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    Pupal size as a proxy for fat content in laboratory-reared and field-collected Drosophila species

    Parker, J. & Johnston, L. A. The proximate determinants of insect size. J. Biol. 5, 15 (2006).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Honěk, A. Intraspecific variation in body size and fecundity in insects: A general relationship. Oikos 66, 483 (1993).Article 

    Google Scholar 
    Kingsolver, J. G. & Huey, R. B. Size, temperature, and fitness: Three rules. Evol. Ecol. Res. 10, 251–268 (2008).
    Google Scholar 
    Beukeboom, L. W. Size matters in insects—An introduction. Entomol. Exp. Appl. 166, 2–3 (2018).Article 

    Google Scholar 
    West, S. A., Flanagan, K. E. & Godfray, H. C. J. The relationship between parasitoid size and fitness in the field, a study of Achrysocharoides zwoelferi (Hymenoptera: Eulophidae). J. Anim. Ecol. 65, 631–639 (1996).Article 

    Google Scholar 
    Sagarra, L. A., Vincent, C. & Stewart, R. K. Body size as an indicator of parasitoid quality in male and female Anagyrus kamali (Hymenoptera: Encyrtidae). Bull. Entomol. Res. 91, 363–367 (2001).CAS 
    PubMed 
    Article 

    Google Scholar 
    Ellers, J., Alphen, J. J. M. V. & Sevenster, J. G. A field study of size–fitness relationships in the parasitoid Asobara tabida. J. Anim. Ecol. 67, 318–324 (1998).Article 

    Google Scholar 
    Armbruster, P. & Hutchinson, R. A. Pupal mass and wing length as indicators of fecundity in Aedes albopictus and Aedes geniculatus (Diptera: Culicidae). J. Med. Entomol. 39, 699–704 (2002).PubMed 
    Article 

    Google Scholar 
    Tantawy, A. O. & Vetukhiv, M. O. Effects of size on fecundity, longevity and viability in populations of Drosophila pseudoobscura. Am. Nat. 94, 395–403 (1960).Article 

    Google Scholar 
    Lefranc, A. & Bundgaard, J. The influence of male and female body size on copulation duration and fecundity in Drosophila melanogaster. Hereditas 132, 243–247 (2004).Article 

    Google Scholar 
    Atkinson, D. Temperature and organism size: A biological law for ectotherms? Adv. Ecol. Res. 25, 1–58 (1994).Article 

    Google Scholar 
    Poças, G. M., Crosbie, A. E. & Mirth, C. K. When does diet matter? The roles of larval and adult nutrition in regulating adult size traits in Drosophila melanogaster. J. Insect Physiol. 139, 104051. https://doi.org/10.1016/j.jinsphys.2020.104051 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Tammaru, T. Determination of adult size in a folivorous moth: constraints at instar level? Ecol. Entomol. 23, 80–89 (1998).Article 

    Google Scholar 
    Miller, R. S. & Thomas, J. L. The effects of larval crowding and body size on the longevity of adult Drosophila melanogaster. Ecology 39, 118–125 (1958).Article 

    Google Scholar 
    Nijhout, H. F. The control of body size in insects. Dev. Biol. 261, 1–9 (2003).CAS 
    PubMed 
    Article 

    Google Scholar 
    Shingleton, A. W., Mirth, C. K. & Bates, P. W. Developmental model of static allometry in holometabolous insects. Proc. R. Soc. B 275, 1875–1885 (2008).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Koenraadt, C. J. M. Pupal dimensions as predictors of adult size in fitness studies of Aedes aegypti (Diptera: Culicidae). J. Med. Entomol. 45, 331–336 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Stillwell, R. C., Dworkin, I., Shingleton, A. W. & Frankino, W. A. Experimental manipulation of body size to estimate morphological scaling relationships in Drosophila. JoVE 56, 3162. https://doi.org/10.3791/3162 (2011).Article 

    Google Scholar 
    Shin, S.-M., Akram, W. & Lee, J.-J. Effect of body size on energy reserves in Culex pipiens pallens females (Diptera: Culicidae). Entomol. Res. 42, 163–167 (2012).Article 

    Google Scholar 
    Mirth, C. K. & Riddiford, L. M. Size assessment and growth control: How adult size is determined in insects. BioEssays 29, 344–355 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    Chown, S. L. & Gaston, K. J. Body size variation in insects: A macroecological perspective. Biol. Rev. 85, 139–169 (2010).PubMed 
    Article 

    Google Scholar 
    Beadle, G. W., Tatum, E. L. & Clancy, C. W. Food level in relation to rate of development and eye pigmentation in Drosophila melanogaster. Biol. Bull. 75, 447–462 (1938).Article 

    Google Scholar 
    Gayon, J. History of the concept of allometry1. Am. Zool. 40, 748–758 (2000).
    Google Scholar 
    Takken, W. et al. Larval nutrition differentially affects adult fitness and Plasmodium development in the malaria vectors Anopheles gambiae and Anopheles stephensi. Parasit. Vectors 6, 345 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Briegel, H. Metabolic relationship between female body size, reserves, and fecundity of Aedes aegypti. J. Insect Physiol. 36, 165–172 (1990).Article 

    Google Scholar 
    Ellers, J. Fat and eggs: An alternative method to measure the trade-off between survival and reproduction in insect parasitoids. Neth. J. Zool. 3, 227–235 (1996).
    Google Scholar 
    González-Tokman, D. et al. Energy storage, body size and immune response of herbivore beetles at two different elevations in Costa Rica. Rev. Biol. Trop. 67, 608–620 (2019).
    Google Scholar 
    Timmermann, S. E. & Briegel, H. Larval growth and biosynthesis of reserves in mosquitoes. J. Insect Physiol. 45, 461–470 (1999).CAS 
    PubMed 
    Article 

    Google Scholar 
    Strohm, E. Factors affecting body size and fat content in a digger wasp. Oecologia 123, 184–191 (2000).PubMed 
    Article 
    ADS 

    Google Scholar 
    Lease, H. M. & Wolf, B. O. Lipid content of terrestrial arthropods in relation to body size, phylogeny, ontogeny and sex. Physiol. Entomol. 36, 29–38 (2011).CAS 
    Article 

    Google Scholar 
    Arrese, E. L. & Soulages, J. L. Insect fat body: Energy, metabolism, and regulation. Annu. Rev. Entomol. 55, 207–225 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kühnlein, R. P. Lipid droplet-based storage fat metabolism in Drosophila. J. Lipid Res. 53, 1430–1436 (2012).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Church, R. B. & Robertson, F. W. A biochemical study of the growth of Drosophila melanogaster. J. Exp. Zool. 162, 337–351 (1966).Article 

    Google Scholar 
    Merkey, A. B., Wong, C. K., Hoshizaki, D. K. & Gibbs, A. G. Energetics of metamorphosis in Drosophila melanogaster. J. Insect Physiol. 57, 1437–1445 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    Nestel, D., Tolmasky, D., Rabossi, A. & Quesada-Allué, L. A. Lipid, carbohydrates and protein patterns during metamorphosis of the Mediterranean fruit fly, Ceratitis capitata (Diptera: Tephritidae). Ann. Entomol. Soc. Am. 96, 237–244 (2003).CAS 
    Article 

    Google Scholar 
    Lee, K. P. & Jang, T. Exploring the nutritional basis of starvation resistance in Drosophila melanogaster. Funct. Ecol. 28, 1144–1155 (2014).Article 

    Google Scholar 
    Hahn, D. A. & Denlinger, D. L. Meeting the energetic demands of insect diapause: Nutrient storage and utilization. J. Insect Physiol. 53, 760–773 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    Tejeda, M. T. et al. Effects of size, sex and teneral resources on the resistance to hydric stress in the tephritid fruit fly Anastrepha ludens. J. Insect Physiol. 70, 73–80 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Hoffmann, A. A., Hallas, R., Anderson, A. R. & Telonis-Scott, M. Evidence for a robust sex-specific trade-off between cold resistance and starvation resistance in Drosophila melanogaster. J. Evol. Biol. 18, 804–810 (2005).CAS 
    PubMed 
    Article 

    Google Scholar 
    Alaux, C., Ducloz, F., Crauser, D. & Le Conte, Y. Diet effects on honeybee immunocompetence. Biol. Lett. 6, 562–565 (2010).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bryk, B., Hahn, K., Cohen, S. M. & Teleman, A. A. MAP4K3 regulates body size and metabolism in Drosophila. Dev. Biol. 344, 150–157 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Gasser, M., Kaiser, M., Berrigan, D. & Stearns, S. C. Life-history correlates of evolution under high and low adult mortality. Evolution 54, 1260–1272 (2000).CAS 
    PubMed 
    Article 

    Google Scholar 
    Chippindale, A. K., Chu, T. J. F. & Rose, M. R. Complex trade-offs and the evolution of starvation resistance in Drosophila melanogaster. Evolution 50, 753 (1996).PubMed 
    Article 

    Google Scholar 
    Kristensen, T. N., Overgaard, J., Loeschcke, V. & Mayntz, D. Dietary protein content affects evolution for body size, body fat and viability in Drosophila melanogaster. Biol. Lett. 7, 269–272 (2011).PubMed 
    Article 

    Google Scholar 
    Juarez-Carreño, S. et al. Body-fat sensor triggers ribosome maturation in the steroidogenic gland to initiate sexual maturation in Drosophila. Cell Rep. 37, 109830 (2021).PubMed 
    Article 
    CAS 

    Google Scholar 
    Markow, T. A. The secret lives of Drosophila flies. Elife 4, e06793 (2015).PubMed Central 
    Article 

    Google Scholar 
    Choma, M. A., Suter, M. J., Vakoc, B. J., Bouma, B. E. & Tearney, G. J. Physiological homology between Drosophila melanogaster and vertebrate cardiovascular systems. Dis. Model. Mech. 4, 411–420 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    Morgan, T. H., Sturtevant, A. H., Muller, H. J. & Bridges, C. B. The Mechanism of Mendelian Heredity (H. Holt, 1923).
    Google Scholar 
    Dobzhansky, T. The influence of the quantity and quality of chromosomal material on the size of the cells in Drosophila melanogaster. Wilhelm Roux Arch. Entwickl Mech. Org. 115, 363–379 (1929).PubMed 
    Article 

    Google Scholar 
    Musselman, L. P. & Kühnlein, R. P. Drosophila as a model to study obesity and metabolic disease. J. Exp. Biol. 221, 163881 (2018).Article 

    Google Scholar 
    DiAngelo, J. R. & Birnbaum, M. J. Regulation of fat cell mass by insulin in Drosophila melanogaster. Mol. Cell. Biol. 29, 6341–6352 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rovenko, B. M. et al. High sucrose consumption promotes obesity whereas its low consumption induces oxidative stress in Drosophila melanogaster. J. Insect Physiol. 79, 42–54 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Hardy, C. M. et al. Obesity-associated cardiac dysfunction in starvation-selected Drosophila melanogaster. Am. J. Physiol.-Regul. Integr. Compar. Physiol. 309, R658–R667 (2015).CAS 
    Article 

    Google Scholar 
    Hardy, C. M. et al. Genome-wide analysis of starvation-selected Drosophila melanogaster—A genetic model of obesity. Mol. Biol. Evol. 35, 50–65 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Musselman, L. P. et al. A high-sugar diet produces obesity and insulin resistance in wild-type Drosophila. Dis. Model. Mech. 4, 842–849 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Henry, Y., Renault, D. & Colinet, H. Hormesis-like effect of mild larval crowding on thermotolerance in Drosophila flies. J. Exp. Biol. 221, 169342 (2018).Article 

    Google Scholar 
    Bulletin, E. P. P. O. Drosophila suzukii. EPPO Bull. 43, 417–424 (2013).Article 

    Google Scholar 
    Bächli, G., Vilela, C. R., Escher, S. A. & Saura, A. The Drosophilidae (Diptera) of Fennoscandia and Denmark (Brill Academic Publishers, 2004).Book 

    Google Scholar 
    Markow, T. A. & O’Grady, P. M. Drosophila: A Guide to Species Identification and Use (Elsevier, 2006).
    Google Scholar 
    Schindelin, J. et al. Fiji: An open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Visser, B. et al. Variation in lipid synthesis, but genetic homogeneity, among Leptopilina parasitic wasp populations. Ecol. Evol. 8, 7355–7364 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Williams, C. M., Thomas, R. H., MacMillan, H. A., Marshall, K. E. & Sinclair, B. J. Triacylglyceride measurement in small quantities of homogenised insect tissue: Comparisons and caveats. J. Insect Physiol. 57, 1602–1613 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2020).Fox, J. & Weisberg, S. An R Companion to Applied Regression 2nd edn. (Sage, 2011).
    Google Scholar 
    Lenth, R., Singmann, H., Love, J., Buerkner, P. & Herve, M. Emmeans: Estimated marginal means, aka least-squares means. R Package Version 1, 3 (2018).
    Google Scholar 
    Burnham, K. P. & Anderson, D. R. A practical information-theoretic approach. In Model Selection and Multimodel Inference (ed. Burnham, K. P.) (Springer, 2002).MATH 

    Google Scholar 
    Crawley, M. J. The R Book (Wiley, 2007).MATH 
    Book 

    Google Scholar 
    Borash, D. J. & Ho, G. T. Patterns of selection: Stress resistance and energy storage in density-dependent populations of Drosophila melanogaster. J. Insect Physiol. 47, 1349–1356 (2001).CAS 
    PubMed 
    Article 

    Google Scholar 
    Klepsatel, P., Procházka, E. & Gáliková, M. Crowding of Drosophila larvae affects lifespan and other life-history traits via reduced availability of dietary yeast. Exp. Gerontol. 110, 298–308 (2018).PubMed 
    Article 

    Google Scholar 
    Henry, Y., Overgaard, J. & Colinet, H. Dietary nutrient balance shapes phenotypic traits of Drosophila melanogaster in interaction with gut microbiota. Comp. Biochem. Physiol. A: Mol. Integr. Physiol. 241, 110626 (2020).CAS 
    Article 

    Google Scholar 
    Ireland, S. & Turner, B. The effects of larval crowding and food type on the size and development of the blowfly, Calliphora vomitoria. Forensic Sci. Int. 159, 175–181 (2006).PubMed 
    Article 

