Philippa Kaur

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain
the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in
Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles
and JavaScript. More

Hughes, C. E. & Atchinson, G. W. The ubiquity of alpine plant radiations: from the Andes to the Hengduan Mountains. N. Phytol. 207, 275–282 (2015).Article 

Google Scholar 
Rahbek, C. et al. Humboldt’s enigma: what causes global patterns of mountain biodiversity? Science 365, 1108–1113 (2019).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Antonelli, A. et al. Geological and climatic influences on mountain biodiversity. Nat. Geosci. 11, 718–725 (2018).ADS 
CAS 
Article 

Google Scholar 
Quintero, I. & Jetz, W. Global elevational diversity and diversification of birds. Nature 555, 246–250 (2018).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Merckx, V. S. F. T. et al. Evolution of endemism on a young tropical mountain. Nature 524, 347–350 (2015).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Körner, C. Alpine Plant Life (Springer, 1999).Smyčka, J. et al. Reprint of: Disentangling drivers of plant endemism and diversification in the European Alps – a phylogenetic and spatially explicit approach. Perspect. Plant Ecol. Evol. Syst. 30, 31–40 (2018).Article 

Google Scholar 
Schönswetter, P., Stehlik, I., Holderegger, R. & Tribsch, A. Molecular evidence for glacial refugia of mountain plants in the European Alps. Mol. Ecol. 14, 3547–3555 (2005).PubMed 
Article 
CAS 

Google Scholar 
Haller, A. von. Enumeratio Methodica Stirpium Helvetiae indigenarum. (Officina Academica Abrami Vandenhoek, 1742).de Candolle, A. Sur les causes de l’inégale distribution des plantes rares dans la chaîne des Alpes. Atti del Congr. Internazionale Bot. Tenuto Firenze. 92–104 (1875).Boucher, F. C., Zimmermann, N. E. & Conti, E. Allopatric speciation with little niche divergence is common among alpine Primulaceae. J. Biogeogr. 43, 591–602 (2016).Article 

Google Scholar 
Schneeweiss, G. M. et al. Molecular phylogenetic analyses identify Alpine differentiation and dysploid chromosome number changes as major forces for the evolution of the European endemic Phyteuma (Campanulaceae). Mol. Phylogenet. Evol. 69, 634–652 (2013).CAS 
PubMed 
Article 

Google Scholar 
Tkach, N. et al. Molecular phylogenetics, morphology and a revised classification of the complex genus Saxifraga (Saxifragaceae). Taxon 64, 1159–1187 (2015).Article 

Google Scholar 
Favre, A. et al. Out-of-Tibet: the spatio-temporal evolution of Gentiana (Gentianaceae). J. Biogeogr. 43, 1967–1978 (2016).Article 

Google Scholar 
Kadereit, J. W., Griebeler, E. M. & Comes, H. Quaternary diversification in European alpine plants: pattern and process. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 359, 265–274 (2004).PubMed 
PubMed Central 
Article 

Google Scholar 
Xing, Y. & Ree, R. H. Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot. Proc. Natl Acad. Sci. 114, E3444–E3451 (2017).CAS 
PubMed 
PubMed Central 

Google Scholar 
Lagomarsino, L. P., Condamine, F. L., Antonelli, A., Mulch, A. & Davis, C. C. The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae). N. Phytol. 210, 1430–1442 (2016).Article 

Google Scholar 
Ding, W. N., Ree, R. H., Spicer, R. A. & Xing, Y. W. Ancient orogenic and monsoon-driven assembly of the world’s richest temperate alpine flora. Science 369, 578–581 (2020).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Roquet, C., Boucher, F. C., Thuiller, W. & Lavergne, S. Replicated radiations of the alpine genus Androsace (Primulaceae) driven by range expansion and convergent key innovations. J. Biogeogr. 40, 1874–1886 (2013).PubMed 
PubMed Central 
Article 

Google Scholar 
Luebert, F. & Muller, L. A. H. Biodiversity from mountain building. Front. Genet. 6, (2015).Zachos, J. C., Dickens, G. R. & Zeebe, R. E. An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics. Nature 451, 279–283 (2008).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Haffer, J. Speciation in Colombian forest birds west of the Andes. Am. Museum Novit. 2294, 1–58 (1967).Aguilée, R., Claessen, D. & Lambert, A. Adaptive radiation driven by the interplay of eco-evolutionary and landscape dynamics. Evolution 67, 1291–1306 (2013).PubMed 
Article 

Google Scholar 
Feng, G., Mao, L., Sandel, B., Swenson, N. G. & Svenning, J. C. High plant endemism in China is partially linked to reduced glacial-interglacial climate change. J. Biogeogr. 43, 145–154 (2016).Article 

Google Scholar 
Molina-Venegas, R., Aparicio, A., Lavergne, S. & Arroyo, J. Climatic and topographical correlates of plant palaeo- and neoendemism in a Mediterranean biodiversity hotspot. Ann. Bot. 119, 229–238 (2017).PubMed 
Article 

Google Scholar 
Saladin, B. et al. Rapid climate change results in long-lasting spatial homogenization of phylogenetic diversity. Nat. Commun. 11, 1–8 (2020).Article 
CAS 

Google Scholar 
Hughes, C. & Eastwood, R. Island radiation on a continental scale: exceptional rates of plant diversification after uplift of the Andes. Proc. Natl Acad. Sci. 103, 10334–10339 (2006).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Pouchon, C. et al. Phylogenomic analysis of the explosive adaptive radiation of the Espeletia complex (Asteraceae) in the tropical Andes. Syst. Biol. 67, 1041–1060 (2018).CAS 
PubMed 
Article 

Google Scholar 
Kadereit, J. W. The role of in situ species diversification for the evolution of high vascular plant species diversity in the European Alps—a review and interpretation of phylogenetic studies of the endemic flora of the Alps. Perspect. Plant Ecol. Evol. Syst. 26, 28–38 (2017).Article 

Google Scholar 
Escobar García, P. et al. Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (Senecio carniolicus, Asteraceae). Mol. Ecol. 21, 1255–1270 (2012).PubMed 
PubMed Central 
Article 

Google Scholar 
Lohse, K., Nicholls, J. A. & Stone, G. N. Inferring the colonization of a mountain range-refugia vs. nunatak survival in high alpine ground beetles. Mol. Ecol. 20, 394–408 (2011).CAS 
PubMed 
Article 

Google Scholar 
Stehlik, I. Resistance or emigration? Response of alpine plants to the ice ages. Taxon 52, 499–510 (2003).Article 

Google Scholar 
Schneeweiss, G. M. & Schönswetter, P. A re-appraisal of nunatak survival in arctic-alpine phylogeography. Mol. Ecol. 20, 190–192 (2011).PubMed 
Article 

Google Scholar 
Westergaard, K. B. et al. Glacial survival may matter after all: Nunatak signatures in the rare European populations of two west-arctic species. Mol. Ecol. 20, 376–393 (2011).PubMed 
Article 

Google Scholar 
Bettin, O., Cornejo, C., Edwards, P. J. & Holderegger, R. Phylogeography of the high alpine plant Senecio halleri (Asteraceae) in the European Alps: In situ glacial survival with postglacial stepwise dispersal into peripheral areas. Mol. Ecol. 16, 2517–2524 (2007).CAS 
PubMed 
Article 

Google Scholar 
Tomasello, S., Karbstein, K., Hodač, L., Paetzold, C. & Hörandl, E. Phylogenomics unravels Quaternary vicariance and allopatric speciation patterns in temperate-montane plant species: a case study on the Ranunculus auricomus species complex. Mol. Ecol. 29, 2031–2049 (2020).PubMed 
Article 

Google Scholar 
Ozenda, P. L’endémisme au niveau de l’ensemble du Système alpin. Acta Bot. Gall. 142, 753–762 (1995).Article 

Google Scholar 
Rolland, J., Lavergne, S. & Manel, S. Combining niche modelling and landscape genetics to study local adaptation: A novel approach illustrated using alpine plants. Perspect. Plant Ecol. Evol. Syst. 17, 491–499 (2015).Article 

Google Scholar 
Alvarez, N. et al. History or ecology? Substrate type as a major driver of spatial genetic structure in Alpine plants. Ecol. Lett. 12, 632–640 (2009).PubMed 
Article 

Google Scholar 
Gao, Y.-D., Gao, X.-F. & Harris, A. Species boundaries and parapatric speciation in the complex of alpine shrubs, Rosa sericea (Rosaceae), based on population genetics and ecological tolerances. Front. Plant Sci. 10, 1–16 (2019).Article 

Google Scholar 
Knox, E. B. Adaptive radiation of African montane plants. In Adaptive Speciation (eds. Dieckmann, U., Doebeli, M., Metz, J. A. J. & Tautz, D.) 345–361 (Cambridge University Press, 2004).Segar, S. T. et al. Speciation in a keystone plant genus is driven by elevation: a case study in New Guinean Ficus. J. Evol. Biol. 30, 512–523 (2017).CAS 
PubMed 
Article 

Google Scholar 
Pouchon, C. et al. Phylogenetic signatures of ecological divergence and leapfrog adaptive radiation in Espeletia. Am. J. Bot. 108, 113–128 (2021).CAS 
PubMed 
Article 

Google Scholar 
Luebert, F. & Weigend, M. Phylogenetic insights into Andean plant diversification. Front. Ecol. Evol. 2, 1–17 (2014).Article 

Google Scholar 
Nagy, L. & Grabherr, G. The Biology of Alpine Habitats (Oxford University Press, 2009).Louca, S. & Pennell, M. W. Extant timetrees are consistent with a myriad of diversification histories. Nature 580, 502–505 (2020).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Goldberg, E. E., Lancaster, L. T. & Ree, R. H. Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Syst. Biol. 60, 451–465 (2011).PubMed 
Article 

