolates, green for the putative green algal secondary endosymbiosis in cabozoans, and blue for the
haptophyte tertiary replacement either in the dinoflagellate common ancestor or only in fucoxanthin-containing taxa. Cabozoan monophyly
has not been substantiated with molecular phylogenetic data therefore the line leading from the Euglenozoa to the chlorarachniophytes is
dashed. Cases of potential gene transfer from green algae in the common ancestor of apicomplexans and dinoflagellates are not shown in
this figure. Plastid loss in the ciliates is shown with the open red box and plastid degeneration in the apicomplexans is shown with the dashed
red line. CB denotes the primary endosymbiosis that gave rise to the proto-algal ancestor of the red, green, and glaucophyte algae.

BioEssays 26.1 57
 15211878, 2004, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/bies.10376 by Universitat De Barcelona, Wiley Online Library on [22/10/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Review articles

and through the union of groups such as the Chromista that 2. Margulis L. Origin of Eucaryotic Cells. New Haven: Yale University Press;
had yet to be proven using other loci. 1970. 349 pp.
3. Gray MW. The endosymbiont hypothesis revisited. Int Rev Cytol 1992;
Perhaps most exciting is the mounting evidence(21,75) for 141:233–357.
a green algal influence in the alveolates. Kohler et al.(75) 4. Bhattacharya D, Medlin L. The phylogeny of plastids: A review based on
originally suggested a green algal origin of the apicoplast comparisons of small subunit ribosomal RNA coding regions. J Phycol
1995;31:489–498.
based on phylogenetic analyses of the highly divergent tufA 5. Delwiche CF. Tracing the thread of plastid diversity through the tapestry
gene. This relatively weakly supported result was recently of life. Am Nat 1999;154(S4):S164–S177.
buttressed by the findings of Funes et al.(21) who identified a 6. McFadden GI. Primary and secondary endosymbiosis and the origin of
plastids. J Phycol 2001;37:951–959.
unique nuclear-encoded cox2 (mitochondrial cytochrome c 7. Reumann S, Davila-Aponte J, Keegstra K. The evolutionary origin of the
oxidase subunit II gene) in apicomplexans and in some protein-translocating channel of chloroplastic envelope membranes:
green algae that is split into two coding regions (cox2a, cox2b). identification of a cyanobacterial homolog. Proc Natl Acad Sci USA 1999;
96:784–789.
Phylogenetic analysis supports the monophyly of the COX- 8. Foth BJ, Ralph SA, Tonkin CJ, Struck NS, Fraunholz M, Roos DS,
IIA þ COXIIB sequence in greens and apicomplexans, imply- Cowman AF, McFadden GI. Dissecting apicoplast targeting in the
ing a single origin of these split genes in a green alga, and its malaria parasite Plasmodium falciparum. Science 2003;299:705–708.
9. Martin W, Herrmann RG. Gene transfer from organelles to the nucleus:
lateral transfer into the apicomplexans presumably after how much, what happens, and why? Plant Physiol 1998;118:9–17.
endosymbiosis.(21,64) Funes et al.(76) and Waller et al.(77) have 10. Blanchard JL, Lynch M. Organellar genes: why do they end up in the
recently provided differing interpretations of the COXII data nucleus? Trends Genet 2000;16:315–320.
11. Gray MW, et al. Genome structure and gene content in protist mito-
and its support for a green algal endosymbiosis in the chondrial DNAs. Nucleic Acids Res 1998;26:865–878.
apicomplexans. Interestingly, analysis of our initial Alexan- 12. Moreira D, Le Guyader H, Philippe H. The origin of red algae and the
drium cDNA set shows the presence of multiple green algal evolution of chloroplasts. Nature 2000;405:69–72.
