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    A latitudinal gradient of deep-sea invasions for marine fishes

    Hillebrand, H. On the generality of the latitudinal diversity gradient. Am. Nat. 163, 192–211 (2004).
    Google Scholar 
    Pianka, E. R. Latitudinal gradients in species diversity: a review of concepts. Am. Nat. 100, 33–46 (1966).
    Google Scholar 
    Mannion, P. D., Upchurch, P., Benson, R. B. J. & Goswami, A. The latitudinal biodiversity gradient through deep time. Trends Ecol. Evol. 29, 42–50 (2014).
    Google Scholar 
    Jablonski, D., Roy, K. & Valentine, J. W. Out of the tropics: evolutionary dynamics of the latitudinal diversity gradient. Science 314, 102–106 (2006).ADS 
    CAS 

    Google Scholar 
    Alexander Pyron, R. & Wiens, J. J. Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity. Proc. R. Soc. B Biol. Sci. 280, 1–10 (2013).
    Google Scholar 
    Allen, A. P. & Gillooly, J. F. Assessing latitudinal gradients in speciation rates and biodiversity at the global scale. Ecol. Lett. 9, 947–954 (2006).
    Google Scholar 
    Wright, S., Keeling, J. & Gillman, L. The road from Santa Rosalia: a faster tempo of evolution in tropical climates. Proc. Natl Acad. Sci. USA 103, 7718–7722 (2006).ADS 
    CAS 

    Google Scholar 
    Rolland, J., Condamine, F. L., Jiguet, F. & Morlon, H. Faster speciation and reduced extinction in the tropics contribute to the mammalian latitudinal diversity gradient. PLoS Biol. 12, e1001775 (2014).
    Google Scholar 
    Rabosky, D. L. et al. An inverse latitudinal gradient in speciation rate for marine fishes. Nature 559, 392–395 (2018).ADS 
    CAS 

    Google Scholar 
    Igea, J. & Tanentzap, A. J. Angiosperm speciation speeds up near the poles. Ecol. Lett. 23, 1–40 (2020).
    Google Scholar 
    Weir, J. T. & Schluter, D. The latitudinal gradient in recent speciation and extinction rates of birds and mammals. Science 315, 1574–1576 (2007).ADS 
    CAS 

    Google Scholar 
    Rabosky, D. L. & Huang, H. A robust semi-parametric test for detecting trait-dependent diversification. Syst. Biol. 65, 181–193 (2016).
    Google Scholar 
    Hansen, J. et al. Global temperature change. Proc. Natl Acad. Sci. USA 103, 14288–14293 (2006).ADS 
    CAS 

    Google Scholar 
    Huey, R. B. & Kingsolver, J. G. Climate warming, resource availability, and the metabolic meltdown of ectotherms. Am. Nat. 194, E140–E150 (2019).
    Google Scholar 
    Gerringer, M. E., Linley, T. D., Jamieson, A. J., Goetze, E. & Drazen, J. C. Pseudoliparis swirei sp. Nov.: A newly-discovered hadal snailfish (Scorpaeniformes: Liparidae) from the Mariana Trench. Zootaxa 4358, 161–177 (2017).
    Google Scholar 
    Childress, J. J. Are there physiological and biochemical adaptations of metabolism in deep-sea animals? Trends Ecol. Evol. 10, 30–36 (1995).CAS 

    Google Scholar 
    Seibel, B. A. & Drazen, J. C. The rate of metabolism in marine animals: environmental constraints, ecological demands and energetic opportunities. Philos. Trans. R. Soc. B Biol. Sci. 362, 2061–2078 (2007).CAS 

    Google Scholar 
    Eme, D., Anderson, M. J., Myers, E. M. V., Roberts, C. D. & Liggins, L. Phylogenetic measures reveal eco-evolutionary drivers of biodiversity along a depth gradient. Ecography 43, 689–702 (2020).
    Google Scholar 
    Costello, M. J. & Chaudhary, C. Marine biodiversity, biogeography, deep-sea gradients, and conservation. Curr. Biol. 27, R511–R527 (2017).CAS 

    Google Scholar 
    Brown, A. & Thatje, S. Explaining bathymetric diversity patterns in marine benthic invertebrates and demersal fishes: Physiological contributions to adaptation of life at depth. Biol. Rev. 89, 406–426 (2014).
    Google Scholar 
    Zintzen, V., Anderson, M. J., Roberts, C. D., Harvey, E. S. & Stewart, A. L. Effects of latitude and depth on the beta diversity of New Zealand fish communities. Sci. Rep. 7, 1–10 (2017).CAS 

    Google Scholar 
    Coleman, R. R., Copus, J. M., Coffey, D. M., Whitton, R. K. & Bowen, B. W. Shifting reef fish assemblages along a depth gradient in Pohnpei, Micronesia. PeerJ 2018, 1–30 (2018).
    Google Scholar 
    Neat, F. C. & Campbell, N. Proliferation of elongate fishes in the deep sea. J. Fish. Biol. 83, 1576–1591 (2013).CAS 

    Google Scholar 
    Martinez, C. M. et al. The deep sea is a hot spot of fish body shape evolution. Ecol. Lett. 24, 1788–1799 (2021).
    Google Scholar 
    Webb, P. Introduction to Oceanography (Online OER textbook, 2017).Hanly, P. J., Mittelbach, G. G. & Schemske, D. W. Speciation and the latitudinal diversity gradient: Insights from the global distribution of endemic fish. Am. Nat. 189, 604–615 (2017).
    Google Scholar 
    Tedesco, P. A., Paradis, E., Lévêque, C. & Hugueny, B. Explaining global-scale diversification patterns in actinopterygian fishes. J. Biogeogr. 44, 773–783 (2017).
    Google Scholar 
    Cooney, C. R., Seddon, N. & Tobias, J. A. Widespread correlations between climatic niche evolution and species diversification in birds. J. Anim. Ecol. 85, 869–878 (2016).
    Google Scholar 
    Title, P. O. & Burns, K. J. Rates of climatic niche evolution are correlated with species richness in a large and ecologically diverse radiation of songbirds. Ecol. Lett. 18, 433–440 (2015).
    Google Scholar 
    Seeholzer, G. F., Claramunt, S. & Brumfield, R. T. Niche evolution and diversification in a Neotropical radiation of birds (Aves: Furnariidae). Evolution 71, 702–715 (2017).
    Google Scholar 
    Kozak, K. H. & Wiens, J. J. Accelerated rates of climatic-niche evolution underlie rapid species diversification. Ecol. Lett. 13, 1378–1389 (2010).
    Google Scholar 
    Schnitzler, J., Graham, C. H., Dormann, C. F., Schiffers, K. & Peter Linder, H. Climatic niche evolution and species diversification in the cape flora, South Africa. J. Biogeogr. 39, 2201–2211 (2012).
    Google Scholar 
    Ghezelayagh, A. et al. Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous. Nat. Ecol. Evol. 1–10. https://doi.org/10.1038/s41559-022-01801-3 (2022).Polato, N. R. et al. Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains. Proc. Natl Acad. Sci. USA 115, 12471–12476 (2018).ADS 
    CAS 

    Google Scholar 
    Rohde, K. Latitudinal gradients in species diversity: the search for the primary cause. Oikos 65, 514–527 (1992).
    Google Scholar 
    O’Hara, T. D., Hugall, A. F., Woolley, S. N. C., Bribiesca-Contreras, G. & Bax, N. J. Contrasting processes drive ophiuroid phylodiversity across shallow and deep seafloors. Nature 565, 636–639 (2019).ADS 

    Google Scholar 
    Losos, J. B. Adaptive radiation, ecological opportunity, and evolutionary determinism. Am. Nat. 175, 623–639 (2010).
    Google Scholar 
    Hulsey, C. D., Roberts, R. J., Loh, Y. H. E., Rupp, M. F. & Streelman, J. T. Lake Malawi cichlid evolution along a benthic/limnetic axis. Ecol. Evol. 3, 2262–2272 (2013).CAS 

    Google Scholar 
    Woolley, S. N. C. et al. Deep-sea diversity patterns are shaped by energy availability. Nature 533, 393–396 (2016).ADS 
    CAS 

    Google Scholar 
    Pigot, A. L., Owens, I. P. F. & Orme, C. D. L. The environmental limits to geographic range expansion in birds. Ecol. Lett. 13, 705–715 (2010).
    Google Scholar 
    Gerringer, M. E., Linley, T. D. & Nielsen, J. G. Revision of the depth record of bony fishes with notes on hadal snailfishes (Liparidae, Scorpaeniformes) and cusk eels (Ophidiidae, Ophidiiformes). Mar. Biol. 168, 1–9 (2021).
    Google Scholar 
    Kolora, S. R. R. et al. Origins and evolution of extreme life span in Pacific Ocean rockfishes. Science 374, 842–847 (2021).ADS 
    CAS 

    Google Scholar 
    Rutschmann, S. et al. Parallel ecological diversification in Antarctic notothenioid fishes as evidence for adaptive radiation. Mol. Ecol. 20, 4707–4721 (2011).
    Google Scholar 
    Wilson, L. A. B., Colombo, M., Hanel, R., Salzburger, W. & Sánchez-Villagra, M. R. Ecomorphological disparity in an adaptive radiation: opercular bone shape and stable isotopes in Antarctic icefishes. Ecol. Evol. 3, 3166–3182 (2013).
    Google Scholar 
    Ingram, T. Speciation along a depth gradient in a marine adaptive radiation. Proc. R. Soc. B. 278, 613–618 (2011).
    Google Scholar 
    Hyde, J. R., Kimbrell, C. A., Budrick, J. E., Lynn, E. A. & Vetter, R. D. Cryptic speciation in the vermilion rockfish (Sebastes miniatus) and the role of bathymetry in the speciation process. Mol. Ecol. 17, 1122–1136 (2008).CAS 

    Google Scholar 
    Kai, Y., Orr, J. W., Sakai, K. & Nakabo, T. Genetic and morphological evidence for cryptic diversity in the Careproctus rastrinus species complex (Liparidae) of the North Pacific. Ichthyol. Res. 58, 143–154 (2011).
    Google Scholar 
    Gerringer, M. E. et al. Habitat influences skeletal morphology and density in the snailfishes (family Liparidae). Front. Zool. 18, 1–22 (2021).
    Google Scholar 
    Saveliev, P. A. & Metelyov, E. A. Species composition and distribution of eelpouts (Zoarcidae, Perciformes, Actinopterygii) in the northwestern Sea of Okhotsk in summer. Prog. Oceanogr. 196, 102605 (2021).
    Google Scholar 
    Quattrini, A. M. et al. Niche divergence by deep-sea octocorals in the genus Callogorgia across the continental slope of the Gulf of Mexico. Mol. Ecol. 22, 4123–4140 (2013).
    Google Scholar 
    Zardus, J. D., Etter, R. J., Chase, M. R., Rex, M. A. & Boyle, E. E. Bathymetric and geographic population structure in the pan-Atlantic deep-sea bivalve Deminucula atacellana (Schenck, 1939). Mol. Ecol. 15, 639–651 (2006).CAS 

    Google Scholar 
    Schüller, M. Evidence for a role of bathymetry and emergence in speciation in the genus Glycera (Glyceridae, Polychaeta) from the deep Eastern Weddell Sea. Polar Biol. 34, 549–564 (2011).
    Google Scholar 
    Smith, W. L., Everman, E. & Richardson, C. Phylogeny and taxonomy of flatheads, scorpionfishes, sea robins, and stonefishes (Percomorpha: Scorpaeniformes) and the evolution of the lachrymal saber. Copeia 106, 94–119 (2018).
    Google Scholar 
    Jamon, M., Renous, S., Gasc, J. P., Bels, V. & Davenport, J. Evidence of force exchanges during the six-legged walking of the bottom-dwelling fish,Chelidonichthys lucerna. J. Exp. Zool. 307A, 542–547 (2007).
    Google Scholar 
    McCune, A. R. & Carlson, R. L. Twenty ways to lose your bladder: common natural mutants in zebrafish and widespread convergence of swim bladder loss among teleost fishes. Evol. Dev. 6, 246–259 (2004).
    Google Scholar 
    Rabosky, D. L. Speciation rate and the diversity of fishes in freshwaters and the oceans. J. Biogeogr. 47, 1207–1217 (2020).
    Google Scholar 
    Daane, J. M. et al. Historical contingency shapes adaptive radiation in Antarctic fishes. Nat. Ecol. Evol. 3, 1102–1109 (2019).
    Google Scholar 
    Mu, Y. et al. Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea. PLoS Genet. 17, e1009530 (2021).CAS 

    Google Scholar 
    Yancey, P. H., Gerringer, M. E., Drazen, J. C., Rowden, A. A. & Jamieson, A. Marine fish may be biochemically constrained from inhabiting the deepest ocean depths. Proc. Natl Acad. Sci. USA 111, 4461–4465 (2014).ADS 
    CAS 

    Google Scholar 
    Janzen, D. Why mountain passes are higher in the tropics. Am. Nat. 101, 233–249 (1967).
    Google Scholar 
    Kozak, K. H. & Wiens, J. J. Climatic zonation drives latitudinal variation in speciation mechanisms. Proc. R. Soc. B: Biol. Sci. 274, 2995–3003 (2007).
    Google Scholar 
    Sheldon, K. S., Huey, R. B., Kaspari, M. & Sanders, N. J. Fifty years of mountain passes: a perspective on Dan Janzen’s classic article. Am. Nat. 191, 553–565 (2018).
    Google Scholar 
    Muñoz, M. M. & Bodensteiner, B. L. Janzen’s hypothesis meets the bogert effect: connecting climate variation, thermoregulatory behavior, and rates of physiological evolution. Integr. Organ. Biol. 1, oby002 (2019).
    Google Scholar 
    Santidrián Tomillo, P., Fonseca, L., Paladino, F. V., Spotila, J. R. & Oro, D. Are thermal barriers ‘higher’ in deep sea turtle nests? PLoS ONE 12, 1–14 (2017).
    Google Scholar 
    Brown, J. H. Why marine islands are farther apart in the tropics. Am. Nat. 183, 842–846 (2014).
    Google Scholar 
    Jablonski, D. et al. Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient. Proc. Natl Acad. Sci. USA 110, 10487–10494 (2013).ADS 
    CAS 

    Google Scholar 
    Hattermann, T. Antarctic thermocline dynamics along a narrow shelf with easterly winds. J. Phys. Oceanogr. 48, 2419–2443 (2018).ADS 

    Google Scholar 
    Robison, B. H. What drives the diel vertical migrations of Antarctic midwater fish? J. Mar. Biol. Ass. 83, 639–642 (2003).
    Google Scholar 
    Bourgeaud, L. et al. Climatic niche change of fish is faster at high latitude and in marine environments. Preprint at bioRxiv https://doi.org/10.1101/853374 (2019).Pie, M. R. et al. The evolution of latitudinal range limits in tropical reef fishes: heritability, limits, and inverse Rapoport’s rule. J. Biogeogr. 00, 1–12 (2021).
    Google Scholar 
    Powell, M. G. & Glazier, D. S. Asymmetric geographic range expansion explains the latitudinal diversity gradients of four major taxa of marine plankton. Paleobiology 43, 196–208 (2017).
    Google Scholar 
    Lawson, A. M. & Weir, J. T. Latitudinal gradients in climatic-niche evolution accelerate trait evolution at high latitudes. Ecol. Lett. 17, 1427–1436 (2014).
    Google Scholar 
    Boag, T. H., Gearty, W. & Stockey, R. G. Metabolic tradeoffs control biodiversity gradients through geological time. Curr. Biol. 31, 2906–2913.e3 (2021).CAS 