Google Scholar 
Goldberg, E. E. & Igić, B. Tempo and mode in plant breeding system evolution. Evolution 66, 3701–3709 (2012).PubMed 
Article 

Google Scholar 
Gitzendanner, M., Soltis, P., Yi, T.-S., Li, D.-Z. & Soltis, D. Plastome Phylogenetics: 30 years of inferences into plant evolution. In Advances in Botanical Research 293–313 (Elsevier, 2018).Birks, H. H. The late-quaternary history of arctic and alpine plants. Plant Ecol. Divers. 1, 135–146 (2008).Article 

Google Scholar 
Mai, D. Tertiäre Vegetationsgeschichte Europas—Metoden und Ergebnisse. (Gustav Fischer Verlag, 1995).Svenning, J. C. Deterministic Plio-Pleistocene extinctions in the European cool-temperate tree flora. Ecol. Lett. 6, 646–653 (2003).Article 

Google Scholar 
Fauquette, S. et al. The Alps: a geological, climatic and human perspective on vegetation history and modern plant diversity. In Mountains, Climate and Biodiversity (eds. Hoorn, C., Perrigo, A. & Antonelli, A.) 413 (Wiley-Blackwell, 2018).Mráz, P. et al. Vascular plant endemism in the Western Carpathians: spatial patterns, environmental correlates and taxon traits. Biol. J. Linn. Soc. 119, 630–648 (2016).Article 

Google Scholar 
Puşcaş, M. et al. Post-glacial history of the dominant alpine sedge Carex curvula in the European Alpine System inferred from nuclear and chloroplast markers. Mol. Ecol. 17, 2417–2429 (2008).PubMed 
Article 
CAS 

Google Scholar 
Puşcaş, M., Taberlet, P. & Choler, P. No positive correlation between species and genetic diversity in European alpine grasslands dominated by Carex curvula. Divers. Distrib. 14, 852–861 (2008).Article 

Google Scholar 
Magyari, E. K. et al. Late Pleniglacial vegetation in eastern-central Europe: are there modern analogues in Siberia? Quat. Sci. Rev. 95, 60–79 (2014).ADS 
Article 

Google Scholar 
Prodon, R., Thibault, J. C. & Dejaifve, P. A. Expansion vs. compression of bird altitudinal ranges on a Mediterranean island. Ecology 83, 1294–1306 (2002).Article 

Google Scholar 
Moen, D. & Morlon, H. Why does diversification slow down? Trends Ecol. Evol. 29, 190–197 (2014).PubMed 
Article 

Google Scholar 
Aguilée, R., Gascuel, F., Lambert, A. & Ferriere, R. Clade diversification dynamics and the biotic and abiotic controls of speciation and extinction rates. Nat. Commun. 9, 1–13 (2018).Article 
CAS 

Google Scholar 
Vargas, P. Molecular evidence for multiple diversification patterns of alpine plants in Mediterranean Europe. Taxon 52, 463–476 (2003).Article 

Google Scholar 
Kruckeberg, A. R. An essay: the stimulus of unusual geologies for plant speciation. Syst. Bot. 11, 455–463 (1986).Article 

Google Scholar 
Cowling, R. M. & Holmes, P. M. Endemism and speciation in a lowland flora from the Cape Floristic Region. Biol. J. Linn. Soc. 47, 367–383 (1992).Article 

Google Scholar 
Lexer, C. et al. Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae). Mol. Ecol. 23, 4373–4386 (2014).CAS 
PubMed 
Article 

Google Scholar 
Anacker, B. L. & Strauss, S. Y. The geography and ecology of plant speciation: range overlap and niche divergence in sister species. Proc. R. Soc. B Biol. Sci. 281, 20132980 (2014).Article 

Google Scholar 
Moore, A. J. & Kadereit, J. W. The evolution of substrate differentiation in Minuartia series Laricifoliae (Caryophyllaceae) in the European Alps: in situ origin or repeated colonization? Am. J. Bot. 100, 2412–2425 (2013).PubMed 
Article 

Google Scholar 
Guggisberg, A. et al. The genomic basis of adaptation to calcareous and siliceous soils in Arabidopsis lyrata. Mol. Ecol. 27, 5088–5103 (2018).PubMed 
Article 

Google Scholar 
Gigon, A. Vergleich alpiner Rasen auf Silikat- und auf Karbonatboden—Konkurrenz—und Stickstofformenversuche sowie standortskundliche Untersuchungen im Nardetum und im Seslerietum bei Davos. (ETH Zuerich, 1971).Davies, M. S. & Snaydon, R. W. Physiological differences among populations of Anthoxanthum odoratum L. collected from the park grass experiment, Rothamsted. I. Response to calcium. J. Appl. Ecol. 10, 33–45 (1973).Article 

Google Scholar 
Snaydon, R. W. Rapid population differentiation in mosaic environment. I. The response of Anthoxantum odoratum populations to soils. Evolution 24, 257–269 (1970).CAS 
PubMed 
Article 

Google Scholar 
Zohlen, A. & Tyler, G. Soluble inorganic tissue phosphorus and calcicole-calcifuge behaviour of plants. Ann. Bot. 94, 427–432 (2004).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Kassen, R., Llewellyn, M. & Rainey, P. B. Ecological contraints on diversification in a model adaptive radiation. Nature 431, 984–988 (2004).ADS 
CAS 
PubMed 
Article 

Google Scholar 
MacLean, R. C., Bell, G. & Rainey, P. B. The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens. Proc. Natl Acad. Sci. USA 101, 8072–8077 (2004).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Rabosky, D. L. & Goldberg, E. E. Model inadequacy and mistaken inferences of trait-dependent speciation. Syst. Biol. 64, 340–355 (2015).CAS 
PubMed 
Article 

Google Scholar 
Kolář, F. et al. Northern glacial refugia and altitudinal niche divergence shape genome-wide differentiation in the emerging plant model Arabidopsis arenosa. Mol. Ecol. 25, 3929–3949 (2016).PubMed 
Article 

Google Scholar 
Dentant, C. & Lavergne, S. Plantes de haute montagne: état des lieux, évolution et analyse diachronique dans le massif des Écrins (France). Bull. Soc. linn. Provence 64, 83–98 (2013).
Google Scholar 
Dentant, C. The highest vascular plants on Earth. Alp. Bot. 128, 97–106 (2018).Article 

Google Scholar 
Boucher, F. C. et al. Reconstructing the origins of high‐alpine niches and cushion life form in the genus Androsace sl (Primulaceae). Evolution 66, 1255–1268 (2012).PubMed 
Article 

Google Scholar 
Boucher, F. C., Lavergne, S., Basile, M., Choler, P. & Aubert, S. Evolution and biogeography of the cushion life form in angiosperms. Perspect. Plant Ecol. Evol. Syst. 20, 22–31 (2016).Article 

Google Scholar 
Schönswetter, P. & Schneeweiss, G. M. Is the incidence of survival in interior Pleistocene refugia (nunataks) underestimated? Phylogeography of the high mountain plant Androsace alpina (Primulaceae) in the European Alps revisited. Ecol. Evol. 9, 4078–4086 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Aeschimann, D., Rasolofo, N. & Theurillat, J. P. Analyse de la flore des Alpes. 2: Diversité et chorologie. Candollea 66, 225–253 (2011).Article 

Google Scholar 
Ebersbach, J. et al. In and out of the Qinghai-Tibet Plateau: divergence time estimation and historical biogeography of the large arctic-alpine genus Saxifraga L. J. Biogeogr. 44, 900–910 (2017).Article 

Google Scholar 
Hannon, G. FASTX. http://hannonlab.cshl.edu/fastx_toolkit/ (2014).Coissac, E. The ORGanelle ASseMbler 1.0.3. https://git.metabarcoding.org/org-asm/org-asm/wikis/home (2016).Shaw, J. et al. Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: the tortoise and the hare IV. Am. J. Bot. 101, 1987–2004 (2014).PubMed 
Article 

Google Scholar 
Mansion, G. et al. How to handle speciose clades? Mass taxon-sampling as a strategy towards illuminating the natural history of Campanula (Campanuloideae). PLoS ONE 7, e50076 (2012).Rossi, M. Taxonomy, phylogeny and reproductive ecology of Gentiana lutea L (University in Bologna, 2011).Hämmerli, M. Molecular Aspects in Systematics of Gentiana Sect. Calathianae Froel (Université de Neuchâtel, 2007).Hungerer, K. B. & Kadereit, J. W. The phylogeny and biogeography of Gentiana L. sect. Ciminalis (Adans.) Dumort.: A historical interpretation of distribution ranges in the European high mountains. Perspect. Plant Ecol. Evol. Syst. 1, 121–135 (1998).Article 

Google Scholar 
Ranwez, V., Harispe, S., Delsuc, F. & Douzery, E. J. P. MACSE: Multiple alignment of coding SEquences accounting for frameshifts and stop codons. PLoS One 6, e22594 (2011).Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552 (2000).CAS 
PubMed 
Article 

Google Scholar 
Kück, P. & Meusemann, K. FASconCAT: convenient handling of data matrices. Mol. Phylogenet. Evol. 56, 1115–1118 (2010).PubMed 
Article 
CAS 

Google Scholar 
Katoh, K., Kuma, K. I., Toh, H. & Miyata, T. MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511–518 (2005).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Bouckaert, R. et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 10, 1–6 (2014).Article 
CAS 

