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    Genetic structure in neotropical birds with different tolerance to urbanization

    Biamonte, E., Sandoval, L., Chacón, E. & Barrantes, G. Effect of urbanization on the avifauna in a tropical metropolitan area. Landsc. Ecol. 26, 183–194 (2011).Article 

    Google Scholar 
    Fahrig, L. Effects of habitat fragmentation on biodiversity. Annu. Rev. Ecol. Evol. Syst. 34, 487–515 (2003).Article 

    Google Scholar 
    Montgomery, M. R. The urban transformation of the developing world. Science 319, 761–764 (2008).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    Nuissl, H. & Siedentop, S. Urbanisation and Land Use Change. In Sustainable Land Management in a European Context: A Co-Design Approach (eds Weith, T. et al.) 75–99 (Springer International Publishing, 2021). https://doi.org/10.1007/978-3-030-50841-8_5.Chapter 

    Google Scholar 
    Scolozzi, R. & Geneletti, D. A multi-scale qualitative approach to assess the impact of urbanization on natural habitats and their connectivity. Environ. Impact Assess. Rev. 36, 9–22 (2012).Article 

    Google Scholar 
    Pauchard, A., Aguayo, M., Peña, E. & Urrutia, R. Multiple effects of urbanization on the biodiversity of developing countries: The case of a fast-growing metropolitan area (Concepción, Chile). Biol. Conserv. 127, 272–281 (2006).Article 

    Google Scholar 
    Xu, X., Xie, Y., Qi, K., Luo, Z. & Wang, X. Detecting the response of bird communities and biodiversity to habitat loss and fragmentation due to urbanization. Sci. Total Environ. 624, 1561–1576 (2018).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    Bélisle, M. & St. Clair, C. C. Cumulative effects of barriers on the movements of forest birds. Conserv. Ecol. 5, 9; http://www.consecol.org/vol5/iss2/art9 (2001).Blair, R. B. Land use and avian species diversity along an urban gradient. Ecol. Appl. 6, 506–519 (1996).Article 

    Google Scholar 
    Tremblay, M. A. & St Clair, C. C. Permeability of a heterogeneous urban landscape to the movements of forest songbirds. J. Appl. Ecol. 48, 679–688 (2011).Article 

    Google Scholar 
    Johnson, M. T. J. & Munshi-South, J. Evolution of life in urban environments. Science 358, 8327 (2017).Article 
    CAS 

    Google Scholar 
    Isaksson, C. Impact of Urbanization on Birds. In Bird Species: How They Arise, Modify and Vanish (ed. Tietze, D. T.) 235–257 (Springer International Publishing, Berlin, 2018). https://doi.org/10.1007/978-3-319-91689-7_13.Chapter 

    Google Scholar 
    Miles, L. S., Rivkin, L. R., Johnson, M. T. J., Munshi-South, J. & Verrelli, B. C. Gene flow and genetic drift in urban environments. Mol. Ecol. 28, 4138–4151 (2019).PubMed 
    Article 

    Google Scholar 
    Delaney, K. S., Riley, S. P. D. & Fisher, R. N. A rapid, strong, and convergent genetic response to urban Habitat fragmentation in four divergent and widespread vertebrates. PLoS ONE 5, e12767 (2010).PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar 
    Unfried, T. M., Hauser, L. & Marzluff, J. M. Effects of urbanization on Song Sparrow (Melospiza melodia) population connectivity. Conserv. Genet. 14, 41–53 (2013).Article 

    Google Scholar 
    Brewer, V. N., Lane, S. J., Sewall, K. B. & Mabry, K. E. Effects of low-density urbanization on genetic structure in the Song Sparrow. PLoS ONE 15, e0234008 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Björklund, M., Ruiz, I. & Senar, J. C. Genetic differentiation in the urban habitat: the great tits (Parus major) of the parks of Barcelona city. Biol. J. Linn. Soc. 99, 9–19 (2010).Article 

    Google Scholar 
    Perrier, C. et al. Great tits and the city: Distribution of genomic diversity and gene–environment associations along an urbanization gradient. Evol. Appl. 11, 593–613 (2018).PubMed 
    Article 

    Google Scholar 
    Tan, D. J. X. et al. Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis. Sci. Rep. 8, 12804 (2018).PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar 
    McRae, B. H., Dickson, B. G., Keitt, T. H. & Shah, V. B. Using circuit theory to model connectivity in ecology, evolution, and conservation. Ecology 89, 2712–2724 (2008).PubMed 
    Article 

    Google Scholar 
    Howell, S. N. G. & Webb, S. A Guide to the Birds of Mexico and Northern Central America (Oxford University Press, 1995).
    Google Scholar 
    Sandoval, L. & Mennill, D. J. Breeding biology of White-eared Ground-sparrow (Melozone leucotis), with a description of a new nest type. Ornitol. Neotropical 23, 225–234 (2012).
    Google Scholar 
    Stiles, F. G. & Skutch, A. F. A Guide to the Birds of Costa Rica (Cornell University Press, 1989).
    Google Scholar 
    Carlson, T. N. & Sanchez-Azofeifa, G. A. Satellite remote sensing of land use changes in and around San José Costa Rica. Remote Sens. Environ. 70, 247–256 (1999).Article 
    ADS 

    Google Scholar 
    Sánchez, J. E., Criado, J., Sánchez, C. & Sandoval, L. Costa Rica. In Important Bird Areas of Americas: priority sites for biodiversity conservation (eds Davendish, C. et al.) 149–156 (Birdlife International, 2009).
    Google Scholar 
    Sandoval, L. et al. The forgotten habitats in conservation: early successional vegetation. Rev. Biol. Trop. 67, 36–52 (2019).Article 

    Google Scholar 
    Juárez, R., Chacón-Madrigal, E. & Sandoval, L. Urbanization has opposite effects on the territory size of two passerine birds. Avian Res. 11, 11 (2020).Article 

    Google Scholar 
    Skutch, A. F. Life history of the Southern House Wren. Condor 55, 121–149 (1953).Article 

    Google Scholar 
    Johnson, L. S. House Wren (Troglodytes aedon), Version 10. In Birds of the World (ed. Poole, A. F.) (Cornell Lab of Ornithology, 2020).
    Google Scholar 
    Markowski, M. et al. Genetic structure of urban and non-urban populations differs between two common parid species. Sci. Rep. 11, 10428. https://doi.org/10.1038/s41598-021-89847-4 (2021).CAS 
    Article 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar 
    Mueller, J. C. et al. Evolution of genomic variation in the burrowing owl in response to recent colonization of urban areas. Proc. R. Soc. B Biol. Sci. 285, 20180206 (2018).Article 

    Google Scholar 
    Vangestel, C. et al. Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient. Heredity 109, 163–172 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Joyce, A. T. Land Use Change in Costa Rica: 1966–2006, as Influenced by Social, Economic, Political, and Environmental Factors (Litografía e imprenta LIL, 2016).
    Google Scholar 
    Fuchs, E. J. & Hamrick, J. L. Mating system and pollen flow between remnant populations of the endangered tropical tree, Guaiacum sanctum (Zygophyllaceae). Conserv. Genet. 12, 175–185 (2011).Article 

    Google Scholar 
    Stevens, K., Harrisson, K. A., Hogan, F. E., Cooke, R. & Clarke, R. H. Reduced gene flow in a vulnerable species reflects two centuries of habitat loss and fragmentation. Ecosphere 9, e02114 (2018).Article 

    Google Scholar 
    Quesada-Román, A., Villalobos-Portilla, E. & Campos-Durán, D. Hydrometeorological disasters in urban areas of Costa Rica Central America. Environ. Hazards 20, 264–278 (2021).Article 

    Google Scholar 
    Muñoz, P., García-Rodríguez, A. & Sandoval, L. Urbanization, habitat extension and spatial pattern, threaten a Costa Rican endemic bird. Rev. Biol. Trop. 69, 170–180 (2021).
    Google Scholar 
    Sandoval, L., Bitton, P. P., Doucet, S. M. & Mennill, D. J. Analysis of plumage, morphology, and voice reveals species-level differences between two subspecies of Prevost’s Ground-sparrow Melozone biarcuata (Prévost and Des Murs) (Aves: Emberizidae). Zootaxa 3895, 103–116 (2014).PubMed 
    Article 

    Google Scholar 
    Arguedas, N. & Parker, P. G. Seasonal migration and genetic population structure in House Wrens. Condor 102, 517–528 (2000).Article 

    Google Scholar 
    Pujol, R. & Pérez, E. Crecimiento urbano en la región metropolitana de San José, Costa Rica. Una exploración espacial y temporal de los determinantes del cambio de uso del suelo, 1986–2010. Lincoln Institute of Land Policy https://www.lincolninst.edu/sites/default/files/pubfiles/2242_1578_Pujol_WP13RP1SP.pdf (2012).Sandoval, L., Dabelsteen, T. & Mennill, D. J. Transmission characteristics of solo songs and duets in a neotropical thicket habitat specialist bird. Bioacoustics 24, 289–306 (2015).Article 

    Google Scholar 
    Sandoval, L., Méndez, C. & Mennill, D. J. Vocal behaviour of White-eared Ground-sparrows (Melozone leucotis) during the breeding season: repertoires, diel variation, behavioural contexts, and individual distinctiveness. J. Ornithol. 157, 1–12 (2016).Article 

    Google Scholar 
    Carro, M. E., Llambías, P. E., Mahler, B. & Fernández, G. J. Contrasting patterns of natal dispersal of a south temperate House Wren population at local and regional scales. J. Ornithol. 162, 895–907 (2021).Article 

    Google Scholar 
    Garrigues, R. & Dean, R. The Birds of Costa Rica: A Field Guide (Cornell University Press, 2014).
    Google Scholar 
    Sandoval, L., Epperly, K. L., Klicka, J. & Mennill, D. J. The biogeographic and evolutionary history of an endemic clade of Middle American sparrows: Melozone and Aimophila (Aves: Passerellidae). Mol. Phylogenet. Evol. 110, 50–59 (2017).PubMed 
    Article 

    Google Scholar 
    MacGregor-Fors, I. & Escobar-Ibáñez, J. F. Birds from Urban Latin America, Where Economic Inequality and Urbanization Meet Biodiversity. In Avian Ecology in Latin American Cityscapes (eds MacGregor-Fors, I. & Escobar-Ibáñez, J. F.) 1–10 (Springer International Publishing, 2017). https://doi.org/10.1007/978-3-319-63475-3_1.Chapter 

    Google Scholar 
    MacGregor-Fors, I. & García-Arroyo, M. Who Is Who in the City? Bird Species Richness and Composition in Urban Latin America. In Avian Ecology in Latin American Cityscapes (eds MacGregor-Fors, I. & Escobar-Ibáñez, J. F.) 33–55 (Springer International Publishing, 2017). https://doi.org/10.1007/978-3-319-63475-3_3.Chapter 

    Google Scholar 
    Lande, R. & Barrowclough, G. F. Effective population size, genetic variation, and their use in population management. In Viable Populations for Conservation (ed. Soulé, M. E.) 87–124 (Cambridge University Press, 1987). https://doi.org/10.1017/CBO9780511623400.007.Chapter 

    Google Scholar 
    Newman, D. & Pilson, D. Increased probability of extinction due to decreased genetic effective population size: Experimental populations of Clarkia Pulchella. Evolution 51, 354–362 (1997).PubMed 
    Article 

    Google Scholar 
    Longmire, J. L., Maltbie, M. & Baker, R. J. Use of ‘Lysis Buffer’ in DNA isolation and its implication for museum collections (Museum of Texas Tech University, 1997).Book 

    Google Scholar 
    Bulgin, N. L., Gibbs, H. L., Vickery, P. & Baker, A. J. Ancestral polymorphisms in genetic markers obscure detection of evolutionarily distinct populations in the endangered Florida grasshopper sparrow (Ammodramus savannarum floridanus). Mol. Ecol. 12, 831–844 (2003).CAS 
    PubMed 
    Article 

    Google Scholar 
    Hanotte, O. et al. Isolation and characterization of microsatellite loci in a passerine bird: the reed bunting Emberiza schoeniclus. Mol. Ecol. 3, 529–530 (1994).CAS 
    PubMed 
    Article 

    Google Scholar 
    Jeffery, K. J., Keller, L. F., Arcese, P. & Bruford, M. W. The development of microsatellite loci in the song sparrow, Melospiza melodia (Aves) and genotyping errors associated with good quality DNA. Mol. Ecol. Notes 1, 11–13 (2001).CAS 
    Article 

    Google Scholar 
    Petren, K. Microsatellite primers from Geospiza fortis and cross-species amplification in Darwin’s finches. Mol. Ecol. 7, 1782–1784 (1998).CAS 
    PubMed 
    Article 

    Google Scholar 
    Brar, R. K. et al. Eleven microsatellite loci isolated from the banded wren (Thryothorus pleurostictus). Mol. Ecol. Notes 7, 69–71 (2007).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Cabe, P. R. & Marshall, K. E. Microsatellite loci from the house wren (Troglodytes aedon). Mol. Ecol. Notes 1, 155–156 (2001).CAS 
    Article 

    Google Scholar 
    R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing https://www.R-project.org/ (2021).RStudio Team. RStudio: integrated development environment for R. RStudio http://www.rstudio.com/ (2021).Goudet, J. hierfstat, a package for r to compute and test hierarchical F-statistics. Mol. Ecol. Notes 5, 184–186 (2005).Article 

    Google Scholar 
    Weir, B. S. & Cockerham, C. C. Estimating F-Statistics for the analysis of population structure. Evolution 38, 1358–1370 (1984).CAS 
    PubMed 

    Google Scholar 
    Jombart, T. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Earl, D. A. & vonHoldt, B. M. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4, 359–361 (2012).Article 

    Google Scholar 
    Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol. 14, 2611–2620 (2005).CAS 
    PubMed 
    Article 