    Google Scholar 
    Near, T. J. et al. Ancient climate change, antifreeze, and the evolutionary diversification of Antarctic fishes. Proc. Natl Acad. Sci. USA 109, 3434–3439 (2012).ADS 
    CAS 

    Google Scholar 
    Hotaling, S., Borowiec, M. L., Lins, L. S. F., Desvignes, T. & Kelley, J. L. The biogeographic history of eelpouts and related fishes: Linking phylogeny, environmental change, and patterns of dispersal in a globally distributed fish group. Mol. Phylogenet. Evol. 162, 107211 (2021).
    Google Scholar 
    Thatje, S., Hillenbrand, C.-D., Mackensen, A. & Larter, R. Life hung by a thread: endurance of Antarctic fauna in glacial periods. Ecology 89, 682–692 (2008).
    Google Scholar 
    Keller, I. & Seehausen, O. Thermal adaptation and ecological speciation. Mol. Ecol. 21, 782–799 (2012).CAS 

    Google Scholar 
    Deutsch, C., Penn, J. L. & Seibel, B. Metabolic trait diversity shapes marine biogeography. Nature 585, 557–562 (2020).ADS 
    CAS 

    Google Scholar 
    Labeyrie, L. D., Duplessy, J. C. & Blanc, P. L. Variations in mode of formation and temperature of oceanic deep waters over the past 125,000 years. Nature 327, 477–482 (1987).ADS 
    CAS 

    Google Scholar 
    Boag, T. H., Stockey, R. G., Elder, L. E., Hull, P. M. & Sperling, E. A. Oxygen, temperature and the deep-marine stenothermal cradle of Ediacaran evolution. Proc. R. Soc. B: Biol. Sci. 285, 2011724 (2018).
    Google Scholar 
    Koslow, J. A. Community structure in North Atlantic deep-sea fishes. Prog. Oceanogr. 31, 321–338 (1993).ADS 

    Google Scholar 
    Brunn, A. The abyssal fauna: its ecology, distribution, and origin. Nature 177, 1105–1108 (1956). Fr.ADS 

    Google Scholar 
    Gaither, M. R. et al. Depth as a driver of evolution in the deep sea: Insights from grenadiers (Gadiformes: Macrouridae) of the genus Coryphaenoides. Mol. Phylogenet. Evol. 104, 73–82 (2016).
    Google Scholar 
    Eastman, J. T. Evolution and diversification of Antarctic notothenioid fishes. Am. Zool. 31, 93–110 (1991).
    Google Scholar 
    Quattrini, A. M., Gómez, C. E. & Cordes, E. E. Environmental filtering and neutral processes shape octocoral community assembly in the deep sea. Oecologia 183, 221–236 (2017).ADS 

    Google Scholar 
    Stefanoudis, P. V. et al. Depth-dependent structuring of reef fish assemblages from the shallows to the rariphotic zone. Front. Mar. Sci. 6, 1–16 (2019).
    Google Scholar 
    Zintzen, V., Anderson, M. J., Roberts, C. D. & Diebel, C. E. Increasing variation in taxonomic distinctness reveals clusters of specialists in the deep sea. Ecography 34, 306–317 (2011).
    Google Scholar 
    Price, S. A., Claverie, T., Near, T. J. & Wainwright, P. C. Phylogenetic insights into the history and diversification of fishes on reefs. Coral Reefs 34, 997–1009 (2015).ADS 

    Google Scholar 
    Weber, M. G., Wagner, C. E., Best, R. J., Harmon, L. J. & Matthews, B. Evolution in a Community Context: On Integrating Ecological Interactions and Macroevolution. Trends Ecol. Evol. 32, 291–304 (2017).
    Google Scholar 
    Linley, T. D. et al. Fishes of the hadal zone including new species, in situ observations and depth records of Liparidae. Deep Sea Res. Part I Oceanogr. Res. Pap. 114, 99–110 (2016).ADS 

    Google Scholar 
    Jamieson, A. J., Linley, T. D., Eigler, S. & Macdonald, T. A global assessment of fishes at lower abyssal and upper hadal depths (5000 to 8000 m). Deep Sea Res. Part I Oceanogr. Res. Pap. 103642. https://doi.org/10.1016/j.dsr.2021.103642 (2021).Boers, N. Observation-based early-warning signals for a collapse of the Atlantic meridional overturning circulation. Nat. Clim. Chang. 11, 680–688 (2021).ADS 

    Google Scholar 
    Paulus, E. Shedding light on deep-sea biodiversity—a highly vulnerable habitat in the face of anthropogenic change. Front. Mar. Sci. 8, 667048 (2021).Froese, R. & Pauly, D. FishBase. FishBase www.fishbase.org (2019).Boettiger, C., Lang, D. T. & Wainwright, P. C. Rfishbase: exploring, manipulating and visualizing FishBase data from R. J. Fish. Biol. 81, 2030–2039 (2012).CAS 

    Google Scholar 
    Revell, L. J. phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).
    Google Scholar 
    Harmon, L. J., Weir, J. T., Brock, C. D., Glor, R. E. & Challenger, W. GEIGER investigating evolutionary radiations. Bioinformatics 24, 129–131 (2008).CAS 

    Google Scholar 
    Karstensen, J., Stramma, L. & Visbeck, M. Oxygen minimum zones in the eastern tropical Atlantic and Pacific oceans. Prog. Oceanogr. 77, 331–350 (2008).ADS 

    Google Scholar 
    Sutton, T. T. et al. A global biogeographic classification of the mesopelagic zone. Deep Sea Res. Part I: Oceanogr. Res. Pap. 126, 85–102 (2017).ADS 

    Google Scholar 
    Alfaro, M. E. et al. Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary. Nat. Ecol. Evol. 2, 688–696 (2018).
    Google Scholar 
    Magnuson-Ford, K. & Otto, S. P. Linking the investigations of character evolution and species diversification. Am. Nat. 180, 225–245 (2012).
    Google Scholar 
    Goldberg, E. E. & Igić, B. Tempo and mode in plant breeding system evolution. Evolution 66, 3701–3709 (2012).
    Google Scholar 
    Rabosky, D. L. & Goldberg, E. E. Model inadequacy and mistaken inferences of trait-dependent speciation. Syst. Biol. 64, 340–355 (2015).CAS 

    Google Scholar 
    Beaulieu, J. M. & O’Meara, B. C. Detecting hidden diversification shifts in models of trait-dependent speciation and extinction. Syst. Biol. 65, 583–601 (2016).
    Google Scholar 
    Adams, D. C., Collyer, M. L. & Kaliontzopoulou, A. Geomorph: Software for geometric morphometric analyses. R package version 3.1.0. (2019).Collyer, M. L. & Adams, D. C. RRPP: An r package for fitting linear models to high-dimensional data using residual randomization. Methods Ecol. Evol. 9, 1772–1779 (2018).
    Google Scholar 
    Title, P. O. & Rabosky, D. L. Tip rates, phylogenies and diversification: What are we estimating, and how good are the estimates? Methods Ecol. Evol. 10, 821–834 (2019).
    Google Scholar 
    Freckleton, R. P., Phillimore, A. B. & Pagel, M. Relating traits to diversification: a simple test. Am. Nat. 172, 102–115 (2008).
    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).ADS 
    CAS 

    Google Scholar 
    Louca, S. & Pennell, M. W. Extant timetrees are consistent with a myriad of diversification histories. Nature 580, 502–505 (2020).ADS 
    CAS 

    Google Scholar 
    May, M. R. & Moore, B. R. A Bayesian approach for inferring the impact of a discrete character on rates of continuous-character evolution in the presence of background-rate variation. Syst. Biol. 69, 530–544 (2020).
    Google Scholar 
    Höhna. et al. RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language. Syst. Biol. 65, 726–736 (2016).
    Google Scholar 
    Burress, E. D. & Muñoz, M. M. Ecological opportunity from innovation, not islands, drove the anole lizard adaptive radiation. Syst. Biol. 0, 1–12 (2021).
    Google Scholar 
    Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901–904 (2018).CAS 

    Google Scholar 
    Ives, A. R. & Helmus, M. R. Phylogenetic metrics of community similarity. Am. Nat. 176, E128–E142 (2010).
    Google Scholar 
    Costello, M. J. & Breyer, S. Ocean depths: the mesopelagic and implications for global warming. Curr. Biol. 27, R36–R38 (2017).CAS 

    Google Scholar  More

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    Flickering flash signals and mate recognition in the Asian firefly, Aquatica lateralis

    Flash recordingAll field recording and experiments were performed at the paddy field in the Northern Chita Peninsula, Aichi Prefecture, central Japan, in June and July between 2003 and 2016. The ambient temperature at the firefly’s active period was measured using a thermometer. The flashes were recorded with a digital video camera (NV-GS-400, Panasonic, Japan) mounted on a tripod at a height of 30–50 cm from ground and a distance of 1.0–1.5 m away from the specimen. Isolated specimens were selected for recording to exclude the background light from other nontarget specimens. When another specimen appeared near the target specimen, the video recording was cancelled. When a female copulated during video recording in the field, her flashes until 1 min before copulation were regarded as those of a ‘receptive female’. To record the flashes of a ‘mated female’, the female specimens already mated were prepared in aquariums (because virgin and mated females cannot be distinguished in the field): the eggs were obtained from wild female specimens collected one year before at the same field and reared to adults; immediately after emergence the virgin female was confined in a small container with two cultured males for two nights to facilitate copulation. As the parents of the reared specimens were collected from the observation field (same genetic background), the rearing temperature was almost the same as that of the natural field, the emergence period of the cultured specimens overlapped with that of the natural population, the adult body sizes of the reared and natural specimens were indistinguishable, and the flash pattern of the cultured mated females was indistinguishable from that of the wild (potentially) mated females. Thus, we believe that there was no influence of different rearing environments, i.e., the flash behavior of the cultured mated female specimens is expected to be substantially the same as that of wild mated female specimens. To distinguish them from wild (potentially) mated females, the elytra of cultured mated females were marked with colored ink before placing them in the field, and after three days, the flashes of ink-marked specimens were recorded. Of note, we never observed male attraction and copulation in any of the mated females used for field observation; thus, the mated females were unreceptive.Waveform analysisSequential still images were captured from video files at 30 frames per second using VirtualDub (GPL), and then the light intensities in the images were qualified (8-bit linear gray scaling from black to white at 0–255) using ImageJ software. In this study, we defined ‘flash’ as a luminescent waveform from baseline to baseline and ‘flickering’ as fluctuation above baseline in a single flash. The waveforms containing a saturated signal (255, white) were omitted. The waveforms of the maximum signal value lower than 50 were also omitted because of the difficulty in separating signal and noise. Approximately 10–90 waveforms per individual were analyzed; thus, the effect of the occasional interruption of the flash recording by the specimen’s movement and/or vegetation swinging between the specimen and the video camera is statistically ignorable. FD is defined as the time interval between the beginning and the end of a flash (Fig. S1). Flicker intensity (FI) was defined as$${text{FI}} = left{ {begin{array}{*{20}l} {mathop {max }limits_{1 le i le n} left( {frac{{{text{min}}left( {p_{i} ,p_{i + 1} } right) – t_{i} }}{{min left( {p_{i} , p_{i + 1} } right) + t_{i} }}} right)} hfill & {{text{if}} , n ge 1} hfill \ 0 hfill & {{text{if}} , n = 0} hfill \ end{array} } right.$$where p, t, and n denote the peak and the trough (local extrema) in the waveform of a flash and the number of toughs in the flash, respectively (Fig. S1). In total, we measured the FD and FI values of 347, 94, and 355 waveforms from 13 sedentary males, 7 receptive females, and 8 mated females, respectively. We did not consider the flash brightness as a factor because the measured value of the light intensity depends largely on the distance between the light source and the detector; thus, the actual brightness of the lantern cannot be practically measured in the field.e-FireflyFor male attraction experiments, we built an electronic LED device, the e-firefly, to generate patterned flashes with various FDs and FIs using a chip LED (green type, λmax = 568 nm, Everlight Electronics, Taiwan; Figs. S2 and S3) with a microcontroller PIC16F628A (Microchip Technology, USA) (see Figs. S4-S5). An example of the program for the microcontroller is shown in Supplementary Data S1. The brightness was constant in all programs. Flickering frequency ranged between 5–12 Hz, which corresponds to that of sedentary male flashes (approximately 10 Hz)15. To prevent direct access of the attracted specimen to the light source, the chip LED was covered by a steel net painted green (see Fig. S2). For flying male attraction experiments, when the male landed within a 100-mm distance from the e-firefly, we judged the attraction to be a success; otherwise, it was a failure. For sedentary male attraction experiments, the e-firefly was placed 200–300 mm away from the sedentary male. When the approaching male touched the steel net covering the e-firefly, to warrant a positive approach, we measured the time the male remained on the net. If the male did not move away from the net for more than 2 min, we judged the attraction to be a success (strict criterion for judgment); otherwise, it was a failure.Spectral measurementThe luminescence spectra of e-firefly and A. lateralis were measured using a Flame-S spectrophotometer (Ocean Insight, USA). The living A. lateralis specimens were anesthetized on ice and frozen at − 20 °C until use. The lantern started luminescence by thawing at room temperature, and the spectrum was measured during luminescence (within 5 min).Statistical analysisFirst, we considered a discriminant analysis using a logistic regression model that discriminates between receptive females and others in the observational data. We fitted several models with combinations of FD and FI, quadratic terms of FD and FI (FD2, FI2), interaction of FD and FI (FD (times) FI), and temperature (T) as explanatory variables. Based on Akaike’s information criteria (AIC) values and model simplicity, we chose the logistic regression model with FD, FI, FD2 and T as explanatory variables. Let (p)(({varvec{x}})) denote the conditional probability that a flash is from a receptive female given ({varvec{x}}=left(mathrm{FD},mathrm{ FI},mathrm{ T}right)) and (widehat{p})(({varvec{x}})) denote its estimate. The coefficients of the logistic regression model are estimated as follows.
    [Model for the observational data with temperature (T)]
    $$begin{gathered} {text{log}}frac{{hat{p}}}{{1 – hat{p}}} = begin{array}{*{20}l} { – 32.26 + 69.69 times FD – 43.47 times FI – 76.63 times FD^{2} + 0.87 times T} hfill \ {~quad left( {6.50} right)quad quad left( {15.37} right)quad quad quad left( {8.56} right)quad quad quad quad left( {17.44} right)quad quad quad left( {0.19} right)~~} hfill \ end{array} hfill \ quad {text{AIC: 84}}{text{.75}} hfill \ end{gathered}$$[Model for the observational data without temperature (T)]$$begin{gathered} {text{log}}frac{{hat{p}}}{{1 – hat{p}}} = begin{array}{*{20}l} { – 7.69~ + 47.57 times FD~ – 38.29 times FI~ – 52.86 times FD^{2} ~} hfill \ {~;left( {1.86} right)quad quad left( {9.68} right)quad quad quad left( {7.08} right)quad quad quad quad left( {11.38} right)~~} hfill \ end{array} hfill \ quad {text{AIC: 114}}{text{.89}} hfill \ end{gathered}$$where values in parentheses indicate standard deviations. The same applies hereafter. Temperature (T) is included in the model not because it affects the occurrence of receptive females but because it affects the FD and/or FI of receptive females. The AIC value increased by 30, which is substantial, when temperature was excluded from the model.Figure 2 shows the FD and FI of each flash from receptive females, mated females and males with the discriminant boundaries of receptive females from others for (p=0.5).We next considered a discriminant analysis for the experimental data. Let ({q}^{f}({varvec{x}})) denote the conditional probability that a flying male is attracted to a flash of ({varvec{x}}=left(mathrm{FD},mathrm{ FI},mathrm{ T}right)) and lands, and ({widehat{q}}^{f}({varvec{x}})) denote its estimate. Among several models we fit, the smallest AIC value is attained by the logistic regression model with FD, FI and T as explanatory variables, but the AIC is not much different from the model with FD and FI only.
    [Model for flying males with temperature (T)]
    $$begin{gathered} {text{log}}frac{{hat{q}^{f} }}{{1 – hat{q}^{f} }} = begin{array}{*{20}l} { – 0.74~~ – 2.42 times FD – 16.82 times FI + 0.31 times T} hfill \ {~;left( {4.01} right)quad quad left( {0.83} right)quad quad quad left( {4.88} right)quad quad quad quad left( {0.20} right)~} hfill \ end{array} hfill \ quad {text{AIC}}:66.96 hfill \ end{gathered}$$