Google Scholar 
Bouckaert, R. R. & Drummond, A. J. bModelTest: Bayesian phylogenetic site model averaging and model comparison. BMC Evol. Biol. 17, 1–11 (2017).Article 

Google Scholar 
Morlon, H. Phylogenetic approaches for studying diversification. Ecol. Lett. 17, 508–525 (2014).PubMed 
Article 

Google Scholar 
Aeschimann, D., Lauber, K., Moser, D. M. & Theurillat, J. P. Flora Alpina (Editions Belin, 2004).Castroviejo, S. Flora Iberica (Real Jardin Botanico CSIC, 2012).Goliášová, K. & Michalková, E. Flóra Slovenska (Vydavateľstvo Slovenskej akadémie vied, 2012).Speta, E. & Rákosy, L. Wildpflanzen Siebenbürgen (Naturhistorisches Museum Wien, 2010).Sarić, M. Flora Srbije (Srpska akademija nauka i umetnosti, 1992).Schönswetter, P. & Schneeweiss, G. M. Androsace komovensis sp. nov., a long mistaken local endemic from the southern Balkan Peninsula with biogeographic links to the Eastern Alps. Taxon 58, 544–549 (2009).Article 

Google Scholar 
Schönswetter, P., Magauer, M. & Schneeweiss, G. M. Androsace halleri subsp. nuria Schönsw. & Schneew. (Primulaceae), a new taxon from the eastern Pyrenees (Spain, France). Phytotaxa 201, 227–232 (2015).Article 

Google Scholar 
Schneeweiss, G. M. & Schonswetter, P. The wide but disjunct range of the European mountain plant Androsace lactea L. (Primulaceae) reflects Late Pleistocene range fragmentation and post-glacial distributional stasis. J. Biogeogr. 37, 2016–2025 (2010).
Google Scholar 
Webb, D. A. & Gornall, R. J. Saxifrages of Europe (Timber Press, 1989).GBIF. https://www.gbif.org/ (2018).Körner, C. et al. A global inventory of mountains for bio-geographical applications. Alp. Bot. 127, 1–15 (2017).Article 

Google Scholar 
Anacker, B. L., Whittall, J. B., Goldberg, E. E. & Harrison, S. P. Origins and consequences of serpentine endemism in the California flora. Evolution 65, 365–376 (2011).PubMed 
Article 

Google Scholar 
Morlon, H. et al. RPANDA: An R package for macroevolutionary analyses on phylogenetic trees. Methods Ecol. Evol. 7, 589–597 (2016).Article 

Google Scholar 
Burnham, K. & Anderson, D. Model Selection and Multimodel Inference (Springer, 2002).Fitzjohn, R. G., Maddison, W. P. & Otto, S. P. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Syst. Biol. 58, 595–611 (2009).PubMed 
Article 

Google Scholar 
O’Meara, B. C. & Beaulieu, J. M. Past, future, and present of state-dependent models of diversification. Am. J. Bot. 103, 792–795 (2016).PubMed 
Article 

Google Scholar 
Beaulieu, J. M. & O’Meara, B. C. Detecting hidden diversification shifts in models of trait-dependent speciation and extinction. Syst. Biol. 65, 583–601 (2016).PubMed 
Article 

Google Scholar 
Herrera-Alsina, L., Van Els, P. & Etienne, R. S. Detecting the dependence of diversification on multiple traits from phylogenetic trees and trait data. Syst. Biol. 68, 317–328 (2019).PubMed 
Article 

Google Scholar 
Onstein, R. E. et al. To adapt or go extinct? The fate of megafaunal palm fruits under past global change. Proc. R. Soc. B Biol. Sci. 285, (2018).Rabosky, D. L. & Goldberg, E. E. FiSSE: a simple nonparametric test for the effects of a binary character on lineage diversification rates. Evolution 71, 1432–1442 (2017).PubMed 
Article 

Google Scholar 
Holland, B. R., Ketelaar-Jones, S., O’Mara, A. R., Woodhams, M. D. & Jordan, G. J. Accuracy of ancestral state reconstruction for non-neutral traits. Sci. Rep. 10, 1–10 (2020).Article 
CAS 

Google Scholar 
Ree, R. H. & Sanmartín, I. Conceptual and statistical problems with the DEC+J model of founder-event speciation and its comparison with DEC via model selection. J. Biogeogr. 45, 741–749 (2018).Article 

Google Scholar 
Schoener, T. W. Nonsynchronous spatial overlap of lizards in patchy habitats. Ecology 51, 408–418 (1970).Article 

Google Scholar 
Zhang, J. spaa: SPecies Association Analysis 0.2.2. https://cran.r-project.org/package=spaa (2016).Smyčka, J. Tempo and drivers of plant diversification in the European mountain system. multidiv, https://doi.org/10.5281/zenodo.6341727 (2022). More

Brienen, R. J. W. et al. Long-term decline of the Amazon carbon sink. Nature 519, 344–348 (2015).CAS 
PubMed 
Article 

Google Scholar 
Hubau, W. et al. Asynchronous carbon sink saturation in African and Amazonian tropical forests. Nature 579, 80–87 (2020).CAS 
PubMed 
Article 

Google Scholar 
Zuleta, D., Duque, A., Cardenas, D., Muller-Landau, H. C. & Davies, S. J. Drought-induced mortality patterns and rapid biomass recovery in a terra firme forest in the Colombian Amazon. Ecology 98, 2538–2546 (2017).PubMed 
Article 

Google Scholar 
Phillips, O. L. et al. Drought sensitivity of the Amazon rainforest. Science 323, 1344–1347 (2009).CAS 
PubMed 
Article 

Google Scholar 
Powers, J. S. et al. A catastrophic tropical drought kills hydraulically vulnerable tree species. Glob. Chang. Biol. 26, 3122–3133 (2020).PubMed 
Article 

Google Scholar 
Bennett, A. C. et al. Resistance of African tropical forests to an extreme climate anomaly. Proc. Natl Acad. Sci. USA 118, e2003169118 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Brodribb, T. J., Powers, J., Cochard, H. & Choat, B. Hanging by a thread? Forests and drought. Science 368, 261–266 (2020).CAS 
PubMed 
Article 

Google Scholar 
McDowell, N. G. et al. Pervasive shifts in forest dynamics in a changing world. Science 368, (2020).Pan, Y. et al. A large and persistent carbon sink in the world’s forests. Science 333, 988–993 (2011).CAS 
PubMed 
Article 

Google Scholar 
Matthews, H. D. et al. An integrated approach to quantifying uncertainties in the remaining carbon budget. Commun. Earth Environ. 2, 7 (2021).Article 

Google Scholar 
Girardin, C. A. J. et al. Nature-based solutions can help cool the planet—if we act now. Nature 593, 191–194 (2021).CAS 
PubMed 
Article 

Google Scholar 
Friedlingstein, P. et al. Earth Syst. Sci. Data 14, 1917–2005 (2022)
Google Scholar 
Choat, B. et al. Triggers of tree mortality under drought. Nature 558, 531–539 (2018).CAS 
PubMed 
Article 

Google Scholar 
Rowland, L. et al. Death from drought in tropical forests is triggered by hydraulics not carbon starvation. Nature 528, 119–122 (2015).CAS 
PubMed 
Article 

Google Scholar 
Lloyd, J. & Farquhar, G. D. Effects of rising temperatures and [CO2] on the physiology of tropical forest trees. Phil. Trans. R. Soc. B 363, 1811–1817 (2008).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
O’Sullivan, O. S. et al. Thermal limits of leaf metabolism across biomes. Glob. Chang. Biol. 23, 209–223 (2017).PubMed 
Article 

Google Scholar 
Grossiord, C. et al. Plant responses to rising vapor pressure deficit. New Phytol. 226, 1550–1566 (2020).PubMed 
Article 

Google Scholar 
Rifai, S. W., Li, S. & Malhi, Y. Coupling of El Niño events and long-term warming leads to pervasive climate extremes in the terrestrial tropics. Environ. Res. Lett. 14, 105002 (2019).CAS 
Article 

Google Scholar 
Rifai, S. W. et al. ENSO drives interannual variation of forest woody growth across the tropics. Phil. Trans. R. Soc. B 373, 20170410 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Smith, M. N. et al. Empirical evidence for resilience of tropical forest photosynthesis in a warmer world. Nat. Plants 6, 1225–1230 (2020).CAS 
PubMed 
Article 

Google Scholar 
Malhi, Y. et al. Exploring the likelihood and mechanism of a climate-change-induced dieback of the Amazon rainforest. Proc. Natl Acad. Sci. USA 106, 20610–20615 (2009).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
McDowell, N., Allen, C. D. & Anderson‐Teixeira, K. Drivers and mechanisms of tree mortality in moist tropical forests. New Phytol. 219, 851–869 (2018).PubMed 
Article 

Google Scholar 
McDowell, N. et al. Mechanisms of plant survival and mortality during drought: why do some plants survive while others succumb to drought? New Phytol. 178, 719–739 (2008).PubMed 
Article 

Google Scholar 
Bauman, D. et al. Tropical tree growth sensitivity to climate is driven by species intrinsic growth rate and leaf traits. Glob. Chang. Biol. 28, 1414–1432 (2022).PubMed 
Article 

Google Scholar 
Esquivel-Muelbert, A. et al. Tree mode of death and mortality risk factors across Amazon forests. Nat. Commun. 11, 5515 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Anderegg, W. R. L., Anderegg, L. D. L., Kerr, K. L. & Trugman, A. T. Widespread drought-induced tree mortality at dry range edges indicates that climate stress exceeds species’ compensating mechanisms. Glob. Chang. Biol. 25, 3793–3802 (2019).PubMed 
Article 

