全 文 ：Journal of Systematics and Evolution 46 (3): 287–306 (2008) doi: 10.3724/SP.J.1002.2008.08035
(formerly Acta Phytotaxonomica Sinica) http://www.plantsystematics.com
Phylogeny and evolution of charophytic algae and land plants
Yin-Long QIU*
(Department of Ecology & Evolutionary Biology, The University Herbarium, University of Michigan, Ann Arbor, MI 48109-1048, USA)
Abstract Charophytic algae and land plants together make up a monophyletic group, streptophytes, which
represents one of the main lineages of multicellular eukaryotes and has contributed greatly to the change of the
environment on earth in the Phanerozoic Eon. Significant progress has been made to understand phylogenetic
relationships among members of this group by phylogenetic studies of morphological and molecular data over the
last twenty-five years. Mesostigma viride is now regarded as among the earliest diverging unicellular organisms in
streptophytes. Characeae are the sister group to land plants. Liverworts represent the first diverging lineage of
land plants. Hornworts and lycophytes are extant representatives of bryophytes and vascular plants, respectively,
when early land plants changed from gametophyte to sporophyte as the dominant generation in the life cycle.
Equisetum, Psilotaceae, and ferns constitute the monophyletic group of monilophytes, which are sister to seed
plants. Gnetales are related to conifers, not to angiosperms as previously thought. Amborella, Nymphaeales,
Hydatellaceae, Illiciales, Trimeniaceae, and Austrobaileya represent the earliest diverging lineages of extant
angiosperms. These phylogenetic results, together with recent progress on elucidating genetic and developmental
aspects of the plant life cycle, multicellularity, and gravitropism, will facilitate evolutionary developmental studies
of these key traits, which will help us to gain mechanistic understanding on how plants adapted to environmental
challenges when they colonized the land during one of the major transitions in evolution of life.
Key words charophytes, evolution, gravitropism, land plants, life cycle, multicellularity, origin, phragmoplast,
phylogeny, plasmodesmata, the tree of life.
The origin of land plants (embryophytes) was one
of the major events in history of life; it irreversibly
changed the evolutionary course of life and the envi-
ronment on earth (Graham, 1993; Gray, 1993; Kenrick
& Crane, 1997; Hagemann, 1999; Gensel & Edwards,
2001). To gain a full understanding of how such a
major evolutionary transition was unfolded, it is not
only necessary to study the event itself, but also
essential to investigate other events and processes that
led to and happened after the origin of land plants,
which undoubtedly contributed to the evolutionary
success of this large clade of photosynthetic eukaryo-
tes. A fully resolved phylogeny of major lineages of
land plants and their algal relatives represents a foun-
dation for comparative biological research on extant
and extinct organisms to elucidate the nature of these
events. Until recently, however, critical parts of the
phylogeny of land plants and their close algal relatives
had remained elusive, despite one and half century’s
effort by plant systematists on exploring morphologi-
cal, ultrastructural, phytochemical, and serological
characters since Charles Darwin (1859) proposed that
all life shared common descent. Over the last
twenty-five years, a rapid progress has been made in
molecular systematics, as development of PCR,
cloning, automated DNA sequencing technology, and
high-speed computing hardware and software has
permitted extensive surveys of living organisms. For
the first time in the history of biology, an unprece-
dented amount of historical information encoded in
the genomes has become available to rigorous quanti-
tative analysis for resolving many difficult phyloge-
netic problems. In this paper, I will review the recent
progress on phylogenetic reconstruction of charo-
phytic algae and land plants. Because phylogenetic
hypotheses play an important role in shaping our
understanding of evolution of organisms, I will also
discuss implications of the new phylogenetic hy-
potheses on several key aspects of plant evolution,
especially focusing on recent progress in genetic and
developmental biological studies of the plant life
cycle, multicellularity, and gravitropism. Hopefully,
this dual focus approach will bring a more compre-
hensive understanding on evolution of plants.
1 Phylogeny of charophytic algae and land
plants
Reconstructing phylogeny of organisms has been

———————————
Received: 20 March 2008 Accepted: 6 May 2008
* Author for correspondence. Email: ylqiu@umich.edu; Tel.: 1-734-764-
8279, Fax: 1-734-763-0544.
Journal of Systematics and Evolution Vol. 46 No. 3 2008 288
one of the main goals of evolutionary biologists ever
since the publication of Charles Darwin’s theory of
evolution (Darwin, 1859). In fact, biologists before
the mid-1800’s were already pursuing the inter-
connected relationships among organisms in their
classification work (Mayr, 1982). Formulation of
cladistic principles by Hennig (1966) and others in the
1960s–’70s established a clear conceptual framework
to uncover relationships among organisms through
examination of their similarities and differences. The
rise of molecular biology and advancement of com-
puter science in the 1980’s unlocked an unprecedented
amount of information and analytical power for
quantitative analyses, making it possible to realize the
dream of reconstructing the Tree of Life (Haeckel,
1866). However, the development path of phyloge-
netics has not been without detour. Early morpho-
logical cladistic studies made a great contribution to
systematics by establishing the first explicit phyloge-
netic frameworks for many groups of organisms, but
mis-interpretation of character homology and under-
estimation of homoplasy resulted in some major
erroneous hypotheses. During the early phase of
molecular systematics, use of single genes, often
without extensive taxon sampling, produced a bewil-
dering array of competing phylogenetic hypotheses,
creating an impression that molecular phylogenetic
analysis was just another one of those methodological
innovations that came and went. Fortunately, this
dilemma was soon ended with the invention of auto-
mated DNA sequencing technology, which enabled
most systematists to use several genes, often from one
to several cellular compartments, to conduct phyloge-
netic studies for virtually any group of organisms.
With extensive taxon sampling, this multigene ap-
proach, dubbed the supermatrix approach, has proven
most effective to tackle difficult phylogenetic prob-
lems (Delsuc et al., 2005). More recently, genomic
scale data have been applied to phylogenetic recon-
struction of organisms, but this approach has so far
received only mixed results, primarily because of
analytical errors amplified by the imbalance of under-
sampling of taxa and over-sampling of characters
(Leebens-Mack et al., 2005; Brinkmann & Philippe,
2008; Heath et al., 2008). One contribution emerging
from phylogenomic studies is the analyses of genomic
structural changes, which have been done back in the
early days of molecular systematics. This type of
analyses, because of character selection based on
frequency of changes and a large number of them
available in entirely sequenced genomes, can provide
independent data sets and is often quite informative in
resolving difficult phylogenetic problems (Kelch et
al., 2004; Jansen et al., 2007). Furthermore, as high
through-put sequencing technology develops, which
allows increased taxon sampling, and our ability to
understand and solve problems in phylogenomic
studies enhances (Brinkmann & Philippe, 2008),
phylogenomic analysis is likely to become more
commonly used to resolve difficult phylogenetic
issues. Following the tradition in systematics of using
all sources of data, modern phylogeneticists have
much more information and many more tools to
unravel the historical patterns among organisms
resulted from evolution. Clearly, a lot of progress has
been made on clarifying phylogenetic patterns among
organisms by taking an integrated approach.