    Google Scholar 
    Saunders, D. S. & Bee, A. Effects of larval crowding on size and fecundity of the blow fly, Calliphora vicina (Diptera: Calliphoridae). EJE 92, 615–622 (2013).
    Google Scholar 
    Ziegler, R. Changes in lipid and carbohydrate metabolism during starvation in adult Manduca sexta. J. Comp. Physiol. B 161, 125–131 (1991).CAS 
    PubMed 
    Article 

    Google Scholar 
    Ojeda-Avila, T., Arthur Woods, H. & Raguso, R. A. Effects of dietary variation on growth, composition, and maturation of Manduca sexta (Sphingidae: Lepidoptera). J. Insect Physiol. 49, 293–306 (2003).CAS 
    PubMed 
    Article 

    Google Scholar 
    Borash, D. J., Gibbs, A. G., Joshi, A. & Mueller, L. D. A genetic polymorphism maintained by natural selection in a temporally varying environment. Am. Nat. 151, 148. https://doi.org/10.1086/286108 (1998).CAS 
    Article 
    PubMed 

    Google Scholar 
    Klepsatel, P., Knoblochová, D., Girish, T. N., Dircksen, H. & Gáliková, M. The influence of developmental diet on reproduction and metabolism in Drosophila. BMC Evol. Biol. 20, 93 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Matzkin, L. M., Johnson, S., Paight, C., Bozinovic, G. & Markow, T. A. Dietary protein and sugar differentially affect development and metabolic pools in ecologically diverse Drosophila. J. Nutr. 141, 1127–1133 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    Musselman, L. P. et al. Role of fat body lipogenesis in protection against the effects of caloric overload in Drosophila. J. Biol. Chem. 288, 8028–8042 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Reeve, M. W., Fowler, K. & Partridge, L. Increased body size confers greater fitness at lower experimental temperature in male Drosophila melanogaster. J. Evol. Biol. 13, 836–844 (2000).Article 

    Google Scholar 
    Lounibos, L. P. et al. Does temperature affect the outcome of larval competition between Aedes aegypti and Aedes albopictus?. J. Vector Ecol. 27, 86–95 (2002).CAS 
    PubMed 

    Google Scholar 
    Bergland, A. O., Genissel, A., Nuzhdin, S. V. & Tatar, M. Quantitative trait loci affecting phenotypic plasticity and the allometric relationship of ovariole number and thorax length in Drosophila melanogaster. Genetics 180, 567–582 (2008).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Holm, S. et al. A comparative perspective on longevity: The effect of body size dominates over ecology in moths. J. Evol. Biol. 29, 2422–2435 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Nunney, L. The response to selection for fast larval development in Drosophila melanogaster and its effect on adult weight: An example of a fitness trade-off. Evolution 50, 1193–1204 (1996).PubMed 
    Article 

    Google Scholar 
    Partridge, L. & Farquhar, M. Lifetime mating success of male fruitflies (Drosophila melanogaster) is related to their size. Anim. Behav. 31, 871–877 (1983).Article 

    Google Scholar 
    Markow, T. A. & Ricker, J. P. Male size, developmental stability, and mating success in natural populations of three Drosophila species. Heredity 69, 122–127 (1992).PubMed 
    Article 

    Google Scholar 
    Wikelski, M. & Romero, L. M. Body size, performance and fitness in galapagos marine iguanas. Integr. Comp. Biol. 43, 376–386 (2003).PubMed 
    Article 

    Google Scholar 
    van Buskirk, J. & Crowder, L. B. Life-history variation in marine turtles. Copeia 1994, 66–81 (1994).Article 

    Google Scholar 
    Broderick, A. C., Glen, F., Godley, B. J. & Hays, G. C. Variation in reproductive output of marine turtles. J. Exp. Mar. Biol. Ecol. 288, 95–109 (2003).Article 

    Google Scholar 
    Wauters, L. A. et al. Effects of spatio-temporal variation in food supply on red squirrel Sciurus vulgaris body size and body mass and its consequences for some fitness components. Ecography 30, 51–65 (2007).Article 

    Google Scholar 
    Lindström, J. Early development and fitness in birds and mammals. Trends Ecol. Evol. 14, 343–348 (1999).PubMed 
    Article 

    Google Scholar 
    Reim, C., Teuschl, Y. & Blanckenhorn, W. U. Size-dependent effects of temperature and food stress on energy reserves and starvation resistance in yellow dung flies. Evol. Ecol. Res. 8, 1215–1234 (2006).
    Google Scholar 
    Kölliker-Ott, U. M., Blows, M. W. & Hoffmann, A. A. Are wing size, wing shape and asymmetry related to field fitness of Trichogramma egg parasitoids? Oikos 100, 563–573 (2003).Article 

    Google Scholar 
    Knapp, M. Relative importance of sex, pre-starvation body mass and structural body size in the determination of exceptional starvation resistance of Anchomenus dorsalis (Coleoptera: Carabidae). PLoS ONE 11, e0151459 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Lue, C.-H. et al. DROP: Molecular voucher database for identification of Drosophila parasitoids. Mol. Ecol. Resour. 21, 2437–2454 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Visser, B. et al. Loss of lipid synthesis as an evolutionary consequence of a parasitic lifestyle. Proc. Natl. Acad. Sci. 107, 8677–8682 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Visser B et al. Why do
    many parasitoids lack adult triglyceride accumulation, despite functioning fatty acid biosynthesis machinery? EcoEvoRxiv:
    https://doi.org/10.32942/osf.io/zpf4jArakawa, R., Miura, M. & Fujita, M. Effects of host species on the body size, fecundity, and longevity of Trissolcus mitsukurii (Hymenoptera: Scelionidae), a solitary egg parasitoid of stink bugs. Appl. Entomol. Zool. 39, 177–181 (2004).Article 

    Google Scholar 
    Visser, B., Alborn, H.T., Rondeaux, S. et al. Phenotypic plasticity explains apparent reverse evolution of fat synthesis in parasitic
    wasps. Sci Rep 11, 7751 (2021). https://doi.org/10.1038/s41598-021-86736-8.Krüger, A. P. et al. Effects of irradiation dose on sterility induction and quality parameters of Drosophila suzukii (Diptera: Drosophilidae). J. Econ. Entomol. 111, 741–746 (2018).PubMed 
    Article 

    Google Scholar 
    Nikolouli, K. et al. Sterile insect technique and Wolbachia symbiosis as potential tools for the control of the invasive species Drosophila suzukii. J. Pest Sci. 91, 1–15 (2017).
    Google Scholar 
    Nikolouli, K., Sassù, F., Mouton, L., Stauffer, C. & Bourtzis, K. Combining sterile and incompatible insect techniques for the population suppression of Drosophila suzukii. J. Pest Sci. 93, 647–661 (2020).CAS 
    Article 

    Google Scholar 
    Calkins, C. O. & Parker, A. G. Sterile insect quality. In Sterile Insect Technique (eds Dyck, V. A. et al.) 269–296 (Springer, 2005).Chapter 

    Google Scholar  More

  • in

    Limited acclimation of early life stages of the coral Seriatopora hystrix from mesophotic depth to shallow reefs

    Hughes, T. P. et al. Global warming and recurrent mass bleaching of corals. Nature 543, 373–377 (2017).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Glynn, P. W. Coral reef bleaching: facts, hypotheses and implications. Glob. Chang. Biol. 2, 495–509 (1996).ADS 
    Article 

    Google Scholar 
    Riegl, B. & Piller, W. E. Possible refugia for reefs in times of environmental stress. Int. J. Earth Sci. 92, 520–531 (2003).Article 

    Google Scholar 
    Hinderstein, L. M. et al. Theme section on ‘Mesophotic Coral Ecosystems: Characterization, Ecology, and Management’. Coral Reefs 29, 247–251 (2010).ADS 
    Article 

    Google Scholar 
    Bongaerts, P., Ridgway, T., Sampayo, E. M. & Hoegh-Guldberg, O. Assessing the ‘deep reef refugia’ hypothesis: Focus on Caribbean reefs. Coral Reefs 29, 309–327 (2010).Article 

    Google Scholar 
    Smith, T. B. et al. Caribbean mesophotic coral ecosystems are unlikely climate change refugia. Global Change Biol. 22, 2756–2765 (2016).ADS 
    Article 

    Google Scholar 
    Frade, P. R. et al. Deep reefs of the Great Barrier Reef offer limited thermal refuge during mass coral bleaching. Nat. Commun. 9, 3447 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Holstein, D. M., Paris, C. B., Vaz, A. C. & Smith, T. B. Modeling vertical coral connectivity and mesophotic refugia. Coral Reefs 35, 23–37 (2016).ADS 
    Article 

    Google Scholar 
    Prasetia, R., Sinniger, F., Hashizume, K. & Harii, S. Reproductive biology of the deep brooding coral Seriatopora hystrix: Implications for shallow reef recovery. PLoS ONE 12, e0177034 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Shlesinger, T., Grinblat, M., Rapuano, H., Amit, T. & Loya, Y. Can mesophotic reefs replenish shallow reefs? Reduced coral reproductive performance casts a doubt. Ecology 99, 421–437 (2018).PubMed 
    Article 

    Google Scholar 
    Gleason, D. F. & Hofmann, D. K. Coral larvae: From gametes to recruits. J. Exp. Mar. Bio. Ecol. 408, 42–57 (2011).Article 

    Google Scholar 
    Hughes, T. P. & Tanner, J. E. Recruitment failure, life histories, and long-term decline of Caribbean corals. Ecology 81, 2250–2263 (2000).Article 

    Google Scholar 
    Bongaerts, P. et al. Deep reefs are not universal refuges: Reseeding potential varies among coral species. Sci. Adv. 3, e1602373 (2017).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    van Oppen, M. J. H., Bongaerts, P., Underwood, J. N., Peplow, L. M. & Cooper, T. F. The role of deep reefs in shallow reef recovery: An assessment of vertical connectivity in a brooding coral from west and east Australia. Mol. Ecol. 20, 1647–1660 (2011).PubMed 
    Article 

    Google Scholar 
    Cohen, I. & Dubinsky, Z. Long term photoacclimation responses of the coral Stylophora pistillata to reciprocal deep to shallow transplantation: Photosynthesis and calcification. Front. Mar. Sci. 2, 45 (2015).Article 

    Google Scholar 
    Eyal, G. et al. Euphyllia paradivisa, a successful mesophotic coral in the northern Gulf of Eilat/Aqaba, Red Sea. Coral Reefs 35, 91–102 (2016).ADS 
    Article 

    Google Scholar 
    Ben-Zvi, O. et al. Photophysiology of a mesophotic coral 3 years after transplantation to a shallow environment. Coral Reefs 39, 903–913 (2020).Article 

    Google Scholar 
    Murata, N., Takahashi, S., Nishiyama, Y. & Allakhverdiev, S. I. Photoinhibition of photosystem II under environmental stress. Biochim. Biophys. Acta Bioenerget. 1767, 414–421 (2007).CAS 
    Article 

    Google Scholar 
    Takahashi, S. & Murata, N. How do environmental stresses accelerate photoinhibition?. Trends Plant Sci. 13, 178–182 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Cumbo, V. R., Baird, A. H. & van Oppen, M. J. H. The promiscuous larvae: Flexibility in the establishment of symbiosis in corals. Coral Reefs 32, 111–120 (2013).ADS 
    Article 

    Google Scholar 
    Little, A. F., Van Oppen, M. J. H. & Willis, B. L. Flexibility in algal endosymbioses shapes growth in reef corals. Science 304, 1492–1494 (2004).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Sinniger, F., Morita, R. & Harii, S. ‘Locally extinct’ coral species Seriatopora hystrix found at upper mesophotic depths in Okinawa. Coral Reefs 32, 153 (2013).ADS 
    Article 

    Google Scholar 
    Sinniger, F. et al. Overview of the mesophotic coral ecosystems around Sesoko Island, Okinawa, Japan. Galaxea J. Coral Reef Stud. 24, 69–76 (2022).Article 

    Google Scholar 
    Loya, Y. et al. Coral bleaching: the winners and the losers. Ecol. Lett. 4, 122–131 (2001).Article 

    Google Scholar 
    van Woesik, R., Sakai, K., Ganase, A. & Loya, Y. Revisiting the winners and the losers a decade after coral bleaching. Mar. Ecol. Prog. Ser. 434, 67–76 (2011).ADS 
    Article 

    Google Scholar 
    Sinniger, F., Prasetia, R., Yorifuji, M., Bongaerts, P. & Harii, S. Seriatopora diversity preserved in upper mesophotic coral ecosystems in Southern Japan. Front. Mar. Sci. 4, 155 (2017).Article 

    Google Scholar 
    Atoda, K. The larva and postlarval development of some reef-building corals. V. Seriatopora hystrix. Sci. Rep. Tohoku Univ. 19, 33–39 (1951).
    Google Scholar 
    Hata, T. et al. Coral larvae are poor swimmers and require fine-scale reef structure to settle. Sci. Rep. 7, 2249 (2017).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Harii, S. & Kayanne, H. Larval dispersal, recruitment, and adult distribution of the brooding stony octocoral Heliopora coerulea on Ishigaki Island, southwest Japan. Coral Reefs 22, 188–196 (2003).Article 

    Google Scholar 
    Mulla, A. J., Lin, C. H., Takahashi, S. & Nozawa, Y. Photo-movement of coral larvae influences vertical positioning in the ocean. Coral Reefs 40, 1297–1306 (2021).Article 

    Google Scholar 
    Figueiredo, J., Baird, A. H., Harii, S. & Connolly, S. R. Increased local retention of reef coral larvae as a result of ocean warming. Nat. Clim. Chang. 4, 498–502 (2014).ADS 
    Article 

    Google Scholar 
    Shanks, A. L., Largier, J., Brink, L., Brubaker, J. & Hooff, R. Demonstration of the onshore transport of larval invertebrates by the shoreward movement of an upwelling front. Limnol. Oceanogr. 45, 230–236 (2000).ADS 
    Article 

    Google Scholar 
    Singh, T. et al. Long-term trends and seasonal variations in environmental conditions in Sesoko Island, Okinawa, Japan. Galaxea J. Coral Reef Stud. 24, 121–133 (2022).Article 

