More stories

  • in

    Below ground efficiency of a parasitic wasp for Drosophila suzukii biocontrol in different soil types

    Di Giacomo, G., Hadrich, J., Hutchison, W. D., Peterson, H. & Rogers, M. Economic impact of spotted wing drosophila (Diptera: Drosophilidae) yield loss on minnesota raspberry farms: A grower survey. J. Integr. Pest Manag. https://doi.org/10.1093/jipm/pmz006 (2019).Article 

    Google Scholar 
    Farnsworth, D. et al. Economic analysis of revenue losses and control costs associated with the spotted wing drosophila, Drosophila suzukii (Matsumura), in the California raspberry industry. Pest. Manag. Sci. 73, 1083–1090. https://doi.org/10.1002/ps.4497 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Beers, E. H., Van Steenwyk, R. A., Shearer, P. W., Coates, W. W. & Grant, J. A. Developing Drosophila suzukii management programs for sweet cherry in the western United States. Pest Manag. Sci. 67, 1386–1395. https://doi.org/10.1002/ps.2279 (2011).CAS 
    Article 
    PubMed 

    Google Scholar 
    Tait, G. et al. Drosophila suzukii (Diptera: Drosophilidae): A decade of research towards a sustainable integrated pest management program. J. Econ. Entomol. 114, 1950–1974. https://doi.org/10.1093/jee/toab158 (2021).Article 
    PubMed 

    Google Scholar 
    Daane, K. M. et al. First exploration of parasitoids of Drosophila suzukii in South Korea as potential classical biological agents. J. Pest Sci. 89, 823–835. https://doi.org/10.1007/s10340-016-0740-0 (2016).ADS 
    Article 

    Google Scholar 
    Abram, P. K. et al. New records of Leptopilina, Ganaspis, and Asobara species associated with Drosophila suzukii in North America, including detections of L. japonica and G. brasiliensis. J. Hymenoptera Res. 78, 1–17. https://doi.org/10.3897/jhr.78.55026 (2020).Article 

    Google Scholar 
    Chabert, S., Allemand, R., Poyet, M., Eslin, P. & Gibert, P. Ability of European parasitoids (Hymenoptera) to control a new invasive Asiatic pest, Drosophila suzukii. Biol. Control 63, 40–47. https://doi.org/10.1016/j.biocontrol.2012.05.005 (2012).Article 

    Google Scholar 
    Gonzalez-Cabrera, J., Moreno-Carrillo, G., Sanchez-Gonzalez, J. A., Mendoza-Ceballos, M. Y. & Arredondo-Bernal, H. C. Single and Combined Release of Trichopria drosophilae (Hymenoptera: Diapriidae) to Control Drosophila suzukii (Diptera: Drosophilidae). Neotrop. Entomol. 48, 949–956. https://doi.org/10.1007/s13744-019-00707-3 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    Rossi Stacconi, M. V., Grassi, A., Ioriatti, C. & Anfora, G. Augmentative releases of Trichopria drosophilae for the suppression of early season Drosophila suzukii populations. Biocontrol 64, 9–19. https://doi.org/10.1007/s10526-018-09914-0 (2018).CAS 
    Article 

    Google Scholar 
    Poyet, M. et al. The wide potential trophic niche of the asiatic fruit fly Drosophila suzukii: The key of its invasion success in temperate Europe?. PLoS ONE 10, e0142785. https://doi.org/10.1371/journal.pone.0142785 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Mazzetto, F. et al. Drosophila parasitoids in northern Italy and their potential to attack the exotic pest Drosophila suzukii. J. Pest Sci. 89, 837–850. https://doi.org/10.1007/s10340-016-0746-7 (2016).Article 

    Google Scholar 
    Wang, X. G., Kacar, G., Biondi, A. & Daane, K. M. Foraging efficiency and outcomes of interactions of two pupal parasitoids attacking the invasive spotted wing drosophila. Biol. Control 96, 64–71. https://doi.org/10.1016/j.biocontrol.2016.02.004 (2016).Article 

    Google Scholar 
    Rossi Stacconi, M. V. et al. Host location and dispersal ability of the cosmopolitan parasitoid Trichopria drosophilae released to control the invasive spotted wing Drosophila. Biol. Control 117, 188–196. https://doi.org/10.1016/j.biocontrol.2017.11.013 (2018).Article 

    Google Scholar 
    Esteban-Santiago, J. M., Rodríguez-Leyva, E., Lomeli-Flores, J. R. & González-Cabrera, J. Demographic parameters of Trichopria drosophilae in three host species. Entomol. Exp. Appl. 169, 330–337. https://doi.org/10.1111/eea.13026 (2021).CAS 
    Article 

    Google Scholar 
    Häussling, B. J. M., Lienenluke, J. & Stokl, J. The preference of Trichopria drosophilae for pupae of Drosophila suzukii is independent of host size. Sci. Rep. 11, 995. https://doi.org/10.1038/s41598-020-80355-5 (2021).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wang, X. G., Kacar, G., Biondi, A. & Daane, K. M. Life-history and host preference of Trichopria drosophilae, a pupal parasitoid of spotted wing drosophila. Biocontrol 61, 387–397. https://doi.org/10.1007/s10526-016-9720-9 (2016).CAS 
    Article 

    Google Scholar 
    Woltz, J. M. & Lee, J. C. Pupation behavior and larval and pupal biocontrol of Drosophila suzukii in the field. Biol. Control 110, 62–69. https://doi.org/10.1016/j.biocontrol.2017.04.007 (2017).Article 

    Google Scholar 
    Ballman, E. S., Collins, J. A. & Drummond, F. A. Pupation behavior and predation on Drosophila suzukii (Diptera: Drosophilidae) Pupae in Maine wild blueberry fields. J. Econ. Entomol. 110, 2308–2317. https://doi.org/10.1093/jee/tox233 (2017).Article 
    PubMed 

    Google Scholar 
    Guillén, L., Aluja, M. N., Equihua, M. & Sivinski, J. Performance of two fruit fly (Diptera: Tephritidae) pupal parasitoids (Coptera haywardi [Hymenoptera: Diapriidae] and Pachycrepoideus vindemiae [Hymenoptera: Pteromalidae]) under different environmental soil conditions. Biol. Control 23, 219–227. https://doi.org/10.1006/bcon.2001.1011 (2002).Article 

    Google Scholar 
    Yi, C. et al. Life history and host preference of Trichopria drosophilae from Southern China, one of the effective pupal parasitoids on the Drosophila species. Insects 11, 103. https://doi.org/10.3390/insects11020103 (2020).Article 
    PubMed Central 

    Google Scholar 
    BoychevaWoltering, S., Romeis, J. & Collatz, J. Influence of the rearing host on biological parameters of Trichopria drosophilae, a potential biological control agent of Drosophila suzukii. Insects. https://doi.org/10.3390/insects10060183 (2019).Article 

    Google Scholar 
    Otto, M. & Mackauer, M. The developmental strategy of an idiobiont ectoparasitoid, Dendrocerus carpenteri: Influence of variations in host quality on offspring growth and fitness. Oecologia 117, 353–364. https://doi.org/10.1007/s004420050668 (1998).ADS 
    Article 
    PubMed 

    Google Scholar 
    Bates, D., Machler, M., Bolker, B. M. & Walker, S. C. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48. https://doi.org/10.18637/jss.v067.i01 (2015).Article 

    Google Scholar 
    R: A Language and Environment for Statistical Computing (Vienna, Austria, 2008).Johnson, S. N. & Gregory, P. J. Chemically-mediated host-plant location and selection by root-feeding insects. Physiol. Entomol. 31, 1–13. https://doi.org/10.1111/j.1365-3032.2005.00487.x (2006).CAS 
    Article 

    Google Scholar 
    Bezerra Da Silva, C. S., Park, K. R., Blood, R. A. & Walton, V. M. Intraspecific competition affects the pupation behavior of spotted-wing drosophila (Drosophila suzukii). Sci. Rep. 9, 7775. https://doi.org/10.1038/s41598-019-44248-6 (2019).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Renkema, J. M. & Devkota, S. Pupation depth of spotted wing drosophila (Drosophila suzukii) and effects of field sanitation in Florida strawberries. Viii Int. Strawberry Symp. 1156, 849–855. https://doi.org/10.17660/ActaHortic.2017.1156.125 (2017).Article 

    Google Scholar 
    Tsitsipis, J. A. & Papanicolaou, E. P. Pupation depth in artificially reared olive fruits-flies Dacus-oleae (Diptera, Tephritidae), as affected by several physical characteristics of the substrates. Annales De Zoologie Ecologie Animale 11, 31–40 (1979).
    Google Scholar 
    Dimou, I., Koutsikopoulos, C., Economopoulos, A. P. & Lykakis, J. Depth of pupation of the wild olive fruit fly, Bactrocera (Dacus) oleae (Gmel.) (Dipt., Tephritidae), as affected by soil abiotic factors. J. Appl. Entomol. 127, 12–17. https://doi.org/10.1046/j.1439-0418.2003.00686.x (2003).Article 

    Google Scholar 
    de Belle, J. S., Hilliker, A. J. & Sokolowski, M. B. Genetic localization of foraging (for): A major gene for larval behavior in Drosophila melanogaster. Genetics 123, 157–163. https://doi.org/10.1093/genetics/123.1.157 (1989).Article 
    PubMed 

    Google Scholar 
    Sokolowski, M. B. et al. Ecological genetics and behaviour of Drosophila melanogaster larvae in nature. Anim. Behav. 34, 403–408. https://doi.org/10.1016/S0003-3472(86)80109-9 (1986).Article 

    Google Scholar 
    Rodriguez, L., Sokolowski, M. B. & Shore, J. S. Habitat selection by Drosophila melanogaster larvae. J. Evol. Biol. 5, 61–70. https://doi.org/10.1046/j.1420-9101.1992.5010061.x (1992).Article 

    Google Scholar 
    McIntosh, H., Atucha, A., Townsend, P. A., Hills, W. B. & Guédot, C. Plastic mulches reduce adult and larval populations of Drosophila suzukii in fall-bearing raspberry. J. Pest. Sci. 95, 525–536. https://doi.org/10.1007/s10340-021-01456-2 (2021).Article 

    Google Scholar 
    Ballman, E. & Drummond, F. Larval movement of spotted wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae). J. Kansas Entomol. Soc. 92, 412–421. https://doi.org/10.2317/0022-8567-92.1.412 (2019).Article 

    Google Scholar  More

  • in

    Influence of spatial characteristics of green spaces on microclimate in Suzhou Industrial Park of China

