LETTER Doi:10.1038/Nature14949

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, Jo´zsef Geml1,2, Rene´ Geurts13, Barbara Gravendeel1,2,14, Peter Hovenkamp1, Paul Imbun11, Isa Ipor15, Steven B. Janssens16, Merlijn Jocque´17,18, 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, meaning that parts of the endemic biota may be relicts, and other but the evolutionary origins of their unique biotas are poorly components may be novel in character4,5. understood4. In varying degrees, local and regional extinction, Disentangling these possibilities for a single tropical montane long-distance colonization, and local recruitment may all contrib- biodiversity hot spot requires molecular phylogenetic study of a large ute to the exceptional character of these communities5. Also, it is number of fauna and flora elements. However, with only few excep- debated whether mountain endemics mostly originate from local tions11,12, evolutionary studies in such hot spots have been limited lowland taxa, or from lineages that reach the mountain by long- to single taxa13,14. This precludes broad understanding of the evolu- range dispersal from cool localities elsewhere6. Here we investigate tionary and biogeographic origins of an endemic biota as a whole4. the evolutionary routes to endemism by sampling an entire trop- We investigated the evolutionary routes to endemism by sampling ical mountain biota on the 4,095-metre-high Mount Kinabalu in an entire tropical mountain biota on the UNESCO World Heritage site Sabah, East Malaysia. We discover that most of its unique biodi- of Gunung Kinabalu in Sabah, East Malaysia. We demonstrate that versity is younger than the mountain itself (6 million years), and most of its unique biodiversity is younger than the mountain itself and comprises a mix of immigrant pre-adapted lineages and descen- comprises a mix of immigrant pre-adapted lineages as well as descen- dants from local lowland ancestors, although substantial shifts dants from local lowland ancestors. from lower to higher vegetation zones in this latter group were At 4,095 m, Kinabalu is the tallest mountain between the Himalayas rare. These insights could improve forecasts of the likelihood of and New Guinea. It is a solitary ‘sky island’, having emerged during the extinction and ‘evolutionary rescue’7 in montane biodiversity hot Pliocene and early Pleistocene as a granite pluton within the surround- spots under climate change scenarios. ing sandstone of the Crocker Range, the latter having formed much In mountainous areas of the humid tropics, steep environmental earlier, between the Eocene and the early Miocene15. Because of the gradients coincide with high primary productivity and relative cli- area’s tectonic activity, as well as Pleistocene sea level changes, the matic stability to sustain large numbers of species, often with strik- exact historical progression of its elevation above sea level is not ing degrees of endemism at higher elevations1,8. It has therefore been known, but it is likely that a major rise, even beyond today’s elevation, recognized that tropical mountains are biodiversity hot spots of great of Kinabalu, as well as the central spine of the Crocker Range, took conservation value1, especially because endemics on mountain tops place between 6 million years ago and today (for more geological are vulnerable to becoming trapped and then annihilated as a result background see Methods). Since the early days of its exploration16, of global warming2,3. Kinabalu has been famous for its extremely high biological diversity, The evolutionary origins of these unique biotas, however, are poorly especially its richness in endemic species, with endemism proportions understood4. Like other insular habitats9, the endemic biota of an reaching 25–30% for some taxa17. isolated mountain results from complex dynamics among coloniza- To unravel the origins of the exceptionally rich Kinabalu biota, we tion, in situ speciation, and local extinction. Each of these factors is mounted a Malaysian–Dutch expedition in which 47 taxonomists dependent on the age and size of the habitat, and on the environmental worked at 37 localities, spanning the full range of elevations (Fig. 1). contrast between the insular habitat and its matrix10. In the case of We used Sanger sequencing to sequence one or more fast-evolving loci a tropical mountain top, an added complication is the fact that for 1,852 individuals, belonging to 18 genera representing gastropods, climate fluctuations may have widened and restricted the geographic annelids, insects, arachnids, vertebrates, pteridophytes, bryophytes, range over which the montane conditions have extended in the past, and angiosperms. We also obtained 3.7 million basidiomycete

1Naturalis 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, Norbyva¨gen 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. 17Royal 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, Zu¨ lpicher Strasse 47b, D-50674 Cologne, Germany. 20Natuurmuseum Fryslaˆn, 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.

Summit trail Sayap Kinabalu Sayap 2 Park Laban Rata

Summit trail Layang Laban Rata Kampong Kiau Poring Borneo Layang Layang Layang

Kinabalu Park HQ Kiansom Tun Fuad Kota Stephen Park Mamut Kinabalu Moyog

Inobong Kisada 0-500 m 2,000–2,500 m Sugud 2 Gunung Alab Sugud Long Gong Kugan 500–1,000 m 2,500–3,000 m Crocker 1,000–1,500 m 3,000–3,500 m Mahua Range Park 1,500–2,000 m 3,500–4,000 m 10 km 4,000–4,500 m

Figure 1 | Map of the study area. Inset left, location of the study area in the indicated with red markers, ten additional sampling sites with blue markers. World and in Borneo. Inset middle, detail of the summit trail in Kinabalu Park. Not indicated separately are 15 sites along the summit trail, and four sites very The eight expedition stations in Kinabalu Park and Crocker Range Park are close to Mahua, Gunung Alab, and Inobong. and glomeromycete ITS2 rDNA sequences from soil cores with ion fall within the past 6 million years, the time span during which semiconductor sequencing. In addition, we retrieved data from eight Kinabalu is likely to have reached its present elevation. Only two previously published single-taxon studies on vascular plants. endemics, the frog Kalophrynus baluensis and the flowering plant We analysed all data within a phylogenetic framework to estimate Ilex kinabaluensis, are markedly older than the mountain itself. the times of origin of endemic species, and to determine whether These may be explained as artefactual if we failed to identify the endemic species had descended from local or distant congeners closest non-endemic sister lineage, thereby inflating their recon- (Methods, Fig. 2, Extended Data Table 1 and Extended Data Figs 1–9). structed age, or if these species are actually not endemics, but more Note that we define ‘endemic’ as restricted to the area in which widespread. Alternatively, they may truly be old endemics that evolved our expedition took place. Although the present study offers the during cooler periods at lower elevations in Borneo before Kinabalu’s most comprehensive evolutionary analysis of any mountain biota to formation. date, the taxa covered are, by necessity, an uneven and fragmentary Our phylogenetic and biogeographicanalyses(ExtendedDataTable1 sampling of the full diversity. Nonetheless, we expect that our and Extended Data Figs 1–4, 7–9) suggest the existence of two categories results are representative for the Kinabalu biota as a whole, as our of endemics18:‘eccentric’(12taxa)and‘centric’(25taxa).Theeccentric selected taxa encompass organisms with a wide variety of phylogen- type of endemic has sister taxa that occur either in temperate climates etic backgrounds, ecologies, and life history traits. (seven cases) or in other tropical mountains outside of Borneo (five Similar to Mesoamerican endemic cloud forest seed plants and cases). To this group belong all bryophytes, pteridophytes, some of the vertebrates11, our molecular dating results show that the estimated fungal lineages and also the endemics in the flowering plant groups mean stem-node ages of 33 endemic species span a wide range, from Hedyotis, Ilex, Impatiens, Ranunculus and Euphrasia,andtheanimals 0.12 million years to 14.6 million years (Fig. 3). However, 76% of these Coeliccia and Tritetrabdella.Eccentricendemicspredominantlyoccurat

bcI. chinesis (Yunnan) Impatiens I. hawkeri (New Guinea) I. platypetala (Bali) I. usambarensis (Tanzania) C. spp. (2,040–2,100 m) I. walleriana (Eastern Africa) I. serpens (Tanzania) I. thamnoidea (Tanzania) I. pseudohamata (Tanzania) I. balsamina (India) C. sp. (1,900 m) Ptomaphaginus I. cuspidata (South India) C. collinitus (Germany) I. ﬂaccida (South India) C. sp. (2,900 m) a I. latifolia (South India) P. n. sp. (Sugud) C. sp. (1,900 m) I. aureliana (China: Yunnan) C. vitreopileatus (New Zealand) P. bryantioides (Poring) I. poilanei (Vietnam) I. eberhardtii (Vietnam) I. chevalieri (Vietnam) C. spp. (2,900 m) P. bryantioides

(Kota Kinabalu & Kiansom) OTU_26541_mid

I. kinabaluensis C. sp. (1,000 m) (Kinabalu HQ, Gn. Alab, P. latimanus (Sayap) C. sp. (2,100 m) Poring) C. lustrabilis (Norway) C. delibutus (Germany) P. kinabaluensis C. rotundisporus (Australia) (Kinabalu HQ & Gn. Alab) C. sp. (2,900 m) C. sp. (2,900 m) C. sp. (1,900 m) P. similipes (Sugud) C. calyptratus (USA) 0-500 m 2,000–2,500 m C. glaucopus (Germany) P. similipes (Sugud) 500–1,000 m 2,500–3,000 m C. cliduchus (Germany) 1,000–1,500 m 3,000–3,500 m C. argutus (Norway) 1,500–2,000 m 3,500–4,000 m C. austroturmalis (Chile) P. similipes (Sayap) Cortinarius C. sp. (2,040–2,100 m)

Figure 2 | Examples of phylogenetic reconstructions. a, Centric endemism zone at which they occur (see legend). High-elevation endemics in a and b are (Ptomaphaginus). b, Eccentric endemism (Impatiens). c, Centric endemism indicated in red. For support values and other details on these and other trees, superimposed on eccentric endemism (detail of the Cortinarius phylogeny). see Extended Data Figs 1–4. Clades are coloured with the same colour scheme as in Fig. 1, by elevational

4,000 Frogs from their ancestral niche. The fact that the endemic biota of Kinabalu Insects appears to be composed largely of pre-adapted (eccentric) species and 3,500 Arachnids locally derived (centric), ecologically conserved endemics is in line Snails with niche conservatism24. 3,000 Leeches We suggest that our novel approach of molecular dating of multiple Conifers 2,500 clades be applied to larger communities in this and other tropical Ferns montane biodiversity hot spots25. In combination, such information Mosses 2,000 should allow a detailed dissection of the relative roles of ecological Flowering plants speciation, colonization and habitat filtering in the formation of

Elevation (m) 1,500 endemic biotas in this and other tropical mountains. Moreover, such understanding could improve predictions of the likelihood of extinc- 1,000 tion and evolutionary rescue of endemic species experiencing chan- ging climate conditions7. 500 Online Content Methods, along with any additional Extended Data display items 0 and Source Data, are available in the online version of the paper; references unique 0 25 30 5 10 15 20 to these sections appear only in the online paper. Divergence time (million years) Received 9 December 2014; accepted 14 July 2015. Figure 3 | Elevations and ages for endemic species. Elevations (mid-points, minima and maxima) and dates of origination derived from molecular Published online 12 August 2015. dating (averages and 95% credible intervals) for endemic species; eccentric 1. Ko¨rner, C. & Spehn, E. M. Mountain Biodiversity: a Global Assessment (Parthenon, species (see main text) are indicated with a black circle. The vertical dashed line Boca Raton, 2002). indicates the oldest possible date for Kinabalu to have reached its current 2. Chen, I. C. et al. Elevation increases in moth assemblages over 42 years on a elevation. For details, see Extended Data Figs 5 and 6. tropical mountain. Proc. Natl Acad. Sci. USA 106, 1479–1483 (2009). 3. La Sorte, F. A. & Jetz, W. Projected range contractions of montane biodiversity under global warming. Proc. R. Soc. Lond. B 277, 3401–3410 (2010). high elevations (mean lower elevational boundary, 2,212 m; s.d., 837 m), 4. Graham, C. H. et al. The origin and maintenance of montane diversity: integrating they are strict Kinabalu endemics (they do not occur on nearby, lower evolutionary and ecological processes. Ecography 37, 711–719 (2014). 5. Cadena, C. D. et al. Latitude, elevational climatic zonation and speciation in New mountains), and are further characterized by high dispersal capacities World vertebrates. Proc. R. Soc. Lond. B 279, 194–201 (2012). (one, two and seven clades with eccentric endemism have small, medium 6. Rodrı´guez-Castan˜ eda, G. et al. Tropical forests are not flat: how mountains affect and large dispersal, respectively). herbivore diversity. Ecol. Lett. 13, 1348–1357 (2010). 7. Schiffers, K., Borne, E. C., Lavergne, S., Thuiller, W. & Travis, J. M. J. Limited The centric type of endemic has sister taxa that occur locally, in the evolutionary rescue of locally adapted populations facing climate change. Phil. Borneo lowlands. Six out of the eight endemic animal species, some of Trans. R. Soc. Lond. B 368, 20120083 (2013). the fungal lineages, the conifers, and 17 of the 20 flowering plants 8. Hoorn, C., Mosbrugger, V., Mulch, A. & Antonelli, A. Biodiversity from mountain belong to this type. Centric endemics occur on average at lower eleva- building. Nat. Geosci. 6, 154 (2013). 9. Warren, B. H. et al. Islands as model systems in ecology and evolution: prospects tions (mean lower elevational boundary, 1,724 m; s.d., 728 m) and fifty years after MacArthur–Wilson. Ecol. Lett. 18, 200–217 (2015). tend to have lower dispersal capacities than the eccentric endemics 10. Watson, D. M. A conceptual framework for studying species composition in (eight, seven and ten clades with centric endemism have small, med- fragments, islands and other patchy ecosystems. J. Biogeogr. 29, 823–834 (2002). 11. Ornelas, J. F. et al. Comparative phylogeographic analyses illustrate the complex ium and large dispersal, respectively). Some centric endemics are evolutionary history of threatened cloud forests of northern Mesoamerica. PLoS not strict Kinabalu endemics, as they are also found on other moun- ONE 8, e56283 (2013). tains in Kinabalu’s vicinity. Our ancestral state reconstructions 12. Madrin˜a´n, S., Corte´s, A. J. & Richardson, J. E. Pa´ramo is the world’s fastest evolving and coolest biodiversity hotspot. Front. Genet. 4, 192 (2013). (Supplementary Table 6) confirm a pattern of altitudinal bottom-up 13. Barkman, T. J. & Simpson, B. B. Origin of high-elevation Dendrochilum species cladogenesis in the centric endemics, with 8 out of 11 species ranging (Orchidaceae) endemic to Mount Kinabalu, Sabah, Malaysia. Syst. Bot. 26, partially or entirely outside of the 95% credibility interval for the 658–669 (2001). reconstructed elevation of the most recent common ancestor, and 14. Gawin, D. F. et al. Patterns of avian diversification in Borneo: the case of the endemic Mountain Black-eye (Chlorocharis emiliae). Auk 131, 86–99 (2014). the remaining 3 out of 11 falling entirely within this interval. When 15. Cottam, M. A. et al. Neogene rock uplift and erosion in northern Borneo: evidence we performed the same analysis with Kitayama’s (ref. 19) seven vegeta- from the Kinabalu granite, Mount Kinabalu. J. Geol. Soc. Lond. 170, 805–816 tion zones, rather than elevation, we found that only three of these (2013). 16. Whitehead, J. Exploration of Mount Kina Balu, North Borneo (Gurney & Jackson, eight elevation shifts may represent a shift towards a higher vegetation London, 1893). zone. This suggests that, even in high-elevation centric endemics, sub- 17. Wong, K. M. & Phillips, A. Kinabalu, Summit of Borneo (Sabah Society & Sabah stantial niche shifts are rare. Niche conservatism is probably even Parks, Kota Kinabalu, 1996). 18. van Steenis, C. G. G. J. Plant geography of the mountain flora of Mt. Kinabalu. Proc. underestimated, since the Massenerhebung effect causes an upward R. Soc. Lond. B 161, 7–38 (1964). shift of vegetation zones on Kinabalu compared with other Bornean 19. Kitayama, K. An altitudinal transect study of the vegetation on Mount Kinabalu, mountains14,20. Borneo. Vegetatio 102, 149–171 (1992). Our multi-taxon study shows that Kinabalu’s biodiversity hot spot 20. Grubb, P. J. Interpretation of Massenerhebung effect on tropical mountains. Nature 229, 44–45 (1971). is of recent origin. This means the mountain is an evolutionary 21. Favre, A. et al. The role of the uplift of the Qinghai–Tibetan Plateau for the evolution cradle, accumulating neo-endemics, as has been suggested for other of Tibetan biotas. Biol. Rev. Camb. Philos. Soc. 90, 236–253 (2015). young, high-elevation biodiversity hot spots at low latitudes21, such 22. Schwery, O. et al. As old as the mountains: the radiations of the Ericaceae. New 22 8 Phytol. 207, 355–367 (2015). as the Tibetan plateau , the Andean highlands , and Afrotropical 23. Price, T. D. et al. Niche filling slows the diversification of Himalayan songbirds. volcanoes23. However, probably as a consequence of the rapid emer- Nature 509, 222–225 (2014). gence of the mountain15 and its unique alpine summit conditions19, 24. Crisp, M. D. et al. Phylogenetic biome conservatism on a global scale. Nature 458, 754–756 (2009). many of these neo-endemics have not evolved by drastic niche 25. Culmsee, H. & Leuschner, C. Consistent patterns of elevational change in tree shifts from local ancestors, but rather by immigration of pre-adapted taxonomic and phylogenetic diversity across Malesian mountain forests. propagules from elsewhere. This explains the multiple independent J. Biogeogr. 40, 1997–2010 (2013). colonization events in some taxa (for example, Glomus, Rhododendron Supplementary Information is available in the online version of the paper. and Coeliccia). In addition, local lowland taxa have also generated Acknowledgements We acknowledge the mountain guides of Sabah Parks for their montane species, but although some of these have reached vegetation help with material collection, ongoing assistance to continuing research in the area, and zones above 2,000 m, most do not show substantial niche shifts away recent efforts following the 5 June 2015 earthquake. R. Butoˆt, M. de Jong, and

B. Driessen carried out DNA extractions and PCRs. P. Wilkie provided a tissue sample the Forest Research Centre researchers, J. B. Dawat, M. Gumbilil, A. J. Jaimin, Jei. for Payena. For the fungi, T. Semenova extracted DNA from the soil samples and Jumian, Jem. Jumian, J. L. Yukang, P. J. Miun, M. A. T. Mustapha, and B. Saludin assisted E. Duijm generated the reads on the Ion Torrent sequencer. B. Blankevoort and in the field. T. Siew of Borneo Indah Sdn. Bhd. was the local supplier for consumables E. J. Bosch prepared Fig. 1. J. Holloway (Natural History Museum, London, UK), I. Das and field equipment. We thank the ESEB Outreach Fund and the Treub Foundation for (Universiti Malaysia Sarawak), and T. S. Liew (Naturalis, UMS) provided background on funding outreach activities in Kinabalu Park and the Crocker Range Park. N. Raes Kinabalu endemism, and R. Hall (University of London) on its geological history. helped with the niche modelling. 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 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., supplied by the Sabah Biodiversity Centre. Besides institutional support via R.R., and M.L. conceived and guided the study. M.Sch. and V.S.F.T.M. wrote the paper. Netherlands FES-funding, this project received funding via grants 821.01.002 and K.H., F.S. and K.B. administrated all samples and sequences. K.H. and L.E.B. were 825.12.007 of the Netherlands Organization for Scientific Research, the Alberta 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., Mennega Foundation, the Ecology Fund of the Royal Netherlands Academy of Sciences, 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., the Uyttenboogaart-Eliasen Foundation, and Pro Acarologia Basiliensis. G. van Uffelen, 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. van Vugt, and P. Kessler (Botanic Gardens, Leiden) and T. de Winter, G. Thijsse, R.R. and M.Sch. collected material in the field and identified it following current B. Hoeksema, H. Dautzenberg, J. Mols, and E. van Nieukerken (Naturalis) gave advice on 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 transportation of specimens. Artist I. Kopelman and Naturalis general director E. van M.Sch. conducted the analyses. 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, Author Information GenBank accession numbers for newly determined sequences respectively. P. Basintal, E. van Huis and E. Smets supervised the expedition as directors are: KF369344, KF492848, KF839944–KF839949, KM378672–KM378719, for the organizing institutions. Media coverage and communications were facilitated by KM489525–KM489544, KM982697–KM982715, KP152323–KP152394, J. van Alphen, A. Mohd. R. P. Dahlan, K. de Greef, A. Kromhout, J. Schilthuizen, KP978313–KP979097, KR002164–KR002181, KR030167–KR030238 and E. E. Soudi, L. Stek, A. Taminiau, and M. Z. Abdul Wahab. Sabah Parks staff members KR232819–KR232836. A large portion of the data is also publicly available on BOLD L. Apin, B. Busin, B. Butit, J. Gampoyo, G. Gangko, B. Gangku, S. Gangku, P. Gimpiton, (www.boldsystems.org), as dataset DS–KINA (http://dx.doi.org/10.5883/DS-KINA). M. Gunggutou, T. Gunggutou, G. Gunsalam, J. Guntabid, I. Isnain, K. Ag. Jalil, Y. Johalin, Voucher specimens have been archived in public natural history collections. Reprints R. M. Karim, Y. Kumin, D. Laban, A. Lahi, J. Lapidin, M. Latim, N. Maidin, N. Majuakim, and permissions information is available at www.nature.com/reprints. The authors R. Miadin, Y. Miki, M. Moguring, H. Mujih, F. Simin, K. C. Sion, D. Sumbin, D. Tingoh, declare no competing financial interests. Readers are welcome to comment on the E. Yakin, were invaluable for all manner of logistics and other support before, during, online version of the paper. Correspondence and requests for materials should be and after the expedition, in the field and at the stations and administrative offices. For addressed to M.Sch. ([email protected]).