    Google Scholar 
    Roth, M. S., Fan, T.-Y. & Deheyn, D. D. Life history changes in coral fluorescence and the effects of light intensity on larval physiology and settlement in Seriatopora hystrix. PLoS ONE 8, e59476 (2013).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Mundy, C. N. & Babcock, R. C. Role of light intensity and spectral quality in coral settlement: Implications for depth-dependent settlement?. J. Exp. Mar. Bio. Ecol. 223, 235–255 (1998).Article 

    Google Scholar 
    Nesa, B., Baird, A. H., Harii, S., Yakovleva, I. & Hidaka, M. Algal symbionts increase DNA damage in coral planulae exposed to sunlight. Zool. Stud. 51, 12–17 (2012).CAS 

    Google Scholar 
    Cunning, R. & Baker, A. C. Excess algal symbionts increase the susceptibility of reef corals to bleaching. Nat. Clim. Change 3, 259–262 (2013).ADS 
    Article 

    Google Scholar 
    Nakamura, T. Mass coral bleaching event in Sekisei lagoon observed in the summer of 2016. J. Jpn. Coral Reef Soc. 19, 29–40 (2017).Article 

    Google Scholar 
    Sakai, K., Singh, T. & Iguchi, A. Bleaching and post-bleaching mortality of Acropora corals on a heat-susceptible reef in 2016. PeerJ 7, e8138 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Edmunds, P. J., Gates, R. D. & Gleason, D. F. The biology of larvae from the reef coral Porites astreoides, and their response to temperature disturbances. Mar. Biol. 139, 981–989 (2001).Article 

    Google Scholar 
    Baker, A. C. Reef corals bleach to survive change. Nature 411, 765–766 (2001).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Bongaerts, P. et al. Adaptive divergence in a scleractinian coral: Physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats. BMC Evol. Biol. 11, 303 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Einbinder, S. et al. Novel adaptive photosynthetic characteristics of mesophotic symbiotic microalgae within the reef-building coral, Stylophora pistillata. Front. Mar. Sci. 3, 195 (2016).Article 

    Google Scholar 
    Rogers, C. S., Fitz, H. C., Gilnack, M., Beets, J. & Hardin, J. Scleractinian coral recruitment patterns at Salt River submarine canyon, St. Croix, U.S. Virgin Islands. Coral Reefs 3, 69–76 (1984).ADS 
    Article 

    Google Scholar 
    Maida, M., Collb, J. C. & Sammarco, P. W. Shedding new light on scleractinian coral recruitment. J. Exp. Mar. Biol. Ecol. 180, 189–202 (1994).Article 

    Google Scholar 
    Sato, M. Mortality and growth of juvenile coral Pocillopora damicornis (Linnaeus). Coral Reefs 4, 27–33 (1985).ADS 
    Article 

    Google Scholar 
    Nozawa, Y. Micro-crevice structure enhances coral spat survivorship. J. Exp. Mar. Biol. Ecol. 367, 127–130 (2008).Article 

    Google Scholar 
    Gleason, D. F. & Wellington, G. M. Ultraviolet radiation and coral bleaching. Nature 365, 836–838 (1993).ADS 
    Article 

    Google Scholar 
    Shlesinger, T. & Loya, Y. Depth-dependent parental effects create invisible barriers to coral dispersal. Commun. Biol. 4, 1–10 (2021).Article 

    Google Scholar 
    Groves, S. H. et al. Growth rates of Porites astreoides and Orbicella franksi in mesophotic habitats surrounding St. Thomas, US Virgin Islands. Coral Reefs 37, 345–354 (2018).ADS 
    Article 

    Google Scholar 
    Al-Horani, F. A., Al-Moghrabi, S. M. & De Beer, D. The mechanism of calcification and its relation to photosynthesis and respiration in the scleractinian coral Galaxea fascicularis. Mar. Biol. 142, 419–426 (2003).CAS 
    Article 

    Google Scholar 
    Jiang, L. et al. Increased temperature mitigates the effects of ocean acidification on the calcification of juvenile Pocillopora damicornis, but at a cost. Coral Reefs 37, 71–79 (2018).ADS 
    Article 

    Google Scholar 
    Jurriaans, S. & Hoogenboom, M. O. Thermal performance of scleractinian corals along a latitudinal gradient on the Great Barrier Reef. Philos. Trans. R. Soc. B Biol. Sci. 374, 20180546 (2019).CAS 
    Article 

    Google Scholar 
    Brown, B. E. et al. Diurnal changes in photochemical efficiency and xanthophyll concentrations in shallow water reef corals: evidence for photoinhibition and photoprotection. Coral Reefs 18, 99–105 (1999).Article 

    Google Scholar 
    Salih, A., Larkum, A., Cox, G., Kühl, M. & Hoegh-Guldberg, O. Fluorescent pigments in corals are photoprotective. Nature 408, 850–853 (2000).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Matz, M. V., Marshall, N. J. & Vorobyev, M. Are corals colorful?. Photochem. Photobiol. 82, 345–350 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    Haddock, S. H. D. & Dunn, C. W. Fluorescent proteins function as a prey attractant: Experimental evidence from the hydromedusa Olindias formosus and other marine organisms. Biol. Open 4, 1094–1104 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Eyal, G. et al. Spectral diversity and regulation of coral fluorescence in a mesophotic reef habitat in the Red Sea. PLoS ONE 10, 1–19 (2015).Article 
    CAS 

    Google Scholar 
    Ben-Zvi, O., Eyal, G. & Loya, Y. Light-dependent fluorescence in the coral Galaxea fascicularis. Hydrobiologia 759, 15–26 (2015).Article 

    Google Scholar 
    Roth, M. et al. Fluorescent proteins in dominant mesophotic reef-building corals. Mar. Ecol. Prog. Ser. 521, 63–79 (2015).ADS 
    CAS 
    Article 

    Google Scholar 
    Ben-Zvi, O., Eyal, G. & Loya, Y. Response of fluorescence morphs of the mesophotic coral Euphyllia paradivisa to ultra-violet radiation. Sci. Rep. 9, 1–9 (2019).CAS 
    Article 

    Google Scholar 
    Hughes, T. P. et al. Coral reefs in the Anthropocene. Nature 546, 82–90 (2017).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Oliver, E. C. J. et al. Longer and more frequent marine heatwaves over the past century. Nat. Commun. 9, 1324 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Nakamura, T., van Woesik, R. & Yamasaki, H. Photoinhibition of photosynthesis is reduced by water flow in the reef-building coral Acropora digitifera. Mar. Ecol. Prog. Ser. 301, 109–118 (2005).ADS 
    Article 

    Google Scholar  More

  • in

    Applying the concept of liquid biopsy to monitor the microbial biodiversity of marine coastal ecosystems

    Brierley AS, Kingsford MJ. Impacts of climate change on marine organisms and ecosystems. Curr Biol. 2009;19:R602–R614.CAS 
    PubMed 
    Article 

    Google Scholar 
    Gissi E, Manea E, Mazaris AD, Fraschetti S, Almpanidou V, Bevilacqua S, et al. A review of the combined effects of climate change and other local human stressors on the marine environment. Sci Total Environ. 2021;755:142564.CAS 
    PubMed 
    Article 

    Google Scholar 
    Carella F, Antuofermo E, Farina S, Salati F, Mandas D, Prado P, et al. In the wake of the ongoing mass mortality events: co-occurrence of Mycobacterium, Haplosporidium and other pathogens in Pinna nobilis collected in Italy and Spain (Mediterranean Sea). Front Mar Sci. 2020;7:48.Article 

    Google Scholar 
    Seuront L, Nicastro KR, Zardi GI, Goberville E. Decreased thermal tolerance under recurrent heat stress conditions explains summer mass mortality of the blue mussel Mytilus edulis. Sci Rep. 2019;9:17498.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Fey SB, Siepielski AM, Nussle S, Cervantes-Yoshida K, Hwan JL, Huber ER, et al. Recent shifts in the occurrence, cause, and magnitude of animal mass mortality events. Proc Natl Acad Sci USA. 2015;112:1083–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Scarpa F, Sanna D, Azzena I, Mugetti D, Cerruti F, Hosseini S, et al. Multiple non-species-specific pathogens possibly triggered the mass mortality in Pinna nobilis. Life. 2020;10:238.CAS 
    PubMed Central 
    Article 

    Google Scholar 
    Bradley M, Kutz SJ, Jenkins E, O’Hara TM. The potential impact of climate change on infectious diseases of Arctic fauna. Int J Circumpolar Health. 2005;64:468–77.PubMed 
    Article 

    Google Scholar 
    Beyer J, Green NW, Brooks S, Allan IJ, Ruus A, Gomes T, et al. Blue mussels (Mytilus edulis spp.) as sentinel organisms in coastal pollution monitoring: a review. Mar Environ Res. 2017;130:338–65.CAS 
    PubMed 
    Article 

    Google Scholar 
    Siravegna G, Marsoni S, Siena S, Bardelli A. Integrating liquid biopsies into the management of cancer. Nat Rev Clin Oncol. 2017;14:531–48.CAS 
    PubMed 
    Article 

    Google Scholar 
    Wan JCM, Massie C, Garcia-Corbacho J, Mouliere F, Brenton JD, Caldas C, et al. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer. 2017;17:223–38.CAS 
    PubMed 
    Article 

    Google Scholar 
    Mandel P, Metais P. Nuclear acids in human blood plasma. Comptes Rendus Séances Soc Biol Filiales. 1948;142:241–3.CAS 

    Google Scholar 
    Bronkhorst AJ, Ungerer V, Holdenrieder S. The emerging role of cell-free DNA as a molecular marker for cancer management. Biomol Detect Quantif. 2019;17:100087.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ignatiadis M, Sledge GW, Jeffrey SS. Liquid biopsy enters the clinic – implementation issues and future challenges. Nat Rev Clin Oncol. 2021;18:297–312.PubMed 
    Article 

    Google Scholar 
    Lo YM, Corbetta N, Chamberlain PF, Rai V, Sargent IL, Redman CW, et al. Presence of fetal DNA in maternal plasma and serum. Lancet. 1997;350:485–7.CAS 
    PubMed 
    Article 

    Google Scholar 
    Moufarrej MN, Wong RJ, Shaw GM, Stevenson DK, Quake SR. Investigating pregnancy and its complications using circulating cell-free RNA in women’s blood during gestation. Front Pediatr. 2020;8:605219.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Oellerich M, Sherwood K, Keown P, Schutz E, Beck J, Stegbauer J, et al. Liquid biopsies: donor-derived cell-free DNA for the detection of kidney allograft injury. Nat Rev Nephrol. 2021;17:591–603.CAS 
    PubMed 
    Article 

    Google Scholar 
    Wong FC, Lo YM. Prenatal diagnosis innovation: genome sequencing of maternal plasma. Annu Rev Med. 2016;67:419–32.CAS 
    PubMed 
    Article 

    Google Scholar 
    Gu W, Deng X, Lee M, Sucu YD, Arevalo S, Stryke D, et al. Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids. Nat Med. 2021;27:115–24.CAS 
    PubMed 
    Article 

    Google Scholar 
    Huang YF, Chen YJ, Fan TC, Chang NC, Chen YJ, Midha MK, et al. Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females. BMC Med Genom. 2018;11:16.Article 
    CAS 

    Google Scholar 
    Goggs R, Jeffery U, LeVine DN, Li RHL. Neutrophil-extracellular traps, cell-free DNA, and immunothrombosis in companion animals: a review. Vet Pathol. 2020;57:6–23.CAS 
    PubMed 
    Article 

    Google Scholar 
    Kowarsky M, De Vlaminck I, Okamoto J, Neff NF, LeBreton M, Nwobegabay J, et al. Cell-free DNA reveals potential zoonotic reservoirs in non-human primates. BioRxiv. 2018;481093.Caza F, Bernet E, Veyrier FJ, Betoulle S, St-Pierre Y. Hemocytes released in seawater act as Trojan horses for spreading of bacterial infections in mussels. Sci Rep. 2020;10:19696.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Andrew S. FastQC: a quality control tool for high throughput sequence data. 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc.Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27:2957–63.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Morgulis A, Gertz EM, Schäffer AA, Agarwala R. A fast and symmetric DUST implementation to mask low-complexity DNA sequences. Comput Biol. 2006;13:1028–40.CAS 
    Article 

    Google Scholar 
    Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674–6.CAS 
    PubMed 
    Article 

    Google Scholar 
    Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15:R46.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Cuccuru G, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, et al. Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics. 2014;30:1928–9.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinform. 2011;12:385.Article 

    Google Scholar 
    Lüskow F, Riisgård H. In situ filtration rates of blue mussels (Mytilus edulis) measured by an open-top chamber method. OJMS. 2018;8:395–406.Article 

    Google Scholar 
    Szpechcinski A, Struniawska R, Zaleska J, Chabowski M, Orlowski T, Roszkowski K, et al. Evaluation of fluorescence-based methods for total vs. amplifiable DNA quantification in plasma of lung cancer patients. J Physiol Pharmacol. 2008;59:675–81.PubMed 

    Google Scholar 
    Tissot C, Toffart AC, Villar S, Souquet PJ, Merle P, Moro-Sibilot D, et al. Circulating free DNA concentration is an independent prognostic biomarker in lung cancer. Eur Respir J. 2015;46:1773–80.CAS 
    PubMed 
    Article 

    Google Scholar 
    Kustanovich A, Schwartz R, Peretz T, Grinshpun A. Life and death of circulating cell-free DNA. Cancer Biol Ther. 2019;20:1057–67.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Prouteau A, Denis JA, De Fornel P, Cadieu E, Derrien T, Kergal C, et al. Circulating tumor DNA is detectable in canine histiocytic sarcoma, oral malignant melanoma, and multicentric lymphoma. Sci Rep. 2021;11:877.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Vandewoestyne M, Van Hoofstat D, Franssen A, Van Nieuwerburgh F, Deforce D. Presence and potential of cell free DNA in different types of forensic samples. For Sci Int Genet. 2013;7:316–20.CAS 
    Article 