1.1 Phylogeny of charophytic algae
Characeae, Coleochaete, Desmidiaceae, and
Zygnemataceae (all of Charophyceae), together with
Fritschiella, Oedogonium, and Ulothrix (all of
Chlorophyta, see Lewis & McCourt, 2004), were
among the green algae that were discussed as potential
relatives of land plants from the mid 1800’s to the
early 1900’s (Pringsheim, 1860, 1878; Celakovsky,
1874; Bower, 1890, 1908, 1935; Fritsch, 1916; Svede-
lius, 1927). Characeae were in fact often mistaken to
be higher multicellular plants and placed together with
mosses, e.g., in Celakovsky (1874). However, it was
not until the discovery of the phragmoplast in Chara,
Coleochaete, and Spirogyra around 1970 that the
status of these algae as the closest algal relatives of
land plants was firmly established (Pickett-Heaps,
1967, 1975; Fowke & Pickett-Heaps, 1969; Pickett-
Heaps & Marchant, 1972; Marchant & Pickett-Heaps,
1973). A formal circumscription of Charophyceae by
Mattox and Stewart in 1984, based on information
from cell division and ultrastructure of the flagellar
apparatus, largely defined membership of this impor-
tant group of green algae, which included: Chloroky-
bales, Klebsormidiales, Zygnematales, Coleo-
chaetales, and Charales. Recent studies, mostly mo-
lecular phylogenetic ones, have accumulated a large
body of evidence to support the hypothesis that land
plants indeed had a charophytic ancestry (Delwiche et
al., 1989; Manhart & Palmer, 1990; Melkonian et al.,
1995; Chapman et al., 1998; Karol et al., 2001; Peter-
sen et al., 2006; Lemieux et al., 2007; Turmel et al.,
2007). However, two questions have figured con-
spicuously in studies of these algae over the last
twenty-five years. One concerns whether the scaly
green flagellate alga Mesostigma viride Lauterborn is
a member of charophytes or not. The other asks which
group of charophytes represents the sister lineage of
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289
land plants.
Mesostigma viride was not in Charophyceae as
originally circumscribed by Mattox and Stewart
(1984), yet the species was shown to have a multilay-
ered structure (MLS) in its flagellar apparatus that is
very similar to that of charophytes and land plants
(Rogers et al., 1981; Melkonian, 1989). Since these
two studies, molecular phylogenetic analyses have
obtained conflicting results, with two main different
positions for the taxon. Two early molecular phy-
logenetic studies, analyzing nuclear encoded small
subunit (SSU) rRNA gene and actin gene respectively,
placed the species at the base of streptophytes (i.e.,
charophytes + land plants) (Melkonian et al., 1995;
Bhattacharya et al., 1998). However, a phylogenomic
study analyzing both entire chloroplast genome se-
quences and genomic structural changes showed that
the species represented the first diverging lineage in
Viridiplantae (i.e., Prasinophyceae, Chlorophyta, and
Streptophyta) (Lemieux et al., 2000). It was quickly
pointed out that this result might be an analytical
artifact caused by sparse taxon sampling (Qiu & Lee,
2000). Several recent studies, either analyzing se-
quences of more genes from nuclear, mitochondrial,
and chloroplast genomes or surveying distribution of
nuclear gene families, have confirmed a streptophytic
affinity of the species (Karol et al., 2001; Kim et al.,
2006; Nedelcu et al., 2006; Petersen et al., 2006;
Rodriguez-Ezpeleta et al., 2007). More importantly,
the original authors who published the result of plac-
ing Mesostigma as the sister to the rest of Viridiplan-
tae have analyzed a data set with significantly in-
creased taxon sampling (including almost all major
lineages of land plants as well as many green and
other algae) and more varieties of methods. They
conclude that the species is indeed a member of
streptophytes, specifically being sister to Chlorokybus
atmophyticus, and that the two taxa constitute the first
diverging lineage within streptophytes (Lemieux et
al., 2007) (Fig. 1).
Although claimed to be a monophyletic group
when formally defined (Mattox & Stewart, 1984),
charophytes are now clearly established as a para-
phyletic group (Bremer, 1985; Mishler & Churchill,
1985; Sluiman, 1985; Melkonian et al., 1995; Chap-
man et al., 1998; Karol et al., 2001; Qiu et al., 2006b,
2007; Lemieux et al., 2007; Turmel et al., 2007). A
question that has intrigued many botanists who study
the green algae-land plants transition is which one of
the extant charophyte lineages is sister to land plants.
While Coleochaete was favored as the closest extant
algal relative of land plants in an early cladistic analy-
sis of morphological and biochemical characters
(Graham et al., 1991), two recent molecular phyloge-
netic studies, with sufficient sampling of taxa and
genes (from all three cellular compartments), have
suggested that Charales are sister to land plants with
moderate to strong bootstrap support (Karol et al.,
2001; Qiu et al., 2006b) (Fig. 1). This hypothesis is
also consistent with the data from group II intron
distribution in the chloroplast genome as well as gene
content, gene order, and intron composition in the
mitochondrial genome of charophytes and land plants
(Turmel et al., 2003, 2006, 2007). However, a phy-
logenomic analysis of 76 chloroplast proteins and
genes has challenged this view, indicating that Zyg-
nematales are sister to land plants (Turmel et al.,
2006). Two factors might have contributed to this
result. One is the highly rearranged chloroplast
genomes in the two zygnematalean taxa that have
been investigated, Staurastrum punctulatum and
Zygnema circumcarinatum, both of which lack an
inverted repeat typically present in the chloroplast
genomes of photosynthetic eukaryotes (Turmel et al.,
2007). It has been known for some time that loss of
the inverted repeat can cause dramatic rearrangement
in the chloroplast genome and produce many autapo-
morphic (unique) structural changes (Palmer &
Thompson, 1982). The other is the two large evolu-
tionary gaps involved in the taxa analyzed, one
between Mesostigma/Chlorokybus and Staurastrum/
Zygnema/Chaetosphaeridium/Chara, and the other
between the latter group and land plants. These large
evolutionary gaps can easily lead phylogenetic analy-
sis astray, particularly in phylogenomic analyses of
gene-rich, taxon-sparse sequence matrices, where
taxon-character imbalance is so severe that systematic
biases in the data sets become virtually irremovable
(Delsuc et al., 2005; Leebens-Mack et al., 2005;
Brinkmann & Philippe, 2008; Heath et al., 2008).
While the zygnematalean ancestry of land plants
hypothesis certainly should not be abandoned yet,
further work in three areas can help to test whether it
is an analytical artifact. First, chloroplast genomes of
more taxa need to be analyzed, including Klebsormi-
dium, Entransia, Coleochaete, and more members of
Charales and Zygnematales. Second, a parallel study
of mitochondrial genomes needs to be conducted, as
the data from this genome already shows incongru-
ence with those from chloroplast genomes (Turmel et
al., 2007). Finally, more analyses using the superma-
trix approach to sample many nuclear, mitochondrial,
and chloroplast genes can help to distinguish the two
hypotheses.
Journal of Systematics and Evolution Vol. 46 No. 3 2008 290




Fig. 1. A representative phylogeny of charophytic algae and land plants. The thicker lines are roughly proportional to the species numbers in the
clades (the clades with <500 species are drawn with thin lines). Major evolutionary changes or evolution of major features are labeled at some nodes.


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291
In addition to progress on these two major ques-
tions, one recent development in phylogenetic inves-
tigation of charophytic algae involves the fresh water
species Entransia fimbricata Hughes. It was only
discovered about half century ago (Hughes, 1948) and
was placed in Zygnemataceae tentatively (see
McCourt et al., 2000). In a major molecular phyloge-
netic survey of Zygnematales, the species was shown
to be placed outside of the order and instead was
grouped with Chaetosphaeridium with weak bootstrap
support (McCourt et al., 2000). Three later studies
with more broad sampling of charophytes showed that
Entransia was sister to Klebsormidium with moderate
to strong bootstrap support (Karol et al., 2001; Turmel
et al., 2002; Sluiman et al., 2008). The study by
Sluiman et al. (2008) also reported that another ob-
scure green algal taxon, Hormidiella, might belong to
Klebsormidiales, a position originally proposed based
on ultrastructural evidence (Lokhorst et al., 2000).
These two examples, together with the recent resolu-
tion of phylogenetic position for Mesostigma, demon-
strate that charophytes are vastly under-studied rela-
tive to their importance in our quest to understand the
origin of land plants. Future research should place
some emphasis on diversity exploration in this group
of green algae of pivotal importance, as recently
stressed elsewhere (Lewis & McCourt, 2004). More
missing links may be discovered that will fill large
gaps among currently divergent groups and facilitate
phylogenomic and other evolutionary studies.