    Google Scholar 
    Shah, V. B. & McRae, B. Circuitscape: A Tool for Landscape Ecology. in Proceedings of the 7th Python in Science Conference (eds. Varoquaux, G., Vaught, T. & Millman, J.) 62–65 (2008).Ortiz-Malavasi, E. Atlas digital de costa rica está a disposición del público. Invest. TEC 23, 1659–3383 (2015).
    Google Scholar 
    McRae, B., Shirk, A. & Platt, J. Gnarly landscape utilities: Resistance and habitat calculator user guide. The Nature Conservancy https://circuitscape.org/gnarly-landscape-utilities/ (2013).Kass, J. M. et al. Wallace: A flexible platform for reproducible modeling of species niches and distributions built for community expansion. Methods Ecol. Evol. 9, 1151–1156 (2018).Article 

    Google Scholar  More

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    Mapping the distribution and tree canopy cover of Jacaranda mimosifolia and Platanus × acerifolia in Johannesburg’s urban forest

    Lawrence, H. In City Trees: A Historical Geography from the Renaissance through to the Nineteenth Century (Charlottesville and London: University of Virginia Press, 2006, Lewis Mumford. The City in History: Its Origins, Its Transformations and Its Prospects (San Diego: Harvest Book Harcourt, 1961).Frawley, J. Campaigning for street trees, Sydney botanic gardens, 1890s–1920s. Environ. Hist. 15(3), 303–322. https://doi.org/10.3197/096734009X12474738199953 (2009).Article 

    Google Scholar 
    Seburanga, J. L., Kaplin, B. A., Zhang, Q.-X. & Gatesire, T. Amenity trees and green space structure in urban settlements of Kigali, Rwanda. Urban. For. Urban Green. 13(84–9313), 84–93. https://doi.org/10.1016/j.ufug.2013.08.001 (2014).Article 

    Google Scholar 
    Wilson, E. H. Northern trees in southern lands. J. Arnold Arbor. 4(2), 61–90 (1923).Article 

    Google Scholar 
    Gwedla, N. & Shackleton, C. M. Population size and development history determine street tree distribution and composition within and between Eastern Cape towns, South Africa. Urban. For. Urban. Gree. 25, 11–18. https://doi.org/10.1016/j.ufug.2017.04.014 (2017).Article 

    Google Scholar 
    Jacobs, A. B., Macdonald, E. & Rofé, Y. In The Boulevard Book: History, Evolution, Design of Multiway Boulevards (MIT Press, Cambridge, MA 2002), Robinson, W. The Parks and Gardens of Paris Considered in Relation to the Wants of Other Cities and of Private and Public Gardens (McMillan and Co., London , 1878).Akbari, A. H., Pomerantz, M. & Taha, H. Cool surfaces and shade trees to reduce energy use and improve air quality in urban. Sol. Energy. 70(3), 295–310 (2001).ADS 
    Article 

    Google Scholar 
    Roy, S., Byrne, J. & Pickering, C. A systematic quantitative review of urban tree benefits, costs, and assessment methods across cities in different climatic zones. Urban For. Urban Green. 11, 351–363. https://doi.org/10.1016/j.ufug.2012.06.006 (2012).Article 

    Google Scholar 
    Schäffler, A. & Swilling, M. Valuing green infrastructure in an urban environment under pressure—The Johannesburg case. Ecol. Econ. 86, 246–257. https://doi.org/10.1016/j.ecolecon.2012.05.008 (2013).Article 

    Google Scholar 
    Santamour, F. S. Trees for urban planting: Diversity, uniformity and common sense. In Proceedings of the 7th Conference of the Metropolitan Tree Improvement Alliance (METRIA), vol. 7, 57–65 (1990).Shams, Z. I. Changes in diversity and composition of flora along a corridor of different land uses in Karachi over 20 years: caUses and implications. Urban. For. Urban Green. 17, 71–79. https://doi.org/10.1016/j.ufug.2016.03.002 (2016).Article 

    Google Scholar 
    Kambites, C. & Owen, S. Renewed prospects for green infrastructure planning in the UK. Plan. Prac. Res. 21(94), 483–496. https://doi.org/10.1080/02697450601173413 (2006).Article 

    Google Scholar 
    Cho, M. A., Malahlelac, O. & Ramoeloa, A. Assessing the utility WorldView-2 imagery for tree species mapping in South African subtropical humid forest and the conservation implications: Dukuduku forest patch as case study. Int. J. Appl. Earth. Obs. 38, 349–357. https://doi.org/10.1016/j.jag.2015.01.015 (2015).Article 

    Google Scholar 
    Niculescu, S., Lardeux, C., Grigoras, I., Hanganu, J. & David, L. Synergy between LiDAR, RADARSAT-2, and spot-5 images for the detection and mapping of wetland vegetation in the Danube Delta. IEEE J Sel. Top. Appl. Earth. Obs. Remote Sens. 9, 3651–3666 (2016).ADS 
    Article 

    Google Scholar 
    Lefebvre, A., Picand, P.-A. & Sannier, C. Mapping tree cover in European cities: Comparison of classification algorithms for an operational production framework. In 2015 Joint Urban Remote Sensing Event (JURSE), IEEE, 1–4 (2015) https://doi.org/10.1109/JURSE.2015.7120511.Wyndham, C. H., Strydom, N. B., Van Rensburg, A. J. & Rogers, G. G. Effects on maximal oxygen intake of acute changes in altitude in a deep mine. J. Appl. Physiol. 29(5), 552–555 (1970).CAS 
    Article 

    Google Scholar 
    Hegnauer, R. Chemotaxonomie der Pflanzen, vol. 3, 268–281 (Birkhäuser Verlag, Basel, 1964).Mabberley, D. J. The Plant-Book, 2nd edn. 87, 368–369 (Cambridge University Press, Cambridge, 1997).Gachet, M. S. & Schühly, W. Jacaranda—An ethnopharmacological and phytochemical review. J. Ethnopharmacol. 121, 14–27. https://doi.org/10.1016/j.jep.2008.10.015 (2009).CAS 
    Article 
    PubMed 

    Google Scholar 
    Gilman, E. F. & Watson, D. G. Jacaranda mimosifolia. Fact Sheet ST-317, Environmental Horticulture Department, Florida Cooperative Extension Service, University of Florida, Gainesville, http://www.ci.milpitas.ca.gov/_pdfs/council/2016/021616/item_04.pdf Accessed 6 June 2020 (1993).Dineva, S. B. Comparative studies of the leaf morphology and structure of white ash Fraxinus americana L. and London plane tree Platanus acerifolia Willd growing in polluted area. Dendrobiology 52, 3–8 (2004).
    Google Scholar 
    Liu, G., Li, Z. & Bao, M. Colchicine-induced chromosome doubling in Platanus acerifolia and its effect on plant morphology. Euphytica 157, 145–154. https://doi.org/10.1007/s10681-007-9406-6 (2007).Article 

    Google Scholar 
    Henry, A. & Flood, M. G. The history of the London plane, Platanus acerifolia, with notes on the Genus Platanus. Proc. R. Irish Acad Sect. B Biol. Geol. Chem. Sci. 35, 9–28 (1919).
    Google Scholar 
    Chavez, P. S. Image-based atmospheric corrections revisited and improved. Photogram. Eng. Rem. S. 62, 1025–1036 (1996).
    Google Scholar 
    Riano, D., Chuvieco, E., Salas, J. & Aguado, I. Assessment of different topographic corrections in Landsat-T. M. data for mapping vegetation types. IEEE Trans. Geosci. Remote Sens. 41, 1056–1061. https://doi.org/10.1109/TGRS.2003.811693 (2003).ADS 
    Article 

    Google Scholar 
    Rouse J. W., Haas, R. H., Schell, J. A. & Deering, D. W. Proceedings of the Third Earth Resources Technology Satellite-1 Symposium, Greenbelt, USA: NASASP-351; 1974. Monitoring vegetation system in the great plains with ERTS, 3010–3017 (1974).R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/ (2021).Du, Y. et al. New hyperspectral discrimination measure for spectral characterization. Opt. Eng. 43(8), 1777–1786 (2004).ADS 
    Article 

    Google Scholar 
    Bhattacharyya, A. On a measure of divergence between two statistical populations defined by their probability distributions’. Bull. Calcutta Math. Soc. 35, 99–109 (1943).MathSciNet 
    MATH 

    Google Scholar 
    Bruzzone, L., Roli, F. & Serpico, S. B. An extension to multiclass cases of the Jefferys-Matusita distance. IEEE Trans. Pattern. Anal. Mach. Intell. 33, 1318–1321 (1995).
    Google Scholar 
    Kaufman, Y. & Remer, L. Detection of forests using mid-IR reflectance: An application for aerosol studies. IEEE Trans. Geosci. Remote Sens. 32(3), 672–683 (1994).ADS 
    Article 

    Google Scholar 
    Padma, S. & Sanjeevi, S. Jeffries Matusita based mixed-measure for improved spectral matching in hyperspectral image analysis. Int. J. Appl. Earth. Obs. 32, 138–151. https://doi.org/10.1016/j.jag.2014.04.001 (2014).Article 

    Google Scholar 
    Kavzoglu, T. & Mather, P. M.. The use of feature selection techniques in the context of artificial neural networks. In Proceedings of the 26th Annual Conference of the Remote Sensing Society (CD-ROM), 12–14 September (Leicester, UK, 2000).Gunal, S. & Edizkan, R. Subspace based feature selection for pattern recognition. Info. Sci. 178, 3716–3726. https://doi.org/10.1016/j.ins.2008.06.001 (2008).Article 

    Google Scholar 
    Tolpekin, V. A. & Stein, A. Quantification of the effects of land-cover-class spectral separability on the accuracy of markov-random-field-based superresolution mapping. IEEE Trans. Geosci. Remote Sens. 47(9), 3283–3297. https://doi.org/10.1109/TGRS.2009.2019126 (2009).ADS 
    Article 

    Google Scholar 
    Paterson, M., Lucas, R. M. & Chisholm, L. Differentiation of selected Australian woodland species using CASI data. In Proceedings IEEE International Geoscience and Remote Sensing Symposium, 643–645 (University of New South Wales, Australia, 2001).Richards, J. A. & Jai, X. Remote Sensing Digital Analysis: An Introduction, 4th edition (Springer, Berlin, 1999).Veraverbeke, S., Harris, S. & Hook, S. Evaluating spectral indices for burned area discrimination using MODIS/ASTER (MASTER) airborne simulator data. Remote Sens. Environ. 115, 2702–2709. https://doi.org/10.1016/j.rse.2011.06.010 (2011).ADS 
    Article 

    Google Scholar 
    Breiman, L. Random forests. Mach. Learn. 45, 5–32 (2001).Article 

    Google Scholar 
    Georganos, S. et al. Geographical random forests: a spatial extension of the random forest algorithm to address spatial heterogeneity in remote sensing and population modelling. Geocarto Int. https://doi.org/10.1080/10106049.2019.1595177 (2019).Article 

    Google Scholar 
    Mellor, A., Haywood, A., Stone, C. & Jones, S. The performance of random forests in an operational setting for large area sclerophyll forest classification. Remote Sens. 5, 2838–2856. https://doi.org/10.3390/rs5062838 (2013).ADS 
    Article 

    Google Scholar 
    Congalton, R. G. Accuracy assessment and validation of remotely sensed and other spatial information. Int. J. Wildland. Fire. 10, 321–328 (2001).Article 

    Google Scholar 
    Thomas, I. L., Ching, N. P., Benning, V. M. & D’aguanno, J. A. Review Article A review of multi-channel indices of class separability. Int. J. Remote Sens. 8(3), 331–350. https://doi.org/10.1080/01431168708948645 (1987).Article 

    Google Scholar 
    Mausel, P. W., Kramber, W. J. & Lee, J. K. Optimum band selection for supervised classification of multispectral data. Photogramm. Eng. Remote. Sens. 56(1), 55–60 (1990).
    Google Scholar 
    Singh, A. Some clarifications about the pairwise divergence measure in remote sensing. Int. J. Remote Sens. 5(3), 623–627. https://doi.org/10.1080/01431168408948845 (1984).Article 

    Google Scholar 
    Kumar, P. et al. A statistical significance of differences in classification accuracy of crop types using different classification algorithms. Geocarto Int. 32(2), 206–224. https://doi.org/10.1080/10106049.2015.1132483 (2017).Article 

    Google Scholar 
    McPherson, E. G., Simpson, J. R., Peper, P. J., Xiao, Q. & Wu, C. Los Angeles 1-Million Tree Canopy Cover Assessment. General Technical Report PSW-GTR-207. U.S. Department of Agriculture Forest Service Pacific Southwest Research Station. Albany, CA, 1–64 (2008).Rahimizadeh, N., Kafaky, S. B., Sahebi, M. R. & Mataji, A. Forest structure parameter extraction using SPOT-7 satellite data by object- and pixel-based classification methods. Environ. Monit. Assess. 192, 43. https://doi.org/10.1007/s10661-019-8015-x (2020).Article 

    Google Scholar 
    McRoberts, R. E. Satellite image-based maps: Scientific inference or pretty pictures?. Remote. Sens. Environ. 115, 715–724. https://doi.org/10.1016/j.rse.2010.10.013 (2011).ADS 
    Article 

    Google Scholar 
    McRoberts, R. E. Probability- and model-based approaches to inference for proportion forest using satellite imagery as ancillary data. Remote. Sens. Environ. 114, 1017–1025. https://doi.org/10.1016/j.rse.2009.12.013 (2010).ADS 
    Article 

    Google Scholar 
    Kokubu, Y., Hara, S. & Tani, A. Mapping seasonal tree canopy cover and leaf area using worldview-2/3 satellite imagery: A megacity-scale case study in Tokyo urban area. Remote. Sens. 12(9), 1505. https://doi.org/10.3390/rs12091505 (2020).Article 

    Google Scholar 
    Johannesburg City Parks and Zoo. 2018. The city that’s a rain forest. http://www.jhbcityparks.com/index.php/street-trees-contents-29. Accessed 14 June 2020.Tesfamichael, S. G., Newete, S. W., Adam, E. & Dubula, B. Field spectroradiometer and simulated multispectral bands for discriminating invasive species from morphologically similar cohabitant plants. GIsci. Remote Sens. 55(3), 417–436. https://doi.org/10.1080/15481603.2017.1396658 (2018).Article 