    Google Scholar 
    Kowarsky M, Camunas-Soler J, Kertesz M, De Vlaminck I, Koh W, Pan W, et al. Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA. Proc Natl Acad Sci USA. 2017;114:9623–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Meddeb R, Dache ZAA, Thezenas S, Otandault A, Tanos R, Pastor B, et al. Quantifying circulating cell-free DNA in humans. Sci Rep. 2019;9:5220.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Li YF, Yang N, Liang X, Yoshida A, Osatomi K, Power D, et al. Elevated seawater temperatures decrease microbial diversity in the gut of Mytilus coruscus. Front Physiol. 2018;9:839.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Musella M, Wathsala R, Tavella T, Rampelli S, Barone M, Palladino G, et al. Tissue-scale microbiota of the Mediterranean mussel (Mytilus galloprovincialis) and its relationship with the environment. Sci Total Environ. 2020;717:137209.CAS 
    PubMed 
    Article 

    Google Scholar 
    Thompson JR, Randa MA, Marcelino LA, Tomita-Mitchell A, Lim E, Polz MF. Diversity and dynamics of a north atlantic coastal Vibrio community. Appl Environ Microbiol. 2004;70:4103–10.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pfister CA, Meyer F, Antonopoulos DA. Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling. PLoS One. 2010;5:e10518.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Galand PE, Casamayor EO, Kirchman DL, Potvin M, Lovejoy C. Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing. ISME J. 2009;3:860–9.CAS 
    PubMed 
    Article 

    Google Scholar 
    Korzhenkov AA, Toshchakov SV, Bargiela R, Gibbard H, Ferrer M, Teplyuk AV, et al. Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity. Microbiome. 2019;7:11.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Spain EA, Johnson SC, Hutton B, Whittaker JM, Lucieer V, Watson SJ, et al. Shallow seafloor gas emissions near Heard and McDonald Islands on the Kerguelen Plateau, southern Indian Ocean. Earth Space Sci. 2020;7:e2019EA000695.Article 

    Google Scholar 
    Farías L, Florez-Leiva L, Besoain V, Sarthou G, Fernández C. Dissolved greenhouse gases (nitrous oxide and methane) associated with the naturally iron-fertilized Kerguelen region (KEOPS 2 cruise) in the Southern Ocean. Biogeosciences. 2015;12:1925–40.Article 

    Google Scholar 
    Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, et al. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. Proc Natl Acad Sci USA. 2014;111:4274–9.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Levasseur A, Andreani J, Delerce J, Bou Khalil J, Robert C, La Scola B, et al. Comparison of a modern and fossil pithovirus reveals its genetic conservation and evolution. Genome Biol Evol. 2016;8:2333–9.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kelley JL, Brown AP, Therkildsen NO, Foote AD. The life aquatic: advances in marine vertebrate genomics. Nat Rev Genet. 2016;17:523–34.CAS 
    PubMed 
    Article 

    Google Scholar 
    Colmer SF, Luethy D, Abraham M, Stefanovski D, Hurcombe SD. Utility of cell-free DNA concentrations and illness severity scores to predict survival in critically ill neonatal foals. PLoS One. 2021;16:e0242635.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rushton JG, Ertl R, Klein D, Tichy A, Nell B. Circulating cell-free DNA does not harbour a diagnostic benefit in cats with feline diffuse iris melanomas. J Feline Med Surg. 2019;21:124–32.PubMed 
    Article 

    Google Scholar 
    Tagawa M, Shimbo G, Inokuma H, Miyahara K. Quantification of plasma cell-free DNA levels in dogs with various tumors. J Vet Diagn Investig. 2019;31:836–43.CAS 
    Article 

    Google Scholar 
    Shi J, Zhang R, Li J, Zhang R. Size profile of cell-free DNA: a beacon guiding the practice and innovation of clinical testing. Theranostics. 2020;10:4737–48.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Fernando MR, Jiang C, Krzyzanowski GD, Ryan WL. Analysis of human blood plasma cell-free DNA fragment size distribution using EvaGreen chemistry based droplet digital PCR assays. Clin Chim Acta. 2018;483:39–47.CAS 
    PubMed 
    Article 

    Google Scholar 
    Findlay AJ. Microbial impact on polysulfide dynamics in the environment. FEMS Microbiol Lett. 2016;363:fnw103.PubMed 
    Article 
    CAS 

    Google Scholar 
    Jørgensen BB, Findlay AJ, Pellerin A. The biogeochemical sulfur cycle of marine sediments. Front Microbiol. 2019;10:849.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Teske A, Brinkhoff T, Muyzer G, Moser DP, Rethmeier J, Jannasch HW. Diversity of thiosulfate-oxidizing bacteria from marine sediments and hydrothermal vents. Appl Environ Microbiol. 2000;66:3125–33.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zhang X, Du Z, Zheng R, Luan Z, Qi F, Cheng K, et al. Development of a new deep-sea hybrid Raman insertion probe and its application to the geochemistry of hydrothermal vent and cold seep fluids. Deep Sea Res Part I Oceanogr Res Pap. 2017;123:1–12.Article 
    CAS 

    Google Scholar 
    Egger M, Riedinger N, Mogollón JM, Jørgensen BB. Global diffusive fluxes of methane in marine sediments. Nat Geosci. 2018;11:421–5.CAS 
    Article 

    Google Scholar 
    Ansorge R, Romano S, Sayavedra L, Kupczok A, Tegetmeyer HE, Dubilier N, et al. Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels. Nat Microbiol. 2019;4:2487–97.PubMed 
    Article 
    CAS 

    Google Scholar 
    Russell SL, Pepper-Tunick E, Svedberg J, Byrne A, Ruelas Castillo J, Vollmers C, et al. Horizontal transmission and recombination maintain forever young bacterial symbiont genomes. PLoS Genet. 2020;16:e1008935.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, et al. The marine viromes of four oceanic regions. PLoS Biol. 2006;4:e368.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Li Z, Pan D, Wei G, Pi W, Zhang C, Wang JH, et al. Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. ISME J. 2021;15:2366–78.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Thongsripong P, Chandler JA, Kittayapong P, Wilcox BA, Kapan DD, Bennett SN. Metagenomic shotgun sequencing reveals host species as an important driver of virome composition in mosquitoes. Sci Rep. 2021;11:8448.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Koonin EV, Krupovic M, Agol VI. The Baltimore classification of viruses 50 years later: how does it stand in the light of virus evolution? Microbiol Mol Biol Rev. 2021;85:e0005321.PubMed 
    Article 

    Google Scholar 
    Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, et al. Global organization and proposed megataxonomy of the virus world. Microbiol Mol Biol Rev. 2020;84:e00061–19.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Breitbach S, Tug S, Simon P. Circulating cell-free DNA: an up-coming molecular marker in exercise physiology. Sports Med. 2012;42:565–86.PubMed 
    Article 

    Google Scholar 
    Preissner KT, Herwald H. Extracellular nucleic acids in immunity and cardiovascular responses: between alert and disease. Thromb Haemost. 2017;117:1272–82.PubMed 
    Article 

    Google Scholar 
    Schwarzenbach H. Circulating nucleic acids as biomarkers in breast cancer. Breast Cancer Res. 2013;15:211.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Murphy DJ. Freezing resistance in intertidal invertebrates. Annu Rev Physiol. 1983;45:289–99.CAS 
    PubMed 
    Article 

    Google Scholar 
    Robledo JAF, Yadavalli R, Allam B, Espinosa EP, Gerdol M, Greco S, et al. From the raw bar to the bench: bivalves as models for human health. Dev Comp Immunol. 2019;92:260–82.Article 

    Google Scholar 
    Cowart DA, Murphy KR, Cheng CC. Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula. Mar Genom. 2018;37:148–60.Article 

    Google Scholar 
    Parducci L, Bennett KD, Ficetola GF, Alsos IG, Suyama Y, Wood JR, et al. Ancient plant DNA in lake sediments. New Phytol. 2017;214:924–42.CAS 
    PubMed 
    Article 

    Google Scholar 
    Mariani S, Baillie C, Giuliano C, Riesgo A. Sponges as natural environmental DNA samplers. Curr Biol. 2019;29:R401–R402.CAS 
    PubMed 
    Article 

    Google Scholar 
    Weber S, Brink L, Wörner M, Künzel S, Veith M, Teubner D, et al. Molecular diet analysis in zebra and quagga mussels (Dreissena spp.) and an assessment of the utility of aquatic filter feeders as biological eDNA filters. BioRxiv. 2021; 432951.Caza F, Joly de Boissel PG, Villemur R, Betoulle S, St-Pierre Y. Liquid biopsies for omics-based analysis in sentinel mussels. Plos One. 2019;14:e0223525.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Hunter ME, Ferrante JA, Meigs-Friend G, Ulmer A. Improving eDNA yield and inhibitor reduction through increased water volumes and multi-filter isolation techniques. Sci Rep. 2019;9:5259.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Burkhardt W III, Calci KR. Selective accumulation may account for shellfish-associated viral illness. Appl Environ Microbiol. 2000;66:1375–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Di Girolamo R, Liston J, Matches J. Ionic bonding, the mechanism of viral uptake by shellfish mucus. Appl Environ Microbiol. 1977;33:19–25.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Metzger MJ, Reinisch C, Sherry J, Goff SP. Horizontal transmission of clonal cancer cells causes leukemia in soft-shell clams. Cell. 2015;161:255–63.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Metzger MJ, Villalba A, Carballal MJ, Iglesias D, Sherry J, Reinisch C, et al. Widespread transmission of independent cancer lineages within multiple bivalve species. Nature. 2016;534:705–9.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Canesi L, Gallo G, Gavioli M, Pruzzo C. Bacteria–hemocyte interactions and phagocytosis in marine bivalves. Microsc Res Tech. 2002;57:469–76.PubMed 
    Article 

    Google Scholar 
    Andruszkiewicz EA, Koseff JR, Fringer OB, Ouellette NT, Lowe AB, Edwards CA, et al. Modeling environmental DNA transport in the coastal ocean using Lagrangian particle tracking. Front Mar Sci. 2019;6:477.Article 

    Google Scholar 
    Wood ZT, Lacoursière-Roussel A, LeBlanc F, Trudel M, Kinnison MT, Garry McBrine C, et al. Spatial heterogeneity of eDNA transport improves stream assessment of threatened salmon presence, abundance, and location. Front Ecol Evol. 2021;9:650717.Article 

    Google Scholar 
    Rand AC, Jain M, Eizenga JM, Musselman-Brown A, Olsen HE, Akeson M, et al. Mapping DNA methylation with high-throughput nanopore sequencing. Nat Methods. 2017;14:411–3.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Simpson JT, Workman RE, Zuzarte PC, David M, Dursi LJ, Timp W. Detecting DNA cytosine methylation using nanopore sequencing. Nat Methods. 2017;14:407–10.CAS 
    PubMed 
    Article 

    Google Scholar 
    Cavalli G, Heard E. Advances in epigenetics link genetics to the environment and disease. Nature. 2019;571:489–99.CAS 
    PubMed 
    Article 

    Google Scholar 
    Fan G, Song Y, Yang L, Huang X, Zhang S, Zhang M, et al. Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K). Gigascience. 2020;9:giaa080.PubMed 
    PubMed Central 
    Article 

    Google Scholar  More

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    Understanding the spatial distribution and hot spots of collared Bornean elephants in a multi-use landscape