1.2 Phylogeny of land plants—bryophytes
The monophyly of land plants has been robustly
established by phylogenetic analyses of morphological
and biochemical data (Bremer, 1985; Mishler &
Churchill, 1985; Kenrick & Crane, 1997), multigene
supermatrices (Qiu et al., 2006b, 2007), and chloro-
plast genome sequences and gene content (Lemieux et
al., 2007), although an early morphological cladistic
study suggested that land plants may not be a strictly
monophyletic group (Sluiman, 1985). This is one of
the few major phylogenetic issues for which there was
much controversy in the pre-cladistic days but explicit
phylogenetic studies quickly reached a consensus. On
the other hand, relationships among basal lineages of
land plants have been vigorously debated over the last
twenty-five years, from morphological cladistic
studies to molecular phylogenetic analyses of genome
sequences and multigene supermatrices. Three ques-
tions are at the center of the debate. First, do bryo-
phytes constitute a mono- or paraphyletic group? If
they form a paraphyletic group, two questions then
follow. Which group of bryophytes represents the first
diverging lineage of land plants, and which lineage is
sister to vascular plants?
Two early cladistic studies of morphological and
biochemical characters concluded that bryophytes
were a paraphyletic group (Mishler & Churchill,
1984; Bremer, 1985). This hypothesis was later
confirmed by two analyses of somewhat different
morphological data sets (Kenrick & Crane, 1997;
Renzaglia et al., 2000). However, two studies of
spermatogenesis characters reached a conclusion that
bryophytes represent a monophyletic group (Garbary
et al., 1993; Renzaglia et al., 2000). Two recent
studies of entire chloroplast genome sequences,
sampling one species each from liverworts, mosses,
and hornworts, also recovered a monophyletic group
of bryophytes, which is sister to vascular plants
(Nishiyama et al., 2004; Goremykin & Hellwig,
2005). On the other hand, an extensive survey of three
mitochondrial group II introns across 350 diverse land
plants and several red and green algae showed that
liverworts exhibit the same condition of lacking the
introns as the algae, supporting the paraphyly hy-
pothesis (Qiu et al., 1998). This conclusion was
recently reinforced by an expanded study of 28 mito-
chondrial group II introns in a smaller number of taxa
(Qiu et al., 2006b). Most recently, parsimony and
likelihood analyses of a multigene supermatrix with
extensive taxon sampling of bryophytes and vascular
plants have shown that the paraphyly of bryophytes is
virtually indisputable (Qiu et al., 2006b). In consid-
eration of all above-cited studies, it is clear that the
paraphyly hypothesis of bryophytes has strong support
from diverse sources of data, whereas the monophyly
hypothesis is only supported by the studies that suffer
from weakness in either character or taxon sampling.
Hence, the paraphyly of bryophytes can be regarded
as one of the most clearly established aspects of the
early land plant phylogeny (Fig. 1).
Identifying the earliest diverging lineage of land
plants can provide significant insight into the algae-
land plants transition. Early cladistic studies of mor-
phological and biochemical data suggested that liver-
worts occupied such a position (Mishler & Churchill,
1984; Bremer, 1985; Kenrick & Crane, 1997). This
hypothesis, however, was challenged by at least four
subsequent analyses, one on morphological and
developmental characters (Renzaglia et al., 2000) and
three on multigene matrices (Nishiyama & Kato,
1999; Nickrent et al., 2000; Renzaglia et al., 2000),
which all argued that hornworts represented the sister
lineage to the rest of land plants. A large survey of
three mitochondrial group II introns, on the other
Journal of Systematics and Evolution Vol. 46 No. 3 2008 292
hand, provided some of the most unequivocal evi-
dence supporting liverworts as the basalmost lineage
in land plants (Qiu et al., 1998). This result was later
corroborated by an independent study of chloroplast
genomic structural changes as well as an expanded
survey of 28 mitochondrial group II introns (Kelch et
al., 2004; Qiu et al., 2006b). Furthermore, two phy-
logenomic analyses of entire chloroplast genome
sequences, after sufficient taxon sampling of major
land plant lineages was achieved, produced the same
topology (Wolf et al., 2005; Qiu et al., 2006b). Fi-
nally, both parsimony and likelihood analyses of a
multigene supermatrix with extensive taxon sampling
across all major lineages of land plants resolved the
liverworts’ basalmost position in land plants with
strong support (Qiu et al., 2006b).
The paraphyly of bryophytes and the basalmost
position of liverworts in land plants were resolved in
three early cladistic studies of morphological and
biochemical data (Mishler & Churchill, 1984; Bremer,
1985; Kenrick & Crane, 1997), and they stood tests by
numerous molecular phylogenetic analyses over the
last twenty-five years. However, the status of mosses
as the sister lineage to vascular plants established in
those studies was challenged very early on by mo-
lecular studies. Hornworts were often recovered as
sister to vascular plants in some early single gene
analyses (Lewis et al., 1997; Samigullin et al., 2002;
Dombrovska & Qiu, 2004). More convincing evi-
dence for this position of hornworts came in several
recent studies of chloroplast and mitochondrial ge-
nomic structural features (Malek & Knoop, 1998;
Kelch et al., 2004; Groth-Malonek et al., 2005) and
phylogenomic analyses of entire chloroplast genome
sequences (Wolf et al., 2005; Qiu et al., 2006b). In
particular, phylogenetic analyses of a supermatrix
with dense taxon sampling in charophytes, bryo-
phytes, pteridophytes, and seed plants have provided
decisive support to the position of hornworts as the
sister to vascular plants (Qiu et al., 2006b). In retro-
spect, the early morphological cladistic studies
mis-interpreted analogy of vascularized conducting
tissues in moss sporophytes and vasculature in vascu-
lar plants. On the other hand, development of nutri-
tionally largely independent sporophytes in hornworts
(Stewart & Rodgers, 1977), a key character syndrome
that facilitates completion of alternation of generations
during early evolution of land plants, has been greatly
under-appreciated (Qiu et al., 2006b, 2007). This is an
exemplar case where new molecular phylogenetic
results lead to discovery of previously neglected
morphological and developmental characters and
consequently greatly enhance our understanding of
plant phylogeny and evolution through reciprocal
illumination (Hennig, 1966).
1.3 Phylogeny of land plants—pteridophytes
While the knowledge of extinct fossil taxa is es-
sential for our understanding of the origin and evolu-
tion of vascular plants, I will limit this review mostly
to studies of extant plants in order to keep the paper
within a reasonable length. Among several extant
basal vascular plant lineages, Psilotaceae were often
compared to extinct early vascular plants Rhyniopsida
and were suggested to be sister to the rest of extant
vascular plants in a morphological cladistic study
(Bremer, 1985). However, discovery of a 30 kb
inversion in the chloroplast genome shared by all
vascular plants except lycophytes, which exhibit the
same condition as bryophytes, clinched the status of
lycophytes as the earliest diverging lineage among
extant vascular plants (Raubeson & Jansen, 1992).
This result has recently been confirmed by completely
sequenced chloroplast genomes of Physcomitrella
patens (Sugiura et al., 2003), Anthoceros formosae
(Kugita et al., 2003), Huperzia lucidula (Wolf et al.,
2005), and Psilotum nudum (Wakasugi et al., unpub-
lished). In Selaginella uncinata, however, there is a
shorter (20 kb) inversion in the same region of the
chloroplast genome that appears to show the same
condition as non-lycophyte vascular plants (Tsuji et
al., 2007). Nevertheless, adjacent genes immediately
outside of this inversion still exhibit the same order as
those in Huperzia lucidula, thus suggesting that this
species acquired a superficially similar inversion via
an independent genome rearrangement event. Re-
cently, the position of lycophytes as the sister to other
vascular plants has also been corroborated by analyses
of a multigene supermatrix with extensive sampling of
all major land plant lineages (Qiu et al., 2007) (Fig.
1).
