TAXON 59 (1) • February 2010: 57–67
Devos & al. • Phylogeny and biogeography of Euryops
A multi-locus phylogeny of Euryops (Asteraceae, Senecioneae)
augments support for the “Cape to Cairo” hypothesis of floral
migrations in Africa
NicolasD evos,1,4 Nigel P. Barker,1 Bertil Nordenstam2 & Ladislav Mucina3,5
1 Molecular Ecology and Systematics Group, Department of Botany, Rhodes University, P.O. Box 94, Grahamstown, 6140, South Africa
2 Department of Phanerogamic Botany, Swedish Museum of Natural History, Box 50007, 104 05 Stockholm, Sweden
3 Department of Botany & Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
4 Institute of Botany, University of Liege, B-22 Sart Tilman, 4000 Liege, Belgium
5 Department of Environmental and Aquatic Sciences, Curtin University of Technology, GPO Box U1987, Perth, WA 6945, Australia
Author for correspondence: Nicolas Devos, ndevos@ulg.ac.be
Abstract With about 100 species, Euryops (Cass.) Cass. ranks among the most speciose genera of the tribe Senecioneae
(Asteraceae). The genus has its greatest diversity in South Africa, and displays an interesting disjunct distribution with most of
the taxa found in southern Africa and a group of eight endemic species confined to the mountains of tropical East Africa and
northeastern Africa. Molecular phylogenetic analyses of DNA sequence data from three chloroplast fragments and the nuclear
ITS region were used to reconstruct the evolutionary history of 41 Euryops species in order to unravel species relationships
and to determine the origin of the disjunct Afromontane taxa. Our results show a lack of support and resolution in the internal
structure of the trees, but also reveal strong incongruence between the ITS and cpDNA datasets as assessed by Bayes Factors.
We hypothesise that this is a consequence of the isolation and divergence of many populations over a short time period at some
point in the history of the genus. Molecular dating based on our phylogenetic tree suggests that the genus diversified in South
Africa around four million years ago. The origin of the East African species, dated at 1.9 Ma, well after the uplift of the East
African mountains, is consistent with a scenario of a single dispersal event from South Africa northwards into the tropical East
African mountains where diversification occurred, creating a monophyletic group of regional Afromontane endemics.
Keywords Asteraceae; Bayes Factors; chloroplast DNA; disjunct distribution; Euryops; ITS; lineage sorting: migration routes;
molecular dating; radiation; topological incongruence
INTRODUCTION
The genus Euryops (Cass.) Cass., revised by Nordenstam
(1968a), comprises 97 described species plus another five
awaiting description or recently described (Nordenstam & al.,
2009; Nordenstam & al., in prep.). Along with Othonna L., it
is the largest genus (in terms of number of species and lowerrank taxa) in the subtribe Othonninae (Asteraceae, Senecioneae), which also includes smaller genera such as Gymnodiscus Less. (two species, only found in South Africa), Hertia
Less. (about ten species, found in Africa and Southwest Asia,
five of which occur in South Africa), and Lopholaena DC.
(18 species, found in southern Africa). With the exception of
one annual herb (E. annuus Compt.), all members of Euryops
are perennial shrubs characterised by coriaceous leaves and
yellow or orange-flowered capitula on simple peduncles usually devoid of leaves or bracts. A comprehensive view of the
evolutionary relationships within the genus is still lacking.
However, based on various vegetative and floral morphological characters, the genus was divided into six sections
(Euryops sects. Angustifoliae, Euryops, Chrysops, Brachypus,
Psilosteum, Leptorrhiza)—all believed to represent groups
having monophyletic origins (Nordenstam, 1968a).
Euryops is restricted to Africa, except for one species,
E. arabicus Steud., which is found in Arabia and Socotra
as well as in the Horn of Africa (Nordenstam, 1968a, 1969;
Fig. 1). The greatest diversity of the genus occurs in southern
Africa, mostly restricted to South Africa. While several species are confined to fynbos shrublands of the Cape Floristic
Region (CFR), the genus cannot be considered as a true “Cape
clade” sensu Linder (2003) as it does not comprise at least
50% of Cape endemics. Chorological analysis of the genus
indicates that the greatest concentration of species is found in
the region of the highest peaks and mountain blocks along the
Great Escarpment, spanning the Mpumalanga escarpment in
the northeast of South Africa, the Drakensberg, the Sneeuberg
in the Eastern Cape through to the Hantam mountains straddling the border of the Western and Northern Cape Provinces
(Fig. 1). Not all species are found at high altitudes, and many
of the low-altitude taxa are quite widespread, such as those
found in the Albany Centre of Endemism (Fig. 1; Nordenstam,
1968a, 1969). While the genus is an important component of
the Cape flora, it generally appears to be restricted to more
peripheral mountain regions of the CFR close to or linked to
the Great Escarpment.
Eight species of Euryops are confined to the high mountains of tropical East Africa, Ethiopia, Somalia and southwestern Arabia (Fig. 1; Nordenstam, 1968a, 1969). The East
African and Ethiopian species form part of the Afromontane
flora. They are found only at high altitudes in one or a few
57
Devos & al. • Phylogeny and biogeography of Euryops
of the high mountain ranges of Tanzania, Kenya and Ethiopia. Euryops elgonensis Mattf. is endemic on Mount Elgon
(Kenya), E. dacrydioides Oliv. in Hook. is found only on
Mount Kilimanjaro (Tanzania), E. brownei S. Moore occurs on
four mountains (Kenya, Aberdare, Meru, Cherangani), E. arabicus Steud. occurs on high mountains in Somalia, Socotra and
southern Arabia, E. pinifolius A. Rich. is found on the high
mountains of Ethiopia, E. prostratus B. Nord. is endemic to the
Bale mountains (Ethiopia), E. antinorii S. Moore is endemic to
the Soha mountains (Ethiopia), whereas E. jacksonii S. Moore
is restricted to the Aberdares and the Mau escarpment (Kenya).
The ecology of these high-altitude taxa resembles that of the
endemic taxa of high mountains of South Africa such as the
Drakensberg and Sneeuberg. Because of this similarity in
ecology and morphology, these two disjunct species groups
are believed to be closely related (Nordenstam, 1968a, 1969).
The floristic affinities between the CFR, the Greater
Drakensberg (incl. Northern Escarpment, Southern Drakensberg, Sneeuberg and possibly also Amathole Mountains) and
the East African Afromontane centre have been well documented (Weimarck, 1941; Killick, 1963, 1978; Wild, 1968;
White, 1978; Linder, 1990; Carbutt & Edwards, 2004; Galley
& Linder, 2006; Galley & al., 2007; Clark & al., 2009). Apart
TAXON 59 (1) • February 2010: 57–67
from Euryops, many other plant lineages are disjunctly distributed between those three endemic centres. However, the
historical origin of those disjunctions remains difficult to understand, and three competing hypotheses have been proposed
towards their explanation. Two of these hypotheses invoke
migration, while the third invokes vicariance. The first migration scenario suggests a northward expansion, with the Drakensberg and other Great Escarpment mountain blocks playing
an important role as ‘stepping-stones’ for lineages migrating
from the Cape northwards into the tropical Afromontane region (Weimarck, 1941; Holland, 1978; Linder, 1994; Galley &
Linder, 2006; Galley & al., 2007). The second migration scenario implies opposite processes—southward migration from
tropical Africa (Levyns, 1938, 1952, 1964; Axelrod & Raven,
1978) followed by radiation in the CFR. In contrast to these
two migration (dispersal) hypotheses, some authors suggested
a vicariance scenario where the current floras in each of the
centres of diversity and endemism represent relics of a once
more widespread floristic stock which underwent fragmentation due to climate change (Adamson, 1958; Wild, 1968). Recent reviews of the available literature (Galley & Linder, 2006;
Galley & al., 2007) suggested that for many of the so-called
“Cape clades” a northward migration took place—a claim
Fig. 1. Satellite image of Africa, with the distribution of Euryops indicated by the black outlines. The inset map of southern Africa indicates the
chorology of Euryops, modified from Nordenstam (1969: map 4) and PRECIS data. Isochores are in 3-species intervals, with highest numbers
for each centre or region provided. Letters in upper case indicate centres of endemism, named following Nordenstam (1969: map 111): A, Albany; B, Barberton; C, Caledon; D, Drakensberg; G, Gariep; S, Sneeuberg; WUK, Western Upper Karoo. Lower case letters indicate centres
as named by Koekemoer (1996): h, Hantam; m, Middelburg.
58
TAXON 59 (1) • February 2010: 57–67
now being considered the prevailing hypothesis explaining the
distribution of many taxa shared between the Cape, the Drakensberg and other Afromontane regions. Euryops is, however,
regarded as an old and widespread member of the African flora
which differentiated in the Paleogene (Nordenstam, 1969),
and therefore may not share the same biogeographic history
common with the typically evolutionary young Cape clades
which served as the basis of the biogeographic syntheses by
Galley & Linder (2006) and Galley & al. (2007).
