Ecology

1.Beauchamp, G. Long-distance migrating species of birds travel in larger groups. Biol. Lett. 7, 692–694 (2011).PubMed 
PubMed Central 
Article 

Google Scholar 
2.Watts, H. E., Cornelius, J. M., Fudickar, A. M., Pérez, J. & Ramenofsky, M. Understanding variation in migratory movements: A mechanistic approach. Gen. Comp. Endocrinol. 256, 112–122 (2018).CAS 
PubMed 
Article 

Google Scholar 
3.Amezaga, J. M., Santamaría, L. & Green, A. J. Biotic wetland connectivity—Supporting a new approach for wetland policy. Acta Oecol. 23, 213–222 (2002).ADS 
Article 

Google Scholar 
4.O’Connell, M. Threats to waterbirds and wetlands: Implications for conservation, inventory and research. Wildfowl 51, 1–16 (2000).
Google Scholar 
5.Darrah, S. E. et al. Improvements to the wetland extent trends (WET) index as a tool for monitoring natural and human-made wetlands. Ecol. Ind. 99, 294–298 (2019).Article 

Google Scholar 
6.BirdLife International. Waterbirds are Showing Widespread Declines, Particularly in Asia. http://www.birdlife.org (2017).7.Maron, M. et al. The many meanings of no net loss in environmental policy. Nat. Sustain. 1, 19–27 (2018).Article 

Google Scholar 
8.He, Q. Conservation: ‘No net loss’ of wetland quantity and quality. Curr. Biol. 29, R1070–R1072 (2019).CAS 
PubMed 
Article 

Google Scholar 
9.Mander, L., Marie-Orleach, L. & Elliott, M. The value of wader foraging behaviour study to assess the success of restored intertidal areas. Estuar. Coast. Shelf Sci. 131, 1–5 (2013).ADS 
Article 

Google Scholar 
10.Choi, C., Gan, X., Hua, N., Wang, Y. & Ma, Z. The habitat use and home range analysis of Dunlin (Calidris alpina) in Chongming Dongtan, China and their conservation implications. Wetlands 34, 255–266 (2014).Article 

Google Scholar 
11.Xia, S. et al. Identifying priority sites and gaps for the conservation of migratory waterbirds in China’s coastal wetlands. Biol. Cons. 210, 72–82 (2017).Article 

Google Scholar 
12.Ramsar Sites Information Service. Mai Po Marshes and Inner Deep Bay. https://rsis.ramsar.org/ris/750 (2021).13.Environment Bureau. Hong Kong Biodiversity Strategy Action Plan 2016–2021 (The Government of the Hong Kong Special Administrative Region, 2016).
Google Scholar 
14.Sung, Y. H., Tse, I. W. L. & Yu, Y. T. Population trends of the Black-faced Spoonbill Platalea minor: Analysis of data from international synchronised censuses. Bird Conserv. Int. 28, 157–167. https://doi.org/10.1017/s0959270917000016 (2017).Article 

Google Scholar 
15.Wei, P. et al. Impact of habitat management on waterbirds in a degraded coastal wetland. Mar. Pollut. Bull. 124, 645–652 (2017).CAS 
PubMed 
Article 

Google Scholar 
16.Cheung, S. C. The politics of wetlandscape: Fishery heritage and natural conservation in Hong Kong. Int. J. Herit. Stud. 17, 36–45 (2011).Article 

Google Scholar 
17.AFCD. Agriculture, Fisheries and Conservation Department (AFCD). Marine Fish Culture, Pond Fish Culture and Oyster Culture. https://www.afcd.gov.hk/english/fisheries/fish_aqu/fish_aqu_mpo/fish_aqu_mpo.html.18.Yu, Y. T., Li, C. H., Tse, I. W. L. & Fong, H. N. F. International Black-Faced Spoonbill Census 2019 (The Hong Kong Bird Watching Society, 2019).
Google Scholar 
19.Pickett, E. J. et al. Cryptic and cumulative impacts on the wintering habitat of the endangered black-faced spoonbill (Platalea minor) risk its long-term viability. Environ. Conserv. 45, 147–154. https://doi.org/10.1017/s0376892917000340 (2018).Article 

Google Scholar 
20.The Hong Kong Bird Watching Society. Black-Faced Spoonbill Population Hits Record High. Number in HK Continues to Decline. Protection of Deep Bay in Urgent Need. https://cms.hkbws.org.hk/cms/ (2020).21.Swennen, C. & Yu, Y. T. Food and feeding behavior of the black-faced spoonbill. Waterbirds 28, 19–27. https://doi.org/10.1675/1524-4695(2005)028[0019:Fafbot]2.0.Co;2 (2005).Article 

Google Scholar 
22.Nichols, R. V., Åkesson, M. & Kjellander, P. Diet assessment based on rumen contents: A comparison between DNA metabarcoding and macroscopy. PLoS ONE 11, e0157977 (2016).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
23.Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C. & Willerslev, E. Towards next-generation biodiversity assessment using DNA metabarcoding. Mol. Ecol. 21, 2045–2050 (2012).CAS 
PubMed 
Article 

Google Scholar 
24.Elbrecht, V., Vamos, E. E., Meissner, K., Aroviita, J. & Leese, F. Assessing strengths and weaknesses of DNA metabarcoding-based macroinvertebrate identification for routine stream monitoring. Methods Ecol. Evol. 8, 1265–1275 (2017).Article 

Google Scholar 
25.McInnes, J. C. et al. Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates. Methods Ecol. Evol. 8, 192–202 (2017).Article 

Google Scholar 
26.Thuo, D. et al. Food from faeces: Evaluating the efficacy of scat DNA metabarcoding in dietary analyses. PLoS ONE 14, e0225805 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
27.De Sousa, L., Silva, S. M. & Xavier, R. DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystem. Environ. DNA 1, 199–214 (2019).Article 

Google Scholar 
28.Ueng, Y. T., Perng, J. J., Wang, J. P., Weng, J. H. & Hou, P. C. Diet of the black-faced spoonbill wintering at Chiku Wetland in Southwestern Taiwan. Waterbirds 29, 185–191 (2006).Article 

Google Scholar 
29.Veen, J., Overdijk, O. & Veen, T. The diet of an endemic subspecies of the Eurasian Spoonbill Platalea leucorodia balsaci, breeding at the Banc d’Arguin, Mauritania. Ardea 100, 123–130 (2012).Article 

Google Scholar 
30.Lee, S. Y. The Mangrove Ecosystem of Deep Bay and the Mai Po Marshes, Hong Kong (Hong Kong University Press, 1999).
Google Scholar 
31.Wong, L. C., Corlett, R. T., Young, L. & Lee, J. S. Comparative feeding ecology of Little Egrets on intertidal mudflats in Hong Kong, South China. Waterbirds 23, 214–225 (2000).
Google Scholar 
32.Yang, K. Y., Lee, S. Y. & Williams, G. A. Selective feeding by the mudskipper (Boleophthalmus pectinirostris) on the microalgal assemblage of a tropical mudflat. Mar. Biol. 143, 245–256 (2003).Article 

Google Scholar 
33.Froese, R., Pauly, D. & eds. FishBase. World Wide Web Electronic Publication. https://www.fishbase.org, version 12/2019 (2019).34.Aguilera, E., Ramo, C. & de le Court, C. Food and feeding sites of the Eurasian spoonbill (Platalea leucorodia) in southwestern Spain. Colon. Waterbirds 19, 159–166 (1996).Article 

Google Scholar 
35.Yu, Y. T. & Swennen, C. K. Habitat use of the black-faced spoonbill. Waterbirds 27, 129–135 (2004).Article 

Google Scholar 
36.World Wide Fund Hong Kong. Mai Po Nature Reserve Habitat Management, Monitoring and Research Plan 2013–2018 (World Wide Fund Hong Kong, 2013).
Google Scholar 
37.Sazima, I. Waterbirds catch and release a poisonous fish at a mudflat in southeastern Australia. Ornithol. Res. 27, 126–128 (2019).Article 

Google Scholar 
38.Marchetti, K. & Price, T. Differences in the foraging of juvenile and adult birds: The importance of developmental constraints. Biol. Rev. 64, 51–70 (1989).Article 

Google Scholar 
39.Jiguet, F. Arthropods in diet of Little Bustards Tetrax tetrax during the breeding season in western France. Bird Study 49, 105–109 (2002).Article 

Google Scholar 
40.Birks, J. D. S. & Dunstone, N. Sex-related differences in the diet of the mink Mustela vison. Ecography 8, 245–252 (1985).Article 

Google Scholar 
41.Mata, V. A. et al. Female dietary bias towards large migratory moths in the European free-tailed bat (Tadarida teniotis). Biol. Lett. 12, 20150988 (2016).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
42.Carreiro, A. R. et al. Metabarcoding, stables isotopes, and tracking: Unraveling the trophic ecology of a winter-breeding storm petrel (Hydrobates castro) with a multimethod approach. Mar. Biol. 167, 14 (2020).CAS 
Article 

Google Scholar 
43.Rose, L. M. Sex differences in diet and foraging behavior in white-faced capuchins (Cebus capucinus). Int. J. Primatol. 15, 95–114 (1994).Article 

Google Scholar 
44.Beeston, R., Baines, D. & Richardson, M. Seasonal and between-sex differences in the diet of Black Grouse Tetrao tetrix. Bird Study 52, 276–281 (2005).Article 

Google Scholar 
45.Durell, S. L. V. D., Goss-Custard, J. D. & Caldow, R. W. G. Sex-related differences in diet and feeding method in the oystercatcher Haematopus ostralegus. J. Anim. Ecol. 62, 205–215 (1993).Article 

Google Scholar 
46.Faegre, S. K., Nietmann, L., Hannon, P., Ha, J. C. & Ha, R. R. Age-related differences in diet and foraging behavior of the critically endangered Mariana Crow (Corvus kubaryi), with notes on the predation of Coenobita hermit crabs. J. Ornithol. 161, 149–158 (2020).Article 

Google Scholar 
47.Dunn, E. K. Effect of age on the fishing ability of sandwich terns Sterna sandvicensis. Ibis 114, 360–366 (1972).Article 

Google Scholar 
48.Watson, M. J. & Hatch, J. J. Differences in foraging performance between juvenile and adult roseate terns at a pre-migratory staging area. Waterbirds 22, 463–465 (1999).Article 

Google Scholar 
49.AEC Limited. Ecological Monitoring and Adaptive Management Advice Services for Lok Ma Chau and West Rail Wetlands. Lok Ma Chau Habitat Creation and Management Plan (AEC Limited, 2019).
Google Scholar 
50.The Hong Kong Bird Watching Society. Hong Kong Fishpond Conservation Scheme Project. https://cms.hkbws.org.hk/cms/ (2020).51.Miya, M. et al. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of more than 230 subtropical marine species. R. Soc. Open Sci. 2, 150088 (2015).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
52.Edgar, R. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461. https://doi.org/10.1093/bioinformatics/btq461 (2010).CAS 
Article 
PubMed 

Google Scholar 
53.Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12. https://doi.org/10.14806/ej.17.1.200 (2011).Article 

Google Scholar 
54.Andrews, S., Krueger, F. & Segonds-Pichon, A. FastQC a Quality Control Tool for High Throughput Sequence Data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).55.Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahe, F. VSEARCH: A versatile open source tool for metagenomics. PeerJ 4, e2584. https://doi.org/10.7717/peerj.2584 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
56.Edgar, R. C. & Flyvbjerg, H. Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics (Oxford, England) 31, 3476–3482. https://doi.org/10.1093/bioinformatics/btv401 (2015).CAS 
Article 

Google Scholar 
57.Edgar, R. C. UNOISE2: Improved error-correction for Illumina 16S and ITS amplicon sequencing. BioRxiv https://doi.org/10.1101/081257 (2016).Article 

Google Scholar 
58.Edgar, R. SINTAX: A simple non-Bayesian taxonomy classifier for 16S and ITS sequences. BioRxiv https://doi.org/10.1101/074161 (2016).Article 

Google Scholar 
59.Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
60.Machida, R. J., Leray, M., Ho, S. L. & Knowlton, N. Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples. Sci. Data 4, 170027. https://doi.org/10.1038/sdata.2017.27 (2017).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
61.Sato, K., Miya, M., Fukunaga, T., Sado, T. & Iwasaki, W. MitoFish and MiFish pipeline: A mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding. Mol. Biol. Evol. 35, 1553–1555 (2018).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
62.Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590-596. https://doi.org/10.1093/nar/gks1219 (2013).CAS 
Article 

Google Scholar 
63.Kahlke, T. & Ralph, P. J. BASTA—Taxonomic classification of sequences and sequence bins using last common ancestor estimations. Methods Ecol. Evol. 10, 100–103. https://doi.org/10.1111/2041-210X.13095 (2019).Article 

Google Scholar 
64.Deagle, B. E. et al. Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?. Mol. Ecol. 28, 391–406. https://doi.org/10.1111/mec.14734 (2019).Article 
PubMed 

Google Scholar 
65.Lahti, L. & Shetty, S. Microbiome R Package Version 1.6.0. http://microbiome.github.io (2012).66.Oksanen, J. et al. vegan: Community Ecology Package Version 2.5–6. https://cran.r-project.org, https://github.com/vegandevs/vegan (2019).67.McMurdie, P. J. & Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217. https://doi.org/10.1371/journal.pone.0061217 (2013).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
68.Martinez-Arbizu, P. pairwiseAdonis: Pairwise Multilevel Comparison Using Adonis. R Package Version 0.3. https://github.com/pmartinezarbizu/pairwiseAdonis (2019).69.Steinberger, A. J. Asteinberger9/seq_scripts: Release v1. https://github.com/asteinberger9/seq_scripts (2018).70.ArcGIS. ArcGIS Version 10.7. https://desktop.arcgis.com/en/arcmap/ (2020). More