METHODS Phylogenetic analysis. We performed initial exploratory alignment and created No statistical methods were used to predetermine sample size. The experiments neighbour-joining trees. This allowed an assessment of individuals that (on the were not randomized and the investigators were not blinded to allocation during basis of cursory morphological examination) had been included as potential experiments and outcome assessment. (undescribed) members of the species complexes of choice. In some cases, the Expedition. Material was sampled chiefly between September 10th and 25th, sequence analysis showed that these individuals were in fact unrelated and such 2012, by the participants of the Crocker Range/Kinabalu Scientific Expedition, sequences were then removed before further analysis. Then, using Geneious (ver- which was conceived, organized, funded and conducted jointly by Sabah Parks sion 6.0.5; created by Biomatters; available from http://www.geneious.com/) as a 25 27 (Malaysia) and Naturalis Biodiversity Center (The Netherlands). The expedition workbench, sequence data were aligned with MUSCLE . We ran ModelTest to was set up with the explicit aim to investigate evolutionary patterns of endemism determine, using Akaike Information Criterion (AIC), the best model of nucleo- (see main text), and participants were selected to maximize taxon coverage and tide substitution per alignment, for each genetic marker separately. We then ecological diversity. The 47 expedition members were asked to identify one or performed a Bayesian analysis using MrBayes 3.2.2 (ref. 28) with settings for 7 more congeneric species complexes (hereafter termed ‘genera’) within their taxon multiple markers unlinked, running two replicates of a minimum of 10 genera- of expertise that included high elevation endemics and preferably also more wide- tions each. Convergence was checked in Tracer (v1.5; ref. 29) and, after discarding spread lowland species (although there is a possibility that this approach would a 25% burn-in, the resulting majority-rule consensus trees were preserved. For the leave out any monotypic endemics, in the groups studied by us, such species are fungal data sets, multiple sequence alignments were built using MUSCLE and, due not known). These, plus outgroup species, were then sampled (using taxon- to the large size of these data sets, phylogenetic analyses of maximum likelihood specific methods; see Supplementary Table 2 for further details) at eight expedition (ML) were carried out in Garli 2.0 (ref. 30) using the GTR1I1G model with stations located at a range of elevations (Fig. 1), and also in additional locations in estimated values of the alpha parameter of the gamma distribution of variable both parks and their vicinity. Data on time, latitude and longitude, elevation, and sites (G) and proportion of invariable sites (I). Clade support was assessed by non- habitat were collected with each sample. Material was subsampled for DNA ana- parametric bootstrap analyses with 100 pseudo-replicates. lysis, mostly in the field, by preserving tissues or entire organisms, usually either Molecular dating. The times of divergence of Mount Kinabalu endemics from in pure ethanol or in silica gel (see Supplementary Table 2 for taxon-specific their most closely related extant relatives were estimated with a molecular clock subsampling and storage). In the case of fungi, mycelial DNA was obtained by approach. We included not only our own data, but also incorporated published bulk extraction from composite soil cores (see Supplementary Table 2 and below). studies on genera other than the ones we sampled. For each genus, taxon sampling In addition to the data collected during the expedition, the expedition members and molecular data used are specified in Supplementary Table 4. All data sets were asked to provide a complete assessment of elevational and geographical were assembled in Geneious (ver. 5.5.6; created by Biomatters; available from distribution for each of the species within their taxon of expertise, based on http://www.geneious.com/). Data sets were pruned to contain a single taxon per published sources and previous collections. species by selecting a random sequence from each species. Sequence alignments Molecular analysis. Upon arrival in the Naturalis DNA barcoding facility, sub- were obtained with the MAFFT (ver. 6.814b) alignment tool implemented in samples were processed in a semi-automated way. DNA extractions on animal Geneious. Divergence time estimates were obtained using a relaxed molecular material were performed on either tissue samples or individual arthropod legs, or clock approach with BEAST (ver. 2.1.3; ref. 31). For each DNA region used, an using whole arthropods in a non-destructive extraction method. DNA was unlinked substitution model was implemented as selected with jModeltest (ver. extracted using the NucleoMag 96 Tissue kit (Macherey-Nagel Gmbh & Co., 2.1.5; ref. 27) under the AIC. For the tree prior, a Yule birth rate prior was selected Du¨ren, Germany) on the KingFisher Flex magnetic particle processor (Thermo with a flat prior on the Yule birth rate. A single clock and tree model was used for Scientific). DNA extractions on plant tissue were performed on dried leaf samples, each analysis. All analyses were run with an uncorrelated log-normal clock model, using the NucleoMag 96 Plant kit (Macherey-Nagel Gmbh & Co., Du¨ren, to which an exponential prior was assigned for both the mean (ucldMEAN; mean Germany). The KingFisher Flex protocols were slightly adjusted from the manu- set at 10.0) and the standard deviation (ucldStdev; mean set at 0.33). Time cal- facturer’s protocol (http://www.thermoscientific.com) to include longer mixing of ibration was done using: (1) fossil constraints; (2) secondary calibration points; or beads with lysed sample and a drying step before elution. A volume of 150 ml was (3) substitution rates, depending on the information available for each particular used for elution in both animal and plant samples. Soil samples containing fungal genus. In cases where suitable fossil or secondary calibration information was not mycelia were processed by pooling 40 cores (for sampling details, see available, we used a priori information about the substitution rate of one of the Supplementary Table 2), resulting in a composite soil sample for each site. gene partitions—as opposed to the ‘fix the mean substitution rate’ option across all Genomic DNA was extracted from 1 g of this sample using the NucleoSpin Soil partitions—to optimize the analyses. The full details on calibration methods used kit (Macherey-Nagel Gmbh & Co., Du¨ren, Germany), according to the manufac- for each taxon are given in Supplementary Table 5. For each run, posterior dis- turer’s protocol. For each sample DNA extraction was carried out twice and tributions of parameters were approximated using a Markov chain Monte Carlo replicates were combined. analysis of 5 3 107 generations, sampling every 5,000 generations, discarding a For each specimen, the accepted barcode marker for its taxon was sequenced, in burn-in of 5 3 106 generations (10%). Convergence of the chains was checked by many cases augmented with one or more other phylogenetically informative loci. evaluating the ESS values of each parameter with Tracer v1.6. Supplementary Tables 1 and 2 provide lists of the loci and primers used for each Biogeographical, elevational and vegetation zone analyses. For each genus, an genus included in the study. Where relevant for outgroup comparison or further independent estimation of the dispersal neighbourhood size was obtained from geographic resolution, we then obtained additional sequences from Borneo or the spatial ecology literature on the genus concerned or related genera, and/or elsewhere from GenBank or from our own, unrelated studies. GenBank accession expert knowledge. We used this information to classify dispersal neighbourhood codes for these are given in Supplementary Table 2. After sequencing, (remains of) (two standard deviations for the distribution of distances between birth and voucher specimens were mostly deposited in the collections of Sabah Parks and/or reproduction for individuals of a certain species) in the genus in question as ‘small’, Naturalis Biodiversity Center. Voucher collection codes are listed in Supple- ,1 km (mostly flightless animals), ‘medium’, 1–100 km (flying or ballooning mentary Table 2. animals, and plants dispersed by flying animals), or ‘large’, .100 km (plants PCR reactions generally contained 18.75 ml ultrapure H2O, 2.5 ml 103 PCR and fungi with very small wind-dispersed seeds or spores). An overview of buffer, 1.0 ml 10 mM of each primer, 0.5 ml 2.5 mM dNTPs and 0.25 ml 5U ml21 dispersal assessments is in Supplementary Table 3. Qiagen Taq. Most PCRs were performed using an initial denaturation step of 180 s Ancestral ranges were estimated for each taxon group under maximum like- at 94 uC, followed by 40 cycles of 15 s at 94 uC, 30 s at 50 uC and 40 s at 72 uC, lihood with BioGeoBears32 using the three-parameter DEC1J model. The ultra- and ended with a final extension of 300 s at 72 uC and pause at 12 uC. metric tree from the Bayesian relaxed molecular clock analysis was used as input Bi-directional Sanger sequencing was performed at either Macrogen (http:// tree. This tree was pruned to include the clade with the endemic species and at least www.macrogen.com) or BaseClear (http://www.baseclear.com). Sequences were one deeper node (for most groups two deeper nodes were included). Each species edited manually (primers trimmed off and obvious reading errors corrected) using was scored to be absent or present in Mount Kinabalu (K), Borneo (B), and the rest Sequencher 4.10.1 (Gene Codes Corporation). For the fungal soil samples, the of the world (W). For each group the analysis was run with equal probability for amplicon library was sequenced using an Ion 318TM Chip in an Ion Torrent exchange between the three areas over the entire diversification time of the tree. Personal Genome Machine (PGM; Life Technologies, Guilford, CT, USA). PCR, The maximum number of areas was assigned as the maximum number of areas sequencing, raw data filtering and all bioinformatic analyses were performed as observed in the extant taxa (either 2 or 3). The optimizations, with the ancestral described in detail previously26. From these fungal soil sequences, we selected non- range with the highest likelihood for each node, are shown in Extended Data redundant sequences of the ectomycorrhizal genus Cortinarius and the arbuscular Figs 7–9). We classify a ‘W’ to ‘K’ or ‘KW’ shift in the lineage leading to a species mycorrhizal genus Glomus because they were distributed along the entire altitu- endemic to Kinabalu as ‘eccentric endemism’. All other ancestral ranges leading dinal range of our sampling. to Kinabalu endemics are scored as ‘centric’.

For each genus sampled during the expedition that showed centric endemism, after this emergence much of Sabah became submerged, although a north–south- we added the elevation at which it had been collected as a continuous character. In oriented mountain belt formed of tightly folded mudstones and sandstones (the BayesTraits 2.0 (ref. 33) we reconstructed ancestral states for elevation at the node future Crocker Range) remained. At the same time, the climate changed from leading to the endemic species and its sister clade using the continuous random seasonal to ever-wet. Mapping of former shelf edges offshore shows that later the walk model which implements a generalized least squares model for continuously Crocker Range widened with time, implying that it became higher in its central varying traits. The elevation of the most-recent common ancestor of the node of parts. Between 8 and 7 Mya a granitic body intruded the crust and cooled rapidly interest was inferred using a MCMC approach on a set of 2,700 trees randomly from ,7 to 5 Mya. Melting could have resulted from a build-up of heat from sampled after the phylogenetic inference with MrBayes (excluding burn-in). The radioactive decay in the deep crust, or from decompression melting following MCMC chain of BayesTraits was run for 106 generations, discarding the results extension. After 6 Mya (the precise timing and duration is not known) the sampled during the first 105 generations as burn-in. We then inspected whether area (including the surrounding Crocker Range) rose further, elevating to the the current range of elevation of the endemic species stretches beyond the 95% point that it was glaciated recently, possibly after a lithospheric root detached credible interval for the most-recent common ancestor. If it stretches above this and sank into the deeper mantle, leading new mantle material to flow into the interval, we considered this indicative of a ‘bottom-up’ scenario, whereas the vacated space below the Crocker Range. Extensive glacial weathering of the sum- reverse would suggest a ‘top-down’ scenario. The results are summarized in mit suggests the mountain had reached its present elevation by at least 1 Mya. Supplementary Table 6. The Pinosuk gravels on Kinabalu’s south-eastern slope are the accumulated ero- In parallel with the elevational analysis, we conducted an analysis in which we sional debris of young glaciation. Today, the mountain is still rising by 0.5 mm coded the vegetation belt(s) as taxon traits. We used the zones defined for Mt. per year. 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 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 montane vegetation (2,000–2,800 m); (v) subalpine vegetation (2,800–3,400 m); gradient. Mol. Ecol. 23, 2452–2472 (2014). (vi) upper subalpine vegetation (3,400–3,700 m); (vii) alpine vegetation (above 27. Posada, D. & Crandall, K. A. Modeltest: testing the model of DNA substitution. 3,700 m). The probabilities at each vegetation belt for the most-recent common Bioinformatics 14, 817–818 (1998). ancestor of the node leading to the endemic clade and its sister group were inferred 28. Ronquist, F. & Huelsenbeck, J. P. MrBayes 3: Bayesian phylogenetic inference with the continuous-time Markov model for discrete data implemented in under mixed models. Bioinformatics 19, 1572–1574 (2003). BayesTraits 2.0. The same input trees were used as for the elevation reconstruction, 29. Rambaut, A. & Drummond, A. J., Tracer v1.5. http://beast.bio.ed.ac.uk/Tracer (2009). and the MCMC was run for 106 generations, discarding the results sampled during 5 30. Zwickl, D. J. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large the first 10 generations as burn-in. The resulting probabilities are shown in Biological Sequence Datasets under the Maximum Likelihood Criterion (The University Supplementary Table 7. of Texas, Austin, 2006). Geological summary. The following is based on refs 15,34 and R. Hall, personal 31. Bouckaert, R. et al. BEAST 2: a software platform for Bayesian evolutionary communication, 2014. analysis. PLOS Comput. Biol. 10, e1003537 (2014). Orogeny in the region began at about 23 million years ago (Mya) as a result of 32. Matzke, N. J. Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model- the northward movement of the Australian plate leading to the collision of testing. Front. Biogeogr. 5, 242–248 (2013). Australia and Southeast Asia in what today is eastern Indonesia. Orogeny in the 33. Meade, A. & Pagel M. BayesTraits, version 2.0. http://www.evolution.rdg.ac.uk Kinabalu area began at about 20 Mya after collision of north Borneo with the (2015). South China continental crust. This led to the emergence of most of Sabah. Soon 34. Hall, R. et al. The Geology of Mount Kinabalu (Sabah Parks, 2008).

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 1 DQ147850 I. hawkeri (Papua New Guinea) RBINS.15993 K. sp.2 DQ147868 I. platypetala (Indonesian, Bali)

RBINS.15994 K. sp.2 1 tbd-I.usambarensis 0.65 RBINS.15995 K. sp.2 1 DQ147892-I.walleriana-African_origin tbd-I.serpens- RBINS.15998 K. sp.2 1 1 1 tbd-I.thamnoidea- RBINS.15999 K. sp.2 1 tbd-I.pseudohamata- RBINS.16000 K. sp.2 DQ147816 I.balsamina (Indian)

RBINS.16001 K. sp.2 0.68 DQ147832 I. cuspidata (India) 1 1 RBINS.16006 K. sp.2 1 DQ147845 I. ﬂaccida (India) 0.78 1 RBINS.16007 K. sp.2 DQ147854 I. lafolia (Indian) DQ147814 I. aureliana (China, Yunnan) RBINS.16009 K. baluensis 1 DQ147869 I. poilanei (Vietnam) RBINS.16010 K. baluensis 1 DQ147839 I. eberhardi (Vietnam) RBINS.16043 K. baluensis 1 FJ826636 I. chevalieri (Vietnam)

RBINS.16063 K. baluensis CM0028 I. kinabaluensis 1 RBINS.16096 K. baluensis CM0015 I. kinabaluensis CM0025 I. kinabaluensis RBINS.16023 K. baluensis 1 FL007 I. kinabaluensis AB611913 K. interlineatus FL033 I. kinabaluensis AB611931 Metaphrynella pollicaris 0.99 FL073 I. kinabaluensis

AB611939 Metaphrynella sundana 0.0070

0.06

Aranea - Myrmarachne EU815599 Ligonipes sp. (Australia) NMF2012-01399.PK357 M.cornuta 1 NMF2012-01399.PK373 M. cornuta 0.84 AY297412 M. assimilis (Philippines) 1 JX145678 M. evidens (Gabon) Begoniaceae - Begonia JX145679 M. foenisex (Gabon) 0.79 NMF2012-01399.PK210 M. hanoii DCT07-24 B. masoniana (China) JX145676 M. cf. gedongensis (Malaysia) 1 NMF2012-01399.PK068 M. malayana NMF2012-01399.PK069 M. malayana DCT08-102 B. kingiana (Malaysia) NMF2012-01399.PK249 M. malayana 0.75 NMF2012-01399.PK254 M. malayana NMF2012-01399.PK259 M. malayana 0.86 NMF2012-01399.PK261 M. malayana PH115 B. spec2 NMF2012-01399.PK262 M. malayana NMF2012-01399.PK267 M. malayana NMF2012-01399.PK285 M. malayana LLF141 B. amphioxus NMF2012-01399.PK291 M. malayana 0.99 NMF2012-01399.PK293 M. malayana 0.57 0.85 NMF2012-01399.PK298 M. malayana DCT09-03 B.pendula (Malaysia) NMF2012-01399.PK301 M. malayana NMF2012-01399.PK303 M. malayana 1 0.87 NMF2012-01399.PK305 M. malayana NMF2012-01399.PK307 M. malayana FL066 B.cauliﬂora NMF2012-01399.PK308 M. malayana 1 NMF2012-01399.PK311 M. malayana NMF2012-01399.PK312 M. malayana FL065 B.cauliﬂora NMF2012-01399.PK315 M. malayana NMF2012-01399.PK317 M. malayana 0.89 1 NMF2012-01399.PK137 M. malayana SNP25535_1 B.vaccinioides NMF2012-01399.PK144 M. malayana 1 NMF2012-01399.PK158 M. malayana 0.68 1 NMF2012-01399.PK083 M. malayana SNP25535_2 B.vaccinioides 1 NMF2012-01399.PK097 M. malayana 1 NMF2012-01399.PK098 M. malayana NMF2012-01399.PK103 M. malayana NMF2012-01399.PK109 M. malayana FL040 B. burbidgei NMF2012-01399.PK116 M. malayana 1 NMF2012-01399.PK245 M. malayana 1 NMF2012-01399.PK248 M. malayana DCT07-26 B. burbidgei NMF2012-01399.PK250 M. malayana NMF2012-01399.PK263 M. malayana NMF2012-01399.PK265 M. malayana FL062 B. spec1 0.98 NMF2012-01399.PK266 M. malayana NMF2012-01399.PK286 M. malayana NMF2012-01399.PK255 M. malayana NMF2012-01399.PK290 M. malayana FL075 B. imbricata NMF2012-01399.PK316 M. malayana NMF2012-01399.PK304 M. malayana 0.98 NMF2012-01399.PK306 M. malayana FL071 B. beryllae NMF2012-01399.PK320 M. malayana 1 NMF2012-01399.PK051 M. sp.4 NMF2012-01399.PK052 M. sp.4 FL074 B. cf. beryllae 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 0.0030 0.73 NMF2012-01399.PK264 M. nov.sp.2 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 0.72 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 1 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 0.96 NMF2012-01399.PK179 M. mariaelenae 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 0.4

Athyriaceae - Athyium

EU329066andEU329109-Deparia.lobatocrenata-Japan EU329064andEU329107-Deparia.petersenii-Japan 1 EU329065andEU329108-Deparia.conilii-Japan 0.95 EU329068 EU329111 Diplazium hachijoense (Japan) 1 EU329067 EU329110 Diplazium nipponicum (Japan) 0.6 e4002185646 Diplazium simplicivenium 0.91 EU329047 EU329090 A. sheareri (Japan) 1 1 EU329029 EU329073 A. cuspidatum (China) EU329042 EU329085 A. niponicum (Japan) 1 EU329063 EU329106 Cornopteris decurren alata (Japan) 1 EU329060 EU329103 Cornopteris christenseniana (Japan) 0.99 1 EU329062 EU329105 Cornopteris crenulatoserrulata (Japan) EU329061 EU329104 Cornopteris christenseniana (Japan) 0.69 EU329038 EU329081 A. melanolepis (Japan) 1 EU329027 EU329071 A. brevifrons (Japan) 0.99 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 0.96 EU329050 EU329093 A. tashiroi (Japan) 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 0.64 0.85 e4002185621 A. clemensiae e4002185526 A. clemensiae 0.99 e4002185538 A. clemensiae 1 EU329030 EU329074 A. deltoidofrons (Japan) 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 e4002185691 A. amoenum 0.81 1 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 0.99 EU329053 EU329096 A. viridescenpe (Japan) 1 EU329057 EU329100 A. x akiense (Japan) 3500-4000m EU329044 EU329087 A. otophorum (Japan) 3000-3500m 0.75 EU329043 EU329086 A. oblitescens (Japan) 2500-3000m EU329049 EU329092 A. strigillosum (Japan) 1 2000-2500m EU329035 EU329078 A. iseanum var. angussectum (Japan) 1500-2000m 1 1 EU329058 EU329101 A. x hisatsuanum (Japan) 1000-1500m EU329034 EU329077 A. iseanum (Japan) 500-1000m 0.03 0-500m 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.

