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    Microbiomes of microscopic marine invertebrates do not reveal signatures of phylosymbiosis

    Gilbert, S. F., Sapp, J. & Tauber, A. I. A symbiotic view of life: we have never been individuals. Q. Rev. Biol. 87, 325–341 (2012).PubMed 
    Article 

    Google Scholar 
    Bass, D., Stentiford, G. D., Wang, H.-C., Koskella, B. & Tyler, C. R. The pathobiome in animal and plant diseases. Trends Ecol. Evol. 34, 996–1008 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Husnik, F. & Keeling, P. J. The fate of obligate endosymbionts: reduction, integration, or extinction. Curr. Opin. Genet. Dev. 58-59, 1–8 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Berg, G. et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8, 103 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kwong, W. K. & Moran, N. A. Gut microbial communities of social bees. Nat. Rev. Microbiol. 14, 374–384 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Hammer, T. J., Janzen, D. H., Hallwachs, W., Jaffe, S. P. & Fierer, N. Caterpillars lack a resident gut microbiome. Proc. Nat Acad. Sci. USA 114, 9641–9646 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Holt, C. C., van der Giezen, M., Daniels, C. L., Stentiford, G. D. & Bass, D. Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus). ISME J. 14, 531–543 (2020).PubMed 
    Article 

    Google Scholar 
    Pollock, F. J. et al. Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny. Nat. Commun. 9, 4921 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Thomas, T. et al. Diversity, structure and convergent evolution of the global sponge microbiome. Nat. Commun. 7, 11870 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Engelberts, J. P. et al. Characterization of a sponge microbiome using an integrative genome-centric approach. ISME J. 14, 1100–1110 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ley, R. E. et al. Evolution of mammals and their gut microbes. Science 320, 1647–1651 (2008).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Mallot, E. K. & Amato, K. R. Host specificity of the gut microbiome. Nat. Rev. Microbiol. 19, 639–653 (2021).Article 
    CAS 

    Google Scholar 
    Colston, T. J. & Jackson, C. R. Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown. Mol. Ecol. 25, 3776–3800 (2016).PubMed 
    Article 

    Google Scholar 
    Levin, D. et al. Diversity and functional landscapes in the microbiota of animals in the wild. Science 372, eabb5352 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Nishida, A. H. & Ochman, H. Rates of gut microbiome divergence in mammals. Mol. Ecol. 27, 1884–1897 (2013).Article 

    Google Scholar 
    Brooks, A. W., Kohl, K. D., Brucker, R. M., van Opstal, E. J. & Bordenstein, S. R. Phylosymbiosis: relationships and functional effects of microbial communities across host evolutionary history. PLoS Biol. 14, e2000225 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Mazel, F. et al. Is host filtering the main driver of phylosymbiosis across the tree of life? mSystems 3, https://doi.org/10.1128/mSystems.00097-18 (2018).Lutz, H. L. et al. Ecology and host identity outweigh evolutionary history in shaping the bat microbiome. mBio 4, 6 (2019).
    Google Scholar 
    Grond, K. et al. No evidence for phylosymbiosis in Western chipmunk species. FEMS Microbiol. Ecol. 96, fiz182 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Song, S. J. et al. Comparative analyses of vertebrate gut microbiomes reveal convergence between birds and bats. mBio 11, 1 (2020).Article 

    Google Scholar 
    Trevelline, B. K., Sosa, J., Hartup, B. K. & Kohl, K. D. A bird’s-eye view of phylosymbiosis: weak signatures of phylosymbiosis among all 15 species of cranes. Proc. R. Soc. B 287, 20192988 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Muegge, B. D. et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970–974 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Youngblut, N. D. et al. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nat. Commun. 10, 2200 (2019).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Amato, K. R. et al. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J. 13, 576–587 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Moeller, A. H. et al. Social behavior shapes the chimpanzee pan-microbiome. Sci. Adv. 2, e1500997 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Eckert, E. M., Anicic, N. & Fontaneto, D. Freshwater zooplankton microbiome composition is highly flexible and strongly influenced by the environment. Mol. Ecol. 30, 1545–1558 (2021).PubMed 
    Article 

    Google Scholar 
    Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–228 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bik, H. M. Microbial metazoa are microbes too. mSystems 4, e00109–e00119 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Schuelke, T., Pereira, T. J., Hardy, S. M. & Bik, H. M. Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats. Mol. Ecol. 27, 1930–1951 (2018).PubMed 
    Article 

    Google Scholar 
    Guidetti, R. et al. Further insights in the Tardigrada microbiome: phylogenetic position and prevalence of infection of four new Alphaproteobacteria putative endosymbionts. Zool. J. Linn. Soc. 188, 925–937 (2020).Article 

    Google Scholar 
    Giere, O. Meiobenthology (Springer-Verlag, 2009).Laumer, C. E. et al. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proc. R. Soc. B 286, 20190831 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Hammer, T. J., Sanders, J. G. & Fierer, N. Not all animals need a microbiome. FEMS Microbiol. Lett. 366, fnz117 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Alejandre-Colomo, C. et al. Cultivable Winogradskyella species are genomically distinct from the sympatric abundant candidate species. ISME Commun. 1, 51 (2021).Article 

    Google Scholar 
    Husnik, F. et al. Bacterial and archaeal symbioses with protists. Curr. Biol. 31, R862–R877 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Salje, J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat. Rev. Microbiol. 19, 375–390 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Neave, M. J., Apprill, A., Ferrier-Pagès, C. & Voolstra, C. R. Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas. Appl. Microbiol. Biotechnol. 100, 8315–8324 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Weiland-Bräuer, N. et al. Composition of bacterial communities associated with Aurelia aurita changes with compartment, life stage, and population. Appl. Environ. Microbiol. 81, 6038–6052 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Bik, E. M. et al. Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nat. Commun. 7, 10516 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Burns, A. R. et al. Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development. ISME J. 10, 655–664 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    McFall-Ngai, M. Adaptive immunity: care for the community. Nature 445, 153 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    Ruehland, C. & Dubilier, N. Gamma- and epsilonproteobacterial ectosymbionts of a shallow-water marine worm are related to deep-sea hydrothermal vent ectosymbionts. Environ. Microbiol. 12, 2312–2326 (2010).CAS 
    PubMed 

    Google Scholar 
    Gruber-Vodicka, H. R. et al. Two intracellular and cell-type specific bacterial symbionts in the placozoan Trichoplax H2. Nat. Microbiol. 4, 1465–1474 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Schockaert, E. R. in Methods for the Examination of Organismal Diversity in Soils and Sediments (ed. Hall, G. S.) 211–225 (CABI, 1996).Higgins, R. P. in Introduction to the Study of Meiofauna (eds. Higgins, R. P. and Thiel, H.) 328–331 (SIP, 1988).Schram, M. D. & Davison, P. G. Irwin Loops—a history and method of constructing homemade loops. Trans. Kans. Acad. Sci. 115, 35–40 (1903).Article 

    Google Scholar 
    Medlin, L., Elwood, H. J., Stickel, S. & Sogin, M. L. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71, 491–499 (1988).CAS 
    PubMed 
    Article 

    Google Scholar 
    Bower, S. M. et al. Preferential PCR amplification of parasitic protistan small subunit rDNA from metazoan tissues. J. Eukaryot. Microbiol. 51, 325–332 (2004).CAS 
    PubMed 
    Article 