The surveyed, rainfed commercial soybean fields were spread across the U.S. north-central region (Supplementary Fig. S1 online) with a latitudinal gradient evident for maturity group (MG). The number of fields (n) was distributed evenly across the three years (2014: n = 812, 2015: n = 960, 2016: n = 966). Among the 2738 fields, 833 (or 30.4%) were sprayed with foliar fungicides. Out of the 833 fields sprayed with foliar fungicides, 623 (74.8%) had also been sprayed with foliar insecticides.A t-test estimate of the yield difference between all fields sprayed with foliar fungicides and those which were not was 0.46 t/ha (95% confidence interval [CI] of 0.39 to 0.52 t/ha). When t-tests were applied to fields within TEDs (the 12 TEDs with the most fields), half of the 95% CIs included zero, indicative of possibly no yield increase due to foliar fungicides over unsprayed fields in those TEDs (Supplementary Fig. S2 online). A linear mixed model with random slopes and intercepts for the fungicide effect within TEDs returned an estimated yield gain of 0.33 t/ha due to foliar fungicide use. A simpler model without random slopes for foliar fungicide was a worse fit to the data. Together these basic tests were indicative of heterogenous effects concerning foliar fungicides and yield gain, implying other global (regional) and local (field specific) conditions may be involved as factors.A tuned random forest (RF) model fitted to the entire dataset (all 2738 observations) overpredicted soybean yield at low actual yields, and underpredicted at the high-yield end (Supplementary Fig. S3 online). However, as 99% of the residual values were less than or equal to |0.25 t/ha| which corresponded to less than 7% of the average yield, we proceeded with the interpretation of the fit RF model. The mean predicted soybean yield (global average) was 3.79 t/ha (minimum = 1.13 t/ha, maximum = 6.02 t/ha, standard deviation = 0.81 t/ha, root mean squared error between the observed and predicted yields = 0.1 t/ha).At the global model level, location (latitude; a surrogate for other unmeasured variables) and sowing date (day of year from Jan 01) were the two variables most associated with yield (Fig. 1), consistent with the central importance of early planting to soybean yield5,13. Soil-related properties (pH and organic matter content of the topsoil) were also associated with yield (Fig. 1). Management-related variables such as foliar fungicide, insecticide and herbicide applications were of intermediate importance, and other management variables (row spacing, seed treatments, starter fertilizer) were on the lower end of the importance spectrum in predicting soybean yield (Fig. 1). Insecticide and fungicide seed treatments were poorly associated with soybean yield increases as has been previously shown8,40. The relatively lower importance of row spacing is consistent with previous analyses of this variable from soybean grower data6. The dataset we analyzed did not contain enough observations to include artificial drainage as a variable, which has been shown to influence soybean yield, presumably by allowing earlier sowing14.Figure 1Importance of management-based variables in a random forest model predicting soybean yield. Feature importance was measured as the ratio of model error, after permuting the values of a feature, to the original model error. A predictor was unimportant if the ratio was 1. Points are the medians of the ratio over all the permutations (repeated 20 times). The bars represent the range between the 5% and 95% quantiles. Sowing date was the number of days from Jan 01. Growing degree days and the aridity index were annualized categorical constructs used within the definition of technology extrapolation domains (TEDs). Foliar fungicide or insecticide use, seed treatment use, starter fertilizer use, lime and manure applications were all binary variables for the use (or not) of the practice. Iron deficiency was likewise binary (symptoms were observed or not). Topsoil texture, plant available water holding capacity in the rooting zone, row spacing, and herbicide program were categorical variables with five, seven, five, and four levels, respectively.Full size imageThe strongest pairwise interactions included that between sowing date and latitude. Delayed sowing at higher latitudes decreased yield by about 1 t/ha relative to the highest yielding fields sown early in the more southerly locations (Supplementary Fig. S4 online). Further examination of the interactions showed that the yield difference between sprayed and unsprayed fields increased with later sowing, indicative of a greater fungicide benefit in later-planted fields (Fig. 2). This would seem to conflict with the results of a recent meta-analysis in which soybean yields responded better when foliar fungicides were applied to early-planted fields27, but in that study there was also the confounding effect of higher-than-average rainfall between sowing and the R3 growth stage. With respect to latitude, the global difference in yield between sprayed and unsprayed fields decreased as one moved further north (Fig. 2), suggesting that foliar fungicides were of more benefit when applied to the more southerly located fields, which do tend to experience more or prolonged conditions conducive to foliar diseases than the northern fields22,24.Figure 2Two-way partial dependence plots of the global effects of (i) foliar fungicide use and sowing date (left panel), and (ii) foliar fungicide use and latitude (right panel) on soybean yield. The black plotted curves are the yield differences between fields that were sprayed or not sprayed with foliar fungicides. Smoothed versions of the curves are shown in blue.Full size imageFocusing on model interpretation at the local level, we examined the Shapley φ values (see the “Methods” section for more information) associated with foliar fungicide applications for different subsets (s) and cohorts (c) of fields within the data (see Supplementary Table S1 online). The 1st subset (s1) was comprised of the 20 highest-yielding fields among those sprayed with foliar fungicides (s1c1) and the 20 highest-yielding fields among those which were not sprayed (s1c2) in each of the 12 technology extrapolation domains (TEDs) in the data matrix with adequate numbers of fields for comparisons (see also Supplementary Table S2 online; Supplementary Fig. S5 online maps the field locations within these 12 TEDs). A TED is a region (not necessarily spatially contiguous) with similar biophysical properties41. Predicted yields within these cohorts were mainly above the global average of 3.79 t/ha, except in TED 602303 (Fig. 3), which corresponded to fields in North Dakota (Supplementary Fig. S5). In most cases Shapley φ values for foliar fungicide use exhibited a positive contribution to the yield above the global average. If these cohorts of fields represented high-yielding environments within each TED, then foliar fungicide sprays contributed positively up to 0.3 t/ha in the yield increase above the global average in s1c1. However, among high-yielding fields in s1c2, the penalty for not spraying was less than 0.1 t/ha. This finding supports the contention that fungicide sprays are most worthwhile in high-yielding environments. Supplementary Fig. S6 online complements Fig. 3 by summarizing the Shapley φ values in another visual format. The overall mean predicted yield for the unsprayed (s1c2) fields was slightly higher (by 0.1 t/ha) than that for the sprayed (s1c1) fields (Supplementary Fig. S6 online). This difference may have been driven by the higher variability in yields among the two cohorts (particularly for TEDs 403603, 602303, 403703, and 303603), or underlying differences in other management factors. Also, the number of sprayed fields in each of these four TEDs was at the target sampling boundary of 20 fields per TED (Supplementary Table S2 online).Figure 3Shapley phi values attributed to foliar fungicide use for two cohorts of fields within the 12 technology extrapolation domains (TEDs) with the most fields. Within each TED, the cohorts are the 20 highest-yielding fields among those sprayed with foliar fungicides and the 20 highest-yielding fields among those which were unsprayed.Full size imageThe Shapley φ values for fungicide use were well-separated among the four cohorts of fields of s2 (Fig. 4, Supplementary Table S1 online). The fields within s2 were selected across the entire dataset and not by TED membership. The lowest-yielding fields (s2c2 & s2c4) were all below the global yield average, whereas the converse was true of the highest-yielding fields (s2c1 & s2c3). Among the lowest-yielding fields, foliar fungicides were mainly associated with a positive, but less than 0.2 t/ha, effect on yield (s2c2), and other factors were responsible for dropping a field’s yield to below the global average. Amongst the highest-yielding fields (s2c1), foliar fungicides were associated with between 0.15 and 0.35 t/ha of the yield above the global average. These Shapley φ values for the contribution of foliar fungicides are consistent with estimates of the yield response to foliar fungicides from a meta-analytic perspective27. Given that the individual yields in s2c1 & s2c3 were 1 to 2 t/ha above the global average, other location-driven factors such as early sowing (Fig. 1) were the larger drivers of yield in these cases. However, there was only a negligible or small ( More

1.Lohr, T. A Short Story About the Geological History of the Pamir (University of Mining and Technology Freiberg, 2001).
Google Scholar 
2.Safarov, N. National Strategy and Action Plan on Conservation and Sustainable Use of Biodiversity (Governmental Working Group of the Republic of Tajikistan, 2003).
Google Scholar 
3.Nowak, A., Nowak, S. & Nobis, M. Distribution patterns, ecological characteristic and conservation status of endemic plants of Tadzhikistan: A global hotspot of diversity. J. Nat. Conserv. 19, 296–305 (2011).Article 

Google Scholar 
4.Nowak, A. et al. Red List of vascular plants of Tajikistan: The core area of the Mountains of Central Asia global biodiversity hotspot. Sci. Rep. 10, 6235 (2020).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
5.Bagheri, A., Maassoumi, A. A., Rahiminejad, M. R., Brassac, J. & Blattner, F. R. Molecular phylogeny and divergence times of Astragalus section Hymenostegis: An analysis of a rapidly diversifying species group in Fabaceae. Sci. Rep. 7, 14033 (2017).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
6.Mittermeier, R. A. et al. Hotspots Revisited: Earth’s Biologically Richest and Most Threatened Terrestrial Ecoregions. (Conservation International, 2005).7.Abramowski, U. et al. Pleistocene glaciations of Central Asia: Results from 10Be surface exposure ages of erratic boulders from the Pamir (Tajikistan), and the Alay-Turkestan range (Kyrgyzstan). Quat. Sci. Rev. 25, 1080–1096 (2006).ADS 
Article 

Google Scholar 
8.Cowling, R. M. & Lombard, A. T. Heterogeneity, speciation/extinction history and climate: Explaining regional plant diversity patterns in the Cape Floristic Region. Divers. Distrib. 8, 163–179 (2002).Article 

Google Scholar 
9.Steinbauer, M. J. et al. Topography-driven isolation, speciation and a global increase of endemism with elevation. Glob. Ecol. Biogeogr. 25, 1097–1107 (2016).Article 

Google Scholar 
10.López-Pujol, J., Zhang, F. M., Sun, H. Q., Ying, T. S. & Ge, S. Centres of plant endemism in China: Places for survival or for speciation?. J. Biogeogr. 38, 1267–1280 (2011).Article 

Google Scholar 
11.Chen, X.-Y. & He, F. Speciation and endemism under the model of island biogeography. Ecology 90, 39–45 (2009).PubMed 
Article 
PubMed Central 

Google Scholar 
12.Bruchmann, I. & Hobohm, C. Factors that create and increase endemism. In Endemism in Vascular Plants (ed. Hobohm, C.) 51–68 (Springer, 2014).Chapter 

Google Scholar 
13.Dynesius, M. & Jansson, R. Evolutionary consequences of changes in species’ geographical distributions driven by Milankovitch climate oscillations. Proc. Natl. Acad. Sci. U. S. A. 97, 9115–9120 (2000).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
14.Vetaas, O. R. & Grytnes, J. A. Distribution of vascular plant species richness and endemic richness along the Himalayan elevation gradient in Nepal. Glob. Ecol. Biogeogr. 11, 291–301 (2002).Article 

Google Scholar 
15.Mucina, L. & Wardell-Johnson, G. W. Landscape age and soil fertility, climatic stability, and fire regime predictability: Beyond the OCBIL framework. Plant Soil 341, 1–23 (2011).CAS 
Article 

Google Scholar 
16.Tzedakis, P. C. Museums and cradles of Mediterranean biodiversity. J. Biogeogr. 36, 1033–1034 (2009).Article 

Google Scholar 
17.Kreft, H. & Jetz, W. Global patterns and determinants of vascular plant diversity. Proc. Natl. Acad. Sci. U. S. A. 104, 5925–5930 (2007).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
18.Noroozi, J., Pauli, H., Grabherr, G. & Breckle, S. W. The subnival-nival vascular plant species of Iran: A unique high-mountain flora and its threat from climate warming. Biodivers. Conserv. 20, 1319–1338 (2011).Article 

Google Scholar 
19.Pauli, H., Gottfried, M., Dirnböck, T., Dullinger, S. & Grabherr, G. Assessing the long-term dynamics of endemic plants at summit habitats. In Alpine Biodiversity in Europe (eds Nagy, L. et al.) 195–207 (Springer, 2003).Chapter 

Google Scholar 
20.Agakhanjanz, O. & Breckle, S. W. Origin and evolution of the mountain flora in middle asia and neighbouring mountain regions. In Arctic and Alpine Biodiversity: Patterns, Causes and Ecosystem Consequences Ecological Studies (Analysis and Synthesis) Vol. 113 (eds Chapin, F. S. & Körner, C.) 63–80 (Springer, 1995).
Google Scholar 
21.Noroozi, J., Akhani, H. & Willner, W. Phytosociological and ecological study of the high alpine vegetation of Tuchal mountains (Central Alborz, Iran). Phytocoenologia 40, 293–321 (2010).Article 

Google Scholar 
22.Goldblatt, P. & Manning, J. C. Plant Diversity of the Cape Region of Southern Africa. Ann. Mo. Bot. Gard. 89, 281–302 (2002).Article 

Google Scholar 
23.Bond, P. & Goldblatt, P. Plants of the Cape fora: a descriptive catalogue. J. S Afr. Bot. Suppl. 13, 1–455 (1984).
Google Scholar 
24.Panda, R. M., Behera, M. D., Roy, P. S. & Biradar, C. Energy determines broad pattern of plant distribution in Western Himalaya. Ecol. Evol. 7, 10850–10860 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
25.Nowak, A., Nowak, S., Nobis, M. & Nobis, A. A report on the conservation status of segetal weeds in Tajikistan. Weed Res. 54, 635–648 (2014).Article 