Google Scholar 
Aguirre-Gutiérrez, J. et al. Drier tropical forests are susceptible to functional changes in response to a long-term drought. Ecol. Lett. 22, 855–865 (2019).PubMed 
Article 

Google Scholar 
Aguirre-Gutiérrez, J. et al. Long-term droughts may drive drier tropical forests towards increased functional, taxonomic and phylogenetic homogeneity. Nat. Comm. 11, 3346 (2020).Article 

Google Scholar 
Meir, P., Mencuccini, M. & Dewar, R. C. Drought-related tree mortality: addressing the gaps in understanding and prediction. New Phytol. 207, 28–33 (2015).PubMed 
Article 

Google Scholar 
Sullivan, M. J. P. et al. Long-term thermal sensitivity of Earth’s tropical forests. Science 368, 869–874 (2020).CAS 
PubMed 
Article 

Google Scholar 
Yuan, W. et al. Increased atmospheric vapor pressure deficit reduces global vegetation growth. Sci. Adv. 5, eaax1396 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
McMahon, S. M., Arellano, G. & Davies, S. J. The importance and challenges of detecting changes in forest mortality rates. Ecosphere 10, e02615 (2019).Article 

Google Scholar 
Trugman, A. T. et al. Tree carbon allocation explains forest drought-kill and recovery patterns. Ecol. Lett. 21, 1552–1560 (2018).CAS 
PubMed 
Article 

Google Scholar 
Trugman, A. T., Anderegg, L. D. L., Anderegg, W. R. L., Das, A. J. & Stephenson, N. L. Why is tree drought mortality so hard to predict? Trends Ecol. Evol. 36, 520–532 (2021).PubMed 
Article 

Google Scholar 
Phillips, O. L. et al. Drought–mortality relationships for tropical forests. New Phytol. 187, 631–646 (2010).PubMed 
Article 

Google Scholar 
Aleixo, I. et al. Amazonian rainforest tree mortality driven by climate and functional traits. Nat. Clim. Change 9, 384–388 (2019).Article 

Google Scholar 
Lingenfelder, M. & Newbery, D. M. On the detection of dynamic responses in a drought-perturbed tropical rainforest in Borneo. Plant Ecol. 201, 267–290 (2009).Article 

Google Scholar 
McDowell, N. G. et al. The interdependence of mechanisms underlying climate-driven vegetation mortality. Trends Ecol. Evol. 26, 523–532 (2011).PubMed 
Article 

Google Scholar 
Zuleta, D. et al. Individual tree damage dominates mortality risk factors across six tropical forests. New Phytol. 233, 705–721 (2022).PubMed 
Article 

Google Scholar 
Fontes, C. G. et al. Dry and hot: the hydraulic consequences of a climate change-type drought for Amazonian trees. Phil. Trans. R. Soc. B 373, 20180209 (2018).Chave, J. et al. Towards a worldwide wood economics spectrum. Ecol. Lett. 12, 351–366 (2009).PubMed 
Article 

Google Scholar 
Peters, J. M. R. et al. Living on the edge: a continental-scale assessment of forest vulnerability to drought. Glob. Chang. Biol. 27, 3620–3641 (2021).PubMed 
Article 

Google Scholar 
Yang, J., Cao, M. & Swenson, N. G. Why functional traits do not predict tree demographic rates. Trends Ecol. Evol. 33, 326–336 (2018).PubMed 
Article 

Google Scholar 
Espírito-Santo, F. D. B. et al. Size and frequency of natural forest disturbances and the Amazon forest carbon balance. Nat. Commun. 5, 3434 (2014).PubMed 
Article 

Google Scholar 
Chambers, J. Q. et al. The steady-state mosaic of disturbance and succession across an old-growth Central Amazon forest landscape. Proc. Natl Acad. Sci. USA 110, 3949–3954 (2013).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Rifai, S. W. et al. Landscape-scale consequences of differential tree mortality from catastrophic wind disturbance in the Amazon. Ecol. Appl. 26, 2225–2237 (2016).PubMed 
Article 

Google Scholar 
López, J., Way, D. A. & Sadok, W. Systemic effects of rising atmospheric vapor pressure deficit on plant physiology and productivity. Glob. Chang. Biol. 27, 1704–1720 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Brando, P. M. et al. Abrupt increases in Amazonian tree mortality due to droughttextendashfire interactions. Proc. Natl Acad. Sci. USA 111, 6347–6352 (2014).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Phillips, O. L. et al. Pattern and process in Amazon tree turnover, 1976–2001. Phil. Trans. R. Soc. Lond. B 359, 381–407 (2004).CAS 
Article 

Google Scholar 
Harris, R. M. B. et al. Biological responses to the press and pulse of climate trends and extreme events. Nat. Clim. Change 8, 579–587 (2018).Article 

Google Scholar 
Andrus, R. A., Chai, R. K., Harvey, B. J., Rodman, K. C. & Veblen, T. T. Increasing rates of subalpine tree mortality linked to warmer and drier summers. J. Ecol. 109, 2203–2218 (2021).Article 

Google Scholar 
Murphy, H. T., Bradford, M. G., Dalongeville, A., Ford, A. J. & Metcalfe, D. J. No evidence for long-term increases in biomass and stem density in the tropical rain forests of Australia. J. Ecol. 101, 1589–1597 (2013).Article 

Google Scholar 
Bennett, A. C., McDowell, N. G., Allen, C. D. & Anderson-Teixeira, K. J. Larger trees suffer most during drought in forests worldwide. Nat. Plants 1, 15139 (2015).PubMed 
Article 

Google Scholar 
Chitra-Tarak, R. et al. Hydraulically-vulnerable trees survive on deep-water access during droughts in a tropical forest. New Phytol. 231, 1798–1813 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Anderegg, W. R. L. et al. Meta-analysis reveals that hydraulic traits explain cross-species patterns of drought-induced tree mortality across the globe. Proc. Natl Acad. Sci. USA 113, 5024–5029 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Taylor, T. C., Smith, M. N., Slot, M. & Feeley, K. J. The capacity to emit isoprene differentiates the photosynthetic temperature responses of tropical plant species. Plant Cell Environ. 42, 2448–2457 (2019).CAS 
PubMed 
Article 

Google Scholar 
Arellano, G., Zuleta, D. & Davies, S. J. Tree death and damage: a standardized protocol for frequent surveys in tropical forests. J. Veg. Sci. 32, e12981 (2021).Article 

Google Scholar 
Bradford, M. G., Murphy, H. T., Ford, A. J., Hogan, D. L. & Metcalfe, D. J. Long-term stem inventory data from tropical rain forest plots in Australia. Ecology 95, 2362 (2014).Article 

Google Scholar 
Johnson, D. J. et al. Climate sensitive size-dependent survival in tropical trees. Nat. Ecol. Evol. 2, 1436–1442 (2018).PubMed 
Article 

Google Scholar 
Needham, J., Merow, C., Chang-Yang, C.-H., Caswell, H. & McMahon, S. M. Inferring forest fate from demographic data: from vital rates to population dynamic models. Proc. Biol. Sci. 285, 20172050 (2018).PubMed 
PubMed Central 

Google Scholar 
Lewis, S. L. et al. Tropical forest tree mortality, recruitment and turnover rates: calculation, interpretation and comparison when census intervals vary. J. Ecol. 92, 929–944 (2004).Article 

Google Scholar 
Reeves, J., Chen, J., Wang, X. L., Lund, R. & Lu, Q. Q. A review and comparison of changepoint detection techniques for climate data. J. Appl. Meteorol. Climatol. 46, 900–915 (2007).Article 

Google Scholar 
Clark, J. S., Bell, D. M., Kwit, M. C. & Zhu, K. Competition-interaction landscapes for the joint response of forests to climate change. Glob. Chang. Biol. 20, 1979–1991 (2014).PubMed 
Article 

Google Scholar 
Oliva, J., Stenlid, J. & Martínez-Vilalta, J. The effect of fungal pathogens on the water and carbon economy of trees: implications for drought-induced mortality. New Phytol. 203, 1028–1035 (2014).CAS 
PubMed 
Article 

Google Scholar 
Franklin, J. F., Shugart, H. H. & Harmon, M. E. Tree death as an ecological process. Bioscience 37, 550–556 (1987).Article 

Google Scholar 
Yanoviak, S. P. et al. Lightning is a major cause of large tree mortality in a lowland neotropical forest. New Phytol. 225, 1936–1944 (2020).PubMed 
Article 

Google Scholar 
Preisler, Y., Tatarinov, F., Grünzweig, J. M. & Yakir, D. Seeking the ‘point of no return’ in the sequence of events leading to mortality of mature trees. Plant Cell Environ. 44, 1315–1328 (2020).PubMed 
Article 

Google Scholar 
Aragão, L. E. O. C. et al. Spatial patterns and fire response of recent Amazonian droughts. Geophys. Res. Lett. 34, L07701 (2007).Article 

Google Scholar 
Malhi, Y. et al. The linkages between photosynthesis, productivity, growth and biomass in lowland Amazonian forests. Glob. Chang. Biol. 21, 2283–2295 (2015).PubMed 
Article 

Google Scholar 
Hutchinson, M. F., Xu, T., Kesteven, J. L., Marang, I. J. & Evans, B. J.ANUClimate v2.0, NCI Australia. https://doi.org/10.25914/60a10aa56dd1b (2021).Abatzoglou, J. T., Dobrowski, S. Z., Parks, S. A. & Hegewisch, K. C. TerraClimate, a high-resolution global dataset of monthly climate and climatic water balance from 1958–2015. Sci. Data 5, 170191 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Carscadden, K. A. et al. Niche breadth: causes and consequences for ecology, evolution, and conservation. Q. Rev. Biol. 95, 179–214 (2020).Article 

