American Journal of Botany 87(9): 1300–1308. 2000.
OLEMONIACEAE PHYLOGENY AND CLASSIFICATION
IMPLICATIONS OF SEQUENCE DATA FROM THE
Herbarium and Department of Botany & Plant Pathology, Michigan State University, East Lansing, Michigan 48824-1312 USA;
Herbarium and Division of Biology, Kansas State University, Manhattan, Kansas 66506-4901 USA; and
Section of Integrative
Biology, Plant Resources Center, and Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712 USA
The chloroplast gene ndhF was used to study phylogenetic relationships of the Polemoniaceae at two levels: among members of
the Ericales and among genera of the family. Sequence data for interfamilial analyses consisted of 2266 bp for 14 members of the
Ericales, including four species of the Polemoniaceae, plus three outgroup taxa. The Polemoniaceae were found to be related to
Diospyros, Fouquieria, the Primulales, Rhododendron, and Impatiens, but relationships among taxa were generally not well supported.
The precise position of the Polemoniaceae within the Ericales remains obscure. Data for intrafamilial analyses consisted of 1031 bp
for 27 species of the Polemoniaceae, including at least one species from most genera of the family, plus ﬁve outgroup taxa. A single
most parsimonious tree was identiﬁed. The analyses suggested that subfamily Cobaeoideae, excluding Loeselia, is monophyletic and
that Huthia is sister to Cantua. Acanthogilia was sister to the remainder of subfamily Cobaeoideae. Subfamily Polemonioideae plus
Loeselia formed four subclades that were strongly supported as monophyletic and represent the major lineages of the subfamily.
Key words: Acanthogilia; classiﬁcation; Ericales; Huthia; Loeselia; molecular phylogeny; ndhF; Polemoniaceae.
The Polemoniaceae is a relatively small but highly diverse
family with ;350 species. The species are distributed primar-
ily in North America, and many are endemic to the western
United States (Grant, 1998a). The family and its constituent
genera and species have served as model systems for many
systematic and evolutionary studies (e.g., Epling and Dob-
zhansky, 1942; Wright, 1943; Grant, 1959; Grant and Grant,
1965; Harborne and Smith, 1978; Carlquist, Eckhart, and
Michener, 1984; Paige and Whitham, 1985; Schlichting and
Levin, 1986; Campbell, 1989; Waser and Price, 1989; Barrett,
Harder, and Worley, 1996). The family is taxonomically com-
plex, and generic delimitation has been controversial and un-
stable (e.g., Greene, 1887; Grant, 1959, 1998a; Johnson and
The ﬁrst molecular phylogenetic study of the Polemoniaceae
was that of Steele and Vilgalys (1994) based on partial se-
quences of the chloroplast encoded gene matK. Their inves-
tigation was followed by a second study based on a more
variable region of the same gene (Johnson and Soltis, 1995;
Johnson et al., 1996) and by another based on sequences of
the internal transcribed spacer (ITS) regions of nuclear ribo-
somal DNA (Porter, 1996). In addition, Grant (1998a) pro-
posed a phylogeny based on both morphology and published
sequence data; however, it was assembled using evolutionary
systematics rather than cladistic methodology. Several phylo-
Manuscript received 10 August 1999; revision accepted 10 December
The authors thank Frank Axelrod, Mark Chase, Amy David, Wendy Hodg-
son, Leigh Johnson, Ki-Joong Kim, Kathy Kron, Robert Patterson, Cynthia
Morton, Mark Porter, and Stanley Spencer for providing plant material, DNA
samples, and DNA sequences, and Jan Barber, Les Goertzen, Mark Mayﬁeld,
Amanda Posto, Anna Wiese, Dieter Wilken, Rachel Williams, and an anon-
ymous reviewer for helpful comments on an earlier version of the manuscript.
Support was provided by the National Science Foundation (LAP, DEB-
9412174; CJF, DEB-9623386; RKJ, DEB-9318279) and by a Garden Club of
America/World Wildlife Fund Scholarship in Tropical Botany to LAP.
Author for correspondence (e-mail email@example.com).
genetic studies have provided insight into evolution at lower
taxonomic levels (e.g., in Ipomopsis [Wolf, Soltis, and Soltis,
1993]; Navarretia [Spencer and Porter, 1997]; Cobaea [Prather
and Jansen, 1998]; and Phlox [Ferguson, Kra¨mer, and Jansen,
1999]). Two recent studies (Porter and Johnson, 1998; John-
son, Soltis, and Soltis, 1999) have focused on the position of
the Polemoniaceae in the Ericales (sensu Angiosperm Phylog-
eny Group, 1998).
Concurrent with the interest in Polemoniaceae phylogenet-
ics has been a resurgence of interest in classiﬁcation of the
family. Grant’s early studies, especially Natural history of the
phlox family (Grant, 1959), revolutionized Polemoniaceae
classiﬁcation and have served as the foundation for Polemon-
iaceae systematics for the last 40 yr. Grant (1998a) recently
contributed a modiﬁed classiﬁcation of the entire family that
incorporated morphological and molecular data that had ac-
cumulated since 1959. At many levels the new classiﬁcation
and molecular phylogenies correspond with his 1959 classiﬁ-
cation, supporting in large part the basic tenets of the earlier
work. In addition to Grant’s contribution, several other work-
ers have recently contributed to tribal (Porter, 1998a), generic
(Grant, 1998b; Grant and Day, 1998; Porter, 1998a, b), or sub-
generic (Day, 1993; Prather, 1994, 1999; Spencer and Porter,
1997; Ferguson, Kra¨mer, and Jansen, 1999) classiﬁcation.
