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    Population genomic signatures of the oriental fruit moth related to the Pleistocene climates

    Hewitt, G. M. Genetic consequences of climatic oscillations in the Quaternary. Philos. Trans. R. Soc. Lond. Ser. B, Biol. Sci. 359, 183–195 (2004).CAS 

    Google Scholar 
    Hewitt, G. The genetic legacy of the Quaternary ice ages. Nature 405, 907–913 (2000).CAS 
    PubMed 

    Google Scholar 
    Abellán, P., Benetti, C. J., Angus, R. B. & Ribera, I. A review of Quaternary range shifts in European aquatic Coleoptera. Glob. Ecol. Biogeogr. 20, 87–100 (2011).
    Google Scholar 
    Geber, M. A. Ecological and evolutionary limits to species geographic ranges. Am. Naturalist 178, S1–S5 (2011).
    Google Scholar 
    Miller, T. E. X. et al. Eco-evolutionary dynamics of range expansion. Ecology 101, e03139 (2020).PubMed 

    Google Scholar 
    Clark, P. U. et al. The last glacial maximum. Science 325, 710 (2009).CAS 
    PubMed 

    Google Scholar 
    Bidegaray-Batista, L. et al. Imprints of multiple glacial refugia in the Pyrenees revealed by phylogeography and palaeodistribution modelling of an endemic spider. Mol. Ecol. 25, 2046–2064 (2016).CAS 
    PubMed 

    Google Scholar 
    Stone, G. N. et al. Tournament ABC analysis of the western Palaearctic population history of an oak gall wasp, Synergus umbraculus. Mol. Ecol. 26, 6685–6703 (2017).PubMed 

    Google Scholar 
    Walton, W., Stone, G. N. & Lohse, K. Discordant Pleistocene population size histories in a guild of hymenopteran parasitoids. Mol. Ecol. https://doi.org/10.1111/mec.16074 (2021).Grant, K. M. et al. Sea-level variability over five glacial cycles. Nat. Commun. 5, 5076 (2014).CAS 
    PubMed 

    Google Scholar 
    Ye, Z., Zhu, G., Chen, P., Zhang, D. & Bu, W. Molecular data and ecological niche modelling reveal the Pleistocene history of a semi-aquatic bug (Microvelia douglasi douglasi) in East Asia. Mol. Ecol. 23, 3080–3096 (2014).CAS 
    PubMed 

    Google Scholar 
    Wei, S. J. et al. Population genetic structure and approximate Bayesian computation analyses reveal the southern origin and northward dispersal of the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) in its native range. Mol. Ecol. 24, 4094–4111 (2015).PubMed 

    Google Scholar 
    Petit, R. et al. Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300, 1563–1565 (2003).CAS 
    PubMed 

    Google Scholar 
    Hoffmann, A. A. & Sgro, C. M. Climate change and evolutionary adaptation. Nature 470, 479–485 (2011).CAS 
    PubMed 

    Google Scholar 
    Hewitt, G. M. Speciation, hybrid zones and phylogeography—or seeing genes in space and time. Mol. Ecol. 10, 537–549 (2001).CAS 
    PubMed 

    Google Scholar 
    Bradburd, G. S. & Ralph, P. L. Spatial population genetics: it’s about time. Annu. Rev. Ecol., Evol. Syst. 50, 427–449 (2019).
    Google Scholar 
    de Lafontaine, G., Ducousso, A., Lefevre, S., Magnanou, E. & Petit, R. J. Stronger spatial genetic structure in recolonized areas than in refugia in the European beech. Mol. Ecol. 22, 4397–4412 (2013).PubMed 

    Google Scholar 
    Hoban, S., Dawson, A., Robinson, J. D., Smith, A. B. & Strand, A. E. Inference of biogeographic history by formally integrating distinct lines of evidence: genetic, environmental niche and fossil. Ecography 42, 1991–2011 (2019).
    Google Scholar 
    Stone, G. N. et al. The phylogeographical clade trade: tracing the impact of human‐mediated dispersal on the colonization of northern Europe by the oak gallwasp Andricus kollari. Mol. Ecol. 16, 2768–2781 (2007).PubMed 

    Google Scholar 
    McGaughran, A., Laver, R. & Fraser, C. Evolutionary responses to warming. Trends Ecol. Evol. 36, 591–600 (2021).PubMed 

    Google Scholar 
    van Boheemen, L. A. & Hodgins, K. A. Rapid repeatable phenotypic and genomic adaptation following multiple introductions. Mol. Ecol. 29, 4102–4117 (2020).PubMed 

    Google Scholar 
    Ruegg, K. et al. Ecological genomics predicts climate vulnerability in an endangered southwestern songbird. Ecol. Lett. 21, 1085–1096 (2018).PubMed 

    Google Scholar 
    Fitzpatrick, M. C. & Keller, S. R. Ecological genomics meets community-level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation. Ecol. Lett. 18, 1–16 (2015).PubMed 

    Google Scholar 
    Sun, Y., Bossdorf, O., Grados, R. D., Liao, Z. & Müller-Schärer, H. Rapid genomic and phenotypic change in response to climate warming in a widespread plant invader. Glob. Change Biol. 26, 6511–6522 (2020).
    Google Scholar 
    Høye, T. T. Arthropods and climate change-arctic challenges and opportunities. Curr. Opin. Insect Sci. 41, 40–45 (2020).PubMed 

    Google Scholar 
    Maino, J. L., Kong, J. D., Hoffmann, A. A., Barton, M. G. & Kearney, M. R. Mechanistic models for predicting insect responses to climate change. Curr. Opin. Insect Sci. 17, 81–86 (2016).PubMed 

    Google Scholar 
    Hoffmann, A. A., Weeks, A. R. & Sgrò, C. M. Opportunities and challenges in assessing climate change vulnerability through genomics. Cell 184, 1420–1425 (2021).CAS 
    PubMed 

    Google Scholar 
    van der Geest, L. P. S. & Evenhuis, H. H. World Crop Pests 5: Tortricid Pests Their Biology, Natural Enemies and Control. Vol. 5 (Elsevier, 1991).Wan, F. H. et al. A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance. Nat. Commun. 10, https://doi.org/10.1038/s41467-41019-12175-41469 (2019).Kirk, H., Dorn, S. & Mazzi, D. Worldwide population genetic structure of the oriental fruit moth (Grapholita molesta), a globally invasive pest. BMC Ecol. 13, 12 (2013).PubMed 
    PubMed Central 

    Google Scholar 
    Torriani, M. V., Mazzi, D., Hein, S. & Dorn, S. Structured populations of the oriental fruit moth in an agricultural ecosystem. Mol. Ecol. 19, 2651–2660 (2010).CAS 
    PubMed 

    Google Scholar 
    Song, W. et al. Multiple refugia from penultimate glaciations in East Asia demonstrated by phylogeography and ecological modelling of an insect pest. BMC Evolut. Biol. 18, 152 (2018).
    Google Scholar 
    SuomMainen, E. in Chromosome Today Vol. 2 (eds. Darlington, C. D. & Lewis, K. R.) 122–138 (Plenum Press, 1969).Nguyen, P. et al. Neo-sex chromosomes and adaptive potential in tortricid pests. Proc. Natl Acad. Sci. USA 110, 6931–6936 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Fuková, I., Nguyen, P. & Marec, F. E. Codling moth cytogenetics: karyotype, chromosomal location of rDNA, and molecular differentiation of sex chromosomes. Genome 48, 1083–1092 (2005).PubMed 

    Google Scholar 
    Cao, L. J. et al. Local climate adaptation and gene flow in the native range of two co-occurring fruit moths with contrasting invasiveness. Mol. Ecol. 30, 4204–4219 (2021).CAS 
    PubMed 

    Google Scholar 
    Caprioli, M. et al. Clock gene variation is associated with breeding phenology and maybe under directional selection in the migratory barn swallow. PLoS ONE 7, 7 (2012).
    Google Scholar 
    Krabbenhoft, T. J. & Turner, T. F. clock gene evolution: seasonal timing, phylogenetic signal, or functional constraint? J. Heredity 105, 407–415 (2014).
    Google Scholar 
    Zhang, J. et al. Comparative transcriptomes analysis of the wing disc between two silkworm strains with different size of wings. PLoS ONE 12, e0179560 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    Zhu, Q. S., Arakane, Y., Beeman, R. W., Kramer, K. J. & Muthukrishnan, S. Functional specialization among insect chitinase family genes revealed by RNA interference. Proc. Natl Acad. Sci. USA 105, 6650–6655 (2008).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chen, C., Yang, H., Tang, B., Yang, W.-J. & Jin, D.-C. Identification and functional analysis of chitinase 7 gene in white-backed planthopper, Sogatella furcifera. Comp. Biochem. Physiol. B-Biochem. Mol. Biol. 208, 19–28 (2017).PubMed 

    Google Scholar 
    Yang, X. et al. Characterization and functional analysis of chitinase family genes involved in nymph-adult transition of Sogatella furcifera. Insect Sci. 28, 901–916 (2021).CAS 
    PubMed 

    Google Scholar 
    Pesch, Y. Y., Riedel, D., Patil, K. R., Loch, G. & Behr, M. Chitinases and Imaginal disc growth factors organize the extracellular matrix formation at barrier tissues in insects. Sci. Rep. 6, 18340 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Charron, Y. et al. The serpin Spn5 is essential for wing expansion in Drosophila melanogaster. Int. J. Dev. Biol. 52, 933–942 (2008).CAS 
    PubMed 

    Google Scholar 
    Charlesworth, B., Campos, J. L. & Jackson, B. C. Faster-X evolution: theory and evidence from Drosophila. Mol. Ecol. 27, 3753–3771 (2018).CAS 
    PubMed 

    Google Scholar 
    Meisel, R. P. & Connallon, T. The faster-X effect: integrating theory and data. Trends Genet. 29, 537–544 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sayres, M. A. W. Genetic diversity on the sex chromosomes. Genome Biol. Evol. 10, 1064–1078 (2018).
    Google Scholar 
    Ellegren, H. The different levels of genetic diversity in sex chromosomes and autosomes. Trends Genet. 25, 278–284 (2009).CAS 
    PubMed 

    Google Scholar 
    Ellegren, H. & Galtier, N. Determinants of genetic diversity. Nat. Rev. Genet. 17, 422–433 (2016).CAS 
    PubMed 

    Google Scholar 
    Pool, J. E. et al. Population genomics of sub-saharan Drosophila melanogaster: African diversity and non-african admixture. PLoS Genet. 8, e1003080–e1003080 (2012).PubMed 
    PubMed Central 

    Google Scholar 
    Sackton, T. B. et al. Positive selection drives faster-Z evolution in silkmoths. Evolution 68, 2331–2342 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    Fraisse, C., Picard, M. A. L. & Vicoso, B. The deep conservation of the Lepidoptera Z chromosome suggests a non-canonical origin of the W. Nat. Commun. 8, https://doi.org/10.1038/s41467-017-01663-5 (2017).Sahara, K., Yoshido, A. & Traut, W. Sex chromosome evolution in moths and butterflies. Chromosome Res. 20, 83–94 (2012).CAS 
    PubMed 

    Google Scholar 
    Ma, C. et al. Mitochondrial genomes reveal the global phylogeography and dispersal routes of the migratory locust. Mol. Ecol. 21, 4344–4358 (2012).PubMed 

    Google Scholar 
    Zhang, B., Edwards, O., Kang, L. & Fuller, S. Russian wheat aphids (Diuraphis noxia) in China: native range expansion or recent introduction? Mol. Ecol. 21, 2130–2144 (2012).CAS 
    PubMed 

    Google Scholar 
    Provan, J. & Bennett, K. Phylogeographic insights into cryptic glacial refugia. Trends Ecol. Evol. 23, 564–571 (2008).PubMed 

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

    Google Scholar 
    Zhang, S. P., Xu, X. L., Wang, W. W., Yang, W. Y. & Liang, W. Clock gene is associated with individual variation in the activation of reproductive endocrine and behavior of Asian short toed lark. Sci. Rep. 7, 8 (2017).CAS 

    Google Scholar 
    Liedvogel, M., Szulkin, M., Knowles, S. C. L., Wood, M. J. & Sheldon, B. C. Phenotypic correlates of Clock gene variation in a wild blue tit population: evidence for a role in seasonal timing of reproduction. Mol. Ecol. 18, 2444–2456 (2009).PubMed 

    Google Scholar 
    Saino, N. et al. Migration phenology and breeding success are predicted by methylation of a photoperiodic gene in the barn swallow. Sci. Rep. 7, 10 (2017).
    Google Scholar 
    e Silva, O. A. B. N., Bernardi, D., Botton, M. & Garcia, M. S. Biological characteristics of Grapholita molesta (Lepidoptera: Tortricidae) induced to diapause in laboratory. J. Insect Sci. 14, 217 (2014).
    Google Scholar 
    Renfree, M. B. & Shaw, G. Diapause. Annu. Rev. Physiol. 62, 353–375 (2000).CAS 
    PubMed 

    Google Scholar 
    Ochocki, B. M. & Miller, T. E. X. Rapid evolution of dispersal ability makes biological invasions faster and more variable. Nat. Commun. 8, 8 (2017).
    Google Scholar 
    Ochocki, B. M., Saltz, J. B. & Miller, T. E. X. Demography-dispersal trait correlations modify the eco-evolutionary dynamics of range expansion. Am. Naturalist 195, 231–246 (2020).
    Google Scholar 
    Travis, J. M. J. & Dytham, C. Dispersal evolution during invasions. Evolut. Ecol. Res. 4, 1119–1129 (2002).
    Google Scholar 
    Phillips, B. L., Brown, G. P. & Shine, R. Life-history evolution in range-shifting populations. Ecology 91, 1617–1627 (2010).PubMed 

    Google Scholar 
    Shine, R., Brown, G. P. & Phillips, B. L. An evolutionary process that assembles phenotypes through space rather than through time. Proc. Natl Acad. Sci. USA 108, 5708–5711 (2011).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Perkins, T. A., Phillips, B. L., Baskett, M. L. & Hastings, A. Evolution of dispersal and life history interact to drive accelerating spread of an invasive species. Ecol. Lett. 16, 1079–1087 (2013).PubMed 

    Google Scholar 
    Phillips, B. L. & Perkins, T. A. Spatial sorting as the spatial analogue of natural selection. Theor. Ecol. 12, 155–163 (2019).
    Google Scholar 
    Angert, A. L., Bontrager, M. G. & Ågren, J. What do we really know about adaptation at range edges? Annu. Rev. Ecol., Evol. Syst. 51, 341–361 (2020).
    Google Scholar 
    Hoffmann, A. A. & Rieseberg, L. H. Revisiting the impact of inversions in evolution: From population genetic markers to drivers of adaptive shifts and speciation? Annu. Rev. Ecol. Evol. Syst. 39, 21–42 (2008).PubMed 
    PubMed Central 

