Vincent etal. 2015 Nature

Vincent etal. 2015 Nature
LETTER
doi:10.1038/nature14949
Evolution of endemism on a young tropical mountain
Vincent S. F. T. Merckx1,2, Kasper P. Hendriks1,3, Kevin K. Beentjes1, Constantijn B. Mennes1, Leontine E. Becking1,4,5,
Katja T. C. A. Peijnenburg1,6, Aqilah Afendy7, Nivaarani Arumugam7,8, Hugo de Boer1,9,10, Alim Biun11, Matsain M. Buang11,
Ping-Ping Chen1, Arthur Y. C. Chung12, Rory Dow1, Frida A. A. Feijen1, Hans Feijen1, Cobi Feijen-van Soest1, József Geml1,2,
René Geurts13, Barbara Gravendeel1,2,14, Peter Hovenkamp1, Paul Imbun11, Isa Ipor15, Steven B. Janssens16, Merlijn Jocqué17,18,
Heike Kappes1,19, Eyen Khoo12, Peter Koomen20, Frederic Lens1,2, Richard J. Majapun12, Luis N. Morgado1, Suman Neupane21,
Nico Nieser1, Joan T. Pereira12, Homathevi Rahman7, Suzana Sabran12, Anati Sawang7, Rachel M. Schwallier1, Phyau-Soon Shim11{,
Harry Smit1, Nicolien Sol1, Maipul Spait11, Michael Stech1, Frank Stokvis1, John B. Sugau12, Monica Suleiman7, Sukaibin Sumail11,
Daniel C. Thomas1,22,23, Jan van Tol1, Fred Y. Y. Tuh11, Bakhtiar E. Yahya7, Jamili Nais11, Rimi Repin11, Maklarin Lakim11 &
Menno Schilthuizen1,2,7
Tropical mountains are hot spots of biodiversity and endemism1–3,
but the evolutionary origins of their unique biotas are poorly
understood4. In varying degrees, local and regional extinction,
long-distance colonization, and local recruitment may all contribute to the exceptional character of these communities5. Also, it is
debated whether mountain endemics mostly originate from local
lowland taxa, or from lineages that reach the mountain by longrange dispersal from cool localities elsewhere6. Here we investigate
the evolutionary routes to endemism by sampling an entire tropical mountain biota on the 4,095-metre-high Mount Kinabalu in
Sabah, East Malaysia. We discover that most of its unique biodiversity is younger than the mountain itself (6 million years), and
comprises a mix of immigrant pre-adapted lineages and descendants from local lowland ancestors, although substantial shifts
from lower to higher vegetation zones in this latter group were
rare. These insights could improve forecasts of the likelihood of
extinction and ‘evolutionary rescue’7 in montane biodiversity hot
spots under climate change scenarios.
In mountainous areas of the humid tropics, steep environmental
gradients coincide with high primary productivity and relative climatic stability to sustain large numbers of species, often with striking degrees of endemism at higher elevations1,8. It has therefore been
recognized that tropical mountains are biodiversity hot spots of great
conservation value1, especially because endemics on mountain tops
are vulnerable to becoming trapped and then annihilated as a result
of global warming2,3.
The evolutionary origins of these unique biotas, however, are poorly
understood4. Like other insular habitats9, the endemic biota of an
isolated mountain results from complex dynamics among colonization, in situ speciation, and local extinction. Each of these factors is
dependent on the age and size of the habitat, and on the environmental
contrast between the insular habitat and its matrix10. In the case of
a tropical mountain top, an added complication is the fact that
climate fluctuations may have widened and restricted the geographic
range over which the montane conditions have extended in the past,
meaning that parts of the endemic biota may be relicts, and other
components may be novel in character4,5.
Disentangling these possibilities for a single tropical montane
biodiversity hot spot requires molecular phylogenetic study of a large
number of fauna and flora elements. However, with only few exceptions11,12, evolutionary studies in such hot spots have been limited
to single taxa13,14. This precludes broad understanding of the evolutionary and biogeographic origins of an endemic biota as a whole4.
We investigated the evolutionary routes to endemism by sampling
an entire tropical mountain biota on the UNESCO World Heritage site
of Gunung Kinabalu in Sabah, East Malaysia. We demonstrate that
most of its unique biodiversity is younger than the mountain itself and
comprises a mix of immigrant pre-adapted lineages as well as descendants from local lowland ancestors.
At 4,095 m, Kinabalu is the tallest mountain between the Himalayas
and New Guinea. It is a solitary ‘sky island’, having emerged during the
Pliocene and early Pleistocene as a granite pluton within the surrounding sandstone of the Crocker Range, the latter having formed much
earlier, between the Eocene and the early Miocene15. Because of the
area’s tectonic activity, as well as Pleistocene sea level changes, the
exact historical progression of its elevation above sea level is not
known, but it is likely that a major rise, even beyond today’s elevation,
of Kinabalu, as well as the central spine of the Crocker Range, took
place between 6 million years ago and today (for more geological
background see Methods). Since the early days of its exploration16,
Kinabalu has been famous for its extremely high biological diversity,
especially its richness in endemic species, with endemism proportions
reaching 25–30% for some taxa17.
To unravel the origins of the exceptionally rich Kinabalu biota, we
mounted a Malaysian–Dutch expedition in which 47 taxonomists
worked at 37 localities, spanning the full range of elevations (Fig. 1).
We used Sanger sequencing to sequence one or more fast-evolving loci
for 1,852 individuals, belonging to 18 genera representing gastropods,
annelids, insects, arachnids, vertebrates, pteridophytes, bryophytes,
and angiosperms. We also obtained 3.7 million basidiomycete
1
Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands. 2Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands. 3Groningen Institute for
Evolutionary Life Sciences, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands. 4Wageningen University & Research centre, Marine Animal Ecology Group, PO Box 338, 6700 AH
Wageningen, The Netherlands. 5Department of Environmental Science, Policy, & Management, University of California Berkeley, 130 Mulford Hall #3114, Berkeley, California 94720, USA. 6Institute for
Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands. 7Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah,
Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia. 8Faculty of Earth Science, Universiti Malaysia Kelantan, Jeli Campus, Locked bag No.100, 17600 Jeli, Kelantan Darul Naim, Malaysia. 9Department of
Organismal Biology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden. 10Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, NO-0318 Oslo, Norway. 11Sabah Parks, Lot 45 &
46, Level 1-5, Blok H, KK Times Square, 88806 Kota Kinabalu, Sabah, Malaysia. 12Forest Research Centre, Sabah Forestry Department, P.O. Box 1407, 90175 Sandakan, Sabah, Malaysia. 13Wageningen
University, Department of Plant Sciences, Laboratory of Molecular Biology, 6700AP Wageningen, The Netherlands. 14University of Applied Sciences Leiden, Zernikedreef 11, 2333 CK Leiden,
The Netherlands. 15Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia. 16Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium.
17
Royal Belgian Institute of Natural Sciences, Aquatic and Terrestrial Ecology, Vautierstraat 29, 1000 Brussels, Belgium. 18Rutgers, The State University of New Jersey, Department of Biological Sciences,
195 University Avenue, Boyden Hall, Newark, New Jersey 07102, USA. 19Zoological Institute, University of Cologne, Zülpicher Strasse 47b, D-50674 Cologne, Germany. 20Natuurmuseum Fryslân,
Schoenmakersperk 2, 8911 EM Leeuwarden, The Netherlands. 21EEB Department, University of Connecticut, 75 N. Eagleville Road, Storrs, Connecticut 06269-3043, USA. 22School of Biological Sciences,
University of Hong Kong, Pok Fu Lam Road, Hong Kong, China. 23Singapore Botanic Gardens, 1 Cluny Road, 259569 Singapore, Republic of Singapore.
{Deceased.
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RESEARCH LETTER
Summit trail
Sayap
Layang
Layang
Borneo
Kinabalu
Park
Sayap 2
Laban Rata
Summit trail
Laban Rata
Kampong Kiau
Layang Layang
Poring
Kinabalu Park HQ
Kota
Kinabalu
Kiansom
Tun Fuad
Stephen Park
Mamut
Moyog
Inobong
Sugud
Sugud 2 Kisada
Gunung Alab
Long Gong Kugan
Crocker
Mahua
Range Park
0-500 m
500–1,000 m
1,000–1,500 m
1,500–2,000 m
10 km
2,000–2,500 m
2,500–3,000 m
3,000–3,500 m
3,500–4,000 m
4,000–4,500 m
Figure 1 | Map of the study area. Inset left, location of the study area in the
World and in Borneo. Inset middle, detail of the summit trail in Kinabalu Park.
The eight expedition stations in Kinabalu Park and Crocker Range Park are
indicated with red markers, ten additional sampling sites with blue markers.
Not indicated separately are 15 sites along the summit trail, and four sites very
close to Mahua, Gunung Alab, and Inobong.
and glomeromycete ITS2 rDNA sequences from soil cores with ion
semiconductor sequencing. In addition, we retrieved data from eight
previously published single-taxon studies on vascular plants.
We analysed all data within a phylogenetic framework to estimate
the times of origin of endemic species, and to determine whether
endemic species had descended from local or distant congeners
(Methods, Fig. 2, Extended Data Table 1 and Extended Data Figs 1–9).
Note that we define ‘endemic’ as restricted to the area in which
our expedition took place. Although the present study offers the
most comprehensive evolutionary analysis of any mountain biota to
date, the taxa covered are, by necessity, an uneven and fragmentary
sampling of the full diversity. Nonetheless, we expect that our
results are representative for the Kinabalu biota as a whole, as our
selected taxa encompass organisms with a wide variety of phylogenetic backgrounds, ecologies, and life history traits.
Similar to Mesoamerican endemic cloud forest seed plants and
vertebrates11, our molecular dating results show that the estimated
mean stem-node ages of 33 endemic species span a wide range, from
0.12 million years to 14.6 million years (Fig. 3). However, 76% of these
fall within the past 6 million years, the time span during which
Kinabalu is likely to have reached its present elevation. Only two
endemics, the frog Kalophrynus baluensis and the flowering plant
Ilex kinabaluensis, are markedly older than the mountain itself.
These may be explained as artefactual if we failed to identify the
closest non-endemic sister lineage, thereby inflating their reconstructed age, or if these species are actually not endemics, but more
widespread. Alternatively, they may truly be old endemics that evolved
during cooler periods at lower elevations in Borneo before Kinabalu’s
formation.
Our phylogenetic and biogeographic analyses (Extended Data Table 1
and Extended Data Figs 1–4, 7–9) suggest the existence of two categories
of endemics18: ‘eccentric’ (12 taxa) and ‘centric’ (25 taxa). The eccentric
type of endemic has sister taxa that occur either in temperate climates
(seven cases) or in other tropical mountains outside of Borneo (five
cases). To this group belong all bryophytes, pteridophytes, some of the
fungal lineages and also the endemics in the flowering plant groups
Hedyotis, Ilex, Impatiens, Ranunculus and Euphrasia, and the animals
Coeliccia and Tritetrabdella. Eccentric endemics predominantly occur at
b
I. chinesis (Yunnan)
I. hawkeri (New Guinea)
I. platypetala (Bali)
I. usambarensis (Tanzania)
I. walleriana (Eastern Africa)
I. serpens (Tanzania)
I. thamnoidea (Tanzania)
I. pseudohamata (Tanzania)
I. balsamina (India)
I. cuspidata (South India)
I. flaccida (South India)
I. latifolia (South India)
Ptomaphaginus
a
P. n. sp. (Sugud)
c
Impatiens
C. spp. (2,040–2,100 m)
C. sp. (1,900 m)
C. collinitus (Germany)
C. sp. (2,900 m)
C. sp. (1,900 m)
I. aureliana (China: Yunnan)
I. poilanei (Vietnam)
I. eberhardtii (Vietnam)
I. chevalieri (Vietnam)
P. bryantioides (Poring)
C. vitreopileatus (New Zealand)
C. spp. (2,900 m)
P. bryantioides
(Kota Kinabalu & Kiansom)
OTU_26541_mid
I. kinabaluensis
(Kinabalu HQ, Gn. Alab,
Poring)
P. latimanus (Sayap)
C. sp. (1,000 m)
P. kinabaluensis
(Kinabalu HQ & Gn. Alab)
P. similipes (Sugud)
P. similipes (Sugud)
P. similipes (Sayap)
0-500 m
500–1,000 m
1,000–1,500 m
1,500–2,000 m
2,000–2,500 m
2,500–3,000 m
3,000–3,500 m
3,500–4,000 m
Figure 2 | Examples of phylogenetic reconstructions. a, Centric endemism
(Ptomaphaginus). b, Eccentric endemism (Impatiens). c, Centric endemism
superimposed on eccentric endemism (detail of the Cortinarius phylogeny).
Clades are coloured with the same colour scheme as in Fig. 1, by elevational
Cortinarius
zone at which they occur (see legend). High-elevation endemics in a and b are
indicated in red. For support values and other details on these and other trees,
see Extended Data Figs 1–4.
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C. sp. (2,100 m)
C. lustrabilis (Norway)
C. delibutus (Germany)
C. rotundisporus (Australia)
C. sp. (2,900 m)
C. sp. (2,900 m)
C. sp. (1,900 m)
C. calyptratus (USA)
C. glaucopus (Germany)
C. cliduchus (Germany)
C. argutus (Norway)
C. austroturmalis (Chile)
C. sp. (2,040–2,100 m)
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LETTER RESEARCH
4,000
Frogs
Insects
Arachnids
Snails
Leeches
Conifers
Ferns
Mosses
Flowering plants
3,500
Elevation (m)
3,000
2,500
2,000
1,500
1,000
500
0
0
5
10
15
20
25
30
from their ancestral niche. The fact that the endemic biota of Kinabalu
appears to be composed largely of pre-adapted (eccentric) species and
locally derived (centric), ecologically conserved endemics is in line
with niche conservatism24.
We suggest that our novel approach of molecular dating of multiple
clades be applied to larger communities in this and other tropical
montane biodiversity hot spots25. In combination, such information
should allow a detailed dissection of the relative roles of ecological
speciation, colonization and habitat filtering in the formation of
endemic biotas in this and other tropical mountains. Moreover, such
understanding could improve predictions of the likelihood of extinction and evolutionary rescue of endemic species experiencing changing climate conditions7.
Online Content Methods, along with any additional Extended Data display items
and Source Data, are available in the online version of the paper; references unique
to these sections appear only in the online paper.
Divergence time (million years)
Figure 3 | Elevations and ages for endemic species. Elevations (mid-points,
minima and maxima) and dates of origination derived from molecular
dating (averages and 95% credible intervals) for endemic species; eccentric
species (see main text) are indicated with a black circle. The vertical dashed line
indicates the oldest possible date for Kinabalu to have reached its current
elevation. For details, see Extended Data Figs 5 and 6.
high elevations (mean lower elevational boundary, 2,212 m; s.d., 837 m),
they are strict Kinabalu endemics (they do not occur on nearby, lower
mountains), and are further characterized by high dispersal capacities
(one, two and seven clades with eccentric endemism have small, medium
and large dispersal, respectively).
The centric type of endemic has sister taxa that occur locally, in the
Borneo lowlands. Six out of the eight endemic animal species, some of
the fungal lineages, the conifers, and 17 of the 20 flowering plants
belong to this type. Centric endemics occur on average at lower elevations (mean lower elevational boundary, 1,724 m; s.d., 728 m) and
tend to have lower dispersal capacities than the eccentric endemics
(eight, seven and ten clades with centric endemism have small, medium and large dispersal, respectively). Some centric endemics are
not strict Kinabalu endemics, as they are also found on other mountains in Kinabalu’s vicinity. Our ancestral state reconstructions
(Supplementary Table 6) confirm a pattern of altitudinal bottom-up
cladogenesis in the centric endemics, with 8 out of 11 species ranging
partially or entirely outside of the 95% credibility interval for the
reconstructed elevation of the most recent common ancestor, and
the remaining 3 out of 11 falling entirely within this interval. When
we performed the same analysis with Kitayama’s (ref. 19) seven vegetation zones, rather than elevation, we found that only three of these
eight elevation shifts may represent a shift towards a higher vegetation
zone. This suggests that, even in high-elevation centric endemics, substantial niche shifts are rare. Niche conservatism is probably even
underestimated, since the Massenerhebung effect causes an upward
shift of vegetation zones on Kinabalu compared with other Bornean
mountains14,20.
Our multi-taxon study shows that Kinabalu’s biodiversity hot spot
is of recent origin. This means the mountain is an evolutionary
cradle, accumulating neo-endemics, as has been suggested for other
young, high-elevation biodiversity hot spots at low latitudes21, such
as the Tibetan plateau22, the Andean highlands8, and Afrotropical
volcanoes23. However, probably as a consequence of the rapid emergence of the mountain15 and its unique alpine summit conditions19,
many of these neo-endemics have not evolved by drastic niche
shifts from local ancestors, but rather by immigration of pre-adapted
propagules from elsewhere. This explains the multiple independent
colonization events in some taxa (for example, Glomus, Rhododendron
and Coeliccia). In addition, local lowland taxa have also generated
montane species, but although some of these have reached vegetation
zones above 2,000 m, most do not show substantial niche shifts away
Received 9 December 2014; accepted 14 July 2015.
Published online 12 August 2015.
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Supplementary Information is available in the online version of the paper.
Acknowledgements We acknowledge the mountain guides of Sabah Parks for their
help with material collection, ongoing assistance to continuing research in the area, and
recent efforts following the 5 June 2015 earthquake. R. Butôt, M. de Jong, and
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RESEARCH LETTER
B. Driessen carried out DNA extractions and PCRs. P. Wilkie provided a tissue sample
for Payena. For the fungi, T. Semenova extracted DNA from the soil samples and
E. Duijm generated the reads on the Ion Torrent sequencer. B. Blankevoort and
E. J. Bosch prepared Fig. 1. J. Holloway (Natural History Museum, London, UK), I. Das
(Universiti Malaysia Sarawak), and T. S. Liew (Naturalis, UMS) provided background on
Kinabalu endemism, and R. Hall (University of London) on its geological history.
R. Etienne (University of Groningen), R. Hall (University of London) and F. Bossuyt (Free
University Brussels) read a draft of the paper. Collection and export permits were
supplied by the Sabah Biodiversity Centre. Besides institutional support via
Netherlands FES-funding, this project received funding via grants 821.01.002 and
825.12.007 of the Netherlands Organization for Scientific Research, the Alberta
Mennega Foundation, the Ecology Fund of the Royal Netherlands Academy of Sciences,
the Uyttenboogaart-Eliasen Foundation, and Pro Acarologia Basiliensis. G. van Uffelen,
R. van Vugt, and P. Kessler (Botanic Gardens, Leiden) and T. de Winter, G. Thijsse,
B. Hoeksema, H. Dautzenberg, J. Mols, and E. van Nieukerken (Naturalis) gave advice on
transportation of specimens. Artist I. Kopelman and Naturalis general director E. van
Huis (Naturalis) accompanied the expedition participants in the field. J. Gunsalam and
P. Jilan (Sabah Parks Board of Trustees) officiated the opening and closing ceremony,
respectively. P. Basintal, E. van Huis and E. Smets supervised the expedition as directors
for the organizing institutions. Media coverage and communications were facilitated by
J. van Alphen, A. Mohd. R. P. Dahlan, K. de Greef, A. Kromhout, J. Schilthuizen,
E. E. Soudi, L. Stek, A. Taminiau, and M. Z. Abdul Wahab. Sabah Parks staff members
L. Apin, B. Busin, B. Butit, J. Gampoyo, G. Gangko, B. Gangku, S. Gangku, P. Gimpiton,
M. Gunggutou, T. Gunggutou, G. Gunsalam, J. Guntabid, I. Isnain, K. Ag. Jalil, Y. Johalin,
R. M. Karim, Y. Kumin, D. Laban, A. Lahi, J. Lapidin, M. Latim, N. Maidin, N. Majuakim,
R. Miadin, Y. Miki, M. Moguring, H. Mujih, F. Simin, K. C. Sion, D. Sumbin, D. Tingoh,
E. Yakin, were invaluable for all manner of logistics and other support before, during,
and after the expedition, in the field and at the stations and administrative offices. For
the Forest Research Centre researchers, J. B. Dawat, M. Gumbilil, A. J. Jaimin, Jei.
Jumian, Jem. Jumian, J. L. Yukang, P. J. Miun, M. A. T. Mustapha, and B. Saludin assisted
in the field. T. Siew of Borneo Indah Sdn. Bhd. was the local supplier for consumables
and field equipment. We thank the ESEB Outreach Fund and the Treub Foundation for
funding outreach activities in Kinabalu Park and the Crocker Range Park. N. Raes
helped with the niche modelling.
Author Contributions M. Sch., V.S.F.T.M., M.Sp., M.M.B., C.B.M., L.E.B., K.T.C.A.P., J.N.,
R.R., and M.L. conceived and guided the study. M.Sch. and V.S.F.T.M. wrote the paper.
K.H., F.S. and K.B. administrated all samples and sequences. K.H. and L.E.B. were
responsible for DNA sampling in the field. V.S.F.T.M., A.A., N.A., A.B., P.-P.C., A.Y.C.C., R.D.,
H.F., C.F.-v.S., J.G., R.G., P.H., P.I., I.I., M.J., H.K., E.K., P.K., F.L., R.J.M., L.N.M., N.N., J.T.P.,
H.R., S.S., A.S., R.M.S., P.-S.S., H.S., N.S., J.B.S., M.Sul., S.Sum., J.v.T., F.Y.Y.T., B.E.Y., C.B.M.,
R.R. and M.Sch. collected material in the field and identified it following current
taxonomy. K.H., V.S.F.T.M., H.d.B., F.A.A.F., J.G., B.G., P.H., S.B.J., S.N., M.St., D.C.T. and
M.Sch. conducted the analyses.
Author Information GenBank accession numbers for newly determined sequences
are: KF369344, KF492848, KF839944–KF839949, KM378672–KM378719,
KM489525–KM489544, KM982697–KM982715, KP152323–KP152394,
KP978313–KP979097, KR002164–KR002181, KR030167–KR030238 and
KR232819–KR232836. A large portion of the data is also publicly available on BOLD
(www.boldsystems.org), as dataset DS–KINA (http://dx.doi.org/10.5883/DS-KINA).
Voucher specimens have been archived in public natural history collections. Reprints
and permissions information is available at www.nature.com/reprints. The authors
declare no competing financial interests. Readers are welcome to comment on the
online version of the paper. Correspondence and requests for materials should be
addressed to M.Sch. (Menno.Schilthuizen@naturalis.nl).
3 5 0 | N AT U R E | VO L 5 2 4 | 2 0 AU G U S T 2 0 1 5
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Macmillan Publishers Limited. All rights reserved
LETTER RESEARCH
METHODS
No statistical methods were used to predetermine sample size. The experiments
were not randomized and the investigators were not blinded to allocation during
experiments and outcome assessment.
Expedition. Material was sampled chiefly between September 10th and 25th,
2012, by the participants of the Crocker Range/Kinabalu Scientific Expedition,
which was conceived, organized, funded and conducted jointly by Sabah Parks
(Malaysia) and Naturalis Biodiversity Center (The Netherlands). The expedition
was set up with the explicit aim to investigate evolutionary patterns of endemism
(see main text), and participants were selected to maximize taxon coverage and
ecological diversity. The 47 expedition members were asked to identify one or
more congeneric species complexes (hereafter termed ‘genera’) within their taxon
of expertise that included high elevation endemics and preferably also more widespread lowland species (although there is a possibility that this approach would
leave out any monotypic endemics, in the groups studied by us, such species are
not known). These, plus outgroup species, were then sampled (using taxonspecific methods; see Supplementary Table 2 for further details) at eight expedition
stations located at a range of elevations (Fig. 1), and also in additional locations in
both parks and their vicinity. Data on time, latitude and longitude, elevation, and
habitat were collected with each sample. Material was subsampled for DNA analysis, mostly in the field, by preserving tissues or entire organisms, usually either
in pure ethanol or in silica gel (see Supplementary Table 2 for taxon-specific
subsampling and storage). In the case of fungi, mycelial DNA was obtained by
bulk extraction from composite soil cores (see Supplementary Table 2 and below).
In addition to the data collected during the expedition, the expedition members
were asked to provide a complete assessment of elevational and geographical
distribution for each of the species within their taxon of expertise, based on
published sources and previous collections.
Molecular analysis. Upon arrival in the Naturalis DNA barcoding facility, subsamples were processed in a semi-automated way. DNA extractions on animal
material were performed on either tissue samples or individual arthropod legs, or
using whole arthropods in a non-destructive extraction method. DNA was
extracted using the NucleoMag 96 Tissue kit (Macherey-Nagel Gmbh & Co.,
Düren, Germany) on the KingFisher Flex magnetic particle processor (Thermo
Scientific). DNA extractions on plant tissue were performed on dried leaf samples,
using the NucleoMag 96 Plant kit (Macherey-Nagel Gmbh & Co., Düren,
Germany). The KingFisher Flex protocols were slightly adjusted from the manufacturer’s protocol (http://www.thermoscientific.com) to include longer mixing of
beads with lysed sample and a drying step before elution. A volume of 150 ml was
used for elution in both animal and plant samples. Soil samples containing fungal
mycelia were processed by pooling 40 cores (for sampling details, see
Supplementary Table 2), resulting in a composite soil sample for each site.