Incorporating phylogenetic information into classiﬁcation
has proven to be sometimes challenging and even controver-
sial, but this provides yet another arena in which the Pole-
moniaceae might serve as a model system. Some examples of
controversy are the generic disposition of the many disparate
elements now included in Gilia s.l. (e.g., Grant, 1998a, b;
Grant and Day, 1998; Porter, 1998a, b), tribal classiﬁcation of
subfamily Polemonioideae (Grant, 1998a; Grant and Day,
1998; Porter, 1998a), and the status of the genera Microsteris
(e.g., Patterson and Wilken, 1993; Grant, 1998a; Ferguson,
Kra¨mer, and Jansen, 1999) and Loeseliastrum (e.g., Porter,
1996; Grant, 1998a).
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RATHER ET AL
HYLOGENY OF THE
1. Voucher information for species from which ndhF sequences were generated. An asterisk (*) by a species indicates that only the 3
ERICALES (except Polemoniaceae)
Ardisia crenata Sims
Fouquieria columnaris (Kellogg) Kellogg ex Curran
Jacquinia umbellata A. DC.
Kron 3001 (NCU)
Prather 1927 (MSC)
Axelrod 4552 (UPRRP)
Acanthogilia gloriosa (Brandegee) A. G. Day & Moran*
Aliciella latifolia (S. Watson) J. M. Porter*
Allophyllum divaricatum (Nutt.) A. D. Grant & V. E.
Bonplandia geminiﬂora Cav.*
Cantua buxifolia Juss. ex Lam*
Porter & Heil 7987 (SJNM)
Porter & Machen 10253 (RSA)
Prather 1350 (TEX)
Cultivated, San Francisco State University
Cultivated, San Francisco State University
Cobaea scandens Cav.
Collomia linearis Nutt.*
Eriastrum sapphirinum (Eastw.) H. Mason*
Gilia leptalea (A. Gray) Greene*
Gilia scabra Brandegee*
Gilia sp. nov.*
Giliastrum rigidulum (Benth.) Rydb.
Gymnosteris parvula (Rydb.) A. Heller*
Huthia coerulea Brand*
Patterson, s. n. (RSA)
Prather 1605 (MSC)
Prather 1441 (TEX)
Johnson 93124 (WS)
Porter & Machen 11542 (RSA)
Porter & Heil 7991 (SJNM)
Porter 8723 (RSA)
Patterson s. n. (WS)
Hodgson 7924 (F)
Ipomopsis aggregata (Pursh) V. E. Grant*
Ipomopsis tenuifolia (A. Gray) V. E. Grant*
Langloisia matthewsii (A. Gray) Greene*
Langloisia setosissima (Torr. & A. Gray) Greene*
Leptodactylon californicum Hook. & Arn.*
Linanthus ciliatus (Benth.) Greene*
Loeselia glandulosa (Cav.) G. Don*
Prather 1618 (MSC)
Prather 1440 (TEX)
Prather 1411 (TEX)
Liston 741-3 (TEX)
Prather 1348 (TEX)
Prather 1397 (TEX)
Porter & Campbell 9231 (SJNM)
Microsteris gracilis (Hook.) Greene*
Navarretia intertexta (Benth.) Hook.*
Phlox pilosa L.
Polemonium foliosissimum A. Gray*
Polemonium pauciﬂorum S. Watson*
David 274 (TEX)
Spencer 568-84 (RSA)
Ferguson 455 (MO)
Porter 7576 (SJNM)
Hinton 19393 (TEX)
The preﬁx GBAN- has been added to link the online version of American Journal of Botany to GenBank, but is not part of the actual accession
Our understanding of Polemoniaceae phylogenetics has ad-
vanced considerably and the classiﬁcation has been improved,
yet many uncertainties remain. Here we discuss implications
of new data from the cpDNA gene ndhF on phylogeny and
classiﬁcation. We focus on several issues related to the follow-
ing taxonomic groups: (1) the order Ericales, (2) the subfamily
Cobaeoideae, including Huthia, (3) the genus Acanthogilia, (4)
the genus Loeselia, and (5) the subfamily Polemonioideae. We
review the current state of Polemoniaceae phylogenetics and
focus attention on the remaining questions. Furthermore, we
discuss the ongoing attempts to reconcile molecular phyloge-
nies of the family with morphological variation and to incor-
porate these data into the classiﬁcation of the family. Finally
we illustrate why it is important to take a conservative and
holistic approach to nomenclature in the Polemoniaceae.
MATERIALS AND METHODS
Sampling—Two sets of analyses were performed. The ﬁrst included rep-
resentatives of the Polemoniaceae and other ericalean families (interfamilial
relationships) and the second included species representing genera of the Po-
lemoniaceae (intrafamilial relationships). For the analysis of interfamilial re-
lationships, we used 11 sequences from other sources (Olmstead, Sweere, and
Wolfe, 1993; Olmstead et al., 2000): Anagallis arvensis L. (GenBank acces-
sion GBAN-AF130212), Camellia japonica L. (GBAN-AF130216), Cornus
ﬂorida L. (GBAN-AF130220), Diospyros texana Scheele (GBAN-
AF130213), Garrya elliptica Dougl. ex Lindl. (GBAN-AF147714), Halesia
tetraptera L. (GBAN-AF130222), Impatiens biﬂora Walt. (GBAN-
AF130210), Nicotiana tabacum L. (GBAN-L14953), Phlox drummondii
Hook. (GBAN-AF130211), Rhododendron mucronulatum Turcz. (GBAN-
AF130209), and Styrax americana Lam. (GBAN-AF130215). In addition, we
sequenced the ndhF coding region for six species (Table 1). We attempted to
sample Diapensiaceae but were unable to amplify ndhF from any DNA sam-
ples that we obtained. The data matrix included four species from the Pole-
moniaceae, ten from potentially related families, and three outgroup taxa
(Cornus, Garrya, and Nicotiana).