13. Stibitz T, Keeling P, Bhattacharya D. Symbiotic origin of a novel actin
genes in this taxon that is sister to apicomplexans (J.D.H., gene in the cryptophyte Pyrenomonas helgolandii. Mol Biol Evol 2000;
H.S.Y., and D.B. unpublished results), supporting the findings 17:1731–1738.
of Funes et al.(21,76) In our estimation, these exciting results 14. Kies L. Zur systematischen Einordnung von Cyanophora paradoxa,
Gloeochaete wittrockiana und Glaucocystis nostochinearum. Ber Deu-
are either due to multiple gene transfers from different green tsch Bot Ges Bd 1979;92:445–454.
algae or a ‘‘hidden’’ green algal endosymbiosis that occurred 15. Kies L, Kremer BP. Typification of the Glaucocystophyta. Taxon 1986;
at least in the common ancestor of apicomplexans and 35:128–133.
16. Graham LD, Wilcox LW. Algae. New Jersey: Prentice-Hall Incorporated;
dinoflagellates. Addition of other completed genome se- 2000. 700 pp.
quences (e.g., Plasmodium falciparum)(78) to the analyses 17. Melkonian M. Phylum Chlorophyta: introduction to the Chlorophyta. In:
should provide the data to test this idea. We also predict that Margulis L, Corliss JO, Melkonian M, Chapman DJ, editors. Handbook of
Protoctista. Boston: Jones and Bartlett Publishers Incorporated; 1990.
genomics projects will, in the near future, turn up other p 597–599.
examples of gene transfer in chromalveolates and in other 18. Raven P, Evert RF, Eichhorn SE. Biology of Plants. New York: Bedford,
protists that have had a photosynthetic ancestry. Groups that Freeman, and Worth Publishing Group; 1998. 875 pp.
19. Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D,
contain, or at one time contained, a secondary or tertiary Stoebe B, Hasegawa M, Penny D. Evolutionary analysis of Arabidopsis,
plastid will likely encode nuclear genes that have arisen cyanobacterial, and chloroplast genomes reveals plastid phylogeny and
through lateral gene transfer from the eukaryotic endosym- thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci
USA 2002;99:12246–12251.
biont(s), much like the case found for the genes of cyanobac- 20. Keeling PJ, Palmer JD. Lateral transfer at the gene and subgenic levels
terial origin in Arabidopsis.(19) in the evolution of eukaryotic enolase. Proc Natl Acad Sci USA 2001;
These events may best be interpreted under the ‘‘Russian 98:10745–10750.
21. Funes S, Davidson E, Reyes-Prieto A, Magallón S, Herion P, King MP.
Doll Paradigm’’ in which each round of endosymbiosis leads to González-Halphen D. A green algal apicoplast ancestor. Science 2002;
large-scale gene transfer that significantly reshapes the 298:2155.
nuclear genome of the host. This process, schematically 22. Ludwig M, Gibbs SP. Are the nucleomorphs of cryptomonads and
Chlorarachnion the vestigial nuclei of eukaryotic endosymbionts? Ann
portrayed in the nuclear chromosomes shown in Fig. 1, is akin Acad Sci NY 1987;503:198–211.
to nested Russian dolls and is predicted to be a driving force in 23. Gibbs S. The evolution of algal chloroplasts. In: Lewin RA, editor. Origins
generating eukaryotic biodiversity by providing a major influx of Plastids. New York: Chapman and Hall Company; 1993. p 107–121.
24. Bhattacharya D, Medlin L, Wainright PO, Ariztia EV, Bibeau C, Stickel SK,
of novel genes into protistan genomes. Sogin ML. Algae containing chlorophylls aþc are polyphyletic: Molecular
evolutionary analysis of the Chromophyta. Evolution 1992;46:1801–
Acknowledgments 1817.
25. McFadden GI. Plastids and protein targeting. J Euk Microbiol 1999;
Figure 1 is based on an image created by NSF graphic artist 46:339–346.
Kirk D. Woellert. 26. Douglas SE, Murphy CA, Spencer DF, Gray MW. Molecular evidence
that cryptomonad algae are chimaeras of two phylogenetically distinct
unicellular eukaryotes. Nature 1991;350:148–151.