The objectives of our work were: (1) to reconstruct a species-level phylogeny of Euryops using sequence data from
four regions: the nuclear ribosomal internal transcribed spacer
(ITS) region, the trnL-trnF and trnT-trnL spacers of the chloroplast genome, and the chloroplast rps16 region; (2) to assess
the phylogenetic relationships of the high-altitude Euryops
species in order to better understand the origin of the disjunct
distribution displayed by Euryops; and (3) to shed light on the
time of origin of Euryops using molecular dating techniques
taking into account phylogenetic uncertainty and variation in
rate of evolution between lineages in the tree.
MATERIALS AND METHODS
Plant material. — Forty-one of the ninety-seven Euryops
species recognised by Nordenstam (1968a) were sampled for
this study. Multiple accessions were sampled whenever possible so as to assess species monophyly. This sampling strategy
increased the number of terminal accessions for the ingroup
to 65. Several representatives of each one of the six sections
recognised within Euryops were included in our sample. Based
on the Senecioninae phylogeny of Pelser & al. (2007), Gymnodiscus capillaris Less., Othonna sedifolia DC., O. carnosa
Less., O. euphorbioides Hutch., O. eriocarpa (DC.) Sch. Bip.
and Hertia pallens (Benth. & Hook. f.) Kuntze were selected
as outgroups.
The vast majority of the samples used in this study were
collected from the field in South Africa and preserved in silica gel for subsequent DNA extraction (Chase & Hills, 1991).
Herbarium vouchers for these specimens are deposited at the
Selmar Schönland Herbarium (GRA) and at the Herbarium of
Stellenbosch University (STEU). These samples were supplemented by leaf material from further herbarium sheets housed
at GRA, Uppsala Herbarium (UPS) and the East African Herbarium (EA) (see Appendix for details).
DNA extraction, amplification, and sequencing. — Total
genomic DNA was isolated from about 1 cm² of dried leaf tissue using a CTAB extraction protocol (Doyle & Doyle, 1987),
but without the RNAase treatment. Three chloroplast DNA
regions (rps16, trnT-trnL, trnL-trnF) and the ITS region of the
nuclear ribosomal DNA were amplified and sequenced. The
primers rps16-F and rps16-2R (Oxelman & al., 1997) were used
to amplify and sequence the rps16 gene. The primers trnA and
trnB (Taberlet & al., 1991) and, trnC and trnF (Taberlet & al.,
1991) were used to amplifly and sequence the trnT-trnL and
trnL-trnF loci, respectively. The ITS region was amplified
and sequenced using the ITS4 (White & al., 1990) and ITS5
Devos & al. • Phylogeny and biogeography of Euryops
(Stanford & al., 2000) primers. The PCR products obtained
were purified using the PCR purification kit (Promega, Madison, Wisconsin, U.S.A.). Sequencing reactions were performed
in both directions using the BigDye® Terminator v.3.1 cycle
sequencing kit (Applied Biosystems, Foster City, California,
U.S.A.) and the same primers as used for PCR amplifications.
It is well known that the ITS region in plants often harbors extensive sequence variation, due to processes such as
duplication, pseudogene decay or incomplete concerted evolution (Alvarez & Wendel, 2003). As a result, ITS sequences
obtained from different species could in fact represent multiple paralogues that would produce a wrong estimate of the
phylogenetic relationships between the species sampled when
used in a phylogenetic analysis. We cannot be sure that all
our sequences are orthologues. However, every single PCR
reaction produced only one ITS amplicon and consequently,
no cloning was required before sequencing. Direct sequencing of those amplicons produced clean chromatographs and
no double peaks were found. This suggests that the universal
ITS primers used were amplifying a single ITS copy. We do
not have any reason to believe that those universal primers are
actually preferentially amplifying different paralogues in the
different accessions sequenced for this study.
Sequence alignment. — Forward and reverse sequences
were assembled and edited using Sequencher v.4.8 (Gene
Codes Corporation, 1998). Contigs were aligned manually
using MacClade 4.1 (Maddison & Maddison, 1992), with gaps
inserted where necessary to preserve positional homology.
Positions that were ambiguously aligned were excluded from
the analyses. All sequences determined for this study were deposited in GenBank (see Appendix for accession numbers) and
sequence alignments were deposited in TreeBase (http://www
.treebase.org) under matrix accession number M4908.
Phylogenetic a nalyses. — Phylogenetic relationships
were assessed from the data using Bayesian inference (BI)
as implemented by MrBayes v.3.1 (Ronquist & Huelsenbeck,
2003). The models for nucleotide substitutions that best fitted
each of the datasets being analyzed (either the ITS or cpDNA)
were selected using the Akaike Information Criterion (AIC;
Akaike, 1974). This was done using MrModeltest v.2.2 (Nylander, 2004) in conjunction with PAUP* (Swofford, 2002).
The prior distributions for the parameters in those models were
set as follows: a flat Dirichlet prior was used for both stationary
state frequencies and nucleotide substitution, a uniform prior
was used on the shape parameter of the gamma distribution
of rate variation (uniform [0.0, 200.00]), and an exponential
prior, Exp(10), was used for branch lengths, and all trees were
assumed to be equally likely.
The nuclear and chloroplast partitions were analyzed separately to identify possible incongruence between partitions.
Potential conflict in the signals displayed by the different partitions was searched for by comparing both topologies and posterior probabilities obtained from each one of the two datasets.
Taxa that seemed to have an incongruent position supported by
more than 0.95 posterior probabilities in the topologies being
compared were pruned prior to combining the ITS and cpDNA
datasets. For each dataset (ITS, cpDNA and combined), three
59
Devos & al. • Phylogeny and biogeography of Euryops
independent runs were carried out using MrBayes v.3.1 (Ronquist & Huelsenbeck, 2003). Each run consisted of one chain
that ran from a random starting tree for a total of three million
generations. Trees were sampled every 10,000th generation.
For the combined dataset, model parameters (with the exception of branch lengths and topology) were unlinked using the
“unlink” command in MrBayes such that each partition in the
combined analysis had its own set of parameters. Convergence
of parameters between the three runs was confirmed by checking that standard deviation of split frequencies was below 0.01
and that the potential scale reduction factor was close to 1 for
all parameters estimated. After discarding the burn-in, outputs
from the three runs were combined for final inference of posterior probabilities of both trees and model parameters.
Incongruence and hypotheses testing. — Congruence
between the ITS and cpDNA datasets was statistically tested
with the parsimony-based ILD test of Farris & al. (1994) as
implemented in PAUP* v.4.0b10 using the heuristic search option with random sequence addition (100 random replications)
and TBR branch-swapping. This ILD-test, also known as the
partition homogeneity test in PAUP* (Swofford, 2002), has been
commonly used to assess topological congruence and more
generally combinability between partitions prior to phylogenetic
analysis of large heterogeneous datasets. However, the ILD test
has been strongly criticised as a measure of dataset heterogeneity and, consequently, as a test for combinability (Cunningham,
1997; Yoder & al., 2001; Barker & Lutzoni, 2002).
As an alternative, the use of Bayes Factors within a Bayesian framework has been recently proposed to test for congruence between partitions (Irestedt & al., 2004; Nylander & al.,
2004). The Bayesian approach of phylogenetic inference provides, through the calculation of Bayes Factors (hereafter BF),
a convenient way for comparing how well two models describe
the processes generating a dataset X (Kass & Raftery, 1995).
Unlike a hierarchical likelihood ratio test, the models compared by mean of BF do not need to be hierarchically nested.
BF is calculated as the ratio of the marginal likelihoods f(X|Mi)
of the models being compared, B12 = f(X|M1) / f(X|M2). The
marginal likelihood of a model is difficult to calculate accurately but can be roughly estimated as the harmonic mean
of the likelihood values of the MCMC samples (Newton &
Raftery, 1994). A value > 10 for 2 log B12 has been suggested
as a very strong evidence that model 1 is far superior than the
alternative model at describing the processes generating the
dataset X (Kass & Raftery, 1995).
This Bayes Factor model selection approach is used here
to explore the potential incongruence between the ITS and the
cpDNA partitions either with or without the taxa identified by
eye as incongruent. The two models being compared when
testing for incongruence between partitions are: (1) a “onetree” model under which the two partitions were constrained
to evolve on the same topology; and (2) a “two-tree” model
under which the two partitions are allowed to explore the treespace separately (“unlink” command in MrBayes). In both
analyses, model parameters and branch-lengths were unlinked
across the partitions. For both models, three independent runs
with one chain each were run from a random starting tree for
60
TAXON 59 (1) • February 2010: 57–67
a total of three million generations. Model parameters and
tree topologies were sampled every 10,000 generations. After
convergence had been confirmed and the burn-in discarded,
harmonic means were calculated over all three runs using the
“sump” command in MrBayes. Twice the difference between
the harmonic mean of the log-likelihoods of the “one-tree”
model and the “two-tree” model was then computed.
