More stories

  • in

    Deforestation is the turning point for the spreading of a weedy epiphyte: an IBM approach

    1.de Wet, J. M. J. & Harlan, J. R. Weeds and domesticates: Evolution in the man-made habitat. Econ. Bot. 29(2), 99–108. https://doi.org/10.1007/BF02863309 (1975).Article 

    Google Scholar 
    2.Ceballos, G. et al. Accelerated modern human—Induced species losses: Entering the sixth mass extinction. Sci. Adv. 1(June), 1–6. https://doi.org/10.1126/sciadv.1400253 (2015).Article 

    Google Scholar 
    3.Wilcove, D. S. Nest predation in forest tracts and the decline of migratory songbirds. Ecology 66(4), 1211–1214 (1985).Article 

    Google Scholar 
    4.Airoldi, L. & Bulleri, F. Anthropogenic disturbance can determine the magnitude of opportunistic species responses on marine urban infrastructures. PLoS ONE https://doi.org/10.1371/journal.pone.0022985 (2011).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    5.Baker, H. G. The evolution of weeds. Annu. Rev. Ecol. Syst. 5, 1–24. https://doi.org/10.2307/2096877 (1974).ADS 
    Article 

    Google Scholar 
    6.Richardson, D. M. et al. Naturalization and invasion of alien plants: Concepts and definitions. Divers. Distrib. 6, 93–107 (2008).Article 

    Google Scholar 
    7.van Etten, M. L., Conner, J. K., Chang, S. M. & Baucom, R. S. Not all weeds are created equal: A database approach uncovers differences in the sexual system of native and introduced weeds. Ecol. Evol. 7(8), 2636–2642. https://doi.org/10.1002/ece3.2820 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    8.Booth, B. D. & Swanton, C. J. Assembly theory applied to weed communities 50th Anniversary—Invited Article Assembly theory applied to weed communities. Weed Sci. 50(3), 2–13. https://doi.org/10.1614/0043-1745(2002)050 (2002).CAS 
    Article 

    Google Scholar 
    9.Kuester, A., Conner, J. K., Culley, T. & Baucom, R. S. How weeds emerge: A taxonomic and trait-based examination using United States data. New Phytol. 202(3), 1055–1068. https://doi.org/10.1111/nph.12698 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    10.van Kleunen, M. et al. The ecology and evolution of alien plants. Annu. Rev. Ecol. Evol. Syst. https://doi.org/10.1146/annurev-ecolsys-110617-062654 (2018).Article 

    Google Scholar 
    11.de Bona, S. et al. Spatio-temporal dynamics of density-dependent dispersal during a population colonisation. Ecol. Lett. 22, 634–644 (2019).PubMed 
    Article 

    Google Scholar 
    12.Baker, H. G. Self-compatibility and establishment after “long-distance” dispersal. Evolution 9(3), 347. https://doi.org/10.2307/2405656 (1955).Article 

    Google Scholar 
    13.Razanajatovo, M. et al. Plants capable of selfing are more likely to become naturalized. Nat. Commun. 7, 13313. https://doi.org/10.1038/ncomms13313 (2016).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    14.Vallejo-Marín, M., Dorken, M. E. & Barrett, S. C. H. The ecological and evolutionary consequences of clonality for plant mating. Annu. Rev. Ecol. Evol. Syst. 41(1), 193–213. https://doi.org/10.1146/annurev.ecolsys.110308.120258 (2010).Article 

    Google Scholar 
    15.Rodger, J. G., Van Kleunen, M. & Johnson, S. D. Pollinators, mates and Allee effects: The importance of self-pollination for fecundity in an invasive lily. Funct. Ecol. 27(4), 1023–1033. https://doi.org/10.1111/1365-2435.12093 (2013).Article 

    Google Scholar 
    16.Barrett, S. C. H. & Harder, L. D. The ecology of mating and its evolutionary consequences in seed plants. Annu. Rev. Ecol. Evol. Syst. https://doi.org/10.1146/annurev-ecolsys-110316-023021 (2017).Article 

    Google Scholar 
    17.Klimeš, L., Klimešová, J., Hendriks, R. & van Groenendael, J. Clonal plant architecture: A comparative analysis of form and function. In The Ecology and Evolution of Clonal Plants (eds De Kroon, H. & Van Groenendael, J. M.) 1–29 (Backhuys, 1997).
    Google Scholar 
    18.Barrett, S. C. H. Influences of clonality on plant sexual reproduction. Proc. Natl. Acad. Sci. 112(29), 8859–8866. https://doi.org/10.1073/pnas.1501712112 (2015).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    19.Heywood, J. S. Spatial analysis of genetic variation in plant populations. Annu. Rev. Ecol. Syst. 22, 335–355 (1991).Article 

    Google Scholar 
    20.Barrett, S. C. H. Evolution of mating systems: Outcrossing versus selfing. In The Princeton Guide to Evolution (ed. Losos, J. B.) 356–362 (Princeton University Press, 2013).
    Google Scholar 
    21.Barrett, S. C. H., Arunkumar, R. & Wright, S. I. The demography and population genomics of evolutionary transitions to self-fertilization in plants. Philos. Trans. R. Soc. B Biol. Sci. 369(1648), 20130344 (2014).Article 

    Google Scholar 
    22.Picó, F. X., Quintana-Ascencio, P. F., Mildén, M., Ehrlén, J. & Pfingsten, I. Modelling the effects of genetics and habitat on the demography of a grassland herb. Basic Appl. Ecol. 10(2), 122–130. https://doi.org/10.1016/j.baae.2008.02.006 (2009).Article 

    Google Scholar 
    23.Ellstrand, N. C. & Roose, M. L. Patterns of genotypic diversity in clonal plant species. Am. J. Bot. 74, 123–131 (1987).Article 

    Google Scholar 
    24.Loh, R., Scarano, F. R., Alves-Ferreira, M. & Salgueiro, F. Implications of clonality to population genetic structure of the nurse species Aechmea nuducaulis (L.) Griseb. (Bromeliaceae). Bot. J. Linn. Soc. 178, 329–341 (2015).Article 

    Google Scholar 
    25.Hedrick, P. W. Purging inbreeding depression and the probability of extinction: Full-sib mating. Heredity 73, 363–372. https://doi.org/10.1038/hdy.1994.183 (1994).Article 
    PubMed 

    Google Scholar 
    26.Arunkumar, R., Ness, R. W., Wright, S. I. & Barrett, S. C. H. The evolution of selfing is accompanied by reduced efficacy of selection and purging of deleterious mutations. Genetics 199(3), 817–829. https://doi.org/10.1534/genetics.114.172809 (2015).Article 
    PubMed 

    Google Scholar 
    27.Pannell, J. R. & Barrett, S. C. H. Baker’s law revisited: Reproductive assurance in a metapopulation. Evolution 52(3), 657–668. https://doi.org/10.2307/2411261 (1998).Article 
    PubMed 

    Google Scholar 
    28.Hamrick, J. L. & Trapnell, D. W. Using population genetic analyses to understand seed dispersal patterns. Acta Oecologica 37, 641–649 (2011).ADS 
    Article 

    Google Scholar 
    29.Côrtes, M. C. et al. Low plant density enhances gene dispersal in the Amazonian understory herb Heliconia acuminata. Mol. Ecol. 22, 5716–5729 (2013).PubMed 
    Article 
    CAS 

    Google Scholar 
    30.Trapnell, D. W., Hamrick, J. L., Ishibashi, C. D. & Kartzinel, T. R. Genetic inference of epiphytic orchid colonization; it may only take one. Mol. Ecol. 22, 3680–3692. https://doi.org/10.1111/mec.12338 (2013).Article 
    PubMed 

    Google Scholar 
    31.Chung, M. Y. et al. Fine-scale genetic structure in populations of the spring ephemeral herb Megaleranthis saniculifolia (Ranunculaceae). Flora Morphol. Distrib. Funct. Ecol. Plants 240, 16–24 (2018).
    Google Scholar 
    32.Roberts, N. R., Dalton, P. J. & Jordan, G. J. Epiphytic ferns and bryophytes of Tasmanian tree-ferns: A comparison of diversity and composition between two host species. Austral Ecol. 30(2), 146–154. https://doi.org/10.1111/j.1442-9993.2005.01440.x (2005).Article 

    Google Scholar 
    33.Cardelús, C. L. & Chazdon, R. L. Inner-crown microenvironments of two emergent tree species in a lowland wet forest. Biotropica 37(2), 238–244. https://doi.org/10.1111/j.1744-7429.2005.00032.x (2005).Article 

    Google Scholar 
    34.Quaresma, A. C., Piedade, M. T. F., Wittmann, F. & ter Steege, H. Species richness, composition, and spatial distribution of vascular epiphytes in Amazonian black-water floodplain forests. Biodivers. Conserv. 27(8), 1981–2002. https://doi.org/10.1007/s10531-018-1520-3 (2018).Article 

    Google Scholar 
    35.Claver, F. K., Alaniz, J. R. & Caldíz, D. O. Tillandsia spp.: Epiphytic weeds of trees and bushes. For. Ecol. Manag. 6(4), 367–372. https://doi.org/10.1016/0378-1127(83)90044-0 (1983).Article 

    Google Scholar 
    36.Bartoli, C. G., Beltrano, J., Fernández, L. V. & Caldíz, D. O. Control of the epiphytic weeds Tillandsia recurvata and Tillandsia aeranthos with different herbicides. For. Ecol. Manage. 59, 289–294 (1993).Article 

    Google Scholar 
    37.Flores-Palacios, A., García-Franco, J. G. & Capistrán-Barradas, A. Biomass, phorophyte specificity and distribution of Tillandsia recurvata in a tropical semi-desert environment (Chihuahuan Desert, Mexico). Plant Ecology and Evolution 148(1), 68–75 (2015).Article 

    Google Scholar 
    38.Birge, W. I. The anatomy and some biological aspects of the “ball moss”, Tillandsia recurvata, 1–24. L. Bull. Univ. Tex. 194(20) (1911).39.Smith, L. B. & Downs, R. J. Tillandsioideae (Bromeliaceae). In Flora Neotropica Monograph 14(2), 663–1492 (1977).40.Hewitt, G. M. (1996). Some genetic consequences of ice ages, and their role in speciation. Biological Journal of the Linnaean Society, 58(July), 247–276. Retrieved from papers3://publication/uuid/B9DB7D5E-D6AE-404C-BFFC-9F813345329441.McWilliams, E. Chronology of the Natural Range Expansion of Tillandsia recurvata (Bromeliaceae) in Texas. Contributions to Botany 15(2), 343–346 (1992).42.Flores-Palacios, A., Barbosa-Duchateau, C. L., Valencia-Díaz, S., Capistrán-Barradas, A. & García-Franco, J. G. Direct and indirect effects of Tillandsia recurvata on Prosopis laevigata in the Chihuahua desert scrubland of San Luis Potosi, Mexico. J. Arid Environ. 104, 88–95. https://doi.org/10.1016/j.jaridenv.2014.02.010 (2014).ADS 
    Article 