For the analysis of intrafamilial relationships, we sequenced over 1 kilobase
(kb) from the 39 region of ndhF from 26 species, including at least one species
from each genus of the Polemoniaceae (Table 1), except the recently estab-
lished genera Maculigilia and Tintinabulum (Grant, 1998b). There has been
some confusion concerning the identity of G. scabra in the literature. Gilia
scabra of Johnson et al. (1996) and Porter (1996), as well as G. cf. scabra
of Porter and Johnson (1998) is identical to the taxon we have called Gilia
sp. nov. The earlier studies included DNA from an undescribed species that
was confused with, and referred to as, G. scabra. The new species is currently
being described by J. M. Porter (personal communication) who kindly fur-
nished samples of plant tissue from both species, which are included here
We used the following combinations of outgroup taxa because the sister
group relationships of the Polemoniaceae remain obscure: (1) Diospyros, (2)
Fouquieria, (3) the Primulales (Anagallis, Ardisia, and Jacquinia), (4) all ﬁve
aforementioned taxa simultaneously, and (5) Fouquieria and Diospyros. Pre-
liminary analyses resulted in a single tree that was topologically identical
regardless of outgroup combination; therefore combination 5 was used in all
1302 [Vol. 87A
Fig. 1. One of three most parsimonious trees identiﬁed from analysis of
interfamilial relationships in the Ericales (sensu Angiosperm Phylogeny
Group, 1998) based on ndhF sequence data with gaps scored as missing data
(gap treatment 1; 1809 steps, CI
5 0.565, RI 5 0.571). Values along branch-
es indicate number of steps. Polemoniaceae species are shown in boldface.
DNA extraction and ampliﬁcation—Total DNA was extracted from fresh
or dried leaf material, the latter sometimes from herbarium specimens. The
DNA extraction methods of Doyle and Doyle (1987) were used for fresh
material and those of Loockerman and Jansen (1996) for dried material. A
double-stranded DNA fragment was ampliﬁed using the ndhF primers of Jan-
sen (1992). For those taxa for which the entire coding region was sequenced,
the gene was ampliﬁed in two segments. Ampliﬁcation components and pa-
rameters followed the protocol of Kim and Jansen (1995) except that hot-start
or touchdown polymerase chain reaction (PCR) methods were sometimes em-
Product puriﬁcation and sequencing—Products were sequenced manually
or on an automated sequencer. Samples that were manually sequenced were
puriﬁed with glass beads as described by Kim and Jansen (1994). Samples
sequenced with the automated sequencer were puriﬁed by spin columns either
directly (QIAquick PCR Puriﬁcation Kit, Qiagen, New Castle, Delaware,
USA) or following separation in an agarose gel (QIAquick Gel Extraction
Kit, Qiagen). Manual sequencing was performed using the snap-chill tech-
nique described by Kim and Jansen (1994), except that termination reactions
were carried out at 428C. Automated sequencing was performed on an ABI
377 DNA sequencer (Applied Biosystems, Inc., Foster City, California, USA).
Sequencing was accomplished with the same primers used by Kim and Jansen
Phylogenetic analyses—Sequences were manually aligned. For the analy-
ses of interfamilial relationships, the ﬁrst 26 bp of the coding region were
excluded because these data were missing for most taxa. For the analyses of
intrafamilial relationships, we used only the 39 end of the sequence beginning
with bp 1262 relative to tobacco. Insertion/deletion (indel) events were treated
in four ways: (1) as missing data, (2) as missing data and each gap scored as
an additional binary character equal in weight to a base substitution, (3), as
additional binary characters with gap regions deleted from the matrix, and (4)
as a new state (i.e., a ﬁfth base). The alignment is available on request from
the ﬁrst author.
Parsimony methods were implemented using PAUP* (version 4.0b2; Swof-
ford, 1999). Heuristic searches were performed using TREE BISECTION RE-
CONNECTION, COLLAPSE, and MULTREES options. The STEEPESTDE-
SCENT option was not in effect. One hundred replicate searches with random
taxon-entry were used to search for multiple islands of most parsimonious
trees (Maddison, 1991; Page, 1993). The amount of support for monophyletic
groups was assessed using 10000 bootstrap replicates (Felsenstein, 1985) with
100 addition-sequence replicates per bootstrap replicate for the interfamilial
analysis and ten addition-sequence replicates for the intrafamilial analysis.
Bootstrap analyses were performed using gap treatment 1 only.
Interfamilial relationships—Of the 2266 bp of aligned se-
quence data, 861 sites (38.0%) were variable and 501 (22.1%)
were potentially phylogenetically informative. Four of 13 in-
dels (30.8%) were potentially phylogenetically informative.
Missing sequence data constituted 1.05% of the data matrix,
and there were no missing data for indels in the interfamilial
analyses. For gap treatments 1, 2, and 4, a topologically iden-
tical set of three most parsimonious trees was identiﬁed (Fig.
1; treatment 1: 1809 steps, consistency index excluding un-
informative characters [CI
] 5 0.565, retention index [RI] 5
0.571; treatment 2: 1822 steps, CI
5 0.566, RI 5 0.572;
treatment 4: 1902 steps, CI
5 0.572, RI 5 0.573). There were
two unresolved nodes in the strict consensus of these three
trees (Fig. 2). Six most parsimonious trees (1780 steps, CI
0.564, RI 5 0.568) were identiﬁed by the search using gap
treatment 3. Three of those six trees corresponded to the set
of trees from the searches using other gap treatments. The
strict consensus of six trees is topologically consistent, but less
resolved than the strict consensus of the former sets of three
(Fig. 2). We favor the strict consensus tree for gap treatments
1, 2, and 4 and use it as the basis of discussion, because many
phylogenetically informative sites are deleted from the matrix
using gap treatment 3.