References 27. McFadden GI, Gilson PR, Waller RF. Molecular phylogeny of chlorar-
1. Mereschkowsky C. Über Natur und Ursprung der Chromatophoren im achniophytes based on plastid rRNA and rbcL sequences. Arch
Pflanzenreiche. Biol Zentralbl 1905;25:593–604. Protistenkd 1995;145:231–239.

58 BioEssays 26.1
 15211878, 2004, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/bies.10376 by Universitat De Barcelona, Wiley Online Library on [22/10/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Review articles

28. Van de Peer Y, Rensing SA, Maier U-G, De Wachter R. Substitution rate 52. Walne PL, Kivic PA. Phylum Euglenida. In: Margulis L, Corliss JO,
calibration of small subunit rRNA identifies chlorarachniophyte endo- Melkonian M, Chapman DJ, editors. Handbook of Protoctista. Boston:
symbionts as remnants of green algae. Proc Natl Acad Sci USA 1996; Jones and Bartlett Publishers Incorporated; 1990. p 270–287.
93:7732–7736. 53. Hannaert V, Saavedra E, Duffieux F, Szikora J-P, Rigden DJ, Michels
29. Gilson PR, McFadden GI. Good things in small packages: the tiny PAM, Opperdoes FR. Plant-like traits associated with metabolism of
genomes of chlorarachniophyte endosymbionts. BioEssays 1997;19: Trypanosoma parasites. Proc Natl Acad Sci USA 2003;100:1067–
167–173. 1071.
30. Douglas S, Zauner S, Fraunholz M, Beaton M, Penny S, Deng LT, Wu X, 54. Martin W, Borst P. Secondary loss of chloroplasts in trypanosomes. Proc
Reith M, Cavalier-Smith T, Maier UG. The highly reduced genome of an Natl Acad Sci USA 2003;100:765–767.
enslaved algal nucleus. Nature 2001;410:1091–1096. 55. Cavalier-Smith T. A revised six-kingdom system of life. Biol Rev Camb
31. Cavalier-Smith T. Chloroplast evolution: secondary symbiogenesis and Philos Soc 1998;73:203–266.
multiple losses. Curr Biol 2002;12:R62–R64. 56. Bhattacharya D, Helmchen T, Melkonian M. Molecular evolutionary
32. Gajadhar AA, Marquardt WC, Hall R, Gunderson J, Ariztia-Carmona EV, analyses of nuclear-encoded small subunit ribosomal RNA identify an
Sogin ML. Ribosomal RNA sequences of Sarcocystis muris, Theileria independent rhizopod lineage containing the Euglyphidae and the
annulata and Crypthecodinium cohnii reveal evolutionary relation- Chlorarachniophyta. J Euk Microbiol 1995;42:65–69.
ships among apicomplexans, dinoflagellates, and ciliates. Mol Biochem 57. Cavalier-Smith T, Chao EE. Molecular phylogeny of the free-living
Parasitol 1991;45:147–154. archezoan Trepomonas agilis and the nature of the first eukaryote. J
33. Cavalier-Smith T. The kingdom Chromista: origin and systematics. In: Mol Evol 1996;43:551–562.
Round FE, Chapman DJ, editors. Progress in Phycological Research 58. Keeling PJ. Foraminifera and Cercozoa are related in actin phylogeny:
(Vol. 4). Bristol: Biopress Limited; 1986. p 309–347. two orphans find a home? Mol Biol Evol 2001;18:1551–1557.
34. Cavalier-Smith T. Membrane heredity and early chloroplast evolution. 59. Bhattacharya D, Helmchen T, Bibeau C, Melkonian M. Comparisons of
Trends Plant Sci 2000;5:174–182. small subunit ribosomal RNAs reveal the evolutionary position of the
35. Cavalier-Smith T. Principles of protein and lipid targeting in secondary Glaucocystophyta. Mol Biol Evol 1995;12:415–420.
symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins 60. Helmchen T, Bhattacharya D, Melkonian M. Analyses of ribosomal
and the eukaryote family tree. J Eukaryot Microbiol 1999;46:347–366. RNA sequences from glaucocystophyte cyanelles provide new insights
36. Gillott M. Phylum Cryptophyta (Cryptomonads). In: Margulis L, Corliss into the evolutionary relationships of plastids. J Mol Evol 1995;41:203–
JO, Melkonian M, Chapman DJ, editors. Handbook of Protoctista. 210.
