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Modern survivors of once more diverse lineages are
Modern survivors of once more diverse lineages are

/ www.sciencexpress.org / 20 October 2011 / Page 1 / 10.1126/science.1209926
Modern survivors of once more diverse lineages are
regarded as living fossils, particularly when characterized
by morphological stasis. Cycads are often cited as a classic
example, reaching their greatest diversity during the
Jurassic-Cretaceous (199.6-65.5 million years ago), then
dwindling to their present diversity of ~300 species as
flowering plants rose to dominance. Using fossilcalibrated
molecular phylogenies, we show that cycads
underwent a near synchronous global re-diversification
beginning in the late Miocene, followed by a slowdown
toward the Recent. Although the cycad lineage is ancient,
our timetree indicates that living cycad species are not
much older than ~12 million years. These data reject the
hypothesized role of dinosaurs in generating extant
diversity and the designation of today’s cycad species as
living fossils.
Living fossils and evolutionary relicts are surviving
representatives of once diverse or abundant groups. They are
significant because they originated tens or even hundreds of
millions of years ago, yet have persisted with little
morphological change. Well-known examples include the
coelacanth, the horseshoe crab, the Ginkgo tree and the
cycads (Cycadophyta) (1), indicate they originated before the
mid-Permian. They apparently reached their peak
morphologically, geographically and in taxic diversity in the
Jurassic-Cretaceous (2–4). Their subsequent decline has been
attributed to competition with flowering plants (1, 5, 6) and
also to the loss of dinosaurs as dispersal agents (3); however,
numerical analyses testing a coradiation between dinosaurs
and cycads are inconclusive (7).
Fossil-calibrated phylogenies (timetrees) were used to test
whether living cycads are relics or whether their
morphological conservation might mask more recent
diversification events. To estimate the ages of living cycad
species, we sampled the nuclear gene phytochrome P (PHYP)
from two-thirds of living cycads (199 of the ~300 recognized
species (8)), using proportional sampling within the large
genera (9). Our sampling included all of the 11 currently
recognized genera [including Chigua, which is nested within
Zamia (10, 11)]. We also assembled plastid data matrices
from published rbcL and matK sequences (Tables 1 and S1).
These matrices had fewer taxa, but they allowed us to test the
results of ages estimated from the PHYP data. Topologies
were inferred from single and combined gene regions, and the
divergence times between the extant lineages were estimated
by subjecting the trees to relaxed molecular clock analysis
with penalized likelihood and to strict molecular clock
analysis with the Langley-Fitch method (12); Bayesian
searches for topologies and divergence times were conducted
using an uncorrelated lognormal relaxed clock (13). The
fossil record was used to assign minimum age constraints on
three internal nodes and to provide a fixed age constraint for
the divergence time between the cycads and their outgroups.
Note that the use of a fixed age constraint, coupled with the
incompleteness of the fossil record means that the inferred
ages underestimate the true divergence times.
The timetree derived from the PHYP data was used to
assess changes in diversification rates within genera using the
gamma (γ) statistic (14) and per-myr diversification rates
(15). To account for the effect of undersampling we also
calculated the rates assuming all the missing taxa had
originated in the last time bin. Despite this very conservative
approach, the results support the conclusion that after
radiating, diversification rates in the genera decreased (table
S7).
Our phylogenetic analysis did not produce any surprises
topologically: the relationships inferred from the PHYP data
(and from the combined PHYP, rbcL, and matK data) are
consistent with well-supported nodes resolved in previously
published trees (10, 11, 16, 17). While the remarkably short
Recent Synchronous Radiation of a Living Fossil
N. S. Nagalingum,
1,2,3* C. R. Marshall,
2 T. B. Quental,
2,4 H. S. Rai1
,
5 D. P. Little,
6 S. Mathews1
*
1
Arnold Arboretum of Harvard University, 22 Divinity Ave, Cambridge, MA 02138, USA. 2
University of California Museum of
Paleontology, 1101 Valley Life Sciences Building, University of California Berkeley, Berkeley, CA 94720-4780, USA. 3
National Herbarium of New South Wales, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney NSW 2000,
Australia. 4
Departamento de Ecologia, Universidade Estadual de São Paulo (USP), São Paulo - SP, Brazil. 5
Department of
Wildland Resources, 5230 Old Main Hill, Utah State University, Logan, UT 84322-5230, USA. 6
Cullman Program for
Molecular Systematics, The New York Botanical Garden, Bronx, NY 10458-5126 USA.