Molecular dating. — Both the ITS and cpDNA datasets
were analyzed using a relaxed Bayesian approach as implemented in BEAST v.1.4.8 (Drummond & al., 2006; Drummond & Rambaut, 2007). In contrast to other dating methods,
BEAST uses a Bayesian Markov chain Monte Carlo method
to simultaneously estimate topology along with the node ages
(Drummond & al., 2002). All BEAST analyses were run in the
absence of topological constraints under a general time reversible model of nucleotide substitution with rate variation among
sites modeled using a gamma shape parameter with four rate
categories. Molecular evolution model parameters used flat
priors, whilst tree priors were modeled according to a Yule
speciation process. The divergence dates estimated were integrated over the various tree topologies sampled throughout the
MCMC analysis, and weighted in proportion to their posterior
probabilities. The MCMC chains were each run for 40 million
generations, and parameters were sampled every 1000th generation. Inspection of the results using Tracer v.1.4 (Rambaut &
Drummond, 2007) confirmed that stationarity and acceptable
mixing of the sampled parameters was achieved. Trees were
summarised as maximum clade credibility trees after removing, as a burn-in, the first 20% of samples.
In the absence of fossil evidence in Euryops, all analyses
were calibrated by setting a prior on the mean rate of nucleotide substitution under the uncorrelated log-normal relaxed
molecular clock (ucld.mean parameter in BEAST). For the ITS
dataset, estimates of absolute rate of molecular evolution found
in the literature were used as prior and uncertainties around
those estimates were factored using a uniform distribution
characterised by a maximum and minimum rate of 0.0078
and 0.003 substitutions per site per million years, respectively.
Richardson & al. (2001a) lists a variety of ITS divergence
rates which generally fall into a range of 1.72 × 10 –3 substitutions per site per million years (s/s/My) in the Saxifragaceae
(Vargas & al., 1998) to a more rapid 7.83 × 10 –3 s/s/My in the
Asteraceae (Sang & al., 1995). The average Asteraceae mutation rate can be calculated as 5.21 × 10 –3 s/s/My (based on an
average calculated from Richardson & al.’s list of Asteraceae
mutation rates) with a lower extreme of 3 × 10 –3 s/s/My (from
the Hawaiian silverswords; Baldwin & Sanderson, 1998), and
a higher extreme of 7.83 × 10 –3 s/s/My (from Robinsonia DC.;
Sang & al., 1995).
Based on estimates presented in Palmer (1991), the average
absolute rate of nucleotide substitution across a large number
of chloroplast genes is 5 × 10 –4 s/s/My. As this estimate has
been calculated across a large variety of land plants and various chloroplast genes, it has to be used with caution. It indeed
includes both synonymous and non-synonymous substitutions and is likely to underestimate substitution rates for noncoding regions. We however factored uncertainties around
TAXON 59 (1) • February 2010: 57–67
Devos & al. • Phylogeny and biogeography of Euryops
that estimate by using as a prior a normal distribution with
a standard deviation of 1 × 10 –4 centred at 5 × 10 –4 s/s/My.
This prior distribution was placed, as for the ITS analysis, on
the mean rate of nucleotide substitution parameter (ucld.mean
parameter in BEAST).
RESULTS
A total of 662 aligned base pairs was obtained from the
ITS1 + 5.8S + ITS2 regions, 762 bp from the rps16 region, 841
bp from the trnL-trnF region and 346 bp from part of the
trnT-trnL region. Of the 1949 characters included in the complete cpDNA dataset, 1694 were constant, 146 were parsimony
informative and 388 were identified by the Bayesian analysis
as unique site patterns under a GTR + Γ model of nucleotide
substitution. Of the 662 aligned base pairs from the ITS dataset, 407 were constant, 179 were identified as parsimony
informative and 270 were identified bye the Bayesian analysis
as unique site patterns under a GTR + Γ model of nucleotide
substitution.
According to the Akaike information criterion (AIC),
the parameter-rich GTR + Γ model of nucleotide substitution
was the best fit for both the ITS and cpDNA partitions. After
discarding a burn-in of 20 trees for each one of the three independent runs, the posterior distribution of topologies was
inferred and is presented for each analysis as a 50% majority
rule consensus tree (Figs. 2, 3).
The trees obtained from the analysis of the individual partitions (ITS and cpDNA, including rps16, trnL-F and trnT-L)
differ in topology and degree of resolution. The parsimonybased ILD test revealed significant incongruence between the
ITS and cpDNA datasets (P = 0.01). Bayes Factors also showed
extensive incongruence between both partitions. Comparison
of a model which allow the ITS and cpDNA datasets to evolve
on separate topology (i.e., independent evolutionary histories)
to a model in which both partitions share the same evolutionary
history (same topology) gave a 2logBF of 358.24. This value
strongly suggests that an unlinked model (“two-tree” model) is
superior to the model assuming a common evolutionary history
for both partitions and as a consequence indicates strong conflict
between the nuclear and chloroplast DNA evolutionary histories.
1
Fig. 2. Phylogenetic relationships of Euryops inferred
from sequences of three chloroplast DNA regions
(trnL-trnF, trnT-trnL, rps16). Fifty percent majority rule
consensus tree of 840 trees sampled by a MCMC chain
using the program MrBayes. Posterior probabilities are
indicated above branches. Marked clades are discussed
within the text. Mountain or alpine species endemic to
the Drakensberg and Sneeuberg Mountains of the Great
Escarpment are in bold. East African species of Euryops
are indicated by a grey box. All other species are from
non-mountainous region of South Africa. Divergence
dates for the major nodes in million years (Ma) are also
given and discussed in the text.
2.2 Ma
(0.8–4.7)
5.0 Ma
(2.3–9.5)
9.9 Ma
(4.7–17.7)
1
18.34 Ma
(9.1–33.5)
21.3 Ma
(10.6–37.8)
1
1
1
1
1
Clade A
E. montanus
E. decumbens
E. petraeus
E. annae
E. lateriflorus #1
E. lateriflorus #2
1 1
E. multifidus
E. subcarnosus
E. dregeanus #1
E. dregeanus #2
E. othonnoides #1
E. brevilobus
1
E. othonnoides #2
E. abrotanifolius #1
E. abrotanifolius #2
1
1 1 0.95 E. speciosissimus #1
E. speciosissimus #2
1
0.51
E. abrotanifolius #3
E. abrotanifolius #4
E. abrotanifolius #5
E. abrotanifolius #6
E. pectinatus
E. tenuissimus #1
E. tenuissimus #1
E. linifolius
E. brownei
Clade B
E. arabicus #1
1
E. arabicus #2
1
E. arabicus #3
E. prostratus
East Africa
0.99
E. dacrydioides
E. dacrydioides
E. pinifolius
E. trilobus
1
E. lateriflorus #3
E. lateriflorus #4
E. empetrifolius
0.55
E. evansii #1
0.56
E. evansii #2
E. evansii #3
E. acraeus
Clade C
E. munitus
E. euryopoides #1
E. brachypodus #1
0.67
E. brachypodus #2
E. hypnoides
0.99
E. spathaceus #1
1
E. spathaceus #2
0.99
E. anthemoides #1
E. anthemoides #2
E. hebecarpus
E. ericoides
E. ericifolius
E. ursinoides
E. euryopoides #2
E. candollei
0.97
Clade D
E. algoensis
E. virgineus #1
E. virgineus #2
E. galpinii
E. tysonii
E. annuus
Hertia pallens
Othonna sedifolia #1
O. sedifolia #2
O. carnosa
Othonna sp. nov.
1
O. eriocarpa
O. euphorbioides
Gymnodiscus capillaris #1
G. capillaris #2
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TAXON 59 (1) • February 2010: 57–67
Devos & al. • Phylogeny and biogeography of Euryops
Thirty-two terminals with conflicting positions between
the ITS and cpDNA trees were pruned before combining the
datasets. Those terminals were identified by eye and considered as having an incongruent position only if their respective
positions in both trees were supported by posterior probabilities of 0.95 or above. Despite the fact that many taxa with an
incongruent position were removed, both datasets remained
incongruent: a Bayes Factor of 25.6 indicating that a model
in which each partition is allowed to have its own topology is
significantly better than a model in which both partitions are
evolving along the same topology. It is worth noting however
that this value is 14 times smaller than the Bayes Factor obtained when no taxa were pruned.
Both the ITS and cpDNA tree resolved Euryops as a wellsupported (posterior probability of 1) monophyletic group with
the only annual species (E. annuus) sister to a well supported
(posterior probability of 1) clade representing the perennial
species of the genus (Figs. 2, 3). This clade was divided into
a series of well-supported lineages indicated in Figs. 2 and 3
by letters A–E. Clades are named identically between trees in
Figs. 2 and 3, as each one of those clades has some elements of
commonality in terms of species membership. The Bayesian
inference invariably failed to recover the relationships between
these well-supported lineages. Species relationships within
these lineages are mainly unresolved and strongly conflicting between the ITS and cpDNA tree topologies. Clade D
includes three species in the cpDNA tree (Fig. 2) while the
same lineage D includes five species in the ITS tree (Fig. 3).
