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• Wei S., Tseng Y.-P. & Zelený D.* (submitted): The ecological characteristics of the safe sites for early-stage establishment of Chamaecyparis obtusa var. formosana seedlings in Taiwan. bioRχiv, https://doi.org/10.1101/2023.05.15.540728
• Huang C.-L & Zelený D.* (submitted): Integrating several analytical methods to assess strength of ecological processes behind metacommunity assembly.
• Helsen K., Viana J.L., Lin T.-Y, Kuo L.-Y. & Zelený D.* (resubmitted): Comparing trait syndromes between Taiwanese subtropical terrestrial and epiphytic ferns and lycophytes at the species and community level. bioRχiv, https://doi.org/10.1101/2021.09.06.459074

• Chao A., Chiu C.-H., Hu K.-H., Zelený D. (2023): Revisiting Alwyn H. Gentry’s forest transect data: latitudinal beta diversity patterns are revealed using a statistical sampling-model-based approach. Japanese Journal of Statistics and Data Science, https://doi.org/10.1007/s42081-023-00214-1
• Chao A., Thorn S., Chiu C.-H., Moyes F., Hu K.-H., Chazdon R.L., Wu J., Magnago L.F.S., Dornelas M., Zelený D., Colwell R.K. and Magurran A.E. (2023): Rarefaction and extrapolation with beta diversity under a framework of Hill numbers: The iNEXT.beta3D standardization. Ecological Monographs, e1588, https://doi.org/10.1002/ecm.1588
• Chytrý M., Pillar V.D., Price J.N., Wagner V., Wiser S.K. & Zelený D. (2023): The benefits of publishing in society-owned scientific journals. Applied Vegetation Science, 26:e12705 https://doi.org/10.1111/avsc.12705 (Open Access)

• Zelený D., Helsen K. & Lee Y.-N. (2022): Extending the CWM approach to intraspecific trait variation: how to deal with overly optimistic standard tests? bioRχiv, https://doi.org/10.1101/2021.09.09.459685
• Ottaviani G., Méndez-Castro F.E., Conti L., Zelený D., Chytrý M., Doležal J., Jandová V., Altman J. & Klimešová J. (2022): Sticking around: Plant persistence strategies on edaphic islands. Diversity and Distribution, 28:1850-1862 https://doi.org/10.1111/ddi.13586
• Helsen K., Shen Y.-C., Lin T.-Y., Chen C.-F., Huang C.-M., Li C.-F. & Zelený D.* (2022): Climate and soil differentially affect species, trait and diversity patterns of woody overstory and fern understory in a subtropical forest along an elevation gradient in Taiwan. Journal of Vegetation Science, 33:e13130. https://doi.org/10.1111/jvs.13130, free to read pdf
• Conti L., Méndez-Castro F.E., Chytrý M., Götzenberger L., Hájek M., Horsák M., Jiménez-Alfaro B., Klimešová J., Zelený D. and Ottaviani G. (2022). Insularity promotes plant persistence strategies in edaphic island systems. Global Ecology and Biogeography. 31:753-764. https://doi.org/10.1111/geb.13465
• Chen C.-F., Li C.-F., Huang C.-M., Lin H.-Y. and Zelený D.* (2022): Secondary succession on landslides in submontane forests of central Taiwan: environmental drivers and restoration strategies. Applied Vegetation Science, 25:e12635. https://doi.org/10.1111/avsc.12635, free to read pdf
• Doležal J., Altman J., Jandová V., Chytrý M., Conti L., Méndez-Castro F.E., Klimešová J., Zelený D. & Ottaviani G. (2022): Climate warming and extended droughts drive establishment and growth dynamics in temperate grassland plants. Agricultural and Forest Meteorology, 313: 108762. https://doi.org/10.1016/j.agrformet.2021.108762