Google Scholar 
26.Nobis, M., Gudkova, P. D., Nowak, A., Sawicki, J. & Nobis, A. A synopsis of the genus Stipa (Poaceae) in Middle Asia, including a key to species identyfication, an annoted checklist and phytogeographical analyses. Ann. Missouri Bot. Gard. 105, 1–63 (2020).Article 

Google Scholar 
27.Thompson, J. N. The Geographic Mosaic of coevolution (Chicago Univ Press, 2005).Book 

Google Scholar 
28.Thompson, J. N. Four central points about coevolution. Evol. Educ. Outreach 3, 7–13 (2010).Article 

Google Scholar 
29.Thrall, P. H., Hochberg, M. E., Burdon, J. J. & Bever, J. D. Coevolution of symbiotic mutualists and parasites in a community context. Trends Ecol. Evol. 22, 120–126 (2007).PubMed 
Article 
PubMed Central 

Google Scholar 
30.Navarro-Fernández, C. M., Aroca, R. & Barea, J. M. Influence of arbuscular mycorrhizal fungi and water regime on the development of endemic Thymus species in dolomitic soils. Appl. Soil Ecol. 48, 31–37 (2011).Article 

Google Scholar 
31.Zubek, S., Nobis, M., Błaszkowski, J., Mleczko, P. & Nowak, A. Fungal root endophyte associations of plants endemic to the Pamir Alay Mountains of Central Asia. Symbiosis 54, 139–149 (2011).PubMed 
PubMed Central 
Article 

Google Scholar 
32.Lambers, H., Chapin, F. S. III. & Pons, T. L. Plant Physiological Ecology (Springer, 2008).Book 

Google Scholar 
33.Lambers, H., Brundrett, M. C., Raven, J. A. & Hopper, S. D. Plant mineral nutrition in ancient landscapes: High plant species diversity on infertile soils is linked to functional diversity for nutritional strategies. Plant Soil 334, 11–31 (2010).CAS 
Article 

Google Scholar 
34.Hopper, S. D. OCBIL theory: Towards an integrated understanding of the evolution, ecology and conservation of biodiversity on old, climatically buffered, infertile landscapes. Plant Soil 322, 49–86 (2009).CAS 
Article 

Google Scholar 
35.Ellison, A. M. & Gotelli, N. J. Energetics and the evolution of carnivorous plants – Darwin’s ‘most wonderful plants in the world’. J. Exp. Bot. 60, 19–42 (2009).CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
36.Merckx, V., Bidartondo, M. I. & Hynson, N. A. Myco-heterotrophy: When fungi host plants. Ann. Bot. 104, 1255–1261 (2009).PubMed 
PubMed Central 
Article 

Google Scholar 
37.Huang, B. H. et al. Differential genetic responses to the stress revealed the mutation-order adaptive divergence between two sympatric ginger species. BMC Genom. 19, 692 (2018).Article 
CAS 

Google Scholar 
38.Turner, J. R. G., Gatehouse, C. M. & Core, C. A. Does solar energy control organic diversity? Butterflies moths and the British climate. Oikos 48, 195–205 (1987).Article 

Google Scholar 
39.Körner, C. Why are there global gradients in species richness? Mountains might hold the answer. Trends Ecol. Evol. 15, 513–514 (2000).Article 

Google Scholar 
40.Makhmadaliev, B., Novikov, V., Kayumov, A., Karimov, U. & Perdomo, M. National Action Plan of the Republic of Tajikistan for Climate Change Mitigation. (Tajik Met Service, 2003).41.Nedzvedskiy, A. P. Geologicheskoe stroenye. In Atlas Tajikskoi SSR (eds Narzikulov, I. K. & Stanyukovich, K. W.) 14–15 (Akademia Nauk Tajikskoi SSR, 1968).
Google Scholar 
42.Latipova, W. A. Kolichestvo osadkov. In Atlas Tajikskoi SSR (eds Narzikulov, I. K. & Stanyukovich, K. W.) 68–69 (Akademia Nauk Tajikskoi SSR, 1968).
Google Scholar 
43.Narzikulov, I. K. & Stanyukovich, K. W. Atlas Tajikskoi SSR. (Akademia Nauk Tajikskoi SSR, 1968).44.Rivas-Martínez, S., Rivas-Sáenz, S. & Penas, Á. Worldwide bioclimatic classification system. Glob. Geobot. 1, 1–638 (2011).
Google Scholar 
45.Djamali, M., Brewer, S., Breckle, S. W. & Jackson, S. T. Climatic determinism in phytogeographic regionalization: A test from the Irano-Turanian region, SW and Central Asia. Flora Morphol. Distrib. Funct. Ecol. Plants 207, 237–249 (2012).
Google Scholar 
46.Ovchinnikov, P. N. Flora Tadzhikskoi SSR. T. I, Paprotnikoobraznye – Zlaki. (Izdatelstvo Akademii Nauk SSSR, 1957).47.Ovchinnikov, P. N. Flora Tadzhikskoi SSR. T. II, Osokovye—Orkhidnye. (Izdatelstvo Akademii Nauk SSSR, 1963).48.Ovchinnikov, P. N. Flora Tadzhikskoi SSR. T. III, Opekhovye—Gvozdichnye. (Izdatelstvo Nauka, 1968).49.Ovchinnikov, P. N. Flora Tadzhikskoi SSR. T. IV, Rogolistnikovye—Rozotsvetnye. (Izdatelstvo Nauka, 1975).50.Ovchinnikov, P. N. Flora Tadzhikskoi SSR. T. V, Krestotsvetne—Bobovye. (Izdatelstvo Nauka, 1978).51.Ovchinnikov, P. N. Flora Tadzhikskoi SSR. T. VI, Bobovye (rod Astragal). (Izdatelstvo Nauka, 1981).52.Kochkareva, T. F. Flora Tadzhikskoi SSR. T. VIII. Kermekovye—Podorozhnikovye. (Izdatelstvo Nauka, 1986).53.Kinzikaeva, G. K. Flora Tadzhikskoi SSR. T. IX. Marenovye – Slozhnotsvetnye. (Izdatelstvo Nauka, 1988).54.Rasulova, M. R. Flora Tadzhikskoi SSR. T. X, Slozhnotsvetnye. (Izdatelstvo Nauka, 1991).55.Grubov, V. I. Schlussbetrachtung zum Florenwerk ‘Rastenija Central’noj Azii’ [Die Pflanzen Zentralasiens] und die Begründung der Eigenständigkeit der mongolischen Flora. Feddes Repert. 121, 7–13 (2010).Article 

Google Scholar 
56.Jarvis, A., Reuter, H. I., Nelson, A. & Guevara, E. Hole-filled SRTM for the globe Version 4, available from the CGIAR-CSI SRTM 90m Database (http://srtm.csi.cgiar.org). (2008).57.Karger, D. N. et al. Climatologies at high resolution for the earth’s land surface areas. Sci. Data 4, 170122 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
58.Zuur, A. F., Ieno, E. N. & Erik, H. W. G. Meesters A Beginner’s Guide to R (Springer, 2009).MATH 
Book 

Google Scholar 
59.Dormann, C. F. et al. Collinearity: A review of methods to deal with it and a simulation study evaluating their performance. Ecography 36, 027–046 (2013).Article 

Google Scholar 
60.Wood, S. N. Generalized Additive Models An Introduction with R (Chapman and Hall/CRC, 2017).MATH 
Book 

Google Scholar 
61.Therneau, T. & Atkinson, B. rpart: Recursive Partitioning and Regression Trees. R package version 4.1-13 (2018).62.De’ath, G. & Fabricius, K. E. Classification and regression trees: A powerful yet simple technique for ecological data analysis. Ecology 81, 3178–3192 (2000).Article 

Google Scholar  More

1.Otto, S. P. Adaptation, speciation and extinction in the Anthropocene. Proc. R. Soc. B 285, 20182047 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
2.Moritz, C. & Agudo, R. The future of species under climate change: Resilience or decline?. Science 341, 504–508 (2013).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
3.Parmesan, C. & Hanley, M. E. Plants and climate change: Complexities and surprises. Ann. Bot. 116, 849–864 (2015).PubMed 
PubMed Central 
Article 

Google Scholar 
4.Soltis, P. S. & Soltis, D. E. The role of genetic and genomic attributes in the success of polyploids. Proc. Natl. Acad. Sci. U.S.A. 97, 7051–7057 (2000).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
5.Barker, M. S., Husband, B. C. & Chris Pires, J. Spreading winge and flying high: The evolutionary importance of polyploidy after a century of study. Am. J. Bot. 103, 1139–1145 (2016).CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
6.Van De Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017).PubMed 
Article 
CAS 
PubMed Central 

Google Scholar 
7.Madlung, A. Polyploidy and its effect on evolutionary success: Old questions revisited with new tools. Heredity (Edinb) 110, 99–104 (2013).CAS 
Article 

Google Scholar 
8.Soltis, D. E., Visger, C. J., Marchant, B. D. & Soltis, P. S. Polyploidy: Pitfalls and paths to a paradigm. Am. J. Bot. 103, 1146–1166 (2016).PubMed 
Article 
PubMed Central 

Google Scholar 
9.Ramsey, J. Polyploidy and ecological adaptation in wild yarrow. Proc. Natl. Acad. Sci. U.S.A. 108, 7096–7101 (2011).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
10.Oswald, B. P. & Nuismer, S. L. Neopolyploidy and diversification in Heuchera grossulariifolia. Evolution 65, 1667–1679 (2011).PubMed 
PubMed Central 
Article 

Google Scholar 
11.Kolář, F., Čertner, M., Suda, J., Schönswetter, P. & Husband, B. C. Mixed-ploidy species: Progress and opportunities in polyploid research. Trends Plant Sci. https://doi.org/10.1016/j.tplants.2017.09.011 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
12.Fowler, N. L. & Levin, D. A. Critical factors in the establishment of allopolyploids. Am. J. Bot. 103, 1236–1251 (2016).PubMed 
Article 
PubMed Central 

Google Scholar 
13.Husband, B. C., Baldwin, S. J. & Suda, J. The incidence of polyploidy in natural plant populations: Major patterns and evolutionary processes. In Plant Genome Diversity 2: Physical Structure, Behaviour and Evolution of Plant Genomes (eds Leitch, I. et al.) 255–276 (Springer, 2013).Chapter 

Google Scholar 
14.Te Beest, M. et al. The more the better? The role of polyploidy in facilitating plant invasions. Ann. Bot. 109, 19–45 (2012).Article 

Google Scholar 
15.Watanabe, K. The cytogeography of the genus Eupatorium (Compositae)—A review. Plant Species Biol. 1, 99–116 (1986).CAS 
Article 

Google Scholar 
16.Novak, S. J., Soltis, D. E. & Soltis, P. S. Ownbey’s Tragopogons: 40 years later. Am. J. Bot. 78, 1586–1600 (1991).Article 

Google Scholar 
17.Van Dijk, P. & Bakx-Schotman, T. Chloroplast DNA phylogeography and cytotype geography in autopolyploid Plantago media. Mol. Ecol. 6, 345–352 (1997).Article 

Google Scholar 
18.Martin, S. L. & Husband, B. C. Influence of phylogeny and ploidy on species ranges of North American angiosperms. J. Ecol. 97, 913–922 (2009).Article 

Google Scholar 
19.Suda, J., Kron, P., Husband, B. C. & Trávníček, P. Flow cytometry and ploidy: Applications in plant systematics, ecology and evolutionary biology. in Flow Cytometry with Plant Cells 103–130 (Wiley, 2007). https://doi.org/10.1002/9783527610921.ch5.20.Ramsey, J. & Ramsey, T. S. Ecological studies of polyploidy in the 100 years following its discovery. Philos. Trans. R. Soc. Lond. B Biol. Sci. 369, 1–76 (2014).Article 

Google Scholar 
21.Goldblatt, P. Polyploidy in angiosperms: Monocotyledons. In Polyploidy. Basic Life Sciences Vol. 13 (ed. Lewis, W. H.) 219–239 (Springer, 1980).
Google Scholar 
22.Levy, A. A. & Feldman, M. The impact of polyploidy on grass genome evolution. Plant Physiol. 130, 1587–1593 (2002).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
23.Kellogg, A. Flowering Plants Monocots Poaceae Vol. 13 (Springer, 2015).
Google Scholar 
24.Estep, M. C. et al. Allopolyploidy, diversification, and the Miocene grassland expansion. Proc. Natl. Acad. Sci. 111, 15149–15154 (2014).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
25.Minaya, M. et al. Contrasting dispersal histories of broad- and fine-leaved temperate Loliinae grasses: Range expansion, founder events, and the roles of distance and barriers. J. Biogeogr. 44, 1980–1993 (2017).Article 

Google Scholar 
26.Torrecilla, P. & Catalán, P. Phylogeny of broad-leaved and fine-leaved Festuca lineages (Poaceae) based on nuclear ITS sequences. Syst. Bot. 27, 241–251 (2002).
Google Scholar 
27.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 (2008).28.Meusel, H., Jäger, E. & Weinert, E. Vergleichende Chorologie der Zentral-europäischen Flora (G. Fischer, 1965).
Google Scholar 
29.Kiedrzyński, M., Zielińska, K. M., Kiedrzyńska, E. & Jakubowska-Gabara, J. Regional climate and geology affecting habitat availability for a relict plant in a plain landscape: The case of Festuca amethystina L. in Poland. Plant Ecol. Divers. 8, 331–341 (2015).Article 

Google Scholar 
30.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, 1359–1370 (2017).Article 