    Google Scholar 
    Wellenreuther, M. & Bernatchez, L. Eco-evolutionary genomics of chromosomal inversions. Trends Ecol. Evol. 33, 427–440 (2018).PubMed 

    Google Scholar 
    Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Vurture, G. W. et al. GenomeScope: Fast reference-free genome profiling from short reads. Bioinformatics (Oxford, England) 33, https://doi.org/10.1093/bioinformatics/btx153 (2017).Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017).CAS 
    PubMed 
    PubMed Central 

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

    Google Scholar 
    Roach, M. J., Schmidt, S. A. & Borneman, A. R. Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinforma. 19, 460 (2018).CAS 

    Google Scholar 
    Neva, C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).
    Google Scholar 
    Dudchenko et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).CAS 
    PubMed 

    Google Scholar 
    Cheng, T. et al. Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest. Nat. Ecol. Evol. 1, 1747–1756 (2017).PubMed 

    Google Scholar 
    Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Tarailo-Graovac, M. & Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinforma. 25, unit 4.10 (2009).
    Google Scholar 
    Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lagesen, K. et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108 (2007).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Cantarel, B. L. et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18, 188–196 (2008).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Korf, I. Gene finding in novel genomes. BMC Bioinforma. 5, 59 (2004).
    Google Scholar 
    Stanke, M. & Waack, S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19, ii215–ii225 (2003).PubMed 

    Google Scholar 
    Brian, J. H. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654–5666 (2003).
    Google Scholar 
    Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).PubMed 
    PubMed Central 

    Google Scholar 
    Huerta-Cepas, J. et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol. Biol. Evol. 34, 2115–2122 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309–D314 (2019).CAS 
    PubMed 

    Google Scholar 
    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).PubMed 
    PubMed Central 

    Google Scholar 
    McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Knaus, B. J. & Grünwald, N. J. vcfr: a package to manipulate and visualize variant call format data in R. Mol. Ecol. Resour. 17, 44–53 (2017).CAS 
    PubMed 

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

    Google Scholar 
    Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. (Austin) 6, 80–92 (2012).CAS 

    Google Scholar 
    Zhang, C., Dong, S. S., Xu, J. Y., He, W. M. & Yang, T. L. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics 35, 1786–1788 (2019).CAS 
    PubMed 

    Google Scholar 
    Gautier, M. & Vitalis, R. Inferring Population Histories Using Genome-Wide Allele Frequency Data. Mol. Biol. Evol. 30, 654–668 (2013).CAS 
    PubMed 

    Google Scholar 
    Terhorst, J., Kamm, J. A. & Song, Y. S. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nat. Genet. 49, 303–309 (2017).CAS 
    PubMed 

    Google Scholar 
    Keightley, P. D. et al. Estimation of the spontaneous mutation rate in Heliconius melpomene. Mol. Biol. Evol. 32, 239–243 (2015).CAS 
    PubMed 

    Google Scholar 
    Ahn, J. J., Yang, C. Y. & Jung, C. Model of Grapholita molesta spring emergence in pear orchards based on statistical information criteria. J. Asia-Pac. Entomol. 15, 589–593 (2012).
    Google Scholar 
    Amat, C., Bosch-Serra, D., Avilla, J. & Escudero Colomar, L. A. Different Population Phenologies of Grapholita molesta (Busck) in Two Hosts and Two Nearby Regions in the NE of Spain. Insects 12, https://doi.org/10.3390/insects12070612 (2021).Li, H. & Ralph, P. Local PCA shows how the effect of population structure differs along the genome. Genetics 211, 289–304 (2019).CAS 
    PubMed 

    Google Scholar 
    Todesco, M. et al. Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature 584, 602–607 (2020).CAS 
    PubMed 

    Google Scholar 
    Yu, G., Wang, L.-G., Han, Y. & He, Q.-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics 16, 284–287 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wei, S. J. et al. Population genomic signatures of the oriental fruit moth related to the Pleistocene climates. Dryad Digital Repository. https://doi.org/10.5061/dryad.6wwpzgmzm (2021). More

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    Settling moths are the vital component of pollination in Himalayan ecosystem of North-East India, pollen transfer network approach revealed

    Potts, S. G. et al. Global pollinator declines: Trends, impacts and drivers. Trends Ecol. Evol. 25, 345–353 (2010).PubMed 

    Google Scholar 
    Kearns, C. A., Inouye, D. W. & Waser, N. M. ENDANGERED MUTUALISMS: The conservation of plant-pollinator interactions. Annu. Rev. Ecol. Syst. 29, 83–112 (1998).
    Google Scholar 
    Ollerton, J., Winfree, R. & Tarrant, S. How many flowering plants are pollinated by animals?. Oikos 120, 321–326 (2011).
    Google Scholar 
    Labandeira, C. C. A paleobiologic perspective on plant–insect interactions. Curr. Opin. Plant Biol. 16, 414–421 (2013).PubMed 

    Google Scholar 
    Faegri, K. & Van Der Pijl, L. Principles of Pollination Ecology. (Elsevier Science, 2014).Bhutia, J. & Sharma, B. Diversity of Pollinators/ Visitors in Namchi, South Sikkim, India. 487–498 (2020).Torres-Vanegas, F. et al. Tropical deforestation reduces plant mating quality by shifting the functional composition of pollinator communities. J. Ecol. 109, 1730–1746 (2021).
    Google Scholar 
    Macgregor, C. J., Pocock, M. J. O., Fox, R. & Evans, D. M. Pollination by nocturnal Lepidoptera, and the effects of light pollution: A review. Ecol. Entomol. 40, 187–198 (2015).PubMed 

    Google Scholar 
    Macgregor, C. J., Williams, J. H., Bell, J. R. & Thomas, C. D. Moth biomass increases and decreases over 50 years in Britain. Nat. Ecol. Evol. 3, 1645–1649 (2019).PubMed 

    Google Scholar 
    Chamorro, S., Heleno, R., Olesen, J. M., McMullen, C. K. & Traveset, A. Pollination patterns and plant breeding systems in the Galápagos: A review. Ann. Bot. 110, 1489–1501 (2012).PubMed 
    PubMed Central 

    Google Scholar 
    Ramirez, N. Pollination specialization and time of pollination on a tropical Venezuelan plain: Variations in time and space. Bot. J. Linn. Soc. 145, 1–16 (2004).
    Google Scholar 
    Walton, R. E., Sayer, C. D., Bennion, H. & Axmacher, J. C. Nocturnal pollinators strongly contribute to pollen transport of wild flowers in an agricultural landscape. Biol. Lett. 16, 20190877 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    Young, H. J. Diurnal and nocturnal pollination of Silene alba (Caryophyllaceae). Am. J. Bot. 89, 433–440 (2002).PubMed 

    Google Scholar 
    Maeda, M., Maguchi, S., Nakamaru, Y., Takagi, D. & Fukuda, S. Prospective study of pollen dispersal prediction and identifying the usefulness of different parameters. Nihon Jibiinkoka Gakkai Kaiho 109, 455–460 (2006).PubMed 

    Google Scholar 
    Bertin, R. I. & Willson, M. F. Effectiveness of diurnal and nocturnal pollination of two milkweeds. Can. J. Bot. 58, 1744–1746 (1980).
    Google Scholar 
    Morse, D. H. & Fritz, R. S. Contributions of diurnal and nocturnal insects to the pollination of common milkweed (Asclepias syriaca L.) in a pollen-limited system. Oecologia 60, 190–197 (1983).Jennersten, O. & Morse, D. H. The quality of pollination by diurnal and nocturnal insects visiting common milkweed Asclepias syriaca. Am. Midl. Nat. 125, 18 (1991).
    Google Scholar 
    Miyake, T. & Yahara, T. Why does the flower of Lonicera japonica open at dusk?. Can. J. Bot. 76, 1806–1811 (1998).
    Google Scholar 
    Atwater, M. M. Diversity and nectar hosts of flower-settling moths within a Florida sandhill ecosystem. J. Nat. Hist. 47, 2719–2734 (2013).
    Google Scholar 
    Grant, V. & Grant, K. A. Hawkmoth pollination of Mirabilis longiflora (Nyctaginaceae). Proc. Natl. Acad. Sci. 80, 1298–1299 (1983).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Willmott, A. P. & Burquez, A. The pollination of Merremia palmeri (Convolvulaceae): Can Hawk moths be trusted?. Am. J. Bot. 83, 1050 (1996).
    Google Scholar 
    Wasserthal, L. T. The Pollinators of the Malagasy Star Orchids Angraecum sesquipedale, A. sororium and A. compactum and the Evolution of Extremely Long Spurs by Pollinator Shift. Bot. Acta 110, 343–359 (1997).Miyake, T., Yamaoka, R. & Yahara, T. Floral scents of hawkmoth-pollinated flowers in Japan. J. Plant Res. 111, 199–205 (1998).CAS 

    Google Scholar 
    Luyt, R. & Johnson, S. D. Hawkmoth pollination of the African epiphytic orchid Mystacidium venosum, with special reference to flower and pollen longevity. Plant Syst. Evol. 228, 49–62 (2001).
    Google Scholar 
    Rust, R. W., Vaissire, B. E. & Westrich, P. Pollinator biodiversity and floral resource use in Ecballium elaterium (Cucurbitaceae), a Mediterranean endemic. Apidologie 34, 29–42 (2003).
    Google Scholar 
    Jürgens, A., Witt, T. & Gottsberger, G. Flower scent composition in Dianthus and Saponaria species (Caryophyllaceae) and its relevance for pollination biology and taxonomy. Biochem. Syst. Ecol. 31, 345–357 (2003).
    Google Scholar 
    Oliveira, P. E., Gibbs, P. E. & Barbosa, A. A. Moth pollination of woody species in the Cerrados of Central Brazil: A case of so much owed to so few?. Plant Syst. Evol. 245, 41–54 (2004).
    Google Scholar 
    Morimoto, Y., Gikungu, M. & Maundu, P. Pollinators of the bottle gourd (Lagenaria siceraria) observed in Kenya. Int. J. Trop. Insect Sci. 24, (2004).Willmer, P. Pollination and floral ecology. (Princeton University Press, 2011). https://doi.org/10.1515/9781400838943.Mitchell, T. C., Dötterl, S. & Schaefer, H. Hawk-moth pollination and elaborate petals in Cucurbitaceae: The case of the Caribbean endemic Linnaeosicyos amara. Flora Morphol. Distrib. Funct. Ecol. Plants 216, 50–56 (2015).Chakraborty, P., Smith, B. & Basu, P. Pollen transport in the dark: Hawkmoths prefer non crop plants to crop plants in an agricultural landscape. Proc. Zool. Soc. 71, 299–303 (2018).
    Google Scholar 
    Proctor, M., Yeo, P. & Lack, A. The natural history of pollination. (Timber Press, 1996).Funamoto, D. & Sugiura, S. Settling moths as potential pollinators of Uncaria rhynchophylla (Rubiaceae). Eur. J. Entomol. 113, 497–501 (2016).
    Google Scholar 
    Funamoto, D. & Sugiura, S. Relative importance of diurnal and nocturnal pollinators for reproduction in the early spring flowering shrub Stachyurus praecox (Stachyuraceae). Plant Species Biol. 36, 94–101 (2021).
    Google Scholar 
    Buxton, M. N., Anderson, B. J. & Lord, J. M. The secret service—analysis of the available knowledge on moths as pollinators in New Zealand / Te pepe huna—he tātarihaka o te mātauraka rakahau ki kā pepe hai whakaaiai ki Aotearoa me Te Waipounamu. N. Z. J. Ecol. 42, 1–9 (2018).
    Google Scholar 
    Hahn, M. & Brühl, C. A. The secret pollinators: An overview of moth pollination with a focus on Europe and North America. Arthropod-Plant Interact. 10, 21–28 (2016).
    Google Scholar 
    Makholela, T. & Manning, J. C. First report of moth pollination in Struthiola ciliata (Thymelaeaceae) in southern Africa. South Afr. J. Bot. 72, 597–603 (2006).CAS 

    Google Scholar 
    Okamoto, T., Kawakita, A. & Kato, M. Floral adaptations to nocturnal moth pollination in Diplomorpha (Thymelaeaceae). Plant Species Biol. 23, 192–201 (2008).
    Google Scholar 
    Paul, M. Impact of urbanization on moth (Insecta: Lepidoptera: Heterocera) diversity across different urban landscapes of Delhi India. Acta Ecol. Sin. 41, 204–209 (2021).
    Google Scholar 
    Subhakar, G. & Sreedevi, K. Nocturnal insect pollinator diversity in bottle gourd and ridge gourd in southern Andhra Pradesh. Curr. Biot. 9, 137–144 (2015).
    Google Scholar 
    Chakraborty, P., Chatterjee, S., Smith, B. M. & Basu, P. Seasonal dynamics of plant pollinator networks in agricultural landscapes: How important is connector species identity in the network?. Oecologia 196, 825–837 (2021).ADS 
    PubMed 

    Google Scholar 
    Chakraborty, P., Mukherjee, P. A., Laha, S. & Gupta, S. K. The influence of floral traits on insect foraging behaviour on medicinal plants in an urban garden of eastern India. J. Trop. Ecol. 37, 200–207 (2021).CAS 

    Google Scholar 
    King, C., Ballantyne, G. & Willmer, P. G. Why flower visitation is a poor proxy for pollination: Measuring single-visit pollen deposition, with implications for pollination networks and conservation. Methods Ecol. Evol. 4, 811–818 (2013).
    Google Scholar 
    Devoto, M., Bailey, S., Craze, P. & Memmott, J. Understanding and planning ecological restoration of plant–pollinator networks. Ecol. Lett. 15, 319–328 (2012).PubMed 

    Google Scholar 
    Saunders, M. E. Insect pollinators collect pollen from wind-pollinated plants: Implications for pollination ecology and sustainable agriculture. Insect Conserv. Divers. 11, 13–31 (2018).
    Google Scholar 
    Ssymank, A., Kearns, C. A., Pape, T. & Thompson, F. C. Pollinating Flies (Diptera): A major contribution to plant diversity and agricultural production. Biodiversity 9, 86–89 (2008).
    Google Scholar 
    Rader, R. et al. Non-bee insects are important contributors to global crop pollination. Proc. Natl. Acad. Sci. 113, 146–151 (2016).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Garibaldi, L. A. et al. Wild pollinators enhance fruit set of crops regardless of honey bee abundance. Science 339, 1608–1611 (2013).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Gong, Y.-B. et al. Wind or insect pollination? Ambophily in a subtropical gymnosperm Gnetum parvifolium (Gnetales): Ambophily in Gnetum. Plant Species Biol. 31, 272–279 (2016).
    Google Scholar 
    Niklas, K. J. A Biophysical Perspective on the Pollination Biology of Ephedra nevadensis and E. trifurca. Bot. Rev. 81, 28–41 (2015).Kato, M., Inoue, T. & Nagamitsu, T. Pollination biology of Gnetum (Gnetaceae) in a LOWLAND MIXED DIPTEROCARP forest in Sarawak. Am. J. Bot. 82, 862–868 (1995).
    Google Scholar 
    Celedón-Neghme, C., Santamaría, L. & González-Teuber, M. The role of pollination drops in animal pollination in the Mediterranean gymnosperm Ephedra fragilis (Gnetales). Plant Ecol. 217, 1545–1552 (2016).
    Google Scholar 
    Costa, A. C. G. & Machado, I. C. Flowering dynamics and pollination system of the sedge Rhynchospora ciliata (Vahl) Kükenth (Cyperaceae): does ambophily enhance its reproductive success?: Ambophily in Rhynchospora ciliata. Plant Biol. 14, 881–887 (2012).CAS 
    PubMed 