Cortinariaceae - Cortinarius

GU234083 Hebeloma mesophaeum OTU 2041 OTU 15011 Coleoptera - Ptomaphaginus OTU 8218 GQ159827.1 Cornarius purpurascens AY669520.1 Cornarius nanceiensis RMNH.INS.549243 Prionochaeta harmandi (Japan) OTU 5338 1 RMNH.INS.555623 Ptomaphaginus ater AY669521.1 Cornarius populinus AY174797.1 Cornarius saginus RMNH.INS.555624-Ptomaphaginus ater OTU 9222 1 RMNH.INS.555632 Ptomaphaginus nr. fagei OTU 14845 1 FJ039613.1 Cornarius balteatus RMNH.INS.555633 Ptomaphaginus.nr. fagei OTU 1594 GU233350.1 Cornarius anauensis 0.88 RMNH.INS.555618 Ptomaphaginus n.sp. bryan complex OTU 9813 RMNH.INS.555621 Ptomaphaginus n.sp. bryan complex OTU 27167 1 FJ039619.1 Cornarius herpecus 1 RMNH.INS.555620 Ptomaphaginus n.sp. bryan complex FJ039622.1 Cornarius herpecus FJ039621.1 Cornarius herpecus RMNH.INS.555622 Ptomaphaginus n.sp. bryan complex EU821686.1 Cornarius salor RMNH.INS.555619 Ptomaphaginus n.sp. bryan complex GU233329.1 Cornarius aerugineoconicus OTU 2542 RMNH.INS.555607 Ptomaphaginus latescens AY033104.1 Cornarius elacapus OTU 13359 1 RMNH.INS.555591 Ptomaphaginus bryanoides OTU 1859 RMNH.INS.555594 Ptomaphaginus bryanoides OTU 15334 AY669677.1 Cornarius fulvoconicus RMNH.INS.555645 Ptomaphaginus bryanoides AJ889977.1 Cornarius torvus EU433388.1 Cornarius agathosmus RMNH.INS.555677 Ptomaphaginus bryanoides OTU 504 RMNH.INS.555600 Ptomaphaginus bryanoides OTU 9276 OTU 8686 RMNH.INS.555598 Ptomaphaginus bryanoides OTU 116 OTU 4229 0.79 1 RMNH.INS.555599 Ptomaphaginus bryanoides OTU 1668 RMNH.INS.549268 Ptomaphaginus bryanoides OTU 3529 0.95 OTU 10831 RMNH.INS.555644 Ptomaphaginus bryanoides OTU 10378 OTU 5366 0.98 RMNH.INS.555637 Ptomaphaginus bryanoides EU821656.1 Cornarius traganus RMNH.INS.549270 Ptomaphaginus bryanoides FJ039542.1 Cornarius serpes FJ717541.1 Cornarius saniosus RMNH.INS.549271 Ptomaphaginus bryanoides OTU 1074 1 OTU 12791 RMNH.INS.549269 Ptomaphaginus bryanoides AY669658.1 Cornarius umbrinolens RMNH.INS.555626 Ptomaphaginus bryanoides AY669667.1 Cornarius helvolus FJ039572.1 Cornarius venustus 1RMNH.INS.555627 Ptomaphaginus bryanoides AY669670.1 Cornarius anthracinus 0.86 AY669688.1 Cornarius biformis RMNH.INS.555628 Ptomaphaginus bryanoides GQ159813.1 Cornarius saturninus 1 RMNH.INS.555625 Ptomaphaginus bryanoides AY669687.1 Cornarius umbilicatus OTU 2471 RMNH.INS.555610 Ptomaphaginus similipes OTU 6606 OTU 12519 1 RMNH.INS.555609 Ptomaphaginus similipes OTU 1496 RMNH.INS.555616 Ptomaphaginus similipes OTU 26469 AY669681.1 Cornarius malachius RMNH.INS.555612 Ptomaphaginus similipes OTU 9572 0.92 OTU 601 RMNH.INS.555593 Ptomaphaginus similipes OTU 26865 RMNH.INS.555592 Ptomaphaginus similipes OTU 18561 OTU 25211 1 1 RMNH.INS.555681 Ptomaphaginus similipes OTU 10559 AM713178.1 Cornarius assiduus RMNH.INS.549263 Ptomaphaginus similipes OTU 16806 RMNH.INS.555680 Ptomaphaginus similipes DQ499466.1 Cornarius boulderensis GQ159914.1 Cornarius fulvescens 1 RMNH.INS.555685 Ptomaphaginus similipes AY669679.1 Cornarius subserpes OTU 5651 RMNH.INS.555611 Ptomaphaginus c.f. lamanus OTU 11821 RMNH.INS.555601 Ptomaphaginus kinabaluensis OTU 2564 AY669665.1 Cornarius hinnuleus 0.85 RMNH.INS.555631 Ptomaphaginus kinabaluensis AY669673.1 Cornarius rubricosus RMNH.INS.555629 Ptomaphaginus kinabaluensis GQ159883.1 Cornarius candelaris OTU 17537 1 RMNH.INS.555602 Ptomaphaginus kinabaluensis OTU 11785 OTU 12030 RMNH.INS.555604 Ptomaphaginus kinabaluensis FJ039708.1 Cornarius sp. RMNH.INS.555605 Ptomaphaginus kinabaluensis OTU 13067 GQ159774.1 Cornarius turibulosus RMNH.INS.555603 Ptomaphaginus kinabaluensis AY669686.1 Cornarius evernius AF430292.1 Cornarius brunneus RMNH.INS.555606 Ptomaphaginus kinabaluensis EU266692.1 Cornarius genlis AJ236072.2 Cornarius pholideus 0.08 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 Dicranaceae - Dicranoloma DQ097876.1 Cornarius callisteus OTU 6025 OTU 5985 OTU 19 AF146376 AF144112 Mesotus celatus AF112147.1 Dermocybe austroveneta AF135067 AF140696 Dicnemon calycinum AY669632.1 Cornarius walkeri AF389160.1 Cornarius amoenus 0.73 AF129587 AF144113 Dicranum polysetum AY669595.1 Cornarius rubellus 0.76 AF135075 AF144116 Paraleucobryum enerve AJ236064.2 Cornarius rubellus OTU 14254 1 KF423995 KF423641 Holomitrium arboreum OTU 3192 OTU 14516 KF423992 KF423638 Holomitrium crispulum GU233342.1 Cornarius picoides DQ462604 DQ464186 D. chilense (Chile) OTU 13297 AY174782.1 Cornarius infractus DQ462594 DQ464193 D. billarderi (New Zealand) OTU 3972 DQ462595 DQ464194 D. billarderi (Chile) OTU 14800 0.95 1 OTU 26181 1 DQ462596 DQ464196 D. billarderi (Rwanda) OTU 727 OTU 14618 DQ462597 DQ464197 D. billarderi (Reunion) OTU 6126 1 e4002189780 D. blumii OTU 4057 0.97 AY669583.1 Cornarius malicorius e4002189776 D. blumii FJ039596.1 Cornarius humboldtensis e4002189814 D. blumii OTU 3916 0.65 FJ039701.1 Cornarius sp. DQ462598 DQ464188 D. robustum (New Zealand) GQ159873.1 Cornarius tubarius 1 OTU 17187 1 DQ462599 DQ464189 D. robustum (New Zealand) OTU 468 DQ462600 DQ464190 D. robustum (Chile) AY082608.1 Dermocybe cinnamomea AY669585.1 Cornarius olivaceofuscus DQ462601 DQ464191 D. robustum (Chile) FJ157089.1 Cornarius neosanguineus KF423978 KF423621 D. cylindrothecium (Russia) FJ157116.1 Cornarius neosanguineus OTU 580 0.91 L0092869 e4002189708 D. diaphanoneurum (Australia) OTU 14542 OTU 4810 1 DQ462607 DQ464184 D. menziesii (New Zealand) OTU 27315 DQ485179 D. menziesii (Australia) OTU 197 1 OTU 11469 e4002189763 D. brevisetum OTU 4748 0.57 e4002189823 D. braunii EU821667.1 Cornarius phoeniceus FJ039591.1 Cornarius smithii 1 e4002189740 D. braunii FJ039594.1 Cornarius idahoensis e4002189766 D. braunii AY669581.1 Cornarius palustris 1 GQ159882.1 Cornarius chrysolitus 1 e4002189764 D. braunii FJ039601.1 Cornarius olivaceopictus AF539707.1 Cornarius luteostriatulus e4002189788 D. brevisetum AF539708.1 Cornarius obscurooliveus MS4_e4002189774 D. brevisetum GU233323.1 Cornarius alienatus OTU 12584 MS9_e4002189739 D. brevisetum 0.99 OTU 12602 MS2_e4002189750 D. brevisetum AY669588.1 Cornarius collinitus OTU 7973 MS3_e4002189762 D. brevisetum OTU 12746 0.86 OTU 17155 DQ485176 D. leichhardi (Australia) OTU 16366 0.84 e4002189743 D. havilandii OTU 25865 OTU 25299 e4002189755 D. havilandii OTU 2634 e4002189767 D. havilandii OTU 21065 0.96 OTU 19102 e4002189779 D. havilandii OTU 18261 GU233334.1 Cornarius vitreopileatus L0856682 e4002189720 D. havilandii OTU 1813 DQ462605 DQ485175 D. dicarpum (New Zealand) DQ652235.1 Cornarius lustrabilis 0.66 OTU 1149 1 0.84 L0856640 e4002189709 D. sp. (Indonesia) OTU 4508 1 L0093198 e4002189685 D. reflexum (Indonesia) OTU 7114 EU525980.1 Cornarius calyptratus e4002189775 D. reflexum AY174787.1 Cornarius glaucopus AY669558.1 Cornarius langei 0.99 e4002189787_D_reflexum_Kinabalu_Sayap AY669535.1 Cornarius argutus 0.99 DQ485178 D. fasciatum (Australia) AY669587.1 Cornarius delibutus AY669612.1 Cornarius rotundisporus 1 DQ462606 DQ464185 D. plurisetum (New Zealand) AF539730.1 Cornarius austroturmalis DQ485174 D. plurisetum (New Zealand) OTU 1023 OTU 2153 0.82 e4002189777 D. assimile OTU 18981 OTU 19822 1 e4002189789 D. assimile OTU 19034 e4002189741 D. assimile OTU 26933 OTU 2553 e4002189802 D. assimile OTU 17207 e4002189765 D. assimile OTU 18659 1 OTU 26171 e4002189742 D. assimile OTU 26541 OTU 23750 e4002189790 D. assimile OTU 12474 e4002189815 D. assimile OTU 2644 OTU 19460 e4002189791 D. assimile OTU 9147 e4002189768 D. assimile OTU 5013 OTU 9521 e4002189827 D. assimile FJ039611.1 Cornarius duracinus GQ159908.1 Cornarius pseudocandelaris OTU 26194 OTU 7849 GQ159860.1 Cornarius velenovskyi OTU 17175 0.02 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 Diptera - Diopsidae OTU 17985 OTU 10720 RMNH.INS.557960 Eurydiopsis sarawakensis OTU 16037 OTU 9069 OTU 18957 RMNH.INS.557894 Teleopsis nr. quinqueguata OTU 14593 OTU 22118 RMNH.INS.557959 Teleopsis nr breviscopium OTU 24443 1 OTU 3600 RMNH.INS.555156 Teleopsis longiconus sp.n. OTU 4725 1 OTU 11980 OTU 15329 Teleopsis longiconus sp.n.V1 OTU 9940 OTU 13013 RMNH.INS.555159 Teleopsis nr. sexguata OTU 8619 0.88 0.89 OTU 12349 RMNH.INS.555161 Cyrtodiopsis nr. dalmanni sp. 2 OTU 12484 1 EU655655.1 Cornarius rapaceotomentosus Cyrtodiopsis nr. dalmanni sp.1 IIX3 DQ663411.1 Cornarius sanc-felicis 1 EU655660.1 Cornarius insignibulbus EU057001.1 Cornarius jardinensis RMNH.INS.555162 Cyrtodiopsis nr. dalmanni sp. 1 EU056976.1 Cornarius magnivelatus 0.98 OTU 26725 RMNH.INS.555160 Teleopsis sabah sp. 1 OTU 12377 OTU 19253 RMNH.INS.555128 Teleopsis pallifacies OTU 12260 1 OTU 752 EU660953.1 Cornarius cretax 1 RMNH.INS.557968 Teleopsis pallifacies OTU 5187 0.87 OTU 1410 1 RMNH.INS.555138 Teleopsis pallifacies OTU 15101 OTU 27038 Teleopsis pallifacies IV5 OTU 14504 OTU 14517 OTU 4929 RMNH.INS.557898 Teleopsis scapulistylus sp.n. OTU 14916 0.93 OTU 14512 RMNH.INS.557932 Teleopsis pseudogracilifemur sp.n. OTU 9017 1 OTU 2674 RMNH.INS.555116 Teleopsis pseudogracilifemur sp.n. OTU 24339 OTU 18369 OTU 15128 0.7 RMNH.INS.555122 Teleopsis pseudogracilifemur sp.n. AF539736.1 Cornarius olivaceobubalinus OTU 4232 0.97 Teleopsis_gracilifemur sp.n. V2 OTU 6233 1 OTU 3490 RMNH.INS.555117 Teleopsis gracilifemur sp.n. OTU 10798 0.98 OTU 2456 RMNH.INS.555127 Teleopsis gracilifemur sp.n. OTU 8407 OTU 18770 OTU 857 RMNH.INS.557902 Teleopsis sabah sp.2 OTU 26840 0.52 OTU 3898 1 RMNH.INS.555141 Teleopsis nr. discrepans sp. C AY669654.1 Cornarius spilomeus OTU 133 1 Teleopsis discrepans XIII1 FJ039604.1 Cornarius ochrophyllus OTU 7587 OTU 3280 RMNH.INS.555146 Teleopsis nr. discrepans sp. A OTU 3693 1 OTU 11718 0.73 RMNH.INS.557903 Teleopsis sp. 2 OTU 5836 AY669596.1 Cornarius bolaris RMNH.INS.557945 Teleopsis nr. discrepans sp. B OTU 8827 AY669645.1 Cornarius anomalus EF420146.1 Cornarius sericeolazulinus FJ039651.1 Cornarius anomalovelatus OTU 4234 0.02 OTU 6434 GQ159887.1 Cornarius anomalovelatus OTU 8855 OTU 10556 AY669646.1 Cornarius caninus GQ159900.1 Cornarius rigens AY669637.1 Cornarius schlerophyllarum OTU 406 3500-4000m OTU 23850 3000-3500m 5 changes 2500-3000m 2000-2500m “up” 1500-2000m “mid” 1000-1500m “low” 500-1000m 0-500m Extended Data Figure 2 | Phylogenetic reconstructions for Coleoptera, Dicranaceae, Diptera and Cortinariaceae. Details of materials and methods used are given in Supplementary Table 2.

Ericaceae - Rhododendron

GU176637 AF394258 R. camtschacum SNP21936 R. borneense SNP21921 R. cuneifolium Hirudinea - Tritetrabdella 0.76 SNP28514 R. cuneifolium SNP28515 R. cuneifolium 0.53 HQ203161 P. pungens (Australia) SNP28516 R. cf. cuneifolium SNP32302 R. ericoides SP13407 H. sp. 0.97 SNP32303 R. ericoides SNP21925 R. simulans SP13398 T. kinabaluensis kinabaluensis SNP21906 R. rugosum SNP21908 R. buri SP13306 T. kinabaluensis kinabaluensis- SNP28504 R. rugosum 1 0.99 0.62 SNP28508 R. rugosum SP13383 T. kinabaluensis inobongensis SNP28510 R. rugosum SNP32301 R. buxifolium SNP32304 R. buxifolium SP13382 T. kinabaluensis inobongensis 1 0.89 1 SNP32306 R. buxifolium SNP32307 R. buxifolium SP13381 T. kinabaluensis inobongensis SNP21909 R cf. rugosum 1 SNP21912 R sp. SP13380 T. kinabaluensis inobongensis 0.57 SNP21918 R. cf. rugosum SNP21932 R. praetervisum HQ203194 T. scandens (Thailand) 0.99 SNP21943 R. suaveolens SNP21944 R. praetervisum HQ322465 T. taiwana (Taiwan) 0.95 SNP21905 R. suaveolens 1 1 0.91 SNP21934 R. suaveolens 1 HQ322464 T. taiwana (Taiwan) SNP21933 R. orbiculatum 0.58 1 SNP21955 R. orbiculatum HQ322466 T. taiwana (Taiwan) 0.56 SNP21910 R. stapﬁanum SNP21926 R. cf. stapﬁanum 0.54 0.89 HQ203195 T. taiwana (China) SNP21914 R. suaveolens 1 1 SNP21929 R. suaveolens AB685259 T. taiwana (China) SNP21919 R. javanicum SNP21922 R. crassifolium 1 HQ322468 T. taiwana (Taiwan) SNP32305 R. lowii SNP28513 R. lowii HQ322469 T. taiwana (Taiwan) SNP21907 R. bagobonum 0.99 SNP21915 R. stenophyllum 0.91 SNP21927 R stenophyllum HQ322463 T. taiwana (Taiwan) 0.87 0.55 SNP28505 R. stenophyllum SNP28517 R. stenophyllum HQ322467 T. taiwana (Taiwan) SNP28518 R. sp. 0.04 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 Gastropoda - Philalanka SNP21911 R. exuberans SNP21916 R p. HQ171582-Zospeum exiguum (Slovenia) SNP21930 R x. planecostatum HQ171529 Carychium mexicanum (USA) 0.93 SNP21935 R. javanicum 1 SNP21939 R. javanicum SP13428 Ibycus rachelae SNP21904 R. crassifolium SNP21923 R. crassifolium JX988066 Subulina octona 1 SNP21937 R. crassifolium SP13507 Philalanka sp.1 1 SNP21938 R. crassifolium SNP21940 R. crassifolium 1 1 SP13508 Philalanka sp.1 SNP21941 R. crassifolium SP13509 Philalanka sp.1

SP13506 Philalanka sp.1 0.0070 1 1 SP13492 Philalanka sp.3 SP13511 Philalanka sp.3

Hemiptera - Rhagovelia 0.97 SP13510 Philalanka sp.2 RMNH.INS.555452 Mesovelia horvathi SP13519 Philalanka thienemanni RMNH.INS.555246 R. samardaca 1 SP13520 Philalanka thienemanni RMNH.INS.555247 R. samardaca RMNH.INS.555248 R. samardaca SP13521 Philalanka thienemanni RMNH.INS.555245 R. samardaca SP13522 Philalanka thienemanni RMNH.INS.555244 R. samardaca 1 1 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 SP13518 Philalanka thienemanni 0.54 RMNH.INS.555252 R. samardaca RMNH.INS.555253 R. samardaca RMNH.INS.555251 R. samardaca 0.05 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 RMNH.INS.555221 R. silau 1 RMNH.INS.555228 R. silau 1 RMNH.INS.555238 R. silau

0.73 RMNH.INS.555224 R. silau 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

1 RMNH.INS.555270 R. simulata 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 OTU 27338 37 OTU 13007 99 AM713409 Glomus eburneum AM713407 Glomus eburneum OTU 5708 OTU 24836 64 65 59 OTU 13666 56 OTU 8632 36 OTU 9223 OTU 8446 48 87 OTU 5542 42 OTU 21220 19 79 OTU 29948 OTU 8741 96 OTU 8898 32 OTU 6588 31 OTU 35053 94 OTU 4196 73 OTU 1606 22 OTU 6655 93 OTU 21224 OTU 5441 90 56 OTU 7081 45 OTU 34472 55 OTU 18850 OTU 3458 24 37 92OTU 5233 30 OTU 21530 60 OTU 16590 27 OTU 26364 69 OTU 29995 OTU 33992 AJ972462 Glomus diaphanum 23 GU059549 Glomus indicum OTU 21269 89 AJ849467 Glomus xanthium 100OTU 27453 14 OTU 34383 OTU 14114 100OTU 12813 10 43 OTU 11936 60 AY035654 Glomus clarum 35 OTU 17823 12 OTU 20507 100 OTU 23633 18 OTU 32979 100 OTU 20709 25 OTU 12112 87 OTU 24971 98 AJ437106 Glomus sinuosum J437105 Glomus sinuosum OTU 20927 98 OTU 27919 57 OTU 10293 33 OTU 29430 25 FM865572 Glomus intraradices 33 44 FM992400 Glomus proliferum 56 FM865573 Glomus intraradices 66 FM865562 Glomus intraradices 30 88 FM865561 Glomus intraradices FM865568 Glomus intraradices 100 EF989103 Glomus intraradices EF989105 Glomus intraradices AJ557009 Glomus intraradices 46 57 80 AJ567351 Glomus intraradices 95 FJ009600 Glomus intraradices 77 FJ009598 Glomus intraradices 68 AJ567764 Glomus intraradices 3500-4000m 70 3000-3500m 40 2500-3000m 37 51 2000-2500m 74 1500-2000m 1000-1500m 500-1000m 0-500m 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.

Nepenthaceae - Nepenthes

AF315885 N. pervillei (Seychelles) L.4149369 N. chaniana L.4149370 N. chaniana L.4149371 N. tentaculata 0.97 L.4149375-6 N. lowii 0.99 L.4149378 N. lowii 1 L.4149124 N. lowii L.4149373 N. lowii L.4149380 N. fusca 1 L.4149381 N. fusca L.4149382 N. fusca L.4149368 N. fusca L.4149091 N. tentaculata 1 L.4149120 N. tentaculata L.4149115 N. tentaculata L.4149101 N. tentaculata L.4149099 N. tentaculata L.4149088 N. tentaculata 1 L.4149087 N. tentaculata L.4149086 N. tentaculata L.4149098 N. tentaculata L.4149097 N. tentaculata 0.83 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 1 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 L.4149092 N. gracilis L.4149078 N. gracilis 0.99 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 0.99 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

0.2

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 RMNH.INS.503932 C. didyma (Terengganu Malaysia) WJJO de Wilde & BEE de Wilde-Duyes 21409 (L) Salomonia cantoniensis 0.72 RMNH.INS.506468 C. cyanomelas (Hong Kong) RMNH.INS.506487 C. cyanomelas (Hong Kong) 1 RMNH.INS.506475 C. cyanomelas (Hong Kong) CM030 (L) E. elongata RMNH.INS.509175 C. poungyi (Thailand) 1 RMNH.INS.509174 C. poungyi (Thailand) 1 CM032 (L) E. elongata RMNH.INS.505734 C. poungyi (Thailand) 0.98 RMNH.INS.501058 C. albicauda (Malaysia)

RMNH.INS.501072 C. albicauda (Malaysia) CM011 (L) E. papuana 1 1 RMNH.INS.506849 C. albicauda (Malaysia) 0.95 RMNH.INS.507675 C. sp. 0.83 RMNH.INS.507677 C. sp. 1 CM013 (L) E. kinabaluensis RMNH.INS.507678 C. sp. RMNH.INS.507662 C. sp. 1 0.98 RMNH.INS.228944 C. octogesima (Malaysia) CM002-1 (L) E. pallida RMNH.INS.506836 C. octogesima (Malaysia) 1 0.95 0.55 RMNH.INS.503977 C. octogesima (Singapore) CM002-2 (L) E. pallida 0.9 RMNH.INS.503978 C. octogesima (Singapore) 1 RMNH.INS.501021 C. octogesima (Singapore) RMNH.INS.507775 C. nemoricola 0.74 CM009 (L) E. pallida RMNH.INS.507780 C. nemoricola 1 RMNH.INS.507782 C. nemoricola RMNH.INS.506294 C. nemoricola (Sarawak Malaysia) CM006 (L) E. pallida 0.69 1 1 RMNH.INS.506304 C. nemoricola (Sarawak Malaysia) RMNH.INS.507768 C. nemoricola 0.99 RMNH.INS.507792 C. nemoricola CM001-1 (L) E. pallida RMNH.INS.507793 C. nemoricola RMNH.INS.507721 C. nemoricola 1 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

cB042 O. pubescens (NewGuinea) Trombidiformes - Hygrobates

cB019 H. ﬁssispula (Borneo) 1 RMNH.ACA.1438 Atracdes cf. propatulus FL011 H. sp. (Philippensis ) 1

FL031 H. sp. (Philippensis) RMNH.ACA.1429 Atracdes cognatus

bZ030 H. valetoniana (NewGuinea) 1 cA092 H. schlechteri (NewGuinea) RMNH.ACA.1360 H. acupalpis 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

FL047 H. pulchella. var. magnispula 1 RMNH.ACA.1370 H. hamatus 1 FL048 H. pulchella. var. magnispula 0.74

FL046 H. pulchella RMNH.ACA.1352 H. hamatoides 1 FL042 H. pulchella 0.71 0.91 RMNH.ACA.1353 H. hamatoides FL039 H. pulchella

FL038 H. pulchella RMNH.ACA.1354 H. hamatoides FL050 H. macrostegia 1

FL055 H. macrostegia RMNH.ACA.1355 H. hamatoides

FL054 H. macrostegia 1 FL049 H. macrostegia RMNH.ACA.1357 H. hamatoides

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.