    Google Scholar 
    McPherson, E. G., Simpsona, J. R., Xiao, Q. & Wu, C. Million trees Los Angeles canopy cover and benefit assessment. Landsc. Urban. Plan. 99, 40–50 (2011).Article 

    Google Scholar 
    Baines, O., Wilkes, P. & Disney, M. Quantifying urban forest structure with open-access remote sensing data sets. Urban For. Urban Green. 50, 126653. https://doi.org/10.1016/j.ufug.2020.126653 (2020).Article 

    Google Scholar 
    Nowak, D. J. et al. Measuring and analyzing urban tree cover. Landsc. Urban Plan. 36, 49–57 (1996).Article 

    Google Scholar 
    Estoque, R. C. et al. Remotely sensed tree canopy cover-based indicators for monitoring global sustainability and environmental initiatives. Environ. Res. Lett. 16, 044047. https://doi.org/10.1088/1748-9326/abe5d9 (2021).ADS 
    CAS 
    Article 

    Google Scholar 
    Paap, T., de Beer, W., Migliorini, D., Nel, W. J. & Wingfield, M. J. The polyphagous shot hole borer (PSHB) and its fungal symbiont Fusarium euwallaceae: A new invasion in South Africa Trudy. Aust. Plant. Pathol. 47, 231–237. https://doi.org/10.1007/s13313-018-0545-0 (2018).Article 

    Google Scholar  More

  • in

    Experimental evidence challenges the presumed defensive function of a “slow toxin” in cycads

    Cox, P. A., Banack, S. A. & Murch, S. J. Biomagnification of cyanobacterial neurotoxins and neurodegenerative disease among the Chamorro people of Guam. Proc. Natl. Acad. Sci. U.S.A. 100, 13380–13383 (2003).ADS 
    CAS 
    Article 

    Google Scholar 
    Brand, L. E., Pablo, J., Compton, A., Hammerschlag, N. & Mash, D. C. Cyanobacterial blooms and the occurrence of the neurotoxin, beta-N-methylamino-L-alanine (BMAA), in south Florida aquatic food webs. Harmful Algae 9, 620–635 (2010).CAS 
    Article 

    Google Scholar 
    Metcalf, J. S., Banack, S. A., Richer, R. & Cox, P. A. Neurotoxic amino acids and their isomers in desert environments. J. Arid Environ. 112, 140–144 (2015).ADS 
    Article 

    Google Scholar 
    Violi, J. P., Mitrovic, S. M., Colville, A., Main, B. J. & Rodgers, K. J. Prevalence of (beta)-methylamino-L-alanine (BMAA) and its isomers in freshwater cyanobacteria isolated from eastern Australia. Ecotoxicol. Environ. Saf. 172, 72–81 (2019).CAS 
    Article 

    Google Scholar 
    Jonasson, S. et al. Transfer of a cyanobacterial neurotoxin within a temperate aquatic ecosystem suggests pathways for human exposure. Proc. Natl. Acad. Sci. 107, 9252–9257 (2010).ADS 
    CAS 
    Article 

    Google Scholar 
    Metcalf, J. et al. Toxin analysis of freshwater cyanobacterial and marine harmful algal blooms on the west coast of Florida and implications for estuarine environments. Neurotox. Res. 39, 27–35 (2021).CAS 
    Article 

    Google Scholar 
    Cox, P. A. et al. Cyanobacteria and BMAA exposure from desert dust: a possible link to sporadic ALS among Gulf War veterans. Amyotroph. Lateral Scler. 10, 109–117 (2009).CAS 
    Article 

    Google Scholar 
    Charlton, T. S., Marini, A. M., Markey, S. P., Norstog, K. & Duncan, M. W. Quantification of the neurotoxin 2-amino-3-(methylamino)-propanoic acid (BMAA) in Cycadales. Phytochemistry 31, 3429–3432 (1992).CAS 
    Article 

    Google Scholar 
    Whiting, M. G. Toxicity of cycads. Econ. Bot. 17, 270–302 (1963).Article 

    Google Scholar 
    Cox, P. A., Davis, D. A., Mash, D. C., Metcalf, J. S. & Banack, S. A. Dietary exposure to an environmental toxin triggers neurofibrillary tangles and amyloid deposits in the brain. Proc. R. Soc. B: Biol. Sci. 283, 20152397 (2016).Article 

    Google Scholar 
    Scott, L. L. & Downing, T. G. A single neonatal exposure to BMAA in a rat model produces neuropathology consistent with neurodegenerative diseases. Toxins 10, 22 (2018).Article 

    Google Scholar 
    Roy, U. et al. Metabolic profiling of zebrafish (Danio rerio) embryos by NMR spectroscopy reveals multifaceted toxicity of (beta)-methylamino-L-alanine (BMAA). Sci. Rep. 7, 1–12 (2017).ADS 
    Article 

    Google Scholar 
    Purdie, E. L., Metcalf, J. S., Kashmiri, S. & Codd, G. A. Toxicity of the cyanobacterial neurotoxin (beta)-N-methylamino-L-alanine to three aquatic animal species. Amyotroph. Lateral Scler. 10, 67–70 (2009).CAS 
    Article 

    Google Scholar 
    Brenner, E. D. et al. Arabidopsis mutants resistant to s (+)-(beta)-methyl-(alpha), (beta)-diaminopropionic acid, a cycad-derived glutamate receptor agonist. Plant Physiol. 124, 1615–1624 (2000).CAS 
    Article 

    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 
    Article 

    Google Scholar 
    Koi, S. & Daniels, J. Life history variations and seasonal polyphenism in Eumaeus atala (Lepidoptera: Lycaenidae). Florida Entomol. 100, 219–229 (2017).Article 

    Google Scholar 
    Koi, S. A butterfly picks its poison: Cycads (Cycadaceae), integrated pest management and Eumaeus atala Poey (Lepidoptera: Lycaenidae). Entomol. Ornithol. Herpetol. 6 (2017).Brenner, E. D., Stevenson, D. W. & Twigg, R. W. Cycads: Evolutionary innovations and the role of plant-derived neurotoxins. Trends Plant Sci. 8, 446–452 (2003).CAS 
    Article 

    Google Scholar 
    Prado, A. The cycad herbivores. Bull. Soc. D’entomol. Quebec 18, 3–6 (2011).
    Google Scholar 
    Popova, A. & Koksharova, O. Neurotoxic non-proteinogenic amino acid (beta)-N-methylamino-L-alanine and its role in biological systems. Biochem. Mosc. 81, 794–805 (2016).CAS 
    Article 

    Google Scholar 
    Salzman, S., Whitaker, M. R. L. & Pierce, N. E. Cycad-feeding insects share a core gut microbiome. Biol. J. Lin. Soc. 123, 728–738 (2018).Article 

    Google Scholar 
    Whitaker, M. R. & Salzman, S. Ecology and evolution of cycad-feeding Lepidoptera. Ecol. Lett. 23, 1862–1877 (2020).Article 

    Google Scholar 
    Zhou, X., Escala, W., Papapetropoulos, S., Bradley, W. G. & Zhai, R. G. BMAA neurotoxicity in Drosophila. Amyotroph. Lateral Scler. 10, 61–66 (2009).CAS 
    Article 

    Google Scholar 
    Zhou, X., Escala, W., Papapetropoulos, S. & Zhai, R. G. (beta)-N-methylamino-L-alanine induces neurological deficits and shortened life span in Drosophila. Toxins 2, 2663–2679 (2010).CAS 
    Article 

    Google Scholar 
    Mekdara, N. T. et al. A novel lenticular arena to quantify locomotor competence in walking fruit flies. J. Exp. Zool. A Ecol. Genet. Physiol. 317, 382–394 (2012).Article 

    Google Scholar 
    Goto, J. J., Koenig, J. H. & Ikeda, K. The physiological effect of ingested (beta)-N-methylamino-L-alanine on a glutamatergic synapse in an in vivo preparation. Comp. Biochem. Physiol. Part C: Toxicol. Pharmacol. 156, 171–177 (2012).CAS 

    Google Scholar 
    Okle, O., Rath, L., Galizia, C. G. & Dietrich, D. R. The cyanobacterial neurotoxin (beta)-N-methylamino-L-alanine (BMAA) induces neuronal and behavioral changes in honeybees. Toxicol. Appl. Pharmacol. 270, 9–15 (2013).CAS 
    Article 

    Google Scholar 
    Spencer, P. S. et al. Guam amyotrophis lateral sclerosis-parkinsonism-dementia linked to a plant excitant neurotoxin. Science 237, 517–522 (1987).ADS 
    CAS 
    Article 

    Google Scholar 
    Bernays, E. A. & Chapman, R. F. Host-plant selection by phytophagous insects. In Host-Plant Selection by Phytophagous Insects. Contemporary Topics in Entomology, vol. 2, 201–213 (Springer, Boston, MA, 1994).Zandt, P. A. V. Plant defense, growth, and habitat: A comparative assessment of constitutive and induced resistance. Ecology 88, 1984–1993 (2007).Article 

    Google Scholar 
    Duncan, M. W. Role of the cycad neurotoxin BMAA in the amyotrophic lateral sclerosi-parkisonism dementia complex of the Western Pacific. Adv. Neurol. 56, 301–310 (1991).CAS 
    PubMed 

    Google Scholar 
    Banack, S. A. & Cox, P. A. Distribution of the neurotoxic nonprotein amino acid BMAA in Cycas micronesica. Bot. J. Linn. Soc. 143, 165–168 (2003).Article 

    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria (2021).Therneau, T. M. A Package for Survival Analysis in R. R package version 3.2-11 (2021).Kassambara, A., Kosinski, M. & Biecek, P. survminer: Drawing Survival Curves using ’ggplot2’. R package version 0.4.9 (2021).Pennington, Z. T. et al. eztrack: An open-source video analysis pipeline for the investigation of animal behavior. Sci. Rep. 9, 1–11 (2019).Article 

    Google Scholar 
    Pérez, F. & Granger, B. E. IPython: A system for interactive scientific computing. Comput. Sci. Eng. 9, 21–29 (2007).Article 

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

    Google Scholar 
    Karlsson, O., Roman, E. & Brittebo, E. B. Long-term cognitive impairments in adult rats treated neonatally with (beta)-N-methylamino-L-alanine. Toxicol. Sci. 112, 185–195 (2009).CAS 
    Article 

    Google Scholar 
    Whitaker, M. R. L., Salzman, S., Gratacos, X. & Tucker Lima, J. Localized overabundance of an otherwise rare butterfly threatens endangered cycads. Florida Entomol. 103, 519–522 (2021).Article 

    Google Scholar 
    Backmann, P. et al. Delayed chemical defense: Timely expulsion of herbivores can reduce competition with neighboring plants. Am. Nat. 193, 125–139 (2019).Article 

    Google Scholar 
    Yáñez-Espinosa, L. & Sosa-Sosa, F. Population structure of Dioon purpusii rose in Oaxaca, Mexico. Neotrop. Biol. Conserv. 2, 46–54 (2007).
    Google Scholar 
    Robbins, R. K. et al. A switch to feeding on cycads generates parallel accelerated evolution of toxin tolerance in two clades of Eumaeus caterpillars (Lepidoptera: Lycaenidae). Proc. Natl. Acad. Sci.118 (2021).Grunseich, J. M., Thompson, M. N., Aguirre, N. M. & Helms, A. M. The role of plant-associated microbes in mediating host-plant selection by insect herbivores. Plants 9, 6 (2020).CAS 
    Article 

    Google Scholar 
    Zhang, Y. & Whalen, J. K. Production of the neurotoxin beta-N-methylamino-L-alanine may be triggered by agricultural nutrients: An emerging public health issue. Water Res. 170, 115335 (2020).CAS 
    Article 

    Google Scholar  More

  • in

    Relationships between species richness and ecosystem services in Amazonian forests strongly influenced by biogeographical strata and forest types