The monophyly of the four Polemoniaceae taxa was strong-
ly supported (Fig. 2; 100% bootstrap value), as was the mono-
phyly of the Primulales (100% bootstrap value). Diospyros
was sister to the Polemoniaceae, albeit with poor bootstrap
support (37%). Fouquieria was placed in a trichotomy with
the Polemoniaceae–Diospyros clade and a clade of the Pri-
mulales plus Impatiens and Rhododendron, but this clade had
poor bootstrap support (29%). Halesia was strongly supported
as sister to Styrax (100% bootstrap value). The relationship
among the Halesia–Styrax clade, Camellia, and the clade of
the remaining ingroup taxa was unresolved (Fig. 2).
Intrafamilial relationships—Of the 1031 bp of aligned se-
quence data used in the intrafamilial analyses, 404 sites
(39.2%) were variable and 235 (22.8%) were potentially phy-
logenetically informative. Seven of 13 indels (53.8%) were
potentially phylogenetically informative. Missing sequence
data constituted 1.05% of the data matrix and three indel cells
(0.72%) were scored as missing. The topology within the Po-
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RATHER ET AL
HYLOGENY OF THE
Fig. 2. Strict consensus of three most parsimonious trees from analyses
of interfamilial relationships in the Ericales based on ndhF sequence data
using gap treatments 1, 2, and 4. See text for details. Bootstrap values (10000
replicates; gap treatment 1) are shown along branches. Asterisks (*) indicate
additional nodes that collapse in the strict consensus of six most parsimonious
trees identiﬁed when scoring gaps as additional binary characters with gap
regions deleted from the matrix (gap treatment 3). Polemoniaceae species are
shown in boldface.
lemoniaceae was identical regardless of which outgroup or
outgroup combination was used (trees not shown) and discus-
sion below is limited to analyses with Diospyros and Fou-
quieria as outgroups. Regardless of gap treatment, a single,
topologically identical, most parsimonious tree (Fig. 3) was
identiﬁed (treatment 1: 797 steps, CI
5 0.601, RI 5 0.691;
treatment 2: 809 steps, CI
5 0.603, RI 5 0.694; treatment 3:
771 steps, CI
5 0.601, RI 5 0.693; treatment 4: 865 steps,
5 0.612, RI 5 0.704).
There was a basal split between two major Polemoniaceae
lineages (Fig. 3). The ﬁrst was composed of Acanthogilia,
Bonplandia, Cantua, Cobaea, and Huthia, but was weakly
supported (Fig. 3; 52% bootstrap support). This lineage cor-
responds to Grant’s (1998a) subfamily Cobaeoideae excluding
Loeselia, and we will refer to this as the Cobaeoideae clade.
The clade consisting of Bonplandia, Cantua, Cobaea, and Hu-
thia will be referred to as the ‘‘core’’ Cobaeoideae. Within this
clade, Huthia was strongly supported (100% bootstrap sup-
port) as sister to Cantua (Fig. 3).
The second lineage was composed of the remainder of the
genera and was strongly supported (98% bootstrap support).
It corresponds for the most part to Grant’s (1998a) subfamily
Polemonioideae, and we will refer to it as the Polemonioideae
clade. This lineage included four subclades (following the no-
menclature of Porter, 1996): (1) Polemonium, (2) the Gilieae
subclade (Allophyllum, Collomia, Gilia leptalea, and Navar-
retia), (3) the Linanthieae subclade (Gymnosteris, Leptodac-
tylon, Linanthus, Microsteris, and Phlox), and (4) the Loese-
lieae subclade (Aliciella, Giliastrum, Eriastrum, Gilia scabra,
Gilia sp. nov., Ipomopsis, Langloisia [incl. Loeseliastrum],
and Loeselia). The Loeselieae subclade was sister to the re-
maining three, and Polemonium was sister to a clade com-
posed of the Gilieae and Linanthieae subclades. Monophyly
of each of these four subclades was strongly supported ($92%
bootstrap values), but there was poor support (54–65% boot-
strap values) for nodes resolving the relationships among these
Interfamilial relationships—The ndhF phylogeny (Fig. 1)
places the Polemoniaceae within the Ericales (sensu Angio-
sperm Phylogeny Group, 1998) in agreement with other mo-
lecular analyses (reviewed in Porter and Johnson, 1998). In
contrast, the traditional placement of the Polemoniaceae has
been near the Hydrophyllaceae or Convolvulaceae, for exam-
ple in the Solanales of Dahlgren (1980) and Cronquist (1981).
The sister-group relationship of Diospyros and the Polemoni-
aceae (Fig. 2) is poorly supported and has not been uncovered
by other molecular analyses. However, a large number of po-
tential sister-group relationships have been proposed by vari-
ous cladistic analyses, and there is no consensus among studies
(see Fig. 1 in Porter and Johnson, 1998). Low bootstrap values
and a lack of resolution at the node uniting the Polemoni-
aceae–Diospyros lineage with two others, Fouquieria and a
clade consisting of the Primulales, Impatiens, and Rhododen-
dron (Fig. 2), prevent us from making any strong conclusions;
precise relationships of the Polemoniaceae to these families
This study is the fourth molecular study to focus on resolv-
ing the phylogenetic position of the Polemoniaceae (Porter and
Johnson, 1998; Johnson et al., 1996; Johnson, Soltis, and Sol-
tis, 1999). These four investigations complement broader com-
parisons (e.g., Olmstead et al., 1992; Chase et al., 1993; Mor-
ton et al., 1996). Overall, results of molecular studies are in-
consistent from analysis to analysis with regard to precise
placement of the family, and many nodes in critical areas are
poorly supported. Resolution of relationships among these
groups will require a concerted effort and involve sampling of
many taxa and genes.
Intrafamilial relationships—The ndhF phylogeny is largely
congruent with other molecular phylogenies and is in general
agreement with Grant’s (1998a) classiﬁcation. There are, how-
ever, some important differences among our results, other mo-
lecular phylogenies, and Grant’s classiﬁcation. These differ-
ences result from disparate phylogenetic hypotheses, conﬂict-
ing perspectives on how to incorporate phylogenetic infor-
mation into classiﬁcation, or a combination of these sources.