Google Scholar 
Swenson, N. G. et al. A reframing of trait–demographic rate analyses for ecology and evolutionary biology. Int. J. Plant Sci. 181, 33–43 (2020).Article 

Google Scholar 
Morueta-Holme, N. et al. Habitat area and climate stability determine geographical variation in plant species range sizes. Ecol. Lett. 16, 1446–1454 (2013).PubMed 
PubMed Central 
Article 

Google Scholar 
Brum, M. et al. Hydrological niche segregation defines forest structure and drought tolerance strategies in a seasonal Amazon forest. J. Ecol. 107, 318–333 (2019).Article 

Google Scholar 
Chitra-Tarak, R. et al. The roots of the drought: hydrology and water uptake strategies mediate forest-wide demographic response to precipitation. J. Ecol. 106, 1495–1507 (2018).Article 

Google Scholar 
Boria, R. A., Olson, L. E., Goodman, S. M. & Anderson, R. P. Spatial filtering to reduce sampling bias can improve the performance of ecological niche models. Ecol. Modell. 275, 73–77 (2014).Article 

Google Scholar 
Farquhar, G. D., von Caemmerer, S. & Berry, J. A. A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species. Planta 149, 78–90 (1980).CAS 
PubMed 
Article 

Google Scholar 
Duursma, R. A. Plantecophys—an R package for analysing and modelling leaf gas exchange data. PLoS ONE 10, e0143346 (2015).PubMed 
PubMed Central 
Article 

Google Scholar 
De Kauwe, M. G. et al. A test of the ‘one-point method’ for estimating maximum carboxylation capacity from field-measured, light-saturated photosynthesis. New Phytol. 210, 1130–1144 (2016).PubMed 
Article 

Google Scholar 
Bloomfield, K. J. et al. The validity of optimal leaf traits modelled on environmental conditions. New Phytol. 221, 1409–1423 (2019).CAS 
PubMed 
Article 

Google Scholar 
McElreath, R. Statistical Rethinking: A Bayesian Course with Examples in R and STAN (CRC Press, 2020).“RStan: the R interface to Stan.” R package version 2.21.2. http://mc-stan.org/ (Stan Development Team, 2020).Bürkner, P.-C. brms: An R package for Bayesian multilevel models using Stan. J. Stat. Softw. 80, 1–28 (2017).Article 

Google Scholar 
R Core Team. R: a language and environment for statistical computing. https://www.R-project.org/ (R Foundation for Statistical Computing, 2021).Dinerstein, E. et al. An ecoregion-based approach to protecting half the terrestrial realm. Bioscience 67, 534–545 (2017).PubMed 
PubMed Central 
Article 

Google Scholar  More

Kelly, A. E. & Goulden, M. L. Rapid shifts in plant distribution with recent climate change. Proc. Natl. Acad. Sci. U.S.A. 105, 11823–11826. https://doi.org/10.1073/pnas.0802891105 (2008).ADS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Wiens, J. J. Climate-related local extinctions are already widespread among plant and animal species. PLoS Biol. 14, e2001104. https://doi.org/10.1371/journal.pbio.2001104 (2016).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Swinnen, J., Burkitbayeva, S., Schierhorn, F., Prishchepov, A. V. & Müller, D. Production potential in the “bread baskets” of Eastern Europe and Central Asia. Global Food Secur. 14, 38–53. https://doi.org/10.1016/j.gfs.2017.03.005 (2017).Article 

Google Scholar 
Henry, R. J. Innovations in plant genetics adapting agriculture to climate change. Curr. Opin. Plant Biol. 56, 168–173. https://doi.org/10.1016/j.pbi.2019.11.004 (2020).Article 
PubMed 

Google Scholar 
Stokes, C. & Howden, M. Adapting Agriculture to Climate Change: Preparing Australian Agriculture, Forestry and Fisheries for the Future (Csiro Publishing, 2010).Book 

Google Scholar 
Bräutigam, K. et al. Epigenetic regulation of adaptive responses of forest tree species to the environment. Ecol. Evol. 3, 399–415. https://doi.org/10.1002/ece3.461 (2013).Article 
PubMed 
PubMed Central 

Google Scholar 
Yaish, M. W., Colasanti, J. & Rothstein, S. J. The role of epigenetic processes in controlling flowering time in plants exposed to stress. J. Exp. Bot. 62, 3727–3735. https://doi.org/10.1093/jxb/err177 (2011).CAS 
Article 
PubMed 

Google Scholar 
Yaish, M. W. DNA methylation-associated epigenetic changes in stress tolerance of plants. In Molecular Stress Physiology of Plants (eds Rout, G. R. & Das, A. B.) 427–440 (Springer India, 2013).Chapter 

Google Scholar 
Suji, K. K. & Joel, A. J. An epigenetic change in rice cultivars underwater stress conditions. Electron. J. Plant Breed. 1, 1142–1143 (2010).
Google Scholar 
Peng, H. & Zhang, J. Plant genomic DNA methylation in response to stresses: Potential applications and challenges in plant breeding. Prog. Nat. Sci. 19, 1037–1045. https://doi.org/10.1016/j.pnsc.2008.10.014 (2009).CAS 
Article 

Google Scholar 
Baduel, P. & Colot, V. The epiallelic potential of transposable elements and its evolutionary significance in plants. Philos. Trans. R. Soc. B 376, 20200123. https://doi.org/10.1098/rstb.2020.0123 (2021).CAS 
Article 

Google Scholar 
Labra, M. et al. Analysis of cytosine methylation pattern in response to water deficit in pea root tips. Plant Biol. 4, 694–699. https://doi.org/10.1055/s-2002-37398 (2002).CAS 
Article 

Google Scholar 
Wang, W.-S. et al. Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.). J. Exp. Bot. 62, 1951–1960. https://doi.org/10.1093/jxb/erq391 (2011).CAS 
Article 
PubMed 

Google Scholar 
Šmarda, P., Bureš, P., Horová, L., Foggi, B. & Rossi, G. Genome size and GC content evolution of Festuca: Ancestral expansion and subsequent reduction. Ann. Bot. 101, 421–433. https://doi.org/10.1093/aob/mcm307 (2008).CAS 
Article 
PubMed 

Google Scholar 
Tomczyk, P. P., Kiedrzyński, M., Jedrzejczyk, I., Rewers, M. & Wasowicz, P. The transferability of microsatellite loci from a homoploid to a polyploid hybrid complex: An example from fine-leaved Festuca species (Poaceae). PeerJ 8, e9227. https://doi.org/10.7717/peerj.9227 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Piękoś-Mirkowa, H. & Mirek, Z. Distribution patterns and habitats of endemic vascular plants in the Polish Carpathians. Acta Soc. Bot. Pol. 78, 321–326 (2009).Article 

Google Scholar 
Kiedrzyński, M., Zielińska, K. M., Rewicz, A. & Kiedrzyńska, E. Habitat and spatial thinning improve the Maxent models performed with incomplete data. J. Geophys. Res. Biogeosci. 122(6), 1359–1370. https://doi.org/10.1002/2016JG003629 (2017).Article 

Google Scholar 
Rewicz, A. et al. Morphometric traits in the fine-leaved fescues depend on ploidy level: The case of Festuca amethystina L. PeerJ 6, e5576. https://doi.org/10.7717/peerj.5576 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Kiedrzyński, M. et al. Tetraploids expanded beyond the mountain niche of their diploid ancestors in the mixed-ploidy grass Festuca amethystina L. Sci. Rep. 11, 18735 (2021).ADS 
Article 

Google Scholar 
Mounger, J. et al. Epigenetics and the success of invasive plants. Philos. Trans. R. Soc. B 376, 20200117. https://doi.org/10.1098/rstb.2020.0117 (2021).CAS 
Article 

Google Scholar 
Bewick, A. J. & Schmitz, R. J. Epigenetics in the wild. Elife 4, e07808. https://doi.org/10.7554/eLife.07808 (2015).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Sahu, P. P. et al. Epigenetic mechanisms of plant stress responses and adaptation. Plant Cell Rep. 32(8), 1151–1159. https://doi.org/10.1007/s00299-013-1462-x (2013).CAS 
Article 
PubMed 

Google Scholar 
Alonso, C. et al. Interspecific variation across angiosperms in global DNA methylation: Phylogeny, ecology and plant features in tropical and Mediterranean communities. New Phytol. 224(2), 949–960. https://doi.org/10.1111/nph.16046 (2019).CAS 
Article 
PubMed 

Google Scholar 
Angers, B., Castonguay, E. & Massicotte, R. Environmentally induced phenotypes and DNA methylation: How to deal with unpredictable conditions until the next generation and after. Mol. Ecol. 19(7), 1283–1295. https://doi.org/10.1111/j.1365-294X.2010.04580.x (2010).CAS 
Article 
PubMed 

Google Scholar 
Batog, J. & Wawro, A. Process of obtaining bioethanol from sorghum biomass using genome shuffling. Cellul. Chem. Technol. 53, 459–467 (2019).CAS 
Article 

Google Scholar 
Richards, C. L., Schrey, A. W. & Pigliucci, M. Invasion of diverse habitats by few Japanese knotweed genotypes is correlated with epigenetic differentiation. Ecol. Lett. 15, 1016–1025. https://doi.org/10.1111/j.1461-0248.2012.01824.x (2012).Article 
PubMed 

Google Scholar 
Li, N. et al. DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids. New Phytol. 223(2), 979–992. https://doi.org/10.1111/nph.15820 (2019).CAS 
Article 
PubMed 