Athyrium Orchidaceae – Dendrochilum Hedyotis

Hymenasplenium_unilaterale 53,85 Elaeis_oleifera 22,78 Asplenium_bulbiferum Nypa_fruticans Carphalea_madagascariensis 83,63 Thelypteris_palustris Musella_lasiocarpa 16,89 Batopedina_pulvinellata 60,29 11,01 Paraknoxia_parviflora 99,02 71,74 Homalosorus_pycnocarpos Anigozanthos_flavidus Dibrachionostylus_kaessneri 62,42 Astelia 18,76 Oldenlandia_rupicola_cC034_Africa Woodsia_polystichoides 66,17 Lanaria 1,66 Hedyotis_nana_cA094_NewGuinea 107,11 Hedyotis_trichoclada_cB029_NewGuine Blechnum_spicant 58,84 Empodium 22,75 4,09 Neanotis_nummularia_cC028_Ceylon 81,52 51,58 32,34 Hypoxis 2,35 Neanotis_nummulariformis_cC029_Ceyl Woodwardia_japonica 11,63 1,66 Neanotis_wightiana_bS011_IndiaSEAsi Rhodohypoxis 11,28 Neanotis_formosana_cC026_Taiwan Deparia_conilii Neuwiedia 1,41 Neanotis_gracilis_SN89_Asia 4,23 39,33 Deparia_petersenii 102,79 Apostasia 0,88Hedyotis_lindleyana_cB023_Asia 75,08 2,39 0,58Neanotis_hirsuta_bS009_Asia Paphiopedilum 5,64 Deparia_lobatocrenata 23,48 1,26 Hedyotis_pahompokae_bS042_Thailand Phragmipedium Neanotis_calycina_SN13_Asia Diplazium_simplicivenium 35,38 4,08 Selenipedium 1,36 Neanotis_indica_cC030_India 67,59 29,06 Diplazium_nipponicum 32,84 Neanotis_monosperma_cC027_India 17,95 77,54 Cypripedium 9,64 Arcytophyllum_muticum Vanilla Arcytophyllum_thymifolium Diplazium_hachijoense 27,61 18,65 Oldenlandia_microtheca 57,81 Cleistes Athyrium_niponicum 34,34 12,25 Stenaria_nigricans Pogonia 9,25 Houstonia_caerulea 14,96 Athyrium_cuspidatum 23,36 8,01 Houstonia_longifolia posterior 58,63 9,4 Codonorchis Oldenlandia_fastigiata 71,7 Disperis 14,34 Athyrium_sheareri 50,15 7,01 Hedythyrsus_spermacocinus 1 Disa 20,83 Mitrasacmopsis_quadrivalvis Cornopteris_crenulatoserrulata 40,12 19,91 Oldenlandia_echinulosa 18,79 Monadenia 7,42 Oldenlandia_geophila Cornopteris_christenseniana 33,32 Habenaria 4,11 Oldenlandia_nervosa 40,21 1,58 posterior Cornopteris_decurrenti 23,91 Platanthera 9,01 Hedyotis_coronaria_cB040_Asia 54,79 16,46 Spermacoce_hispida Athyrium_filix_femina 1 Orchis 39,46 14,44 Oldenlandia_salzmannii Chiloglottis 25,98 6,72 Oldenlandia_tenuis 2,64 69,66 35,08 Athyrium_brevifrons Diuris 19,89 6,48 Cordylostigma_microcala 0,96 40,24 Cordylostigma_virgata_cB032 Athyrium_melanolepis Microtis 14,53 33,36 13,38 1,68 Oldenlandia_umbellata_SN84_Asia 34,28 Eriochilus Oldenlandia_umbellata_cC025_Asia Athyrium_atkinsonii 49,73 9,33 Oldenlandia_wiedemannii Chloraea Oldenlandia_duemmeri_cB041 12,01 Athyrium_rupestre 6,17 2,65 45,06 Pterostylis Oldenlandia_taborensis 10,22 Athyrium_nikkoense Megastylis Oldenlandia_capensis_var_capensis 4,39 3,1 Oldenlandia_densa_robinsonii_bB92 6,55 42,7 Exalaria 24,39 1,56 Athyrium_yokoscense 7,64 3,63 Oldenlandia_nematocaulis 2,15 Ponthieva Oldenlandia_wauensis 21,17 Athyrium_kirisimaense 40,35 27,82 1,51 Oldenlandia_corymbosa_bB72 0,7 Altenstenia 1,35 Oldenlandia_erecta_SN2_Asia Athyrium_tashiroi 25,34 Spiranthes 0,74 62,55 16,38 Oldenlandia_erecta_cB024_Asia Athyrium_tozanense 38,38 Sarcoglottis Oldenlandia_cherevensis_cA054_SEAsi 8,99 Synaptantha_tillaeacea Athyrium_clemensiae Pachyplectron Oldenlandia_mitrasacmoides Dossinia 18,9 Kadua_affinis 32 13,61 Athyrium_nakanoi Ludisia 6,62 Kadua_fluviatilis 23,13 4,77 Kadua_parvula 8,51 Athyrium_deltoidofrons Goodyera 17,77 9,89 16,83 18,61 4,57 Oldenlandia_biflora 2,32 Platythelys Oldenlandia_pterita Athyrium_neglectum 5,99 Oldenlandia_biflora_bB067 0,43 Palmorchis 4,09 Leptopetalum_foetidum_cB044_Pacific Athyrium_vidalii 41,37 Listera 15,31 2,49 13,5 24,46 16,7 Leptopetalum_grayii_bZ041_Japan Athyrium_amoenum Epipactis Oldenlandia_angustifolia_cB014_Indi 1,55 Oldenlandia_tenelliflora Sobralia 1,01 Athyrium_arisanense 42,67 Oldenlandia_tenelliflora_cA089_Asia Nervilia 11,6 Oldenlandia_pinifolia_bS031_IndiaSE 9,68 Athyrium_strigillosum 49,86 31,18 6,66 Oldenlandia_verticillata_SN5_Asia 11,86 Dendrobium_kingianum 10,18 Oldenlandia_gracilipes_cA061_Thaila 7,13 Athyrium_iseanum 25,37 Dendrobium_crystallinum 8,73 8,93 Oldenlandia_stocksii_cC022_India 1,28 Dendrobium_officinale 6,51 Oldenlandia_lancifolia Athyrium_x_hisatsuanum 36,41 15,98 5,34 Oldenlandia_galioides 10,72 45,44 Pleione 3,97 Oldenlandia_herbacea_cB058 Athyrium_eremicola 2,42 5,25 19,66 Coelogyne_cristata 0,76Oldenlandia_brachypoda_SN88_Asia Athyrium_wardii 17,05 Dendrochilum_scriptum Oldenlandia_diffusa_bS3_Asia Oldenlandia_ovatifolia_bZ044_SEAsia 7,66 Dendrochilum_glumaceum Athyrium_x_tokashikii 2,18 Hedyotis_pachycarpa_bZ011_Asia 7,42 1,27 Dendrochilum_cobbianum Oldenlandia_chrysotricha_bZ040_Chin Athyrium_clivicola 37,86 4,92 1,34 Oldenlandia_chrysotricha_bR100_Chin 0,44 Agrostophyllum_majus 0,57Oldenlandia_chrysotricha_bR99_China Athyrium_setuligerum 25,83 Earina_autumnalis 13,54 16,71 4,22 Oldenlandia_auricularia_cB013_Asia 4,19 Athyrium_kuratae Earina_valida 2,85 Oldenlandia_auricularia_cC020_Ceylo 0,88 32,87 2,28 Hedyotis_costata_bS41_Asia Eria 0,79Hedyotis_vestita_bS40_Asia 0 Athyrium_subrigescens 31,03 6,71 3,22 2,7 Wullschlaegelia 1,9 Oldenlandia_auricularia_cC021_Fiji Athyrium_viridescentipe 27,06 Masdevallia Oldenlandia_lapeyrousii_cA097_NewGu 35,81 23,76 2,83 Oldenlandia_lineata_bS6_IndiaSEAsia 1,41Athyrium_x_akiense Cattleya posterior 1,12 Oldenlandia_lineata_cB010_IndiaSEAs 0,53 Calanthe Hedyotis_scandens_cA052_Asia Athyrium_oblitescens 1 Hedyotis_capitellata_bZ031_SEAsia 0,23 0 34,71 Phalaenopsis 5,85 Athyrium_otophorum 4,81 Hedyotis_capitellata_bR98_SEAsia 32,69 Cymbidium Oldenlandia_scabra_cB025_IndiaSEAsi Galeandra 4,09 1,74 Hedyotis_sp_bZ013_Vietnam 13,87 0,95Oldenlandia_contracta_bZ008 29,37 Mormodes 2,952,63 Hedyotis_ampliflora_cB056_China 23,14 Bifrenaria Hedyotis_dianxiensis_bZ048_China 14,69 Lycaste 2,79 Hedyotis_obliquinervis_bZ009_Asia 12,7 1,01Hedyotis_sp_bZ018_Vietnam 19 Maxillaria 2,04 Hedyotis_sp_bZ020_Vietnam Zygopetalum 1,29 Hedyotis_pitardiana_bZ023 0,42Hedyotis_sp_bZ021_Vietnam Begonia 17,13 Vitekorchis 0,68Hedyotis_sp_bZ025_Vietnam 14,35 Stanhopea 0,27 9,21 Oldenlandia_hedyotidea_cB006_Asia Gongora Dentella_repens Begonia_oxyloba_ndhA_ndhF_rpl32 8,78 Pentodon_pentandrus_Zambia 18,71 QUA_goudotii09_02167ndhA_ndhF_rpl32 Kohautia_coccinea 17,14 TET_polygonoides09_02176ndhA_ndhF_rpl32 8,35 Kohautia_cynanchica 10,12 Begonia_poculifera 22,09 Oldenlandia_herbacea_var_herbacea 6,6 Begonia_sutherlandii 17,77 Oldenlandia_rosulata Begonia_dregei 28,53 15,31 Amphiasma_merenkyanum_cB033 12,34 SOL_radicans09_02177ndhA_ndhF_rpl32 11,17 10,18 Dendrochilum Pentanopsis_fragrans 9,58 GIR_nelumbifolia09_02171ndhA_ndhF_rpl32 8,12 Oldenlandia_stricta_cC023_India BAR_boliviensis09_02161phu_ndhA_ndhF_rpl32 7,12 Oldenlandia_affinis Begonia_dipetala 2,48 Oldenlandia_affinis_bZ039 22,41 13,02 Begonia_samahensis Oldenlandia_angolensis 2,09 Begonia_socotrana Coelogyne_cristata 4,37 27,33 5,84 Oldenlandia_goreensis 6,2 Begonia_malabarica Oldenlandia_trinervia_cC024_Asia 15,11 Begonia_floccifera Dendrochilum_dewildei 3,98 Oldenlandia_uniflora REI_hymenophylla10_00613 9,94 10,61 2,65 Dendrochilum_karoense Agathisanthemum_quadricostatum_cC03 IGN_smithiae10_00615 4,66 Agathisanthemum_chlorophyllum_cB031 14,62 11,67 Begonia_tenuifolia 1,29 2,51 Agathisanthemum_globosum 4,58 PAR_elisabethae10_00618 8,83 Dendrochilum_ovatum 3,89 Lelya_osteocarpa 3,15 Begonia_aff_elisabethae 2,69 13,9 2,26 0,43Agathisanthemum_bojeri 18,37 PAR_spec_Thailand110_00620 Dendrochilum_cobbianum Lelya_prostrata_cB039 Begonia_grandis 23,43 Oldenlandia_ternata_bZ027_SEAsia ALI_alicida10_00614 0,5 12,61 3,51 Dendrochilum_graciliscapum 0,21Hedyotis_parryi_cB057_China 2,69 Begonia_spec_China1 Oldenlandia_tetrangularis_cB052_SEA 11,35 DIP_spec_Thailand210_00622 5,38 2,92 Dendrochilum_arachnites Pleiocraterium_verticillare_bS39_In DIP_spec_Thailand310_00624 7,8 Hedyotis_purpurascens_cC032_India 7,38 REI_brandisiana10_00619 0,4 7,34 10,87 5,6 Dendrochilum_glumaceum 11,49 Hedyotis_articularis_bP48_India 4,67 DIP_demissa10_00617 5,66 Hedyotis_stylosa_bS34_India DIP_aceroides10_00623 2,93 Hedyotis_swertioides_India 9,27 Begonia_flagellaris posterior Dendrochilum_dewindtianum Hedyotis_sp_cB011 Begonia_versicolor 0,4 5,25 Oldenlandia_benguetensis_cB026_SEAs 4,83 Begonia_venusta 1 Dendrochilum_tenompokense 7,59 2,23 10,04 Hedyotis_decora_cB005_Thailand 1,45 Begonia_decora Oldenlandia_vachellii_cB007_China Begonia_pavonina 4,93 2,31 Dendrochilum_cupulatum 3,59 Hedyotis_acutangula_cB002_Asia Begonia_sikkimensis 2,7 15,76 5,61 1,41 4,64 Oldenlandia_bracteosa_cB004_China 0,54Begonia_palmata Dendrochilum_haslamii Oldenlandia_bodinieri_cB012_China Begonia_sizemoreae 1,71 0,6 3,24 Hedyotis_shenzhenensis Begonia_hatacoa 8,93 5,95 1,68 Hedyotis_shiuyingiae_cB018_China 4,95 4,11 Begonia_spec_China2 Dendrochilum_exasperatum Hedyotis_ovata_VH048 3,17 Begonia_aff_multangula 1,09 Hedyotis_rivalis_bZ035_Malaysia 1,33 Begonia_robusta Dendrochilum_gibbsiae 0 5,14 2,51 0,58 Hedyotis_uncinella_bZ038_China 4,55 0,29Begonia_multangula 0,53 4,69 Hedyotis_korrorensis_aT83_Pacific Begonia_areolata Dendrochilum_joclemensii 1,64 Hedyotis_megalantha_aT99 Begonia_roxburghii 2,22 2,15 2,69 0,32Hedyotis_novoguinensis_cA093_NewGui SPH_obovoidea10_00621 Dendrochilum_alatum 6,92 Hedyotis_sp_SKP946 3,22 Begonia_silletensis 0,43 8,56 Oldenlandia_paridifolia_TM3165_Chin 1,81 Begonia_acetosella 0,54 1,6 Dendrochilum_corrugatum Oldenlandia_paridifolia_TM3167_Chin 0,99 Begonia_longifolia 4,86 Hedyotis_cantoniensis_cA056_China Begonia_aptera 1,31 Dendrochilum_kamborangense 0,9 Oldenlandia_lancea_cB003_China 4,33 Begonia_masoniana 0,49Hedyotis_caudatifolia Begonia_morsei 0,3 0,31Hedyotis_caudatifolia_cB027_China Begonia_spec_Sumbawa1 Dendrochilum_stachyodes Hedyotis_caudatifolia_cB037_China 5,93 Begonia_goegoensis 0,71 5,69 1,11 4,38 0,56Oldenlandia_consanguinea 3,54 Begonia_sudjanae Dendrochilum_trusmadiense 4,81 Oldenlandia_consanguinea_aT79_China posterior 10,01 Begonia_muricata 1,6 0,42 Oldenlandia_assimilis 12,54 Begonia_nigritarum Dendrochilum_muluense 0,8 Oldenlandia_assimilis_cB055_China 1 6,58 Begonia_cleopatrae 0,48Oldenlandia_melli_bZ036_China 6,03 Begonia_fenicis Dendrochilum_grandiflorum 5,14 Hedyotis_cantoniensis 2,2 Begonia_hernandioides 2,07 Hedyotis_xinyiensis 0,51Begonia_chloroneura 7,75 2,85 0,94 Dendrochilum_transversum 2,39 Hedyotis_yangchunensis 10,75 Begonia_kingiana 3,52 Oldenlandia_pulcherrima Begonia_doloisii_concat_D350_PH115 Hedyotis_effusa_aT081_Asia 7,18 Begonia_amphioxus_concat_DCT2012 0,51 Dendrochilum_alpinum 2,44 Oldenlandia_tenuipes Begonia_pendula_DCT2012 0,05 0,92 2,73 0,25Hedyotis_effusa 0,92 Begonia_cauliflora_aff_D364_FL066_concat Dendrochilum_pterogyne Oldenlandia_tenuipes_bZ037_China 2,4 FL065_Begonia_cauliflora_aff_concat_D344 0,35 Hedyotis_communis_cA055_China 9,39 Begonia_vaccinioides_D351_ndhA_concat Dendrochilum_pseudoscriptum 2,47 2,15 0,15 0,12Hedyotis_sp_bZ022_Vietnam 1,12 Begonia_vaccinioides_D353_concat 0,1 Hedyotis_sp_bZ024_Vietnam Begonia_burbidgei_D363_FL040_concat Dendrochilum_scriptum 3,15 Hedyotis_cathayana_TM3214_China 0,34Begonia_burbidgei_DCT2012 1,4 0 2,84 Hedyotis_minutopuberula_TM3219_Chin Begonia_imbricata_D365_FL075_concat 1,52 Oldenlandia_prostrata_bZ043_SEAsia 0,68 FL062_Begonia_inobongensis_concat_D342 2,51 0,43 Oldenlandia_cryptantha_TM3202_China 9,04 0,16FL071_Begonia_beryllae_concat_D345 1,88 Hedyotis_cheniana_TM3190_China FL074_Begonia_cf_beryllae_cf_D347 6,48 0,18Oldenlandia_hainanensis_cB028_China Begonia_bracteata 3,67 Begonia_verecunda Hedyotis_sp_cA050 2,83 Oldenlandia_pubescens_cB042_NewGuin 1,73 BRA_specSumatra08_02319 Dicranoloma (ITS rate ﬁ xed) Hedyotis_fissistipula_cB019_Borneo BRA_resecta08_00204 3,53 2,38 Hedyotis_philippensis_cB043_Asia PET_wrayi10_00642_extraction 5,83 0,37Hedyotis_rigida_bZ042_SEAsia 3,74 Begonia_multijugata 3,15 2,48 Hedyotis_macrostegia_Borneo 1,15 PET_spec1Borneo07_00575 0,97Hedyotis_pulchella_bZ029_Borneo 4,15 Begonia_chlorosticta AF146376_AF144112_Mesotus_celatus_OUTGROUP 2,05 Oldenlandia_nutans_bS27_NewGuinea 6,63 PET_harauensis09_01011 5,17 1,15 Hedyotis_schlechteri_cA092_NewGuine 1,47 Begonia_laruei AF135067_AF140696_Dicnemon_calycinum 0,95 2,94 PET_aff_congesta09_00060 Hedyotis_valetoniana_bZ030_NewGuine 0,24PET_specKalimantan09_01013 AF129587_AF144113_Dicranum_polysetum Hedyotis_membranacea_SN78_India 0,09Begonia_corrugata 3,51 0,68 1,31 Hedyotis_coprosmoides_bS14_Ceylon PET_specSumbawa09_01015 AF135075_AF144116_Paraleucobryum_enerve 4,29 Hedyotis_tridentata_bS36_Ceylon Begonia_serratipetala 1,79 Hedyotis_rhinophylla_aT90_Ceylon 1,04 KF423995_KF423641_Holomitrium_arboreum 3,31 1,96 Hedyotis_nodulosa_bS26_Ceylon Begonia_brevirimosa 0,71 0,6Metabolos_rugosus_bS7_SEAsia 5,67 4,61 3,44 PET_specPhilippines08_03026 KF423992_KF423638_Holomitrium_crispulum 0,28 2,53 Begonia_negrosensis 3,26 0,08Metabolos_decipiens_cC016_Ceylon 1,67 Begonia_poliloensis DQ462604_DQ464186_D_chilense_Chile 2,36 Metabolos_decipiens_cC017_Ceylon 4,26 Begonia_symsanguinea Hedyotis_fruticosa_aT85_India 3,4 DQ462594_DQ464193_D_billarderi_New_Zealand Hedyotis_lawsoniae_aT98_Ceylon 0,58Begonia_strigosa 0,05 2,041,3 Hedyotis_obscura_bS29_Ceylon 4 Begonia_argenteomarginata 0,88 PET_specNewGuinea09_01016 DQ462595_DQ464194_D_billarderi_Chile Hedyotis_trimenii_bS37_India 3,37 1,83 0,23 1,83 Hedyotis_thwaitesii_SN79_India 2,09 PET_weigallii09_01017 DQ462596_DQ464196_D_billarderi_Rwanda 1,04 Hedyotis_dendroides_bS2_Ceylon 5,16 PET_spec1Papua08_02330 2,69 0,05 0,76 PET_hekensis08_02227 DQ462597_DQ464197_D_billarderi_Reunion 1,41 Hedyotis_lessertiana_var_lessertian 1,88 Begonia_varipeltata Hedyotis_quinquenervia_aT97_Ceylon 0,13PET_stevei07_01455 1,1 MS52_e4002189780_D_blumii_Kinabalu_Gunung_Alab 0,950,4Hedyotis_flavescens_SN61_Ceylon 2,99 Hedyotis_gardnerii_bS016_Ceylon 0,47PET_macintyreana07_01454 0,33 MS20_e4002189776_D_blumii_Kinabalu_L2 0,81Hedyotis_lessertiana_var_marginata PET_chiasmogyna07_00577 0,05 0,43Hedyotis_marginata_SN72_Ceylon 2,03 PET_mendumiae07_00578 MS39_e4002189814_D_blumii_Kinabalu_Laban_Rata 1,42 Begonia_masarangensis 0,8 0,85 PET_capituliformis09_01419 DQ462598_DQ464188_D_robustum_New_Zealand 4,61 0,56PET_hispidissima_GLombulan09_01418 0,18 Begonia_siccacaudata DQ462599_DQ464189_D_robustum_New_Zealand 2,66 2,33 0,39 PET_bonthainensis09_01403 DQ462600_DQ464190_D_robustum_Chile 0 0,7 PET_prionota_spec809_01407 0,16 4,13 1,12 PET_didyma08_02240 DQ462601_DQ464191_D_robustum_Chile Ilex (plastid data) 0,74 PET_ozotothrix08_02845 PET_nobiaespec1709_01416 KF423978_KF423621_D_cylindrothecium_Russia 3,9 Begonia_watuwilensis 0,93 1,35 PET_flacca09_01009 MS53_e4002189792_D_sp_Kinabalu_Gunung_Alab PET_lasioura_spec1309_01412 posterior Helwingia_japonica 3,55 2,9 Begonia_koordersii L0092869_e4002189708_D_diaphanoneurum_Australia Ilex_buergeri 2,15 PET_pseudolateralis08_02220ndhA_ndhF_rpl32 1 0,74 Ilex_rugosa 3,18 PET_comestibilis_spec509_01402 DQ462607_DQ464184_D_menziesii_New_Zealand 10,48 0,08 24,3 15,38 Ilex_sebertii 1,47 0,67 PET_vermeulenii_07_01837 DQ485179_D_menziesii_Australia Ilex_pernyi PET_torajana1109_01410 1,81 3,6 1,23 Begonia_guttapila Ilex_collina 0,78 MS11_e4002189763_D_brevisetum_Kinabalu_Sayap 21,35 Ilex_anomala 1,06 PET_aff_mekonggensisspec1209_01411 13,32 PET_rantemarioensis09_01405 0,53 MS35_e4002189766_D_braunii_Kinabalu_L2 5,79 Ilex_verticillata 0,93 PET_sanguineopilosaspec1809_01417 0,09 Ilex_yunnanensis1 MS19_e4002189764_D_braunii_Kinabalu_Sayap 16,24 Ilex_laevigata 0,21 7,71 Ilex_nothofagifolia MS16_e4002189823_D_braunii_Kinabalu_Sayap 13,15 1,49 0,67 0,07 Ilex_shennongjiaensis MS17_e4002189740_D_braunii_Kinabalu_Sayap 73,98 8,97 Ilex_pedunculosa 36,34 7,37 Ilex_liukiuensis MS21_e4002189788_D_brevisetum_Kinabalu_Sayap 4,66 Ilex_theizans2 MS2_e4002189750_D_brevisetum_Kinabalu_Sayap Ilex_mutchagara 0,38 0,03 17,08 Ilex_rubra Coeliccia MS3_e4002189762_D_brevisetum_Kinabalu_Sayap 6,84 0,12 26,52 Ilex_havilandii MS4_e4002189774_D_brevisetum_Kinabalu_Sayap