Google Scholar 
31.Petrova, A. & Kozuharov, S. Citotaxonomicno proucvane na balgarski vidove ot roda Festuca L. in IV Nacionalna Konferencija Po Botanika 1 (ed. Trudova) 16–23 (1987).32.Stählin, A. Morphologische und zytologische Untersuchungen an Gramineen. Wiss. Arch. Landwirtschaft., Abt. A, Pflanzenbau 1, 330–398 (1929).33.Wittmann, H. & Strobl, W. Beitrag zur Kenntnis von Festuca amethystina L. im Bundesland Salzburg. Florist. Mitt. Salzburg 9, 3–8 (1984).34.La Sorte, F. A. & Jetz, W. Projected range contractions of montane biodiversity under global warming. Proc. R. Soc. B Biol. Sci. 277, 3401–3410 (2010).Article 

Google Scholar 
35.Elsen, P. R. & Tingley, M. W. Global mountain topography and the fate of montane species under climate change. Nat. Clim. Change 5, 772–776 (2015).ADS 
Article 

Google Scholar 
36.Šmarda, P., Müller, J., Vraná, J. & Kočí, K. Ploidy level variability of some Central European fescues (Festuca subg. Festuca, Poaceae). Biologia 60, 1–6 (2005).
Google Scholar 
37.Rewicz, A. et al. Morphometric traits in the fine-leaved fescues depend on ploidy level: The case of Festuca amethystina L. PeerJ 2018, e5576 (2018).Article 

Google Scholar 
38.Roleček, J., Dřevojan, P. & Šmarda, P. First record of Festuca amethystina L. from the Transylvanian Basin (Romania). Contrib. Bot. 54, 91–97 (2019).Article 

Google Scholar 
39.Phillips, S. J. & Dudík, M. Modeling of species distribution with Maxent: New extensions and a comprehensive evaluation. Ecograpy 31, 161–175 (2008).Article 

Google Scholar 
40.Segraves, K. A., Thompson, J. N., Soltis, P. S. & Soltis, D. E. Multiple origins of polyploidy and the geographic structure of Heuchera grossulariifolia. Mol. Ecol. 8, 253–262 (1999).Article 

Google Scholar 
41.Levin, D. A. Minority cytotype exclusion in local plant populations. TAXON vol. 24. https://eurekamag.com/pdf/000/000139096.pdf (1975).42.Pils, G. Systematics, distribution, and karyology of the Festuca violacea Group (Poaceae) in the Eastern Alps. Plant Syst. Evol. 136, 73–124 (1980).Article 

Google Scholar 
43.Stebbins, G. L. Chromosomal Evolution in Higher Plants (Addison-Wesley, 1971).
Google Scholar 
44.Stutz, H. C. & Sanderson, S. C. Evolutionary studies in Atriplex: Chromosome races of A. confertifolia (shadscale). Am. J. Bot. 70, 1536–1547 (1983).Article 

Google Scholar 
45.Husband, B. C. & Schemske, D. W. Cytotype distribution at a diploid-tetraploid contact zone in Chamerion (Epilobium) angustifolium (Onagraceae). Am. J. Bot. 85, 1688–1694 (1998).CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
46.Hardy, O. J., Vanderhoeven, S., De Loose, M. & Meerts, P. Ecological, morphological and allozymic differentiation between diploid and tetraploid knapweeds (Centaurea jacea) from a contact zone in the Belgian Ardennes. New Phytol. 146, 281–290 (2000).CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
47.Gauthier, P., Lumaret, R. & Bédécarrats, A. Genetic variation and gene flow in Alpine diploid and tetraploid populations of Lotus (L. alpinus (DC) Schleicher/L. corniculatus L.). I. Insights from morphological and allozyme markers. Heredity (Edinb) 80, 683–693 (1998).CAS 
Article 

Google Scholar 
48.Schönswetter, P. et al. Sympatric diploid and hexaploid cytotypes of Senecio carniolicus (Asteraceae) in the Eastern Alps are separated along an altitudinal gradient. J. Plant Res. 120, 721–725 (2007).PubMed 
Article 
PubMed Central 

Google Scholar 
49.Petit, C., Bretagnolle, F. & Felber, F. Evolutionary consequences of diploid-polyploid hybrid zones in wild species. Trends Ecol. Evol. 14, 306–311 (1999).CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
50.Chumová, Z., Krejčíková, J., Mandáková, T., Suda, J. & Trávníček, P. Evolutionary and taxonomic implications of variation in nuclear genome size: Lesson from the grass genus Anthoxanthum (Poaceae). PLoS One 10, e0133748 (2015).Article 
CAS 

Google Scholar 
51.Marchant, D. B., Soltis, D. E. & Soltis, P. S. Patterns of abiotic niche shifts in allopolyploids relative to their progenitors. New Phytol. 212, 708–718 (2016).Article 
CAS 

Google Scholar 
52.Arrigo, N. et al. Is hybridization driving the evolution of climatic niche in Alyssum montanum. Am. J. Bot. 103, 1348–1357 (2016).PubMed 
Article 
PubMed Central 

Google Scholar 
53.Laport, R. G., Minckley, R. L. & Ramsey, J. Ecological distributions, phenological isolation, and genetic structure in sympatric and parapatric populations of the Larrea tridentata polyploid complex. Am. J. Bot. 103, 1358–1374 (2016).CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
54.Mosquin, T. Evidence for autopolyploidy in Epilobium angustifolium (Onagraceae). Evolution (N. Y.) 21, 713–719 (1967).
Google Scholar 
55.Szafer, W. The mountain element in the flora of Polish Plain. Rozpr. Wydz. Mat. PAU Ser. 3 Dział B 69, 83–196 (1930).
Google Scholar 
56.Kiedrzyński, M., Zielińska, K. M., Kiedrzyńska, E. & Rewicz, A. Refugial debate: On small sites according to their function and capacity. Evol. Ecol. 31, 815–827 (2017).Article 

Google Scholar 
57.Babić, V. P. et al. Temperature and other microclimate conditions in the oak forests on Fruška Gora (Serbia). Therm. Sci. 19, S415–S425 (2015).Article 

Google Scholar 
58.Jakubowska-Gabara, J. Decline of Potentillo albae-Quercetum Libb. 1933 phytocoenoses in Poland. Vegetatio 124, 45–59 (1996).Article 

Google Scholar 
59.Roleček, J. Formalized classification of thermophilous oak forests in the Czech Republic: What brings the Cocktail method?. Preslia 79, 1–21 (2007).
Google Scholar 
60.Indreica, A. Festuca amethystina in the sessile oak forests from upper basin of Olt River. Contrib. Bot. 42, 11–18 (2007).
Google Scholar 
61.Jakubowska-Gabara, J. Festuca amethystina L. In The Polish Red Book of Plants. Pteridophytes and Vascular Plants (eds Kaźmierczakowa, R. et al.) 616–618 (Institute of Nature Conservation PAS, 2014).
Google Scholar 
62.Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G. & Jarvis, A. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25, 1965–1978 (2005).Article 

Google Scholar 
63.Fick, S. E. & Hijmans, R. J. WorldClim 2: New 1-km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302–4315 (2017).Article 

Google Scholar 
64.Wei, T. & Simko, V. R package ‘corrplot’: Visualization of a Correlation Matrix (2017).65.Šmilauer, P. & Lepš, J. Multivariate Analysis of Ecological Data Using CANOCO 5 (Cambridge University Press, 2014). https://doi.org/10.1017/CBO9781139627061.Book 
MATH 

Google Scholar 
66.Wilke, C. O. Ridgeline Plots in ‘ggplot2’. https://wilkelab.org/ggridges/index.html (2021).67.Phillips, S. J., Anderson, R. P. & Schapire, R. E. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190, 231–259 (2006).Article 

Google Scholar 
68.Phillips, S. J., Anderson, R. P., Dudík, M., Schapire, R. E. & Blair, M. E. Opening the black box: An open-source release of Maxent. Ecography (Cop.) 40, 887–893 (2017).Article 

Google Scholar 
69.Warren, D. L. & Seifert, S. Ecological niche modeling in Maxent: The importance of model complexity and the performance of model selection criteria. Ecol. Soc. Am. 21, 335–342 (2011).
Google Scholar 
70.Elith, J. et al. A statistical explanation of MaxEnt for ecologists. Divers. Distrib. 17, 43–57 (2011).Article 

Google Scholar 
71.Warren, D. L., Glor, R. E. & Turelli, M. ENMTools: A toolbox for comparative studies of environmental niche models. Ecography (Cop.) 33, 607–611 (2010).
Google Scholar 
72.Liu, C., Berry, P. M., Dawson, T. P. & Pearson, R. G. Selecting thresholds of occurrence in the prediction of species distributions. Ecography (Cop.) 28, 385–393 (2005).Article 

Google Scholar  More

1.Chesson, P. Mechanisms of maintenance of species diversity. Annu. Rev. Ecol. Syst. 31, 343–366 (2000).Article 

Google Scholar 
2.Wright, J. S. Plant diversity in tropical forests: A review of mechanisms of species coexistence. Oecologia 130, 1–14 (2002).ADS 
PubMed 
Article 

Google Scholar 
3.Janzen, D. H. Herbivores and the number of tree species in tropical forests. Am. Nat. 104, 501–528 (1970).Article 

Google Scholar 
4.Connell, J. On the role of natural enemies in preventing competitive exclusion in some marine animals and rain forest trees. Dyn. Popul. 298, 312 (1971).
Google Scholar 
5.Terborgh, J. W. Toward a trophic theory of species diversity. PNAS 112, 11415–11422 (2015).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
6.Johnson, D. J., Beaulieu, W. T., Bever, J. D. & Clay, K. Conspecific negative density dependence and forest diversity. Science 336, 904–907 (2012).ADS 
CAS 
PubMed 
Article 

Google Scholar 
7.LaManna, J. A. et al. Plant diversity increases with the strength of negative density dependence at the global scale. Science 356, 1389–1392 (2017).ADS 
CAS 
PubMed 
Article 

Google Scholar 
8.Chisholm, R. A. & Muller-Landau, H. C. A theoretical model linking interspecific variation in density dependence to species abundances. Theor. Ecol. 4, 241–253 (2011).Article 

Google Scholar 
9.Mangan, S. A. et al. Negative plant–soil feedback predicts tree-species relative abundance in a tropical forest. Nature 466, 752–755 (2010).ADS 
CAS 
PubMed 
Article 

Google Scholar 
10.Chisholm, R. A. & Fung, T. Comment on “Plant diversity increases with the strength of negative density dependence at the global scale”. Science 360, eaar4685 (2018).PubMed 
Article 
CAS 

Google Scholar 
11.Hülsmann, L. & Hartig, F. Comment on “Plant diversity increases with the strength of negative density dependence at the global scale”. Science 360, eaar2435 (2018).PubMed 
Article 
CAS 

Google Scholar 
12.Detto, M., Visser, M. D., Wright, S. J. & Pacala, S. W. Bias in the detection of negative density dependence in plant communities. Ecol. Lett. 22, 1923–1939 (2019).PubMed 
Article 

Google Scholar 
13.LaManna, J. A. et al. Response to Comment on “Plant diversity increases with the strength of negative density dependence at the global scale”. Science 360, eaar3824 (2018).PubMed 
Article 
CAS 

Google Scholar 
14.LaManna, J. A. et al. Response to Comment on “Plant diversity increases with the strength of negative density dependence at the global scale”. Science 360, eaar5245 (2018).PubMed 
Article 
CAS 

Google Scholar 
15.LaManna, J. A., Mangan, S. A. & Myers, J. A. Conspecific negative density dependence and why its study should not be abandoned. Ecosphere 12, e03322 (2021).Article 

Google Scholar 
16.Gaston, K. J. Global patterns in biodiversity. Nature 405, 220–227 (2000).CAS 
PubMed 
Article 

Google Scholar 
17.Mittelbach, G. G. et al. Evolution and the latitudinal diversity gradient: Speciation, extinction and biogeography. Ecol. Lett. 10, 315–331 (2007).PubMed 
Article 

Google Scholar 
18.Janzen, D. H. Why mountain passes are higher in the tropics. Am. Nat. 101, 233–249 (1967).Article 

Google Scholar 
19.Ricklefs, R. E. & He, F. Region effects influence local tree species diversity. PNAS 113, 674–679 (2016).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
20.Comita, L. S. et al. Testing predictions of the Janzen-Connell hypothesis: A meta-analysis of experimental evidence for distance- and density-dependent seed and seedling survival. J. Ecol. 102, 845–856 (2014).PubMed 
PubMed Central 
Article 

Google Scholar 
21.Currie, D. J. Energy and large-scale patterns of animal- and plant-species richness. Am. Nat. 137, 27–49 (1991).Article 

Google Scholar 
22.Grosso, S. D. et al. Global potential net primary production predicted from vegetation class, precipitation, and temperature. Ecology 89, 2117–2126 (2008).PubMed 
Article 

Google Scholar 
23.Chase, J. M. Stochastic Community Assembly Causes Higher Biodiversity in More Productive Environments. Science 27, (2010).24.O’Brien, E. M. Climatic gradients in woody plant species richness: Towards an explanation based on an analysis of Southern Africa’s woody flora. J. Biogeography 20, 181–198 (1993).Article 

Google Scholar 
25.McCain, C. M. & Grytnes, J.-A. Elevational Gradients in Species Richness. In eLS (American Cancer Society, 2010).26.Barry, R. G. Mountain Weather and Climate (Cambridge University Press, 2008).Book 

Google Scholar 
27.LaManna, J. A., Walton, M. L., Turner, B. L. & Myers, J. A. Negative density dependence is stronger in resource-rich environments and diversifies communities when stronger for common but not rare species. Ecol. Lett. 19, 657–667 (2016).PubMed 
Article 

Google Scholar 
28.Zhu, K., Woodall, C. W., Monteiro, J. V. D. & Clark, J. S. Prevalence and strength of density-dependent tree recruitment. Ecology 96, 2319–2327 (2015).PubMed 
Article 

Google Scholar 
29.Yao, J. et al. Abiotic niche partitioning and negative density dependence across multiple life stages in a temperate forest in northeastern China. J. Ecol. 108, 1299–1310 (2020).Article 