*To whom correspondence should be addressed. E-mail: nathalie.nagalingum@rbgsyd.nsw.gov.au (N.S.N.);
smathews@oeb.harvard.edu (S.M.)
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/ www.sciencexpress.org / 20 October 2011 / Page 2 / 10.1126/science.1209926
terminal branches may raise doubts over the validity of the
defined cycad species, reproductive, morphological and
geographical evidence strongly support their specific status
(18–20).
Unexpectedly, the timetrees indicate that all extant species
(except for those in monotypic genera) derive from recent
divergence events that occurred no later than the late Miocene
to the Pliocene (Fig. 1 and Table 1). Initiation of species
diversification occurred in a very short ~5 myr timeframe for
all of the large genera, that is Cycas, Encephalartos,
Macrozamia, Zamia and Ceratozamia (Fig. 1). Subsequently,
all of these genera show significant declines in diversification
rate, dropping to almost zero in the last ~2 Ma (Fig. 2). Even
when we use our conservative approach for accounting for
the undersampling of extant species, we find that the rates
peaked early in the radiation of each of these genera (table
S7).
The signal of a recent and near-synchronous global
radiation is also detected using different methods, genes and
gene combinations (tables 1 and S2 to S5 and figs. S1, S4, S5,
S8, and S9). It is robust to topological and branch length
uncertainty and to uniform, correlated or uncorrelated rates
across the tree (tables S3 and S4) – at most the minimum
timeframe for the radiation varies from the late MiocenePliocene
to the mid-to late Miocene. Accounting for the
incompleteness of the fossil record yields median (50%)
crown group age estimates for the genera in the mid- to late
Miocene (12.2-6.4 Ma), and maximum (95%) estimates in the
early to mid-Miocene (23.9-9.2 Ma) (tables S4 and S5).
The late Cenozoic radiation reported here is consistent
with the young ages for Encephalartos and Cycas species
(~10 Ma) inferred from rbcL mutation rates (16), and with a
gymnosperm matK and 18S rRNA timetree that includes a
much smaller sampling of cycads (3-6 species per genus)
(21), although the median age estimates from this latter study
extend as far back as the early Miocene. These slightly older
age estimates may have resulted from differences in how key
fossil calibrations were applied (9). Recent divergences have
also been hypothesized within many of the living genera
based on the low genetic diversity characteristic of congeneric
species [e.g., (18, 22, 23) and see also table S8].
Finally, our findings are consistent with data from some
highly specialized insect pollinators of cycads (weevils),
where low inter-specific divergence among mitochondrial
DNA sequences is also suggestive of recent diversification
(24).
The cycad timetree is remarkable for its long branches
subtending the late Cenozoic radiations (Fig. 1). These
suggest “phylogenetic fuses”, where the origin of a clade is
decoupled from its later evolutionary explosion (25). This
hypothesis requires the assumption that the long fuse (branch)
represents a period of low diversity. Alternatively, the long
branches may result from considerable extinction, and this is
consistent with at least three lines of evidence. First, fossil
data indicate that cycads were diverse in the Mesozoic, but
with extinctions occurring toward the end of the Mesozoic (1,
5, 6). Second, a birth-death model used in the Bayesian
analyses (9), yielded a high ratio of extinction to speciation
(relative death rate = 0.97). Finally, numerical simulations
show that long fuses may result from mass extinctions (26).
However, we cannot currently address the exact role of
extinction in shaping the cycad timetree due to a limited
understanding of the Cenozoic cycad fossil record, and to our
current inability to extract accurate data on extinction patterns
from molecular phylogenies (27). Thus, we do not know
whether Cenozoic cycad diversity remained low until the late
Cenozoic radiations reported here, or whether substantial
early- to mid-Cenozoic diversity existed, but was impacted by
major Cenozoic extinctions.
The near-simultaneous initiation of diversification of six of
the living cycad genera across the globe (in Australia, Africa,
south-east Asia, and central America) indicates a single
trigger may have been responsible. During the late Miocene,
the global climate shifted as the world’s landmasses largely
assumed their current positions (28). This closed the last of
the equatorial seaways that had allowed warm tropical water
to circulate the globe, leading to a shift from globally warm,
equable climates to present day cooler, more seasonal
climates (29). The majority of cycad species live in tropical
or subtropical climates in regions of predominantly summer
rainfall (2). Thus, it is possible that cycad diversification was
largely driven by the global climate change that increased the
geographic extent of those subtropical and tropical biomes
that became marked by seasonality. Nonetheless, despite their
recent success, almost two-thirds of cycads are on the IUCN
Red List of Threatened Plants (~62% of cycads are
threatened—the highest value of any plant group) (30). Thus,
their relatively recent radiation does not appear to have
buffered them from high extinction risk, and the threat of
becoming victims of a human-induced sixth mass extinction
(31).