Both these lineages are supported by 0.97 and 0.99 posterior
probabilities in the cpDNA and ITS trees, respectively. Clade
C includes ten species in the cpDNA tree (Fig. 2) and is supported by a posterior probability of 1. Species belonging to this
lineage in the cpDNA tree are distributed in three different
lineages in the ITS tree (clades A, C and E; Fig. 3), all of them
supported by high posterior probabilities values. Two species
(E. spathaceus DC. and E. hebecarpus (DC.) B. Nord.) are
found in clade A, three species (E. munitus (L. f.) B. Nord.,
E. euryopoides (DC.) B. Nord., E. ursinoides B. Nord.) are
found in clade C, while the remaining five species form clade
E in the ITS tree (Fig. 3). Another major conflict concerns five
species (E. trilobus Harv., E. lateriflorus (L. f.) DC., E. empetrifolius DC., E. evansii Schltr., E. acraeus M.D. Hend.) that the
Fig. 3. Phylogenetic relationships of Euryops inferred
from sequences of the internal transcribed spacers of the
nuclear ribosomal DNA. Fifty percent majority rule consensus tree of 840 trees sampled by a MCMC chain using
the program MrBayes. For further details, see Fig. 2.
6.9 Ma
(3.7–11.8)
9.7 Ma
(5.69–16.00)
1
1
0.61
0.99
1
1
Gymnodiscus capillaris #1
G. capillaris #2
62
Clade A
E. montanus
E. decumbens
E. multifidus
E. petraeus
E. annae
1
0.99
E. lateriflorus #1
1
E. lateriflorus #2
0.97
E. lateriflorus #4
E. empetrifolius
0.95
E. lateriflorus #3
0.54 0.90
1
E. spathaceus #1
E. spathaceus #2
1
E. trilobus
3.8 Ma
E. evansii #1
E. tenuissimus #1
(2.16–6.41)
1
E. tenuissimus #1
0.79
E. linifolius
E. hebecarpus
1
E. evansii #2
E. evansii #3
E. othonnoides #1
0.91
E. brevilobus
E. othonnoides #2
0.95
E. pectinatus
E. speciosissimus #1
E. speciosissimus #2
1
E. abrotanifolius #1
E. abrotanifolius #2
1
E. subcarnosus
1
E. dregeanus #1
0.99
E. dregeanus #2
E. abrotanifolius #5
1
E.
abrotanifolius #6
4.3 Ma
1
E. abrotanifolius #3
0.97
E. abrotanifolius #4
(2.46–7.36)
E. brownei
Clade B
E. arabicus #1
0.98
E. arabicus #2
East
E. arabicus #3
0.98
1
E. dacrydioides Africa
E. dacrydioides
E. pinifolius
0.74
E. prostratus
E. munitus
Clade C
0.97
E. euryopoides #1
E. euryopoides #2
E. ursinoides
0.96
Clade D
E. candollei
0.80
E. tysonii
1.9 Ma
E.
algoensis
0.99
(0.8–3.7)
E. virgineus #1
E. virgineus #2
E. acraeus
1
E. brachypodus #1 Clade E
E. brachypodus #2
1
E. anthemoides #1
1
E. anthemoides #2
E. ericoides
E. ericifolius
E. hypnoides
E. galpinii
E. annuus
Othonna eriocarpa
O. euphorbioides
Hertia pallens
O. sedifolia #1
O. sedifolia #2
O. carnosa
Othonna sp. nov.
1
1
0.97
TAXON 59 (1) • February 2010: 57–67
cpDNA tree places, with a posterior probability of 1, within
clade B together with a monophyletic group of East African
high-altitude species (Fig. 2). The ITS tree suggests instead,
that those species are nested within lineages A and D (with
a posterior probability of 0.99; Fig. 2). It is worth noting that
the taxa mentioned above do not represent an exhaustive list
of the species with an apparent incongruent position. They are
just those that display an incongruent position between our
labeled clades. Incongruence is in fact also observed within
those labeled clades.
All the species endemic to the mountains of east and northeast Africa were resolved as a well-supported monophyletic
group, irrespective of dataset (clade B in Figs. 2 and 3). While
those species do not seem to show any close relationship with
the endemic high-altitude species of southern Africa in the
ITS tree, they do show a close relationship with E. evansii
and E. acraeus in the cpDNA tree. These latter two species
are endemic to the highest peaks of the Drakensberg (South
Africa/Lesotho). The remaining South African high-altitude
species earlier suggested as close relatives to the Afromontane
species of East Africa (Nordenstam, 1968a) are spread in multiple lineages, and consequently do not seem to have a single
origin (species in bold, Figs. 2, 3).
The BEAST analyses recovered a posterior distribution
of trees similar to the posterior distribution of trees sampled
by the MrBayes analysis of both the ITS and cpDNA datasets, respectively. The 50% majority rule consensus trees and
the posterior probability values were congruent between both
analyses (data not shown). The divergence time for the major nodes are given in Fig. 3 for the ITS and in Fig. 2 for the
cpDNA dataset. Based on the ITS dataset, the age of the node
corresponding to the putative basal radiation (crown group,
excluding E. annuus) was estimated at 4.33 Ma (95% highest
posterior density: 2.46–7.36; hereafter 95% HPD), while the
age of the most recent common ancestor of the Afromontane
species of East Africa was estimated at 1.9 Ma (95% HPD:
0.81–3.7; Fig. 3). Age estimates based on the cpDNA dataset,
although slightly older than the age estimates obtained from
the analysis of the ITS dataset, had a 95% HPD overlapping the
95% HPD obtained with the ITS dataset. The age of the node
corresponding to the putative basal radiation was estimated at
9.9 Ma (95% HPD: 4.7–17.7), while the age of the most recent
common ancestor of the Afromontane species of East Africa
was estimated at 2.2 Ma (95% HPD: 0.81–4.7; Fig. 2).
DISCUSSION
Phylogenetic relationships and incongruence. — Despite
the use of four loci (2611 bp and 325 parsimony informative
sites), the phylogenies obtained for the individual (ITS and
cpDNA) datasets were largely unresolved. Rapid diversifications are typically characterised in a phylogeny by very short
or nonexistent branches that are extremely difficult to resolve
due to the paucity of shared derived characters (Richardson
& al., 2001a; McCracken & Sorenson, 2005). Unresolved and
poorly supported short branches have also been attributed to
Devos & al. • Phylogeny and biogeography of Euryops
the use of insufficient or inappropriate data for the level of
divergence that is being analysed, and often can be resolved
by including more characters (Maddison, 1989; DeSalle &
al., 1994). However, the loci sequenced here have been used
before in many studies dealing with species-level phylogenies.
Therefore, we do not believe that an inappropriate choice of, or
insufficient, markers would have caused this lack of resolution.
Rather, we suggest that the lack of support and resolution in
the internal structure of the trees could reflect the signature
of the isolation and divergence of many ancestral populations
in a short time frame.
Phylogenetic reconstruction of rapidly radiating species or
lineages is expected to produce strong incongruence among
different gene trees (e.g., Shaw, 2002; Hughes & Vogler, 2004;
McCracken & Sorensen, 2005). Much of this incongruence is
the result of lineage sorting, a random process of retention and
extinction of alleles in a lineage over time (e.g., Pamilo & Nei,
1988; Maddison, 1997; Nichols, 2001). The ILD test found a
significant incongruence (P = 0.01) between the nrDNA and
cpDNA gene partitions in Euryops suggesting the presence
of strongly supported character conflict between the two
partitions. However, presence of significant heterogeneity in
the data does not necessarily imply that the partitions under
investigation have different underlying topologies (Dolphin
& al., 2000). When rate differences between partitions are
too different, the ILD test could indeed suggest significant
heterogeneity despite the partitions having similar underlying
evolutionary histories (Dolphin & al., 2000). Nevertheless,
in a Bayesian framework, the use of Bayes Factors to test for
incongruence between gene partitions also suggested strong
incongruence between the evolutionary histories of the nuclear and chloroplast DNA. Allowing the gene partitions to
have separate topology clearly had a better fit to the data than
a model in which the data partitions are forced to evolve on
the same topology. The strong incongruence between the ITS
and cpDNA datasets argues in favour of a rapid diversification of Euryops. However, other biological processes such as
hybridisation, introgression or paralogy in the ITS dataset are
known to produce incongruence between the phylogenetic
trees estimated from different loci (Maddison, 1997; Nichols,
2001; Seehausen, 2004). The occurrence of such processes
in Euryops cannot be completely ruled out. Distinguishing
between hypotheses of reticulation (hybridisation, introgression and allopolyploidisation) and that of lineage sorting is
extremely difficult because both processes are known to produce similar phylogenetic patterns (Holder & al., 2001). Many
taxa had to be pruned in order to reduce the incongruence observed between the ITS and cpDNA datasets. It is unlikely that
every one of those taxa has originated through hybridisation,
allopolyploidisation or introgression. Spontaneous hybridisation and introgression have been rarely observed in Euryops
and polyploidy seems to have played only a minor role in the
diversification of the genus (Nordenstam, 1968a,b). Only four
polyploid taxa have been identified based on chromosomes
counts of 37 taxa (Nordenstam, 1968b). In two species, viz.,
E. oligoglossus DC. and E. lateriflorus, tetraploids were
found as well as diploids (2n = 20, 40). One of these species
63
Devos & al. • Phylogeny and biogeography of Euryops
(E. lateriflorus) was included in our dataset. Removing it from
the analysis did not reduce the degree of incongruence between
our two partitions. Incomplete lineage sorting due to putatively
recent and fast diversification in the genus is more likely to
be the underlying cause of the strong incongruence observed
between the nuclear and cpDNA datasets. The putative radiation in Euryops is estimated to have occurred sometime
between four millon years ago (based on estimates from the
ITS dataset) and nine millon years ago (based on estimates
from the cpDNA dataset). Whether that time is sufficient for
lineage sorting to be completed is difficult to say because it
is highly dependent on the effective population size at the
time of diversification. However, even if four to nine million
years is sufficient for lineage sorting to become completed,
incongruence between gene trees is still likely to be observed.