    [Model for flying males without temperature (T)]
    $$begin{gathered} {text{log}}frac{{hat{q}^{f} }}{{1 – hat{q}^{f} }} = begin{array}{*{20}l} { – 5.36~ – 1.72 times FD – 13.69 times FI} hfill \ {~;left( {1.49} right)quad quad left( {0.63} right)~quad quad left( {4.09} right)~~} hfill \ end{array} hfill \ quad {text{AIC}}:67.61 hfill \ end{gathered}$$
    For sedentary males, the model with the smallest AIC value includes all the quadratic terms of FI and FD but not temperature. Let ({q}^{s}({varvec{x}})) denote the conditional probability that a sedentary male is attracted to a flash of ({varvec{x}}=left(mathrm{FD},mathrm{ FI},mathrm{ T}right)) and ({widehat{q}}^{s}left({varvec{x}}right)) denote its estimate. The logistic regression model for ({q}^{s}({varvec{x}})) with the best AIC value is given as follows.
    [Model for sedentary males]
    $${text{log}}frac{{hat{q}~^{s} }}{{1 – hat{q}~^{s} }} = begin{array}{*{20}l} { – 0.68~ + 7.84 times FD~ + 48.17 times FI – 5.35 times FD^{2} – 166.70 times FI^{2} – 65.67 times FD times FI} hfill \ {;left( {0.97} right)quad quad quad left( {2.99} right)quad quad quad left( {17.74} right)quad quad quad left( {1.74} right)quad quad quad quad left( {72.34} right)quad quad quad quad left( {17.67} right)~} hfill \ end{array}$$
    Figure 3 shows successes and failures of attraction of flying males on the left and sedentary males on the right with estimated discriminant boundaries.Let us now estimate probabilities that a flying male is attracted and lands or a sedentary male is attracted to a flash when a flash is from a receptive female or when a flash is either from a sedentary male or mated female. The probability that a flying male is attracted and lands when a flash is from a receptive female is a conditional probability and is expressed as follows.$$begin{aligned} Pleft(left.begin{array}{*{20}c} {text{Flying male}} \ {text{is attracted}} \ end{array} right|begin{array}{*{20}c} {text{Receptive }} \ {{text{female}}} \ end{array} right) & = frac{{Pleft( {begin{array}{*{20}c} {text{Flying male}} \ {text{is attracted}} \ end{array} {text{ and }}begin{array}{*{20}c} {text{Receptive }} \ {{text{female}}} \ end{array} } right) }}{{Pleft( {begin{array}{*{20}c} {{text{Receptive}}} \ {{text{female}}} \ end{array} } right)}}, \ Pleft( {begin{array}{*{20}c} {{text{Receptive}}} \ {{text{female}}} \ end{array} } right) & = mathop int_{Omega } Pleft(left. begin{array}{*{20}c} {{text{Receptive}}} \ {{text{female}}} \ end{array} right|{varvec{x}} right)fleft( {varvec{x}} right)d{varvec{x}} = mathop int_{Omega }pleft( {varvec{x}} right) fleft( {varvec{x}} right)d{varvec{x}} hspace{5mm}{text{and}} \ Pleft( {begin{array}{*{20}c} {text{Flying male}} \ {text{is attracted}} \ end{array} {text{ and }}begin{array}{*{20}c} {text{Receptive }} \ {{text{female}}} \ end{array} } right) & = mathop int_{Omega } Pleft(left. begin{array}{*{20}c} {{text{Receptive}}} \ {{text{female}}} \ end{array} right|varvec{x} right)Pleft(left. begin{array}{*{20}c} {text{Flying male}} \ {text{is attracted}} \ end{array} right|{varvec{x}} right)fleft( {varvec{x}} right)d{varvec{x}} \ & = mathop int_{Omega } pleft( varvec{x} right)q^{f} left( {varvec{x}} right)fleft( {varvec{x}} right)d{varvec{x}}mathbf{.} \ end{aligned}$$Integrals are taken over the domain (Omega) of ({varvec{x}}=(FD, FI, T)) of all females and males, and (f({varvec{x}})) is the joint density function of ({varvec{x}}.) Because (f({varvec{x}})) is unknown, we use the empirical distribution of the observational data, and conditional probabilities given ({varvec{x}}) are replaced with their estimates by logistic regression models. Let ({{varvec{x}}}_{i}=left(F{D}_{i}, F{I}_{i}, {T}_{i}right), i=mathrm{1,2},dots N) denote the (i) th observation in the observational data. The estimates of probabilities are given as follows:$$begin{aligned} hat{P}left( {begin{array}{*{20}c} {{text{Receptive}}} \ {{text{female}}} \ end{array} }right) & = frac{1}{N}mathop sum limits_{i = 1}^{n} hat{p}left( {{varvec{x}}_{i} } right) hspace{15mm} {text{and}} \ hat{P}left( {begin{array}{*{20}c} {text{Flying male}} \ {text{is attracted}} \ end{array} {text{ and }}begin{array}{*{20}c} {text{Receptive }} \ {{text{female}}} \ end{array} } right) & = frac{1}{N}mathop sum limits_{i = 1}^{n} hat{p}left( {{varvec{x}}_{i} } right) hat{q}^{f} left( {{varvec{x}}_{i} } right). \ end{aligned}$$Thus,$$hat{P}left( left. begin{array}{*{20}c} {text{Flying male}} \ {text{is attracted}} \ end{array} right| begin{array}{*{20}c} {text{Receptive }} \ {text{female}} \ end{array} right) = frac{{mathop sum nolimits_{i = 1}^{n} hat{p}left( {{varvec{x}}_{i} } right) hat{q}^{f} left( {{varvec{x}}_{i} } right)}}{{mathop sum nolimits_{i = 1}^{n}hat{p}left(varvec{x}_i right)}}.$$Similarly, we have$$begin{aligned} hat{P}left( left.begin{array}{*{20}c} {text{Flying male}} \ {text{is attracted}} \ end{array}right| {text{Others}} right) & = frac{{mathop sum nolimits_{i = 1}^{n} (1 – hat{p}left( {{varvec{x}}_{i} } right)) hat{q}^{f} left( {{varvec{x}}_{i} } right)}}{{mathop sum nolimits_{i = 1}^{n} (1 – hat{p}left( {{varvec{x}}_{i} } right))}} \ hat{P}left( left. begin{array}{*{20}c} {text{Sedentary male}} \ {text{is attracted}} \ end{array} right| begin{array}{*{20}c} {text{Receptive }} \ {text{female}} \ end{array} right)& = frac{{mathop sum nolimits_{i = 1}^{n} hat{p}left( {{varvec{x}}_{i} } right) hat{q}^{s} left( {{varvec{x}}_{i} } right)}}{{mathop sum nolimits_{i = 1}^{n} hat{p}left( varvec{x}_{i} right)}}hspace{15mm} {text{ and}} \hat{P}left(left. begin{array}{*{20}c} {text{Sedentary male}} \ {text{is attracted}} \ end{array}right| {text{Others}} right) & = frac{{mathop sum nolimits_{i = 1}^{n} left( {1 – hat{p}left( varvec{x}_{i} right)} right) hat{q}^{s} left( {varvec{x}_{i} } right)}}{mathop sum nolimits_{i = 1}^{n} left( {1 – hat{p}left( varvec{x}_{i} right)} right)} . \ end{aligned}$$The estimated probabilities are shown in Table 1.Table 1 Estimated probabilities of a flying male and a sedentary male being attracted to flashes from a receptive female and from others.Full size table More

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    Ecological niche model transferability of the white star apple (Chrysophyllum albidum G. Don) in the context of climate and global changes

    IPBES (2019): Summary for policymakers of the global assessment report on biodiversity and ecosystem services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. S. Díaz, J. Settele, E. S. Brondízio E.S., H. T. Ngo, M. Guèze, J. Agard, A. Arneth, P. Balvanera, K. A. Brauman, S. H. M. Butchart, K. M. A. Chan, L. A. Garibaldi, K. Ichii, J. Liu, S. M. Subramanian, G. F. Midgley, P. Miloslavich, Z. Molnár, D. Obura, A. Pfaff, S. Polasky, A. Purvis, J. Razzaque, B. Reyers, R. Roy Chowdhury, Y. J. Shin, I. J. Visseren-Hamakers, K. J. Willis, and C. N. Zayas (eds.). IPBES secretariat, Bonn, Germany. 56 p.FAO. in Global Forest Resources Assessment 2020: Main report. Rome. https://doi.org/10.4060/ca9825en (2020).Millennium Ecosystem Assessment (MA). Ecosystems and Human Well-Being: Synthesis. Island Press, Washington (2005)CBD. Considerations for Implementing International Standards and Codes of Conduct in National Invasive Species. Strategies and Plans. CBD (2011).Semper-Pascual, A. et al. Using occupancy models to assess the direct and indirect impacts of agricultural expansion on species’ populations. Biodivers. Conserv. 29, 3669–3688 (2020).
    Google Scholar 
    IPCC. Provisional State of the Global Climate. 2022. https://storymaps.arcgis.com/stories/5417cd9148c248c0985a5b6d028b0277, Accessed 23rd December 2022.Nunez, S. & Alkemade, R. Exploring interaction effects from mechanisms between climate and land-use changes and the projected consequences on biodiversity. Biodivers. Conserv. 30, 3685–3696 (2021).
    Google Scholar 
    Liu, C., White, M. & Newell, G. Measuring and comparing the accuracy of species distribution models with presence absence data. Ecography 34, 232–243. https://doi.org/10.1111/j.1600-0587.2010.06354.x (2011).Article 
    CAS 

    Google Scholar 
    Hao, T., Elith, J., Lahoz-Monfort, J. J. & Guillera-Arroita, G. Testing whether ensemble modelling is advantageous for maximising predictive performance of species distribution models. Ecography 43, 549–558. https://doi.org/10.1111/ecog.04890 (2020).Article 

    Google Scholar 
    Pearson, G. R., Raxworthy, J. C., Nakamura, M. & Peterson, A. T. Predicting species distributions from small numbers of occurrence records: A test case using cryptic geckos in Madagascar. J. Biogeogr 34, 102–117 (2007).
    Google Scholar 
    Thuiller, W. et al. Niche-based modelling as a tool for predicting the risk of alien plant invasions at a global scale. Glob. Chang. Biol. 11, 2234–2250 (2005).ADS 

    Google Scholar 
    He, Y. et al. Predicting potential global distribution and risk regions for potato cyst nematodes (Globodera rostochiensis and Globodera pallida). Sci. Rep. 12(1), 1–10 (2022).ADS 
    CAS 

    Google Scholar 
    Elith, J., Kearney, M. & Phillips, S. The art of modelling range-shifting species. Methods Ecol. Evol. 1, 330–342 (2010).
    Google Scholar 
    Ashraf, U., Chaudhry, M. N. & Peterson, A. T. Ecological niche models of biotic interactions predict increasing pest risk to olive cultivars with changing climate. Ecosphere 12, e03714. https://doi.org/10.1002/ecs2.3714 (2021).Article 

    Google Scholar 
    Elith, J. et al. A statistical explanation of MaxEnt for ecologists. Divers. Distrib. 17, 43–57 (2011).
    Google Scholar 
    Ganglo, J. C. et al. Ecological niche modeling and strategies for the conservation of Dialium guineense Willd. (Black velvet) in West Africa. Int. J. Biodivers. Conserv. 9, 373–388 (2017).
    Google Scholar 
    Djotan, A. K. G. et al. How far can climate changes help to conserve and restore Garcinia kola Heckel, an extinct species in the wild in Benin (West Africa). Int. J. Biodivers. Conserv. 10, 203–213 (2018).
    Google Scholar 
    Kakpo, S. B. et al. Spatial distribution and impacts of climate change on Milicia excelsa in Benin, West Africa. J. For. Res. 32, 143–150. https://doi.org/10.1007/s11676-019-01069-7 (2021).Article 

    Google Scholar 
    Jung, M. et al. A global map of terrestrial habitat types. Sci. Data 7(1), 1–8 (2020).MathSciNet 