Here we place our data within the context of ongoing issues
in Polemoniaceae phylogenetics and classiﬁcation. We sum-
marize several key differences among studies, explicitly iden-
tify whether the issues are phylogenetic or classiﬁcation relat-
ed, and identify the problems remaining and propose how best
to approach them.
Subfamily Cobaeoideae—The Cobaeoideae clade is one of
two major groups of the Polemoniaceae in the ndhF analyses
(Fig. 3), and the core Cobaeoideae is monophyletic. Other
studies have sampled only three genera of the core Cobaeo-
ideae, Bonplandia, Cantua, and Cobaea, and these three taxa
are monophyletic in most molecular phylogenies (Fig. 4).
There are two exceptions: in the matK study of Steele and
Vilgalys (1994), members of the core Cobaeoideae plus Acan-
thogilia formed an unresolved polytomy at the base of the
Polemoniaceae (Fig. 4B), and in the ITS tree (Porter, 1996;
1304 [Vol. 87A
Fig. 3. Single most parsimonious tree identiﬁed from analysis of intrafamilial relationships of the Polemoniaceae based on ndhF sequence data with gaps
scored as missing data (gap treatment 1; 797 steps, CI
5 0.601, RI 5 0.691). Major clades are indicated on the right. Bootstrap values (10000 replicates; gap
treatment 1) are given above branches. The number of steps is indicated below each branch in italics. Subclade nomenclature follows Porter (1996).
Fig. 4. Simpliﬁed phylogenetic diagrams illustrating relationships of
Acanthogilia to the core Cobaeoideae and Polemonioideae clade as inferred
from six separate molecular phylogenetic analyses. (A) ndhF (from Fig. 3,
this study). (B) matK 1 (from Fig. 3 in Steele and Vilgalys, 1994). (C) matK
2 (from Fig. 3 in Johnson et al., 1996). (D) nad1B (from Fig. 2 in Porter and
Johnson, 1998). (E) ITS (from Fig. 1 in Porter, 1996). (F) 18S (from Fig. 3
in Johnson, Soltis, and Soltis, 1999). Sampling of core Cobaeoideae and Po-
lemonioideae clade varied in each study.
Fig. 4E) these same taxa formed a basal group that was par-
aphyletic to the remainder of the family. However, branches
in the critical portion of the ITS tree were weakly supported
and Porter stated that the branching pattern was ‘‘suspect’’
(Porter, 1996, p. 69).
Our ndhF phylogeny is the only molecular study to include
Huthia. Given our sampling, H. coerulea is sister to Cantua
buxifolia and the relationship is strongly supported. A close
relationship between Huthia and Cantua has long been hy-
pothesized based on the woody habit, simple leaves, actino-
morphic and tubular corollas, and their primarily Andean dis-
tributions. Our results are in agreement with morphology and
current classiﬁcation (Grant, 1998a).
Subfamily Cobaeoideae sensu Grant (1998a) consists of
Acanthogilia, Bonplandia, Cantua, Cobaea, Loeselia, and Hu-
thia. Because the bulk of the molecular evidence suggests that
Bonplandia, Cantua, and Cobaea form a monophyletic group
and because the sister-group relationship between Cantua and
Huthia in the ndhF phylogeny is consistent with morpholog-
ical evidence and classiﬁcation, monophyly of the core Co-
baeoideae is well established. Cobaea is sister to Bonplandia
in the ndhF tree (Fig. 3) and is nested within the Polemoni-
aceae in every molecular analysis. This is an important ﬁnding
because Cobaea has often been placed in other families or
segregated to its own (reviewed in Prather, 1999a). Our data,
September 2000] 1305P
RATHER ET AL
HYLOGENY OF THE
and in fact all molecular analyses, suggest that Loeselia should
be excluded from the subfamily (see below). The relationship
between the core Cobaeoideae and Acanthogilia is unclear and
is discussed in detail below.
Phylogenetic position and classiﬁcation of Acanthogilia—
The position of Acanthogilia as sister to the core Cobaeoideae
in the ndhF phylogeny, albeit with weak support (Fig. 3), is
novel among molecular studies (Fig. 4). In other molecular
studies Acanthogilia always appeared as a basal lineage, al-
though its exact placement varied among phylogenies (Fig. 4).
In the two matK analyses, Acanthogilia was in an unresolved
polytomy at the base of the Polemoniaceae (Fig. 4B, C; Steele
and Vilgalys, 1994; Johnson et al., 1996), a position consistent
with, but less resolved than, the ndhF phylogeny. The nad1B
data placed the core Cobaeoideae as sister to a clade consisting
of Acanthogilia and the Polemonioideae clade (Fig. 4D; Porter
and Johnson, 1998). Based on the ITS data, Acanthogilia was
the sister taxon to the entire family except Bonplandia (Fig.
4E; Porter, 1996). The 18S data placed the genus as sister to
all seven remaining Polemoniaceae taxa sampled, including
Bonplandia, Cantua, and Cobaea (Fig. 4F; Johnson, Soltis,
and Soltis, 1999).
The placement of Acanthogilia in the ndhF phylogeny is in
general agreement with morphological features and classiﬁ-
cation. When erecting the monotypic genus Acanthogilia, Day
and Moran (1986) concluded that it was most closely related
to Cantua, based on morphological and palynological features.
Grant (1998a) placed Acanthogilia in subfamily Cobaeoideae,
based on morphological evidence, but found the genus distinct
enough to place it in its own tribe, tribe Acanthogilieae.