    In this study, the five main characteristics of green spaces that were measured were area, perimeter, perimeter-area ratio, leaf area index, and canopy density. The structure of parameter between them is shown in Table 3.Table 3 Parameter structure of the cooling and humidification effect based on the spatial characteristics of green spaces.Full size tableCorrelation between various spatial characteristics and cooling and humidifying intensity in green spacesSmall-size green spacesFigures 4 and 6 shows the results of linear regressions between spatial characteristics and the cooling effect in small-size green spaces. There were relatively weak correlations between area, perimeter, perimeter-area ratio, leaf area index and cooling intensity, and a strong correlation between canopy density and cooling intensity. Small-size green space has the weakest positive correlation between perimeter-area ratio and cooling intensity (R2 = 0.11), and its canopy density and cooling intensity have the strongest positive correlation (R2 = 0.64). Meanwhile, small-size green space has weakest negative correlation between perimeter and humidifying intensity (R2 = 0.17), and its leaf area index and humidifying intensity have significant positive correlation (R2 = 0.42). Figures 4a and 5a show that for every 1 ha increase in area of small-size green spaces, the cooling intensity increased by 1.026 °C, and the humidifying intensity decreased by 1.56%. Figures 4b and 5b show that for every 100 m increase in perimeter, the cooling intensity decreases by 1.06 °C, and the humidifying intensity decreased by 1.19%. Figures 4c and 5c show that for every 0.01 increase in the perimeter-area ratio, the cooling intensity increases by 1.12 °C, and the humidifying intensity increased by 1.46%. Figures 4d and 5d show that for every 0.1 increase in the leaf area index, the cooling intensity increases by 1.11 °C, and the humidifying intensity increased by 1.12%. Figures 4e and 5e show that each 0.01 increase in the canopy density, the cooling intensity increases by 1.60 °C, and each 0.1 increase in canopy density, the humidifying intensity increased by 1.15% (Fig. 6).
    Figure 4Linear regressions between spatial characteristics and cooling intensity of small-size green spaces.Full size imageFigure 5Linear regressions of spatial characteristics and humidifying intensity of small-size green spaces.Full size imageFigure 6The correlation between the spatial characteristics of small-size green spaces and the intensity of cooling and humidifying (GA means green area; GP means green perimeter; GPAR means green perimeter-area ratio; LAI means leaf area index; CD means canopy density).Full size imageMedium-size green spacesFigures 7 and 9 shows the linear regressions between spatial characteristics and cooling intensity in medium-size green spaces. There was an extremely significant positive correlation between area and cooling intensity, an insignificant positive correlation between the leaf area index and cooling intensity, and a relatively weak negative correlation between the other three characteristics and cooling intensity. Medium-size green space has the weakest negative correlation between canopy density and cooling intensity (R2 = 0.12), and its green area and cooling intensity have the strongest positive correlation (R2 = 0.83). Meanwhile, medium-size green space has weakest negative correlation between perimeter-area ratio and humidifying intensity (R2 = 0.41), and its area and humidifying intensity have most significant positive correlation (R2 = 0.81). Figures 7a and 8a show that for every 1 ha increase in area of medium-size green spaces, the cooling intensity increased by 1.19 °C, and the humidifying intensity increased by 1.24%. Figures 7b and 8b show that for every 100 m increase in perimeter, the cooling intensity decreases by 1.02 °C, and the humidifying intensity increased by 1.17%. Figures 7c and 8c show that for every 0.01 increase in the perimeter-area ratio, the cooling intensity decreases by 1.29 °C, and the humidifying intensity decreased by 2.40%. Figures 7d and 8d show that for every 0.1 increase in the leaf area index, the cooling intensity increases by 1.37 °C, and the humidifying intensity decreased by 1.92%. Figures 7e and 8e show that each 0.01 increase in the canopy density, increases the cooling intensity decreases by 1.23 °C, and the humidifying intensity decreased by 6.48% (Fig. 9).Figure 7Linear regressions between spatial characteristics and cooling intensity of medium-size green spaces.Full size imageFigure 8Linear regressions of spatial characteristics and humidifying intensity of medium-size green spaces.Full size imageFigure 9The correlation between the spatial characteristics of medium-size green spaces and the intensity of cooling and humidifying (GA means green area; GP means green perimeter; GPAR means green perimeter-area ratio; LAI means leaf area index; CD means canopy density).Full size imageLarge-size green spacesFigures 10 and 12 shows the linear regressions between spatial characteristics and cooling intensity in large-size green spaces. There was an insignificant correlation between area and cooling intensity, a weak correlation between canopy density and cooling intensity, and a significant correlation between perimeter, perimeter-area ratio and the leaf area index and cooling intensity. Medium-size green space has the weakest negative correlation between green area and cooling intensity (R2 = 0.35), and its leaf area index and cooling intensity have the strongest positive correlation (R2 = 0.92). Meanwhile, medium-size green space has weakest negative correlation between perimeter-area ratio and humidifying intensity (R2 = 0.11), and its leaf area index and humidifying intensity have most significant positive correlation (R2 = 0.39). Figures 10a and 11a show that for every 1 ha increase in area of large-size green spaces, the cooling intensity decreased by 1.02 °C, and the humidifying intensity decreased by 1.22%. Figures 10b and 11b show that for every 100 m increase in perimeter, the cooling intensity decreases by 1.05 °C, and the humidifying intensity decreased by 1.34%. Figures 10c and 11c show that for every 0.005 increase in the perimeter-area ratio, the cooling intensity decreases by 1.43 °C, and each 0.01 increase in perimeter-area ratio, the humidifying intensity decreased by 1.27%. Figures 10d and 11d show that for every 0.1 increase in the leaf area index, the cooling intensity increases by 2.41 °C, and the humidifying intensity increased by 1.37%. Figures 10e and 11e show that each 0.1 increase in the canopy density, the cooling intensity increased by 3.69 °C, and the humidifying intensity decreased by 2.84% (Fig. 12).Figure 10Linear regressions of spatial characteristics and cooling intensity of large-size green spaces.Full size imageFigure 11Linear regressions of spatial characteristics and humidifying intensity of large-size green spaces.Full size imageFigure 12The correlation between the spatial characteristics of large-size green spaces and the intensity of cooling and humidifying (GA means green area; GP means green perimeter; GPAR means green perimeter-area ratio; LAI means leaf area index; CD means canopy density).Full size imageQuantitative analysis of the microclimatic effects of different types of green spacesQuantitative analysis of the effects of different types of green space on cooling intensityFigure 13 shows the linear regressions between the different types of green spaces and cooling intensity. There were negative correlations between green spaces a short, medium, and long distance from a water body and cooling intensity in small-size green spaces, medium-size green spaces and large-size green spaces. The negative correlation between the distance to a water body and cooling intensity in medium-size green spaces was most significant (R2 = 0.985). The greater the distance to a water body, the lower the cooling intensity. For medium-size green spaces, for every 1/4 increase in the distance ratio, the cooling intensity decreased by 0.81 °C. For small-size green spaces, for every 1/4 increase in the distance ratio, the cooling intensity decreased by 1.04 °C. For large-size green spaces, for every 1/4 increase in the distance ratio, the cooling intensity decreased by 1.36 °C. For small-, medium-, and large-size green spaces, there was a positive correlation between canopy density and cooling intensity. There was a most significant positive correlation between canopy density and cooling intensity in large-size green spaces (R2 = 0.941). The greater the canopy density, the greater the cooling intensity. For large green spaces, for every 0.5 increase in canopy density, the cooling intensity increased by 0.16 °C. For small-size green spaces, for every 0.5 increase in canopy density, the cooling effect increased by 0.15 °C. For medium-size green spaces, for every 0.5 increase in canopy density, the cooling intensity increased by 0.16 °C.Figure 13Linear regressions between the distance from different types of green spaces to water areas, canopy density and cooling intensity.Full size imageQuantitative analysis of the effects of different types of green space on humidifying intensityFigure 14 shows the linear regression between the distance of a green space from a water body, canopy density and humidifying intensity. There was a negative correlation between the distance to a water body and humidifying intensity in small, medium, and large green spaces. The negative correlation between the distance to a water body and humidifying intensity in small green spaces was most significant (R2 = 0.996). The longer the distance, the lower the humidifying intensity. For small green spaces, for every 1/4 in-crease in the distance ratio, the humidifying intensity decreased by 4.23%. For medium-size green spaces, for every 1/4 increase in the distance ratio, the humidifying intensity decreased by 3.02%. For large-size green spaces, for every 1/4 increase in the distance ratio, the humidifying intensity de-creased by 6.14%. For small, medium, and large green spaces, there was a positive correlation between canopy density and humidifying intensity. The positive correlation between canopy density and humidifying intensity in medium-size green spaces was extremely significant (R2 = 0.925). The greater the canopy density, the greater the humidifying intensity. For medium-size green spaces, for every 0.5 increase in canopy density, the humidifying intensity increased by 3.29%. For small-size green spaces, for every 0.5 increase in canopy density, the humidifying intensity increased by 3.17%. For large-size green spaces, for every 0.5 increase in canopy density, the humidifying intensity increased by 4.06% (Fig. 15).
    Figure 14Linear regressions between the distance from different types of green space to water area, canopy density and humidifying intensity.Full size imageFigure 15Correlation of different green space types with water distance, canopy density and cooling and humidifying intensity.Full size imageEffect of shape and area of water bodies on microclimatic effects based on numerical simulationBanded waterWe constructed a numerical simulation model to explore the effects of a simulated increase in water body area on cooling and humidification. Figure 16 shows the simulated distribution characteristics of temperature and relative humidity after a 5% and 10% increase in water area at 14:00 when temperatures were high. The results suggest that between 7:00 and 10:00, with a 5% and 10% increase in water area, the air temperature was basically the same and the cooling effect was insignificant. However, between 12:00 and 19:00 and particularly in the hours between 13:00 and 16:00 when temperatures were highest, a 5% increase in water area produced a significant cooling effect, with a daily average value of 0.05 °C and a maximum value of 0.09 °C. A 10% increase in water area produced an extremely significant cooling effect, with a daily average value of 0.07 °C and a maximum value of 0.14 °C. From 11:00 to 19:00, a 5% increase in water area produced a significant humidifying effect, with a daily average value of 0.08% and a maximum value of 0.17%. A 10% increase produced an extremely significant humidifying effect, with a daily average value of 0.13% and a maximum value of 0.26% (See supplementary file).Figure 16Distribution characteristics of cooling and humidifying effects of simulated increase of banded water area at 14:00. (a) original cooling effect of banded water in the sample area; (b) cooling effect of 5% increase in water area; (c) cooling effect of 10% increase in water area; (d) original humidifying effect of banded water in the sample area; (e) humidifying effect of 5% increase in water area; (f) humidifying effect of 10% increase of water area.Full size imageMassive waterFigure 17 shows the simulated distribution characteristics of the cooling and humidifying effects after a 5% and 10% increase in the water area at 14:00 when temperatures were high. Between 8:00 and 19:00, a 5% and 10% increase in water area produced a significant cooling effect. At 19:00, the numerical simulation result was abnormal when the water area increased by 5% and 10%; at 13:00, the numerical simulation result was also ab-normal when the water area increased by 10%. After excluding the abnormal simulated data, a 5% increase in water area produced a cooling effect, with a daily average value of 0.06 °C and a maximum value of 0.10 °C. A 10% increase in water area produced an extremely significant cooling effect, with a daily average value of 0.10 °C and a maximum value of 0.18 °C. Between 11:00 and 19:00, a 5% increase in water area produced a significant humidifying effect, with a daily average value of 0.05% and a maximum value of 0.13%. A 10% increase in water area produced an extremely significant humidifying effect, with a daily average value of 0.13% and a maximum value of 0.27% (See supplementary file).Figure 17Distribution characteristics of cooling and humidifying effects of simulated increase of massive water area at 14:00. (a) original cooling effect of massive water in the sample area; (b) cooling effect of 5% increase in water area; (c) cooling effect of 10% increase in water area; (d) original humidifying effect of massive water in the sample area; (e) humidifying effect of 5% increase in water area; (f) humidifying effect of 10% increase of water area.Full size imageAnnular waterFigure 18 shows the simulated distribution characteristics of the cooling and humidifying effects after a 5% and 10% increase in the area of the annular water body at 14:00 when temperatures were high. Between 7:00 and 19:00, a 5% and 10% increase in water area produced a significant cooling effect. Between 11:00 and 16:00 when temperatures were high, a 5% increase in water area produced a cooling effect, with a daily average value of 0.06 °C and a maximum value of 0.14 °C°C and a 10% increase in water area produced an extremely significant cooling effect, with a daily average value of 0.13 °C and a maximum value of 0.28 °C. Between 7:00 and 19:00, a 5% and 10% increase in water area produced significant humidifying effects. Between 11:00 and 16:00 when temperatures were high, a 5% increase in water area produced an extremely significant humidifying effect, with a daily average value of 0.17% and a maximum value of 0.39% and a 10% increase in water area produced an extremely significant humidifying effect with a daily average value of 0.38% and a maximum value of 0.81% (See supplementary file).Figure 18Distribution characteristics of cooling and humidifying effects of simulated increase of annular water area at 14:00. (a) original cooling effect of annular water in the sample area; (b) cooling effect of 5% increase in water area; (c) cooling effect of 10% increase in water area; (d) original humidifying effect of annular water in the sample area; (e) humidifying effect of 5% increase in water area; (f) humidifying effect of 10% increase of water area.Full size image More

  • in

    Success of post-fire plant recovery strategies varies with shifting fire seasonality

    Canadell, J. G. et al. Multi-decadal increase of forest burned area in Australia is linked to climate change. Nat. Commun. 12, 6921 (2021).CAS 
    Article 

    Google Scholar 
    Jolly, W. M. et al. Climate-induced variations in global wildfire danger from 1979 to 2013. Nat. Commun. 6, 7537 (2015).CAS 
    Article 

    Google Scholar 
    Jain, P., Wang, X. & Flannigan, M. D. Trend analysis of fire season length and extreme fire weather in North America between 1979 and 2015. Int. J. Wildland Fire 26, 1009–1020 (2017).Article 

    Google Scholar 
    Wotton, B. M. & Flannigan, M. D. Length of the fire season in a changing climate. For. Chronicle 69, 187–192 (1993).
    Google Scholar 
    Collins, L. et al. The 2019/2020 mega-fires exposed Australian ecosystems to an unprecedented extent of high-severity fire. Environ. Res. Lett. 16, 044029 (2021).Article 

    Google Scholar 
    Higuera, P. E. & Abatzoglou, J. T. Record‐setting climate enabled the extraordinary 2020 fire season in the western United States. Glob. Change Biol. 27, 1–2 (2021).Article 

    Google Scholar 
    Nolan, R. H. et al. Limits to post-fire vegetation recovery under climate change. Plant Cell Environ. 44, 3471–3489 (2021).CAS 
    Article 

    Google Scholar 
    Abram, N. J. et al. Connections of climate change and variability to large and extreme forest fires in southeast Australia. Commun. Earth Environ. 2, 8 (2021).Article 

    Google Scholar 
    Dickman, C. R. Ecological consequences of Australia’s “Black Summer” bushfires: managing for recovery. Int. Environ. Assess. Manag. 17, 1162–1167 (2021).Article 

    Google Scholar 
    Swain, D. L. A shorter, sharper rainy season amplifies California wildfire risk. Geophys. Res. Lett. 48, e2021GL092843 (2021).
    Google Scholar 
    Keeley, J. E. Fire intensity, fire severity and burn severity: a brief review and suggested usage. Int. J. Wildland Fire 18, 116–126 (2009).Article 

    Google Scholar 
    He, T., Pausas, J. G., Belcher, C. M., Schwilk, D. W. & Lamont, B. B. Fire-adapted traits of Pinus arose in the fiery Cretaceous. New Phytol. 194, 751–759 (2012).Article 

    Google Scholar 
    Bradstock, R. A. A biogeographic model of fire regimes in Australia: current and future implications. Glob. Ecol. Biogeogr. 19, 145–158 (2010).Article 

    Google Scholar 
    Bowman, D. M., Murphy, B. P., Neyland, D. L., Williamson, G. J. & Prior, L. D. Abrupt fire regime change may cause landscape-wide loss of mature obligate seeder forests. Glob. Change Biol. 20, 1008–1015 (2014).Article 

    Google Scholar 
    Keeley, J. E., Pausas, J. G., Rundel, P. W., Bond, W. J. & Bradstock, R. A. Fire as an evolutionary pressure shaping plant traits. Trends Plant Sci. 16, 406–411 (2011).CAS 
    Article 

    Google Scholar 
    Barrett, K. et al. Postfire recruitment failure in Scots pine forests of southern Siberia. Remote Sens. Environ. 237, 111539 (2020).Article 

    Google Scholar 
    Miller, R. G., Fontaine, J. B., Merritt, D. J., Miller, B. P. & Enright, N. J. Experimental seed sowing reveals seedling recruitment vulnerability to unseasonal fire. Ecol. Appl. 31, e02411 (2021).
    Google Scholar 
    Prior, L. D., Williamson, G. J. & Bowman, D. M. Impact of high-severity fire in a Tasmanian dry eucalypt forest. Austral. J. Bot. 64, 193–205 (2016).Article 

    Google Scholar 
    Brewer, J. S. Long-term population changes of a fire-adapted plant subjected to different fire seasons. Nat. Areas J. 26, 267–273 (2006).Article 