    Google Scholar 
    Huang, L. et al. Beta diversity partitioning and drivers of variations in fish assemblages in a headwater stream: Lijiang River China. Water 11, 680 (2019).CAS 

    Google Scholar 
    Schneider, D., Wink, M., Sporer, F. & Lounibos, P. Cycads: their evolution, toxins, herbivores and insect pollinators. Naturwissenschaften 89, 281–294 (2002).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Wilson, G. W. Insect Pollination in the Cycad Genus Bowenia Hook, ex Hook. f. (Stangeriaceae)1. Biotropica 34, 438–441 (2002).Terry, L. I. et al. Pollination of Australian Macrozamia cycads (Zamiaceae): effectiveness and behavior of specialist vectors in a dependent mutualism. Am. J. Bot. 92, 931–940 (2005).PubMed 

    Google Scholar 
    Intachat, J., Holloway, J. D. & Staines, H. Effects of weather and phenology on the abundance and diversity of geometroid moths in a natural Malaysian tropical rain forest. J. Trop. Ecol. 17, 411–429 (2001).
    Google Scholar 
    Shaheen, H., Ullah, Z., Khan, S. M. & Harper, D. M. Species composition and community structure of western Himalayan moist temperate forests in Kashmir. For. Ecol. Manag. 278, 138–145 (2012).
    Google Scholar 
    Shaheen, H., Mallik, N. M. & Dar, M. E. U. I. Species composition and community structure of subtropical forest stands in western himalayan foothills of kashmir. Pak. J. Bot. 47, 2151–2160 (2015).CAS 

    Google Scholar 
    Bhutia, Y., Gudasalamani, R., Ganesan, R. & Saha, S. Assessing forest structure and composition along the altitudinal gradient in the State of Sikkim, Eastern Himalayas India. Forests 10, 633 (2019).
    Google Scholar 
    Dar, J. A. & Sundarapandian, S. Variation of biomass and carbon pools with forest type in temperate forests of Kashmir Himalaya India. Environ. Monit. Assess. 187, 55 (2015).PubMed 

    Google Scholar 
    Kandel, P. et al. Plant diversity of the Kangchenjunga Landscape, Eastern Himalayas. Plant Divers. 41, 153–165 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    Leonhardt, S. D. & Blüthgen, N. A sticky affair: Resin collection by bornean stingless bees: resin collection by stingless bees. Biotropica 41, 730–736 (2009).
    Google Scholar 
    Nyeko, P., Edwards-Jones, G. & Day, R. K. Honeybee, Apis mellifera (Hymenoptera: Apidae), leaf damage on Alnus species in Uganda: A blessing or curse in agroforestry?. Bull. Entomol. Res. 92, 405–412 (2002).CAS 
    PubMed 

    Google Scholar 
    Koch, H., Corcoran, C. & Jonker, M. Honeydew collecting in malagasy stingless bees (Hymenoptera: Apidae: Meliponini) and observations on competition with invasive ants. Afr. Entomol. 19, 36–41 (2011).
    Google Scholar 
    Santas, L. A. Insects producing honeydew exploited by bees in Greece. Apidologie 14, 93–103 (1983).
    Google Scholar 
    Banza, P., Belo, A. D. F. & Evans, D. M. The structure and robustness of nocturnal Lepidopteran pollen-transfer networks in a Biodiversity Hotspot. Insect Conserv. Divers. 8, 538–546 (2015).
    Google Scholar 
    Walton, R. E., Sayer, C. D., Bennion, H. & Axmacher, J. C. Improving the pollinator pantry: Restoration and management of open farmland ponds enhances the complexity of plant-pollinator networks. Agric. Ecosyst. Environ. 320, 107611 (2021).Dormann, C. F. et al. bipartite: Visualising Bipartite Networks and Calculating Some (Ecological) Indices. (2021).Karmawati, E. & Tobing, S. L. Laboratory biology of Achaea janata L. castor large semi-loopers. Ind. Crops Res. J. 1, 37–42 (1988).
    Google Scholar 
    Labouche, A. & Bernasconi, G. Cost limitation through constrained oviposition site in a plant-pollinator/seed predator mutualism. Funct. Ecol. 27, 509–521 (2013).
    Google Scholar 
    Ramakrishna & Alfred, J. R. B. Faunal resources of India. (Zoological Survey of India, 2007).Lees, D. C. & Zilli, A. Moths: Their Biology, Diversity and Evolution | NHBS Field Guides & Natural History. (London Natural History Museum, 2020).Holloway, J. D. Moths of Borneo. (Malayan Nature Journal, 2001).Plant diversity in the Himalaya hotspot region: a volume to celebrate the completion of university service of Dr. Abhaya Prasad Das. (Bishen Singh Mahendra Pal Singh, 2018).Hampson, G. F. The Fauna of British India, including Ceylon and Burma. vol. 1 1–560 (Taylor and Francis, 1892).Hampson, G. F. The Fauna of British India, including Ceylon and Burma. vol. 2 1–640 (Taylor and Francis, 1894).Hampson, G. F. The Fauna of British India, including Ceylon and Burma. vol. 3 1–582 (Taylor and Francis, 1895).Hampson, G. F. The Fauna of British India, including Ceylon and Burma. vol. 4 1–632 (Taylor and Francis, 1896).Kirti, J. S. & Singh, N. Arctiid moths of India. (Nature Books India, 2015).Kirti, J. S. & Singh, N. Arctiid moths of India. vol. 2 (Nature Books India, 2016).Moths of India. https://www.mothsofindia.org/.iNaturalist. iNaturalist. iNaturalist https://www.inaturalist.org/users/sign_in.Nieukerken, E. J. V. et al. Order Lepidoptera Linnaeus, 1758. In : Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 212–221 (2011).PalDat. https://www.paldat.org/.Global Pollen Project. Global Pollen Project. https://globalpollenproject.org/.Agashe, S. N. & Caulton, E. Pollen and spores: applications with special emphasis on aerobiology and allergy. (Science Publishers, 2009).Bhattacharya, K. et al. A textbook of palynology. (2014).Stephen, A. Pollen—A microscopic wonder of plant kingdom. Int. J. Adv. Res. Biol. Sci. 1, 45–62 (2014).
    Google Scholar 
    Halbritter, H. et al. Illustrated Pollen Terminology. (Springer International Publishing, 2018). doi:https://doi.org/10.1007/978-3-319-71365-6.Dunne, J. A., Williams, R. J. & Martinez, N. D. Food-web structure and network theory: The role of connectance and size. Proc. Natl. Acad. Sci. 99, 12917–12922 (2002).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Rodriguez-Girones, M. A. & Santamaria, L. A new algorithm to calculate the nestedness temperature of presence-absence matrices. J. Biogeogr. 33, 924–935 (2006).
    Google Scholar 
    Blüthgen, N., Menzel, F. & Blüthgen, N. Measuring specialization in species interaction networks. BMC Ecol. 6, 9 (2006).PubMed 
    PubMed Central 

    Google Scholar 
    Tylianakis, J. M., Tscharntke, T. & Lewis, O. T. Habitat modification alters the structure of tropical host–parasitoid food webs. Nature 445, 202–205 (2007).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Blüthgen, N., Menzel, F., Hovestadt, T., Fiala, B. & Blüthgen, N. Specialization, constraints, and conflicting interests in mutualistic networks. Curr. Biol. 17, 341–346 (2007).PubMed 

    Google Scholar 
    Bersier, L.-F., Banašek-Richter, C. & Cattin, M.-F. Quantitative descriptors of food-web matrices. Ecology 83, 2394–2407 (2002).MATH 

    Google Scholar 
    Poisot, T., Lepennetier, G., Martinez, E., Ramsayer, J. & Hochberg, M. E. Resource availability affects the structure of a natural bacteria–bacteriophage community. Biol. Lett. 7, 201–204 (2011).PubMed 

    Google Scholar  More

  • in

    Local adaptation to climate anomalies relates to species phylogeny

    Verdura, J. et al. Biodiversity loss in a Mediterranean ecosystem due to an extreme warming event unveils the role of an engineering gorgonian species. Sci. Rep. 9, 1–11 (2019).CAS 

    Google Scholar 
    Pandori, L. L. M. & Sorte, C. J. B. The weakest link: sensitivity to climate extremes across life stages of marine invertebrates. Oikos 128, 621–629 (2019).
    Google Scholar 
    Palmer, G. et al. Climate change, climatic variation and extreme biological responses. Philos. Trans. R. Soc. B Biol. Sci. 372, 20160144 (2017).Altwegg, R., Visser, V., Bailey, L. D. & Erni, B. Learning from single extreme events. Philos. Trans. R. Soc. B Biol. Sci. 372, 20160141 (2017).
    Google Scholar 
    McDermott Long, O. et al. Sensitivity of UK butterflies to local climatic extremes: which life stages are most at risk? J. Anim. Ecol. 86, 108–116 (2017).PubMed 

    Google Scholar 
    Jentsch, A., Kreyling, J. & Beierkuhnlein, C. A new generation of climate‐change experiments: events, not trends. Front. Ecol. Environ. 5, 365–374 (2007).
    Google Scholar 
    Suggitt, A. J. et al. Habitat associations of species show consistent but weak responses to climate. Biol. Lett. 8, 590–593 (2012).PubMed 
    PubMed Central 

    Google Scholar 
    Trisos, C. H., Merow, C. & Pigot, A. L. The projected timing of abrupt ecological disruption from climate change. Nature 580, 496–501 (2020).CAS 
    PubMed 

    Google Scholar 
    Valladares, F. et al. The effects of phenotypic plasticity and local adaptation on forecasts of species range shifts under climate change. Ecol. Lett. 17, 1351–1364 (2014).PubMed 

    Google Scholar 
    Bush, A. et al. Incorporating evolutionary adaptation in species distribution modelling reduces projected vulnerability to climate change. Ecol. Lett. 19, 1468–1478 (2016).PubMed 

    Google Scholar 
    Stephens, P. A. et al. Consistent response of bird populations to climate change on two continents. Science 352, 84–87 (2016).CAS 
    PubMed 

    Google Scholar 
    Kerr, J. T. et al. Climate change impacts on bumblebees converge across continents. Science 349, 177–180 (2015).CAS 
    PubMed 

    Google Scholar 
    Roy, D. B. et al. Similarities in butterfly emergence dates among populations suggest local adaptation to climate. Glob. Chang. Biol. 21, 3313–3322 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    Titeux, N. et al. The need for large-scale distribution data to estimate regional changes in species richness under future climate change. Divers. Distrib. 23, 1393–1407 (2017).
    Google Scholar 
    Haeler, E., Fiedler, K. & Grill, A. What prolongs a butterfly’s life?: trade-offs between dormancy, fecundity and body size. PLoS One 9, e111955 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    Gonzalez-Suarez, M., Gomez, A. & Revilla, E. Which intrinsic traits predict vulnerability to extinction depends on the actual threatening processes. Ecosphere 4, 1–16 (2013).
    Google Scholar 
    Pacifici, M. et al. Species’ traits influenced their response to recent climate change. Nat. Clim. Chang. 7, 205–208 (2017).
    Google Scholar 
    Kingsolver, J. G. & Watt, W. B. Thermoregulatory strategies in Colias butterflies: thermal stress and the limits to adaptation in temporally varying environments (Colorado). Am. Nat. 121, 32–55 (1983).
    Google Scholar 
    MacLean, H. J., Higgins, J. K., Buckley, L. B. & Kingsolver, J. G. Morphological and physiological determinants of local adaptation to climate in Rocky Mountain butterflies. Conserv. Physiol. 4, 1 (2016).Kingsolver, J. G. & Wiernasz, D. C. Seasonal polyphenism in wing-melanin pattern and thermoregulatory adaptation in Pieris butterflies. Am. Nat. 137, 816–830 (1991).
    Google Scholar 
    Herrando, S. et al. Contrasting impacts of precipitation on Mediterranean birds and butterflies. Sci. Rep. 9, 1–7 (2019).CAS 

    Google Scholar 
    Thomas, J. A. Monitoring change in the abundance and distribution of insects using butterflies and other indicator groups. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 360, 339–357 (2005).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Roy, D. B., Rothery, P., Moss, D., Pollard, E. & Thomas, J. A. Butterfly numbers and weather: predicting historical trends in abundance and the future effects of climate change. J. Anim. Ecol. 70, 201–217 (2008).
    Google Scholar 
    Pöyry, J., Luoto, M., Heikkinen, R. K., Kuussaari, M. & Saarinen, K. Species traits explain recent range shifts of Finnish butterflies. Glob. Chang. Biol. 15, 732–743 (2009).
    Google Scholar 
    Devictor, V. et al. Differences in the climatic debts of birds and butterflies at a continental scale. Nat. Clim. Chang. 2, 121–124 (2012).
    Google Scholar 
    Krauss, J. et al. Habitat fragmentation causes immediate and time-delayed biodiversity loss at different trophic levels. Ecol. Lett. 13, 597–605 (2010).PubMed 
    PubMed Central 

    Google Scholar 
    Eskildsen, A. et al. Ecological specialization matters: long-term trends in butterfly species richness and assemblage composition depend on multiple functional traits. Divers. Distrib. 21, 792–802 (2015).
    Google Scholar 
    Pollard, E. A method for assessing changes in the abundance of butterflies. Biol. Conserv. 12, 115–134 (1977).
    Google Scholar 
    Schmucki, R. et al. A regionally informed abundance index for supporting integrative analyses across butterfly monitoring schemes. J. Appl. Ecol. 53, 501–510 (2016).
    Google Scholar 
    Pollard, E., Lakhani, K. H. & Rothery, P. The detection of density-dependence from a series of annual censuses. Ecology 68, 2046–2055 (1987).CAS 
    PubMed 

    Google Scholar 
    Dooley, C. A., Bonsall, M. B., Brereton, T. & Oliver, T. Spatial variation in the magnitude and functional form of density-dependent processes on the large skipper butterfly Ochlodes sylvanus. Ecol. Entomol. 38, 608–616 (2013).
    Google Scholar 
    Rothery, P., Newton, I., Dale, L. & Wesolowski, T. Testing for density dependence allowing for weather effects. Oecologia 112, 518–523 (1997).PubMed 