Boston: Jones and Bartlett Publishers Incorporated; 1990. p 139–151. 61. Archibald JM, Rogers MB, Toop M, Ishida K-I, Keeling PJ. Lateral gene
37. Green JC, Perch-Nielsen K, Westbroek P. Phylum Prymnesiophyta. In: transfer and the evolution of plastid-targeted proteins in the secondary
Margulis L, Corliss JO, Melkonian M, Chapman DJ, editors. Handbook of plastid-containing alga Bigelowiella natans. Proc Natl Acad Sci USA
Protoctista. Boston: Jones and Bartlett Publishers Incorporated; 1990. 2003;100:7678–7683.
p 293–317. 62. Oliveira M, Bhattacharya D. Phylogeny of the Bangiophycidae (Rhodo-
38. Vivier E, Desportes I. Phylum Apicomplexa. In: Margulis L, Corliss JO, phyta) and the secondary endosymbiotic origin of algal plastids. Am J
Melkonian M, Chapman DJ, editors. Handbook of Protoctista. Boston: Bot 2000;87:482–492.
Jones and Bartlett Publishers Incorporated; 1990. p 549–573. 63. Archibald JM, Keeling PJ. Recycled plastids: a ‘green movement’ in
39. Lynn DH, Small EB. Phylum Ciliophora. In: Margulis L, Corliss JO, eukaryotic evolution. Trends Genet 2002;18:577–584.
Melkonian M, Chapman DJ, editors. Handbook of Protoctista. Boston: 64. Palmer JD. The symbiotic birth and spread of plastids: how many times
Jones and Bartlett Publishers Incorporated; 1990. p 498–523. and whodunit? J Phycol 2003;39:4–12.
40. Taylor FJR. Phylum Dinoflagellata. In: Margulis L, Corliss JO, Melkonian 65. Zhang Z, Green BR, Cavalier-Smith T. Single gene circles in dino-
M, Chapman DJ, editors. Handbook of Protoctista. Boston: Jones and flagellate chloroplast genomes. Nature 1999;400:155–159.
Bartlett Publishers Incorporated; 1990. p 419–437. 66. Yoon HS, Hackett J, Bhattacharya D. A single origin of the peridinin-, and
41. Wilson RJ, et al. Complete gene map of the plastid-like DNA of the fucoxanthin-containing plastids in dinoflagellates through tertiary endo-
malaria parasite Plasmodium falciparum. J Mol Biol 1996;261:155–172. symbiosis. Proc Natl Acad Sci USA 2002b;99:11724–11729.
42. Fast NM, Kissinger JC, Roos DS, Keeling PJ. Nuclear-encoded, plastid- 67. Barbrook AC, Howe CJ. Minicircular plastid DNA in the dinoflagellate
targeted genes suggest a single common origin for apicomplexan and Amphidinium operculatum. Mol Gen Genet 2000;263:152–158.
dinoflagellate plastids. Mol Biol Evol 2001;18:418–426. 68. Barbrook AC, Symington H, Nisbet RE, Larkum A, Howe CJ. Organiza-
43. Yoon HS, Hackett J, Pinto G, Bhattacharya D. The single, ancient origin tion and expression of the plastid genome of the dinoflagellate
of chromist plastids. Proc Natl Acad Sci USA 2002;99:15507–15512. Amphidinium operculatum. Mol Genet Genomics 2001;266:632–638.