Google Scholar 
30.Leigh, E. G. et al. Why do some tropical forests have so many species of trees?. Biotropica 36, 447–473 (2004).
Google Scholar 
31.Terborgh, J. Enemies maintain hyperdiverse tropical forests. Am. Nat. 179, 303–314 (2012).PubMed 
Article 

Google Scholar 
32.Altman, J. et al. Linking spatiotemporal disturbance history with tree regeneration and diversity in an old-growth forest in northern Japan. PPEES 21, 1–13 (2016).
Google Scholar 
33.Kubota, Y., Hirao, T., Fujii, S., Shiono, T. & Kusumoto, B. Beta diversity of woody plants in the Japanese archipelago: The roles of geohistorical and ecological processes. J. Biogeogr. 41, 1267–1276 (2014).Article 

Google Scholar 
34.Mori, A. S. Local and biogeographic determinants and stochasticity of tree population demography. J. Ecol. 107, 1276–1287 (2019).Article 

Google Scholar 
35.Oohata, S. Distribution of tree species along the temperature gradient in the Japan archipelago (ii).: Life form and species distribution. Jap. J. Ecol. 40, 71–84 (1990).ADS 

Google Scholar 
36.Kira, T. A Climatological Interpretation of Japanese Vegetation Zones 21–30 (Springer, 1977).
Google Scholar 
37.Mori, A. S. Environmental controls on the causes and functional consequences of tree species diversity. J. Ecol. 106, 113–125 (2018).Article 

Google Scholar 
38.Suzuki, S. N., Ishihara, M. I. & Hidaka, A. Regional-scale directional changes in abundance of tree species along a temperature gradient in Japan. Glob. Chan. Biol. 21, 3436–3444 (2015).ADS 
Article 

Google Scholar 
39.Hara, M. Analysis of seedling banks of a climax beech forest: Ecological importance of seedling sprouts. Vegetatio 71, 67–74 (1987).
Google Scholar 
40.Homma, K. Effects of snow pressure on growth form and life history of tree species in Japanese beech forest. J. Veg. Sci. 8, 781–788 (1997).Article 

Google Scholar 
41.Gansert, D. Treelines of the Japanese Alps—altitudinal distribution and species composition under contrasting winter climates. Flora 199, 143–156 (2004).Article 

Google Scholar 
42.Hukusima, T. et al. New phytosociological classification of beech forests in Japan. Jpn. J. Ecol. 45, 79–98 (1995).
Google Scholar 
43.Matsui, T. et al. Probability distributions, vulnerability and sensitivity in Fagus crenata forests following predicted climate changes in Japan. J. Veg. Sci. 15, 605–614 (2004).Article 

Google Scholar 
44.Johnson, D. J., Condit, R., Hubbell, S. P. & Comita, L. S. Abiotic niche partitioning and negative density dependence drive tree seedling survival in a tropical forest. Proc. R. Soc. B 284, 20172210 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
45.Ishihara, M. I. et al. Forest stand structure, composition, and dynamics in 34 sites over Japan. Ecol. Res. 26, 1007–1008 (2011).Article 

Google Scholar 
46.Law, R. et al. Ecological information from spatial patterns of plants: Insights from point process theory. J. Ecol. 97, 616–628 (2009).Article 

Google Scholar 
47.Wright, S. J. et al. Reproductive size thresholds in tropical trees: Variation among individuals, species and forests. J. Trop. Ecol. 21, 307–315 (2005).Article 

Google Scholar 
48.Zhu, Y., Comita, L. S., Hubbell, S. P. & Ma, K. Conspecific and phylogenetic density-dependent survival differs across life stages in a tropical forest. J. Ecol. 103, 957–966 (2015).Article 

Google Scholar 
49.Ripley, B. D. Spatial point pattern analysis in ecology. In Develoments in Numerical Ecology (eds Legendre, P. & Legendre, L.) 407–429 (Springer, 1987).Chapter 

Google Scholar 
50.Wiegand, T. & Moloney, K. A. Handbook of Spatial Point-Pattern Analysis in Ecology (CRC Press, 2013).Book 

Google Scholar 
51.Loosmore, N. B. & Ford, E. D. Statistical inference using the G or K point pattern spatial statistics. Ecology 87, 1925–1931 (2006).PubMed 
Article 

Google Scholar 
52.R Core Team. R: A Language and Environment for Statistical Computing (2020).53.Baddeley, A. & Turner, R. spatstat: An R Package for Analyzing Spatial Point Patterns. J. Stat. Soft. 12, 1–42 (2005).Article 

Google Scholar 
54.Wills, C., Condit, R., Foster, R. B. & Hubbell, S. P. Strong density- and diversity-related effects help to maintain tree species diversity in a neotropical forest. PNAS 94, 1252–1257 (1997).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
55.Givnish, T. J. On the causes of gradients in tropical tree diversity. J. Ecol. 87, 193–210 (1999).Article 

Google Scholar 
56.Fibich, P., Vítová, A. & Lepš, J. Interaction between habitat limitation and dispersal limitation is modulated by species life history and external conditions: A stochastic matrix model approach. Comm. Ecol. 19, 9–20 (2018).Article 

Google Scholar 
57.Miyawaki, A. A vegetation ecological view of the Japanese archipelago. Bull. Inst. Environ. Sci. Technol. Yokohama Natl. Univ. 11, 85–101 (1984).
Google Scholar 
58.Mori, A. S. et al. Community assembly processes shape an altitudinal gradient of forest biodiversity. Glo. Ecol. Biogeogr. 22, 878–888 (2013).Article 

Google Scholar 
59.Grime, J. P. Plant Strategies, Vegetation Processes, and Ecosystem Properties (Wiley, 2001).
Google Scholar 
60.Brown, C., Law, R., Illian, J. B. & Burslem, D. F. R. P. Linking ecological processes with spatial and non-spatial patterns in plant communities. J. Ecol. 99, 1402–1414 (2011).Article 

Google Scholar 
61.Bastias, C. C. et al. Species richness influences the spatial distribution of trees in European forests. Oikos 129, 380–390 (2020).Article 

Google Scholar 
62.Hülsmann, L., Chisholm, R. A. & Hartig, F. Is variation in conspecific negative density dependence driving tree diversity patterns at large scales?. Trends Ecol. Evol. 36, 151–163 (2021).PubMed 
Article 

Google Scholar 
63.Damgaard, C. & Weiner, J. It’s about time: A critique of macroecological inferences concerning plant competition. Trends Ecol. Evol. 32, 86–87 (2017).PubMed 
Article 

Google Scholar 
64.Murata, I. et al. Effects of sika deer (Cervus nippon) and dwarf bamboo (Sasamorpha borealis) on seedling emergence and survival in cool-temperate mixed forests in the Kyushu Mountains. J. For. Res. 14, 296–301 (2009).Article 

Google Scholar 
65.Ackerly, D. D. et al. The geography of climate change: Implications for conservation biogeography. Divers. Distrib. 16, 476–487 (2010).Article 

Google Scholar  More

Samples collectionThree sampling campaigns were carried out at the two sample sites (A and B) on the coast of north-western Sicily (Fig. 1a) chosen for this study. The main features of the sites and sampling details are summarized in Table S1 (Supplementary Information). A total of 90 specimens of sea urchins Paracentrotus lividus (45 specimen per each site), 30 l of seawater (15 per site), 40 samples (20 per site) of sea grass Posidonia oceanica (less than 5 cm leaf fragments, according to the institutional and national ethical guidelines) were collected and analyzed together with 30 l of brackish water from site B (15 l from each creek).Figure 1Map of the sampling site. (a) Geographic area, (b) bathymetric chart and (c) relative distance between sample sites; (d, e) close ups of sampling sites. (Images obtained by courtesy of Google Earth Pro and map.openseamap.org).Full size imageThe samplings activity was authorized by the Capitaneria di Porto of Palermo with protocol number: 0029430. In the absence of data about PFOA contamination in the most recent report about chemical contamination in the coastal region subjected to this study31, the choice of sample sites was based on supposedly different status of pollution based on the site position or proximity to human activities (e.g. restaurants, pipeline, sewages, etc.).Site A (see Fig. 1d), was chosen assuming a lower state of pollution based on its position in proximity to Capo Zafferano, at the northern extremity of S. Elia’s bay, with an average depth of 11 m and rocky seabed (see Fig. 1b and Supplementary Information: Table S1). Conversely, Site B (see Fig. 1e was chosen in the same coastal area (only 4.7 km away from Site A) assuming a higher state of pollution due to its position located on the southern side of Solanto promontory, nearby a pipeline and the mouths of two small creeks from inland, with a shallow (3 m) sandy seabed and where a bathing prohibition order is in place32 (see Fig. 1b, c and Supplementary Information: Table S1).The biodistribution of PFOA in the various matrices was evaluated by analyzing sea urchin’s coelomocytes (CC) (90 samples) and coelomic fluid (CF) (90 samples), as well as gonads (G) (63 samples from 32 sea urchins collected in site A and 31 sea urchins collected in site B), or mixed organs (MIX) (27 samples from 13 sea urchins collected in site A and 14 sea urchins collected in site B) consisting of a homogenized mixture of urchin’s inner matrices when gonads were not developed enough for sampling. Due to their mutually exclusive nature the latter two datasets (G and MIX) were merged and labelled as “Gonads or Mixed organs” (GoM) for statistical analysis and graphical representations that needed a uniform dataset of 45 items per site. Further details on the collection of matrices and their labelling are described in the Supplementary Information.The size of the sea urchins (horizontal diameter without spines) ranged between 30 and 51 mm indicating specimen that have lived in their respective site approximately from 3 to 5 years25.PFOA extraction and analysisMaterials, equipment and software are described in the Supplementary Information.PFOA extraction procedures were adapted33 to the type of matrix to be analyzed. Recovery percentages (R %) were checked per each batch of analyses by spiking blank samples with different amounts of PFOA analytical standard before the extraction procedure33.Spiked samples underwent the same extraction procedure of unspiked samples and the percentage of recovery R was calculated according to Eq. 1, where Cspike is the known concentration of spiked PFOA, Dspiked is the instrumental (LC–MS) analytical response of the spiked sample (i.e. the “detected” concentration), Dunspiked is the analytical response of the unspiked sample. R was then used in Eq. 2 to calculate the actual values, [PFOA], of PFOA concentrations in unspiked analyzed samples.$$ {text{R}} = 100 times left( {{text{D}}_{{{text{spiked}}}} – {text{D}}_{{{text{unspiked}}}} } right)/{text{C}}_{{{text{spike}}}} $$
(1)
$$ left[ {{text{PFOA}}} right] = 100 times {text{D}}_{{{text{unspiked}}}} /{text{R}} $$
(2)
With the exception of [PFOA]seawater and [PFOA]creek, which are expressed as nanograms per liter (ppt), all other PFOA concentrations are expressed in nanograms per gram of matrix (ppb).The PFOA standard was used for calibration before each batch of analyses and a linear response (R2  > 0.99) was recorded in the concentration range from 0.1 to 1000 ppb. The RSDs on three replicates were below 10%. LOD (0.1 ppb) and LOQ (1.0 ppb) were quantified by IUPAC method. LC–MS analyses were performed in the negative ion-monitoring mode (see Supplementary Information).For the analysis of P. lividus specimens, an estimate of the total PFOA concentration, [PFOA]TOT in ng/g, in each sea urchin has been calculated considering the sampled weight (W) in grams of each matrix (Eq. 3):$$ left[ {{text{PFOA}}} right]_{{{text{TOT}}}} = left( {{text{W}}_{{{text{CF}}}} left[ {{text{PFOA}}} right]_{{{text{CF}}}} + {text{W}}_{{{text{CC}}}} left[ {{text{PFOA}}} right]_{{{text{CC}}}} + {text{W}}_{{{text{GoM}}}} left[ {{text{PFOA}}} right]_{{{text{GoM}}}} } right)/left( {{text{W}}_{{{text{CF}}}} + {text{W}}_{{{text{CC}}}} + {text{W}}_{{{text{GoM}}}} } right) $$
(3)
Water analysisDuring each one of the 3 sampling campaigns, 2 samples of seawater (5 l from Site A and 5 l from site B) and 2 samples of brackish water (5 l from each creek mouths in site B) were collected for a total of 6 seawater samples and 6 brackish water samples.Samples were checked for the presence of PFOA by solid phase extraction (SPE) (see Supplementary Information) followed by LC–MS analysis34.The percentage of recovery, calculated according to Eq. 1, was R = 120%. [PFOA]seawater and [PFOA]creek concentrations (ng/L) were determined from analytical data according to Eq. 2.
Posidonia oceanica analysisA total of 40 samples of leaves were collected from different individuals of P. oceanica (20 samples from site A and 20 samples from site B). Each sample was cut in tiny pieces and homogenized using an agate mortar and pestle, weighed (0.5 g) and transferred to a glass tube for extraction (see Supplementary Information).The percentage of recovery, calculated according to Eq. 1, was R = 70%. [PFOA]P. oceanica concentrations (ng/g) were determined from analytical data according to Eq. 2.Coelomocytes and coelomic fluid analysisThe coelomic fluid, containing also the coelomocyte population, was taken from all the ninety collected specimens (45 per site) by inserting an ultrathin and sharp needle (32G 0.26 mm × 12 mm) of a 1 mL syringe through the peristomal membrane35. All samples were centrifuged at 4 °C and 1500 rpm for 5 min in a 5804R refrigerated centrifuge (Eppendorf, Germany) thus separating the supernatant coelomic fluid (CF) from the coelomocytes (CC). CF and CC were then weighed and placed in different glass tubes for subsequent PFOA extractions (see Supplementary Information).The percentage of recovery, calculated according to Eq. 1, was R = 28% for CF and R = 68% for CC. [PFOA]CF and [PFOA]CC concentrations (ng/g) were determined from analytical data according to Eq. 2.Gonads analysisThe extraction of PFOA from 63 samples of gonads (32 from Site A and 31 from Site B) was performed with LC–MS grade methanol following the same procedure used for extraction from CF and CC (5 mL for samples greater than 0.5 g samples; 2.5 mL for samples between 0.1 g and 0.5 g). In case of undetected PFOA (considered as zero-values in graphics and statistical data treatment), analyses were repeated for confirmation on concentrated sample extracts.Twenty spiked samples were prepared from the most abundant samples of gonads (10 spiked samples per site), by adding 25 µL of an aqueous 1 mg/L stock solution of PFOA to 0.25 g of gonads samples. The percentage of PFOA recovery from gonads, calculated according to Eq. 1, was R = 73%. [PFOA]G concentrations (ng/g) were determined from analytical data according to Eq. 2.Mixed organs analysisIn 27 specimens of sea urchins (13 from Site A and 14 from Site B), the developmental status was not sufficient to collect at least 0.1 g of gonad sample. For these individuals, organs remaining after CF and CC collection, mainly intestine and undeveloped gonads, were mixed together and extracted similarly to the other matrices.Spiked samples were prepared by adding 25 µL of an aqueous 1 mg/L stock solution of PFOA to 0.25 g of mixed organs (MIX) samples. The percentage of PFOA recovery from MIX, calculated according to Eq. 1, was R = 20%. [PFOA]MIX concentrations (ng/g) were determined from analytical data according to Eq. 2.Statistical analyses and graphical data representationThe distribution of PFOA concentrations in all the sampled matrices from collected sea urchins is graphically represented by box and jitter plot (Fig. 2) where the 25–75 percentiles are drawn using a box; minimum and maximum are shown at the end of the thin lines (whiskers), while the median is marked as a horizontal line in the boxfitting. Statistical tests and linear fittings were used to evaluate data significance and correlations (see Supplementary Information).Figure 2Box and jitter plot showing the concentrations of PFOA found in the Coelomic Fluid (CF) Coelomocytes (CC) and Gonads or Mixed organs (GoM), as well as the total PFOA concentration (TOT), in 45 specimens of P. lividus collected from Site A (left side) and in 45 specimens of P. lividus collected from Site B (right side).Full size imageA permutational multivariate analysis of variance PERMANOVA36 was performed to evaluate the differences in the PFOA concentrations between the two groups of sea urchins collected from site A and site B. The experimental design comprised of one factor (Site) two levels (fixed and orthogonal) and four variables corresponding to the concentrations of PFOA in each type of sample analysed (coelomocytes, coelomic fluid, gonad or mixed organs) including the estimated total PFOA concentration. Each term in the analysis was tested by 999 random permutations.Finally, Principal Component Analysis (PCA) (see Supplementary Information: PCA tables and graphs) was performed on a dataset, containing five variables. Specifically sea urchin’s size and PFOA concentrations in each type of sample (CF, CC, and GoM) as well as in the entire sea urchin (TOT), to verify the multivariate nature of data in a relatively small number of dimensions, thus limiting the loss of information. More