    Google Scholar 
    43.Benzing, D. H. Bromeliaceae: Profile of an Adaptive Radiation (Cambridge University Press, 2000).Book 

    Google Scholar 
    44.Benzing, D. H. Air Plants: Epiphytes and Aerial Gardens (Cornell University Press, 2012).Book 

    Google Scholar 
    45.Foster, M. D. Blueprint of the jungle as depicted by the altitude of growth of the Bromeliadswith notes on the culture of certain tropical epiphytes. Bull. N. Y. Bot. Garden 46, 9–16 (1945).
    Google Scholar 
    46.Soltis, D. E., Gilmartin, A. J., Rieseberg, L. & Gardner, S. Genetic variation in the epiphytes Tillandsia ionantha and T. recurvata (Bromeliaceae). Am. J. Bot. 74(4), 531–537 (1987).CAS 
    Article 

    Google Scholar 
    47.Orozco-Ibarrola, O. A., Flores-Hernández, P. S., Victoriano-Romero, E., Corona-López, A. M. & Flores-Palacios, A. Are breeding system and florivory associated with the abundance of Tillandsia species (Bromeliaceae)?. Bot. J. Linn. Soc. 177(1), 50–65. https://doi.org/10.1111/boj.12225 (2015).Article 

    Google Scholar 
    48.Chilpa-Galván, N. et al. Seed traits favouring dispersal and establishment of six epiphytic Tillandsia (Bromeliaceae) species. Seed Sci. Res. https://doi.org/10.1017/S0960258518000247 (2018).Article 

    Google Scholar 
    49.Southwood, T. & Kennedy, C. Trees as islands. Oikos 41(3), 359–371. https://doi.org/10.2307/3544094 (1983).Article 

    Google Scholar 
    50.Burns, K. C. Network properties of an epiphyte metacommunity. J. Ecol. 95(5), 1142–1151 (2007).Article 

    Google Scholar 
    51.Trapnell, D. W., Hamrick, J. L. & Nason, J. D. Three-dimensional fine-scale genetic structure of the neotropical epiphytic orchid, Laelia rubescens. Mol. Ecol. 13, 1111–1118 (2004).CAS 
    PubMed 
    Article 

    Google Scholar 
    52.Torres, E., Riofrío, M.-L. & Iriondo, J. M. Complex fine-scale spatial genetic structure in Epidendrum rhopalostele: an epiphytic orchid. Heredity https://doi.org/10.1038/s41437-018-0139-1 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    53.Victoriano-Romero, E., Valencia-Díaz, A., Toledo-Hernández, V. H. & Flores-Palacios, A. Dispersal limitation of Tillandsia species correlates with rain and host structure in a central Mexican tropical dry forest. PLoS ONE 12(2), e0171614 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    54.Martins, S. E. (2009). Flora fanerogâmica do estado de São Paulo. FAPESP: Instituto de Botânica.55.Chaves, C. J. N., Dyonisio, J. C. J. C. & Rossatto, D. R. D. R. Host trait combinations drive abundance and canopy distribution of atmospheric bromeliad assemblages. AoB Plants 8(October 2015), plw010. https://doi.org/10.1093/aobpla/plw010 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    56.Epps, C. W. & Keyghobadi, N. Landscape genetics in a changing world: Disentangling historical and contemporary influences and inferring change. Mol. Ecol. 24(24), 6021–6040. https://doi.org/10.1111/mec.13454 (2015).Article 
    PubMed 

    Google Scholar 
    57.Cushman, S. A., Shirk, A. & Landguth, E. L. Separating the effects of habitat area, fragmentation and matrix resistance on genetic differentiation in complex landscapes. Landsc. Ecol. 27(3), 369–380. https://doi.org/10.1007/s10980-011-9693-0 (2012).Article 

    Google Scholar 
    58.Jackson, N. D. & Fahrig, L. Habitat amount, not habitat configuration, best predicts population genetic structure in fragmented landscapes. Landsc. Ecol. 31(5), 951–968. https://doi.org/10.1007/s10980-015-0313-2 (2016).Article 

    Google Scholar 
    59.Grimm, V. & Railsback, S. F. Individual-Based Modelling and Ecology (Princeton University Press, 2005).MATH 
    Book 

    Google Scholar 
    60.Csilléry, K., Blum, M. G. B., Gaggiotti, O. E. & François, O. Approximate Bayesian Computation (ABC) in practice. Trends Ecol. Evol. 25(7), 410–418. https://doi.org/10.1016/j.tree.2010.04.001 (2010).Article 
    PubMed 

    Google Scholar 
    61.Udupa, S. M. & Baum, M. High mutation rate and mutational bias at (TAA)n microsatellite loci in chickpea (Cicer arietinum L.). Mol. Genet. Genom. 265(6), 1097–1103. https://doi.org/10.1007/s004380100508 (2001).CAS 
    Article 

    Google Scholar 
    62.Anmarkrud, J. A., Kleven, O., Bachmann, L. & Lifjeld, J. T. Microsatellite evolution: Mutations, sequence variation, and homoplasy in the hypervariable avian microsatellite locus HrU10. BMC Evol. Biol. 8(1), 1–10. https://doi.org/10.1186/1471-2148-8-138 (2008).CAS 
    Article 

    Google Scholar 
    63.Marriage, T. N. et al. Direct estimation of the mutation rate at dinucleotide microsatellite loci in Arabidopsis thaliana (Brassicaceae). Heredity 103(4), 310–317. https://doi.org/10.1038/hdy.2009.67 (2009).CAS 
    Article 
    PubMed 

    Google Scholar 
    64.Bernal, R., Valverde, T. & Hernández-Rosas, L. Habitat preference of the epiphyte Tillandsia recurvata (Bromeliaceae) in a semi-desert environment in Central Mexico. Can. J. Bot. 83(10), 1238–1247 (2005).Article 

    Google Scholar 
    65.Chaves, C. J. & Rossatto, D. R. Unravelling intricate interactions among atmospheric bromeliads with highly overlapping niches in seasonal systems. Plant Biol. 22(2), 243–251 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    66.Vekemans, X. & Hardy, O. J. New insights from fine-scale spatial genetic structure analyses in plant populations. Mol. Ecol. 13(4), 921–935. https://doi.org/10.1046/j.1365-294X.2004.02076.x (2004).CAS 
    Article 
    PubMed 

    Google Scholar 
    67.Ward, S. Genetic analysis of invasive plant populations at different spatial scales. Biol. Invasions 8(3), 541–552. https://doi.org/10.1007/s10530-005-6443-8 (2006).Article 

    Google Scholar 
    68.Pettengill, J. B., Briscoe Runquist, R. D. & Moeller, D. A. Mating system divergence affects the distribution of sequence diversity within and among populations of recently diverged subspecies of Clarkia xantiana (Onagraceae). Am. J. Bot. 103(1), 99–109. https://doi.org/10.3732/ajb.1500147 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    69.Atwater, D. Z., Fletcher, R. A., Dickinson, C. C., Paterson, A. H. & Barney, J. N. Evidence for fine-scale habitat specialization in an invasive weed. J. Plant Ecol. 11(2), 189–199. https://doi.org/10.1093/jpe/rtw124 (2018).Article 

    Google Scholar 
    70.Li, J. & Dong, M. Fine-scale clonal structure and diversity of invasive plant Mikania micrantha H.B.K. and its plant parasite Cuscuta campestris Yunker. Biol. Invasions 11(3), 687–695. https://doi.org/10.1007/s10530-008-9283-5 (2009).MathSciNet 
    Article 

    Google Scholar 
    71.Ren, M. X., Cafasso, D., Cozzolino, S. & Pinheiro, F. Extensive genetic differentiation at a small geographical scale: Reduced seed dispersal in a narrow endemic marsh orchid, Anacamptis robusta. Bot. J. Linn. Soc. 183(3), 429–438. https://doi.org/10.1093/botlinnean/bow017 (2017).Article 

    Google Scholar 
    72.Barluenga, M. et al. Fine-scale spatial genetic structure and gene dispersal in Silene latifolia. Heredity 106(1), 13–24. https://doi.org/10.1038/hdy.2010.38 (2011).CAS 
    Article 
    PubMed 

    Google Scholar 
    73.Charbonneau, A. et al. Weed evolution: Genetic differentiation among wild, weedy, and crop radish. Evol. Appl. https://doi.org/10.1111/eva.12699 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    74.Sagnard, F., Oddou-Muratorio, S., Pichot, C., Vendramin, G. G. & Fady, B. Effects of seed dispersal, adult tree and seedling density on the spatial genetic structure of regeneration at fine temporal and spatial scales. Tree Genet. Genomes 7(1), 37–48. https://doi.org/10.1007/s11295-010-0313-y (2011).Article 

    Google Scholar 
    75.Counsens, R. & Mortimer, M. Dynamics of Weed Populations (Cambridge University Press, 1995).Book 

    Google Scholar 
    76.Loreau, M. et al. Unifying sources and sinks in ecology and Earth sciences. Biol. Rev. 88, 365–379 (2013).PubMed 
    Article 

    Google Scholar 
    77.dos Santos, L. S. et al. Generalized Allee effect model. Theory Biosci. 133, 117–124 (2014).PubMed 

    Google Scholar 
    78.Spruch, L. et al. Modeling community assembly on growing habitat “islands”: A case study on trees and their vascular epiphyte communities. Theor. Ecol. 12, 1–17 (2019).Article 

    Google Scholar 
    79.Einzmann, H. J. R. & Zotz, G. “No signs of saturation”: long-term dynamics of vascular epiphyte communities in a human-modified landscape. Biodivers. Conserv. 26, 1393–1410 (2017).Article 

    Google Scholar 
    80.Belinchón, R., Harrison, P. J., Mair, L., Várkonyi, G. & Snäll, T. Local epiphyte establishment and future metapopulation dynamics in landscapes with different spatiotemporal properties. Ecology 98(3), 741–750. https://doi.org/10.1002/ecy.1686 (2017).Article 
    PubMed 

    Google Scholar 
    81.Vergara-Torres, C. A., Pacheco-Álvarez, M. C. & Flores-Palacios, A. Host preference and host limitation of vascular epiphytes in a tropical dry forest of central Mexico. J. Trop. Ecol. 26(6), 563–570. https://doi.org/10.1017/S0266467410000349 (2010).Article 

    Google Scholar 
    82.Barrett, S. C. H. & Kohn, J. R. Genetic and evolutionary consequences of small population size in plants: Implications for conservation. In Genetics and Conservation of Rare Plants (eds Falk, D. A. & Holsinge, K. E.) 3–30 (Oxford University Press, 1991).
    Google Scholar 
    83.Nathan, R., Horn, H. S., Chave, J. & Levin, S. A. Mechanistic models for tree seed dispersal by wind in dense forests and open landscapes. In Seed Dispersal and Frugivory-Ecologie, Evolution, Conservation 69–82 (2002). https://doi.org/10.1079/9780851995250.006984.Cousens, R. et al. Dispersal in Plants. A Population Perspective (Oxford University Press, 2008).Book 