• Biurrun I., Pielech R., Dembicz I, … Zelený D., … Dengler J. (2021): Benchmarking plant diversity of Palaearctic grasslands and other open habitats. Journal of Vegetation Science 4: e13050. https://doi.org/10.1111/jvs.13050 (Behind the paper post on vegsciblog.org)
• Mendez-Castro F.E., Conti L., Chytrý M., Jiménez-Alfaro B., Hájek M., Horsák M., Zelený D., Malavasi M. & Ottaviani G. (2021): What defines insularity for plants in edaphic islands? Ecography, 44: 1249-1258. https://doi.org/10.1111/ecog.05650
• Chytrý M., Danihelka J., Kaplan Z., Wild J., Holubová D., Novotný P., Řezníčková M., Rohn M., Dřevojan P., Grulich V., Klimešová J., Lepš J., Lososová Z., Pergl J., Sádlo J., Šmarda P., Štěpánková P., Tichý L., Axmanová I., Bartušková A., Blažek P., Chrtek J. Jr., Fischer F. M., Guo W.-Y., Herben T., Janovský Z., Konečná M., Kühn I., Moravcová L., Petřík P., Pierce S., Prach K., Prokešová H., Štech M., Těšitel J., Těšitelová T., Večeřa M., Zelený D. & Pyšek P. (2021): Pladias Database of the Czech Flora and Vegetation. Preslia, 93: 1–87. https://doi.org/10.23855/preslia.2021.001

• Zelený D. & Lin P.-Y. (2020): Using tea bags to estimate the rate of soil organic matter decomposition in a Taiwanese forest. IAVS Bulletin, 2020/3, 31-33. https://doi.org/10.21570/BUL-202003-5, pdf, video from the field
• Chao A., Kubota Y., Zelený D., Chiu C.-H., Li C.-F., Kusumoto B., Yasuhara M., Thorn S., Wei C.-L., Costello M.J. & Colwell R.K. (2020): Quantifying sample completeness and comparing diversities among assemblages. Ecological Research, 35, 292–314. https://doi.org/10.1111/1440-1703.12102
• Chudomelová M. & Zelený D. (2020): Tracing the signs of local dispersal in the temperate forest understorey using spatially structured vegetation data. Journal of Vegetation Science, 31, 84–94. https://doi.org/10.1111/jvs.12835, read-only pdf, Behind the paper post on vegsciblog.org

• Kattge J., Bönisch G., Díaz S., Lavorel S., Prentice I. C., Leadley P., Tautenhahn S., Gijsbert D., … Zelený D., … Wirth C. (2019): TRY plant trait database – enhanced coverage and open access. Global Change Biology, 26, 119–188. https://doi.org/10.1111/gcb.14904
• Zelený D. & Chytrý M. (2019): Ecological Specialization Indices for species of the Czech flora. Preslia 91: 93–-116. https://doi.org/10.23855/preslia.2019.093, pdf, Appendix 1, Supplementary online information on GitHub
• Zelený D. & Fidelis, A. (2019): About travel awards to annual symposium by IAVS Global Sponsorship Committee. IAVS Bulletin, 4, 14–16. https://doi.org/10.21570/BUL-201904-2, pdf
• Wiser, S., Zelený, D., Diekmann, M., Fidelis, A., Janišová, M., Loidi, J. & Minchin, P. (2019): Meet the new IAVS Governing Board. IAVS Bulletin, 4, 2–13. https://doi.org/10.21570/BUL-201904-1, pdf

• Zelený D. (2018): Which results of the standard test for community weighted mean approach are too optimistic? Journal of Vegetation Science 29: 953–966. https://doi.org/10.1111/jvs.12688, read-only pdf, preprint on bioRχiv, Plain language summary on vegsciblog.org, blog post on blog.davidzeleny.net
• Chytrý M., Tichý L., Dřevojan P., Sádlo J. & Zelený D. (2018): Ellenberg-type indicator values for the Czech flora. Preslia 90: 83–-103. https://doi.org/10.23855/preslia.2018.083, pdf, Appendix 1