    Google Scholar 
    Keith, D. A., Holman, L., Rodoreda, S., Lemmon, J. & Bedward, M. Plant functional types can predict decade‐scale changes in fire‐prone vegetation. J. Ecol. 95, 1324–1337 (2007).Article 

    Google Scholar 
    Savage, M., Mast, J. N. & Feddema, J. J. Double whammy: high-severity fire and drought in ponderosa pine forests of the Southwest. Can. J. For. Res. 43, 570–583 (2013).Article 

    Google Scholar 
    Miller, R. G. et al. Mechanisms of fire seasonality effects on plant populations. Trends Ecol. Evol. 34, 1104–1117 (2019).Article 

    Google Scholar 
    Tangney, R., Merritt, D. J., Fontaine, J. B. & Miller, B. P. Seed moisture content as a primary trait regulating the lethal temperature thresholds of seeds. J. Ecol. 107, 1093–1105 (2019).Article 

    Google Scholar 
    Tangney, R. et al. Seed dormancy interacts with fire seasonality mechanisms. Trends Ecol. Evol. 35, 1057–1059 (2020).Article 

    Google Scholar 
    Bowman, D. M. et al. The human dimension of fire regimes on Earth. J. Biogeogr. 38, 2223–2236 (2011).Article 

    Google Scholar 
    Knapp, E. E., Estes, B. L. & Skinner, C. N. Ecological effects of prescribed fire season: a literature review and synthesis for managers. Gen. Tech. Rep. https://doi.org/10.2737/PSW-GTR-224 (2009).Miller, R. G. et al. Fire seasonality mechanisms are fundamental for understanding broader fire regime effects. Trends Ecol. Evol. 35, 869–871 (2020).Article 

    Google Scholar 
    Keeley, J. E. & Syphard, A. D. Twenty-first century California, USA, wildfires: fuel-dominated vs. wind-dominated fires. Fire Ecol. 15, 24 (2019).Article 

    Google Scholar 
    Lamont, B. B., Enright, N. J. & He, T. Fitness and evolution of resprouters in relation to fire. Plant Ecol. 212, 1945–1957 (2011).Article 

    Google Scholar 
    Pausas, J. G. & Bradstock, R. A. Fire persistence traits of plants along a productivity and disturbance gradient in mediterranean shrublands of south‐east Australia. Glob. Ecol. Biogeogr. 16, 330–340 (2007).Article 

    Google Scholar 
    Pausas, J. G. & Keeley, J. E. Evolutionary ecology of resprouting and seeding in fire-prone ecosystems. New Phytol. 204, 55–65 (2014).Article 

    Google Scholar 
    Fairman, T. A., Bennett, L. T. & Nitschke, C. R. Short-interval wildfires increase likelihood of resprouting failure in fire-tolerant trees. J. Environ. Manag. 231, 59–65 (2019).Article 

    Google Scholar 
    Pyke, G. H. Fire-stimulated flowering: a review and look to the future. Critic. Rev. Plant Sci. 36, 179–189 (2017).Article 

    Google Scholar 
    Zirondi, H. L., Ooi, M. K. J. & Fidelis, A. Fire-triggered flowering is the dominant post-fire strategy in a tropical savanna. J. Veg. Sci. 32, e12995 (2021).Article 

    Google Scholar 
    Howe, H. F. Response of Zizia aurea to seasonal mowing and fire in a restored Prairie. Am. Midl. Nat. 141, 373–380 (1999).Article 

    Google Scholar 
    Thompson, K. Seeds and seed banks. New Phytol. 106, 23–34 (1987).Article 

    Google Scholar 
    Baskin, C. C. & Baskin, J. M. Seeds: Ecology, Biogeography, and Evolution of Dormancy and Germination 2nd edn (Academic Press, 2001).Alvarado, V. & Bradford, K. J. A hydrothermal time model explains the cardinal temperatures for seed germination. Plant Cell Environ. 25, 1061–1069 (2002).Article 

    Google Scholar 
    Mackenzie, B. D. E., Auld, T. D., Keith, D. A., Hui, F. K. C. & Ooi, M. K. J. The effect of seasonal ambient temperatures on fire-stimulated germination of species with physiological dormancy: a case study using boronia (Rutaceae). PLoS One 11, e0156142 (2016).Article 
    CAS 

    Google Scholar 
    Ooi, M. K. J. Delayed emergence and post-fire recruitment success: effects of seasonal germination, fire season and dormancy type. Austral. J. Bot. 58, 248–256 (2010).Article 

    Google Scholar 
    Bond, W. Fire survival of Cape Proteaceae-influence of fire season and seed predators. Vegetatio 56, 65–74 (1984).Article 

    Google Scholar 
    Keith, D. A., Dunker, B. & Driscoll, D. A. Dispersal: the eighth fire seasonality effect on plants. Trends Ecol. Evol. 35, 305–307 (2020).Article 

    Google Scholar 
    Paroissien, R. & Ooi, M. K. J. Effects of fire season on the reproductive success of the post-fire flowerer Doryanthes excelsa. Environ. Exp. Bot. 192, 104634 (2021).Article 

    Google Scholar 
    Furlaud, J. M., Prior, L. D., Williamson, G. J. & Bowman, D. M. J. S. Bioclimatic drivers of fire severity across the Australian geographical range of giant Eucalyptus forests. J. Ecol. 109, 2514–2536 (2021).Article 

    Google Scholar 
    Thomsen, A. M. & Ooi, M. K. J. Shifting season of fire and its interaction with fire severity: Impacts on reproductive effort in resprouting plants. Ecol. Evol. 12, e8717 (2022).Article 

    Google Scholar 
    Fill, J. M. & Crandall, R. M. Stronger evidence needed for global fire season effects. Trends Ecol. Evol. 35, 867–868 (2020).Article 

    Google Scholar 
    Jump, A. S. & Peñuelas, J. Running to stand still: adaptation and the response of plants to rapid climate change. Ecol. Lett. 8, 1010–1020 (2005).Article 

    Google Scholar 
    Inouye, D. W. Climate change and phenology. Wiley Interdiscip. Rev. Clim. Change n/a, e764 (2022).
    Google Scholar 
    Enright, N. J., Marsula, R., Lamont, B. B. & Wissel, C. The ecological significance of canopy seed storage in fire-prone environments: a model for non-sprouting shrubs. J. Ecol. 86, 946–959 (1998).Article 

    Google Scholar 
    Setterfield, S. A. The impact of experimental fire regimes on seed production in two tropical eucalypt species in northern Australia. Austral. J. Ecol. 22, 279–287 (1997).Article 

    Google Scholar 
    Collette, J. C. & Ooi, M. K. J. Evidence for physiological seed dormancy cycling in the woody shrub Asterolasia buxifolia and its ecological significance in fire-prone systems. Plant Biol. 22, 745–749 (2020).CAS 
    Article 

    Google Scholar 
    Setterfield, S. A. Seedling establishment in an Australian tropical savanna: effects of seed supply, soil disturbance and fire. J. Appl. Ecol. 39, 949–959 (2002).Article 

    Google Scholar 
    Russell-Smith, J. & Edwards, A. C. Seasonality and fire severity in savanna landscapes of monsoonal northern Australia. Int. J. Wildland Fire 15, 541–550 (2006).Article 

    Google Scholar 
    Whitehead, P. J., Purdon, P., Russell-Smith, J., Cooke, P. M. & Sutton, S. The management of climate change through prescribed Savanna burning: Emerging contributions of indigenous people in Northern Australia. Public Adm. Dev. 28, 374–385 (2008).Article 

    Google Scholar 
    Prior, L. D., Williams, R. J. & Bowman, D. M. Experimental evidence that fire causes a tree recruitment bottleneck in an Australian tropical savanna. J. Tropical Ecol. 26, 595–603 (2010).Abatzoglou, J. T., Williams, A. P. & Barbero, R. Global emergence of anthropogenic climate change in fire weather indices. Geophys. Res. Lett. 46, 326–336 (2019).Article 

    Google Scholar 
    Ferreira, L. N., Vega-Oliveros, D. A., Zhao, L., Cardoso, M. F. & Macau, E. E. N. Global fire season severity analysis and forecasting. Comput. Geosci. 134, 104339 (2020).Article 

    Google Scholar 
    Flannigan, M. et al. Global wildland fire season severity in the 21st century. For. Ecol. Manag. 294, 54–61 (2013).Article 

    Google Scholar 
    Ansley, R. J. & Castellano, M. J. Prickly pear cactus responses to summer and winter fires. Rangel. Ecol. Manag. 60, 244–252 (2007).Article 

    Google Scholar 
    Ansley, R. J., Kramp, B. A. & Jones, D. L. Honey mesquite (Prosopis glandulosa) seedling responses to seasonal timing of fire and fireline intensity. Rangel. Ecol. Manag. 68, 194–203 (2015).Article 

    Google Scholar 
    Armstrong, G. & Legge, S. The post-fire response of an obligate seeding Triodia species (Poaceae) in the fire-prone Kimberley, north-west Australia. Int. J. Wildland Fire 20, 974–981 (2012).Article 

    Google Scholar 
    Bellows, R. S., Thomson, A. C., Helmstedt, K. J., York, R. A. & Potts, M. D. Damage and mortality patterns in young mixed conifer plantations following prescribed fires in the Sierra Nevada, California. For. Ecol. Manag. 376, 193–204 (2016).Article 

    Google Scholar 
    Beyers, J. L. & Wakeman, C. D. Season of burn effects in southern California chaparral. In Second interface between ecology and land development in California 45–55 (Occidental College, CA, 2000).Bowen, B. J. & Pate, J. S. Effect of season of burn on shoot recovery and post‐fire flowering performance in the resprouter Stirlingia latifolia R. Br.(Proteaceae). Austral Ecol. 29, 145–155 (2004).Article 

    Google Scholar 
    Casals, P., Valor, T., Rios, A. & Shipley, B. Leaf and bark functional traits predict resprouting strategies of understory woody species after prescribed fires. For. Ecol. Manag. 429, 158–174 (2018).Article 

    Google Scholar 
    Céspedes, B., Torres, I., Luna, B., Pérez, B. & Moreno, J. M. Soil seed bank, fire season, and temporal patterns of germination in a seeder-dominated Mediterranean shrubland. Plant Ecol. 213, 383–393 (2012).Article 

    Google Scholar 
    Clabo, D. C. & Clatterbuck, W. K. Shortleaf pine (Pinus echinata, Pinaceae) seedling sprouting responses: Clipping and burning effects at various seedling ages and seasons. J. Torrey Bot. Soc. 146, 96–110 (2019).Article 

    Google Scholar 
    Drewa, P. B. Effects of fire season and intensity on Prosopis glandulosa Torr. var. glandulosa. Int. J. Wildland Fire 12, 147–157 (2003).Article 

    Google Scholar 
    Drewa, P. B., Platt, W. J. & Moser, E. B. Fire effects on resprouting of shrubs in headwaters of southeastern longleaf pine savannas. Ecology 83, 755–767 (2002).Article 

    Google Scholar 
    Drewa, P. B., Thaxton, J. M. & Platt, W. J. Responses of root‐crown bearing shrubs to differences in fire regimes in Pinus palustris (longleaf pine) savannas: exploring old‐growth questions in second‐growth systems. Appl. Veg. Sci. 9, 27–36 (2006).
    Google Scholar 
    Ellsworth, L. M. & Kauffman, J. B. Seedbank responses to spring and fall prescribed fire in mountain big sagebrush ecosystems of differing ecological condition at Lava Beds National Monument, California. J. Arid Environ. 96, 1–8 (2013).Article 

    Google Scholar 
    Fairfax, R. et al. Effects of multiple fires on tree invasion in montane grasslands. Landsc. Ecol. 24, 1363–1373 (2009).Article 

    Google Scholar 
    Fill, J. M., Welch, S. M., Waldron, J. L. & Mousseau, T. A. The reproductive response of an endemic bunchgrass indicates historical timing of a keystone process. Ecosphere 3, 1–12 (2012).Article 

    Google Scholar 
    Grant, C. Post-burn vegetation development of rehabilitated bauxite mines in Western Australia. For. Ecol. Manag. 186, 147–157 (2003).Article 

    Google Scholar 
    Hajny, K. M., Hartnett, D. C. & Wilson, G. W. Rhus glabra response to season and intensity of fire in tallgrass prairie. Int. J. Wildland Fire 20, 709–720 (2011).Article 

    Google Scholar 
    Holmes, P. A comparison of the impacts of winter versus summer burning of slash fuel in alien-invaded fynbos areas in the Western Cape. Southern African For. J. 192, 41–50 (2001).Article 

    Google Scholar 
    Jasinge, N., Huynh, T. & Lawrie, A. Consequences of season of prescribed burning on two spring-flowering terrestrial orchids and their endophytic fungi. Austr. J. Bot. 66, 298–312 (2018).Article 

    Google Scholar 
    Jasinge, N., Huynh, T. & Lawrie, A. Changes in orchid populations and endophytic fungi with rainfall and prescribed burning in Pterostylis revoluta in Victoria, Australia. Ann. Bot. 121, 321–334 (2018).CAS 
    Article 

    Google Scholar 
    Kauffman, J. & Martin, R. Sprouting shrub response to different seasons and fuel consumption levels of prescribed fire in Sierra Nevada mixed conifer ecosystems. For. Sci. 36, 748–764 (1990).
    Google Scholar 
    Keyser, T. L., Greenberg, C. H. & McNab, W. H. Season of burn effects on vegetation structure and composition in oak-dominated Appalachian hardwood forests. For. Ecol. Manag. 433, 441–452 (2019).Article 

    Google Scholar 
    Knox, K. & Clarke, P. J. Fire season and intensity affect shrub recruitment in temperate sclerophyllous woodlands. Oecologia 149, 730–739 (2006).CAS 
    Article 

    Google Scholar 
    Lamont, B. B. & Downes, K. S. Fire-stimulated flowering among resprouters and geophytes in Australia and South Africa. Plant Ecol. 212, 2111–2125 (2011).Article 

    Google Scholar 
    Lesica, P. & Martin, B. Effects of prescribed fire and season of burn on recruitment of the invasive exotic plant, Potentilla recta, in a semiarid grassland. Restoration Ecol. 11, 516–523 (2003).Article 

