Directory UMM :Data Elmu:jurnal:P:PlantScience:Plant Science_BioMedNet:001-020:
trends in plant science
Reviews
30 Müller, M. and Knudsen, S. (1993) The nitrogen response of a barley C-hordein
promoter is controlled by positive and negative regulation of the GCN4 and
endosperm box. Plant J. 4, 343–355
31 Rao, V.V. et al. (1992) Developmental changes of L-lysine–ketoglutaric acid
reductase in rat brain and liver. Comp. Biochem. Physiol. B Biochem. Mol. Biol.
103, 221–224
32 Markovitz, P.J. et al. (1984) Familial hyperlysinemias. J. Biol. Chem. 259,
11643–11646
33 Deleu, C. et al. (1999) Three new osmotic stress-regulated cDNAs identified by
differential display polymerase chain reaction in rapeseed leaf discs. Plant Cell
Environ. 22, 979–988
34 Feller, A. et al. (1994) Repression of the genes for lysine biosynthesis in
Saccharomyces cerevisiae is caused by limitation of Lys14-dependent
transcriptional activation. Mol. Cell. Biol. 14, 6411–6418
35 Verhage, M. et al. (2000) Synaptic assembly of the brain in the absence of
neurotransmitter secretion. Science 287, 864–869
36 Lam, H.M. et al. (1998) Glutamic acid receptor genes in plants. Nature 396,
125–126
37 Nanjo, T. et al. (1999) Biological functions of proline in morphogenesis and
osmotolerance revealed in antisense transgenic Arabidopsis thaliana. Plant J. 18,
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Paulo Arruda*, Edson L. Kemper, Fabio Papes and Adilson Leite
are at the Centro de Biologia Molecular e Engenharia Genética,
Universidade Estadual de Campinas, 13083-970, Campinas, SP,
Brazil. Paulo Arruda is also in the Departamento de Genética e
Evolução, IB, Universidade Estadual de Campinas, 13083-970,
Campinas, SP, Brazil.
*Author for correspondence (tel 155 19 788 1137; fax 155 19 788
1089; e-mail [email protected]).
Recent progress in reconstructing
angiosperm phylogeny
Robert K. Kuzoff and Charles S. Gasser
In the past year, the study of angiosperm phylogeny has moved from tentative inferences
based on relatively small data matrices into an era of sophisticated, multigene analyses and
significantly greater confidence. Recent studies provide both strong statistical support and
mutual corroboration for crucial aspects of angiosperm phylogeny. These include identifying
the earliest extant lineages of angiosperms, confirming Amborella as the sister of all other
angiosperms, confirming some previously proposed lineages and redefining other groups
consistent with their phylogeny. This phylogenetic framework enables the exploration of both
genotypic and phenotypic diversification among angiosperms.
U
nderstanding the phylogenetic relationships among the principal lineages, or clades (Box 1), of angiosperms is essential for
elucidating the evolutionary events that underlie the diversification and ascension of this ecologically dominant plant group. We
also need to reconstruct flowering-plant phylogeny to facilitate comparative studies of plant development, metabolism, reproduction,
pathology and genomics. For these and other reasons, reconstructing
angiosperm phylogeny has been a major goal of plant systematists.
The state of knowledge before 1999
Attempts to unravel the overall phylogeny of angiosperms through
cladistic analysis date back more than a decade1,2. Goals of such
studies include identifying the composition of major lineages, the
relationships among them and the earliest lineages (first-branching
clades) of flowering plants. Analyses reported before 1999 were typically based on relatively small non-molecular2,3 or single-gene4–6
data matrices, with some exceptions7,8. Many results generated during this period constituted noteworthy advances that were largely
upheld by subsequent work. For example, several clades were identified, including the eudicots, rosids and asterids; some previously
proposed groups, including the Hamameliidae and Dilleniidae, were
also shown to be assemblages of distantly related species2,4–6,8,9.
However, although a potentially accurate picture of angiosperm phylogeny was taking shape, the plant-systematic and larger biological
communities did not place great confidence in it.
In addition to obvious instances of conflict among the earlier studies, systematists were aware of several other problems that tempered
330
August 2000, Vol. 5, No. 8
their enthusiasm. One major concern was that statistical support for
putative clades and the relationships among them was generally low,
if investigated. A second concern was that earlier studies relied
exclusively on parsimony as an optimality criterion in data analysis.
However, in parsimony analyses of DNA sequences, long branches
in a tree separated by short internodes can attract each other artifactually because of chance substitutions of identical nucleotides at
homologous sequence positions10,11. Such long-branch attraction can
be engendered by using distantly related outgroups. This is because
the branch leading to the outgroups attracts another long branch to
the base of the ingroup (Box 1). Alternatively it can be engendered
by insufficient taxon sampling, because taxonomically large groups
are represented only by sparse, long branches in an analysis9,12–14.
A third concern about these earlier studies was that the available
analysis protocols and computer programs employed were not well
suited to analysing complex phylogenies (those with large numbers
of taxa5,15,16). Consequently, analyses of some complex phylogenies
had to be stopped by the investigators before they could be completed4–6. Finally, it became clear that the amount of data being analyzed was not sufficient to resolve the phylogenetic problems
addressed, both because there were too few phylogenetically informative characters9,12,15 and because some of the apparently informative characters were potentially biased and misleading9,17.
Breakthroughs during the past year
Beginning in late 1999, several more-rigorous, multigene studies
have been published that address phylogenetic relationships among
1360 - 1385/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved. PII: S1360-1385(00)01685-X
trends in plant science
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Five recent studies
Tree
A hypothesis of phylogenetic relationships (branching order) for a
group of species (sometimes genes) inferred through phylogenetic
analysis25–27,32 of DNA or protein sequences, non-molecular data, or
a combination of these, sampled from each species (Fig. I). The root
is generally determined by the position of the branch connecting outgroup (black) and ingroup (colored) species. The first branch (earliest-diverging lineage) within the ingroup is the sister group to all
other ingroup species. The most recent common ancestor (MRCA)
of all ingroup species is represented by the node adjacent to the root
of the tree. A tree is composed of hierarchically nested clades (phylogenetic branches or lineages) of organisms, each comprising a
MRCA for that group and all its descendants. All nodes in a completely resolved tree are bifurcating. An unresolved node is a polytomy (clade Y).
Outgroup
Species
First branch of ingroup
Root
of
tree
Species A
Species G
Species B
MRCA of
A to G
Species C
Clade Y
Clade Z
Species D
MRCA of
B to F
Species E
Species F
Fig. I.
Clade X
One of the recent landmark studies18 focused on relationships near
the phylogenetic root of angiosperms, using a fairly novel approach
to identify these earliest branches that does not involve sampling
outgroups. All other seed plants are distantly related to angiosperms
and their use as outgroups might hinder phylogeny reconstruction.
To circumvent this problem, species were sampled for two paralogous phytochrome genes, phyA and phyC, that are duplicated only
among angiosperms. Sequences of these genes from 26 species (chosen to represent the angiosperm lineages thought to be the most
basal) were aligned and analyzed in concert. In the resulting phylogenetic network (an unrooted tree), there is a branch that connects
two largely symmetrical halves; one comprising all the phyA genes,
the other all the phyC genes. The position of this connecting branch
was used to root both halves, producing two highly concordant trees.
Several studies before 1999 indicated the positive effect on phylogenetic accuracy of increasing the number of characters sampled
per species9,12,13,15. In a recent study22, the sequences of
17 chloroplast genes (~13.4 kb) were sampled from each of 21
species, representing three gymnosperm and 18 putative basal
angiosperm lineages. Primary goals of this study were to identify the
first-branching lineages of angiosperms, to assess the effects of
greatly increased character sampling and to determine the phylogenetic usefulness of 14 previously untested chloroplast genes. Importantly, phylogenetic analyses were conducted with and without gymnosperm outgroups, to explore whether this would affect the
relationships at the base of the angiosperms22.