    Google Scholar 
    85.Snäll, T., Ehrlén, J. & Rydin, H. Colonization-extinction dynamics of an epiphyte metapopulation in a dynamic landscape. Ecology 86(1), 106–115 (2005).Article 

    Google Scholar 
    86.Ruiz-Cordova, J. P., Toledo-Hernández, V. H. & Flores-Palacios, A. The effect of substrate abundance in the vertical stratification of bromeliad epiphytes in a tropical dry forest (Mexico). Flora Morphol. Distrib. Funct. Ecol. Plants 209(8), 375–384. https://doi.org/10.1016/j.flora.2014.06.003 (2014).Article 

    Google Scholar 
    87.Flores-Palacios, A., Bustamante-Molina, A. B., Corona-López, A. M. & Valencia-Díaz, S. Seed number, germination and longevity in wild dry forest Tillandsia species of horticultural value. Scientia Hortic. 187, 72–79 (2015).Article 

    Google Scholar 
    88.Goodman, R., & Herold, M. (2014). Why maintaining tropical forests is essential and urgent for a stable climate. Center for Global Development Working Paper, (385).89.Seymour, F. & Busch, J. Why Forests? Why Now?: The Science, Economics, and Politics of Tropical Forests and Climate Change (Brookings Institution Press, 2016).
    Google Scholar 
    90.Stephenson, N. L. et al. Rate of tree carbon accumulation increases continuously with tree size. Nature 507(7490), 90–93 (2014).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    91.Tel-Zur, N., Abbo, S., Myslabodsky, D. & Mizrahi, Y. Modified CTAB procedure for DNA isolation from epiphytic cacti of genera Hylocereus and Selenicereus (Cactaceae). Plant Mol. Biol. Rep. 17, 249–254 (1999).CAS 
    Article 

    Google Scholar 
    92.Chaves, C. J. N., Aoki-Gonçalves, F., Leal, B. S. S., Rossatto, D. R. & Palma-Silva, C. Transferability of nuclear microsatellite markers to the atmospheric bromeliads Tillandsia recurvata and T. aeranthos (Bromeliaceae). Braz. J. Bot. 41, 931–935. https://doi.org/10.1007/s40415-018-0494-4 (2018).Article 

    Google Scholar 
    93.Keenan, K., Mcginnity, P., Cross, T. F., Crozier, W. W. & Prodöhl, P. A. DiveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors. Methods Ecol. Evol. https://doi.org/10.1111/2041-210X.12067 (2013).Article 

    Google Scholar 
    94.Slatkin, M. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139, 457–462 (1995).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    95.Nei, M. Genetic distances between populations. Am. Nat. 106, 283–292 (1972).Article 

    Google Scholar 
    96.Edwards, A. W. F. Distance between populations on the basis of gene frequencies. Biometrics 27, 873–881 (1971).CAS 
    PubMed 
    Article 

    Google Scholar 
    97.Reynolds, J. B., Weir, B. S. & Cockerham, C. C. Estimation of the coancestry coefficient: Basis for a short-term genetic distance. Genetics 105, 767–779 (1983).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    98.Kamvar, Z. N., Tabima, J. F. & Grünwald, N. J. Poppr: An R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ https://doi.org/10.7717/peerj.281 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    99.Paradis, E. pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26, 419–420 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    100.Excoffier, L., Smouse, P. E. & Quattro, J. M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131, 479–491. https://doi.org/10.1007/s00424-009-0730-7 (1992).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    101.Loiselle, B. A., Sork, V. L., Nason, J. & Graham, C. Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am. J. Bot. 82(11), 1420–1425 (1995).Article 

    Google Scholar 
    102.Bailleul, D., Stoeckel, S. & Arnaud-Haond, S. RClone: A package to identify MultiLocus Clonal Lineages and handle clonal data sets in r. Methods Ecol. Evol. 7(8), 966–970. https://doi.org/10.1111/2041-210X.12550 (2016).Article 

    Google Scholar 
    103.Harrison, S. et al. Beta diversity on geographic gradients in Britain. J. Anim. Ecol. 61(1), 151–158 (1992).Article 

    Google Scholar 
    104.Jost, L. Partitioning diversity into independent alpha and beta components. Ecology 88(10), 2427–2439. https://doi.org/10.1890/07-1861.1 (2007).Article 
    PubMed 

    Google Scholar 
    105.Charney, N. & Record, S. Vegetarian: Jost diversity measures for community data. https://cran.r-project.org/web/packages/vegetarian/index.html (2012). Accessed Jul 2018.106.Wilensky, U. NetLogo (Northwestern University, Center for Connected Learning and Computer-Based Modeling, 1999).
    Google Scholar 
    107.Grimm, V. et al. A standard protocol for describing individual-based and agent-based models. Ecol. Model. 198(1–2), 115–126. https://doi.org/10.1016/j.ecolmodel.2006.04.023 (2006).Article 

    Google Scholar 
    108.Grimm, V. et al. The ODD protocol: A review and first update. Ecol. Model. 221(23), 2760–2768. https://doi.org/10.1016/j.ecolmodel.2010.08.019 (2010).Article 

    Google Scholar 
    109.Kooijman, B. & Kooijman, S. A. L. M. Dynamic Energy Budget Theory for Metabolic Organisation (Cambridge University Press, 2010).
    Google Scholar 
    110.Sibly, R. M. et al. Representing the acquisition and use of energy by individuals in agent-based models of animal populations. Methods Ecol. Evol. 4(2), 151–161 (2013).Article 

    Google Scholar 
    111.Johnston, A. S. A., Hodson, M. E., Thorbek, P., Alvarez, T. & Sibly, R. M. An energy budget agent-based model of earthworm populations and its application to study the effects of pesticides. Ecol. Model. 280, 5–17 (2014).CAS 
    Article 

    Google Scholar 
    112.van der Vaart, E., Johnston, A. S. A. & Sibly, R. M. Predicting how many animals will be where: How to build, calibrate and evaluate individual-based models. Ecol. Model. 326, 113–123 (2016).Article 

    Google Scholar 
    113.Garza, J. C. & Williamson, E. G. Detection of reduction in population size using data from microsatellite loci. Mol. Ecol. 10, 305–318 (2001).CAS 
    PubMed 
    Article 

    Google Scholar 
    114.Excoffier, L., Laval, G. & Schneider, S. Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evol. Bioinform. Online 1, 47–50 (2005).CAS 
    Article 

    Google Scholar 
    115.Csilléry, K., François, O. & Blum, M. G. abc: An R package for approximate Bayesian computation (ABC). Methods Ecol. Evol. 3(3), 475–479 (2012).Article 

    Google Scholar 
    116.Pastur, G. M., Lencinas, M. V., Cellini, J. M. & Mundo, I. Diameter growth: Can live trees decrease?. Forestry 80(1), 83–88. https://doi.org/10.1093/forestry/cpl047 (2007).Article 

    Google Scholar  More

  • in

    Plant defence to sequential attack is adapted to prevalent herbivores

    1.Karban, R. The ecology and evolution of induced responses to herbivory and how plants perceive risk. Ecol. Entomol. 45, 1–9 (2020).Article 

    Google Scholar 
    2.Heil, M. Plastic defence expression in plants. Evol. Ecol. 24, 555–569 (2010).Article 

    Google Scholar 
    3.Erb, M. & Reymond, P. Molecular interactions between plants and insect herbivores. Annu. Rev. Plant Biol. 70, 527–557 (2019).CAS 
    Article 

    Google Scholar 
    4.Ohgushi, T. Indirect interaction webs: herbivore-induced effects through trait change in plants. Annu. Rev. Ecol. Evol. Syst. 36, 81–105 (2005).Article 

    Google Scholar 
    5.Poelman, E. H., van Loon, J. J. A., van Dam, N. M., Vet, L. E. M. & Dicke, M. Herbivore-induced plant responses in Brassica oleracea prevail over effects of constitutive resistance and result in enhanced herbivore attack. Ecol. Entomol. 35, 240–247 (2010).Article 

    Google Scholar 
    6.Erb, M., Meldau, S. & Howe, G. A. Role of phytohormones in insect-specific plant reactions. Trends Plant Sci. 17, 250–259 (2012).CAS 
    Article 

    Google Scholar 
    7.Soler, R. et al. Plant-mediated facilitation between a leaf-feeding and a phloem-feeding insect in a brassicaceous plant: from insect performance to gene transcription. Funct. Ecol. 26, 156–166 (2012).Article 

    Google Scholar 
    8.Thaler, J. S., Humphrey, P. T. & Whiteman, N. K. Evolution of jasmonate and salicylate signal crosstalk. Trends Plant Sci. 17, 260–270 (2012).CAS 
    Article 

    Google Scholar 
    9.Ehrlich, P. R. & Raven, P. H. Butterflies and plants—a study in coevolution. Evolution 18, 586–608 (1964).Article 

    Google Scholar 
    10.Labandeira, C. C., Johnson, K. R. & Wilf, P. Impact of the terminal Cretaceous event on plant–insect associations. Proc. Natl Acad. Sci. USA 99, 2061–2066 (2002).CAS 
    Article 

    Google Scholar 
    11.Ramos, S. E. & Schiestl, F. P. Rapid plant evolution driven by the interaction of pollination and herbivory. Science 364, 193–196 (2019).CAS 
    Article 

    Google Scholar 
    12.Züst, T. et al. Natural enemies drive geographic variation in plant defenses. Science 338, 116–119 (2012).Article 

    Google Scholar 
    13.Agrawal, A. A. Specificity of induced resistance in wild radish: causes and consequences for two specialist and two generalist caterpillars. Oikos 89, 493–500 (2000).Article 

    Google Scholar 
    14.Moreira, X., Abdala‐Roberts, L. & Castagneyrol, B. Interactions between plant defence signalling pathways: evidence from bioassays with insect herbivores and plant pathogens. J. Ecol. 106, 2353–2364 (2018).Article 

    Google Scholar 
    15.Voelckel, C. & Baldwin, I. T. Herbivore-induced plant vaccination. Part II. Array-studies reveal the transience of herbivore-specific transcriptional imprints and a distinct imprint from stress combinations. Plant J. 38, 650–663 (2004).CAS 
    Article 

    Google Scholar 
    16.Caarls, L., Pieterse, C. M. J. & Van Wees, S. C. M. How salicylic acid takes transcriptional control over jasmonic acid signaling. Front. Plant Sci. 6, 170 (2015).Article 

    Google Scholar 
    17.Proietti, S. et al. Genome-wide association study reveals novel players in defense hormone crosstalk in Arabidopsis. Plant Cell Environ. 41, 2342–2356 (2018).CAS 
    Article 

    Google Scholar 
    18.Davidson-Lowe, E., Szendrei, Z. & Ali, J. G. Asymmetric effects of a leaf-chewing herbivore on aphid population growth. Ecol. Entomol. 44, 81–92 (2019).Article 