    Google Scholar 
    Moreno, J. M. et al. Rainfall patterns after fire differentially affect the recruitment of three Mediterranean shrubs. Biogeosciences 8, 3721–3732 (2011).Article 

    Google Scholar 
    Mulligan, M. K. & Kirkman, L. K. Burning influences on wiregrass (Aristida beyrichiana) restoration plantings: natural seedling recruitment and survival. Restor. Ecol. 10, 334–339 (2002).Article 

    Google Scholar 
    Nield, A. P., Enright, N. J. & Ladd, P. G. Fire-stimulated reproduction in the resprouting, non-serotinous conifer Podocarpus drouynianus (Podocarpaceae): the impact of a changing fire regime. Popul. Ecol. 58, 179–187 (2016).Article 

    Google Scholar 
    Norden, A. H. & Kirkman, L. K. Persistence and prolonged winter dormancy of the federally endangered Schwalbea Americana L.(Scrophulariaceae) following experimental management techniques. Nat. Areas J. 24, 129–134 (2004).
    Google Scholar 
    Olson, M. S. & Platt, W. J. Effects of habitat and growing season fires on resprouting of shrubs in longleaf pine savannas. Vegetatio 119, 101–118 (1995).Article 

    Google Scholar 
    Ooi, M. K. The importance of fire season when managing threatened plant species: a long-term case-study of a rare Leucopogon species (Ericaceae). J. Environ. Manag. 236, 17–24 (2019).Article 

    Google Scholar 
    Pavlovic, N. B., Leicht-Young, S. A. & Grundel, R. Short-term effects of burn season on flowering phenology of savanna plants. Plant Ecology 212, 611–625 (2011).Article 

    Google Scholar 
    Payton, I. J. & Pearce, H. G. Fire-Induced Changes to the Vegetation of Tall-Tussock (Chionochloa rigida) Grassland Ecosystems. (Department of Conservation Wellington, New Zealand, 2009).Peguero, G. & Espelta, J. M. Disturbance intensity and seasonality affect the resprouting ability of the neotropical dry-forest tree Acacia pennatula: do resources stored below-ground matter? J. Tropical Ecol. 28, 539–546 (2011).Risberg, L. & Granström, A. Exploiting a window in time. Fate of recruiting populations of two rare fire-dependent Geranium species after forest fire. Plant Ecol. 215, 613–624 (2014).Article 

    Google Scholar 
    Rodríguez-Trejo, D. A., Castro-Solis, U. B., Zepeda-Bautista, M. & Carr, R. J. First year survival of Pinus hartwegii following prescribed burns at different intensities and different seasons in central Mexico. Int. J. Wildland Fire 16, 54–62 (2007).Article 

    Google Scholar 
    Russell, M., Vermeire, L., Ganguli, A. & Hendrickson, J. Fire return interval and season of fire alter bud banks. Rangel. Ecol. Manag.72, 542–550 (2019).Article 

    Google Scholar 
    Russell-Smith, J., Whitehead, P. J., Cook, G. D. & Hoare, J. L. Response of Eucalyptus‐dominated savanna to frequent fires: lessons from Munmarlary, 1973–1996. Ecol. Monogr. 73, 349–375 (2003).Article 

    Google Scholar 
    Schmidt, I. B., Sampaio, A. B. & Borghetti, F. Effects of the season on sexual reproduction and population structure of Heteropterys pteropetala (Adr. Juss.), Malpiguiaceae, in areas of Cerrado sensu stricto submitted to biennial fires. Acta Bot. Brasilica 19, 927–934 (2005).Article 

    Google Scholar 
    Shepherd, B. J., Miller, D. L. & Thetford, M. Fire season effects on flowering characteristics and germination of longleaf pine (Pinus palustris) savanna grasses. Restor. Ecol. 20, 268–276 (2012).Article 

    Google Scholar 
    Spier, L. P. & Snyder, J. R. Effects of wet-and dry-season fires on Jacquemontia curtisii, a south Florida pine forest endemic. Nat. Areas J. 18, 350–357 (1998).
    Google Scholar 
    Tsafrir, A. et al. Fire season modifies the perennial plant community composition through a differential effect on obligate seeders in eastern Mediterranean woodlands. Appl. Veg. Sci. 22, 115–126 (2019).Article 

    Google Scholar 
    Vander Yacht, A. L. et al. Vegetation response to canopy disturbance and season of burn during oak woodland and savanna restoration in Tennessee. For. Ecol. Manag. 390, 187–202 (2017).Article 

    Google Scholar 
    Vidaller, C., Dutoit, T., Ramone, H. & Bischoff, A. Fire increases the reproduction of the dominant grass Brachypodium retusum and Mediterranean steppe diversity in a combined burning and grazing experiment. Appl. Veg. Sci. 22, 127–137 (2019).Article 

    Google Scholar 
    Williams, P. R., Congdon, R. A., Grice, A. C. & Clarke, P. J. Soil temperature and depth of legume germination during early and late dry season fires in a tropical eucalypt savanna of north‐eastern Australia. Austral Ecol. 29, 258–263 (2004).Article 

    Google Scholar 
    Williams, P. R., Congdon, R. A., Grice, A. C. & Clarke, P. J. Germinable soil seed banks in a tropical savanna: seasonal dynamics and effects of fire. Austral Ecol. 30, 79–90 (2005).Article 

    Google Scholar 
    Zhao, H. et al. Ecophysiological influences of prescribed burning on wetland plants: a case study in Sanjiang Plain wetlands, northeast China. Fresenius Environ. Bull 20, 2932–2938 (2011).CAS 

    Google Scholar 
    Pick, J. L., Nakagawa, S. & Noble, D. W. Reproducible, flexible and high‐throughput data extraction from primary literature: The metaDigitise r package. Methods in Ecol. Evol. 10, 426–431 (2019).Article 

    Google Scholar 
    Team, R. C. R: A Language and Environment for Statistical Computing. https://www.R-project.org/ (2020).Higgins, J. P. et al. Cochrane Handbook for Systematic Reviews of Interventions. (John Wiley & Sons, 2019).Lüdecke, D., Lüdecke, M. D. & David, B. W. Package ‘esc’. https://strengejacke.github.io/esc (2017).Schwarzer, G. meta: An R package for meta-analysis. R news 7, 40–45 (2007).
    Google Scholar 
    Borenstein, M., Hedges, L. V., Higgins, J. P. & Rothstein, H. R. A basic introduction to fixed‐effect and random‐effects models for meta‐analysis. Res. Synth. Methods 1, 97–111 (2010).Article 

    Google Scholar 
    Harrer, M., Cuijpers, P., Furukawa, T. A. & Ebert, D. D. Doing Meta-Analysis with R: a Hands-on Guide. (Chapman and Hall, 2019).Wilke, C. O., Wickham, H. & Wilke, M. C. O. Package ‘cowplot’. Streamlined Plot Theme and Plot Annotations for ‘ggplot2 (Cowplot, 2019).Fill, J. M., Davis, C. N. & Crandall, R. M. Climate change lengthens southeastern USA lightning‐ignited fire seasons. Glob. Change Biol. 25, 3562–3569 (2019).Article 

    Google Scholar 
    Halofsky, J. E., Peterson, D. L. & Harvey, B. J. Changing wildfire, changing forests: the effects of climate change on fire regimes and vegetation in the Pacific Northwest, USA. Fire Ecol. 16, 4 (2020).Article 

    Google Scholar 
    Kraaij, T., Cowling, R. M., van Wilgen, B. W., Rikhotso, D. R. & Difford, M. Vegetation responses to season of fire in an aseasonal, fire-prone fynbos shrubland. PeerJ 5, e3591 (2017).Article 

    Google Scholar 
    Peel, M. C., Finlayson, B. L. & McMahon, T. A. Updated world map of the Köppen-Geiger climate classification. Hydrol. Earth Syst. Sci. 11, 1633–1644 (2007).Article 

    Google Scholar 
    Murphy, B. P. et al. Fire regimes of Australia: a pyrogeographic model system. J. Biogeogr. 40, 1048–1058 (2013).Article 

    Google Scholar 
    McColl-Gausden, S. C., Bennett, L. T., Duff, T. J., Cawson, J. G. & Penman, T. D. Climatic and edaphic gradients predict variation in wildland fuel hazard in south-eastern Australia. Ecography 43, 443–455 (2020).Article 

    Google Scholar 
    Pausas, J. G. & Keeley, J. E. Evolutionary ecology of resprouting and seeding in fire‐prone ecosystems. New Phytol. 204, 55–65 (2014).Article 

    Google Scholar 
    Lamont, B. B., Maitre, D. C. L., Cowling, R. M. & Enright, N. J. Canopy seed storage in woody plants. Bot. Rev. 57, 277–317 (1991).Article 

    Google Scholar 
    Tangney, R. et al. Data supporting: Success of post-fire plant recovery strategies varies with shifting fire seasonality. Zenodo https://doi.org/10.5061/dryad.7sqv9s4t5 (2022).Rothstein, H. R., Sutton, A. J. & Borenstein, M. Publication Bias in Meta-Analysis: Prevention, Assessment and Adjustments (John Wiley & Sons, 2006).Head, M. L., Holman, L., Lanfear, R., Kahn, A. T. & Jennions, M. D. The extent and consequences of P-hacking in science. PLoS Biol. 13, e1002106 (2015).Article 
    CAS 

    Google Scholar 
    Egger, M., Smith, G. D., Schneider, M. & Minder, C. Bias in meta-analysis detected by a simple, graphical test. BMJ 315, 629–634 (1997).CAS 
    Article 

    Google Scholar 
    Simonsohn, U., Nelson, L. D. & Simmons, J. P. P-curve: a key to the file-drawer. J. Exp. Psychol.Gen. 143, 534 (2014).Article 

    Google Scholar  More

  • in

    Modeling the impact of genetically modified male mosquitoes in the spatial population dynamics of Aedes aegypti