On the basis of several Monte Carlo computer simulations
(method reviewed in Ref. 28), it has been argued that the judicious
addition of species to phylogenetic analyses of taxonomically large
groups can break up otherwise long branches and improve the accuracy of results12–14. A third recent study19 attempted to improve the
accuracy of an inferred angiosperm phylogeny by increased sampling of both the number of species (560) and the nucleotides per
species (4733) relative to earlier studies4–8. The genes sampled were
Box 1. Glossary
Sister to rest
of ingroup
principal angiosperm lineages18–24. This surge in publications has
been facilitated by extensive collaboration among international
researchers, automated sequencing technology, advances in phylogenetic analysis software and access to increasingly powerful personal computers. Some recent inquiries focus on relationships near
the phylogenetic root of the flowering plants18,20–22 and others
explore a broader range of angiosperm phylogeny19,23,24. These studies use data matrices of between two18,23 and 17 (Ref. 22) complete,
aligned gene sequences, and include up to 560 species19,24. Inferring
trees from such large data matrices and assessing the statistical support for recovered clades have been facilitated by innovations in
phylogenetic analysis software16,25–27. Major relationships elucidated
by these analyses are generally not novel but, collectively, they provide abundant corroboration for each other as well as previously
unrealized levels of statistical support.
Although the strategies used in recent investigations differ appreciably, taken together, they strongly support a suite of conclusions
for overall angiosperm phylogeny18–22,24. First, these recent studies
identify Amborella trichopoda as the sister group of all other
angiosperms. Second, the next two successive branches in the
angiosperm tree are the Nymphaeales and the ‘ITA’ (Illiciaceae,
Schisandraceae, Trimeniaceae and Austrobaileyaceae) clade;
Amborella, the Nymphaeales and ITA are known as the ‘ANITA’
clades20 (Figs 1 and 2). Third, the composition of several major lineages of angiosperms (Table 1) is consistent among all these studies
(Table 2). Fourth, these studies, taken together, suggest that several
relationships among these lineages have been confidently resolved,
although several relationships remain unclear (Fig. 2).
Trends in Plant Science
Bootstrapping
A technique for assessing how strongly phylogenetic data support
clades in a tree29. The characters in the original data set are sampled,
with replacement, until a new data set of the same size as the orig
inal is generated. The generated data set is analyzed phylogenetically and a summary tree produced. These two steps, constituting
one replicate, are repeated a specified number of times. Bootstrap
values represent the percentage of summary trees supporting a
particular clade. Replicates can propagate biases present in the
original data matrix.
Parsimony jackknifing
A technique for assessing how strongly phylogenetic data support
clades in a tree25. Replicate data matrices are generated through independent and random deletion of characters from the original data
matrix until a user-defined fraction [typically 0.5 or 1 2 (1 4 e)] of
the original characters remain. Summary trees are produced for each
replicate data matrix through parsimony analysis. Jackknife values
are the percentage of summary trees that support a clade. Replicates
can propagate biases present in the original data matrix.
August 2000, Vol. 5, No. 8
331
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(a)
(b)
(c)
(d)
Fig. 1. Flowers of representatives from ANITA clades. Amborella, the Nymphaeales and the
ITA (Illiciaceae, Schisandraceae, Trimeniaceae and Austrobaileyaceae) clade are known as the
‘ANITA’ clades20. (a) Female flower of Amborella trichopoda (photograph courtesy of Sandra
K. Floyd). Amborella comprises one species of dioecious, woody shrub endemic to New
Caledonia. Flowers have a spirally arranged, undifferentiated perianth, a small hypanthium and
either numerous more-or-less laminar stamens (male flower) or 4–8 distinct, urn-shaped
carpels, with unfused margins (female flower). (b) Flower of Nymphaea sp. (Nymphaeales;
photograph courtesy of Gregory M. Plunkett). Nymphaea comprises ~50 species of aquatic,
rhizomatous cosmopolitanly distributed herbs. Flowers are bisexual with several undifferentiated tepals, numerous more-or-less laminar stamens, numerous united carpels, with fused margins, and an inferior ovary. (c) Flower of Austrobaileya scandens (Austrobaileyaceae, ITA
clade; photograph courtesy of Susana Magallón). Austrobaileya comprises one species of evergreen liana found in NE Australia. Flowers have numerous, undifferentiated, spirally arranged
tepals, several spirally arranged, more-or-less laminar stamens, and 10–13 distinct carpels with
unfused margins. (d) Flower of Illicium sp. (Illiciaceae, ITA clade; photograph courtesy of
Douglas E. Soltis), Illicium comprises ~42 species of shrubs and small trees, distributed in eastern Asia and southern North America. Flowers are bisexual, with a spirally arranged, undifferentiated perianth, spirally arranged stamens with short, thick filaments, and carpels with
partially fused margins. All descriptions are based on Refs 33,51.
rbcL and atpB from the chloroplast genome, and nuclear 18S rDNA.
Because of the increased sampling of species, this study was the
most-rigorous test of the monophyly of major angiosperm groups yet
published. The many species included in this study merited the use
of alternatives to standard computational techniques. For example,
they used a recently developed search algorithm called the Ratchet16
(implemented by NONA 2.0, Ref 26) that finds shorter trees in parsimony analyses of complex phylogenies more quickly than other
available algorithms. Also, because traditional heuristic parsimony
bootstrapping29 with this number of species was impractical, this
study used a more rapid method, parsimony jackknifing25 (Box 1) to
assess the support for inferred clades (Table 2).
The evolution of individual genes or genomes used in phylogeny
reconstruction is generally not well understood and might have a
negative impact on phylogenetic analyses. In a fourth recent study20,
five genes from three genomes (nuclear, chloroplast and mitochondrial) were sampled from 105 species, representing all major gymnosperm and putative basal angiosperm lineages. The sampled
genes, encompassing 8733 aligned nucleotides, were the same as
those used in the third study, above19, with the addition of two mito332
August 2000, Vol. 5, No. 8
chondrial genes, matR and atp1. Sampling
three genomes with potentially different histories and modes of inheritance (the nuclear
genome is biparentally inherited but the
chloroplast and mitochondrial genomes are
generally uniparentally inherited) might mitigate the effects of possible cryptic biases present in the individual genes or genomes. In
addition, separate phylogenetic analyses were
conducted for each of the five genes included
in the study20.
For reasons discussed above, a fifth study21
also sampled five genes representing all three
plant genomes (totaling 6564 nucleotides) for
51 species from several major angiosperm and
gymnosperm lineages. These genes are
nuclear 18S rDNA, chloroplast atpB and three
mitochondrial genes (mtSSU, cox1 and rps2).
In addition, the sequence data were analyzed
with and without gymnosperm outgroups and
a series of likelihood ratio tests (method
reviewed in Ref. 30) were conducted to determine whether the position of Amborella as sister to all other angiosperms was significantly
better than alternative candidates for this position. Although the other studies discussed
above relied solely on parsimony, which can
produce misleading results under certain circumstances10,11, the data in this study21 were
reanalyzed using a model-based approach to
phylogenetic inference called maximumlikelihood estimation31,32 (MLE). This analysis should be less sensitive to branch-length
disparity, provided that the model of sequence
evolution used is appropriate.
Mutual corroboration
Although there is always room to question
phylogenetic results10,11,22, taken together, the
five studies reviewed above provide a wellsupported picture of angiosperm phylogeny
(Fig. 2; Table 2) that withstands a variety of
potential criticisms. Although the effects of
taxon12–14 and character9,12,13,15 sampling can
dramatically affect the accuracy of inferred phylogenies, altering
these factors across a wide range (21 versus 560 species and 2.2 versus 13.4 kb per species; Table 2) did not alter the relationships among
basal branches or the composition of major angiosperm lineages.