    Google Scholar 
    Poor, E. E., Scheick, B. K. & Mullinax, J. M. Multiscale consensus habitat modeling for landscape level conservation prioritization. Sci. Rep. 10(1), 1–13 (2020).
    Google Scholar 
    Schüßler, D., Mantilla-Contreras, J., Stadtmann, R., Ratsimbazafy, J. H. & Radespiel, U. Identification of crucial stepping stone habitats for biodiversity conservation in northeastern Madagascar using remote sensing and comparative predictive modeling. Biodivers. Conserv. 29, 2161–2184 (2020).
    Google Scholar 
    Campos-Cerqueira, M. et al. Climate change is creating a mismatch between protected areas and suitable habitats for frogs and birds in Puerto Rico. Biodivers. Conserv. 30, 3509–3528 (2021).
    Google Scholar 
    Biddle, R. et al. The value of local community knowledge in species distribution modelling for a threatened Neotropical parrot. Biodivers. Conserv. 30, 1803–1823 (2021).
    Google Scholar 
    Costa, A. et al. Modelling the amphibian chytrid fungus spread by connectivity analysis: Towards a national monitoring network in Italy. Biodivers. Conserv. 30(10), 2807–2825 (2021).
    Google Scholar 
    Konowalik, K. & Nosol, A. Evaluation metrics and validation of presence-only species distribution models based on distributional maps with varying coverage. Sci. Rep. 11(1), 1–15 (2021).
    Google Scholar 
    Borgelt, J., Sicacha-Parada, J., Skarpaas, O. & Verones, F. Native range estimates for red-listed vascular plants. Sci. Data 9(1), 1–12 (2022).
    Google Scholar 
    Brychkova, G. et al. Climate change and land-use change impacts on future availability of forage grass species for Ethiopian dairy systems. Sci. Rep. 12(1), 1–16 (2022).
    Google Scholar 
    Carrara, R. & Roig-Juñent, S. A. Maps of potential biodiversity: when the tools for regional conservation planning clash with species ecological niches. Biodivers. Conserv. 31(2), 651–665 (2022).
    Google Scholar 
    Critchlow, R. et al. Multi-taxa spatial conservation planning reveals similar priorities between taxa and improved protected area representation with climate change. Biodivers. Conserv. 31(2), 683–702 (2022).
    Google Scholar 
    González-Orozco, C. E., Porcel, M., Rodriguez-Medina, C. & Yockteng, R. Extreme climate refugia: A case study of wild relatives of cacao (Theobroma cacao) in Colombia. Biodivers. Conserv. 31(1), 161–182 (2022).
    Google Scholar 
    Karami, S., Ejtehadi, H., Moazzeni, H., Vaezi, J. & Behroozian, M. Minimal climate change impacts on the geographic distribution of Nepeta glomerulosa, medicinal species endemic to southwestern and central Asia. Sci. Rep. 12(1), 1–10 (2022).ADS 
    CAS 

    Google Scholar 
    Montemayor, S. I., Besteiro, S. I. & del Río, M. G. Integrating ecological and biogeographical tools for the identification of conservation areas in two Neotropical biogeographic provinces in Argentina based on phytophagous insects. Biodivers. Conserv. 31(7), 1969–1986 (2022).
    Google Scholar 
    da Silva, L. B. et al. How future climate change and deforestation can drastically affect the species of monkeys endemic to the eastern Amazon, and priorities for conservation. Biodivers. Conserv. 31(3), 971–988 (2022).
    Google Scholar 
    Yousefi, M. & Naderloo, R. Global habitat suitability modeling reveals insufficient habitat protection for mangrove crabs. Sci. Rep. 12(1), 1–9 (2022).
    Google Scholar 
    Yudaputra, A. et al. Habitat preferences, spatial distribution and current population status of endangered giant flower Amorphophallus titanum. Biodivers. Conserv. 31(3), 831–854 (2022).
    Google Scholar 
    Gomes, V. H. et al. Species distribution modelling: Contrasting presence-only models with plot abundance data. Sci. Rep. 8(1), 1–12 (2018).
    Google Scholar 
    Hoveka, L. N., van der Bank, M., Bezeng, B. S. & Davies, T. J. Identifying biodiversity knowledge gaps for conserving South Africa’s endemic flora. Biodivers. Conserv. 29, 2803–2819 (2020).
    Google Scholar 
    Macdonald, D. W. et al. Predicting biodiversity richness in rapidly changing landscapes: Climate, low human pressure or protection as salvation?. Biodivers. Conserv. 29, 4035–4057 (2020).
    Google Scholar 
    Peng, Y., Feng, J., Sang, W. & Axmacher, J. C. Geographical divergence of species richness and local homogenization of plant assemblages due to climate change in grasslands. Biodivers. Conserv. 31(3), 797–810 (2022).
    Google Scholar 
    Rincón, V. et al. Connectivity of Natura 2000 potential natural riparian habitats under climate change in the Northwest Iberian Peninsula: Implications for their conservation. Biodivers. Conserv. 31(2), 585–612 (2022).MathSciNet 

    Google Scholar 
    Leta, S. et al. Modeling the global distribution of Culicoides imicola: An Ensemble approach. Sci. Rep. 9(1), 1–9 (2019).ADS 
    CAS 

    Google Scholar 
    Messina, J. P. et al. The current and future global distribution and population at risk of dengue. Nat. Microbiol. 4(9), 1508–1515 (2019).CAS 

    Google Scholar 
    Redding, D. W. et al. Impacts of environmental and socio-economic factors on emergence and epidemic potential of Ebola in Africa. Nat. Commun. 10, 4531 (2019).ADS 

    Google Scholar 
    Klitting, R. et al. Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades. Nat. Commun. 13(1), 1–15 (2022).
    Google Scholar 
    Li, Y. P., Gao, X., An, Q., Sun, Z. & Wang, H. B. Ecological niche modeling based on ensemble algorithms to predicting current and future potential distribution of African swine fever virus in China. Sci. Rep. 12(1), 1–11 (2022).ADS 

    Google Scholar 
    Oppel, S., Schaefer, H. M., Schmidt, V. & Schröder, B. How much suitable habitat is left for the last known population of the Pale-headed Brush-Finch?. The Condor 106, 429–434 (2004).
    Google Scholar 
    Heikkinen, R. K., Marmion, M. & Luoto, M. Does the interpolation accuracy of species distribution models come at the expense of transferability?. Ecography 35, 276–288 (2012).
    Google Scholar 
    Manzoor, S. A., Griffiths, G. & Lukac, M. Species distribution model transferability and model grain size–finer may not always be better. Sci. Rep. 8(1), 1–9 (2018).
    Google Scholar 
    Yates, K. L. et al. Outstanding challenges in the transferability of ecological models. Trends Ecol. Evol. 33, 790–802. https://doi.org/10.1016/j.tree.2018.08.001 (2018).Article 

    Google Scholar 
    Gantchoff, M. G. et al. Distribution model transferability for a wide-ranging species, the Gray Wolf. Sci. Rep. 12(1), 1–11 (2022).
    Google Scholar 
    Lyam, P. T., Adeyemi, T. O. & Ogundipe, O. T. Distribution modelling of Chrysophyllum albidum G. Don. in South-West Nigeria. J. Nat. Environ. Sci. 3, 7–14 (2012).
    Google Scholar 
    Orwa, C., Mutua, A., Kindt, R., Jamnadass, R., & Simons, A. Agroforestree Database: a tree reference and selection guide version 4.0. World Agroforestry Centre, Kenya. http://www.worldagroforestry.org/af/treedb/ (2009).Bolanle-Ojo, O. T. & Onyekwelu, J. C. Socio-economic importance of Chrysophyllum albidum G. Don. Rainforest and derived savanna ecosystems of Ondo state, Nigeria. Eur. J. Agric. For. Res. 2, 43–51 (2014).
    Google Scholar 
    Ugwu, J. A. & Umeh, V. C. Assessment of African star apple (Chrysophyllum albidum) fruit damage due to insect pests in Ibadan Southwest Nigeria. Res. J. For. 9, 87–92 (2015).
    Google Scholar 
    Akoegninou, A., Van der Burg, W. J. & Van der Maesen, L. J. G. in Flore Analytique du Bénin (No. 06.2). Backhuys Publishers. (2006).Houessou, L. G., Lougbegnon, T. O., Gbesso, F. G., Anagonou, L. E. & Sinsin, B. Ethno-botanical study of the African star apple (Chrysophyllum albidum G. Don) in the Southern Benin (West Africa). J. Ethnobiol. Ethnomed. 8, 1–10 (2012).
    Google Scholar 
    Lougbégnon, O. T., Nassi, K. M. & Gbesso, G. H. F. Ethnobotanique quantitative de l’usage de Chrysophyllum albidum G. Don par les populations locales au Bénin. J. Appl. Biosci. 95, 9028–9038 (2015).
    Google Scholar 
    Nartey, D., Gyesi, J. N., & Borquaye, L. S. Chemical composition and biological activities of the essential oils of Chrysophyllum albidum G. Don (African star apple). Biochem. Res. Int. 2021 (2021).Olajide, O., Udo, E. S., & Out, D. O. Diversity and population of timber tree species producing valuable non-timber products in two tropical rainforests in cross river state, Nigeria. J. Agric. Soc. Sci. ISSN Print 1813–2235 (2008)Platts, P. J., Omeny, P. & Marchant, R. AFRICLIM: High-resolution climate projections for ecological applications in Africa. Afr. J. Ecol. 53, 103–108 (2015).
    Google Scholar 
    Hajima, T. et al. Development of the MIROC-ES2L Earth system model and the evaluation of biogeochemical processes and feedbacks. Geosci. Model Dev. 13, 2197–2244 (2020).ADS 

    Google Scholar 
    Aiello-Lammens, M. E., Boria, R. A., Radosavljevic, A., Vilela, B. & Anderson, R. P. An R package for spatial thinning of species occurrence records for use in ecological niche models. Ecography 38, 541–545 (2015).
    Google Scholar 
    Lannuzel, G., Balmot, J., Dubos, N., Thibault, M. & Fogliani, B. High-resolution topographic variables accurately predict the distribution of rare plant species for conservation area selection in a narrow-endemism hotspot in New Caledonia. Biodivers. Conserv. 30, 963–990 (2021).
    Google Scholar 
    Scales, K. L. et al. Scale of inference: On the sensitivity of habitat models for wide-ranging marine predators to the resolution of environmental data. Ecography 40, 210–220 (2017).
    Google Scholar 
    Fick, S. E. & Hijmans, R. J. (2017) WorldClim 2: New 1km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37(12), 4302–4315 (2017).
    Google Scholar 
    Center for International Earth Science Information Network: CIESIN—Columbia University. 2021. Gridded Population of the World, Version 4 (GPWv4): Administrative Unit Center Points with Population Estimates, Revision 11. Palisades, NY: NASA Socioeconomic Data and Applications Center (SEDAC). Last Accessed 7th December, 2021. https://doi.org/10.7927/H4BC3WMT (2018)Eyring, V. et al. Overview of the coupled model intercomparison project phase 6 (CMIP6) experimental design and organization. Geosci. Model Dev. 9, 1937–1958. https://doi.org/10.5194/gmd-9-1937-2016 (2016).Article 
    ADS 

    Google Scholar 
    Dormann, C. F. et al. Collinearity: A review of methods to deal with it and a simulation study evaluating their performance. Ecography 36, 27–46 (2013).
    Google Scholar 
    Naimi, B. & Araújo, M. B. sdm: A reproducible and extensible R platform for species distribution modelling. Ecography 39, 368–375. https://doi.org/10.1111/ecog.01881 (2016).Article 

    Google Scholar 
    R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/ (2020)Phillips, S. J., Anderson, R. P. & Schapire, R. E. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190, 231–259 (2006).
    Google Scholar 
    Elith, J., Leathwick, J. R. & Hastie, T. A working guide to boosted regression trees. J. Anim. Ecol. 77, 802–813 (2008).CAS 

    Google Scholar 
    Breiman, L. Random forests. Mach. Learn. 45, 5–32. https://doi.org/10.1023/A:1010933404324 (2001).Article 
    MATH 

    Google Scholar 
    Zheng, B. & Agresti, A. Summarizing the predictive power of a generalized linear model. Stat. Med. 19, 1771–1781 (2000).CAS 

    Google Scholar 
    Hastie, T. J. in Generalized Additive Models, Statistical models, 249–307 (Routledge, 2017).Friedman, J. H. Multivariate adaptive regression splines. Ann. Stat. 19, 1–67 (1991).MathSciNet 
    MATH 

    Google Scholar 
    Allouche, O., Tsoar, A. & Kadmon, R. Assessing the accuracy of species distribution models: Prevalence, kappa and the true skill statistic (TSS). J. Appl. Ecol. 43, 1223–1232 (2006).
    Google Scholar 
    Barbet-Massin, M., Jiguet, F., Albert, C. H. & Thuiller, W. Selecting pseudo-absences for species distribution models: How, where and how many?. Methods Ecol. Evol. 3, 327–338 (2012).
    Google Scholar 
    QGIS Development Team. QGIS geographic information system. Open Source Geospatial Foundation Project. http://qgis.osgeo.org (2021)Fandohan, B. et al. Women’s traditional knowledge, use value, and the contribution of tamarind (Tamarindus indica L.) to rural households’ cash income in Benin. Econ. Bot. 64, 248–259 (2010).
    Google Scholar 
    Gouwakinnou, G. N., Lykke, A. M., Assogbadjo, A. E. & Sinsin, B. Local knowledge, pattern and diversity of use of Sclerocarya birrea. J. Ethnobiol. Ethnomed. 7, 1–9 (2011).
    Google Scholar 
    O’Donnell, M. S. & Ignizio, D. A. Bioclimatic predictors for supporting ecological applications in the conterminous United States. US Geological Surv. Data Ser. 691, 4–9 (2012).
    Google Scholar 
    United Nations. 2022. World population projected to reach 9.8 billion in 2050, and 11.2 billion in 2100. https://www.un.org/en/desa/world-population-projected-reach-98-billion-2050-and-112-billion-2100, Accessed 25th December 2022 .Gbesso, F. H. G., Tente, B. H. A., Gouwakinnou, G. N. & Sinsin, B. A. Influence des changements climatiques sur la distribution géographique de Chrysophyllum albidum G. Don (Sapotaceae) au Benin. Int. J. Biol. Chem. Sci. 7, 2007–2018 (2013).
    Google Scholar 
    Elith, J. et al. Novel methods improve prediction of species’ distributions from occurrence data. Ecography 29, 129–151 (2006).
    Google Scholar 
    Mi, C., Huettmann, F., Guo, Y., Han, X. & Wen, L. Why choose random forest to predict rare species distribution with few samples in large undersampled areas? Three Asian crane species models provide supporting evidence. Peer J. 5, e2849. https://doi.org/10.7717/peerj.2849 (2017).Article 

    Google Scholar 
    Segurado, P. & Araujo, M. B. An evaluation of methods for modelling species distributions. J. Biogeogr. 31, 1555–1568 (2004).
    Google Scholar 
    Pearson, R. G. et al. Model-based uncertainty in species range prediction. J. Biogeogr. 33, 1704–1711 (2006).
    Google Scholar 
    Dambros, C. et al. The role of environmental filtering, geographic distance and dispersal barriers in shaping the turnover of plant and animal species in Amazonia. Biodivers. Conserv. 29, 3609–3634 (2020).
    Google Scholar  More

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    What it would take to bring back the dodo

    The flightless dodo went extinct in the seventeenth century. Biotech company Colossal Biosciences plans to resurrect it.Credit: Hart, F/Bridgeman Images