    Google Scholar 
    Oliver, T. H. et al. Interacting effects of climate change and habitat fragmentation on drought-sensitive butterflies. Nat. Clim. Chang. 5, 941–946 (2015).
    Google Scholar 
    Stefanescu, C., Carnicer, J. & Peñuelas, J. Determinants of species richness in generalist and specialist Mediterranean butterflies: the negative synergistic forces of climate and habitat change. Ecography 34, 353–363 (2011).
    Google Scholar 
    Essens, T., van Langevelde, F., Vos, R. A., Van Swaay, C. A. M. & WallisDeVries, M. F. Ecological determinants of butterfly vulnerability across the European continent. J. Insect Conserv. 21, 439–450 (2017).
    Google Scholar 
    Tolman, T. & Lewington, R. Butterflies of Europe (Harper Collins, 2008).Dapporto, L. et al. Integrating three comprehensive data sets shows that mitochondrial DNA variation is linked to species traits and paleogeographic events in European butterflies. Mol. Ecol. Resour. 19, 1623–1636 (2019).CAS 
    PubMed 

    Google Scholar 
    Hewitt, G. M. Post-glacial re-colonization of European biota. Biol. J. Linn. Soc. Lond. 68, 87–112 (2008).
    Google Scholar 
    Dincă, V. et al. High resolution DNA barcode library for European butterflies reveals continental patterns of mitochondrial genetic diversity. Commun. Biol. 4, 1–11 (2021).
    Google Scholar 
    Fei, S. et al. Divergence of species responses to climate change. Sci. Adv. 3, e1603055 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    Macgregor, C. J. et al. Climate-induced phenology shifts linked to range expansions in species with multiple reproductive cycles per year. Nat. Commun. 10, 1–10 (2019).CAS 

    Google Scholar 
    Dapporto, L. & Dennis, R. L. H. The generalist–specialist continuum: testing predictions for distribution and trends in British butterflies. Biol. Conserv. 157, 229–236 (2013).
    Google Scholar 
    MacLean, S. A. & Beissinger, S. R. Species’ traits as predictors of range shifts under contemporary climate change: a review and meta-analysis. Glob. Chang. Biol. 23, 4094–4105 (2017).PubMed 

    Google Scholar 
    Morlon, H. et al. Spatial patterns of phylogenetic diversity. Ecol. Lett. 14, 141–149 (2011).PubMed 
    PubMed Central 

    Google Scholar 
    Kraft, N. J. B. et al. Community assembly, coexistence and the environmental filtering metaphor. Funct. Ecol. 29, 592–599 (2015).
    Google Scholar 
    Razgour, O. et al. Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections. Proc. Natl Acad. Sci. USA 116, 10418–10423 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Vanden Broeck, A. et al. Gene flow and effective population sizes of the butterfly Maculinea alcon in a highly fragmented, anthropogenic landscape. Biol. Conserv. 209, 89–97 (2017).
    Google Scholar 
    Haldane, J. B. S. Theoretical genetics of autopolyploids. J. Genet. 22, 359–372 (1930).
    Google Scholar 
    Tigano, A. & Friesen, V. L. Genomics of local adaptation with gene flow. Mol. Ecol. 25, 2144–2164 (2016).PubMed 

    Google Scholar 
    Pfeifer, S. P. et al. The evolutionary history of Nebraska deer mice: local adaptation in the face of strong gene flow. Mol. Biol. Evol. 35, 792–806 (2018).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Reusch, T. B. H. & Wood, T. E. Molecular ecology of global change. Mol. Ecol. 16, 3973–3992 (2007).CAS 
    PubMed 

    Google Scholar 
    DeLong, J. P. & Gibert, J. P. Gillespie eco-evolutionary models (GEMs) reveal the role of heritable trait variation in eco-evolutionary dynamics. Ecol. Evol. 6, 935–945 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    Atkins, K. E. & Travis, J. M. J. Local adaptation and the evolution of species’ ranges under climate change. J. Theor. Biol. 266, 449–457 (2010).CAS 
    PubMed 

    Google Scholar 
    Hampe, A. & Petit, R. J. Conserving biodiversity under climate change: the rear edge matters. Ecol. Lett. 8, 461–467 (2005).PubMed 

    Google Scholar 
    Mills, S. C. et al. European butterfly populations vary in sensitivity to weather across their geographical ranges. Glob. Ecol. Biogeogr. 26, 1374–1385 (2017).
    Google Scholar 
    Van Dyck, H., Bonte, D., Puls, R., Gotthard, K. & Maes, D. The lost generation hypothesis: could climate change drive ectotherms into a developmental trap? Oikos 124, 54–61 (2015).
    Google Scholar 
    Hu, G. et al. Environmental drivers of annual population fluctuations in a trans-Saharan insect migrant. Proc. Natl Acad. Sci. USA 118, 2102762118 (2021).
    Google Scholar 
    Merlin, C. & Liedvogel, M. The genetics and epigenetics of animal migration and orientation: birds, butterflies and beyond. J. Exp. Biol. 222, jeb191890 (2019).Wiemers, M. et al. An updated checklist of the European butterflies (Lepidoptera, Papilionoideae). Zookeys 2018, 9–45 (2018).
    Google Scholar 
    Dennis, E. B., Freeman, S. N., Brereton, T. & Roy, D. B. Indexing butterfly abundance whilst accounting for missing counts and variability in seasonal pattern. Methods Ecol. Evol. 4, 637–645 (2013).
    Google Scholar 
    Radchuk, V., Turlure, C. & Schtickzelle, N. Each life stage matters: the importance of assessing the response to climate change over the complete life cycle in butterflies. J. Anim. Ecol. 82, 275–285 (2013).PubMed 

    Google Scholar 
    Metzger, M. J. et al. A high-resolution bioclimate map of the world: a unifying framework for global biodiversity research and monitoring. Glob. Ecol. Biogeogr. 22, 630–638 (2013).
    Google Scholar 
    Carnicer, J. et al. A unified framework for diversity gradients: the adaptive trait continuum. Glob. Ecol. Biogeogr. 22, 6–18 (2013).
    Google Scholar 
    Klok, E. J. & Klein Tank, A. M. G. Updated and extended European dataset of daily climate observations. Int. J. Climatol. 29, 1182–1191 (2009).
    Google Scholar 
    Haylock, M. R. et al. A European daily high-resolution gridded data set of surface temperature and precipitation for 1950-2006. J. Geophys. Res. Atmos. 113, D20119 (2008).
    Google Scholar 
    Marsh, T. J. The UK drought of 2003: a hydrological review. Weather 59, 224–230 (2004).
    Google Scholar 
    Voyer, A. G. & Garamszegi, L. Z. An introduction to phylogenetic path analysis. in Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology (eds Garamszegi, L. Z. & Mundry, R.) 201–229 (Springer Berlin Heidelberg, 2014).Pagel, M. Inferring the historical patterns of biological evolution. Nature 401, 877–884 (1999).CAS 
    PubMed 

    Google Scholar 
    Pöyry, J. et al. The effects of soil eutrophication propagate to higher trophic levels. Glob. Ecol. Biogeogr. 26, 18–30 (2017).
    Google Scholar 
    Münkemüller, T. et al. How to measure and test phylogenetic signal. Methods Ecol. Evol. 3, 743–756 (2012).
    Google Scholar 
    Bates, D., Maechler, M., Bolker, B. & Walker, S. Fitting Linear Mixed-Effects Models Using lme4. J. Stat. Softw. 67, 1–48 (2015).
    Google Scholar 
    Bartoń, K. MuMIn: Multi-model inference. R package version 1.10.5. (2014).Revell, L. J. phytools: An R package for phylogenetic comparative biology (and other things). MEE. 3, 217–223 (2012).
    Google Scholar 
    Briere, J. F., Pracros, P., Le Roux, A. Y. & Pierre, J. S. A novel rate model of temperature-dependent development for arthropods. Environ. Entomol. 28, 22–29 (1999).
    Google Scholar 
    Shi, P. & Ge, F. A comparison of different thermal performance functions describing temperature-dependent development rates. J. Therm. Biol. 35, 225–231 (2010).
    Google Scholar 
    Angilletta, M. J., Wilson, R. S., Navas, C. A. & James, R. S. Tradeoffs and the evolution of thermal reaction norms. Trends Ecol. Evol. 18, 234–240 (2003).
    Google Scholar 
    Zeuss, D., Brandl, R., Brändle, M., Rahbek, C. & Brunzel, S. Global warming favours light-coloured insects in Europe. Nat. Commun. 5, 1–9 (2014).
    Google Scholar  More

  • in

    Forest fragmentation impacts the seasonality of Amazonian evergreen canopies

    Peñuelas, J., Rutishauser, T. & Filella, I. Ecology. Phenology feedbacks on climate change. Science 324, 887–888 (2009).PubMed 

    Google Scholar 
    Phillips, O. L. et al. Drought sensitivity of the Amazon rainforest. Science 323, 1344–1347 (2009).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Richardson, A. D. et al. Climate change, phenology, and phenological control of vegetation feedbacks to the climate system. Agric. Meteorol. 169, 156–173 (2013).
    Google Scholar 
    Wu, J. et al. Leaf development and demography explain photosynthetic seasonality in Amazon evergreen forests. Science 351, 972–976 (2016).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Wright, J. S. et al. Rainforest-initiated wet season onset over the southern Amazon. Proc. Natl. Acad. Sci. USA 114, 8481–8486 (2017).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hilker, T. et al. Vegetation dynamics and rainfall sensitivity of the Amazon. Proc. Natl. Acad. Sci. USA 111, 16041–16046 (2014).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Girardin, C. A. J. et al. Seasonal trends of Amazonian rainforest phenology, net primary productivity, and carbon allocation. Glob. Biogeochem. Cycles 30, 700–715 (2016).ADS 
    CAS 

    Google Scholar 
    Maeda, E. E. et al. Consistency of vegetation index seasonality across the Amazon rainforest. Int. J. Appl. Earth Obs. Geoinf. 52, 42–53 (2016).ADS 

    Google Scholar 
    Saleska, S. R. et al. Dry-season greening of Amazon forests. Nature 531, E4–E5 (2016). vol.CAS 
    PubMed 

    Google Scholar 
    Chen, X. et al. Vapor pressure deficit and sunlight explain seasonality of leaf phenology and photosynthesis across amazonian evergreen broadleaved forest. Global Biogeochem. Cycles https://doi.org/10.13140/2.1.5019.5520 (2021).Hashimoto, H. et al. New generation geostationary satellite observations support seasonality in greenness of the Amazon evergreen forests. Nat. Commun. 12, 684 (2021).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Brando, P. M. et al. Seasonal and interannual variability of climate and vegetation indices across the Amazon. Proc. Natl. Acad. Sci. USA 107, 14685–14690 (2010).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wu, J. et al. Seasonality of Central Amazon forest leaf flush using tower-mounted RGB camera. In AGU Fall Meeting https://doi.org/10.13140/2.1.5019.5520 (2014).Huete, A. R. et al. Amazon rainforests green-up with sunlight in dry season. Geophys. Res. Lett. https://doi.org/10.1029/2005GL025583 (2006).Restrepo-Coupe, N. et al. What drives the seasonality of photosynthesis across the Amazon basin? A cross-site analysis of eddy flux tower measurements from the Brasil flux network. Agric. Meteorol. 182-183, 128–144 (2013).
    Google Scholar 
    Manoli, G., Ivanov, V. Y. & Fatichi, S. Dry-season greening and water stress in Amazonia: the role of modeling leaf phenology. J. Geophys. Res. Biogeosci. 123, 1909–1926 (2018).
    Google Scholar 
    Guan, K. et al. Photosynthetic seasonality of global tropical forests constrained by hydroclimate. Nat. Geosci. 8, 284–289 (2015).ADS 
    CAS 

    Google Scholar 
    Lopes, A. P. et al. Leaf flush drives dry season green-up of the Central Amazon. Remote Sens. Environ. 182, 90–98 (2016).ADS 

    Google Scholar 
    Smith, M. N. et al. Seasonal and drought-related changes in leaf area profiles depend on height and light environment in an Amazon forest. N. Phytol. 222, 1284–1297 (2019).
    Google Scholar 
    Mitchell Aide, T. Herbivory as a selective agent on the timing of leaf production in a tropical understory community. Nature 336, 574–575 (1988).
    Google Scholar 
    Myneni, R. B. et al. Large seasonal swings in leaf area of Amazon rainforests. Proc. Natl. Acad. Sci. USA 104, 4820–4823 (2007).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wu, J. et al. Partitioning controls on Amazon forest photosynthesis between environmental and biotic factors at hourly to interannual timescales. Glob. Chang. Biol. 23, 1240–1257 (2017).ADS 
    PubMed 

    Google Scholar 
    Nunes, M. H. et al. Recovery of logged forest fragments in a human-modified tropical landscape during the 2015-16 El Niño. Nat. Commun. 12, 1526 (2021).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Vasconcelos, H. L. & Luizão, F. J. Litter production and litter nutrient concentrations in a fragmented Amazonian landscape. Ecol. Appl. 14, 884–892 (2004).
    Google Scholar 
    Laurance, W. F. et al. Rain forest fragmentation and the proliferation of successional trees. Ecology 87, 469–482 (2006).PubMed 

    Google Scholar 
    Uriarte, M. et al. Impacts of climate variability on tree demography in second growth tropical forests: the importance of regional context for predicting successional trajectories. Biotropica 48, 780–797 (2016).
    Google Scholar 
    Ewers, R. M. & Banks-Leite, C. Fragmentation impairs the microclimate buffering effect of tropical forests. PLoS One 8, e58093 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chave, J. et al. Regional and seasonal patterns of litterfall in tropical South America. Biogeosciences 7, 43–55 (2010).ADS 

    Google Scholar 
    Barros, F. et al. Hydraulic traits explain differential responses of Amazonian forests to the 2015 El Niño-induced drought. N. Phytol. 223, 1253–1266 (2019).CAS 