Google Scholar 
Róis, A. S. et al. Epigenetic rather than genetic factors may explain phenotypic divergence between coastal populations of diploid and tetraploid Limonium spp. (Plumbaginaceae) in Portugal. BMC Plant Biol. 13(1), 205. https://doi.org/10.1186/1471-2229-13-205 (2013).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Li, A. et al. DNA methylation in genomes of several annual herbaceous and woody perennial plants of varying ploidy as detected by MSAP. Plant Mol. Biol. Rep. 29, 784–793. https://doi.org/10.1007/s11105-010-0280-3 (2011).ADS 
CAS 
Article 

Google Scholar 
Sokolova, D. A., Vengzhen, G. S. & Kravets, A. P. An Analysis of the correlation between the changes in satellite DNA methylation patterns and plant cell responses to the stress. Cell Bio 2, 163–171. https://doi.org/10.4236/cellbio.2013.23018 (2013).CAS 
Article 

Google Scholar 
Johnson, L. I. & Tricker, P. J. Epigenomic plasticity within populations: Its evolutionary significance and potential. Heredity 105, 113–121. https://doi.org/10.1038/hdy.2010.25 (2010).CAS 
Article 
PubMed 

Google Scholar 
Zheng, X. et al. Transgenerational variations in DNA methylation induced by drought stress in two rice varieties with distinguished difference to drought resistance. PLoS One 8(11), e80253. https://doi.org/10.1371/journal.pone.0080253 (2013).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Karan, R., DeLeon, T., Biradar, H. & Subudhi, P. K. Salt Stress induced variation in DNA methylation pattern and its influence on gene expression in contrasting rice genotypes. PLoS One 7(6), e40203. https://doi.org/10.1371/journal.pone.0040203 (2012).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Richards, C. L. & Pigliucci, M. Epigenetic inheritance. A decade into the extended evolutionary synthesis. Paradigmi 38, 463–494. https://doi.org/10.30460/99624 (2020).Article 

Google Scholar 
Chelaifa, H., Monnier, A. & Ainouche, M. Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina × townsendii and Spartina anglica (Poaceae). New Phytol. 186(1), 161–174. https://doi.org/10.1111/j.1469-8137.2010.03179.x (2010).CAS 
Article 
PubMed 

Google Scholar 
Al-Lawati, A., Al-Bahry, S., Victor, R., Al-Lawati, A. H. & Yaish, M. W. Salt stress alters DNA methylation levels in alfalfa (Medicago spp.). Genet. Mol. Res. 15, 15018299. https://doi.org/10.4238/gmr.15018299 (2016).CAS 
Article 
PubMed 

Google Scholar 
Lewandowska-Gnatowska, E. et al. Is DNA methylation modulated by wounding-induced oxidative burst in maize?. Plant Physiol. Biochem. 82, 202–208. https://doi.org/10.1016/j.plaphy.2014.06.003 (2014).CAS 
Article 
PubMed 

Google Scholar 
Marfil, C. et al. Changes in grapevine DNA methylation and polyphenols content induced by solar ultraviolet-B radiation, water deficit and abscisic acid spray treatments. Plant Physiol. Biochem. 135, 287–294. https://doi.org/10.1016/j.plaphy.2018.12.021 (2019).CAS 
Article 
PubMed 

Google Scholar 
Zedek, F. et al. Endopolyploidy is a common response to UV-B stress in natural plant populations, but its magnitude may be affected by chromosome type. Ann. Bot. 126(5), 883–889. https://doi.org/10.1093/aob/mcaa109 (2020).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Pandey, N. & Pandey-Rai, S. Deciphering UV-B-induced variation in DNA methylation pattern and its influence on regulation of DBR2 expression in Artemisia annua L. Planta 242(4), 869–879. https://doi.org/10.1007/s00425-015-2323-3 (2015).CAS 
Article 
PubMed 

Google Scholar 
Molinier, J. Genome and epigenome surveillance processes underlying UV exposure in plants. Genes 8(11), 316. https://doi.org/10.3390/genes8110316 (2017).CAS 
Article 
PubMed Central 

Google Scholar 
Niederhuth, C. E. et al. Widespread natural variation of DNA methylation within angiosperms. Genome Biol. 17, 194. https://doi.org/10.1186/s13059-016-1059-0 (2016).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Lira-Medeiros, C. F. et al. Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS One 5, e10326. https://doi.org/10.1371/journal.pone.0010326 (2010).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Richards, C. L., Verhoeven, K. J. F. & Bossdorf, O. Evolutionary significance of epigenetic variation. In Plant Genome Diversity Vol. 1 (eds Wendel, J. F. et al.) 257–274 (Springer Vienna, 2012).Chapter 

Google Scholar 
Paun, O. et al. Stable epigenetic effects impact adaptation in allopolyploid orchids (Dactylorhiza: Orchidaceae). Mol. Biol. Evol. 27, 2465–2473. https://doi.org/10.1093/molbev/msq150 (2010).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Xie, H. et al. Global DNA methylation patterns can play a role in defining terroir in grapevine (Vitis vinifera cv. Shiraz). Front. Plant Sci. 8, 130398. https://doi.org/10.3389/fpls.2017.01860 (2017).Article 

Google Scholar 
Herrera, C. M. & Bazaga, P. Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis. New Phytol. 187(3), 867–876. https://doi.org/10.1111/j.1469-8137.2010.03298.x (2010).CAS 
Article 
PubMed 

Google Scholar 
Portis, E., Acquadro, A., Comino, C. & Lanteri, S. Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP). Plant Sci. 166, 169–178. https://doi.org/10.1016/j.plantsci.2003.09.004 (2004).CAS 
Article 

Google Scholar 
R Core Team. R: A language and environment for statistical computing. http://www.R-project.org (R Foundation for Statistical Computing, 2013).Schloerke, B. et al. GGally: Extension to “ggplot2” R package version 2.1.0. https://CRAN.R-project.org/package=GGally (2021).StatSoft, Inc. STATISTICA (Data Analysis Software System), Version 10. http://www.statsoft.com (2011).Tomczyk, P. Phenotypic measurement of inbreeding depression in grasses—An overview of traits (Fenotypowe miary depresji wsobnej u traw—przegląd cech). Wiad. Bot. https://doi.org/10.5586/wb.2019.005 (2019).Article 

Google Scholar 
Fick, S. E. & Hijmans, R. J. WorldClim 2: new 1km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37(12), 4302–4315. https://doi.org/10.1002/joc.5086 (2017).Article 

Google Scholar 
Fox, J. & Weisberg, S. An {R} Companion to Applied Regression (Sage Publications, 2019).
Google Scholar  More

DataAll data was processed and analyzed using R (R Core Team, Version 4.0.3).Dengue case data were collected and shared by the Alcaldía de Medellín, Secretaría de Salud. In Medellin, dengue case surveillance is conducted by public health institutions that classify and report all cases that meet the WHO clinical dengue case criteria for a probable case to Medellin’s Secretaría de Salud through SIVIGILA (“el Sistema Nacional de Vigilancia en Salud Publica). All case data were de-identified and aggregated to the SIT Zone level.Human public transit usage and movement data were collected and shared by the Área Metropolitana del Valle de Aburrá for 50–200 respondents per SIT Zone. The “Encuestas Origen Destino” (Origen Destination Surveys) were conducted in 2005, 2011, and 2016 and published in 2006, 2012, and 2017, with survey methods described by the Área Metropolitana del Valle de Aburrá25. Survey respondents include a randomly selected subset of all Medellin residents in each SIT zone regardless of whether they use public transit or not. Survey respondents reported the start and end locations, purpose for travel, and mode of travel for all movement over the last 24 h from the time the survey was administered. Respondents reported all modes of movement, including public transit, private transit, and movement on foot. The results of the survey published in 2017 are published online by the Área Metropolitana del Valle de Aburrá26, and select data are available through the geodata-Medellin open data portal27. The results and data of the survey published in 2012 are not publicly available and were obtained directly from the Área Metropolitana del Valle de Aburrá.The public transit usage survey data were also used to extract socioeconomic data to the SIT zone; surveyors also reported basic demographic data including household Estrato, which was averaged per SIT zone to estimate zone socioeconomic status. “Estrato” measures socioeconomic status on a scale from 1 (lowest) to 6 (highest). This system is used by the government of Colombia to allocate public services and subsidies (Law 142, 1994). Data from the public transit usage survey were used to extract socioeconomic status data because it is the only location available where the spatial scale of the data matched the spatial scale of the SIT zone.Data on the location of Medellín public transit lines was downloaded as shape files from the geodata-Medellín open data portal27 and subset for each year to the set of transit lines that was available in that year. Data on the opening date of each Medellín public transit line was taken from the Medellín metro website28.Because census data at the zone level were not available for this study and only exists for 2005 and 2018, we used population estimates for each year downloaded from the WorldPop project29 and aggregated by SIT zone. The accuracy of WorldPop estimates were checked against available census data for 2005 and 2018 at the comuna level, accessed via the geodata- Medellín open data portal27.Ethical considerationsNo human subjects research was conducted. All data used was de-identified, and the analysis was conducted on a database of cases meeting the clinical criteria for dengue with no intervention or modification of biological, physical, psychological, or social variables. All methods were performed in accordance with the relevant guidelines and regulations.Data analysisQuantifying public transit usage and distance from nearest transit lineTo quantify public transit usage, we determined if each respondent reported using the metro, metroplus, or ruta alimentadora (supplementary bus route system integrated with the metro system) in the last 24 h. We then calculated the percent of respondents using the public transit system at least once for each SIT zone.To quantify the distance to the nearest public transit line, we calculated the distance from the center point of each zone to the closest metro, metroplus, tranvía, metrocable, ruta alimentadora, or escalera eléctrica. This was recalculated for each year, including new transit lines that were added within that year.Spatial autoregressive models of dengue incidenceDengue incidence per year at the level of the SIT zone was modeled using a fixed effects spatial panel model by maximum likelihood (R package splm30) as described in31. Our fixed effects were socioeconomic status, distance from public transit, a two-way interaction between these factors, and year. To weight dengue cases by population per SIT zone, the model contained a log offset of population per zone per year. Dengue case counts were log transformed after adding one to account for zones with zero dengue cases in a given year. Year was analyzed as a categorical variable to avoid smoothing epidemic years. All continuous variables were scaled to enable comparison of effect size. Because these panel models require balanced data across time, data was truncated to SIT zones that had data for all years available (247 remaining of 291). Spatial dependency was evaluated, and the model was selected using the Hausman specification test and locally robust panel Lagrange Multiplier tests for spatial dependence. Based on a significant Hausman specification test result, which indicates a poor specification of the random effect model, a fixed effect model was chosen. This result is supported by the fact that we had a nearly exhaustive sample of SIT zones in the Medellin metro area. Lagrange multiplier tests were used to determine the most appropriate spatial dependency specifications. Based on the results of the Lagrange multiplier tests, a Spatial Autoregressive (SAR) model was the most appropriate to incorporate spatial dependency; a SAR model considers that the number of dengue cases in a SIT zone depends on the number in neighboring zones.Because public transit usage was a measurement taken during just two of the study years, we constructed an additional fixed effects spatial panel model by maximum likelihood model of dengue incidence in just 2011 and 2016 that included ridership as an additional predictor variable. Our fixed effects were year, socioeconomic status, distance from public transit, a two-way interaction between socioeconomic status and distance from public transit, percent utilizing public transit, and a two-way interaction between socioeconomic status and percent utilizing public transit. As in our model of all years, the model contained a log offset of population per zone per year and dengue case counts were log transformed after adding one to account for zones with zero dengue cases in a given year, year was analyzed as a categorical variable, and all continuous variables were scaled to enable comparison of effect size. The data was truncated to SIT zones that had data for all years available (251 remaining of 291). We used the same model selection process, and again a fixed effect model was chosen, and based on the results of the Lagrange multiplier tests, a Spatial Autoregressive (SAR) model was determined the most appropriate to incorporate spatial dependency. More