Long-branch attraction, whether it is due to the use of distantly
related outgroups or to the presence of long ingroup branches, also
does not appear to have had a negative impact on these
phylogenetic results:
• Relationships near the root of the tree and the composition of
major lineages were not affected by the removal of distantly
related outgroups from analyses18,21,22.
• The first three branches in the trees from the five studies summarized above are not especially long compared with other branches
in each of these studies18–22.
• MLE provides corroboration for the branch positions that were
inferred through parsimony analysis and several likelihood ratio
tests detected no better rootings21.
Hence, although long-branch attraction among the earliest angiosperm lineages cannot be decisively ruled out, it is unlikely that it
affected these results.
trends in plant science
Reviews
95/-
Other Conifers
Extant
gymnosperms
Pinaceae
100/100/100
Gnetales
Ginkgo
100/-
Cycads
Amborella
100/100
100/100
90/65
Nymphaeales
100/98
ITA
100/99
Chloranthales
Ceratophyllum
98/72
99/83
100/93
71/-
Monocots
Magnoliales
Angiosperms
Impact and implications
Phenotypic evolution
100/94
100/-
ANITA clades
Finally, these principal findings are not
likely to be the result of cryptic-gene or
genome biases. The positions of Amborella
and the other ANITA clades in independent
analyses of at least five individual genes representing all plant genomes6,18,20,23 and five
multigene matrices18–22 strongly suggests that
all these sources of data contain a significant,
concordant phylogenetic signal. By far the
simplest explanation for the congruence of
these studies and their strong statistical support is that they have each accurately inferred
elements of the underlying organismal phylogeny.
Eudicots
The collective findings of the above studies
Laurales
100/97
67/97/71
provide a phylogenetic framework that
100/94
Winterales
enables additional research on several classi83/cal problems in angiosperm evolution. For
Piperales
100/88
example, there is tremendous interest in
100/98
Ranunculales
reconstructing the patterns of diversification
86/84 Proteales
among angiosperms for a variety of attributes
100/99
100/100
including floral and vegetative morphology,
Sabiaceae
91/59
metabolism, modes of reproduction, con100/100 Trochodendrales
stituent gene families, and genomes18–22,33.
100/100 Buxaceae and
This can be accomplished by mapping those
Didymelaceae
characters onto individual trees, tracing their
98/87
-/100
Caryophyllales
evolution throughout the phylogeny and
-/99
Asterids
reconstructing character states for ancestral
-/100
-/60
taxa (e.g. using MacClade 3.07, Ref. 34).
Rosids
Comparisons of features of families in the
Trends in Plant Science
ANITA clades, in their phylogenetic context,
provide insight into the origin and early
52
Fig. 2. Simplified ‘supertree’ based on five recent multigene phylogenies for
diversification of flowering plants18,20,21,33.
angiosperms18–22. The supertree is the strict consensus of 36 shortest trees recovered from a
For example, the vegetative body of the combranch-and-bound analysis of clades in individual multigene studies (source trees) using
mon ancestor of all extant angiosperms probmatrix representation with parsimony52 and a weighting scheme based on the support values
ably had a woody habit, vessel-less wood,
of branches in the source trees (,50% 5 1; 51–70% 5 2; 71–90% 5 3; 91–100% 5 4).
unilacunar leaf nodes with two traces, leaves
Support values for clades in the supertree are based on parsimony bootstrap29 (blue) and
with chloranthoid teeth along their margins
jackknife25 (red) analyses from two source trees (‘2’ indicates ,50% support). Support values from other source trees are listed in Table 2. Relationships among gymnosperms shown
and no ethereal oils. Flowers of this common
here are consistent with recent results from analyses of seed plants36. Abbreviations: ITA
ancestor probably had an undifferentiated
clade, consists of Illiciaceae, Schisandraceae, Trimeniaceae and Austrobaileyaceae.
perianth arranged in more than two cycles or
series, perianth appendages that were unfused
above the base and anthers that shed pollen
towards the center of the flower. Carpels in these flowers were urn- Genetic basis of phenotypic evolution
shaped (ascidiate), were not attached to one another (apocarpous) In general, understanding genotypic or phenotypic diversification
and had margins that did not fuse completely but were closed at requires knowledge of an organismal phylogeny to specify the
maturity by secretions. An herbaceous habit, ethereal oils, wood locations, frequency and directionality of character state changes
with vessels, differentiated sepals and petals, and complete carpel within a lineage. The phylogenetic results discussed above provide
closure probably evolved after the origin of flowering plants. These the requisite framework to dissect the evolution of genes, gene
derived features might have contributed to the rapid diversification families and genomes, and to relate these events to morphological
of later-evolved angiosperm lineages (Table 1). The emerging pic- evolution. Molecular and phylogenetic dissection of petal and
ture of the earliest angiosperms differs appreciably from previously ovule evolution illustrate this point (additional examples are
proposed models for the first angiosperms (reviewed in Refs 35–37). reviewed in Ref. 38).
Recent results from studies of all the seed-plant groups suggest
It has been argued on the basis of comparative morphology that,
that the extant gymnosperms form a monophyletic group that is the among angiosperms, superficially similar petals have evolved sevsister lineage to the angiosperms20,36,37 (Fig. 2). This contradicts eral times from either stamens (andropetals) or sepals (bracteosome earlier models that placed one group of gymnosperms, the petals)38. How frequently each has occurred can be elucidated only
Gnetales, as the sister to all angiosperms. Consequently, future by the combined analysis of comparative morphology and geneclues to the morphological transitions that led to the origin of the expression and gene-family evolution in the context of angiosperm
angiosperms will come largely from fossil33,36 and comparative phylogeny38–40. Recent results indicate that, among the eudicots, sepmolecular-genetic data37,38.
arate lineages of AP3 homologs have been recruited in independent
August 2000, Vol. 5, No. 8
333
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Genome evolution
Table 1. Several lineages (clades) of flowering plants recognized in recent
phylogenetic analyses43
Clade
Families
(species)
Examples
Amborella
1 (1)
Amborella trichopoda
Nymphaeales
2 (81)
Water lilies (Nymphaea spp.)
‘ITA’a
4 (95)
Star anise (Illicium verum)
Chloranthales
1 (75)
Chloranthus, Ascarina
Ceratophyllum
1 (6)
Ceratophyllum
Monocots
102 (65 000)
Grasses, orchids, palms
Magnoliales
6 (2700)
Magnolia, tulip tree (Liriodendron tulipifera)
Laurales
7 (3400)
Sassafras, avocado (Persea americana)
Winterales
2 (73)
Winter’s bark (Drimys)
Piperales
4 (3500)
Black pepper (Piper)
Ranunculales
7 (4400)
Buttercup (Ranunculus spp.), poppy (Papaver spp.)
Proteales
3 (1600)
Sacred lotus (Nelumbo), plane (Platanus spp.)
Caryophyllales
26 (9400)
Cactus (Cactaceae), beet (Beta vulgaris),
spinach (Spinacia oleracea)
Asterids
107 (87 000)
Sunflower (Helianthus spp.), carrot, tomato, holly
(Ilex spp.), snapdragon (Antirrhinum majus)
A comparison of the molecular phylogeny of
group-I introns and overall angiosperm phylogeny suggests that group-I introns have
been independently acquired ~1000 times by
various angiosperms44. Whether these introns
have been acquired independently from fungal donors or through horizontal transfer
from plants is unclear but it has important
implications for the potential for genetic
transfer from genetically engineered crop
species to local flora. Resolving this question will depend on expanded analyses of
group-I introns in the context of angiosperm
phylogeny.
Phylogenetic analysis of genome size
among the grasses reveals a predominantly unidirectional trend towards genomic ‘obesity’45.