Ancestral polymorphism will eventually disappear as each
descendant lineage becomes fixed for a different set of alleles
or haplotypes, but the incongruences between gene trees and
species trees that ancestral polymorphisms have generated
would persist (McCracken & Sorensen, 2005).
Our age estimates (i.e 4.33 [2.46–7.36] million years for
the ITS and 9.9 [4.7–17.7] million years for the cpDNA) place
the diversification of Euryops at the end of the Miocene, early
Pliocene. This timing coincides with the strong upwelling of
the cold Benguela Current waters along the west coast of South
Africa and as a consequence the onset of aridity in the region
(Marlow & al., 2000; Linder, 2003; de Menocal, 2004). “Sudden” aridification and climatic change during the late Miocene
and early Pliocene is assumed to have initiated such explosive
speciation on a range of continents (e.g., Richardson & al.,
2001a; Hughes & Eastwood, 2006; Moore & Jansen, 2006,
Linder, 2008) and especially in the Cape Floristic Region (e.g.,
Linder & al., 1992; Richardson & al., 2001b; Linder, 2003;
Verboom & al., 2003; Klak & al., 2004).
The lack of resolution and the incongruence between gene
trees challenge the interpretation of the evolutionary history
of Euryops. Nevertheless, it is worth noting that both datasets
resolve the only annual species of Euryops as sister to the
remainder of the genus (i.e., a lineage of ca. 90 perennial species). The long branch leading to this annual species could be
explained by high rate of nucleotide substitution. It has been
shown in numerous comparative studies that annual plants
display a higher rate of molecular evolution compared with
perennials (Andreasen & Baldwin, 2001). This pattern has
been partialy explained by differences in generation times,
efficiency of DNA repair or replication, and difference in
population sizes between annual and perennial plants. The
lack of diversification in this annual lineage is however puzzling especially if annuals are indeed harboring faster rate of
molecular evolution. High exctinction rate on the other hand
could explain the long branch length and would help explain
the apparent absence of radiation in this lineage.
Biogeographic patterns. — Although the inferred relationships are incongruent across loci and not well resolved,
some interesting biogeographic patterns become evident. The
most clear of these is the monophyletic origin of all the Euryops species endemic to the high mountains of East Africa.
64
TAXON 59 (1) • February 2010: 57–67
Many taxa that are most diverse in southern Africa and more
specifically in the CFR have, like Euryops, outliers that form
part of the Afromontane flora in northeastern tropical Africa
(Weimarck, 1933, 1936). The interpretation of molecular phylogenies produced for the lineages displaying disjunct distribution between southern Africa and the uplands of tropical
East Africa supports the idea that the Afromontane taxa are
derived from the Cape clades from one or several migrations
northwards, from the CFR (Galley & Linder, 2006; Galley
& al., 2007). The cpDNA dataset indicates that in Euryops,
the Afromontane species form a very well supported monophyletic group, nested within an otherwise southern clade. In
fact, the outgroups used represent genera that are only found
in Southern Africa and have been identified by Pelser & al.
(2007) as the closest relatives of Euryops. The phylogenetic
tree produced by Pelser & al. (2007) includes most of the
genera of the tribe Senecioneae and leaves no doubt that the
whole Othoninnae subtribe is a group that originated and diversified in southern Africa. The position of the Afromontane
species is thus consistent with a scenario of a radiation from
a single immigration into the East African mountains and
corroborates Galley & al.’s (2007) interpretation of the same
disjunction observed in other taxa such as Restionaceae and
Pentaschistis (Nees) Spach (Poaceae). Moreover, the crown
group age of this monophyletic East African lineage (1.9 million years based on the ITS dataset and 2.2 million years
based on the cpDNA dataset) is consistent with a scenario of
a recent migration event as opposed to a scenario of vicariance of a once more widespread flora in Africa that receded
due to climatic changes, combined with the uplift of the East
African mountains, which occurred much earlier (middle-late
Miocene) during the development of the East African Rift
System (Chorowicz, 2005). The estimated age of 1.9–2.2 million years for the East African clade is generally somewhat
younger than the ages of East African clades and dispersal
or migration events estimated by Galley & al. (2007: table 1).
It would be tempting to suggest that these tropical Afromontane species originated from an ancestral species closely
related to one of the extant high-altitude species from South
Africa. Nordenstam (1968a) noted a close morphological affinity between E. prostratus B. Nord. from Ethiopia and the
two alpine endemics (E. decumbens B. Nord., E. montanus
Schltr.) from the Drakensberg in South Africa. In both the ITS
and cpDNA gene trees, E. decumbens and E. montanus are
closely related to each other with strong support. However,
they do not show any close relationship with E. prostratus
nor with any of the other East African Afromontane species.
Nordenstam (1968a) also noted the close affinity between
E. brownei and E. acraeus, endemics of East Africa and
Drakensberg, respectively. Interestingly, the cpDNA gene
tree resolved E. acraeus and E. evansii, another endemic from
the Drakensberg, within the Afromontane East African clade
(clade B, Fig. 2) that includes E. brownei. The Afromontane
species of tropical Africa could thus have originated from
a northward migration of an ancient high-altitude ancestral
species related to the extant alpine endemics E. acraeus and
E. evansii.
TAXON 59 (1) • February 2010: 57–67
The Great Escarpment of South Africa (including both the
Drakensberg and Sneeuberg) is an important centre of diversity
for Euryops and other high-altitude taxa. Nordenstam (1969)
noted that there were 16 endemic species in this region, and a
further two new species have been recently discovered from
the Sneeuberg (Nordenstam & al., 2009). However, unlike the
species of East Africa, the species found in the Drakensberg
and Sneeuberg mountains do not seem to be closely related.
This suggests that local diversification (i.e., diversification
from a single ancestor) has not occurred in these regions, but
that the diversity is a consequence of multiple migrations or
a consequence of these mountains acting as refugial habitats.
The absence of local diversification in the Drakensberg has
also been found in both the Restionaceae and Pentaschistis
(Poaceae; Galley & al., 2007). In contrast, the diversity of
the genus Disa Bergius (Orchidaceae) and the tribe Irideae
(Iridaceae) in the Drakensberg is a consequence of in situ
diversification following multiple migration events (Galley
& al., 2007). These authors implicate the role of pollinator
specificity as a factor driving in situ speciation: the windpollinated grass genus Pentaschistis and Restionaceae have
not radiated in situ, whereas the biotic (and probably specialist)
pollination syndromes of Disa and Irideae may have driven
speciation following successful colonisation. Euryops, with
its presumably typical asteraceous generalist pollination syndrome would, like the wind-pollinated examples cited above,
probably not speciate as readily following migration into a new
region. A more-intensively sampled and completely resolved
species phylogeny will however be needed in order to reconstruct ancestral distribution ranges from which directionality
of migration events can be rigorously addressed.
CONCLUSIONS
The strong topological incongruence between our gene
trees, combined with the lack of support and resolution in
the internal structure of both the ITS and cpDNA trees led
us to suggest that the genus Euryops has radiated in southern
Africa within a short time period. Molecular dating of both
ITS and cpDNA trees suggest that the radiation has taken place
during late Miocene, early Pliocene. This period coincides
with drastic climatic changes in South Africa and has been
shown to have initiated explosive species radiation in various
plant groups such as Ruschioideae (Klak & al., 2004), Gazania
(Howis & al., 2009), Phylica (Richardson & al., 2001b) and
Zygophyllum (Bellstedt & al., 2008).