1.Chittka, L. & Raine, N. E. Recognition of flowers by pollinators. Curr. Opin. Plant Biol. 9, 428–435 (2006).PubMed 
Article 
PubMed Central 

Google Scholar 
2.Raguso, R. A. Flowers as sensory billboards: Progress towards an integrated understanding of floral advertisement. Curr. Opin. Plant Biol. 7, 434–440 (2004).PubMed 
Article 
PubMed Central 

Google Scholar 
3.Goulson, D., Stout, J. C. & Hawson, S. A. Can flower constancy in nectaring butterflies be explained by Darwin’s interference hypothesis?. Oecologia 112, 225–231 (1997).ADS 
CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
4.Goulson, D. & Wright, N. P. Flower constancy in the hoverflies Episyrphus balteatus (Degeer) and Syrphus ribesii (L.) (Syrphidae). Behav. Ecol. 9, 213–219 (1998).Article 

Google Scholar 
5.Von Arx, M., Goyret, J., Davidowitz, G. & Raguso, R. A. Floral humidity as a reliable sensory cue for profitability assessment by nectar-foraging hawkmoths. Proc. Natl. Acad. Sci. 109, 9471–9476 (2012).ADS 
Article 

Google Scholar 
6.Leonard, A. S., Dornhaus, A. & Papaj, D. R. Forget-me-not: Complex floral displays, inter-signal interactions, and pollinator cognition. Curr. Zool. 57, 215–224 (2011).Article 

Google Scholar 
7.Vaknin, Y., Gan-Mor, S., Bechar, A., Ronen, B. & Eisikowitch, D. The role of electrostatic forces in pollination. Plant Syst. Evol. 222, 133–142. https://doi.org/10.1007/bf00984099 (2000).Article 

Google Scholar 
8.Bowker, G. E. & Crenshaw, H. C. Electrostatic forces in wind-pollination—Part 2: Simulations of pollen capture. Atmos. Environ. 41, 1596–1603 (2007).ADS 
CAS 
Article 

Google Scholar 
9.Erickson, E. Surface electric potentials on worker honeybees leaving and entering the hive. J. Apic. Res. 14, 141–147 (1975).Article 

Google Scholar 
10.Edwards, D. Electrostatic charges on insects due to contact with different substrates. Can. J. Zool. 40, 579–584 (1962).Article 

Google Scholar 
11.Vaknin, Y., Gan-Mor, S., Bechar, A., Ronen, B. & Eisikowitch, D. Pollen and Pollination 133–142 (Springer, 2000).Book 

Google Scholar 
12.Eskov, E. & Sapozhnikov, A. Mechanism of generation and perception of electric fields by honey bees. Biofizika 21, 1097–1102 (1976).CAS 

Google Scholar 
13.Clarke, D., Whitney, H., Sutton, G. & Robert, D. Detection and learning of floral electric fields by bumblebees. Science 340, 66–69 (2013).ADS 
CAS 
PubMed 
Article 

Google Scholar 
14.Bowker, G. E. & Crenshaw, H. C. Electrostatic forces in wind-pollination—Part 1: Measurement of the electrostatic charge on pollen. Atmos. Environ. 41, 1587–1595 (2007).ADS 
CAS 
Article 

Google Scholar 
15.Gan-Mor, S., Schwartz, Y., Bechar, A., Eisikowitch, D. & Manor, G. Relevance of electrostatic forces in natural and artificial pollination. Can. Agric. Eng. 37, 189–194 (1995).
Google Scholar 
16.Colin, M., Richard, D. & Chauzy, S. Measurement of electric charges carried by bees: Evidence of biological variations. J. Bioelectr. 10, 17–32 (1991).Article 

Google Scholar 
17.Pinillos, V. & Cuevas, J. Artificial pollination in tree crop production. Horticult. Rev. 2, 2 (2008).
Google Scholar 
18.Corbet, S. A., Beament, J. & Eisikowitch, D. Are electrostatic forces involved in pollen transfer?. Plant Cell Environ. 5, 125–129 (1982).Article 

Google Scholar 
19.Inouye, D. W., Larson, B. M., Ssymank, A. & Kevan, P. G. Flies and flowers III: Ecology of foraging and pollination. J. Pollin. Ecol. 16, 115–133 (2015).Article 

Google Scholar 
20.Kanstrup, J. & Olesen, J. M. Plant-flower visitor interactions in a neotropical rain forest canopy: Community structure and generalisation level. The Scand. Assoc. Pollin. Ecol. honours knut Fægri 2, 33–42 (2000).
Google Scholar 
21.Orford, K. A., Vaughan, I. P. & Memmott, J. The forgotten flies: The importance of non-syrphid Diptera as pollinators. Proc. R. Soc. B Biol. Sci. 282, 20142934 (2015).Article 

Google Scholar 
22.Sakurai, A. & Takahashi, K. Flowering phenology and reproduction of the Solidago virgaurea L. complex along an elevational gradient on M t N orikura, central Japan. Plant Sp. Biol. 32, 270–278 (2017).Article 

Google Scholar 
23.Forup, M. L., Henson, K. S., Craze, P. G. & Memmott, J. The restoration of ecological interactions: Plant–pollinator networks on ancient and restored heathlands. J. Appl. Ecol. 45, 742–752 (2008).Article 

Google Scholar 
24.Solomon, M. & Kendall, D. Pollination by the syrphid fly, Eristalis tenax. (1970).25.Kendall, D., Wilson, D., Guttridge, C. & Anderson, H. Testing Eristalis as a pollinator of covered crops. Long Ashton Res. Stn. Rep. 1971, 120–121 (1971).
Google Scholar 
26.Ohsawa, R. & Namai, H. The effect of insect pollinators on pollination and seed setting in Brassica campestris cv. Nozawana and Brassica juncea cv Kikarashina. Jpn. J. Breed. 37, 453–463 (1987).ADS 
Article 

Google Scholar 
27.Jauker, F. & Wolters, V. Hover flies are efficient pollinators of oilseed rape. Oecologia 156, 819–823 (2008).ADS 
PubMed 
Article 

Google Scholar 
28.Rader, R. et al. Alternative pollinator taxa are equally efficient but not as effective as the honeybee in a mass flowering crop. J. Appl. Ecol. 46, 1080–1087 (2009).Article 

Google Scholar 
29.Kalmijn, A. J. The electric sense of sharks and rays. J. Exp. Biol. 55, 371–383 (1971).CAS 
PubMed 
Article 

Google Scholar 
30.Clarke, D., Morley, E. & Robert, D. The bee, the flower, and the electric field: Electric ecology and aerial electroreception. J. Comp. Physiol. A. 203, 737–748 (2017).Article 

Google Scholar 
31.Greggers, U. et al. Reception and learning of electric fields in bees. Proc. R. Soc. B Biol. Sci. 280, 20130528 (2013).Article 

Google Scholar 
32.Casas, J. & Dangles, O. Physical ecology of fluid flow sensing in arthropods. Annu. Rev. Entomol. 55, 505–520 (2010).CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
33.Tautz, J. & Rostás, M. Honeybee buzz attenuates plant damage by caterpillars. Curr. Biol. 18, R1125–R1126 (2008).CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
34.Bathellier, B., Steinmann, T., Barth, F. G. & Casas, J. Air motion sensing hairs of arthropods detect high frequencies at near-maximal mechanical efficiency. J. R. Soc. Interface 9, 1131–1143 (2011).PubMed 
PubMed Central 
Article 

Google Scholar 
35.Newland, P. L. et al. Static electric field detection and behavioural avoidance in cockroaches. J. Exp. Biol. 211, 3682–3690 (2008).PubMed 
Article 

Google Scholar 
36.Sutton, G. P., Clarke, D., Morley, E. L. & Robert, D. Mechanosensory hairs in bumblebees (Bombus terrestris) detect weak electric fields. Proc. Natl. Acad. Sci. 113, 7261–7265 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
37.Wędzony, M. & Filek, M. Changes of electric potential in pistils of Petunia hybrida Hort. and Brassica napus L. during pollination. Acta Physiol. Plantarum 20, 291–297 (1998).Article 

Google Scholar 
38.Stout, J. C. & Goulson, D. The use of conspecific and interspecific scent marks by foraging bumblebees and honeybees. Anim. Behav. 62, 183–189 (2001).Article 

Google Scholar 
39.Weiss, M. R. Floral color change: A widespread functional convergence. Am. J. Bot. 82, 167–185 (1995).Article 

Google Scholar 
40.Waser, N. M. & Price, M. V. Pollinator behaviour and natural selection for flower colour in Delphinium nelsonii. Nature 302, 422 (1983).ADS 
Article 

Google Scholar 
41.Shimozawa, T., Murakami, J. & Kumagai, T. Sensors and Sensing in Biology and Engineering 145–157 (Springer, 2003).Book 

Google Scholar 
42.Khan, S. & Hanif, H. Diversity and fauna of hoverflies (Syrphidae) in Chakwal, Pakistan. Int. J of Zool. Stud. 1, 22–23 (2016).
Google Scholar 
43.Khan, S. A. & Hanif, H. First record and redescription of Cheilosia albipila syrphid flies from Punjab, Pakistan. Int. J. Zool. Res. 1, 2 (2016).
Google Scholar 
44.Shehzad, A. et al. Faunistic study of hover flies (Diptera: Syrphidae) of Pakistan. Orient. Insects 51, 197–220 (2017).Article 

Google Scholar 
45.Nicholas, S., Thyselius, M., Holden, M. & Nordström, K. Rearing and long-term maintenance of eristalis tenax hoverflies for research studies. JoVE https://doi.org/10.3791/57711 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
46.Gilbert, F. S. Foraging ecology of hoverflies: Morphology of the mouthparts in relation to feeding on nectar and pollen in some urban species. Ecol. Entomol. 2, 2 (1981).
Google Scholar 
47.Nicholas, S., Thyselius, M., Holden, M. & Nordström, K. Rearing and long-term maintenance of Eristalis tenax hoverflies for research studies. J. Vis. Exp. JoVE 2, 2 (2018).
Google Scholar 
48.Hogg, B. N., Bugg, R. L. & Daane, K. M. Attractiveness of common insectary and harvestable floral resources to beneficial insects. Biol. Control 56, 76–84 (2011).Article 

Google Scholar 
49.McGonigle, D. F., Jackson, C. W. & Davidson, J. L. Triboelectrification of houseflies (Musca domestica L.) walking on synthetic dielectric surfaces. J. Electrostat. 54, 167–177 (2002).Article 

Google Scholar 
50.Koh, K., Montgomery, C., Clarke, D., Morley, E. & Robert, D. in Journal of Physics: Conference Series. 012001 (IOP Publishing).51.Rycroft, M., Israelsson, S. & Price, C. The global atmospheric electric circuit, solar activity and climate change. J. Atmos. Solar Terr. Phys. 62, 1563–1576 (2000).ADS 
CAS 
Article 