Whether genomes evolve towards greater
size in general among angiosperms can now
be explored in other well-defined angiosperm
lineages. Genome doubling through polyploidy is a common phenomenon in the history of angiosperms and is especially
prevalent in crop species42. The number of
polyploid origins and their parentage, consequences for gene evolution and biochemical
impact can now be dissected in the context of
overall angiosperm phylogeny.
Classification
Several authors have discussed the inadequacies of previously available classification systems for flowering plants9,35,46. Foremost
Rosids
149 (77 000)
Maple (Acer spp.), apple, pea, rose, Arabidopsis
among their concerns is that these classifia
cations are at odds with robust results of pub‘ITA’ clade comprises Illiciaceae, Schisandraceae, Trimeniaceae and Austrobaileyaceae.
lished phylogenetic analyses. In an effort to
address this need, the Angiosperm Phylogeny
evolutionary events to determine petal identity in the Ranunculales Group (APG), a consortium of over 40 plant systematists, has proand in the Rosids and Asterids39,40. Among the grasses, AP3- posed a working classification of angiosperms into orders and some
homolog expression is conserved in petals but other genetic factors higher-level groupings46. Their provisional classification system was
have been altered, converting the familiar petals into lodicules38,41. based on results of single4–6 and preliminary multigene19 studies. The
Although the directionality of change in these cases is fairly uncon- additional phylogenetic results summarized above are entirely controversial, the exact origins and frequency of these transformations cordant with their classification system, suggesting that it should be
remain unclear. Determining these will require testing additional retained and extended. The proposed APG classification is useful for
organisms, selected according to the available phylogeny. In addi- facilitating communication within and among disciplines of biology
tion, an understanding of the general applicability of other aspects of and presentation of fruitful research to the broader community.
floral development in model organisms will be achieved through
future phylogenetically informed research42.
Future directions
The Arabidopsis INNER NO OUTER (INO) gene has been shown Although much of the overall angiosperm phylogeny is now confito be essential for the asymmetric growth of ovule outer integu- dently resolved, polytomies (Box 1) among magnoliid clades,
ments43. Gene-expression patterns in wild-type and mutant Ara- Ceratophyllum and the monocots, as well as within the eudicots,
bidopsis were compatible with INO acting either to establish require additional study (Fig. 2). The enormous effort that has
abaxial–adaxial polarity in ovules or to promote outer integument already been put into these studies might lead to pessimism about
outgrowth directly. The phylogenetic results discussed above permit the prospects for additional progress. Fortunately, there are several
the selection of angiosperm lineages that are radially symmetrical resources that can be brought to bear on the problem, which will
and bitegmic or asymmetrical (polar) and unitegmic in order to test clarify relationships further. For example, several available sources
the two models by examining the ancestral function of INO of data have not been fully exploited. Morphological data are being
orthologs through comparative gene-expression studies. Tests of reanalyzed in light of the results discussed above to reveal previous
these two models through comparative study of expression of INO misleading homology assessments, enhancing their utility in suborthologs isolated from diverse species, selected according to the lat- sequent analyses and facilitating the incorporation of crucial fossil
est phylogenies, are in progress [R. Kuzoff et al., unpublished data33,35,36.
(http://www.ou.edu/cas/botany-micro/botany2000/section2/
Similar analyses of molecular data9,15,22,23 will reveal hidden tenabstracts/28.shtml)].
dencies in nucleotide substitution and permit the generation of
334
August 2000, Vol. 5, No. 8
trends in plant science
Reviews
Table 2. Recent molecular phylogenetic analyses of angiospermsa
Study (sequences rbcL
analyzed)
(Ref. 4)
18S rDNA
(Ref. 6)
atpB
(Ref. 23)b
phyA, C
(Ref. 18)c
17-cp genes
(Ref. 22)
3 genes
(rbcL, atpB,
18S rDNA)19d
5 genes (rbcL,
atpB, 18S rDNA,
matR, atp1)20
5 genes (atpB,
18S rDNA, cox1,
rps2, mtSSU)21
Genomes (genes) Cp (1)
Nuc (1)
Cp (1)
Nuc (2)
Cp (17)
Nuc (1),
Cp (2)
Nuc (1), Cp (2),
Mt (2)
Nuc (1), Cp (1),
Mt (3)
Nucleotides
1428
1855
1460
2208
~13 400
4733
8733
6564
Species
499
228
357
26
21
560
105
51
Amborella is
first branch
2
1
1
1, 92%,
83%
1, 69%
1, 65%
1, 90%
1, 89%
ANITA clades
adjacent to root
2
1
(1 some
Piperales)
1
1, 86%
1, 94%
1, 71%
1, 97%
1, 92%
Nymphaeales
1
1
1, 100%
1, 100%
1, 100%
1, 100%
1, 100%
1, 100%
Chloranthales
1
1
1, 59%
1 sampled
Not sampled
1, 99%
1, 100%
1 sampled
Monocots
1
Almost
(2 1 species)
Almost
(1 1 species)
1, 100%
1, 93%
1, 95%
1, 99%
1, 92%
Magnoliales
1
1
1
1, 100%
1 sampled
1, 93%
1, 100%
1, .90%
Laurales
1
1
1, 68%
1, 100%
1 sampled
1, 97%
1, 100%
1, .90%
Winterales
1
1
1, 94%
1, 99%
1 sampled
1, 94%
1, 100%
1 sampled
Piperales
1
2
1
1, 100%
1, 99%
1, 88%
1, 100%
1
Eudicots
1
Almost
(1 3 orders)
1
1, 100%
1, 100%
1, 99%
1, 100%
1, 100%
Rosids
1
Almost
(1 1 order)
1 sampled
1, 60%
Not sampled
1
Asterids
1
Almost
(1 1 order)
1 sampled
1, 99%
Not sampled
1, .90%
Almost
Not sampled
(2 1 order)
1, 66%
Not sampled
a
Clades that are recovered (1) or not recovered (2) and bootstrap support values29 (unless otherwise indicated) are indicated in each analysis. Names for lineages
generally follow Ref. 46, except for Winterales and Chloranthales, which were recognized in more recent analyses19,20. ‘1 sampled’ indicates clades that were not
tested for monophyly, because only one species was sampled.
b
Although both atpB and rbcL sequences were analyzed23, results summarized here are based on atpB alone.
c
Bootstrap values were inferred for the clade comprising all species other than Amborella in the separate phyA and phyC trees18; all other bootstrap values in this
analysis came from the analysis of concatenated phyA and phyC sequences.
d
Jackknife values were used25 rather than bootstrap values29 to assess support for clades recovered in this study.
Abbreviations: Nuc, nuclear; Cp, chloroplast; Mt, mitochondrial.
more-realistic models of sequence evolution. These clarified models
will inform and increase the accuracy of subsequent model-based
phylogenetic analyses30–32. Also, the molecules used in several of the
analyses described above18,21,22 and elsewhere47 can be sampled from
additional species and combined with existing data for more detailed
analyses of relationships within principal angiosperm clades, such as
the monocots, eudicots, rosids and asterids. Other complex phylogenies, in the grasses for example, required as many as eight independent data sets before complete resolution with strong support was
achieved48.
Computational strategies such as compartmentalization5,49,50, in
which large, well-supported clades are replaced in an analysis by an
inferred ancestral state for that clade, also appear to be promising. In
fact, an expanded analysis of 26S rDNA (Ref. 47) and other
sequences20 using such compartmentalization of angiosperm clades
has produced complete resolution among the basal lineages and with
stronger support than was achieved previously (M. Zanis et al., pers.
commun.). We are optimistic that angiosperm phylogenetics will
progress rapidly on its present course, facilitating additional comparative studies and fuller exploitation of knowledge garnered from
model research organisms.