    By pooling the results of the entire known range analysis of 14 GPS-collared elephants living in the Kinabatangan, our study suggests that this populations range covers at least 628 km2 (Table 3). Nine different locations were identified as hot spots, representing 266.9 km2 or 43% of this range, suggesting that just under half is highly used and/or frequented (Fig. 1). We found that the size of individual’s hot spots was positively related to the size of the entire range, meaning the larger the entire range the larger the summed area of an elephants hot spots. On average, hot spots represented a relatively small percent of an animal’s entire range (ranging from 4 to 20%, averaging 12%, Table 3). However, time spent within these hot spots ranged from 10 to 60% (averaging 34% across elephants, Table 5), with time spent in hot spots being related to the overall size of the hot spots (the larger the hot spot the more time elephants spent in them).Identifying the location of these hot spots is essential in designing appropriate management practices in collaboration with land users and identifying the best location for elephant corridors. In the last 25 years, forest cover in the Lower Kinabatangan has been drastically reduced and fragmented46, eroding the biodiversity value of this landscape. Today, this region has little remaining forests, and what is left is insufficient for sustaining the local elephant population10. Moreover, forests are highly fragmented along the Kinabatangan River, with a number of bottlenecks constraining elephant movements9. The situation in this landscape is getting worse because of further land clearances for agriculture, namely oil palm; as well as for the highly controversial Sukau Bridge and new road/highway that is planned for the region.Our analyses revealed a highly significant difference between the average proportions of protected area, unprotected forest, and oil palm estate extents within the elephant’s entire range; and a substantive, but not significant, difference across these land use/land cover types within hot spots (Table SI 4). At the individual level, there was a highly significant negative relationship between the proportion of protected areas and oil palm estates both within the elephant’s entire range and within the hot spots.At the pooled level, we found that around 45% of the entire known range and hot spots were within forested environments (280.44 km2 and 120.29 km2 respectively). Our results showed strong fidelity of certain elephants to these forested habitats. Our k-means cluster analysis found that within elephant entire ranges and hot spots, two out of the three cluster groups had high or very high usage of forests. Both cluster 1, for the entire range, and cluster 1 for hot spots extents, had five females that on average used forest environments 90% of their time, with protected areas being used 64% and 59%, and unprotected forested being used on average 26% and 31%, respectively (Table 7).Individuals in cluster 2, for the entire range analysis, on average, spent 73% of their time in forests (57% of this in protected areas and 16% in unprotected forests; Table 7). For the hot spot analysis, the individuals in cluster 2 spent on average 65% of their time in forests (52% of this in the unprotected forests and 13% in protected forests; Table 7). Elephants within these clusters were all females. Our results suggest that forest may be of particular importance for females as they had forest as their dominant land cover type within their entire range, hot spot extents and time spent analyses (Fig. 3, Table 5). Several studies have shown that adult females influence and guide the movement patterns and habitat utilization for their family group and that females in family units tend to inhabit less risky areas, such as within natural forest habitat60,61,62.However, the unprotected forest is at risk. We identified about 8% (or 49 km2) of forest identified within the pooled entire known range were not protected, with half potentially being on state land, and the remaining half on land titles of various types (Table SI 4). For the pooled hot spot areas, unprotected forest was proportionally higher, comprising of 11% (or 29 km2) of the total extent, with 54% being potentially on State land and 46% on land titles (Table SI 4). Protecting these forests would be an essential and efficient way to secure key elephant habitat since all collared individuals were using these forest fragments in their entire range (averaging 11%, and ranging from 8 to 18%), and hot spot extents (averaging 20%, and ranging from 0 to 53%) (Table SI 4, Fig. 3). On average, 24% of time was spent in unprotected forests within hot spots, though this varied widely from 0% (for the male elephant known as Gading) to 61% (for the female matriarch named Jasmine) (Table 5). In fact, five females had large proportions of their hot spot extents (24–53%) in unprotected forests, spending substantial periods of their time (33–61%) within these threatened areas.Our findings show that unprotected forests around the villages of Bilit and Sukau, were of particular significance (Figs. 1, 2). These unprotected forests largely consist of lowland dry forest, seasonally flooded swamp forest, and swamp forest, which are considered important habitats for elephants for feeding, resting and moving47,63. Within these forests, and along the forest margins and river banks there are also natural open grasslands that consist of Phragmites karka and Dinochloa scabrida that provide essential forage, mainly in the riparian areas for elephants9,21,23. Forested environments are also considered to be important in providing natural refugee from human activities and disturbance. For example, elephants have been documented to form significantly larger group sizes, as well as engaging in significantly more social interactions, in natural forest habitat compared to, for example, oil palm landscapes63. Adult females, generally, avoid areas considered unsafe for their respective social units, are more selective in the resources they use, and require regular access to water because of the presence of young64,65,66. This may be why our results, strongly suggest that forest habitats seem to be most important for adult females.Another significant issue faced by these elephants is the threat from the controversial planned Sukau bridge and road/highway that is set out in the Sabah Structure Plan, an overarching policy document for the State58. Currently, a new road/highway is under construction on the northern bank of the village of Sukau, and this has already cleared areas of unprotected forest. This public road could link to a potential new bridge that would cross over the Kinabatangan River, cutting through unprotected forest and a protected area (Lower Kinabatangan Wildlife Sanctuary), before going through oil palm estates then through another protected area to the south and through the Tabin elephant population range. For the Kinabatangan, creating a public highway will cut the elephant population range into two parts (Figs. 2, 3). All collared elephants use this area, as it is a key bottleneck and the only alternative option to pass around Sukau village9. We found that nine elephants have hot spots that intersect or meet up with the current road (which will be up-graded and get considerably busier) and/or the planned road/highway alignment (Figs. SI 1 and 2). For these elephants, we calculated that they spent from 2 to 44% (average 14%) of their time within these hot spots (Table 4). Our statistical analyses suggest that if the road/highway goes ahead it will have a significant impact on the elephants’ behaviour with respect to time spent in the hot spots. Indeed, this infrastructure project could have dire consequences for these elephants and their family groups, by disrupting their ranging patterns and segmenting the entire elephant range into two (Figs. 2, 4). The existing road in Batu Putih has already proven to be an impassable barrier for this elephant population, as no elephants have been observed crossing this road since the early 2000s14. For elephants that do try and cross, vehicle collisions may become a significant threat to elephants and drivers alike67, and potentially increasing human–elephant conflict in the nearby villages, as well as in plantations14,68,69, exacerbating an already difficult situation for this small and fragmented population.Results from the pooled analysis show that about 53% of the entire known population range is within oil palm estates; and 51% for the pooled hot spots (Fig. 3, Table SI 4). Our k-means clustering analysis grouped 6 elephants into cluster 3 that on average spent 57% of time in oil palm estates; and 7 elephants into cluster 2 within the hot spot analysis that on average spent 73% of their time in oil palm estates (Table 6). All the males, were clustered within these groups (Table 5). In fact, the three collared males were amongst the highest users of oil palm estates (Fig. 3, Table SI4, and 5). This could be related to a ‘‘high risk, high gain’’ strategy, often adopted by males to increase body size and enhance reproductive success32,33,60. However, it is interesting to see that three females (Ita, Ratu and Koyah) and their respective social units, also seemed to have high levels of oil palm use, while other individuals had zero or very little use of oil palm (e.g. Aqeela, Jasmin, Sandi, Kasih; Table SI 4, Fig. 3). Differential choices may result from differences in individual knowledge and experience with people during past encounters, for example70,71.We identified that collared elephants were ranging in 11 known oil palm estates, with the five most regularly used being Melangking Oil Palm Plantation (with 12 elephants entire range overlapping with this estate and six hot spots), IOI Corporation (with 11 overlapping entire ranges, and eight hot spots), Genting Plantations (14 and seven, respectively), Sime Darby Plantation (five and two, respectively), and Karangan Agriculture (8 and 2, respectively) (Table 6; Fig. 4). Presence of bottlenecks and barriers (e.g. electric fences) may explain hot spot occurrences in these estates, as well as feeding opportunities, management strategies of specific estates, and historical and seasonal ranges.Linear features like major highways, electric fences and drainage ditches hamper elephant movements within the Lower Kinabatangan9. A previous study identified 20 bottlenecks in the Lower Kinabatangan with the two main ones (of 9 km and 6.5 km in length) found around the village of Sukau9. In addition, the unplanned and chaotic erection of electric fences by large estates and smallholdings has disrupted significantly elephant movement patterns and resulted in artificial hot spots for certain individuals (e.g. Liun, Ita, Gading and Sejati)35,72. Electric fences have widely been used to mitigate human–elephant conflicts. The establishment of fences rarely consider the traditional elephant routes nor the location of existing fences in neighbouring estates. If elephants manage to enter such areas, they often become trapped and experience difficulties in returning to nearby forests, exacerbating conflicts with people35.Certain estates such as Melangking Oil Palm Plantation have allowed elephants to roam freely in their estate (Muhammad Al-Shafieq, personal communication). Since 2017, this plantation has shown a drastic reduction in damages to their oil palms following the removal of their permanent electric fences surrounding their entire estate. Instead, this plantation is using a temporary electric fencing regime around newly planted palm areas. Concurrently, they now do not push elephants out of their estate, which can explain why Melangking Oil Palm Plantation is a significant hotspot in the region.Another reason why elephant ranges incorporate oil palm estates is to move between forest patches that are becoming completely isolated following forest conversion, as is the case close to Sukau (Fig. SI1 and SI2; Fig. 1). Unlike other elephant species that increase their speed of movement rates in highly disturbed areas27,30,66, the Bornean elephant has been observed doing the opposite, which may explain some of the hot spots within oil palm estates. This movement strategy may allow for better vigilance as seen on a few occasions when elephants spent 2–5 days in the Bukit Melapi-Yu Kwang Corridor, near the village of Sukau, before leaving the area (Othman, personal observation).Hot spots in the oil palm landscape can also be explained by feeding opportunities, since elephants feed on palm shoots, leaves and hearts73. Elephants are known to eat the shoots of newly planted oil palms, often killing the palms and causing significant economic damages35. Since 2010, many estates located in the Lower Kinabatangan have started a new palm rotation. Palms are replanted every 25 years. A new rotation includes land clearing, bole and root mass removal, and the shredding or chipping of felled palms. Elephants are attracted to the shredded palm hearts since it gives them easy access to one of their favourite food72. This particular behaviour does not cause economic damage, and some estate managers allow the elephants to stay and forage in the chipping areas. This was documented for several collared elephants, whose hot spots and time spent were particularly high within oil palm (e.g. Gading and Sandy, two males; and Ratu and Ita, two females). Once the shredded palms have dried, however, elephants will leave these areas and move elsewhere. Within oil palm estates, some elephants have been found to travel more directly and rapidly suggesting ‘exploratory’ behaviour, which could be associated with searching for young palms or areas of palm felling and chipping of palm hearts15.Lastly, elephants may still be using their historical range that used to be covered with forest before conversion to oil palm. Other factors potentially explaining the relatively high use of oil palm estates include seasonal variations of ranging patterns. Indeed events of drought or floods limit the access to various parts of the floodplain and will tend to confine the animals in some areas9,63.In Sabah the state authorities have recorded at least 200 elephant deaths from the year 2010 to 2021 and most of these have occurred on, or near, oil palm estates14,74,75,76. Deaths from non-natural causes are largely due to poisoning (both accidental and intentional), gunshot wounds, poaching for tusks and other body parts, and snares35. Stopping killing and enabling a safe coexistence between people and elephants within multiple-use landscapes that are dominated by oil palm is one of the key strategies developed in the Bornean Elephant Action Plan for Sabah (2020–2029), which was endorsed by the State14. Based on our results in Lower Kinabatangan, a series of recommendations are proposed.This study underscores the importance of remaining forested areas for the Lower Kinabatangan elephant population. Full protection of all forest fragments left in the Lower Kinabatangan is urgently needed. Several official mechanisms are available to fulfil this request that has been proposed for the past 20 years by various organizations46.The current network of forests available in the Lower Kinabatangan is too small and fragmented to sustain a viable elephant population. Forest corridors must be created across the landscape through reforestation exercises, whilst concurrently undertaking enrichment planting of native understory forage within forested areas as this may minimize the need for elephants to search for easily accessible food in high-risk oil palm landscapes21,22,23.Current governmental plans to build a road bridge and public road/highway linking the southern bank of the Kinabatangan River to Tabin Wildlife Reserve to the south will irreversibly impact the Lower Kinabatangan elephant population by cutting the current range into two isolated parts. This will impact the elephants ranging patterns, potentially even fragmenting the already small population into two groups, and potentially leading to elephant deaths by vehicle collisions (which is becoming increasingly common in Peninsular Malaysia), and increase the risk of poaching activities, all resulting in a decrease in the genetic diversity of the, already small and isolated, population14,67.Eventually, the future of the Kinabatangan elephant population resides in improving land use and management practices within oil palm estates currently used by elephants. We recommend that priority should be given at improving elephant movements in oil palm estates by removing unnecessary man-made barriers and only cautiously installing temporary electric fences to protect sensitive areas. For example, the use of electric fences around mature oil palm and areas whereby palms are being removed and chipped could be prohibited, and electric fences permitted solely for protecting oil palm nurseries, new plantings and young oil palms (e.g. up to 7–8 years old), and staff and office quarters. This would greatly allow for landscape permeability for elephants, and other species that need to cross the landscape for their ecological and biological needs14.A handful of guidelines exist to assist oil palm managers and staff in managing elephant populations in their respective estates72,77. However, there is a need for a more comprehensive set of guidelines, which delineate better practices with the aim to increase the protection of people and elephants outside protected areas. Guidelines should specify “do’s” and “don’ts” (based on best available data and knowledge) of actions needed before, during and after elephants visit oil palm estates and smallholdings.Sabah now is in an interesting transition within their palm oil sector. On the 21st October 2015, the Sabah State Cabinet committed to produce 100% certified sustainable palm oil, by 2025, under the Roundtable for Sustainable palm Oil (RSPO) Jurisdictional Certification approach. Under this approach, areas of High Conservation Value and areas identified within the High Carbon Stock Approach need specific management and monitoring, in order to comply with RSPO principles and criteria78,79,80. Sabah government can use this platform to build an integrated landscape level approach to better manage landscapes within known elephant ranges (which is considered a High Conservation Value species) to allow for a safe and permeable movement through the landscape.Eventually, long-term survival of the Bornean elephant will mainly depend on how people and elephants can co-exist. It is our hope that this study illustrates the importance of protecting all forested habitat and effectively managing areas outside of protected areas to allow for long-term elephant coexistence with humans in this landscape. More

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    Salinity of irrigation water selects distinct bacterial communities associated with date palm (Phoenix dactylifera L.) root

    Ramoliya, P. & Pandey, A. Effect of salinization of soil on emergence, growth and survival of seedlings of Cordia rothii. For. Ecol. Manage. 176, 185–194 (2003).Article 

    Google Scholar 
    Müller, H. M. et al. The desert plant Phoenix dactylifera closes stomata via nitrate-regulated SLAC1 anion channel. New Phytol. 216, 150–162 (2017).PubMed 
    Article 
    CAS 

    Google Scholar 
    Hazzouri, K. M. et al. Prospects for the study and improvement of abiotic stress tolerance in date palms in the post-genomics era. Front. Plant Sci. 11, 293 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Abdelfattah, M. A. Integrated suitability assessment: A way forward for land use planning and sustainable development in Abu Dhabi, United Arab Emirates. Arid Land Res. Manage. 27, 41–64 (2013).Article 

    Google Scholar 
    Al-Muaini, A. et al. Water requirements for irrigation with saline groundwater of three date-palm cultivars with different salt-tolerances in the hyper-arid United Arab Emirates. Agric. Water Manage. 222, 213–220 (2019).Article 

    Google Scholar 
    Guo, H., Shi, X., Ma, L., Yang, T. & Min, W. Long-term irrigation with saline water decreases soil nutrients, diversity of bacterial communities, and cotton yields in a gray desert soil in China. Pol. J. Environ. Stud. 29, 4077–4088 (2020).CAS 
    Article 

    Google Scholar 
    Blaskó, L. Salinity, physical effects on soils. In Encyclopedia of Agrophysics (eds Gliński, J. et al.) 723–725 (Springer, 2011).Chapter 

    Google Scholar 
    Rengasamy, P. Irrigation water quality and soil structural stability: A perspective with some new insights. Agronomy 8, 72 (2018).Article 
    CAS 

    Google Scholar 
    Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T. & Singh, B. K. Plant–microbiome interactions: From community assembly to plant health. Nat. Rev. Microbiol. 18, 607–621 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Masmoudi, K. et al. Metagenomics of beneficial microbes in abiotic stress tolerance of date palm. In The Date Palm Genome, Vol. 2: Omics and Molecular Breeding (eds Al-Khayri, J. M. et al.) 203–214 (Springer, 2021).Chapter 