    Google Scholar 
    19.Eisenring, M., Glauser, G., Meissle, M. & Romeis, J. Differential impact of herbivores from three feeding guilds on systemic secondary metabolite induction, phytohormone levels and plant-mediated herbivore interactions. J. Chem. Ecol. 44, 1178–1189 (2018).CAS 
    Article 

    Google Scholar 
    20.Züst, T. & Agrawal, A. A. Mechanisms and evolution of plant resistance to aphids. Nat. Plants 2, 15206 (2016).Article 

    Google Scholar 
    21.Ali, J. G., Agrawal, A. A. & Fox, C. Asymmetry of plant-mediated interactions between specialist aphids and caterpillars on two milkweeds. Funct. Ecol. 28, 1404–1412 (2014).Article 

    Google Scholar 
    22.Bidart-Bouzat, M. G. & Kliebenstein, D. An ecological genomic approach challenging the paradigm of differential plant responses to specialist versus generalist insect herbivores. Oecologia 167, 677–689 (2011).Article 

    Google Scholar 
    23.Ali, J. G. & Agrawal, A. A. Specialist versus generalist insect herbivores and plant defense. Trends Plant Sci. 17, 293–302 (2012).CAS 
    Article 

    Google Scholar 
    24.Mertens, D. et al. Predictability of biotic stress structures plant defence evolution. Trends Ecol. Evol. 36, 444–456 (2021).Article 

    Google Scholar 
    25.Appel, H. M. et al. Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores. Front. Plant Sci. 5, 20 (2014).
    Google Scholar 
    26.Hedges, L. V., Gurevitch, J. & Curtis, P. S. The meta-analysis of response ratios in experimental ecology. Ecology 80, 1150–1156 (1999).Article 

    Google Scholar 
    27.Connell, J. H. Diversity and the coevolution of competitors, or the ghost of competition past. Oikos 35, 131–138 (1980).Article 

    Google Scholar 
    28.Barton, K. E. & Koricheva, J. The ontogeny of plant defense and herbivory: characterizing general patterns using meta-analysis. Am. Nat. 175, 481–493 (2010).Article 

    Google Scholar 
    29.Barbosa, P., Letourneau, D. K. & Agrawal A. A. (eds) Insect Outbreaks Revisited (Wiley-Blackwell, 2012).30.Bischoff, A. & Trémulot, S. Differentiation and adaptation in Brassica nigra populations: interactions with related herbivores. Oecologia 165, 971–981 (2011).Article 

    Google Scholar 
    31.Schlinkert, H. et al. Plant size as determinant of species richness of herbivores, natural enemies and pollinators across 21 Brassicaceae species. PLoS ONE 10, e0135928 (2015).Article 

    Google Scholar 
    32.Snoeren, T. A. L., Broekgaarden, C. & Dicke, M. Jasmonates differentially affect interconnected signal-transduction pathways of Pieris rapae-induced defenses in Arabidopsis thaliana. Insect Sci. 18, 249–258 (2011).CAS 
    Article 

    Google Scholar 
    33.Leon-Reyes, A. et al. Salicylate-mediated suppression of jasmonate-responsive gene expression in Arabidopsis is targeted downstream of the jasmonate biosynthesis pathway. Planta 232, 1423–1432 (2010).CAS 
    Article 

    Google Scholar 
    34.Broekgaarden, C., Voorrips, R. E., Dicke, M. & Vosman, B. Transcriptional responses of Brassica nigra to feeding by specialist insects of different feeding guilds. Insect Sci. 18, 259–272 (2011).CAS 
    Article 

    Google Scholar 
    35.Fernández de Bobadilla, M. et al. Insect species richness affects plant responses to multi‐herbivore attack. New Phytol. https://doi.org/10.1111/nph.17228 (2021).36.Johnson, J. B. & Omland, K. S. Model selection in ecology and evolution. Trends Ecol. Evol. 19, 101–108 (2004).Article 

    Google Scholar 
    37.Zuur, A. F., Ieno, E. N., Walker, N., Saveliev, A. A. & Smith, G. M. Mixed Effects Models and Extensions in Ecology with R (Springer, 2009).38.Pinheiro, J., Bates, D., DebRoy, S. & Sarkar, D. nlme: Linear and nonlinear mixed effects models. R package version 3.1-141 https://CRAN.R-project.org/package=nlme (2019).39.Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).Article 

    Google Scholar 
    40.Zeileis, A. & Hothorn, T. Diagnostic checking in regression relationships. R News 2, 7–10 (2002).
    Google Scholar 
    41.Lenth, R. emmean: Estimated marginal means, aka least-squares means. R package version 1.2.3 https://CRAN.R-project.org/package=emmeans (2018).42.R Core Team. R: A Language and Environment for Statistical Computing version 3.2.4 (R Foundation for Statistical Computing, 2016).43.Lajeunesse, M. J. On the meta‐analysis of response ratios for studies with correlated and multi‐group designs. Ecology 92, 2049–2055 (2011).Article 

    Google Scholar  More

  • in

    Diurnal oscillations in gut bacterial load and composition eclipse seasonal and lifetime dynamics in wild meerkats

    Effects of storage and technical variationWe first validated our methods by assessing the effect of storage and technical variation on microbiome composition. To quantify the effect of the two storage methods on bacterial composition in fresh samples, we performed a separate pilot study with nine faecal samples sourced from nine captive meerkats at Zurich University. Samples were immediately frozen after collection, and then either freeze-dried or kept frozen at −80 °C for seven days. Microbiome composition clustered strongly by sample identity in their beta diversity (Supplementary Fig. 1b), and storage did not significantly affect composition (Weighted Unifrac: F = 0.7, p = 0.52; Unweighted Unifrac: F = 1.0, p = 0.37). Across samples analysed in this study, storage had significant yet small effects on estimated bacterial load, with frozen samples overall having slightly lower estimated abundance (t = 7.2, p  More

  • in

    Biological activity of chitosan inducing resistance efficiency of rice (Oryza sativa L.) after treatment with fungal based chitosan

    1.Chaney, R. L., Kim, W. I., Kunhikrishnan, A., Yang, J. E. & Ok, Y. S. Integrated management strategies for arsenic and cadmium in rice paddy environments. Geoderma 270, 1–116. https://doi.org/10.1016/j.geoderma.2016.03.001 (2016).ADS 
    Article 

    Google Scholar 
    2.Nakashima, K., Yamaguchi-Shinozaki, K. & Shinozaki, K. The transcriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat. Front. Plant Sci. 5, 170. https://doi.org/10.3389/fpls.2014.00170 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    3.Senthil-Nathan, S. Physiological and biochemical effect of neem and other Meliaceae plants secondary metabolites against Lepidopteran insects. Front. Physiol. 4, 359. https://doi.org/10.3389/fphys.2013.00359 (2013).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    4.Kalaivani, K., Maruthi-Kalaiselvi, M. & Senthil-Nathan, S. Seed treatment and foliar application of methyl salicylate (MeSA) as a defense mechanism in rice plants against the pathogenic bacterium, Xanthomonas oryzae pv. oryzae. Pest Biochem. Physiol. 171, 104718. https://doi.org/10.1016/j.pestbp.2020.104718 (2021).CAS 
    Article 

    Google Scholar 
    5.Das, G. & Rao, G. J. N. Molecular marker assisted gene stacking for biotic and abiotic stress resistance genes in an elite rice cultivar. Front. Plant Sci. 6, 698. https://doi.org/10.3389/fpls.2015.00698 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    6.Senthil-Nathan, S. A review of biopesticides and their mode of action against insect pests. Environ. Sustain. https://doi.org/10.1007/978-81-322-2056-5_3 (2015).Article 

    Google Scholar 
    7.Shi, W. et al. Grain yield and quality responses of tropical hybrid rice to high night-time temperature. Food Crop Res. 190, 18–25. https://doi.org/10.1016/j.fcr.2015.10.006 (2016).Article 

    Google Scholar 
    8.Farooq, M. et al. Rice direct seeding: Experiences, challenges and opportunities. Soil Till. Res. 111, 87–98. https://doi.org/10.1016/j.still.2010.10.008 (2011).Article 

    Google Scholar 
    9.Brown, J. K. M. Yield penalties of disease resistance in crops. Curr. Opin. Plant Biol. 5, 339–344. https://doi.org/10.1016/S1369-5266(02)00270-4 (2002).CAS 
    Article 
    PubMed 

    Google Scholar 
    10.Liu, H. et al. Antifungal effect and mechanism of chitosan against the rice sheath blight pathogen, Rhizoctonia solani. Biotechnol. Lett. 34, 2291–2298. https://doi.org/10.1007/s10529-012-1035-z (2012).CAS 
    Article 
    PubMed 

    Google Scholar 
    11.Orzali, L., Corsi, B., Forni, C. & Riccinoi, L. Chitosan in agriculture: A new challenge for managing plant disease, biological activities and application of marine polysaccharides. Biol. Act. Appl. Mar. Polysaccharides. 17–36. https://doi.org/10.5772/66840 (2017).
    12.Anosheh, H. P., Sadeghi, H. & Emam, Y. Chemical priming with urea and KNO3 enhances maize hybrids (Zea mays L.) seed viability under abiotic stress. J. Crop Sci. Biotechnol. 14, 289–295. https://doi.org/10.1007/s12892-011-0039-x (2011).Article 

    Google Scholar 
    13.Hänsch, R. & Mendel, R. R. Physiological functions of mineral micronutrients (Cu, Zn, Mn, Fe, Ni, Mo, B, Cl). Curr. Opin. Plant Biol. 12, 259–266. https://doi.org/10.1016/j.pbi.2009.05.006 (2009).CAS 
    Article 
    PubMed 

    Google Scholar 
    14.Savvides, A., Ali, S., Tester, M. & Fotopoulos, V. Chemical priming of plants against multiple abiotic stresses: Mission possible?. Trends Plant Sci. 21, 329–340. https://doi.org/10.1016/j.tplants.2015.11.003 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    15.Kurita, K. Chitin and chitosan: Functional biopolymers from marine crustaceans. Mar. Biotechnol. 8, 203–226. https://doi.org/10.1007/s10126-005-0097-5 (2006).CAS 
    Article 

    Google Scholar 
    16.Hamed, I., Özogul, F. & Regenstein, J. M. Industrial applications of crustacean by-products (chitin, chitosan, and chitooligosaccharides): A review. Trends Food Sci. Technol. 48, 40–50. https://doi.org/10.1016/j.tifs.2015.11.007 (2016).CAS 
    Article 

    Google Scholar 
    17.Badawy, M. E. I. & Rabea, E. I. A. Biopolymer chitosan and its derivatives as promising antimicrobial agents against plant pathogens and their applications in crop protection. Int. J. Carbohydr. Chem. https://doi.org/10.1155/2011/460381 (2011).Article 

    Google Scholar 
    18.Davydova, V. N. et al. Chitosan antiviral activity: Dependence on structure and depolymerization method. Appl. Biochem. Microbiol. 47, 103–108. https://doi.org/10.1134/S0003683811010042 (2011).CAS 
    Article 