    Google Scholar 
    Comeau, A. M., Li, W. K. W., Tremblay, J.-E., Carmack, E. C. & Lovejoy, C. Arctic ocean microbial community structure before and after the 2007 record sea ice minimum. PLoS ONE 6, e27492 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zhang, R.-Y. et al. Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea. BMC Microbiol. 20, 25 (2020).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Lane, D. J. in Nucleic Acid Techniques in Bacterial Systematics (eds Stackebrandt, E. & Goodfellow, M) 115–175 (Wiley, 1991).Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403–1414 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Marcel, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10 (2011).
    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2020).Callahan, B. J. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A. & Callahan, B. J. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome 6, 226 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag, 2016).Love, M. I., Huber, W. & Anders, S. Moderate estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).Kurtz, Z. D. Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput. Biol. 11, e1004226 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Csardi, G. & Nepusz, T. The igraph Software Package for Complex Network Research (InterJournal, 2006).Breiman, L. Random forests. Mach. Learn. 45, 5–32 (2001).Kolde, R. pheatmap: pretty heatmaps. R package version 1.0.12 https://CRAN.R-project.org/package=pheatmap (2015).Lin, H. & Das Peddada, S. Analysis of composition of microbiomes with bias correction. Nat. Commun. 11, 3514 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Oksanen, J. vegan: Community Ecology Package. R package version 2.5.7 https://CRAN.R-project.org/package=vegan (2020).Rouse, G., Pleijel, F. & Tilic, E. Annelida (Oxford Univ. Press, 2022).Ahmed, M. & Holovachov, O. Twenty years after De Ley and Blaxter—How far did we progress in understanding the phylogeny of the phylum Nematoda? Animals 11, 3479 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Van Steenkiste, N. W. L., Herbert, E. R. & Leander, B. S. Species diversity in the marine microturbellarian Astrotorhynchus bifidus sensu lato (Platyhelminthes: Rhabdocoela) from the Northeast Pacific Ocean. Mol. Phylogenet. Evol. 120, 259–273 (2018). More

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    Determinants of variability in signature whistles of the Mediterranean common bottlenose dolphin

    Wilkins, M. R., Seddon, N. R. & Safran, R. J. Evolutionary divergence in acoustic signals: causes and consequences. Trends Ecol. Evol. 28, 156–166 (2013).PubMed 
    Article 

    Google Scholar 
    Wei, C. Sound production and propagation in cetacean. In Neuroendocrine Regulation of Animal Vocalization (eds Rosenfeld, C. S. & Hoffmann, F.) 267–291 (Academic Press, 2021).Chapter 

    Google Scholar 
    Nakakara, F. Social functions of cetacean acoustic communication. Fish. Sci. 68, 298–301 (2002).Article 

    Google Scholar 
    Caldwell, M. C. & Caldwell, D. K. Vocalization of naive captive dolphins in small groups. Science 159, 1121–1123 (1968).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Caldwell, M. C., Caldwell, D. K. & Tyack, P. L. Review of the signature-whistle-hypothesis for the Atlantic bottlenose dolphin. In The bottlenose dolphin (eds Leatherwood, S. & Reeves, R. R.) 199–234 (Academic Press, 1990).Chapter 

    Google Scholar 
    Ford, J. B. Vocal traditions among resident killer whales (Orcinus orca) in coastal waters of British Columbia. Can. J. Zool. 69, 1454–1483 (1991).Article 

    Google Scholar 
    Weilgart, L. & Whitehead, H. Group-specific dialects and geographical variation in coda repertoire in South Pacific sperm whales. Behav. Ecol. Sociobiol. 40, 277–285 (1997).Article 

    Google Scholar 
    Deeck, V. B., Ford, J. K. B. & Spong, P. Dialect change in resident killer whales: implications for vocal learning and cultural transmission. Anim. Behav. 60, 629–638 (2000).Article 

    Google Scholar 
    Chen, Z. & Wiens, J. J. The origins of acoustic communication in vertebrates. Nat. Commun. 11, 369 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Morton, E. S. Sources of selection on avian sounds. Am. Nat. 109, 17–34 (1975).ADS 
    Article 

    Google Scholar 
    Irwin, D. E., Thimgan, M. P. & Irwin, J. H. Call divergence is correlated with geographic and genetic distance in greenish warblers (Phylloscopus trochiloides): A strong role for stochasticity in signal evolution?. J. Evol. Biol. 21, 435–448 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Campbell, P. et al. Geographic variation in the songs of Neotropical singing mice: Testing the relative importance of drift and local adaptation. Evol. 64, 1955–1972 (2010).
    Google Scholar 
    Connor, R. C., Wells, R. S., Mann, J. & Read, A. J. The bottlenose dolphin: Social relationships in a fission-fusion society. In Cetacean societies: Field studies of dolphins and whales (eds Mann, J. et al.) 91–126 (University of Chicago Press, Chicago, 2000).
    Google Scholar 
    Janik, V. M. & Sayigh, L. S. Communication in bottlenose dolphins: 50 years of signature whistle research. J. Comp. Physiol. A https://doi.org/10.1007/s00359-013-0817-7 (2013).Article 

    Google Scholar 
    MacFarlane, N. et al. Signature whistles facilitate reunions and/or advertise identity in Bottlenose Dolphins. JASA 141, 3543 (2017).Article 

    Google Scholar 
    Buckstaff, K. C. Effects of watercraft noise on the acoustic behaviour of bottlenose dolphins, Tursiops truncatus, in Sarasota Bay, Florida. Mar. Mam. Sci. 20, 709–725 (2004).Article 

    Google Scholar 
    Cook, M. L. H., Sayigh, L. S., Blum, J. E. & Wells, R. S. Signature-whistle production in undisturbed free-ranging bottlenose dolphins (Tursiops truncatus). Proc. R. Soc. Lond. B. 271, 1043–1049 (2004).Article 

    Google Scholar 
    Watwood, S. L., Owen, E. C. G., Tyack, P. L. & Wells, R. S. Signature whistle use by temporarily restrained and free-swimming bottlenose dolphins, Tursiops truncatus. Anim. Behav. 69, 1373–1386 (2005).Article 

    Google Scholar 
    Sayigh, L. S., Tyack, P. L., Wells, R. S., Scott, M. D. & Irvine, A. B. Sex difference in signature whistle production of free-ranging bottle-nosed dolphins, Tursiops-truncatus. Beh. Ecol. Soc. 36, 171–177 (1995).Article 

    Google Scholar 
    Tyack, P. L. & Sayigh, L. S. Vocal learning in cetaceans. In Social influences on vocal development (eds Snowdon, C. T. & Hausberger, M.) 208–233 (Cambridge University Press, 1997).Chapter 

    Google Scholar 
    Miksis, J. L., Tyack, P. & Buck, J. R. Captive dolphins, Tursiops truncatus, develop signature whistles that match acoustic features of human-made model sounds. JASA 112, 728–739 (2002).Article 

    Google Scholar 
    Fripp, D. et al. Bottlenose dolphin (Tursiops truncatus) calves appear to model their signature whistles on the signature whistles of community members. Anim. Cogn. 8, 17–26 (2005).PubMed 
    Article 

    Google Scholar 
    Janik, V. M. & Slater, P. J. B. Context-specific use suggests that bottlenose dolphin signature whistles are cohesion calls. Anim. Behav. 56, 829–838 (1998).CAS 
    PubMed 
    Article 

    Google Scholar 
    Sayigh, L. S., Tyack, P. L., Wells, R. S. & Scott, M. D. Signature whistles of free-ranging bottlenose dolphins, Tursiops truncatus: mother offspring comparisons. Behav. Ecol. Sociobiol. 26, 247–260 (1990).Article 

    Google Scholar 
    Watwood, S. L., Tyack, P. L. & Wells, R. S. Whistle sharing in paired male bottlenose dolphins, Tursiops truncatus. Behav. Ecol. Sociobiol. 55, 531–543 (2004).Article 

    Google Scholar 
    Janik, V. M., Dehnhardt, G. & Todt, D. Signature whistle variations in a bottlenosed dolphin, Tursiops truncatus. Behav. Ecol. Sociobiol. 35, 243–248 (1994).Article 

    Google Scholar 
    Esch, H. C., Sayigh, L. S. & Wells, R. S. Quantifying parameters of bottlenose dolphin signature whistles. Mar. Mam. Sci. 24, 976–986 (2009).Article 

    Google Scholar 
    Gridley, T. Geographic and species variation in bottlenose dolphin (Tursiops spp.) signature whistle types. PhD Thesis Biology. University of St Andrews (2011).King, S. L. & Janik, V. M. Bottlenose dolphins can use learned vocal labels to address each other. Proc Natl Acad Sci USA 110, 13216–13221 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kriesell, H., Elwen, S. H., Nastasi, A. & Gridley, T. Identification and characteristics of signature whistles in wild bottlenose dolphins (Tursiops truncatus) from Namibia. PLoS ONE 9, e106317 (2014).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Luis, A. R., Couchinho, M. N. & dos Santos, M. E. Signature whistles in wild bottlenose dolphins: Long term stability and emission rates. Acta Ethol. https://doi.org/10.1007/s10211-015-0230-z (2015).Article 