    A biotech company announced an audacious effort to ‘de-extinct’ the dodo last week. The flightless birds vanished from the island of Mauritius — in the Indian Ocean — in the late seventeenth century, and became emblematic of humanity’s negative impacts on the natural world. Could the plan actually work?Colossal Biosciences, based in Dallas, Texas, has landed US$225 million in investment (including funds from the celebrity Paris Hilton) — having previously announced plans to de-extinct thylacines, an Australian marsupial, and create elephants with woolly mammoth traits. But Colossal’s plans depend on huge advances in genome editing, stem-cell biology and animal husbandry, making success far from certain.“It’s incredibly exciting that there’s that kind of money available,” says Thomas Jensen, a cell and molecular reproductive physiologist at Wells College in Aurora, New York. “I’m not sure that the end goal they’re going for is something that’s super feasible in the near future.”Iridescent pigeonsColossal’s plan starts with the dodo’s closest living relative, the iridescent-feathered Nicobar pigeon (Caloenas nicobarica). The company plans to isolate and culture specialized primordial germ cells (PGCs) — which make sperm and egg-producing cells — from developing Nicobars. Colossal’s scientists would edit DNA sequences in the PGCs to match those of dodos using tools such as CRISPR. These gene-edited PGCs would then be inserted into embryos from a surrogate bird species to generate chimeric — those with DNA from both species — animals that make dodo-like egg and sperm. These could potentially produce something resembling a dodo (Raphus cucullatus).To gene-edit Nicobar pigeon PGCs, scientists first need to identify the conditions that allow these cells to flourish in the laboratory, says Jae Yong Han, an avian-reproduction scientist at Seoul National University. Researchers have done this with chickens, but it will take time to identify the appropriate culture conditions that suit other birds’ PGCs.A greater challenge will be determining the genetic changes that could transform Nicobar pigeons into Dodos. A team including Beth Shapiro, a palaeogeneticist at the University of California, Santa Cruz, who is advising Colossal on the dodo project, has sequenced the dodo genome but has not yet published the results. Dodos and Nicobar pigeons shared a common ancestor that lived around 30 million to 50 million years ago, Shapiro’s team reported in 20161. By comparing the nuclear genomes of the two birds, the researchers hope to identify most of the DNA changes that distinguish between them.Insights from ratsTom Gilbert, an evolutionary biologist at the University of Copenhagen, who also advises Colossal, expects the dodo genome to be of high quality — it comes from a museum sample he provided to Shapiro. But he says that finding all the DNA differences between the two birds is not possible. Ancient genomes are cobbled together from short sequences of degraded DNA, and so are filled with unavoidable gaps and errors. And research he published last year comparing the genome of the extinct Christmas Island rat (Rattus macleari) with that of the Norwegian brown rat (Rattus norvegicus)2 suggests that gaps in the dodo genome could lie in the very DNA regions that have changed the most since its lineage split from that of Nicobar pigeons.Even if researchers could identify every genetic difference, introducing the thousands of changes to PGCs would not be simple. “I’m not sure it’s feasible in the near future,” says Jensen, whose team is encountering difficulties making a single genetic change to the genomes of quail.Focusing on only a subset of DNA changes, such as those that alter protein sequences, could slash the number of edits needed. But it’s still not clear that this would yield anything resembling a wild dodo, says Gilbert. “My worry is that Paris Hilton thinks she’s going to get a dodo that looks like a dodo,” he says.A further problem will be the need to find a large bird, such as an emu (Dromaius novaehollandiae), that can act as the surrogate, says Jensen. “Dodo eggs are much, much larger than Nicobar pigeon eggs, you couldn’t grow a dodo inside of a Nicobar egg.”Chicken embryos are fairly receptive to PGCs from other birds, and Jensen’s team has created chimeric chickens that can produce quail sperm — efforts to generate eggs have failed so far. But he thinks it will be far more challenging to transfer PGCs — particularly heavily gene-edited ones — from one wild bird into another.Conservation boon?Colossal chief executive Ben Lamm acknowledges these hurdles, but argues they aren’t dealbreakers. Work towards dodo de-extinction will help with conservation efforts for other birds, he adds. “It will bring a lot of new technologies to the field of bird conservation,” agrees Jensen.Vikash Tatayah, conservation director at the Mauritian Wildlife Foundation in Vacoas-Phoenix, is also enthusiastic about the attention dodo de-extinction could bring to conservation. “It’s something we would like to embrace,” he says.But he points out that the predators that threatened the dodo in the seventeeth century haven’t gone away, whereas most of its habitat has. “You do have to ask,” he says, “if we could have such money, wouldn’t it be better spent on restoring habitat on Mauritius and preventing species from going extinct?” More

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    Family before work: task reversion in workers of the red imported fire ant, Solenopsis invicta in the presence of brood

    Wilson, E. O. The Insect Societies (Oxford University Press, 1971).
    Google Scholar 
    Beshers, S. N. & Fewell, J. H. Models of division of labor in social insects. Annu. Rev. Entomol. 46, 413–440 (2001).CAS 

    Google Scholar 
    Seeley, T. D. Adaptive significance of the age polyethism schedule in honeybee colonies. Behav. Ecol. Sociobiol. 4, 287–293 (1982).
    Google Scholar 
    Tallamy, D. W. Insect parental care. Bioscience 34, 20–24. https://doi.org/10.2307/1309421 (1984).Article 

    Google Scholar 
    Queller, D. C. Extended parental care and the origin of eusociality. Proc. R. Soc. Lond. Ser. B: Biol. Sci. 256, 105–111. https://doi.org/10.1098/rspb.1994.0056 (1994).Article 
    ADS 

    Google Scholar 
    Bigley, W. S. & Vinson, S. B. Characterization of a brood pheromone isolated from the sexual brood of the imported fire ant, Solenopsis invicta 1,2. Ann. Entomol. Soc. Am. 68, 301–304 (1975).CAS 

    Google Scholar 
    Endler, A. et al. Surface hydrocarbons of queen eggs regulate worker reproduction in a social insect. Proc. Natl. Acad. Sci. USA 101, 2945–2950. https://doi.org/10.1073/pnas.0308447101 (2004).Article 
    ADS 
    CAS 

    Google Scholar 
    Maisonnasse, A., Lenoir, J. C., Beslay, D., Crauser, D. & Le Conte, Y. E-beta-ocimene, a volatile brood pheromone involved in social regulation in the honey bee colony (Apis mellifera). PLoS ONE 5, e13531. https://doi.org/10.1371/journal.pone.0013531 (2010).Article 
    ADS 
    CAS 

    Google Scholar 
    Schultner, E., Oettler, J. & Helantera, H. The role of brood in eusocial hymenoptera. Q. Rev. Biol. 92, 39–78. https://doi.org/10.1086/690840 (2017).Article 

    Google Scholar 
    Amdam, G. V., Hartfelder, K., Norberg, K., Hagen, A. & Omholt, S. W. Altered physiology in worker honey bees (Hymenoptera: Apidae) infested with the mite Varroa destructor (Acari: Varroidae): A factor in colony loss during overwintering? J. Econ. Entomol. 97, 741–747 (2004).
    Google Scholar 
    Calabi, P. & Traniello, J. F. Behavioral flexibility in age castes of the ant Pheidole dentata. J. Insect Behav. 2, 663–677 (1989).
    Google Scholar 
    Gordon, D. W. Dynamics of task switching in harvester ants. Anim. Behav. 38, 194–204 (1989).
    Google Scholar 
    Robinson, G. E. Regulation of division of labor in insect societies. Annu. Rev. Entomol. 37, 637–665. https://doi.org/10.1146/annurev.en.37.010192.003225 (1992).Article 
    CAS 

    Google Scholar 
    Robinson, E. J., Feinerman, O. & Franks, N. R. Flexible task allocation and the organization of work in ants. Proc. R. Soc. B: Biol. Sci. 276, 4373–4380 (2009).
    Google Scholar 
    Nijhout, H. F. & Wheeler, D. E. Juvenile-hormone and the physiological-basis of Insect polymorphisms. Q. Rev. Biol. 57, 109–133. https://doi.org/10.1086/412671 (1982).Article 
    CAS 

    Google Scholar 
    Herb, B. R. et al. Reversible switching between epigenetic states in honeybee behavioral subcastes. Nat. Neurosci. 15, 1371–1373. https://doi.org/10.1038/nn.3218 (2012).Article 
    CAS 

    Google Scholar 
    Kensuke, N. Age polyethism, idiosyncrasy and behavioural flexibility in the queenless ponerine ant, Diacamma sp. J. Ethol. 13, 113–123 (1995).
    Google Scholar 
    Kensuke, N. Does behavioral flexibility compensate or constrain colony productivity? Relationship among age structure, labor allocation, and production of workers in ant colonies. J. Insect Behav. 9, 557–569 (1996).
    Google Scholar 
    Shimoji, H., Kasutani, N., Ogawa, S. & Hojo, M. K. Worker propensity affects flexible task reversion in an ant. Behav. Ecol. 74, 1–8 (2020).
    Google Scholar 
    Bernadou, A., Busch, J. & Heinze, J. Diversity in identity: Behavioral flexibility, dominance, and age polyethism in a clonal ant. Behav. Ecol. Sociobiol. 69, 1365–1375 (2015).
    Google Scholar 
    Kohlmeier, P., Feldmeyer, B. & Foitzik, S. Vitellogenin-like A—Associated shifts in social cue responsiveness regulate behavioral task specialization in an ant. PLoS Biol. 16, e2005747 (2018).
    Google Scholar 
    Tripet, F. & Nonacs, P. Foraging for work and age-based polyethism: The roles of age and previous experience on task choice in ants. Ethology 110, 863–877 (2004).
    Google Scholar 
    Kohlmeier, P., Alleman, A. R., Libbrecht, R., Foitzik, S. & Feldmeyer, B. Gene expression is more strongly associated with behavioural specialisation than with age or fertility in ant workers. Mol. Ecol. https://doi.org/10.1111/mec.14971 (2018).Article 

    Google Scholar 
    Levenbook, L. & Bauer, A. C. The fate of the larval storage protein calliphorin during adult development of Calliphora vicina. Insect Biochem. 14, 77–86 (1984).CAS 

    Google Scholar 
    Zhou, X., Oi, F. M. & Scharf, M. E. Social exploitation of hexamerin: RNAi reveals a major caste-regulatory factor in termites. Proc. Natl. Acad. Sci. 103, 4499–4504 (2006).ADS 
    CAS 

    Google Scholar 
    Zhou, X., Tarver, M. R., Bennett, G., Oi, F. & Scharf, M. Two hexamerin genes from the termite Reticulitermes flavipes: Sequence, expression, and proposed functions in caste regulation. Gene 376, 47–58 (2006).CAS 

    Google Scholar 
    Hawkings, C., Calkins, T. L., Pietrantonio, P. V. & Tamborindeguy, C. Caste-based differential transcriptional expression of hexamerins in response to a juvenile hormone analog in the red imported fire ant (Solenopsis invicta). PLoS ONE 14, e0216800 (2019).CAS 

    Google Scholar 
    Hoffman, E. A. & Goodisman, M. A. Gene expression and the evolution of phenotypic diversity in social wasps. BMC Biol. 5, 1–9 (2007).
    Google Scholar 
    Hunt, J. H., Buck, N. A. & Wheeler, D. E. Storage proteins in vespid wasps: Characterization, developmental pattern, and occurrence in adults. J. Insect Physiol. 49, 785–794 (2003).CAS 

    Google Scholar 
    Colgan, T. J. et al. Polyphenism in social insects: Insights from a transcriptome-wide analysis of gene expression in the life stages of the key pollinator, Bombus terrestris. BMC Genom. 12, 1–20 (2011).
    Google Scholar 
    Cremer, S., Armitage, S. A. & Schmid-Hempel, P. Social immunity. Curr. Biol. 17, R693–R702 (2007).CAS 

    Google Scholar 
    Cremer, S., Pull, C. D. & Fuerst, M. A. Social immunity: Emergence and evolution of colony-level disease protection. Annu. Rev. Entomol. 63, 105–123 (2018).CAS 

    Google Scholar 
    Danihlík, J., Aronstein, K. & Petřivalský, M. Antimicrobial peptides: A key component of honey bee innate immunity: Physiology, biochemistry, and chemical ecology. J. Apic. Res. 54, 123–136 (2015).
    Google Scholar 
    Koch, S. I. et al. Caste-specific expression patterns of immune response and chemosensory related genes in the leaf-cutting ant, Atta vollenweideri. PLoS ONE 8, e81518 (2013).ADS 

    Google Scholar 
    Chardonnet, F. et al. Food searching behaviour of a Lepidoptera pest species is modulated by the foraging gene polymorphism. J. Exp. Biol. 217, 3465–3473 (2014).
    Google Scholar 
    Scheiner, R., Page, R. E. Jr. & Erber, J. Responsiveness to sucrose affects tactile and olfactory learning in preforaging honey bees of two genetic strains. Behav. Brain Res. 120, 67–73 (2001).CAS 

    Google Scholar 
    Wang, Z. et al. Visual pattern memory requires foraging function in the central complex of Drosophila. Learn. Mem. 15, 133–142 (2008).
    Google Scholar 
    Zhou, Y., Lei, Y., Lu, L. & He, Y. Temperature-and food-dependent foraging gene expression in foragers of the red imported fire ant Solenopsis invicta Buren (Hymenoptera: Formicidae). Physiol. Entomol. 45, 1–6 (2020).
    Google Scholar 
    Ingram, K. K. et al. Context-dependent expression of the foraging gene in field colonies of ants: The interacting roles of age, environment and task. Proc. R. Soc. B: Biol. Sci. 283, 20160841 (2016).
    Google Scholar 
    Ingram, K. K., Oefner, P. & Gordon, D. M. Task-specific expression of the foraging gene in harvester ants. Mol. Ecol. 14, 813–818 (2005).CAS 

    Google Scholar 
    Lucas, C. & Sokolowski, M. B. Molecular basis for changes in behavioral state in ant social behaviors. Proc. Natl. Acad. Sci. 106, 6351–6356 (2009).ADS 
    CAS 

    Google Scholar 
    Ben-Shahar, Y. The foraging gene, behavioral plasticity, and honeybee division of labor. J. Comp. Physiol. A. 191, 987–994 (2005).CAS 

    Google Scholar 
    Daugherty, T., Toth, A. & Robinson, G. Nutrition and division of labor: Effects on foraging and brain gene expression in the paper wasp Polistes metricus. Mol. Ecol. 20, 5337–5347 (2011).CAS 

    Google Scholar 
    Morrison, L. W., Porter, S. D., Daniels, E. & Korzukhin, M. D. Potential global range expansion of the invasive fire ant, Solenopsis invicta. Biol. Invasions 6, 183–191 (2004).
    Google Scholar 
    Valles, S. M., Wetterer, J. K. & Porter, S. D. The red imported fire ant (Hymenoptera: Formicidae) in the West Indies: Distribution of natural enemies and a possible test bed for release of self-sustaining biocontrol agents. Fls. Entomol. 98, 1101–1105 (2015).
    Google Scholar 
    Greenberg, L., Vinson, S. & Ellison, S. Nine-year study of a field containing both monogyne and polygyne red imported fire ants (Hymenoptera: Formicidae). Ann. Entomol. Soc. Am. 85, 686–695 (1992).
    Google Scholar 
    Keller, L. & Ross, K. G. Selfish genes: A green beard in the red fire ant. Nature 394, 573–575 (1998).ADS 
    CAS 