Google Scholar 
52.Whitney, H. M., Dyer, A., Chittka, L., Rands, S. A. & Glover, B. J. The interaction of temperature and sucrose concentration on foraging preferences in bumblebees. Naturwissenschaften 95, 845–850 (2008).ADS 
CAS 
PubMed 
Article 

Google Scholar 
53.Stanković, B. & Davies, E. Both action potentials and variation potentials induce proteinase inhibitor gene expression in tomato. FEBS Lett. 390, 275–279 (1996).PubMed 
Article 

Google Scholar  More

1.Pucciarelli, S. et al. Molecular cold-adaptation of protein function and gene regulation: the case for comparative genomic analyses in marine ciliated protozoa. Mar Genomics 2, 57–66. https://doi.org/10.1016/j.margen.2009.03.008 (2009).Article 
PubMed 

Google Scholar 
2.Pucciarelli, S., Marziale, F., Di Giuseppe, G., Barchetta, S. & Miceli, C. Ribosomal cold-adaptation: characterization of the genes encoding the acidic ribosomal P0 and P2 proteins from the Antarctic ciliate Euplotes focardii. Gene 360, 103–110. https://doi.org/10.1016/j.gene.2005.06.007 (2005).CAS 
Article 
PubMed 

Google Scholar 
3.Pucciarelli, S. & Miceli, C. Characterization of the cold-adapted alpha-tubulin from the psychrophilic ciliate Euplotes focardii. Extremophiles 6, 385–389. https://doi.org/10.1007/s00792-002-0268-5 (2002).CAS 
Article 
PubMed 

Google Scholar 
4.Yang, G. et al. Characterization and comparative analysis of psychrophilic and mesophilic alpha-amylases from Euplotes species: a contribution to the understanding of enzyme thermal adaptation. Biochem Biophys Res Commun 438, 715–720. https://doi.org/10.1016/j.bbrc.2013.07.113 (2013).CAS 
Article 
PubMed 

Google Scholar 
5.Prescott, D. M. The DNA of ciliated protozoa. Microbiol Rev 58, 233–267 (1994).CAS 
Article 

Google Scholar 
6.Mollenbeck, M. & Klobutcher, L. A. De novo telomere addition to spacer sequences prior to their developmental degradation in Euplotes crassus. Nucleic Acids Res 30, 523–531 (2002).Article 

Google Scholar 
7.Swart, E. C. et al. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS Biol 11, e1001473. https://doi.org/10.1371/journal.pbio.1001473 (2013).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
8.Heyse, G., Jonsson, F., Chang, W. J. & Lipps, H. J. RNA-dependent control of gene amplification. Proc Natl Acad Sci U S A 107, 22134–22139. https://doi.org/10.1073/pnas.1009284107 (2010).ADS 
Article 
PubMed 
PubMed Central 

Google Scholar 
9.Nowacki, M., Haye, J. E., Fang, W., Vijayan, V. & Landweber, L. F. RNA-mediated epigenetic regulation of DNA copy number. Proc Natl Acad Sci U S A 107, 22140–22144. https://doi.org/10.1073/pnas.1012236107 (2010).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
10.Dayeh, V. R. et al. Comparing a ciliate and a fish cell line for their sensitivity to several classes of toxicants by the novel application of multiwell filter plates to Tetrahymena. Res Microbiol 156, 93–103. https://doi.org/10.1016/j.resmic.2004.08.005 (2005).ADS 
CAS 
Article 
PubMed 

Google Scholar 
11.Detrich, H. W., 3rd, Parker, S. K., Williams, R. C., Jr., Nogales, E. & Downing, K. H. Cold adaptation of microtubule assembly and dynamics. Structural interpretation of primary sequence changes present in the alpha- and beta-tubulins of Antarctic fishes. J Biol Chem 275, 37038–37047. https://doi.org/10.1074/jbc.M005699200 (2000).12.Manka, S. W. & Moores, C. A. Microtubule structure by cryo-EM: snapshots of dynamic instability. Essays Biochem 62, 737–751. https://doi.org/10.1042/EBC20180031 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
13.Inclan, Y. F. & Nogales, E. Structural models for the self-assembly and microtubule interactions of gamma-, delta- and epsilon-tubulin. J Cell Sci 114, 413–422 (2001).CAS 
Article 

Google Scholar 
14.Chiappori, F. et al. Structural thermal adaptation of beta-tubulins from the Antarctic psychrophilic protozoan Euplotes focardii. Proteins 80, 1154–1166. https://doi.org/10.1002/prot.24016 (2012).CAS 
Article 
PubMed 

Google Scholar 
15.Marziale, F. et al. Different roles of two gamma-tubulin isotypes in the cytoskeleton of the Antarctic ciliate Euplotes focardii: remodelling of interaction surfaces may enhance microtubule nucleation at low temperature. FEBS J 275, 5367–5382. https://doi.org/10.1111/j.1742-4658.2008.06666.x (2008).CAS 
Article 
PubMed 

Google Scholar 
16.Pucciarelli, S., Miceli, C. & Melki, R. Heterologous expression and folding analysis of a beta-tubulin isotype from the Antarctic ciliate Euplotes focardii. Eur J Biochem 269, 6271–6277 (2002).CAS 
Article 

Google Scholar 
17.Gromer, S., Urig, S. & Becker, K. The thioredoxin system–from science to clinic. Med Res Rev 24, 40–89. https://doi.org/10.1002/med.10051 (2004).CAS 
Article 
PubMed 

Google Scholar 
18.Birben, E., Sahiner, U. M., Sackesen, C., Erzurum, S. & Kalayci, O. Oxidative stress and antioxidant defense. World Allergy Organ J 5, 9–19. https://doi.org/10.1097/WOX.0b013e3182439613 (2012).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
19.Alin, P., Danielson, U. H. & Mannervik, B. 4-Hydroxyalk-2-enals are substrates for glutathione transferase. FEBS Lett 179, 267–270 (1985).CAS 
Article 

Google Scholar 
20.Juganson, K. et al. Mechanisms of toxic action of silver nanoparticles in the protozoan Tetrahymena thermophila: From gene expression to phenotypic events. Environ Pollut 225, 481–489. https://doi.org/10.1016/j.envpol.2017.03.013 (2017).CAS 
Article 
PubMed 

Google Scholar 
21.Clark, M. S., Fraser, K. P. & Peck, L. S. Antarctic marine molluscs do have an HSP70 heat shock response. Cell Stress Chaperones 13, 39–49. https://doi.org/10.1007/s12192-008-0014-8 (2008).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
22.Tomanek, L. The heat-shock response: its variation, regulation and ecological importance in intertidal gastropods (genus Tegula). Integr Comp Biol 42, 797–807. https://doi.org/10.1093/icb/42.4.797 (2002).CAS 
Article 
PubMed 

Google Scholar 
23.Morimoto, R. I., Kline, M. P., Bimston, D. N. & Cotto, J. J. The heat-shock response: regulation and function of heat-shock proteins and molecular chaperones. Essays Biochem 32, 17–29 (1997).CAS 
PubMed 

Google Scholar 
24.Gonzalez-Aravena, M. et al. HSP70 from the Antarctic sea urchin Sterechinus neumayeri: molecular characterization and expression in response to heat stress. Biol Res 51, 8. https://doi.org/10.1186/s40659-018-0156-9 (2018).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
25.Hofmann, G. E., Buckley, B. A., Airaksinen, S., Keen, J. E. & Somero, G. N. Heat-shock protein expression is absent in the antarctic fish Trematomus bernacchii (family Nototheniidae). J Exp Biol 203, 2331–2339 (2000).CAS 
Article 

Google Scholar 
26.La Terza, A., Papa, G., Miceli, C. & Luporini, P. Divergence between two Antarctic species of the ciliate Euplotes, E. focardii and E. nobilii, in the expression of heat-shock protein 70 genes. Mol Ecol 10, 1061–1067. https://doi.org/10.1046/j.1365-294x.2001.01242.x (2001).27.Klobutcher, L. A. & Farabaugh, P. J. Shifty ciliates: frequent programmed translational frameshifting in euplotids. Cell 111, 763–766 (2002).CAS 
Article 

Google Scholar 
28.Lobanov, A. V. et al. Position-dependent termination and widespread obligatory frameshifting in Euplotes translation. Nat Struct Mol Biol 24, 61–68. https://doi.org/10.1038/nsmb.3330 (2017).CAS 
Article 
PubMed 

Google Scholar 
29.Coordinators, N. R. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 45, D12–D17. https://doi.org/10.1093/nar/gkw1071 (2017).CAS 
Article 

Google Scholar 
30.Pucciarelli, S. et al. Microbial consortium associated with the antarctic marine ciliate Euplotes focardii: an investigation from genomic sequences. Microb Ecol 70, 484–497. https://doi.org/10.1007/s00248-015-0568-9 (2015).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
31.Klobutcher, L. A. et al. Conserved DNA sequences adjacent to chromosome fragmentation and telomere addition sites in Euplotes crassus. Nucleic Acids Res 26, 4230–4240. https://doi.org/10.1093/nar/26.18.4230 (1998).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
32.Aeschlimann, S. H. et al. The draft assembly of the radically organized Stylonychia lemnae macronuclear genome. Genome Biol Evol 6, 1707–1723. https://doi.org/10.1093/gbe/evu139 (2014).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
33.Swart, E. C. (personal communication).34.Cavalcanti, A. R., Stover, N. A., Orecchia, L., Doak, T. G. & Landweber, L. F. Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project. Chromosoma 113, 69–76. https://doi.org/10.1007/s00412-004-0295-3 (2004).CAS 
Article 
PubMed 

Google Scholar 
35.Lozupone, C. A., Knight, R. D. & Landweber, L. F. The molecular basis of nuclear genetic code change in ciliates. Curr Biol 11, 65–74. https://doi.org/10.1016/s0960-9822(01)00028-8 (2001).CAS 
Article 
PubMed 

Google Scholar 
36.Salas-Marco, J. et al. Distinct paths to stop codon reassignment by the variant-code organisms Tetrahymena and Euplotes. Mol Cell Biol 26, 438–447. https://doi.org/10.1128/MCB.26.2.438-447.2006 (2006).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
37.Klobutcher, L. A. Sequencing of random Euplotes crassus macronuclear genes supports a high frequency of +1 translational frameshifting. Eukaryot Cell 4, 2098–2105. https://doi.org/10.1128/EC.4.12.2098-2105.2005 (2005).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
38.Wang, R., Xiong, J., Wang, W., Miao, W. & Liang, A. High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus. Sci Rep 6, 21139. https://doi.org/10.1038/srep21139 (2016).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
39.Turanov, A. A. et al. Genetic code supports targeted insertion of two amino acids by one codon. Science 323, 259–261. https://doi.org/10.1126/science.1164748 (2009).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
40.Maehigashi, T., Dunkle, J. A., Miles, S. J. & Dunham, C. M. Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops. Proc Natl Acad Sci U S A 111, 12740–12745. https://doi.org/10.1073/pnas.1409436111 (2014).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
41.Miceli, C., Ballarini, P., Di Giuseppe, G., Valbonesi, A. & Luporini, P. Identification of the tubulin gene family and sequence determination of one beta-tubulin gene in a cold-poikilotherm protozoan, the antarctic ciliate Euplotes focardii. J Eukaryot Microbiol 41, 420–427. https://doi.org/10.1111/j.1550-7408.1994.tb06100.x (1994).CAS 
Article 
PubMed 

Google Scholar 
42.Ricci, F. et al. The sub-chromosomic macronuclear pheromone genes of the ciliate Euplotes raikovi: comparative structural analysis and insights into the mechanism of expression. J Eukaryot Microbiol 66, 376–384. https://doi.org/10.1111/jeu.12677 (2019).CAS 
Article 
PubMed 

Google Scholar 
43.Wang, R., Liu, J., Di Giuseppe, G. & Liang, A. UAA and UAG may Encode Amino Acid in Cathepsin B Gene of Euplotes octocarinatus. J Eukaryot Microbiol 67, 144–149. https://doi.org/10.1111/jeu.12755 (2020).CAS 
Article 
PubMed 

Google Scholar 
44.Heaphy, S. M., Mariotti, M., Gladyshev, V. N., Atkins, J. F. & Baranov, P. V. Novel ciliate genetic code variants including the reassignment of all three stop codons to sense codons in condylostoma magnum. Mol Biol Evol 33, 2885–2889. https://doi.org/10.1093/molbev/msw166 (2016).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
45.Swart, E. C., Serra, V., Petroni, G. & Nowacki, M. Genetic codes with no dedicated stop codon: context-dependent translation termination. Cell 166, 691–702. https://doi.org/10.1016/j.cell.2016.06.020 (2016).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
46.Roy, B., Leszyk, J. D., Mangus, D. A. & Jacobson, A. Nonsense suppression by near-cognate tRNAs employs alternative base pairing at codon positions 1 and 3. Proc Natl Acad Sci U S A 112, 3038–3043. https://doi.org/10.1073/pnas.1424127112 (2015).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
47.Dunn, J. G., Foo, C. K., Belletier, N. G., Gavis, E. R. & Weissman, J. S. Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. Elife 2, e01179. https://doi.org/10.7554/eLife.01179 (2013).Article 
PubMed 
PubMed Central 

Google Scholar 
48.Frechin, M., Duchene, A. M. & Becker, H. D. Translating organellar glutamine codons: a case by case scenario?. RNA Biol 6, 31–34. https://doi.org/10.4161/rna.6.1.7564 (2009).CAS 
Article 
PubMed 