    Google Scholar 
    Wang, D. W., Würsig, B. & Evans, W. E. Whistles of bottlenose dolphins: Comparisons among populations. Aquatic Mam. 21, 65–77 (1995).
    Google Scholar 
    May-Collado, L. J. & Wartzok, D. A comparison of bottlenose dolphin whistles in the Atlantic Ocean: Factors promoting whistle variation. J. Mammal. 89, 1229–1240 (2008).Article 

    Google Scholar 
    Papale, E. et al. Acoustic divergence between bottlenose dolphin whistles from the Central-Eastern North Atlantic and Mediterranean Sea. Acta Ethol. 17, 155–165 (2014).Article 

    Google Scholar 
    La Manna, G., Rako-Gospić, N., Manghi, M., Picciulin, M. & Sarà, G. Assessing geographical variation on whistle acoustic structure of three Mediterranean populations of common bottlenose dolphin (Tursiops truncatus). Beh. 154, 583–607 (2017).Article 

    Google Scholar 
    La Manna, G. et al. Whistle variation in Mediterranean common bottlenose dolphin: The role of geographical, anthropogenic, social, and behavioral factors. Ecol. Evol. 00, 1–7 (2020).
    Google Scholar 
    Natoli, A., Birkun, A., Aguilar, A., Lopez, A. & Rus Hoelzel, A. Habitat structure and the dispersal of male and female bottlenose dolphins (Tursiops truncatus) based on microsatellite and mitochon-drial DNA analyses. Proc. R. Soc. Lond. B. 272, 1217–2122 (2005).CAS 

    Google Scholar 
    Richardson, W. J., Greene, C. R., Malme, C. I. & Thomson, D. H. Marine mammals and noise (Academic Press, London, 1995).
    Google Scholar 
    Gnone, G., et al. TursioMed: An international project to assess the conservation status of the bottlenose dolphin in the Mediterranean Sea. Final Report (2019).La Manna, G. & Ronchetti, F. Relazione sul monitoraggio della presenza e distribuzione del tursiope Tursiops truncatus nell’area del nord Sardegna comprendente l’Area Marina Protetta Capo Caccia – Isola Piana. Report AMP, 42 (2018).La Manna, G., Ronchetti, F., Sarà, G., Ruiu, A. & Ceccherelli, G. Common bottlenose dolphin protection and sustainable boating: species distribution modeling for effective coastal planning. Front. Mar. Sci. 7, 542648 (2020).Article 

    Google Scholar 
    Pace, D. S. et al. An integrated approach for cetacean knowledge and conservation in the central Mediterranean Sea using research and social media data sources. Aquat. Conserv. 29, 1302–1323 (2019).Article 

    Google Scholar 
    Pace, D. S. et al. Capitoline Dolphins: Residency patterns and abundance estimate of Tursiops truncatus at the Tiber River Estuary (Mediterranean Sea). Biology 10, 275 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pulcini, M., Pace, D. S., La Manna, G., Triossi, F. & Fortuna, C. M. Distribution and abundance estimates of bottlenose dolphins (Tursiops truncatus) around Lampedusa Island (Sicily Channel, Italy). Implications for their management. J. Mar. Biol. Assoc. UK 6, 1175–1184 (2013).
    Google Scholar 
    La Manna, G., Ronchetti, F. & Sarà, G. Predicting common bottlenose dolphin habitat preference to dynamically adapt management measures from a Marine Spatial Planning perspective. Ocean Coast. Manag. 130, 317–327 (2016).Article 

    Google Scholar 
    Santostasi, N. L., Bonizzoni, S., Bearzi, G., Eddy, L. & Gimenez, O. A robust design capture-recapture analysis of abundance, survival and temporary emigration of three odontocete species in the Gulf of Corinth, Greece. PLoS ONE 11, e0166650 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Bearzi, G., Bonizzoni, S. & Gonzalvo, J. Mid-distance movements of common bottlenose dolphins in the coastal waters of Greece. J. Ethol 29, 369–374 (2011).Article 

    Google Scholar 
    Bearzi, G. et al. Dolphins in a scaled-down Mediterranean: The Gulf of Corinth’s odontocetes. In Adv. Mar. Biol. Vol. 75 (eds NotarbartolodiSciara, G. et al.) 297–331 (Academic Press, 2016).
    Google Scholar 
    Pleslić, G. et al. The abundance of common bottlenose dolphins (Tursiops truncatus) in the former special marine reserve of the Cres-Lošinj Archipelago, Croatia. Aquat. Conserv. 25, 125–137 (2015).Article 

    Google Scholar 
    Rako-Gospić, N. et al. Factor associated variations in the home range of a resident Adriatic common bottlenose dolphin population. Mar. Pol. Bul. 124, 234–244 (2017).Article 
    CAS 

    Google Scholar 
    Janik, V. M., King, S. L., Sayigh, L. S. & Wells, R. S. Identifying signature whistles from recordings of groups of unrestrained bottlenose dolphins (Tursiops truncatus). Mar Mam. Sci 29, 1–14 (2013).Article 

    Google Scholar 
    La Manna, G., Manghi, M., Pavan, G., Lo Mascolo, F. & Sarà, G. Behavioural strategy of common bottlenose dolphins (Tursiops truncatus) in response to different kinds of boats in the waters of Lampedusa Island (Italy). Aquat. Conserv. 23, 745–757 (2013).
    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2015).
    Google Scholar 
    Zuur, A. F., Ieno, E. N., Walker, N. J., Saveliev, A. A. & Smith, G. H. Mixed effects models and extensions in ecology with R, 579 (Springer, 2009).MATH 
    Book 

    Google Scholar 
    Garamszegi, L. Z. A simple statistical guide for the analysis of behaviour when data are constrained due to practical or ethical reasons. Anim. Beh. 120, 223–234 (2015).Article 

    Google Scholar 
    Pinheiro, J., Bates, D., DebRoy, S., Sarkar, D., & R Core Team. nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1–137 (2018).Janik, V. M. Source levels and the estimated active space of bottlenose dolphin (Tursiops truncatus) whistles in the Moray Firth, Scotland. J. Comp. Physiol. A Sens. Neural Behav. Physiol 186, 673–680 (2000).CAS 
    Article 

    Google Scholar 
    Quintana-Rizzo, E., Mann, D. A. & Wells, R. S. Estimated communication range of social sounds used by bottlenose dolphins (Tursiops truncatus). JASA 120, 1671–1683 (2006).Article 

    Google Scholar 
    Sayigh, L. S. Development and function of signature whistles of free ranging bottlenose dolphins, Tursiops truncatus. MIT/WHOI joint program (1992).Janik, V. M., Sayigh, L. S. & Wells, R. S. Signature whistle shape conveys identity information to bottlenose dolphins. PNAS 103, 8293–8297 (2006).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Papale, E., Gamba, M., Perez-Gil, M., Martin, V. M. & Giacoma, C. Dolphins adjust species-specific frequency parameters to compensate for increasing background noise. PLoS ONE 10, e0121711 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    La Manna, G., Rako-Gospić, N., Manghi, M. & Ceccherelli, G. Influence of environmental, social and behavioural variables on the whistling of the common bottlenose dolphin (Tursiops truncatus). Behav. Ecol. Sociobiol. 73, 12 (2019).Article 

    Google Scholar 
    Ballard, S. M. & Lee, K. M. The acoustics of marine sediments. JASA 13, 18–18 (2017).
    Google Scholar 
    Smolker, R. & Pepper, J. W. Whistle convergence among allied male bottlenose dolphins (Delphinidae, Tursiops sp). Ethology 105, 595–617 (1999).Article 

    Google Scholar 
    Sayigh, L. S., Esch, H. C., Wells, R. S. & Janik, V. M. Facts about signature whistles of bottlenose dolphins (Tursiops truncatus). Anim. Behav. 74, 1631–1642 (2007).Article 

    Google Scholar 
    Jourdan J., et al. Distribution and abundance of bottlenose dolphin (Tursiops truncatus) along French Provençal coast. In Proceeding of the 30th European Cetacean Society Conference, Madeira (2016).Labach, H. et al. Distribution and abundance of common bottlenose dolphin (Tursiops truncatus) over the French Mediterranean continental shelf. Mar. Mam. Sci. 2021, 1–11 (2021).
    Google Scholar 
    Terranova, F. et al. Signature whistles of the demographic unit of bottlenose dolphins (Tursiops truncatus) inhabiting the Eastern Ligurian Sea: characterisation and comparison with the literature. Eur. Zool. J. 88, 771–781 (2021).Article 

    Google Scholar  More

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    Dark matter-free galaxies, alarming tree deaths and the dawn of farming

    This Hubble image captures a set of galaxies that are unusual because they seem not to have dark matter.Credit: NASA/ESA/P. van Dokkum, Yale Univ.