    Google Scholar 
    19.Park, B. K. & Kim, M. M. Applications of chitin and its derivatives in biological medicine. Int. J. Mol. Sci. 11, 5152–5164. https://doi.org/10.3390/ijms11125152 (2010).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    20.Malerba, M. & Cerana, R. Chitosan effects on plant systems. Int. J. Mol. Sci. 17, 996. https://doi.org/10.3390/ijms17070996 (2016).CAS 
    Article 
    PubMed Central 

    Google Scholar 
    21.Liu, H. et al. Progress and constraints of dry direct-seeded rice in China. J. Food Agric. Environ. 2121, 465–472 (2014).
    Google Scholar 
    22.Li, B., Wang, X., Chen, R., Huangfu, W. & Xie, G. Antibacterial activity of chitosan solution against Xanthomonas pathogenic bacteria isolated from Euphorbia pulcherrima. Carbohydr. Polym. 72, 287–292. https://doi.org/10.1016/j.carbpol.2007.08.012 (2008).CAS 
    Article 

    Google Scholar 
    23.Falcón-Rodríguez, A. B., Cabrera, J. C., Wégria, G., Onderwater, R. C. A., González, G., Nápoles, M. C., Costales, D., Rogers, H. J., Diosdado, E., González, S., Cabrera, G., González, L. & Wattiez, R. Practical use of oligosaccharins in agriculture. In Ist World Congress on the use of biostimulants in agriculture. Acta Hortic. 1009, 195–212 (2012).24.Yin, H. et al. Genome shuffling of Saccharomyces cerevisiae for enhanced glutathione yield and relative gene expression analysis using fluorescent quantitation reverse transcription polymerase chain reaction. J. Microbiol. Methods 127, 188–192. https://doi.org/10.1016/j.mimet.2016.06.012 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    25.Borah, N. et al. Low energy rice stubble management through in situ decomposition. Procedia Environ. Sci. 35, 771–780. https://doi.org/10.1016/j.proenv.2016.07.092 (2016).CAS 
    Article 

    Google Scholar 
    26.Singh, R., Srivastava, M. & Shukla, A. Environmental sustainability of bioethanol production from rice straw in India: A review. Renew. Sustain. Energy Rev. 54, 202–216. https://doi.org/10.1016/j.rser.2015.10.005 (2016).CAS 
    Article 

    Google Scholar 
    27.Mrudula, S. & Murugammal, R. Production of cellulase by Aspergillus niger under submerged and solid state fermentation using coir waste as a substrate. Braz. J. Microbiol. 42, 1119–1127. https://doi.org/10.1590/S1517-83822011000300033 (2011).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    28.El-Sayed, S. M. & Mahdy, M. E. Effect of chitosan on root-knot nematode, Meloidogyne javanica on tomato plants. Int. J. ChemTech Res. 7, 1985–1992 (2015).
    Google Scholar 
    29.Iriti, M. & Varoni, E. M. Chitosan-induced antiviral activity and innate immunity in plants. Environ. Sci. Pollut. Res. 22, 2935–2944. https://doi.org/10.1007/s11356-014-3571-7 (2015).CAS 
    Article 

    Google Scholar 
    30.Orzali, L. et al. Chitosan in agriculture: A new challenge for chitosan in agriculture: A new challenge for managing plant disease managing plant disease. InTech Open Publisher https://doi.org/10.5772/66840 (2017).ADS 
    Article 

    Google Scholar 
    31.Nanda, S., Mohammad, J., Reddy, S. N., Kozinski, J. A. & Dalai, A. K. Pathways of lignocellulosic biomass conversion to renewable fuels. Biomass Convers. Biorefinery 4, 157–191. https://doi.org/10.1007/s13399-013-0097-z (2014).CAS 
    Article 

    Google Scholar 
    32.Aggarwal, N. K., Goyal, V., Saini, A., Yadav, A. & Gupta, R. Enzymatic saccharification of pretreated rice straw by cellulases from Aspergillus niger BK01. 3 Biotech 7, 158. https://doi.org/10.1007/s13205-017-0755-0 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    33.Fatma, H., Abd-EI-Zaher & Fadel, M. Production of bioethanol via enzymatic saccharification of rice straw by cellulase produced by Trichoderma Reesei under solid state fermentation. N. Y. Sci. J., 72–78. http://www.sciencepub.net/newyork (2010).34.Chang, A. K. T., Frias, R. R., Alvarez, L. V., Bigol, U. G. & Guzman, J. P. M. D. Comparative antibacterial activity of commercial chitosan and chitosan extracted from Auricularia sp. Biocatal. Agric. Biotechnol. 17, 189–195. https://doi.org/10.1016/j.bcab.2018.11.016 (2019).Article 

    Google Scholar 
    35.Lizárraga-Paulín, E. G., Miranda-Castro, S. P., Moreno-Martínez, E., Lara-Sagahón, A. V. & Torres-Pacheco, I. Maize seed coatings and seedling sprayings with chitosan and hydrogen peroxide: Their influence on some phenological and biochemical behaviors. J. Zhejiang Univ. Sci. B. 14, 87–96. https://doi.org/10.1631/jzus.B1200270 (2013).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    36.Hadwiger, L. A., Fristensky, B. & Riggleman, R. C. Chitosan, a natural regulator in plant-fungal pathogen interactions, increases crop yields. Chitin Chitosan Relat. Enzymes. https://doi.org/10.1016/b978-0-12-780950-2.50024-1 (1984).Article 

    Google Scholar 
    37.Mrda, J., Crnobarac, J., Dušanić, N., Jocić, S. & Miklič, V. Germination energy as a parameter of seed quality in different sunflower genotypes. Genetika 43, 427–436. https://doi.org/10.2298/GENSR1103427M (2011).Article 

    Google Scholar 
    38.Singh, H. et al. Seed priming techniques in field crops—A review. Agric. Rev. 36, 1–14. https://doi.org/10.18805/ag.v36i4.6662 (2015).Article 

    Google Scholar 
    39.Hameed, A., Sheikh, M. A., Farooq, T., Basra, S. M. A. & Jamil, A. Chitosan priming enhances the seed germination, antioxidants, hydrolytic enzymes, soluble proteins and sugars in wheat seeds. Agrochimica LVII, 31–46 (2013).
    Google Scholar 
    40.Zhou, Y. G. et al. Effects of chitosan on some physiological activity in germinating seed of peanut. J. Peanut Sci. 31, 22–25 (2002).
    Google Scholar 
    41.Samarah, N. H., Wang, H. & Welbaum, G. E. Pepper (Capsicum annuum) seed germination and vigour following nanochitin, chitosan or hydropriming treatments. Seed Sci. Technol. 44, 1–15. https://doi.org/10.15258/sst.2016.44.3.18 (2016).Article 

    Google Scholar 
    42.Chen, J. L. & Zhao, Y. Effect of molecular weight, acid, and plasticizer on the physicochemical and antibacterial properties of β-chitosan based films. J. Food Sci. 77, E127–E136. https://doi.org/10.1111/j.1750-3841.2012.02686.x (2012).CAS 
    Article 
    PubMed 

    Google Scholar 
    43.Kulikov, S. N., Chirkov, S. N., Il’ina, A. V., Lopatin, S. A. & Varlamov, V. P. Effect of the molecular weight of chitosan on its antiviral activity in plants. Appl. Biochem. Microbiol. 42, 200–203. https://doi.org/10.1134/S0003683806020165 (2006).CAS 
    Article 

    Google Scholar 
    44.El Hadrami, A., Adam, L. R., El Hadrami, I. & Daayf, F. Chitosan in plant protection. Mar. Drugs 8, 968–987. https://doi.org/10.3390/md8040968 (2010).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    45.Orzali, L., Forni, C. & Riccioni, L. Effect of chitosan seed treatment as elicitor of resistance to Fusarium graminearum in wheat. Seed Sci. Technol. 42, 132–149. https://doi.org/10.15258/sst.2014.42.2.03 (2014).Article 

    Google Scholar 
    46.Rabea, E. I., Badawy, M. E. T., Stevens, C. V., Smagghe, G. & Steurbaut, W. Chitosan as antimicrobial agent: Applications and mode of action. Biomacromol 4, 1457–1465. https://doi.org/10.1021/bm034130m (2003).CAS 
    Article 

    Google Scholar 
    47.Wang, X., El Hadrami, A., Adam, L. R. & Daayf, F. Differential activation and suppression of potato defence responses by Phytophthora infestans isolates representing US-1 and US-8 genotypes. Plant Pathol. 57, 1026–1037. https://doi.org/10.1111/j.1365-3059.2008.01866.x (2008).CAS 
    Article 

    Google Scholar 
    48.Smits, J. P., Rinzema, A., Tramper, J., Schlösser, E. E. & Knol, W. Accurate determination of process variables in a solid-state fermentation system. Process Biochem. 31, 669–678. https://doi.org/10.1016/S0032-9592(96)00019-2 (1996).CAS 
    Article 

    Google Scholar 
    49.Kalaivani, K., Kalaiselvi, M. M. & Senthil-Nathan, S. Effect of methyl salicylate (MeSA), an elicitor on growth, physiology and pathology of resistant and susceptible rice varieties. Sci. Rep. 6, 1–11 (2016).Article 

    Google Scholar 
    50.Rane, K. D. & Hoover, D. G. An evaluation of alkali and acid treatments for chitosan extraction from fungi. Process Biochem. 28, 115–118 (1993).CAS 
    Article 

    Google Scholar 
    51.Crestini, C., Kovac, B. & Giovannozzi-Sermanni, G. Production of chitosan by fungi. 50, 207–210. https://doi.org/10.1002/bit.260500202 (1996).52.Khalaf, S. A. Production and characterization of fungal chitosan under solid-state fermentation conditions. Int. J. Agric. Biol. 6, 1033–1036 (2004).CAS 

    Google Scholar 
    53.Zhang, Z. T., Chen, D. H. & Chen, L. Preparation of two different serials of chitosan. J. Dong Hua Univ. Engl. Ed. 19, 36–39 (2002).
    Google Scholar 
    54.Chanthini, K. M. et al. Sustainable agronomic strategies for enhancing the yield and nutritional quality of wild tomato Solanum Lycopersicum (l) Var Cerasiforme Mill. Agronomy 9, 311 (2019).CAS 
    Article 

    Google Scholar 
    55.Ellis, R. H. & Roberts, E. H. Improved equations for the prediction of seed longevity. Ann. Bot. 45, 13–30. https://doi.org/10.1093/oxfordjournals.aob.a085797 (1980).Article 

    Google Scholar 
    56.Chanthini, K. M. et al. Biocatalysis and agricultural biotechnology Chaetomorpha antennina (Bory) Kützing derived seaweed liquid fertilizers as prospective bio-stimulant for Lycopersicon esculentum (Mill). Biocatal. Agric. Biotechnol. 20, 101190 (2019).Article 