Genomic DNA was extracted from 1 g of this sample using the NucleoSpin Soil
kit (Macherey-Nagel Gmbh & Co., Düren, Germany), according to the manufacturer’s protocol. For each sample DNA extraction was carried out twice and
replicates were combined.
For each specimen, the accepted barcode marker for its taxon was sequenced, in
many cases augmented with one or more other phylogenetically informative loci.
Supplementary Tables 1 and 2 provide lists of the loci and primers used for each
genus included in the study. Where relevant for outgroup comparison or further
geographic resolution, we then obtained additional sequences from Borneo or
elsewhere from GenBank or from our own, unrelated studies. GenBank accession
codes for these are given in Supplementary Table 2. After sequencing, (remains of)
voucher specimens were mostly deposited in the collections of Sabah Parks and/or
Naturalis Biodiversity Center. Voucher collection codes are listed in Supplementary Table 2.
PCR reactions generally contained 18.75 ml ultrapure H2O, 2.5 ml 103 PCR
buffer, 1.0 ml 10 mM of each primer, 0.5 ml 2.5 mM dNTPs and 0.25 ml 5U ml21
Qiagen Taq. Most PCRs were performed using an initial denaturation step of 180 s
at 94 uC, followed by 40 cycles of 15 s at 94 uC, 30 s at 50 uC and 40 s at 72 uC,
and ended with a final extension of 300 s at 72 uC and pause at 12 uC.
Bi-directional Sanger sequencing was performed at either Macrogen (http://
www.macrogen.com) or BaseClear (http://www.baseclear.com). Sequences were
edited manually (primers trimmed off and obvious reading errors corrected) using
Sequencher 4.10.1 (Gene Codes Corporation). For the fungal soil samples, the
amplicon library was sequenced using an Ion 318TM Chip in an Ion Torrent
Personal Genome Machine (PGM; Life Technologies, Guilford, CT, USA). PCR,
sequencing, raw data filtering and all bioinformatic analyses were performed as
described in detail previously26. From these fungal soil sequences, we selected nonredundant sequences of the ectomycorrhizal genus Cortinarius and the arbuscular
mycorrhizal genus Glomus because they were distributed along the entire altitudinal range of our sampling.
G2015
Phylogenetic analysis. We performed initial exploratory alignment and created
neighbour-joining trees. This allowed an assessment of individuals that (on the
basis of cursory morphological examination) had been included as potential
(undescribed) members of the species complexes of choice. In some cases, the
sequence analysis showed that these individuals were in fact unrelated and such
sequences were then removed before further analysis. Then, using Geneious (version 6.0.5; created by Biomatters; available from http://www.geneious.com/) as a
workbench, sequence data were aligned with MUSCLE25. We ran ModelTest27 to
determine, using Akaike Information Criterion (AIC), the best model of nucleotide substitution per alignment, for each genetic marker separately. We then
performed a Bayesian analysis using MrBayes 3.2.2 (ref. 28) with settings for
multiple markers unlinked, running two replicates of a minimum of 107 generations each. Convergence was checked in Tracer (v1.5; ref. 29) and, after discarding
a 25% burn-in, the resulting majority-rule consensus trees were preserved. For the
fungal data sets, multiple sequence alignments were built using MUSCLE and, due
to the large size of these data sets, phylogenetic analyses of maximum likelihood
(ML) were carried out in Garli 2.0 (ref. 30) using the GTR1I1G model with
estimated values of the alpha parameter of the gamma distribution of variable
sites (G) and proportion of invariable sites (I). Clade support was assessed by nonparametric bootstrap analyses with 100 pseudo-replicates.
Molecular dating. The times of divergence of Mount Kinabalu endemics from
their most closely related extant relatives were estimated with a molecular clock
approach. We included not only our own data, but also incorporated published
studies on genera other than the ones we sampled. For each genus, taxon sampling
and molecular data used are specified in Supplementary Table 4. All data sets
were assembled in Geneious (ver. 5.5.6; created by Biomatters; available from
http://www.geneious.com/). Data sets were pruned to contain a single taxon per
species by selecting a random sequence from each species. Sequence alignments
were obtained with the MAFFT (ver. 6.814b) alignment tool implemented in
Geneious. Divergence time estimates were obtained using a relaxed molecular
clock approach with BEAST (ver. 2.1.3; ref. 31). For each DNA region used, an
unlinked substitution model was implemented as selected with jModeltest (ver.
2.1.5; ref. 27) under the AIC. For the tree prior, a Yule birth rate prior was selected
with a flat prior on the Yule birth rate. A single clock and tree model was used for
each analysis. All analyses were run with an uncorrelated log-normal clock model,
to which an exponential prior was assigned for both the mean (ucldMEAN; mean
set at 10.0) and the standard deviation (ucldStdev; mean set at 0.33). Time calibration was done using: (1) fossil constraints; (2) secondary calibration points; or
(3) substitution rates, depending on the information available for each particular
genus. In cases where suitable fossil or secondary calibration information was not
available, we used a priori information about the substitution rate of one of the
gene partitions—as opposed to the ‘fix the mean substitution rate’ option across all
partitions—to optimize the analyses. The full details on calibration methods used
for each taxon are given in Supplementary Table 5. For each run, posterior distributions of parameters were approximated using a Markov chain Monte Carlo
analysis of 5 3 107 generations, sampling every 5,000 generations, discarding a
burn-in of 5 3 106 generations (10%). Convergence of the chains was checked by
evaluating the ESS values of each parameter with Tracer v1.6.
Biogeographical, elevational and vegetation zone analyses. For each genus, an
independent estimation of the dispersal neighbourhood size was obtained from
the spatial ecology literature on the genus concerned or related genera, and/or
expert knowledge. We used this information to classify dispersal neighbourhood
(two standard deviations for the distribution of distances between birth and
reproduction for individuals of a certain species) in the genus in question as ‘small’,
,1 km (mostly flightless animals), ‘medium’, 1–100 km (flying or ballooning
animals, and plants dispersed by flying animals), or ‘large’, .100 km (plants
and fungi with very small wind-dispersed seeds or spores). An overview of
dispersal assessments is in Supplementary Table 3.
Ancestral ranges were estimated for each taxon group under maximum likelihood with BioGeoBears32 using the three-parameter DEC1J model. The ultrametric tree from the Bayesian relaxed molecular clock analysis was used as input
tree. This tree was pruned to include the clade with the endemic species and at least
one deeper node (for most groups two deeper nodes were included). Each species
was scored to be absent or present in Mount Kinabalu (K), Borneo (B), and the rest
of the world (W). For each group the analysis was run with equal probability for
exchange between the three areas over the entire diversification time of the tree.
The maximum number of areas was assigned as the maximum number of areas
observed in the extant taxa (either 2 or 3). The optimizations, with the ancestral
range with the highest likelihood for each node, are shown in Extended Data
Figs 7–9). We classify a ‘W’ to ‘K’ or ‘KW’ shift in the lineage leading to a species
endemic to Kinabalu as ‘eccentric endemism’. All other ancestral ranges leading
to Kinabalu endemics are scored as ‘centric’.
Macmillan Publishers Limited. All rights reserved
RESEARCH LETTER
For each genus sampled during the expedition that showed centric endemism,
we added the elevation at which it had been collected as a continuous character. In
BayesTraits 2.0 (ref. 33) we reconstructed ancestral states for elevation at the node
leading to the endemic species and its sister clade using the continuous random
walk model which implements a generalized least squares model for continuously
varying traits. The elevation of the most-recent common ancestor of the node of
interest was inferred using a MCMC approach on a set of 2,700 trees randomly
sampled after the phylogenetic inference with MrBayes (excluding burn-in). The
MCMC chain of BayesTraits was run for 106 generations, discarding the results
sampled during the first 105 generations as burn-in. We then inspected whether
the current range of elevation of the endemic species stretches beyond the 95%
credible interval for the most-recent common ancestor. If it stretches above this
interval, we considered this indicative of a ‘bottom-up’ scenario, whereas the
reverse would suggest a ‘top-down’ scenario. The results are summarized in
Supplementary Table 6.
In parallel with the elevational analysis, we conducted an analysis in which we
coded the vegetation belt(s) as taxon traits. We used the zones defined for Mt.
Kinabalu in ref. 19, namely: (i) lowland vegetation (below 600 m); (ii) hill vegetation (600–1,200 m); (iii) lower montane vegetation (1,200–2,000 m); (iv) upper
montane vegetation (2,000–2,800 m); (v) subalpine vegetation (2,800–3,400 m);
(vi) upper subalpine vegetation (3,400–3,700 m); (vii) alpine vegetation (above
3,700 m). The probabilities at each vegetation belt for the most-recent common
ancestor of the node leading to the endemic clade and its sister group were inferred
with the continuous-time Markov model for discrete data implemented in
BayesTraits 2.0. The same input trees were used as for the elevation reconstruction,
and the MCMC was run for 106 generations, discarding the results sampled during
the first 105 generations as burn-in. The resulting probabilities are shown in
Supplementary Table 7.
Geological summary. The following is based on refs 15,34 and R. Hall, personal
communication, 2014.
Orogeny in the region began at about 23 million years ago (Mya) as a result of
the northward movement of the Australian plate leading to the collision of
Australia and Southeast Asia in what today is eastern Indonesia. Orogeny in the
Kinabalu area began at about 20 Mya after collision of north Borneo with the
South China continental crust. This led to the emergence of most of Sabah. Soon
G2015
after this emergence much of Sabah became submerged, although a north–southoriented mountain belt formed of tightly folded mudstones and sandstones (the
future Crocker Range) remained. At the same time, the climate changed from
seasonal to ever-wet. Mapping of former shelf edges offshore shows that later the
Crocker Range widened with time, implying that it became higher in its central
parts. Between 8 and 7 Mya a granitic body intruded the crust and cooled rapidly
from ,7 to 5 Mya. Melting could have resulted from a build-up of heat from
radioactive decay in the deep crust, or from decompression melting following
extension. After 6 Mya (the precise timing and duration is not known) the
area (including the surrounding Crocker Range) rose further, elevating to the
point that it was glaciated recently, possibly after a lithospheric root detached
and sank into the deeper mantle, leading new mantle material to flow into the
vacated space below the Crocker Range. Extensive glacial weathering of the summit suggests the mountain had reached its present elevation by at least 1 Mya.
The Pinosuk gravels on Kinabalu’s south-eastern slope are the accumulated erosional debris of young glaciation. Today, the mountain is still rising by 0.5 mm
per year.
26. Geml, J. et al. Large-scale fungal diversity assessment in the Andean Yungas
forests reveals strong community turnover among forest types along an altitudinal
gradient. Mol. Ecol. 23, 2452–2472 (2014).
27. Posada, D. & Crandall, K. A. Modeltest: testing the model of DNA substitution.
Bioinformatics 14, 817–818 (1998).
28. Ronquist, F. & Huelsenbeck, J. P. MrBayes 3: Bayesian phylogenetic inference
under mixed models. Bioinformatics 19, 1572–1574 (2003).
29. Rambaut, A. & Drummond, A. J., Tracer v1.5. http://beast.bio.ed.ac.uk/Tracer
(2009).
30. Zwickl, D. J. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large
Biological Sequence Datasets under the Maximum Likelihood Criterion (The University
of Texas, Austin, 2006).
31. Bouckaert, R. et al. BEAST 2: a software platform for Bayesian evolutionary
analysis. PLOS Comput. Biol. 10, e1003537 (2014).
32. Matzke, N. J. Probabilistic historical biogeography: new models for founder-event
speciation, imperfect detection, and fossils allow improved accuracy and modeltesting. Front. Biogeogr. 5, 242–248 (2013).
33. Meade, A. & Pagel M. BayesTraits, version 2.0. http://www.evolution.rdg.ac.uk
(2015).
34. Hall, R. et al. The Geology of Mount Kinabalu (Sabah Parks, 2008).
Macmillan Publishers Limited. All rights reserved
LETTER RESEARCH
Anura - Kalophrynus
Balsaminaceae - Impatiens
AB611973 Phrynella pulchra
DQ147849 I. hians Africa
AB611921 Kalophrynus pleurosgma
DQ147825 I. chinensis (China, Yunnan)
1
RBINS.15992 K. sp.1
DQ147850 I. hawkeri (Papua New Guinea)
1
RBINS.15993 K. sp.2
DQ147868 I. platypetala (Indonesian, Bali)
RBINS.15994 K. sp.2
0.65
DQ147892-I.walleriana-African_origin
1
RBINS.15995 K. sp.2
1
RBINS.15998 K. sp.2
1
tbd-I.usambarensis
1
tbd-I.serpenstbd-I.thamnoidea-
1
RBINS.15999 K. sp.2
tbd-I.pseudohamata-
1
RBINS.16000 K. sp.2
DQ147816 I.balsamina (Indian)
RBINS.16001 K. sp.2
1
DQ147832 I. cuspidata (India)
0.68
RBINS.16006 K. sp.2
1
1
DQ147845 I. flaccida (India)
0.78
1
DQ147854 I. lafolia (Indian)
RBINS.16007 K. sp.2
DQ147814 I. aureliana (China, Yunnan)
RBINS.16009 K. baluensis
1
DQ147869 I. poilanei (Vietnam)
RBINS.16010 K. baluensis
DQ147839 I. eberhardi (Vietnam)
1
1
RBINS.16043 K. baluensis
FJ826636 I. chevalieri (Vietnam)
RBINS.16063 K. baluensis
CM0028 I. kinabaluensis
1
CM0015 I. kinabaluensis
RBINS.16096 K. baluensis
1
RBINS.16023 K. baluensis
CM0025 I. kinabaluensis
FL007 I. kinabaluensis
AB611913 K. interlineatus
FL033 I. kinabaluensis
0.99
AB611931 Metaphrynella pollicaris
FL073 I. kinabaluensis
AB611939 Metaphrynella sundana
0.0070
0.06
Aranea - Myrmarachne
1
0.79
0.75
EU815599 Ligonipes sp. (Australia)
NMF2012-01399.PK357 M.cornuta
NMF2012-01399.PK373 M. cornuta
AY297412 M. assimilis (Philippines)
0.84
1
JX145678 M. evidens (Gabon)
JX145679 M. foenisex (Gabon)
NMF2012-01399.PK210 M. hanoii
JX145676 M. cf. gedongensis (Malaysia)
1 NMF2012-01399.PK068 M. malayana
NMF2012-01399.PK069 M. malayana
NMF2012-01399.PK249 M. malayana
NMF2012-01399.PK254 M. malayana
NMF2012-01399.PK259 M. malayana
NMF2012-01399.PK261 M. malayana
0.86
NMF2012-01399.PK262 M. malayana
NMF2012-01399.PK267 M. malayana
NMF2012-01399.PK285 M. malayana
NMF2012-01399.PK291 M. malayana
NMF2012-01399.PK293 M. malayana
0.99
0.85 NMF2012-01399.PK298 M. malayana
NMF2012-01399.PK301 M. malayana
NMF2012-01399.PK303 M. malayana
NMF2012-01399.PK305 M. malayana
0.87
NMF2012-01399.PK307 M. malayana
NMF2012-01399.PK308 M. malayana
NMF2012-01399.PK311 M. malayana
NMF2012-01399.PK312 M. malayana
NMF2012-01399.PK315 M. malayana
NMF2012-01399.PK317 M. malayana
1 NMF2012-01399.PK137 M. malayana
NMF2012-01399.PK144 M. malayana
NMF2012-01399.PK158 M. malayana
0.68
1
NMF2012-01399.PK083 M. malayana
1
NMF2012-01399.PK097 M. malayana
1 NMF2012-01399.PK098 M. malayana
NMF2012-01399.PK103 M. malayana
NMF2012-01399.PK109 M. malayana
NMF2012-01399.PK116 M. malayana
NMF2012-01399.PK245 M. malayana
NMF2012-01399.PK248 M. malayana
NMF2012-01399.PK250 M. malayana
NMF2012-01399.PK263 M. malayana
NMF2012-01399.PK265 M. malayana
NMF2012-01399.PK266 M. malayana
0.98
NMF2012-01399.PK286 M. malayana
NMF2012-01399.PK255 M. malayana
NMF2012-01399.PK290 M. malayana
NMF2012-01399.PK316 M. malayana
NMF2012-01399.PK304 M. malayana
NMF2012-01399.PK306 M. malayana
NMF2012-01399.PK320 M. malayana
1
NMF2012-01399.PK051 M. sp.4
NMF2012-01399.PK052 M. sp.4
1
NMF2012-01399.PK183 M. sp.3
NMF2012-01399.PK206 M. sp.3
0.5
NMF2012-01399.PK256 M. nov.sp.2
1
NMF2012-01399.PK257 M. nov.sp.2
NMF2012-01399.PK260 M. nov.sp.2
0.54
NMF2012-01399.PK264 M. nov.sp.2
0.73
0.72
1
0.4
Begoniaceae - Begonia
DCT07-24 B. masoniana (China)
DCT08-102 B. kingiana (Malaysia)
PH115 B. spec2
LLF141 B. amphioxus
0.57
DCT09-03 B.pendula (Malaysia)
1
FL066 B.cauliflora
1
FL065 B.cauliflora
0.89
SNP25535_1 B.vaccinioides
1
SNP25535_2 B.vaccinioides
FL040 B. burbidgei
1
1
DCT07-26 B. burbidgei
FL062 B. spec1
FL075 B. imbricata
0.98
FL071 B. beryllae
FL074 B. cf. beryllae
0.0030
NMF2012-01399.PK050 M. nov.sp.1
NMF2012-01399.PK036 M. christae
NMF2012-01399.PK073 M. sp.5
1
NMF2012-01399.PK080 M. sp.5
NMF2012-01399.PK081 M. sp.5
NMF2012-01399.PK077 M. sp.5
NMF2012-01399.PK003 M. mariaelenae
NMF2012-01399.PK005 M. mariaelenae
NMF2012-01399.PK009 M. mariaelenae
NMF2012-01399.PK010 M. mariaelenae
NMF2012-01399.PK017 M. mariaelenae
NMF2012-01399.PK027 M. mariaelenae
NMF2012-01399.PK011 M. mariaelenae
NMF2012-01399.PK012 M. mariaelenae
NMF2012-01399.PK013 M. mariaelenae
NMF2012-01399.PK014 M. mariaelenae
NMF2012-01399.PK015 M. mariaelenae
NMF2012-01399.PK016 M. mariaelenae
NMF2012-01399.PK024 M. mariaelenae
NMF2012-01399.PK026 M. mariaelenae
NMF2012-01399.PK007 M. mariaelenae
NMF2012-01399.PK018 M. mariaelenae
NMF2012-01399.PK019 M. mariaelenae
NMF2012-01399.PK008 M. mariaelenae
NMF2012-01399.PK020 M. mariaelenae
NMF2012-01399.PK022 M. mariaelenae
NMF2012-01399.PK023 M. mariaelenae
NMF2012-01399.PK174 M. mariaelenae
NMF2012-01399.PK175 M. mariaelenae
NMF2012-01399.PK179 M. mariaelenae
0.96
NMF2012-01399.PK214 M. mariaelenae
NMF2012-01399.PK216 M. mariaelenae
NMF2012-01399.PK222 M. mariaelenae
NMF2012-01399.PK224 M. mariaelenae
NMF2012-01399.PK246 M. mariaelenae
NMF2012-01399.PK178 M. mariaelenae
NMF2012-01399.PK191 M. mariaelenae
NMF2012-01399.PK247 M. mariaelenae
NMF2012-01399.PK198 M. mariaelenae
NMF2012-01399.PK200 M. mariaelenae
NMF2012-01399.PK213 M. mariaelenae
NMF2012-01399.PK215 M. mariaelenae
NMF2012-01399.PK217 M. mariaelenae
NMF2012-01399.PK219 M. mariaelenae
NMF2012-01399.PK221 M. mariaelenae
NMF2012-01399.PK220 M. mariaelenae
NMF2012-01399.PK223 M. mariaelenae
NMF2012-01399.PK226 M. mariaelenae
NMF2012-01399.PK227 M. mariaelenae
NMF2012-01399.PK244 M. mariaelenae
NMF2012-01399.PK252 M. mariaelenae
NMF2012-01399.PK177 M. mariaelenae
NMF2012-01399.PK186 M. mariaelenae
NMF2012-01399.PK225 M. mariaelenae
NMF2012-01399.PK352 M. mariaelenae
Athyriaceae - Athyium
1
EU329066andEU329109-Deparia.lobatocrenata-Japan
EU329064andEU329107-Deparia.petersenii-Japan
EU329065andEU329108-Deparia.conilii-Japan
0.6
0.91
1
1
0.99
0.99
3500-4000m
3000-3500m
2500-3000m
2000-2500m
1500-2000m
1000-1500m
500-1000m
0-500m
0.03
EU329068 EU329111 Diplazium hachijoense (Japan)
0.95
1
EU329067 EU329110 Diplazium nipponicum (Japan)
e4002185646 Diplazium simplicivenium
EU329047 EU329090 A. sheareri (Japan)
EU329029 EU329073 A. cuspidatum (China)
EU329042 EU329085 A. niponicum (Japan)
1 EU329063 EU329106 Cornopteris decurren alata (Japan)
EU329060 EU329103 Cornopteris christenseniana (Japan)
1
1 EU329062 EU329105 Cornopteris crenulatoserrulata (Japan)
EU329061 EU329104 Cornopteris christenseniana (Japan)
0.69 EU329038 EU329081 A. melanolepis (Japan)
1
EU329027 EU329071 A. brevifrons (Japan)
EU329032 EU329076 A. filix-femina-culvated
EU329041 EU329084 A. nikkoense (Japan)
1
EU329055 EU329098 A. yokoscense (Japan)
1
EU329036 EU329079 A. kirisimaense (Japan)
1 0.7
EU329050 EU329093 A. tashiroi (Japan)
0.96
EU329056 EU329099 A. yokoscense var. dilatatum (Japan)
EU329045 EU329088 A. rupestre (Japan)
EU329026 EU329070 A. atkinsonii (Japan)
EU329051 EU329094-A.tozanense (Japan)
e4002185620 A. clemensiae
e4002185621 A. clemensiae
0.85
0.64
e4002185526 A. clemensiae
e4002185538 A. clemensiae
0.99
EU329030 EU329074 A. deltoidofrons (Japan)
1
EU329052 EU329095 A. vidalii (Japan)
0.96
0.92 EU329040 EU329083 A.neglectum (Japan)
EU329039 EU329082 A. nakanoi (Japan)
e4002185631 A. amoenum
e4002185655 A. amoenum
1 e4002185691 A. amoenum
0.81
e4002185515 A. amoenum
e4002185539 A.amoenum
e4002185551 A. amoenum
EU329025 EU329069 A. arisanense (Japan)
0.75
EU329031 EU329075 A. eremicola (Japan)
1
EU329054 EU329097 A. wardii (Japan)
EU329059 EU329102 A. x tokashikii (Japan)
0.68
EU329046 EU329089 A. setuligerum (Japan)
0.91
1
EU329028 EU329072 A. clivicola (Japan)
0.94 EU329048 EU329091 A. subrigescens (Japan)
EU329037 EU329080 A. kuratae (Japan)
0.57
EU329053 EU329096 A. viridescenpe (Japan)
0.99
1 EU329057 EU329100 A. x akiense (Japan)
0.75 EU329044 EU329087 A. otophorum (Japan)
EU329043 EU329086 A. oblitescens (Japan)
EU329049 EU329092 A. strigillosum (Japan)
1
EU329035 EU329078 A. iseanum var. angussectum (Japan)
1
1 EU329058 EU329101 A. x hisatsuanum (Japan)
EU329034 EU329077 A. iseanum (Japan)
Extended Data Figure 1 | Phylogenetic reconstructions for Anura, Araneae, Athyriaceae, Balsaminaceae and Begoniaceae. Details of materials and methods
used are given in Supplementary Table 2.