    Galaxies without dark matter baffle astronomersScientists have long thought that galaxies cannot form without the gravitational pull of the mysterious material known as dark matter. But one group of astronomers thinks it might have observed a line of 11 galaxies that don’t contain any of the substance, and could all have been created in an ancient collision (P. van Dokkum et al. Nature 605, 435–439; 2022).This kind of system could be used to learn about how galaxies form, and about the nature of dark matter itself. However, some researchers are not convinced that the claim is much more than a hypothesis.The finding centres on two galaxies, called DF2 and DF4, that were described in 2018 and 2019. Their stars moved so slowly that the pull of dark matter was not needed to explain their orbits, so the team concluded that the galaxies contained no dark matter.In the latest research, scientists identified between three and seven new candidates for dark-matter-free galaxies in a line between DF2 and DF4, as well as strange, faint galaxies at either end.“If proven right, this could certainly be exciting for galaxy formation. However, the jury is still out,” says Chervin Laporte, an astronomer at the University of Barcelona in Spain.Northern Australian tree deaths double in 35 yearsThe rate at which trees are dying in the old-growth tropical forests of northern Australia each year has doubled since the 1980s, and researchers say climate change is probably to blame.The findings, published in Nature on 18 May, come from an extraordinary record of tree deaths catalogued at 24 sites in the tropical forests of northern Queensland over the past 49 years (D. Bauman et al. Nature https://doi.org/hv67; 2022).The research team recorded that 2,305 trees across 81 key species had died since 1971. But from the mid-1980s, tree mortality risk increased from an average of 1% a year to 2% a year (see ‘Increasing death rate’). Of the 81 tree species that the team studied, 70% showed an increase in mortality risk over the study period.The study found that the rise in death rate occurred at the same time as a long-term trend of increases in the atmospheric vapour pressure deficit, which is the difference between the amount of water vapour that the atmosphere can hold and the amount of water it does hold at a given time. The higher the deficit, the more water trees lose through their leaves, which can lead to sustained stress and eventually tree death.

    Europe’s first farming populations descend mostly from farmers in the Anatolian peninsula, in what is now Turkey.Credit: Fatih Kurt/Anadolu Agency/Getty

    Ancient DNA maps ‘dawn of farming’Sometime before 12,000 years ago, nomadic hunter-gatherers in the Middle East made one of the most important transitions in human history: they began staying put and took to farming.Two ancient-DNA studies have now homed in on the identity of the hunter-gatherers who settled down.Researchers sequenced the genomes of 15 hunter-gatherers and early farmers who lived in southwest Asia and Europe, along a key migration routes into Europe — the Danube River (N. Marchi et al. Cell https://doi.org/gp49rr; 2022).The team found that ancient farmers in Anatolia — now Turkey — descended from repeated mixing between distinct hunter-gatherer groups from Europe and the Middle East. These groups first split at the height of the last Ice Age, some 25,000 years ago. Modelling suggests that the western groups nearly died out, before rebounding as the climate warmed.Once established in Anatolia, the researchers found, early farmers moved west into Europe in a stepping-stone-like way, beginning around 8,000 years ago. They mixed occasionally — but not extensively — with local hunter-gatherers.The findings chime with those of a similar ancient-genomics study posted on the bioRxiv preprint server this month (M. E. Allentoft. et al. Preprint at bioRxiv https://doi.org/hv7g; 2022). More

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    VenomMaps: Updated species distribution maps and models for New World pitvipers (Viperidae: Crotalinae)