    In this study we analysed how tree and arborescent palm species richness was related to aboveground carbon stock, commercially relevant timber stock, and commercially relevant NTFP abundance in tropical forests, and how these relationships were influenced by environmental stratification at different spatial scales. We found that species richness showed significant relationships with all three ecosystem services stock components, but its relationships were strongly influenced by variation across forest types and biogeographical strata. This is further explained below.Across the Guiana Shield, species richness showed a positive relationship with carbon stock and timber, but not with NTFP abundance. Although relationships only differed in significance among the biogeographical subregions, they differed in direction between terra firme forests and white sand forests. Species richness was positively related to carbon stock and timber stock in terra firme forests, whereas it was negatively related to NTFP abundance in white sand forests. The positive species-carbon relationship across forests of the Guiana Shield is in line with the effects described by hypotheses such as the ‘niche complementarity’ and ‘selection effect’10 and is in line with previous findings at regional spatial scales6,21. To our knowledge, the relationship between species richness and timber stock has not been previously analysed for tropical forests. Interestingly, the observed positive species-timber relationship in terra firme forests of the Guiana Shield contrasts with the negative species-timber relationship found for subtropical forests in both the U.S.A. and Spain20, although this may be explained by the difference in ecosystems. The non-significant species-NTFP abundance relationship across the Guiana Shield and the negative relationship within white sand forests seems to contradict previous findings. Steur et al.24 found a negative species-NTFP abundance relationship for tropical forests in Suriname. However, this negative relationship was found across multiple forest types, including flooded forests that had low species richness and high NTFP abundance. These flooded forests most likely influenced the species-NTFP abundance relationship across all forest types.In contrast to the relationship between species richness and carbon stock, no mechanism has been proposed for how species richness would influence commercial timber stock and NTFP abundance. Although our results suggest that species richness had a positive relationship with timber, the relationship was not found within multiple biogeographical subregions. For NTFP abundance, species richness did not contribute to explaining variation when variation across biogeographical subregions was accounted for (i.e. was included as an explanatory variable). We here tentatively propose that both commercial relevant timber stock and NTFP abundance are driven by variation in species floristic composition, rather than by species richness. For services such as commercial timber and NTFP provisioning, only a subset of all species is relevant (in this study, 9.4% of all morphospecies for timber and 3.8% for NTFPs), and such subsets are likely not random selections. For example, for Suriname, it was found that variation in commercially relevant NTFP abundance was driven by a particularly small selection of NTFP producing species with high abundances (referred to as ‘NTFP oligarchs’)24, and for commercial relevant timber stock, it is commonly known that selections tend to include more abundant than rare species. Additionally, as the relative abundance of species tends to vary across floristic regions in Amazonia, where, for example, certain species are dominant in particular forest types and biogeographical regions31,32, it can be expected that commercial timber stock and NTFP abundance are determined by floristic composition. In support, for NTFP abundance in Suriname tropical forests, Steur et al.24 found that floristic composition was a stronger predictor of NTFP abundance than species richness.Across all of Amazonia, species richness had a positive relationship with carbon stock, but only when variation among biogeographical regions was accounted for. The positive species-carbon relationship across Amazonia partly contrasts with previous findings at continental spatial scales11,13. When variation across climatic and/or edaphic variables was accounted for, Sullivan et al.13 found no significant species-carbon relationship across South-America, while Poorter et al.33 did find a positive relationship across Meso- and South-America. Here, we propose that accounting for differences among biogeographical regions can explain the previously found contrasts at continental spatial scales. In our dataset, for individual regions, we found either a positive relationship or a non-significant, but weakly positive, relationship between carbon stock and species richness (Fig. 2). However, when the data were aggregated across all regions, this resulted in a non-significant, and weakly negative, relationship. This reflects a known statistical phenomenon referred to as a ‘Simpson’s paradox’34, in which a relationship appears in multiple distinct groups but disappears or reverses when the groups are combined. Additional post-hoc tests of leaving one region out at a time showed that this pattern was not dependent of any particular biogeographical region. This is the first time that an analysis based on empirical data provides evidence for a Simpson’s paradox in species-ecosystem service relationships.It is likely that the observed differences in carbon stock across the biogeographical regions of Amazonia are influenced by multiple factors. For example, the biogeographical regions used in our analyses were recognised according to differences in substrate history, geological age and floristic composition, which could all contribute to variation in carbon stock. The substrate history and geological age of the biogeographical regions have been related to differences in soil fertility35, while multiple spatial gradients in floristic composition identified across the Amazon coincide with a spatial gradient in wood density28. However, further analysis is needed to obtain better insight into the relative contributions of these and other variables to explain the observed variation in carbon stock across the biogeographical regions. This requires data on multiple environmental variables, including floristic composition, climatic variables such as the length of the dry period, soil conditions, and intensity of disturbance.In our analyses, terra firme forests determined the relationship of species richness with the carbon stock, timber stock, and NTFP abundance across the datasets. Although this is most likely the effect of unequal sample sizes, with terra firme forests being the dominant forest type in terms of sample size (n = 130 vs. n = 21 for the Guiana Shield dataset; n = 257 vs. n = 26 for the Amazonia dataset), we expect that the observed relationships reflect the general pattern. Terra firme forests are the most dominant forest type in terms of geographical area32 and were representatively sampled. Regardless, the analyses per forest type had added value. The significant relationship between species richness and NTFP abundance in white sand forests across the Guiana Shield would otherwise have been overlooked.Due to the known scarcity of reliable and adequate information on which timber and NTFP species are being commercially traded36,37,38,39, we used a fixed set of timber and NTFP species to apply across the Guiana Shield plots. However, in reality, timber and NTFP species can be expected to vary according to socio-economic factors, such as culture, access, and harvest costs, which may change over space and time. Therefore, estimates of timber stock and NTFP abundance can be expected to differ across spatial gradients, and thus, their possible relationships with species richness cannot be easily generalised. To circumvent this, timber stock and NTFP abundance would have to be estimated on the basis of ‘flexible’ species selections that can change according to local socio-economic contexts. To this end, detailed information on both commercially relevant timber and NTFP species is urgently needed. Yet, for our study area, we did not observe major differences in selected species, and we included broad selections of species, which should make timber stock and NTFP abundance robust against small deviations in species selection. It must be noted that our approach of quantifying commercial relevant timber stock and NTFP abundance does not consider the value of timber and NTFPs for subsistence use. In addition, NTFPs can also be derived from other growth forms, such as lianas, shrubs and herbs. Last, because NTFP production data was not available we used NTFP abundance as a proxy for NTFP stock, following similar assessments of NTFP stock 24,40. A limitation of this approach is that each NTFP species individual has an equal contribution to NTFP stock, whereas it can be expected that large individuals may have a larger contribution than smaller individuals and that production volumes can differ for different types of NTFPs, for example barks vs. seeds.Our findings illustrate the importance of considering environmental stratification and spatial scale when analysing relationships between biodiversity and ecosystem services. First, environmental stratification can help detect relationships that are otherwise obscured by environmental heterogeneity. For example, although the association between species richness and carbon stock across Amazonia was relatively weak (explaining ~ 3% of total variation vs. ~ 15% in the Guiana Shield) and was obscured by variation in carbon stock across biogeographical strata, by using environmental stratification the positive relationship remained detectable. Second, environmental heterogeneity tends to vary with spatial scale; therefore, its importance needs to be checked according to spatial scale. For example, at the regional scale of the Guiana Shield, biogeographical subregions explained a moderate amount of variation in carbon stock (~ 20%), while at the spatial scale of Amazonia, biogeographical regions explained more than half of total variation in carbon stock (~ 55%). Such an increase and ultimate importance of variation across biogeographical strata might also explain the absence of a significant relationship between species richness and carbon stock across African and/or Asian tropical forests as reported by Sullivan et al.13.In our analyses, we found evidence of a positive relationship between species richness and carbon stock across and within Amazonia. This supports the notion that win–win scenarios are possible in conservation approaches, where, for example, REDD+ can be expected to help conserve tropical forests that contain large amounts of carbon stock and high concentrations of species9. However, we conclude that species richness is not always a strong predictor of biomass-based ecosystem services. In our analyses, NTFP abundance was not driven by species richness, and we ultimately expect the same for timber stock. We expect that differences in floristic composition, linked to differences across forest types and biogeographical strata, will be more relevant than species richness in explaining variation in timber stock and NTFP abundance. This would mean that conserving timber and NTFP related ecosystem services requires the development of additional region-specific strategies that account for differences in floristic composition. For example, areas with high concentrations of timber or NTFPs could be considered in the designation of multiple use protected areas41, such as the extractive reserves in Brazil, or be included as ‘high conservation value areas’ (HCVAs) in sustainable forest management certification42. More

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    Active lithoautotrophic and methane-oxidizing microbial community in an anoxic, sub-zero, and hypersaline High Arctic spring

    Pollard W, Omelon C, Andersen D, McKay C. Perennial spring occurrence in the Expedition Fiord area of western Axel Heiberg Island, Canadian High Arctic. Can J Earth Sci. 1999;36:105–20.CAS 
    Article 

    Google Scholar 
    Andersen DT. Cold springs in permafrost on Earth and Mars. J Geophys Res. 2002;107:4–1-4-7.
    Google Scholar 
    Niederberger TD, Perreault NN, Tille S, Lollar BS, Lacrampe-Couloume G, Andersen D, et al. Microbial characterization of a subzero, hypersaline methane seep in the Canadian High Arctic. ISME J. 2010;4:1326–39.CAS 
    PubMed 
    Article 

    Google Scholar 
    Goordial J, Lamarche-Gagnon G, Lay CY, Whyte L. Left out in the cold: life in cryoenvironments. In: Seckbach J, Oren A, Stan-Lotter H, editors. Polyextremophiles. New York: Springer; 2013. p. 335–64.Gilichinsky D, Rivkina E, Bakermans C, Shcherbakova V, Petrovskaya L, Ozerskaya S, et al. Biodiversity of cryopegs in permafrost. FEMS Microbiol Ecol. 2005;53:117–28.CAS 
    PubMed 
    Article 

    Google Scholar 
    Rivkina EM, Friedmann EI, McKay CP, Gilichinsky DA. Metabolic activity of permafrost bacteria below the freezing point. Appl Environ Microbiol. 2000;66:3230–3.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Brown MV, Bowman JP. A molecular phylogenetic survey of sea-ice microbial communities (SIMCO). FEMS Microbiol Ecol. 2001;35:267–75.CAS 
    PubMed 
    Article 

    Google Scholar 
    Murray AE, Kenig F, Fritsen CH, McKay CP, Cawley KM, Edwards R, et al. Microbial life at -13 degrees C in the brine of an ice-sealed Antarctic lake. Proc Natl Acad Sci USA. 2012;109:20626–31.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Orosei R, Lauro SE, Pettinelli E, Cicchetti A, Coradini M, Cosciotti B, et al. Radar evidence of subglacial liquid water on Mars. Science. 2018;361:490–3.CAS 
    PubMed 
    Article 

    Google Scholar 
    Lauro SE, Pettinelli E, Caprarelli G, Guallini L, Pio Rossi A, Mattei E, et al. Multiple subglacial water bodies below the south pole of Mars unveiled by new MARSIS data. Nat Astron. 2021;5:63–70.Article 

    Google Scholar 
    Bishop JL, Yesilbas M, Hinman NW, Burton ZFM, Englert PAJ, Toner JD, et al. Martian subsurface cryosalt expansion and collapse as trigger for landslides. Sci Adv. 2021;7:1–13.
    Google Scholar 
    Allen CC, Oehler DZ. A case for ancient springs in Arabia Terra, Mars. Astrobiology. 2008;8:1093–112.CAS 
    PubMed 
    Article 

    Google Scholar 
    Battler MM, Osinski GR, Banerjee NR. Mineralogy of saline perennial cold springs on Axel Heiberg Island, Nunavut, Canada and implications for spring deposits on Mars. Icarus. 2013;224:364–81.CAS 
    Article 

    Google Scholar 
    Leask EK, Ehlmann BL. Evidence for deposition of chloride on Mars from small‐volume surface water events into the Late Hesperian‐Early Amazonian. AGU Adv. 2022;3:1–19.Article 

    Google Scholar 
    Howell SM, Pappalardo RT. NASA’s Europa Clipper-a mission to a potentially habitable ocean world. Nat Commun. 2020;11:1–4.Article 

    Google Scholar 
    Farley KA, Williford KH, Stack KM, Bhartia R, Chen A, de la Torre M, et al. Mars 2020 mission overview. Space Sci Rev. 2020;216:1–41.Article 

    Google Scholar 
    Kargel JS, Kaye JZ, Head JW, Marion GM, Sassen R, Crowley JK, et al. Europa’s crust and ocean: origin, composition, and the prospects for life. Icarus. 2000;148:226–65.CAS 
    Article 

    Google Scholar 
    Taubner RS, Pappenreiter P, Zwicker J, Smrzka D, Pruckner C, Kolar P, et al. Biological methane production under putative Enceladus-like conditions. Nat Commun. 2018;9:1–11.CAS 
    Article 

    Google Scholar 
    Lamarche-Gagnon G, Comery R, Greer CW, Whyte LG. Evidence of in situ microbial activity and sulphidogenesis in perennially sub-0 degrees C and hypersaline sediments of a high Arctic permafrost spring. Extremophiles. 2015;19:1–15.CAS 
    PubMed 
    Article 

    Google Scholar 
    Lay CY, Mykytczuk NC, Yergeau E, Lamarche-Gagnon G, Greer CW, Whyte LG. Defining the functional potential and active community members of a sediment microbial community in a high-arctic hypersaline subzero spring. Appl Environ Microbiol. 2013;79:3637–48.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Menzel P, Ng KL, Krogh A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun. 2016;7:1–9.Article 

    Google Scholar 
    Gruber-Vodicka HR, Seah BKB, Pruesse E. phyloFlash: rapid small-subunit rRNA profiling and targeted assembly from metagenomes. mSystems. 2020;5:1–16.Article 

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

    Google Scholar 
    Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3:1–15.Article 

    Google Scholar 
    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Chen IA, Chu K, Palaniappan K, Ratner A, Huang J, Huntemann M, et al. The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Res. 2020;49:D751–D63.PubMed Central 
    Article 

    Google Scholar 
    Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Sundaramurthi JC, Lee J, et al. Genomes OnLine Database (GOLD) v.8: overview and updates. Nucleic Acids Res. 2020;49:D723–D733.PubMed Central 
    Article 

    Google Scholar 
    Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2019;36:1925–7.PubMed Central 

    Google Scholar 
    Schmieder R, Edwards R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE. 2011;6:1–11.Article 

    Google Scholar 
    Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kopylova E, Noe L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28:3211–7.CAS 
    PubMed 
    Article 

    Google Scholar 
    Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–9.CAS 
    PubMed 
    Article 

    Google Scholar 
    Royo-Llonch M, Sanchez P, Ruiz-Gonzalez C, Salazar G, Pedros-Alio C, Sebastian M, et al. Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean. Nat Microbiol. 2021;6:1561–74.CAS 
    PubMed 
    Article 

    Google Scholar 
    Ghosh W, Dam B. Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea. FEMS Microbiol Rev. 2009;33:999–1043.CAS 
    PubMed 
    Article 

    Google Scholar 
    Boden R. Reclassification of Halothiobacillus hydrothermalis and Halothiobacillus halophilus to Guyparkeria gen. nov. in the Thioalkalibacteraceae fam. nov., with emended descriptions of the genus Halothiobacillus and family Halothiobacillaceae. Int J Syst Evol Microbiol. 2017;67:3919–28.CAS 
    PubMed 
    Article 

    Google Scholar 
    Sorokin DY, Abbas B, van Zessen E, Muyzer G. Isolation and characterization of an obligately chemolithoautotrophic Halothiobacillus strain capable of growth on thiocyanate as an energy source. FEMS Microbiol Lett. 2014;354:69–74.CAS 
    PubMed 
    Article 