Despite the lack of resolution and the incongruence between our gene trees, it was possible to resolve some aspects
of the phylogenetic relationships within Euryops and interpret
those within a plausible biogeographic framework. In particular, the Afromontane species have radiated following a single
immigration event into the East African mountains, which
corroborates Galley & al.’s (2007) interpretation of the same
disjunction observed in other taxa such as Restionaceae and
Pentaschistis (Poaceae) and augments support for the “Cape
to Cairo” hypothesis of floral migrations in Africa.
Devos & al. • Phylogeny and biogeography of Euryops
ACKNOWLEDGMENTS
The authors gratefully acknowledge the National Research Foundation of South Africa for financial support (through grant 2069059 to
N.P.B., grant 2069036 to L.M. and a Postdoctoral Fellowship to N. Devos). Seranne Howis provided technical assistance, Robert McKenzie and
Peter Teske helped during the field work. We thank the South African
National Biodiversity Institute for providing access to distribution data
of Euryops from the PRECIS system. Mats Thulin of Uppsala University Herbarium kindly supplied leaf material of Euryops arabicus and
E. dacrydioides, and Siro Masinde of the National Herbarium in Nairobi,
Kenya, provided material of some East African taxa of the genus.
LITERATURE CITED
Adamson, R.S. 1958. The Cape as an ancient African flora. Advancem.
Sci. 58: 1–10.
Akaike, H. 1974. A new look at the statistical model identification.
IEEE Trans. Autom. Control 19: 716–723.
Alvarez, I. & Wendel, J.F. 2003. Ribosomal ITS sequences and plant
phylogenetic inference. Molec. Phylog. Evol. 29: 417–434.
Andreasen, K. & Baldwin, B.G. 2001. Unequal evolutionary rates between annual and perennial lineages of checker mallows (Sidalcea,
Malvaceae): Evidence from 18S-26S rDNA internal and external
transcribed spacers. Molec. Biol. Evol. 18: 936–944.
Axelrod, D.I. & Raven, P.H. 1978. Late Cretaceous and Tertiary
vegetation history of Africa. Pp. 79–130 in: Werger, M.J.A. (ed.),
Biogeography and ecology of southern Africa. The Hague: Dr.
W. Junk.
Baldwin, B.G. & Sanderson, M.J. 1998. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proc. Natl.
Acad. Sci. U.S.A. 95: 9402–9406.
Barker, F.K. & Lutzoni, F. 2002. The utility of the incongruence
length difference test. Syst. Biol. 51: 625–637.
Bellstedt, D.U., van Zyl, L., Marais, E.M., Bytebier, B., de Villiers, C.A., Makwarela, A.M. & Dreyer, L.L. 2008. Phylogenetic
relationships, character evolution and biogeography of southern
African members of Zygophyllum (Zygophyllaceae) based on three
plastid regions. Molec. Phylog. Evol. 47: 932–949.
Carbutt, C. & Edwards, T.J. 2004. Cape elements on high-altitude
corridors and edaphic islands: Historical aspects and preliminary
phytogeography. Syst. Geogr. Pl. 71: 1033–1061.
Chase, M.W. & Hills, H.H. 1991. Silica gel: An ideal material for field
preservation of leaf samples for DNA studies. Taxon 40: 215–220.
Chorowicz, J. 2005. The East African rift system. J. Afr. Earth Sci.
43: 379–410.
Clark, V.R., Barker, N.P. & Mucina, L. 2009. The Sneeuberg: A
new centre of floristic endemism on the Great Escarpment, South
Africa. S. African J. Bot. 75: 196–238.
Cunningham, C.W. 1997. Is congruence between data partitions a
reliable predictor of phylogenetic accuracy? Empirically testing
an iterative procedure for choosing among phylogenetic methods.
Syst. Biol. 46: 464–478.
De Menocal, P.B. 2004. African climate change and faunal evolution
during the Pliocene–Pleistocene. Earth Planet. Sci. Lett. 220: 3–24.
DeSalle, R., Absher, R. & Amato, G. 1994. Speciation and phylogenetic resolution. Trends Ecol. Evol. 9: 297–298.
Dolphin, K., Belshaw, R., Orme, C.D.L. & Quicke, D.L.J. 2000.
Noise and incongruence: Interpreting results of the incongruence
length difference test. Molec. Phylog. Evol. 17: 401–406.
Doyle, J.J. & Doyle, J.L. 1987. Preservation of plant samples for DNA
restriction endonuclease analysis. Taxon 36: 715–722.
Drummond, A.J., Ho, S.Y.W., Phillips, M.J. & Rambaut, A. 2006.
65
Devos & al. • Phylogeny and biogeography of Euryops
Relaxed phylogenetics and dating with confidence. PLoS Biol 4:
e88. doi:10.1371/journal.pbio.0040088.
Drummond, A.J., Nicholls, G.K., Rodrigo, A.G. & Solomon, W.
2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data.
Genetics 161: 1307–1320.
Drummond, A.J. & Rambaut, A. 2007. BEAST: Bayesian evolutionary
analysis by sampling trees. BMC Evol. Biol. 7: 214. doi:10.1186/14712148-7-214.
Farris, J.S., Källersjö, M., Kluge, A.G. & Bult, C. 1994. Testing
significance of incongruence. Cladistics 10: 315–319.
Galley, C., Bytebier, B., Bellstedt, D.U. & Linder, H.P. 2007. The
Cape element in the Afrotemperate flora: From Cape to Cairo?
Proc. Roy. Soc. London, Ser. B, Biol. Sci. 274: 535–543.
Galley, C. & Linder, H.P. 2006. Geographical affinities of the Cape
flora, South Africa. J. Biogeogr. 33: 236–250.
Gene Codes Corporation. 1998. Sequencher 4.01 reference: Advanced,
user friendly software tools for DNA sequencing. Madison, Wisconsin: Gene Codes Corporation.
Holder, M.T., Anderson, J.A. & Holloway, A.K. 2001. Difficulties
in detecting hybridization. Syst. Biol. 50: 978–982.
Holland, P.G. 1978. An evolutionary biogeography of the genus Aloe.
J. Biogeogr. 5: 213–226.
Howis, S., Barker, N.P. & Mucina, L. 2009. Globally grown, but
poorly known: Species limits and biogeography of Gazania Gaert.
(Asteraceae) inferred from chloroplast and nuclear DNA sequence
data. Taxon 58: 871–882.
Hughes, C. & Eastwood, R. 2006. Island radiation on a continental
scale: Exceptional rates of plant diversification after uplift of the
Andes. Proc. Natl. Acad. Sci. U.S.A. 103: 10334–10339.
Hughes, J. & Vogler, A.P. 2004. The phylogeny of acorn weevils
(genus Curculio) from mitochondrial and nuclear DNA sequences:
The problem of incomplete data. Molec. Phylog. Evol. 32: 601–615.
Irestedt, M., Fjeldså, J., Nylander, J.A.A. & Ericson, P.G.P. 2004.
Phylogenetic relationships of typical antbirds (Thamnophilidae)
and test of incongruence based on Bayes factors. BMC Evol. Biol.
4: 23. doi:10.1186/1471-2148-4-23.
Kass, R.E. & Raftery, A.E. 1995. Bayes factors. J. Amer. Statist.
Assoc. 90: 773–795.
Killick, D.J.B. 1963. An account of the plant ecology of the Cathedral
peak area on the Natal Drakensberg. Mem. Bot. Surv. South Africa
31: 1–178.
Killick, D.J.B. 1978. The Afro-alpine region. Pp. 515–560 in: Werger,
M.J.A. (ed.), Biogeography and ecology of southern Africa. The
Hague: Dr. W. Junk.
Klak, C., Reeves, G. & Hedderson, T. 2004. Unmatched tempo of evolution in Southern African semi-desert ice plants. Nature 427: 63–65.
Koekemoer, M. 1996. An overview of the Asteraceae of southern
Africa. Pp. 95–110 in: Hind, D.J.N. & Beentje, H.J. (eds.), Proceedings of the International Compositae Conference, Kew, 1994, vol.
1, Compositae: Systematics. Kew: Royal Botanic Gardens.
Levyns, M.R. 1938. Some evidence bearing on the past history of the
Cape flora. Trans. Roy. Soc. South Africa 26: 404–424.
Levyns, M.R. 1952. Clues to the past in the Cape flora of today.
S. African J. Sci. 49: 155–164.
Levyns, M.R. 1964. Presidential address, migrations and origin of the
Cape flora. Trans. Roy. Soc. South Africa 37: 85–107.
Linder, H.P. 1990. On the relationship between the vegetation and
floras of the Afromontane and the Cape regions of Africa. Mitt.
Inst. Allg. Bot. Hamburg 23b: 777–790.
Linder, H.P. 1994. Afrotemperate phytogeography: Implications of
cladistic biogeographical analysis. Pp. 913–930 in: Seyani, J.H. &
Chikuni, A.C. (eds.), Proceedings of the 13th Plenary Meeting of
AETFAT, Zomba, Malawi, 2–11 April 1991. Zomba: National Herbarium and Botanic Gardens of Malawi.