44. Van de Peer Y, De Wachter R. Evolutionary relationships among the 69. Hansen G, Daugbjerg N, Henriksen P. Comparative stidy of Gymnodi-
eukaryotic crown taxa taking into account site-to-site rate variation in 18S nium mikimotoi and Gymnodinium aureolum, comb. nov. (¼Gyrodinium
rRNA. J Mol Evol 1997;45:619–630. aureolum) based on morphology, pigment composition, and molecular
45. Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF. A kingdom-level data. J Phycol 2000;36:394–410.
phylogeny of eukaryotes based on combined protein data. Science 70. Hackett JD, Maranda L, Yoon HS, Bhattacharya D. Phylogenetic
2000;290:972–977. evidence for the cryptophyte origin of the plastid of Dinophysis
46. Durnford DG, Deane JA, Tan S, McFadden GI, Gantt E, Green BR. A (Dinophysiales, Dinophyceae). J Phycol 2003;39:440–448.
phylogenetic assessment of the eukaryotic light-harvesting antenna pro- 71. Chesnick JM, Morden CW, Schmieg AM. Identity of the endosymbiont of
teins, with implications for plastid evolution. J Mol Evol 1999;48:59–68. Peridinium foliaceum (Pyrrophyta): analysis of the rbcLS operon. J Phycol
47. Knoll AH. The early evolution of eukaryotes: a geological perspective. 1996;32:850–857.
Science 1992;256:622–627. 72. Watanabe MM, Takeda Y, Sasa T, Inouye I, Suda S, Sawaguchi T,
48. Xiao S, Zhang Y, Knoll AH. Three-dimensional preservation of algae and Chihara M. A green dinoflagellate with chlorophylls a and b morphology
animal embryos in a Neoproterozoic phosphorite. Nature 1998;391:553– fine structure of the chloroplast and chlorophyll composition. J Phycol
558. 1987;23:382–389.
49. Anbar AD, Knoll AH. Proterozoic ocean chemistry and evolution: a 73. Zhang Z, Cavalier-Smith T, Green BR. Evolution of dinoflagellate
bioinorganic bridge. Science 2002;297:1137–1142. unigenic minicircles and the partially concerted divergence of their
50. Saldarriaga JF, Taylor FJ, Keeling PJ, Cavalier-Smith T. Dinoflagellate putative replicon origins. Mol Biol Evol 2002;19:489–500.
nuclear SSU rRNA phylogeny suggests multiple plastid losses and 74. Nozaki H, Matsuzaki M, Takahara M, Misumi O, Kuroiwa H, Hasegawa
replacements. J Mol Evol 2001;53:204–213. M, Shin-I T, Kohara Y, Ogasawara N, Kuroiwa T. The phylogenetic
51. Andersson JO, Roger AJ. A cyanobacterial gene in nonphotosynthetic position of red algae revealed by multiple nuclear genes from
protists-an early chloroplast acquisition in eukaryotes? Curr Biol 2002; mitochondria-containing eukaryotes and an alternative hypothesis on
12:115–119. the origin of plastids. J Mol Evol 2003;56:485–497.

BioEssays 26.1 59
 15211878, 2004, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/bies.10376 by Universitat De Barcelona, Wiley Online Library on [22/10/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Review articles

75. Kohler S, Delwiche CF, Denny PW, Tilney LG, Webster P, Wilson RJ, 78. Gardner MJ, et al. Genome sequence of the human malaria parasite
Palmer JD, Roos DS. A plastid of probable green algal origin in Api- Plasmodium falciparum. Nature 2002;419:498–511.
complexan parasites. Science 1997;275:1485–1489. 79. Rodrı́guez F, Oliver JL, Marin A, Medina JR. The general
76. Funes S, Davidson E, Reyes-Prieto A, Magallon S, Herion P, King MP, stochastic model of nucleotide substitution. J Theor Biol 1990;142:
Gonzalez-Halphen D. Response to Comment on ‘‘A Green Algal Apico- 485–501.
plast Ancestor’’. Science 2003;301:49. 80. Morden CW, Sherwood AR. Continued evolutionary surprises among
77. Waller RF, Keeling PJ, Van Dooren GG, McFadden GI. Comment on dinoflagellates. Proc Natl Acad Sci USA 2002;99:11558–11560.
‘‘A Green Algal Apicoplast Ancestor’’. Science 2003;301:49.

60 BioEssays 26.1