    Google Scholar 
    Boncompagni, E., Østerås, M., Poggi, M.-C. & Le Rudulier, D. Occurrence of choline and glycine betaine uptake and metabolism in the family rhizobiaceae and their roles in osmoprotection. Appl. Environ. Microbiol. 65, 2072–2077 (1999).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Chen, C. & Beattie, G. A. Characterization of the osmoprotectant transporter opuc from Pseudomonas syringae and demonstration that cystathionine-β-synthase domains are required for its osmoregulatory function. J. Bacteriol. 189, 6901–6912 (2007).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rath, H. et al. Management of osmoprotectant uptake hierarchy in Bacillus subtilis via a SigB-dependent antisense RNA. Front. Microbiol. 11, 622 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Singh, R. P. & Jha, P. N. The PGPR Stenotrophomonas maltophilia SBP-9 augments resistance against biotic and abiotic stress in wheat plants. Front. Microbiol. 8, 1945 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ferjani, R. et al. The date palm tree rhizosphere is a niche for plant growth promoting bacteria in the oasis ecosystem. Biomed Res. Int. 2015, 1–10 (2015).Article 

    Google Scholar 
    Sanka Loganathachetti, D., Alhashmi, F., Chandran, S. & Mundra, S. Irrigation water salinity structures the bacterial communities of date palm (Phoenix dactylifera)-associated bulk soil. Front. Plant Sci. https://doi.org/10.3389/fpls.2022.944637 (2022).Article 

    Google Scholar 
    Chen, L. J. et al. An integrative influence of saline water irrigation and fertilization on the structure of soil bacterial communities. J. Agric. Sci. 157, 693–700 (2019).CAS 
    Article 

    Google Scholar 
    Li, Y. Q. et al. Bacterial community in saline farmland soil on the Tibetan plateau: Responding to salinization while resisting extreme environments. BMC Microbiol. 21, 119 (2021).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Mosqueira, M. J. et al. Consistent bacterial selection by date palm root system across heterogeneous desert oasis agroecosystems. Sci. Rep. 9, 4033 (2019).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Cherif, H. et al. Oasis desert farming selects environment-specific date palm root endophytic communities and cultivable bacteria that promote resistance to drought. Environ. Microbiol. Rep. 7, 668–678 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    FAO. Standard Operating Procedure for Soil Electrical Conductivity, Soil/Water, 1:5. (2021).Nelson, D. W. & Sommers, L. E. Total carbon, organic carbon, and organic matter. In Chemical Methods-SSSA Book Series No. 5 (eds Bigham, J. M. et al.) (Soil Science Society of America and American Society of Agronomy, 1996).
    Google Scholar 
    Mizrahi-Man, O., Davenport, E. R. & Gilad, Y. Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: Evaluation of effective study designs. PLoS ONE 8, e53608 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

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

    Google Scholar 
    Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: A versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Martin-Sanchez, P. M. et al. Analysing indoor mycobiomes through a large-scale citizen science study in Norway. Mol. Ecol. 30, 2689–2705 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Dai, T. et al. Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: A case study of microbial communities in the sediments of Hangzhou Bay. FEMS Microbiol. Ecol. 92, 150 (2016).Article 
    CAS 

    Google Scholar 
    Oksanen, J. et al. vegan: Community Ecology Package (2020).Blanchet, F. G., Legendre, P. & Borcard, D. Forward selection of explanatory variables. Ecology 89, 2623–2632 (2008).PubMed 
    Article 

    Google Scholar 
    Emirates Soil Museum. Emirates Soil Museum. https://www.emiratessoilmuseum.org/index.php/ (Accessed 08 July 2022).Jackson, O., Quilliam, R. S., Stott, A., Grant, H. & Subke, J.-A. Rhizosphere carbon supply accelerates soil organic matter decomposition in the presence of fresh organic substrates. Plant Soil 440, 473–490 (2019).CAS 
    Article 

    Google Scholar 
    Xie, E. et al. Short-term effects of salt stress on the amino acids of Phragmites australis root exudates in constructed wetlands. Water 12, 569 (2020).CAS 
    Article 

    Google Scholar 
    Korber, D. R., Choi, A., Wolfaardt, G. M. & Caldwell, D. E. Bacterial plasmolysis as a physical indicator of viability. Appl. Environ. Microbiol. 62, 3939–3947 (1996).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zhang, K. et al. Salinity is a key determinant for soil microbial communities in a desert ecosystem. mSystems 4, e00225 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hessini, K. et al. Interactive effects of salinity and nitrogen forms on plant growth, photosynthesis and osmotic adjustment in maize. Plant Physiol. Biochem. 139, 171–178 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Lammel, D. R. et al. Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures. Microbiome 6, 106 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lopes, L. D., Hao, J. & Schachtman, D. P. Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem. FEMS Microbiol. Ecol. 97, 028 (2021).Article 
    CAS 

    Google Scholar 
    Rousk, J. et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4, 1340–1351 (2010).PubMed 
    Article 

    Google Scholar 
    Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Kumar, A., Mann, A., Kumar, A., Kumar, N. & Meena, B. L. Physiological response of diverse halophytes to high salinity through ionic accumulation and ROS scavenging. Int. J. Phytoremediat. 23, 1041–1051 (2021).CAS 
    Article 

    Google Scholar 
    Kalam, S. et al. Recent understanding of soil acidobacteria and their ecological significance: A critical review. Front. Microbiol. https://doi.org/10.3389/fmicb.2020.580024 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Boukhatem, Z. F., Merabet, C. & Tsaki, H. Plant growth promoting actinobacteria, the most promising candidates as bioinoculants? Front. Agron. https://doi.org/10.3389/fagro.2022.849911 (2022).Article 

    Google Scholar 
    Köberl, M. et al. Comparisons of diazotrophic communities in native and agricultural desert ecosystems reveal plants as important drivers in diversity. FEMS Microbiol. Ecol. 92, 166 (2016).Article 
    CAS 

    Google Scholar 
    Speirs, L. B. M., Rice, D. T. F., Petrovski, S. & Seviour, R. J. The phylogeny, biodiversity, and ecology of the Chloroflexi in activated sludge. Front. Microbiol. 10, 2015 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Hou, Y. et al. Responses of the soil microbial community to salinity stress in maize fields. Biology (Basel) 10, 1114 (2021).CAS 

    Google Scholar 
    Patil, A., Kale, A., Ajane, G., Sheikh, R. & Patil, S. Plant growth-promoting rhizobium: Mechanisms and biotechnological prospective. Rhizobium Biol. Biotechnol. https://doi.org/10.1007/978-3-319-64982-5_7 (2017).Article 

    Google Scholar 
    Lima Guimarães, S. et al. Effects of inoculation of Rhizobium on nodulation and nitrogen accumulation in cowpea subjected to water availabilities. Am. J. Plant Sci. 06, 1378–1384 (2015).Article 

    Google Scholar 
    Ghadbane, M., Medjekal, S., Benderradji, L., Belhadj, H. & Daoud, H. Assessment of arbuscular mycorrhizal fungi status and Rhizobium on date palm (Phoenix dactylifera L.) cultivated in a Pb contaminated soil. In Recent Advances in Environmental Science from the Euro-Mediterranean and Surrounding Regions 2nd edn (eds Ksibi, M. et al.) 703–707 (Springer, 2021).
    Google Scholar 
    Saeed, E. E. et al. Streptomyces globosus UAE1, a potential effective biocontrol agent for black scorch disease in date palm plantations. Front. Microbiol. 8, 1455 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Falagán, C. & Johnson, D. B. Acidibacter ferrireducens gen. nov., sp. nov.: An acidophilic ferric iron-reducing gammaproteobacterium. Extremophiles 18, 1067–1073 (2014).PubMed 
    Article 
    CAS 

    Google Scholar 
    Schulze-Makuch, D. et al. Transitory microbial habitat in the hyperarid Atacama desert. Proc. Natl. Acad. Sci. 115, 2670–2675 (2018).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zhao, K. et al. Actinobacteria associated with Glycyrrhiza inflata Bat. are diverse and have plant growth promoting and antimicrobial activity. Sci. Rep. 8, 13661 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    An, S.-U. et al. Invasive Spartina anglica greatly alters the rates and pathways of organic carbon oxidation and associated microbial communities in an intertidal wetland of the Han river estuary, Yellow Sea. Front. Mar. Sci. 7, 59 (2020).ADS 
    Article 

    Google Scholar 
    Khan, M. A. et al. Rhizospheric Bacillus spp. rescues plant growth under salinity stress via regulating gene expression, endogenous hormones, and antioxidant system of Oryza sativa L.. Front. Plant Sci. 12, 1145 (2021).
    Google Scholar 
    Schimel, J., Balser, T. C. & Wallenstein, M. Microbial stress-response physiology and its implications for ecosystem function. Ecology 88, 1386–1394 (2007).PubMed 
    Article 

    Google Scholar 
    Mukhtar, S., Mehnaz, S., Mirza, M. S., Mirza, B. S. & Malik, K. A. Diversity of bacillus-like bacterial community in the rhizospheric and non-rhizospheric soil of halophytes (Salsola stocksii and Atriplex amnicola), and characterization of osmoregulatory genes in halophilic Bacilli. Can. J. Microbiol. 64, 567–579 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Yeager, C. M. et al. Polysaccharide degradation capability of actinomycetales soil isolates from a semiarid grassland of the colorado plateau. Appl. Environ. Microbiol. 83, e03020-e3116 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ortúzar, M., Trujillo, M. E., Román-Ponce, B. & Carro, L. Micromonospora metallophores: A plant growth promotion trait useful for bacterial-assisted phytoremediation? Sci. Total Environ. 739, 139850 (2020).ADS 
    PubMed 
    Article 
    CAS 

    Google Scholar 
    El-Tarabily, K. A. et al. Growth promotion of Salicornia bigelovii by Micromonospora chalcea UAE1, an endophytic 1-aminocyclopropane-1-carboxylic acid deaminase-producing actinobacterial isolate. Front. Microbiol. 10, 1694 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Carro, L. et al. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci. Rep. 8, 525 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Li, M. et al. Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields. Chin. Med. 15, 85 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rufián, J. S., Rueda-Blanco, J., Beuzón, C. R. & Ruiz-Albert, J. Protocol: An improved method to quantify activation of systemic acquired resistance (SAR). Plant Methods 15, 16 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bhise, K. K., Bhagwat, P. K. & Dandge, P. B. Synergistic effect of Chryseobacterium gleum sp. SUK with ACC deaminase activity in alleviation of salt stress and plant growth promotion in Triticum aestivum L.. 3 Biotech 7, 105 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Cao, C., Tao, S., Cui, Z. & Zhang, Y. Response of soil properties and microbial communities to increasing salinization in the meadow grassland of Northeast China. Microb. Ecol. 82, 722–735 (2021).CAS 
    PubMed 
    Article 

    Google Scholar  More

  • in

    Soil inoculum identity and rate jointly steer microbiomes and plant communities in the field

    Hu ZM, Li SG, Guo Q, Niu SL, He NP, Li LH. et al. A synthesis of the effect of grazing exclusion on carbon dynamics in grasslands in China. Global Change Biol. 2016;22:1385–93.Article 

    Google Scholar 
    Lyu X, Li XB, Gong JR, Wang H, Dang DL, Dou HS, et al. Comprehensive grassland degradation monitoring by remote sensing in Xilinhot, Inner Mongolia, China. Sustainability. 2020;12:3682.Article 

    Google Scholar 
    O’Mara FP. The role of grasslands in food security and climate change. Ann Bot-London. 2012;110:1263–70.Article 

    Google Scholar 
    Bryan BA, Gao L, Ye YQ, Sun XF, Connor JD, Crossman ND, et al. China’s response to a national land-system sustainability emergency. Nature. 2018;559:193–204.CAS 
    PubMed 
    Article 

    Google Scholar 
    Bardgett RD, Bullock JM, Lavorel S, Manning P, Schaffner U, Ostle N. et al. Combatting global grassland degradation. Nat Rev Earth Environ. 2021;2:720–35.Article 

    Google Scholar 
    Chang JF, Ciais P, Gasser T, Smith P, Herrero M, Havlik P, et al. Climate warming from managed grasslands cancels the cooling effect of carbon sinks in sparsely grazed and natural grasslands. Nat Commun. 2021;12:118.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wardle DA, Bardgett RD, Klironomos JN, Setälä H, van der Putten WH, Wall DH. Ecological linkages between aboveground and belowground biota. Science. 2004;304:1629–33.CAS 
    PubMed 
    Article 

    Google Scholar 
    Feeney DS, Crawford JW, Daniell T, Hallett PD, Nunan N, Ritz K, et al. Three-dimensional microorganization of the soil-root-microbe system. Microb Ecol. 2006;52:151–8.PubMed 
    Article 

    Google Scholar 
    Harris J. Soil microbial communities and restoration ecology: Facilitators or followers? Science. 2009;325:573–4.CAS 
    PubMed 
    Article 

    Google Scholar 
    Vecrin MP, Muller S. Top-soil translocation as a technique in the re-creation of species-rich meadows. Appl Veg Sci. 2003;6:271–8.Article 

    Google Scholar 
    Middleton EL, Bever JD. Inoculation with a native soil community advances succession in a grassland restoration. Restor Ecol. 2012;20:218–26.Article 

    Google Scholar 
    Wubs ERJ, van der Putten WH, Bosch M, Bezemer TM. Soil inoculation steers restoration of terrestrial ecosystems. Nat Plants. 2016;2:16107.PubMed 
    Article 

    Google Scholar 
    Wubs ERJ, van Heusden T, Melchers PD, Bezemer TM. Soil inoculation steers plant-soil feedback, suppressing ruderal plant species. Front Ecol Evol. 2019;7:451.Article 

    Google Scholar 
    Bever JD. Feedback between plants and their soil communities in an old field community. Ecology. 1994;75:1965–77.Article 

    Google Scholar 
    Bennett JA, Maherali H, Reinhart KO, Lekberg Y, Hart MM, Klironomos J. Plant-soil feedbacks and mycorrhizal type influence temperate forest population dynamics. Science. 2017;355:181–4.CAS 
    PubMed 
    Article 

    Google Scholar 
    Contos P, Wood JL, Murphy NP, Gibb H. Rewilding with invertebrates and microbes to restore ecosystems: Present trends and future directions. Ecol Evol. 2021;11:7187–200.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Emam T. Local soil, but not commercial AMF inoculum, increases native and non-native grass growth at a mine restoration site. Restor Ecol. 2016;24:35–44.Article 