The questions concerning Acanthogilia involve both phy-
logeny and classiﬁcation: What are its relationships? Is it best
placed in subfamily Cobaeoideae or Polemonioideae, or per-
haps in a third subfamily? Because of the agreement among
morphology, classiﬁcation, and the ndhF phylogeny, as well
as consistency with the phylogenetic position in other cpDNA
studies (Fig. 4), we conclude that Acanthogilia is best included
in subfamily Cobaeoideae. However, among molecular phy-
logenies, lack of resolution and/or weak support for the rela-
tionships to other genera suggest that additional comparisons
are needed to ﬁrmly establish its phylogenetic and taxonomic
Classiﬁcation of Loeselia—The ndhF tree places Loeselia
sister to a clade of two Gilia species, G. scabra and G. sp.
nov., and this clade falls within the Loeselieae subclade. The
ITS (Porter, 1996) and matK (Johnson et al., 1996) phyloge-
nies identiﬁed these same relationships, albeit with different
sampling. In fact, except for nad1B, all molecular studies that
have sampled both taxa have placed Loeselia and G. scabra
in a monophyletic Loeselieae subclade.
Grant hypothesized a close relationship between Loeselia
and some members of the Loeselieae subclade, particularly the
Gilia rigidula group (more or less equivalent to Giliastrum;
Porter, 1998a). In fact, he stated ‘‘it is hypothesized that the
Gilia rigidula group evolved from Loeselia in the Madro-Ter-
tiary ﬂora ...’’(Grant, 1998a, p. 747). It is noteworthy that
Loeselia and Giliastrum, plus a few other taxa, share a rela-
tively recent common ancestor (Fig. 3) and that this pattern
agrees with Grant’s evolutionary hypothesis.
Why then, did Grant place Loeselia in subfamily Cobaeo-
ideae and not in his tribe Gilieae of subfamily Polemonioideae
(Grant, 1998a)? This decision stems from the fact that Grant
did not use a cladistic deﬁnition of monophyly (Grant, 1998a,
p. 748) and chose, rather, to emphasize similarities of Loeselia
to members of subfamily Cobaeoideae. We choose to use a
cladistic deﬁnition of monophyly and therefore include Loe-
selia in subfamily Polemonioideae. The evolutionary relation-
ships are not in conﬂict among previous and current studies;
we merely differ in how we choose to represent those rela-
tionships in classiﬁcation.
We agree that there are many similarities between Loeselia
and some genera of subfamily Cobaeoideae, especially Bon-
plandia. For instance, seeds of the species of subfamily Co-
baeoideae are broadly winged, except for those of Bonplandia,
which are narrowly winged and very similar to wings of Loe-
selia seeds. Wings are absent from seeds of species of subfam-
ily Polemonioideae except for some species of Polemonium
that have ridge-like vestigial ‘‘wings’’ (Grant, 1959). The
small size of chromosomes of Loeselia is also similar to that
of members of subfamily Cobaeoideae, but this information
has been quantiﬁed for few species of Loeselia, and some spe-
cies of subfamily Polemonioideae (e.g., Leptodactylon califor-
nicum) have chromosomes approaching those of Loeselia in
size (ﬁg. 62 in Grant, 1959).
But we also note many similarities to some members of
subfamily Polemonioideae. For example, the chromosome
number of Loeselia species is n 5 9, a number common in
subfamily Polemonioideae, but unknown in subfamily Co-
baeoideae, except in Acanthogilia. The pollen of Loeselia is
not similar to that of any species in subfamily Cobaeoideae,
but is very similar to some species in subfamily Polemonioi-
deae (Stuchlik, 1967a, b; Taylor and Levin, 1975). The veins
of the corolla lobes of Loeselia species are either free, or con-
nected well above the base, both conditions that occur only
among species of subfamily Polemonioideae. All species of
subfamily Cobaeoideae have veins that are connected at the
base, as well as sometimes in the upper lobes (Day and Moran,
1986). Because morphological and cytological evidence is
equivocal, yet molecular data strongly place Loeselia in the
Polemonioideae clade, we choose to place Loeselia in subfam-
Phylogeny and classiﬁcation of subfamily Polemonioi-
deae—Grant’s subfamily Polemonioideae plus Loeselia, our
Polemonioideae clade, is strongly supported as monophyletic.
These genera, which include most species and genera of the
family, also formed a monophyletic group in every other phy-
logeny except for that based on the 18S data, in which Phlox
was sister to the rest of the family except Acanthogilia (Fig.
4F). That placement of Phlox is incongruent with all other
molecular data as well as morphological evidence. The focus
of the 18S study was not on intrafamilial relationships and
sampling within the family was quite limited (eight species),
therefore we urge caution in interpreting the 18S data with
regard to relationships within the Polemoniaceae. The prepon-
derance of evidence strongly supports a monophyletic group
of the genera included in Grant’s subfamily Polemonioideae
plus Loeselia (Fig. 4).
The four major subclades of the Polemonioideae clade in
the ndhF tree are strongly supported (Fig. 3) and provide a
context for grouping genera and species of the subfamily. The
four subclades, Polemonium, Gilieae, Linanthieae, and Loe-
selieae, correspond to groups detected by most other molecular
phylogenetic studies. Except for sampling differences, the sub-
1306 [Vol. 87A
clades are identical to the clades of Porter (1996). The three
latter groups also correspond to the Allophyllum–Gilia splen-
dens clade, Phlox–Gilia ﬁliformis clade, and Ipomopsis–Gilia
subnuda clade, respectively, of Johnson et al. (1996).
The agreement in subclade membership among nearly all
molecular analyses and strong support for monophyly in our
phylogeny allow us to be reasonably certain that these four
groups of the Polemonioideae clade are monophyletic. The
only phylogenetic analysis that suggested any of these groups
is nonmonophyletic was the nad1B study, in which the Lin-
anthieae subclade was polyphyletic (Fig. 3 in Porter and John-
son, 1998). The authors considered placement of the Linan-
thieae members an anomalous result, possibly because of miss-
ing data for those taxa (Porter and Johnson, 1998). Like the
18S study, focus of the nad1B study was on interfamilial re-
lationships, therefore sampling within the Polemoniaceae was
The ndhF phylogeny places the Linanthieae and Gilieae
subclades as sister groups, with Polemonium and the Loese-
lieae subclade as successively more basal lineages. Different
placements have been suggested by other phylogenetic anal-
yses and relationships between subclades typically have been
poorly supported. It appears that the major lineages of the
Polemonioideae clade are well deﬁned, but relationships
among the subclades remain unresolved.