Ilex_tsoi RMNH_INS_500047_Calicnemia_rectangulata_Pahang_Malaysia_OUTGROUP 0,04 18,64 Ilex_oppositifolia MS9_e4002189739_D_brevisetum_Kinabalu_Sayap 13,06 Ilex_purpurea1 1,25 11,22 Ilex_zygophylla DQ485176_D_leichhardtii_Australia 32,54 5,68 Ilex_repanda L0856682_e4002189720_D_havilandii_Kinabalu_Layang_Laya Ilex_x_attenuata 2,1 0,38 13,33 45,88 9,2 Ilex_wallichii2 Calicnemia_chaseni 0,13 MS41_e4002189743_D_havilandii_Kinabalu_Laban_Rata Ilex_vomitoria 0,03 17,72 MS44_e4002189779_D_havilandii_Kinabalu_Laban_Rata 4,05 Ilex_nervulosa 0,08 Ilex_chamaedryfolia 1,68 MS42_e4002189755_D_havilandii_Kinabalu_Laban_Rata 10,27 Ilex_amara 0,03 7,34 MS43_e4002189767_D_havilandii_Kinabalu_Laban_Rata 5,73 Ilex_wallichii1 1,14 Ilex_maingayi Calicnemia_sinensis DQ462605_DQ485175_D_dicarpum_New_Zealand Ilex_triflora 24,11 Ilex_laurina L0856640_e4002189709_D_sp_Indonesia_Java 0,61 0,27 17,52 Ilex_integra1 L0093198_e4002189685_D_reflexum_Indonesia_Sumatra Ilex_kinabaluensis 0,38 Ilex_cymosa MS12_e4002189775_D_reflexum_Kinabalu_Sayap posterior 37,86 14,35 Ilex_microdonta 4,44 Coeliccia_borneensis 0,05 24,18 Ilex_zhejiangensis 0,95 MS13_e4002189787_D_reflexum_Kinabalu_Sayap 1 13,93 Ilex_cassine DQ485178_D_fasciatum_Australia 5,09 Ilex_corallina 1,69Ilex_purpurea2 1,75 DQ462606_DQ464185_D_plurisetum_New_Zealand 36,19 0,1 Ilex_macropoda 0,81 DQ485174_D_plurisetum_New_Zealand Ilex_theizans1 Coeliccia_flavostriata 12,25 Ilex_cornuta2 MS25_e4002189741_D_assimile_Kinabalu_Sayap 26,87 4,26 Ilex_warburgii 0,61 8,91 0,12 MS28_e4002189777_D_assimile_Kinabalu_KNP 5,21 Ilex_dimorphophylla 0,04 18,81 Ilex_spicata MS29_e4002189789_D_assimile_Kinabalu_KNP Ilex_opaca 0,42 35,56 6,33 Ilex_dugesii MS38_e4002189802_D_assimile_Kinabalu_Laban_Rata Coeliccia_flavicauda 15,53 8,23 Ilex_aculeolata 0 MS45_e4002189791_D_assimile_Kinabalu_Gunung_Alab Ilex_brasiliensis 3,82 0,32 13,12 Ilex_bioritsensis MS51_e4002189768_D_assimile_Kinabalu_Gunung_Alab 7,37 Ilex_cornuta1 0,2 0,03 MS48_e4002189827_D_assimile_Kinabalu_Gunung_Alab Ilex_pubescens 22,97 Ilex_longipes Coeliccia_ryukyuensis 0,13 MS27_e4002189765_D_assimile_Kinabalu_Sayap 21,23 Ilex_hylonoma 0,03 8,67 Ilex_paraguariensis MS47_e4002189815_D_assimile_Kinabalu_Gunung_Alab 14 0,1 Ilex_argentina MS33_e4002189742_D_assimile_Kinabalu_KNP 8,29 Ilex_matanoana posterior 0,04 33,57 4,29 Ilex_integerrima 2,17 MS37_e4002189790_D_assimile_Kinabalu_L2 27,02 Ilex_brevicuspis 1 2,92 18,16 Ilex_revoluta RMNH_INS_506468_C_cyanomelas_HongKong 15,47 Ilex_fragilis 6,21 Ilex_fargesii1 3,57 Ilex_nitida 2,11 Ilex_asperula 22,97 Ilex_x_makinoi Dicranoloma (trnL rate ﬁ xed) 16,85 3,51 RMNH_INS_503926_C_didyma_Terengganu_Malaysia 1,82Ilex_maximowicziana 9,79 Ilex_arnhemensis Ilex_fargesii2 5,3 Ilex_leucoclada AF146376_AF144112_Mesotus_celatus_OUTGROUP 18,98 3,44 Ilex_mertensii 2,73 Ilex_spinigera AF135067_AF140696_Dicnemon_calycinum 10,98 Ilex_canariensis RMNH_INS_501058_C_albicauda_Malaysia 30,54 AF129587_AF144113_Dicranum_polysetum 14,58 Ilex_georgei 5,38 1,04 Ilex_rotunda1 AF135075_AF144116_Paraleucobryum_enerve 10,72 5,74 Ilex_geniculata 1,81 2,69 5,56 KF423995_KF423641_Holomitrium_arboreum 2,45 Ilex_decidua 1,08 9,58 Ilex_decidua_var_curtissii KF423992_KF423638_Holomitrium_crispulum Ilex_mucronata RMNH_INS_509175_C_poungyi_Thailand 4,98 5,19 Ilex_x_kiusiana DQ462604_DQ464186_D_chilense_Chile 8,62 7,31 Ilex_cumulicola DQ462594_DQ464193_D_billarderi_New_Zealand Ilex_mitis 0,08 Ilex_discolor 2,26 DQ462595_DQ464194_D_billarderi_Chile 15,13 Ilex_latifolia 2,78 0,35 5,17 Ilex_montana RMNH_INS_507662_C_species_2_1500to1750mASL_KHQ DQ462596_DQ464196_D_billarderi_Rwanda 0 4,08 0,08 1,44Ilex_yunnanensis2 DQ462597_DQ464197_D_billarderi_Reunion 24 Ilex_goshiensis 10,38 Ilex_amelanchier 1,66 MS52_e4002189780_D_blumii_Kinabalu_Gunung_Alab 6,83 Ilex_rotunda2 0,52 MS20_e4002189776_D_blumii_Kinabalu_L2 Ilex_kusanoi 0,08 17,55 3,68 Ilex_liebmannii 1,51 RMNH_INS_507675_C_species_1_500to750mASL_PHS MS39_e4002189814_D_blumii_Kinabalu_Laban_Rata Ilex_wilsonii 1,18 DQ462598_DQ464188_D_robustum_New_Zealand 8,61 3,39 Ilex_sp_Craven 0,28 13,37 Ilex_guianensis posterior DQ462599_DQ464189_D_robustum_New_Zealand 6,17 Ilex_integra2 3,53 0,58 4,77 Ilex_tolucana 1 DQ462600_DQ464190_D_robustum_Chile 3,6 1,19 0,24 2,82 Ilex_micrococca RMNH_INS_503977_C_octogesima_Singapore DQ462601_DQ464191_D_robustum_Chile 12 Ilex_serrata Ilex_sugerokii KF423978_KF423621_D_cylindrothecium_Russia 5,97 Ilex_macrocarpa 1,41 3,91 MS53_e4002189792_D_sp_Kinabalu_Gunung_Alab Ilex_quercetorum 2,52 Ilex_teratopis 0,85 L0092869_e4002189708_D_diaphanoneurum_Australia 10,8 Ilex_crenata Coeliccia_cyaneothorax 1,13 Ilex_pseudobuxus DQ462607_DQ464184_D_menziesii_New_Zealand 5,69 Ilex_cyrtura 0,12 9,45 3,72 DQ485179_D_menziesii_Australia 1,37Ilex_kingiana 0,26 2,75 8,79 Ilex_ficoidea MS11_e4002189763_D_brevisetum_Kinabalu_Sayap Ilex_perado 0 MS35_e4002189766_D_braunii_Kinabalu_L2 Ilex_colchica RMNH_INS_507768_C_nemoricola_500to750mASL_IN 0,79 0,15 6,91 3,85 Ilex_coriacea MS19_e4002189764_D_braunii_Kinabalu_Sayap 2,22 Ilex_ciliospinosa 0,33 4,68 MS16_e4002189823_D_braunii_Kinabalu_Sayap 1,22Ilex_cissoidea 0,1 Ilex_hookeri 2,26 1,03 MS17_e4002189740_D_braunii_Kinabalu_Sayap 4,68 Ilex_glabra 3,24 Ilex_aquifolium MS21_e4002189788_D_brevisetum_Kinabalu_Sayap 3,17 Ilex_dumosa MS2_e4002189750_D_brevisetum_Kinabalu_Sayap Dacrycarpus 0,59 0,05 MS3_e4002189762_D_brevisetum_Kinabalu_Sayap 0,2 MS4_e4002189774_D_brevisetum_Kinabalu_Sayap 0,07 10,43 Phyllocladus_alpinus MS9_e4002189739_D_brevisetum_Kinabalu_Sayap Phyllocladus_trichomanoides 1,88 20,01 Phyllocladus_toatoa DQ485176_D_leichhardtii_Australia 15,69 Ilex (nuclear data) Phyllocladus_aspleniifolius L0856682_e4002189720_D_havilandii_Kinabalu_Layang_Laya 10,41 Phyllocladus_hypophyllus 0,57 Lepidothamnus_intermedius MS41_e4002189743_D_havilandii_Kinabalu_Laban_Rata 0,2 0,05 161,21 61,25 Lagarostrobos_franklinii MS43_e4002189767_D_havilandii_Kinabalu_Laban_Rata 127,01 Manoao_colensoi 0,12 Sundacarpus_amarus MS42_e4002189755_D_havilandii_Kinabalu_Laban_Rata 113,14 43,55 0,05 Helwingia_japonica 17,46 Prumnopitys_andina MS44_e4002189779_D_havilandii_Kinabalu_Laban_Rata 68,15 Prumnopitys_taxifolia 1,67 Ilex_collina Prumnopitys_ladei DQ462605_DQ485175_D_dicarpum_New_Zealand 10,85 1,51Ilex_decidua 148,07 33,15 Ilex_decidua_var_curtissii 1,36Prumnopitys_ferruginea L0856640_e4002189709_D_sp_Indonesia_Java 3,76 Prumnopitys_ferruginoides 0,93 0,42 1,19Ilex_longipes Saxegothaea_conspicua L0093198_e4002189685_D_reflexum_Indonesia_Sumatra 22,58 Ilex_montana 0,57 Ilex_amelanchier Microcachrys_tetragona MS12_e4002189775_D_reflexum_Kinabalu_Sayap 8,4 Ilex_mucronata Pherosphaera_fitzgeraldii 118,87 0,08 20,71 Ilex_cassine Acmopyle_sahniana 1,45 MS13_e4002189787_D_reflexum_Kinabalu_Sayap 2,18 Ilex_x_attenuata 102,93 19,19 Falcatifolium_taxoides DQ485178_D_fasciatum_Australia 7,92 Ilex_cumulicola Falcatifolium_papuanum 3,2 Ilex_rubra 34,37 Dacrydium_cupressinum DQ462606_DQ464185_D_plurisetum_New_Zealand 4,68 0,14 28,57 2,94 Ilex_opaca 15,21 Dacrydium_balansae 1,23 DQ485174_D_plurisetum_New_Zealand Ilex_dugesii 93,46 1,48Dacrydium_guillauminii 0 Ilex_vomitoria 9,5 Dacrydium_beccarii MS25_e4002189741_D_assimile_Kinabalu_Sayap Ilex_paraguariensis 57,28 5,22 0,93 17,02 8,79 Dacrydium_elatum 0,18 MS28_e4002189777_D_assimile_Kinabalu_KNP 73,8 Ilex_laurina Dacrycarpus_dacrydioides 0,07 14,59 7,66 Ilex_discolor Dacrycarpus_imbricatus105 MS29_e4002189789_D_assimile_Kinabalu_KNP Ilex_tolucana 21,65 0,64 9,71 Ilex_nitida 87,55 15,15 5,65 Dacrycarpus_imbricatus106 MS38_e4002189802_D_assimile_Kinabalu_Laban_Rata 24,36 3,78 Ilex_repanda Dacrycarpus_kinabaluensis913 Ilex_amara 11,04 Dacrycarpus_compactus 0,49 MS45_e4002189791_D_assimile_Kinabalu_Gunung_Alab 5,17 1,52 1,43Ilex_chamaedryfolia 8,64 Dacrycarpus_expansus MS51_e4002189768_D_assimile_Kinabalu_Gunung_Alab Ilex_dumosa Dacrycarpus_imbricatus102 0,3 0,05 17,35 Ilex_teratopis 11,18Dacrycarpus_kinabaluensis111 MS48_e4002189827_D_assimile_Kinabalu_Gunung_Alab 15,61 1,01Ilex_crenata Retrophyllum_rospigliosii 0,21 MS27_e4002189765_D_assimile_Kinabalu_Sayap Ilex_mutchagara posterior 14,93 Retrophyllum_comptonii 0,06 7,9 Ilex_revoluta 6,27 Retrophyllum_minus MS47_e4002189815_D_assimile_Kinabalu_Gunung_Alab 5,13 Ilex_triflora 1 0,14 Ilex_maximowicziana 43,96 Nageia_wallichiana MS33_e4002189742_D_assimile_Kinabalu_KNP 6,83 76,41 14,59 Nageia_fleuryi 0,06 Ilex_rugosa 6,54 Nageia_formosensis MS37_e4002189790_D_assimile_Kinabalu_L2 Ilex_aquifolium 1,18 1,34Ilex_perado 29,17 Nageia_nagi 36,43 18,95 10,23 Afrocarpus_mannii 1,72Ilex_colchica 1,57Afrocarpus_gracilior Ilex_spinigera 5,07 Ilex_kinabaluensis Afrocarpus_usambarensis 17,55 1,63 5,52 Ilex_leucoclada 0,66Afrocarpus_dawei Impatiens Ilex_x_makinoi Afrocarpus_falcatus 9,63 Ilex_cornuta1 Podocarpus_smithii Ilex_cornuta2 19,89 14,64 6,83 2,69 1,3Podocarpus_angustifolius Ilex_dimorphophylla Podocarpus_salignus 4,54 Ilex_zhejiangensis 29,01 Iomeiana 1,94 Podocarpus_nubigenus Ikerriae Ilex_integra1 Podocarpus_totara Iglandulifera 13,28 Ilex_hylonoma 24,03 3,78Podocarpus_acutifolius 3,46 Ichungtienensis 10,61 Ilex_x_kiusiana 1,06 posterior Ilex_integra2 60,82 11,73 Podocarpus_hallii 12,81 5,76 1,18 Ibalfourii 7,2 2,9 Podocarpus_gnidioides Iparviflora Ilex_liukiuensis 4,1 1 5,05 Ilex_matanoana 7,83 Podocarpus_cunninghamii 0,96 Iedgeworthii 0,5 5,15 Podocarpus_nivalis 8,47 Iscabrida 11,8 Ilex_mertensii 2,65Podocarpus_lawrencei 19,22 0,52 Idavidi Ilex_latifolia 35,88 Ipurpurea 8,08 Ilex_ciliospinosa Podocarpus_lambertii 6,49 Idesmantha 2,82 Ilex_fargesii1 5,92 Podocarpus_sprucei Itaronensis 5,57 2,78 5,5 2,69 31,84 2,58 Ilex_hookeri 24,99 Podocarpus_parlatorei 1,65 Irectangula 10,37 Ilex_nothofagifolia Podocarpus_henkelii 3,35 Isiculifer Ilex_fargesii2 12,91 Podocarpus_madagascariensis Iaquatilis Ilex_corallina 9,51 2,27 Ifenghwaiana 8,85 Podocarpus_elongatus 17,38 1,47 Icyanantha Ilex_pernyi 3,43Podocarpus_latifolius 0,77 8,16 4,63 Ilex_kingiana 0,76 Iuliginosa 3,01 30,28 Podocarpus_milanjianus Iflanaganae 1,26Ilex_bioritsensis Podocarpus_celatus 4,62 Itinctoria_elegantissima 7,12 Ilex_georgei 2,25 1,12 Ifischeri Ilex_buergeri 8,95 Podocarpus_oleifolius 0,42 2,92 48,76 Podocarpus_guatemalensis Iteitensis 4,35 Ilex_warburgii 1,28Podocarpus_matudae 9,7 Ipallida Ilex_cyrtura 14,87 1,94 Inolitangere 2,41 Ilex_ficoidea 6,94 Podocarpus_purdieanus 1,22 Icapensis Ilex_canariensis Podocarpus_urbanii 5,62 Iuniflora 24,12 Ilex_coriacea 12,56 Podocarpus_sellowii 2,43 9,41 3,18 Iimbicilla 12,37 Ilex_glabra Podocarpus_coriaceus Iforrestii 6,25 Ilex_liebmannii 13,69 2,06 Ifaberi 7,08 Podocarpus_drouynianus Ilex_argentina Podocarpus_spinulosus 1,96 Irubrostriata Ilex_anomala Podocarpus_rumphii Iconchibracteata 17,5 6,02 Ilex_pseudobuxus 8,87 Podocarpus_elatus 1,05 Icampanulata 3,14 Ilex_microdonta 4,85 Iparasitica 29,2 14,78 25,45 15,66 Podocarpus_grayae 6,68 Ihenslowiana Ilex_quercetorum Podocarpus_novae-caledoniae 12,67 5,92 Iclavicornu 12,77 5,13 Ilex_asperula 7,58 Podocarpus_longifoliolatus 3,46 Iviscida Ilex_brevicuspis 4,07 9,6 Ilex_guianensis Podocarpus_lucienii 0,98 Imengtseana 6,61 1,17Podocarpus_sylvestris Imonticola Ilex_brasiliensis 22,13 4,13 Ibegonifolia 8,21 Ilex_theizans2 0 Podocarpus_dispermus 9,69 1,89 Inapoensis 3,87 Ilex_integerrima Podocarpus_neriifolius 1,31 2,52 0,62 Itrichosepala 27,19 Ilex_theizans1 9,5 3,59Podocarpus_archboldii Iyingjiangensis Ilex_pubescens Podocarpus_brassii Ioumina 18,13 6,19 2,97 19,07 0,65Ilex_purpurea1 1,28Podocarpus_ledermannii 1,77 Ikamerunensis_kamerunensis Ilex_purpurea2 Podocarpus_rubens Ikamerunensis_obanensis 14,77 Ilex_rotunda1 Podocarpus_bracteatus 9,1 4,27 Isakerana 2,08 Ilex_rotunda2 13,03 Ihians 7,25 Podocarpus_pilgeri 3,21 1,38 Ipalpebrata 11,4 Ilex_goshiensis 3,19Podocarpus_fasciculus 0,92 Icolumbaria Ilex_wilsonii 0,55Podocarpus_forrestii 2,53 22,41 Ilex_sebertii 1,79 0,56 Imackeyana_zenkeri Podocarpus_chingianus Imackeyana_claeri 25,55 21,13 8,04 Ilex_havilandii 0,93Podocarpus_costalis 1,77 Ipseudomacroptera Ilex_spicata 10,32 0,54 0,63 20,56 Ilex_sp_Craven Podocarpus_macrophyllus 8,32 Imacroptera Podocarpus_affinis posterior Ichinensis 17,08 Ilex_cissoidea 4,84 5,21 Ihawkeri Ilex_oppositifolia Podocarpus_degeneri 1,92 Iplatypetala 15,9 6,04 Ilex_zygophylla 0,97Podocarpus_pallidus 1 8,62 Ibalsamina 13,37 Ilex_maingayi Podocarpus_ramosii 4,24 Ilatifolia 0 7,57 Ilex_arnhemensis 6,91 2,28 24,63 5,72 Podocarpus_sp_PK_2012b 1,77 Icuspidata 9,49 Ilex_wallichii1 3,02Podocarpus_sp_PK_2012a 4,63 Iflaccida Ilex_nervulosa 1,62Podocarpus_polystachyus Iaureliana 7,74 0,83 7,82 5,14 Ilex_cymosa Podocarpus_subtropicalis 3,43 1,29 Ichevalieri Ilex_wallichii2 2,16 Ikinabaluensis Ilex_geniculata Ieberhardtii 10,39 1,64 Ipoilanei 1,58Ilex_laevigata Ikilimanjari Ilex_verticillata 0,81 Ipseudoviola Ilex_pedunculosa 6,18 Iusambarensis 23,13 15,42 Ilex_sugerokii 4,15 1,02 11,44 Ilex_yunnanensis1 0,58 Igordoni 3,79 Epirixanthes 3,49 Iwalleriana Ilex_shennongjiaensis Isodeni 21,25 2,18 Ilex_yunnanensis2 3,24 Ihamata Ilex_mitis 1,01 Iserpens Ilex_micrococca Xanthophyllum_sp 0,47 19,57 10,1 0,19Ithamnoidea Ilex_serrata Eriandra_fragrans Ipseudohamata 16,06 Ilex_kusanoi 5,5 Iengleri_engleri 4,36 Ilex_macrocarpa Imildbraediitelekii 36,67 Carpolobia_alba 0,51 10,6 Ilex_aculeolata Iethiopica 5,42 Ilex_tsoi 54,58 18,16 Iirvingii 7,72 Atroxima_afzeliana 4,79 4,03 Ihochstetteri_hochstetteri 5,64 Ilex_fragilis 0,72 Ihochstetteri_jacquesii Ilex_macropoda Polygala_costaricensis 4,5 Ibequartii 5,31 3,13 Ibriartii 29,43 Ihoehnellii 46,78 Bredemeyera_floribunda 3,69 1,81 Itweediae Ibururiensis Securidaca_longepedunculata 3,24 1 Ipercordata_percordata 3,05 0,36Imannii_CentralAFrica Myrmarachne 15,87 Securidaca_diversifolia Imannii_WestAfrica 5,68 5,21 2,31 0,33Ikeillii_keillii Securidaca_retusa Ikeillii_pubescens 33,53 1,37 Ibombycina 42,16 0,73 Icongolensis EU815599_Ligonipes_sp_Australia_OUTGROUP posterior Monnina_xalapensis 0,44Iniamniamensis Icecilii 31,93 2,66 AY297412_M_assimilis_Philippines 1 Comesperma_esulifolium 4,46 Ihydrogetonoides 0,93 Ipseudozombensis 30,7 Polygala_californica Ieryaleia 0,38 Myrmarachne_japonica Icatati 25,68 Ituberosa Polygala_violacea 4,83 3,14 1,36 0,32 0,58 Ibicaudata PK373_M_cornuta_500to750mASL_PHS 35,75 2,48 Iauricoma Polygala_senega Iinaperta 0,23 1,34 0,51 0,73 Iarachnoides 1,32 Myrmarachne_plataleoides 16,03 Polygala_longicaulis 4,54 Ifurcata 9,72 Ivolkensii 3,6 Iassurgens Myrmarachne_sp_F_FSC_2006 Polygala_paniculata 0 2,87 Iburtoniiburtonii 4,36 Iulugurensis 0,33 Polygala_myrtifolia Idigitata_digitata Myrmarachne_sp_MRB113 1,02 3,79 0,71 Imeruensis_cruciata 0,17 29,97 16,02 Polygala_vulgaris Imeruensis_meruensis JX145678_M_evidens_Gabon Iraphidotrix 3,51 1,74 0,1 3,07 Polygala_amara 1,13 Iconfusa_longicornu Iioides 1,05 JX145679_M_foenisex_Gabon 2,11 3,27 Imazumbaensis Polygala_comosa 0,35Inana 0,83 1,86 Ilukwangulensis JX145676_M_cf_gedongensis_Malaysia 28,69 Polygala_alpicola 1,08 Isylvicola 0,01 0,83 0,18Ipalliderosae_palliderosae Myrmarachne_sp_WPM_2008 Muraltia_karroica Ipalliderosae_lupangaensis posterior 0,61 0,58 13,34 0,23Irubromaculata_rubromaculata 1 Nylandtia_spinosa Irubromaculata_imagiensis Myrmarachne_sp_A_FSC_2006 0,01 Polygala_paucifolia 28,09 Myrmarachne_sp_D_FSC_2006 11,1 0,88 Polygala_chamaebuxus PK210_M_hanoii_1000to1250mASL_MA 24,5 Salomonia_ciliata Hygrobates 7,22 PK068_M_malayana_500to750mASL_PHS Salomonia_cantoniensis 0,88 0,63 19,67 Epirixanthes_elongata Atractides_cognatus Myrmarachne_sp_B_FSC_2006 0,83 13,7 Epirixanthes_pallida 2,9 PK051_M_sp_4_500to750mASL_PHS 9,54 Epirixanthes_papuana posterior 0,76 PK183_M_sp_3_1750to2000mASL_GA 7,23 1 Atractides_cf_propatulus Epirixanthes_kinabaluensis 0,64 PK050_M_nov_sp_1_500to750mASL_PHS 9,55 PK003_M_mariaelenae_1500to1750mASL_KHQ Hygrobates_sp_2 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