Linder, H.P. 2003. The radiation of the Cape flora, southern Africa.
Biol. Rev. 78: 597–638.
66
TAXON 59 (1) • February 2010: 57–67
Linder, H.P. 2008. Plant species radiations: Where, when, why? Philos.
Trans., Ser. B. 363: 3097–3105.
Linder, H.P., Meadows, M.E. & Cowling, R.M. 1992. History of the
Cape Flora. Pp. 113–134 in: Cowling, R.M. (ed.), Fynbos: Nutrients, fire and diversity. Cape Town: Oxford Univ. Press.
Maddison, W. 1989. Reconstructing character evolution on polytomous cladograms. Cladistics 5: 365–377.
Maddison, W.P. 1997. Gene trees in species trees. Syst. Biol. 46: 523–536.
Maddison, W.P. & Maddison, D.R. 1992. MacClade: Analysis of
phylogeny and character evolution, version 4.0. Sunderland, Massachusetts: Sinauer.
Marlow, J.R., Lange, C.B., Walter, G. & Rosell-Melé, A. 2000. Upwelling intensification as part of the Pliocene–Pleistocene climate
transition. Science 290: 2288–2291.
McCracken, K.G. & Sorensen, M.D. 2005. Is homoplasy or lineage
sorting the source of incongruent mtDNA and nuclear gene trees
in the stiff-tailed ducks (Nomonyx oxyura)? Syst. Biol. 54: 35–55.
Moore, M.J. & Jansen, R.K. 2006. Molecular evidence for the age,
origin, and evolutionary history of the American desert plant genus
Tiquilia (Boraginaceae). Molec. Phylog. Evol. 39: 668–687.
Newton, M.A. & Raftery, A.E. 1994. Approximate Bayesian inference by the weighted likelihood bootstrap (with discussion). J. Roy.
Statist. Soc., Ser. B 56: 3–48.
Nichols, R. 2001. Gene trees and species trees are not the same. Trends
Ecol. Evol. 16: 358–364.
Nordenstam, B. 1968a. The genus Euryops. Part I. Taxonomy. Opera
Bot. 20: 1–409.
Nordenstam, B. 1968b. The genus Euryops. Part II. Aspects of morphology and cytology. Bot. Not. 121: 209–232.
Nordenstam, B. 1969. Phytogeography of the genus Euryops (Compositae). A contribution to the phytogeography of southern Africa.
Opera Bot. 23: 1–77.
Nordenstam, B., Clark, V.R., Devos, N. & Barker, N.P. 2009. Two new
species of Euryops (Asteraceae: Senecioneae) from the Sneeuberg,
Eastern Cape Province, South Africa. S. African J. Bot. 75: 144–152.
Nylander, J.A.A. 2004. MrModeltest, version 2. Evolutionary Biology
Centre, Uppsala University: Program distributed by the author.
Nylander, J.A.A., Ronquist, F., Huelsenbeck, J.P. & Nieves-Aldrey,
J.L. 2004. Bayesian phylogenetic analysis of combined data. Syst.
Biol. 53: 47–67.
Oxelman, B., Lidén, M. & Berglund, D. 1997. Chloroplast rps16
intron phylogeny of the tribe Sileneae (Caryophyllaceae). Pl. Syst.
Evol. 206: 393–410.
Palmer, J.D. 1991. Plastid chromosome: Structure and evolution. Pp.
5–53 in: Bogorad, L. & Vasil, I.K. (eds.), The molecular biology
of plastids. San Diego: Academic Press.
Pamilo, P. & Nei, M. 1988. Relationships between gene trees and
species trees. Molec. Biol. Evol. 5: 568–583.
Pelser, P.B., Nordenstam, B., Kadereit, J.W. & Watson, L.E. 2007.
An ITS phylogeny of tribe Senecioneae (Asteraceae) and a new
delimitation of Senecio L. Taxon 56: 1077–1104.
Rambaut, A. & Drummond, A.J. 2007. Tracer, version 1.4. http://
tree.bio.ed.ac.uk/software/tracer/.
Richardson, J.E., Pennington, R.T., Pennington, T.D. & Hollingsworth, P.M. 2001a. Rapid diversification of a species-rich genus
of neotropical rain forest trees. Science 293: 2242–2245.
Richardson, J.E., Weitz, F.M., Fay, M.F., Cronk, Q.C.B., Linder,
H.P., Reeves, G. & Chase, M.W. 2001b. Rapid and recent origin
of species richness in the Cape flora of South Africa. Nature 412:
181–183.
Ronquist, F. & Huelsenbeck, J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574.
Sang, T., Crawford, D.J., Stuessy, T.F. & Silva-O., M. 1995. ITS
sequences and the phylogeny of the genus Robinsonia (Asteraceae).
Syst. Bot. 20: 55–64.
Seehausen, O. 2004. Hybridization and adaptive radiation. Trends
Ecol. Evol. 19: 198–207.
TAXON 59 (1) • February 2010: 57–67
Shaw, K.L. 2002. Conflict between nuclear and mitochondrial DNA
phylogenies of a recent species radiation: What mtDNA reveals
and conceals about modes of speciation in Hawaiian crickets. Proc.
Natl. Acad. Sci. U.S.A. 99: 16122–16127.
Stanford, A.M., Harden, R. & Parks, C.R. 2000. Phylogeny and
biogeography of Juglans (Juglandaceae) based on matK and ITS
sequence data. Amer. J. Bot. 87: 872–882.
Swofford, D.L. 2002. PAUP*: Phylogenetic analysis using parsimony
(*and other methods), version 4. Sunderland, Massachusetts: Sinauer.
Taberlet, P., Gielly, L., Pautou, G. & Bouvet, J. 1991. Universal primers for amplification of three non-coding regions of chloroplast
DNA. Pl. Molec. Biol. 17: 1105–1109.
Vargas, P., Baldwin, B.G. & Constance, L. 1998. Nuclear ribosomal
DNA evidence for a western North American origin of Hawaiian
and South American species of Sanicula (Apiaceae). Proc. Natl.
Acad. Sci. U.S.A. 95: 235–240.
Verboom, G.A., Linder, H.P. & Stock, W.D. 2003. Phylogenetics of the
grass genus Ehrharta Thunb.: Evidence for radiation in the summerarid zone of the South African Cape. Evolution 57: 1008–1021.
Devos & al. • Phylogeny and biogeography of Euryops
Weimarck, H. 1933. Die Verbreitung einiger afrikanisch-montanen
Pflanzengruppen. I–II. Svensk Bot. Tidskr. 27: 400–419.
Weimarck, H. 1936. Die Verbreitung einiger afrikanisch-montanen
Pflanzengruppen. III–IV. Svensk Bot. Tidskr. 30: 36–56.
Weimarck, H. 1941. Phytogeographical groups, centres and intervals
within the Cape flora. Lunds Univ. Arsskrift 37: 1–143.
White, F. 1978. The Afromontane region. Pp. 463–513 in: Werger,
M.J.A. (ed.), Biogeography and ecology of southern Africa. The
Hague: Dr. W. Junk.
White, T.J., Bruns, T., Lee, S. & Taylor, J. 1990. Amplification
and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Pp. 315–324 in: Innis, M.A., Gelfand, D.H., Sninsky,
J.J. & White, T.J. (eds.), PCR protocols: A guide to methods and
applications. San Diego: Academic Press.
Wild, H. 1968. Phytogeography in South Central Africa. Kirkia 6:
197–222.
Yoder, A.D., Irwin, J.A. & Payseur, B.A. 2001. Failure of the ILD
to determine data combinability for slow loris phylogeny. Syst.
Biol. 50: 408–424.
Appendix. Voucher information and GenBank accession numbers for specimens used in this study. Voucher specimens are deposited in the Selmar Schonland Herbarium, Grahamstown, South Africa. Species are grouped according to their affiliation to the Euryops sections described by Nordenstam (1968a).
Section: species: voucher (collector’s name, collector’s number and herbarium), GenBank accessions no. ITS, rps16, trnL-trnF, trnT-trnL
E. sect. Angustifoliae: Euryops acraeus M.D. Hend.: N. Devos CH05 (GRA), EU667472, EU667538, EU670096, EU670158; Euryops algoensis DC.: N.