    Google Scholar 
    57.Murray, P. R., Baron, E. J., Pfaller, M. A., Tenover, F. C. & Yolke, R. H. Manual of clinical Microbiology 6th edn. (American Society of Microbiology Press, 1995).
    Google Scholar 
    58.French, E. R. Efficacy of five methods of inoculating potato plants with Pseudomonas solanacearum. Phytopathology 76, 1078 (1986).
    Google Scholar 
    59.Yasmin, S. et al. Biocontrol of Bacterial Leaf Blight of rice and profiling of secondary metabolites produced by rhizospheric Pseudomonas aeruginosa BRp3. Front. Microbiol. 8, 1895. https://doi.org/10.3389/fmicb.2017.01895 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    60.Hammerschmidt, R. & Kuć, J. Lignification as a mechanism for induced systemic resistance in cucumber. Physiol. Plant Pathol. 20, 61–71. https://doi.org/10.1016/0048-4059(82)90024-8 (1982).CAS 
    Article 

    Google Scholar 
    61.Worthington, C. C. Worthington Enzyme Manual: Enzymes and Related Biochemicals (Worthington Biochemical Corporation, 1988).
    Google Scholar  More

  • in

    Seasonal activity of Dermacentor reticulatus ticks in the era of progressive climate change in eastern Poland

    1.Rubel, F. et al. Geographical distribution of Dermacentor marginatus and Dermacentor reticulatus in Europe. Ticks Tick Borne Dis. 7, 224–233 (2016).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    2.Medlock, J. M. et al. Driving forces for changes in geographical distribution of Ixodes ricinus ticks in Europe. Parasites Vectors 6, 1–11 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    3.Jongejan, F. & Uilenberg, G. The global importance of ticks. Parasitology 129, 3–14 (2004).Article 

    Google Scholar 
    4.Földvári, G., Široký, P., Szekeres, S., Majoros, G. & Sprong, H. Dermacentor reticulatus: a vector on the rise. Parasites Vectors 9, 1–29 (2016).Article 

    Google Scholar 
    5.Ličková, M. et al. Dermacentor reticulatus is a vector of tick-borne encephalitis virus. Ticks Tick Borne Dis. 11, 101414 (2020).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    6.Pawełczyk, A. et al. Long-term study of Borrelia and Babesia prevalence and co-infection in Ixodes ricinus and Dermacentor recticulatus ticks removed from humans in Poland, 2016–2019. Parasites Vectors 14, 1–13 (2021).Article 
    CAS 

    Google Scholar 
    7.Karbowiak, G. et al. The competition between immatures of Ixodes ricinus and Dermacentor reticulatus (Ixodida: Ixodidae) ticks for rodent hosts. J. Med. Entomol. 56, 448–452 (2018).Article 

    Google Scholar 
    8.Karbowiak, G. The occurrence of the Dermacentor reticulatus tick-its expansion to new areas and possible causes. Ann. Parasitol. 60, 37–47 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    9.Drehmann, M. et al. The Spatial Distribution of Dermacentor Ticks (Ixodidae) in Germany: Evidence of a continuing spread of Dermacentor reticulatus. Front. Vet. Sci. 7, 578220 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    10.Sands, B. O., Bryer, K. E. & Wall, R. Climate and the seasonal abundance of the tick Dermacentor reticulatus. Med. Vet. Entomol. https://doi.org/10.1111/mve.12518 (2021).Article 
    PubMed 

    Google Scholar 
    11.Hasle, G. et al. Transport of ticks by migratory passerine birds to Norway. J. Parasitol. 95, 1342–1351 (2009).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    12.Kjær, L. J. et al. A large-scale screening for the taiga tick, Ixodes persulcatus, and the meadow tick, Dermacentor reticulatus, in southern Scandinavia, 2016. Parasites Vectors 12, 1–4 (2019).Article 

    Google Scholar 
    13.García-Sanmartín, J., Barandika, J. F., Juste, R. A., García-Pérez, A. L. & Hurtado, A. Distribution and molecular detection of Theileria and Babesia in questing ticks from northern Spain. Med. Vet. Entomol. 22, 318–325 (2008).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    14.Olivieri, E. et al. The southernmost foci of Dermacentor reticulatus in Italy and associated Babesia canis infection in dogs. Parasites Vectors 9, 1–9 (2016).Article 
    CAS 

    Google Scholar 
    15.Široký, P. et al. The distribution and spreading pattern of Dermacentor reticulatus over its threshold area in the Czech Republic: How much is range of this vector expanding?. Vet. Parasitol. 183, 130–135 (2011).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    16.Hornok, S. & Farkas, R. Influence of biotope on the distribution and peak activity of questing ixodid ticks in Hungary. Med. Vet. Entomol. 23, 41–46 (2009).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    17.Chitimia-Dobler, L. Spatial distribution of Dermacentor reticulatus in Romania. Vet. Parasitol. 214, 219–223 (2015).PubMed 
    Article 

    Google Scholar 
    18.Akimov, I. & Nebogatkin, I. Distribution of Ticks from of the Genus Dermacentor (Acari, Ixodidae) in Ukraine. Vestnik Zoologii 45, 6 (2011).
    Google Scholar 
    19.Kiewra, D., Szymanowski, M., Czułowska, A. & Kolanek, A. The local-scale expansion of Dermacentor reticulatus ticks in Lower Silesia, SW, Poland. Ticks Tick Borne Dis. 12, 101599 (2021).PubMed 
    Article 

    Google Scholar 
    20.Dwużnik-Szarek, D. et al. Monitoring the expansion of Dermacentor reticulatus and occurrence of canine babesiosis in Poland in 2016–2018. Parasites Vectors 14, 1–18 (2021).Article 

    Google Scholar 
    21.Zając, Z., Woźniak, A. & Kulisz, J. Density of Dermacentor reticulatus ticks in eastern Poland. Int. J. Environ. Res. Public Health 17, 2814 (2020).PubMed Central 
    Article 

    Google Scholar 
    22.Ogden, N. H., Ben Beard, C., Ginsberg, H. S. & Tsao, J. I. Possible effects of climate change on ixodid ticks and the pathogens they transmit: Predictions and observations. J. Med. Entomol. 58, 1536–1545 (2020).Article 

    Google Scholar 
    23.Zając, Z., Sędzikowska, A., Maślanko, W., Woźniak, A. & Kulisz, J. Occurrence and Abundance of Dermacentor reticulatus in the habitats of the ecological corridor of the Wieprz river, eastern Poland. Insects 12, 96 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    24.Zając, Z., Bartosik, K. & Woźniak, A. Monitoring Dermacentor reticulatus host-seeking activity in natural conditions. Insects 11, 264 (2020).PubMed Central 
    Article 

    Google Scholar 
    25.Global and European temperature—European Environment Agency. https://www.eea.europa.eu/data-and-maps/indicators/global-and-european-temperature/global-and-european-temperature-assessment-1. Accessed 22 July 2021.26.Średnie i sumy miesięczne. Dane meteorologiczne https://meteomodel.pl/dane/srednie-miesieczne/?imgwid=351220495&par=sndp&max_empty=2. Accessed 22 July 2021.27.Vladimirov, L. N. et al. Quantifying the Northward Spread of Ticks (Ixodida) as climate warms in Northern Russia. Atmosphere 12, 233 (2021).ADS 
    Article 

    Google Scholar 
    28.Mierzejewska, E. J., Alsarraf, M., Behnke, J. M. & Bajer, A. The effect of changes in agricultural practices on the density of Dermacentor reticulatus ticks. Vet. Parasitol. 211, 259–265 (2015).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    29.Zając, Z., Woźniak, A. & Kulisz, J. Infestation of dairy cows by ticks Dermacentor reticulatus (Fabricius, 1794) and Ixodes ricinus (Linnaeus, 1758) in eastern Poland. Ann. Parasitol. 66, 87–96 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    30.Estrada-Peña, A. Climate, niche, ticks, and models: What they are and how we should interpret them. Parasitol. Res. 103, 87–95 (2008).Article 

    Google Scholar 
    31.Süss, J., Klaus, C., Gerstengarbe, F. W. & Werner, P. C. What makes ticks tick? Climate change, ticks, and tick-borne diseases. J. Travel Med. 15, 39–45 (2008).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    32.Paulauskas, A. et al. New localities of Dermacentor reticulatus ticks in the Baltic countries. Ticks Tick Borne Dis. 6, 630–635 (2015).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    33.Kubiak, K. et al. Dermacentor reticulatus ticks (Acari: Ixodidae) distribution in north-eastern Poland: An endemic area of tick-borne diseases. Exp. Appl. Acarol. 75, 289–298 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    34.Silaghi, C., Weis, L. & Pfister, K. Dermacentor reticulatus and Babesia canis in Bavaria (Germany): A georeferenced field study with digital habitat characterization. Pathogens 9, 541 (2020).CAS 
    PubMed Central 
    Article 

    Google Scholar 
    35.Kohn, M. et al. Dermacentor reticulatus in Berlin/Brandenburg (Germany): Activity patterns and associated pathogens. Ticks Tick Borne Dis. 10, 191–206 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    36.Kiewra, D., Czułowska, A., Dyczko, D., Zieliński, R. & Plewa-Tutaj, K. First record of Haemaphysalis concinna (Acari: Ixodidae) in Lower Silesia, SW, Poland. Exp. Appl. Acarol. 77, 449–454 (2019).PubMed 
    Article 

    Google Scholar 
    37.Zieba, P. et al. A new locality of the Haemaphysalis concinna tick (Koch, 1844) in Poland and its role as a potential vector of infectious diseases. Ann. Parasitol. 65, 281–286 (2019).PubMed 

    Google Scholar 
    38.Gray, J. S., Dautel, H., Estrada-Peña, A., Kahl, O. & Lindgren, E. Effects of climate change on ticks and tick-borne diseases in Europe. Interdiscip. Perspect. Infect. Dis. 2009, 593232 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    39.Medlock, J. M. & Leach, S. A. Effect of climate change on vector-borne disease risk in the UK. Lancet Infect. Dis. 15, 721–730 (2015).PubMed 
    Article 

    Google Scholar 
    40.Pfäffle, M., Littwin, N. & Petney, T. Host preferences of immature Dermacentor reticulatus (Acari: Ixodidae) in a forest habitat in Germany. Ticks Tick Borne Dis. 6, 508–515 (2015).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    41.Zając, Z., Bartosik, K., Kulisz, J. & Woźniak, A. Ability of adult Dermacentor reticulatus ticks to overwinter in the temperate climate zone. Biology 9, 145 (2020).PubMed Central 
    Article 

    Google Scholar 
    42.Kiewra, D., Czułowska, A. & Lonc, E. Winter activity of Dermacentor reticulatus (Fabricius, 1794) in the newly emerging population of Lower Silesia, south-west Poland. Ticks Tick Borne Dis. 7, 1124–1127 (2016).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    43.Buczek, A., Bartosik, K. & Zając, Z. Changes in the activity of adult stages of Dermacentor reticulatus (Ixodida: Amblyommidae) induced by weather factors in eastern Poland. Parasites Vectors 7, 245 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    44.Hubálek, Z., Halouzka, J. & Juricova, Z. Host-seeking activity of ixodid ticks in relation to weather variables. J. Vector Ecol. 28, 159–165 (2003).PubMed 
    PubMed Central 