Google Scholar 
49.Wilcox, M. & Nirenberg, M. Transfer RNA as a cofactor coupling amino acid synthesis with that of protein. Proc Natl Acad Sci U S A 61, 229–236. https://doi.org/10.1073/pnas.61.1.229 (1968).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
50.Detrich, H. W. 3rd., Fitzgerald, T. J., Dinsmore, J. H. & Marchese-Ragona, S. P. Brain and egg tubulins from antarctic fishes are functionally and structurally distinct. J Biol Chem 267, 18766–18775 (1992).CAS 
Article 

Google Scholar 
51.Detrich, H. W. 3rd., Johnson, K. A. & Marchese-Ragona, S. P. Polymerization of Antarctic fish tubulins at low temperatures: energetic aspects. Biochemistry 28, 10085–10093 (1989).CAS 
Article 

Google Scholar 
52.Wloga, D. et al. Glutamylation on alpha-tubulin is not essential but affects the assembly and functions of a subset of microtubules in Tetrahymena thermophila. Eukaryot Cell 7, 1362–1372. https://doi.org/10.1128/EC.00084-08 (2008).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
53.Eisen, J. A. et al. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol 4, e286. https://doi.org/10.1371/journal.pbio.0040286 (2006).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
54.Aury, J. M. et al. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444, 171–178. https://doi.org/10.1038/nature05230 (2006).ADS 
CAS 
Article 
PubMed 

Google Scholar 
55.Pucciarelli, S. et al. Distinct functional roles of beta-tubulin isotypes in microtubule arrays of Tetrahymena thermophila, a model single-celled organism. PLoS ONE 7, e39694. https://doi.org/10.1371/journal.pone.0039694 (2012).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
56.Pucciarelli, S. et al. Tubulin folding: the special case of a beta-tubulin isotype from the Antarctic psychrophilic ciliate Euplotes focardii. Polar Biol 36, 1833–1838. https://doi.org/10.1007/s00300-013-1390-9 (2013).Article 

Google Scholar 
57.Pucci, F. & Rooman, M. Physical and molecular bases of protein thermal stability and cold adaptation. Curr Opin Struct Biol 42, 117–128. https://doi.org/10.1016/j.sbi.2016.12.007 (2017).CAS 
Article 
PubMed 

Google Scholar 
58.Aqvist, J., Isaksen, G. V. & Brandsdal, B. O. Computation of enzyme cold adaptation. Nat Rev Chem 1, 0051. https://doi.org/10.1038/s41570-017-0051 (2017).CAS 
Article 

Google Scholar 
59.Lesser, M. P. Oxidative stress in marine environments: biochemistry and physiological ecology. Annu Rev Physiol 68, 253–278. https://doi.org/10.1146/annurev.physiol.68.040104.110001 (2006).CAS 
Article 
PubMed 

Google Scholar 
60.McCord, J. M. & Fridovich, I. Superoxide dismutase. An enzymic function for erythrocuprein (hemocuprein). J Biol Chem 244, 6049–6055 (1969).61.McCord, J. M. & Fridovich, I. Superoxide dismutase: the first twenty years (1968–1988). Free Radic Biol Med 5, 363–369 (1988).CAS 
Article 

Google Scholar 
62.Miller, A. F. Superoxide dismutases: ancient enzymes and new insights. FEBS Lett 586, 585–595. https://doi.org/10.1016/j.febslet.2011.10.048 (2012).CAS 
Article 
PubMed 

Google Scholar 
63.Benov, L. T. & Fridovich, I. Escherichia coli expresses a copper- and zinc-containing superoxide dismutase. J Biol Chem 269, 25310–25314 (1994).CAS 
Article 

Google Scholar 
64.Steinman, H. M. & Ely, B. Copper-zinc superoxide dismutase of Caulobacter crescentus: cloning, sequencing, and mapping of the gene and periplasmic location of the enzyme. J Bacteriol 172, 2901–2910. https://doi.org/10.1128/jb.172.6.2901-2910.1990 (1990).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
65.Antonyuk, S. V., Strange, R. W., Marklund, S. L. & Hasnain, S. S. The structure of human extracellular copper-zinc superoxide dismutase at 1.7 A resolution: insights into heparin and collagen binding. J Mol Biol 388, 310–326. https://doi.org/10.1016/j.jmb.2009.03.026 (2009).66.Marklund, S. L. Extracellular superoxide dismutase and other superoxide dismutase isoenzymes in tissues from nine mammalian species. Biochem J 222, 649–655. https://doi.org/10.1042/bj2220649 (1984).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
67.Bannister, J. V., Bannister, W. H. & Rotilio, G. Aspects of the structure, function, and applications of superoxide dismutase. CRC Crit Rev Biochem 22, 111–180 (1987).CAS 
Article 

Google Scholar 
68.James, E. R. Superoxide dismutase. Parasitol Today 10, 481–484. https://doi.org/10.1016/0169-4758(94)90161-9 (1994).CAS 
Article 
PubMed 

Google Scholar 
69.Ferro, D. et al. Cu, Zn superoxide dismutases from Tetrahymena thermophila: molecular evolution and gene expression of the first line of antioxidant defenses. Protist 166, 131–145. https://doi.org/10.1016/j.protis.2014.12.003 (2015).CAS 
Article 
PubMed 

Google Scholar 
70.Arnaiz, O. & Sperling, L. ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. Nucleic Acids Res 39, D632-636. https://doi.org/10.1093/nar/gkq918 (2011).CAS 
Article 
PubMed 

Google Scholar 
71.Fink, R. C. & Scandalios, J. G. Molecular evolution and structure–function relationships of the superoxide dismutase gene families in angiosperms and their relationship to other eukaryotic and prokaryotic superoxide dismutases. Arch Biochem Biophys 399, 19–36. https://doi.org/10.1006/abbi.2001.2739 (2002).CAS 
Article 
PubMed 

Google Scholar 
72.Lee, Y. M., Friedman, D. J. & Ayala, F. J. Superoxide dismutase: an evolutionary puzzle. Proc Natl Acad Sci U S A 82, 824–828. https://doi.org/10.1073/pnas.82.3.824 (1985).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
73.Pischedda, A. et al. Antarctic marine ciliates under stress: superoxide dismutases from the psychrophilic Euplotes focardii are cold-active yet heat tolerant enzymes. Sci Rep 8, 14721. https://doi.org/10.1038/s41598-018-33127-1 (2018).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
74.Yang, G. et al. Characterization of the first eukaryotic cold-adapted patatin-like phospholipase from the psychrophilic Euplotes focardii: Identification of putative determinants of thermal-adaptation by comparison with the homologous protein from the mesophilic Euplotes crassus. Biochimie 95, 1795–1806. https://doi.org/10.1016/j.biochi.2013.06.008 (2013).CAS 
Article 
PubMed 

Google Scholar 
75.Li, J., Zhou, L., Lin, X., Yi, Z. & Al-Rasheid, K. A. Characterizing dose-responses of catalase to nitrofurazone exposure in model ciliated protozoan Euplotes vannus for ecotoxicity assessment: enzyme activity and mRNA expression. Ecotoxicol Environ Saf 100, 294–302. https://doi.org/10.1016/j.ecoenv.2013.08.021 (2014).CAS 
Article 
PubMed 

Google Scholar 
76.Prast-Nielsen, S., Huang, H. H. & Williams, D. L. Thioredoxin glutathione reductase: its role in redox biology and potential as a target for drugs against neglected diseases. Biochim Biophys Acta 1262–1271, 2011. https://doi.org/10.1016/j.bbagen.2011.06.024 (1810).CAS 
Article 

Google Scholar 
77.Kabani, M. & Martineau, C. N. Multiple hsp70 isoforms in the eukaryotic cytosol: mere redundancy or functional specificity?. Curr Genomics 9, 338–248. https://doi.org/10.2174/138920208785133280 (2008).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
78.La Terza, A., Miceli, C. & Luporini, P. The gene for the heat-shock protein 70 of Euplotes focardii, an Antarctic psychrophilic ciliate. Antarct. Sci. 16, 23–28. https://doi.org/10.1017/S0954102004001774 (2004).ADS 
Article 

Google Scholar 
79.Chen, X. et al. Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors. Mol Ecol Resour 19, 1292–1308. https://doi.org/10.1111/1755-0998.13023 (2019).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
80.Chen, Z. et al. Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish. Proc Natl Acad Sci U S A 105, 12944–12949. https://doi.org/10.1073/pnas.0802432105 (2008).ADS 
Article 
PubMed 
PubMed Central 

Google Scholar 
81.Li, Y. et al. Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis. BMC Genomics 20, 624. https://doi.org/10.1186/s12864-019-5988-3 (2019).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
82.Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. https://doi.org/10.1093/bioinformatics/btu170 (2014).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
83.Andrews, S. (2010).84.Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19, 455–477. https://doi.org/10.1089/cmb.2012.0021 (2012).MathSciNet 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
85.Nikolenko, S. I., Korobeynikov, A. I. & Alekseyev, M. A. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics 14 Suppl 1, S7. https://doi.org/10.1186/1471-2164-14-S1-S7 (2013).86.Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075. https://doi.org/10.1093/bioinformatics/btt086 (2013).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
87.Boscaro, V., Husnik, F., Vannini, C. & Keeling, P. J. Symbionts of the ciliate Euplotes: diversity, patterns and potential as models for bacteria-eukaryote endosymbioses. Proc Biol Sci 286, 20190693. https://doi.org/10.1098/rspb.2019.0693 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
88.Serra, V. et al. Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont “Candidatus Pinguicoccus supinus” sp. nov. Sci Rep 10, 20311. https://doi.org/10.1038/s41598-020-76348-z (2020).89.Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 34, W435-439. https://doi.org/10.1093/nar/gkl200 (2006).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
90.Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323. https://doi.org/10.1186/1471-2105-12-323 (2011).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
91.Conesa, A. et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674–3676. https://doi.org/10.1093/bioinformatics/bti610 (2005).CAS 
Article 
PubMed 

Google Scholar 
92.Gotz, S. et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36, 3420–3435. https://doi.org/10.1093/nar/gkn176 (2008).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
93.Parra, G., Bradnam, K. & Korf, I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23, 1061–1067. https://doi.org/10.1093/bioinformatics/btm071 (2007).CAS 
Article 
PubMed 

Google Scholar 
94.Laslett, D. & Canback, B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32, 11–16. https://doi.org/10.1093/nar/gkh152 (2004).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
95.Gruber, A. R., Lorenz, R., Bernhart, S. H., Neubock, R. & Hofacker, I. L. The Vienna RNA websuite. Nucleic Acids Res 36, W70-74. https://doi.org/10.1093/nar/gkn188 (2008).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
96.Popenda, M. et al. Automated 3D structure composition for large RNAs. Nucleic Acids Res 40, e112. https://doi.org/10.1093/nar/gks339 (2012).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
97.Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152. https://doi.org/10.1093/bioinformatics/bts565 (2012).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
98.Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659. https://doi.org/10.1093/bioinformatics/btl158 (2006).CAS 
Article 
PubMed 

Google Scholar 
99.Shigematsu, M. et al. YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs. Nucleic Acids Res 45, e70. https://doi.org/10.1093/nar/gkx005 (2017).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
100.Bushnell, B., Rood, J. & Singer, E. BBMerge: accurate paired shotgun read merging via overlap. PLoS ONE 12, e0185056. https://doi.org/10.1371/journal.pone.0185056 (2017).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
101.Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. 2011 17, 3. https://doi.org/10.14806/ej.17.1.200 (2011).102.Holmes, A. D., Howard, J. M., Chan, P. P. & Lowe, T. M. tRNA Analysis of eXpression (tRAX): A tool for integrating analysis of tRNAs, tRNA-derived small RNAs, and tRNA modifications. (Submitted) (2020).103.Sievers, F. & Higgins, D. G. Clustal omega. Curr Protoc Bioinformatics 48, 3 13 11–16. https://doi.org/10.1002/0471250953.bi0313s48 (2014).104.Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35, 1547–1549. https://doi.org/10.1093/molbev/msy096 (2018).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
105.Webb, B. & Sali, A. Comparative protein structure modeling using MODELLER. Curr Protoc Bioinform. 54, 5 6 1–5 6 37. https://doi.org/10.1002/cpbi.3 (2016).106.Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46, W296–W303. https://doi.org/10.1093/nar/gky427 (2018).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
107.Ichikawa, M. et al. Tubulin lattice in cilia is in a stressed form regulated by microtubule inner proteins. Proc Natl Acad Sci U S A 116, 19930–19938. https://doi.org/10.1073/pnas.1911119116 (2019).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
108.Chaaban, S. et al. The Structure and Dynamics of C. elegans Tubulin Reveals the Mechanistic Basis of Microtubule Growth. Dev Cell 47, 191–204 e198. https://doi.org/10.1016/j.devcel.2018.08.023 (2018).109.Kikkawa, M. et al. Switch-based mechanism of kinesin motors. Nature 411, 439–445. https://doi.org/10.1038/35078000 (2001).ADS 
CAS 
Article 
PubMed 

Google Scholar 
110.Howes, S. C. et al. Structural differences between yeast and mammalian microtubules revealed by cryo-EM. J Cell Biol 216, 2669–2677. https://doi.org/10.1083/jcb.201612195 (2017).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
111.Ma, M. et al. Structure of the Decorated Ciliary Doublet Microtubule. Cell 179, 909–922 e912. https://doi.org/10.1016/j.cell.2019.09.030 (2019).112.Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001 (2015).ADS 
Article 

Google Scholar 
113.Morrison, T. B., Weis, J. J. & Wittwer, C. T. Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification. Biotechniques 24, 954–958, 960, 962 (1998).114.Pfaffl, M. W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29, e45. https://doi.org/10.1093/nar/29.9.e45 (2001).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
115.Pfaffl, M. W., Horgan, G. W. & Dempfle, L. Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 30, e36. https://doi.org/10.1093/nar/30.9.e36 (2002).Article 
PubMed 
PubMed Central 

Google Scholar  More