The other major breakthrough in pteridophyte
systematics over the last twenty-five years is repre-
sented by identification of a major clade that unites
Equisetum, Psilotaceae and true ferns and placement
of this clade as the sister to seed plants (Fig. 1). This
clade, named monilophytes, was first recognized in a
morphological cladistic analysis on extinct and living
taxa, and it possesses one synapomorphy, mesarch
protoxylem confined to the lobes of the xylem strand
(Kenrick & Crane, 1997). Later, a molecular phy-
logenetic study identified the clade with strong boot-
strap support and also uncovered a highly diagnostic
three codon insertion in the chloroplast gene rps4
(Pryer et al., 2001). A large-scale phylogenetic study
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293
with extensive taxon sampling in bryophytes, pteri-
dophytes, and seed plants have also identified this
clade and placed it as the sister to seed plants with
strong statistical support (Qiu et al., 2007). Resolution
of these relationships represents significant progress
toward achieving a complete understanding on the
origin of seed plants, as early morphological cladistic
studies have had great difficulty to clarify relation-
ships among the so-called fern allies (Equisetum,
Psilotaceae, and lycophytes), ferns, and seed plants
(Bremer, 1985; Garbary et al., 1993).
While placement of Equisetum and Psilotaceae
with true ferns in the monilophyte clade has clarified
relationships among early vascular plants, relation-
ships among these two taxa, two eusporangiate fern
families (Marattiaceae and Ophioglossaceae), and the
clade of leptosporangiate ferns are still not resolved.
The only resolved part here is the sister relationship
between Psilotaceae and Ophioglossaceae, which
receives strong bootstrap support in molecular phy-
logenetic analyses (Pryer et al., 2001; Qiu et al.,
2007). Future studies that sample more genes from
mitochondrial, nuclear, and chloroplast genomes may
offer resolution to this problem.
1.4 Phylogeny of land plants—seed plants
Early morphological cladistic analyses of extinct
and extant taxa concluded that seed plants were a
monophyletic group (Crane, 1985; Doyle &
Donoghue, 1986), although there was a possibility of
biphyletic origin of seed plants (Doyle & Donoghue,
1986). The seed plant monophyly has now been
clearly confirmed by a large-scale molecular phy-
logenetic study that sampled both non-seed plants and
seed plants extensively (Qiu et al., 2007).
The other major finding from several morpho-
logical cladistic analyses of seed plants (Crane, 1985;
Doyle & Donoghue, 1986; Nixon et al., 1994; Roth-
well & Serbet, 1994) was a close relationship between
Gnetales and angiosperms, but this result was almost
never recovered in any molecular study. Instead,
Gnetales were often shown to be sister to Pinaceae
(Goremykin et al., 1996; Winter et al., 1999; Bowe et
al., 2000; Chaw et al., 2000; Frohlich & Parker, 2000;
Gugerli et al., 2001; Magallon & Sanderson, 2002;
Soltis et al., 2002; Burleigh & Mathews, 2004; Qiu et
al., 2007) (Fig. 1) or sometimes to conifers (Chaw et
al., 1997; Burleigh & Mathews, 2004). In analyses of
fast-evolving genes or nucleotide positions, typically
chloroplast genes or 3rd codon positions of other
genes, Gnetales were placed as the sister to all other
seed plants (Magallon & Sanderson, 2002; Rydin et
al., 2002). Only in a study of nuclear 18S and 26S
rRNA genes, Gnetales were shown to be sister to
angiosperms, but with low bootstrap support (Rydin et
al., 2002). Given the kinds and number of genes
sampled, the diversity of taxon sampling schemes
used, and the variety of methods employed in all these
analyses, it is difficult to imagine what types of sys-
tematic errors were present in all these molecular data
sets that would prevent recovery of a close relation-
ship between Gnetales and angiosperms if there was
one. Therefore, it seems reasonable to conclude that
Gnetales are related to conifers rather than to angio-
sperms.
One of the most spectacular discoveries in mo-
lecular systematics over the last two and half decades
is the identification of several basal angiosperm taxa
as the earliest diverging lineages among living angio-
sperms, which include Amborella, Nymphaeales,
Hydatellaceae, and Illiciales/Trimeniaceae/Austrobai-
leya (ANHITA; Fig. 1) (Mathews & Donoghue, 1999;
Parkinson et al., 1999; Qiu et al., 1999; Soltis et al.,
1999; Barkman et al., 2000; Graham & Olmstead,
2000; Saarela et al., 2007). Subsequent analyses
sampling more genes and employing more varieties of
analytical methods have solidified this result (Qiu et
al., 2000, 2001, 2005, 2006a; Zanis et al., 2002;
Borsch et al., 2003; Hilu et al., 2003; Stefanovic et al.,
2004; Leebens-Mack et al., 2005; Jansen et al., 2007;
Moore et al., 2007). Until recently, it was thought that
the diversification pattern among the earliest angio-
sperms could never be resolved despite nearly two
centuries of research (see Qiu et al., 1993). The di-
vergence gap between ANHITA and euangiosperms
(angiosperms exclusive of Amborella, Nymphaeales,
Hydatellaceae, and Illiciales/Trimeniaceae/Austrobai-
leya (Qiu et al., 1999)) in fact is quite large, and has
been identified in most molecular phylogenetic studies
that sample several genes (Parkinson et al., 1999; Qiu
et al., 1999, 2005, 2006a; Graham & Olmstead, 2000;
Soltis et al., 2000; Borsch et al., 2003; Stefanovic et
al., 2004; Jansen et al., 2007; Moore et al., 2007). This
gap has also been independently corroborated by
studies of fossil evidence (Friis et al., 1999) and
morphology (Endress & Igersheim, 2000; Williams &
Friedman, 2002). In retrospect, early appearance of
ANHITA in angiosperm evolution was already de-
tected in the comparative analyses of extant angio-
sperms (Stebbins, 1974; Endress, 1986) and fossil
record (Upchurch, 1984). This is another exemplar
case where phylogenetic relationships, once resolved
by molecular systematic studies, suddenly reveal a
consistent evolutionary pattern in the data that already
existed and are being gathered, shedding significant
Journal of Systematics and Evolution Vol. 46 No. 3 2008 294
light on a long-standing evolutionary enigma—the
origin of angiosperms in this case.
Another spectacular discovery in the recent his-
tory of plant systematics involves the recognition of a
large monophyletic group of angiosperms termed
eudicots (or tricolpates) (Doyle & Hotton, 1991),
which encompasses 75% of extant angiosperm diver-
sity (Mabberley, 1987) (Fig. 1). It was suggested as
early as in the 1930’s that angiosperms with tricolpate
pollen and derived pollen types may represent a
natural group based on extensive surveys of extant and
fossil angiosperm pollen (Wodehouse, 1935, 1936).
Several other authors later supported this hypothesis
from their comparative studies of plant morphology
and pollen (Bailey & Nast, 1943; Hu, 1950; Walker &
Doyle, 1975). In an explicit cladistic analysis of basal
angiosperms using morphological data, the mono-
phyly of eudicots was established for the first time
(Donoghue & Doyle, 1989). However, limited taxon
sampling in that study prevented this finding from
being widely recognized. The first large-scale mo-
lecular phylogenetic analysis of angiosperms using
sequences of the chloroplast gene rbcL established
monophyly of this large group beyond any doubt
(Chase et al., 1993). All major molecular phylogenetic
studies of angiosperms since then have shown that
monophyly of eudicots is one of the best established
aspects of the angiosperm phylogeny (Qiu et al., 1999,
2006a; Savolainen et al., 2000; Soltis et al., 2000; Hilu
et al., 2003; Jansen et al., 2007; Moore et al., 2007).
Evolution of tricolpate pollen turns out to be such an
infrequent event that it happened only twice outside
eudicots, once in Illiciales and once in Arecaceae (the
palm family), and in both cases the pollen develop-
mental pattern is actually different from that in eudi-
cots (see Cronquist, 1981; Qiu et al., 1993). The
history of discovery of this large clade of land plants,
spanning more than half century, demonstrates that
our ability to explore the nature is highly dependent
on advancement of technology. In this particular case,
invention of light microscope, electron microscope,
DNA sequencing techniques, and computer all had an
instrumental role in the eventual recognition of this
major clade of angiosperms.