G2015
Macmillan Publishers Limited. All rights reserved
RESEARCH LETTER
Cortinariaceae - Cortinarius
GU234083 Hebeloma mesophaeum
Coleoptera - Ptomaphaginus
RMNH.INS.549243 Prionochaeta harmandi (Japan)
1 RMNH.INS.555623 Ptomaphaginus ater
RMNH.INS.555624-Ptomaphaginus ater
RMNH.INS.555632 Ptomaphaginus nr. fagei
1
RMNH.INS.555633 Ptomaphaginus.nr. fagei
0.88
RMNH.INS.555618 Ptomaphaginus n.sp. bryan complex
RMNH.INS.555621 Ptomaphaginus n.sp. bryan complex
1
RMNH.INS.555620 Ptomaphaginus n.sp. bryan complex
RMNH.INS.555622 Ptomaphaginus n.sp. bryan complex
RMNH.INS.555619 Ptomaphaginus n.sp. bryan complex
RMNH.INS.555607 Ptomaphaginus latescens
1 RMNH.INS.555591 Ptomaphaginus bryanoides
RMNH.INS.555594 Ptomaphaginus bryanoides
RMNH.INS.555645 Ptomaphaginus bryanoides
RMNH.INS.555677 Ptomaphaginus bryanoides
RMNH.INS.555600 Ptomaphaginus bryanoides
RMNH.INS.555598 Ptomaphaginus bryanoides
RMNH.INS.555599 Ptomaphaginus bryanoides
0.79
1
RMNH.INS.549268 Ptomaphaginus bryanoides
RMNH.INS.555644 Ptomaphaginus bryanoides
0.98
RMNH.INS.555637 Ptomaphaginus bryanoides
RMNH.INS.549270 Ptomaphaginus bryanoides
RMNH.INS.549271 Ptomaphaginus bryanoides
1
RMNH.INS.549269 Ptomaphaginus bryanoides
RMNH.INS.555626 Ptomaphaginus bryanoides
1RMNH.INS.555627 Ptomaphaginus bryanoides
0.86
RMNH.INS.555628 Ptomaphaginus bryanoides
1
RMNH.INS.555625 Ptomaphaginus bryanoides
RMNH.INS.555610 Ptomaphaginus similipes
RMNH.INS.555609 Ptomaphaginus similipes
1
RMNH.INS.555616 Ptomaphaginus similipes
RMNH.INS.555612 Ptomaphaginus similipes
0.92
RMNH.INS.555593 Ptomaphaginus similipes
RMNH.INS.555592 Ptomaphaginus similipes
RMNH.INS.555681 Ptomaphaginus similipes
1
1
RMNH.INS.549263 Ptomaphaginus similipes
RMNH.INS.555680 Ptomaphaginus similipes
1
RMNH.INS.555685 Ptomaphaginus similipes
RMNH.INS.555611 Ptomaphaginus c.f. lamanus
RMNH.INS.555601 Ptomaphaginus kinabaluensis
0.85
RMNH.INS.555631 Ptomaphaginus kinabaluensis
RMNH.INS.555629 Ptomaphaginus kinabaluensis
RMNH.INS.555602 Ptomaphaginus kinabaluensis
1
RMNH.INS.555604 Ptomaphaginus kinabaluensis
RMNH.INS.555605 Ptomaphaginus kinabaluensis
RMNH.INS.555603 Ptomaphaginus kinabaluensis
RMNH.INS.555606 Ptomaphaginus kinabaluensis
1
1
0.95
0.08
Dicranaceae - Dicranoloma
AF146376 AF144112 Mesotus celatus
AF135067 AF140696 Dicnemon calycinum
AF129587 AF144113 Dicranum polysetum
0.73
AF135075 AF144116 Paraleucobryum enerve
0.76
KF423995 KF423641 Holomitrium arboreum
1
KF423992 KF423638 Holomitrium crispulum
DQ462604 DQ464186 D. chilense (Chile)
DQ462594 DQ464193 D. billarderi (New Zealand)
DQ462595 DQ464194 D. billarderi (Chile)
1
0.95
1
DQ462596 DQ464196 D. billarderi (Rwanda)
DQ462597 DQ464197 D. billarderi (Reunion)
1
e4002189780 D. blumii
0.97
e4002189776 D. blumii
e4002189814 D. blumii
0.65
DQ462598 DQ464188 D. robustum (New Zealand)
1
DQ462599 DQ464189 D. robustum (New Zealand)
1
DQ462600 DQ464190 D. robustum (Chile)
DQ462601 DQ464191 D. robustum (Chile)
KF423978 KF423621 D. cylindrothecium (Russia)
L0092869 e4002189708 D. diaphanoneurum (Australia)
0.91
1 DQ462607 DQ464184 D. menziesii (New Zealand)
DQ485179 D. menziesii (Australia)
1
e4002189763 D. brevisetum
0.57
e4002189823 D. braunii
e4002189740 D. braunii
1
e4002189766 D. braunii
1
1
e4002189764 D. braunii
e4002189788 D. brevisetum
MS4_e4002189774 D. brevisetum
MS9_e4002189739 D. brevisetum
0.99
MS2_e4002189750 D. brevisetum
MS3_e4002189762 D. brevisetum
0.86
DQ485176 D. leichhardi (Australia)
e4002189743 D. havilandii
0.84
e4002189755 D. havilandii
e4002189767 D. havilandii
0.96
e4002189779 D. havilandii
L0856682 e4002189720 D. havilandii
DQ462605 DQ485175 D. dicarpum (New Zealand)
0.66
1 0.84
L0856640 e4002189709 D. sp. (Indonesia)
L0093198 e4002189685 D. reflexum (Indonesia)
1
e4002189775 D. reflexum
0.99 e4002189787_D_reflexum_Kinabalu_Sayap
0.99
DQ485178 D. fasciatum (Australia)
1 DQ462606 DQ464185 D. plurisetum (New Zealand)
DQ485174 D. plurisetum (New Zealand)
0.82
e4002189777 D. assimile
e4002189789 D. assimile
1
e4002189741 D. assimile
e4002189802 D. assimile
e4002189765 D. assimile
1
e4002189742 D. assimile
e4002189790 D. assimile
e4002189815 D. assimile
e4002189791 D. assimile
e4002189768 D. assimile
e4002189827 D. assimile
0.02
Diptera - Diopsidae
RMNH.INS.557960 Eurydiopsis sarawakensis
RMNH.INS.557894 Teleopsis nr. quinqueguata
RMNH.INS.557959 Teleopsis nr breviscopium
1
1
RMNH.INS.555156 Teleopsis longiconus sp.n.
Teleopsis longiconus sp.n.V1
RMNH.INS.555159 Teleopsis nr. sexguata
0.88
0.89
RMNH.INS.555161 Cyrtodiopsis nr. dalmanni sp. 2
1
Cyrtodiopsis nr. dalmanni sp.1 IIX3
1
RMNH.INS.555162 Cyrtodiopsis nr. dalmanni sp. 1
0.98
RMNH.INS.555160 Teleopsis sabah sp. 1
RMNH.INS.555128 Teleopsis pallifacies
1
RMNH.INS.557968 Teleopsis pallifacies
1
0.87
RMNH.INS.555138 Teleopsis pallifacies
1
Teleopsis pallifacies IV5
RMNH.INS.557898 Teleopsis scapulistylus sp.n.
0.93
RMNH.INS.557932 Teleopsis pseudogracilifemur sp.n.
1
RMNH.INS.555116 Teleopsis pseudogracilifemur sp.n.
RMNH.INS.555122 Teleopsis pseudogracilifemur sp.n.
0.7
0.97
1
Teleopsis_gracilifemur sp.n. V2
0.98
RMNH.INS.555117 Teleopsis gracilifemur sp.n.
RMNH.INS.555127 Teleopsis gracilifemur sp.n.
RMNH.INS.557902 Teleopsis sabah sp.2
0.52
RMNH.INS.555141 Teleopsis nr. discrepans sp. C
1
1
Teleopsis discrepans XIII1
RMNH.INS.555146 Teleopsis nr. discrepans sp. A
1
RMNH.INS.557903 Teleopsis sp. 2
0.73
RMNH.INS.557945 Teleopsis nr. discrepans sp. B
0.02
3500-4000m
3000-3500m
2500-3000m
2000-2500m
1500-2000m
1000-1500m
500-1000m
0-500m
OTU 2041
OTU 15011
OTU 8218
GQ159827.1 Cornarius purpurascens
AY669520.1 Cornarius nanceiensis
OTU 5338
AY669521.1 Cornarius populinus
AY174797.1 Cornarius saginus
OTU 9222
OTU 14845
FJ039613.1 Cornarius balteatus
OTU 1594
GU233350.1 Cornarius anauensis
OTU 9813
OTU 27167
FJ039619.1 Cornarius herpecus
FJ039622.1 Cornarius herpecus
FJ039621.1 Cornarius herpecus
EU821686.1 Cornarius salor
GU233329.1 Cornarius aerugineoconicus
OTU 2542
AY033104.1 Cornarius elacapus
OTU 13359
OTU 1859
OTU 15334
AY669677.1 Cornarius fulvoconicus
AJ889977.1 Cornarius torvus
EU433388.1 Cornarius agathosmus
OTU 504
OTU 9276
OTU 8686
OTU 116
OTU 4229
OTU 1668
OTU 3529
OTU 10831
OTU 10378
OTU 5366
EU821656.1 Cornarius traganus
FJ039542.1 Cornarius serpes
FJ717541.1 Cornarius saniosus
OTU 1074
OTU 12791
AY669658.1 Cornarius umbrinolens
AY669667.1 Cornarius helvolus
FJ039572.1 Cornarius venustus
AY669670.1 Cornarius anthracinus
AY669688.1 Cornarius biformis
GQ159813.1 Cornarius saturninus
AY669687.1 Cornarius umbilicatus
OTU 2471
OTU 6606
OTU 12519
OTU 1496
OTU 26469
AY669681.1 Cornarius malachius
OTU 9572
OTU 601
OTU 26865
OTU 18561
OTU 25211
OTU 10559
AM713178.1 Cornarius assiduus
OTU 16806
DQ499466.1 Cornarius boulderensis
GQ159914.1 Cornarius fulvescens
AY669679.1 Cornarius subserpes
OTU 5651
OTU 11821
OTU 2564
AY669665.1 Cornarius hinnuleus
AY669673.1 Cornarius rubricosus
GQ159883.1 Cornarius candelaris
OTU 17537
OTU 11785
OTU 12030
FJ039708.1 Cornarius sp.
OTU 13067
GQ159774.1 Cornarius turibulosus
AY669686.1 Cornarius evernius
AF430292.1 Cornarius brunneus
EU266692.1 Cornarius genlis
AJ236072.2 Cornarius pholideus
OTU 9936
AY669607.1 Cornarius basipurpureus
AY669594.1 Cornarius callisteus
EU821663.1 Cornarius huronensis
AY669630.1 Cornarius cannarius
OTU 12419
EU821696.1 Cornarius vibralis
AF539734.1 Cornarius lividus
OTU 416
GQ159773.1 Cornarius valgus
OTU 14041
EU821684.1 Cornarius genlis
GU233333.1 Cornarius aegrotus
OTU 10420
OTU 14591
OTU 18368
OTU 11462
OTU 7233
OTU 5948
DQ097876.1 Cornarius callisteus
OTU 6025
OTU 5985
OTU 19
AF112147.1 Dermocybe austroveneta
AY669632.1 Cornarius walkeri
AF389160.1 Cornarius amoenus
AY669595.1 Cornarius rubellus
AJ236064.2 Cornarius rubellus
OTU 14254
OTU 3192
OTU 14516
GU233342.1 Cornarius picoides
OTU 13297
AY174782.1 Cornarius infractus
OTU 3972
OTU 14800
OTU 26181
OTU 727
OTU 14618
OTU 6126
OTU 4057
AY669583.1 Cornarius malicorius
FJ039596.1 Cornarius humboldtensis
OTU 3916
FJ039701.1 Cornarius sp.
GQ159873.1 Cornarius tubarius
OTU 17187
OTU 468
AY082608.1 Dermocybe cinnamomea
AY669585.1 Cornarius olivaceofuscus
FJ157089.1 Cornarius neosanguineus
FJ157116.1 Cornarius neosanguineus
OTU 580
OTU 14542
OTU 4810
OTU 27315
OTU 197
OTU 11469
OTU 4748
EU821667.1 Cornarius phoeniceus
FJ039591.1 Cornarius smithii
FJ039594.1 Cornarius idahoensis
AY669581.1 Cornarius palustris
GQ159882.1 Cornarius chrysolitus
FJ039601.1 Cornarius olivaceopictus
AF539707.1 Cornarius luteostriatulus
AF539708.1 Cornarius obscurooliveus
GU233323.1 Cornarius alienatus
OTU 12584
OTU 12602
AY669588.1 Cornarius collinitus
OTU 7973
OTU 12746
OTU 17155
OTU 16366
OTU 25865
OTU 25299
OTU 2634
OTU 21065
OTU 19102
OTU 18261
GU233334.1 Cornarius vitreopileatus
OTU 1813
DQ652235.1 Cornarius lustrabilis
OTU 1149
OTU 4508
OTU 7114
EU525980.1 Cornarius calyptratus
AY174787.1 Cornarius glaucopus
AY669558.1 Cornarius langei
AY669535.1 Cornarius argutus
AY669587.1 Cornarius delibutus
AY669612.1 Cornarius rotundisporus
AF539730.1 Cornarius austroturmalis
OTU 1023
OTU 2153
OTU 18981
OTU 19822
OTU 19034
OTU 26933
OTU 2553
OTU 17207
OTU 18659
OTU 26171
OTU 26541
OTU 23750
OTU 12474
OTU 2644
OTU 19460
OTU 9147
OTU 5013
OTU 9521
FJ039611.1 Cornarius duracinus
GQ159908.1 Cornarius pseudocandelaris
OTU 26194
OTU 7849
GQ159860.1 Cornarius velenovskyi
OTU 17175
OTU 19944
OTU 6677
OTU 12976
AY669656.1 Cornarius incisus
AY669655.1 Cornarius acutovelatus
FJ039606.1 Cornarius ceraceus
FJ157003.1 Cornarius acutus
OTU 3231
OTU 12440
AY669651.1 Cornarius cysdiocatenatus
OTU 8882
OTU 6053
AF539727.1 Cornarius pachynemeus
OTU 13501
OTU 17073
OTU 3195
OTU 18150
OTU 15546
OTU 17985
OTU 10720
OTU 16037
OTU 9069
OTU 18957
OTU 14593
OTU 22118
OTU 24443
OTU 3600
OTU 4725
OTU 11980
OTU 15329
OTU 9940
OTU 13013
OTU 8619
OTU 12349
OTU 12484
EU655655.1 Cornarius rapaceotomentosus
DQ663411.1 Cornarius sanc-felicis
EU655660.1 Cornarius insignibulbus
EU057001.1 Cornarius jardinensis
EU056976.1 Cornarius magnivelatus
OTU 26725
OTU 12377
OTU 19253
OTU 12260
OTU 752
EU660953.1 Cornarius cretax
OTU 5187
OTU 1410
OTU 15101
OTU 27038
OTU 14504
OTU 14517
OTU 4929
OTU 14916
OTU 14512
OTU 9017
OTU 2674
OTU 24339
OTU 18369
OTU 15128
AF539736.1 Cornarius olivaceobubalinus
OTU 4232
OTU 6233
OTU 3490
OTU 10798
OTU 2456
OTU 8407
OTU 18770
OTU 857
OTU 26840
OTU 3898
AY669654.1 Cornarius spilomeus
OTU 133
FJ039604.1 Cornarius ochrophyllus
OTU 7587
OTU 3280
OTU 3693
OTU 11718
OTU 5836
AY669596.1 Cornarius bolaris
OTU 8827
AY669645.1 Cornarius anomalus
EF420146.1 Cornarius sericeolazulinus
FJ039651.1 Cornarius anomalovelatus
OTU 4234
OTU 6434
GQ159887.1 Cornarius anomalovelatus
OTU 8855
OTU 10556
AY669646.1 Cornarius caninus
GQ159900.1 Cornarius rigens
AY669637.1 Cornarius schlerophyllarum
OTU 406
OTU 23850
5 changes
“up”
“mid”
“low”
Extended Data Figure 2 | Phylogenetic reconstructions for Coleoptera, Dicranaceae, Diptera and Cortinariaceae. Details of materials and methods used are
given in Supplementary Table 2.
G2015
Macmillan Publishers Limited. All rights reserved
LETTER RESEARCH
Ericaceae - Rhododendron
GU176637 AF394258 R. camtschacum
SNP21936 R. borneense
SNP21921 R. cuneifolium
SNP28514 R. cuneifolium
SNP28515 R. cuneifolium
0.53
SNP28516 R. cf. cuneifolium
SNP32302 R. ericoides
0.97
SNP32303 R. ericoides
SNP21925 R. simulans
SNP21906 R. rugosum
SNP21908 R. buri
SNP28504 R. rugosum
SNP28508 R. rugosum
0.99 0.62
SNP28510 R. rugosum
SNP32301 R. buxifolium
SNP32304 R. buxifolium
0.89 1
SNP32306 R. buxifolium
SNP32307 R. buxifolium
SNP21909 R cf. rugosum
SNP21912 R sp.
0.57 SNP21918 R. cf. rugosum
SNP21932 R. praetervisum
SNP21943 R. suaveolens
0.99
SNP21944 R. praetervisum
0.95
SNP21905 R. suaveolens
0.91
SNP21934 R. suaveolens
1
SNP21933 R. orbiculatum
1 SNP21955 R. orbiculatum
0.56
SNP21910 R. stapfianum
SNP21926 R. cf. stapfianum
0.89
SNP21914 R. suaveolens
1 SNP21929 R. suaveolens
SNP21919 R. javanicum
SNP21922 R. crassifolium
SNP32305 R. lowii
SNP28513 R. lowii
SNP21907 R. bagobonum
SNP21915 R. stenophyllum
0.91
SNP21927 R stenophyllum
0.87
SNP28505 R. stenophyllum
0.55
SNP28517 R. stenophyllum
SNP28518 R. sp.
SNP21917 R. sp.
SNP28509 R. acuminatum
0.5
SNP21913 R. fallacinum
SNP21920 R. fallacinum
1
SNP21928 R. fallacinum
SNP21931 R. fallacinum
0.99 SNP21945 R. fallacinum
SNP21956 R. fallacinum
SNP28502 R. fallacinum
SNP28503 R. fallacinum
SNP21911 R. exuberans
SNP21916 R p.
SNP21930 R x. planecostatum
SNP21935 R. javanicum
0.93
1 SNP21939 R. javanicum
SNP21904 R. crassifolium
SNP21923 R. crassifolium
SNP21937 R. crassifolium
1
SNP21938 R. crassifolium
SNP21940 R. crassifolium
SNP21941 R. crassifolium
Hirudinea - Tritetrabdella
0.76
HQ203161 P. pungens (Australia)
SP13407 H. sp.
SP13398 T. kinabaluensis kinabaluensis
SP13306 T. kinabaluensis kinabaluensis1
SP13383 T. kinabaluensis inobongensis
SP13382 T. kinabaluensis inobongensis
1
SP13381 T. kinabaluensis inobongensis
1
SP13380 T. kinabaluensis inobongensis
HQ203194 T. scandens (Thailand)
HQ322465 T. taiwana (Taiwan)
1
1
HQ322464 T. taiwana (Taiwan)
0.58
HQ322466 T. taiwana (Taiwan)
0.54
HQ203195 T. taiwana (China)
1
AB685259 T. taiwana (China)
1
HQ322468 T. taiwana (Taiwan)
HQ322469 T. taiwana (Taiwan)
0.99
HQ322463 T. taiwana (Taiwan)
HQ322467 T. taiwana (Taiwan)
0.04
Gastropoda - Philalanka
HQ171582-Zospeum exiguum (Slovenia)
HQ171529 Carychium mexicanum (USA)
SP13428 Ibycus rachelae
JX988066 Subulina octona
1
SP13507 Philalanka sp.1
1 SP13508 Philalanka sp.1
1
SP13509 Philalanka sp.1
SP13506 Philalanka sp.1
0.0070
1
1
SP13492 Philalanka sp.3
SP13511 Philalanka sp.3
Hemiptera - Rhagovelia
SP13510 Philalanka sp.2
0.97
RMNH.INS.555452 Mesovelia horvathi
SP13519 Philalanka thienemanni
RMNH.INS.555246 R. samardaca
RMNH.INS.555248 R. samardaca
SP13521 Philalanka thienemanni
RMNH.INS.555245 R. samardaca
SP13522 Philalanka thienemanni
1
RMNH.INS.555244 R. samardaca
1
SP13520 Philalanka thienemanni
1
RMNH.INS.555247 R. samardaca
SP13515 Philalanka thienemanni
RMNH.INS.555243 R. samardaca
SP13523 Philalanka thienemanni
RMNH.INS.555242 R. samardaca
RMNH.INS.555249 R. samardaca
SP13516 Philalanka thienemanni
RMNH.INS.555250 R. samardaca
SP13517 Philalanka thienemanni
1
RMNH.INS.555241 R. samardaca
0.54
SP13518 Philalanka thienemanni
RMNH.INS.555252 R. samardaca
RMNH.INS.555253 R. samardaca
0.05
RMNH.INS.555251 R. samardaca
0.97
RMNH.INS.555254 R. samardaca
RMNH.INS.555255 R. samardaca
0.97
RMNH.INS.555259 R. samardaca
RMNH.INS.555260 R. samardaca
RMNH.INS.555258 R. samardaca
RMNH.INS.555256 R. samardaca
RMNH.INS.555257 R. samardaca
RMNH.INS.555214 R. ranau
RMNH.INS.555215 R. ranau
0.99
RMNH.INS.555219 R. ranau
RMNH.INS.555217 R. ranau
RMNH.INS.555212 R. ranau
0.91
1
1
RMNH.INS.555221 R. silau
RMNH.INS.555228 R. silau
RMNH.INS.555238 R. silau
RMNH.INS.555224 R. silau
0.73
0.62
RMNH.INS.555225 R. silau
0.85
RMNH.INS.555473 R. simulata
0.97
RMNH.INS.555449 R. simulata
RMNH.INS.555474 R. simulata
RMNH.INS.555270 R. simulata
1
RMNH.INS.555445 R. simulata
RMNH.INS.555440 R. simulata
0.95
RMNH.INS.555444 R. simulata
RMNH.INS.555466 R. simulata
RMNH.INS.555471 R. simulata
0.04
Glomeraceae - Glomus
100
37
99
64
19
32
31
22
37
23
OTU 27338
OTU 13007
AM713409 Glomus eburneum
AM713407 Glomus eburneum
OTU 5708
OTU 24836
65
OTU 13666
59
56
OTU 8632
36
OTU 9223
OTU 8446
48
87 OTU 5542
42
OTU 21220
79
OTU 29948
OTU 8741
96 OTU 8898
OTU 6588
OTU 35053
OTU 4196
94
73
OTU 1606
OTU 6655
93
OTU 21224
OTU 5441
OTU
7081
90
56
45
OTU 34472
OTU 18850
55
OTU 3458
24
OTU 5233
92
OTU 21530
30
OTU 16590
60
OTU 26364
27
69
OTU 29995
OTU 33992
AJ972462 Glomus diaphanum
GU059549 Glomus indicum
OTU 21269
AJ849467 Glomus xanthium
89
OTU 27453
100
OTU 34383
OTU 14114
100 OTU 12813
43
OTU 11936
60 AY035654
Glomus clarum
14
10
OTU 17823
35
12
100
18
OTU 20507
OTU 23633
OTU 32979
OTU 20709
OTU 12112
OTU 24971
98 AJ437106 Glomus sinuosum
J437105 Glomus sinuosum
100
25
87
OTU 20927
OTU 27919
OTU 10293
OTU 29430
FM865572 Glomus intraradices
FM992400 Glomus proliferum
FM865573 Glomus intraradices
56
66 FM865562 Glomus intraradices
88 FM865561 Glomus intraradices
FM865568 Glomus intraradices
100 EF989103 Glomus intraradices
EF989105 Glomus intraradices
AJ557009 Glomus intraradices
57
AJ567351 Glomus intraradices
80
95
FJ009600 Glomus intraradices
FJ009598 Glomus intraradices
AJ567764 Glomus intraradices
68
98
57
33
25
33
44
30
46
77
3500-4000m
3000-3500m
2500-3000m
2000-2500m
1500-2000m
1000-1500m
500-1000m
0-500m
70
40
37
51
74
0.3
Extended Data Figure 3 | Phylogenetic reconstructions for Ericaceae, Gastropoda, Glomeraceae, Hemiptera and Hirudinea. Details of materials and
methods used are given in Supplementary Table 2.