    Google Scholar 
    45.Bartosik, K., Wiśniowski, Ł & Buczek, A. Questing behavior of Dermacentor reticulatus adults (Acari: Amblyommidae) during diurnal activity periods in eastern Poland. J. Med. Entomol. 49, 859–864 (2012).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    46.Buczek, A., Bartosik, K., Wisniowski, L. & Tomasiewicz, K. Changes in population abundance of adult Dermacentor reticulatus (Acari: Amblyommidae) in long-term investigations in eastern Poland. Ann. Agric. Environ. Med. 20, 269–272 (2013).PubMed 
    PubMed Central 

    Google Scholar 
    47.Mierzejewska, E. J., Estrada-Peña, A., Alsarraf, M., Kowalec, M. & Bajer, A. Mapping of Dermacentor reticulatus expansion in Poland in 2012–2014. Ticks Tick Borne Dis. 7, 94–106 (2016).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    48.Zając, Z. et al. Environmental determinants of the occurrence and activity of Ixodes ricinus ticks and the prevalance of tick-borne diseases in eastern Poland. Sci. Rep. 11, 15472 (2021).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    49.Kulisz, J., Bartosik, K., Zając, Z., Woźniak, A. & Kolasa, S. Quantitative parameters of the body composition influencing host seeking behavior of Ixodes ricinus adults. Pathogens 10, 706 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    50.Alasmari, S. & Wall, R. Metabolic rate and resource depletion in the tick Ixodes ricinus in response to temperature. Exp. Appl. Acarol. 83, 81–93 (2020).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    51.Zajac, Z., Bartosik, K. & Buczek, A. Factors influencing the distribution and activity of Dermacentor reticulatus (F.) ticks in an anthropopressure-unaffected area in central-eastern Poland. Ann. Agric. Environ Med. 23, 270–275 (2016).PubMed 
    Article 

    Google Scholar 
    52.Bogdaszewska, Z. Range and ecology of Dermacentor reticulatus (Fabricius, 1794) in Mazuria focus. II. Seasonal activity patterns of the adults. Wiad. Parazytol. 50, 731–738 (2004).PubMed 

    Google Scholar 
    53.Razumova, I. V. The activity of Dermacentor reticulatus Fabr. (Ixodidae) ticks in nature. Med. Parasitol. Parasites Dis. 4, 8–14 (1999).
    Google Scholar 
    54.Szymański, S. Seasonal activity of Dermacentor reticulatus (Fabricius, 1794) (Acarina, Ixodidae) in Poland I. Adults. Acta Parasitol. Pol. 31, 247–255 (1987).
    Google Scholar 
    55.Hornok, S. Allochronic seasonal peak activities of Dermacentor and Haemaphysalis spp. under continental climate in Hungary. Vet. Parasitol. 163, 366–369 (2009).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    56.Randolph, S. E. & Storey, K. Impact of microclimate on immature tick-rodent host interactions (Acari: Ixodidae): Implications for parasite transmission. J. Med. Entomol. 36, 741–748 (1999).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    57.Nowak-Chmura, M. Ticks (Ixodida) of Central Europe (Pedagogical University of Cracow Press, 2013).
    Google Scholar  More

  • in

    Elevated wildlife-vehicle collision rates during the COVID-19 pandemic

    Altogether, we found that, while traffic volume declined by  > 7% during the pandemic year (with a maximum monthly decline of nearly 40%), the absolute number of annual WVCs was largely unchanged. This resulted in significant increases of  > 8% in collision rates between vehicles and wildlife during the pandemic year, peaking at a  > 27% nationwide increase in April 2020. Other studies from the first several months of the pandemic documented similar transient declines in the number of WVCs when the pandemic began which then reversed in many jurisdictions as the pandemic progressed and traffic rebounded26,27. We observed a similar pattern over the first five months of the pandemic at the national scale (Fig. 2): WVCs initially declined during the pandemic in step with declines in traffic volume, but then started to increase to baseline levels at a faster rate than traffic, possibly due to behavioral lags by wildlife following traffic-mediated increases in wildlife road use. Though based on coarse-scale data, our research aligns with assertions from studies during27 and prior to the pandemic3,15,16,28,29 that the relationship between traffic volume and WVCs is non-linear.We postulate that the observed non-linear relationship between traffic volume and WVCs is the result of greater use of roads and roadsides by certain wildlife species, namely large mammals (Table S1), in response to decreasing traffic volume, as prior research has suggested3,14,15,16. This explanation is consistent with accounts of various wildlife species making increased use of human spaces during the pandemic17,20,21: with less cars on the roads, wildlife might be less deterred from roads by the noise and light pollution that accompany high traffic volumes9,10,11,20 and perceive roads as less risky, thereby increasing their willingness to attempt road crossings3,8,15,16. Beyond incidentally crossing roads while moving about the landscape8,9, wildlife might be attracted to roads for travel, mates, or other resources8,10,11. Many animals are shown to utilize roads to move efficiently across the landscape11,12, and roads and the surrounding areas are comparatively open, such that wildlife might select roads and roadsides for enhanced visibility to find mates, detect predators, or locate prey10,13. Roadsides also can provide foraging opportunities and essential nutrients for wildlife via abundant, high-quality early successional vegetation and high salt concentrations10,11. As such, decreased road traffic during the pandemic might have caused certain wildlife species to tolerate the risks associated with roads in order to access the benefits of roads and roadsides.An alternative explanation for the observed increases in collision rates is that human driving behavior, rather than animal behavior, changed during the pandemic. With fewer cars on the road, people might drive faster35, rendering it more difficult for both humans and wildlife to avoid collisions3. Preliminary studies from throughout the United States have indeed suggested changes to human driving behavior during the pandemic, with several jurisdictions reporting increased vehicle speeds35,36. Despite reported increases in vehicle speeds, however, the total number of vehicle collisions (the sum of both wildlife and non-wildlife collisions) mirrored trends in traffic volume and declined considerably during the pandemic37,38. Thus, because changes to human behavior appear to have had a minimal effect on vehicle collisions overall, it is unlikely that the observed changes in collision rates are due to increased vehicle speeds alone. Still, we cannot discount the possibility that changes to human driving behavior contributed to the patterns documented here, and future work should more explicitly test the relative effects of changes in traffic volume on both human driving behavior and wildlife space-use, as well as the resultant impacts on WVCs.A greater understanding of human driving behavior would also help explain our findings regarding changes in traffic patterns during the pandemic. Nationwide, the severity of COVID-19 restrictions accounted for a large amount of the variation in changes in monthly traffic volume (R2 = 0.968), but the severity of restrictions was less influential on changes in yearly traffic across states (Tables S3 and S4). Restrictions implemented throughout the pandemic were largely enacted for the purpose of minimizing travel, and other research has demonstrated that these restrictions were effective at reducing human mobility18,21. Our state-level findings, however, imply that it was not only the restrictions themselves that reduced travel, but possibly also the associated anxiety regarding the risk of contracting the SARS-CoV-2 virus, as has been suggested in other studies21,22,23,24; although we observed the greatest declines in traffic volume early in the pandemic (Fig. 2A) when restrictions were most stringent (Fig. S2)21, there was widespread anxiety about the risks posed by SARS-CoV-2 during this time22,23, which likely motivated people to stay home independent of restrictions24. Indeed, anxiety and risk perception might explain the relationship between traffic volume and the other covariates in our top models (Table S4). Declines in traffic were greatest in the most densely populated states (Fig. 4A) and in states that had the highest and the lowest disease burdens (Fig. 4B). The risk of SARS-CoV-2 transmission is greater in more densely populated states due to the close proximity of and frequent interactions amongst people21. As such, people may have altered their road use more in densely populated states as compared to sparsely populated ones due to differing perceptions of disease transmission risk23—though differences in infrastructure in relation to population density likely contributed to this pattern as well39. Similarly, declines in traffic volume in states with larger outbreaks of SARS-CoV-2 might have been driven by increases in the perceived risk of contracting the virus21,23. Alternatively, traffic reductions in states with low disease burdens might reflect increased compliance with stay-at-home orders, and therefore less opportunity for disease spread40,41; essentially, reductions in traffic volume might be the cause of locally low disease burdens therein, rather than a consequence. Altogether, we posit that the observed heterogeneity in traffic volume between states is, at least in part, attributed to differences in the perceived risk posed by the SARS-CoV-2 virus.Regardless of the mechanisms underlying changes in traffic volume and WVCs, our observation that the annual number of WVCs was largely unchanged despite substantive declines in traffic volume has implications for mitigating WVCs going forward. Most directly, the lack of a directional change in WVCs suggests that road traffic levels in the United States are currently such that even large decreases in traffic volume would have minimal long-term effects on the absolute number of WVCs. As such, decreasing collisions by reducing traffic volume would require even larger and longer-lasting changes in traffic than those observed during the pandemic. Since such massive and sustained reductions in traffic are unlikely4,5,6, WVCs in the United States essentially represent a fixed cost as of now, both for human society and wildlife populations. As such, these transient decreases in traffic likely provided minimal reprieve to large mammals from collision-induced mortality, in contrast to speculation that changes in human mobility during the COVID-19 pandemic had substantial positive effects for wildlife populations by freeing wildlife from the pervasive direct and indirect effects of humans17,18,19,20,26,27,42.Indeed, it is possible that short-term decreases in traffic volume might ultimately be harmful to those wildlife species that increased their road use. Although the increases in collision rates we observed at the beginning of the pandemic were rapid and corresponded to nationwide declines in traffic volume (see also26,27), collision rates remained elevated even as traffic approached baseline levels in July (Fig. 2B). If wildlife responses to changes in traffic are asymmetric (i.e., increases in wildlife road use following declines in traffic occur more rapidly than decreases in wildlife road use in response to increased traffic), then short-term declines in traffic volume might lead to net increases in the number WVCs over longer timeframes, ultimately proving detrimental to certain wildlife populations1,3. Future work should evaluate the long-term effects of the pandemic on wildlife populations, specifically with regards to collision-induced mortality17,20,26,27,42.Although the COVID-19 pandemic provided an opportunity to examine the short-term effects of transient decreases in traffic volume on WVCs, the longer-term effects of expanding human populations, greater road densities, and altogether higher traffic volumes on WVCs are less clear. Similar to the increases in wildlife road use in response to decreases in traffic volume theorized here, steady increases in traffic might reduce wildlife road use long-term3,14,15,16; since road traffic is indeed increasing through time4,5,6, we might therefore see declines in WVCs as roads become more effective at repelling wildlife1,3,14. Although these reductions in vehicle-induced wildlife mortality are welcome, this would see roads increasingly serve as barriers to animal movement and gene flow43, further fragmenting already disconnected wildlife populations8. Thus, policy makers and urban planners should invest in infrastructure such as overpasses, underpasses, and fencing that enables wildlife to cross high-traffic roads safely or directs wildlife towards low-risk areas8,9. Even substantive short-term declines in road traffic are not sufficient to mitigate wildlife-vehicle conflict on their own. More