Acknowledgements
We apologize to those whose work could not be included in this review owing to space limitations. We thank Olaf Bininda-Emonds,
Jim Doyle, Sean Graham, Toby Kellogg, Jessie McAbee, Greg
Plunkett, Vincent Savolainen, Doug and Pam Soltis, and Michael
Zanis for helpful discussions, and the Katherine Esau Postdoctoral
Fellowship and the National Science Foundation (IBN-9983354) for
financial support.
August 2000, Vol. 5, No. 8
335
trends in plant science
Reviews
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Robert K. Kuzoff* and Charles S. Gasser are at the Section of
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CA 95616, USA.
*Author for correspondence (tel 11 530 752 3111;
fax 11 530 752 3085; e-mail [email protected]).
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Paulo Arruda*, Edson L. Kemper, Fabio Papes and Adilson Leite
are at the Centro de Biologia Molecular e Engenharia Genética,
Universidade Estadual de Campinas, 13083-970, Campinas, SP,
Brazil. Paulo Arruda is also in the Departamento de Genética e
Evolução, IB, Universidade Estadual de Campinas, 13083-970,
Campinas, SP, Brazil.
*Author for correspondence (tel 155 19 788 1137; fax 155 19 788
1089; e-mail [email protected]).
Recent progress in reconstructing
angiosperm phylogeny
Robert K. Kuzoff and Charles S. Gasser
In the past year, the study of angiosperm phylogeny has moved from tentative inferences
based on relatively small data matrices into an era of sophisticated, multigene analyses and
significantly greater confidence. Recent studies provide both strong statistical support and
mutual corroboration for crucial aspects of angiosperm phylogeny. These include identifying
the earliest extant lineages of angiosperms, confirming Amborella as the sister of all other
angiosperms, confirming some previously proposed lineages and redefining other groups
consistent with their phylogeny. This phylogenetic framework enables the exploration of both
genotypic and phenotypic diversification among angiosperms.
U
nderstanding the phylogenetic relationships among the principal lineages, or clades (Box 1), of angiosperms is essential for
elucidating the evolutionary events that underlie the diversification and ascension of this ecologically dominant plant group. We
also need to reconstruct flowering-plant phylogeny to facilitate comparative studies of plant development, metabolism, reproduction,
pathology and genomics. For these and other reasons, reconstructing
angiosperm phylogeny has been a major goal of plant systematists.
The state of knowledge before 1999
Attempts to unravel the overall phylogeny of angiosperms through
cladistic analysis date back more than a decade1,2. Goals of such
studies include identifying the composition of major lineages, the
relationships among them and the earliest lineages (first-branching
clades) of flowering plants. Analyses reported before 1999 were typically based on relatively small non-molecular2,3 or single-gene4–6
data matrices, with some exceptions7,8. Many results generated during this period constituted noteworthy advances that were largely
upheld by subsequent work. For example, several clades were identified, including the eudicots, rosids and asterids; some previously
proposed groups, including the Hamameliidae and Dilleniidae, were
also shown to be assemblages of distantly related species2,4–6,8,9.
However, although a potentially accurate picture of angiosperm phylogeny was taking shape, the plant-systematic and larger biological
communities did not place great confidence in it.
In addition to obvious instances of conflict among the earlier studies, systematists were aware of several other problems that tempered
330
August 2000, Vol. 5, No. 8
their enthusiasm. One major concern was that statistical support for
putative clades and the relationships among them was generally low,
if investigated. A second concern was that earlier studies relied
exclusively on parsimony as an optimality criterion in data analysis.
However, in parsimony analyses of DNA sequences, long branches
in a tree separated by short internodes can attract each other artifactually because of chance substitutions of identical nucleotides at
homologous sequence positions10,11. Such long-branch attraction can
be engendered by using distantly related outgroups. This is because
the branch leading to the outgroups attracts another long branch to
the base of the ingroup (Box 1). Alternatively it can be engendered
by insufficient taxon sampling, because taxonomically large groups
are represented only by sparse, long branches in an analysis9,12–14.
A third concern about these earlier studies was that the available
analysis protocols and computer programs employed were not well
suited to analysing complex phylogenies (those with large numbers
of taxa5,15,16). Consequently, analyses of some complex phylogenies
had to be stopped by the investigators before they could be completed4–6. Finally, it became clear that the amount of data being analyzed was not sufficient to resolve the phylogenetic problems
addressed, both because there were too few phylogenetically informative characters9,12,15 and because some of the apparently informative characters were potentially biased and misleading9,17.
Breakthroughs during the past year
Beginning in late 1999, several more-rigorous, multigene studies
have been published that address phylogenetic relationships among
1360 - 1385/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved. PII: S1360-1385(00)01685-X
trends in plant science
Reviews
Five recent studies
Tree
A hypothesis of phylogenetic relationships (branching order) for a
group of species (sometimes genes) inferred through phylogenetic
analysis25–27,32 of DNA or protein sequences, non-molecular data, or
a combination of these, sampled from each species (Fig. I). The root
is generally determined by the position of the branch connecting outgroup (black) and ingroup (colored) species. The first branch (earliest-diverging lineage) within the ingroup is the sister group to all
other ingroup species. The most recent common ancestor (MRCA)
of all ingroup species is represented by the node adjacent to the root
of the tree. A tree is composed of hierarchically nested clades (phylogenetic branches or lineages) of organisms, each comprising a
MRCA for that group and all its descendants. All nodes in a completely resolved tree are bifurcating. An unresolved node is a polytomy (clade Y).
Outgroup
Species
First branch of ingroup
Root
of
tree
Species A
Species G
Species B
MRCA of
A to G
Species C
Clade Y
Clade Z
Species D
MRCA of
B to F
Species E
Species F
Fig. I.
Clade X
One of the recent landmark studies18 focused on relationships near
the phylogenetic root of angiosperms, using a fairly novel approach
to identify these earliest branches that does not involve sampling
outgroups. All other seed plants are distantly related to angiosperms
and their use as outgroups might hinder phylogeny reconstruction.
To circumvent this problem, species were sampled for two paralogous phytochrome genes, phyA and phyC, that are duplicated only
among angiosperms. Sequences of these genes from 26 species (chosen to represent the angiosperm lineages thought to be the most
basal) were aligned and analyzed in concert. In the resulting phylogenetic network (an unrooted tree), there is a branch that connects
two largely symmetrical halves; one comprising all the phyA genes,
the other all the phyC genes. The position of this connecting branch
was used to root both halves, producing two highly concordant trees.
Several studies before 1999 indicated the positive effect on phylogenetic accuracy of increasing the number of characters sampled
per species9,12,13,15. In a recent study22, the sequences of
17 chloroplast genes (~13.4 kb) were sampled from each of 21
species, representing three gymnosperm and 18 putative basal
angiosperm lineages. Primary goals of this study were to identify the
first-branching lineages of angiosperms, to assess the effects of
greatly increased character sampling and to determine the phylogenetic usefulness of 14 previously untested chloroplast genes. Importantly, phylogenetic analyses were conducted with and without gymnosperm outgroups, to explore whether this would affect the
relationships at the base of the angiosperms22.
On the basis of several Monte Carlo computer simulations
(method reviewed in Ref. 28), it has been argued that the judicious
addition of species to phylogenetic analyses of taxonomically large
groups can break up otherwise long branches and improve the accuracy of results12–14. A third recent study19 attempted to improve the
accuracy of an inferred angiosperm phylogeny by increased sampling of both the number of species (560) and the nucleotides per
species (4733) relative to earlier studies4–8. The genes sampled were
Box 1. Glossary
Sister to rest
of ingroup
principal angiosperm lineages18–24. This surge in publications has
been facilitated by extensive collaboration among international
researchers, automated sequencing technology, advances in phylogenetic analysis software and access to increasingly powerful personal computers. Some recent inquiries focus on relationships near
the phylogenetic root of the flowering plants18,20–22 and others
explore a broader range of angiosperm phylogeny19,23,24. These studies use data matrices of between two18,23 and 17 (Ref. 22) complete,
aligned gene sequences, and include up to 560 species19,24. Inferring
trees from such large data matrices and assessing the statistical support for recovered clades have been facilitated by innovations in
phylogenetic analysis software16,25–27. Major relationships elucidated
by these analyses are generally not novel but, collectively, they provide abundant corroboration for each other as well as previously
unrealized levels of statistical support.