    In the present work, we extend the base model for the spatial mosquito population dynamics24 to include wild male mosquitoes and genetically modified male mosquitoes. Thus, five populations will be considered: the aquatic mosquito population, including larvae and pupae, the egg mosquito population, the reproductive female mosquito population, the wild male mosquito population, and the genetically modified male population. Similar approaches can be found in the literature25,26.In the following system, we represent mosquito population densities (mosquitoes per m(^2)) by: E – in the egg phase, A – in the aquatic phase, F – female in the reproductive phase, M – wild males, and G – genetically modified male mosquitoes. Due to the very high resistance of the egg phase (up to 450 days27) and as we are interested in an urban spatial macro-scale modeling, we do not consider the mortality in the egg phase. The model is described by the following system of partial differential equations:$$begin{aligned} {left{ begin{array}{ll} partial _t E &{} = alpha beta F M -e E, \ partial _t A &{} = e left( 1 – dfrac{A}{k} right) E -(eta _a+{mu _a})A, \ partial _t F &{} = nabla cdot (D_m nabla F) -mu _f F + reta _{a} A, \ partial _t M &{} = nabla cdot (D_m nabla M) -mu _m M + (1-r)eta _{a} A, \ partial _t G &{} = nabla cdot (D_g nabla G) -mu _{g}G + l, end{array}right. } end{aligned}$$
    (1)
    where ( alpha ) represents the proportion of wild male mosquitoes to the total number of male mosquitoes (wild males + genetically modified males); (beta ) represents the expected quantity of eggs from the successful encounter between wild females and males; e is the egg hatching rate; k is the carrying capacity of the aquatic phase; ( eta _a ) is the emergence rate for mosquitoes from the aquatic phase to the female or male phases; ( mu _a), (mu _f), (mu _m), and (mu _{g}) are the mortality rates of mosquitoes in the aquatic phase, females, males, and genetically modified males, respectively; r is the proportion of females to males (typically (r=0.5)); (l=l(x,y,t)) is the function representing the number of genetically modified mosquitoes released in a unit of time at any point of the domain; (D_m) is the diffusion coefficient of wild mobiles females and males; (D_g) is the diffusion coefficient of genetically modified males. The proposed model (1) can naturally deal with heterogeneous parameters, such as mortality, diffusion, and carrying capacity coefficients. Thus it is possible to model the influence of rain, wind, and human action. In the context of this work, we are considering that the city neighborhood is divided into two environments: houses and streets. Due to lack of data, we restrict the investigated heterogeneity only to the carrying capacity coefficient.The proposed model can be regarded as an extension of other “economic” models20,24 in the effort to qualitatively reproduce the complex phenomena by using as few parameters as possible. Following this idea, the carrying capacity was neglected in the egg phase because of the skip oviposition phenomenon28 i.e., the female lays the number of eggs that the place holds, without more space, she migrates to other environments to finish laying the eggs. We also do not consider this coefficient in the winged phase as limitations in the winged phase were not reported in any study. On the other hand, we consider it in the aquatic phases (larvae and pupae), where it is effective29.The term ( alpha ), which multiplies the probability of encounters between male and female, represents the impact of the insertion of genetically modified males in the mosquito population to the immobile phase and is defined as$$begin{aligned} alpha = left{ begin{array}{cc} 1, &{} text{ if } M=G= 0, \ dfrac{M}{M + G}, &{} text{ otherwise }. end{array} right. end{aligned}$$
    (2)
    Similar modeling approach can be found in the literature16. As the release rate of genetically modified males increases, the alpha value decreases, and, consequently, the probability of encounter between females and wild males also decreases. Thus, there is a greater probability of encounter between genetically modified males and females. This approach presents an advantage, when compared to the models found in the literature25, as System  (1) does not present singularities at the equilibrium states, allowing mathematical analysis and numerical simulations. From the biological point of view, the increment of male wild mosquitoes over some critical value does not affect the egg deposition. At first glance, the term FM can lead to a misunderstanding that such property is not satisfied in the presented model. However, in Section “Equilibrium points considering the application of genetically modified male mosquitoes,” we argue that both male and female populations possess mathematical attractor equilibria, blocking the wild male population from growing beyond this value.Finally, any acceptable population model should be invariant in the definition domain, meaning its solution does not present senseless values. Setting the variable domain as$$begin{aligned} 0 le E(x,y,t)< infty ,;; 0 le A(x,y,t) le k, ;; 0 le F(x,y,t)< infty ,;; 0 le M(x,y,t)< infty ,;; 0 le G(x,y,t) < infty , end{aligned}$$ (3) we can verify that it is invariant under the time evolution by the System (1). To prove this statement, it is sufficient to verify that the vector field defined by the right side of (1) points into the domain when (E, A, F, M, G) approaches the domain boundary. When E approaches zero, the right side of the first equation in (1) is not negative. When A approaches zero, the right side of the second equation in (1) is not negative. When A approaches k (bottom), the first term on the right side of the second equation in (1) tends to zero, while the second term remains negative. Since the term ( nabla cdot (D_m nabla F) ) cannot change the F sign, when F approaches zero, the right side of the third equation in (1) is not negative Since the term ( nabla cdot (D_m nabla M) ) cannot change the M sign, when M approaches zero, the right side of the fourth equation in (1) is not negative. Since the term ( nabla cdot (D_g nabla G) ) cannot change the G sign, when G approaches zero, the right side of the fifth equation in (1) is not negative. In the rest of this section, let us explain how to estimate one-by-one all the parameters used in this model from experimental data available in the literature. It is a challenging task as, typically, the development of the Ae. aegypti mosquito depends on food variation30, temperature variations14,15 and rainfall31. This data is not available in the literature in the organized and systematic form. Because of that, we assume the environment is under optimal conditions of temperature, availability of food, and humidity.How to estimate emergence rate ((eta _a)) The emergence rate describes the rate at which the aquatic phase of the mosquito emerges into the adult phases. In the present model, for simplicity, it was considered that no mosquito from the crossing between genetically modified males and females reaches adulthood. Thus, the emergence rate is calculated on the crossing between females and wild males. Under optimal conditions and feeding distribution, based on the literature30, the emergence rate is 0.5596 (text{ day}^{-1}).How to estimate diffusion coefficients ((D_m,D_g)) The diffusion coefficient is one of the most important parameters describing the mosquitoes’ movement. We use the methodology proposed in the previous work24 to obtain the diffusion coefficient of adult mosquitoes (females and males) and genetically modified males.The estimate is done by assuming that all mosquitoes are released at (0, 0), and their movement is described by the corresponding equation in (1) neglecting other terms than diffusion. The population starts spreading in all directions. We define the spreading distance R(t) as the radius of the region centered in (0, 0) where (90%) of the initial mosquitoes population density is present. In Silva et al.24 it is shown that$$begin{aligned} R(t) = sqrt{4Dt} ;text {erf}^{-1}(0.9). end{aligned}$$ (4) Now corresponding diffusion coefficient is estimated by using the average flight distance of the mosquitoes and the characteristic time related to their life expectancy. Under favorable weather conditions, the average lifetime flight distance of females and males is approximately32,33 65 m, while the same for GM males is34 67.3 m. Based on the literature, we consider that the characteristic time for wild females and males32 is 7 days, and the same for genetically modified males is34 2.17 days. Using (4) we estimate the values for (D_m) and (D_g) summarized in Table 1. It would be natural to consider that the mosquitoes’ movement changes in different environments. Unfortunately, we were unable to find the corresponding experimental data, and because of that, we considered that (D_m) and (D_g) are the same in streets and house blocks.How to estimate mortality rates ((mu _a), (mu _f), (mu _m), (mu _{g}))The mortality coefficient represents an average quantity of mosquitoes in the corresponding phase dying each day. As mentioned before, we disregard the mortality rate in the egg phase, as it is negligible due to its great durability27, it does not affect the numerical results, and it complicates analytical estimates. Thus, the aquatic phase mortality rate coefficient is equal to the same for larvae’s coefficient, which is approximately29 (mu _a = 0.025) (1/day).There is no solid agreement on the mortality rate of male and female wild mosquitoes in the literature. Although some results29,30 suggest they are similar, we follow these authors and consider them equal. Considering both natural death and accidental ones, approximately (10%) of females and male mosquitoes in the adult phase die at each day35. Under optimal conditions, the mortality coefficient can be estimated from this data by using the proposed model (1) by neglecting diffusion and emergence terms in the corresponding equation; details can be found in the previous work24. The resulting parameter values are summarized in Table 1.It would be natural to consider that the mosquitoes mortality rate depends on the environment. Unfortunately, we were unable to find the corresponding experimental data, and because of that, we considered that (mu _a), (mu _f), (mu _m), and (mu _{g}) are the same in streets and house blocks.How to estimate the expected egg number ((beta ))This coefficient represents the average quantity of eggs a wild female lays per day, assuming a successful meeting with a wild male. Considering the number of times a female lays eggs in its lifetime36, the average quantity of eggs per lay and the mosquito’s life expectancy, under favorable conditions, this coefficient is estimated as (beta = 34).How to estimate the hatching rate (e)This coefficient determines the average number of eggs hatching in one day. Experimental data37 suggest that, under optimal humidity conditions, the mean value of the hatch rate coefficient is 0.24 given a temperature of 28 ((^{circ })C), which is considered ideal for mosquito development. This is the value used in the present work.How to estimate carrying capacity coefficient (k)The carrying capacity k represents the space limitation of one phase due to situations present in the environment37,38, such as competition for food among the larvae39. In general, it depends on external factors such as food availability, climate, terrain properties, making direct estimation almost impossible. In the Analytical results section, we show how to estimate this coefficient for each grid block. When considering spatial population dynamics in a heterogeneous environment, carrying capacity is one of the most influential parameters as it varies significantly. For example, house block offer more food and a shelter against natural predators resulting to a larger carrying capacity when compared with street environment. Following the literature32 we assume that the 80% of the mosquito’s breeding places are in houses resulting in the relation (k_h=5k_s), where (k_h) and (k_s) are the carrying capacities of the house blocks and in the streets.Genetically modified mosquitoes release rate (l)Function l(x, y, t) determines how many genetically modified mosquitoes are released in the location (x, y) at time t.In a normal situation, the sex ratio between males and females is 1 : 1. The increment of this proportion favoring GM males increases the probability of females to mate with these mosquitoes. As reported in the literature12,30 the initial launch size is 11 times larger than the adult female population, and it is done in some spots in the city. In this work, we analyze different release strategies maintaining the (11times 1) proportion in some scenarios.Table 1 All parameter values are directly taken or estimated from the literature as explained in section Modeling.Full size table More

  • in

    Faunal communities mediate the effects of plant richness, drought, and invasion on ecosystem multifunctional stability

    DesignPlant richness. Sixteen locally frequent native plant species in the barren mountain areas (around Taizhou University, Zhejiang, China) invaded by the exotic plant Symphyotrichum subulatum60 were selected as the native species pool. These species were chosen because they spanned the dicotyledon plant taxonomy (including 7 Orders, 10 Families, and 14 Genus, in the Class Magnoliopsida), differed widely in their functional traits (related to height, life form, dominance in local communities, and leaf habit) (Supplementary Table 3), and were occasionally found to be associated with the invasive species Symphyotrichum subulatum60 in the local secondary-succession communities. With this species pool, we were able to imitate the locally natural, spatially stochastic, compositionally ruderal, and functionally varied plant community61, which is a typical attribute of the secondary-succession communities in the local barren mountains invaded by the exotic plant Symphyotrichum subulatum. Based on this native species pool, monocultures of each species (16 total), and random mixtures of 2, 4 or 8 species (with 10, 10, or 9 distinct assemblages, respectively) were designed, creating a complete set (Fig. 1d) of 45 different plant assemblages (pots) in total. Each plant assemblage was replicated 6 times, for a total of 270 pots. To eliminate the non-random effects during the 1-year development of the 270 pots, their distributions were randomized, such that not all replicates of an assemblage were next to each other (Fig. 1d–f).DroughtAfter 1-year development of the native plant assemblages, three drought treatments (non-, moderate-, and intensive-drought) were manipulated by adjusting irrigation using automatic drip irrigation systems, with 100%, 50%, and 25% of the equivalent to the amount received in the areas where native species were collected, respectively. Two random complete sets were selected for each drought treatment, each complete set being composed of 45 different plant assemblages (Fig. 1d–f).Exotic plant invasionNine months after drought treatment, the two complete sets (Fig. 1d) of each drought treatment were randomly exposed (invasion) or not exposed to (non-invasion) the invasive species Symphyotrichum subulatum (Michx.) G. L. Nesom (Fig. 1e, f). S. subulatum, an annual herbaceous plant native to North America, is a common invasive species in the subtropical and tropical regions of China18,60, and tends to interact with the native species via, for example, competing for space and resources62,63, enriching for pathogens or herbivores, and changing soil faunal, bacterial or fungal microbiomes18,64,65.ExperimentThe experiment based on the design mentioned above was conducted at Taizhou University, Zhejiang province, China (28.66°N, 121.39°E). The seeds of the 16 native plant species (Supplementary Table 3) and the soil were collected from nearby mountain areas (Wugui, 28.65°N, 121.38°E; Baiyun, 28.67°N, 121.42°E; Beigu, 28.86°N, 121.11°E). The seed-mixtures were obtained by mixing seeds of the 16 species pro rata, in proportion to germination rates. The soil (fine-loamy, mixed, semiative, mosic, Humic Hapludults) was sieved to pass a 2-mm mesh, and thoroughly mixed. 270 plastic pots (72 cm length × 64 cm width × 42 cm depth) were prepared, and each was filled with a 27-cm soil layer, followed by a 10-cm mixture of soil and vermiculite-compost to provide water-, air- and fertility-support for germination, seedling establishment, and plant growth (Supplementary Table 4).Native plant assemblagesAll the 270 pots were placed inside a plastic shelter, which allowed for both air ventilation and protection from rain. Each pot was sown with a seed-mixture of ca. 800 seeds. One month after germination, for each pot, the undesired seedlings were removed manually according to the plant richness design (Fig. 1d–f), and thus 32 vigorous seedlings (with the same number of seedlings per species, e.g., 4 seedlings for each species of the 8-species mixtures) were spatial-evenly retained. In this manner, the plant richness was manipulated for each plant assemblage. During the development of the 270 plant assemblages, the soil volumetric water content was controlled at ca. 20%, which was similar to that of the nearby mountainous soil, using the automatic drip irrigation systems. Weeds and undesired species were removed monthly (Fig. 1f).Drought treatmentAfter 1-year development of native plant assemblages, the drought treatments (non-, moderate-, and intensive-drought) were manipulated according to the experimental design mentioned above (Fig. 1d, e). Two complete sets (Fig. 1d) of different plant assemblages (2 × 45 pots) were selected for each drought treatment. Every other week, 40 pots each drought treatment were randomly selected for measuring soil water content and soil temperature at the depth of 0–20 cm, using the ProCheck analyzer (Decagon, Pullman, Washington, USA), and irrigation was adjusted accordingly using automatic drip irrigation systems. The irrigation for non-, moderate-, or intensive-drought was adjusted to accomplish an irrigation level amounts to 100%, 50%, or 25% that of the mountain areas where seeds were collected. Because of the distinct seasonal temperature and evaporation conditions, the irrigation frequencies were approximately daily in May-September, every other day in March–April and October–December, and weekly in January–February. With this manipulation, the volumetric soil water contents of non-, moderate-, and intensive-drought were controlled within ranges of 13.8–23.4%, 6.8–13.7%, and 1.4–7.4%, respectively, throughout the manipulation of drought treatment (Fig. 1e, f). Eight months after drought introduction, fresh litter was collected form the two replicate pots of each drought treatment, and then oven-dried at 40 °C, cut into ca. 2-cm pieces, and filled into litterbags (2-g litter in each litterbag).Invasion treatmentNine months after drought introduction, one complete set (45 pots) of the plant assemblages (Fig. 1d) from each drought treatment, was chosen and exposed to invasion disturbance by sowing 50 seeds of S. subulatum in each pot, and the other was specified as the non-invasion treatment (Fig. 1e, f). The prepared litterbags were embedded under the litter-layer of each pot (5 litterbags in each pot), correspondingly.SamplingSix months after invasion introduction, one litterbag was collected for litter-fauna extraction. Nine months after invasion, five soil cores (20-cm depth) were collected with augers (6.4 cm in diameter) and mixed for extraction of soil-fauna, and measurement of soil property and enzyme activity (Fig. 1f). The aboveground biomass of both native and invasive plants in each pot was harvested, sorted to species, oven-dried to a constant mass at 80 °C, and weighed. The belowground plant biomass was also sampled, sorted to native and invasive groups, oven-dried, and weighed (Fig. 1f).Plant, litter-, and soil-faunal communitiesPlant communitySince exotic plant invasion was treated as a disturbance factor, the biomass of the invasive species S. subulatum was not included for analyses concerning plant community and ecosystem (multi)functionality. The aboveground biomasses of native plant species in each of the 270 pots were collected for plant community analysis.Litter- and soil-faunal communitiesOne litterbag or fifty grams of mixed-soil samples were used for litter- or soil-fauna extraction using a Tullgren funnel apparatus (dry funnel method)66. The obtained microarthropods were stored in 70% alcohol, identified with double-tube anatomical lens, and classified to Family level. For both litter and soil samples, the numbers (abundances) of all faunal taxa were counted for litter/soil-faunal community analysis.Phylogenetic information of plant, litter-, and soil-faunal communitiesSimilar procedures were used to construct the plant and faunal phylogenetic trees. First, protein sequences of 12 faunal mitochondrial coding genes and 16 plant plastid coding genes (Supplementary Data 1) were obtained by searching plant or faunal taxonomies from NCBI protein database (https://www.ncbi.nlm.nih.gov/protein/) with Edirect software (https://www.ncbi.nlm.nih.gov/books/NBK179288/). All available sequences at plant species level or faunal Family level were fetched. If unavailable, the missing sequences were sampled from plant genus or faunal Order level. Sequoiadendron giganteum and Echinococcus were specified as out-group references for plant and faunal trees, respectively. Then, the sequences of each plant or faunal taxon were clustered at 97% or 90% identity independently, and the centroids were used as representative markers. The markers were aligned with MUSCLE67, followed by concatenation. Finally, using MEGA X68, the maximum likelihood trees were constructed based on BioNJ initial trees69 and 500 bootstrap checking nodal support. The parameters for plant tree construction were specified as follow: 70% partial deletion (with 4824 positions retained) and the best-fit substitution model JTT + G + I + F70,71; parameters for faunal tree: 90% partial deletion (2778 positions) and LG + G + I + F model71,72. The Linux codes for processing the protein sequences were submitted to GitHub (https://github.com/YuanGe-Lab/JZW_2022/tree/main/linux)The plant and faunal taxonomies, representative markers, and marker accessions are provided as Supplementary Data 1.Ecosystem function-related variablesA total of 14 individual function-related variables were collected. These variables belonged to three functional groups: (1) biomass production, including aboveground and belowground biomass of native plants, light interception efficiency, litter-fauna abundance, and soil-fauna abundance; (2) soil properties, including contents of soil organic carbon, soil nitrogen, soil phosphorus, and GRSP (relating to soil physical properties and stocks of carbon and nutrient73); and (3) processes, including rate of litter decomposition, and activities of β-glucosidase, protease, nitrate reductase and dehydrogenase.Light interception efficiency, the fraction of incident photosynthetically active radiation (PAR) intercepted by each plant community canopy, was determined between 12:00 and 14:00 on clear days using LI-191R line PAR sensors (LI-COR Inc., NE, USA), and the mean of 4 measurements (monthly from May to August the third year; Fig. 1f) was used. Total soil organic carbon and nitrogen were measured with an elemental analyzer (vario Max; Elementar, Germany). Total soil phosphorus was determined using the molybdenum blue method with a UV–visible spectrophotometer (Shimadzu, Kyoto, Japan). GRSP was determined using the method described by Shen et al.18. Litter decomposition rate was assessed by embedding litterbags and fitting litter mass loss against decomposition time (Fig. 1f). Enzyme activities were analyzed by the spectrophotometric method using the substrates, p-Nitrophenyl-β-d-glucopyranoside (pNPG; for β-glucosidase), caseinate (protease), nitrate (nitrate reductase) and triphenyltetrazolium chloride (TTC; dehydrogenase)18.Quantifying community stability and multifunctional stabilityCommunity data was comprised of native plant biomasses or faunal abundances, and the associated phylogenetic information. Multifunctionality data was comprised of 14 function-related variables, each variable (V) being transformed (V’) using the formula ({V}^{{prime} }=frac{V-{{{{{rm{min }}}}}}left(Vright)}{{{{{{rm{sd}}}}}}left(Vright)}) to guarantee even contribution to global variance. We calculated community similarity (1 minus Weighted-UniFrac distance) and multifunctional similarity (1 minus Bray–Curtis distance), based on the community data and the multifunctionality data, respectively. The specific subsets of each symmetric similarity matrix were used to assess three different aspects of stability: (1) Invariability (against stochastic fluctuations), reflected as the pairwise similarities (1476 pairs) within treatment groups, at same plant richness*drought*invasion condition; (2) Drought resistance, the similarities (2148 pairs) between drought (moderate- and intensive-drought) and non-drought treatments, at same plant richness*invasion condition; and (3) Invasion resistance, the similarities (n = 1611 pairs) between invasion and non-invasion treatments, at same plant richness*drought condition (Supplementary Fig. 1).We also assessed the three aspects of stability of each individual function in a similar way, but by calculating the similarity using the formula ({{{{{{{mathrm{SIM}}}}}}}}_{{ij}}=1-frac{|{V}_{i}-{V}_{j}|}{{V}_{i}+{V}_{j}}) (Vi and Vj are ith and jth elements in a function vector; SIMij is the similarity between Vi and Vj).Statistics and reproducibilityPERMANOVA (10,000 randomizations) was conducted to test the influences of the manipulated factors on ecosystem multifunctionality or communities of plant, litter- and soil-fauna, using “vegan::adonis” in R74. Mantel test (10,000 randomizations; Spearman’s R) was conducted to test the community-community or the community-multifunctionality relationships, using “vegan::mantel” in R74.As each similarity-pair of each aspect of community or multifunctional stability mentioned above was in strict correspondence to single level of each manipulated factor (plant richness, drought, and invasion) (Supplementary Fig.  1), the direct/indirect effects of treatments on the community or multifunctional stability can be assessed using SEM. To test direct and indirect effects (by modulating community stability) of the manipulated factors on multifunctional stability, we built three SEMs (Fig. 1a–c) based on three different aspects of stability (i.e., invariability, drought resistance, and invasion resistance) under the conditions of corresponding parings of manipulated factors (Supplementary Fig. 1), with the LAVAAN package75. The standardized paths (direct effects) in SEMs can be conceived as the partial correlations after teasing all side effects away. Bootstrapping with 10,000 randomizations was conducted to generate the unbiased mean effect. The significance of effect was tested using a Mantel-like permutation (10,000 randomizations) test76, where the null hypotheses (H0) were that the independent factors plant richness, drought, and invasion, had no direct/indirect effects (effect = 0) on multifunctional stability. Based on H0, permutation procedure was conducted by permuting the index of dependent factors (both columns and rows of a symmetric matrix; Supplementary Fig. 1) simultaneously to gain null models and null effects. p-values (probability of H0 acceptance) were calculated as the percentage of observed positive (or negative) effect that was greater (or less) than the null effects. We also assessed the direct and indirect effects of factors on the stability of each individual function based on the same SEMs, to consolidate our findings on multifunctional stability. The R codes and examples solving the permutation test for the significance of effects derived from SEMs that based on multidimensional similarity (or distance) were submitted to GitHub (https://github.com/YuanGe-Lab/JZW_2022/tree/main/R). All the analyses were conducted using R (https://www.r-project.org).Reporting summaryFurther information on research design is available in the Nature Research Reporting Summary linked to this article. More