Barker NB1908 (GRA), EU667483, EU667547, EU670105, EU670167; Euryops annae E. Phillips: R. Clark CDM4 (GRA), EU667470, EU667537, EU670094,
EU670156; Euryops arabicus Steud.: M. Thulin & A.N. Gifri 8850 (UPS), EU667464, n/a, EU670088, n/a; Euryops arabicus Steud.: Mats Thulin, Abdi Dahir &
Ahmed Osman 9438 (UPS), EU667465, n/a, EU670089, EU670152; Euryops arabicus Steud.: Thulin, Eriksson, Gifri & Langstrom 8134 (UPS), EU667463, n/a,
EU670087, EU670151; Euryops brownei S. Moore: n/a 248 (EA), EU667477, n/a, n/a, n/a; Euryops candollei Harv.: M. Cunningham CC352 (GRA), EU667467,
EU667534, EU670091, EU670153; Euryops dacrydioides Oliv. in Hook: Majda Zumer Z18 (UPS), EU667529, EU667591, EU670147, EU670206; Euryops
dacrydioides Oliv. in Hook: Olov Hedberg 4377 (UPS), EU667528, EU667590, EU670146, n/a; Euryops dregeanus Schltr.: N. Devos ND090905_6 (GRA),
EU667497, EU667560, EU670118, EU670180; Euryops dregeanus Schltr.: N. Devos ND090905_7 (GRA), EU667498, EU667561, EU670119, EU670181; Euryops
empetrifolius DC.: Laidler 529 (PRE), EU667520, EU667582, EU670139, EU670201; Euryops lateriflorus (L. f.) B. Nord.: N. Barker NB1487 (GRA), EU667482,
EU667546, EU670104, EU670166; Euryops lateriflorus (L. f.) B. Nord.: N. Devos ND040905_4 (GRA), EU667491, EU667555, n/a, EU670175; Euryops lateriflorus (L. f.) B. Nord.: N. Devos ND060905_11 (GRA), EU667493, EU667557, EU670114, EU670177; Euryops lateriflorus (L. f.) B. Nord.: N. Devos ND130206
(GRA), EU667504, EU667567, EU670124, EU670187; Euryops linifolius (L.) DC.: N. Devos ND140705_2 (GRA), EU667507, EU667570, EU670127, EU670190;
Euryops multifidus Schltr.: N. Devos ND040905_3 (GRA), EU667490, EU667554, EU670112, EU670174; Euryops petraeus B. Nord.: V. Clark CDM2 (GRA),
EU667468, EU667535, EU670092, EU670154; Euryops pinifolius A. Rich.: M. Thulin & A. Hunde 3930 (UPS), EU667530, EU667592, EU670148, EU670207;
Euryops spathaceus DC.: N. Devos ND120605_2 (GRA), EU667500, EU667563, EU670121, EU670183; Euryops spathaceus DC.: N. Devos ND120605_4 (GRA),
EU667502, EU667565, n/a, EU670185; Euryops subcarnosus subsp. vulgaris DC.: N. Devos ND080905_1 (GRA), EU667495, EU667558, EU670116, EU670178;
Euryops tenuissimus subsp. tenuissimus (L.) DC.: N. Devos ND020905_4 (GRA), EU667489, EU667553, EU670111, EU670173; Euryops tenuissimus subsp.
tenuissimus (L.) DC.: N. Devos ND130705_1 (GRA), EU667505, EU667568, EU670125, EU670188; Euryops tysonii Phill.: M. Cunningham CH08 (GRA),
EU667473, EU667539, EU670097, EU670159; Euryops virgineus (L. f.) DC.: N. Devos ND260805 (GRA), EU667512, EU667575, EU670132, EU670195; Euryops
virgineus (L. f.) DC.: R. McKenzie RM1023 (GRA), EU667521, EU667583, EU670140, EU670202. E. sect. Brachypus: Euryops decumbens B. Nord.: M. Cunningham CH09 (GRA), EU667474, EU667540, EU670098, EU670160; Euryops galpinii Bol.: N. Devos ND081005_4 (GRA), EU667496, EU667559, EU670117,
EU670179; Euryops montanus Schltr.: M. Cunningham 1XT5314 (GRA), EU667462, EU667532, n/a, EU670150; Euryops prostratus B. Nord.: Anderberg 1708
(S), EU667478, EU667542, EU670100, EU670162. E. sect. Chrysops: Euryops abrotanifolius (L.) DC.: R. McKenzie RM1056 (GRA), EU667522, EU667584,
EU670141, EU670203; Euryops abrotanifolius (L.) DC.: N. Devos ND130705_2C (GRA), EU667506, EU667569, EU670126, EU670189; Euryops abrotanifolius (L.) DC.: N. Devos ND160705_5 (GRA), EU667510, EU667573, EU670130, EU670193; Euryops abrotanifolius (L.) DC.: N. Devos ND280805_1 (GRA),
EU667513, EU667576, EU670133, EU670196; Euryops abrotanifolius (L.) DC.: N. Devos ND310805_1 (GRA), EU667516, EU667579, EU670136, EU670198;
Euryops abrotanifolius (L.) DC.: N. Devos ND310805_6 (GRA), EU667518, EU667581, EU670138, EU670200; Euryops evansii subsp. evansii Schltr.: M.
Cunningham CH04 (GRA), EU667471, n/a, EU670095, EU670157; Euryops evansii subsp. parvus Schltr.: N. Devos ND190106 (GRA), EU667511, EU667574,
EU670131, EU670194; Euryops evansii subsp. parvus Schltr.: M. Cunningham CH11 (GRA), EU667475, EU667541, EU670099, EU670161; Euryops trilobus
Harv.: V. Clark CDM3 (GRA), EU667469, EU667536, EU670093, EU670155. E. sect. Euryops: Euryops brevilobus Compt.: N. Devos ND010905_6 (GRA),
EU667488, EU667552, EU670110, EU670172; Euryops othonnoides (DC.) B. Nord.: N. Devos ND010905_1 (GRA), EU667486, EU667550, EU670108, EU670170;
Euryops othonnoides (DC.) B. Nord.: N. Devos ND120905_6 (GRA), EU667503, EU667566, EU670123, EU670186; Euryops pectinatus subsp. pectinatus (L.)
Cass.: N. Devos ND290805_2 (GRA), EU667514, EU667577, EU670134, n/a; Euryops speciosissimus DC.: N. Devos ND310805_4 (GRA), EU667517, EU667580,
EU670137, EU670199; Euryops speciosissimus DC.: R. McKenzie RM1058 (GRA), EU667523, EU667585, EU670142, EU670204. E. sect. Leptorrhiza: Euryops
annuus Compt.: N. Devos ND010905_4 (GRA), EU667487, EU667551, EU670109, EU670171. E. sect. Psilosteum: Euryops anthemoides B. Nord.: N. Devos
ND120605_3 (GRA), EU667501, EU667564, EU670122, EU670184; Euryops anthemoides B. Nord.: T. Dold TD452 (GRA), EU667525, EU667587, n/a, n/a;
Euryops brachypodus (DC.) B. Nord.: N. Devos ND01 (GRA), EU667485, EU667549, EU670107, EU670169; Euryops brachypodus (DC.) B. Nord.: R. McKenzie
RM1108 (GRA), EU667524, EU667586, EU670143, EU670205; Euryops ericifolius (Belang.) B. Nord.: Palmer PALMER3934 (GRA), EU667519, n/a, n/a, n/a;
Euryops ericoides (L. f.) B. Nord.: N. Devos ND160705_3 (GRA), EU667509, EU667572, EU670129, EU670192; Euryops euryopoides (DC.) B. Nord.: Doubell
29 (GRA), EU667476, n/a, n/a, n/a; Euryops euryopoides (DC.) B. Nord.: Youthed 751 (GRA), EU667531, EU667593, EU670149, n/a; Euryops hebecarpus
(DC.) B. Nord.: N. Devos ND160705_1 (GRA), EU667508, EU667571, EU670128, EU670191; Euryops hypnoides B. Nord.: T. Dold TD4700 (GRA), EU667527,
EU667589, EU670145, n/a; Euryops munitus (L. f.) B. Nord.: Brown 130898 (GRA), EU667466, EU667533, EU670090, n/a; Euryops ursinoides B. Nord.: T. Dold
TD4649 (GRA), EU667526, EU667588, EU670144, n/a. Outgroups: Gymnodiscus capillaris (L. f.) Less.: N. Devos ND300805_1 (GRA), EU667515, EU667578,
EU670135, EU670197; Gymnodiscus capillaris (L. f.) Less.: L. Mucina LM110805_3 (GRA), EU667480, EU667544, EU670102, EU670164; Othonna carnosa
Less.: N. Devos ND120605_1 (GRA), EU667499, EU667562, EU670120, EU670182; Othonna eriocarpa (DC.) Sch. Bip.: N. Barker NB1938 (GRA), EU667484,
EU667548, EU670106, EU670168; Othonna euphorbioides Hutch.: N. Devos ND060905_3 (GRA), EU667494, n/a, EU670115, n/a; Othonna sedifolia DC.: N.
Devos ND050905_1 (GRA), EU667492, EU667556, EU670113, EU670176; Othonna sedifolia DC.: L. Mucina LM060605_13 (GRA), EU667479, EU667543,
EU670101, EU670163; Othonna sp. nov.: L. Mucina LM210903_6 (GRA), EU667481, EU667545, EU670103, EU670165.
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