Given their ancient origins, it is remarkable that virtually
all cycad species-level diversity is due to recent speciation
events. Groups of somewhat less ancient plants that also
radiate later in their histories include the Pinaceae,
Ephedraceae, Nymphaeales and Chloranthaceae (32–35),
although diversification within these groups was not as
synchronous, and occurred earlier than the cycad
diversification, during the Oligocene-Miocene. However,
independently evolved lineages of succulents also show an
increased rate of diversification approximately
contemporaneous with the cycad radiations, most likely
triggered by the increased aridity that was correlated with the
shift to increased seasonality (36). The possibility of
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concurrent bursts of speciation across the plant tree of life is
an intriguing pattern that warrants closer assessment.
The fossil-calibrated molecular phylogenies of the cycads
presented here reject the prevailing hypothesis that extant
species are relictual living fossils (2, 4, 6), whose current
diversity was established through interactions in the deep past
with the dinosaurs (3). Their recent radiation suggests that coevolution
of living cycads and their insect pollinators should
be examined over a significantly shorter time period (37–39),
and it may explain low levels of genetic diversity that have
been observed within cycad species (40, 41).
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Acknowledgments: Supported by NSF’s Assembling the
Tree of Life program (grant EF-0629890 to SM). The data
reported in this paper are tabulated in the Supporting
Online Material and archived in Genbank (JN655891-
JN656096), and TreeBase (#11891). We thank M.
Beilstein, M. Clements, and K. Schellenberg for
discussions and assistance; A. Vo for help with cloning
and sequencing; S. Ho for advice on BEAST; J. Hilton for
information regarding fossil ages; M. Sanderson for
suggestions on divergence time analyses; D. Stevenson for
cycad tissue; and the reviewers for suggestions and
comments.
Supporting Online Material
www.sciencemag.org/cgi/content/full/science.1209926/DC1
Materials and Methods
Figs. S1 to S13
Tables S1 to S8
References (42–76)
16 June 2011; accepted 27 September 2011
Published online 20 October 2011; 10.1126/science.1209926
Fig. 1. Cycad chronogram inferred from PHYP data assuming
a relaxed molecular clock (12), and map showing geographic
distribution of genera. (A) Chronogram and distribution
(inset) of genera. Numbered circles mark the ages of fossil
constraints and unnumbered circles mark the inferred ages of
the constrained node (9). Geographic distributions obtained
from (2). (B) Enlarged view of chronogram from A focusing
on the Miocene-Recent. Abbreviations: L. Paleoz, Late
Paleozoic; P, Paleocene; Eoc, Eocene; O, Oligocene; Mi,
Miocene; PPH, Pleistocene-Pliocene-Holocene; Q,
Quaternary; Pli, Pliocene; PH, Pleistocene-Holocene.
Fig. 2. Diversification rates per myr and γ values for the
cycad genera. (A) Cycas, (B) Encephalartos, (C)
Macrozamia, (D) Zamia, and (E) Ceratozamia. Rates and γ
values are shown only for genera with more than 5 species.
All γ values shown are significant, indicating decreasing
diversification rates. The time of initiation of the genus-level
radiations depends on the analysis (the penalized likelihood
analysis is shown here); see Table 1 for alternative
possibilities.
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Table 1. Congruence of crown group ages from nuclear and/or plastid markers. Ages are shown only for genera with more than
5 species. PL, Penalized Likelihood; BI, Bayesian Inference mean age; na, not applicable because only one species was sampled
from the crown group for the genus; dash, marker not used in that analysis (9).
Nuclear: PL Nuclear: BI Nuclear +
plastid PL
(missing data)
Nuclear +
plastid PL
(fully sampled)
Plastid PL
(fully sampled)
# taxa: PHYP 199 199 199 20 —
# taxa: matK — — 34 20 20
# taxa: rbcl — — 59 20 20
Age (My): Cycas 9.77 12.80 8.17 8.68 9.46
Age (My):
Encephalartos
9.21 11.37 8.49 10.25 7.99
Age (My):
Macrozamia
5.36 7.48 5.43 3.33 4.83
Age (My):
Zamia
4.77 11.25 5.77 na na
Age (My):
Ceratozamia
4.37 11.48 4.40 na na
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