• Zelený D. (2017): Bias in community-weighted mean analysis of plant functional traits and species indicator values. bioRχiv (preprint). http://dx.doi.org/10.1101/046946, blog post on blog.davidzeleny.net
• Bonari, G., Fajmon, K., Malenovský, I., Zelený, D., Holuša, J., Jongepierová, I., Kočárek, P., Konvička, O., Uřičář, J. & Chytrý, M. (2017): Management of semi-natural grasslands benefiting both plant and insect diversity: The importance of heterogeneity and tradition. Agriculture, Ecosystems & Environment 246: 243–252. https://doi.org/10.1016/j.agee.2017.06.010
• Wagner V., Chytrý M., Zelený D., von Wehrden H., Brinkert A., Danihelka J., Jansen F., Hölzel N., Kamp J., Lustyk P., Merunková K., Palpurina S., Preislerová Z. & Wesche K. (2017): Regional differences in soil pH niche among dry grassland plants in Eurasia. Oikos, 126: 660–670. https://doi.org/10.1111/oik.03369
• Hawkins B.A., Leroy B., Rodríguez M.Á., Singer A., Vilela B., Villalobos F., Wang X. & Zelený D. (2017): Structural bias in aggregated species‐level variables driven by repeated species co‐occurrences: a pervasive problem in community and assemblage data. Journal of Biogeography, 44: 1199–1211. https://doi.org/10.1111/jbi.12953
• Chudomelová M., Zelený D. & Li C.-F. (2017): Contrasting patterns of fine-scale herb layer species composition in temperate forests. Acta Oecologica, 80: 24–31. https://doi.org/10.1016/j.actao.2017.02.003

• Divíšek J., Storch D., Zelený D. & Culek M. (2016): Towards the spatial coherence of biogeographical regionalizations at subcontinental and landscape scales. Journal of Biogeography, 43: 2489–2501. https://doi.org/10.1111/jbi.12832
• de Bello F., Fibich P., Zelený D., Kopecký M., Mudrák O., Chytrý M., Pyšek P., Wild J., Michalcová D., Sádlo J., Šmilauer P., Lepš J. & Pärtel M. (2016): Measuring size and composition of species pools: a comparison of dark diversity estimates. Ecology and Evolution, 6: 4088–4101. https://doi.org/10.1002/ece3.2169
• Carboni M., Zelený D. & Acosta A. (2016): Measuring ecological specialization along a natural stress gradient using a set of complementary niche breadth indices. Journal of Vegetation Science, 27: 892–903. https://doi.org/10.1111/jvs.12413

• Chytrý M., Zelený D. & Hettenbergerová E. (eds.) (2015): 58th Annual Symposium of the International Association for Vegetation Science: Understanding broad-scale vegetation patterns. 19–24 July 2015, Brno, Czech Republic. Abstracts. Masaryk University, Brno. pdf
• Li C.-F., Zelený D., Chytrý M., Chen M.-Y., Chen T.-Y., Chiou C.-R., Hsia Y.-J., Liu H.-Y., Yang S.-Z., Yeh C.-L., Wang J.-C., Yu C.-F., Lai Y.-J., Guo K. & Hsieh C.-F. (2015): Chamaecyparis mountain cloud forest in Taiwan: ecology and vegetation classification. Ecological Research, 30: 771–791. https://doi.org/10.1007/s11284-015-1284-0, pdf
• Lososová Z., de Bello F., Chytrý M., Kühn I., Pyšek P., Sádlo J., Winter M. & Zelený D. (2015): Alien plants invade more phylogenetically clustered community types and cause even stronger clustering. Global Ecology and Biogeography, 24: 786–794. https://doi.org/10.1111/geb.12317
• Čeplová N., Lososová Z., Zelený D., Chytrý M., Danihelka J., Fajmon K., Láníková D., Preislerová Z., Řehořek V. & Tichý L. (2015): Phylogenetic diversity of central European urban plant communities: effects of alien species and habitat types. Preslia 87: 1-16. pdf

• Horsák M., Zelený D. & Hájek M. (2014): Land snail richness and abundance along a sharp ecological gradient at two sampling scales: disentangling relationships. Journal of Molluscan Studies, 80: 256–264. https://doi.org/10.1093/mollus/eyu027
• Divíšek J., Zelený D., Culek M. & Šťastný K. (2014): Natural habitats matter: determinants of spatial pattern in animal assemblages of the Czech Republic. Acta Oecologica, 59: 7–17. https://doi.org/10.1016/j.actao.2014.05.003
• Michalcová D., Chytrý M., Pechanec V., Hájek O., Jongepier J.W., Danihelka J., Grulich V., Šumberová K., Preislerová Z., Ghisla A., Bacaro B. & Zelený D. (2014): High plant diversity of grasslands in the landscape context: a comparison of contrasting regions in Central Europe. Folia Geobotanica, 49: 117–135 https://doi.org/10.1007/s12224-013-9173-1