G2015
Macmillan Publishers Limited. All rights reserved
RESEARCH LETTER
Nepenthaceae - Nepenthes
AF315885 N. pervillei (Seychelles)
L.4149369 N. chaniana
L.4149370 N. chaniana
L.4149371 N. tentaculata
L.4149375-6 N. lowii
0.99
L.4149378 N. lowii
1
0.97
L.4149124 N. lowii
L.4149373 N. lowii
L.4149380 N. fusca
L.4149381 N. fusca
L.4149382 N. fusca
L.4149368 N. fusca
L.4149091 N. tentaculata
L.4149120 N. tentaculata
L.4149115 N. tentaculata
L.4149101 N. tentaculata
L.4149099 N. tentaculata
L.4149088 N. tentaculata
L.4149087 N. tentaculata
L.4149086 N. tentaculata
L.4149098 N. tentaculata
L.4149097 N. tentaculata
L.4149096 N. tentaculata
L.4149095 N. tentaculata
L.4149390 N. tentaculata
L.4149358 N. tentaculata
L.4149395 N. tentaculata
L.4149110 N. tentaculata
L.4149385 N. tentaculata
L.4149386 N. tentaculata
L.4149387 N. tentaculata
L.4149388 N. tentaculata
L.4149374 N. tentaculata
L.4149379 N. tentaculata
L.4149114 N. mirabilis
L.4149113 N. mirabilis
L.4149112 N. mirabilis
L.4149081 N. mirabilis
L.4149084 N. mirabilis
L.4149084 N. mirabilis
L.4149082 N. mirabilis
L.4149083 N. mirabilis
L.4149089 N. mirabilis
L.4149365 N. gracilis
L.4149377 N. gracilis
L.4149109 N. gracilis
0.99
L.4149383 N. mirabilis
L.4149079 N. mirabilis
1
1
1
0.83
1
L.4149092 N. gracilis
L.4149078 N. gracilis
L.4149080 N. gracilis
L.4149090 N. gracilis
L.4149396 N. gracilis
L.4149384 N. gracilis
L.4149359 N. x hookeriana
1
L.4149361 N. ampullaria
L.4149362 N. ampullaria
L.4149364 N. ampullaria
L.4149367 N. ampullaria
L.4149106 N. edwardsiana
L.4149394 N. x kinabaluensis
L.4149355-6 N. x harryana
L.4149354 N. villosa
L.4149393 N. villosa
L.4149392 N. x kinabaluensis
L.4149391 N.villosa
L.4149357 N. x kinabaluensis
L.4149389 N. villosa
SNP34297 N. rajah
L.4149107 N. villosa
L.4149117 N. edwardsiana
0.98
L.4149074-77 N. edwardsiana
L.4149093 N. edwardsiana
0.99
0.99
0.2
Polygalaceae - Epirixanthes
Odonata - Coeliccia
K'tung 78 6390 Salomonia ciliata
RMNH.INS.500047 Calicnemia rectangulata (Pahang Malaysia)
RMNH.INS.503926 C. didyma (Terengganu Malaysia)
1
WJJO de Wilde & BEE de Wilde-Duyes 21409 (L) Salomonia cantoniensis
RMNH.INS.503932 C. didyma (Terengganu Malaysia)
RMNH.INS.506468 C. cyanomelas (Hong Kong)
0.72
RMNH.INS.506487 C. cyanomelas (Hong Kong)
1
CM030 (L) E. elongata
RMNH.INS.506475 C. cyanomelas (Hong Kong)
1
RMNH.INS.509175 C. poungyi (Thailand)
1
RMNH.INS.509174 C. poungyi (Thailand)
CM032 (L) E. elongata
RMNH.INS.505734 C. poungyi (Thailand)
0.98
RMNH.INS.501058 C. albicauda (Malaysia)
1
RMNH.INS.501072 C. albicauda (Malaysia)
CM011 (L) E. papuana
1
RMNH.INS.506849 C. albicauda (Malaysia)
0.95
RMNH.INS.507675 C. sp.
0.83
1
RMNH.INS.507677 C. sp.
CM013 (L) E. kinabaluensis
RMNH.INS.507678 C. sp.
RMNH.INS.507662 C. sp.
0.98
1
CM002-1 (L) E. pallida
RMNH.INS.228944 C. octogesima (Malaysia)
1
0.55
0.95
RMNH.INS.506836 C. octogesima (Malaysia)
RMNH.INS.503977 C. octogesima (Singapore)
CM002-2 (L) E. pallida
RMNH.INS.503978 C. octogesima (Singapore)
0.9
1
RMNH.INS.501021 C. octogesima (Singapore)
RMNH.INS.507775 C. nemoricola
0.74
1
CM009 (L) E. pallida
RMNH.INS.507780 C. nemoricola
RMNH.INS.507782 C. nemoricola
1
RMNH.INS.506294 C. nemoricola (Sarawak Malaysia)
1 RMNH.INS.506304 C. nemoricola (Sarawak Malaysia)
0.69
CM006 (L) E. pallida
RMNH.INS.507768 C. nemoricola
CM001-1 (L) E. pallida
RMNH.INS.507792 C. nemoricola
0.99
RMNH.INS.507793 C. nemoricola
1
RMNH.INS.507721 C. nemoricola
CM001-2 (L) E. pallida
RMNH.INS.507728 C. nemoricola
RMNH.INS.507734 C. nemoricola
RMNH.INS.507735 C. nemoricola
0.04
0.04
Rubiaceae - Hedyotis
Trombidiformes - Hygrobates
cB042 O. pubescens (NewGuinea)
cB019 H. fissispula (Borneo)
RMNH.ACA.1438 Atracdes cf. propatulus
1
FL011 H. sp. (Philippensis )
1
FL031 H. sp. (Philippensis)
RMNH.ACA.1429 Atracdes cognatus
bZ030 H. valetoniana (NewGuinea)
1
RMNH.ACA.1360 H. acupalpis
cA092 H. schlechteri (NewGuinea)
1
FL077 H. pulchella
RMNH.ACA.1362 H. acupalpis
FL068 H.pulchella
1
1
FL037 H. pulchella
1
RMNH.ACA.1364 H. hamatus
FL035 H. pulchella
1
1
FL047 H. pulchella. var. magnispula
RMNH.ACA.1370 H. hamatus
FL048 H. pulchella. var. magnispula
0.74
RMNH.ACA.1352 H. hamatoides
FL046 H. pulchella
1
0.71
FL042 H. pulchella
0.91
RMNH.ACA.1353 H. hamatoides
FL039 H. pulchella
FL038 H. pulchella
RMNH.ACA.1354 H. hamatoides
1
FL050 H. macrostegia
FL055 H. macrostegia
1
RMNH.ACA.1355 H. hamatoides
FL054 H. macrostegia
RMNH.ACA.1357 H. hamatoides
FL049 H. macrostegia
FL058A H. macrostegia
RMNH.ACA.1351 H. hamatoides
FL052 H. macrostegia
0.0020
0.2
3500-4000m
3000-3500m
2500-3000m
2000-2500m
1500-2000m
1000-1500m
500-1000m
0-500m
Extended Data Figure 4 | Phylogenetic reconstructions for Nepenthaceae, Odonata, Polygalaceae, Rubiaceae and Trombidiformes. Details of materials and
methods used are given in Supplementary Table 2.
G2015
Macmillan Publishers Limited. All rights reserved
LETTER RESEARCH
Athyrium
Hedyotis
Orchidaceae – Dendrochilum
Hymenasplenium_unilaterale
53,85
22,78
Asplenium_bulbiferum
83,63
Thelypteris_palustris
71,74
99,02
60,29
Homalosorus_pycnocarpos
62,42
Woodsia_polystichoides
81,52
Blechnum_spicant
51,58
66,17
107,11
58,84
32,34
Woodwardia_japonica
Deparia_conilii
4,23
Deparia_petersenii
2,39
Deparia_lobatocrenata
75,08
23,48
35,38
32,84
Diplazium_simplicivenium
29,06
67,59
Diplazium_nipponicum
17,95
77,54
Diplazium_hachijoense
57,81
Athyrium_niponicum
14,96
58,63
posterior
1
34,34
Athyrium_cuspidatum
9,4
71,7
Athyrium_sheareri
50,15
40,12
Cornopteris_crenulatoserrulata
18,79
Cornopteris_christenseniana
1,58
Cornopteris_decurrenti
40,21
Athyrium_filix_femina
2,64 Athyrium_brevifrons
0,96
23,91
35,08
40,24
33,36
49,73
Athyrium_rupestre
45,06
42,7
Athyrium_nikkoense
6,55
Athyrium_yokoscense
2,15 Athyrium_kirisimaense
0,7
Athyrium_tashiroi
21,17
7,64
40,35
62,55
27,82
25,34
Athyrium_clemensiae
32
Athyrium_nakanoi
8,51
13,61
23,13
Athyrium_deltoidofrons
2,32 Athyrium_neglectum
0,43
Athyrium_vidalii
13,5
18,61
41,37
24,46
Athyrium_amoenum
Athyrium_arisanense
9,68
11,86
42,67
49,86
Athyrium_strigillosum
7,13
25,37
Athyrium_iseanum
1,28
Athyrium_x_hisatsuanum
10,72
19,66
17,05
Athyrium_wardii
7,66
Athyrium_x_tokashikii
1,27
Athyrium_clivicola
0,44
Athyrium_setuligerum
7,42
4,19
0
8,73
36,41
45,44
Athyrium_eremicola
5,25
16,38
38,38
Athyrium_tozanense
8,99
16,83
16,46
54,79
69,66
Athyrium_atkinsonii
12,01
10,22
19,91
33,32
posterior
1
Athyrium_melanolepis
14,53
34,28
11,63
39,33
102,79
37,86
25,83
Athyrium_kuratae
0,88
Athyrium_subrigescens
16,71
32,87
31,03
2,7
Athyrium_viridescentipe
1,41
Athyrium_x_akiense
0,53
27,06
35,81
Athyrium_oblitescens
0,23
Athyrium_otophorum
0
23,76
34,71
32,69
13,87
29,37
23,14
Begonia
14,69
12,7
19
17,13
14,35
18,71
17,14
Begonia_oxyloba_ndhA_ndhF_rpl32
QUA_goudotii09_02167ndhA_ndhF_rpl32
TET_polygonoides09_02176ndhA_ndhF_rpl32
Begonia_poculifera
Begonia_sutherlandii
Begonia_dregei
SOL_radicans09_02177ndhA_ndhF_rpl32
GIR_nelumbifolia09_02171ndhA_ndhF_rpl32
BAR_boliviensis09_02161phu_ndhA_ndhF_rpl32
Begonia_dipetala
Begonia_samahensis
2,09
Begonia_socotrana
Begonia_malabarica
6,2
Begonia_floccifera
REI_hymenophylla10_00613
IGN_smithiae10_00615
Begonia_tenuifolia
4,58
PAR_elisabethae10_00618
3,15
Begonia_aff_elisabethae
2,26
PAR_spec_Thailand110_00620
Begonia_grandis
ALI_alicida10_00614
Begonia_spec_China1
2,69
DIP_spec_Thailand210_00622
DIP_spec_Thailand310_00624
7,38
REI_brandisiana10_00619
5,6
DIP_demissa10_00617
4,67
DIP_aceroides10_00623
Begonia_flagellaris
Begonia_versicolor
4,83
Begonia_venusta
7,59
2,23
Begonia_decora
1,45
Begonia_pavonina
Begonia_sikkimensis
5,61
1,41
0,54Begonia_palmata
Begonia_sizemoreae
Begonia_hatacoa
Begonia_spec_China2
4,95 4,11
3,17
Begonia_aff_multangula
1,33
Begonia_robusta
0,58 Begonia_multangula
4,55
0,29
Begonia_areolata
Begonia_roxburghii
2,15
SPH_obovoidea10_00621
3,22
Begonia_silletensis
1,81
Begonia_acetosella
1,6
Begonia_longifolia
0,99
Begonia_aptera
Begonia_masoniana
4,33
Begonia_morsei
Begonia_spec_Sumbawa1
5,93
Begonia_goegoensis
4,38
Begonia_sudjanae
3,54
Begonia_muricata
Begonia_nigritarum
6,58
Begonia_cleopatrae
6,03
Begonia_fenicis
2,2
Begonia_hernandioides
0,51Begonia_chloroneura
Begonia_kingiana
Begonia_doloisii_concat_D350_PH115
Begonia_amphioxus_concat_DCT2012
7,18
Begonia_pendula_DCT2012
2,73
Begonia_cauliflora_aff_D364_FL066_concat
0,92
2,4
FL065_Begonia_cauliflora_aff_concat_D344
Begonia_vaccinioides_D351_ndhA_concat
0,15
2,15
Begonia_vaccinioides_D353_concat
1,12
Begonia_burbidgei_D363_FL040_concat
0,34
Begonia_burbidgei_DCT2012
1,4
Begonia_imbricata_D365_FL075_concat
0,68 FL062_Begonia_inobongensis_concat_D342
0,43FL071_Begonia_beryllae_concat_D345
0,16
FL074_Begonia_cf_beryllae_cf_D347
Begonia_bracteata
3,67
Begonia_verecunda
2,83
BRA_specSumatra08_02319
1,73
BRA_resecta08_00204
PET_wrayi10_00642_extraction
3,74
Begonia_multijugata
2,48
PET_spec1Borneo07_00575
1,15
Begonia_chlorosticta
4,15
PET_harauensis09_01011
6,63
1,47
Begonia_laruei
2,94
PET_aff_congesta09_00060
0,24
PET_specKalimantan09_01013
0,09
Begonia_corrugata
PET_specSumbawa09_01015
Begonia_serratipetala
1,04
Begonia_brevirimosa
3,44
5,67
4,61
PET_specPhilippines08_03026
2,53
Begonia_negrosensis
1,67
Begonia_poliloensis
4,26
Begonia_symsanguinea
3,4
Begonia_strigosa
0,58 Begonia_argenteomarginata
4
PET_specNewGuinea09_01016
3,37
PET_weigallii09_01017
2,09
PET_spec1Papua08_02330
5,16
PET_hekensis08_02227
1,88
Begonia_varipeltata
0,13
PET_stevei07_01455
2,99
PET_macintyreana07_01454
0,47PET_chiasmogyna07_00577
2,03
PET_mendumiae07_00578
1,42
Begonia_masarangensis
0,85 PET_capituliformis09_01419
4,61
0,56PET_hispidissima_GLombulan09_01418
Begonia_siccacaudata
2,66
PET_bonthainensis09_01403
PET_prionota_spec809_01407
0,7 PET_didyma08_02240
4,13
1,12
PET_ozotothrix08_02845
0,74 PET_nobiaespec1709_01416
Begonia_watuwilensis
3,9
1,35
PET_flacca09_01009
PET_lasioura_spec1309_01412
3,55 2,9
Begonia_koordersii
2,15
PET_pseudolateralis08_02220ndhA_ndhF_rpl32
3,18
PET_comestibilis_spec509_01402
1,47 0,67 PET_vermeulenii_07_01837
PET_torajana1109_01410
1,230,78 Begonia_guttapila
PET_aff_mekonggensisspec1209_01411
1,06
PET_rantemarioensis09_01405
0,93 PET_sanguineopilosaspec1809_01417
10,12
6,6
12,34
10,18
9,58
13,02
22,41
15,11
10,61
14,62
11,67
13,9
18,37
12,61
11,35
10,87
9,27
15,76
posterior
1
10,01
12,54
10,75
9,39
9,04
0
posterior
1
Dendrochilum_cobbianum
Dendrochilum_graciliscapum
posterior
1
0,4
4,93
2,31
Dendrochilum_arachnites
Dendrochilum_glumaceum
Dendrochilum_dewindtianum
Dendrochilum_tenompokense
Dendrochilum_cupulatum
1,71
Dendrochilum_haslamii
0,6
Dendrochilum_exasperatum
1,09
Dendrochilum_joclemensii
2,69
0,43
1,31
0,3
0,71
0,42
1,6
0
Dendrochilum_gibbsiae
0,53
Dendrochilum_alatum
Dendrochilum_corrugatum
Dendrochilum_kamborangense
Dendrochilum_stachyodes
Dendrochilum_trusmadiense
Dendrochilum_muluense
Dendrochilum_grandiflorum
Dendrochilum_transversum
0,94
0,51
0,35
0
Dendrochilum_alpinum
0,05
Dendrochilum_pterogyne
Dendrochilum_pseudoscriptum
0,1
Dendrochilum_scriptum
Dicranoloma (ITS rate fixed)
AF146376_AF144112_Mesotus_celatus_OUTGROUP
AF135067_AF140696_Dicnemon_calycinum
AF129587_AF144113_Dicranum_polysetum
AF135075_AF144116_Paraleucobryum_enerve
KF423995_KF423641_Holomitrium_arboreum
KF423992_KF423638_Holomitrium_crispulum
DQ462604_DQ464186_D_chilense_Chile
DQ462594_DQ464193_D_billarderi_New_Zealand
0,05
DQ462595_DQ464194_D_billarderi_Chile
0,23
DQ462596_DQ464196_D_billarderi_Rwanda
0,05
DQ462597_DQ464197_D_billarderi_Reunion
MS52_e4002189780_D_blumii_Kinabalu_Gunung_Alab
0,33
MS20_e4002189776_D_blumii_Kinabalu_L2
0,05
MS39_e4002189814_D_blumii_Kinabalu_Laban_Rata
0,8
DQ462598_DQ464188_D_robustum_New_Zealand
0,18
DQ462599_DQ464189_D_robustum_New_Zealand
0,39
DQ462600_DQ464190_D_robustum_Chile
0,16
DQ462601_DQ464191_D_robustum_Chile
KF423978_KF423621_D_cylindrothecium_Russia
0,93
MS53_e4002189792_D_sp_Kinabalu_Gunung_Alab
L0092869_e4002189708_D_diaphanoneurum_Australia
0,74
DQ462607_DQ464184_D_menziesii_New_Zealand
0,08
DQ485179_D_menziesii_Australia
MS11_e4002189763_D_brevisetum_Kinabalu_Sayap
MS35_e4002189766_D_braunii_Kinabalu_L2
0,53
0,09
MS19_e4002189764_D_braunii_Kinabalu_Sayap
0,21
MS16_e4002189823_D_braunii_Kinabalu_Sayap
0,07
0,67
MS17_e4002189740_D_braunii_Kinabalu_Sayap
MS21_e4002189788_D_brevisetum_Kinabalu_Sayap
MS2_e4002189750_D_brevisetum_Kinabalu_Sayap
0,38
0,03
MS3_e4002189762_D_brevisetum_Kinabalu_Sayap
0,12
MS4_e4002189774_D_brevisetum_Kinabalu_Sayap
0,04
MS9_e4002189739_D_brevisetum_Kinabalu_Sayap
DQ485176_D_leichhardtii_Australia
L0856682_e4002189720_D_havilandii_Kinabalu_Layang_Laya
0,38
MS41_e4002189743_D_havilandii_Kinabalu_Laban_Rata
0,130,03
MS44_e4002189779_D_havilandii_Kinabalu_Laban_Rata
0,08
MS42_e4002189755_D_havilandii_Kinabalu_Laban_Rata
0,03
MS43_e4002189767_D_havilandii_Kinabalu_Laban_Rata
DQ462605_DQ485175_D_dicarpum_New_Zealand
L0856640_e4002189709_D_sp_Indonesia_Java
0,61
0,27
L0093198_e4002189685_D_reflexum_Indonesia_Sumatra
0,38
MS12_e4002189775_D_reflexum_Kinabalu_Sayap
0,05
0,95
MS13_e4002189787_D_reflexum_Kinabalu_Sayap
DQ485178_D_fasciatum_Australia
DQ462606_DQ464185_D_plurisetum_New_Zealand
0,1
0,81
DQ485174_D_plurisetum_New_Zealand
MS25_e4002189741_D_assimile_Kinabalu_Sayap
0,61
0,12 MS28_e4002189777_D_assimile_Kinabalu_KNP
0,04
MS29_e4002189789_D_assimile_Kinabalu_KNP
0,42
MS38_e4002189802_D_assimile_Kinabalu_Laban_Rata
MS45_e4002189791_D_assimile_Kinabalu_Gunung_Alab
0,32
MS51_e4002189768_D_assimile_Kinabalu_Gunung_Alab
0,03
0,2
MS48_e4002189827_D_assimile_Kinabalu_Gunung_Alab
0,13 MS27_e4002189765_D_assimile_Kinabalu_Sayap
0,03
MS47_e4002189815_D_assimile_Kinabalu_Gunung_Alab
0,1
MS33_e4002189742_D_assimile_Kinabalu_KNP
0,04
MS37_e4002189790_D_assimile_Kinabalu_L2
0,68
3,51
1,79
0,71
3,26
1,83
2,69
1,1
2,33
posterior
1
1,81
RMNH_INS_500047_Calicnemia_rectangulata_Pahang_Malaysia_OUTGROUP
1,25
2,1
Calicnemia_chaseni
1,68
1,14
Calicnemia_sinensis
Coeliccia_borneensis
1,75
Coeliccia_flavostriata
Coeliccia_flavicauda
0
3,82
Coeliccia_ryukyuensis
2,17
2,92
31,18
Dendrochilum_ovatum
0,4
Coeliccia
posterior
1
39,46
Dendrochilum_karoense
2,92
RMNH_INS_503926_C_didyma_Terengganu_Malaysia
RMNH_INS_501058_C_albicauda_Malaysia
21,35
2,69
AF146376_AF144112_Mesotus_celatus_OUTGROUP
AF135067_AF140696_Dicnemon_calycinum
AF129587_AF144113_Dicranum_polysetum
AF135075_AF144116_Paraleucobryum_enerve
KF423995_KF423641_Holomitrium_arboreum
KF423992_KF423638_Holomitrium_crispulum
DQ462604_DQ464186_D_chilense_Chile
DQ462594_DQ464193_D_billarderi_New_Zealand
0,08
DQ462595_DQ464194_D_billarderi_Chile
0,35
DQ462596_DQ464196_D_billarderi_Rwanda
0,08
DQ462597_DQ464197_D_billarderi_Reunion
MS52_e4002189780_D_blumii_Kinabalu_Gunung_Alab
1,66
0,52
MS20_e4002189776_D_blumii_Kinabalu_L2
0,08
MS39_e4002189814_D_blumii_Kinabalu_Laban_Rata
1,18
DQ462598_DQ464188_D_robustum_New_Zealand
0,28
DQ462599_DQ464189_D_robustum_New_Zealand
0,58
DQ462600_DQ464190_D_robustum_Chile
0,24
DQ462601_DQ464191_D_robustum_Chile
KF423978_KF423621_D_cylindrothecium_Russia
1,41
MS53_e4002189792_D_sp_Kinabalu_Gunung_Alab
L0092869_e4002189708_D_diaphanoneurum_Australia
1,13
DQ462607_DQ464184_D_menziesii_New_Zealand
0,12
DQ485179_D_menziesii_Australia
MS11_e4002189763_D_brevisetum_Kinabalu_Sayap
MS35_e4002189766_D_braunii_Kinabalu_L2
0,79
0,15
MS19_e4002189764_D_braunii_Kinabalu_Sayap
0,33
MS16_e4002189823_D_braunii_Kinabalu_Sayap
0,1
1,03
MS17_e4002189740_D_braunii_Kinabalu_Sayap
MS21_e4002189788_D_brevisetum_Kinabalu_Sayap
MS2_e4002189750_D_brevisetum_Kinabalu_Sayap
0,59
0,05
MS3_e4002189762_D_brevisetum_Kinabalu_Sayap
0,2
MS4_e4002189774_D_brevisetum_Kinabalu_Sayap
0,07
MS9_e4002189739_D_brevisetum_Kinabalu_Sayap
1,88
DQ485176_D_leichhardtii_Australia
L0856682_e4002189720_D_havilandii_Kinabalu_Layang_Laya
0,57
MS41_e4002189743_D_havilandii_Kinabalu_Laban_Rata
0,2 0,05
MS43_e4002189767_D_havilandii_Kinabalu_Laban_Rata
0,12
MS42_e4002189755_D_havilandii_Kinabalu_Laban_Rata
0,05
MS44_e4002189779_D_havilandii_Kinabalu_Laban_Rata
1,67
DQ462605_DQ485175_D_dicarpum_New_Zealand
L0856640_e4002189709_D_sp_Indonesia_Java
0,93
0,42
L0093198_e4002189685_D_reflexum_Indonesia_Sumatra
0,57
MS12_e4002189775_D_reflexum_Kinabalu_Sayap
0,08
MS13_e4002189787_D_reflexum_Kinabalu_Sayap
1,45
DQ485178_D_fasciatum_Australia
DQ462606_DQ464185_D_plurisetum_New_Zealand
0,14
1,23
DQ485174_D_plurisetum_New_Zealand
MS25_e4002189741_D_assimile_Kinabalu_Sayap
0,93
0,18 MS28_e4002189777_D_assimile_Kinabalu_KNP
0,07
MS29_e4002189789_D_assimile_Kinabalu_KNP
0,64
MS38_e4002189802_D_assimile_Kinabalu_Laban_Rata
MS45_e4002189791_D_assimile_Kinabalu_Gunung_Alab
0,49
MS51_e4002189768_D_assimile_Kinabalu_Gunung_Alab
0,3
0,05
MS48_e4002189827_D_assimile_Kinabalu_Gunung_Alab
0,21 MS27_e4002189765_D_assimile_Kinabalu_Sayap
0,06
MS47_e4002189815_D_assimile_Kinabalu_Gunung_Alab
0,14
MS33_e4002189742_D_assimile_Kinabalu_KNP
0,06
MS37_e4002189790_D_assimile_Kinabalu_L2
2,26
2,78
RMNH_INS_507662_C_species_2_1500to1750mASL_KHQ
1,51
4,08
RMNH_INS_507675_C_species_1_500to750mASL_PHS
posterior
1
1,19
3,53
RMNH_INS_503977_C_octogesima_Singapore
0,85
Coeliccia_cyaneothorax
0,26
2,75
0
RMNH_INS_507768_C_nemoricola_500to750mASL_IN
2,26
Dacrycarpus
Phyllocladus_alpinus
Phyllocladus_trichomanoides
Phyllocladus_toatoa
Phyllocladus_aspleniifolius
10,41
Phyllocladus_hypophyllus
Lepidothamnus_intermedius
Lagarostrobos_franklinii
Manoao_colensoi
Sundacarpus_amarus
Prumnopitys_andina
17,46
Prumnopitys_taxifolia
Prumnopitys_ladei
33,15
Prumnopitys_ferruginea
1,36
Prumnopitys_ferruginoides
Saxegothaea_conspicua
Microcachrys_tetragona
Pherosphaera_fitzgeraldii
Acmopyle_sahniana
Falcatifolium_taxoides
19,19
Falcatifolium_papuanum
34,37
Dacrydium_cupressinum
Dacrydium_balansae
15,21
1,48
Dacrydium_guillauminii
9,5
Dacrydium_beccarii
5,22 Dacrydium_elatum
Dacrycarpus_dacrydioides
Dacrycarpus_imbricatus105
21,65
5,65 Dacrycarpus_imbricatus106
15,15
Dacrycarpus_kinabaluensis913
11,04
Dacrycarpus_compactus
1,52
Dacrycarpus_expansus
8,64
Dacrycarpus_imbricatus102
1,18
1
Dacrycarpus_kinabaluensis111
Retrophyllum_rospigliosii
14,93
6,27 Retrophyllum_comptonii
Retrophyllum_minus
Nageia_wallichiana
14,59
Nageia_fleuryi
6,54 Nageia_formosensis
1,18
Nageia_nagi
29,17
Afrocarpus_mannii
1,57
Afrocarpus_gracilior
5,07 Afrocarpus_usambarensis
1,63
Afrocarpus_dawei
0,66
Afrocarpus_falcatus
Podocarpus_smithii
19,89
Podocarpus_angustifolius
1,3
Podocarpus_salignus
29,01
Podocarpus_nubigenus
Podocarpus_totara
24,03
3,78Podocarpus_acutifolius
1,06
Podocarpus_hallii
11,73
Podocarpus_gnidioides
7,83
Podocarpus_cunninghamii
5,15 Podocarpus_nivalis
2,65
Podocarpus_lawrencei
35,88
Podocarpus_lambertii
5,92 Podocarpus_sprucei
2,78