Although the strategies used in recent investigations differ appreciably, taken together, they strongly support a suite of conclusions
for overall angiosperm phylogeny18–22,24. First, these recent studies
identify Amborella trichopoda as the sister group of all other
angiosperms. Second, the next two successive branches in the
angiosperm tree are the Nymphaeales and the ‘ITA’ (Illiciaceae,
Schisandraceae, Trimeniaceae and Austrobaileyaceae) clade;
Amborella, the Nymphaeales and ITA are known as the ‘ANITA’
clades20 (Figs 1 and 2). Third, the composition of several major lineages of angiosperms (Table 1) is consistent among all these studies
(Table 2). Fourth, these studies, taken together, suggest that several
relationships among these lineages have been confidently resolved,
although several relationships remain unclear (Fig. 2).
Trends in Plant Science
Bootstrapping
A technique for assessing how strongly phylogenetic data support
clades in a tree29. The characters in the original data set are sampled,
with replacement, until a new data set of the same size as the orig
inal is generated. The generated data set is analyzed phylogenetically and a summary tree produced. These two steps, constituting
one replicate, are repeated a specified number of times. Bootstrap
values represent the percentage of summary trees supporting a
particular clade. Replicates can propagate biases present in the
original data matrix.
Parsimony jackknifing
A technique for assessing how strongly phylogenetic data support
clades in a tree25. Replicate data matrices are generated through independent and random deletion of characters from the original data
matrix until a user-defined fraction [typically 0.5 or 1 2 (1 4 e)] of
the original characters remain. Summary trees are produced for each
replicate data matrix through parsimony analysis. Jackknife values
are the percentage of summary trees that support a clade. Replicates
can propagate biases present in the original data matrix.
August 2000, Vol. 5, No. 8
331
trends in plant science
Reviews
(a)
(b)
(c)
(d)
Fig. 1. Flowers of representatives from ANITA clades. Amborella, the Nymphaeales and the
ITA (Illiciaceae, Schisandraceae, Trimeniaceae and Austrobaileyaceae) clade are known as the
‘ANITA’ clades20. (a) Female flower of Amborella trichopoda (photograph courtesy of Sandra
K. Floyd). Amborella comprises one species of dioecious, woody shrub endemic to New
Caledonia. Flowers have a spirally arranged, undifferentiated perianth, a small hypanthium and
either numerous more-or-less laminar stamens (male flower) or 4–8 distinct, urn-shaped
carpels, with unfused margins (female flower). (b) Flower of Nymphaea sp. (Nymphaeales;
photograph courtesy of Gregory M. Plunkett). Nymphaea comprises ~50 species of aquatic,
rhizomatous cosmopolitanly distributed herbs. Flowers are bisexual with several undifferentiated tepals, numerous more-or-less laminar stamens, numerous united carpels, with fused margins, and an inferior ovary. (c) Flower of Austrobaileya scandens (Austrobaileyaceae, ITA
clade; photograph courtesy of Susana Magallón). Austrobaileya comprises one species of evergreen liana found in NE Australia. Flowers have numerous, undifferentiated, spirally arranged
tepals, several spirally arranged, more-or-less laminar stamens, and 10–13 distinct carpels with
unfused margins. (d) Flower of Illicium sp. (Illiciaceae, ITA clade; photograph courtesy of
Douglas E. Soltis), Illicium comprises ~42 species of shrubs and small trees, distributed in eastern Asia and southern North America. Flowers are bisexual, with a spirally arranged, undifferentiated perianth, spirally arranged stamens with short, thick filaments, and carpels with
partially fused margins. All descriptions are based on Refs 33,51.
rbcL and atpB from the chloroplast genome, and nuclear 18S rDNA.
Because of the increased sampling of species, this study was the
most-rigorous test of the monophyly of major angiosperm groups yet
published. The many species included in this study merited the use
of alternatives to standard computational techniques. For example,
they used a recently developed search algorithm called the Ratchet16
(implemented by NONA 2.0, Ref 26) that finds shorter trees in parsimony analyses of complex phylogenies more quickly than other
available algorithms. Also, because traditional heuristic parsimony
bootstrapping29 with this number of species was impractical, this
study used a more rapid method, parsimony jackknifing25 (Box 1) to
assess the support for inferred clades (Table 2).
The evolution of individual genes or genomes used in phylogeny
reconstruction is generally not well understood and might have a
negative impact on phylogenetic analyses. In a fourth recent study20,
five genes from three genomes (nuclear, chloroplast and mitochondrial) were sampled from 105 species, representing all major gymnosperm and putative basal angiosperm lineages. The sampled
genes, encompassing 8733 aligned nucleotides, were the same as
those used in the third study, above19, with the addition of two mito332
August 2000, Vol. 5, No. 8
chondrial genes, matR and atp1. Sampling
three genomes with potentially different histories and modes of inheritance (the nuclear
genome is biparentally inherited but the
chloroplast and mitochondrial genomes are
generally uniparentally inherited) might mitigate the effects of possible cryptic biases present in the individual genes or genomes. In
addition, separate phylogenetic analyses were
conducted for each of the five genes included
in the study20.
For reasons discussed above, a fifth study21
also sampled five genes representing all three
plant genomes (totaling 6564 nucleotides) for
51 species from several major angiosperm and
gymnosperm lineages. These genes are
nuclear 18S rDNA, chloroplast atpB and three
mitochondrial genes (mtSSU, cox1 and rps2).
In addition, the sequence data were analyzed
with and without gymnosperm outgroups and
a series of likelihood ratio tests (method
reviewed in Ref. 30) were conducted to determine whether the position of Amborella as sister to all other angiosperms was significantly
better than alternative candidates for this position. Although the other studies discussed
above relied solely on parsimony, which can
produce misleading results under certain circumstances10,11, the data in this study21 were
reanalyzed using a model-based approach to
phylogenetic inference called maximumlikelihood estimation31,32 (MLE). This analysis should be less sensitive to branch-length
disparity, provided that the model of sequence
evolution used is appropriate.
Mutual corroboration
Although there is always room to question
phylogenetic results10,11,22, taken together, the
five studies reviewed above provide a wellsupported picture of angiosperm phylogeny
(Fig. 2; Table 2) that withstands a variety of
potential criticisms. Although the effects of
taxon12–14 and character9,12,13,15 sampling can
dramatically affect the accuracy of inferred phylogenies, altering
these factors across a wide range (21 versus 560 species and 2.2 versus 13.4 kb per species; Table 2) did not alter the relationships among
basal branches or the composition of major angiosperm lineages.
Long-branch attraction, whether it is due to the use of distantly
related outgroups or to the presence of long ingroup branches, also
does not appear to have had a negative impact on these
phylogenetic results:
• Relationships near the root of the tree and the composition of
major lineages were not affected by the removal of distantly
related outgroups from analyses18,21,22.
• The first three branches in the trees from the five studies summarized above are not especially long compared with other branches
in each of these studies18–22.
• MLE provides corroboration for the branch positions that were
inferred through parsimony analysis and several likelihood ratio
tests detected no better rootings21.