Hygrobates_hamatusH20 0

Extended Data Figure 5 | Chronograms for Athyrium, Begonia, Coeliccia, for more details. Node colours represent posterior probabilities. Endemic Dacrycarpus, Epirixanthes, Dendrochilum, Dicranoloma, Impatiens, species printed in red. Hygrobates, Hedyotis, Ilex and Myrmarachne. See Supplementary Table 5

Euphrasia Paphiopedilum Rhododendron Phragmipedium_longifolium 9,14 Bartsia Paphiopedilum_besseae Cassiope_fastigiata 2,77 10,32 Euphrasia_hookeri Phragmipedium_schlimii Cassiope_tetragona 1,21 Rhododendron_camtschaticum Euphrasia_scabra 11,72 4,88 Paphiopedilum_delenatii Rhododendron_redowskianum Euphrasia_formosissima 3,89 5,73 Rhododendron_leptothrium Euphrasia_chrysantha 22,6 Paphiopedilum_malipoense 4,83 2,63 Rhododendron_vialii Euphrasia_taurica Paphiopedilum_micranthum 9,18 Rhododendron_hongkongense 1,07 5,2 Rhododendron_ovatum Euphrasia_petiolaris Paphiopedilum_concolor 26,5 6,54 4,24 Rhododendron_bachii Euphrasia_borneensis 3,56 2,59 Paphiopedilum_niveum Rhododendron_mitriforme 3,55 Euphrasia_philippinensis 12,77 42 Rhododendron_semibarbatum 2,72 Euphrasia_nankotaizanensis Paphiopedilum_gratrixianum Rhododendron_henryi 1,75 1,8 14,44 4,15 Euphrasia_tarokoana Paphiopedilum_exul Rhododendron_latoucheae 1,5 Euphrasia_durietziana Rhododendron_moulmainense 7,61 0,29 5,35 7,35 Euphrasia_transmorrisonensis Paphiopedilum_sangii 22,13 Rhododendron_championiae 2,75 5,63 3,4 Rhododendron_subestipitatum Euphrasia_tricuspidata 9,16 Paphiopedilum_wardii 2,49 8,49 5,38 1,94 Rhododendron_cavaleriei Euphrasia_grandiflora posterior 1,98 Paphiopedilum_superbiens_var_curtisii 5,02 Rhododendron_dayaoshanense Euphrasia_oakesii 1 Rhododendron_westlandii 1,3 Paphiopedilum_glaucophyllum 2,61 6,41 Euphrasia_randii Rhododendron_hancockii 3,67 4,15 Rhododendron_feddei Euphrasia_picta Paphiopedilum_liemianum 36,25 2,86 0,62 0,53 Rhododendron_tutcherae Euphrasia_spectabilis 3,63 posterior 3,12 0,89 Paphiopedilum_primulinum Rhododendron_stamineum Euphrasia_marchesettii 7,22 6,07 19,61 2,89 1 0,37 Paphiopedilum_randsii Rhododendron_mackenzianum Euphrasia_maximowiczii Rhododendron_sanctum 1,8 4,83 1,62 Euphrasia_kerneri Paphiopedilum_philippinense Rhododendron_weyrichii 0,86 Euphrasia_hirtella 2,76 Rhododendron_farrerae 0,44 Paphiopedilum_rothschildianum 10,16 6,7 Euphrasia_disjuncta Rhododendron_reticulatum 2,01 Paphiopedilum_stonei 4,12 Rhododendron_dilatatum 2,68 1,31 Euphrasia_subarctica 1,16 Rhododendron_kiyosumense 8,22 0,46 8,11 Euphrasia_parviflora Paphiopedilum_kolopakingii Rhododendron_mayebarae 0,21 3,28 Euphrasia_rostkoviana Paphiopedilum_glanduliferum Rhododendron_viscistylum 1,03 6,65 5,91 Euphrasia_glabrescens 1,24 Rhododendron_lagopus Paphiopedilum_wilhelminiae 4,69 0,57Euphrasia_vigursii 17,08 Rhododendron_tashiroi 0,19 3,88 Rhododendron_mariesii 4,16 Paphiopedilum_adductum 3,48 Euphrasia_officinalis Rhododendron_wadanum Euphrasia_insignis 3,57 Paphiopedilum_dianthum Rhododendron_serpyllifolium Euphrasia_cuneata 0,32 8,78 Rhododendron_indicum 6,73 Paphiopedilum_parishii 3,98 Euphrasia_callosa 2,13 27,9 Rhododendron_tsusiophyllum 4,45 6,3 Euphrasia_mirabilis Paphiopedilum_haynaldianum 12,4 Rhododendron_boninense 0,93 7,37 Rhododendron_kaempferi 5 5,63 Euphrasia_disperma Paphiopedilum_lowii Rhododendron_kiusianum 5,96 4,03 Euphrasia_revoluta 9,13 Rhododendron_transiens 2,62 Paphiopedilum_victoria-regina 5,01 5,33 Euphrasia_cockayniana Rhododendron_macrosepalum Euphrasia_antarctica Paphiopedilum_druryi 7,56 Rhododendron_amanoi 7,38 3,34 Euphrasia_alsa 2,46 Paphiopedilum_spicerianum posterior 6,29 Rhododendron_scabrum 5,16 Rhododendron_yakuinsulare 2,71 Euphrasia_phragmostoma 4,79 1 1,19 Paphiopedilum_charlesworthii 4,21 Rhododendron_eriocarpum 0,42 2,57 Euphrasia_collina Rhododendron_tosaense 0,61 Paphiopedilum_villosum_var_boxallii Euphrasia_dinarica Rhododendron_albiflorum 0,07 12,91 Rhododendron_albrechtii Euphrasia_pectinata Paphiopedilum_insigne 17,79 3,78 Rhododendron_nipponicum 2,36 Euphrasia_regelii 14,96 Paphiopedilum_barbatum Rhododendron_schlippenbachii 4,43 1,87 Euphrasia_kashmiriana 1,4 1,48 Paphiopedilum_appletonianum Rhododendron_tomentosum_subsp_tomentosum Euphrasia_fedtschenkoana 0,46 Rhododendron_micranthum Euphrasia_wettsteinii Paphiopedilum_callosum Rhododendron_ferrugineum 0,42 0 Rhododendron_virgatum 3,29 Euphrasia_foulaensis 2,04 Paphiopedilum_lawrenceanum 18,93 7,08 Rhododendron_primuliflorum 2,15 Euphrasia_arctica 11,69 0,18 Paphiopedilum_fowliei 6,42 Rhododendron_fastigiatum Euphrasia_confusa 2,81 0,97 Rhododendron_rubiginosum 1,56 0,85 Paphiopedilum_sukhakulii Euphrasia_fennica 16,62 Rhododendron_trichocladum 0 0,36 0,14 10,57 2,87 Euphrasia_salisburgensis Paphiopedilum_tonsum 7,69 Rhododendron_pachypodum 7,25 Rhododendron_mucronulatum Euphrasia_micrantha 1,32 25,14 5,92 1,23 Paphiopedilum_mastersianum Rhododendron_edgeworthii Euphrasia_stricta 0,71 9,5 0,72 Rhododendron_mollicomum Euphrasia_nemorosa Paphiopedilum_violascens 3,67 Rhododendron_racemosum 2,25 Euphrasia_christii 1,06 6,37 0,95 Paphiopedilum_hennisianum 16,62 Rhododendron_spiciferum Euphrasia_alpina 3,94 0,79 Paphiopedilum_ciliolare Rhododendron_scabrifolium 1,72 Euphrasia_cisalpina 2,52 Rhododendron_duclouxii 0,64 1,81 1,31 Euphrasia_inopinata Paphiopedilum_javanicum_var_virens Rhododendron_spinuliferum 0,66Euphrasia_minima Rhododendron_santapaui 0,36 12,05 Rhododendron_borneense Euphrasia_tetraquetra 5,72 Rhododendron_cuneifolium 2,87 Philalanka Rhododendron_ericoides Rhododendron_acuminatum 22,46 14,6 4,09 Zospeum_spelaeum Rhododendron_fallacinum Rhododendron_crassifolium Kalophrynus 4,61 Rhododendron_bagobonum HQ171582_Zospeum_exiguum_Slovenia 10,91 2,92 6,33 Rhododendron_stenophyllum 8,12 3,08 Zospeum_alpestre Rhododendron_exuberans 4,01 Rhododendron_javanicum Callulina_kreffti posterior 1,53 2,43 Zospeum_isselianum 9,58 Rhododendron_lowii 54,22 Breviceps_fuscus 1 4,59 Rhododendron_rugosum 4,29 29,94 Zospeum_pretneri Rhododendron_buxifolium Breviceps_mossambicus 0 6,25 Rhododendron_praetervisum 2,67 5,13 Rhododendron_stapfianum Kaloula_pulchra Zospeum_frauenfeldi 4,07 Rhododendron_orbiculatum 0,63 2,83 40,37 Ramanella_cf_obscura_MNHN_2000_628 Zospeum_subobesum Rhododendron_suaveolens 21,4 Rhododendron_canadense 34,74 AB611973_Phrynella_pulchra SP13428_Ibycus_rachelae_1000to1250mASL_MA 13,64 Rhododendron_occidentale 7,82 Rhododendron_luteum 27,46 AB611931_Metaphrynella_pollicaris 5,4 15,37 JX988066_Subulina_octona_unknown Rhododendron_molle 68,65 48,85 19,96 AB611939_Metaphrynella_sundana 19,66 Rhododendron_aureum 12,01 10,65 Rhododendron_maximum SP13507_Philalanka_spec1_250to500mASL_IN 8,57 AB611921_Kalophrynus_pleurostigma Rhododendron_ponticum 9,01 SP13492_Philalanka_spec3_500to750mASL_PHS Rhododendron_vernicosum 18,33 MJ65_K_sp_2_500to750mASL_IN 14,19 9,26 Rhododendron_irroratum 6,66 4,04 SP13510_Philalanka_spec2_1000to1250mASL_MA Rhododendron_formosanum 16,39 MJ81_K_baluensis_1750to2000mASL_GA 19,72 3,56 Rhododendron_agastum 11,74 4,39 14,47 MJ64_K_sp_1_500to750mASL_IN SP13519_Philalanka_thienemanni_1000to1250mASL_M Rhododendron_delavayi Rhododendron_sinogrande 10,68 7,39 AB611913_K_interlineatus Carychium_ibazoricum 9,72 Rhododendron_grande 60,18 1,26 Rhododendron_forrestii Asterophrys_turpicola Carychium_minimum 3,81 Rhododendron_campylocarpum 37,99 3,02 Rhododendron_lukiangense Cophixalus_sp_SJR3271 8,74 5,73 Carychium_clappi 2,62 Rhododendron_wardii 1,98 Chiasmocleis_shudikarensis 0,64 Rhododendron_anthosphaerum Carychium_floridanum Rhododendron_selense 35,78 2,71 posterior Syncope_hudsoni 7,16 Rhododendron_decorum 2,21 3,19 Carychium_exiguum Rhododendron_cyanocarpum 1 2,11 49,42 Phrynomantis_annectens Rhododendron_neriiflorum 30,17 1,4 0 Carychium_exile Rhododendron_aberconwayi Phrynomantis_bifasciatus 1,04 58,51 6,31 Rhododendron_alutaceum 42,56 HQ171529_Carychium_mexicanum_USA 3,22 1,21Rhododendron_aganniphum Elachistocleis_ovalis 0,7 2,19 Rhododendron_beesianum 34,89 Dermatonotus_muelleri Rhododendron_bureavii 6,31 1,09Rhododendron_fulvum 29,24 0,59 Hypopachus_variolosus Ptomaphaginus Rhododendron_rex_subsp_fictolacteum 18,93 Gastrophryne_carolinensis Rhododendron_rubropunctatum Rhododendron_williamsianum 5,1 2,34 55,9 Dyscophus_antongilii RMNH_INS_549243_Prionochaeta_harmandi_Japan Rhododendron_auriculatum 20,77 4,23 Rhododendron_floccigerum Dyscophus_insularis 3,42 Rhododendron_glischrum Dytiscus_dauricus 1,89 Rhododendron_dimitrum 47,32 Micryletta_inornata 1,89 Rhododendron_argyrophyllum 1,55 0,15 0,61 Calluella_guttulata Rhododendron_fortunei 41,53 25,88 Dytiscus_alaskanus Microhyla_butleri 38,18 Microhyla_pulchra 0,88 Carabus_lewisianus 53,15 32,43 Microhyla_heymonsi 0,06 28,48 Carabus_kimurai Ranunculus Glyphoglossus_molossus posterior Paradoxophyla_palmata 0,12 1 Carabus_albrechti 29,56 Anemone_quinquefolia Scaphiophryne_calcarata 5,17 Isopyrum_thalictroides 7,54 Coptis_trifolia 0,1 2,26 Coptis_quinquefolia 47,98 Otophryne_pyburni 2,14 Carabus_yamato 3,41 Coptis_japonica 0,48 Coptis_lutescens 2,41 Coptis_chinensis Anodonthyla_boulengerii 0,06 1,46 Coptis_deltoidea 46,69 24,02 1,07 Coptis_omeiensis Carabus_japonicus 0,64 Coptis_teeta Anodonthyla_montana Kumlienia_hystricula 9,27 3,57 Peltocalathos_baurii 29,63 Platypelis_grandis 2,19 Callianthemoides_semiverticillatus 1,73 Hamadryas_delfinii RMNH_INS_555623_Ptomaphaginus_ater_3000to3250mASL_L2 4,39 Beckwithia_andersonii Plethodontohyla_brevipes 1,34 Cyrtorhyncha_ranunculina 27,07 2,85 Oxygraphis_polypetala 0,98 2,41 Arcteranthis_cooleyae Rhombophryne_alluaudi RMNH_INS_555618_Ptomaphaginus_n_sp_bryanti_complex_2750to3000mASL_ 0,97 Trautvetteria_grandis 24,54 16,95 1,97 Halerpestes_cymbalaria 0 1,02 Halerpestes_uniflora Rhombophryne_testudo 0,7 7,03 Coptidium_lapponicum 21,61 1,05 Coptidium_pallasii RMNH_INS_555632_Ptomaphaginus_nr_fagei_1750to2000mASL_GA 2,45 Ficaria_fascicularis Stumpffia_psologlossa 1,17 Ficaria_verna 14,32 1,99 Myosurus_minimus Stumpffia_pygmaea Ceratocephala_falcata 1,42 Ceratocephala_orthoceras RMNH_INS_555607_Ptomaphaginus_latescens_1500to1750mASL_KHQ 6,52 Krapfia_clypeata 1,27 Laccopetalum_giganteum Ranunculus_thora 1,05 Ranunculus_hybridus 1,6 0,69 Ranunculus_brevifolius_subsp_brevifolius RMNH_INS_555598_Ptomaphaginus_bryantioides_250to500mASL_Kiansom 5,65 Ranunculus_glacialis 1,37 Ranunculus_cacuminis Nepenthes (ITS) 2,97 Ranunculus_aconitifolius 1,19 0,49 Ranunculus_platanifolius 1,05 RMNH_INS_555592_Ptomaphaginus_similipes_250to500mASL_Sugud 0,82 Ranunculus_kuepferi_subsp_orientalis 0 0,56 Ranunculus_seguieri 2,08 Ranunculus_gramineus Drosophyllum_lusitanicum 5,33 1,2 Ranunculus_acetosellifolius 0,66 0,88 Ranunculus_pyrenaeus 36,21 RMNH_INS_555603_Ptomaphaginus_kinabaluensis_1500to1750mASL_KHQ 0,59 Ranunculus_amplexicaulis Ancistrocladus_tectorius 1,93 0,18Ranunculus_parnassiifolius_subsp_parnassiifolius 27,11 0,42 Ranunculus_crenatus Triphyophyllum_peltatum 0,69 Ranunculus_magellensis 14,03 1,63 Ranunculus_traunfellneri Dioncophyllum_thollonii RMNH_INS_555611_Ptomaphaginus_cf_latimanus_750to1000mASL_SA 4,03 0,95 Ranunculus_alpestris 0,64 Ranunculus_bilobus Nepenthes_ampullaria Ranunculus_lyallii 2,56 Ranunculus_apiifolius 2,25 Ranunculus_gmelinii 53,45 Nepenthes_rafflesiana 0,68 Ranunculus_collinus 17,91 2,93 Payena 4,61 1,88 Ranunculus_papulentus Nepenthes_hemsleyana Ranunculus_sceleratus 1,58 1,06 Ranunculus_fuegianus 8,84 0,68 Ranunculus_hyperboreus Nepenthes_gracilis2 1,45 Ranunculus_natans 0,71 Ranunculus_radicans 5,71 Nepenthes_mirabilis Sarcosperma_laurinum 1,31 3,22 Ranunculus_sphaerospermus 1,48 Eberhardtia_aurata posterior 1,01 0,55 Ranunculus_nipponicus Nepenthes_kamotiana Omphalocarpum_pachysteloides 0,75 Ranunculus_trichophyllus 32,1 0,36 Ranunculus_peltatus_subsp_peltatus 38,68 Sideroxylon_oxyacanthum 1 Ranunculus_penicillatus_subsp_pseudofluitans Nepenthes_tentaculata 11,14 Xantolis_siamensis Ranunculus_rufosepalus 36,47 0,92 Ranunculus_gelidus Nepenthes_northiana Englerophytum_natalense 0,8 Ranunculus_adoneus 31,72 Poutera_firma_EDNA09_01389 0,75 Ranunculus_cardiophyllus Ranunculus_pedatifidus Nepenthes_villosa 75,68 24,31 Pouteria_sp 0,59 19,5 1,25 0,38 Ranunculus_nivalis 48,14 10,56 Pouteria_maclayana_EDNA09_00990 0,75 Ranunculus_pygmaeus 5,47 Nepenthes_villosa3 Pouteria_sp_EDNA09_02322 Ranunculus_micranthus posterior 1,36 0,48 Ranunculus_notabilis 27,06 Sideroxylon_salicifolium 0,33 Nepenthes_villosa2 0,89 0,2 Ranunculus_carpaticola 1 3,07 18,39 Argania_spinosa Ranunculus_cassubicifolius Nepenthes_edwardsiana3 Sideroxylon_mascatense Ranunculus_punctatus Ranunculus_longicaulis 1,34 Sideroxylon_wightianum 0,73 0,25 Ranunculus_pseudohirculus Nepenthes_edwardsiana2 68,99 40,95 9,49 Sideroxylon_inerme 4,24 0,53 Ranunculus_hirtellus 14,6 Sideroxylon_marginatum 0,49 Ranunculus_brotherusii Nepenthes_x_kinabaluensis 25,31 0,19Ranunculus_pulchellus 24,97 31,84 Sideroxylon_marmulano 0,41 Ranunculus_cf_pseudopygmaeus_KE2011 5,58 Nepenthes_rajah2 39,04 20,06 Sideroxylon_saxorum 0,33 Ranunculus_nephelogenes 10,03 0,22Ranunculus_membranaceus 1,55 6,63 Sideroxylon_betsimisarakum Ranunculus_meyeri Nepenthes_rajah 29,74 Sideroxylon_majus 1,34 Ranunculus_aquatilis Sideroxylon_cubense 0,62 Ranunculus_hydrophilus 10,84 Nepenthes_lowii 1,69Sideroxylon_repens 2,43 Ranunculus_alismifolius 17,9 Ranunculus_lingua 4,23 Nepenthes_glandulifera Sideroxylon_floribundum 1,85 0,37 Ranunculus_flammula 34,27 11,2 0,1Ranunculus_reptans 1,84 Sideroxylon_capiri 1,58 Ranunculus_lateriflorus Nepenthes_chaniana 7,17 Sideroxylon_foetidissimum 0,94 7,56 3,88 0,61 Ranunculus_flagelliformis Sideroxylon_tepicense 1,31 Ranunculus_ophioglossifolius Nepenthes_maxima Ranunculus_volkensii Sideroxylon_lanuginosum 0,92 0,83 0,69 Ranunculus_cheirophyllus 22,16 5,15 Nepenthes_boschiana 53,33 Sideroxylon_reclinatum Ranunculus_ficariifolius 1,72Sideroxylon_lycioides Ranunculus_bonariensis 3,79 0,56 Ranunculus_neapolitanus Nepenthes_hurrelliana 25,54 Sideroxylon_tenax 1,01 Ranunculus_bulbosus_subsp_bulbosus 2,17 Sideroxylon_persimile 0,81 0,15Ranunculus_polyanthemos Nepenthes_fusca 17,92 Nesoluma_polynesiacum 0,37 Ranunculus_serpens_subsp_nemorosus 1,24 1,61 0,16Ranunculus_submarginatus Nepenthes_vogelii 14,46 Sideroxylon_occidentale Ranunculus_sardous Sideroxylon_obtusifolium 2,27 Ranunculus_pensylvanicus 11,51 Ranunculus_amerophyllus Nepenthes_campanulata 9,15 Sideroxylon_horridum 1,01 Ranunculus_chinensis 3,49 0,81 0,53 13,52 Sideroxylon_angustum 0,34 Ranunculus_cantoniensis Nepenthes_truncata 7,47 Sideroxylon_americanum 0,65 Ranunculus_silerifolius 4,23 3,77 Ranunculus_lowii 5,14 Sideroxylon_confertum 0,43 Ranunculus_saruwagedicus Nepenthes_peltata 3,35 Sideroxylon_obovatum 1,97 0,37 Ranunculus_brassii 2,06 0,32 Ranunculus_basilobatus Nepenthes_ventricosa Sideroxylon_picardae 0,15Ranunculus_pseudolowii 19,97 9,05 Lecomtedoxa_klaineana Ranunculus_peduncularis Nepenthes_alata 35,28 Neolemonniera_clitandrifolia 0,94 Ranunculus_caprarum Ranunculus_raeae Northia_seychellana Ranunculus_tenuirostris Nepenthes_specatabilis 31,42 1,2 0,92 Capurodendron_androyense 1,78 0,5 Ranunculus_multifidus 18,29 5,93 Nepenthes_gymnamphora Inhambanella_henriquesii 1,08 Ranunculus_pinnatus Baillonella_toxisperma_EDNA09_01453 Ranunculus_trilobus 3,34 47,79 0,69 Ranunculus_cornutus Nepenthes_insignis 20,72 Vitellaria_paradoxa 1,63 0,47 Ranunculus_marginatus 1,63 17,35 0,33 Ranunculus_muricatus Vitellariopsis_marginata 0 Ranunculus_macounii 15,89 