  • in

    John Macfarlane was the first to recognize Eukaryota as a group

    Woese, C. R., Kandler, O. & Wheelis, M. L. Proc. Natl Acad. Sci. USA 87, 4576–4579 (1990).CAS 
    Article 

    Google Scholar 
    Sapp, J. Microbiol. Mol. Biol. Rev. 69, 292–305 (2005).CAS 
    Article 

    Google Scholar 
    Chatton, É. Ann. Sci. Nat. Zool. 8, 1–84 (1925).
    Google Scholar 
    Soyer-Gobillard, M.-O. & Schrevel, J. The Discoveries and Artistic Talents of Édouard Chatton and André Lwoff, Famous Biologists (Cambridge Scholars Publishing, 2020).Macfarlane, J. M. The Causes and Course of Organic Evolution: A Study in Bioenergics (Macmillan, 1918).Haeckel, E. Systematische Phylogenie. Erster Theil (Verlag von Georg Reimer, 1894).Stanier, R. Y., Douderoff, M. & Adelberg, E. The Microbial World 2nd edn (Prentice Hall, 1963).Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J. & Embley, T. M. Nat. Ecol. Evol. 4, 138–147 (2020).Article 

    Google Scholar 
    Steckbeck, W. Science 98, 487–488 (1943).CAS 
    Article 

    Google Scholar 
    Creese, M. R. S. & Creese, T. M. Ladies in the Laboratory III (Scarecrow Press, 2010). More

  • in

    Cover crop-driven shifts in soil microbial communities could modulate early tomato biomass via plant-soil feedbacks

    Mariotte, P. et al. Plant–soil feedback: Bridging natural and agricultural sciences. Trends Ecol. Evol. 33, 129–142 (2018).PubMed 
    Article 

    Google Scholar 
    Daryanto, S., Fu, B., Wang, L., Jacinthe, P. A. & Zhao, W. Quantitative synthesis on the ecosystem services of cover crops. Earth-Sci. Rev. 185, 357–373 (2018).ADS 
    CAS 
    Article 

    Google Scholar 
    Shackelford, G. E., Kelsey, R. & Dicks, L. V. Effects of cover crops on multiple ecosystem services: Ten meta-analyses of data from arable farmland in California and the Mediterranean. Land Use Policy 88, 104204 (2019).Article 

    Google Scholar 
    McDaniel, M. D., Tiemann, L. K. & Grandy, A. S. Does agricultural crop diversity enhance soil microbial biomass and organic matter dynamics? A meta-analysis. Ecol. Appl. 24, 560–570 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Wittwer, R. A., Dorn, B., Jossi, W. & van der Heijden, M. G. A. A. Cover crops support ecological intensification of arable cropping systems. Sci. Rep. 7, 41911 (2017).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Chahal, I. & Van Eerd, L. L. Cover crops increase tomato productivity and reduce nitrogen losses in a temperate humid climate. Nutr. Cycl. Agroecosyst. 119, 195–211 (2021).CAS 
    Article 

    Google Scholar 
    Belfry, K. D., Trueman, C., Vyn, R. J., Loewen, S. A. & Van Eerd, L. L. Winter cover crops on processing tomato yield, quality, pest pressure, nitrogen availability, and profit margins. PLoS ONE 12, 1–17 (2017).Article 
    CAS 

    Google Scholar 
    Wall, L. G. et al. Changes of paradigms in agriculture soil microbiology and new challenges in microbial ecology. Acta Oecologica 95, 68–73 (2019).ADS 
    Article 

    Google Scholar 
    Schmidt, R., Gravuer, K., Bossange, A. V., Mitchell, J. & Scow, K. Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil. PLoS ONE 13, 1–19 (2018).
    Google Scholar 
    Schmidt, R., Mitchell, J. & Scow, K. Cover cropping and no-till increase diversity and symbiotroph:saprotroph ratios of soil fungal communities. Soil Biol. Biochem. 129, 99–109 (2019).CAS 
    Article 

    Google Scholar 
    Ali, A. et al. Hiseq base molecular characterization of soil microbial community, diversity structure, and predictive functional profiling in continuous cucumber planted soil affected by diverse cropping systems in an intensive greenhouse region of Northern China. Int. J. Mol. Sci. 20, 2619 (2019).CAS 
    PubMed Central 
    Article 

    Google Scholar 
    Kim, N., Zabaloy, M. C., Guan, K. & Villamil, M. B. Do cover crops benefit soil microbiome? A meta-analysis of current research. Soil Biol. Biochem. 142, 107701 (2020).CAS 
    Article 

    Google Scholar 
    Vukicevich, E., Lowery, T., Bowen, P., Úrbez-Torres, J. R. & Hart, M. Cover crops to increase soil microbial diversity and mitigate decline in perennial agriculture. A review. Agron. Sustain. Dev. 36, 1–14 (2016).CAS 
    Article 

    Google Scholar 
    Nevins, C. J., Nakatsu, C. & Armstrong, S. Characterization of microbial community response to cover crop residue decomposition. Soil Biol. Biochem. 127, 39–49 (2018).CAS 
    Article 

    Google Scholar 
    Peralta, A. L., Sun, Y., McDaniel, M. D. & Lennon, J. T. Crop rotational diversity increases disease suppressive capacity of soil microbiomes. Ecosphere 9, e02235 (2018).Article 

    Google Scholar 
    Cloutier, M. L. et al. Fungal community shifts in soils with varied cover crop treatments and edaphic properties. Sci. Rep. 10, 1–15 (2020).Article 
    CAS 

    Google Scholar 
    Finney, D. M., Buyer, J. S. & Kaye, J. P. Living cover crops have immediate impacts on soil microbial community structure and function. J. Soil Water Conserv. 72, 361–373 (2017).Article 

    Google Scholar 
    Calderón, F. J., Nielsen, D., Acosta-Martínez, V., Vigil, M. F. & Lyon, D. Cover crop and irrigation effects on soil microbial communities and enzymes in semiarid agroecosystems of the central great plains of North America. Pedosphere 26, 192–205 (2016).Article 
    CAS 

    Google Scholar 
    Romdhane, S. et al. Cover crop management practices rather than composition of cover crop mixtures affect bacterial communities in no-till agroecosystems. Front. Microbiol. 10, 1–11 (2019).Article 

    Google Scholar 
    Blanco-Canqui, H. & Lal, R. Crop residue removal impacts on soil productivity and environmental quality. CRC. Crit. Rev. Plant Sci. 28, 139–163 (2009).CAS 
    Article 

    Google Scholar 
    Turmel, M. S., Speratti, A., Baudron, F., Verhulst, N. & Govaerts, B. Crop residue management and soil health: A systems analysis. Agric. Syst. 134, 6–16 (2015).Article 

    Google Scholar 
    Yang, Q., Wang, X. & Shen, Y. Comparison of soil microbial community catabolic diversity between rhizosphere and bulk soil induced by tillage or residue retention. J. Soil Sci. Plant Nutr. https://doi.org/10.4067/S0718-95162013005000017 (2013).Article 

    Google Scholar 
    Tang, H. et al. Tillage and crop residue incorporation effects on soil bacterial diversity in the double-cropping paddy field of southern China. Arch. Agron. Soil Sci. 67, 435–446 (2021).CAS 
    Article 

    Google Scholar 
    Zhang, Y. et al. Long-term harvest residue retention could decrease soil bacterial diversities probably due to favouring oligotrophic lineages. Microb. Ecol. 76, 771–781 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhang, C. et al. Straw retention efficiently improves fungal communities and functions in the fallow ecosystem. BMC Microbiol. 21, 52 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Chahal, I. & Van Eerd, L. L. Cover crop and crop residue removal effects on temporal dynamics of soil carbon and nitrogen in a temperate, humid climate. PLoS ONE 15, e0235665 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Chahal, I. & Van Eerd, L. L. Evaluation of commercial soil health tests using a medium-term cover crop experiment in a humid, temperate climate. Plant Soil 427, 351–367 (2018).CAS 
    Article 

    Google Scholar 
    Ruis, S. J. & Blanco-Canqui, H. Cover crops could offset crop residue removal effects on soil carbon and other properties: A review. Agron. J. 109, 1785–1805 (2017).CAS 
    Article 