    The custom code used to clean occurrence records and construct SDMs is available at (github.com/RhettRautsaw/ VenomMaps). We used the following R16 packages for data cleaning, manipulation, species distribution modeling, and Shiny app creation: tidyverse17 readxl18, data.table19, sf20, sp21,22, rgdal23, raster24, smoothr25, ape26, phytools27, argparse28, parallel16, memuse29, dismo30, rJava31, concaveman32, spThin33, usdm34, ENMeval35, kuenm36, shiny37, leaflet38, leaflet.extras39, leaflet.extras240, RColorBrewer41, ggpubr42, ggtext43, and patchwork44.Updating occurrence record taxonomyOur goal was to update and reconstruct the distributions of New World pitvipers. We used the Reptile Database45 (May 2021) as our primary source for current taxonomy which included the following genera: Agkistrodon, Atropoides, Bothriechis, Bothrocophias, Bothrops, Cerrophidion, Crotalus, Lachesis, Metlapilcoatlus, Mixcoatlus, Ophryacus, Porthidium, and Sistrurus. However, to ensure we captured all New World pitvipers records, we incorporated all members of the family Viperidae (all vipers and pitvipers) into our pipeline for updating occurrence record taxonomy (i.e., to account for errors in the recorded latitude, longitude, or if subfamily was not recorded).First, we collected global occurrence records for “Viperidae” from GBIF (downloaded 2021-08-19)46, Bison (downloaded 2021-08-19)47, HerpMapper (only New World taxa; downloaded 2021-08-19)48, Brazilian Snake Atlas49, BioWeb (downloaded 2021-07-07)50, unpublished data/databases from RMR, GJV, EPH, LRVA, MM, and CLP, and georeferenced literature records totaling 373,673 species-level records, 292,425 of which are New World pitvipers. Given the fluidity of taxonomy, records were often associated with outdated names. For example, Crotalus mitchelli pyrrhus was elevated to Crotalus pyrrhus51, but may still be recorded as the former in a given repository (e.g., GBIF). To correct taxonomy in our database, we checked records against a list of synonyms found on the Reptile Database and compared them to current taxonomy. If species and subspecies columns matched the same taxon (or no subspecies was recorded), then species IDs were not altered. If species and subspecies IDs did not match the same taxon, we updated taxonomy by minimizing the number of changes required to a given character string. We then manually checked all changes.Constructing distribution mapsNext, we collected preliminary distribution maps from the International Union for Conservation of Nature (IUCN; downloaded 2018-11-27)52, Global Assessment of Reptile Distributions (GARD) v1.153, Heimes54, Campbell and Lamar55, and unpublished maps. We manually curated distribution maps for all New World pitvipers in QGIS using the occurrence records, previous distribution maps, and recent publications for each taxon (note that distributions for Old World Viperidae have not yet been updated). We used a digital relief map (maps-for-free.com) and The Nature Conservancy Terrestrial Ecoregions (TNG.org)56 to identify clear distribution boundaries (e.g., mountains). We then clipped the final distributions to a land boundary (GADM v3.6)57 and smoothed the distribution using the the “chaikin” method in the R package smoothr25.Occurrence-distribution overlapOur initial taxonomy check was only concerned with records for which a subspecies was recorded and had since been elevated to species status. Therefore, many records with no assigned subspecies likely remained associated with an incorrect or outdated generic and/or specific identification. Fortunately, taxonomic changes are typically associated with changes in the species’ expected distribution. For example, when Crotalus simus was resurrected from C. durissus, the distribution of C. durissus was split: the northern portion of its range in Central America now represented the resurrected species (C. simus) and the southern portion of its range remained C. durissus55. Yet, occurrence records in Central America often remain labelled as C. durissus in data repositories. Therefore, we spatially joined records with the newly reconstructed species distribution maps to determine if they overlapped with their expected distribution (Old World taxa were joined with the GARD 1.1 distributions53).Briefly, we developed a custom function (occ_cleaner.R) to perform the spatial join and update taxonomy. First, we calculated the distance for each record to the 20 nearest distributions within 50 km (full overlap resulted in a distance of 0 m). Next, we calculated the phylogenetic distance between the recorded species ID and each species with which that record overlapped using the tree from Zaher et al.58 and adding taxa based on recent clade-specific publications (bind.tip2.R; see github.com/RhettRautsaw/VenomMaps for full list of references and details). If records overlapped with their expected species, no changes were made. If records fell outside of their expected distribution, we filtered the potential overlapping and nearby species (within 50 km) to minimize phylogenetic distance. If multiple species were equally distant (i.e., share the same common ancestor), we attempted to minimize geographic distance. If multiple species remained equally distant in both phylogenetic and geographic distance, we flagged the record to be manually checked. We also flagged records if a species’ taxonomy had changed and records were additionally flagged as potentially dubious if the taxonomic change had a phylogenetic divergence greater than 5 million years. We manually checked all flagged records and returned records to their original species ID if species identity remained uncertain. We flagged these records as potentially dubious, along with records that fell outside of their expected distribution (within 50 km), and removed all flagged records for species distribution modeling. Our final cleaned database contained 344,998 global records, of which 275,087 were New World pitvipers.Species distribution modelingWe attempted to infer SDMs for the 158 species of New World pitvipers currently recognized by the Reptile Database (May 2021) and additionally modeled the three subspecies of Crotalus ravus separately based on recommendations for species status elevation by Blair et al.59 for a total of 160 species. We developed a unix-executable R script (autokuenm.R) designed to take occurrence records, distribution maps, and environmental data and prepare these data for species distribution modeling with kuenm36. We chose to use kuenm – and MaxEnt v3.4.460 – because it has been shown to have good predictive power61 and fine-tuning of this algorithm has performance comparable to more computationally intensive ensembles62,63. Additionally, MaxEnt allows for flexibility in parameter selection64 and can function entirely with presence data14.Prior to autokuenm, to account for sampling/spatial bias during SDM, we created a bias file by using the pooled New World pitviper occurrence records as representative background data65,66,67,68. Specifically, we converted occurrence records to a raster and performed two-dimensional kernel density estimation (kde2d) with the MASS package with default settings69 and rescaled the kernel density by a factor of 1000 and rounded to three decimal places. This was then used as input to factor out sampling bias by MaxEnt. We then ran autokuenm, which is designed to subset/partition the cleaned occurrence records for a given species and prepare additional files for SDM. We first defined M-areas – or areas accessible to a given species – using the World Wildlife Fund Terrestrial Ecoregions70. Biogeographic regions represent distributional limits for many species and are reasonable hypotheses for the areas accessible to a given species71,72. To do this, we created alpha hulls from the subset of occurrence records for a given species using concaveman32 with default settings. We then identified regions with at least 20% of the region covered by the alpha hull and merged these regions together to form our final M-area. All environmental layers and the bias file were cropped to this M-area which was used as the geographic extent for modeling. We then randomly selected 5% of records to function as an independent test set for final model evaluation. Next, we generated 2000 random background points across the cropped environmental layers and used ENMeval to partition occurrence records into four sets using the checkerboard2 pattern35. Note that the background points here were not used in MaxEnt. One of the four partitions was selected at random to be used as the testing set; the remaining three partitions were used for training the MaxEnt models. If the number of occurrence records in the independent test set was less than five, then we used the training partition for final model creation and used the testing partition for final model evaluation.We tested the top-contributing variables from three sets of environmental layers: (1) bioclimatic variables, (2) EarthEnv topographic variables73, and (3) a combination of these variables. To select the top-contributing variables in each set, we wrote a custom function (SelectVariables) which used a combination of MaxEnt permutation importance and Variable Inflation Factors (VIF) to remove collinearity while keeping the variables that contributed the most to the model. Compared with variable selection via principal component analysis loadings, the permutation importance and VIF methodology demonstrated significant improvement in MaxEnt model fit. First, we designed SelectVariables to run MaxEnt using dismo::maxent with default settings and then extracted the permutation importance. We removed variables if they had 0% permutation importance. Next, we calculated VIF with usdm::vif and then iteratively removed variables by selecting the variables with two highest VIF values and removing whichever variable had the lowest permutation importance. We then recalculated VIF and repeated the process until the maximum VIF value was less than 10. Finally, we recalculated permutation importance with the remaining variables using dismo::maxent with default settings and removed variables with less than 1% permutation importance to create the final variable sets. This process was done for each species independently.With the final environmental variable, testing, and training sets, we generated SDMs using kuenm. First, we created candidate calibration models with multiple combinations of regularization multipliers (0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 8, 10), feature classes (l, q, h, lq, lp, lt, lh, qp, qt, qh, pt, ph, th, lqp, lqt, lqh, lpt, lph, lth, qpt, qph, qth, pth, lqpt, lqph, lqth, lpth, qpth, lqpth), and sets of environmental predictors (bioclimatic, topographic, combination) totaling 2,958 candidate models per species. We then ran each model in parallel using GNU Parallel74. Next, we evaluated the candidate models and selected the best models using statistical significance (partial ROC), prediction ability (omission rates; OR), and model complexity (AICc) with the “kuenm_ceval” function with default settings. Specifically, models were only considered if they were statistically significant and had an OR less than 5%. If no models passed the OR criteria, the models with the minimal OR were considered. Finally, any remaining models were filtered to those within 2 AICc of the top model (Supplementary Table 1). In addition to evaluating and comparing all models together, we evaluated bioclimatic-only and combination-only models separately since these two sets of environmental variables were expected to be the best performing models given the ubiquity of bioclimatic variables in species distribution modeling (Supplementary Table 1).We generated 10 bootstrap replicates for each of the “best” calibration models using the “kuenm_mod” function. We also performed jackknifing to assess variable importance and models were output in raw format. We evaluated the final models using “kuenm_feval” with default settings. To select the best model for each comparative set (i.e., all, bioclimatic-only, and combination-only sets), we filtered the final evaluation results to minimize the OR and maximize the AUC ratio (Supplementary Table 2). If multiple models remained and were considered equally competitive, we averaged these models together (Supplementary Table 3). Because we performed three different set of comparisons, there were three “best” models per species, so we again aimed to minimize the OR and maximize the AUC ratio to select a final model for each species (Supplementary Table 4). We then converted our final models into cloglog format for visualization and threshold the models using a 10th percentile training presence cutoff (Fig. S2). Both conversion and thresholding functions are provided as R functions (raw2log, raw2clog, raster_threshold in functions.R; github.com/RhettRautsaw/VenomMaps). More

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    Bottom-up estimates of reactive nitrogen loss from Chinese wheat production in 2014

    Literature reviewWe conducted a comprehensive review of relevant literature published since 1995. Studies were extracted from the China National Knowledge Infrastructure and Web of Science using the following keywords: “N (nitrogen) loss OR NO (nitric oxide) emission OR N2O (nitrous oxide) emission OR NH3 (ammonia volatilization) emission OR NO3− (nitric leaching) OR N (nitrogen) runoff AND wheat AND China”. We excluded the following types of experiment: experiments not covering the entire wheat growing season, experiments conducted in greenhouses or laboratories, experiments without zero-N control, and experiments including manure, controlled release fertilizer, or inhibitors. In total, we extracted 941 observations from 138 articles, consisting of 121 observations of NO emission, 383 of N2O emission, 185 of NH3 emission, 188 of NO3− leaching, and 64 of Nr runoff. We also extracted data on N application rates, and climate and soil variables (Fig. 1). Missing climate data were obtained from China Meteorological Data Network (https://data.cma.cn/), miss values of soil organic carbon (SOC) and total N content were obtained from the National Scientific Fertilizer Network (http://kxsf.soilbd.com/), and missing soil silt, clay, sand content, bulk density, cation exchange capacity (CEC), and pH data were obtained from the Harmonized World Soil Database (HWSD) v. 1.2 (http://www.fao.org/soils-portal/soil-survey/soilmaps-and-databases/harmonized-world-soildatabase-v12/en). Based on this dataset, the EFs of Nr loss pathways were calculated by the following equation:$$E{F}_{i}=left({E}_{treatment}{rm{-}}{E}_{control}right){rm{/}}N;applied$$
    (1)
    where i = 1–5, represented NO, N2O, NH3, NO3− leaching and Nr runoff, respectively. Etreatment is the loss rate of experimental treatments with applied N fertilizer, Econtrol is the loss rate of experimental control without applied N fertilizer, and N applied is the N application rate corresponding to Etreatment. The resulting data was used to develop RF models to predict EFs of the five Nr loss pathways.Fig. 1The generate framework of the Nr loss from Chinese wheat system (Nr-Wheat) 1.0 database.Full size imageRF modelsRF models outperformed empirical models in previous studies15,18,19. We employed RF models to predict the EFs of NO, N2O, NH3, NO3− leaching, and Nr runoff. Environmental factors were selected via redundancy analysis20. Redundancy analysis, a basic ordination technique for gradients analysis, produces an ordination summarizing the variation in several response variables that can be best explained by a matrix of explanatory variables based on multiple linear regression. We conducted redundancy analysis using Canoco 5 to further analyze the effects of 10 environmental factors, including 4 soil physical factors (bulk density, silt, clay, and sand content), 4 soil chemical factors (pH, SOC, CEC and total N content), and 2 weather factors (total rainfall and mean temperature during the wheat growing period) of different EFs. Ultimately, the dataset of each pathway contained an ensemble of different environmental factors (Table 1).Table 1 Environmental factors were employed to build RF model for each pathway and total explanatory rates.Full size tableWhen establishing the RF model, the first step was to select k features from a total of m (k  More