Podocarpus_parlatorei
24,99
Podocarpus_henkelii
12,91
Podocarpus_madagascariensis
9,51
Podocarpus_elongatus
3,43Podocarpus_latifolius
0,76
30,28
Podocarpus_milanjianus
Podocarpus_celatus
2,25
Podocarpus_oleifolius
8,95
Podocarpus_guatemalensis
1,28
Podocarpus_matudae
14,87
Podocarpus_purdieanus
6,94
Podocarpus_urbanii
12,56
Podocarpus_sellowii
9,41
Podocarpus_coriaceus
Podocarpus_drouynianus
7,08
Podocarpus_spinulosus
Podocarpus_rumphii
8,87
4,85 Podocarpus_elatus
Podocarpus_grayae
15,66
25,45
Podocarpus_novae-caledoniae
7,58
Podocarpus_longifoliolatus
4,07 Podocarpus_lucienii
1,17
Podocarpus_sylvestris
22,13
Podocarpus_dispermus
Podocarpus_neriifolius
Podocarpus_archboldii
9,5
3,59Podocarpus_brassii
18,13
6,19 Podocarpus_ledermannii
1,28
Podocarpus_rubens
Podocarpus_bracteatus
13,03 7,25
Podocarpus_pilgeri
Podocarpus_fasciculus
3,19
0,55
Podocarpus_forrestii
1,79
Podocarpus_chingianus
0,93
Podocarpus_costalis
10,32
0,54
Podocarpus_macrophyllus
Podocarpus_affinis
4,84 Podocarpus_degeneri
0,97
Podocarpus_pallidus
8,62
Podocarpus_ramosii
6,91
Podocarpus_sp_PK_2012b
3,02Podocarpus_sp_PK_2012a
1,62
Podocarpus_polystachyus
0,83
Podocarpus_subtropicalis
10,43
20,01
15,69
161,21
61,25
127,01
113,14
43,55
68,15
148,07
118,87
102,93
93,46
57,28
87,55
posterior
1
43,96
76,41
60,82
48,76
0
0
73,98
8,97
7,37
36,34
32,54
45,88
posterior
1
37,86
36,19
35,56
33,57
30,54
12,81
8,47
19,22
17,38
9,7
13,69
12,67
9,69
9,1
8,32
posterior
1
7,82
Xanthophyllum_sp
Eriandra_fragrans
36,67
Carpolobia_alba
18,16
Atroxima_afzeliana
Polygala_costaricensis
29,43
Bredemeyera_floribunda
46,78
Securidaca_longepedunculata
15,87
Securidaca_diversifolia
5,68
posterior
1
Securidaca_retusa
33,53
42,16
Monnina_xalapensis
31,93
Comesperma_esulifolium
30,7
Polygala_californica
25,68
Polygala_violacea
35,75
Polygala_senega
16,03
Polygala_longicaulis
9,72
Polygala_paniculata
0
Polygala_myrtifolia
29,97
16,02
Polygala_vulgaris
3,07
Polygala_amara
2,11 Polygala_comosa
0,83
Polygala_alpicola
28,69
Muraltia_karroica
13,34
28,09
Ilex (nuclear data)
Helwingia_japonica
10,85
3,76
22,58
8,4
Nylandtia_spinosa
7,92
73,8
posterior
1
0
Myrmarachne
EU815599_Ligonipes_sp_Australia_OUTGROUP
AY297412_M_assimilis_Philippines
0,38
Myrmarachne_japonica
0,32
PK373_M_cornuta_500to750mASL_PHS
0,23
0,51
1,32
Myrmarachne_plataleoides
Myrmarachne_sp_F_FSC_2006
0,33
Myrmarachne_sp_MRB113
0,17
JX145678_M_evidens_Gabon
0,1
JX145679_M_foenisex_Gabon
1,05
JX145676_M_cf_gedongensis_Malaysia
0,01
Myrmarachne_sp_WPM_2008
posterior
1
0,58
Myrmarachne_sp_A_FSC_2006
0,01
Myrmarachne_sp_D_FSC_2006
Polygala_paucifolia
11,1
Polygala_chamaebuxus
24,5
7,22
19,67
Salomonia_ciliata
0,88
Hygrobates
PK210_M_hanoii_1000to1250mASL_MA
7,23
0,63
Myrmarachne_sp_B_FSC_2006
Atractides_cognatus
Epirixanthes_pallida
9,54
PK068_M_malayana_500to750mASL_PHS
0,88
Salomonia_cantoniensis
Epirixanthes_elongata
13,7
0,83
2,9
Epirixanthes_papuana
Ilex_collina
1,51Ilex_decidua
Ilex_decidua_var_curtissii
Ilex_longipes
1,19
Ilex_montana
Ilex_amelanchier
Ilex_mucronata
Ilex_cassine
2,18 Ilex_x_attenuata
Ilex_cumulicola
3,2
Ilex_rubra
4,68
Ilex_opaca
28,57
2,94 Ilex_dugesii
Ilex_vomitoria
Ilex_paraguariensis
8,79
17,02
Ilex_laurina
14,59
Ilex_discolor
7,66
Ilex_tolucana
9,71
Ilex_nitida
3,78
24,36
Ilex_repanda
Ilex_amara
5,17
1,43Ilex_chamaedryfolia
Ilex_dumosa
17,35
Ilex_teratopis
Ilex_crenata
15,61
1,01
Ilex_mutchagara
7,9
Ilex_revoluta
5,13
Ilex_triflora
Ilex_maximowicziana
6,83
Ilex_rugosa
Ilex_aquifolium
1,34Ilex_perado
10,23
18,95
1,72 Ilex_colchica
Ilex_spinigera
Ilex_kinabaluensis
17,55
Ilex_leucoclada
5,52
Ilex_x_makinoi
9,63
Ilex_cornuta1
14,64
6,83
2,69 Ilex_cornuta2
Ilex_dimorphophylla
4,54
Ilex_zhejiangensis
1,94 Ilex_integra1
Ilex_hylonoma
13,28
Ilex_x_kiusiana
10,61
Ilex_integra2
7,2
2,9
Ilex_liukiuensis
5,05
Ilex_matanoana
0,5
Ilex_mertensii
11,8
Ilex_latifolia
Ilex_ciliospinosa
8,08
2,82 Ilex_fargesii1
5,57
31,84
2,58 Ilex_hookeri
10,37
Ilex_nothofagifolia
Ilex_fargesii2
Ilex_corallina
8,85
Ilex_pernyi
4,63
Ilex_kingiana
8,16
3,01
1,26Ilex_bioritsensis
Ilex_georgei
7,12
Ilex_buergeri
2,92 Ilex_warburgii
4,35
2,41 Ilex_cyrtura
Ilex_ficoidea
Ilex_canariensis
24,12
Ilex_coriacea
12,37
Ilex_glabra
6,25
Ilex_liebmannii
Ilex_argentina
Ilex_anomala
6,02
17,5
Ilex_pseudobuxus
3,14
Ilex_microdonta
14,78
29,2
Ilex_quercetorum
Ilex_asperula
5,13
12,77
Ilex_brevicuspis
Ilex_guianensis
9,6
6,61
Ilex_brasiliensis
8,21
Ilex_theizans2
3,87
2,52 Ilex_integerrima
Ilex_theizans1
27,19
Ilex_pubescens
Ilex_purpurea1
19,07
0,65
Ilex_purpurea2
14,77
Ilex_rotunda1
2,08 Ilex_rotunda2
Ilex_goshiensis
11,4
Ilex_wilsonii
22,41
Ilex_sebertii
Ilex_havilandii
25,55
21,13
8,04
Ilex_spicata
20,56
Ilex_sp_Craven
Ilex_cissoidea
17,08
Ilex_oppositifolia
6,04
15,9
Ilex_zygophylla
Ilex_maingayi
13,37
7,57
Ilex_arnhemensis
24,63
5,72
Ilex_wallichii1
9,49
Ilex_nervulosa
7,74
Ilex_cymosa
5,14
Ilex_wallichii2
Ilex_geniculata
10,39
1,58Ilex_laevigata
Ilex_verticillata
Ilex_pedunculosa
23,13
15,42
Ilex_sugerokii
11,44
Ilex_yunnanensis1
3,79
Ilex_shennongjiaensis
2,18 Ilex_yunnanensis2
21,25
Ilex_mitis
Ilex_micrococca
10,1
19,57
Ilex_serrata
Ilex_kusanoi
16,06
4,36
Ilex_macrocarpa
Ilex_aculeolata
10,6
5,42
Ilex_tsoi
7,72
Ilex_fragilis
5,64
Ilex_macropoda
20,71
36,43
Epirixanthes
54,58
0
Impatiens
Iomeiana
Ikerriae
Iglandulifera
3,46
Ichungtienensis
Ibalfourii
5,76
1,18
Iparviflora
4,1
Iedgeworthii
0,96
Iscabrida
Idavidi
0,52 Ipurpurea
Idesmantha
6,49
Itaronensis
5,5
2,69
Irectangula
1,65
Isiculifer
3,35
Iaquatilis
2,27
Ifenghwaiana
1,47
0,77 Icyanantha
Iuliginosa
Iflanaganae
4,62
Itinctoria_elegantissima
1,12
0,42Ifischeri
Iteitensis
Ipallida
1,94
Inolitangere
1,22
Icapensis
5,62
Iuniflora
2,43
Iimbicilla
3,18
Iforrestii
2,06
Ifaberi
Irubrostriata
1,96
Iconchibracteata
Icampanulata
1,05
Iparasitica
6,68
Ihenslowiana
5,92
Iclavicornu
3,46
Iviscida
Imengtseana
0,98
Imonticola
4,13
Ibegonifolia
1,89
Inapoensis
1,31
0,62 Itrichosepala
Iyingjiangensis
Ioumina
2,97
Ikamerunensis_kamerunensis
1,77
Ikamerunensis_obanensis
4,27
Isakerana
Ihians
1,38
3,21
Ipalpebrata
0,92
Icolumbaria
2,53
0,56 Imackeyana_zenkeri
Imackeyana_claeri
1,77
Ipseudomacroptera
0,63 Imacroptera
Ichinensis
5,21
Ihawkeri
1,92
Iplatypetala
Ibalsamina
4,24
Ilatifolia
2,28
Icuspidata
1,77
Iflaccida
4,63
Iaureliana
Ichevalieri
3,43
1,29
Ikinabaluensis
2,16
Ieberhardtii
1,64
Ipoilanei
Ikilimanjari
0,81
Ipseudoviola
6,18
Iusambarensis
4,15
1,02
Igordoni
0,58 Iwalleriana
3,49
Isodeni
3,24
Ihamata
1,01
Iserpens
0,47 Ithamnoidea
0,19
Ipseudohamata
5,5
Iengleri_engleri
0,51 Imildbraediitelekii
Iethiopica
Iirvingii
4,79 4,03
0,72 Ihochstetteri_hochstetteri
Ihochstetteri_jacquesii
Ibequartii
4,5
3,13
Ibriartii
5,31
Ihoehnellii
3,69
1,81
Itweediae
Ibururiensis
3,24
1
Ipercordata_percordata
3,05
0,36Imannii_CentralAFrica
Imannii_WestAfrica
Ikeillii_keillii
2,31
5,21
0,33
Ikeillii_pubescens
1,37
Ibombycina
0,73 Icongolensis
0,44Iniamniamensis
Icecilii
2,66
Ihydrogetonoides
4,46
Ipseudozombensis
0,93
Ieryaleia
Icatati
Ituberosa
3,14
4,83
1,36
0,58 Ibicaudata
Iauricoma
2,48
Iinaperta
1,34
Iarachnoides
0,73 Ifurcata
4,54
Ivolkensii
3,6
Iassurgens
2,87
Iburtoniiburtonii
4,36
Iulugurensis
Idigitata_digitata
1,02
3,79
0,71 Imeruensis_cruciata
Imeruensis_meruensis
Iraphidotrix
3,51
1,74
Iconfusa_longicornu
1,13
Iioides
3,27
Imazumbaensis
0,35Inana
1,86
Ilukwangulensis
Isylvicola
1,08
Ipalliderosae_palliderosae
0,83 0,18
Ipalliderosae_lupangaensis
0,61 Irubromaculata_rubromaculata
0,23
Irubromaculata_imagiensis
5,79
7,71
13,15
1,08
4,98
RMNH_INS_509175_C_poungyi_Thailand
3,6
13,32
16,24
1,04
5,38
1,81
Helwingia_japonica
Ilex_buergeri
Ilex_rugosa
Ilex_sebertii
Ilex_pernyi
Ilex_collina
Ilex_anomala
Ilex_verticillata
Ilex_yunnanensis1
Ilex_laevigata
Ilex_nothofagifolia
Ilex_shennongjiaensis
Ilex_pedunculosa
Ilex_liukiuensis
4,66
Ilex_theizans2
Ilex_mutchagara
17,08
Ilex_rubra
6,84
Ilex_havilandii
26,52
Ilex_tsoi
18,64
Ilex_oppositifolia
13,06
Ilex_purpurea1
11,22
Ilex_zygophylla
5,68
Ilex_repanda
Ilex_x_attenuata
13,33
Ilex_wallichii2
9,2
Ilex_vomitoria
17,72
Ilex_nervulosa
4,05
Ilex_chamaedryfolia
10,27
Ilex_amara
7,34
Ilex_wallichii1
5,73
Ilex_maingayi
Ilex_triflora
24,11
Ilex_laurina
Ilex_integra1
17,52
Ilex_kinabaluensis
Ilex_cymosa
14,35
Ilex_microdonta
24,18
Ilex_zhejiangensis
13,93
Ilex_cassine
5,09
1,69Ilex_corallina
Ilex_purpurea2
Ilex_macropoda
Ilex_theizans1
Ilex_cornuta2
12,25
4,26
26,87
Ilex_warburgii
8,91
Ilex_dimorphophylla
5,21
Ilex_spicata
18,81
Ilex_opaca
6,33
Ilex_dugesii
15,53
Ilex_aculeolata
8,23
Ilex_brasiliensis
13,12
Ilex_bioritsensis
7,37
Ilex_cornuta1
Ilex_pubescens
Ilex_longipes
22,97
Ilex_hylonoma
21,23
8,67
Ilex_paraguariensis
14
Ilex_argentina
8,29
Ilex_matanoana
4,29
Ilex_integerrima
27,02
Ilex_brevicuspis
18,16
Ilex_revoluta
15,47
Ilex_fragilis
6,21
Ilex_fargesii1
3,57
Ilex_nitida
Ilex_asperula
22,97
Ilex_x_makinoi
16,85
3,51
Ilex_maximowicziana
1,82Ilex_arnhemensis
9,79
Ilex_fargesii2
5,3
Ilex_leucoclada
18,98
3,44
Ilex_mertensii
Ilex_spinigera
10,98
Ilex_canariensis
Ilex_georgei
14,58
Ilex_rotunda1
5,74
Ilex_geniculata
10,72
5,56
Ilex_decidua
2,45 Ilex_decidua_var_curtissii
9,58
Ilex_mucronata
5,19
Ilex_x_kiusiana
8,62
Ilex_cumulicola
7,31
Ilex_mitis
Ilex_discolor
15,13
Ilex_latifolia
5,17
Ilex_montana
1,44Ilex_yunnanensis2
Ilex_goshiensis
24
10,38
Ilex_amelanchier
6,83
Ilex_rotunda2
Ilex_kusanoi
3,68
17,55
Ilex_liebmannii
Ilex_wilsonii
Ilex_sp_Craven
8,61
3,39
Ilex_guianensis
13,37
6,17
Ilex_integra2
4,77
Ilex_tolucana
3,6
Ilex_micrococca
2,82 Ilex_serrata
12
Ilex_sugerokii
5,97
Ilex_macrocarpa
3,91
2,52 Ilex_quercetorum
Ilex_teratopis
10,8
Ilex_crenata
Ilex_pseudobuxus
5,69
Ilex_cyrtura
9,45
3,72
Ilex_kingiana
1,37
Ilex_ficoidea
8,79
Ilex_perado
Ilex_colchica
3,85
6,91
Ilex_coriacea
2,22 Ilex_ciliospinosa
4,68
Ilex_cissoidea
1,22
Ilex_hookeri
4,68
Ilex_glabra
3,24
Ilex_aquifolium
3,17
Ilex_dumosa
10,48
15,38
24,3
Dicranoloma (trnL rate fixed)
2,73
2,35
1,66
Ilex (plastid data)
RMNH_INS_506468_C_cyanomelas_HongKong
2,11
1,66
4,09
5,64
Dendrochilum_dewildei
1,29
3,51
5,38
11,01
11,28
Coelogyne_cristata
2,65
8,83
Carphalea_madagascariensis
Batopedina_pulvinellata
Paraknoxia_parviflora
Dibrachionostylus_kaessneri
Oldenlandia_rupicola_cC034_Africa
Hedyotis_nana_cA094_NewGuinea
Hedyotis_trichoclada_cB029_NewGuine
Neanotis_nummularia_cC028_Ceylon
Neanotis_nummulariformis_cC029_Ceyl
Neanotis_wightiana_bS011_IndiaSEAsi
Neanotis_formosana_cC026_Taiwan
1,41 Neanotis_gracilis_SN89_Asia
0,88Hedyotis_lindleyana_cB023_Asia
0,58
Neanotis_hirsuta_bS009_Asia
Hedyotis_pahompokae_bS042_Thailand
1,26 Neanotis_calycina_SN13_Asia
4,08
1,36 Neanotis_indica_cC030_India
Neanotis_monosperma_cC027_India
Arcytophyllum_muticum
9,64
Arcytophyllum_thymifolium
18,65
27,61
Oldenlandia_microtheca
12,25
Stenaria_nigricans
9,25
Houstonia_caerulea
8,01
23,36
Houstonia_longifolia
Oldenlandia_fastigiata
14,34
Hedythyrsus_spermacocinus
7,01
Mitrasacmopsis_quadrivalvis
20,83
Oldenlandia_echinulosa
7,42
Oldenlandia_geophila
4,11
Oldenlandia_nervosa
Hedyotis_coronaria_cB040_Asia
9,01
Spermacoce_hispida
14,44
Oldenlandia_salzmannii
6,72
25,98
Oldenlandia_tenuis
19,89
Cordylostigma_microcala
6,48
Cordylostigma_virgata_cB032
13,38
1,68 Oldenlandia_umbellata_SN84_Asia
Oldenlandia_umbellata_cC025_Asia
Oldenlandia_wiedemannii
9,33
Oldenlandia_duemmeri_cB041
2,65
6,17
Oldenlandia_taborensis
Oldenlandia_capensis_var_capensis
4,39 3,1
Oldenlandia_densa_robinsonii_bB92
24,39
1,56 Oldenlandia_nematocaulis
3,63
Oldenlandia_wauensis
1,51 Oldenlandia_corymbosa_bB72
1,35 Oldenlandia_erecta_SN2_Asia
0,74Oldenlandia_erecta_cB024_Asia
Oldenlandia_cherevensis_cA054_SEAsi
Synaptantha_tillaeacea
Oldenlandia_mitrasacmoides
18,9
Kadua_affinis
6,62
Kadua_fluviatilis
4,77
Kadua_parvula
17,77
9,89
Oldenlandia_biflora
4,57
Oldenlandia_pterita
5,99
Oldenlandia_biflora_bB067
4,09
Leptopetalum_foetidum_cB044_Pacific
2,49
Leptopetalum_grayii_bZ041_Japan
16,7 15,31
Oldenlandia_angustifolia_cB014_Indi
1,55 Oldenlandia_tenelliflora
1,01 Oldenlandia_tenelliflora_cA089_Asia
11,6
Oldenlandia_pinifolia_bS031_IndiaSE
6,66
Oldenlandia_verticillata_SN5_Asia
10,18
Oldenlandia_gracilipes_cA061_Thaila
8,93
Oldenlandia_stocksii_cC022_India
6,51
Oldenlandia_lancifolia
15,98
5,34
Oldenlandia_galioides
3,97
Oldenlandia_herbacea_cB058
2,42
Oldenlandia_brachypoda_SN88_Asia
0,76Oldenlandia_diffusa_bS3_Asia
Oldenlandia_ovatifolia_bZ044_SEAsia
Hedyotis_pachycarpa_bZ011_Asia
Oldenlandia_chrysotricha_bZ040_Chin
1,34
Oldenlandia_chrysotricha_bR100_Chin
4,92
0,57
Oldenlandia_chrysotricha_bR99_China
13,54
Oldenlandia_auricularia_cB013_Asia
4,22 2,85
Oldenlandia_auricularia_cC020_Ceylo
2,28
Hedyotis_costata_bS41_Asia
0,79Hedyotis_vestita_bS40_Asia
3,22
6,71
Oldenlandia_auricularia_cC021_Fiji
1,9
Oldenlandia_lapeyrousii_cA097_NewGu
2,83
Oldenlandia_lineata_bS6_IndiaSEAsia
1,12 Oldenlandia_lineata_cB010_IndiaSEAs
Hedyotis_scandens_cA052_Asia
Hedyotis_capitellata_bZ031_SEAsia
5,85
Hedyotis_capitellata_bR98_SEAsia
4,81
Oldenlandia_scabra_cB025_IndiaSEAsi
1,74
4,09
0,95Hedyotis_sp_bZ013_Vietnam
Oldenlandia_contracta_bZ008
2,95
Hedyotis_ampliflora_cB056_China
2,63
Hedyotis_dianxiensis_bZ048_China
Hedyotis_obliquinervis_bZ009_Asia
2,79
1,01 Hedyotis_sp_bZ018_Vietnam
2,04
Hedyotis_sp_bZ020_Vietnam
Hedyotis_pitardiana_bZ023
1,290,42
Hedyotis_sp_bZ021_Vietnam
0,68
Hedyotis_sp_bZ025_Vietnam
0,27
Oldenlandia_hedyotidea_cB006_Asia
Dentella_repens
8,78
Pentodon_pentandrus_Zambia
Kohautia_coccinea
8,35
Kohautia_cynanchica
22,09
Oldenlandia_herbacea_var_herbacea
17,77
Oldenlandia_rosulata
15,31
Amphiasma_merenkyanum_cB033
28,53
11,17
Pentanopsis_fragrans
8,12
Oldenlandia_stricta_cC023_India
7,12
Oldenlandia_affinis
2,48
Oldenlandia_affinis_bZ039
Oldenlandia_angolensis
4,37
Oldenlandia_goreensis
27,33
5,84
Oldenlandia_trinervia_cC024_Asia
3,98
Oldenlandia_uniflora
9,94
Agathisanthemum_quadricostatum_cC03
Agathisanthemum_chlorophyllum_cB031
4,66
2,51
Agathisanthemum_globosum
3,89
Lelya_osteocarpa
2,69
Agathisanthemum_bojeri
0,43
Lelya_prostrata_cB039
23,43
Oldenlandia_ternata_bZ027_SEAsia
0,5Hedyotis_parryi_cB057_China
0,21
Oldenlandia_tetrangularis_cB052_SEA
Pleiocraterium_verticillare_bS39_In
7,8
Hedyotis_purpurascens_cC032_India
7,34
Hedyotis_articularis_bP48_India
11,49
5,66
Hedyotis_stylosa_bS34_India
2,93
Hedyotis_swertioides_India
Hedyotis_sp_cB011
5,25
Oldenlandia_benguetensis_cB026_SEAs
Hedyotis_decora_cB005_Thailand
10,04
Oldenlandia_vachellii_cB007_China
3,59
Hedyotis_acutangula_cB002_Asia
2,7
Oldenlandia_bracteosa_cB004_China
4,64
Oldenlandia_bodinieri_cB012_China
3,24
Hedyotis_shenzhenensis
1,68 Hedyotis_shiuyingiae_cB018_China
5,95
8,93
Hedyotis_ovata_VH048
Hedyotis_rivalis_bZ035_Malaysia
5,14
2,51
Hedyotis_uncinella_bZ038_China
Hedyotis_korrorensis_aT83_Pacific
4,69
1,64 Hedyotis_megalantha_aT99
2,22
Hedyotis_novoguinensis_cA093_NewGui
0,32
Hedyotis_sp_SKP946
8,56 6,92
Oldenlandia_paridifolia_TM3165_Chin
0,54
Oldenlandia_paridifolia_TM3167_Chin
4,86
Hedyotis_cantoniensis_cA056_China
0,9 Oldenlandia_lancea_cB003_China
0,49
Hedyotis_caudatifolia
0,31
Hedyotis_caudatifolia_cB027_China
Hedyotis_caudatifolia_cB037_China
5,69
1,11 Oldenlandia_consanguinea
0,56
Oldenlandia_consanguinea_aT79_China
4,81
Oldenlandia_assimilis
0,8 Oldenlandia_assimilis_cB055_China
0,48
Oldenlandia_melli_bZ036_China
5,14
Hedyotis_cantoniensis
2,07
Hedyotis_xinyiensis
7,75
2,85
Hedyotis_yangchunensis
2,39
Oldenlandia_pulcherrima
3,52
Hedyotis_effusa_aT081_Asia
2,44
Oldenlandia_tenuipes
0,92Hedyotis_effusa
0,25
Oldenlandia_tenuipes_bZ037_China
Hedyotis_communis_cA055_China
2,47
Hedyotis_sp_bZ022_Vietnam
0,12
Hedyotis_sp_bZ024_Vietnam
3,15
Hedyotis_cathayana_TM3214_China
2,84 1,52 Hedyotis_minutopuberula_TM3219_Chin
Oldenlandia_prostrata_bZ043_SEAsia
2,51
Oldenlandia_cryptantha_TM3202_China
1,88
Hedyotis_cheniana_TM3190_China
0,18
6,48
Oldenlandia_hainanensis_cB028_China
Hedyotis_sp_cA050
Oldenlandia_pubescens_cB042_NewGuin
Hedyotis_fissistipula_cB019_Borneo
3,53 2,38
Hedyotis_philippensis_cB043_Asia
0,37
5,83
Hedyotis_rigida_bZ042_SEAsia
3,15
Hedyotis_macrostegia_Borneo
0,97Hedyotis_pulchella_bZ029_Borneo
2,05
Oldenlandia_nutans_bS27_NewGuinea
5,17
1,15 Hedyotis_schlechteri_cA092_NewGuine
0,95Hedyotis_valetoniana_bZ030_NewGuine
Hedyotis_membranacea_SN78_India
Hedyotis_coprosmoides_bS14_Ceylon
1,31
Hedyotis_tridentata_bS36_Ceylon
4,29
Hedyotis_rhinophylla_aT90_Ceylon
3,31 1,96 0,6Hedyotis_nodulosa_bS26_Ceylon
Metabolos_rugosus_bS7_SEAsia
0,28
Metabolos_decipiens_cC016_Ceylon
0,08
Metabolos_decipiens_cC017_Ceylon
2,36
Hedyotis_fruticosa_aT85_India
Hedyotis_lawsoniae_aT98_Ceylon
Hedyotis_obscura_bS29_Ceylon
2,041,3
0,88Hedyotis_trimenii_bS37_India
1,831,04 Hedyotis_thwaitesii_SN79_India
0,76Hedyotis_dendroides_bS2_Ceylon
1,41 Hedyotis_lessertiana_var_lessertian
Hedyotis_quinquenervia_aT97_Ceylon
Hedyotis_flavescens_SN61_Ceylon
0,95
0,4
Hedyotis_gardnerii_bS016_Ceylon
0,81Hedyotis_lessertiana_var_marginata
0,43
Hedyotis_marginata_SN72_Ceylon
16,89
18,76
22,75
Dendrochilum
1,49
4,44
9,21
Elaeis_oleifera
Nypa_fruticans
Musella_lasiocarpa
Anigozanthos_flavidus
Astelia
Lanaria
Empodium
Hypoxis
Rhodohypoxis
Neuwiedia
Apostasia
Paphiopedilum
Phragmipedium
Selenipedium
Cypripedium
Vanilla
Cleistes
Pogonia
Codonorchis
Disperis
Disa
Monadenia
Habenaria
Platanthera
Orchis
Chiloglottis
Diuris
Microtis
Eriochilus
Chloraea
Pterostylis
Megastylis
Exalaria
Ponthieva
Altenstenia
Spiranthes
Sarcoglottis
Pachyplectron
Dossinia
Ludisia
Goodyera
Platythelys
Palmorchis
Listera
Epipactis
Sobralia
Nervilia
Dendrobium_kingianum
Dendrobium_crystallinum
Dendrobium_officinale
Pleione
Coelogyne_cristata
Dendrochilum_scriptum
Dendrochilum_glumaceum
2,18
Dendrochilum_cobbianum
Agrostophyllum_majus
Earina_autumnalis
Earina_valida
Eria
Wullschlaegelia
Masdevallia
Cattleya
Calanthe
Phalaenopsis
Cymbidium
Galeandra
Mormodes
Bifrenaria
Lycaste
Maxillaria
Zygopetalum
Vitekorchis
Stanhopea
Gongora
posterior
1
PK051_M_sp_4_500to750mASL_PHS
PK183_M_sp_3_1750to2000mASL_GA
0,76
Atractides_cf_propatulus
Epirixanthes_kinabaluensis
PK050_M_nov_sp_1_500to750mASL_PHS
0,64
9,55
Hygrobates_sp_2
PK003_M_mariaelenae_1500to1750mASL_KHQ
0,49
0,12
0
PK073_M_sp_5_500to750mASL_PHS
0,33
3,72
PK256_M_nov_sp_2_1000to1250mASL_MA
Hygrobates_hamatoides
0,25
PK036_M_christae_2500to2750mASL_L2
0
1,71
Hygrobates_hamatus
1,23
0
Extended Data Figure 5 | Chronograms for Athyrium, Begonia, Coeliccia,
Dacrycarpus, Epirixanthes, Dendrochilum, Dicranoloma, Impatiens,
Hygrobates, Hedyotis, Ilex and Myrmarachne. See Supplementary Table 5
G2015
Hygrobates_hamatusH20
for more details. Node colours represent posterior probabilities. Endemic
species printed in red.