Hence, although long-branch attraction among the earliest angiosperm lineages cannot be decisively ruled out, it is unlikely that it
affected these results.
trends in plant science
Reviews
95/-
Other Conifers
Extant
gymnosperms
Pinaceae
100/100/100
Gnetales
Ginkgo
100/-
Cycads
Amborella
100/100
100/100
90/65
Nymphaeales
100/98
ITA
100/99
Chloranthales
Ceratophyllum
98/72
99/83
100/93
71/-
Monocots
Magnoliales
Angiosperms
Impact and implications
Phenotypic evolution
100/94
100/-
ANITA clades
Finally, these principal findings are not
likely to be the result of cryptic-gene or
genome biases. The positions of Amborella
and the other ANITA clades in independent
analyses of at least five individual genes representing all plant genomes6,18,20,23 and five
multigene matrices18–22 strongly suggests that
all these sources of data contain a significant,
concordant phylogenetic signal. By far the
simplest explanation for the congruence of
these studies and their strong statistical support is that they have each accurately inferred
elements of the underlying organismal phylogeny.
Eudicots
The collective findings of the above studies
Laurales
100/97
67/97/71
provide a phylogenetic framework that
100/94
Winterales
enables additional research on several classi83/cal problems in angiosperm evolution. For
Piperales
100/88
example, there is tremendous interest in
100/98
Ranunculales
reconstructing the patterns of diversification
86/84 Proteales
among angiosperms for a variety of attributes
100/99
100/100
including floral and vegetative morphology,
Sabiaceae
91/59
metabolism, modes of reproduction, con100/100 Trochodendrales
stituent gene families, and genomes18–22,33.
100/100 Buxaceae and
This can be accomplished by mapping those
Didymelaceae
characters onto individual trees, tracing their
98/87
-/100
Caryophyllales
evolution throughout the phylogeny and
-/99
Asterids
reconstructing character states for ancestral
-/100
-/60
taxa (e.g. using MacClade 3.07, Ref. 34).
Rosids
Comparisons of features of families in the
Trends in Plant Science
ANITA clades, in their phylogenetic context,
provide insight into the origin and early
52
Fig. 2. Simplified ‘supertree’ based on five recent multigene phylogenies for
diversification of flowering plants18,20,21,33.
angiosperms18–22. The supertree is the strict consensus of 36 shortest trees recovered from a
For example, the vegetative body of the combranch-and-bound analysis of clades in individual multigene studies (source trees) using
mon ancestor of all extant angiosperms probmatrix representation with parsimony52 and a weighting scheme based on the support values
ably had a woody habit, vessel-less wood,
of branches in the source trees (,50% 5 1; 51–70% 5 2; 71–90% 5 3; 91–100% 5 4).
unilacunar leaf nodes with two traces, leaves
Support values for clades in the supertree are based on parsimony bootstrap29 (blue) and
with chloranthoid teeth along their margins
jackknife25 (red) analyses from two source trees (‘2’ indicates ,50% support). Support values from other source trees are listed in Table 2. Relationships among gymnosperms shown
and no ethereal oils. Flowers of this common
here are consistent with recent results from analyses of seed plants36. Abbreviations: ITA
ancestor probably had an undifferentiated
clade, consists of Illiciaceae, Schisandraceae, Trimeniaceae and Austrobaileyaceae.
perianth arranged in more than two cycles or
series, perianth appendages that were unfused
above the base and anthers that shed pollen
towards the center of the flower. Carpels in these flowers were urn- Genetic basis of phenotypic evolution
shaped (ascidiate), were not attached to one another (apocarpous) In general, understanding genotypic or phenotypic diversification
and had margins that did not fuse completely but were closed at requires knowledge of an organismal phylogeny to specify the
maturity by secretions. An herbaceous habit, ethereal oils, wood locations, frequency and directionality of character state changes
with vessels, differentiated sepals and petals, and complete carpel within a lineage. The phylogenetic results discussed above provide
closure probably evolved after the origin of flowering plants. These the requisite framework to dissect the evolution of genes, gene
derived features might have contributed to the rapid diversification families and genomes, and to relate these events to morphological
of later-evolved angiosperm lineages (Table 1). The emerging pic- evolution. Molecular and phylogenetic dissection of petal and
ture of the earliest angiosperms differs appreciably from previously ovule evolution illustrate this point (additional examples are
proposed models for the first angiosperms (reviewed in Refs 35–37). reviewed in Ref. 38).
Recent results from studies of all the seed-plant groups suggest
It has been argued on the basis of comparative morphology that,
that the extant gymnosperms form a monophyletic group that is the among angiosperms, superficially similar petals have evolved sevsister lineage to the angiosperms20,36,37 (Fig. 2). This contradicts eral times from either stamens (andropetals) or sepals (bracteosome earlier models that placed one group of gymnosperms, the petals)38. How frequently each has occurred can be elucidated only
Gnetales, as the sister to all angiosperms. Consequently, future by the combined analysis of comparative morphology and geneclues to the morphological transitions that led to the origin of the expression and gene-family evolution in the context of angiosperm
angiosperms will come largely from fossil33,36 and comparative phylogeny38–40. Recent results indicate that, among the eudicots, sepmolecular-genetic data37,38.
arate lineages of AP3 homologs have been recruited in independent
August 2000, Vol. 5, No. 8
333
trends in plant science
Reviews
Genome evolution
Table 1. Several lineages (clades) of flowering plants recognized in recent
phylogenetic analyses43
Clade
Families
(species)
Examples
Amborella
1 (1)
Amborella trichopoda
Nymphaeales
2 (81)
Water lilies (Nymphaea spp.)
‘ITA’a
4 (95)
Star anise (Illicium verum)
Chloranthales
1 (75)
Chloranthus, Ascarina
Ceratophyllum
1 (6)
Ceratophyllum
Monocots
102 (65 000)
Grasses, orchids, palms
Magnoliales
6 (2700)
Magnolia, tulip tree (Liriodendron tulipifera)
Laurales
7 (3400)
Sassafras, avocado (Persea americana)
Winterales
2 (73)
Winter’s bark (Drimys)
Piperales
4 (3500)
Black pepper (Piper)
Ranunculales
7 (4400)
Buttercup (Ranunculus spp.), poppy (Papaver spp.)
Proteales
3 (1600)
Sacred lotus (Nelumbo), plane (Platanus spp.)
Caryophyllales
26 (9400)
Cactus (Cactaceae), beet (Beta vulgaris),
spinach (Spinacia oleracea)
Asterids
107 (87 000)
Sunflower (Helianthus spp.), carrot, tomato, holly
(Ilex spp.), snapdragon (Antirrhinum majus)
A comparison of the molecular phylogeny of
group-I introns and overall angiosperm phylogeny suggests that group-I introns have
been independently acquired ~1000 times by
various angiosperms44. Whether these introns
have been acquired independently from fungal donors or through horizontal transfer
from plants is unclear but it has important
implications for the potential for genetic
transfer from genetically engineered crop
species to local flora. Resolving this question will depend on expanded analyses of
group-I introns in the context of angiosperm
phylogeny.
Phylogenetic analysis of genome size
among the grasses reveals a predominantly unidirectional trend towards genomic ‘obesity’45.
Whether genomes evolve towards greater
size in general among angiosperms can now
be explored in other well-defined angiosperm
lineages. Genome doubling through polyploidy is a common phenomenon in the history of angiosperms and is especially
prevalent in crop species42. The number of
polyploid origins and their parentage, consequences for gene evolution and biochemical
impact can now be dissected in the context of
overall angiosperm phylogeny.