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    Cash and action are needed to avert a biodiversity crisis

    Ambitious new targets are needed to conserve nature by protecting parks and species.Credit: Tang Dehong/VCG/Getty

    It will take ample time and money to slow the world’s catastrophic loss of plant and animal species — and right now, both are running dangerously low. This year, nations are due to agree to an action plan to protect global biodiversity at the 15th Conference of the Parties (COP15) to the United Nations Convention on Biological Diversity. But the meeting is already two years late because of the pandemic, and China, which will host the conference in Kunming, has yet to set a new date.Now, conflicts over financing are adding to the tension. Conservation groups and advocates suggest that rich nations must donate at least US$60 billion annually to help less-affluent ones to fund projects such as protecting areas where wildlife can thrive and tackling the illegal wildlife trade that is driving hundreds of species to extinction. This is much more than the $4 billion to $10 billion that they are estimated to be spending today, and well below the amount they are giving low- and middle-income countries (LMICs) to fight climate change, which reached around $50 billion in 2019 according to one estimate. Yet limited overseas development funds are spread ever thinner as donors deal with the pandemic and now the fallout from Russia’s invasion of Ukraine. This is where COP15 is meant to deliver: as well as agreeing to the action plan, called the Global Biodiversity Framework, nations will be encouraged to pledge more money.A mix of public and private money has started to trickle in. Currently, biodiversity funding on the table ahead of COP15 amounts to roughly $5.2 billion per year, according to estimates by a group of five leading conservation organizations. Most comes from six governments, including France, the United Kingdom and Japan, and the European Union. In April, the Global Environment Facility (GEF) — a multilateral fund to support international environmental agreements — announced that, over the next four years, around $1.9 billion will go to projects dedicated to biodiversity. However, it’s unclear how much of this will come from the coffers that donor countries have already pledged.Some cash for conservation is coming from private philanthropic donors — such as $2 billion committed by entrepreneur Jeff Bezos last year. And starting in 2020, a group of financial institutions (now 89 of them) promised to annually report their financing activities and investments that affect biodiversity, and to move away from those that do harm — a form of ecological accounting that could help to shrink the budget needed to protect biodiversity. Donors will need to reach much deeper into their pockets to meet the demands of LMICs, the custodians of much of the world’s biodiversity. In March, a group of LMICs, led by Gabon, asked for $100 billion per year in new funding when officials met in Geneva, Switzerland, to discuss progress on the Global Biodiversity Framework. The LMICs want the money placed in a new multilateral fund for biodiversity, separate from, but complementary to, the GEF.Aside from cash, the fund will need to find a new home and structure — and there are a few options. A proposal from Brazil, circulated at the Geneva meeting, suggests the fund be governed by a board of 24 members, with an equal number from rich and lower-income nations. The board would be responsible for funding decisions and would prioritize projects that help to achieve the biodiversity convention’s goals. The pitch generated interest among some countries, but also concerns that it’s an attempt by Brazil to divert attention from its failure over the past few years to protect the Amazon rainforest and prevent other environmental harm.Another option is the Kunming Biodiversity Fund, which China announced in October last year to help LMICs to safeguard their ecosystems. It allocated 1.5 billion yuan (US$223 million) to seed the fund and invited other countries to contribute, but so far none has. Sources knowledgeable about the fund say that donor countries are reluctant to pitch in because China is holding on too tightly to the reins and is not involving others in its deliberations. Details of how the fund will operate are scarce, but Nature has learnt that China is floating the idea of housing it at the Asian Infrastructure Investment Bank (AIIB), based in Beijing. Set up in 2016, the AIIB has $100 billion in total capital and 105 members, including Germany, France and the United Kingdom. The AIIB has big green plans. By 2025, it wants half of all infrastructure projects it finances to focus on climate issues. With rigorous oversight and transparency, the AIIB would make a good home for the Kunming fund.As countries prepare to meet in Nairobi on 20–26 June in a last-ditch attempt to push the biodiversity framework forwards before COP15, China, as the host, must urgently provide stronger leadership on financing, including more transparency and engagement. Progress will require quick, generous contributions from donor nations — which should prioritize grants, not loans, for biodiversity projects.Holding the COP15 meeting must be a priority, too. As China tightens restrictions in the face of a COVID-19 surge, some researchers fear that delays will stretch on, stalling conservation work and leaving less time to meet biodiversity targets. China must either commit to holding the meeting this year or let it proceed elsewhere. One option being quietly discussed is moving the meeting to Canada — home of the United Nations biodiversity convention’s secretariat — and this deserves consideration. The world needs an ambitious biodiversity plan now — nature cannot wait. More

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    Mulching impact of Jatropha curcas L. leaves on soil fertility and yield of wheat under water stress

    Khamraev, Sh. R. & Bezborodov, Yu. G. Results of research on the reduction of physical evaporation of moisture from the cotton fields. Sci. World 2(33), 86–93 (2016).
    Google Scholar 
    Khan, A. U. et al. Production of organic fertilizers from rocket seed (Eruca sativa L.), chicken peat and Moringa oleifera leaves for growing linseed under water deficit stress. Sustainability 13(1), 1–19 (2021).CAS 

    Google Scholar 
    Patil Shirish, S., Kelkar Tushar, S. & Bhalerao Satish, A. Mulching: A soil and water conservation practice. Res. J. Agric For. Sci. 1(3), 26–29 (2013).
    Google Scholar 
    Matkovic, A. et al. Mulching as a physical weed control method applicable in medicinal plants cultivations. J. Lekovite Sirovine 35, 37–51 (2015).Article 

    Google Scholar 
    Nawaz, A., Lal, R., Shrestha, R. K. & Farooq, M. Mulching affects soil properties and greenhouse gas emissions under long-term no-till and plough-till systems in alfisol of Central Ohio. Land Degrad. Dev. 28(2), 673–681 (2016).Article 

    Google Scholar 
    Brant, V. et al. Splash erosion in maize crops under conservation management in combination with Shallow Strip-tillage before Sowing. Soil Water Res. 12(2), 106–116 (2017).CAS 
    Article 

    Google Scholar 
    Kumar, R. et al. Effect of plant spacing and organic mulch on growth, yield and quality of natural sweetener plant Stevia and soil fertility in western Himalayas. Int. J. Plant Prod. 8(3), 311–334 (2014).ADS 

    Google Scholar 
    Seleiman, M. F. & Kheir, A. M. S. Maize productivity, heavy metals uptake and their availability in contaminated clay and sandy alkaline soils as affected by inorganic and organic amendments. Chemosphere 204, 514–522 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Seleiman, M. F. & Kheir, A. M. S. Saline soil properties, quality and productivity of wheat grown with bagasse ash and thiourea in different climatic zones. Chemosphere 193, 538–546 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Chakraborty, D. et al. Effect of mulching on soil and plant water status, and the growth and yield of wheat (Triticum aestivum L.) in a semi-arid environment. Agric. Water Manag. 95(12), 1323–1334 (2008).Article 