Besides these two major findings, recent mo-
lecular phylogenetic analyses of large data sets with
extensive sampling of genes and taxa have greatly
clarified relationships among angiosperms (Hilu et al.,
2003; Qiu et al., 2005, 2006a). Overall, euangio-
sperms can be divided into five monophyletic groups:
Ceratophyllum, Chloranthaceae, eudicots, magnoliids
(which include two pairs of sister taxa, Canel-
lales/Piperales and Magnoliales/Laurales), and mono-
cots. Currently, relationships among three large clades
with significant diversity, magnoliids, monocots, and
eudicots, have been resolved differently in studies
using multigene and phylogenomic data sets. In a
study of analyzing 8 mitochondrial, chloroplast, and
nuclear genes from 144 taxa with a compatibility
method, magnoliids and eudicots were shown to be
sister to each other, and they were sister to monocots
(Qiu & Estabrook, 2008). However, in two analyses of
entire chloroplast genome sequences, monocots were
sister to eudicots, and together they were sister to
magnoliids (Jansen et al., 2007; Moore et al., 2007).
Because the power of the compatibility method in
resolving deep phylogenetic patterns remains rela-
tively untested, and phylogenomic studies have often
suffered from systematic errors in data sets (Delsuc et
al., 2005; Leebens-Mack et al., 2005; Brinkmann &
Philippe, 2008; Heath et al., 2008), it is best to view
relationships among the major angiosperm lineages as
unresolved at present.
2 Evolutionary implications of a newly
reconstructed phylogeny of charophytic
algae and land plants
From the above review, it is clear that our under-
standing on the phylogeny of charophytic algae and
land plants has been significantly improved over the
last two and half decades (Fig. 1). Several cladistic
analyses of mostly morphological characters for the
first time formulated explicit phylogenetic hypotheses
on relationships among major lineages of these pho-
tosynthetic eukaryotes (Mishler & Churchill, 1984,
1985; Bremer, 1985; Crane, 1985; Doyle &
Donoghue, 1986; Donoghue & Doyle, 1989; Graham
et al., 1991; Kenrick & Crane, 1997). These hypothe-
ses served as paradigms for guiding evolutionary
studies of various aspects of these organisms during
this period, for example, origin of sporopollenin in
charophytes (Delwiche et al., 1989), fertilization in
Gnetales and angiosperms (Friedman, 1990) and auxin
metabolism in early land plants (Sztein et al., 1995;
Cooke et al., 2002, 2004). Undoubtedly, these mor-
phological cladistic studies represented a major step
forward from traditional taxonomy, enforcing a
rigorous criterion on identifying homologous charac-
ters and defining strictly monophyletic groups. Nev-
ertheless, these studies also had their limitations,
especially in making mis-interpretation of some of the
morphological characters and under-estimating the
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295
extent of homoplasy in plant evolution. Molecular
phylogenetic studies, in particular those based on
supermatrices and infrequent genomic structural
changes, have a greater resolution power because of
access to a much larger amount of historical informa-
tion and higher quality characters (Manhart & Palmer,
1990; Raubeson & Jansen, 1992; Chase et al., 1993;
Qiu et al., 1998, 1999, 2006a, b, 2007; Bowe et al.,
2000; Chaw et al., 2000; Graham & Olmstead, 2000;
Savolainen et al., 2000; Soltis et al., 2000; Karol et al.,
2001; Pryer et al., 2001; Hilu et al., 2003; Burleigh &
Mathews, 2004; Kelch et al., 2004). These molecular
studies have remedied to a good extent the weakness
of morphological cladistic studies, by circumventing
the problem of relying on a few morphological char-
acters that might have experienced convergent evolu-
tion due to similar selection pressure. As a result, the
combined use of morphology and molecules in rigor-
ous quantitative analyses over the last twenty-five
years has led to one of the most rapid growth periods
in our knowledge on evolutionary relationships among
organisms.
The significantly improved organismal phylog-
eny is providing a momentum for the pendulum of
evolutionary research to swing back to the study of
mechanisms and processes. It allows tracing
macro-evolutionary patterns among major clades of
organisms on large scales and helps formulating
hypotheses on mechanisms and processes of some
major evolutionary transitions. The emergence of
evolutionary developmental biology will further
catalyze this transformation by providing experimen-
tal approaches to test the hypotheses. This interplay
among studies of phylogenetic patterns, developmen-
tal mechanisms, and evolutionary processes in a large
diversity of organisms is likely to lead to a new level
of understanding on functioning and evolution of life
in general. Charophytes and land plants together
represent one of the major lineages in eukaryotic
evolution, which spans the diversity from unicellular
aquatic algae to highly evolved multicellular angio-
sperms. Studies of their evolutionary patterns and
developmental mechanisms under a new phylogenetic
framework will help us not only to understand how
this major clade has evolved, but also to learn how
eukaryotes in general adapt to environment challenges
during several major evolutionary transitions that were
not unique to plants, e.g., from unicellularity to mul-
ticellularity, from a gravity-water buoyancy environ-
ment to a gravity-air buoyancy environment, and from
a haploid gametophyte to a diploid sporophyte as the
dominant generation in the life cycle. Below, I will
review and discuss recent progress on genetic, devel-
opmental, and cell biological studies of several plant
traits, which, when investigated with an evolutionary
developmental approach under the new phylogenetic
hypotheses, are likely to further our understanding of
plant evolution.
2.1 Evolution of life cycle in land plants
One of the most interesting and important, but
somehow recently neglected, aspects of plant evolu-
tion is the change of life cycle in various lineages of
charophytic algae and land plants. The phylogeny of
these organisms as currently understood (Fig. 1) and
their order of appearance in the fossil record (Gray,
1993; Taylor & Taylor, 1993; Kenrick & Crane, 1997;
Wellman et al., 2003) clearly demonstrate a trend of
expansion of the diploid sporophyte generation with
concomitant reduction of the haploid gametophyte
generation. However, had the phylogenetic pattern not
been clear, it would have been much more difficult, if
not impossible, to detect this trend based purely on
fossil evidence.
Three issues in the phylogeny of charophytic al-
gae and early land plants, all resolved over the last
several decades, can directly affect interpretation of
evolution of life cycle in land plants. First, charo-
phytes, rather than Ulvophyceae in Chlorophyta, are
identified as the closest algal relatives of land plants.
Although this relationship was recognized based on
surveys of cell division and ultrastructure of the
flagellar apparatus among green algae and land plants
(Pickett-Heaps, 1975; Mattox & Stewart, 1984),
phylogenetic analyses of morphological and molecular
data provided robust assurance and independent
corroboration to this result (Manhart & Palmer, 1990;
Melkonian et al., 1995; Chapman et al., 1998; Karol et
al., 2001; Lemieux et al., 2007; Turmel et al., 2007).
Second, the monophyly of land plants was much less
certain in the pre-cladistic time, and an early morpho-
logical cladistic study even expressed doubt on the
issue (Sluiman, 1985). However, cladistic studies of
morphological and biochemical data firmly estab-
lished monophyly of land plants (Bremer, 1985;
Mishler & Churchill, 1985; Kenrick & Crane, 1997).
Recent phylogenetic analyses of molecular data have
provided further and more convincing evidence to
support this conclusion (Qiu et al., 2006b, 2007;
Lemieux et al., 2007; Turmel et al., 2007). Finally, the
paraphyly of bryophytes, though established by some
early morphological cladistic studies (Mishler &
Churchill, 1984; Bremer, 1985), has been challenged
by both morphological and molecular phylogenetic
analyses from time to time (Garbary et al., 1993;
Journal of Systematics and Evolution Vol. 46 No. 3 2008 296
Renzaglia et al., 2000; Nishiyama et al., 2004; Gore-
mykin & Hellwig, 2005). The recent large scale
analyses of multigene supermatrices and a broad
survey of mitochondrial group II introns, all with
extensive taxon sampling across land plants, have
decisively resolved this issue (Qiu et al., 1998, 2006b,
2007). Failure to resolve any of these issues would
have resulted in a much less clear phylogenetic pat-
tern, impeding investigation of the origin of land
plants and evolution of alternation of generations.