  • in

    Improving pesticide-use data for the EU

    Gene Expression and Therapy Group, King’s College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, Guy’s Hospital, London, UKRobin Mesnage & Michael N. AntoniouCentre for Ecology, Evolution & Behaviour, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, UKEdward A. Straw, Mark J. F. Brown & Ellouise LeadbeaterHeartland Health Research Alliance, Port Orchard, WA, USACharles BenbrookANSES, Sophia Antipolis Laboratory, Unit of Honey Bee Pathology, Sophia Antipolis, FranceMarie-Pierre ChauzatAgricultural Economics and Policy Group, ETH Zürich, Zürich, SwitzerlandRobert FingerSchool of Life Sciences, University of Sussex, Brighton, UKDave GoulsonBC3 — Basque Centre for Climate Change, Scientific Campus of the University of Basque Country, Leioa, SpainAna López-BallesterosCentre D’Études Biologiques de Chizé, UMR 7372, CNRS & La Rochelle Université, Villiers-en-bois, FranceNiklas MöhringInstitute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, SwitzerlandPeter NeumannSchool of Agriculture and Food Science, University College Dublin, Dublin, IrelandEdward A. Straw, Dara Stanley & Linzi J. ThompsonDepartment of Botany, School of Natural Sciences, Trinity College Dublin, Dublin, IrelandJane C. Stout & Elena ZiogaDepartment of Ecoscience, Aarhus University, Aarhus, DenmarkChristopher J. ToppingSchool of Chemical Sciences, Glasnevin Campus, Dublin City University, Dublin, IrelandBlánaid WhiteInstitute of Zoology, University of Natural Resources and Life Sciences, Vienna, Vienna, AustriaJohann G. ZallerCorrespondence to
    Robin Mesnage or Edward A. Straw. More

  • in

    Advice on comparing two independent samples of circular data in biology

    Type-I errorIn the case of two identical unimodal von Mises distributions, seven tests did not maintain Type-I error near the nominal 5% level, at least when sample sizes were small. These tests were the Kuiper two-sample test, the non equal concentration parameters approach ANOVA, the P-test, the Watson’s large-sample nonparametric test, the Watson–Williams test and the Rao dispersion test (Fig. 2). The Type-I error results were similar for the unimodal wrapped skew-normal distribution, except that the Wallraff test and Fisher’s method also showed Type-I error inflation (Fig. S1). No other methods showed evidence of failure to control Type-I error rate across different testing situations (Figs. S2–S5), except for the Log-likelihood ratio ANOVA in the case of two identical asymmetrical bimodal distributions (Fig. S3). In summary, only eight out of 18 tests reliably controlled the Type-I error rate near the nominal 5% level across all the situations investigated. These included five tests for identical distribution, the Watson’s U2 test, the Large-sample Mardia–Watson–Wheeler test, the Watson-Wheeler test, the embedding approach ANOVA, the MANOVA approach, the Rao polar test for differences in mean direction, and two tests for differences in concentration, the Levene’s test and the concentration test. We focus only on these tests in our explorations of statistical power.Figure 2Type-I error of all tests using von Mises distributions for different sample sizes: 10 and 10 (A), 20 and 20 (B), 50 and 50 (C), 20 and 30 (D) and 10 and 50 (E). Concentration (κ, kappa) increases for both distributions from 0 to 8. Tests are grouped according to their null hypotheses.Full size imagePower to detect differences in concentrationThe most powerful test to detect concentration differences between two von Mises distributions was the MANOVA approach, which offered superior power especially at lower sample sizes (Fig. 3). The Watson’s U2 test was also very powerful, followed by the Watson–Wheeler and the Large-sample Mardia–Watson–Wheeler tests with only marginally lower power. The embedding approach ANOVA had lower power, but, notably, was still more powerful than the Concentration test and Levene’s test, both specifically designed to detect differences in concentration. As expected, the Rao polar test was not sensitive to differences in concentration. The general results for two unimodal wrapped skew-normal distributions were comparable to the results for unimodal von Mises distributions, with the only exception of superior performance of Levene’s test in situations with highly asymmetric samples sizes (Fig. S6).Figure 3Power of all included tests when comparing von Mises distributions of differing concentrations using different sample sizes: 10 and 10 (A), 20 and 20 (B), 50 and 50 (C), 20 and 30 (D) and 10 and 50 (E). The first distribution is fixed at κ = 0, the second increases from 0 towards 8.Full size imageWhen comparing axial von Mises distributions, only the Watson’s U2 test offered acceptable power (Fig. S7). For the symmetrical trimodal distributions, overall power was very low, and again, only the Watson’s U2 providing some power (Fig. S8). The asymmetrical bimodal (Fig. S9) situation showed acceptable power of the MANOVA approach and Watson’s U2, however, for the asymmetrical trimodal distribution power was low with the Watson’s U2 providing the best results (Fig. S10).Power to detect differences in the mean/medianThe power to detect angular differences between two von Mises distributions was highest for the MANOVA approach at small sample sizes (n = 10), followed by the Watson’s U2, Watson-Wheeler test and the Large-sample Mardia-Watson-Wheeler test (Fig. 4). Notably, the Levene’s test also showed acceptable power levels, clearly failing to detect specifically concentration differences (to which it was less sensitive, see Fig. 4). The concentration test was not sensitive to the differences in mean direction. Special cases were the embedding approach ANOVA and the Rao polar test. The ANOVA approach showed, with the exception of very unequal sample sizes (n = 10/50), a unimodal response, with increasing power levels from 0° to 90° difference, but then rapidly decreasing power towards 180° difference. The Rao polar test showed an even stranger pattern, with, at higher sample sizes, very good power when the difference was either around 45° or 135°, but with power levels dropping to 0.05 in between these two peaks (at 90°). The results were similar for the wrapped skew-normal distribution, with the exceptions that the Rao polar test showed strongly reduced power and switched from a bimodal to a unimodal power curve with a peak around 60°, and the Levene’s test completely lost its power (Fig. S11).Figure 4Power of all included tests when comparing von Mises distributions (kappa for both = 2) of differing directions using different sample sizes: 10 and 10 (A), 20 and 20 (B), 50 and 50 (C), 20 and 30 (D) and 10 and 50 (E). The first distribution is fixed at 0°, the second increases from 0° towards 180.Full size imageFor axial distributions, only the Watson’s U2 test offered acceptable power levels, although large sample sizes (~ n = 100) were required for the power to reach over 50% (Fig. S12). All other tests failed to detect the difference in mean direction between two axial distributions. For symmetric trimodal distributions none of the tests used was sensitive to differences in mean direction (Fig. S13).When comparing asymmetrical bimodal distributions, the general trends were similar to the unimodal case. However, over all sample sizes the MANOVA approach offered the best power. The Watson–Wheeler test was considerably less powerful in this situation, as were the Watson’s U2 test and the Large-sample Mardia–Watson–Wheeler test (Fig. S14). The Levene’s test showed a unimodal-shaped power curve. The asymmetrical trimodal situation was, again, similar to the asymmetrical bimodal situation (Fig. S15), with the exception of the Levene’s test, which showed steady power increase with angular difference (instead of the hump-shaped curve).Power to detect differences in distribution typeWhen comparing a unimodal and an axial bimodal distribution, which increased similarly in concentration, we found that the MANOVA approach again offered the best power in particular at low samples sizes, followed by the Watson’s U2 test, the Large-sample Mardia–Watson–Wheeler test and Watson–Wheeler test (Fig. 5). While the embedding approach ANOVA and the Levene’s test had varying but usable power levels, the concentration test was only sensitive to such differences at low concentration values. The Rao polar test was not sensitive to such differences.Figure 5Power of all included tests when comparing von Mises distributions of differing number of modes (unimodal and axially bimodal) using different sample sizes: 10 and 20 (A), 20 and 40 (B), 50 and 100 (C), 20 and 60 (D) and 10 and 100 (E). The concentration (κ) of both increases from 0 to 8.Full size imageThe picture was only marginally different when comparing a von Mises with a wrapped skew-normal distribution (Fig. S16). For low sample sizes (n = 10) the MANOVA approach offered great power, followed by the embedding approach ANOVA. The latter offered good power throughout the range of sample sizes tested, followed by the Watson’s U2 test, the Large-sample Mardia–Watson–Wheeler test and Levene’s test. Also, the Rao polar test showed lower, but acceptable sensitivity to distribution type. The concentration test only showed very low power, that (as expected) increased with increasing concentrations of the respective distributions.We summarize the results obtained in the power analysis in Table 2. In all situations, either the Watson’s U2 test or the MANOVA approach offered the best power.Table 2 Ranking of tests based on the power comparisons for the main scenarios encountered in potential data sets (using different distributions: unimodal, axial, asymmetrical bimodal, symmetrical trimodal, asymmetrical trimodal), in cases were only one test performed acceptable the others ranks were left blank (see Table 1 for abbreviations).Full size tableReal data examplesTesting the performance of the robust tests on real data sets revealed, predominantly, the expected test behavior. In the example of homing pigeons where a difference in concentration was expected, all tests, with the exception of the Rao polar test and, notably, the concentration test, showed a significant difference between the distributions (Fig. 6A). Therefore, we can conclude, in accordance with the respective publication19, that sectioning of the olfactory nerve disrupted the homing behavior of pigeons.Figure 6Results from example data. Shown are results of pigeon (A), ant (B) and bat orientations (C). Control groups are on the left panels and experimental groups on the right. The tests are abbreviated according to Table 1, significant test results are indicated in red with asterisk and non-significant in blue. For each circular plot directional data is shown as dots on the circle (each dot is one individual), the arrows represent the mean direction and the dashed line the 95% confidence interval.Full size imageIn the ant example, where no difference between the groups was expected, there was no significant difference between the distributions detected by most of the tests (Fig. 6B). Only the concentration test showed a significant difference. Based on the other tests we would conclude that there was no biological meaningful difference between the two distributions. Therefore, ants appear to be able to transfer visual information from one eye to the other.In the bat example, where a difference in mean direction was expected, the Watson’s U2, the Mardia–Watson–Wheeler, Watson-Wheeler test and the MANOVA approach showed a significant difference (Fig. 6C). Notably, the Rao polar, Levene’s, and concentration tests and the embedding approach ANOVA failed to show a significant difference. At least for the Rao polar test, one would have expected a significant difference, as the two distributions are clearly 180° apart. This outcome concurs with our simulation results where the Rao polar test failed to distinguish distributions on the same and orthogonal axes (Fig. 4). As the results of the tests where quite mixed this example highlights the need for choosing a test with appropriate power to detect the expected differences. Based on the results of the most powerful tests, we conclude that the bats showed a mirrored orientation, as expected in the experimental design. More