    Google Scholar 
    Zhao, M. et al. Intercropping affects genetic potential for inorganic nitrogen cycling by root-associated microorganisms in Medicago sativa and Dactylis glomerata. Appl. Soil Ecol. 119, 260–266 (2017).ADS 
    Article 

    Google Scholar 
    Wardle, D. A. et al. Ecological linkages between aboveground and belowground biota. Science (80-). 304, 1629–1633 (2004).ADS 
    CAS 
    Article 

    Google Scholar 
    Xiong, C. et al. Host selection shapes crop microbiome assembly and network complexity. New Phytol. 229, 1091–1104 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    McDaniel, M. D., Grandy, A. S., Tiemann, L. K. & Weintraub, M. N. Eleven years of crop diversification alters decomposition dynamics of litter mixtures incubated with soil. Ecosphere 7, e01426 (2016).Article 

    Google Scholar 
    Buyer, J. S., Teasdale, J. R., Roberts, D. P., Zasada, I. A. & Maul, J. E. Factors affecting soil microbial community structure in tomato cropping systems. Soil Biol. Biochem. 42, 831–841 (2010).CAS 
    Article 

    Google Scholar 
    Fernandez-Gnecco, G. et al. Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas. FEMS Microbiol. Ecol. 97, 1–14 (2021).Article 
    CAS 

    Google Scholar 
    Semenov, M. V., Krasnov, G. S., Semenov, V. M. & van Bruggen, A. H. C. Long-term fertilization rather than plant species shapes rhizosphere and bulk soil prokaryotic communities in agroecosystems. Appl. Soil Ecol. 154, 103641 (2020).Article 

    Google Scholar 
    White, C. M. & Weil, R. R. Forage radish cover crops increase soil test phosphorus surrounding radish taproot holes. Soil Sci. Soc. Am. J. 75, 121–130 (2011).ADS 
    CAS 
    Article 

    Google Scholar 
    Schulz, M., Marocco, A., Tabaglio, V., Macias, F. A. & Molinillo, J. M. G. Benzoxazinoids in rye allelopathy—From discovery to application in sustainable weed control and organic farming. J. Chem. Ecol. 39, 154–174 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    Cheng, F. & Cheng, Z. Research progress on the use of plant allelopathy in agriculture and the physiological and ecological mechanisms of allelopathy. Front. Plant Sci. 6, 1020 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    Thapa, V. R., Ghimire, R., Acosta-Martínez, V., Marsalis, M. A. & Schipanski, M. E. Cover crop biomass and species composition affect soil microbial community structure and enzyme activities in semiarid cropping systems. Appl. Soil Ecol. 157, 103735 (2021).Article 

    Google Scholar 
    Drost, S. M., Rutgers, M., Wouterse, M., de Boer, W. & Bodelier, P. L. E. Decomposition of mixtures of cover crop residues increases microbial functional diversity. Geoderma 361, 114060 (2020).ADS 
    CAS 
    Article 

    Google Scholar 
    Di Rauso Simeone, G., Müller, M., Felgentreu, C. & Glaser, B. Soil microbial biomass and community composition as affected by cover crop diversity in a short-term field experiment on a podzolized Stagnosol-Cambisol. J. Plant Nutr. Soil Sci. 183, 539–549 (2020).Article 
    CAS 

    Google Scholar 
    Maul, J. E. et al. Microbial community structure and abundance in the rhizosphere and bulk soil of a tomato cropping system that includes cover crops. Appl. Soil Ecol. 77, 42–50 (2014).Article 

    Google Scholar 
    Huang, J. et al. Allocation and turnover of rhizodeposited carbon in different soil microbial groups. Soil Biol. Biochem. 150, 107973 (2020).CAS 
    Article 

    Google Scholar 
    Strickland, M. S. & Rousk, J. Considering fungal:bacterial dominance in soils—Methods, controls, and ecosystem implications. Soil Biol. Biochem. 42, 1385–1395 (2010).CAS 
    Article 

    Google Scholar 
    Leff, J. W. et al. Predicting the structure of soil communities from plant community taxonomy, phylogeny, and traits. ISME J. 12, 1794–1805 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Milcu, A. et al. Functionally and phylogenetically diverse plant communities key to soil biota. Ecology 94, 1878–1885 (2013).PubMed 
    Article 

    Google Scholar 
    Lozupone, C. A., Hamady, M., Kelley, S. T. & Knight, R. Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. 73, 1576–1585 (2007).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lay, C.-Y., Hamel, C. & St-Arnaud, M. Taxonomy and pathogenicity of Olpidium brassicae and its allied species. Fungal Biol. 122, 837–846 (2018).PubMed 
    Article 

    Google Scholar 
    Liu, L., Zhu, K., Wurzburger, N. & Zhang, J. Relationships between plant diversity and soil microbial diversity vary across taxonomic groups and spatial scales. Ecosphere 11, e02999 (2020).
    Google Scholar 
    Hartwright, L. M., Hunter, P. J. & Walsh, J. A. A comparison of Olpidium isolates from a range of host plants using internal transcribed spacer sequence analysis and host range studies. Fungal Biol. 114, 26–33 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Barel, J. M. et al. Winter cover crop legacy effects on litter decomposition act through litter quality and microbial community changes. J. Appl. Ecol. 56, 132–143 (2019).CAS 
    Article 

    Google Scholar 
    Austin, E. E., Wickings, K., McDaniel, M. D., Robertson, G. P. & Grandy, A. S. Cover crop root contributions to soil carbon in a no-till corn bioenergy cropping system. GCB Bioenergy 9, 1252–1263 (2017).CAS 
    Article 

    Google Scholar 
    Bai, Z., Liang, C., Bodé, S., Huygens, D. & Boeckx, P. Phospholipid 13C stable isotopic probing during decomposition of wheat residues. Appl. Soil Ecol. 98, 65–74 (2016).Article 

    Google Scholar 
    Põlme, S. et al. FungalTraits: A user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Divers. 105, 1–16 (2020).Article 

    Google Scholar 
    Pepe, A., Giovannetti, M. & Sbrana, C. Lifespan and functionality of mycorrhizal fungal mycelium are uncoupled from host plant lifespan. Sci. Rep. 8, 1–10 (2018).
    Google Scholar 
    Frey, S. D. Mycorrhizal fungi as mediators of soil organic matter dynamics. Annu. Rev. Ecol. Evol. Syst. 50, 237–259 (2019).Article 

    Google Scholar 
    Saleem, M., Hu, J. & Jousset, A. More than the sum of its parts: Microbiome biodiversity as a driver of plant growth and soil health. Annu. Rev. Ecol. Evol. Syst. 50, 145–168 (2019).Article 

    Google Scholar 
    Wei, Z. et al. Initial soil microbiome composition and functioning predetermine future plant health. Sci. Adv. 5, 1–12 (2019).
    Google Scholar 
    Ozimek, E. & Hanaka, A. Mortierella species as the plant growth-promoting fungi present in the agricultural soils. Agriculture 11, 7 (2020).Article 
    CAS 

    Google Scholar 
    Li, F. et al. Mortierella elongata’s roles in organic agriculture and crop growth promotion in a mineral soil. L. Degrad. Dev. 29, 1642–1651 (2018).Article 

    Google Scholar 
    Sansinenea, E. Bacillus spp.: As plant growth-promoting bacteria. in Secondary Metabolites of Plant Growth Promoting Rhizomicroorganisms: Discovery and Applications 225–237 (Springer, 2019). https://doi.org/10.1007/978-981-13-5862-3_11.Palaniyandi, S. A., Yang, S. H., Zhang, L. & Suh, J.-W. Effects of actinobacteria on plant disease suppression and growth promotion. Appl. Microbiol. Biotechnol. 97, 9621–9636 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    Jung, M.-Y. et al. Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities. ISME J. 16, 272–283 (2022).CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhong, Y. et al. Microbial community assembly and metabolic function during wheat straw decomposition under different nitrogen fertilization treatments. Biol. Fertil. Soils 56, 697–710 (2020).CAS 
    Article 

    Google Scholar 
    Liu, X. et al. Decomposing cover crops modify root-associated microbiome composition and disease tolerance of cash crop seedlings. Soil Biol. Biochem. 160, 108343 (2021).CAS 
    Article 

    Google Scholar 
    Larkin, R. P., Griffin, T. S. & Honeycutt, C. W. Rotation and cover crop effects on soilborne potato diseases, tuber yield, and soil microbial communities. Plant Dis. 94, 1491–1502 (2010).PubMed 
    Article 

    Google Scholar 
    van der Putten, W. H., Bradford, M. A., Brinkman, E. P., van de Voorde, T. F. J. & Veen, G. F. Where, when and how plant–soil feedback matters in a changing world. Funct. Ecol. 30, 1109–1121 (2016).Article 

    Google Scholar 
    Menalled, U. D., Seipel, T. & Menalled, F. D. Farming system effects on biologically mediated plant–soil feedbacks. Renew. Agric. Food Syst. 36, 1–7 (2021).Article 

    Google Scholar 
    Fierer, N. & Jackson, J. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl. Environ. Microbiol. 71, 4117 (2005).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Vainio, E. J. & Hantula, J. Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycol. Res. 104, 927–936 (2000).CAS 
    Article 

    Google Scholar 
    Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. 108, 4516–4522 (2011).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    White, T. J., Bruns, T., Lee, S. & Taylor, J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: A Guide to Methods and Applications (eds Innis, M. A. et al.) 315–322 (Academic Press, 1990).

    Google Scholar 
    Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rivers, A. R., Weber, K. C., Gardner, T. G., Liu, S. & Armstrong, S. D. ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. F1000Research 7, 1418 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—Approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Bokulich, N. A. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6, 90 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    Abarenkov, K. et al. UNITE QIIME release for Fungi. https://doi.org/10.15156/bio/786385 (2020).R Core Team. R: A Language and Environment for Statistical Computing. (2020).Oksanen, J. et al. vegan: Community Ecology Package. (2020).Anderson, M. J., Gorley, R. N. & Clarke, K. R. PERMANOVA+ for PRIMER: Guide to Software and Statistical Methods. (PRIMER-E, 2008).Anderson, M. J. & Willis, T. J. Canonical analysis of principal coordinates: A useful method of constrained ordination for ecology. Ecology 84, 511–525 (2003).Article 

    Google Scholar 
    Cáceres, M. D. & Legendre, P. Associations between species and groups of sites: Indices and statistical inference. Ecology 90, 3566–3574 (2009).PubMed 
    Article 

    Google Scholar 
    Fernandes, A. D. et al. Unifying the analysis of high-throughput sequencing datasets: Characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis. Microbiome 2, 15 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar  More

  • in

    Molecular phylogenies map to biogeography better than morphological ones

    Harvey, P. H. & Pagel, M. D. The comparative method in evolutionary biology. Vol. 239 (Oxford University Press, 1991).Oyston, J. W., Hughes, M., Wagner, P. J., Gerber, S. & Wills, M. A. What limits the morphological disparity of clades? Interface Focus 5, 0042 (2015).Article 

    Google Scholar 
    Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K. & Mooers, A. O. The global diversity of birds in space and time. Nature 491, 444–448 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Webb, C. O. Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am. Naturalist 156, 145–155 (2000).Article 

    Google Scholar 
    Purvis, A., Gittleman, J. L. & Brooks, T. Phylogeny and conservation. (Cambridge University Press, 2005).Page, R. D. M. Parallel phylogenies: reconstructing the history of host-parasite assemblages. Cladistics 10, 155–173 (1994).Article 

    Google Scholar 
    Weaver, S. C. & Vasilakis, N. Molecular evolution of dengue viruses: contributions of phylogenetics to understanding the history and epidemiology of the preeminent arboviral disease. Infect., Genet. Evolution 9, 523–540 (2009).CAS 
    Article 

    Google Scholar 
    Tassy, P. Trees before and after Darwin. J. Zool. Syst. Evolut. Res. 49, 89–101 (2011).Article 

    Google Scholar 
    Heather, J. M. & Chain, B. The sequence of sequencers: The history of sequencing DNA. Genomics 107, 1–8 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Pyron, R. A. Post-molecular systematics and the future of phylogenetics. Trends Ecol. Evolution 30, 384–389 (2015).Article 

    Google Scholar 
    Sansom, R. S. & Wills, M. A. Differences between hard and soft phylogenetic data. Proc. R. Soc. B: Biol. Sci. 284, 20172150 (2017).Article 

    Google Scholar 
    Scotland, R. W., Olmstead, R. G. & Bennett, J. R. Phylogeny reconstruction: the role of morphology. Syst. Biol. 52, 539–548 (2003).PubMed 
    Article 

    Google Scholar 
    Regier, J. C. et al. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463, 1079–1083 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Callender-Crowe, L. M. & Sansom, R. S. Osteological characters of birds and reptiles are more congruent with molecular phylogenies than soft characters are. Zool. J. Linn. Soc. 194, 1–13 (2022).Article 

    Google Scholar 
    Wahlberg, N. et al. Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers. Proc. R. Soc. B: Biol. Sci. 272, 1577–1586 (2005).CAS 
    Article 

    Google Scholar 
    He, L. et al. A molecular phylogeny of selligueoid ferns (Polypodiaceae): Implications for a natural delimitation despite homoplasy and rapid radiation. Taxon 67, 237–249 (2018).Article 

    Google Scholar 
    Fernández, R., Edgecombe, G. D. & Giribet, G. Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies. Sci. Rep. 8, 1–7 (2018).
    Google Scholar 
    Eme, L., Spang, A., Lombard, J., Stairs, C. W. & Ettema, T. J. G. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15, 711–723 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Asher, R. J., Bennett, N. & Lehmann, T. The new framework for understanding placental mammal evolution. BioEssays 31, 853–864 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    Shoshani, J. & McKenna, M. C. Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data. Mol. Phylogenetics Evolution 9, 572–584 (1998).CAS 
    Article 

    Google Scholar 
    Beck, R. M. D. & Baillie, C. Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny. Proc. R. Soc. B: Biol. Sci. 285, 20181632 (2018).Article 