Alternatively, if some of these three issues were
resolved with different outcomes, e.g., Ulvophyceae
were identified as the closest algal relatives of land
plants, or bryophytes were shown to form a mono-
phyletic group sister to vascular plants, an entirely
different hypothesis, the homologous hypothesis
(Pringsheim, 1878), than the one discussed below
would have to be considered to explain the origin of
land plants and evolution of life cycle in land plants.
The phylogenetic pattern among charophytic al-
gae and early land plants inferred from morphological
and molecular data sheds significant light on two
major events in the history of plant life: colonization
of land and change from a haploid gametophyte to a
diploid sporophyte as the dominant generation in the
life cycle. One school of thoughts, often known as the
antithetic hypothesis, first developed Celakovsky in
1874 and later greatly expanded by Bower (1890,
1908, 1935) and others (Campbell, 1924; Svedelius,
1927; Smith, 1955), actually used a phylogenetic
scheme that is largely congruent to what is recon-
structed now to explain evolutionary changes at these
two major events. These authors examined and com-
pared developmental patterns of life cycle in various
algal and plant lineages by following this phylogenetic
scheme. They hypothesized that land plants originated
as a consequence of interpolation of a new phase
(sporophyte generation) into the life cycle of some
green algae that were more likely related to today’s
charophytes. They further suggested that as early land
plants (mosses as recognized by those early botanists)
evolved, the sporophyte generation expanded through
structural elaboration and progressive sterilization of
potentially sporogenesis tissues and ultimately became
a free-living dominant generation as seen in the life
cycle of ferns and seed plants. It is noteworthy that the
different ploidy levels of gametophyte and sporophyte
generations (Strasburger, 1894) and meiosis (Van
Beneden, 1883) (see Hamoir, 1992) were both dis-
covered after Celakovsky (1874) had proposed this
hypothesis. Hence, one has to be amazed by the power
of comparative developmental biology, which can
only be realized when there is a correct phylogenetic
framework to guide interpretation of the observed
pattern.
The third major event in plant evolution is the
origin of seed plants (and the origin of angiosperms
can be regarded as an extension of this process). This
event has not been so much targeted in the study of
evolution of life cycle in land plants, particularly in
the debate between the antithetic (Celakovsky, 1874;
Bower, 1890; Campbell, 1924; Svedelius, 1927;
Smith, 1955) and the homologous hypotheses (Pring-
sheim, 1878). Equally puzzling is that despite intense
interest in the origins of seed plants and angiosperms
throughout the entire last century, few have looked at
the problems from a life cycle evolutionary develop-
mental perspective, with perhaps one exception
(Takhtajan, 1976), who alluded to neoteny as one of
the possible mechanisms contributing to the origin of
angiosperms. What has received most attention is
emergence of new structures such as seeds and flow-
ers (Crane, 1985; Doyle & Donoghue, 1986; Frohlich
& Parker, 2000; Theissen et al., 2000), but equally
important aspects during this phase of land plant
evolution are reduction of gametophytes and further
increase of male meiocyte number per fertilization
event (this number, in a non-heterospory situation,
was already greatly increased when the sporophyte
became a dominant generation during the origin of
vascular plants). These evolutionary changes are
obvious when reproductive cycles of seed plants,
monilophytes, and lycophytes (Gifford & Foster,
1989) are compared under a phylogenetic framework,
which again has only been available from recent
phylogenetic analyses of morphological and molecular
data (Kenrick & Crane, 1997; Pryer et al., 2001; Qiu
et al., 2007). More importantly, these changes fit the
trend of sporophyte expansion and gametophyte
reduction since plants colonized the land (Fig. 1).
Adaptive significance of this trend in life cycle change
lies in the fact that it allows generation of a larger
number of genetically different gametes through
increase of the meiocyte number, which then leads to
occupation of more variable environmental niches on
the land than in the water by more genetically variable
offspring after fertilization (Svedelius, 1927).
Once this macro-evolutionary trend is revealed, it
becomes relatively straightforward to design an
integrated experimental strategy to explore develop-
mental mechanisms that have shaped the pattern of
life cycles in extant land plants, though it will take
many years to elucidate these mechanisms. The study
of developmental events in the life cycle, especially
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297
the control of timing of meiosis initiation, has been
pursued for many years in the fungal system,
Schizosaccharomyces pombe. One particular gene that
has been identified to play an important role in meio-
sis initiation is mei2, which encodes an RNA-binding
protein that is essential for premeiotic DNA synthesis
and the commitment to meiosis (Watanabe & Yama-
moto, 1994). This gene is likely to be conserved
among protists, fungi, and plants (Jeffares et al.,
2004). In green algae and land plants, it appears that
the gene has undergone a major duplication event,
with one gene family (TEL) involved in cell differen-
tiation in shoot and root meristems (Jeffares et al.,
2004; Veit et al., 1998) and the other (AML) playing a
role in vegetative meristem activity as well as meiosis
in Arabidopsis thaliana (Kaur et al., 2006). It is no
coincidence that both meiosis and mitosis are targets
of action by this gene family, as cell divisions in
vegetative and reproductive growth are key processes
to regulate in order to mold the life cycle of a certain
lineage. Hence, genes controlling the timing of mitosis
and meiosis should be high priority targets to investi-
gate in the effort to understand evolution of the life
cycle in land plants. Since the primary focus of this
review is on the phylogeny, no other genes will be
discussed here though many have been identified (Ma,
2005; Hamant et al., 2006). The above example is
provided merely to show that it is feasible to take an
evolutionary developmental approach to study mecha-
nistic aspects of evolution of life cycle in land plants.
2.2 Transition from unicellularity to multicellu-
larity in streptophytes
Land plants represent one of the most successful
groups and the most sophisticated kinds of multicel-
lular organisms (Hagemann, 1999). The transition
from uni- to multicellularity actually took place before
they came onto land, and the current phylogeny
suggests that it happened either in the common ances-
tor of all streptophytes or shortly after the origin of
this clade (Fig. 1). Placement of Mesostigma viride, a
unicellular organism, is critical to pinpoint the origin
of multicellularity in this part of eukaryotic evolution.
Since there is no longer any dispute on its inclusion
within charophytes (Karol et al., 2001; Kim et al.,
2006; Nedelcu et al., 2006; Petersen et al., 2006;
Lemieux et al., 2007; Rodriguez-Ezpeleta et al.,
2007), it is reasonable to suggest that multicellularity
evolved in the common ancestor of streptophytes or
later, because the green algae below this node on the
phylogeny, Prasinophyceae, are all unicellular (Bal-
dauf, 2003; Lewis & McCourt, 2004). On the other
hand, whether Mesostigma alone (Karol et al., 2001;
Petersen et al., 2006) or together with Chlorokybus
(Qiu et al., 2006b; Lemieux et al., 2007) is sister to all
other streptophytes has not been clearly resolved.
Hence, it is also likely that multicellularity evolved
shortly after the origin of streptophytes, particularly in
consideration of the sarcinoid organization in Chloro-
kybus atmophyticus, which is a packet of a few cells
held together by a gelatinous matrix without plas-
modesma connection (van den Hoek et al., 1995)—a
quasi-state of multicellularity. Regardless of these
topological variations, the currently resolved phy-
logenetic relationships among early diverging charo-
phytic algae provide a sound evolutionary framework
under which the transition from uni- to multicellular-
ity can be meaningfully investigated.
Multicellularity evolved more than two dozens of
times in bacteria, archaea, and eukaryotes (Bonner,
1999; Grosberg & Strathmann, 2007). It confers
several advantages to organisms by enhancing their
metabolic and reproductive capabilities (Niklas, 1997;
Grosberg & Strathmann, 2007). First, the sheer in-
crease of physical size allows the organisms to use
resource from the environment better than their uni-
cellular competitors. Because the cell size increase has
an upper bound constrained by physico-chemical
properties of phospholipids, proteins, and other com-
pounds that make up the plasma membrane and cell
wall, multicellularity provides the only solution to the
problems of out-competing other organisms when
resource stays the same or decreases in the environ-
ment, or increasing metabolic activity in a re-
source-richer environment. Multicellularity also
ensures better protection of genetic material than
unicellularity. Second, once multicellularity emerges,
functional differentiation and specialization (division
of labor) among cells in an organism will confer a
greater fitness to its metabolism and reproduction.