    Google Scholar 
    Ahmad, Z. I., Ansar, M., Iqbal, M. & Minhas, N. M. Effect of planting geometry and mulching on moisture conservation, weed control and wheat growth under rainfed conditions. Pak. J. Bot. 39(4), 1189–1195 (2007).
    Google Scholar 
    Teame, G. Effect of organic mulches and land preparation methods on soil moisture and sesame productivity. Afr. J. Agric. Res. 12(38), 2836–2843 (2017).Article 

    Google Scholar 
    Lehar, L., Wardiyati, T., Moch Dawam, M. & Suryanto, A. Influence of mulch and plant spacing on yield of Solanum tuberosum L. cv. Nadiya at medium altitude. Int. Food Res. J. 24(3), 1338–1344 (2017).CAS 

    Google Scholar 
    Arash, K. The evaluation of water use efficiency in common bean (Phaseolus vulgaris L.) in irrigation condition and mulch. Sci. Agric. 2(3), 60–64 (2013).
    Google Scholar 
    Artyszak, A., Gozdowski, D. & Kucińska, K. The yield and technological quality of sugar beet roots cultivated in mulches. Plant Soil Environ. 60(10), 464–469 (2014).Article 

    Google Scholar 
    Brittaine, R. & Lutaladio, N. Jatropha: A Smallholder Bioenergy Crop. The Potential for Pro-poor Development Integrated Crop Management, Vol. 8 (IFAD/FAO, 2010). http://www.fao.orgElbehri, A., Segerstedt, A. & Liu, P. Biofuels and the sustainability challenge: A global assessment of sustainability issues, trends and policies for biofuels and related feedstocks. Food and Agric. Organ. United Nations (FAO) xvi-174 (2013).King, A. J. et al. Potential of Jatropha curcas as a source of renewable oil and animal feed. J. Exp. Bot. 60(10), 2897–2905 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    Raheman, H. 14 Jatropha. Handbook of Bioenergy Crop Plants, 315–345 (2012).Ullah, F., Bano, A. & Nosheen, A. Sustainable measures for biodiesel. Effects 36(23), 2621–2628 (2014).CAS 

    Google Scholar 
    Irshad, M. et al. Evaluation of Jatropha curcas L. leaves mulching on wheat growth and biochemical attributes under water stress. BMC Plant Biol. 21(1), 1–12 (2021).Article 
    CAS 

    Google Scholar 
    Dieye, T. et al. The effect of Jatropha curcas L. leaf litter decomposition on soil carbon and nitrogen status and bacterial community structure (Senegal). J. Soil Sci. Environ Manag. 7(3), 32–44 (2016).CAS 
    Article 

    Google Scholar 
    Kafi, M. & Salehi, M. Kochia scoparia as a model plant to explore the impact of water deficit on halophytic communities. Pak. J. Bot. 44, 257–262 (2012).
    Google Scholar 
    Yang, Y. M., Liu, X. J., Li, W. Q. & Li, C. Z. Effect of different mulch materials on winter wheat production in desalinized soil in Heilonggang region of North China. J. Zhejiang Univ. Sci. B 7(11), 858–867 (2006).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Xie, Z. K., Wang, Y. J. & Li, F. M. Effect of plastic mulching on soil water use and spring wheat yield in arid region of northwest China. Agric. Water Manag. 75(1), 71–83 (2005).Article 

    Google Scholar 
    Khan, R. H., Anwar-ul-Haq, K. & Sajjad, M. R. Effect of different types of mulches on grain yield and yield components of wheat (Triticum aestivum) under rainfed condition. J. Biol. Agric. Healthc. 4(12), 85–91 (2014).
    Google Scholar 
    Weidhuner, A., Afshar, R. K., Luo, Y., Battaglia, M. & Sadeghpour, A. Particle size affects nitrogen and carbon estimate of a wheat cover crop. Agron. J. 111(6), 3398–3402 (2019).CAS 
    Article 

    Google Scholar 
    Ding, Z. et al. The integrated effect of salinity, organic amendments, phosphorus fertilizers, and deficit irrigation on soil properties, phosphorus fractionation and wheat productivity. Sci. Rep. 10(1), 1–13 (2020).Article 
    CAS 

    Google Scholar 
    Rummana, S., Amin, A. K. M. R., Islam, M. S. & Faruk, G. M. Effect of irrigation and mulch materials on growth and yield of wheat. Bang. Agron. J. 21(1), 71–76 (2018).Article 

    Google Scholar 
    Richard, L. A. Diagnosis and improvement of saline and alkaline soils. Handbook No. 60 (US Depart. Agric., 1954).McLean, E. O. Soil pH and lime requirement. Methods of Soil Analysis: Part 2 Chemical and Microbiological Properties, Vol. 9, 199–224 (1983).Walkley, A. A critical examination of a rapid method for determining organic carbon in soils—Effect of variations in digestion conditions and of inorganic soil constituents. Soil Sci. 63, 251–264 (1947).ADS 
    CAS 
    Article 

    Google Scholar 
    Singleton, V. L., Orthofer, R. & Lamuela-Raventos, R. M. Analysis of total phenols and other oxidation substrates and antioxidants by means of Folin–Ciocalteu reagent. Methods Enzymol. 299, 152–178 (1999).CAS 
    Article 

    Google Scholar 
    Vance, E. D., Brookes, P. C. & Jenkinson, D. S. An extraction method for measuring soil microbial biomass C. Soil Biol. Biochem. 19, 703–707 (1987).CAS 
    Article 

    Google Scholar 
    Bremner, J. M. & Mulvaney, C. S. Nitrogen-total. In Methods of Soil Analysis. Part 2. Chemical and Microbiological Properties (eds Page, A. L. et al.) 595–624 (Soil Sci. Society America, 1982).
    Google Scholar 
    Steel, R. G. D., Torrie, J. H. & Dickey, D. A. Principles and Procedures of Statistics: A Biometrical Approach 3rd edn, 246 (McGraw-Hill, 1997).
    Google Scholar 
    Brady, N. C. & Weil, R. R. Soil colloids: Seat of soil chemical and physical acidity. Nat. Prop. Soils 5(13), 311–358 (2008).
    Google Scholar 
    Scharenbroch, B. C. & Lloyd, J. E. Particulate organic matter and soil nitrogen availability in urban landscapes. Arboricul. Urb. For. 32(4), 180–191 (2006).Article 

    Google Scholar 
    Bhadha, J. H., Capasso, J. M., Khatiwada, R., Swanson, S. & LaBorde, C. Raising soil organic matter content to improve water holding capacity. UF/IFAS 1–5 (2017).Chalker-Scott, L. Impact of mulches on landscape plants and the environment—A review. J. Environ. Hortic. 25(4), 239–249 (2007).Article 

    Google Scholar 
    Liu, Z., Fu, B., Zheng, X. & Liu, G. Plant biomass, soil water content and soil N:P ratio regulating soil microbial functional diversity in a temperate steppe: A regional scale study. Soil Biol. Biochem. 42(3), 445–450 (2010).CAS 
    Article 

    Google Scholar 
    Bai, S. H., Blumfield, T. J. & Reverchon, F. The impact of mulch type on soil organic carbon and nitrogen pools in a sloping site. Biol. Fertil. Soils 50(1), 37–44 (2014).Article 

    Google Scholar 
    Yang, H. et al. The combined effects of maize straw mulch and no-tillage on grain yield and water and nitrogen use efficiency of dry-land winter wheat (Triticum aestivum L.). Soil Tillage Res. 197, 104485 (2020).Article 

    Google Scholar 
    Li, X. J. et al. Abscisic acid pretreatment enhances salt tolerance of rice seedlings: Proteomic evidence. Biochim. Biophys. Acta (BBA) Proteins Proteomics 1804(4), 929–940 (2010).CAS 
    Article 

    Google Scholar 
    Fang, S., Xie, B., Liu, D. & Liu, J. Effects of mulching materials on nitrogen mineralization, nitrogen availability and poplar growth on degraded agricultural soil. New For. 41(2), 147–162 (2011).Article 