    Google Scholar 
    Meier DV, Pjevac P, Bach W, Hourdez S, Girguis PR, Vidoudez C, et al. Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents. ISME J. 2017;11:1545–58.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Headd B, Engel AS. Evidence for niche partitioning revealed by the distribution of sulfur oxidation genes collected from areas of a terrestrial sulfidic spring with differing geochemical conditions. Appl Environ Microbiol. 2013;79:1171–82.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Preisig O, Zufferey R, Thoney-Meyer L, Appleby CA, Hennecke H. A high-affinity cbb3-type cytochrome oxidase terminates the symbiosis-specific respiratory chain of Bradyrhizobium japonicum. J Bacteriol. 1996;178:1532–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Mikucki JA, Pearson A, Johnston DT, Turchyn AV, Farquhar J, Schrag DP, et al. A contemporary microbially maintained subglacial ferrous “ocean”. Science. 2009;324:397–400.CAS 
    PubMed 
    Article 

    Google Scholar 
    Ruff SE, Biddle JF, Teske AP, Knittel K, Boetius A, Ramette A. Global dispersion and local diversification of the methane seep microbiome. Proc Natl Acad Sci USA. 2015;112:4015–20.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lloyd KG, Lapham L, Teske A. An anaerobic methane-oxidizing community of ANME-1b archaea in hypersaline Gulf of Mexico sediments. Appl Environ Microbiol. 2006;72:7218–30.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Maignien L, Parkes RJ, Cragg B, Niemann H, Knittel K, Coulon S, et al. Anaerobic oxidation of methane in hypersaline cold seep sediments. FEMS Microbiol Ecol. 2013;83:214–31.CAS 
    PubMed 
    Article 

    Google Scholar 
    Campen R, Kowalski J, Lyons WB, Tulaczyk S, Dachwald B, Pettit E, et al. Microbial diversity of an Antarctic subglacial community and high-resolution replicate sampling inform hydrological connectivity in a polar desert. Environ Microbiol. 2019;21:2290–306.PubMed 
    Article 

    Google Scholar 
    Cooper ZS, Rapp JZ, Carpenter SD, Iwahana G, Eicken H, Deming JW. Distinctive microbial communities in subzero hypersaline brines from Arctic coastal sea ice and rarely sampled cryopegs. FEMS Microbiol Ecol. 2019;95:1–15.Article 

    Google Scholar 
    Winkel M, Mitzscherling J, Overduin PP, Horn F, Winterfeld M, Rijkers R, et al. Anaerobic methanotrophic communities thrive in deep submarine permafrost. Sci Rep. 2018;8:1–13.CAS 

    Google Scholar 
    Lay CY, Mykytczuk NC, Niederberger TD, Martineau C, Greer CW, Whyte LG. Microbial diversity and activity in hypersaline high Arctic spring channels. Extremophiles. 2012;16:177–91.CAS 
    PubMed 
    Article 

    Google Scholar 
    Bhattarai S, Cassarini C, Lens PNL. Physiology and distribution of archaeal methanotrophs that couple anaerobic oxidation of methane with sulfate reduction. Microbiol Mol Biol Rev. 2019;83:1–31.Article 

    Google Scholar 
    Kleindienst S, Ramette A, Amann R, Knittel K. Distribution and in situ abundance of sulfate-reducing bacteria in diverse marine hydrocarbon seep sediments. Environ Microbiol. 2012;14:2689–710.CAS 
    PubMed 
    Article 

    Google Scholar 
    Timmers PH, Welte CU, Koehorst JJ, Plugge CM, Jetten MS, Stams AJ. Reverse methanogenesis and respiration in methanotrophic archaea. Archaea. 2017;2017:1–22.Article 

    Google Scholar 
    Leu AO, Cai C, McIlroy SJ, Southam G, Orphan VJ, Yuan Z, et al. Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae. ISME J. 2020;14:1030–41.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Haroon MF, Hu S, Shi Y, Imelfort M, Keller J, Hugenholtz P, et al. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature. 2013;500:567–70.CAS 
    PubMed 
    Article 

    Google Scholar 
    Cai C, Leu AO, Xie GJ, Guo J, Feng Y, Zhao JX, et al. A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. ISME J. 2018;12:1929–39.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Oshkin IY, Wegner CE, Luke C, Glagolev MV, Filippov IV, Pimenov NV, et al. Gammaproteobacterial methanotrophs dominate cold methane seeps in floodplains of West Siberian rivers. Appl Environ Microbiol. 2014;80:5944–54.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Cabrol L, Thalasso F, Gandois L, Sepulveda-Jauregui A, Martinez-Cruz K, Teisserenc R, et al. Anaerobic oxidation of methane and associated microbiome in anoxic water of Northwestern Siberian lakes. Sci Total Environ. 2020;736:1–16.Article 

    Google Scholar 
    Orcutt B, Boetius A, Elvert M, Samarkin V, Joye SB. Molecular biogeochemistry of sulfate reduction, methanogenesis and the anaerobic oxidation of methane at Gulf of Mexico cold seeps. Geochim Cosmochim Acta. 2005;69:4267–81.CAS 
    Article 

    Google Scholar 
    Knittel K, Losekann T, Boetius A, Kort R, Amann R. Diversity and distribution of methanotrophic archaea at cold seeps. Appl Environ Microbiol. 2005;71:467–79.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Schubert CJ, Coolen MJ, Neretin LN, Schippers A, Abbas B, Durisch-Kaiser E, et al. Aerobic and anaerobic methanotrophs in the Black Sea water column. Environ Microbiol. 2006;8:1844–56.CAS 
    PubMed 
    Article 

    Google Scholar 
    Wang J, Hua M, Cai C, Hu J, Wang J, Yang H, et al. Spatial-temporal pattern of sulfate-dependent anaerobic methane oxidation in an intertidal zone of the East China Sea. Appl Environ Microbiol. 2019;85:1–15.
    Google Scholar 
    Dyksma S, Bischof K, Fuchs BM, Hoffmann K, Meier D, Meyerdierks A, et al. Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. ISME J. 2016;10:1939–53.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Perreault NN, Greer CW, Andersen DT, Tille S, Lacrampe-Couloume G, Lollar BS, et al. Heterotrophic and autotrophic microbial populations in cold perennial springs of the high Arctic. Appl Environ Microbiol. 2008;74:6898–907.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Cordero PRF, Bayly K, Man Leung P, Huang C, Islam ZF, Schittenhelm RB, et al. Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival. ISME J. 2019;13:2868–81.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Nigro LM, Elling FJ, Hinrichs KU, Joye SB, Teske A. Microbial ecology and biogeochemistry of hypersaline sediments in Orca Basin. PLoS ONE. 2020;15:1–25.Article 

    Google Scholar 
    Rath KM, Fierer N, Murphy DV, Rousk J. Linking bacterial community composition to soil salinity along environmental gradients. ISME J. 2019;13:836–46.CAS 
    PubMed 
    Article 

    Google Scholar 
    Yoon JH, Lee MH, Kang SJ, Oh TK. Salegentibacter salinarum sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol. 2008;58:365–9.CAS 
    PubMed 
    Article 

    Google Scholar 
    Sangwan N, Xia F, Gilbert JA. Recovering complete and draft population genomes from metagenome datasets. Microbiome. 2016;4:1–11.Article 

    Google Scholar 
    Goordial J, Raymond-Bouchard I, Zolotarov Y, de Bethencourt L, Ronholm J, Shapiro N, et al. Cold adaptive traits revealed by comparative genomic analysis of the eurypsychrophile Rhodococcus sp. JG3 isolated from high elevation McMurdo Dry Valley permafrost, Antarctica. FEMS Microbiol Ecol. 2016;92:1–11.
    Google Scholar 
    Laso-Perez R, Wegener G, Knittel K, Widdel F, Harding KJ, Krukenberg V, et al. Thermophilic archaea activate butane via alkyl-coenzyme M formation. Nature. 2016;539:396–401.CAS 
    PubMed 
    Article 

    Google Scholar 
    Dombrowski N, Teske AP, Baker BJ. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat Commun. 2018;9:1–13.CAS 
    Article 

    Google Scholar 
    Oren A. Thermodynamic limits to microbial life at high salt concentrations. Environ Microbiol. 2011;13:1908–23.CAS 
    PubMed 
    Article 

    Google Scholar 
    Gunde-Cimerman N, Plemenitas A, Oren A. Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations. FEMS Microbiol Rev. 2018;42:353–75.CAS 
    PubMed 
    Article 

    Google Scholar 
    Hechler T, Pfeifer F. Anaerobiosis inhibits gas vesicle formation in halophilic. Archaea Mol Microbiol. 2009;71:132–45.CAS 
    PubMed 
    Article 

    Google Scholar 
    Stokke R, Roalkvam I, Lanzen A, Haflidason H, Steen IH. Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments. Environ Microbiol. 2012;14:1333–46.CAS 
    PubMed 
    Article 

    Google Scholar 
    Wegener G, Krukenberg V, Riedel D, Tegetmeyer HE, Boetius A. Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria. Nature. 2015;526:587–90.CAS 
    PubMed 
    Article 

    Google Scholar 
    Skennerton CT, Chourey K, Iyer R, Hettich RL, Tyson GW, Orphan VJ. Methane-fueled syntrophy through extracellular electron transfer: uncovering the genomic traits conserved within diverse bacterial partners of anaerobic methanotrophic archaea. mBio. 2017;8:1–14.Article 

    Google Scholar 
    Krukenberg V, Riedel D, Gruber-Vodicka HR, Buttigieg PL, Tegetmeyer HE, Boetius A, et al. Gene expression and ultrastructure of meso- and thermophilic methanotrophic consortia. Environ Microbiol. 2018;20:1651–66.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Youssef NH, Rinke C, Stepanauskas R, Farag I, Woyke T, Elshahed MS. Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’. ISME J. 2015;9:447–60.CAS 
    PubMed 
    Article 

    Google Scholar 
    Castelle CJ, Brown CT, Anantharaman K, Probst AJ, Huang RH, Banfield JF. Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nat Rev Microbiol. 2018;16:629–45.CAS 
    PubMed 
    Article 

    Google Scholar 
    Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013;499:431–7.CAS 
    PubMed 
    Article 

    Google Scholar 
    Dombrowski N, Lee JH, Williams TA, Offre P, Spang A. Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. FEMS Microbiol Lett. 2019;366:1–12.Article 

    Google Scholar 
    Wong HL, MacLeod FI, White RA 3rd, Visscher PT, Burns BP. Microbial dark matter filling the niche in hypersaline microbial mats. Microbiome. 2020;8:1–14.Article 

    Google Scholar 
    Schut GJ, Nixon WJ, Lipscomb GL, Scott RA, Adams MW. Mutational analyses of the enzymes involved in the metabolism of hydrogen by the hyperthermophilic archaeon Pyrococcus furiosus. Front Microbiol. 2012;3:1–6.Article 

    Google Scholar 
    Ruuskanen MO, Colby G, St. Pierre KA, St. Louis VL, Aris‐Brosou S, Poulain AJ. Microbial genomes retrieved from High Arctic lake sediments encode for adaptation to cold and oligotrophic environments. Limnol Oceanogr. 2020;65:S233–S247.CAS 
    Article 

    Google Scholar 
    Vigneron A, Cruaud P, Lovejoy C, Vincent WF. Genomic evidence of functional diversity in DPANN archaea, from oxic species to anoxic vampiristic consortia. ISME Commun. 2022;2:1–10.Article 

    Google Scholar 
    Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996–1004.CAS 
    PubMed 
    Article 

    Google Scholar 
    Meheust R, Castelle CJ, Matheus Carnevali PB, Farag IF, He C, Chen LX, et al. Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog. ISME J. 2020;14:2907–22.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Hahn CR, Farag IF, Murphy CL, Podar M, Elshahed MS, Youssef NH. Microbial diversity and sulfur cycling in an early earth analogue: from ancient novelty to modern commonality. mBio. https://doi.org/10.1128/mbio.00016-22. (in press).Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y. The I-TASSER Suite: protein structure and function prediction. Nat Methods. 2015;12:7–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rummel JD, Beaty DW, Jones MA, Bakermans C, Barlow NG, Boston PJ, et al. A new analysis of Mars “Special Regions”: findings of the second MEPAG Special Regions Science Analysis Group (SR-SAG2). Astrobiology. 2014;14:887–968.PubMed 
    Article 

    Google Scholar 
    Harris RL, Schuerger AC, Wang W, Tamama Y, Garvin ZK, Onstott TC. Transcriptional response to prolonged perchlorate exposure in the methanogen Methanosarcina barkeri and implications for Martian habitability. Sci Rep. 2021;11:1–16.Article 

    Google Scholar 
    Webster CR, Mahaffy PR, Atreya SK, Moores JE, Flesch GJ, Malespin C, et al. Background levels of methane in Mars’ atmosphere show strong seasonal variations. Science. 2018;360:1093–6.CAS 
    PubMed 
    Article 

    Google Scholar 
    Oehler DZ, Etiope G. Methane seepage on Mars: where to look and why. Astrobiology. 2017;17:1233–64.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Marlow JJ, Larowe DE, Ehlmann BL, Amend JP, Orphan VJ. The potential for biologically catalyzed anaerobic methane oxidation on ancient Mars. Astrobiology. 2014;14:292–307.CAS 
    PubMed 
    Article 

    Google Scholar 
    Ji M, Greening C, Vanwonterghem I, Carere CR, Bay SK, Steen JA, et al. Atmospheric trace gases support primary production in Antarctic desert surface soil. Nature. 2017;552:400–3.CAS 
    PubMed 
    Article 

    Google Scholar 
    Berg JS, Ahmerkamp S, Pjevac P, Hausmann B, Milucka J, Kuypers MMM. How low can they go? Aerobic respiration by microorganisms under apparent anoxia. FEMS Microbiol Rev. 2022;fuac006. https://doi.org/10.1093/femsre/fuac006.Berg JS, Pjevac P, Sommer T, Buckner CRT, Philippi M, Hach PF, et al. Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters. Environ Microbiol. 2019;21:1611–26.CAS 
    PubMed 
    Article 