Complexity will be achieved through structural (mor-
phological), metabolic (chemical, physiological, and
behavioral), and reproductive differentiation, with
formation of tissues, organs, and member groups
within a social group. Indeed, empirical analyses have
detected a positive correlation between size and
complexity (Bell & Mooers, 1997; Bonner, 2004).
Finally, because the life span of a cell is constrained
by physico-chemical properties of carbohydrates,
phospholipids, fatty acids, amino acids, proteins,
nucleic acids, and other compounds that make up the
cell, multicellular organisms have an advantage of
out-living unicellular competitors.
Development of multicellularity depends on two
basic processes at the cellular level, cell cohesion and
Journal of Systematics and Evolution Vol. 46 No. 3 2008 298
cell-cell exchange of information and materials (Al-
berts et al., 1989). At present, little is known about
cell cohesion during the transition from uni- to multi-
cellularity in early streptophytes. In comparison, more
information is available on plasmodesmata-cytoplas-
mic bridges that connect adjacent cells and allow
exchange of hormones, RNAs, carbohydrates, pro-
teins, and other compounds between cells (Lucas &
Lee, 2004). In eukaryotes, plasmodesmata have
evolved several times independently, in Fungi, Phae-
ophyta, Chlorophyta, and Streptophyta (Lucas et al.,
1993; Raven, 1997). Evolution of this cell-cell com-
munication/transportation device in early strepto-
phytes has undoubtedly contributed to the success of
building large complex multicellular organisms in this
lineage of eukaryotes. Among all extant charophytes,
Mesostigma viride is probably the only ancestrally
unicellular organisms. Chlorokybus atmophyticus is
sarcinoid (no plasmodesma), exhibiting a primitive
type of multicellularity. The three genera of Klebsor-
midiales, Klebsormidium, Entransia, and Hormidiella
(Lewis & McCourt, 2004; Sluiman et al., 2008), all
contain unbranched filamentous species (Hughes,
1948; van den Hoek et al., 1995; Lokhorst et al., 2000;
Cook, 2004). There are no plasmodesmata connecting
cells in species of Klebsormidium (van den Hoek et
al., 1995) and Entransia (M. E. Cook, personal com-
munication); no information about plasmodesmata is
currently available in Hormidiella. Zygnematales
contain a large number of unicellular, colonial, or
unbranched filamentous species. The phylogenetic
distribution of plasmodesmata in charophytes
(McCourt et al., 2000; Karol et al., 2001) suggests that
unicellularity in this group might have been secondar-
ily derived. So far, no plasmodesmata have been
reported in any species of Zygnematales (van den
Hoek et al., 1995). Coleochaetales and Charales are
the only multicellular charophytic algae that have
plasmodesmata connecting their cells (Franceschi et
al., 1994; van den Hoek et al., 1995; Cook et al.,
1997). From their distribution on the currently re-
solved phylogeny of charophytes and land plants (Fig.
1), it seems reasonable to suggest that plasmodesmata
evolved in the common ancestor of Coleochaetales,
Charales, and land plants.
Another structure that has likely contributed to
evolution of multicellularity in streptophytes, and
particularly formation of the three-dimensional plant
body, is the phragmoplast, which is a unique ar-
rangement of vesicles and microtubules during cyto-
kinesis whereby microtubules are oriented perpen-
dicular to the plane of cytokinesis (Fowke &
Pickett-Heaps, 1969; Pickett-Heaps, 1975). It is found
primarily in Zygnematales, Coleochaetales, Charales,
and land plants (Pickett-Heaps, 1967; Fowke &
Pickett-Heaps, 1969; Marchant & Pickett-Heaps,
1973); elsewhere it is only found in Trentepohliales of
Chlorophyta (Chapman & Henk, 1986). Klebsormi-
dium, though lacking a clear phragmoplast, exhibits
two characteristics required for evolution of the
structure: an ingrowing cleavage furrow and a persis-
tent system of interzonal microtubules separating
daughter nuclei and derived from a spindle apparatus
(Floyd et al., 1972; Pickett-Heaps & Marchant, 1972).
Hence, it seems that the phragmoplast evolved shortly
after streptophytes originated, as can be inferred from
its distribution on the phylogeny of charophytes and
land plants (Fig. 1). It has been suggested that the
phragmoplast is perhaps essential for organisms to
achieve a two- to three-dimensional pattern of cell
division, instead of a one-dimensional, filamentous
type of simple division, to develop complex plant
bodies (Hagemann, 1999; Pickett-Heaps et al., 1999).
Hagemann (1999) in particular has argued that the
type of cell division involving formation of a phrag-
moplast is related to the unique way of cell wall
construction in land plants, which are multicellular
organisms that grow against the direction of gravity in
a less buoyant medium (air, in comparison to water
for most algae) and have few, if any, parallels in
eukaryotes. These ideas are certainly consistent with
the pattern of morphological complexity of plant
bodies exhibited by various charophyte and land plant
lineages on the phylogeny (Fig. 1).
The plasmodesmata and phragmoplasts, the evo-
lution of which seems not dependent on each other,
may have been largely responsible for evolution of
multicellularity in streptophytes (Lucas et al., 1993;
Franceschi et al., 1994; Hagemann, 1999). Identifica-
tion of genes encoding various components of both
structures will significantly increase our understand-
ing on how multicellularity was achieved step by step
during the transition of photosynthetic eukaryotes
from the aquatic to the terrestrial environment. The
knowledge accumulated from cell biology research
over the last several decades has laid down a solid
foundation (Pickett-Heaps et al., 1999; Lucas & Lee,
2004), but fine-scale evolutionary genetic and devel-
opmental studies are needed to elucidate the process
of uni- to multicellularity transition in streptophytes.
Finally, it should be added that uni- to multicellularity
transition actually happened twice during streptophyte
evolution: once at the gametophyte whole organism
level in early evolution of charophytes and another at
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299
the sporophyte level during the origin of land plants
(only part of the organism was involved in Characeae
and liverworts). For the latter, a life cycle with the
diploid sporophyte generation being dominant (Sve-
delius, 1927; Coelho et al., 2007; McManus & Qiu,
2008) and origin of lignin (for cell cohesion) probably
have also contributed to the building of large and
complex multicellular plant bodies.
2.3 Origin and evolution of gravitropism in
streptophytes
Land plants, as the major primary producers in
the terrestrial ecosystem, have developed a body plan
of a vertical axis with photosynthetic organs (leaves)
in the air and absorption-anchorage organs (roots or
rhizoids) in the soil. Although this body plan is best
manifested in seed plants (Cooke et al., 2004), proto-
typic forms are found in pteridophytes, bryophytes,
and Characeae. Gravitropism has played an instru-
mental role in the origin and evolution of this body
plan, as streptophytes undergo the transition from
free-swimming/planktonic green algae such as
Mesostigma viride and Zygnematales to aquatic
rhizophytic Characeae (Raven & Edwards, 2001), and
to land-grown bryophytes, pteridophytes and seed
plants. Essentially, two types of cells, “root” and
“shoot” meristematic cells that respond to gravity
positively and negatively, are responsible for building
this body plan. Though gravity has always accompa-
nied life on earth (Volkmann & Baluska, 2006), in no
time has it figured so conspicuously in influencing
evolution of organisms as during the water-land
transition of plants, since no other organisms have
built a body with the size and mass of giant sequoia or
eucalyptus trees. Hence, elucidating the origin and
evolution of gravitropism in streptophytes will not
only help us to understand the origin and evolution of
land plants, but also provide insight into the role of
gravity in shaping evolution of life.