    Google Scholar 
    Brum, M. et al. Hydrological niche segregation defines forest structure and drought tolerance strategies in a seasonal Amazon forest. J. Ecol. 107, 318–333 (2019).
    Google Scholar 
    Signori-Müller, C. et al. Non-structural carbohydrates mediate seasonal water stress across Amazon forests. Nat. Commun. 12, 2310 (2021).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Coelho de Souza, F. et al. Evolutionary heritage influences Amazon tree ecology. Proc. Biol. Sci. https://doi.org/10.1098/rspb.2016.1587 (2016).Hansen, M. C. et al. The fate of tropical forest fragments. Sci. Adv. 6, eaax8574 (2020).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Morton, D. C. et al. Amazon forests maintain consistent canopy structure and greenness during the dry season. Nature 506, 221–224 (2014).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Draper, F. C. et al. Amazon tree dominance across forest strata. Nat. Ecol. Evol. 5, 757–767 (2020).
    Google Scholar 
    Calders, K. et al. Monitoring spring phenology with high temporal resolution terrestrial LiDAR measurements. Agric. Meteorol. 203, 158–168 (2015).
    Google Scholar 
    Disney, M. Terrestrial LiDAR: a three-dimensional revolution in how we look at trees. N. Phytol. 222, 1736–1741 (2019).
    Google Scholar 
    Tang, H. & Dubayah, R. Light-driven growth in Amazon evergreen forests explained by seasonal variations of vertical canopy structure. Proc. Natl. Acad. Sci. USA 114, 2640–2644 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Laurance, W. F. et al. An Amazonian rainforest and its fragments as a laboratory of global change. Biol. Rev. Camb. Philos. Soc. 93, 223–247 (2018).PubMed 

    Google Scholar 
    Correction for Tang and Dubayah, Light-driven growth in Amazon evergreen forests explained by seasonal variations of vertical canopy structure. Proc. Natl. Acad. Sci. USA 116, 9137 (2019).Ma, L. et al. Characterizing the three-dimensional spatiotemporal variation of forest photosynthetically active radiation using terrestrial laser scanning data. Agric. Meteorol. 301-302, 108346 (2021).
    Google Scholar 
    Laurans, M., Hérault, B., Vieilledent, G. & Vincent, G. Vertical stratification reduces competition for light in dense tropical forests. Ecol. Manag. 329, 79–88 (2014).
    Google Scholar 
    Garcia, M. N. et al. Importance of hydraulic strategy trade-offs in structuring response of canopy trees to extreme drought in Central Amazon. Oecologia https://doi.org/10.1007/s00442-021-04924-9 (2021).Giardina, F. et al. Tall Amazonian forests are less sensitive to precipitation variability. Nat. Geosci. 11, 405–409 (2018).ADS 
    CAS 

    Google Scholar 
    Brando, P. Tree height matters. Nat. Geosci. 11, 390–391 (2018).ADS 
    CAS 

    Google Scholar 
    Stark, S. C. et al. Amazon forest carbon dynamics predicted by profiles of canopy leaf area and light environment. Ecol. Lett. 15, 1406–1414 (2012).PubMed 

    Google Scholar 
    Pyle, E. H. et al. Dynamics of carbon, biomass, and structure in two Amazonian forests. J. Geophys. Res. https://doi.org/10.1029/2007JG000592 (2008).Gorgens, E. B. et al. Resource availability and disturbance shape maximum tree height across the Amazon. Glob. Chang. Biol. 27, 177–189 (2021).ADS 
    PubMed 

    Google Scholar 
    Oliveira, R. S. et al. Linking plant hydraulics and the fast-slow continuum to understand resilience to drought in tropical ecosystems. N. Phytol. 230, 904–923 (2021).
    Google Scholar 
    Falster, D. S. & Westoby, M. Leaf size and angle vary widely across species: what consequences for light interception? N. Phytol. 158, 509–525 (2003).
    Google Scholar 
    Chavana-Bryant, C. et al. Leaf aging of Amazonian canopy trees as revealed by spectral and physiochemical measurements. N. Phytol. 214, 1049–1063 (2017).CAS 

    Google Scholar 
    Brando, P. M. et al. Drought effects on litterfall, wood production and belowground carbon cycling in an Amazon forest: results of a throughfall reduction experiment. Philos. Trans. R. Soc. Lond. B Biol. Sci. 363, 1839–1848 (2008).PubMed 
    PubMed Central 

    Google Scholar 
    Wang, D., Momo Takoudjou, S. & Casella, E. LeWoS: a universal leaf-wood classification method to facilitate the 3D modelling of large tropical trees using terrestrial LiDAR. Methods Ecol. Evol. 11, 376–389 (2020).
    Google Scholar 
    Grossiord, C. et al. Plant responses to rising vapor pressure deficit. N. Phytol. 226, 1550–1566 (2020).
    Google Scholar 
    Smith, M. N. et al. Empirical evidence for resilience of tropical forest photosynthesis in a warmer world. Nat. Plants 6, 1225–1230 (2020).CAS 
    PubMed 

    Google Scholar 
    Aleixo, I. et al. Amazonian rainforest tree mortality driven by climate and functional traits. Nat. Clim. Chang. 9, 384–388 (2019).ADS 

    Google Scholar 
    Lohbeck, M. et al. Successional changes in functional composition contrast for dry and wet tropical forest. Ecology 94, 1211–1216 (2013).PubMed 

    Google Scholar 
    Lambers, H. & Oliveira, R. S. in Plant Physiological Ecology (eds. Lambers, H. & Oliveira, R. S.) 385–449 (Springer International Publishing, 2019).Reich, P. B. Key canopy traits drive forest productivity. Proc. Biol. Sci. 279, 2128–2134 (2012).PubMed 
    PubMed Central 

    Google Scholar 
    Albiero-Júnior, A., Venegas-González, A., Camargo, J. L. C., Roig, F. A. & Tomazello-Filho, M. Amazon forest fragmentation and edge effects temporarily favored understory and midstory tree growth. Trees https://doi.org/10.1007/s00468-021-02172-1 (2021).Doughty, C. E. et al. Drought impact on forest carbon dynamics and fluxes in Amazonia. Nature 519, 78–82 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    San-José, M., Werden, L., Peterson, C. J., Oviedo-Brenes, F. & Zahawi, R. A. Large tree mortality leads to major aboveground biomass decline in a tropical forest reserve. Oecologia https://doi.org/10.1007/s00442-021-05048-w (2021).Qin, Y. et al. Carbon loss from forest degradation exceeds that from deforestation in the Brazilian Amazon. Nat. Clim. Chang. 11, 442–448 (2021).Brinck, K. et al. High resolution analysis of tropical forest fragmentation and its impact on the global carbon cycle. Nat. Commun. 8, 14855 (2017).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Duffy, P. B., Brando, P., Asner, G. P. & Field, C. B. Projections of future meteorological drought and wet periods in the Amazon. Proc. Natl. Acad. Sci. USA 112, 13172–13177 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Silva Junior, C. H. L. et al. Persistent collapse of biomass in Amazonian forest edges following deforestation leads to unaccounted carbon losses. Sci. Adv. 6, eaaz8360 (2020).Forrest, J. & Miller-Rushing, A. J. Toward a synthetic understanding of the role of phenology in ecology and evolution. Philos. Trans. R. Soc. Lond. B Biol. Sci. 365, 3101–3112 (2010).PubMed 
    PubMed Central 

    Google Scholar 
    Park, J. Y. et al. Quantifying leaf phenology of individual trees and species in a tropical forest using unmanned aerial vehicle (UAV) images. Remote Sens. 11, 1534 (2019).ADS 

    Google Scholar 
    Dubayah, R. et al. The global ecosystem dynamics investigation: high-resolution laser ranging of the Earth’s forests and topography. Egypt. J. Remote Sens. Space Sci. 1, 100002 (2020).
    Google Scholar 
    Coomes, D. A. et al. Area-based vs tree-centric approaches to mapping forest carbon in Southeast Asian forests from airborne laser scanning data. Remote Sens. Environ. 194, 77–88 (2017).ADS 

    Google Scholar 
    Calders, K. et al. Terrestrial laser scanning in forest ecology: expanding the horizon. Remote Sens. Environ. 251, 112102 (2020).ADS 

    Google Scholar 
    Nobre, C. A. et al. Land-use and climate change risks in the Amazon and the need of a novel sustainable development paradigm. Proc. Natl. Acad. Sci. USA 113, 10759–10768 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Almeida, D. R. A. et al. Persistent effects of fragmentation on tropical rainforest canopy structure after 20 yr of isolation. Ecol. Appl. 29, e01952 (2019).PubMed 

    Google Scholar 
    Wilkes, P. et al. Data acquisition considerations for terrestrial laser scanning of forest plots. Remote Sens. Environ. 196, 140–153 (2017).ADS 

    Google Scholar 
    Vincent, G. et al. Mapping plant area index of tropical evergreen forest by airborne laser scanning. A cross-validation study using LAI2200 optical sensor. Remote Sens. Environ. 198, 254–266 (2017).ADS 

    Google Scholar 
    Pimont, F., Allard, D., Soma, M. & Dupuy, J.-L. Estimators and confidence intervals for plant area density at voxel scale with T-LiDAR. Remote Sens. Environ. 215, 343–370 (2018).ADS 

    Google Scholar 
    Vincent, G., Pimont, F. & Verley, P. A note on PAD/LAD Estimators Implemented in AMAPVox 1.7.https://doi.org/10.23708/1AJNMP (2021)Ross, J. The radiation regime and architecture of plant stands (Springer, 1981).Béland, M., Widlowski, J.-L., Fournier, R. A., Côté, J.-F. & Verstraete, M. M. Estimating leaf area distribution in savanna trees from terrestrial LiDAR measurements. Agric. Meteorol. 151, 1252–1266 (2011).
    Google Scholar 
    Almeida, D. R. Ade et al. Optimizing the remote detection of tropical rainforest structure with airborne LiDAR: leaf area profile sensitivity to pulse density and spatial sampling. Remote Sens. 11, 92 (2019).ADS 

    Google Scholar 
    Qie, L. et al. Long-term carbon sink in Borneo’s forests halted by drought and vulnerable to edge effects. Nat. Commun. 8, 1966 (2017).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Росс, Ю. & Ross, J. The radiation regime and architecture of plant stands (Springer Science & Business Media, 1981).Berry, Z. C. & Goldsmith, G. R. Diffuse light and wetting differentially affect tropical tree leaf photosynthesis. N. Phytol. 225, 143–153 (2020).CAS 

    Google Scholar 
    Mercado, L. M. et al. Impact of changes in diffuse radiation on the global land carbon sink. Nature 458, 1014–1017 (2009).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    USGS. LP DAAC—MCD18A1. https://lpdaac.usgs.gov/products/mcd18a1v006/ (2008).Maeda, E. E. et al. Large-scale commodity agriculture exacerbates the climatic impacts of Amazonian deforestation. Proc. Natl. Acad. Sci. USA 118, e2023787118 (2021).Engelbrecht, B. M. J. et al. Drought sensitivity shapes species distribution patterns in tropical forests. Nature 447, 80–82 (2007).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Zellweger, F. et al. Forest microclimate dynamics drive plant responses to warming. Science 368, 772–775 (2020).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Wild, J. et al. Climate at ecologically relevant scales: a new temperature and soil moisture logger for long-term microclimate measurement. Agric. Meteorol. 268, 40–47 (2019).
    Google Scholar 
    Camargo, J. L. C. & Kapos, V. Complex edge effects on oil moisture and microclimate in Central Amazonian forest. J. Trop. Ecol. 11, 205–221 (1995).
    Google Scholar 
    Zuur, A., Ieno, E. N., Walker, N., Saveliev, A. A. & Smith, G. M. Mixed Effects Models and Extensions in Ecology with R (Springer Science & Business Media, 2009).Malhi, Y., Phillips, O. L. & Laurance, W. F. Forest-climate interactions in fragmented tropical landscapes. Philos. Trans. R. Soc. Lond. B Biol. Sci. 359, 345–352 (2004).
    Google Scholar  More

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    Unexpectedly minor nitrous oxide emissions from fluvial networks draining permafrost catchments of the East Qinghai-Tibet Plateau

    Variability of N2O concentrations and fluxesAll sampled streams and rivers were supersaturated on all dates (117.9–242.5%, n = 342 samples from 114 site visits) in N2O with respect to the atmosphere. Dissolved N2O concentrations fluctuated between 10.2 and 18.9 nmol L−1 with an average of 12.4 ± 1.7 nmol L−1, which is one-third of the global average3 (37.5 nmol L−1; Supplementary Table 3). Significantly higher N2O concentrations were observed in spring (P  More

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    Community-based rangeland management in Namibia improves resource governance but not environmental and economic outcomes