    Google Scholar 
    Moradi J, Vicentini F, Simackova H, Pizl V, Tajovsky K, Stary J. An investigation into the long-term effect of soil transplant in bare spoil heaps on survival and migration of soil meso and macrofauna. Ecol Eng. 2018;110:158–64.Article 

    Google Scholar 
    Carbajo V, den Braber B, van der Putten WH, De Deyn GB. Enhancement of late successional plants on ex-arable land by soil inoculations. Plos One. 2011;6:e21943.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ma W, Liang XS, Wang ZW, Luo WT, Yu Q, Han XG. Resistance of steppe communities to extreme drought in northeast China. Plant Soil. 2022;473:181–194.IUSS Working Group WRB. World Reference Base for Soil Resources 2014, update 2015 International soil classification system for naming soils and creating legends for soil maps. World Soil Resources Reports No. 106. FAO, Rome, 2015.Jaunatre R, Buisson E, Dutoit T. Topsoil removal improves various restoration treatments of a Mediterranean steppe (La Crau, southeast France). Appl Veg Sci. 2014;17:236–45.Article 

    Google Scholar 
    Kuo S. Methods of soil analysis. Part 3: chemical methods. Soil Science Society of America: Madison, 1996.Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. P Natl Acad Sci USA. 2008;105:10583–8.CAS 
    Article 

    Google Scholar 
    De Beeck MO, Lievens B, Busschaert P, Declerck S, Vangronsveld J, Colpaert JV. Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies. Plos One. 2014;9:e97629.Article 

    Google Scholar 
    Magoč T, Salzberg SL. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27:2957–63.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.CAS 
    PubMed 
    Article 

    Google Scholar 
    Chen SF, Zhou YQ, Chen YR, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Edgar RC. UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.CAS 
    PubMed 
    Article 

    Google Scholar 
    Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb. 2007;73:5261–7.CAS 
    Article 

    Google Scholar 
    Quast C, Pruesse E, Gerken J, Peplies J, Yarza P, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012;41:590–6.Article 
    CAS 

    Google Scholar 
    Kõljalg U, Larsson K-H, Abarenkov K, Nilsson RH, Alexander IJ, Eberhardt U, et al. UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytol. 2005;166:1063–8.PubMed 
    Article 
    CAS 

    Google Scholar 
    Oostenbrink M. Estimating nematode populations by some selected methods. Nematology, Chapel Hill, 1960.Townshend JL. A modification and evaluation of the apparatus for the Oostenbrink direct cotton wool filter extraction method. Nematologica. 1963;9:106–10.Article 

    Google Scholar 
    Bongers T. De Nematoden van Nederland. In: Vormgeving en technische realisatie. Uitgeverij Pirola, Schoorl, 1994.Ahmad W, Jairjpuri MS. Mononchida: the predaceous nematodes. Nematology Monographs and Perspectives. Brill, Boston, 2010.Li Q, Liang WJ, Zhang XK, Mahamood M. Soil nematodes of grasslands in Northern China. Academic Press: San Diego, 2017.Wu ZY, Raven PH, Hong DY. Flora of China. Science Press: Beijing, 2013.Munson SM, Long AL, Wallace CSA, Webb RH. Cumulative drought and land-use impacts on perennial vegetation across a North American dryland region. Appl Veg Sci. 2016;19:430–41.Article 

    Google Scholar 
    Li YH, Wang W, Liu ZL, Jiang S. Grazing gradient versus restoration succession of leymus chinensis (Trin.) Tzvel. grassland in inner mongolia. Restor Ecol. 2008;16:572–83.Article 

    Google Scholar 
    Liang C, Michalk DL, Millar GD. The ecology and growth patterns of Cleistogenes species in degraded grasslands of eastern Inner Mongolia, China. J Appl Ecol. 2002;39:584–94.Article 

    Google Scholar 
    Liu ZG, Li ZQ. Effects of different grazing regimes on the morphological traits of Carex duriuscula on the Inner Mongolia steppe. China. New Zeal J Agr Res. 2010;53:5–12.Article 

    Google Scholar 
    Liu M, Gong JR, Pan Y, Luo QP, Zhai ZW, Yang LL, et al. Response of dominant grassland species in the temperate steppe of Inner Mongolia to different land uses at leaf and ecosystem levels. Photosynthetica. 2018;56:921–31.Article 

    Google Scholar 
    Bates D, Machler M, Bolker BM, Walker SC. Fitting linear mixed-effects models using lme4. J Stat Softw. 2015;67:1–48.Article 
    CAS 

    Google Scholar 
    Dixon P. Vegan, a package of R functions for community ecology. J Veg Sci. 2003;14:927–30.Article 

    Google Scholar 
    McMurdie PJ, Holmes S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. Plos One. 2013;8:e61217.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.CAS 
    PubMed 
    Article 

    Google Scholar 
    De Cáceres M, Legendre P, Moretti M. Improving indicator species analysis by combining groups of sites. Oikos. 2010;119:1674–84.Article 

    Google Scholar 
    Hartman K, van der Heijden MGA, Wittwer RA, Banerjee S, Walser JC, Schlaeppi K. Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming. Microbiome. 2018;6:14.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Aitchison J. A new approach to null correlations of proportions. Mathematical Geology. 1981;13:175–89.Article 

    Google Scholar 
    Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. Plos Comput Biol. 2015;11:e1004226.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Cao YP, Lin W, Li HZ. Two-sample tests of high-dimensional means for compositional data. Biometrika. 2018;105:115–32.Article 

    Google Scholar 
    Csardi G, Nepusz T. The igraph software package for complex network research. InterJ Complex Syst. 2006;1695:1–9.Banerjee S, Schlaeppi K, van der Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol. 2018;16:567–76.CAS 
    PubMed 
    Article 

    Google Scholar 
    Banerjee S, Schlaeppi K, van der Heijden MGA. Reply to ‘Can we predict microbial keystones?’. Nat Rev Microbiol. 2019;17:194–194.CAS 
    PubMed 
    Article 

    Google Scholar 
    Zheng HP, Yang TJ, Bao YZ, He PP, Yang KM, Mei XL, et al. Network analysis and subsequent culturing reveal keystone taxa involved in microbial litter decomposition dynamics. Soil Biol Biochem. 2021;157:108230.CAS 
    Article 

    Google Scholar 
    Kardol P, Wardle DA. How understanding aboveground-belowground linkages can assist restoration ecology. Trends Ecol Evol. 2010;25:670–9.PubMed 
    Article 

    Google Scholar 
    Wubs ERJ, van der Putten WH, Mortimer SR, Korthals GW, Duyts H, Wagenaar R, et al. Single introductions of soil biota and plants generate long-term legacies in soil and plant community assembly. Ecol Lett. 2019;22:1145–51.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    St-Denis A, Kneeshaw D, Belanger N, Simard S, Laforest-Lapointe I, Messier C. Species-specific responses to forest soil inoculum in planted trees in an abandoned agricultural field. Appl Soil Ecol. 2017;112:1–10.Article 

    Google Scholar 
    Kitto JAJ, Gray DP, Greig HS, Niyogi DK, Harding JS. Meta-community theory and stream restoration: evidence that spatial position constrains stream invertebrate communities in a mine impacted landscape. Restor Ecol. 2015;23:284–91.Article 

    Google Scholar 
    Ofek M, Hadar Y, Minz D. Ecology of root colonizing Massilia (Oxalobacteraceae). Plos One. 2012;7:e40117.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lyu D, Backer R, Smith DL. Three plant growth-promoting rhizobacteria alter morphological development, physiology, and flower yield of Cannabis sativa L. Ind Crop Prod. 2022;178:114583.CAS 
    Article 

    Google Scholar 
    Kulmatiski A, Beard KH. Long-term plant growth legacies overwhelm short-term plant growth effects on soil microbial community structure. Soil Biol Biochem. 2011;43:823–30.CAS 
    Article 

    Google Scholar 
    Brewer TE, Handley KM, Carini P, Gilbert JA, Fierer N. Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’. Nat Microbiol. 2017;2:16198.Article 
    CAS 

    Google Scholar 
    Reme J. Development and present state of close-to-nature silviculture. J Landscape Ecol. 2018;11:17–32.Article 

    Google Scholar  More

  • in

    Author Correction: A new wave of marine fish invasions through the Panama and Suez canals

    Authors and AffiliationsSmithsonian Tropical Research Institute – STRI, Balboa, Republic of PanamaGustavo A. Castellanos-Galindo, D. Ross Robertson, Diana M. T. Sharpe & Mark E. TorchinLeibniz Centre for Tropical Marine Research (ZMT), Bremen, GermanyGustavo A. Castellanos-GalindoAuthorsGustavo A. Castellanos-GalindoD. Ross RobertsonDiana M. T. SharpeMark E. TorchinCorresponding authorCorrespondence to
    Gustavo A. Castellanos-Galindo. More

  • in

    Invasive brown treesnakes (Boiga irregularis) move short distances and have small activity areas in a high prey environment

    Nathan, R. et al. A movement ecology paradigm for unifying organismal movement research. Proc. Natl. Acad. Sci. 105, 19052–19059 (2008).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lima, S. L. & Dill, L. M. Behavioral decisions made under the risk of predation: A review and prospectus. Can. J. Zool. 68, 619–640 (1990).Article 

    Google Scholar 
    Kays, R., Crofoot, M. C., Jetz, W. & Wikelski, M. Terrestrial animal tracking as an eye on life and planet. Science 348, 1122–1133. https://doi.org/10.1126/science.aaa2478 (2015).CAS 
    Article 

    Google Scholar 
    Allen, A. M. & Singh, N. J. Linking movement ecology with wildlife management and conservation. Front. Ecol. Evol. 3, 1–13. https://doi.org/10.3389/fevo.2015.00155 (2016).ADS 
    Article 

    Google Scholar 
    Fraser, K. C. et al. Tracking the conservation promise of movement ecology. Front. Ecol. Evol. https://doi.org/10.3389/fevo.2018.00150 (2018).Article 

    Google Scholar 
    Boutin, S. Food supplementation experiments with terrestrial vertebrates: Patterns, problems, and the future. Can. J. Zool. 68, 203–220 (1990).Article 

    Google Scholar 
    Adams, E. S. Approaches to the study of territory size and shape. Annu. Rev. Ecol. Syst. 32, 277–303. https://doi.org/10.1146/annurev.ecolsys.32.081501.114034 (2001).Article 

    Google Scholar 
    Ruffino, L., Salo, P., Koivisto, E., Banks, P. B. & Korpimaki, E. Reproductive responses of birds to experimental food supplementation: A meta-analysis. Front. Ecol. Evol. 11, 1–13. https://doi.org/10.1186/s12983-014-0080-y (2014).CAS 
    Article 

    Google Scholar 
    Taylor, E. N., Malawy, M. A., Browning, D. M., Lemar, S. V. & DeNardo, D. F. Effects of food supplementation on the physiological ecology of female western diamond-backed rattlesnakes (Crotalus atrox). Oecologia 144, 206–213. https://doi.org/10.1007/s00442-005-0056-x (2005).ADS 
    Article 
    PubMed 

    Google Scholar 
    Wasko, D. K. & Sasa, M. Food resources influence spatial ecology, habitat selection, and foraging behavior in an ambush-hunting snake (Viperidae: Bothrops asper): An experimental study. Zoology 115, 179–187. https://doi.org/10.1016/j.zool.2011.10.001 (2012).Article 
    PubMed 

    Google Scholar 
    Glaudas, X. & Alexander, G. J. Food supplementation affects the foraging ecology of a low-energy, ambush-foraging snake. Behav. Ecol. Sociobiol. 71, 1–11. https://doi.org/10.1007/s00265-016-2239-3 (2017).Article 

    Google Scholar 
    Secor, S. M. & Nagy, K. A. Bioenergetic correlates of foraging mode for the snakes Crotalus cerastes and Masticophis flagellum. Ecology 75, 1600–1614 (1994).Article 

    Google Scholar 
    Christy, M. T., Savidge, J. A., Yackel Adams, A. A., Gragg, J. E. & Rodda, G. H. Experimental landscape reduction of wild rodents increases movements in the invasive brown treesnake (Boiga irregularis). Manag. Biol. Invasions 8, 455–467. https://doi.org/10.3391/mbi.2017.8.4.01 (2017).Article 

    Google Scholar 
    Neilson, E. W., Avgar, T., Burton, A. C., Broadley, K. & Boutin, S. Animal movement affects interpretation of occupancy models from camera-trap surveys of unmarked animals. Ecosphere 9, 1–15. https://doi.org/10.1002/ecs2.2092 (2018).Article 

    Google Scholar 
    Efford, M. G. & Dawson, D. K. Occupancy in continuous habitat. Ecosphere 3, 1–15. https://doi.org/10.1890/ES11-00308.1 (2012).Article 

    Google Scholar 
    Tang, Z., Huang, Q., Wu, H., Kuang, L. & Fu, S. The behavioral response of prey fish to predators: The role of predator size. PeerJ 5, 1–13. https://doi.org/10.7717/peerj.3222 (2017).Article 

    Google Scholar 
    Thorsen, M., Shorten, R., Lucking, R. & Lucking, V. Norway rats (Rattus norvegicus) on Fregate Island, Seychelles: The invasion; subsequent eradication attempts and implications for the island’s fauna. Biol. Cons. 96, 133–138 (2000).Article 

    Google Scholar 
    Rodda, G. H. Foraging behavior of the brown tree snake, Boiga irregularis. Herpetol. J. 2, 110–114 (1992).
    Google Scholar 
    Savidge, J. A. Extinction of an island forest avifauna by an introduced snake. Ecology 68, 660–668 (1987).Article 

    Google Scholar 
    Rodda, G. H., McCoid, M. J., Fritts, T. H. & Campbell, E. W. III. Population trends and limiting factors in Boiga irregularis. In Problem Snake Management: The Habu and the Brown Treesnake (eds Rodda, G. H. et al.) 236–256 (Cornell University Press, 1999).Chapter 

    Google Scholar 
    Yackel Adams, A. A., Lardner, B., Knox, A. J. & Reed, R. N. Inferring the absence of an incipient population during a rapid response for an invasive species. PLoS ONE 13, 1–13 (2018).Article 
    CAS 