    Google Scholar 
    Stamenković V, Ward LM, Mischna M, Fischer WW. O2 solubility in Martian near-surface environments and implications for aerobic life. Nat Geosci. 2018;11:905–9.Article 

    Google Scholar  More

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    Application of humic acid and biofertilizers changes oil and phenolic compounds of fennel and fenugreek in intercropping systems

    FennelThe main effect of fertilization (F) significantly impacted all measured parameters of fennel. Intercropping (I) pattern affected all parameters except plant height and 1000-seed weight. Significant I × F interactions occurred for umbel number, seed yield, essential oil content (EO), EO yield, oil content, and oil yield (Table 2).Table 2 Analysis of variance for the effect of cropping pattern and fertilization on evaluated traits in fennel.Full size tablePlant heightThe tallest fennel plants (125.8 cm) occurred in the sole cropping (Fs), while the shortest plants (98.6 cm) occurred in 1F:2FG. Across intercropping patterns, the Fs treatment had 28%, 14%, 11% taller fennel plants than 1F:2FG, 2F:2FG, and 2F:4FG, respectively (Fig. 1A). Compared to the unfertilized control, HA and BFS increased fennel plant height by 10% and 13%, respectively (Fig. 1B).Figure 1Means comparison for the main effects of cropping patterns [Fs (fennel sole cropping), 1F:2FG, 2F:2FG, 2F:4FG (ratios of fennel and fenugreek in the intercropping patterns)] on plant height (A), and fertilization [C (control), HA (humic acid), BFS (biofertilizers)] on plant height (B) and 1000-seed weight (C) of fennel. Different lower-case letters above the bars indicate significant (p ≤ 0.05) differences.Full size image1000-seed weightCompared to the unfertilized control (3.9 g per 1000 seeds), BFS and HA increased the 1000-seed weight of fennel by 24.1% and 14.5% (4.9 and 4.5 g per 1000 seeds), respectively (Fig. 1C).Umbel numberThe fennel sole cropping fertilized with HA produced the most umbels of fennel (51.5), while 2F:4FG without fertilization produced the least (32). Averaged across fertilizer types within each intercropping system, 1F:2FG, 2F:2FG, and 2F:4FG had 21.1%, 16.3%, and 26.7% fewer umbels than fennel sole cropping, respectively. Across intercropping systems, HA and BFS increased the umbel number by 17.8% and 16.5% compared with the unfertilized control, respectively (Fig. 2A).Figure 2Means comparison for the interaction effect of fertilization [C (control), HA (humic acid), BFS (biofertilizers)] and different cropping patterns [Fs (fennel sole cropping), 1F:2FG, 2F:2FG, 2F:4FG (ratios of fennel and fenugreek in the intercropping patterns)] on umbel number (A) and seed yield (B) of fennel. Different lower-case letters above the bars indicate significant (p ≤ 0.05) differences.Full size imageSeed yieldThe different intercropping patterns had lower fennel seed yields than fennel sole cropping. Sole cropping fertilized with BFS and HA produced the highest fennel seed yields (2233 and 2209 kg ha–1, respectively), followed by unfertilized sole cropping (1960 kg ha–1). The lowest seed yields occurred in the unfertilized controls in 1F:2FG (933 kg ha–1) and 2F:4FG (1033 kg ha–1). Averaged across fertilization treatments, fennel seed yield in 1F:2FG, 2F:2FG, and 2F:4FG decreased by 41.7, 26.8, and 36.3%, respectively, compared to fennel sole cropping (Fs). Averaged across intercropping patterns, HA and BFS increased fennel seed yield by 33.3% and 39.5% compared with the unfertilized control, respectively (Fig. 2B).Essential oil content and yieldThe different intercropping patterns produced higher EO contents of fennel than fennel sole cropping. The highest absolute EO content of fennel (4.22%) occurred in 2F:2FG fertilized with BFS, although this did not statistically differ from the 2F:2FG fertilized with HA (4.04%) or 2F:4FG fertilized with HA or BFS (3.8% and 4.00%, respectively) (Fig. 3A). The lowest EO contents occurred in the unfertilized control (2.38%), HA (2.55%), and BFS (2.57%) in the Fs system. Averaged across fertilization treatments, the EO content of fennel in 1F:2FG, 2F:2FG, and 2F:4FG increased by 36%, 52%, and 44% compared to fennel sole cropping, respectively. Within each intercropping pattern, and with the exception of Fs, the HA and BFS treatments had higher EO contents of fennel, none of which significantly differed, increasing by 25% and 29%, respectively (Fig. 3A).Figure 3Means comparison for the interaction effect of fertilization [C (control), HA (humic acid), BFS (biofertilizers)] and different cropping patterns [Fs (fennel sole cropping), 1F:2FG, 2F:2FG, 2F:4FG (ratios of fennel and fenugreek in the intercropping patterns)] on essential oil content (A), essential oil yield (B), oil content (C), and oil yield (D) of fennel. Different lower-case letters above the bars indicate significant (p ≤ 0.05) differences.Full size imageMaximum EO yields of fennel occurred with HA or BFS applied in 2F:2FG (65.2 and 66.6 kg ha–1) and 2F:4FG (60.7 and 65.5 kg ha–1), respectively, while the lowest EO yields occurred in the unfertilized control in 1F:2FG (27.2 kg ha–1), 2F:2FG (33.2 kg ha–1), and 2F:4FG (32.1 kg ha–1). Averaged across intercropping patterns, the EO yield of fennel increased by 66.1% and 74.7% with HA and BFS, respectively (Fig. 3B).Fennel essential oil compositionGC–FID and GC–MS analyses identified 14 components in the fennel EO (representing 97.4–99.9% of the total composition) (Table 3), with the main constituents being trans-anethole (78.3–84.85%), estragole (3.02–7.17%), fenchone (4.14–7.52%), and limonene (3.15–4.88%). The highest percentage of (E)-anethole, estragole, and fenchone occurred in 2F:2FG with BFS. The highest limonene content occurred in 2F:4 FG with HA. The relative contents of trans-anethole, fenchone, and limonene increased by 3.9%, 16.6%, and 8.4% compared with fennel sole cropping. Notably, the contents of most compounds increased with HA and BFS. Compared to the unfertilized control, trans-anethole, fenchone, and limonene contents increased by 2.9%, 21.5%, and 7.9% with BFS and 2.3%, 22.4%, and 11.9% with HA, respectively (Table 3).Table 3 Proportion of fennel essential oil constituents under different cropping patterns and fertilization.Full size tableFennel oil content and yieldAmong the studied treatments, the highest fennel oil content occurred with HA or BFS application in 1F:2FG (16.3% and 16.6%) and 2F:2FG (16.3% and 17.4%), respectively. The lowest fennel oil contents occurred in the unfertilized control, HA, and BFS treatments (12.5%, 12.8%, and 12.9%, respectively) under fennel sole cropping, and the unfertilized control in 2F:4FG (12.6%). Averaged across fertilizer treatments, fennel oil content in 1F:2FG, 2F:2FG, and 2F:4FG increased by 22.8%, 26.0%, and 12.6% compared with fennel sole cropping, respectively. Across intercropping patterns, HA and BFS increased fennel oil content by 13.5% and 16.5%, respectively (Fig. 3C).The maximum oil yield of fennel (318.6 kg ha–1) occurred in 2F:2FG fertilized with BFS, while the lowest oil yield (129.3 kg ha–1) occurred in 1F:2FG without fertilization. Across intercropping patterns, HA and BFS increased fennel oil yield by 50.8% and 62.6%, respectively (Fig. 3D).Oil compoundsGC–FID and GC–MS analyses identified nine constituents that represented 94.3–97.9% of the total fennel oil composition. The main oil constituents were oleic acid (39.2–48.3%), linoleic acid (17.1–24.8%), stearic acid (10.9–15.4%), lauric acid (10.1–14.00%), and arachidic acid (2.2–3.4%). The highest oleic and linoleic acid contents occurred in 2F:4FG and 2F:2FG fertilized with BFS, respectively. Across fertilizer treatments, oleic and linoleic acid contents increased by 6% and 21%, respectively, under different intercropping patterns compared with fennel sole cropping. Across systems, HA and BFS enhanced oleic acid content by 1.8% and 8% and linoleic acid by 7.9% and 8.2%, respectively, compared with the unfertilized control. The highest percentage of stearic and lauric acids occurred in the unfertilized control of fennel sole cropping. Conversely, the lowest stearic and lauric acid contents occurred in 2F:2FG and 2F:4FG fertilized with BFS, 16.1% and 14.2% higher than fennel sole cropping, respectively. Finally, HA and BFS decreased stearic acid content by an average of 5.4% and 7.2%, respectively (Table 4).Table 4 Proportion of fennel oil constituents under different cropping patterns and fertilization.Full size tablePhenolic compoundsThe main phenolic compounds of fennel were chlorogenic acid (10.4–15.3 ppm), quercetin (7.0–17.2 ppm), and cinnamic acid (4.1–8.9 ppm). The highest chlorogenic acid and quercetin contents occurred in 2F:2FG fertilized with BFS and HA, respectively, while the lowest contents occurred in the fennel sole cropping system without fertilizer. Averaged across the three intercropping patterns, the chlorogenic acid and quercetin contents were 18.5% and 80.1% higher than the fennel sole cropping system. The chlorogenic acid and quercetin contents increased by 13% and 17% with BFS and 22% and 15% with HA, respectively (Table 5).Table 5 Concentration of phenolic compounds in fennel under different cropping patterns and fertilization.Full size tableFenugreekThe main effects of intercropping (I) pattern (C) and fertilizer (F) were significant for all parameters analyzed in fenugreek. Significant I × F interactions occurred for plant height, pod number per plant, seed yield, oil content, and oil yield of fenugreek (Table 6).Table 6 Analysis of variance for the effects of cropping patterns and fertilization on evaluated traits in fenugreek.Full size tablePlant heightThe 2F:2FG intercropping system fertilized with BFS produced the tallest fenugreek plants (63 cm), followed by 1F:2FG with BFS (53.3 cm) and 2F:4FG with BFS (56 cm), and 2F:2FG with HA (55 cm). The unfertilized control produced the shortest fenugreek plants (42 cm) in the sole cropping. Most fertilizer treatments across different intercropping patterns produced taller fenugreek plants than their sole cropping counterparts. Across fertilizer treatments, 1F:2FG, 2F:2FG, and 2F:4FG produced 16.2%, 26.8%, and 14.6% taller fenugreek plants than sole cropping, respectively. Across cropping patterns, BFS and HA increased fenugreek plant height by 5.7% and 15.2% compared with the unfertilized control, respectively (Fig. 4A).Figure 4Means comparison for the interaction effect of fertilization [C (control), HA (humic acid), BFS (biofertilizers)] and different cropping patterns [FGs (fenugreek sole cropping), 1F:2FG, 2F:2FG, 2F:4FG (ratios of fennel and fenugreek in the intercropping patterns)] on plant height (A) and pod number per plant (B) of fenugreek. Different lower-case letters above the bars indicate significant (p ≤ 0.05) differences.Full size imagePod number per plantThe fenugreek sole cropping with BFS and HA and 2F:4FG with BFS produced the most pods per plant (21.3, 20.3, and 20, respectively), while the unfertilized controls in 1F:2FG, 2F:2FG, and 2F:4FG produced the least (11.6, 12, and 13.3, respectively). Across fertilization treatments, 1F:2FG, 2F:2FG, and 2F:4FG had 30.1%, 25.6%, and 14.3% fewer pods per plant, respectively, than the fenugreek sole cropping system. Across cropping systems, HA and BFS increased pod number per plant in fenugreek by 25% and 33%, respectively, relative to the corresponding sole cropping (Fig. 4B).Seed number per podAcross fertilization treatments, fenugreek sole cropping produced the most seeds per pod (7.09), followed by 2F:4FG (6.02), 2F:2FG (4.93), and 1F:2FG (4.41) (Fig. 5A). In relative terms, sole cropping produced 60.5%, 43.9%, and 17.6% more seeds per pod than 1F:2FG, 2F:2FG, and 2F:4FG (Fig. 5A). Across cropping patterns, BFS and HA increased seed number per pod by 8.1% and 17.4% compared with the unfertilized control, respectively (Fig. 5B).Figure 5Means comparison for the main effects of cropping patterns [FGs (fenugreek sole cropping), 1F:2FG, 2F:2FG, 2F:4FG (ratios of fennel and fenugreek in the intercropping patterns)] on seed number per pod (A) and 1000-seed weight (C), and fertilization [C (control), HA (humic acid), BFS (biofertilizers)] on seed number per pod (B) and 1000-seed weight (D) of fennel. Different lower-case letters above the bars indicate significant (p ≤ 0.05) differences.Full size image1000-seed weightAmong different cropping patterns, sole cropping and 1F:2FG produced the highest (10.45 g) and lowest (8.34 g) fenugreek seed weights, respectively. In relative terms, fenugreek sole cropping produced 25.3%, 21.8%, and 12.4% higher seed weights than 1F:2FG, 2F:2FG, and 2F:4FG, respectively (Fig. 5C). Across cropping patterns, BFS and HA increased fenugreek seed weight by 3.7% and 5.7% compared with the control, respectively (Fig. 5D).Seed yieldMeans comparisons showed that sole cropping produced higher fenugreek seed yields than intercropping patterns. Sole cropping with BFS (1240 kg ha–1) and HA (1217 kg ha–1) produced the highest seed yields followed by the unfertilized control (Fig. 6A). The unfertilized control in 1F:2FG (437 kg ha–1) and 2F:2FG (467 kg ha–1) produced the lowest fenugreek seed yields. In all cases, and within each cropping pattern, BFS and HS produced higher fenugreek seed yields than the unfertilized control. As a result, BFS and HA increased fenugreek seed yield by 25.2% and 31.5% compared with the unfertilized control, respectively (Fig. 6A).Figure 6Means comparison for the interaction effects of fertilization [C (control), HA (humic acid), BFS (biofertilizers)] and different cropping patterns [FGs (fenugreek sole cropping), 1F:2FG, 2F:2FG, 2F:4FG (ratios of fennel and fenugreek in the intercropping patterns)] on seed yield (A), oil content (B), and oil yield (C) of fenugreek. Different lower-case letters above the bars indicate significant (p ≤ 0.05) differences.Full size imageOil content and yieldThe 2F:2FG cropping pattern with BFS produced the highest fenugreek oil content (8.3%), while the unfertilized control in sole cropping produced the lowest (5.9%). Across fertilizer treatments, 1F:2FG, 2F:2 FG, and 2F:4 FG produced 11.7%, 18.5%, and 15.7% higher fenugreek oil contents than sole cropping, respectively. In the 2F:2FG and 2F:4FG cropping patterns, BFS produced higher oil content (%) than HA. As a result, across cropping patterns, HA and BFS increased fenugreek oil content by 12.3% and 19.4%, respectively (Fig. 6B).Sole cropping with HA and BFS and 2F:2FG with BFS produced the highest fenugreek oil yields (77.1, 80.0, and 74.4 kg ha–1, respectively), while the unfertilized controls in 1F:2FG and 2F:4FG produced the lowest (27.51 and 29.8 kg ha–1, respectively). The 1F:2FG, 2F:2FG, and 2F:4FG cropping patterns produced 45.9%, 20.7%, and 41.5% lower fenugreek oil yields than fenugreek sole cropping, respectively. Moreover, except for sole cropping, BFS produced the highest fenugreek oil yield, followed by HA and the unfertilized control (Fig. 6C).Oil compoundsGC–FID and GC–MS analyses identified seven constituents (representing 91.09–99.27% of the total composition) in fenugreek oil. The main oil constituents were linoleic acid (26.1–37.1%), linolenic acid (16.9–22.4%), oleic acid (15.1–21.2%), palmitic acid (11.2–17.1%), lauric acid (5.0–12.3%), and myristic acid (3.1–6.4%). The highest linoleic and oleic acid percentages occurred in 1F:2FG and 2F:4FG with BFS. The 1F:2FG cropping pattern with BFS also had the highest linolenic acid percentage. The fenugreek sole cropping system without fertilization (control) had the lowest content of these three compounds. The intercropping patterns had 17%, 18.2%, and 17.1% higher oleic, linoleic, and linolenic acid contents than fenugreek sole cropping. In addition, HA and BFS increased oleic acid content by 15.6% and 8.8%, linoleic acid content by 12.8% and 7%, and linolenic acid content by 7.5% and 12.9%, respectively. Fenugreek sole cropping without fertilization produced the highest lauric acid and palmitic contents, 29.33% and 22.81% higher than the intercropping patterns (Table 7).Table 7 Proportion of fenugreek oil constituents under different cropping patterns and fertilization.Full size tablePhenolic compoundsThe main phenolic compounds in fenugreek were chlorogenic acid (2.01–5.49 ppm), caffeic acid (2.42–4.93 ppm), quercetin (1.98–4.45 ppm), comaric (1.09–2.43 ppm), apigenin (1.97–2.99 ppm), and gallic acid (1.76–2.92 ppm). The 2F:2FG cropping pattern with HA produced the highest quercetin and gallic acid contents, and 2F:4FG with HA produced the highest chlorogenic and caffeic acid contents. The 2F:2FG and 2F:4FG cropping patterns with BFS produced the highest comaric and apigenin contents, respectively. In contrast, fenugreek sole cropping without fertilization produced the lowest contents of the abovementioned compounds (Table 8).Table 8 Proportion of fenugreek concentration of phenolic compounds under different cropping patterns and fertilization.Full size tableLand equivalent ratio (LER)The 2F:4FG and 2F:2FG intercropping patterns treated with BFS had the highest partial LERs for fennel (0.82) and fenugreek (0.72), respectively. In addition, 2F:2FG with BFS and 1F:2FG without fertilization produced the highest (1.42) and lowest (0.86) total LERs, respectively (Fig. 7).Figure 7Partial and total land equivalent ratio (LER) for seed yields of different fennel and fenugreek intercropping patterns [1F:2FG, 2F:2FG, 2F:4FG (ratios of fennel and fenugreek in the intercropping patterns)] and fertilization [C (Control), HA (humic acid), BFS (biofertilizers)]. Different lower-case letters above the bars indicate significant (p ≤ 0.05) differences.Full size image More