• Chytrý M., Zelený D., Navrátilová J. & Sádlo J. (2013): Boreokontinentální jehličnaté lesy (Vaccinio-Picetea). Boreo-continental coniferous forests (Vaccinio-Picetea). In.: Chytrý M. (ed.), Vegetace České Republiky 4. Lesní a křovinná vegetace. Vegetation of the Czech Republic 4. Forest and Scrub Vegetation. Academia, Praha. pp. 380–432. Project website, pdf
• Hettenbergerová E., Horsák M., Chandran R., Hájek M., Zelený D. & Dvořáková J. (2013): Patterns of land snail assemblages along a fine-scale moisture gradient. Malacologia 56: 31–42. https://doi.org/10.4002/040.056.0227
• Chang L.-W., Zelený D.*, Li C.-F., Chiu S.-T. & Hsieh C.-F. (2013): Better environmental data may reverse conclusions about niche- and dispersal-based processes in community assembly. Ecology 94: 2145–2151. https://doi.org/10.1890/12-2053.1, pdf
• Li C.-F., Chytrý M., Zelený D., Chen M.-Y., Chen T.-Y., Chiou C.-R., Hsia Y.-J., Liu H.-Y., Yang S.-Z., Yeh C.-L., Wang J.-C., Yu C.-F., Lai Y.-J., Chao W.-C. & Hsieh C.-F. (2013): Classification of Taiwan forest vegetation. Applied Vegetation Science, 16: 698–719. https://doi.org/10.1111/avsc.12025, related website with CoDeK application
• Hettenbergerová E., Hájek M., Zelený D., Jiroušková J. & Mikulášková E. (2013): Changes in species richness and species composition of vascular plants and bryophytes along a moisture gradient. Preslia, 85: 369–388. pdf
• Fajmonová Z., Zelený D., Syrovátka V., Vončina G. & Hájek M. (2013): Distribution of habitat specialists in semi-natural grasslands. Journal of Vegetation Science, 24: 616–627. https://doi.org/10.1111/jvs.12005

• Lin C.-T., Li C.-F., Zelený D., Chytrý M., Nakamura Y., Chen M.-Y., Chen T.-Y., Hsia Y.-J., Hsieh C.-F., Liu H.-Y., Wang J.-C., Yang S.-Z., Yeh C.-L. & Chiou C.-R. (2012): Classification of the high-mountain coniferous forests in Taiwan. Folia Geobotanica, 47: 373–401 (www)
• Axmanová I., Tichý L., Fajmonová Z., Hájková P., Hettenbergerová E., Li C.-F., Merunková K., Nejezchlebová M., Otýpková Z., Vymazalová M. & Zelený D. (2012): Estimation of herbaceous biomass from species composition and cover. Applied Vegetation Science, 15: 580–589 (www)
• Zelený D. (2012): Poznámky k používání průměrných Ellenbergových indikačních hodnot při analýze vegetačních dat [Notes to the use of mean Ellenberg indicator values in vegetation analyses]. Zprávy České Botanické Společnosti, 47: 159–178 (pdf, related website)
• Chytrý M., Ermakov N., Danihelka J., Hájek M., Hájková P., Horsák M., Kočí M., Kubešová S., Lustyk P., Otýpková Z., Pelánková B., Valachovič M. & Zelený D. (2012): High species richness in hemiboreal forests of the northern Russian Altai, southern Siberia. Journal of Vegetation Science, 23:605–616 (www)
• Axmanová I., Chytrý M., Zelený D., Li C.-F., Vymazalová M., Danihelka J., Horsák M., Kočí M., Kubešová S., Lososová Z., Otýpková Z., Tichý L., Martynenko V.B., Baisheva E., Schuster B. & Diekmann M. (2012): The species richness–productivity relationship in the herb layer of European deciduous forests. Global Ecology and Biogeography, 21: 657–667 (www)
• Zelený D. & Schaffers A.P. (2012): Too good to be true: pitfalls of using mean Ellenberg indicator values in vegetation analyses. Journal of Vegetation Science, 23: 419–431 (www, read-only pdf, software for modified permutation test, blog post)