    Google Scholar 
    Vinson, S. B. Impact of the invasion of the imported fire ant. Insect Sci. 20, 439–455 (2013).
    Google Scholar 
    Tschinkel, W. R. The Fire Ants (Harvard University Press, 2006).
    Google Scholar 
    Cassill, D. L. & Tschinkel, W. R. Task selection by workers of the fire ant Solenopsis invicta. Behav. Ecol. Sociobiol. 45, 301–310 (1999).
    Google Scholar 
    Mirenda, J. T. & Vinson, S. B. Division of labour and specification of castes in the red imported fire ant Solenopsis invicta Buren. Anim. Behav. 29, 410–420 (1981).
    Google Scholar 
    Wilson, E. O. Division of labor in fire ants based on physical castes (Hymenoptera: Formicidae: Solenopsis). J. Kansas Entomol. Soc. 51, 615–636 (1978).
    Google Scholar 
    Sorensen, A., Busch, T. M. & Vinson, S. B. Behavioral flexibility of temporal subcastes in the fire ant, Solenopsis invicta in response to food. Psyche 91, 319–331 (1984).
    Google Scholar 
    Bigley, W. S. & Vinson, S. B. Characterization of a brood pheromone isolated from the sexual brood of the imported fire ant, Solenopsis invicta. Ann. Entomol. Soc. Am. 2, 301–304 (1975).
    Google Scholar 
    Bajracharya, P., Lu, H. L. & Pietrantonio, P. V. The red imported fire ant (Solenopsis invicta Buren) kept Y not F: Predicted sNPY endogenous ligands deorphanize the short NPF (sNPF) receptor. PLoS ONE 9(10), e109590 (2014).ADS 

    Google Scholar 
    Castillo, P. Short neuropeptide F receptor in the worker brain of the red imported fire ant (Solenopsis invicta Buren) and methodology for RNA interference M.S. thesis, Texas A&M University (2015).Castillo, P. & Pietrantonio, P. V. Differences in sNPF receptor-expressing neurons in brains of fire ant (Solenopsis invicta Buren) worker subcastes: Indicators for division of labor and nutritional status? PLoS ONE 8, e83966 (2013).ADS 

    Google Scholar 
    Cassill, D. L. & Tschinkel, W. R. Allocation of liquid food to larvae via trophallaxis in colonies of the fire ant, Solenopsis invicta. Anim. Behav. 3, 801–813 (1995).
    Google Scholar 
    Cassill, D. L., Stuy, A. & Buck, R. G. Emergent properties of food distribution among fire ant larvae. J. Theor. Biol. 3, 371–381 (1998).ADS 

    Google Scholar 
    Dussutour, A. & Simpson, S. J. Communal nutrition in ants. Curr. Biol. 19, 740–744. https://doi.org/10.1016/j.cub.2009.03.015 (2009).Article 
    CAS 

    Google Scholar 
    Petralia, R. S. & Vinson, S. B. Feeding in the larvae of the imported fire ant, Solenopsis invicta: Behavior and morphological adaptations. Ann. Entomol. Soc. Am. 71, 643–648 (1978).
    Google Scholar 
    Petralia, R. S. & Vinson, S. B. Developmental morphology of larvae and eggs of the imported fire ant, Solenopsis invicta. Ann. Entomol. Soc. Am. 72, 472–484 (1979).
    Google Scholar 
    Chen, J. Advancement on techniques for the separation and maintenance of the red imported fire ant colonies. Insect Sci. 14, 1–4 (2007).
    Google Scholar 
    Banks, W. A. et al. (Agricultural Research (Southern Region), Science and Education…, 1981).Valles, S. M. & Porter, S. D. Identification of polygyne and monogyne fire ant colonies (Solenopsis invicta) by multiplex PCR of Gp-9 alleles. Insectes Soc. 2, 199–200 (2003).
    Google Scholar 
    Schmittgen, T. D. & Livak, K. J. Analyzing real-time PCR data by the comparative CT method. Nat. Protoc. 3, 1101 (2008).CAS 

    Google Scholar 
    Cheng, D., Zhang, Z., He, X. & Liang, G. Validation of reference genes in Solenopsis invicta in different developmental stages, castes and tissues. PLoS ONE 8, e57718. https://doi.org/10.1371/journal.pone.0057718 (2013).Article 
    ADS 
    CAS 

    Google Scholar 
    Qiu, H.-L., Zhao, C.-Y. & He, Y.-R. On the molecular basis of division of labor in Solenopsis invicta (Hymenoptera: Formicidae) workers: RNA-seq analysis. J. Insect Sci. 17, 48 (2017).
    Google Scholar 
    Chen, J. et al. Role of the foraging gene in worker behavioral transition in the red imported fire ant, Solenopsis invicta (Hymenoptera: Formicidae). Pest Manag. Sci. https://doi.org/10.1002/ps.6921 (2022).Article 

    Google Scholar 
    Shorter, J. R. & Tibbetts, E. A. The effect of juvenile hormone on temporal polyethism in the paper wasp Polistes dominulus. Insectes Soc. 56, 7–13 (2009).
    Google Scholar 
    Pankiw, T., Page, R. E. Jr. & Kim Fondrk, M. Brood pheromone stimulates pollen foraging in honey bees (Apis mellifera). Behav. Ecol. Sociobiol. 44, 193–198. https://doi.org/10.1007/s002650050531 (1998).Article 

    Google Scholar 
    Smedal, B., Brynem, M., Kreibich, C. D. & Amdam, G. V. Brood pheromone suppresses physiology of extreme longevity in honeybees (Apis mellifera). J. Exp. Biol. 212, 3795–3801. https://doi.org/10.1242/jeb.035063 (2009).Article 
    CAS 

    Google Scholar 
    Solis, C. R. & Strassmann, J. E. Presence of brood affects caste differentiation in the social wasp, Polistes exclamans Viereck (Hymenoptera, Vespidae). Funct. Ecol. 4, 531–541. https://doi.org/10.2307/2389321 (1990).Article 

    Google Scholar 
    Traynor, K. S. Decoding Brood Pheromone: The Releaser and Primer Effects of Young and Old Larvae on Honey Bee (Apis mellifera) Workers (Arizona State University, 2014).
    Google Scholar 
    Wagoner, K. M., Spivak, M. & Rueppell, O. Brood affects hygienic behavior in the honey bee (Hymenoptera: Apidae). J. Econ. Entomol. 111, 2520–2530. https://doi.org/10.1093/jee/toy266 (2018).Article 
    CAS 

    Google Scholar 
    Nijhout, H. F. & Wheeler, D. E. Juvenile hormone and the physiological basis of insect polymorphisms. Q. Rev. Biol. 57, 109–133 (1982).CAS 

    Google Scholar  More

  • in

    Genomic architecture of migration timing in a long-distance migratory songbird

    Davidson, S. C. et al. Ecological insights from three decades of animal movement tracking across a changing arctic. Science 370, 712–715 (2020).ADS 
    CAS 

    Google Scholar 
    Cohen, J. M., Lajeunesse, M. J. & Rohr, J. R. A global synthesis of animal phenological responses to climate change. Nat. Clim. Chang. 8, 224–228 (2018).ADS 

    Google Scholar 
    Both, C., Bouwhuis, S., Lessells, C. M. & Visser, M. E. Climate change and population declines in a long-distance migratory bird. Nature 441, 81–83 (2006).ADS 
    CAS 

    Google Scholar 
    Studds, C. E. & Marra, P. P. Rainfall-induced changes in food availability modify the spring departure programme of a migratory bird. Proc. R. Sci. B. 278, 3437–3443 (2011).
    Google Scholar 
    González, A. M., Bayly, N. J. & Hobson, K. A. Earlier and slower or later and faster: spring migration pace linked to departure time in a Neotropical migrant songbird. J. Anim. Ecol. 89, 2840–2851 (2020).
    Google Scholar 
    Liedvogel, M., Åkesson, S. & Bensch, S. The genetics of migration on the move. Trends Ecol. Evol. 26, 561–569 (2011).
    Google Scholar 
    Caprioli, M. et al. Clock gene variation is associated with breeding phenology and maybe under directional selection in the migratory barn swallow. PLoS ONE 7, e35140 (2012).ADS 
    CAS 

    Google Scholar 
    Mettler, R., Segelbacher, G. & Schaefer, M. H. Interactions between a candidate gene for migration (ADCYAP1), morphology and sex predict spring arrival in blackcap populations. PLoS ONE 10, e0144587 (2015).
    Google Scholar 
    Bazzi, G. et al. Clock gene polymorphism and scheduling of migration: a geolocator study of the barn swallow Hirundo rustica. Sci. Rep. 5, 12443 (2015).ADS 

    Google Scholar 
    Saino, N. et al. Polymorphism at the Clock gene predicts phenology of long-distance migratoin in birds. Mol. Ecol. 24, 1758–1773 (2015).CAS 

    Google Scholar 
    Bossu, C. M. et al. Clock-linked genes underlie seasonal migratory timing in a diurnal raptor. Proc. R. Soc. B. 289, 20212507 (2022).CAS 

    Google Scholar 
    O’Malley, K. G., Ford, M. J. & Hard, J. J. Clock polymorphism in Pacific salmon: evidence for variable selection along a latitudinal gradient. Proc. R. Soc. B. 277, 3703–3714 (2010).
    Google Scholar 
    Peterson, M. P. et al. Variation in candidate genes CLOCK and ADCYAP1 does not consistently predict differences in migratory behavior in the songbird genus Junco. F1000Research 2 (2013).McKinnon, E. A. & Ten Love, O. P. years tracking the migrations of small landbirds: Lessons learned in the golden age of bio-logging. Auk 135, 834–856 (2018).
    Google Scholar 
    Fraser, K. C. et al. Continent-wide tracking to determine migratory connectivity and tropical habitat associations of a declining aerial insectivore. Proc. R. Soc. B. 279, 4901–4906 (2012).
    Google Scholar 
    Neufeld, L. R. et al. Breeding latitude is associated with the timing of nesting and migration around the annual calendar among purple martin Progne subis populations. J. Ornithol. 162, 1009–1024 (2021).
    Google Scholar 
    Peona, V. et al. Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise. Mol. Ecol. 21(1), 263–286 (2020).
    Google Scholar 
    Coelho, L. A., Musher, L. J. & Cracraft, J. A multireference-based whole genome assembly for the obligate ant-following antbird, Rhegmatorhina melanosticta (Thamnophilidae). Diversity 11(19), 144 (2019).CAS 

    Google Scholar 
    Zhou, X., Carbonetto, P. & Stephens, M. Polygenic modeling with Bayesian sparse linear mixed models. PLoS Genet. 9, e1003264 (2013).CAS 

    Google Scholar 
    Fuller, Z. L. et al. Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching. Science 369(6501) (2019).Jones, S., Pfister-Genskow, M., Benca, R. M. & Cirelli, C. Molecular correlates of sleep and wakefulness in the brain of the white-crowned sparrow. J. Neurochem. 105, 46–62 (2008).CAS 

    Google Scholar 
    Ma, C. et al. Sleep regulation by neurotensinergic neurons in a thalamo-amygdala circuit. Neuron 103 (2019).Wong, J. M. & Eirin-Lopez, J. M. Evolution of methyltransferase-like (METTL) proteins in metazoan: a complex gene family involved in epitranscriptomic regulation and other epigenetic processes. Mol. Biol. Evol. 38, 5309–5327 (2021).CAS 

    Google Scholar 
    Jia, Z. et al. ACSS3 in brown fast drives propionate catabolism and its deficiency leads to autophagy and systemic metabolic dysfunction. Clin. Transl. Med. 12, e665 (2022).CAS 

    Google Scholar 
    Muller, F. et al. Towards a conceptual framework for explaining variation in nocturnal departure time of songbird migrants. Mov. Ecol. 4, 24 (2016).
    Google Scholar 
    Fraser, K. C. et al. Individual variability in migration timing can explain long-term population-level advances in a songbird. Front. Ecol. Evol. 7, 324 (2019).ADS 

    Google Scholar 
    Barret, R. D. H. & Schluter, D. Adaptation from standing genetic variation. Trends Ecol. Evol. 23(1), 38–44 (2008).
    Google Scholar 
    Colodro-Conde, L. et al. A direct test of the diathesis-stress model for depression. Mol. Psychiatry 23, 1590–1596 (2017).
    Google Scholar 
    Dudbridge, F. Power and predictive accuracy of polygenic risk scores. PLOS Genetics 9(4) (2013).Lavallée, C. D. et al. The use of nocturnal flights for barrier crossing in a diurnally migrating songbird. Mov. Ecol. 9, 21 (2021).
    Google Scholar 
    Saino, N. et al. Migration phenology and breeding success are predicted by methylation of a photoperiodic gene in the barn swallow. Sci. Rep. 7, 45412 (2017).ADS 
    CAS 

    Google Scholar 
    Henry, R. A. et al. Changing the selectivity of p300 by acetyl-CoA modulation of histone acetylation. ACS Chem. Biol 10, 146–156 (2015).CAS 

    Google Scholar 
    Sun, H., Skorgerbø, G., Wang, Z., Liu, W. & Li, Y. Structural relationships between highly conserved elements and genes in vertebrate genomes. PLoS ONE 3, e3727 (2008).ADS 

    Google Scholar 
    Chin, C. S. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods 13, 1050–1054 (2016).CAS 

    Google Scholar 
    Chin, C. S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569 (2013).CAS 

    Google Scholar 
    Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017).CAS 

    Google Scholar 
    Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).ADS 

    Google Scholar 
    Coombe, L. et al. ARKS: Chromosome-scale scaffolding of human genome drafts with linked read kmers. BMC Bioinform. 19, 1–10 (2018).
    Google Scholar 
    Campbell, M. S., Holt, C., Moore, B. & Yandell, M. Genome annotation and curation using MAKER and MAKER‐P. Curr. Protocols Bioinform. 48, 4.11.1–4.11.39 (2014).Malmberg, M. M. et al. Evaluation and recommendations for routine genotyping using skim whole genome re-sequencing in canola. Front. Plant. Sci. 9 (2018).Browning, B. L. & Browning, S. R. Genotype imputation with millions of reference samples. Am. J. Hum. Genet. 98, 116–126 (2016).CAS 

    Google Scholar 
    Golicz, A. A., Bayer, P. E. & Edwards, D. Skim-based genotyping by sequencing. Methods Mol. Biol. 1245, 257–270 (2015).CAS 

    Google Scholar 
    Hill, R. D. Theory of geolocation by light levels. In B. J. L. Boeuf, & R. M. Laws (Ed.), Elephant seals: Population ecology, behaviour and physiology, pp. 227–236. Berkeley, CA: University of California Press (1994).Wotherspoon, S., Summer, M. & Lisovski, S. BAStag: basic data processing for light based geolocation archival tags. Version 0.1.3. (2016).Lisovski, S. & Hahn, S. GeoLight-processing and anslysing light-based geolocator data in R. Methods Ecol. Evol. 3, 1055–1059 (2012).
    Google Scholar 
    Gompert, Z., Lucas, L. K., Nice, C. C. & Buerkle, C. A. Genome divergence and the genetic architecture of barriers to gene flow between Lycaeides idas and L. melissa. Evolution 67, 2498–2514 (2013).
    Google Scholar 
    Pfeifer, S. P. et al. The evolutionary history of Nebraska deer mice: local adaptation in the face of strong gene flow. Mol. Biol. Evol. 35, 792–806 (2018).CAS 

    Google Scholar 
    Purcell, S. et al. PLINK: a toolset for whole-genome association and population-based linkage analysis. Am. J. Hum. Genet. 81, 559–575 (2007).CAS 