As an example we consider the phylogenetic position of
Polemonium. The ITS data placed Polemonium in a mono-
phyletic group with the Linanthieae and Gilieae subclades, al-
beit with different sister-group relationships than in the ndhF
phylogeny (Porter, 1996). In the 18S phylogeny, Polemonium
was sister to a lineage consisting of the Loeselieae and Gilieae
subclades. The results from the matK studies were inconsis-
tent. The Steele and Vilgalys (1994) study supported Pole-
monium as sister to a lineage consisting of the Linanthieae and
Gilieae subclades, in agreement with the ndhF data. The John-
son and Soltis (1995) phylogeny placed Polemonium sister to
the Linanthieae subclade only, while the phylogeny of Johnson
et al. (1996) placed Polemonium as sister to the remainder of
the Polemonioideae clade, as did the nad1B data (Porter and
Johnson, 1998). Grant suggested that Polemonium, especially
section Polemonium, may have been one of the earliest derived
members of the temperate lineage (Grant, 1998a, p. 748) and
molecular data are in general agreement with his hypothesis.
The tribal classiﬁcation of subfamily Polemonioideae is cer-
tain to be one of the major issues of Polemoniaceae classiﬁ-
cation in the near future. In Grant’s (1998a) revision, tribal
circumscriptions within the subfamily were largely the same
as in his 1959 treatment except that Navarretia was moved
from the Gilieae to the Polemonieae, and Leptodactylon and
Linanthus were excluded from the Gilieae and included in the
newly erected tribe Leptodactyloneae. Concurrently, Porter
(1998a) recognized two tribes not treated by Grant, tribe Phlo-
gieae (our Linanthieae subclade) and tribe Loeselieae (our
Loeselieae subclade). Porter’s tribe Phlogieae is an expanded
Leptodactyloneae, and his tribe Loeselieae is essentially
Grant’s (1998a) tribe Gilieae plus Loeselia, but excluding
many species included in Gilia, most notably the type of Gilia,
The bulk of molecular evidence from several genes (see
above) supports Porter’s new tribes. However, if those tribes
are recognized, all that would remain of tribe Gilieae would
be Gilia s.s., whereas the Polemonieae would include Allo-
phyllum, Collomia, Navarretia, and Polemonium. Based on
molecular data tribe Polemonieae would not be monophyletic.
If the Gilieae were expanded to include Allophyllum, Collom-
ia, and Navarretia (the Gilieae subclade) and if the Polemon-
ieae were restricted to Polemonium alone, all the tribes would
be monophyletic based on the molecular phylogenies. The
question is whether molecular analyses should be the basis for
Molecules and morphology—The degree to which it is ap-
propriate to use morphological characters vs. molecular data
in classiﬁcation of the Polemoniaceae has recently become an
issue. Grant (1998a, p. 750; 1998b, pp. 82–84) and Grant and
Day (1998, pp. 379–380) have emphasized morphological data
and criticized what they perceived as an overemphasis on mo-
lecular data, especially by Johnson et al. (1996) and Porter
(1996). Grant went so far as to say (1998b, p. 84) ‘‘In any
incongruence between the evidence from one or two genes and
that from multifactorial phenotypic characters, the latter must
be given great weight.’’ On the other hand, Porter (1998a, b)
emphasized molecular data when making nomenclatural
changes, although not to the exclusion of discussions of mor-
Every recent student of the Polemoniaceae has agreed, at
least implicitly, that data from both morphology and molecules
can be valuable indicators of relationship and are therefore
likely to be useful in classiﬁcation. The recent discussions of
the utility of different types of data, however, have been some-
times misleading for two reasons. First, the molecular data
have been analyzed using cladistic methodology, while the
morphological characters were analyzed using evolutionary
systematics (Grant, 1998a). Differing methodology could lead
to different outcomes regardless of whether there is conﬂict
among data sets. Second, the conﬂict discussed thus far in the
literature is primarily between molecular data and morpholog-
ical characters that have been traditionally considered impor-
tant, i.e. those used in classiﬁcation. It has not been shown
that there is conﬂict between morphological characters, in gen-
eral, and molecular data.
Detailed study of morphological features combined with
phylogenetic analyses is the only appropriate method to ad-
dress potential conﬂicts between morphological and molecular
data. This is a very difﬁcult task at the intergeneric level be-
cause of the remarkable morphological diversity within and
among genera. But it is an important future goal for Pole-
moniaceae systematists and is absolutely critical to under-
standing evolution in the family. Phylogenetic analyses of
morphological data are not unheard of at lower levels in the
Polemoniaceae. Three such studies exist: the Ipomopsis spi-
cata complex (Wilken and Hartman, 1991), Navarretia (Spen-
cer and Porter, 1997), and Cobaea (Prather, 1999b). The latter
two are the only examples for which molecular phylogenies
have also been estimated (Spencer and Porter, 1997; Prather
and Jansen, 1998). Interestingly, comparisons of molecular and
morphological phylogenies revealed much congruence. How-
ever, these studies found some morphological characters tra-
ditionally used in sectional circumscription to be homoplasious
when examined in a phylogenetic context and advised against
continued use of those morphological characters.
A comparison of molecular and morphological data using
cladistic methodology would not allay the concerns of those
people, including Grant, who object to cladistic methodology
in the ﬁrst place. But it would at least allow the question to
be reﬁned (i.e., is it the methodology that leads to different
September 2000] 1307P
RATHER ET AL
HYLOGENY OF THE
conclusions regarding phylogeny and classiﬁcation, or is it
conﬂict between types of data?).