    Theory of changeAt the heart of the of CBRLM’s theory of change is the assumption that improvements in the ecological sub-system provide a sustainable resource base for increased livestock production and marketing34. The ecological sub-system, however, depends on a functioning economic sub-system because herd owners must be able to destock quickly in response to adverse ecological circumstances. The theory holds that the most important constraint on the economic sub-system is unproductive herds and low-quality cattle because farmers are unwilling to sell their cattle when they command low market prices. Therefore, improvements in rangeland grazing management need to be complemented by improvements in information and access to livestock markets, herd structures, and animal husbandry practices.Crucially, changes to the ecological, economic, and livestock sub-systems rely on effective community governance and collective-action capacity in CBRLM communities. This is because rangeland grazing management practices can be easily undermined by non-participating herd owners inside or outside the GA. The theory therefore calls for investments at multiple levels of the social-ecological system to ensure that improvements in certain program areas are not undermined by failures in others34. The CBRLM implementers believed that previous rangeland development programs were undermined by a failure to account for the linkages among sub-systems, which motivated them to design a more holistic intervention34.Intervention componentsCBRLM was a multi-faceted package of administrative, educational, financial, and technical support. Implementation of the package was designed as an experimental treatment to assist in project assessment. To select study areas for evaluation, GOPA identified 38 RIAs with sufficiently low density of people, livestock, and bush cover to enable the implementation of new group-grazing plans, one of the core treatment components. The evaluation team randomly assigned 19 RIAs to treatment and 19 RIAs to control (see Randomization for details). GOPA implemented CBRLM in up to seven GAs within each treatment RIA.MobilizationGOPA conducted pre-mobilization meetings with TAs and other stakeholders in the second half of 2010 to identify GA communities most likely to participate in CBRLM34. Early mobilization efforts focused on soliciting community buy-in for the cornerstone principles of CBRLM, including community-planned grazing, combined herding of cattle, and efficient livestock management. There is also substantial evidence from qualitative surveys that some community members were motivated to participate in the CBRLM by prospects for water infrastructure development by GOPA34.While almost 100 GAs were initially mobilized for the project, by 2014 GOPA was targeting resources and support towards 58 GAs based on community receptivity and the discretion of CBRLM management. In each GA, GOPA worked principally with households owning 10 or more cattle, although other community members benefitted from participation in a “Small Stock Pass-on Scheme” and a variety of training activities, which are described below.Rangeland grazing managementThe core aim of CBRLM was to shift how communities approached livestock grazing, forage conservation, and risk management by encouraging two key practices: planned grazing and combined herding. Planned grazing entails rotating a community’s cattle to a new pasture on a regular basis in accordance with a written plan. The goal was to preserve grass for the dry season and allow grazed pastures more time to recover. Combined herding entails grouping many owners’ cattle into one large herd and herding them in a tight bunch. This practice is meant to concentrate animal impact on rangeland, minimize cattle losses, and increase the likelihood that cows are exposed to bulls, thus increasing the pregnancy and calving rates of the entire herd. The scientific and practical rationale behind these practices is reviewed in Supplementary Note 2.GOPA staff developed grazing plans with each participating community and taught them planned grazing and combined herding via field-based training sessions. These followed a “training of trainers” approach in which GOPA recruited field facilitators from each community, taught them the principles of CBRLM, and tasked them with training their fellow participating pastoralists.Livestock managementGOPA taught participants some best practices in animal husbandry, including structuring herds to maximize productivity (by increasing the proportion of bulls and reducing the proportion of oxen and cattle over the age of 10 years), providing vaccinations and supplements, and deworming34. Additionally, to support the introduction of more bulls into herds, the project implemented a “bull scheme” in which participating communities were given the opportunity to collectively buy certified breeding bulls at a subsidized price. Communities were meant to repay the cost of the bulls either with cash or in-kind trades of goats. Goats collected in this repayment process fed into the small stock pass-on scheme under which participating community members nominated households to receive goats from GOPA. GOPA requested that communities nominate households that owned few or no livestock and were led by youth and/or women. When GOPA received goats as payment for loaned bulls, they would pass them on to nominated households. The recipients were then expected to pass on the offspring of the goats they received to other disadvantaged households.Cattle marketingCBRLM also sought to increase participants’ marketing of cattle to generate revenue from livestock raising and encourage offtake of unproductive animals34. Community facilitators and project experts provided participating herd owners with information about market opportunities and ideal herd composition, and encouraged flexible offtake in response to forage shortages. In 2013, GOPA invested in the development of regional livestock cooperatives that held local auctions and helped farmers transport their animals to markets. Finally, GOPA invested in identifying international export opportunities for CBRLM farmers to Zimbabwe and Angola, although these were generally not successful31.Community developmentThe project sought to institutionalize community-level governance to organize and enforce collective activities like planned grazing, water point maintenance, and financing of livestock inputs. The central management unit of each GA was a new Grazing Area Committee consisting of five to 10 elected community members. The project encouraged participating communities to collectively cover operational expenses in their GA through a GA fund managed by the committee. Among these expenses were the payments to herders, costs of diesel for water pumps and maintenance of water infrastructure, financing collective livestock vaccination campaigns, and any other collective expenses that would support operation of the GA. CBRLM supported every GA fund with a 1:1 matched subsidy. The matched subsidy was limited by a ceiling amount determined by the estimated number of cattle in a GA. GOPA also instructed committees to maintain “GA record books” to track grazing plans, record meeting minutes, and keep logs of community members’ participation and financial contributions.Water infrastructureGOPA upgraded water infrastructure at a total of 84 sites throughout the NCAs to facilitate planned grazing and combined herding. Water infrastructure improvement included minor upgrades like water tanks and drinking troughs, and larger investments such as the installation of diesel and solar pump systems, the drilling and installation of boreholes, and the construction of pipelines, deep wells, and a large earthen dam31.Intervention timelineThe timeline for major components of the research process and CBRLM roll-out is illustrated in Supplementary Fig. 1. The research team conducted the random assignments and the implementation team began community mobilization in early 2010. Formal enrollment in CBRLM began in early 2011. The program implementer conducted mobilization in two waves: they mobilized 11 of 19 RIAs in 2010 and the remaining 8 RIAs in 2011. The evaluation team conducted qualitative data collection to inform the design of social and cattle surveys prior to project end 2014; social surveys in 2014 and 2016; rangeland surveys in the wet and dry seasons of 2016; a cattle survey in 2016; and a household economic survey in 2017.Cumulative GA-level implementation is illustrated in Supplementary Fig. 2. The project implementer first formally reported enrollment and field visits in April 2011. The implementer achieved nearly full targeted enrollment (50 GAs) by November 11, although some grazing areas were added or subtracted thereafter. Mobilization exceeded enrollment because some grazing area communities chose not to participate in the program and some enrolled in the program and then dropped out. The program averaged between 25 and 50 field visits per month over the project period. A field visit consisted of a week-long community meeting about grazing-plan development and implementation, animal husbandry and budget training, and marketing opportunities.RandomizationThe unit of randomization is the RIA, an intervention zone with a locally recognized boundary. Each RIA falls under the jurisdiction of a single local governing body, known as a Traditional Authority (TA). As noted above, RIAs contain five to 15 GAs where a community of producers share water and forage resources. Grazing areas do not have legally defined boundaries. A herd owner’s ability to move among GAs is variable.GOPA mapped 41 RIAs prior to randomization. Three contiguous RIAs in the north-central region, composed of two treatment RIAs and one control RIA, were omitted from the study post-randomization because reexamination of baseline density of bushland vegetation deemed them unviable for CBRLM implementation. These are the three RIAs without sampled GAs in Fig. 1. The other 38 RIAs were randomly assigned to either receive the CBRLM treatment (19 RIAs) or serve as controls (19 RIAs).The randomization was stratified by TA to ensure that at least one RIA was assigned to the treatment in each TA. The research team then re-randomized the sample units until seven variables were balanced (a p value of 0.33 or higher for an omnibus f test of all seven variables) between treatment and control: (1) Presence of forest; (2) number of households; (3) number of cattle; (4) cattle density per unit area; (5) quality of water sources; (6) presence of community-based organizations (CBOs); and (7) overlap with complementary interventions (see Supplementary Table 1). For future researchers, we recommend re-randomizing a set number of times and choosing the re-randomization with the highest balance35. These variables and indicator variables for TA are included as covariates in all analyses.Sample selectionIn the original sampling strategy, the project implementer was asked to predict the GAs where they would implement the project if the RIA were assigned to treatment. However, there was limited overlap between the GAs that the implementer predicted and the GAs where CBRLM was ultimately implemented. Therefore, the evaluation team devised a revised sampling strategy in 2013, which proceeded in four steps:

    1.

    Map GAs in sampled RIAs: The evaluation team traveled to all 38 RIAs and worked with TAs and Namibian Agricultural Extension (AE) officers to map all the GAs in each RIA. The team mapped 171 GAs in control RIAs and 213 GAs in treatment RIAs.

    2.

    Collect pre-program data on GAs: The evaluation team collected information on pre-program characteristics of each GA from interviews with TAs and AE staff, the Namibian national census36, and the Namibian Atlas37. The latter has a geo-referenced database on climate, ecology, and livestock for the nation.

    3.

    Predict CBRLM enrollment for treatment GAs: The researchers used these data in a logistic regression to predict the probability that each GA would enroll in CBRLM and would adopt the CBRLM interventions based on pre-program characteristics. For example, the model found that GAs with more existing water infrastructure, strong social cohesion, and adequate cell phone service were more likely to be enrolled in the program. The variables used to predict CBRLM adoption were: (1) Presence of water installations (yes/no); (2) carrying capacity of the land (above/below the regional median); (3) community’s readiness to change (high/very high); (4) community’s social cohesion (high/very high); (5) spillover effects from neighbors; (6) quality of herders and herder turnover; (7) presence of members of the Himba ethnic group; (8) the TA’s readiness to change; (9) cell phone coverage; and (10) primary housing material (mud, clay, or brick).

    4.

    Generate sample of GAs in treatment and control RIAs: The evaluation team applied the statistical model (above) to all GAs in the sample and set a cut-off point to separate GAs that were likely to adopt the CBRLM program vs. those that were unlikely to do so. In treatment RIAs, the model predicted 52 GAs, of which 37 were formally enrolled in CBRLM and 15 were not. In control RIAs, 71 GAs met or exceeded the cutoff; they offer the best counter-factual estimate of which GAs would have enrolled in the program had their RIA received treatment.

    Data collectionThe names, survey questions, and variable constructions for all outcomes included in the analysis are available at the AEA RCT Registry (ID number: AEARCTR-0002723). See Supplementary Methods for a list of definitions of variables depicted in Fig. 2 and 3.Social surveysSocial surveys were intended to assess the effect of CBRLM on community behaviors, community dynamics, knowledge, and attitudes. All data were collected using electronic tablets with the SurveyCTO software38.The primary unit of analysis for household respondents is the manager of the cattle kraal (holding pen). Researchers conducted surveys with kraal managers, rather than heads of households, for three reasons. First, many kraals contain cattle owned by multiple households, and decisions about grazing practices, cattle treatment, and participation in grazing groups are generally made at the kraal level. Second, many cattle-owning households do not directly oversee the day-to-day activities of their cattle (many live outside the GA), and so would be unable to answer questions about key outcomes, such as livestock management behaviors and community dynamics39. Finally, enrollment in CBRLM occurred at the kraal, rather than household, level.In 2014, the research team worked with local headmen and other community members to generate a complete census of kraals in every sampled Grazing Area (GA) that contained 10 or more cattle at the start of the program (an eligibility requirement for enrollment in CBRLM). The research team randomly sampled up to 11 community members for participation in the 2014 kraal manager survey. Surveys were conducted in the manager’s local language and lasted ~45 min. Alongside the 2014 survey, teams of two surveyors visited all grazing areas where at least one respondent reported participating in a community grazing group or community combined herd to corroborate reported behaviors through direct observation.To assess the persistence of CBRLM’s effects on behaviors, community dynamics, knowledge, and attitudes, the research team conducted a follow-up survey of kraal managers in 2016, two years after program end. The survey team randomly sampled two additional kraals in each grazing area to account for the possibility of attrition. The 2016 survey lasted approximately one hour on average, and included an expanded list of questions about governance, social conflict, and collective action as well as new survey modules on cattle marketing, cattle movement, and livestock management. In 2017, the research team randomly sampled three kraals in each grazing area to conduct direct observation audits of key rangeland grazing-management behaviors.To assess the effects of CBRLM on economic outcomes, the research team conducted a household-level survey in 2017, three years after program end. The survey instrument asked detailed questions on topics that could not be answered by kraal managers, such as household consumption, income, food security, and savings. To select households for this survey, during the 2016 survey the research team asked kraal managers to list all households that owned cattle in the manager’s kraal, then randomly selected one household from each kraal. Alongside the 2017 survey, the research team conducted an in-depth survey with the local headman of all 123 GAs in the sample. The headman survey focused on historical background about the grazing area, as well as the headman’s perceptions of rangeland and livestock issues.Cattle dataThe cattle component was intended to assess effects of CBRLM on cattle numbers, body condition, and productivity. The variables of key interest involved the average liveweight and body condition, calving rates, and average market value of cattle, as well as overall herd structures.The data collection protocols closely followed standards from livestock assessments elsewhere in Sub-Saharan Africa40. The research team randomly selected up to six kraals in each GA to participate in the cattle survey. The survey team mobilized selected herds during multiple community visits to ensure all herds were accounted for. Herd owners were compensated for the costs of rounding up animals and weighed cattle received anti-parasite treatment (“dipping”)41. A total of 19,875 cattle from 669 herds were weighed.The data-collection process for each herd proceeded in six steps. First, surveyors worked with herd managers to round up all cattle that regularly stayed in the selected cattle kraal. Once cattle had been brought to the designated location for data collection, they were passed through a mobile crush pen and scale. As each animal passed through the crush pen, a survey team member recorded the animal type (i.e., bull, ox, cow, calf) and used a SurveyCTO randomizer to calculate whether the animal was randomly selected for assessment. The random number generator was set to randomly select approximately 30 cattle from each herd for weighing. If the animal was selected, the survey team kept the animal on the scale and recorded its weight and body condition. A semi-subjective 1–5 scale, commonly used by livestock buyers in the NCAs (see Supplementary Fig. 3), was adjusted to a 0–4 scale used to determine formal market pricing. The team then placed the animal in a neck clamp and estimated the animal’s age by dentition (but extremely young calves were aged visually). Each animal was marked as it moved through the crush pen to ensure that it was assessed only once. In addition to assessing randomly selected animals, the survey team weighed and aged all bulls in the herd. The cattle survey yielded average cattle weight, age, and body condition for 19,875 animals across all treatment and control GAs, as well as estimates of calving rates, ratios of bulls to cows, and ratios of productive to unproductive animals.Rangeland dataThe rangeland ecology research was intended to assess treatment effects on vegetation and soil surface conditions. Full research details, including field technician training protocols, are available elsewhere42. The data collection approach followed methods commonly used in Africa43,44. Extended definitions of variables depicted in Fig. 3 and Table 2 are available in the “Supplementary Methods” section.The rationale for how the ecological variables presented in Fig. 3 translate into assessments of rangeland condition or health is based on forage and soil characteristics from a livestock production perspective25. The highest quality forages for cattle on rangelands are perennial grasses, since annual grasses are more ephemeral in terms of nutritive value and productivity. Herbaceous forbs often have the poorest forage quality for large grazers because of their low fiber content and risks of containing toxic chemicals. When rangelands are degraded by over-grazing, perennial grasses are reduced and replaced by annual grasses and forbs. This trend reflects animal diet selectivity that favors consumption of the perennial plants. Reversing such trends via management interventions can be difficult. The main option is to reduce grazing pressure and hope that perennial grasses can outcompete annuals and become reestablished over time. Another option is to implement a grazing rotation that allows perennial grasses to recover after a grazing period.Increases in annual grasses are documented to occur as one outcome of chronic overgrazing in Namibia45,46. In 2016, annual grasses were 5-times more abundant than perennial grasses in our study area. When over-grazing occurs, most plant material is harvested and less is available for the pool of organic matter (OM) for the topsoil. Less OM (e.g., plant litter) on the soil surface means that more soil is also exposed to wind and rain, accelerating erosion. The GAs in our research occur on various soil types and landscapes, some of which are more susceptible to erosion than others. Silty soils on slopes are vulnerable to erosion, for example, while sandy soils on level sites are less vulnerable25.On-the-ground sampling was conducted in all 123 selected GAs along an 800-km zone running West to East. Elevations ranged from 750 to 1700 masl (West) and 1050 to 1120 masl (East). Within each sampled GA, up to 12 1-ha (square) sampling sites were initially chosen using coordinates generated randomly from latitude and longitude coordinates in a satellite image of the GA47. About 17% of sites were later removed from the sample based on their close proximity to landscape disturbances or inaccessibility by field technicians. Overall, 972 sites were analyzed in the wet season and 885 in the dry season of 2016, two years after the implementation phase of CBRLM had ended.The geographic center-point for a sampling site was generated using a spatially constrained random distribution algorithm applied to the satellite image, and the field team navigated to the center-point coordinates using GPS technology. The team took photographs and recorded descriptive information including elevation, slope, aspect, other landscape features, vegetation type, dominant plant species, soil type, soil erosion, and degree of grazing or browsing pressure, and proximity to high impact areas such as trails, water points, and villages.At the center point, the survey team then established two perpendicular transects, each 100 m in length and crossing at the middle. The resulting four, 50-m transect lines ran according to each cardinal direction (N, S, E, W) as determined with a compass. Technicians then placed 1-m notched sampling sticks at randomized locations along each transect line and recorded what plants or other materials (i.e., stone, wood, leaf litter, animal dung, etc.) were located under or above the notches of the sampling sticks. These data points were tabulated to calculate percent cover for various categories of vegetation; there were n = 200 data points per site based on 40 stick placements and 5 notches per stick. This method enabled precise calculation of cover values for herbaceous (i.e., grass, forb) and diminutive woody plants (i.e., small shrubs, seedlings, saplings, etc.). Tree cover was estimated from point data collected via a small adjustment in the approach42. Herbaceous species were identified in wet seasons but not in dry seasons due to senescence during the latter.Quadrat sampling supplemented the notched stick approach. Random placements of a 1-m2 quadrat frame within the sampling site allowed for 20 estimates of a soil surface condition score ranging from 1 (poor) to 2 (moderate) or 3 (good)42. Poor was indicated by smooth soil surfaces, absence of litter, having poor infiltration and signs of erosion such as rills, pedestals, or terracettes; good was indicated by rough soil surfaces, abundant litter, seedlings evident, and lack of evidence of erosion. Herbaceous biomass was estimated in the quadrats and weighed to estimate herbaceous biomass.StatisticsIndex creationIndex construction for socioeconomic variables was composed of several steps48. For each response variable we first signed all component variables such that a higher sign is a positive outcome, i.e., in line with CBRLM’s intended impacts. Then we standardized each component by subtracting its control group mean and dividing by its control group standard deviation. We computed the mean of the standardized components of the index and standardized the sum once again by the control group sum’s mean and standard deviation. When the value of one component in an index was missing, we computed the index average from the remaining components. See Tables 3–6 for index components.Calculation of average treatment effectsThe estimate of interest is the Average Treatment Effect (ATE), or the average change in an outcome generated by assignment to CBRLM. We estimate the ATE using standard Ordinary Least Squares regression and control for variables used in stratification. Regressions for rangeland outcome variables include a unique set of controls, including rainfall over the project period, rainfall in the year of data collection, grazing area cattle density, grazing area ecological zones, and a remote-sensing estimate of pre-project biomass. The core model takes the form:$$hat{Y}=alpha +{beta }_{1}T+{{{{{boldsymbol{beta }}}}}}{{{{{bf{X}}}}}}$$
    (1)
    where T represents treatment assignment and X represents pre-treatment covariates used to test for balance during re-randomizations. The results capture the intention-to-treat (ITT) effect rather than the effect of treatment-on-treated (TOT). ITT is more appropriate than TOT in this context for two principal reasons. First, it is more relevant for policymakers – the effect of policies should account for imperfect compliance. Second, “uptake” is not well-defined, and certainly not a binary concept, for CBRLM since many communities and community members complied partially, complied with some but not all components, and complied for some but not all of the time.Standard errors and p valuesWe report two-tailed p values for all analyses. For each outcome, we show the two-tailed p value from a standard Ordinary Least Squares (OLS) regression with standard errors clustered at the level of the RIA, the unit of randomization49. We also calculate two-tailed p values using Randomization Inference (RI). To calculate RI p values, we re-run the randomization procedure (described above) 10,000 times and generate an Average Treatment Effect (ATE) under each hypothetical randomization. The p value is the percent of re-randomizations that generate a treatment effect that is either equal to, or larger in absolute value than, the true ATE.Multiple hypotheses correctionWe calculate q values to account for families of outcome indices with multiple hypotheses50. The q value represents the minimum false discovery rate at which the null hypothesis would be rejected for a given test. We pre-specified five families of indices:

    1.

    Behavioral outcomes (all in 2014): Grazing planning, Grazing-plan adherence, Herding practices, and Herder management.

    2.

    Behavioral outcomes (all in 2016): Grazing planning, Grazing-plan adherence, Herding practices, and Herder management.

    3.

    Primary material outcomes: Cattle herd value (2016), Herd productivity (2016), Household income (2017), Household expenditures (2017), Household livestock wealth (2017).

    4.

    Secondary material outcomes: Time use (2017), Resilience (2017), Female empowerment (2017), Diet (2017), and Herd structure (2016).

    5.

    Mechanisms: Collective Action (2014, 2016), Community Governance (2014, 2016), Community disputes (2014, 2016), Trust (2014), Self and community efficacy (2014, 2017), and Knowledge (2016).

    Heterogeneous treatment effects analysisWe are interested in whether the effect of CBRLM was impacted by lower rainfall in some grazing areas during the project period. We evaluated heterogeneous treatment effects by rainfall in grazing areas using a variety of measures of rainfall, including aggregate rainfall during the project period and deviation in aggregate rainfall from the ten-year mean during the project period.For simplicity, Supplementary Tables 5 and 6 present the results of analysis of the interaction between treatment and a binary indicator of low rainfall. To construct this indicator, for each GA we first compute the absolute difference between mean rainfall during the project and mean rainfall during the 10 years prior (2000–2010). We divide the absolute difference by mean rainfall during the 10 years prior to produce a relative (%) difference. We then determine the median relative difference over all GAs. For each GA, we assign the value 1 to the low rainfall indicator if the relative difference for the GA is less than the median relative difference over all GAs; we assign 0 otherwise. The results are consistent when we use alternative rainfall measures.Spillovers analysisBecause CBRLM grazing areas were more likely to experience external incursions by cattle herds from outside the community, we test for spillovers. Specifically, we are interested in whether control grazing areas near treatment areas were affected by having a treatment grazing area nearby. We conducted the spillovers analysis only on control group grazing areas. For each control group grazing area, we measured the distance to the border of the nearest treatment grazing area. We created a binary measure taking the value 1 if the distance between the control group grazing area and nearest treatment group grazing area is below the median distance, and 0 otherwise. We find no evidence of spillover effects. The results are presented in Supplementary Table 7.Ethical considerationsApproval for this study was obtained from the Institutional Review Boards at Yale University (1103008148), Innovations for Poverty Action (253.11March-001), and Northwestern University (STU00205556-CR0001). The program was conceived, designed, and implemented by the Millennium Challenge Account compact between the Millennium Challenge Corporation and the Government of Namibia. The research team did not participate in program design or implementation. Communities and individual farmers were informed that they were free to withdraw from participation in evaluation activities at any time. The random assignment of the program was appropriate given the uncertainty around the program’s effect, and the Government of Namibia committed to implementing the program in control areas if the evaluation showed positive results.The research team took a number of steps to ensure the autonomy and well-being of study participants. First, we designed the survey and data collection protocols after considerable qualitative field work to ensure that questions about sensitive issues (e.g., cattle wealth, cattle losses, attitudes towards the Traditional Authority) were phrased appropriately and did not engender adverse emotional or social consequences. Second, all survey activities were reviewed and approved by the MCA compact, Regional Governors, and Traditional Authorities. Third, surveys were conducted with informed consent and in private to ensure that information remained private and respondents were as comfortable as possible during the survey. Finally, the research team disseminated findings on market prices and rangeland condition to communities and regional Agriculture Extension Officers.We received no negative reports about the community reception of the survey from surveyors during the evaluation. Two cows were injured during the cattle weighing exercise, and the owner was financially compensated in line with a compensation agreement made with all farmers prior to the cattle weighing exercise.Reporting summaryFurther information on research design is available in the Nature Research Reporting Summary linked to this article. More

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    Diversity of rice rhizosphere microorganisms under different fertilization modes of slow-release fertilizer

    Xin, F. et al. Large increases of paddy rice area, gross primary production, and grain production in Northeast China during 2000–2017. Sci. Total Environ. 711, 135–183. https://doi.org/10.1016/j.scitotenv.2019.135183 (2020).CAS 
    Article 

    Google Scholar 
    Du, B. et al. Deep fertilizer placement improves rice growth and yield in zero tillage. Appl. Ecol. Environ. Res. 16, 8045–8054. https://doi.org/10.15666/aeer/1606_80458054 (2018).Article 

    Google Scholar 
    Ni, B., Liu, M., Lü, S., Xie, L. & Wang, Y. Environmentally friendly slow-release nitrogen fertilizer. J. Agric. Food Chem. 59, 10169–10175. https://doi.org/10.1021/jf202131z (2011).CAS 
    Article 
    PubMed 

    Google Scholar 
    Zhu, C. et al. Mechanized transplanting with side deep fertilization increases yield and nitrogen use efficiency of rice in Eastern China. Sci. Rep. 9, 5653. https://doi.org/10.1038/s41598-019-42039-7 (2019).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Tilman, D., Cassman, K. G., Matson, P. A., Naylor, R. & Polasky, S. Agricultural sustainability and intensive production practices. Nature 418, 671–677. https://doi.org/10.1038/nature01014 (2002).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Sharma, B. et al. Recycling of organic wastes in agriculture: An environmental perspective. Int. J. Environ. Res. 13, 409–429. https://doi.org/10.1007/s41742-019-00175-y (2019).CAS 
    Article 

    Google Scholar 
    Pan, S. et al. Benefits of mechanized deep placement of nitrogen fertilizer in direct-seeded rice in South China. Field Crops Res. 203, 139–149. https://doi.org/10.1016/j.fcr.2016.12.011 (2017).Article 

    Google Scholar 
    Shahena, S., Rajan, M., Chandran, V. & Mathew, L. Conventional methods of fertilizer release. In Controlled Release Fertilizers for Sustainable Agriculture (eds Lewu, F. B. et al.) 1–24 (Academic Press, 2021). https://doi.org/10.1016/B978-0-12-819555-0.00001-7.Chapter 

    Google Scholar 
    Wang, C. et al. Effects of different fertilization methods on ammonia volatilization from rice paddies. J. Clean. Prod. 295, 126299. https://doi.org/10.1016/j.jclepro.2021.126299 (2021).CAS 
    Article 

    Google Scholar 
    Wu, Q. et al. Effects of different types of slow- and controlled-release fertilizers on rice yield. J. Integr. Agric. 20, 1503–1514. https://doi.org/10.1016/S2095-3119(20)63406-2 (2021).CAS 
    Article 

    Google Scholar 
    Mahajan, G., Kumar, V. & Chauhan, B. S. Rice production in India. In Rice production worldwide (eds Chauhan, B. et al.) 53–91 (Springer International Publishing, 2017). https://doi.org/10.1007/978-3-319-47516-5_3.Chapter 

    Google Scholar 
    Opoku-Kwanowaa, Y., Furaha, R. K., Yan, L. & Wei, D. Effects of planting field on groundwater and surface water pollution in China. Clean-Soil Air Water 48, 1900452. https://doi.org/10.1002/clen.201900452 (2020).CAS 
    Article 

    Google Scholar 
    Lin, W. et al. The effects of chemical and organic fertilizer usage on rhizosphere soil in tea orchards. PLoS ONE 14, e0217018. https://doi.org/10.1371/journal.pone.0217018 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sempeho, S. I., Kim, H. T., Mubofu, E. & Hilonga, A. Meticulous overview on the controlled release fertilizers. Adv. Chem. 1–16, 2014. https://doi.org/10.1155/2014/363071 (2014).Article 

    Google Scholar 
    Trenkel, M. E. Controlled-Release and Stabilized Fertilizers in Agriculture 1–156 (International Fertilizer Industry Association, 1997).
    Google Scholar 
    Lawrencia, D. et al. Controlled release fertilizers: A review on coating materials and mechanism of release. Plants 10, 238. https://doi.org/10.3390/plants10020238 (2021).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Tang, S. et al. Studies on the mechanism of single basal application of controlled-release fertilizers for increasing yield of rice (Oryza safiva L.). Agric. Sci. China 6, 586–596. https://doi.org/10.1016/S1671-2927(07)60087-X (2007).CAS 
    Article 

    Google Scholar 
    Zheng, Y. et al. Effects of mixed controlled release nitrogen fertilizer with rice straw biochar on rice yield and nitrogen balance in northeast china. Sci. Rep. 10, 9452. https://doi.org/10.1038/s41598-020-66300-6 (2020).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ransom, C. J., Jolley, V. D., Blair, T. A., Sutton, L. E. & Hopkins, B. G. Nitrogen release rates from slow- and controlled-release fertilizers influenced by placement and temperature. PLoS ONE 15, e0234544. https://doi.org/10.1371/journal.pone.0234544 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Soni, R., Kumar, V., Suyal, D. C., Jain, L. & Goel, R. Metagenomics of plant rhizosphere microbiome. In Understanding host-microbiome interactions—an omics approach (eds Singh, R. et al.) 193–205 (Springer, 2017). https://doi.org/10.1007/978-981-10-5050-3_12.Chapter 

    Google Scholar 
    Kumar, A. Phosphate solubilizing bacteria in agriculture biotechnology: Diversity, mechanism and their role in plant growth and crop yield. Int. J. Adv. Res. 4, 116–124. https://doi.org/10.21474/IJAR01/111 (2016).Article 

    Google Scholar 
    Arjun, J. K. Metagenomic analysis of bacterial diversity in the rice rhizosphere soil microbiome. Biotechnol. Bioinf. Bioeng 1, 361–367 (2011).
    Google Scholar 
    Zhao, J. et al. Responses of bacterial communities in arable soils in a rice-wheat cropping system to different fertilizer regimes and sampling times. PLoS ONE 9, e85301. https://doi.org/10.1371/journal.pone.0085301 (2014).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Huang, M. et al. Soil bacterial communities in three rice-based cropping systems differing in productivity. Sci. Rep. 10, 9867. https://doi.org/10.1038/s41598-020-66924-8 (2020).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hayatsu, M. A novel function of controlled-release nitrogen fertilizers. Microbes Environ. 29, 121–122. https://doi.org/10.1264/jsme2.ME2902rh (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Aslam, Z., Yasir, M., Yoon, H. S., Jeon, C. O. & Chung, Y. R. Diversity of the bacterial community in the rice rhizosphere managed under conventional and no-tillage practices. J. Microbiol. 51, 747–756. https://doi.org/10.1007/s12275-013-2528-8 (2013).Article 
    PubMed 

    Google Scholar 
    Min, J. et al. Mechanical side-deep fertilization mitigates ammonia volatilization and nitrogen runoff and increases profitability in rice production independent of fertilizer type and split ratio. J. Clean. Prod. 316, 128370. https://doi.org/10.1016/j.jclepro.2021.128370 (2021).CAS 
    Article 

    Google Scholar 
    Ke, J. et al. Combined controlled-released nitrogen fertilizers and deep placement effects of N leaching, rice yield and N recovery in machine-transplanted rice. Agr. Ecosyst. Environ. 265, 402–412. https://doi.org/10.1016/j.agee.2018.06.023 (2018).CAS 
    Article 

    Google Scholar 
    Cardinale, B. J. et al. Effects of biodiversity on the functioning of trophic groups and ecosystems. Nature 443, 989–992. https://doi.org/10.1038/nature05202 (2006).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336. https://doi.org/10.1038/nmeth.f.303 (2010).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Li, P. et al. Different regulation of soil structure and resource chemistry under animal- and plant-derived organic fertilizers changed soil bacterial communities. Appl. Soil. Ecol. 165, 104020. https://doi.org/10.1016/j.apsoil.2021.104020 (2021).Article 