Young cerebrospinal fluid probably improves the conductivity of the neurons in ageing mice.Credit: Qilai Shen/Bloomberg/Getty

Young brain fluid improves memory in old miceCerebrospinal fluid (CSF) from young mice can improve memory function in older mice, researchers report in Nature (T. Iram et al. Nature 605, 509–515; 2022).A direct brain infusion of young CSF probably improves the conductivity of the neurons in ageing mice, which improves the process of making and recalling memories.CSF is a cocktail of essential ions and nutrients that cushions the brain and spinal cord and is essential for normal brain development. But as mammals age, CSF loses some of its punch. Those changes might affect cells related to memory, says co-author Tal Iram, a neuroscientist at Stanford University in California.The researchers found that young CSF helps ageing mice to generate more early-stage oligodendrocytes, cells in the brain that produce the insulating sheath around nerve projections and help to maintain brain function.The team suggest that the improvements are largely due to a specific protein in the fluid.“This is super exciting from the perspective of basic science, but also looking towards therapeutic applications,” says Maria Lehtinen, a neurobiologist at Boston Children’s Hospital in Massachusetts.Gender bias worms its way into parasite namingA study examining the names of nearly 3,000 species of parasitic worm discovered in the past 20 years reveals a markedly higher proportion named after male scientists than after female scientists — and a growing appetite for immortalizing friends and family members in scientific names.Robert Poulin, an ecological parasitologist at the University of Otago in Dunedin, New Zealand, and his colleagues combed through papers published between 2000 and 2020 that describe roughly 2,900 new species of parasitic worm (R. Poulin et al. Proc. R. Soc. B https://doi.org/htqn; 2022). The team found that well over 1,500 species were named after their host organism, where they were found or a prominent feature of their anatomy.

Source: R. Poulin et al. Proc. R. Soc. B https://doi.org/htqn (2022)

Many others were named after people, ranging from technical assistants to prominent politicians. But just 19% of the 596 species named after eminent scientists were named after women, a percentage that barely changed over the decades (see ‘Parasite name game’). Poulin and his colleagues also noticed an upward trend in the number of parasites named after friends, family members and even pets of the scientists who formally described them. This practice should be discouraged, Poulin argues.

Sea anemones turn oxybenzone into a light-activated agent that can bleach and kill corals.Credit: Georgette Douwma/Getty

Anemones suggest why sunscreen turns toxic in seaA common but controversial sunscreen ingredient that is thought to harm corals might do so because of a chemical reaction that causes it to damage cells in the presence of ultraviolet light.Researchers have discovered that sea anemones, which are similar to corals, make the sun-blocking molecule oxybenzone water-soluble by tacking a sugar onto it. This inadvertently turns oxybenzone into a molecule that — instead of blocking UV light — is activated by sunlight to produce free radicals that can bleach and kill corals. The animals “convert a sunscreen into something that’s essentially the opposite of a sunscreen”, says Djordje Vuckovic, an environmental engineer at Stanford University in California.It’s not clear how closely these laboratory-based studies mimic the reality of reef ecosystems. The concentration of oxybenzone at a coral reef can vary widely, depending on factors such as tourist activity and water conditions. And other factors threaten the health of coral reefs; these include climate change, ocean acidification, coastal pollution and overfishing. The study, published on 5 May (D. Vuckovic et al. Science 376, 644–648; 2022) does not show where oxybenzone ranks in the list. More

Australia’s tropical rainforests are some of the oldest in the world.Credit: Alexander Schenkin

The rate of tree dying in the old-growth tropical forests of northern Australia each year has doubled since the 1980s, and researchers say climate change is probably to blame.The findings, published today in Nature1, come from an extraordinary record of tree deaths catalogued at 24 sites in the tropical forests of northern Queensland over the past 49 years.“Trees are such long-living organisms that it really requires huge amounts of data to be able to detect changes in such rare events as the death of a tree,” says lead author David Bauman, a plant ecologist at the University of Oxford, UK. The sites were initially surveyed every two years, then every three to four years, he explains, and the analysis focused on 81 key species.Bauman and his team recorded that 2,305 of these trees have died since 1971. But they calculated that, from the mid-1980s, tree mortality risk increased from an average of 1% a year to 2% a year (See ‘Increasing death rate’).

Bauman says that trees help to slow global warming because they absorb carbon dioxide, so an increase in tree deaths reduces forests’ carbon-capturing ability. “Tropical forests are critical to climate change, but they’re also very vulnerable to it,” he explains.Climate changeThe study found that the rise in death rate occurred at the same time as a long-term trend of increases in the atmospheric vapour pressure deficit, which is the difference between the amount of water vapour that the atmosphere can hold and the amount of water it does hold at a given time. The higher the deficit, the more water trees lose through their leaves. “If the evaporative demand at the leaf level can’t be matched by water absorption in fine roots, it can lead to leaves wilting, whole branches dying and, if the stress is sustained, to tree death,” Bauman says.The researchers looked at other climate-related trends — including rising temperatures and an estimate of drought stress in soils — but they found that the drying atmosphere had the strongest effect. “What we show is that this increase [in tree mortality risk] also closely followed the increase in atmospheric water stress, or the drying power of air, which is a consequence of the temperature increase due to climate change,” Bauman explains.Of the 81 tree species that the team studied, 70% showed an increase in mortality risk over the study period, including the Moreton Bay chestnut (Castanospermum australe), white aspen (Medicosma fareana) and satin sycamore (Ceratopetalum succirubrum).The authors also saw differences in mortality in the same tree species across plots, depending on how high the atmospheric vapour pressure deficit was in each plot.“This is one data set where the trees have been monitored in reasonably good detail since the early ’70s, and this is a really top-notch analysis of it,” says Belinda Medlyn, an ecosystem scientist at University of Western Sydney, Australia.But she says that more experiments are needed to determine whether the vapour pressure deficit is the biggest climate-related contributor to the increase in tree deaths. More