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    Do habitat and elevation promote hybridization during secondary contact between three genetically distinct groups of warbling vireo (Vireo gilvus)?

    Abbott RJ, Brennan AC (2014) Altitudinal gradients, plant hybrid zones and evolutionary novelty. Philos Trans R Soc B Biol Sci 369:6–9Article 

    Google Scholar 
    Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge, MABook 

    Google Scholar 
    Baldassarre DT, White TA, Karubian J, Webster MS (2014) Genomic and morphological analysis of a semipermeable avian hybrid zone suggests asymmetrical introgression of a sexual signal. Evolution 68:2644–2657PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Barr KR, Dharmarajan G, Rhodes OE, Lance R, Leberg PL (2007) Novel microsatellite loci for the study of the black-capped vireo (Vireo atricapillus). Mol Ecol Notes 7:1067–1069CAS 
    Article 

    Google Scholar 
    Barton NH, Gale KS (1993) Hybrid zones and the evolutionary process. In: Harrison RG (ed.) Hybrid Zones and the Evolutionary Process. Oxford University Press, New York, NY
    Google Scholar 
    Barton NH, Hewitt GM (1989) Adaption, speciation and hybrid zones. Nature 341:497–503CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Billerman SM, Murphy MA, Carling MD (2016) Changing climate mediates sapsucker (Aves: Sphyrapicus) hybrid zone movement. Ecol Evol 6:7976–7990PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bell RC, Irian CG (2019) Phenotypic and genetic divergence in reed frogs across a mosaic hybrid zone on São Tomé Island. Biol J Linn Soc 128:672–680Article 

    Google Scholar 
    Bensch S, Price T, Kohn J (1997) Isolation and characterization of microsatellite loci in a Phylloscopus warbler. Mol Ecol 6:91–92CAS 
    PubMed 
    Article 

    Google Scholar 
    Bradbury IR, Bowman S, Borza T, Snelgrove PVR, Hutchings JA, Berg PR et al. (2014) Long distance linkage disequilibrium and limited hybridization suggest cryptic speciation in Atlantic cod. PLoS ONE 9:e106330Article 
    CAS 

    Google Scholar 
    Brelsford A, Irwin DE (2009) Incipient speciation despite little assortative mating: the yellow-rumped warbler hybrid zone. Evolution 63:3050–3060PubMed 
    Article 

    Google Scholar 
    Burg TM, Croxall JP (2004) Global population structure and taxonomy of the wandering albatross species complex. Mol Ecol 13:2345–2355CAS 
    PubMed 
    Article 

    Google Scholar 
    Carling MD, Zuckerberg B (2011) Spatio-temporal changes in the genetic structure of the Passerina bunting hybrid zone. Mol Ecol 20:1166–1175PubMed 
    Article 

    Google Scholar 
    Carling MD, Thomassen HA (2012) The role of environmental heterogeneity in maintaining reproductive isolation between hybridizing Passerina (Aves: Cardinalidae) buntings. Int J Ecol 2012:295463Article 

    Google Scholar 
    Carpenter AM, Graham BA, Spellman GM, Klicka J, Burg TM (2021) Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes). Zool J Linn Soc zlab036 https://doi.org/10.1093/zoolinnean/zlab036Cicero C, Johnson NK (1998) Molecular phylogeny and ecological diversification in a clade of New World songbirds (genus Vireo). Mol Ecol 7:1359–1370CAS 
    PubMed 
    Article 

    Google Scholar 
    Chenuil A, Cahill AE, Délémontey N, Du Salliant du Luc E, Fanton H (2019) Problems and questions posed by cryptic species. A framework to guide future studies. Assessing to conserving biodiversity. History, philosophy and theory of the life sciences, Vol. 24. Springer. Daubenmire, Cham
    Google Scholar 
    Cheviron ZA, Brumfield RT (2012) Genomic insights into adaptation to high-altitude environments. Heredity 108:354–361CAS 
    PubMed 
    Article 

    Google Scholar 
    Coyne JA, Orr HA (2004) Speciation. Sinauer and Associates, Sunderland, Massachusetts
    Google Scholar 
    Culumber ZW, Shepard DB, Colemans SW, Rosenthal GG, Tobler M (2012) Physiological adaptation along environmental gradients and replicated hybrid zone structure in swordtails (Teleostei: Xiphophorus). J Evol Biol 25:1800–1814CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Dubay SG, Witt CC (2014) Differential high-altitude adaptation and restricted gene flow across a mid-elevation hybrid zone in Andean tit-tyrant flycatchers. Mol Ecol 23:3551–3565PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Garroway CJ, Bowman J, Cascaden TJ, Holloway GL, Mahan CG, Malcolm JR et al. (2010) Climate change induced hybridization in flying squirrels. Glob Chang Biol 16:113–121Article 

    Google Scholar 
    Grabenstein KC, Taylor SA (2018) Breaking barriers: Causes, consequences, and experimental utility of human-mediated hybridization. Trends Ecol Evol 33:198–212PubMed 
    Article 

    Google Scholar 
    Graham BA, Cicero C, Strickland D, Woods JG, Coneybeare H, Dohms KM et al. (2021) Cryptic genetic diversity and cytonuclear discordance characterize contact among Canada jay (Perisoreus canadensis) morphotypes in western North America. Biol J Linn Soc 132:725–740Article 

    Google Scholar 
    Hammer Ø, Harper DA, Ryan PD (2001) Paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9Haselhorst MSH, Parchman TL, Buerkle CA (2019) Genetic evidence for species cohesion, substructure and hybrids in spruce. Mol Ecol 28:2029–2045PubMed 
    Article 

    Google Scholar 
    Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A (2005) Very high resolution interpolated climate surfaces for global land areas. Int J Climatol 25:1965–1978Article 

    Google Scholar 
    Hawley DM (2005) Isolation and characterization of eight microsatellite loci from the house finch (Carpodactus mexicanus). Mol Ecol Notes 5:443–445CAS 
    Article 

    Google Scholar 
    Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol 2:e312PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Hewitt GM (1988) Hybrid zones-natural laboratories for evolutionary studies. Trends Ecol Evol 3:158–167CAS 
    PubMed 
    Article 
    PubMed Central 

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

    Google Scholar 
    Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A (2005) Very high resolution interpolated climate surfaces for global land areas. Int J Climatol 25:1965–1978Article 

    Google Scholar 
    Hindley JA, Graham BA, Pulgarin-R PC, Burg TM (2018) The influence of latitude, geographic distance, and habitat discontinuities on genetic variation in a high latitude montane species. Sci Rep. 8:11846CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Hinojosa JC, Koubínová D, Szenteczki MA, Pitteloud C, Dincă V, Alvarez N et al. (2019) A mirage of cryptic species: Genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris. Mol Ecol 28:3857–3868PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Res 9:1322–1332Article 

    Google Scholar 
    Irwin DE (2020) Assortative mating in hybrid zones is remarkably ineffective in promoting speciation. Evolution 195:E150–E167
    Google Scholar 
    Johnson NK (1995) Speciation in vireos. I. Macrogeographic patterns of allozymic variation in the Vireo solitarius complex in the contiguous United States. Condor 97:903–919Article 

    Google Scholar 
    Johnson NK, Cicero C (2004) New mitochondrial DNA data affirm the importance of Pleistocene speciation in North American birds. Evolution 58:1122–1130PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Larson EL, Tinghitella RM, Taylor SA (2019) Insect hybridization and climate change. Front Ecol Evol 7:348Article 

    Google Scholar 
    Legendre P, Fortin M-J (2010) Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data. Mol Ecol Resour 10:831–844PubMed 
    Article 

    Google Scholar 
    Lovell SF, Lein MR, Rogers SM (2021) Cryptic speciation in the warbling vireo (Vireo gilvus). Ornithology 138:ukaa071Article 

    Google Scholar 
    MacDonald ZG, Dupuis JR, Davis CS, Acorn JH, Nielsen SE, Sperling FAH (2020) Gene flow and climate-associated genetic variation in a vagile habitat specialist. Mol Ecol 29:3889–3906PubMed 
    Article 

    Google Scholar 
    Manthey JD, Klicka J, Spellman GM (2011) Cryptic diversity in a widespread North American songbird: phylogeography of the brown creeper (Certhia americana). Mol Phylogenet Evol 58:502–512PubMed 
    Article 

    Google Scholar 
    Marchetti K, Price T, Richman A (1995) Correlates of wing morphology with foraging behaviour and migration distance in the genus Phylloscopus. J Av Biol 26:177–181Article 

    Google Scholar 
    Martin H, Touzet P, Dufay M, Gode C, Schmitt E, Lahiani E et al. (2017) Lineages of Silene nutans developed rapid, strong, asymmetric postzygotic reproductive isolation in allopatry. Evolution 71:1519–1531CAS 
    PubMed 
    Article 

    Google Scholar 
    Martinez JG, Soler JJ, Soler M, Moller AP, Burke T (1999) Comparative population structure and gene flow of a brood parasite, the great spotted cuckoo (Clamator glandarius) and its primary host, the magpie (Pica pica). Evolution 53:269–278CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Mettler RD, Spellman GM (2009) A hybrid zone revisited: Molecular and morphological analysis of the maintenance, movement, and evolution of a Great Plains avian (Cardinalidae: Pheucticus) hybrid zone. Mol Ecol 18:3256–3267CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Meirmans PG, Van Tienderen PH (2004) GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Notes 4:792–794Article 