Macmillan Publishers Limited. All rights reserved
RESEARCH LETTER
Euphrasia
Paphiopedilum
Rhododendron
Phragmipedium_longifolium
Bartsia
Euphrasia_hookeri
Euphrasia_scabra
Euphrasia_formosissima
Euphrasia_chrysantha
Euphrasia_taurica
1,07
Euphrasia_petiolaris
6,54
Euphrasia_borneensis
3,55
Euphrasia_philippinensis
2,72
Euphrasia_nankotaizanensis
1,75
Euphrasia_tarokoana
1,5
Euphrasia_durietziana
7,61
0,29
Euphrasia_transmorrisonensis
Euphrasia_tricuspidata
5,38
8,49
Euphrasia_grandiflora
Euphrasia_oakesii
1,3
6,41
Euphrasia_randii
Euphrasia_picta
0,62
Euphrasia_spectabilis
3,12
0,89
Euphrasia_marchesettii
0,37
Euphrasia_maximowiczii
Euphrasia_kerneri
1,62
0,86 Euphrasia_hirtella
0,44
Euphrasia_disjuncta
Euphrasia_subarctica
1,31
8,22
0,46Euphrasia_parviflora
0,21
1,03 Euphrasia_rostkoviana
Euphrasia_glabrescens
0,57Euphrasia_vigursii
0,19
Euphrasia_officinalis
Euphrasia_insignis
Euphrasia_cuneata
6,73
Euphrasia_callosa
4,45
6,3
Euphrasia_mirabilis
Euphrasia_disperma
5,96
4,03
Euphrasia_revoluta
2,62
Euphrasia_cockayniana
5,33
Euphrasia_antarctica
7,38
3,34
Euphrasia_alsa
2,71
Euphrasia_phragmostoma
0,42
Euphrasia_collina
Euphrasia_dinarica
Euphrasia_pectinata
2,36
Euphrasia_regelii
1,87
Euphrasia_kashmiriana
4,43
1,4
Euphrasia_fedtschenkoana
Euphrasia_wettsteinii
0,42
Euphrasia_foulaensis
3,29
Euphrasia_arctica
2,15
0,18
Euphrasia_confusa
0,97
Euphrasia_fennica
0,36
Euphrasia_salisburgensis
2,87
Euphrasia_micrantha
1,23
Euphrasia_stricta
0,72
Euphrasia_nemorosa
2,25
Euphrasia_christii
0,95
Euphrasia_alpina
1,72
Euphrasia_cisalpina
1,31
Euphrasia_inopinata
0,66 Euphrasia_minima
0,36
Euphrasia_tetraquetra
9,14
Paphiopedilum_besseae
2,77
3,89
26,5
posterior
1
0
Paphiopedilum_malipoense
2,63
4,83
9,18
Paphiopedilum_micranthum
5,2
Paphiopedilum_concolor
3,56
4,24
Paphiopedilum_niveum
12,77
Paphiopedilum_gratrixianum
1,8
42
Paphiopedilum_exul
5,35
Paphiopedilum_sangii
2,75
9,16
22,13
Paphiopedilum_wardii
1,94
posterior
1
Paphiopedilum_superbiens_var_curtisii
Paphiopedilum_glaucophyllum
3,67
7,22
Paphiopedilum_liemianum
0,53
Paphiopedilum_primulinum
6,07
36,25
Paphiopedilum_randsii
1,8
Paphiopedilum_philippinense
2,76
Paphiopedilum_rothschildianum
2,01
Paphiopedilum_stonei
1,16
6,65
Paphiopedilum_kolopakingii
Paphiopedilum_glanduliferum
1,24
Paphiopedilum_wilhelminiae
4,16
Paphiopedilum_adductum
Paphiopedilum_dianthum
0,32
Paphiopedilum_parishii
3,57
2,13
27,9
Paphiopedilum_haynaldianum
0,93
5
Paphiopedilum_lowii
Paphiopedilum_victoria-regina
Paphiopedilum_druryi
2,46
Paphiopedilum_spicerianum
4,79
1,19
Paphiopedilum_charlesworthii
posterior
1
0,61 Paphiopedilum_villosum_var_boxallii
0,07
Paphiopedilum_insigne
3,78
Paphiopedilum_barbatum
1,48
0
Paphiopedilum_appletonianum
0,46
Paphiopedilum_callosum
2,04
Paphiopedilum_lawrenceanum
Paphiopedilum_fowliei
1,56 0,85
Paphiopedilum_sukhakulii
0,14
Paphiopedilum_tonsum
1,32
0,71
25,14
Paphiopedilum_mastersianum
Paphiopedilum_violascens
1,06
Paphiopedilum_hennisianum
0,79 Paphiopedilum_ciliolare
0,64
Paphiopedilum_javanicum_var_virens
Philalanka
22,46
Zospeum_spelaeum
HQ171582_Zospeum_exiguum_Slovenia
8,12
Callulina_kreffti
54,22
3,08
Zospeum_alpestre
1,53
posterior
1
Breviceps_fuscus
Zospeum_isselianum
4,59
29,94
Zospeum_pretneri
Breviceps_mossambicus
2,67
Kaloula_pulchra
40,37
AB611973_Phrynella_pulchra
27,46
Zospeum_subobesum
21,4
SP13428_Ibycus_rachelae_1000to1250mASL_MA
AB611931_Metaphrynella_pollicaris
15,37
19,96
JX988066_Subulina_octona_unknown
AB611939_Metaphrynella_sundana
12,01
SP13507_Philalanka_spec1_250to500mASL_IN
AB611921_Kalophrynus_pleurostigma
18,33
9,01
SP13492_Philalanka_spec3_500to750mASL_PHS
MJ65_K_sp_2_500to750mASL_IN
16,39
6,66
MJ81_K_baluensis_1750to2000mASL_GA
14,47
SP13510_Philalanka_spec2_1000to1250mASL_MA
3,56
19,72
SP13519_Philalanka_thienemanni_1000to1250mASL_M
MJ64_K_sp_1_500to750mASL_IN
10,68
Carychium_ibazoricum
AB611913_K_interlineatus
60,18
1,26
Asterophrys_turpicola
Carychium_minimum
37,99
Cophixalus_sp_SJR3271
Carychium_clappi
5,73
0,64
Chiasmocleis_shudikarensis
Carychium_floridanum
35,78
Syncope_hudsoni
2,21
Phrynomantis_annectens
49,42
30,17
42,56
Carychium_exiguum
1,4
0
Phrynomantis_bifasciatus
58,51
Carychium_exile
1,04
HQ171529_Carychium_mexicanum_USA
Elachistocleis_ovalis
34,89
Dermatonotus_muelleri
29,24
0
Zospeum_frauenfeldi
0,63
Ramanella_cf_obscura_MNHN_2000_628
34,74
48,85
posterior
1
11,72
Paphiopedilum_delenatii
5,73
22,6
Kalophrynus
68,65
Cassiope_fastigiata
Cassiope_tetragona
Rhododendron_camtschaticum
Rhododendron_redowskianum
Rhododendron_leptothrium
Rhododendron_vialii
Rhododendron_hongkongense
Rhododendron_ovatum
Rhododendron_bachii
Rhododendron_mitriforme
Rhododendron_semibarbatum
Rhododendron_henryi
4,15
14,44
Rhododendron_latoucheae
Rhododendron_moulmainense
7,35
Rhododendron_championiae
3,4
Rhododendron_subestipitatum
5,63
2,49Rhododendron_cavaleriei
1,98
Rhododendron_dayaoshanense
5,02
Rhododendron_westlandii
2,61
Rhododendron_hancockii
Rhododendron_feddei
4,15
2,86
Rhododendron_tutcherae
3,63
Rhododendron_stamineum
19,61
2,89
Rhododendron_mackenzianum
Rhododendron_sanctum
4,83
Rhododendron_weyrichii
Rhododendron_farrerae
6,7
10,16
Rhododendron_reticulatum
4,12
Rhododendron_dilatatum
2,68
Rhododendron_kiyosumense
8,11
Rhododendron_mayebarae
3,28
Rhododendron_viscistylum
5,91
Rhododendron_lagopus
4,69
Rhododendron_tashiroi
17,08
3,88
Rhododendron_mariesii
3,48
Rhododendron_wadanum
Rhododendron_serpyllifolium
8,78
Rhododendron_indicum
3,98
Rhododendron_tsusiophyllum
Rhododendron_boninense
12,4
7,37
Rhododendron_kaempferi
5,63
Rhododendron_kiusianum
9,13
Rhododendron_transiens
5,01
Rhododendron_macrosepalum
7,56
Rhododendron_amanoi
6,29
Rhododendron_scabrum
5,16
Rhododendron_yakuinsulare
4,21
Rhododendron_eriocarpum
2,57
Rhododendron_tosaense
Rhododendron_albiflorum
12,91
Rhododendron_albrechtii
17,79
Rhododendron_nipponicum
14,96
Rhododendron_schlippenbachii
Rhododendron_tomentosum_subsp_tomentosum
Rhododendron_micranthum
Rhododendron_ferrugineum
Rhododendron_virgatum
18,93
7,08
Rhododendron_primuliflorum
11,69
6,42
Rhododendron_fastigiatum
2,81
Rhododendron_rubiginosum
16,62
Rhododendron_trichocladum
10,57
7,69
Rhododendron_pachypodum
7,25
Rhododendron_mucronulatum
5,92
Rhododendron_edgeworthii
9,5
Rhododendron_mollicomum
3,67
Rhododendron_racemosum
6,37
16,62
Rhododendron_spiciferum
3,94
Rhododendron_scabrifolium
2,52 Rhododendron_duclouxii
1,81
Rhododendron_spinuliferum
Rhododendron_santapaui
12,05
Rhododendron_borneense
5,72
Rhododendron_cuneifolium
2,87
Rhododendron_ericoides
Rhododendron_acuminatum
14,6
4,09
Rhododendron_fallacinum
Rhododendron_crassifolium
4,61
Rhododendron_bagobonum
2,92
10,91
Rhododendron_stenophyllum
6,33
Rhododendron_exuberans
4,01
Rhododendron_javanicum
2,43
9,58
Rhododendron_lowii
Rhododendron_rugosum
4,29
Rhododendron_buxifolium
6,25
Rhododendron_praetervisum
5,13
Rhododendron_stapfianum
4,07
Rhododendron_orbiculatum
2,83
Rhododendron_suaveolens
Rhododendron_canadense
13,64
Rhododendron_occidentale
7,82
Rhododendron_luteum
5,4
Rhododendron_molle
Rhododendron_aureum
19,66
10,65
Rhododendron_maximum
8,57
Rhododendron_ponticum
Rhododendron_vernicosum
14,19
9,26
Rhododendron_irroratum
4,04
Rhododendron_formosanum
Rhododendron_agastum
4,39
11,74
Rhododendron_delavayi
Rhododendron_sinogrande
7,39
Rhododendron_grande
9,72
Rhododendron_forrestii
3,81
Rhododendron_campylocarpum
3,02 Rhododendron_lukiangense
8,74
2,62 Rhododendron_wardii
1,98
Rhododendron_anthosphaerum
Rhododendron_selense
2,71
7,16
Rhododendron_decorum
3,19
Rhododendron_cyanocarpum
2,11
Rhododendron_neriiflorum
Rhododendron_aberconwayi
Rhododendron_alutaceum
6,31 3,22
1,21Rhododendron_aganniphum
0,7
Rhododendron_beesianum
2,19
Rhododendron_bureavii
1,09Rhododendron_fulvum
6,31
0,59
Rhododendron_rex_subsp_fictolacteum
Rhododendron_rubropunctatum
Rhododendron_williamsianum
5,1
2,34
Rhododendron_auriculatum
4,23
Rhododendron_floccigerum
3,42
Rhododendron_glischrum
1,89 Rhododendron_dimitrum
1,89
Rhododendron_argyrophyllum
0,61
Rhododendron_fortunei
10,32
Phragmipedium_schlimii
1,21
4,88
Hypopachus_variolosus
18,93
Ptomaphaginus
Gastrophryne_carolinensis
RMNH_INS_549243_Prionochaeta_harmandi_Japan
Dyscophus_antongilii
55,9
20,77
Dyscophus_insularis
47,32
Dytiscus_dauricus
Micryletta_inornata
0,15
1,55
Calluella_guttulata
41,53
Dytiscus_alaskanus
25,88
2,59
Microhyla_butleri
38,18
Microhyla_pulchra
32,43
53,15
Carabus_lewisianus
0,88
Ranunculus
0,06
Microhyla_heymonsi
28,48
Carabus_kimurai
Glyphoglossus_molossus
posterior
1
Paradoxophyla_palmata
29,56
0,12
Carabus_albrechti
5,17
Scaphiophryne_calcarata
47,98
Otophryne_pyburni
0,1
2,14
24,02
RMNH_INS_555623_Ptomaphaginus_ater_3000to3250mASL_L2
0,98
Rhombophryne_alluaudi
24,54
4,39
RMNH_INS_555618_Ptomaphaginus_n_sp_bryanti_complex_2750to3000mASL_
16,95
Rhombophryne_testudo
7,03
0,7
21,61
RMNH_INS_555632_Ptomaphaginus_nr_fagei_1750to2000mASL_GA
Stumpffia_psologlossa
1,99
14,32
Stumpffia_pygmaea
6,52
RMNH_INS_555607_Ptomaphaginus_latescens_1500to1750mASL_KHQ
Nepenthes (ITS)
1,6
RMNH_INS_555598_Ptomaphaginus_bryantioides_250to500mASL_Kiansom
1,05
5,33
0,66
RMNH_INS_555603_Ptomaphaginus_kinabaluensis_1500to1750mASL_KHQ
Ancistrocladus_tectorius
27,11
0,42
Triphyophyllum_peltatum
14,03
RMNH_INS_555611_Ptomaphaginus_cf_latimanus_750to1000mASL_SA
Dioncophyllum_thollonii
Nepenthes_ampullaria
53,45
17,91
Nepenthes_rafflesiana
2,93
Nepenthes_hemsleyana
8,84
4,61
Nepenthes_mirabilis
1,48
Nepenthes_kamotiana
32,1
38,68
36,47
Nepenthes_tentaculata
Nepenthes_northiana
Nepenthes_villosa
31,72
75,68
48,14
Nepenthes_villosa3
1,36
Nepenthes_villosa2
5,47
27,06
3,07
Nepenthes_edwardsiana3
1,34
Nepenthes_edwardsiana2
14,6
40,95
68,99
Nepenthes_x_kinabaluensis
24,97
5,58
31,84
39,04
Nepenthes_rajah2
1,55
Nepenthes_rajah
29,74
Nepenthes_lowii
10,84
4,23
1,84
7,56
Nepenthes_glandulifera
34,27
Nepenthes_chaniana
Nepenthes_maxima
5,15
22,16
53,33
Nepenthes_boschiana
3,79
Nepenthes_hurrelliana
2,17 Nepenthes_fusca
1,24
Nepenthes_vogelii
Nepenthes_campanulata
13,52
Nepenthes_truncata
4,23
19,97
Nepenthes_peltata
Nepenthes_ventricosa
9,05
35,28
Nepenthes_alata
31,42
Nepenthes_specatabilis
5,93
18,29
Nepenthes_gymnamphora
3,34
1,63
15,89
47,79
Nepenthes_insignis
Nepenthes_bongso
Nepenthes_reinwardtiana
40,08
Nepenthes_benstonei
11,5
Nepenthes_macfarlanei
0
3,22
8,14
Nepenthes_singalana
3,22
2,73
2,52
6,36
Nepenthes_kongkandana
posterior
1
35,84
Nepenthes_vieillardii
Nepenthes_andamana
Nepenthes_gracillima
2,4
3,29
Nepenthes_sanguinea
Nepenthes_alba
1,29
Nepenthes_ramispina
2,28
Nepenthes_albomarginata
1,27
Nepenthes_bokorensis
34,47
Nepenthes (matK)
Drosophyllum_lusitanicum
Ancistrocladus_abbreviatus
Habropetalum_dawei
11,37
Triphyophyllum_peltatum
5,27
Dioncophyllum_thollonii
Nepenthes_macrovulgaris
5,6
Nepenthes_bicalcarata
Nepenthes_bellii
1,18
Nepenthes_merrilliana
7,87
Nepenthes_insignis
4,81
Nepenthes_sibuyanensis
3,64
Nepenthes_ventricosa
0,63
Nepenthes_burkei
Nepenthes_murudensis
15,85
3,21
Nepenthes_muluensis
7,38
Nepenthes_glabrata
4,44
Nepenthes_hamata
Nepenthes_faizaliana
13,87
6,46
Nepenthes_lowii
4,03
Nepenthes_clipeata
2,69
Nepenthes_ephippiata
8,55
Nepenthes_mira
3,59
Nepenthes_alata
Nepenthes_stenophylla
6,66
2,51
Nepenthes_fusca
1,95
Nepenthes_burbidgeae
5,06
Nepenthes_pilosa
1,5
Nepenthes_eymae
3,53
Nepenthes_maxima
2,88
Nepenthes_veitchii
Nepenthes_reinwardtiana
Nepenthes_mikei
10,02
Nepenthes_gracillima
7,1
Nepenthes_sanguinea
4,52
Nepenthes_ramispina
0,66
Nepenthes_macfarlanei
14,34
Nepenthes_petiolata
2,65
Nepenthes_truncata
6,24
Nepenthes_edwardsiana2
Nepenthes_edwardsiana3
4,46
1,02
Nepenthes_rajah
3,5
Nepenthes_villosa3
12,36
2,45
Nepenthes_villosa2
8,57
1,75 Nepenthes_rajah2
1,05
Nepenthes_villosa_2
Nepenthes_boschiana
Nepenthes_thorelii
2,14 Nepenthes_rafflesiana
7,36
0,72
Nepenthes_albomarginata
6,71
Nepenthes_gracilis2
2,13
Nepenthes_mapuluensis
4,13
Nepenthes_hirsuta
9,91
1,59 Nepenthes_ampullaria
0,47
Nepenthes_mirabilis
Nepenthes_tobaica
3,62
Nepenthes_lavicola
Nepenthes_spathulata
6,11
2,96
Nepenthes_talangensis
0,68
Nepenthes_aristolochioides
5,01
Nepenthes_densiflora
3,01
Nepenthes_singalana
7,58
0,96
Nepenthes_diatas
Nepenthes_bongso
1,17
Nepenthes_gymnamphora
Nepenthes_dubia
5,09
1,45
Nepenthes_inermis
Nepenthes_adnata
4,37 2,43
Nepenthes_longifolia
Nepenthes_spectabilis
3,89
1,7
Nepenthes_ovata
2,79
Nepenthes_eustachya
2,51
Nepenthes_sumatrana
1,62
Nepenthes_rhombicaulis
38,11
24,32
53,03
30,88
posterior
1
20,42
0
31,37
0
29
Sarcosperma_laurinum
Eberhardtia_aurata
Omphalocarpum_pachysteloides
Sideroxylon_oxyacanthum
11,14
Xantolis_siamensis
Englerophytum_natalense
Poutera_firma_EDNA09_01389
24,31
Pouteria_sp
19,5
Pouteria_maclayana_EDNA09_00990
10,56
Pouteria_sp_EDNA09_02322
Sideroxylon_salicifolium
Argania_spinosa
18,39
Sideroxylon_mascatense
Sideroxylon_wightianum
Sideroxylon_inerme
9,49
Sideroxylon_marginatum
25,31
Sideroxylon_marmulano
20,06
Sideroxylon_saxorum
10,03
Sideroxylon_betsimisarakum
6,63
Sideroxylon_majus
1,69Sideroxylon_cubense
Sideroxylon_repens
17,9
Sideroxylon_floribundum
11,2
Sideroxylon_capiri
7,17
Sideroxylon_foetidissimum
3,88
Sideroxylon_tepicense
Sideroxylon_lanuginosum
0,83
1,72Sideroxylon_reclinatum
Sideroxylon_lycioides
0,56
Sideroxylon_tenax
25,54
Sideroxylon_persimile
Nesoluma_polynesiacum
17,92
Sideroxylon_occidentale
14,46
Sideroxylon_obtusifolium
11,51
9,15
3,49 Sideroxylon_horridum
Sideroxylon_angustum
7,47
Sideroxylon_americanum
5,14
Sideroxylon_confertum
3,35 Sideroxylon_obovatum
2,06 Sideroxylon_picardae
Lecomtedoxa_klaineana
Neolemonniera_clitandrifolia
Northia_seychellana
Capurodendron_androyense
Inhambanella_henriquesii
Baillonella_toxisperma_EDNA09_01453
20,72
Vitellaria_paradoxa
17,35
Vitellariopsis_marginata
0,75
Vitellariopsis_cuneata
0,28
Vitellariopsis_dispar
26,01
Mimusops_obovata
7,39
Mimusops_elengi
4,89
Mimusops_caffra
3,07 Mimusops_comorensis
2,49 Mimusops_zeyheri
22,99
Tieghemella_heckelii
Autranella_congolensis
22,12
3,06 Labramia_costata
Labramia_mayottensis
15,87
20,87
Faucherea_parvifolia
5,35
2,07 Labourdonnaisia_calophylloides
Labourdonnaisia_revoluta
18,53
Manilkara_concolor
11,44
Manilkara_zapota
Manilkara_hexandra
16,2
10,51
Manilkara_kauki
14,21
Letestua_durissima
8,82
Manilkara_obovata
6,74
Manilkara_discolor
Palaquium_impressionervium_EDNA09_00720
Palaquium_clarkeanum_EDNA09_00716
Palaquium_rufolanigerum_EDNA09_01133
7,56
2,11 Palaquium_microphyllum
0,97
Palaquium_microphyllum_EDNA09_02312
25,76
6,05
Palaquium_sumatranum_EDNA09_00955
3,41 Palaquium_rostratum_EDNA09_00956
1,23
Palaquium_pseudorostratum_EDNA09_01131
0,31
Palaquium_rigidum_EDNA09_01129
18,08
Palaquium_sp_EDNA09_02320
8,63
Palaquium_dasyphyllum_EDNA07_01936
6,88
Palaquium_formosanum_EDNA09_00722
4,2
Palaquium_sericeum_EDNA09_02304
0,57
Palaquium_sericeum_EDNA09_01452
Palaquium_quercifolium_EDNA09_01451
10,45
4,67
Palaquium_galactoxylon_EDNA09_00987
0,85
Palaquium_sp_EDNA09_00989
Aulandra_longifolia
4,62
Diploknema_oligomera
8,66 5,49
Palaquium_calophyllum_EDNA09_00992
4,56
Palaquium_eriocalyx_EDNA09_00993
3,58
1 Palaquium_leiocarpum_EDNA09_01130
Palaquium_oxleyanum_EDNA09_00719
7,1
Palaquium_cryptocarifolium_EDNA09_01144
0,84
Palaquium_herveyi_EDNA09_01141
Palaquium_xanthochymum_EDNA09_00721
5,13
Palaquium_gutta_EDNA09_00717
6,39
4,02
Palaquium_ridleyi_EDNA09_01132
1,09
Palaquium_hexandrum_EDNA09_01142
0,59
6,19
Palaquium_walsurifolium_EDNA09_01135
Palaquium_obovatum_EDNA09_00718
Palaquium_beccarianum_EDNA09_00952
5,15
0,42
Palaquium_maingayi_EDNA09_00957
4,23