    Google Scholar 
    Clark, L., Clark, C. & Siers, S. Brown tree snake methods and approaches for control. In Ecology and Management of Terrestrial Vertebrate Invasive Species in the United States (eds Pitt, W. C. et al.) 107–134 (CRC Press, 2018).
    Google Scholar 
    Christy, M. T., Yackel Adams, A. A., Rodda, G. H., Savidge, J. A. & Tyrrell, C. L. Modelling detection probabilities to evaluate management and control tools for an invasive species. J. Appl. Ecol. 47, 106–113 (2010).Article 

    Google Scholar 
    Tyrrell, C. L. et al. Evaluation of trap capture in a geographically closed population of brown treesnakes on Guam. J. Appl. Ecol. 46, 128–135 (2009).Article 

    Google Scholar 
    Siers, S. R., Yackel Adams, A. A. & Reed, R. N. Behavioral differences following ingestion of large meals and consequences for management of a harmful invasive snake: A field experiment. Ecol. Evol. 8, 10075–10093 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Santana-Bendix, M. A. Movements, Activity Patterns and Habitat Use of Boiga irregularis (Colubridae), an Introduced Predator in the Island of Guam (University of Arizona, 1994).
    Google Scholar 
    Tobin, M. E., Sugihara, R. T., Pochop, P. A. & Linnell, M. A. Nightly and seasonal movements of Boiga irregularis on Guam. J. Herpetol. 33, 281–291 (1999).Article 

    Google Scholar 
    Lardner, B., Savidge, J. A., Reed, R. N. & Rodda, G. H. Movements and activity of juvenile brown treesnakes (Boiga irregularis). Copeia 2014, 428–436 (2014).Article 

    Google Scholar 
    Siers, S. R., Savidge, J. A. & Reed, R. N. Invasive brown treesnake movements at road edges indicate road-crossing avoidance. J. Herpetol. 48, 500–505 (2014).Article 

    Google Scholar 
    Wiewel, A. S., Yackel Adams, A. A. & Rodda, G. H. Distribution, density, and biomass of introduced small mammals in the southern Marian Islands. Pac. Sci. 63, 205–222 (2009).Article 

    Google Scholar 
    Camp, R. J., Amidon, F. A., Marshall, A. P. & Pratt, T. K. Bird populations on the island of Tinian; Persistence despite wholesale loss of native forests. Pac. Sci. 66, 283–298. https://doi.org/10.2984/66.3.3 (2012).Article 

    Google Scholar 
    Lardner, B., Yackel Adams, A. A., Knox, A. J., Savidge, J. A. & Reed, R. N. Do observer fatigue and taxon bias compromise visual encounter surveys for small vertebrates?. Wildl. Res. 46, 127–135 (2019).Article 

    Google Scholar 
    Mathies, T., Levine, B., Engeman, R. & Savidge, J. A. Pheromonal control of the invasive brown treesnake: Potency of female sexual attractiveness pheromone varies with ovarian state. Int. J. Pest Manag. https://doi.org/10.1080/09670874.2013.784374 (2013).Article 

    Google Scholar 
    Boback, S. M., Nafus, M. G., Yackel Adams, A. A. & Reed, R. N. Use of visual surveys and radiotelemetry reveals sources of detection bias for a cryptic snake at low densities. Ecosphere https://doi.org/10.1002/ecs2.3000 (2020).Article 

    Google Scholar 
    Harper, G. A. & Rutherford, M. Home range and population density of black rats (Rattus rattus) on a seabird island: A case for a marine subsidised effect?. N. Z. J. Ecol. 40, 219–228 (2016).
    Google Scholar 
    Hochachka, W. M., Martin, K., Doyle, F. & Krebs, C. J. Monitoring vertebrate populations using observational data. Can. J. Zool. 78, 521–529 (2000).Article 

    Google Scholar 
    Wiewel, A. S., Yackel Adams, A. A. & Rodda, G. H. Evaluating abundance estimate precision and the assumptions of a count-based index for small mammals. J. Wildl. Manag. 73, 761–771. https://doi.org/10.2193/2008-180 (2009).Article 

    Google Scholar 
    Fauteux, D. et al. Evaluation of invasive and non-invasive methods to monitor rodent abundance in the Arctic. Ecosphere 9, 1–18. https://doi.org/10.1002/ecs2.2124 (2018).Article 

    Google Scholar 
    Siers, S. R. et al. Assessment of brown treesnake activity and bait take following large-scale snake suppression in Guam. (ed APHIS USDA, WS, NWRC) (Final Report QA-2438, Hilo, HI, 2018).McQueen, D. J., Post, J. R. & Mills, E. L. Trophic relationships in fresh-water pelagic ecosystems. Can. J. Fish. Aquat. Sci. 43, 1571–1581 (1986).Article 

    Google Scholar 
    Sih, A., Crowley, P., McPeek, M., Petranka, J. & Strohmeier, K. Predation, competition, and prey communities: A review of field experiments. Annu. Rev. Ecol. Syst. 16, 269–311 (1985).Article 

    Google Scholar 
    Dorcas, M. E. et al. Severe mammal declines coincide with proliferation of invasive Burmese pythons in Everglades National Park. Proc. Natl. Acad. Sci. 109, 2418–2422. https://doi.org/10.1073/pnas.1115226109 (2012).ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    de Miranda, E. B. P. The plight of reptiles as ecological actors in the tropics. Front. Ecol. Evol. 5, 1–15. https://doi.org/10.3389/fevo.2017.00159 (2017).Article 

    Google Scholar 
    Campbell, E. W. III., Yackel Adams, A. A., Converse, S. J., Fritts, T. H. & Rodda, G. H. Do predators control prey species abundance? An experimental test with brown treesnakes on Guam. Ecology 93, 1194–1203 (2012).PubMed 
    Article 

    Google Scholar 
    Lindell, L. E. & Forsman, A. Density effects and snake predation: Prey limitation and reduced growth rate of adders at high density of conspecifics. Can. J. Zool. 74, 1000–1007 (1996).Article 

    Google Scholar 
    Schoener, T. W., Spiller, D. A. & Losos, J. B. Predation on a common Anolis lizard: Can the food-web effects of a devastating predator be reversed?. Ecol. Monogr. 72, 383–407 (2002).Article 

    Google Scholar 
    McCleery, R. A. et al. Marsh rabbit mortalities tie pythons to the precipitous decline of mammals in the Everglades. Proc. R. Soc. Lond. 282, 20150120. https://doi.org/10.1098/rspb.2015.0120 (2015).Article 

    Google Scholar 
    Plummer, M. V. & Congdon, J. D. Radiotelemetric study of activity and movements of racers (Coluber constrictor) associated with a Carolina bay in South Carolina. Copeia 1994, 20–26 (1994).Article 

    Google Scholar 
    Madsen, T. & Shine, R. Seasonal migration of predators and prey—A study of pythons, and rats in tropical Australia. Ecology 77, 149–156 (1996).Article 

    Google Scholar 
    Chandler, C. J., Van Helden, B., Close, P. G. & Speldewinde, P. C. 2D or not 2D? Three-dimensional home range analysis better represents space use by an arboreal mammal. Acta Oecol. 105, 103576. https://doi.org/10.1016/j.actao.2020.103576 (2020).Article 

    Google Scholar 
    Udyawer, V., Simpfendorfer, C. A. & Heupel, M. R. Diel patterns in three-dimensional use of space by sea snakes. Anim. Biotelem. 3, 1–9. https://doi.org/10.1186/s40317-015-0063-6 (2015).Article 

    Google Scholar 
    Shine, R. Reproduction in Australian elapid snakes II. Female reproductive cycles. Aust. J. Zool. 25, 655–666 (1977).Article 

    Google Scholar 
    Murcia, C. Edge effects in fragmented forests: Implications for conservation. Trends Ecol. Evol. 10, 58–62 (1995).CAS 
    PubMed 
    Article 

    Google Scholar 
    Matlack, G. R. Microenvironment variation within and among forest edge sites in the eastern United States. Biol. Cons. 66, 185–194 (1993).Article 

    Google Scholar 
    Kapos, V. Effects of isolation on the water status of forest patches in the Brazilian Amazon. Trop. Ecol. 5, 173–185 (1989).Article 

    Google Scholar 
    Williams-Linera, G. Vegetation structure and environmental conditions of forest edges in Panama. J. Ecol. 78, 356–373 (1990).Article 

    Google Scholar 
    Matlack, G. R. Vegetation dynamics of the forest edge: Trends in space and successional time. J. Ecol. 82, 113–123 (1994).Article 

    Google Scholar 
    Chen, J., Franklin, J. F. & Spies, T. A. Vegetation responses to edge environments in old-growth douglas-fir forests. Ecol. Appl. 2, 387–396 (1992).PubMed 
    Article 

    Google Scholar 
    Gates, J. E. Powerline corridors, edge effects, and wildlife in forested landscapes of the central Appalachians. In Wildlife and Habitats in Managed Landscapes (eds Rodiek, J. E. & Bolen, E. G.) 13–32 (Island Press, 1991).
    Google Scholar 
    Kroodsma, R. L. Edge effect on breeding forest birds along a power-line corridor. J. Appl. Ecol. 19, 361–370 (1982).Article 

    Google Scholar 
    Morgan, K. A. & Gates, J. E. Bird population patterns in forest edge and strip vegetation at Remington Farms, Maryland. J. Wildl. Manag. 46, 933–944 (1982).Article 

    Google Scholar 
    Weatherhead, P. J. & Charland, M. B. Habitat selection in an Ontario population of the snake, Elaphe obsoleta. J. Herpetol. 19, 12–19 (1985).Article 

    Google Scholar 
    Durner, G. M. & Gates, J. E. Spatial ecology of black rat snakes on Remington Farms, Maryland. J. Wildl. Manag. 57, 812–826 (1993).Article 

    Google Scholar 
    Mushinsky, H. R. Foraging ecology. In Snakes: Ecology and Evolutionary Biology (eds Seigel, R. A. et al.) 302–334 (Macmillan Publishing Company, 1987).
    Google Scholar 
    Fritts, T. H., Scott, N. J. Jr. & Smith, B. J. Trapping Boiga irregularis on Guam using bird odors. J. Herpetol. 23, 189–192 (1989).Article 

    Google Scholar 
    Shivik, J. A. Brown tree snake response to visual and olfactory cues. J. Wildl. Manag. 62, 105–111 (1998).Article 

    Google Scholar 
    Simkova, O., Frydlova, P., Zampachova, B., Frynta, D. & Landova, E. Development of behavioral profile in the Northern common boa (Boa imperator): Repeatable independent traits or personality?. PLoS ONE 12, 1–35. https://doi.org/10.1371/journal.pone.0177911 (2017).CAS 
    Article 

    Google Scholar 
    Fritts, T. H., McCoid, M. J. & Gomez, D. M. Dispersal of snakes to extralimital islands: Incidents of the brown treesnake, Boiga irregularis, dispersing to islands in ships and aircraft. In Problem Snake Management: The Habu and the Brown Treesnake (eds Rodda, G. H. et al.) 209–223 (Cornell University Press, 1999).
    Google Scholar 
    Yackel Adams, A. A. et al. Can we prove that an undetected species is absent? Evaluating whether brown treesnakes are established on the island of Saipan using surveillance and expert opinion. Manag. Biol. Invas. 12, 901–926 (2021).Article 

    Google Scholar 
    Siers, S. R. & Savidge, J. A. Restoration Plan for the Habitat Management Unit, Naval Support Activity Andersen, Guam 1–238 (Colorado State University, 2017).
    Google Scholar 
    Dorr, B. S., Clark, C. S. & Savarie, P. (USDA APHIS WS National Wildlife Research Center, Fort Collins, CO, 2016).Reinert, H. K. & Cundall, D. An improved surgical implantation method for radio-tracking snakes. Copeia 1982, 702–705 (1982).Article 

    Google Scholar 
    Shine, R. Strangers in a strange land: Ecology of the Australian colubrid snakes. Copeia 1991, 120–131 (1991).Article 

    Google Scholar 
    Savidge, J. A., Qualls, F. J. & Rodda, G. H. Reproductive biology of the brown tree snake, Boiga irregularis (Reptilia: Colubridae), during colonization of Guam and comparison with that in their native range. Pac. Sci. 61, 191–199 (2007).Article 

    Google Scholar 
    Yackel Adams, A. A. & Nafus, M. G. Brown Treesnake visual survey and radiotelemetry data, Guam 2015: U.S. Geological Survey data release. https://doi.org/10.5066/P939BM0W (2020).Savidge, J. A. Food habits of Boiga irregularis, an introduced predator on Guam. J. Herpetol. 22, 275–282 (1988).Article 

    Google Scholar 
    Reed, R. N. & Boback, S. M. Does body size predict dates of species description among North American and Australian reptiles and amphibians?. Glob. Ecol. Biogeogr. 11, 41–47 (2002).Article 

    Google Scholar 
    Duong, T. ks: Kernel density estimation and kernel discriminant analysis for multivariate data in R. J. Stat. Softw. 21, 1–16 (2007).Article 

    Google Scholar 
    R Foundation for Statistical Computing. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2017).
    Google Scholar 
    Simpfendorfer, C. A., Olsen, E. M., Heupel, M. R. & Moland, E. Three-dimensional kernel utilization distributions improve estimates of space use in aquatic animals. Can. J. Fish. Aquat. Sci. 69, 565–572 (2012).Article 

    Google Scholar 
    Gitzen, R. A., Millspaugh, J. J. & Kernohan, B. J. Bandwidth selection for fixed-kernel analysis of animal utilization distributions. J. Wildl. Manag. 70, 1334–1344 (2006).Article 

    Google Scholar 
    Cooper, N. W., Sherry, T. W. & Marra, P. P. Modeling three-dimensional space use and overlap in birds. Auk 131, 681–693 (2014).Article 

    Google Scholar 
    ArcGIS Desktop (Environmental Systems Research, 2017).Nafus, M. G., Boback, S. M., Klug, P. E., Yackel Adams, A. A. & Reed, R. N. Brown treesnake movement following snake suppression in the Habitat Management Unit on Northern Guam from 2015. U.S Geological Survey data release. https://doi.org/10.5066/P95QJ2PE (2022). More