Some recent changes in classiﬁcation, such as Grant’s trans-
fer of Navarretia from tribe Gilieae to tribe Polemonieae, re-
sulted from consideration of both morphological and molec-
ular data. We support this practice. The ultimate goal should
be to ﬁnd consensus among all data and to explain any con-
ﬂict, not merely to ﬁnd morphological characters that support
molecular phylogenies. The studies on Navarretia (Spencer
and Porter, 1997) and Cobaea (Prather and Jansen, 1998;
Prather, 1999a, b) provide examples of this endeavor.
A cautionary note on nomenclature—Systematists gener-
ally recognize that there are two main goals of plant classiﬁ-
cation. Classiﬁcation should reﬂect our understanding of phy-
logeny and provide a system that can be easily used to refer
to plants (Cantino, Wagstaff, and Olmstead, 1998). Both of
these goals are extremely important and every effort should
be made to achieve them in tandem. Unfortunately, the dual
goals are sometimes in conﬂict. Given the conﬂict discussed
in this paper and the likelihood that still more nomenclatural
changes will be made in the near future, the Polemoniaceae
may exemplify the problem of developing a classiﬁcation that
meets these dual goals.
At present we advocate a conservative approach to nomen-
clatural changes in the Polemoniaceae. For this reason we fol-
low Grant (1998a) in recognizing the monotypic genus Mi-
crosteris, while some workers include the species in Phlox as
P. gracilis E. Greene. The recognition of Microsteris is equiv-
ocal based on ITS sequences and cpDNA restriction site data
of Phlox given current sampling of the major lineages (Fer-
guson, Kra¨mer, and Jansen, 1999; C. Ferguson and R. Jansen,
unpublished data). If further study suggests that Phlox is par-
aphyletic to Microsteris or detailed morphological studies
across the range of variation lead to a strong argument that
characters used to segregate Microsteris are weak or problem-
atic, it would be reasonable to reduce the genus to synonymy
We also follow Grant (1998a) in including Loeseliastrum in
Langloisia (5Langloisia s.l.). Little is to be gained by segre-
gating three species between two genera, because they are
morphologically very similar. There is more diversity between
pairs of species in other genera [e.g., Cobaea scandens Cav.
and C. penduliﬂora (H. Karst.) Hook. f. or Loeselia glandulosa
(Cav.) G. Don and L. mexicana (Lam.) Brand] than among
these three taxa. The phylogenetic relationships of these spe-
cies are troublesome because Loeseliastrum was paraphyletic
to Eriastrum and Langloisia s.s. in the ITS tree (Porter, 1996).
Notably, Langloisia s.l. is monophyletic in the cpDNA phy-
logenies (Fig. 3; Johnson et al., 1996). Subsuming Loeselias-
trum does not remedy the potential problem of paraphyly but
it does minimize a rather cumbersome nomenclature. This is-
sue is best resolved in context of the phylogeny of the entire
Loeselieae subclade; until such an undertaking is completed
we advocate following Grant (1998a).
Perhaps the example that best highlights our concerns re-
garding nomenclature is the ultimate disposition of species
currently placed in Gilia s.l. The situation is extremely com-
plex. In Grant’s (1998a) revision he kept Gilia s.l. intact, with
much the same composition as in the 1959 treatment (Grant,
1959). Contemporaneously, Porter (1998a, b) segregated Ali-
ciella and Giliastrum from Gilia s.l. Later, Grant (1998b) re-
classiﬁed Gilia and reduced Porter’s Aliciella and Giliastrum
to synonymy within Gilia and simultaneously segregated from
Gilia s.l. two additional genera, Maculigilia and Tintinabulum.
Additionally, Grant transferred one species of Gilia, G. tener-
rima A. Gray, to Allophyllum (Grant, 1998b). Later, that same
taxon was transferred to Tintinabulum, as T. tenerrimum (A.
Gray) A. Day & V. Grant and four more species of Gilia were
transferred to Allophyllum (Grant and Day, 1998). Based on
molecular phylogenies there are several remaining Gilia spe-
cies, aside from those already transferred or split into the four
genera mentioned above, that render the genus polyphyletic.
The recent trend has been to segregate most of the lineages
into separate genera, whence came Aliciella, Giliastrum, Ma-
culigilia, and Tintinabulum. If this continues, we estimate that
there will be at least four, and possibly more, additional genera
segregated from Gilia s.l.
This situation is not unique to Gilia. Based on a perusal of
available molecular evidence, many genera may not be mono-
phyletic (Ipomopsis, Langloisia s.l., Linanthus, Leptodactylon,
and Navarretia). We suggest that if these taxa are studied in
context of their respective lineages with comprehensive sam-
pling, preferably with both molecular and morphological data,
we may discover that some of the genera are monophyletic,
rendering nomenclatural changes unnecessary. Furthermore, if
the phylogeny of a lineage is well understood it may reveal
that, when nonmonophyly occurs, some of the species could
be accommodated in existing genera. Thus, an increasingly
cumbersome taxonomy would be avoided.
The ndhF data provide insight into several important issues
of Polemoniaceae phylogeny. Perhaps most interestingly, the
data support monophyly of subfamily Cobaeoideae (excluding
Loeselia) and suggest that Acanthogilia is basal to other mem-
bers of the subfamily. Furthermore, for the ﬁrst time, molec-
ular data are available for Huthia and indicate that the genus
is sister to Cantua. The subclades of the Polemonioideae clade
identiﬁed by ndhF are identical in composition, allowing for
sampling differences, to those identiﬁed by most other molec-
ular analyses. This provides convincing evidence for mono-
phyly of the four lineages. Because some relationships differ
from analysis to analysis, and some relationships are weakly
supported, we promote a cautious approach in incorporating
molecular data into classiﬁcation and nomenclature and sug-
gest that phylogenetic analyses of morphological data are sore-
ly needed at the generic level in the Polemoniaceae.
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