Palaquium_brassii_EDNA09_01385
2,89 Palaquium_amboinense
1,04
Palaquium_lobbianum_EDNA09_02319
2,14 Isonandra_compta_EDNA09_00984
Isonandra_sp
22,54
Madhuca_crassipes
0,42
Madhuca_utilis
20,82
Isonandra_perakensis_EDNA09_00998
14,91
Isonandra_lanceolata_EDNA09_02321
Burckella_sp_EDNA09_02325
10,39
Burckella_macropoda_EDNA09_00995
7,72
Burckella_polymera_EDNA09_01388
Madhuca_hainanensis
Madhuca_longifolia_EDNA09_02311
18,62
23,61
Diploknema_siamensis_EDNA09_2330
15,98
Diploknema_butyracea
21,03
Payena_acuminata
8,5
Payena_maingayi_EDNA09_00988
16,15
Payena_lucida_EDNA09_02306
22,5
11,14
Payena_leerii_EDNA09_02317
5,59
Payena_ferruginea_EDNA09_02314
3,8
e4003829276_P_gigas_830mASL_OL
3,07 e4003829322_P_microphylla_627mASL_IN
1,56e4003829348_P_kinabaluensis_844mASL_OL
0,67
Payena_obscura_EDNA09_02313
22,48
Madhuca_pachyphylla_EDNA09_01386
6,28
Madhuca_fulva_EDNA09_00985
5,02
Madhuca_microphylla
7,59
Madhuca_oblongifolia_EDNA09_01379
Madhuca_malaccensis_EDNA09_00958
4,44 1,33
Madhuca_laurifolia_EDNA09_02184
3,93
Madhuca_palembanica
3,3
Madhuca_korthalsii_EDNA09_01380
15,52
2,58 Madhuca_sericea_EDNA09_01378
1,25
Madhuca_elmeri_EDNA09_02183
0,67
Madhuca_sarawakensis_EDNA09_01136
Madhuca_leucodermis
Madhuca_palida_EDNA09_01139
5,2
Madhuca_curtisii_EDNA09_02307
9,27
0,99
Madhuca_sp_nov_EDNA09_01383
Madhuca_kunstleri_EDNA09_01138b
7,8
4,75
Madhuca_erythrophylla_EDNA09_01137
3,56
Madhuca_lancifolia_EDNA09_01382
6,04
Madhuca_prolixa_EDNA09_01381
4,64 2,49 Madhuca_barbata_EDNA09_01143
Madhuca_kuchingensis_EDNA09_01134
4,12
Madhuca_kingiana_EDNA09_00954
3,64
Madhuca_motleyana
56,82
39,46
24,52
53,03
34,51
13,28
31,8
16,07
17,89
66,83
59,36
32,21
11,76
38,57
102,14
57,72
34,07
77,19
34,38
37,1
26,52
14,01
71,34
49,39
39,36
19,41
32,6
23,38
53,91
16,11
68,88
34,93
posterior
1
39,82
33,16
48,92
44,13
42,76
7,68
40,79
28,07
25,59
61,82
38,74
16,47
32,58
13,75
23,48
18,96
40,81
50,11
24,5
43,03
25,45
45,63
38,32
8,57
33,24
26,22
16,72
37,24 33,18
31,92
35,98
27,67
24,3
32,9
13,71
29,23
22,84
0
18,43
14,07
12,1
16,55
13,82
8,73
8,5
39,86
9,33
posterior
1
37,17
35,7
0
29,34
Extended Data Figure 6 | Chronograms for Euphrasia, Kalophrynus,
Nepenthes, Paphiopedilum, Philalanka, Ptomaphaginus, Payena,
Trichosanthes, Rhododendron, Ranunculus, Tritetrabdella and
G2015
29
6,13
4,49
Momordica_charantia
Lagenaria_siceraria
Austrobryonia_micrantha
Bryonia_dioica
Ecballium_elaterium
Hodgsonia_heteroclita
Nothoalsomitra_suberosa
Luffa_echinata
Luffa_operculata
Luffa_acutangula
Luffa_graveolens
Luffa_aegyptiaca
Linnaeosicyos_amara
Cyclanthera_pedata
Sicyos_angulatus
Marah_macrocarpus
Echinocystis_lobata
Trichosanthes_auriculata
Trichosanthes_postarii1
0,49
Trichosanthes_postarii2
Trichosanthes_subvelutina2
Trichosanthes_subvelutina1
20,76
6,57
Trichosanthes_subvelutina3
Trichosanthes_nervifolia
7,31
2,31 Trichosanthes_cucumerina1
19,92
Trichosanthes_cucumerina2
13,99
Gymnopetalum_tubiflorum3
2,98
Gymnopetalum_tubiflorum1
1,3 Gymnopetalum_tubiflorum2
16,52
Trichosanthes_dioica
Trichosanthes_beccariana
8,38
Trichosanthes_adhaerens
13,22
6,21
Trichosanthes_pendula
4,54
Trichosanthes_mucronata
10,95
Trichosanthes_pilosa_var._roseipulpa
5,44
Trichosanthes_baviensis
4,2
Trichosanthes_pilosa2
7,19
Trichosanthes_holtzei
3,76
Trichosanthes_pilosa1
1,33Trichosanthes_pilosa4
Trichosanthes_villosa2
3,41
Trichosanthes_villosa1
Trichosanthes_villosa5
12,36
3,55
Trichosanthes_villosa3
7,11
Trichosanthes_kerrii
0,79
Trichosanthes_villosa4
4,15
Trichosanthes_phonsenae1
3,06
23,87
Trichosanthes_phonsenae2
Trichosanthes_reticulinervis
17,73
Trichosanthes_smilacifolia
Trichosanthes_truncata3
5,98
21,26
Trichosanthes_truncata1
0,61
Trichosanthes_truncata2
Trichosanthes_miyagii
15,66
Trichosanthes_homophylla
4,97
Trichosanthes_hylonoma
9,35
5,89
Trichosanthes_rosthornii1
2,48
Trichosanthes_rosthornii2
8,17
Trichosanthes_multiloba1
0,95
Trichosanthes_multiloba2
6,47
Trichosanthes_kirilowii_var._japonica1
3,22
Trichosanthes_kirilowii_var._japonica3
1,63
Trichosanthes_kirilowii_var._japonica2
Gymnopetalum_scabrum2
7,34
Gymnopetalum_scabrum3
3,42
Gymnopetalum_scabrum1
Trichosanthes_laeoica1
23,57
7,2
Trichosanthes_edulis
4,73
Trichosanthes_dentifera
3,74
Trichosanthes_laeoica2
13,26
Trichosanthes_odontosperma1
5,21
Trichosanthes_pilosa3
8,76
Trichosanthes_odontosperma2
2,91
Trichosanthes_odontosperma3
Trichosanthes_pubera_var._fissisepala2
Trichosanthes_pubera_var._rubriflos1
4,79
1,18Trichosanthes_pubera_var._fissisepala1
2,87
1,43 Trichosanthes_pubera_var._rubriflos2
Trichosanthes_tricuspidata_subsp._tricuspidata
Trichosanthes_wallichiana
14,38
Trichosanthes_schlechteri
23,81
13,52
Gymnopetalum_chinense
6,54
Gymnopetalum_orientale
1,23Trichosanthes_quinquangulata1
Trichosanthes_quinquangulata2
12,16
Trichosanthes_inthanonensis2
18,03
Trichosanthes_bracteata
5,5
2,62
Trichosanthes_lepiniana2
4,47
Trichosanthes_inthanonensis1
2,46
Trichosanthes_tricuspidata_subsp._javanica
3,38
Trichosanthes_lepiniana1
1,48 Trichosanthes_lepiniana3
15,38
Trichosanthes_fissibracteata
5,55
Trichosanthes_laceribractea3
8,55
Trichosanthes_laceribractea1
5,04
Trichosanthes_laceribractea2
Trichosanthes_pedata
6,95
Trichosanthes_quinquefolia
8,08
Trichosanthes_pallida1
13,19
2,63
Trichosanthes_pallida2
9,97
Trichosanthes_wawrae
5,57
Trichosanthes_papuana
3,39
Trichosanthes_pentaphylla1
1,69 Trichosanthes_pentaphylla2
12,33
Trichosanthes_celebica
6,16
Trichosanthes_elmeri
Trichosanthes_sepilokensis
10,18
4,87
Trichosanthes_montana_subsp._crassipes
3,82
Trichosanthes_montana_subsp._montana
8,55
Trichosanthes_borneensis
5,81
Trichosanthes_globosa
7,58
Trichosanthes_intermedia
6,12
Trichosanthes_kinabaluensis
3,75
Trichosanthes_obscura
0,64
Tritetrabdella
Hirudinaria_manillensis
Haemadipsa_rjukjuana
4,47
Haemadipsa_sylvestris
3,33
Haemadipsa_ornata
4,83
Haemadipsa_hainana
16,67
4,41
Haemadipsa_japonica_japonica
3,33
Haemadipsa_zeylanica_montivindicis
2,68
Haemadipsa_picta
Haemadipsa_cavatuses
8,64
6,39
0,73
4,38
posterior
1
SP13383_T_kinabalensis_inobongensis_250to500mASL_IN
SP13398_T_kinabalensis_kinabalensis_1750to2000mASL_G
Tritetrabdella_scandens
3,22
Tritetrabdella_taiwana_C
2,89
0,87
7,23
Tritetrabdella_taiwana_A
Tritetrabdella_taiwana_B
Domanibdella_EB_2010
Nesophilaemon_skottsbergii
Domanibdella_palmyrae
Idiobdella_seychellensis
3,96
21,1
22,56
0
5,35
44,34
83,97
3,77
1,07
1,73
6,25
Orchidaceae – Paphiopedilum
Anigozanthos_flavidus
Musella_lasiocarpa
Elaeis_oleifera
Nypa_fruticans
Astelia
Lanaria
Empodium
Hypoxis
Rhodohypoxis
Apostasia
Neuwiedia
Vanilla
Cleistes
Pogonia
Cypripedium
Selenipedium
Phragmipedium
Paphiopedilum_delenatii
Paphiopedilum_haynaldianum
Codonorchis
Disperis
Disa
Monadenia
Habenaria
Orchis
Platanthera
Diuris
Chiloglottis
Eriochilus
Microtis
Chloraea
Pterostylis
Megastylis
Exalaria
Ponthieva
Altenstenia
Sarcoglottis
Spiranthes
Pachyplectron
Dossinia
Ludisia
Goodyera
Platythelys
Palmorchis
Epipactis
Listera
Sobralia
Nervilia
Dendrobium_kingianum
Dendrobium_officinale
Dendrobium_crystallinum
Calanthe
Pleione
Agrostophyllum_majus
Earina_autumnalis
Earina_valida
Eria
Wullschlaegelia
Cattleya
Masdevallia
Phalaenopsis
Cymbidium
Galeandra
Mormodes
Bifrenaria
Lycaste
Maxillaria
Zygopetalum
Vitekorchis
Gongora
Stanhopea
4,24
Trichosanthes
7,89
60,75
posterior
1
1,46
2,19
3,49
50,28
106,78
4,03
Payena
Nepenthes_gracilis2
5,71
posterior
1
5,65
RMNH_INS_555592_Ptomaphaginus_similipes_250to500mASL_Sugud
0
Drosophyllum_lusitanicum
36,21
0,48
2,41
Plethodontohyla_brevipes
27,07
Anemone_quinquefolia
Isopyrum_thalictroides
Coptis_trifolia
Coptis_quinquefolia
Coptis_japonica
Coptis_lutescens
Coptis_chinensis
Coptis_deltoidea
Coptis_omeiensis
Coptis_teeta
Kumlienia_hystricula
Peltocalathos_baurii
Callianthemoides_semiverticillatus
Hamadryas_delfinii
Beckwithia_andersonii
1,34
Cyrtorhyncha_ranunculina
2,85
Oxygraphis_polypetala
Arcteranthis_cooleyae
2,41
0,97
Trautvetteria_grandis
1,97
Halerpestes_cymbalaria
1,02
Halerpestes_uniflora
Coptidium_lapponicum
1,05
Coptidium_pallasii
2,45
Ficaria_fascicularis
1,17
Ficaria_verna
Myosurus_minimus
Ceratocephala_falcata
1,42
Ceratocephala_orthoceras
Krapfia_clypeata
1,27
Laccopetalum_giganteum
Ranunculus_thora
1,05
Ranunculus_hybridus
0,69
Ranunculus_brevifolius_subsp_brevifolius
Ranunculus_glacialis
Ranunculus_cacuminis
1,37
2,97
Ranunculus_aconitifolius
1,19
0,49
Ranunculus_platanifolius
0,82
Ranunculus_kuepferi_subsp_orientalis
0,56
Ranunculus_seguieri
2,08
Ranunculus_gramineus
1,2
Ranunculus_acetosellifolius
0,88
Ranunculus_pyrenaeus
0,59
Ranunculus_amplexicaulis
0,18Ranunculus_parnassiifolius_subsp_parnassiifolius
1,93
Ranunculus_crenatus
0,69
Ranunculus_magellensis
1,63
Ranunculus_traunfellneri
0,95
Ranunculus_alpestris
0,64
Ranunculus_bilobus
Ranunculus_lyallii
Ranunculus_apiifolius
2,56
Ranunculus_gmelinii
2,25
Ranunculus_collinus
0,68
1,88
Ranunculus_papulentus
Ranunculus_sceleratus
1,58
1,06
Ranunculus_fuegianus
0,68
Ranunculus_hyperboreus
1,45
Ranunculus_natans
0,71
Ranunculus_radicans
1,31
Ranunculus_sphaerospermus
3,22
Ranunculus_nipponicus
1,01
0,55
Ranunculus_trichophyllus
0,75
Ranunculus_peltatus_subsp_peltatus
0,36 Ranunculus_penicillatus_subsp_pseudofluitans
Ranunculus_rufosepalus
0,92
Ranunculus_gelidus
0,8
Ranunculus_adoneus
0,75
Ranunculus_cardiophyllus
Ranunculus_pedatifidus
0,59
1,25
0,38 Ranunculus_nivalis
Ranunculus_pygmaeus
0,75
Ranunculus_micranthus
0,48
Ranunculus_notabilis
0,33 Ranunculus_carpaticola
0,89
0,2 Ranunculus_cassubicifolius
Ranunculus_punctatus
Ranunculus_longicaulis
0,73
0,25 Ranunculus_pseudohirculus
0,53
Ranunculus_hirtellus
0,49 0,19Ranunculus_brotherusii
Ranunculus_pulchellus
0,41
Ranunculus_cf_pseudopygmaeus_KE2011
0,33 Ranunculus_nephelogenes
0,22Ranunculus_membranaceus
Ranunculus_meyeri
1,34
Ranunculus_aquatilis
0,62
Ranunculus_hydrophilus
2,43
Ranunculus_alismifolius
Ranunculus_lingua
0,37 Ranunculus_flammula
1,85
0,1
Ranunculus_reptans
Ranunculus_lateriflorus
1,58
0,94
Ranunculus_flagelliformis
0,61
Ranunculus_ophioglossifolius
1,31
Ranunculus_volkensii
0,92
Ranunculus_cheirophyllus
0,69
Ranunculus_ficariifolius
Ranunculus_bonariensis
Ranunculus_neapolitanus
Ranunculus_bulbosus_subsp_bulbosus
1,01
Ranunculus_polyanthemos
0,81
0,15
0,37 Ranunculus_serpens_subsp_nemorosus
Ranunculus_submarginatus
1,61
0,16
Ranunculus_sardous
2,27
Ranunculus_pensylvanicus
Ranunculus_amerophyllus
1,01
Ranunculus_chinensis
0,81 0,53
Ranunculus_cantoniensis
0,34 Ranunculus_silerifolius
0,65
Ranunculus_lowii
0,43
Ranunculus_saruwagedicus
1,97
0,37 Ranunculus_brassii
0,32 Ranunculus_basilobatus
0,15
Ranunculus_pseudolowii
Ranunculus_peduncularis
0,94
Ranunculus_caprarum
Ranunculus_raeae
Ranunculus_tenuirostris
1,2 0,92
Ranunculus_multifidus
1,78
0,5
Ranunculus_pinnatus
1,08
Ranunculus_trilobus
0,69
Ranunculus_cornutus
0,47
1,63
0,33 Ranunculus_marginatus
Ranunculus_muricatus
Ranunculus_macounii
0,42
Ranunculus_repens
Ranunculus_oreophytus
1,421,22
Ranunculus_diffusus
1,02
Ranunculus_orthorhynchus
0,57
Ranunculus_maclovianus
1,26
3,1
0,3 Ranunculus_hawaiensis
Ranunculus_mauiensis
Ranunculus_septentrionalis
1,01 0,75
Ranunculus_petiolaris
0,95
Ranunculus_acriformis
0,61
0,25 Ranunculus_fascicularis
Ranunculus_hispidus
Ranunculus_arvensis
1,66
Ranunculus_sojakii
0,76
Ranunculus_caucasicus
0,51
Ranunculus_brutius
0,3 Ranunculus_dissectus_subsp_napellifolius
2,87
Ranunculus_pinardi
Ranunculus_sericeus
2,18
Ranunculus_constantinopolitanus
0,99
Ranunculus_grandiflorus
1,77
0,66
Ranunculus_strigillosus
Ranunculus_chius
0,39
1,45
Ranunculus_parviflorus
Ranunculus_stagnalis
0,46
Ranunculus_tembensis
1,3
Ranunculus_baldshuanicus
0,96
0,45
Ranunculus_cassius
0,83
0,29 Ranunculus_occidentalis
Ranunculus_uncinatus
1,1
Ranunculus_kotschyi
0,42
Ranunculus_velutinus
2,93
Ranunculus_granatensis
0,9
0,23 Ranunculus_serbicus
Ranunculus_laetus
0,73 0,43
Ranunculus_taisanensis
0,63
Ranunculus_lanuginosus
0,5
Ranunculus_acris
0,25 Ranunculus_glabriusculus
0,2 Ranunculus_japonicus
Ranunculus_brachylobus
0,33 Ranunculus_breyninus
0,66
Ranunculus_buhsei
0,48
0,34 Ranunculus_cappadocicus
Ranunculus_amblyolobus
Ranunculus_cortusifolius
Ranunculus_gregarius
1,33
0,8
Ranunculus_bullatus
0,99
Ranunculus_spicatus
2,13
0,74
Ranunculus_ollissiponensis
0,38 Ranunculus_pseudomillefoliatus
0,24 Ranunculus_paludosus
Ranunculus_regelianus
0,86
Ranunculus_macropodoides
0,59
Ranunculus_papyrocarpus
1,81
1,23
Ranunculus_makaluensis
Ranunculus_leptorrhynchus
0,9
0,08
Ranunculus_linearilobus
0,68
Ranunculus_afghanicus
0,46
Ranunculus_aucheri
0,29 Ranunculus_elbrusensis
0,11
Ranunculus_termei
Ranunculus_carpaticus
1,66
Ranunculus_villarsii
0,88
Ranunculus_marschlinsii
0,55
Ranunculus_pseudomontanus
0,71
0,43
Ranunculus_carinthiacus
0,31 Ranunculus_aduncus
0,61
0,19Ranunculus_venetus
Ranunculus_gouanii
0,48
Ranunculus_pollinensis
1,55
0,34 Ranunculus_apenninus
0,24 Ranunculus_montanus
0,17Ranunculus_sartorianus
Ranunculus_millefoliatus
1,05
Ranunculus_heterorrhizus
0,74
Ranunculus_illyricus
Ranunculus_cicutarius
1,39
0,81
Ranunculus_hierosolymitanus
0,57
Ranunculus_millefolius
0,33 Ranunculus_macrorrhynchus
1,2
Ranunculus_garganicus
Ranunculus_gracilis
0,97 0,63
Ranunculus_asiaticus
0,91
Ranunculus_oxyspermus
0,64 0,33 Ranunculus_argyreus
Ranunculus_damascenus
0,54
Ranunculus_psilostachys
0,39
0,27 Ranunculus_sprunerianus
Ranunculus_rumelicus
2,26
3,41
3,57
9,27
Platypelis_grandis
0
7,54
Carabus_japonicus
Anodonthyla_montana
29,63
Carabus_yamato
0,06
Anodonthyla_boulengerii
46,69
Phytobdella_meyeri
2,68
Planobdella_sp_EB_2010
3,37
Malagabdella_fallax
3,26
Malagabdella_vagans
2,76
5,76
Malagabdella_niarchosorum
Philaemon_gloriosi
3,81
Leiobdella_sp_EB_2010
3,26
Neoterrabdella_australis
Chtonobdella_whitmani
4,75
2,71
Chtonobdella_bilineata
2,01
Philaemon_sp_brown_EB_2010
4,21
Philaemon_cf_grandis_EB_2010
3,01
Philaemon_sp_green_EB_2010
3,48
0
Philaemon_mediorubra
2,89
Philaemon_pungens
Weinmannia
63,37
48,62
87,63
27,91
Brunellia
Cephalotus_follicularis
Karrabina_benthamiana
Spiraeopsis_celebica
Caldcluvia_paniculata
Ackama_rosifolia
Caldcluvia_paniculosa
Eucryphia_cordifolia
18,73
Eucryphia_moorei
Codia_discolor
Pullea_glabra
Callicoma_serratifolia
Vesselowskya
Weinmannia_trichosperma
Weinmannia_tinctoria
14,25
Weinmannia_tomentosa
9,55
2,02
Weinmannia_myrtifolia
5,1
Weinmannia_bangii
2,97 Weinmannia_elattantha
1,64Weinmannia_auriculata
0,96
Weinmannia_sp_Bradford_435
Cunonia_macrophylla
16,94
Cunonia_montana
8,79
Cunonia_balansae
6,34
Cunonia_atrorubens
3,94
Cunonia_pulchella
Cunonia_capensis
Pancheria_engleriana
2,45
Pancheria_phylliraeoides
11,8
Pancheria_reticulata
5,27
Pancheria_brunhesii
2
Pancheria_hirsuta
Weinmannia_clemensiae
Weinmannia_exigua
9,23
2,62
Weinmannia_richii
5,89
Weinmannia_fraxinea
0,94
Weinmannia_hooglandii
Weinmannia_dichotoma
4,57
Weinmannia_serrata
Weinmannia_racemosa
15,97
2,02
Weinmannia_silvicola
Weinmannia_vitiensis
12,63 9,41
Weinmannia_sp_Bradford_837
Weinmannia_parviflora
10,81
1,78
Weinmannia_samoensis
6,09
Weinmannia_raiateensis
2,06
Weinmannia_vescoi
Weinmannia_sp_Bradford_655
6,79
Weinmannia_madagascariensis
3,45
Weinmannia_rutenbergii
Weinmannia_marojejyensis
16,98
6,78
Weinmannia_humbertiana
3,14
Weinmannia_minutiflora
10,02
Weinmannia_bojeriana
6,66
Weinmannia_stenostachya
3,91
Weinmannia_arguta
2,05
Weinmannia_sanguisugarum
20,18
10,6
63,68
42,57
32,41
59,78
posterior
1
50,63
39,86
34,24
25
22,7
28,67
24,56
0
22,88
Weinmannia. See Supplementary Table 5 for more details. Node colours
represent posterior probabilities. Endemic species printed in red.