    Google Scholar 
    Choi, S. W., Mak, T. S. & O’Reilly, P. F. Tutorial: a guide to performing polygenic risk score analysis. Nat Protoc 15, 2759–2772 (2020).CAS 

    Google Scholar 
    Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).CAS 

    Google Scholar 
    Cruickshank, T. E. & Hahn, M. W. Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Mol. Ecol. 23, 3133–3157 (2014).
    Google Scholar 
    Vijay, N. et al. Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex. Nat. Commun. 7, 13195 (2016).ADS 
    CAS 

    Google Scholar 
    Delmore, K. et al. The evolutionary history and genomics of European blackcap migration. eLife 9, e54462 (2020). More

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    Mangrove reforestation provides greater blue carbon benefit than afforestation for mitigating global climate change

    Literature search and screeningOur analysis included a systematic literature search and was conducted by following the PRISMA protocol55 (Supplementary Fig. 7). We searched through Web of Science and China National Knowledge Infrastructure (CNKI) platforms by using keywords listed in Supplementary Table 3. A total of 3299 potentially relevant articles were found (Mandarin and English). The availability of peer-reviewed datasets associated with these published articles11,15,56,57,58,59 and online databases (The Sustainable Wetlands Adaptation and Mitigation Program (SWAMP) database, https://www2.cifor.org/swamp) were also considered. We then removed a significant number of articles through title screening, leaving 551 articles for further inspection.For these remaining articles, we used a four-step critique process to screen their title, abstract, and full text. We determined that firstly, they must provide carbon density data for at least one of the four mangrove carbon pools (i.e., aboveground biomass, belowground biomass, sediment organic carbon, or total ecosystem carbon). Secondly, articles needed to state the forest age or the starting date of the restoration action. For those studies providing only age intervals (e.g., 10–25 years, >66 years), we excluded them from the analysis. Thirdly, a description of prior land use was required. From these, mangrove restoration could be divided into two categories—reforestation and afforestation—on whether mangroves previously existed in that location. For reforestation, the initial conditions for inclusion were: (1) abandoned agricultural/aquacultural sites built previously by excavating mangrove forests, (2) clear-felled mangrove lands after wars, timber harvest, and silvicultural management, and (3) mangrove forests with mortality due to spraying of defoliants and hydrological alteration caused by the construction of embankments. We compared the carbon densities of reforested mangroves among sites with different causes of degradation/deforestation, and no significant difference is found (Supplementary Fig. 9). For those reforested mangroves, we assumed they would be protected and conserved by local governments and non-government organizations, so that there will not be human-driven degradation or deforestation in the near future. However, we acknowledge that a fraction of mangrove reforestation is managed for wood production, which means logging would happen at a certain interval after reforestation at these sites. For these logging sites, we used their reported measurements after clear-cut, such as 0-, 5-, 10-, 15-, and 25-year post-harvest sites in Sundarbans, Bangladesh60. On the other hand, the future occurrence of natural-driven deforestation (e.g., cyclones) is difficult to predict, and thus not considered in our study. For afforestation, the initial condition for inclusion was the presence of non-mangrove habitat immediately before afforestation began, such as mudflats, seagrass, saltmarsh, coral reef, or denuded areas. In most cases, reforestation and afforestation were undertaken through active planting without much re-engineering4, but for reforestation, natural regeneration could have, and in many places likely did, augment recruitment61. Moreover, we only considered mangrove succession that started from near-barren land with an insignificant amount of biomass, and introductions of exotic species to degraded areas with sparse trees were not incorporated. Lastly, if the forest age or prior land use type was not given, the articles needed to specify the location of sampling plots (latitude, longitude). With the coordinates matching, prior land use type and establishment dates were sometimes identifiable through remote sensing (Supplementary Fig. 10). For those articles sharing the same restoration sites but showing different aspects of the data collection, we combined the results and considered the collective work as one source. Based on the space-for-time method, data in the control sites before mangrove restoration actions were also collected as a paired site of restoration (e.g., abandoned ponds before mangrove reforestation; mudflats before mangrove afforestation). In total, we obtained data from 379 mangrove restoration sites described by 106 articles.Data extractionWe extracted aboveground living biomass carbon (AGC), belowground living biomass carbon (BGC), sediment carbon (SCS), and total ecosystem carbon (TECS) density from the 106 original data sources. In most cases, numeric values were provided. For those data not provided numerically but graphed, we determined values from figures with the application of GetData Graph Digitizer (http://getdata-graph-digitizer.com/).Among the articles, aboveground and belowground biomass (Mg ha−1) data were obtained using either a harvesting method (empirical) or an allometric method (calculation). Aboveground biomass represented the sum of stem, leaf, and branch dry weight, and we included prop root biomass when Rhizophora spp. were present. For soil coring methods that determined belowground biomass or sediment carbon density, belowground biomass was considered the dry weight of living coarse and fine roots multiplied by the ratio of core area to land surface area62. For allometric methods, trunk diameter at breast height (DBH, ~1.3 m) and tree height were used to calculate aboveground and belowground biomass by species-specific or common allometric equations63. These equations were also used to calculate the belowground biomass when articles provided plot information (DBH, height) but not belowground biomass (Supplementary Table 4). Total biomass was calculated as the sum of aboveground and belowground biomass. Deadwood and pneumatophore biomass were not included in our analysis; these data are rarely provided and/or methods of determination are inconsistent among global studies64. Some articles provided total biomass and shoot/root biomass ratio (S/R), and in such cases, above- and belowground biomass data were obtained through calculation as follows:$${{{{{rm{Aboveground}}}}}},{{{{{rm{biomass}}}}}}={{{{{rm{Total}}}}}},{{{{{rm{biomass}}}}}}times frac{frac{S}{R}}{frac{S}{R}+1}$$
    (1)
    $${{{{{rm{Belowground}}}}}},{{{{{rm{biomass}}}}}}={{{{{rm{Total}}}}}},{{{{{rm{biomass}}}}}}times frac{1}{frac{S}{R}+1}$$
    (2)
    For those articles measuring carbon content, study-specific carbon conversion factors were used to transform biomass to biomass carbon density (Mg C ha−1). If carbon content data were not provided, we converted aboveground and belowground biomass to carbon density by applying a conversion of 0.47 and 0.39, respectively65. The aboveground biomass carbon density was divided by its corresponding age to get the average aboveground biomass carbon accumulation rate (Mg C ha−1 yr−1).For sediment carbon density (SCS, Mg C ha−1), we selected the top 1 m because this depth equated to the most commonly reported depth and could reflect the impact of root mass input in the deeper depth66, which is also consistent with recent blue carbon standing stock assessment guidance64,67. Sediment carbon stock was calculated by multiplying sediment organic carbon content (SOC, %) by bulk density (BD, g cm−3), integrated over depth (cm). For studies that reported sediment carbon stock to More

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    Asynchrony in coral community structure contributes to reef-scale community stability

    Parmesan, C. Ecological and evolutionary responses to recent climate change. Annu. Rev. Ecol. Evol. Syst. 37, 637–669 (2006).
    Google Scholar 
    Elahi, R. et al. Recent trends in local-scale marine biodiversity reflect community structure and human impacts. Curr. Biol. 25, 1938–1943 (2015).CAS 

    Google Scholar 
    Harley, C. D. G. Climate change, keystone predation, and biodiversity loss. Science 334, 1124–1127 (2011).ADS 
    CAS 

    Google Scholar 
    Poloczanska, E. S. et al. Global imprint of climate change on marine life. Nat. Clim. Change 3, 919–925 (2013).ADS 

    Google Scholar 
    Bellwood, D. R., Hughes, T. P., Folke, C. & Nyström, M. Confronting the coral reef crisis. Nature 429, 827–833 (2004).ADS 
    CAS 

    Google Scholar 
    Moreno-Mateos, D. et al. Anthropogenic ecosystem disturbance and the recovery debt. Nat. Commun. 8, 14163 (2017).ADS 
    CAS 

    Google Scholar 
    Newman, E. A. Disturbance ecology in the Anthropocene. Front. Ecol. Evol. 7, 147 (2019).
    Google Scholar 
    Mittelbach, G. G. et al. What is the observed relationship between species richness and productivity?. Ecology 82, 2381–2396 (2001).
    Google Scholar 
    van Nes, E. H. & Scheffer, M. Implications of spatial heterogeneity for catastrophic regime shifts in ecosystems. Ecology 86, 1797–1807 (2005).
    Google Scholar 
    Tylianakis, J. M. et al. Resource heterogeneity moderates the biodiversity-function relationship in real world ecosystems. Plos Biol. 6, e122 (2008).
    Google Scholar 
    Loreau, M. et al. In Metacommunities: Spatial Dynamics and Ecological Communities (eds Holyoak, M. et al.) (The University of Chicago Press, 2005).
    Google Scholar 
    Loreau, M. From Populations to Ecosystems (Princeton University Press, 2010). https://doi.org/10.1515/9781400834167.vii.Book 

    Google Scholar 
    Moreira, E. F., Boscolo, D. & Viana, B. F. Spatial heterogeneity regulates plant-pollinator networks across multiple landscape scales. PLoS ONE 10, e0123628 (2015).
    Google Scholar 
    Costanza, J. K., Moody, A. & Peet, R. K. Multi-scale environmental heterogeneity as a predictor of plant species richness. Landsc. Ecol. 26, 851–864 (2011).
    Google Scholar 
    Hughes, T. P. et al. Global warming transforms coral reef assemblages. Nature 556, 492–496 (2018).ADS 
    CAS 

    Google Scholar 
    Nyström, M., Graham, N. A. J., Lokrantz, J. & Norström, A. V. Capturing the cornerstones of coral reef resilience: Linking theory to practice. Coral Reefs 27, 795–809 (2008).ADS 

    Google Scholar 
    Virah-Sawmy, M., Gillson, L. & Willis, K. J. How does spatial heterogeneity influence resilience to climatic changes? Ecological dynamics in southeast Madagascar. Ecol. Monogr. 79, 557–574 (2009).
    Google Scholar 
    Wilson, D. S. Complex interactions in metacommunities, with implications for biodiversity and higher levels of selection. Ecology 73, 1984–2000 (1992).
    Google Scholar 
    Leibold, M. A. et al. The metacommunity concept: A framework for multi-scale community ecology. Ecol. Lett. 7, 601–613 (2004).
    Google Scholar 
    Briggs, C. J. & Hoopes, M. F. Stabilizing effects in spatial parasitoid–host and predator–prey models: A review. Theor. Popul. Biol. 65, 299–315 (2004).MATH 

    Google Scholar 
    Wang, S., Haegeman, B. & Loreau, M. Dispersal and metapopulation stability. PeerJ 3, e1295 (2015).
    Google Scholar 
    Tilman, D. The ecological consequences of changes in biodiversity: A search for general principles. Ecology 80, 1455–1474 (1999).
    Google Scholar 
    Loreau, M., Mouquet, N. & Gonzalez, A. Biodiversity as spatial insurance in heterogeneous landscapes. Proc. Natl. Acad. Sci. 100, 12765–12770 (2003).ADS 
    CAS 

    Google Scholar 
    Yachi, S. & Loreau, M. Biodiversity and ecosystem productivity in a fluctuating environment: The insurance hypothesis. Proc. Natl. Acad. Sci. 96, 1463–1468 (1999).ADS 
    CAS 

    Google Scholar 
    Bouvier, T. et al. Contrasted effects of diversity and immigration on ecological insurance in marine bacterioplankton communities. PLoS ONE 7, e37620 (2012).ADS 
    CAS 

    Google Scholar 
    Hammond, M., Loreau, M., Mazancourt, C. & Kolasa, J. Disentangling local, metapopulation, and cross-community sources of stabilization and asynchrony in metacommunities. Ecosphere 11, e03078 (2020).
    Google Scholar 
    Lamy, T., Legendre, P., Chancerelle, Y., Siu, G. & Claudet, J. Understanding the spatio-temporal response of coral reef fish communities to natural disturbances: Insights from beta-diversity decomposition. PLoS ONE 10, e0138696 (2015).
    Google Scholar 
    Lamy, T. et al. Species insurance trumps spatial insurance in stabilizing biomass of a marine macroalgal metacommunity. Ecology 100, e02719 (2019).
    Google Scholar 
    Stier, A. C., Shelton, A. O., Samhouri, J. F., Feist, B. E. & Levin, P. S. Fishing, environment, and the erosion of a population portfolio. Ecosphere https://doi.org/10.1002/ecs2.3283 (2020).Article 

    Google Scholar 
    Burgess, S. C. et al. Beyond connectivity: How empirical methods can quantify population persistence to improve marine protected-area design. Ecol. Appl. 24, 257–270 (2014).
    Google Scholar 
    Saenz-Agudelo, P., Jones, G. P., Thorrold, S. R. & Planes, S. Connectivity dominates larval replenishment in a coastal reef fish metapopulation. Proc. R. Soc. B Biol. Sci. 278, 2954–2961 (2011).
    Google Scholar 
    Wood, S., Paris, C. B., Ridgwell, A. & Hendy, E. J. Modelling dispersal and connectivity of broadcast spawning corals at the global scale. Glob. Ecol. Biogeogr. 23, 1–11 (2014).
    Google Scholar 
    Loreau, M. et al. Biodiversity as insurance: From concept to measurement and application. Biol. Rev. https://doi.org/10.1111/brv.12756 (2021).Article 

    Google Scholar 
    Thibaut, L. M. & Connolly, S. R. Understanding diversity–stability relationships: Towards a unified model of portfolio effects. Ecol. Lett. 16, 140–150 (2013).
    Google Scholar 
    Wilcox, K. R. et al. Asynchrony among local communities stabilises ecosystem function of metacommunities. Ecol. Lett. 20, 1534–1545 (2017).
    Google Scholar 
    Loreau, M. & de Mazancourt, C. Species synchrony and its drivers: Neutral and nonneutral community dynamics in fluctuating environments. Am. Nat. 172, E48–E66 (2008).
    Google Scholar 
    Loreau, M. & Mazancourt, C. Biodiversity and ecosystem stability: A synthesis of underlying mechanisms. Ecol. Lett. 16, 106–115 (2013).
    Google Scholar 
    Gross, K. et al. Species richness and the temporal stability of biomass production: A new analysis of recent biodiversity experiments. Am. Nat. 183, 1–12 (2014).
    Google Scholar 
    Sullaway, G. H., Shelton, A. O. & Samhouri, J. F. Synchrony erodes spatial portfolios of an anadromous fish and alters availability for resource users. J. Anim. Ecol. https://doi.org/10.1111/1365-2656.13575 (2021).Article 

    Google Scholar 
    Adjeroud, M., Augustin, D., Galzin, R. & Salvat, B. Natural disturbances and interannual variability of coral reef communities on the outer slope of Tiahura (Moorea, French Polynesia): 1991 to 1997. Mar. Ecol. Prog. Ser. 237, 121–131 (2002).ADS 

    Google Scholar 
    Adjeroud, M. et al. Recurrent disturbances, recovery trajectories, and resilience of coral assemblages on a South Central Pacific reef. Coral Reefs 28, 775–780 (2009).ADS 