    Google Scholar 
    Zou, Z. T. & Zhang, J. Z. Morphological and molecular convergences in mammalian phylogenetics. Nat. Commun. 7, 1–9 (2016).
    Google Scholar 
    Hillis, D. M. Molecular versus morphological approaches to systematics. Annu. Rev. Ecol. Syst. 18, 23–42 (1987).Article 

    Google Scholar 
    Thompson, N. Alfred Russell Wallace Contributions to the theory of Natural Selection, 1870, and Charles Darwin and Alfred Wallace, ‘On the Tendency of Species to form Varieties’ (Papers presented to the Linnean Society 30th June 1858). (Routledge, 2004).Croizat, L. Panbiogeography; or an introductory synthesis of zoogeography, phytogeography, and geology, with notes on evolution, systematics, ecology, anthropology, etc., Vol. 1, 2a & 2b (Published by the author, Caracas., 1958).Means, J. C. & Marek, P. E. Is geography an accurate predictor of evolutionary history in the millipede family Xystodesmidae? PeerJ 5, e3854 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wills, M. A., Barrett, P. M. & Heathcote, J. F. The modified gap excess ratio (GER*) and the stratigraphic congruence of dinosaur phylogenies. Syst. Biol. 57, 891–904 (2008).PubMed 
    Article 

    Google Scholar 
    Fisher, D. C. Stratocladistics: integrating temporal data and character data in phylogenetic inference. Annu. Rev. Ecol., Evolution Syst. 39, 365–385 (2008).Article 

    Google Scholar 
    Lazarus, D. B. & Prothero, D. R. The role of stratigraphic and morphologic data in phylogeny. J. Paleontol. 58, 163–172 (1984).
    Google Scholar 
    Camerini, J. R. Evolution, biogeography, and maps: an early history of Wallace’s Line. Isis 84, 700–727 (1993).CAS 
    PubMed 
    Article 

    Google Scholar 
    Upchurch, P., Hunn, C. A. & Norman, D. B. An analysis of dinosaurian biogeography: evidence for the existence of vicariance and dispersal patterns caused by geological events. Proc. R. Soc. B: Biol. Sci. 269, 613–621 (2002).Article 

    Google Scholar 
    Ferreira, G. S., Bronzati, M., Langer, M. C. & Sterli, J. Phylogeny, biogeography and diversification patterns of side-necked turtles (Testudines: Pleurodira). R. Soc. Open Sci. 5, 171773 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ronquist, F. & Sanmartín, I. Phylogenetic methods in biogeography. Annu. Rev. Ecol., Evolution, Syst. 42, 441–464 (2011).Article 

    Google Scholar 
    IUCN. The IUCN Red List of Threatened Species. Version 2019-2., https://www.iucnredlist.org (2019).GBIF.org. GBIF Home Page, https://www.gbif.org/ (2019).Uetz, P., Freed, P., Aguilar, R. & Hošek, J. The reptile database., http://www.reptiledatabase.org (2019).Archie, J. W. Homoplasy excess ratios: new indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index. Syst. Zool. 38, 253–269 (1989).Article 

    Google Scholar 
    Wilkinson, M. On phylogenetic relationships within Dendrotriton (Amphibia: Caudata: Plethodontidae) is there sufficient evidence? Herpetological J. 7, 55–65 (1997).
    Google Scholar 
    O’Connor, A. & Wills, M. A. Measuring stratigraphic congruence across trees, higher taxa, and time. Syst. Biol. 65, 792–811 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Colless, D. H. Review of phylogenetics: the theory and practice of phylogenetic systematics. Syst. Zool. 31, 100–104 (1982).Article 

    Google Scholar 
    Lartillot, N. & Philippe, H. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philos. Trans. R. Soc. B: Biol. Sci. 363, 1463–1472 (2008).Article 

    Google Scholar 
    Sansom, R. S., Choate, P. G., Keating, J. N. & Randle, E. Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees. Biol. Lett. 14, 20180263 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rosa, B. B., Melo, G. A. & Barbeitos, M. S. Homoplasy-based partitioning outperforms alternatives in Bayesian analysis of discrete morphological data. Syst. Biol. 68, 657–671 (2019).PubMed 
    Article 

    Google Scholar 
    Lucena, D. A. & Almeida, E. A. Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae). Zool. J. Linn. Soc. 194, 36–79 (2022).Article 

    Google Scholar 
    O’Reilly, J. E. et al. Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data. Biol. Lett. 12, 20160081 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Smith, M. R. Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets. Biol. Lett. 15, 20180632 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wiens, J. The role of morphological data in phylogeny reconstruction. Syst. Biol. 53, 653–661 (2004).PubMed 
    Article 

    Google Scholar 
    O’Leary, M. A. & Kaufman, S. G. MorphoBank 3.0: Web application for morphological phylogenetics and taxonomy., http://www.morphobank.org (2012).de Queiroz, A. & Gatesy, J. The supermatrix approach to systematics. Trends Ecol. Evolution 22, 34–41 (2007).Article 

    Google Scholar 
    Wilkinson, M. A comparison of two methods of character construction. Cladistics 11, 297–308 (1995).Article 

    Google Scholar 
    Brazeau, M. D. Problematic character coding methods in morphology and their effects. Biol. J. Linn. Soc. 104, 489–498 (2011).Article 

    Google Scholar 
    Drummond, A. J., Ho, S. Y. W., Phillips, M. J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    O’Reilly, J. E., Puttick, M. N., Pisani, D. & Donoghue, P. C. Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data. Palaeontology 61, 105–118 (2018).PubMed 
    Article 

    Google Scholar 
    Keating, J. N., Sansom, R. S., Sutton, M. D., Knight, C. G. & Garwood, R. J. Morphological phylogenetics evaluated using novel evolutionary simulations. Syst. Biol. 69, 897–912 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Makarenkov, V. et al. Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees. BMC Evolut. Biol. 10, 1–16 (2010).Article 
    CAS 

    Google Scholar 
    Stayton, C. T. The definition, recognition, and interpretation of convergent evolution, and two new measures for quantifying and assessing the significance of convergence. Evolution 69, 2140–2153 (2015).PubMed 
    Article 

    Google Scholar 
    Sattler, R. Homology – a continuing challenge. Syst. Bot. 9, 382–394 (1984).Article 

    Google Scholar 
    Jenner, R. A. & Schram, F. R. The grand game of metazoan phylogeny: rules and strategies. Biol. Rev. 74, 121–142 (1999).Article 

    Google Scholar 
    Pisani, D. & Wilkinson, M. Matrix representation with parsimony, taxonomic congruence, and total evidence. Syst. Biol. 51, 151–155 (2002).PubMed 
    Article 

    Google Scholar 
    Arcila, D. et al. Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria). Syst. Biol. 70, 1123–1144 (2021).PubMed 
    Article 

    Google Scholar 
    Felsenstein, J. Phylogenies and the comparative method. Am. Naturalist 125, 1–15 (1985).Article 

    Google Scholar 
    Bremer, K. Branch support and tree stability. Cladistics 10, 295–304 (1994).Article 

    Google Scholar 
    Johnson, W. E. et al. The late Miocene radiation of modern Felidae: a genetic assessment. Science 311, 73–77 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    Van der Made, J. Biogeography and climatic change as a context to human dispersal out of Africa and within Eurasia. Quat. Sci. Rev. 30, 1353–1367 (2011).Article 

    Google Scholar 
    May, F., Rosenbaum, B., Schurr, F. M. & Chase, J. M. The geometry of habitat fragmentation: Effects of species distribution patterns on extinction risk due to habitat conversion. Ecol. Evolution 9, 2775–2790 (2019).Article 

    Google Scholar 
    Swofford, D. L. et al. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50, 525–539 (2001).CAS 
    PubMed 
    Article 

    Google Scholar 
    Jaeger, J. J. & Martin, M. African marsupials – vicariance or dispersion? Nature 312, 379–379 (1984).Article 

    Google Scholar 
    Smith, B. T. et al. The drivers of tropical speciation. Nature 515, 406–409 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Simkanin, C. et al. Exploring potential establishment of marine rafting species after transoceanic long-distance dispersal. Glob. Ecol. Biogeogr. 28, 588–600 (2019).Article 

    Google Scholar 
    Raxworthy, C. J., Forstner, M. R. J. & Nussbaum, R. A. Chameleon radiation by oceanic dispersal. Nature 415, 784–787 (2002).CAS 
    PubMed 
    Article 

    Google Scholar 
    Stehli, F. G. & Webb, S. D. The great American biotic interchange., Vol. 4 (Springer Science & Business Media, 2013).Ronquist, F. Dispersal-vicariance analysis: A new approach to the quantification of historical biogeography. Syst. Biol. 46, 195–203 (1997).Article 

    Google Scholar 
    Ricklefs, R. E. & Bermingham, E. The concept of the taxon cycle in biogeography. Glob. Ecol. Biogeogr. 11, 353–361 (2002).Article 

    Google Scholar 
    Ma, H. An analysis of the equilibrium of migration models for biogeography-based optimization. Inf. Sci. 180, 3444–3464 (2010).Article 

    Google Scholar 
    Yiming, L., Niemelä, J. & Dianmo, L. Nested distribution of amphibians in the Zhoushan archipelago, China: can selective extinction cause nested subsets of species? Oecologia 113, 557–564 (1998).CAS 
    PubMed 
    Article 

    Google Scholar 
    Crisci, J. V., Katinas, L. & Posadas, P. Historical Biogeography: An Introduction. (Harvard University Press, 2003).Chen, R. et al. Adaptive innovation of green plants by horizontal gene transfer. Biotechnol. Adv. 46, 107671 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Schönknecht, G., Weber, A. P. & Lercher, M. J. Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution. BioEssays 36, 9–20 (2014).PubMed 
    Article 
    CAS 

    Google Scholar 
    Smith, A. B. Echinoderm phylogeny: morphology and molecules approach accord. Trends Ecol. Evolution 7, 224–229 (1992).CAS 
    Article 

    Google Scholar 
    Bateman, R. M., Hilton, J. & Rudall, P. J. Morphological and molecular phylogenetic context of the angiosperms: contrasting the ‘top-down’ and ‘bottom-up’ approaches used to infer the likely characteristics of the first flowers. J. Exp. Bot. 57, 3471–3503 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    Morris, J. L. et al. The timescale of early land plant evolution. Proc. Natl Acad. Sci. 115, E2274–E2283 (2018).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Richter, S. The Tetraconata concept: hexapod-crustacean relationships and the phylogeny of Crustacea. Org. Diversity Evolution 2, 217–237 (2002).Article 

    Google Scholar 
    Dunn, C. W. et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452, 745–749 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Caravas, J. & Friedrich, M. Of mites and millipedes: recent progress in resolving the base of the arthropod tree. BioEssays 32, 488–495 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Howard, R. J. et al. The Ediacaran origin of Ecdysozoa: integrating fossil and phylogenomic data. J. Geol. Soc. https://doi.org/10.1144/jgs2021-107 (2022).Newman, M. E. J. A model of mass extinction. J. Theor. Biol. 189, 235–252 (1997).CAS 
    PubMed 
    Article 

    Google Scholar 
    Cobbett, A., Wilkinson, M. & Wills, M. A. Fossils impact as hard as living taxa in parsimony analyses of morphology. Syst. Biol. 56, 753–766 (2007).PubMed 
    Article 

    Google Scholar 
    Ruta, M., Krieger, J., Angielczyk, K. & Wills, M. A. The evolution of the tetrapod humerus: morphometrics, disparity, and evolutionary rates. Earth Environ. Sci. Trans. R. Soc. Edinb. 109, 351–369 (2018).
    Google Scholar 
    Puttick, M. N., Thomas, G. H. & Benton, M. J. High rates of evolution preceded the origins of birds. Evolution 68, 1497–1510 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Sansom, R. S. & Wills, M. A. Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees. Sci. Rep. 3, 1–5 (2013).Article 

    Google Scholar 
    Brinkworth, A., Sansom, R. & Wills, M. A. Phylogenetic incongruence and homoplasy in the appendages and bodies of arthropods: why broad character sampling is best. Zool. J. Linn. Soc. 187, 100–116 (2019).Article 

    Google Scholar 
    Brown, J. W. & Smith, S. A. The past sure is tense: on interpreting phylogenetic divergence time estimates. Syst. Biol. 67, 340–353 (2018).PubMed 
    Article 

    Google Scholar 
    Barba-Montoya, J., Dos Reis, M. & Yang, Z. H. Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating. Mol. Phylogenetics Evolution 114, 386–400 (2017).CAS 
    Article 

    Google Scholar 
    Sanderson, M. J. & Donoghue, M. J. Patterns of variation in levels of homoplasy. Evolution 43, 1781–1795 (1989).PubMed 
    Article 

    Google Scholar 
    Alroy, J. Fossilworks: Gateway to the Paleobiology Database, http://fossilworks.org (2019).Benton, M. J. The Fossil Record 2. (Chapman & Hall, 1993).Cohen, K. M., Harper, D. A. T. & Gibbard, P. L. ICS International Chronostratigraphic Chart 2021/02, http://www.stratigraphy.org/ (2021).Gradstein, F. & Ogg, J. Geologic time scale 2004–why, how, and where next! Lethaia 37, 175–181 (2004).Article 

    Google Scholar 
    Rohde, R. A. The GeoWhen Database, (2005).O’Leary, M. A. et al. The placental mammal ancestor and the post–K-Pg radiation of placentals. Science 339, 662–667 (2013).PubMed 
    Article 
    CAS 

    Google Scholar 
    Kluge, A. G. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Biol. 38, 7–25 (1989).Article 

    Google Scholar 
    Tolson, P. J. Phylogenetics of the boid snake genus Epicrates and Caribbean vicariance theory. Occasional Pap. Mus. Zool., Univ. Mich. 715, 1–68 (1987).
    Google Scholar 
    Clopper, C. J. & Pearson, E. S. The use of confidence or fiducial limits illustrated in the case of the binomial. Biometrika 26, 404–413 (1934).Article 

    Google Scholar  More