Macmillan Publishers Limited. All rights reserved
LETTER RESEARCH
BioGeoBEARS DEC+J on Dacrycarpus M0_unconstrained
ancstates: global optim, 3 areas max. d=0.0479; e=0; j=0; LnL=−11.60
BioGeoBEARS DEC+J on Athyrium M0_unconstrained
ancstates: global optim, 2 areas max. d=0; e=0; j=0.0344; LnL=−8.42
W
W Dacrycarpus_dacrydioides
W
W Athyrium_filix_femina
W
W
W
BioGeoBEARS DEC+J on Epirixanthes M0_unconstrained
ancstates: global optim, 3 areas max. d=0.149; e=0; j=0; LnL=−2.69
KBWSalomonia_cantoniensis
KBW
W W Athyrium_melanolepis
W
W W Athyrium_brevifrons
W
W
W
W
W
W
W
W
W
W
KBW
K
W Athyrium_rupestre
W
W
W
W Athyrium_nikkoense
KBWDacrycarpus_imbricatus105
W
W Athyrium_yokoscense
W
KBWSalomonia_ciliata
KBW
W W Athyrium_tashiroi
W
W
W W Athyrium_kirisimaense
W Athyrium_atkinsonii
W
W
W Athyrium_tozanense
W
KBW
W
KBWEpirixanthes_pallida
K
WW Athyrium_vidalii
W
WW Athyrium_neglectum
W
W
W
KBWDacrycarpus_imbricatus106
KBW
K
W Athyrium_deltoidofrons
W
K Athyrium_amoenum
K
W
W
KBW
W
W Athyrium_nakanoi
W
W
W
W
W
K Dacrycarpus_kinabaluensis913
K
K Athyrium_clemensiae
K
W
W
W Athyrium_wardii
W
KBW
K
K K Dacrycarpus_kinabaluensis111
W
W
W
W
W Athyrium_eremicola
W
K Epirixanthes_kinabaluensis
K
W
W Athyrium_viridescentipe
KBW
W
W
W
W W
W
W
W
W WW Athyrium_x_akiense
W W
W
W Athyrium_otophorum
W
W
W
W Athyrium_oblitescens
KBW
KBWDacrycarpus_imbricatus102
K
K
W W Athyrium_subrigescens
W
W
W
W
W
W
KBW
K
W W Athyrium_kuratae
KBWEpirixanthes_papuana
K
W
W W
W
W Athyrium_x_tokashikii
W W Dacrycarpus_expansus
W
WW Athyrium_setuligerum
WW
WW Athyrium_clivicola
W
W
W Athyrium_strigillosum
W
W
W
W
W Athyrium_x_hisatsuanum
W
W
W W
W
W W Dacrycarpus_compactus
W Athyrium_iseanum
KBWEpirixanthes_elongata
K
W Athyrium_arisanense
W
60
50
40
30
20
10
0
Millions of years ago
35
30
25
20
15
10
5
25
20
15
0
10
5
0
Millions of years ago
Millions of years ago
BioGeoBEARS DEC+J on Dendrochilum M0_unconstrained
ancstates: global optim, 3 areas max. d=0.4531; e=0; j=0.0092; LnL=−15.86
BioGeoBEARS DEC+J on Euphrasia M0_unconstrained
ancstates: global optim, 2 areas max. d=0; e=0; j=0.071; LnL=−2.96
BioGeoBEARS DEC+J on Begonia M0_unconstrained
ancstates: global optim, 2 areas max. d=0.8061; e=0; j=0; LnL=−3.54
B Dendrochilum_cupulatum
B
W Euphrasia_philippinensis
W
KB Begonia_amphioxus
K
K Dendrochilum_joclemensii
K
KB
B
KB
K
KB Dendrochilum_gibbsiae
KB
KB
B
KB Dendrochilum_tenompokense
KB
W Euphrasia_tarokoana
W
KB Dendrochilum_dewindtianum
KB
K Dendrochilum_transversum
K
KB Begonia_cf_beryllae
W W
W
W
K K Dendrochilum_scriptum
KB
W W Euphrasia_transmorrisonensis
K
K
K
KB
K
W
W
KB
B
K
W Euphrasia_nankotaizanensis
W
KB Dendrochilum_haslamii
B
K
W
KB
B
KB Begonia_pendula
K
W
KB Dendrochilum_exasperatum
B
KB
K
K
K K Dendrochilum_pseudoscriptum
W
W
K
K
KK Dendrochilum_pterogyne
K
K
K
K
K
KB Begonia_imbricata
K
W W Euphrasia_durietziana
K
KK Dendrochilum_alpinum
K Dendrochilum_grandiflorum
K
K
K
W
B Dendrochilum_trusmadiense
B
KB
K
K
K
K
K
K Begonia_vaccinioides
K
K
K
5
4
3
2
2.5
2
1.5
1
0.5
W
W
K Dendrochilum_corrugatum
1
K Dendrochilum_alatum
0
10
8
6
4
2
0
Millions of years ago
BioGeoBEARS DEC+J on Dicranoloma M0_unconstrained
ancstates: global optim, 3 areas max. d=0.2702; e=0; j=0; LnL=−30.34
0
W Euphrasia_taurica
W
Millions of years ago
KB Begonia_cauliflora
W Euphrasia_petiolaris
W
K Dendrochilum_kamborangense
K
K
K
K Dendrochilum_stachyodes
K
K
K
K
K
K
K Euphrasia_borneensis
K
B
B
K Begonia_burbidgei
K
B Dendrochilum_muluense
B
K
K
BioGeoBEARS DEC+J on Hedyotis M0_unconstrained
ancstates: global optim, 3 areas max. d=0.1289; e=0; j=0.0812; LnL=−15.92
Millions of years ago
KB D_sp_Kinabalu_Gunung_Alab
KB
BioGeoBEARS DEC+J on Coeliccia M0_unconstrained
ancstates: global optim, 3 areas max. d=0.0615; e=0; j=0.0588; LnL=−14.15
W D_cylindrothecium
W
W D_diaphanoneurum
W
W Coeliccia_ryukyuensis
W
W Oldenlandia_nutans_bS27_New
W
W
W
W
W
W Oldenlandia_pubescens_cB042
W
KBW
W
W D_menziesii
W
W
W
W
W RMNH_INS_503926_C_didyma
W
W
KBW D_brevisetum
W
W Hedyotis_valetoniana_bZ030_N
W
W
W
KBW
W
WW
KBW D_braunii
W
W
W
W C_cyanomelas
W
W
W
W
K
W
W
W
W
W Hedyotis_schlechteri_cA092_N
K
KB Hedyotis_pulchella_bZ029_Bor
D_havilandii
KBW D_assimile
W
W
W
W
W
W D_plurisetum
W
W C_albicauda
W
K
W
KBW D_reflexum
W
W
W
W
W
K Hedyotis_macrostegia_Borneo
K
W
K C_species_2
K
K
W D_fasciatum
W
W
W
W
W
W
W
W
K
W C_poungyi
W
W
W
W D_leichhardtii
KW
W
W
W D_sp_Indonesia
W
B
W
K
K
K
BWC_octogesima
B
W
W
W
W
KBW
W
KB
KB C_nemoricola
5
B
2
1.5
1
KBW D_billarderi
W
B Hedyotis_fissistipula_cB019_B
B
KB
B
2.5
KBWHedyotis_philippensis_cB043_A
B
B
KBW D_blumii
B
B
3
KBW
W D_robustum
W
W
KBW
B
W D_chilense
W
K
BWHedyotis_rigida_bZ042_SEAsia
W D_dicarpum
K C_species_1
K
0.5
B Coeliccia_cyaneothorax
4
3
2
1
0
Millions of years ago
5
4
3
2
1
0
Millions of years ago
0
Millions of years ago
Extended Data Figure 7 | Ancestral range estimations for Athyrium, Begonia, Coeliccia, Dacrycarpus, Dendrochilum, Dicranoloma, Epirixanthes,
Euphrasia and Hedyotis. See Methods for further details. The trees are alphabetically ordered by genus name.
G2015
Macmillan Publishers Limited. All rights reserved
RESEARCH LETTER
BioGeoBEARS DEC+J on Hygrobates M0_unconstrained
ancstates: global optim, 2 areas max. d=0.433; e=0; j=0.1711; LnL=−1.20
KB Hygrobates_sp_2
K
BioGeoBEARS DEC+J on Paphiopedilum M0_unconstrained
ancstates: global optim, 3 areas max. d=0.0149; e=0; j=0.0848; LnL=−8.51
BioGeoBEARS DEC+J on Kalophrynus M0_unconstrained
ancstates: global optim, 3 areas max. d=0.0057; e=0; j=0.1631; LnL=−5.42
W Paphiopedilum_primulinum
W
KBWK_pleurostigma
KBW
W
W
W Paphiopedilum_liemianum
W
W
W
K K_sp_2
K
W Paphiopedilum_glaucophyllum
W
KBW
K
K Paphiopedilum_rothschildianum
K
BW
KB Hygrobates_hamatus
KB
B
B
W K_interlineatus
W
B Paphiopedilum_kolopakingii
B
K
K
B
B
K
K
B Paphiopedilum_stonei
B
BW
BW
KB
K
K K_sp_1
K
BWPaphiopedilum_philippinense
BW
K
K
BW
BW
W Paphiopedilum_randsii
W
K Hygrobates_hamatoides
K
7
6
4
2
5
4
3
2
1
0
Millions of years ago
K K_baluensis
K
8
6
0
Millions of years ago
50
40
30
20
10
BioGeoBEARS DEC+J on Payena M0_unconstrained
ancstates: global optim, 3 areas max. d=0.0575; e=0; j=0.1107; LnL=−12.85
0
Millions of years ago
BioGeoBEARS DEC+J on Ilex M0_unconstrained
ancstates: global optim, 2 areas max. d=0; e=0; j=0.0109; LnL=−4.85
BWPayena_lucida_EDNA09_0230
B
BioGeoBEARS DEC+J on Myrmarachne M0_unconstrained
ancstates: global optim, 2 areas max. d=5; e=0; j=1.9; LnL=−1.49
W Ilex_rugosa
W
W
W
W Ilex_maximowicziana
W
KB PK050_M_nov_sp_1_500to750
B
K Ilex_kinabaluensis
K
W Ilex_integra1
W
W
W
W Ilex_dimorphophylla
W
W
W
W
W
W
W
W
W
W
W Ilex_cornuta2
W
W Ilex_cornuta1
W
W
W Ilex_x_kiusiana
W
W
W
W
W
W
WW Ilex_mertensii
W
WW Ilex_matanoana
W
W
W Ilex_nothofagifolia
W
W
W
W Ilex_fargesii1
W
W
W Ilex_ficoidea
W
W Ilex_cyrtura
W
W Ilex_pernyi
W
W
KB
K
W Ilex_buergeri
W
W
W
W
W
W Ilex_kingiana
K PK003_M_mariaelenae_1500to
K
W
W Ilex_georgei
W
W
W
W Ilex_bioritsensis
B
W
W Ilex_colchica
15
W
W
W Ilex_perado
W
10
5
10
5
0
Millions of years ago
W
W
W Ilex_aquifolium
KB PK210_M_hanoii_1000to1250m
B
0.8
0
0.6
0.4
0.2
BioGeoBEARS DEC+J on Philalanka M0_unconstrained
ancstates: global optim, 2 areas max. d=0; e=0; j=3; LnL=−1.17
0
Millions of years ago
Millions of years ago
BioGeoBEARS DEC+J on Nepenthes M0_unconstrained
ancstates: global optim, 3 areas max. d=0.0074; e=0; j=0.0156; LnL=−29.45
W Iaureliana
W
B Nepenthes_northiana
B
K Nepenthes_x_kinabaluensis
K
K
K
K Nepenthes_rajah
K
KB Nepenthes_lowii
KB
K
K
KB
B
B Nepenthes_chaniana
B
B
B
B Nepenthes_glandulifera
B
KB
B
B
B
B
B
B
B Nepenthes_boschiana
B
B
B
B
B
B Nepenthes_hurrelliana
K Nepenthes_villosa
K
K Nepenthes_edwardsiana2
K
W Nepenthes_peltata
W
W Nepenthes_truncata
W
BW
B Nepenthes_campanulata
B
W Nepenthes_alata
W
W
W
W
W
W Nepenthes_ventricosa
W
W
W
W
W
W
W
W
W
W
BWNepenthes_reinwardtiana
W Nepenthes_benstonei
W
W
W
W
W
W Nepenthes_macfarlanei
WW
W Nepenthes_singalana
WWW
W Nepenthes_kongkandana
WW
W
W
W
W
K Ikinabaluensis
K
W Nepenthes_insignis
W Nepenthes_specatabilis
W
W
B SP13519_Philalanka_thienema
B
W Nepenthes_bongso
W
W
W
W
B
W Nepenthes_gymnamphora
W
W
W
W Ieberhardtii
W
K
K
W
W
W
B Nepenthes_fusca
K
K
KBW
W
B Nepenthes_vogelii
B
B
KBW
K SP13510_Philalanka_spec2_10
K
K
K
W Ipoilanei
W
K
K
W Nepenthes_maxima
W
KBW
W
B SP13492_Philalanka_spec3_50
B
BioGeoBEARS DEC+J on Impatiens M0_unconstrained
ancstates: global optim, 2 areas max. d=0; e=0; j=0.2671; LnL=−2.56
W
B e4003829276_P_gigas_830mA
W Ilex_spinigera
W
W
W
KB e4003829322_P_microphylla_6
B
B
W
W
W W
B
W Ilex_warburgii
W
W
15
B
KB PK073_M_sp_5_500to750mAS
KB
W
W
W
W
20
B
W Ilex_corallina
W
25
KB
K
KB
W Ilex_fargesii2
WW
30
K e4003829348_P_kinabaluensis
W Ilex_ciliospinosa
W
W
W
B
K
W
W
W
W
B
KB PK256_M_nov_sp_2_1000to12
B
W Ilex_hookeri
W
B
B
W
W
W
W
W
BWPayena_obscura_EDNA09_023
KB
B
W Ilex_latifolia
W
W
B
W Ilex_hylonoma
W
W
KB
K
W Ilex_integra2
W
W
KB PK036_M_christae_2500to275
B
W Ilex_liukiuensis
W
W
B
B
W
W
W
B Payena_ferruginea_EDNA09_0
B
W Ilex_leucoclada
W
W
KB PK183_M_sp_3_1750to2000m
B
KK
W Ilex_x_makinoi
W
W
B
W Ilex_zhejiangensis
W
BWPayena_leerii_EDNA09_02317
B
W
W
W
W Nepenthes_andamana
W Nepenthes_vieillardii
W
W W Nepenthes_bokorensis
W
W
W BWNepenthes_albomarginata
W
B SP13507_Philalanka_spec1_25
B
W
W W Nepenthes_ramispina
W
W
W W
W
25
W Ichevalieri
W
4
3
2
1
20
15
10
5
W
W W Nepenthes_alba
W
W
W
W
W Nepenthes_sanguinea
W Nepenthes_gracillima
4
3
2
1
0
Millions of years ago
0
Millions of years ago
0
Millions of years ago
Extended Data Figure 8 | Ancestral range estimations for Hygrobates, Ilex, Impatiens, Kalophrynus, Myrmarachne, Nepenthes, Paphiopedilum, Payena
and Philalanka. See Methods for further details. The trees are alphabetically ordered by genus name.
G2015
Macmillan Publishers Limited. All rights reserved
LETTER RESEARCH
BioGeoBEARS DEC+J on Teleopsis M0_unconstrained
ancstates: global optim, 3 areas max. d=0.0173; e=0; j=0.1103; LnL=−24.05
BioGeoBEARS DEC+J on Ptomaphaginus M0_unconstrained
ancstates: global optim, 3 areas max. d=0.5097; e=0; j=0.6198; LnL=−4.20
W
B Ptomaphaginus_bryantioides
B
BioGeoBEARS DEC+J on Weinmannia M0_unconstrained
ancstates: global optim, 3 areas max. d=6e−04; e=0; j=0; LnL=−12.42
W Teleopsis_adjacens
W W Weinmannia_hooglandii
KBW
KBW
KBWWeinmannia_fraxinea
KBW
B
B
KBW
KB
W Weinmannia_richii
W
W
W
KBW
KBW
B
B
KBW
KB Teleopsis_nr_discrepans_sp_C
W Weinmannia_exigua
W
K Weinmannia_clemensiae
K
KB Teleopsis_discrepans
B
B
B
W Weinmannia_sp_Bradford_655
W
W
W
W
W
B Teleopsis_sabah_sp_2
B
KBW
W Weinmannia_marojejyensis
W Weinmannia_humbertiana
W
W
W
BB
W Weinmannia_minutiflora
W
W
W
B
B
W
W
B Teleopsis_nr_discrepans_sp_B
B
W Weinmannia_madagascariensi
W
W
W
W
KBW
B
B
KB Ptomaphaginus_cf_latimanus
B
W Weinmannia_rutenbergii
W
W Weinmannia_bojeriana
W
B Teleopsis_sp_2
B
W
W
W
W
W
B
B
K
K
W
B
B
B Teleopsis_nr_discrepans
B
W
W
W Weinmannia_stenostachya
W
W
W Weinmannia_arguta
W
W Weinmannia_silvicola
W
W
W
K Teleopsis_pseudogracilifemur
W
W
W
B
W Weinmannia_dichotoma
W
W
W
W
W
W
W
W
W
W
W
W Teleopsis_rubicunda
W
W
W
W
W Cunonia_macrophylla
W
W
B Teleopsis_sabah
W
W
W
W
W
W
W
W Cunonia_montana
W Cunonia_balansae
W
W
15
KB Ptomaphaginus_latescens
10
5
W Cunonia_pulchella
W
W
K
W Pancheria_brunhesii
W Cunonia_capensis
W
W Teleopsis_trichophora
B
W Pancheria_hirsuta
W
W
W
W
W Pancheria_engleriana
W Pancheria_reticulata
W
B
W
W Pancheria_phylliraeoides
W
W
W Teleopsis_breviscopium
W
W
B Ptomaphaginus_similipes
B
W Weinmannia_parviflora
W
W
W
W
W Weinmannia_samoensis
W Weinmannia_serrata
W
KB Teleopsis_pallifacies
W Weinmannia_raiateensis
W
W
W
B
W Weinmannia_vescoi
W
W
B Teleopsis_scapulistylus
B
B
W Weinmannia_vitiensis
W
W
W
W
B
W Weinmannia_sp_Bradford_837
W
W
W
KBW
B
K
K
W
W
K
B
W
W
W
K
B
K Ptomaphaginus_kinabaluensis
W Weinmannia_racemosa
KB Teleopsis_gracilifemur
K
K
W Weinmannia_sanguisugarum
W
W Cunonia_atrorubens
0
Millions of years ago
35
2
1.5
1
0.5
0
25
20
15
10
5
0
BioGeoBEARS DEC+J on Trichosanthes M0_unconstrained
ancstates: global optim, 3 areas max. d=0.019; e=0; j=0.2724; LnL=−9.98
BioGeoBEARS DEC+J on Ranunculus M0_unconstrained
ancstates: global optim, 2 areas max. d=0; e=0; j=0.0742; LnL=−3.50
B Trichosanthes_sepilokensis
B
W Ranunculus_chinensis
W
BW
B
W
W
30
Millions of years ago
Millions of years ago
BWTrichosanthes_montana
BW
W Ranunculus_silerifolius
W
W
W
W Ranunculus_cantoniensis
W
B Trichosanthes_intermedia
B
W
W
BW
B Ranunculus_lowii
B
B
B
B Trichosanthes_obscura
B
W
W
W Ranunculus_saruwagedicus
W
B
B
K Trichosanthes_kinabaluensis
K
W
W
B
B
W Ranunculus_brassii
W
W
W
W
W Ranunculus_pseudolowii
W
W Trichosanthes_globosa
W
W
W
W
W
W Ranunculus_basilobatus
W
BWTrichosanthes_borneensis
W
W Ranunculus_amerophyllus
W
10
8
6
4
2
0
Millions of years ago
1
0.8
0.6
0.4
0.2
0
Millions of years ago
BioGeoBEARS DEC+J on Tritetrabdella M0_unconstrained
ancstates: global optim, 2 areas max. d=0; e=0; j=0.3937; LnL=−1.83
BioGeoBEARS DEC+J on Rhododendron M0_unconstrained
ancstates: global optim, 3 areas max. d=0.1291; e=0.0222; j=0; LnL=−38.63
K
W Haemadipsa_cavatuses
W
W Rhododendron_santapaui
W
K Rhododendron_ericoides
K
KW
K
K
KB Rhododendron_cuneifolium
K
KB
K
KB Rhododendron_borneense
K
K Rhododendron_buxifolium
K
K
K
W Tritetrabdella_scandens
W
KB Rhododendron_rugosum
K
W
K
K
KB Rhododendron_praetervisum
K
K
K
K
KB Rhododendron_stapfianum
K
W
W
K
K
KB Rhododendron_suaveolens
K
K
K
KB
KBWRhododendron_orbiculatum
K
K
K
KB Rhododendron_lowii
KBW
KBWRhododendron_javanicum
K
K
KB Rhododendron_exuberans
K
K
K
K
K
W Tritetrabdella_taiwana_A
W
KBW
K
KB
K
KB Rhododendron_crassifolium
K
K
K
K
KB Rhododendron_stenophyllum
KBW
K
K
K
KBWRhododendron_bagobonum
K SP13398_T_kinabalensis_kina
K
KB Rhododendron_fallacinum
KB
K
K
K Rhododendron_acuminatum
6
4
2
0
Millions of years ago
15
10
5
0
Millions of years ago
Extended Data Figure 9 | Ancestral range estimations for Ptomaphaginus, Ranunculus, Rhododendron, Teleopsis, Trichosanthes, Tritetrabdella and
Weinmannia. See Methods for further details. The trees are alphabetically ordered by genus name.
G2015
Macmillan Publishers Limited. All rights reserved
RESEARCH LETTER
Extended Data Table 1 | Details for all studied endemic taxa
Plants are highlighted in green, fungi in blue, and animals in brown.
* For clade numbering in Cortinarius, see Supplementary Table 2.
** Centric/eccentric status determined via biogeographic analysis (see Extended Data 4).
*** For definitions and sources, see Supplementary Table 3.
**** K, Mount Kinabalu; T, Mount Tambuyukon; C, Crocker Range; TM, Mount Trus Madi.
***** Manuscript name.
G2015
Macmillan Publishers Limited. All rights reserved
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