Classification
Several authors have discussed the inadequacies of previously available classification systems for flowering plants9,35,46. Foremost
Rosids
149 (77 000)
Maple (Acer spp.), apple, pea, rose, Arabidopsis
among their concerns is that these classifia
cations are at odds with robust results of pub‘ITA’ clade comprises Illiciaceae, Schisandraceae, Trimeniaceae and Austrobaileyaceae.
lished phylogenetic analyses. In an effort to
address this need, the Angiosperm Phylogeny
evolutionary events to determine petal identity in the Ranunculales Group (APG), a consortium of over 40 plant systematists, has proand in the Rosids and Asterids39,40. Among the grasses, AP3- posed a working classification of angiosperms into orders and some
homolog expression is conserved in petals but other genetic factors higher-level groupings46. Their provisional classification system was
have been altered, converting the familiar petals into lodicules38,41. based on results of single4–6 and preliminary multigene19 studies. The
Although the directionality of change in these cases is fairly uncon- additional phylogenetic results summarized above are entirely controversial, the exact origins and frequency of these transformations cordant with their classification system, suggesting that it should be
remain unclear. Determining these will require testing additional retained and extended. The proposed APG classification is useful for
organisms, selected according to the available phylogeny. In addi- facilitating communication within and among disciplines of biology
tion, an understanding of the general applicability of other aspects of and presentation of fruitful research to the broader community.
floral development in model organisms will be achieved through
future phylogenetically informed research42.
Future directions
The Arabidopsis INNER NO OUTER (INO) gene has been shown Although much of the overall angiosperm phylogeny is now confito be essential for the asymmetric growth of ovule outer integu- dently resolved, polytomies (Box 1) among magnoliid clades,
ments43. Gene-expression patterns in wild-type and mutant Ara- Ceratophyllum and the monocots, as well as within the eudicots,
bidopsis were compatible with INO acting either to establish require additional study (Fig. 2). The enormous effort that has
abaxial–adaxial polarity in ovules or to promote outer integument already been put into these studies might lead to pessimism about
outgrowth directly. The phylogenetic results discussed above permit the prospects for additional progress. Fortunately, there are several
the selection of angiosperm lineages that are radially symmetrical resources that can be brought to bear on the problem, which will
and bitegmic or asymmetrical (polar) and unitegmic in order to test clarify relationships further. For example, several available sources
the two models by examining the ancestral function of INO of data have not been fully exploited. Morphological data are being
orthologs through comparative gene-expression studies. Tests of reanalyzed in light of the results discussed above to reveal previous
these two models through comparative study of expression of INO misleading homology assessments, enhancing their utility in suborthologs isolated from diverse species, selected according to the lat- sequent analyses and facilitating the incorporation of crucial fossil
est phylogenies, are in progress [R. Kuzoff et al., unpublished data33,35,36.
(http://www.ou.edu/cas/botany-micro/botany2000/section2/
Similar analyses of molecular data9,15,22,23 will reveal hidden tenabstracts/28.shtml)].
dencies in nucleotide substitution and permit the generation of
334
August 2000, Vol. 5, No. 8
trends in plant science
Reviews
Table 2. Recent molecular phylogenetic analyses of angiospermsa
Study (sequences rbcL
analyzed)
(Ref. 4)
18S rDNA
(Ref. 6)
atpB
(Ref. 23)b
phyA, C
(Ref. 18)c
17-cp genes
(Ref. 22)
3 genes
(rbcL, atpB,
18S rDNA)19d
5 genes (rbcL,
atpB, 18S rDNA,
matR, atp1)20
5 genes (atpB,
18S rDNA, cox1,
rps2, mtSSU)21
Genomes (genes) Cp (1)
Nuc (1)
Cp (1)
Nuc (2)
Cp (17)
Nuc (1),
Cp (2)
Nuc (1), Cp (2),
Mt (2)
Nuc (1), Cp (1),
Mt (3)
Nucleotides
1428
1855
1460
2208
~13 400
4733
8733
6564
Species
499
228
357
26
21
560
105
51
Amborella is
first branch
2
1
1
1, 92%,
83%
1, 69%
1, 65%
1, 90%
1, 89%
ANITA clades
adjacent to root
2
1
(1 some
Piperales)
1
1, 86%
1, 94%
1, 71%
1, 97%
1, 92%
Nymphaeales
1
1
1, 100%
1, 100%
1, 100%
1, 100%
1, 100%
1, 100%
Chloranthales
1
1
1, 59%
1 sampled
Not sampled
1, 99%
1, 100%
1 sampled
Monocots
1
Almost
(2 1 species)
Almost
(1 1 species)
1, 100%
1, 93%
1, 95%
1, 99%
1, 92%
Magnoliales
1
1
1
1, 100%
1 sampled
1, 93%
1, 100%
1, .90%
Laurales
1
1
1, 68%
1, 100%
1 sampled
1, 97%
1, 100%
1, .90%
Winterales
1
1
1, 94%
1, 99%
1 sampled
1, 94%
1, 100%
1 sampled
Piperales
1
2
1
1, 100%
1, 99%
1, 88%
1, 100%
1
Eudicots
1
Almost
(1 3 orders)
1
1, 100%
1, 100%
1, 99%
1, 100%
1, 100%
Rosids
1
Almost
(1 1 order)
1 sampled
1, 60%
Not sampled
1
Asterids
1
Almost
(1 1 order)
1 sampled
1, 99%
Not sampled
1, .90%
Almost
Not sampled
(2 1 order)
1, 66%
Not sampled
a
Clades that are recovered (1) or not recovered (2) and bootstrap support values29 (unless otherwise indicated) are indicated in each analysis. Names for lineages
generally follow Ref. 46, except for Winterales and Chloranthales, which were recognized in more recent analyses19,20. ‘1 sampled’ indicates clades that were not
tested for monophyly, because only one species was sampled.
b
Although both atpB and rbcL sequences were analyzed23, results summarized here are based on atpB alone.
c
Bootstrap values were inferred for the clade comprising all species other than Amborella in the separate phyA and phyC trees18; all other bootstrap values in this
analysis came from the analysis of concatenated phyA and phyC sequences.
d
Jackknife values were used25 rather than bootstrap values29 to assess support for clades recovered in this study.
Abbreviations: Nuc, nuclear; Cp, chloroplast; Mt, mitochondrial.
more-realistic models of sequence evolution. These clarified models
will inform and increase the accuracy of subsequent model-based
phylogenetic analyses30–32. Also, the molecules used in several of the
analyses described above18,21,22 and elsewhere47 can be sampled from
additional species and combined with existing data for more detailed
analyses of relationships within principal angiosperm clades, such as
the monocots, eudicots, rosids and asterids. Other complex phylogenies, in the grasses for example, required as many as eight independent data sets before complete resolution with strong support was
achieved48.
Computational strategies such as compartmentalization5,49,50, in
which large, well-supported clades are replaced in an analysis by an
inferred ancestral state for that clade, also appear to be promising. In
fact, an expanded analysis of 26S rDNA (Ref. 47) and other
sequences20 using such compartmentalization of angiosperm clades
has produced complete resolution among the basal lineages and with
stronger support than was achieved previously (M. Zanis et al., pers.
commun.). We are optimistic that angiosperm phylogenetics will
progress rapidly on its present course, facilitating additional comparative studies and fuller exploitation of knowledge garnered from
model research organisms.
Acknowledgements
We apologize to those whose work could not be included in this review owing to space limitations. We thank Olaf Bininda-Emonds,
Jim Doyle, Sean Graham, Toby Kellogg, Jessie McAbee, Greg
Plunkett, Vincent Savolainen, Doug and Pam Soltis, and Michael
Zanis for helpful discussions, and the Katherine Esau Postdoctoral
Fellowship and the National Science Foundation (IBN-9983354) for
financial support.
August 2000, Vol. 5, No. 8
335
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Robert K. Kuzoff* and Charles S. Gasser are at the Section of
Molecular and Cellular Biology, University of California, Davis,
CA 95616, USA.
*Author for correspondence (tel 11 530 752 3111;
fax 11 530 752 3085; e-mail [email protected]).