    Google Scholar 
    Wang, J. et al. Wheat and rice growth stages and fertilization regimes alter soil bacterial community structure, but not diversity. Front. Microbiol. https://doi.org/10.3389/fmicb.2016.01207 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gu, Y., Zhang, X., Tu, S. & Lindström, K. Soil microbial biomass, crop yields, and bacterial community structure as affected by long-term fertilizer treatments under wheat-rice cropping. Eur. J. Soil Biol. 45, 239–246. https://doi.org/10.1016/j.ejsobi.2009.02.005 (2009).CAS 
    Article 

    Google Scholar 
    Niu, J. et al. Insight into the effects of different cropping systems on soil bacterial community and tobacco bacterial wilt rate: Effects of different copping systems. J. Basic Microbiol. 57, 3–11. https://doi.org/10.1002/jobm.201600222 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Wu, T., Qin, Y. & Li, M. Intercropping of tea (Camellia sinensis L.) and Chinese chestnut: Variation in the structure of rhizosphere bacterial communities. J. Soil Sci. Plant Nutr. 21, 2178–2190. https://doi.org/10.1007/s42729-021-00513-0 (2021).CAS 
    Article 

    Google Scholar 
    Li, Y. C. et al. Variations of rhizosphere bacterial communities in tea (Camellia sinensis L.) continuous cropping soil by high-throughput pyrosequencing approach. J. Appl. Microbiol. 121, 787–799. https://doi.org/10.1111/jam.13225 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    Bei, Q., Moser, G., Müller, C. & Liesack, W. Seasonality affects function and complexity but not diversity of the rhizosphere microbiome in European temperate grassland. Sci. Total Environ. 784, 147036. https://doi.org/10.1016/j.scitotenv.2021.147036 (2021).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    You, J., Das, A., Dolan, E. M. & Hu, Z. Ammonia-oxidizing archaea involved in nitrogen removal. Water Res. 43, 1801–1809. https://doi.org/10.1016/j.watres.2009.01.016 (2009).CAS 
    Article 
    PubMed 

    Google Scholar 
    Chuang, S. et al. Potential effects of Rhodococcus qingshengii strain djl-6 on the bioremediation of carbendazim-contaminated soil and the assembly of its microbiome. J. Hazard. Mater. 414, 125496. https://doi.org/10.1016/j.jhazmat.2021.125496 (2021).CAS 
    Article 
    PubMed 

    Google Scholar 
    Luo, D. et al. The anaerobic oxidation of methane in paddy soil by ferric iron and nitrate, and the microbial communities involved. Sci. Total Environ. 788, 147773. https://doi.org/10.1016/j.scitotenv.2021.147773 (2021).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Premnath, N. et al. A crucial review on polycyclic aromatic hydrocarbons—Environmental occurrence and strategies for microbial degradation. Chemosphere 280, 130608. https://doi.org/10.1016/j.chemosphere.2021.130608 (2021).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Makino, A. Photosynthesis, grain yield, and nitrogen utilization in rice and wheat. Plant Physiol. 155, 125–129. https://doi.org/10.1104/pp.110.165076 (2011).CAS 
    Article 
    PubMed 

    Google Scholar 
    Sun, L., Lu, Y., Yu, F., Kronzucker, H. J. & Shi, W. Biological nitrification inhibition by rice root exudates and its relationship with nitrogen-use efficiency. New Phytol. 212, 646–656. https://doi.org/10.1111/nph.14057 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    Coskun, D., Britto, D. T., Shi, W. & Kronzucker, H. J. How plant root exudates shape the nitrogen cycle. Trends Plant Sci. 22, 661–673. https://doi.org/10.1016/j.tplants.2017.05.004 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Qiang, S. et al. Deep placement of mixed controlled-release and conventional urea improves grain yield, nitrogen use efficiency of rainfed spring maize. Arch. Agronomy Soil Sci. 67, 1848–1858. https://doi.org/10.1080/03650340.2020.1817396 (2021).CAS 
    Article 

    Google Scholar 
    Hou, P. et al. Deep fertilization with controlled-release fertilizer for higher cereal yield and N utilization in paddies: The optimal fertilization depth. Agronomy J. https://doi.org/10.1002/agj2.20772 (2021).Article 

    Google Scholar 
    Zhu, S., Vivanco, J. M. & Manter, D. K. Nitrogen fertilizer rate affects root exudation, the rhizosphere microbiome and nitrogen-use-efficiency of maize. Appl. Soil. Ecol. 107, 324–333. https://doi.org/10.1016/j.apsoil.2016.07.009 (2016).Article 

    Google Scholar  More

  • in

    Quantifying fish otolith mineralogy for trace-element chemistry studies

    Morrongiello, J. R., Thresher, R. E. & Smith, D. C. Aquatic biochronologies and climate change. Nat. Clim. Change 2, 849 (2012).ADS 
    Article 

    Google Scholar 
    Pracheil, B. M., Hogan, J. D., Lyons, J. & McIntyre, P. B. Using hard-part microchemistry to advance conservation and management of North American freshwater fishes. Fisheries 39, 451–465 (2014).Article 

    Google Scholar 
    Starrs, D., Ebner, B. C. & Fulton, C. J. All in the ears: Unlocking the early life history biology and spatial ecology of fishes. Biol. Rev. 91, 86–105 (2016).Article 

    Google Scholar 
    Limburg, K. E. Otolith strontium traces environmental history of subyearling American shad Alosa sapidissima. Mar. Ecol. Progr. Ser. 119, 25–35 (1995).ADS 
    Article 

    Google Scholar 
    Kennedy, B. P., Klaue, A., Blum, J. D., Folt, C. L. & Nislow, K. H. Reconstructing the lives of fish using Sr isotopes in otoliths. Can. J. Fish. Aquat. Sci. 59, 925–929 (2002).Article 

    Google Scholar 
    Hogan, J. D., Blum, M. J., Gilliam, J. F., Bickford, N. & McIntyre, P. B. Consequences of alternative dispersal strategies in a putatively amphidromous fish. Ecology 95, 2397–2408 (2014).Article 

    Google Scholar 
    Carlson, A. K., Phelps, Q. E. & Graeb, B. D. S. Chemistry to conservation: using otoliths to advance recreational and commercial fisheries management. J. Fish Biol. 90, 505–527 (2017).CAS 
    Article 

    Google Scholar 
    Campana, S. E. Chemistry and composition of fish otoliths: pathways, mechanisms and applications. Mar. Ecol. Prog. Ser. 188, 263–297 (1999).ADS 
    CAS 
    Article 

    Google Scholar 
    Pracheil, B. M. et al. Sturgeon and paddlefish (Acipenseridae) sagittal otoliths are composed of the calcium carbonate polymorphs vaterite and calcite. J. Fish Biol. 90, 549–558 (2017).CAS 
    Article 

    Google Scholar 
    Pracheil, B. M., George, R. & Chakoumakos, B. C. Significance of otolith calcium carbonate crystal structure diversity to microchemistry studies. Rev. Fish Biol. Fish. 29, 569–588 (2019).Article 

    Google Scholar 
    Nehrke, G., Poigner, H., Wilhelms-Dick, D., Brey, T. & Abele, D. Coexistence of three calcium carbonate polymorphs in the shell of the Antarctic clam Laternula elliptica. Geochem. Geophys. Geosyst. 13(5), 15. https://doi.org/10.1029/2011GC003996 (2012).CAS 
    Article 

    Google Scholar 
    Wassenburg, J. A. et al. Determination of aragonite trace element distribution coefficients from speleothem calcite–aragonite transitions. Geochim. Cosmochim. Acta 190, 347–367 (2016).ADS 
    CAS 
    Article 

    Google Scholar 
    Tzeng, W. N. et al. Misidentification of the migratory history of anguillid eels by Sr/Ca ratios of vaterite otoliths. Mar. Ecol. Prog. Ser. 348, 285–295 (2007).ADS 
    CAS 
    Article 

    Google Scholar 
    Gauldie, R. W. Effects of temperature and vaterite replacement on the chemistry of metal ions in the otoliths of Oncorhynchus tshawytscha. Can. J. Fish. Aquat. Sci. 53, 2015–2026 (1996).CAS 
    Article 

    Google Scholar 
    Reimer, T. et al. Rapid growth causes abnormal vaterite formation in farmed fish otoliths. J. Exp. Biol. 220, 2965–2969 (2017).PubMed 

    Google Scholar 
    Coll-Lladó, C., Giebichenstein, J., Webb, P. B. & Bridges, C. R. Ocean acidification promotes otolith growth and calcite deposition in gilthead sea bream (Sparus aurata) larvae. Sci. Rep. 8, 8384 (2018).ADS 
    Article 

    Google Scholar 
    Loeppky, A. R. et al. Influence of ontogenetic development, temperature, and pCO2 on otolith calcium carbonate polymorph composition in sturgeons. Sci. Rep. 11(1), 1–10 (2021).Article 

    Google Scholar 
    Melancon, S., Fryer, B. J., Ludsin, S. A., Gagnon, J. E. & Yang, Z. Effects of crystal structure on the uptake of metals by lake trout (Salvelinus namaycush) otoliths. Can. J. Fish. Aquat. Sci. 62, 2609–2619 (2005).CAS 
    Article 

    Google Scholar 
    Veinott, G. I., Porter, T. R. & Nasdala, L. Using Mg as a proxy for crystal structure and Sr as an indicator of marine growth in vaterite and aragonite otoliths of aquaculture rainbow trout. Trans. Am. Fish. Soc. 138, 1157–1165 (2009).CAS 
    Article 

    Google Scholar 
    Loeppky, A. R., Chakoumakos, B. C., Pracheil, B. M. & Anderson, W. G. Otoliths of sub-adult Lake Sturgeon Acipenser fulvescens contain aragonite and vaterite calcium carbonate polymorphs. J. Fish Biol. 94, 810–814 (2019).CAS 
    Article 

    Google Scholar 
    Vignon, M. When the presence of a vateritic otolith has morphological effect on its aragonitic partner: Trans-lateral compensation induces bias in microecological patterns in one-side-only vateritic otolith. Can. J. Fish. Aquat. Sci. 77, 285–294 (2020).Article 

    Google Scholar 
    Clarke, A. D., Telmer, K. H. & Mark Shrimpton, J. Elemental analysis of otoliths, fin rays and scales: A comparison of bony structures to provide population and life-history information for the Arctic grayling (Thymallus arcticus). Ecol. Freshw. Fish 16, 354–361 (2007).Article 

    Google Scholar 
    Campana, S. E., Chouinard, G. A., Hanson, J. M., Frechet, A. & Brattey, J. Otolith elemental fingerprints as biological tracers of fish stocks. Fish. Res. 46, 343–357 (2000).Article 

    Google Scholar 
    Gauldie, R. W. Continuous and discontinuous growth in the otolith of Macruronus novaezelandiae (Merlucciidae: Teleostei). J. Morphol. 216(3), 271–294 (1993).CAS 
    Article 

    Google Scholar 
    Long, J. M., Snow, R. A., Pracheil, B. M. & Chakoumakos, B. C. Morphology and composition of Goldeye (Hiodontidae; Hiodon alosoides) otoliths. J. Morphol. 282(4), 511–519 (2021).CAS 
    Article 

    Google Scholar 
    Chakoumakos, B. C., Pracheil, B. M., Koenigs, R. P., Bruch, R. M. & Feygenson, M. Empirically testing vaterite structural models using neutron diffraction and thermal analysis. Sci. Rep. 6, 36799 (2016).ADS 
    CAS 
    Article 

    Google Scholar 
    David, A. W., Grimes, C. B. & Isely, J. J. Vaterite sagittal otoliths in hatchery-reared juvenile red drums. Progres. Fish-Cult. 56(4), 301–303 (1994).Article 

    Google Scholar 
    Tomás, J. & Geffen, A. J. Morphometry and composition of aragonite and vaterite otoliths of deformed laboratory reared juvenile herring from two populations. J. Fish Biol. 63(6), 1383–1401 (2003).Article 

    Google Scholar 
    Kamhi, S. R. On the structure of vaterite CaCO3. Acta Crystallogr. A 16(8), 770–772 (1963).CAS 
    Article 

    Google Scholar 
    Kartnaller, V., Ribeiro, E. M., Venancio, F., Rosariob, F. & Cajaiba, J. Preferential incorporation of sulfate into calcite polymorphs during calcium carbonate precipitation: an experimental approach. CrystEngComm 20, 2241–2244 (2018).CAS 
    Article 

    Google Scholar 
    Paquette, J. & Reeder, R. J. Relationship between surface structure, growth mechanism, and trace element incorporation in calcite. Geochim. Cosmochim. Acta 59(4), 735–749 (1995).ADS 
    CAS 
    Article 

    Google Scholar 
    Hüssy, K. & Mosegaard, H. Atlantic cod (Gadus morhua) growth and otolith accretion characteristics modelled in a bioenergetics context. Can. J. Fish. Aquat. Sci. 61(6), 1021–1031 (2004).Article 

    Google Scholar 
    Fablet, R. et al. Shedding light on fish otolith biomineralization using a bioenergetic approach. PLoS ONE 6(11), e27055 (2011).ADS 
    CAS 
    Article 

    Google Scholar 
    Naslund, A. W., Davis, B. E., Hobbs, J. A., Fangue, N. A. & Todgham, A. E. Warming, not CO2-acidified seawater, alters otolith development of juvenile Antarctic emerald rockcod (Trematomus bernacchii). Polar Biol. 44(9), 1917–1923 (2021).Article 

    Google Scholar 
    Coll-Lladó, C. et al. Pilot study to investigate the effect of long-term exposure to high pCO2 on adult cod (Gadus morhua) otolith morphology and calcium carbonate deposition. Fish Physiol. Biochem. 48, 1879–1891 (2021).Article 

    Google Scholar 
    Söllner, C. et al. Control of crystal size and lattice formation by starmaker in otolith biomineralization. Science 302(5643), 282–286 (2003).ADS 
    Article 

    Google Scholar 
    Rodriguez-Carvajal, J. FULLPROF: A program for Rietveld refinement and pattern matching analysis. In Satellite Meeting on Powder Diffraction of the XV Congress of the IUCr (Vol. 127) (1990).Roisnel, T. & Rodríquez-Carvajal, J. WinPLOTR: A windows tool for powder diffraction pattern analysis. Mater. Sci. 378(1), 118–123 (2001).
    Google Scholar 
    Momma, K. & Izumi, F. VESTA: A three-dimensional visualization system for electronic and structural analysis. J. Appl. Crystallogr. 41(3), 653–658 (2008).CAS 
    Article 

    Google Scholar 
    Slater, J. C. Atomic radii in crystals. J. Chem. Phys. 41(10), 3199–3205 (1964).ADS 
    CAS 
    Article 

    Google Scholar  More