Nepenthes_bongso 0,75Vitellariopsis_cuneata 0,42 Ranunculus_repens 0,28Vitellariopsis_dispar Ranunculus_oreophytus Nepenthes_reinwardtiana 1,421,22 Ranunculus_diffusus 40,08 26,01 Mimusops_obovata 1,02 7,39 0,57 Ranunculus_orthorhynchus Nepenthes_benstonei Mimusops_elengi 1,26 Ranunculus_maclovianus 4,89 Mimusops_caffra 3,1 0,3 Ranunculus_hawaiensis 11,5 Nepenthes_macfarlanei 3,07 Ranunculus_mauiensis 2,49 Mimusops_comorensis 1,01 Ranunculus_septentrionalis 22,99 Mimusops_zeyheri 0,75 Ranunculus_petiolaris 3,22 Nepenthes_singalana posterior 0,95 Ranunculus_acriformis 0 8,14 Tieghemella_heckelii 0,61 Ranunculus_fascicularis 3,22 Nepenthes_kongkandana Autranella_congolensis 0,25 Ranunculus_hispidus 1 22,12 Labramia_costata Ranunculus_arvensis 2,73 35,84 3,06 1,66 Ranunculus_sojakii Nepenthes_vieillardii Labramia_mayottensis 0,76 Ranunculus_caucasicus 2,52 20,87 15,87 Faucherea_parvifolia 0,51 Ranunculus_brutius 6,36 Nepenthes_andamana 5,35 Labourdonnaisia_calophylloides 2,87 0,3 Ranunculus_dissectus_subsp_napellifolius 2,07 Ranunculus_pinardi Nepenthes_gracillima 18,53 Labourdonnaisia_revoluta Ranunculus_sericeus 2,4 Manilkara_concolor 2,18 Ranunculus_constantinopolitanus 11,44 0,99 Ranunculus_grandiflorus Nepenthes_sanguinea Manilkara_zapota 1,77 0,66 Ranunculus_strigillosus 16,2 Manilkara_hexandra Ranunculus_chius 3,29 Nepenthes_alba 10,51 Manilkara_kauki 1,45 0,39 Ranunculus_parviflorus 1,29 14,21 Letestua_durissima 0,46 Ranunculus_stagnalis Nepenthes_ramispina 8,82 Ranunculus_tembensis 2,28 Manilkara_obovata 1,3 0,96 Ranunculus_baldshuanicus 6,74 Manilkara_discolor 0,45 Ranunculus_cassius Nepenthes_albomarginata 0,83 Ranunculus_occidentalis 1,27 Palaquium_impressionervium_EDNA09_00720 0,29 Ranunculus_uncinatus Nepenthes_bokorensis 1,1 Palaquium_clarkeanum_EDNA09_00716 0,42 Ranunculus_kotschyi 34,47 Palaquium_rufolanigerum_EDNA09_01133 Ranunculus_velutinus 7,56 2,93 0,9 Ranunculus_granatensis 2,11 Palaquium_microphyllum 0,23Ranunculus_serbicus 0,97Palaquium_microphyllum_EDNA09_02312 0,73 Ranunculus_laetus 25,76 6,05 0,43 Ranunculus_taisanensis Palaquium_sumatranum_EDNA09_00955 0,63 Ranunculus_lanuginosus 3,41 Palaquium_rostratum_EDNA09_00956 0,5 Ranunculus_acris 1,23Palaquium_pseudorostratum_EDNA09_01131 0,25 Ranunculus_glabriusculus Nepenthes (matK) 0,31 0,2 Ranunculus_japonicus 18,08 Palaquium_rigidum_EDNA09_01129 Ranunculus_brachylobus Palaquium_sp_EDNA09_02320 0,33 Ranunculus_breyninus 8,63 0,66 Ranunculus_buhsei Palaquium_dasyphyllum_EDNA07_01936 0,48 Ranunculus_cappadocicus Drosophyllum_lusitanicum 6,88 Palaquium_formosanum_EDNA09_00722 0,34 Ranunculus_amblyolobus 4,2 38,11 Ancistrocladus_abbreviatus Palaquium_sericeum_EDNA09_02304 Ranunculus_cortusifolius 0,57 1,33 Ranunculus_gregarius 24,32 Habropetalum_dawei Palaquium_sericeum_EDNA09_01452 0,8 Ranunculus_bullatus 11,37 10,45 Palaquium_quercifolium_EDNA09_01451 2,13 0,99 Ranunculus_spicatus Triphyophyllum_peltatum 4,67 Palaquium_galactoxylon_EDNA09_00987 0,74 Ranunculus_ollissiponensis 5,27 0,85 0,38 Ranunculus_pseudomillefoliatus Dioncophyllum_thollonii Palaquium_sp_EDNA09_00989 0,24 Ranunculus_paludosus Nepenthes_macrovulgaris Aulandra_longifolia Ranunculus_regelianus 5,6 4,62 0,86 Nepenthes_bicalcarata Diploknema_oligomera 0,59 Ranunculus_macropodoides 8,66 5,49 Ranunculus_papyrocarpus Nepenthes_bellii Palaquium_calophyllum_EDNA09_00992 1,81 1,23 Ranunculus_makaluensis 1,18 4,56 Palaquium_eriocalyx_EDNA09_00993 0,9 Ranunculus_leptorrhynchus 53,03 Nepenthes_merrilliana 3,58 0,08Ranunculus_linearilobus 7,87 1 Palaquium_leiocarpum_EDNA09_01130 0,68 Ranunculus_afghanicus Nepenthes_insignis Palaquium_oxleyanum_EDNA09_00719 0,46 Ranunculus_aucheri 4,81 Nepenthes_sibuyanensis 7,1 0,29 31,37 Palaquium_cryptocarifolium_EDNA09_01144 0,11Ranunculus_elbrusensis 3,64 Nepenthes_ventricosa 0,84Palaquium_herveyi_EDNA09_01141 Ranunculus_termei 0,63 1,66 Ranunculus_carpaticus Nepenthes_burkei Palaquium_xanthochymum_EDNA09_00721 0,88 Ranunculus_villarsii Nepenthes_murudensis 6,395,13 Palaquium_gutta_EDNA09_00717 Ranunculus_marschlinsii 15,85 3,21 0,710,55 Ranunculus_pseudomontanus Nepenthes_muluensis 4,02 Palaquium_ridleyi_EDNA09_01132 0,43 Ranunculus_carinthiacus 7,38 1,09Palaquium_hexandrum_EDNA09_01142 0,31 Ranunculus_aduncus 30,88 Nepenthes_glabrata 6,19 0,59 0,61 0,19Ranunculus_venetus 4,44 Palaquium_walsurifolium_EDNA09_01135 Ranunculus_gouanii Nepenthes_hamata Palaquium_obovatum_EDNA09_00718 0,48 Ranunculus_pollinensis 1,55 0,34 Ranunculus_apenninus Nepenthes_faizaliana 5,15 Palaquium_beccarianum_EDNA09_00952 0,24 13,87 6,46 Nepenthes_lowii 0 0,42Palaquium_maingayi_EDNA09_00957 0,17Ranunculus_montanus 4,23 Ranunculus_sartorianus 4,03 Nepenthes_clipeata Palaquium_brassii_EDNA09_01385 Ranunculus_millefoliatus 2,69 2,89 1,05 Ranunculus_heterorrhizus Nepenthes_ephippiata 1,04Palaquium_amboinense 0,74 Ranunculus_illyricus 8,55 Palaquium_lobbianum_EDNA09_02319 Ranunculus_cicutarius Nepenthes_mira 1,39 0,81 Ranunculus_hierosolymitanus 3,59 Isonandra_compta_EDNA09_00984 0,57 Nepenthes_alata 2,14 Isonandra_sp 0,33 Ranunculus_millefolius Nepenthes_stenophylla 1,2 Ranunculus_macrorrhynchus 6,66 22,54 Madhuca_crassipes Ranunculus_garganicus 2,51 Nepenthes_fusca 0,42Madhuca_utilis Ranunculus_gracilis posterior 20,42 1,95 20,82 0,97 0,63 Ranunculus_asiaticus Nepenthes_burbidgeae 14,91 Isonandra_perakensis_EDNA09_00998 0,91 Ranunculus_oxyspermus 1 5,06 Nepenthes_pilosa Isonandra_lanceolata_EDNA09_02321 0,64 Ranunculus_argyreus 1,5 0,33 Ranunculus_damascenus Nepenthes_eymae 29 Burckella_sp_EDNA09_02325 0,54 Ranunculus_psilostachys 3,53 10,39 Burckella_macropoda_EDNA09_00995 0,39 Nepenthes_maxima 7,72 0,27 Ranunculus_sprunerianus 2,88 Burckella_polymera_EDNA09_01388 Ranunculus_rumelicus Nepenthes_veitchii Madhuca_hainanensis Nepenthes_reinwardtiana Madhuca_longifolia_EDNA09_02311 23,61 18,62 Nepenthes_mikei 15,98 Diploknema_siamensis_EDNA09_2330 10,02 Diploknema_butyracea Nepenthes_gracillima 21,03 7,1 Nepenthes_sanguinea 8,5 Payena_acuminata Tritetrabdella 4,52 Nepenthes_ramispina Payena_maingayi_EDNA09_00988 0,66 22,5 16,15 Payena_lucida_EDNA09_02306 Nepenthes_macfarlanei 11,14 Payena_leerii_EDNA09_02317 14,34 Nepenthes_petiolata 2,65 5,59 Payena_ferruginea_EDNA09_02314 Hirudinaria_manillensis Nepenthes_truncata 3,8 e4003829276_P_gigas_830mASL_OL 6,24 Nepenthes_edwardsiana2 3,07 e4003829322_P_microphylla_627mASL_IN Haemadipsa_rjukjuana 1,56 Nepenthes_edwardsiana3 e4003829348_P_kinabaluensis_844mASL_OL 4,47 4,46 1,02 0,67Payena_obscura_EDNA09_02313 Haemadipsa_sylvestris Nepenthes_rajah 22,48 3,33 3,5 Madhuca_pachyphylla_EDNA09_01386 Haemadipsa_ornata Nepenthes_villosa3 6,28 Madhuca_fulva_EDNA09_00985 4,83 12,36 2,45 5,02 8,57 Nepenthes_villosa2 Madhuca_microphylla Haemadipsa_hainana 1,75 Nepenthes_rajah2 7,59 Madhuca_oblongifolia_EDNA09_01379 16,67 1,05 4,41 Nepenthes_villosa_2 4,44 Madhuca_malaccensis_EDNA09_00958 Haemadipsa_japonica_japonica 1,33Madhuca_laurifolia_EDNA09_02184 Nepenthes_boschiana 3,93 3,33 Haemadipsa_zeylanica_montivindicis Nepenthes_thorelii Madhuca_palembanica 3,3 Madhuca_korthalsii_EDNA09_01380 2,68 7,36 2,14 Nepenthes_rafflesiana Haemadipsa_picta 0,72 15,52 2,58 Madhuca_sericea_EDNA09_01378 Nepenthes_albomarginata 1,25Madhuca_elmeri_EDNA09_02183 Haemadipsa_cavatuses 6,71 Nepenthes_gracilis2 0,67 2,13 Madhuca_sarawakensis_EDNA09_01136 8,64 Nepenthes_mapuluensis Madhuca_leucodermis SP13383_T_kinabalensis_inobongensis_250to500mASL_IN 6,39 4,13 Nepenthes_hirsuta Madhuca_palida_EDNA09_01139 0,73 9,91 5,2 SP13398_T_kinabalensis_kinabalensis_1750to2000mASL_G 1,59 Nepenthes_ampullaria 9,27 Madhuca_curtisii_EDNA09_02307 0,47 0,99Madhuca_sp_nov_EDNA09_01383 4,38 Nepenthes_mirabilis Tritetrabdella_scandens 7,8 Madhuca_kunstleri_EDNA09_01138b posterior Nepenthes_tobaica 4,75 3,62 Madhuca_erythrophylla_EDNA09_01137 1 3,22 Tritetrabdella_taiwana_C Nepenthes_lavicola 3,56 Madhuca_lancifolia_EDNA09_01382 6,04 2,89 6,11 Nepenthes_spathulata Madhuca_prolixa_EDNA09_01381 Tritetrabdella_taiwana_A 2,96 Nepenthes_talangensis 4,64 Madhuca_barbata_EDNA09_01143 0,87 0,68 2,49 Madhuca_kuchingensis_EDNA09_01134 7,23 Tritetrabdella_taiwana_B 5,01 Nepenthes_aristolochioides 4,12 Nepenthes_densiflora Madhuca_kingiana_EDNA09_00954 3,64 Madhuca_motleyana Domanibdella_EB_2010 3,01 Nepenthes_singalana 7,58 0,96 Nesophilaemon_skottsbergii Nepenthes_diatas 3,49 Nepenthes_bongso 1,17 Domanibdella_palmyrae Nepenthes_gymnamphora Nepenthes_dubia Trichosanthes 5,35 Idiobdella_seychellensis 0 5,09 1,45 Nepenthes_inermis 6,25 Phytobdella_meyeri Nepenthes_adnata 3,96 2,68 4,37 2,43 Nepenthes_longifolia Momordica_charantia Planobdella_sp_EB_2010 Nepenthes_spectabilis Lagenaria_siceraria 3,37 3,89 1,7 Malagabdella_fallax Nepenthes_ovata 56,82 Austrobryonia_micrantha 2,79 39,46 Bryonia_dioica 3,26 Nepenthes_eustachya 24,52 Malagabdella_vagans 2,51 Ecballium_elaterium 5,76 2,76 Nepenthes_sumatrana 53,03 Malagabdella_niarchosorum 1,62 34,51 Hodgsonia_heteroclita Nepenthes_rhombicaulis Nothoalsomitra_suberosa Luffa_echinata Philaemon_gloriosi 50,28 13,28 Luffa_operculata 3,81 Leiobdella_sp_EB_2010 7,89 Luffa_acutangula 3,26 6,13 Luffa_graveolens Neoterrabdella_australis 4,49 Luffa_aegyptiaca Linnaeosicyos_amara 4,75 Chtonobdella_whitmani Orchidaceae – Paphiopedilum 44,34 31,8 Cyclanthera_pedata 2,71 16,07 Sicyos_angulatus Chtonobdella_bilineata 21,1 Marah_macrocarpus 2,01 17,89 Echinocystis_lobata Philaemon_sp_brown_EB_2010 4,21 Anigozanthos_flavidus Trichosanthes_auriculata Philaemon_cf_grandis_EB_2010 60,75 8,5 Musella_lasiocarpa 0,49Trichosanthes_postarii1 3,01 83,97 Trichosanthes_postarii2 Philaemon_sp_green_EB_2010 Elaeis_oleifera 22,56 Trichosanthes_subvelutina2 3,48 Nypa_fruticans 39,86 20,76 9,33 Trichosanthes_subvelutina1 0 Philaemon_mediorubra 6,57 Trichosanthes_subvelutina3 2,89 Astelia Philaemon_pungens 66,83 posterior Trichosanthes_nervifolia Lanaria 7,31 106,78 59,36 Trichosanthes_cucumerina1 Empodium 1 19,92 2,31 Trichosanthes_cucumerina2 32,21 Hypoxis 13,99 11,76 Gymnopetalum_tubiflorum3 Rhodohypoxis 2,98 Gymnopetalum_tubiflorum1 1,3 Apostasia Gymnopetalum_tubiflorum2 Weinmannia 102,14 38,57 16,52 Neuwiedia Trichosanthes_dioica Vanilla Trichosanthes_beccariana 57,72 13,22 8,38 Trichosanthes_adhaerens Brunellia Cleistes 6,21 Trichosanthes_pendula 63,37 34,07 4,54 Cephalotus_follicularis Pogonia Trichosanthes_mucronata 37,17 10,95 77,19 Cypripedium 29 Trichosanthes_pilosa_var._roseipulpa Karrabina_benthamiana 34,38 5,44 Selenipedium Trichosanthes_baviensis 48,62 Spiraeopsis_celebica 37,1 4,2 Trichosanthes_pilosa2 Phragmipedium 7,19 87,63 27,91 26,52 Trichosanthes_holtzei Caldcluvia_paniculata Paphiopedilum_delenatii 3,76 Trichosanthes_pilosa1 14,01 1,33 20,18 Ackama_rosifolia Paphiopedilum_haynaldianum Trichosanthes_pilosa4 10,6 71,34 Codonorchis Caldcluvia_paniculosa 3,41 Trichosanthes_villosa2 49,39 Disperis Trichosanthes_villosa1 63,68 Eucryphia_cordifolia Disa 12,36 Trichosanthes_villosa5 18,73 39,36 19,41 3,55 Trichosanthes_villosa3 Eucryphia_moorei Monadenia 7,11 Trichosanthes_kerrii 32,6 Habenaria 0,79 Codia_discolor Trichosanthes_villosa4 42,57 23,38 Orchis 4,15 Trichosanthes_phonsenae1 Pullea_glabra 16,11 23,87 3,06 59,78 32,41 53,91 Platanthera Trichosanthes_phonsenae2 Callicoma_serratifolia 68,88 Diuris Trichosanthes_reticulinervis 34,93 17,73 Vesselowskya Chiloglottis Trichosanthes_smilacifolia posterior 39,82 Trichosanthes_truncata3 Eriochilus posterior Weinmannia_trichosperma 21,26 5,98 Trichosanthes_truncata1 50,63 1 33,16 0,61 Weinmannia_tinctoria 48,92 Microtis Trichosanthes_truncata2 1 14,25 Chloraea 15,66 Trichosanthes_miyagii Weinmannia_tomentosa 35,7 Trichosanthes_homophylla 9,55 2,02 44,13 Pterostylis 4,97 Weinmannia_myrtifolia Megastylis 9,35 Trichosanthes_hylonoma 5,89 Trichosanthes_rosthornii1 5,1 42,76 Exalaria 2,48 Weinmannia_bangii 7,68 Trichosanthes_rosthornii2 39,86 Ponthieva 8,17 2,97 Weinmannia_elattantha 40,79 Trichosanthes_multiloba1 28,07 Altenstenia 0,95Trichosanthes_multiloba2 1,64 6,47 Weinmannia_auriculata 61,82 25,59 Sarcoglottis Trichosanthes_kirilowii_var._japonica1 0,96 16,47 3,22 Trichosanthes_kirilowii_var._japonica3 Weinmannia_sp_Bradford_435 38,74 Spiranthes 1,63 Trichosanthes_kirilowii_var._japonica2 Cunonia_macrophylla Pachyplectron Gymnopetalum_scabrum2 Dossinia 7,34 16,94 Cunonia_montana 32,58 13,75 Gymnopetalum_scabrum3 Ludisia 3,42 Gymnopetalum_scabrum1 8,79 23,48 34,24 Cunonia_balansae Goodyera Trichosanthes_laeoica1 6,34 18,96 23,57 7,2 Cunonia_atrorubens Platythelys Trichosanthes_edulis 3,94 4,73 Trichosanthes_dentifera 25 Palmorchis 3,74 Cunonia_pulchella 0 13,26 Trichosanthes_laeoica2 40,81 Epipactis Cunonia_capensis 24,5 Trichosanthes_odontosperma1 Listera 5,21 8,76 Trichosanthes_pilosa3 Pancheria_engleriana Sobralia Trichosanthes_odontosperma2 22,7 2,45 50,11 43,03 2,91 Trichosanthes_odontosperma3 Pancheria_phylliraeoides Nervilia 29,34 11,8 Trichosanthes_pubera_var._fissisepala2 Pancheria_reticulata Dendrobium_kingianum Trichosanthes_pubera_var._rubriflos1 25,45 Dendrobium_officinale 4,79 1,18 5,27 Pancheria_brunhesii 45,63 8,57 Trichosanthes_pubera_var._fissisepala1 Dendrobium_crystallinum 2,87 2 1,43Trichosanthes_pubera_var._rubriflos2 Pancheria_hirsuta Calanthe Trichosanthes_tricuspidata_subsp._tricuspidata 33,24 28,67 Weinmannia_clemensiae 38,32 Pleione Trichosanthes_wallichiana 14,38 Agrostophyllum_majus 23,81 Trichosanthes_schlechteri 9,23 Weinmannia_exigua 13,52 Gymnopetalum_chinense 2,62 26,22 Earina_autumnalis 6,54 Weinmannia_richii 16,72 Gymnopetalum_orientale 37,24 Earina_valida 5,89 33,18 1,23Trichosanthes_quinquangulata1 Weinmannia_fraxinea Eria Trichosanthes_quinquangulata2 0,94 31,92 12,16 Trichosanthes_inthanonensis2 Weinmannia_hooglandii Wullschlaegelia 18,03 27,67 Cattleya Trichosanthes_bracteata Weinmannia_dichotoma 35,98 24,3 5,5 2,62 Trichosanthes_lepiniana2 4,57 Masdevallia 4,47 Trichosanthes_inthanonensis1 Weinmannia_serrata Phalaenopsis 2,46 3,38 Trichosanthes_tricuspidata_subsp._javanica 24,56 Weinmannia_racemosa Cymbidium Trichosanthes_lepiniana1 15,97 2,02 32,9 1,48 Weinmannia_silvicola Galeandra Trichosanthes_lepiniana3 29,23 13,71 15,38 Trichosanthes_fissibracteata Weinmannia_vitiensis Mormodes 5,55 12,63 9,41 8,55 Trichosanthes_laceribractea3 Weinmannia_sp_Bradford_837 22,84 Bifrenaria Trichosanthes_laceribractea1 14,07 Lycaste 5,04 12,1 Trichosanthes_laceribractea2 10,81 Weinmannia_parviflora Maxillaria 1,78 0 18,43 6,95 Trichosanthes_pedata 0 Weinmannia_samoensis Zygopetalum 8,08 Trichosanthes_quinquefolia 6,09 Trichosanthes_pallida1 22,88 Weinmannia_raiateensis 16,55 Vitekorchis 13,19 2,63 2,06 13,82 Gongora 9,97 Trichosanthes_pallida2 Weinmannia_vescoi 8,73 Trichosanthes_wawrae Stanhopea 5,57 Trichosanthes_papuana Weinmannia_sp_Bradford_655 3,39 Trichosanthes_pentaphylla1 1,69 6,79 Weinmannia_madagascariensis 12,33 Trichosanthes_pentaphylla2 3,45 Weinmannia_rutenbergii 6,16 Trichosanthes_celebica Trichosanthes_elmeri 16,98 Weinmannia_marojejyensis Trichosanthes_sepilokensis 10,18 4,87 Trichosanthes_montana_subsp._crassipes 6,78 Weinmannia_humbertiana 3,82 3,14 Trichosanthes_montana_subsp._montana Weinmannia_minutiflora 8,55 Trichosanthes_borneensis 10,02 5,81 Trichosanthes_globosa Weinmannia_bojeriana 7,58 Trichosanthes_intermedia 6,66 6,12 Weinmannia_stenostachya Trichosanthes_kinabaluensis 3,91 3,75 Trichosanthes_obscura Weinmannia_arguta 2,05 Weinmannia_sanguisugarum