    Google Scholar 
    Houghton, J. T. Climate Change 2001: The Scientific Basis 419–470 (2001).Johnson, D. et al. Plant community composition affects the biomass, activity and diversity of microorganisms in limestone grassland soil. Eur. J. Soil Sci. 54(4), 671–678 (2003).Article 

    Google Scholar 
    Johnson, M. J., Lee, K. Y. & Scow, K. M. DNA finger printing reveals links among agricultural crops, soil properties, and the composition of soil microbial communities. Geoderma 114, 279–303 (2003).ADS 
    Article 

    Google Scholar 
    Nielsen, N. M., Winding, A. & Binnerup, S. Microorganisms as Indicators of Soil Health 15–16 (Ministry of the Environment, National Environ. Res. Inst., 2002).
    Google Scholar 
    Wilkinson, S. C. et al. PLFA profiles of microbial communities in decomposing conifer litters subject to moisture stress. Soil Biol. Biochem. 34(2), 189–200 (2002).CAS 
    Article 

    Google Scholar 
    Drenovsky, R. E., Vo, D., Graham, K. J. & Scow, K. M. Soil water content and organic carbon availability are major determinants of soil microbial community composition. Microb. Ecol. 48(3), 424–430 (2004).CAS 
    PubMed 
    Article 

    Google Scholar 
    Liu, Y. Y., Yao, H. Y. & Huang, C. Y. Influence of soil moisture regime on microbial community diversity and activity in a paddy soil. Acta Pedol. Sin. 43, 828–834 (2006).
    Google Scholar 
    Jensen, K. D., Beier, C., Michelsen, A. & Emmett, B. A. Effects of experimental drought on microbial processes in two temperate heathlands at contrasting water conditions. Appl. Soil Ecol. 24(2), 165–176 (2003).Article 

    Google Scholar 
    Stoklosa, A., Hura, T., Stupnicka-Rodzynkiewicz, E., Dabkowska, T. & Lepiarczyk, A. The influence of plant mulches on the content of phenolic compounds in soil and primary weed infestation of maize. Acta. Agron. Bot. 61(2), 205–219 (2008).
    Google Scholar 
    Ohno, T. Oxidation of phenolic acid derivatives by soil and its relevance to allelopathic activity. J. Environ. Qual. 30(5), 1631–1635 (2001).CAS 
    PubMed 
    Article 

    Google Scholar 
    Farooq, S., Shahid, M., Khan, M. B., Hussain, M. & Farooq, M. Improving the productivity of bread wheat by good management practices under terminal drought. J. Agric. Crop Sci. 201(3), 173–188 (2015).Article 

    Google Scholar 
    Madani, A., Rad, A. S., Pazoki, A., Nourmohammadi, G. & Zarghami, R. Wheat (Triticum aestivum L.) grain filling and dry matter partitioning responses to source: Sink modifications under postanthesis water and nitrogen deficiency. Acta Sci. Agron. 32, 145–151 (2010).CAS 
    Article 

    Google Scholar 
    Deng, X. P., Shan, L., Zhang, H. & Turner, N. C. Improving agricultural water use efficiency in arid and semiarid areas of China. Agric. Water Manag. 80(1–3), 23–40 (2006).Article 

    Google Scholar 
    Athar, H. R., Khan, A. & Ashraf, M. Inducing salt tolerance in wheat by exogenously applied ascorbic acid through different modes. J. Plant Nutr. 32, 1799–1817 (2009).CAS 
    Article 

    Google Scholar 
    Luo, et al. Dual plastic film and straw mulching boosts wheat productivity and soil quality under the El Nino in semiarid Kenya. Sci. Total Environ. 738, 139808 (2020).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Duan, et al. Improvement of wheat productivity and soil quality by arbuscular mycorrhizal fungi is density-and moisture-dependent. Agron. Sustain. Dev. 41(1), 1–12 (2021).Article 
    CAS 

    Google Scholar  More

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    Enhanced silica export in a future ocean triggers global diatom decline

    Mesocosm experimentsSi:Nexport measurementsBetween 2010 and 2014, we conducted five in situ mesocosm experiments to assess impacts of OA on natural plankton communities. Study sites covered a large latitudinal gradient (28 °N–79 °N) and diverse oceanic environments/ecosystems (Extended Data Fig. 1 and Extended Data Table 1). Sample collection and processing was conducted every 1 or 2 days throughout the experiments. Sinking particulate matter was obtained from sediment traps attached to the bottom of each mesocosm, thereby collecting the entire material sinking down in the enclosed water column36. Processing of sediment trap samples followed a previous protocol37. Samples for particulate matter suspended in the water column were collected with depth-integrating water samplers (HYDRO-BIOS) and filtered following standard procedures. Biogenic silica was leached from the sediment trap samples and filters by alkaline pulping (0.1 M NaOH at 85 °C). After 135 min the leaching process was terminated with 0.05 M H2SO4 and dissolved silica was measured spectrophotometrically38. Carbon and nitrogen content were determined using an elemental CN analyser (EuroEA)39.Analysis of OA impactsTo test for a systemic influence of OA on Si:Nexport, we synthesized the datasets from the different experiments and (i) conducted a meta-analysis to quantify effect sizes, and (ii) computed probability density estimates. Because the experimental design, the range of CO2 treatments, and the time periods for our analysis of Si:Nexport varied to some extent among experiments (Extended Data Table 1), we pooled mesocosms for ambient conditions and in the ({{p}}_{{{rm{CO}}}_{2}}) range of ~700–1,000 μatm (‘OA treatment’), corresponding to end-of-century values according to RCP 6.0 and 8.5 emission scenarios15. Effect sizes were calculated as log-transformed response ratios lnRR, an approach commonly used in meta-analysis40:$${rm{l}}{rm{n}}{rm{R}}{rm{R}}={rm{l}}{rm{n}}{X}_{{rm{O}}{rm{A}}}-{rm{l}}{rm{n}}{X}_{{rm{c}}{rm{o}}{rm{n}}{rm{t}}{rm{r}}{rm{o}}{rm{l}}},$$where X is the arithmetic mean of Si:Nexport ratios under OA and ambient conditions (Extended Data Table 1). Effect sizes 0 indicate that the effect was positive. Effects are considered statistically significant when 95% confidence intervals (calculated from pooled standard deviations) do not overlap with zero. The overall effect size across all studies was computed by weighing individual effect sizes according to their variance, following the common methodology for meta-analyses40. In addition, we computed probability densities of Si:Nexport based on kernel density estimation, which better accounts for data with skewed or multimodal distributions41. Another advantage of this approach is that it does not require the calculation of temporal means. Instead, the entire data timeseries can be incorporated into the analysis, thus retaining information about temporal variability. Confidence intervals of the density estimates were calculated with a bootstrapping approach using data resampling (1,000 permutations)41. The resulting probability density plots can be interpreted analogously to histograms. Differences among ambient and OA conditions are considered statistically significant when confidence intervals of the probability density distributions do not overlap. Numbers for suspended and sinking Si, C and N (and their respective ratios) for the analysis period are given in Extended Data Table 2.Analysis of pH effects on Si:N in global sediment trap dataWe analysed a recent compilation of global sediment trap data (674 locations collected between 1976 and 2012)35. The aim of this analysis was to assess the influence of pH on opal dissolution in the world ocean. In contrast to the mesocosm experiments, where export fluxes were measured only at one depth, the global dataset provides depth-resolved information, enabling us to examine the vertical change in the Si:N ratio of sinking particulate matter and how this correlates with pH. It has long been known that the silica content of sinking particles increases with depth, as opal dissolution is less efficient than organic matter remineralization25,42. The resulting accumulation of Si relative to N can be quantified as the change in Si:N with increasing depth, that is, the slope of the relationship of depth versus Si:N (ΔSi:N, in units of m−1). Our approach is analogous to previous studies, which used vertical profiles of Si:C as a proxy for differential dissolution/remineralization of opal and organic matter, and its regional variability in the ocean24,42. We extracted all data that (I) included simultaneous measurements of Si and N, and (II) contained vertical profiles with at least three depth levels (so that ΔSi:N [m−1] can be calculated). We then calculated linear regressions for individual Si:N profiles and subsequently extracted those for which Si:N displayed a statistically significant relationship with depth (p  More