    Google Scholar 
    Pratchett, M. S., Trapon, M., Berumen, M. L. & Chong-Seng, K. Recent Disturbances Augment Community Shifts in Coral Assemblages in Moorea, French Polynesia (SpringerLink, 2011). https://doi.org/10.1007/s00338-010-0678-2.Book 

    Google Scholar 
    Kayal, M. et al. Predator crown-of-thorns starfish (Acanthaster planci) outbreak, mass mortality of corals, and cascading effects on reef fish and benthic communities. PLoS ONE 7, e47363 (2012).ADS 
    CAS 

    Google Scholar 
    McWilliam, M., Pratchett, M. S., Hoogenboom, M. O. & Hughes, T. P. Deficits in functional trait diversity following recovery on coral reefs. Proc. R. Soc. B 287, 20192628 (2020).
    Google Scholar 
    Hoegh-Guldberg, O. et al. Coral reefs under rapid climate change and ocean acidification. Science 318, 1737–1742 (2007).ADS 
    CAS 

    Google Scholar 
    Penin, L., Adjeroud, M., Schrimm, M. & Lenihan, H. S. High spatial variability in coral bleaching around Moorea (French Polynesia): Patterns across locations and water depths. C. R. Biol. 330, 171–181 (2007).
    Google Scholar 
    Adam, T. C. et al. Herbivory, connectivity, and ecosystem resilience: Response of a coral reef to a large-scale perturbation. PLoS ONE 6, e23717 (2011).ADS 
    CAS 

    Google Scholar 
    Edmunds, P. et al. Why more comparative approaches are required in time-series analyses of coral reef ecosystems. Mar. Ecol. Prog. Ser. 608, 297–306 (2019).ADS 

    Google Scholar 
    Pérez-Rosales, G. et al. Documenting decadal disturbance dynamics reveals archipelago-specific recovery and compositional change on Polynesian reefs. Mar. Pollut. Bull. 170, 112659 (2021).
    Google Scholar 
    Bruno, J. F. & Selig, E. R. Regional decline of coral cover in the Indo-Pacific: Timing, extent, and subregional comparisons. PLoS ONE 2, e711 (2007).ADS 

    Google Scholar 
    Jackson, J. B. C. et al. Status and trends of Caribbean coral reefs. Global Coral Reef Monitoring Network, IUCN, Gland, Switzerland (2014)Edmunds, P. J. Implications of high rates of sexual recruitment in driving rapid reef recovery in Mo’orea, French Polynesia. Sci. Rep. 8, 16615 (2018).ADS 

    Google Scholar 
    Burgess, S. C., Johnston, E. C., Wyatt, A. S. J., Leichter, J. J. & Edmunds, P. J. Response diversity in corals: Hidden differences in bleaching mortality among cryptic Pocillopora species. Ecology https://doi.org/10.1002/ecy.3324 (2021).Article 

    Google Scholar 
    Holbrook, S. J. et al. Recruitment drives spatial variation in recovery rates of resilient coral reefs. Sci. Rep. 8, 7338 (2018).ADS 

    Google Scholar 
    Guest, J. R. et al. A framework for identifying and characterising coral reef “oases” against a backdrop of degradation. J. Appl. Ecol. 55, 2865–2875 (2018).
    Google Scholar 
    Hench, J. L., Leichter, J. J. & Monismith, S. G. Episodic circulation and exchange in a wave-driven coral reef and lagoon system. Limnol. Oceanogr. 53, 2681–2694 (2008).ADS 

    Google Scholar 
    Barry, J. P. & Dayton, P. K. Ecological heterogeneity. Ecol. Stud. https://doi.org/10.1007/978-1-4612-3062-5_14 (1991).Article 

    Google Scholar 
    Edmunds, P. & Bruno, J. The importance of sampling scale in ecology: Kilometer-wide variation in coral reef communities. Mar. Ecol. Prog. Ser. 143, 165–171 (1996).ADS 

    Google Scholar 
    Lough, J. M., Anderson, K. D. & Hughes, T. P. Increasing thermal stress for tropical coral reefs: 1871–2017. Sci. Rep. 8, 6079 (2018).ADS 
    CAS 

    Google Scholar 
    van Oppen, M. J. H. & Lough, J. M. Coral bleaching, patterns, processes, causes and consequences. Ecol. Stud. https://doi.org/10.1007/978-3-319-75393-5_14 (2018).Article 

    Google Scholar 
    Monismith, S. G. Hydrodynamics of coral reefs. Annu. Rev. Fluid Mech. 39, 37–55 (2007).ADS 
    MATH 

    Google Scholar 
    Edmunds P. Of Moorea Coral Reef LTER. MCR LTER: Coral Reef: Long-term Population and Community Dynamics: Corals, ongoing since 2005. knb-lter-mcr.4.33 https://doi.org/10.6073/pasta/1f05f1f52a2759dc096da9c24e88b1e8 (2020).Cowles, J. et al. Resilience: insights from the U.S. Long-term ecological research network. Ecosphere 12, e03434 (2021).
    Google Scholar 
    Beijbom, O. et al. Towards automated annotation of benthic survey images: Variability of human experts and operational modes of automation. PLoS ONE 10, e0130312 (2015).
    Google Scholar 
    Veron, J. E. N. Corals of the world, v. 1–3. Australian Institute of Marine Science (2000)Washburn, L of Moorea Coral Reef LTER. MCR LTER: Coral Reef: Ocean Currents and Biogeochemistry: salinity, temperature and current at CTD and ADCP mooring FOR01 from 2004 ongoing. knb-lter-mcr.30.36doi:10.6073/pasta/124d19950c5234bf1937661989dcced7 (2021).Safaie, A. et al. High frequency temperature variability reduces the risk of coral bleaching. Nat. Commun. 9, 1671 (2018).ADS 

    Google Scholar 
    Dean, R. G. & Dalrymple, R. A. Water Wave Mechanics for Engineers and Scientists. Advanced Series on Ocean Engineering Vol. 2 (World Scientific, 1991).
    Google Scholar 
    Carroll, A., Harrison, P. & Adjeroud, M. Sexual reproduction of Acropora reef corals at Moorea, French Polynesia. Coral Reefs 25, 93–97 (2006).ADS 

    Google Scholar 
    Han, X., Adam, T. C., Schmitt, R. J., Brooks, A. J. & Holbrook, S. J. Response of herbivore functional groups to sequential perturbations in Moorea, French Polynesia. Coral Reefs 35, 999–1009 (2016).ADS 

    Google Scholar 
    Clarke, K. R. Non-parametric multivariate analyses of changes in community structure. Austral Ecol. 18, 117–143 (1993).
    Google Scholar 
    Clarke, K. R., Somerfield, P. J. & Chapman, M. G. On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray–Curtis coefficient for denuded assemblages. J. Exp. Mar. Biol. Ecol. 330, 55–80 (2006).
    Google Scholar 
    RStudio Team. RStudio: Integrated development for R. RStudio, PBC, Boston, MA URL http://www.rstudio.com/ (2021).Oksanen J. et al. vegan: Community ecology package. R package version 2.5–7. https://CRAN.R-project.org/package=vegan (2020).Wickham, et al. Welcome to the Tidyverse. J. Open Source Softw. 4(43), 1686. https://doi.org/10.21105/joss.01686 (2019).Article 
    ADS 

    Google Scholar 
    Corlett, R. T. The Anthropocene concept in ecology and conservation. Trends Ecol. Evol. 30, 36–41 (2015).
    Google Scholar 
    Williams, G. J. et al. Coral reef ecology in the Anthropocene. Funct. Ecol. 33, 1014–1022 (2019).
    Google Scholar 
    Walther, G.-R. et al. Ecological responses to recent climate change. Nature 416, 389–395 (2002).ADS 
    CAS 

    Google Scholar 
    Walther, G.-R. Community and ecosystem responses to recent climate change. Philos. Trans. R. Soc. B Biol. Sci. 365, 2019–2024 (2010).
    Google Scholar 
    Cinner, J. E. et al. Bright spots among the world’s coral reefs. Nature 535, 416–419 (2016).ADS 
    CAS 

    Google Scholar 
    Grman, E., Lau, J. A., Schoolmaster, D. R. & Gross, K. L. Mechanisms contributing to stability in ecosystem function depend on the environmental context. Ecol. Lett. 13, 1400–1410 (2010).
    Google Scholar 
    Schindler, D. E. et al. Population diversity and the portfolio effect in an exploited species. Nature 465, 609–612 (2010).ADS 
    CAS 

    Google Scholar 
    Doak, D. F. et al. The statistical inevitability of stability-diversity relationships in community ecology. Am. Nat. 151, 264–276 (1998).CAS 

    Google Scholar 
    Isbell, F. I., Polley, H. W. & Wilsey, B. J. Biodiversity, productivity and the temporal stability of productivity: Patterns and processes. Ecol. Lett. 12, 443–451 (2009).
    Google Scholar 
    Connell, J. H. Diversity in tropical rain forests and coral reefs author. Science 199, 1302–1310 (1978).ADS 
    CAS 

    Google Scholar 
    Plaisance, L., Caley, M. J., Brainard, R. E. & Knowlton, N. The diversity of coral reefs: What are we missing?. PLoS ONE 6, e25026 (2011).ADS 
    CAS 

    Google Scholar 
    Williams, G. J. et al. Biophysical drivers of coral trophic depth zonation. Mar. Biol. 165, 60 (2018).
    Google Scholar 
    Moritz, C. et al. Long-term monitoring of benthic communities reveals spatial determinants of disturbance and recovery dynamics on coral reefs. Mar. Ecol. Prog. Ser. 672, 141–152 (2021).ADS 

    Google Scholar 
    Dietzel, A. et al. The spatial footprint and patchiness of large scale disturbances on coral reefs. Global Change Biol. 27, 4825–4838 (2021).CAS 

    Google Scholar 
    Leichter, J. et al. Biological and physical interactions on a tropical island coral reef: Transport and retention processes on Moorea, French Polynesia. Oceanography 26, 52–63 (2011).
    Google Scholar 
    Porter, J. W. et al. Population trends among Jamaican reef corals. Nature 294, 249–250 (1981).ADS 

    Google Scholar 
    Graham, N. A. J., Jennings, S., MacNeil, M. A., Mouillot, D. & Wilson, S. K. Predicting climate-driven regime shifts versus rebound potential in coral reefs. Nature 518, 94–97 (2015).ADS 
    CAS 

    Google Scholar 
    Whittaker, R. H. & Levin, S. A. The role of mosaic phenomena in natural communities. Theor. Popul. Biol. 12, 117–139 (1977).CAS 

    Google Scholar 
    Karlson, R. H. & Hurd, L. E. Disturbance, coral reef communities, and changing ecological paradigms. Coral Reefs 12, 117–125 (1993).ADS 

    Google Scholar 
    Stoddart, D. R. Effects of Hurricane Hattie on the British Honduras reefs and cays, October 30–31, 1961. Atoll Res. Bull. 95, 1–142 (1963).
    Google Scholar 
    Witman, J. D. Physical disturbance and community structure of exposed and protected reefs: A case study from St. John U.S. Virgin Islands. Integr. Comp. Biol. 32, 641–654 (1992).
    Google Scholar 
    Thorson, J. T., Scheuerell, M. D., Olden, J. D. & Schindler, D. E. Spatial heterogeneity contributes more to portfolio effects than species variability in bottom-associated marine fishes. Proc. R. Soc. B 285, 20180915 (2018).
    Google Scholar 
    Mellin, C., MacNeil, M. A., Cheal, A. J., Emslie, M. J. & Caley, M. J. Marine protected areas increase resilience among coral reef communities. Ecol. Lett. 19, 629–637 (2016).
    Google Scholar 
    Beyer, H. L. et al. Risk-sensitive planning for conserving coral reefs under rapid climate change. Conserv. Lett. 11, e12587 (2018).
    Google Scholar 
    Harrison, H. B., Bode, M., Williamson, D. H., Berumen, M. L. & Jones, G. P. A connectivity portfolio effect stabilizes marine reserve performance. Proc. Natl. Acad. Sci. 117, 25595–25600 (2020).ADS 
    CAS 

    Google Scholar 
    Walter, J. A. et al. The spatial synchrony of species richness and its relationship to ecosystem stability. Ecology https://doi.org/10.1002/ecy.3486 (2021).Article 

    Google Scholar 
    Wang, S., Lamy, T., Hallett, L. M. & Loreau, M. Stability and synchrony across ecological hierarchies in heterogeneous metacommunities: Linking theory to data. Ecography 42, 1200–1211 (2019).
    Google Scholar 
    Catano, C. P., Fristoe, T. S., LaManna, J. A. & Myers, J. A. Local species diversity, β-diversity and climate influence the regional stability of bird biomass across North America. Proc. R. Soc. B 287, 20192520 (2020).
    Google Scholar 
    Roscher, C. et al. Identifying population- and community-level mechanisms of diversity–stability relationships in experimental grasslands. J. Ecol. 99, 1460–1469 (2011).
    Google Scholar 
    Downing, A. L., Brown, B. L. & Leibold, M. A. Multiple diversity–stability mechanisms enhance population and community stability in aquatic food webs. Ecology 95, 173–184 (2014).
    Google Scholar 
    Moran, P. The statistical analysis of the Canadian Lynx cycle. Aust. J. Zool. 1, 291–298 (1953).
    Google Scholar 
    Townsend, D. L. & Gouhier, T. C. Spatial and interspecific differences in recruitment decouple synchrony and stability in trophic metacommunities. Theor. Ecol. 12, 319–327 (2019).
    Google Scholar 
    Yeager, M. E., Gouhier, T. C. & Hughes, A. R. Predicting the stability of multitrophic communities in a variable world. Ecology 101, e02992 (2020).
    Google Scholar 
    Hughes, T. P. et al. Emergent properties in the responses of tropical corals to recurrent climate extremes. Curr. Biol. https://doi.org/10.1016/j.cub.2021.10.046 (2021).Article 

    Google Scholar 
    Jackson, J. B. C. Morphological strategies of sessile animals. In Biology and Systematics of Colonial Organisms (eds Larwood, G. & Rosen, B. R.) 499–555 (Academic, 1979).
    Google Scholar 
    Sammarco, P. W. & Andrews, J. C. Localized dispersal and recruitment in Great Barrier Reef Corals: The helix experiment. Science 239, 1422–1424 (1988).ADS 
    CAS 

    Google Scholar 
    Edmunds, P. J. Unusually high coral recruitment during the 2016 El Niño in Mo’orea, French Polynesia. PLoS ONE 12, e0185167 (2017).
    Google Scholar 
    Bull, G. Distribution and abundance of coral plankton. Coral Reefs 4, 197–200 (1986).ADS 

    Google Scholar 
    Hodgson, G. Abundance and distribution of planktonic coral larvae in Kaneohe Bay, Oahu, Hawaii. Mar. Ecol. Prog. Ser. 26, 61–71 (1985).ADS 

    Google Scholar 
    Edmunds, P. J. Vital rates of small reef corals are associated with variation in climate. Limnol. Oceanogr. 66, 901–913 (2021).ADS 

    Google Scholar  More