Parasites have frequently been observed on the gills of coleoid cephalopods during ROV dives in the mesopelagic waters of the Monterey Submarine Canyon. Here, we demonstrate that at least two parasite species can be distinguished from ROV-collected specimens. Based on morphology, the first parasite was identified as the protist Hochbergia cf. moroteuthensis. Although the original description of H. moroteuthensis struggled to assign a taxonomic rank, the authors noted that the presence of trichocysts and an apical pore bear similarities to those of dinoflagellates in an encysted life stage29,30. Using Sanger sequencing and dinoflagellate cyst-specific primers, we confirm this parasite to be a dinoflagellate that forms a sister group to members of the Oodinium genus. The second parasite could not be matched to any documented morphological descriptions, and DNA barcoding was only able to resolve a short sequence that does not provide for a reliable identification.Hochbergia moroteuthensis appears to be a common parasite of midwater cephalopods and has previously been collected off the gills of twenty cephalopod species29,30. These include five taxa investigated here (C. calyx, V. infernalis, Galiteuthis spp., Gonatus spp. and Japetella diaphana), with Taonius sp. new to the list. While H. cf. moroteuthensis found in this study was somewhat smaller than the type series (0.5–1.4 mm versus 1.19–1.99)30, it was within the range of those reported by McLean et al.29 on the squids Stigmatoteuthis dofleini Pfeffer, 1912 and Abralia trigonura Berry, 1913 (i.e. 0.56 to 1.10 mm on average in length)29. The latter authors noticed that parasite size, color (i.e. white to yellow) and thecal plate morphology may differ between host species, which could indicate multiple Hochbergia species. It should, however, be noted that it is unknown whether H. moroteuthensis maximum growth is dependent on host size or whether the investigated parasites were simply in different growth stages given the study’s relatively small samples sizes. Although we did not compare H. cf. moroteuthensis morphology across hosts in great detail, the partial 18S rRNA sequences obtained for parasites on Gonatus berryi and Chiroteuthis calyx were identical. Further research is therefore warranted to investigate species-specific parasite differences and speciation among hosts.The genetic relatedness between H. cf. moroteuthensis and its Oodinium sister group is further supported by several morphological features. First, the lack of distinct dinoflagellate characters, ovoid shape and the presence of trichocysts, have also been noted for Oodinium cysts41,42,43. McLean et al.29 further reported that the nucleus of the single-celled H. moroteuthensis cyst contains diffuse chromatin, a feature unlike most dinoflagellates that possess well-defined rod-like chromosomes42. Remarkably, dinoflagellates within Oodinium are known to alternate between both non-dinokaryotic and dinokaryotic nuclei within their life cycles, which could explain H. moroteuthensis’ diffuse chromatin42,43. Similarities between H. moroteuthensis and Oodinium further extend to the parasitic life style with primarily pelagic hosts. Dinoflagellates in the Oodinium genus are all known to be ectoparasitic, infecting ctenophores, chaetognaths, annelids, larvaceans and a hydromedusa41,43,44,45,46.In spite of these similarities, there are also several noteworthy morphological differences between H. moroteuthensis and members of the Oodinium genus. Young Oodinium cysts generally have a white to yellow coloring, with older cysts taking a yellow–brown or dark brown tint41,43,44. Oodinium cysts also possess relatively simple thecal plates and above all, have a distinct peduncle, or stalk, with which they attach to the host and which is thought to serve as feeding apparatus41,43,47. Maximum lengths for Oodinium cysts have been reported up to 0.39 mm43,46. In contrast, cysts in H. moroteuthensis possess a white to yellow coloring, an intricate pattern of triangular plates, reach sizes up to 1.99 mm long, and have a simple holdfast area with an oval aperture that likely anchors them to the host30. Currently, both Oodinium and Hochbergia form a genetically distinct clade within the Dinophyceae and analysis of further specimens and genetic markers might provide more insight into their relatedness and specialization on primarily pelagic hosts. Additionally, analysis of fast- and slow-evolving genetic markers might resolve the polytomy observed in the phylogenetic trees, which were also present in the phylogenetic reconstruction of the DINOREF reference database by Mordret et al.32.The genetic similarity of H. cf. moroteuthensis to an unidentified eukaryote from the water column and the fact that we encountered the protozoans in an encysted stage, strongly suggests that these dinoflagellates infect their cephalopod hosts through a free-living life stage. Many parasitic dinoflagellates, including Oodinium, alternate between a motile free-living stage—the dinospore—that forms a vegetative feeding stage—the trophont—upon attachment to the host41,47,48. During this vegetative stage, the trophont grows greatly in size but without cellular division. Once mature, the trophont detaches from the host to divide into multiple flagellated dinospores. The dinospores disperse into the water column, free to infect new hosts (Fig. 6)41,47,48.Figure 6Theorized life cycle of Hochbergia moroteuthensis. (a) The vegetative trophont (feeding life stage) grows without cellular division on the cephalopod’s gills. (b) The mature trophont detaches and (c) divides into motile dinospores, (d) free to infect new hosts in the water column. Illustration (b) trophont adapted from Shinn & McLean30.Full size imageSuch a free-living life stage is consistent with H. moroteuthensis’ wide geographic distribution. Free-living dinospores are easily dispersed by ocean currents, and observations in both the North Pacific Ocean and the Gulf of Mexico could indicate large-scale ocean connectivity, potentially beyond the distribution reported here29. This dispersal may also offer H. moroteuthensis a wide range of infection possibilities and explain why trophonts are found in twenty-one different cephalopod taxa. Nevertheless, population genetic structure needs to be investigated, as it is currently unknown if the parasites represent multiple species.Free-living dinospores might also explain H. moroteuthensis’ location on the exterior gill tissue. With dinospores free in the water column, the fastest pathway to a cephalopod’s interior is through ‘inhalation’. In this process, cephalopods actively force water through their gills, making these the first organs Hochbergia would encounter. Respiratory organs give direct access to the cephalopod’s blood stream, and therefore offer a suitable environment (i.e. nutrient and oxygen rich) for development into a trophont. Gills also provide interstices that could simply trap dinospores. Either way, there was only one occasion (i.e. out of 355) where trophonts were seen on other body parts besides the gills (Fig. 4e). In comparison, several Oodinium parasites are also known to attach to specific host-body parts, apparently preferring sites involved in locomotor movement. For instance, Oodinium jordani McLean & Nielsen, 1989 is known to attach to the fin of the chaetognath Sagitta elegans Verrill, 187346, while O. pouchetti is mostly found on the tail of appendicularians41, and Oodinium sp. collected off various ctenophores appears to prefer attachment close to or within the beating comb rows44. Whether these surface areas offer highest encounter rates or provide a physical benefit such as enhanced oxygenation remains unknown.The increased prevalence of H. cf. moroteuthensis observed in the most abundant cephalopod, Chiroteuthis, and in the other adult cephalopods is in line with infection dynamics known from other wildlife parasites, where the probability of a parasitic infection increases with host density and age49,50,51. Following this, dinospores in the Monterey Submarine Canyon have more opportunities to encounter common squids like Chiroteuthis52 and longer-lived cephalopods. Alternatively, it is possible that the increased parasite load in adults is simply the result of larger gill surface areas when compared to juveniles. However, when comparing prevalence between host species, it should be noted that the maximum adult sizes for C. calyx (up to 100 mm in mantle length, ML) are smaller than those of Galiteuthis (500 mm ML), Taonius (660 mm ML) and Japetella (144 mm ML) among specimens found in the Monterey Submarine Canyon53,54.Other factors that might explain the observed prevalence include parasite preferences for host physiology (e.g. respiration rates) or confinement to a certain depth range18. Although Chiroteuthis, Galiteuthis, Taonius and Japetella partially overlap in their depth distributions, Chiroteuthis generally remains above the core of the oxygen minimum zone, located around 700 m in Monterey Bay52,55. Galiteuthis, on the other hand, has a bimodal distribution, with older individuals known to migrate below the oxygen minimum core52,55,56. If dinospore viability is restricted to more shallow depths, the probability of infection for Galiteuthis could decrease when living at deeper depths. This is further supported by Taonius, which showed a comparable bimodal distribution to Galiteuthis52 and shared a similar parasite prevalence. Furthermore, Japetella is the deepest living cephalopod investigated and harbored relatively few Hochbergia trophonts. In spite of this, it is unknown how long it takes for H. moroteuthensis dinospores to develop into mature trophonts and over what time frames they may accumulate on their hosts. Lab-based experiments with Oodinium sp. on the ctenophore Beroe abyssicola Mortensen, 1927 showed that trophonts needed approximately 20 days to grow from 35 µm in length to their mature size of 350 µm at 10 °C44. Given that H. moroteuthensis can grow over five times larger and lives at colder temperatures depending on its host distribution, growth periods may be substantially longer.When looking at the prevalence of H. cf. moroteuthensis over time, only Taonius appeared to be showing an increase in infected individuals over the years. Present results, however, are insufficient to determine whether this increase is the result of environmental change or part of natural variability. We therefore recommend continued monitoring to determine long term trends. Based on the monthly prevalence, it is likely that Chiroteuthis acts as a reservoir for Hochbergia parasites throughout the year. Galiteuthis, Japetella and Taonius show more seasonal dynamics. It may be that the reported seasonality is related to upwelling events or environmental cues promoting dinospore formation (e.g. increasing temperatures)50. Alternatively, cephalopods might be more susceptible to infections in certain months, or have higher resistance in others. Taonius, for example, had a markedly lower parasite load on average than Galiteuthis despite similar prevalence estimates (Tables 1 and 2), potentially indicating some sort of resistance mechanism. More research is warranted to confirm any host resistance and the influence of depth or seasonal effects.The other parasite type found in ROV-collected specimens of Vampyroteuthis infernalis and Gonatus spp. needs further characterization. Although DNA barcoding was able to resolve a short sequence that potentially places it within the phylum Apicomplexa, it appears more likely that this genetic material originated from contamination with a different parasite. Apicomplexa reported in cephalopods generally infect the digestive tract and are morphologically different from the parasites observed here19.In conclusion, our findings highlight the need for further investigation of cephalopods and their gill parasites. Considering that parasites influence biodiversity and that cephalopods form key links in pelagic food webs, future research should be focused at assessing potential effects on cephalopod physiology. For example, if H. moroteuthensis limits longevity or reproduction in common squids like C. calyx, then changes in parasite abundance might result in cascading effects on abundance of Chiroteuthis’ prey, predators and competitors. Additionally, baseline estimates of parasite prevalence are crucial to fully understand whether midwater host-parasite systems are at risk from increasing anthropogenic stressors and how they will change over time. While ROV observations have proven key to estimate prevalence and infection intensity here, trawled specimens continue to be valuable for verification of parasite species and obtaining material for genetic analyses, even if slightly damaged. We therefore recommend combining ROV observations with periodic trawling in future studies, since ROVs may not reveal smaller parasites, early infections or parasites in animals with tissue that is not transparent. More