The phylogeny of charophytic algae and land
plants as currently reconstructed (Fig. 1) shows that
gravitropism in streptophytes likely evolved in the
common ancestor of Characeae and land plants,
because both groups are rhizophytes (Raven & Ed-
wards, 2001) and other charophytes are either
free-swimming/planktonic or epiphytic in aquatic or
terrestrial habitats (van den Hoek et al., 1995). In
some early phylogenetic studies of streptophytes and
green algae using nuclear 18S rDNA data, Characeae
were shown to be the first diverging lineage among
charophytes (Kranz et al., 1995; Friedl, 1997). The
cladistic analysis of morphological and biochemical
characters placed Coleochaete as the closest extant
algal relative of land plants (Graham et al., 1991).
Both topologies suggest either two independent
origins of gravitropism in Characeae and land plants
separately or loss of the trait in some charophytes.
These scenarios are not entirely without any merit
since rhizophytes are also found in Chlorophyta
(Raven & Edwards, 2001), and gravitropism has
clearly evolved more than once in eukaryotes. How-
ever, the current strong support from two multigene
analyses clearly favors the position of Characeae as
the sister to land plants (Karol et al., 2001; Qiu et al.,
2007). Thus, the best hypothesis at present is that
gravitropism evolved only once in streptophytes.
Gravitropism in Characeae has been studied at
the cellular level in great details (Braun & Limbach,
2006). In general, actin has been shown to be inti-
mately involved in gravity sensing and polarized cell
growth in this system. Actomyosin plays a key role in
gravity sensing by first coordinating the position of
statoliths, which are BaSO4-crystall-filled vesicles
(different from starch-filled amyloplasts in angio-
sperms). Upon a change in the cell’s orientation
relative to the direction of gravity, it directs sediment-
ing statoliths to specific areas of the plasma mem-
brane, where contact with membrane-bound grav-
isensor molecules elicits short gravitropic pathways.
In controlling polarized cell growth, actin and a steep
gradient of cytoplasmic free calcium make up crucial
components of a feedback mechanism. So far, only
limited knowledge on the role of auxin in regulating
rhizoid growth and gravitropism has been obtained in
Chara (Klambt et al., 1992; Cooke et al., 2002).
In Arabidopsis thaliana, a lot more information
has been learned about gravitropism from fine-scale
genetic analyses conducted over the last ten years. A
family of genes (named PIN after pin-formed mutants)
encoding auxin efflux carrier proteins have been
isolated (Galweiler et al., 1998; Paponov et al., 2005).
It is demonstrated that upon gravity stimulation, the
PIN3 protein, positioned symmetrically at the plasma
membrane of the root columella cells, rapidly relocal-
izes at the lateral plasma membrane surface and to
vesicles that cycle in an actin-dependent manner,
which provides a mechanism for redirecting auxin
flux to trigger asymmetric growth (Friml et al., 2002;
Palme et al., 2006). Recently, it has been shown that
five PIN genes (PIN1, 2, 3, 4, and 7) collectively
control auxin distribution to regulate cell division and
expansion in the primary root, and that they work with
another family of genes (PLT for PLETHORA) to
specify the meristematic identity of cells in the root
(Blilou et al., 2005). In another recent paper, sterol
Journal of Systematics and Evolution Vol. 46 No. 3 2008 300
composition has been implicated in polar localization
of the PIN2 protein, which also encodes an auxin
transporter and directs root gravitropism (Men et al.,
2008). This body of work basically confirms the
classical view that auxin, via its basipetal transport, is
the main secondary messenger regulating gravitropic
growth (Boonsirichai et al., 2002), but has revealed
much more genetic insight on mechanisms how plants
respond to gravity.
The detailed genetic and cell biological studies of
gravitropism in Characeae and Arabidopsis set a stage
for broad-scale evolutionary investigation of the
phenomenon. A third line of work that may aid this
research is the isolation of various gravitropic mutants
in two mosses, Physcomitrella patens (Knight et al.,
1991) and Ceratodon purpureus (Wagner et al., 1997;
Cove & Quatrano, 2006). Given the momentum of
research on Physcomitrella, it is conceivable that the
genes will be isolated from these mutants soon. Thus
far, the PIN genes have been found in both eudicots
and monocots (Paponov et al., 2005). It will be desir-
able to extend isolation of this family of genes and the
PLT genes, which mediate patterning of the root stem
cell niche in Arabidopsis (Aida et al., 2004), to gym-
nosperms and pteridophytes, since the root apical
meristem first appeared at the beginning of vascular
plant evolution. Further, the search of the PIN genes
should be pursued in bryophytes and Characeae.
Although there is lack of evidence at present to sup-
port a hypothesis that gravitropism in Characeae and
all land plants is controlled by the same genetic
machinery, it is logical to expect so. A generally
consistent evolutionary pattern of auxin metabolism
and transport in Characeae, bryophytes, pteridophytes,
and seed plants offers some optimism in this hypothe-
sis (Cooke et al., 2002). When the algae colonized the
land, among various challenges they face (desiccation,
nutrient shortage, less buoyancy, UV, and sperm-
locomotion hindrance), absorption of water and
nutrients was the first they had to deal with in order to
survive, and gravitropism had to have evolved before
the algae moved onto the land so that underground
organs could develop to overcome this challenge.
Moreover, a brief examination of morphology of the
organisms along the phylogeny also supports such a
hypothesis. Characeae, liverworts, mosses, hornworts,
and vascular plants all have rhizoids or roots, which
are all gravity-sensing and underground organs. The
shoot negative gravitropism has not been studied as
much as the root positive gravitropism, but the evolu-
tionary history of the shoot portrays a similar and
virtually universal role of negative gravitropism in
shoot development. At the gametophytic level,
Characeae, Haplomitrium, some leafy liverworts,
Takakia and acrocarpous mosses all have a vertical
upward growing axis. At the sporophytic level,
Haplomitrium, simple thalloid and leafy liverworts, all
mosses, hornworts, and vascular plants also have such
an organ. In development of multicellular organisms,
cell polarity is the fundamental problem that organ-
isms have to solve during evolution (Cove, 2000).
During evolution of streptophytes, gravity had clearly
provided the most decisive environmental cue for
polarity establishment once these plants became
anchored on the soil. Therefore, the current exquisite
genetic information obtained from Arabidopsis and
the emerging results from studies of Characeae and
Physcomitrella provide a solid foundation to investi-
gate the origin and evolution of gravitropism in
charophytic algae and land plants.
In summary, the last twenty-five years witnessed
one of the most rapid growth periods in the history of
systematics. For the phylogeny of charophytic algae
and land plants, not only the backbone, which was
proposed even before morphological cladistic studies,
has been confirmed with rigorous quantitative analy-
ses of morphological and molecular data, but also
many important details crucial for our understanding
of some major evolutionary transitions have been
clarified by mostly molecular phylogenetic studies.
This progress on one hand brings us closer toward our
goal of reconstructing the Tree of Life (Haeckel,
1866), and on the other hand sets the stage for new
endeavors to explore how major evolutionary transi-
tions in evolution of plant life happened. Advances in
genetics and developmental biology in particular offer
a great opportunity to integrate the knowledge from
model organisms such as Physcomitrella and Arabi-
dopsis and the new phylogenetic information on
lineages that preceded and followed some major
transitions, e.g., Coleochaetaceae/Characeae and the
origin of gravitropism, and hornworts/lycophytes and
alternation of generations in the life cycle of early
land plants. This integrated multidisciplinary approach
is likely to help us to gain mechanistic understanding
on how some of the major evolutionary events in the
plant history were unfolded.
Acknowledgements I would like to express my
gratitude to Christiane Anderson, Peter K. Endress,
and Michael J. Wynne for help with literature search
and translation, and to Todd J. Cooke, Hilary A.
McManus and Paul G. Wolf for suggestions on im-
provement of the manuscript. I also would like to
QIU: Plant phylogeny and evolution

301
thank the National Science Foundation (USA), the
National Natural Science Foundation of China, and
DIVERSITAS (bioGENESIS program) for financial
support.
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