• Axmanová I., Zelený D., Li C.-F. & Chytrý M. (2011): Environmental factors influencing herb layer productivity in Central European oak forests: insights from soil and biomass analyses and a phytometer experiment. Plant and Soil, 342: 183–194 (www)

• Chytrý M., Danihelka J., Axmanová I., Božková J., Hettenbergerová E., Li C.-F., Rozbrojová Z., Sekulová L., Tichý L., Vymazalová M. & Zelený D. (2010): Floristic diversity of an eastern Mediterranean dwarf shrubland: the importance of soil pH. Journal of Vegetation Science, 21: 1125–1137 (www)
• Zelený D., Li C.-F. & Chytrý M. (2010): Pattern of local plant species richness along a gradient of landscape topographical heterogeneity: result of spatial mass effect or environmental shift? Ecography, 33:578–589 (pdf)
• Tichý L., Hájek M. & Zelený D. (2010): Imputation of environmental variables for vegetation plots based on compositional similarity. Journal of Vegetation Science, 21: 88–95 (www)

• Roleček J., Tichý L., Zelený D. & Chytrý M. (2009): Modified TWINSPAN classification in which the hierarchy respects cluster heterogeneity. Journal of Vegetation Science, 20:596–602
• Zelený D. (2009): Co-occurrence based assessment of species habitat specialization is affected by the size of species pool: reply to Fridley et al. (2007). Journal of Ecology, 97:10–17
• Zelený D. (2009): Jak se „botanizuje“ na Tchaj-wanu. Ekolist 4

• Zelený D. & Li C.-F. (2008): Vegetace suchých acidofilních trávníků v oblasti třebíčského žulosyenitového plutonu [Dry acidophilous grassland vegetation in the area of Třebíč's granosyenite pluton]. Acta Rerum Naturalium, 5: 177–194
• Zelený D. (2008): Lesní vegetace v údolí Vltavy severně od Zlaté Koruny (okres Český Krumlov) [Forest vegetation in the Vltava river valley north of Zlatá Koruna (district of Český Krumlov)]. Zprávy České Botanické Společnosti, 43: 111–169
• Zelený D. (2008): 'Taiwan? A mají tam vůbec nějaký les?' ['Taiwan? And is there some forest?'] Živa 56 (1): 17–19

• Zelený D. & Chytrý M. (2007): Environmental control of vegetation pattern in deep river valleys of the Bohemian Massif. Preslia, 79: 205–222
• Hájková P., Hájek M., Apoštolová I., Zelený D., Dítě D. (2007): Shifts in the ecological behaviour of plant species between two distant regions: evidence from the base richness gradient in mires. Journal of Biogeography, 35: 282–294
• Hájek M., Tichý L., Schamp B.S., Zelený D., Roleček J., Hájková P., Apostolová I. & Dítě D. (2007): Testing the Species Pool Hypothesis for mire vegetation: exploring the influence of pH specialists and habitat history. Oikos 116: 1311–1322
• Boublík K. & Zelený D. (2007): Plant communities of silver fir forests in southeastern Bohemia. Tuexenia, 27: 73–90
• Zelený D. (2007): Deep river valleys - one of the hot spots of biodiversity in Central Europe. Yearly Journal of Taiwan Biodiversity Association 2007 (into Chinese translated by Ching-Feng Li)

• Zelený D. (2006): Výskyt vegetace širokolistých suchých trávníků svazu Bromion u Nové Vsi na Třebíčsku. [Occurrence of broad-leaved semi-dry grasslands of the Bromion alliance close to village Nová Ves, district of Třebíč (Czech Republic)] Acta Rerum Naturalium, Jihlava, 2: 39–44

• Zelený D., Šraitová D., Mašková Z. & Květ J. (2001): Management effects on a mountain meadow plant community. Silva Gabreta, 7: 45–54