Extended Data Figure 6 | Chronograms for Euphrasia, Kalophrynus, Weinmannia. See Supplementary Table 5 for more details. Node colours Nepenthes, Paphiopedilum, Philalanka, Ptomaphaginus, Payena, represent posterior probabilities. Endemic species printed in red. Trichosanthes, Rhododendron, Ranunculus, Tritetrabdella and

BioGeoBEARS DEC+J on Athyrium M0_unconstrained BioGeoBEARS DEC+J on Dacrycarpus M0_unconstrained BioGeoBEARS DEC+J on Epirixanthes M0_unconstrained ancstates: global optim, 2 areas max. d=0; e=0; j=0.0344; LnL=−8.42 ancstates: global optim, 3 areas max. d=0.0479; e=0; j=0; LnL=−11.60 ancstates: global optim, 3 areas max. d=0.149; e=0; j=0; LnL=−2.69

Dacrycarpus_dacrydioides W W Athyrium_filix_femina W W KBW KBWSalomonia_cantoniensis

W W W W Athyrium_melanolepis W W W W Athyrium_brevifrons

W W Athyrium_rupestre K KBW W W W W W W Athyrium_nikkoense W KBWDacrycarpus_imbricatus105

W W W W Athyrium_yokoscense W

W W KBW Salomonia_ciliata W W WW Athyrium_tashiroi KBW W W WW Athyrium_kirisimaense

W W W Athyrium_atkinsonii K K Dacrycarpus_kinabaluensis913

K K Athyrium_clemensiae W W W W Athyrium_tozanense W KBW W KBW

W W Athyrium_nakanoi K KBWEpirixanthes_pallida W Athyrium_vidalii W W W KBW KBWDacrycarpus_imbricatus106 W W W W K WW Athyrium_neglectum W W

W W Athyrium_deltoidofrons

K K Athyrium_amoenum

W W W W Athyrium_wardii K W W K K Dacrycarpus_kinabaluensis111 KBW W W W W Athyrium_eremicola K K Epirixanthes_kinabaluensis W W Athyrium_viridescentipe W KBW W W WW Athyrium_x_akiense

W W W W W W WW Athyrium_otophorum WW KBWKBWDacrycarpus_imbricatus102 W W K K WW Athyrium_oblitescens

W W Athyrium_subrigescens W W W W W W K KBW W W Athyrium_kuratae K KBWEpirixanthes_papuana W W Athyrium_x_tokashikii W W W W Dacrycarpus_expansus W W WW Athyrium_setuligerum W W WW Athyrium_clivicola W W W W Athyrium_strigillosum

W W W W Athyrium_x_hisatsuanum W W W W Dacrycarpus_compactus W W W W Athyrium_iseanum K KBWEpirixanthes_elongata W W Athyrium_arisanense 60 50 40 30 20 10 0 Millions of years ago 25 20 15 10 5 0 35 30 25 20 15 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 BioGeoBEARS DEC+J on Begonia M0_unconstrained ancstates: global optim, 2 areas max. d=0; e=0; j=0.071; LnL=−2.96 ancstates: global optim, 2 areas max. d=0.8061; e=0; j=0; LnL=−3.54 B B Dendrochilum_cupulatum

W W Euphrasia_philippinensis

K KB Begonia_amphioxus K K Dendrochilum_joclemensii B KB K KB

KB KB Dendrochilum_gibbsiae

B KB W W B KB Dendrochilum_exasperatum W W Euphrasia_nankotaizanensis K KB B KB

B KB Dendrochilum_haslamii K KB Begonia_pendula

KB KB Dendrochilum_tenompokense W W K B KB W W Euphrasia_tarokoana KB KB Dendrochilum_dewindtianum

K K Dendrochilum_transversum K KB Begonia_cf_beryllae W W

K K Dendrochilum_scriptum W W W W Euphrasia_transmorrisonensis KB K K K K

K KB K K Dendrochilum_pseudoscriptum W W K K

KK Dendrochilum_pterogyne K K K K K KB Begonia_imbricata K K W W Euphrasia_durietziana KK Dendrochilum_alpinum

K K Dendrochilum_grandiflorum K K W

K K B B Dendrochilum_muluense K K Euphrasia_borneensis B B K K Begonia_burbidgei B B Dendrochilum_trusmadiense

K KB

K K Dendrochilum_stachyodes K K K K W W Euphrasia_petiolaris Dendrochilum_kamborangense K K K K K K

Begonia_vaccinioides W W K K K K Dendrochilum_corrugatum

K K

K K Dendrochilum_alatum W W Euphrasia_taurica

543210 10 8 6 4 2 0 Millions of years ago Millions of years ago K KB Begonia_cauliflora

BioGeoBEARS DEC+J on Dicranoloma M0_unconstrained BioGeoBEARS DEC+J on Hedyotis M0_unconstrained 2.5 2 1.5 1 0.5 0 ancstates: global optim, 3 areas max. d=0.2702; e=0; j=0; LnL=−30.34 ancstates: global optim, 3 areas max. d=0.1289; e=0; j=0.0812; LnL=−15.92 Millions of years ago

KB KB D_sp_Kinabalu_Gunung_Alab W W Oldenlandia_pubescens_cB042

BioGeoBEARS DEC+J on Coeliccia M0_unconstrained W KBW ancstates: global optim, 3 areas max. d=0.0615; e=0; j=0.0588; LnL=−14.15 W W D_cylindrothecium

W W D_diaphanoneurum W W Coeliccia_ryukyuensis W W Oldenlandia_nutans_bS27_New W W W W

W W D_menziesii

W W W W W W RMNH_INS_503926_C_didyma W KBW D_brevisetum W W Hedyotis_valetoniana_bZ030_N W W W KBW WW W KBW D_braunii W W W W W C_cyanomelas W W D_leichhardtii W W Hedyotis_schlechteri_cA092_N W KW W W W W K K D_havilandii W

W W C_poungyi W KBW D_assimile

W W K KB Hedyotis_pulchella_bZ029_Bor W W W W W W W D_plurisetum W W W W C_albicauda K K

W W D_fasciatum

K K Hedyotis_macrostegia_Borneo W W W W W KBW D_reflexum W W C_species_2 K K W W

W W D_sp_Indonesia W W

B BWHedyotis_rigida_bZ042_SEAsia W W D_dicarpum K K K K C_species_1

B KBW W W D_chilense

K KBW KBWHedyotis_philippensis_cB043_A K W W D_robustum B BWC_octogesima W W W W B B

W KBW D_blumii W KBW B B

KB KB C_nemoricola W KBW D_billarderi B B Hedyotis_fissistipula_cB019_B

B KB 543210 543210 Millions of years ago Millions of years ago B B Coeliccia_cyaneothorax

3 2.5 2 1.5 1 0.5 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.

BioGeoBEARS DEC+J on Hygrobates M0_unconstrained BioGeoBEARS DEC+J on Kalophrynus M0_unconstrained BioGeoBEARS DEC+J on Paphiopedilum M0_unconstrained ancstates: global optim, 2 areas max. d=0.433; e=0; j=0.1711; LnL=−1.20 ancstates: global optim, 3 areas max. d=0.0057; e=0; j=0.1631; LnL=−5.42 ancstates: global optim, 3 areas max. d=0.0149; e=0; j=0.0848; LnL=−8.51

Hygrobates_sp_2 W W Paphiopedilum_primulinum K KB KBW KBWK_pleurostigma

W W

W W Paphiopedilum_liemianum

W W

K K K_sp_2 W W Paphiopedilum_glaucophyllum KBW

K K K Paphiopedilum_rothschildianum

KB KB Hygrobates_hamatus B B

W W K_interlineatus B B Paphiopedilum_kolopakingii K K

B B

K K B B Paphiopedilum_stonei BW BW

K KB

K K K_sp_1 BW BWPaphiopedilum_philippinense

K K BW BW

W W Paphiopedilum_randsii

K K Hygrobates_hamatoides 76543210 Millions of years ago K K K_baluensis 86420 Millions of years ago BioGeoBEARS DEC+J on Payena M0_unconstrained 50 40 30 20 10 0 ancstates: global optim, 3 areas max. d=0.0575; e=0; j=0.1107; LnL=−12.85 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 B BWPayena_lucida_EDNA09_0230 BioGeoBEARS DEC+J on Myrmarachne M0_unconstrained ancstates: global optim, 2 areas max. d=5; e=0; j=1.9; LnL=−1.49

W W Ilex_rugosa W W W W Ilex_maximowicziana B KB PK050_M_nov_sp_1_500to750 K K Ilex_kinabaluensis

W W Ilex_integra1 B BWPayena_leerii_EDNA09_02317 W W W W Ilex_zhejiangensis B W W W W Ilex_dimorphophylla W W W W W W Ilex_cornuta2

W W B PK183_M_sp_3_1750to2000m W W W W Ilex_cornuta1 KB KK W W Ilex_x_makinoi W W B B Payena_ferruginea_EDNA09_0 W W Ilex_leucoclada

W W W Ilex_x_kiusiana B B

WW Ilex_mertensii W W W W W W WW Ilex_matanoana PK036_M_christae_2500to275 W W B KB W W W W Ilex_liukiuensis W W K KB W W Ilex_integra2 B BWPayena_obscura_EDNA09_023

W W Ilex_hylonoma B KB

W W Ilex_latifolia W W B B W W Ilex_nothofagifolia B B W W W W B KB PK256_M_nov_sp_2_1000to12 W W Ilex_hookeri W W W W Ilex_fargesii1 K e4003829348_P_kinabaluensis W K W W W W W W W Ilex_ciliospinosa K KB KB B B W W Ilex_fargesii2

W W Ilex_corallina W W W W Ilex_ficoidea KB KB PK073_M_sp_5_500to750mAS W W W W W W Ilex_cyrtura W W B KB e4003829322_P_microphylla_6 W W Ilex_warburgii W W B B Ilex_buergeri K KB W W W W W W Ilex_pernyi

W W W W Ilex_kingiana K K PK003_M_mariaelenae_1500to W W W W Ilex_georgei W W W W Ilex_bioritsensis B B e4003829276_P_gigas_830mA

W W Ilex_spinigera W W W W Ilex_colchica W W 15 10 5 0 W W Ilex_perado W W Millions of years ago W W Ilex_aquifolium B KB PK210_M_hanoii_1000to1250m

BioGeoBEARS DEC+J on Philalanka M0_unconstrained 30 25 20 15 10 5 0 0.8 0.6 0.4 0.2 0 ancstates: global optim, 2 areas max. d=0; e=0; j=3; LnL=−1.17 Millions of years ago Millions of years ago

B B SP13492_Philalanka_spec3_50 BioGeoBEARS DEC+J on Impatiens M0_unconstrained BioGeoBEARS DEC+J on Nepenthes M0_unconstrained ancstates: global optim, 2 areas max. d=0; e=0; j=0.2671; LnL=−2.56 ancstates: global optim, 3 areas max. d=0.0074; e=0; j=0.0156; LnL=−29.45

W W Iaureliana B B Nepenthes_northiana K K Nepenthes_x_kinabaluensis K K K K Nepenthes_rajah

KB KB Nepenthes_lowii K K B KB B B Nepenthes_chaniana B B K K B B Nepenthes_glandulifera B KB KBW W W Nepenthes_maxima

B B B B Nepenthes_boschiana K K K K SP13510_Philalanka_spec2_10 B B B B Nepenthes_vogelii B B B B Nepenthes_fusca B B W W Ipoilanei B B Nepenthes_hurrelliana

K K Nepenthes_villosa K K W KBW KBW K K Nepenthes_edwardsiana2

W W Nepenthes_peltata K K W W W W Nepenthes_truncata W W W BW B B Nepenthes_campanulata

W W Nepenthes_alata W W W W W W Nepenthes_ventricosa B W W Nepenthes_gymnamphora SP13519_Philalanka_thienema W W Ieberhardtii W W Nepenthes_bongso B B W W W W W W W W W W Nepenthes_insignis

W W Nepenthes_specatabilis

W W W BWNepenthes_reinwardtiana

W W Nepenthes_benstonei W W W W W W Nepenthes_macfarlanei

W WW W Nepenthes_singalana W W WWW W Nepenthes_kongkandana WW W W Nepenthes_andamana WW W W Nepenthes_vieillardii K Ikinabaluensis K W W W W Nepenthes_bokorensis W W W BWNepenthes_albomarginata B B SP13507_Philalanka_spec1_25 W W W W Nepenthes_ramispina W W W W W W Nepenthes_alba 43210 W W W W Nepenthes_sanguinea W W Millions of years ago W W Nepenthes_gracillima

25 20 15 10 5 0

W W Ichevalieri Millions of years ago

43210 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.

BioGeoBEARS DEC+J on Ptomaphaginus M0_unconstrained BioGeoBEARS DEC+J on Teleopsis M0_unconstrained BioGeoBEARS DEC+J on Weinmannia M0_unconstrained ancstates: global optim, 3 areas max. d=0.5097; e=0; j=0.6198; LnL=−4.20 ancstates: global optim, 3 areas max. d=0.0173; e=0; j=0.1103; LnL=−24.05 ancstates: global optim, 3 areas max. d=6e−04; e=0; j=0; LnL=−12.42

W W Teleopsis_adjacens B B Ptomaphaginus_bryantioides W W Weinmannia_hooglandii KBW KBW B B KBWKBWWeinmannia_fraxinea KBW KBW W Weinmannia_richii KB KB Teleopsis_nr_discrepans_sp_C W W W B B KBW KBW W W Weinmannia_exigua

K K Weinmannia_clemensiae B KB Teleopsis_discrepans B B W W Weinmannia_sp_Bradford_655 W W W W Weinmannia_rutenbergii W W B B Teleopsis_sabah_sp_2 W W Weinmannia_madagascariensi

W W W W Weinmannia_marojejyensis KBW KBW B B W W B KB Ptomaphaginus_cf_latimanus W W Weinmannia_minutiflora Teleopsis_nr_discrepans_sp_B B B W W B W W Weinmannia_humbertiana B W W BB W W Weinmannia_bojeriana B B Teleopsis_sp_2 W W W W Weinmannia_stenostachya B B W W W W Weinmannia_sanguisugarum K K W W W Weinmannia_arguta B B B B Teleopsis_nr_discrepans W W W W W Weinmannia_silvicola W W W W Weinmannia_racemosa K KB Teleopsis_gracilifemur W W Weinmannia_sp_Bradford_837 W W B K W W K K Ptomaphaginus_kinabaluensis W W Weinmannia_vitiensis

K K Teleopsis_pseudogracilifemur W W W W Weinmannia_vescoi B B KBW W W K K W W Weinmannia_raiateensis W W W W W W Weinmannia_samoensis B B Teleopsis_scapulistylus B B W W W W Weinmannia_parviflora

B W W Weinmannia_serrata B KB Teleopsis_pallifacies W W W W Weinmannia_dichotoma

W W W W Pancheria_phylliraeoides W W W W Teleopsis_breviscopium W W Pancheria_engleriana Ptomaphaginus_similipes W W W W B B W W Pancheria_reticulata B W W W W Pancheria_hirsuta W W Teleopsis_rubicunda W W W W W W W W Pancheria_brunhesii

W W W W Cunonia_capensis W Teleopsis_trichophora W W W Cunonia_macrophylla

W W W W Cunonia_montana

W W Cunonia_balansae B B Teleopsis_sabah W W W W W W Cunonia_pulchella W W W W Cunonia_atrorubens K KB Ptomaphaginus_latescens 15 10 5 0 Millions of years ago 35 30 25 20 15 10 5 0 21.510.50 Millions of years ago Millions of years ago 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 B Trichosanthes_sepilokensis

W W Ranunculus_chinensis B BW

W W BW BWTrichosanthes_montana

W W Ranunculus_silerifolius

W W

W W Ranunculus_cantoniensis B B Trichosanthes_intermedia

W W BW

B B Ranunculus_lowii B B

B B Trichosanthes_obscura

W W W W Ranunculus_saruwagedicus B B

K K Trichosanthes_kinabaluensis W W B B W W Ranunculus_brassii W

W W

W W Ranunculus_pseudolowii W W Trichosanthes_globosa

W W

W W Ranunculus_basilobatus

W BWTrichosanthes_borneensis

W W Ranunculus_amerophyllus 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 W W Haemadipsa_cavatuses

W W Rhododendron_santapaui

K K Rhododendron_ericoides K KW K K

K KB Rhododendron_cuneifolium K KB

K KB Rhododendron_borneense

K K Rhododendron_buxifolium

K K W W Tritetrabdella_scandens

K KB Rhododendron_rugosum W

K K K KB Rhododendron_praetervisum

K K K K KB Rhododendron_stapfianum W W K K K KB Rhododendron_suaveolens

K KB

Rhododendron_orbiculatum K K K KBW

K KB Rhododendron_lowii W W Tritetrabdella_taiwana_A K KBW

KBW KBWRhododendron_javanicum K KB K K K KB Rhododendron_exuberans

K K K K K KB Rhododendron_crassifolium

K K K KB Rhododendron_stenophyllum

K KBW

K KBWRhododendron_bagobonum

K K SP13398_T_kinabalensis_kina K KB Rhododendron_fallacinum

K KB

Rhododendron_acuminatum K K 6420 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.

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,seeSupplementaryTable2. ** 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.