    Google Scholar 
    Nowakowski JK, Szulc J, Remisiewicz M (2014) The further the flight, the longer the wing: relationship between wing length and migratory distance in Old World reed and bush warblers (Acrocephalidae and Locustellidae). Ornis Fennica 91:178–186
    Google Scholar 
    Pavolova A, Amos JN, Joseph L, Loynes K, Austin JJ, Keogh JS et al. (2013) Perched at the mito-nuclear crossroads: divergent mitochondrial lineages correlate with environment in the face of ongoing nuclear gene flow in an Australian bird. Evol 67:3412–3428Article 
    CAS 

    Google Scholar 
    Piertney SB, Marquiss M, Summers R (1998) Characterization of tetranucleotide microsatellite markers in the Scottish crossbill (Loxia scotica). Mol Ecol 7:1261–1263CAS 
    PubMed 
    Article 

    Google Scholar 
    Porras-Hurtado L, Ruiz Y, Santos C, Phillips C, Carracedo A, Lareu MV (2013) An overview of STRUCTURE: Applications, parameter settings, and supporting software. Front Genet 4:98PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Reding DM, Castañeda-Rico S, Shirazi S, Hofman CA, Cancellare IA, Lance SL et al. (2021) Mitochondrial genomes of the United States distribution of gray fox (Urocyon cinereoargenteus) reveal a major phylogeographic break at the Great Plains suture zone. Front Ecol Evol. https://doi.org/10.3389/fevo.2021.666800.Richardson DS, Jury FL, Dawson DA, Salgueiro P, Komdeur J, Burke T (2003) Fifty Seychelles warbler (Acrocephalus sechellensis) microsatellite loci polymorphic in Sylviidae species and their cross-species amplification in other passerine birds. Mol Ecol 9:2225–2230Article 

    Google Scholar 
    Riordan EC, Gugger PF, Ortego J, Smith C, Gaddis K, Thompson P et al. (2016) Association of genetic and phenotypic variability with geography and climate in three southern California oaks. Am J Bot 103:73–85PubMed 
    Article 

    Google Scholar 
    Rush AC, Cannings RJ, Irwin DE (2009) Analysis of multilocus DNA reveals hybridization in a contact zone between Empidonax flycatchers. J Avian Biol 40:614–624Article 

    Google Scholar 
    Sartor CC, Cushman SA, Wan HY, Kretschmer R, Pereira JA, Bou N et al. (2021) The role of the environment in the spatial dynamics of an extensive hybrid zone between two neotropical cats. J Evol Biol 34:614–627PubMed 
    Article 

    Google Scholar 
    Schukman JM, Lira-Noriega A, Townsend Peterson A (2011) Multiscalar ecological characterization of Say’s and eastern phoebes and their zone of contact in the Great Plains. Condor 113:372–384Article 

    Google Scholar 
    Seehausen O, Takimoto G, Roy D, Jokela J (2008) Speciation reversal and biodiversity dynamics with hybridization in changing environments. Mol Ecol 17:30–44PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Semenchuk GP (1992) The Atlas of Breeding Birds of Alberta. Fed. of Alberta Naturalists, Edmonton, p 243
    Google Scholar 
    Peakall R, Smouse PE (2012) GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research–an update. Bioinformatics 28:2537–2539CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Sorenson MD, Ast JC, Dimcheff DE, Yuri T, Mindell DP (1999) Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol Phylogent Evol 12:105–114CAS 
    Article 

    Google Scholar 
    Spellman GM, Klicka J (2007) Phylogeography of the white-breasted nuthatch (Sitta carolinensis): diversification in North American pine and oak woodlands. Mol Ecol 16:1729–1740CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Stenzler LM, Fitzpatrick JW (2002) Isolation of microsatellite loci in the Florida scrub jay Aphelocoma coerulescens. Mol Ecol Notes 2:547–550CAS 
    Article 

    Google Scholar 
    Swenson NG (2006) GIS-based niche models reveal unifying climatic mechanisms that maintain location of avian hybrid zones in a North America suture zone. J Evol Biol. 19:717–725CAS 
    PubMed 
    Article 

    Google Scholar 
    Swenson NG, Howard DJ (2005) Clustering of contact zones, hybrid zones, and phylogeographic breaks in North America. Am Nat 166:581–591PubMed 
    Article 

    Google Scholar 
    Tarr CL, Fleischer RC (1998) Primers for polymorphic GT microsatellites isolated from the Mariana crow, Corvus kubaryi. Mol Ecol 7:253–255CAS 
    PubMed 
    Article 

    Google Scholar 
    Tarroso P, Pereira RJ, Martínez-Freiría F, Godinho R, Brito JC (2014) Hybridization at an ecotone: Ecological and genetic barriers between three Iberian vipers. Mol Ecol 23:1108–1123CAS 
    PubMed 
    Article 

    Google Scholar 
    Taylor SA, Larson EL, Harrison RG (2015) Hybrid zones: windows on climate change. Trends Ecol Evol 30:398–406PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Toews DPL, Mandic M, Richards JG, Irwin DE (2014) Migration, mitochondria and the yellow-rumped warbler. Evolution 68:241–255CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Toews DPL, Campagna L, Taylor SA, Balakrishnan CN, Baldassarre DT, Deane-Coe PE et al. (2016) Genomic approaches to understanding population divergence and speciation in birds. Auk 133:13–30Article 

    Google Scholar 
    Toews DPL, Irwin DE (2008) Cryptic speciation in a Holarctic passerine revealed by genetic and bioacoustic analyses. Mol Ecol 17:2691–2705CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    van Els P, Cicero C, Klicka J (2012) High latitudes and high genetic diversity: Phylogeography of a widespread boreal bird, the gray jay (Perisoreus canadensis). Mol Phylogenet Evol 63:456–465PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Voelker G, Rohwer S (1998) Contrasts in scheduling of molt and migration in eastern and western warbling vireos. Auk 155:142–155Article 

    Google Scholar 
    Walsh J, Billerman SM, Rohwer VG, Butcher BG, Lovette IJ (2020) Genomic and plumage variation across the controversial Baltimore and Bullock’s oriole hybrid zone. Auk 137:1–15Article 

    Google Scholar 
    Walsh J, Rowe RJ, Olsen BJ, Shriver WG, Kovach AI (2016) Genotype-environment associations support a mosaic hybrid zone between two tidal marsh birds. Ecol Evol 6:279–294PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Walsh P, Metzger D, Higuchi R (1991) Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10:506–513CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Weir JT, Schluter D (2004) Ice sheets promote speciation in boreal birds. Proc R Soc B 271:1881–1887PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Williams JW (2003) Variations in tree cover in North America since the last glacial maximum. Glob Planet Change 35:1–23Article 

    Google Scholar 
    Williams DA, Berg EC, Hale AM, Hughes CR (2004) Characterization of microsatellites for parentage studies of white-throated magpie-jays (Calocitta formosa) and brown jays (Cyanocorax morio). Mol Ecol Notes 4:509–511CAS 
    Article 

    Google Scholar 
    Zwartjes PW (2001) Genetic structuring among migratory populations of the black-whiskered vireo, with a comparison to the red-eyed vireo. Condor 103:439–448Article 

    Google Scholar  More

  • in

    RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels

    Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, et al. Uncovering Earth’s virome. Nature. 2016;536:425–30.CAS 
    PubMed 

    Google Scholar 
    Anderson PK, Cunningham AA, Patel NG, Morales FJ, Epstein PR, Daszak P. Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers. Trends Ecol Evol. 2004;19:535–44.PubMed 

    Google Scholar 
    Taylor LH, Latham SM, Woolhouse MEJ. Risk factors for human disease emergence. Philos Trans R Soc B Biol Sci. 2001;356:983–9.CAS 

    Google Scholar 
    White R, Murray S, Rohweder M. Pilot analysis of global ecosystems: grassland ecosystems. 2000 World Resources Institute. Washington, DC.Zhao Y, Liu Z, Wu J. Grassland ecosystem services: a systematic review of research advances and future directions. Landsc Ecol. 2020;35:793–814.
    Google Scholar 
    Trubl G, Jang HBin, Roux S, Emerson JB, Solonenko N, Vik DR, et al. Soil viruses are underexplored players in ecosystem carbon processing. mSystems. 2018;3:e00076–18.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Jang HBin, et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nat Microbiol. 2018;3:870–80.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zablocki O, Adriaenssens EM, Frossard A, Seely M, Ramond J-B, Cowan D. Metaviromes of extracellular soil viruses along a Namib desert aridity gradient. Genome Announc. 2017;5:e01470–16.PubMed 
    PubMed Central 

    Google Scholar 
    Jin M, Guo X, Zhang R, Qu W, Gao B, Zeng R. Diversities and potential biogeochemical impacts of mangrove soil viruses. Microbiome. 2019;7:58.PubMed 
    PubMed Central 

    Google Scholar 
    Adriaenssens EM, Kramer R, Van Goethem MW, Makhalanyane TP, Hogg I, Cowan DA. Environmental drivers of viral community composition in Antarctic soils identified by viromics. Microbiome. 2017;5:83.PubMed 
    PubMed Central 

    Google Scholar 
    Williamson KE, Fuhrmann JJ, Wommack KE, Radosevich M. Viruses in soil ecosystems: an unknown quantity within an unexplored territory. Annu Rev Virol. 2017;4:201–19.CAS 
    PubMed 

    Google Scholar 
    Starr EP, Nuccio EE, Pett-Ridge J, Banfield JF, Firestone MK. Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil. Proc Natl Acad Sci. 2019;116:25900–8.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wu R, Davison MR, Gao Y, Nicora CD, Mcdermott JE, Burnum-Johnson KE, et al. Moisture modulates soil reservoirs of active DNA and RNA viruses. Commun Biol. 2021;4:1–11.
    Google Scholar 
    Hurwitz BL, Sullivan MB. The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One. 2013;8:e57355.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol. 2018;3:754–66.CAS 
    PubMed 

    Google Scholar 
    Wolf YI, Kazlauskas D, Iranzo J, Lucía-Sanz A, Kuhn JH, Krupovic M, et al. Origins and evolution of the Global RNA virome. MBio. 2018;9:e02329–18.PubMed 
    PubMed Central 

    Google Scholar 
    Shi M, Lin XD, Tian JH, Chen LJ, Chen X, Li CX, et al. Redefining the invertebrate RNA virosphere. Nature. 2016;540:539–43.CAS 

    Google Scholar 
    Callanan J, Stockdale SR, Shkoporov A, Draper LA, Ross RP, Hill C. Expansion of known ssRNA phage genomes: from tens to over a thousand. Sci Adv. 2020;6:eaay5981.CAS 
    PubMed 
    PubMed Central 

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

    Google Scholar 
    Cobbin JC, Charon J, Harvey E, Holmes EC, Mahar JE. Current challenges to virus discovery by meta-transcriptomics. Curr Opin Virol. 2021;51:48–55.CAS 
    PubMed 

    Google Scholar 
    Trubl G, Hyman P, Roux S, Abedon ST. Coming-of-age characterization of soil viruses: a user’s guide to virus isolation, detection within metagenomes, and viromics. Soil Syst. 2020;4:1–34. MDPI AG.
    Google Scholar 
    Santos-Medellin C, Zinke LA, ter Horst AM, Gelardi DL, Parikh SJ, Emerson JB. Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities. ISME J. 2021;15:1–15.
    Google Scholar 
    Adriaenssens EM, Farkas K, Harrison C, Jones DL, Allison HE, McCarthy AJ. Viromic analysis of wastewater input to a river catchment reveals a diverse assemblage of RNA viruses. mSystems. 2018;3:e00025–18.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bibby K, Peccia J. Identification of viral pathogen diversity in sewage sludge by metagenome analysis. Environ Sci Technol. 2013;47:1945–51.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Culley A. New insight into the RNA aquatic virosphere via viromics. Virus Res. 2018;244:84–89.CAS 
    PubMed 

    Google Scholar 
    Withers E, Hill PW, Chadwick DR, Jones DL. Use of untargeted metabolomics for assessing soil quality and microbial function. Soil Biol Biochem. 2020;143:107758.CAS 

    Google Scholar 
    Trubl G, Solonenko N, Chittick L, Solonenko SA, Rich VI, Sullivan MB. Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient. PeerJ. 2016;4:e1999.PubMed 
    PubMed Central 

    Google Scholar 
    Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 2011;17:10.
    Google Scholar 
    Joshi N, Fass J. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files. 2011.Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27:863–4.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kopylova E, Noé L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28:3211–7.CAS 
    PubMed 

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

    Google Scholar 
    Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2014;12:59–60. Nature Publishing Group.PubMed 

    Google Scholar 
    Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S. et al.MEGAN Community Edition – interactive exploration and analysis of large-scale microbiome sequencing data.PLOS Comput Biol. 2016;12:e1004957PubMed 
    PubMed Central 

    Google Scholar 
    Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 2010;11:119.
    Google Scholar 
    Mistry J, Finn RD, Eddy SR, Bateman A, Punta M. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res. 2013;41:e121–e121.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658–9.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum information about an uncultivated virus genome (MIUViG). Nat Biotechnol. 2018;37:29–37.PubMed 
    PubMed Central 

    Google Scholar 
    Germain P-L, Vitriolo A, Adamo A, Laise P, Das V, Testa G. RNAontheBENCH: computational and empirical resources for benchmarking RNAseq quantification and differential expression methods. Nucleic Acids Res. 2016;44:5054–67.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package. 2019.Wickham H. ggplot2: elegant graphics for data analysis. 2016. Springer-Verlag New York.Conway JR, Lex A, Gehlenborg N. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics. 2017;33:2938–40.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Katoh K. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–66.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490.PubMed 
    PubMed Central 

    Google Scholar 
    Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47:W256–W259.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Roux S, Emerson JB, Eloe-Fadrosh EA, Sullivan MB. Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ. 2017;5:e3817.PubMed 
    PubMed Central 

    Google Scholar 
    Ayllón MA, Turina M, Xie J, Nerva L, Marzano SYL, Donaire L, et al. ICTV virus taxonomy profile: botourmiaviridae. J Gen Virol. 2020;101:454–5.PubMed 
    PubMed Central 

    Google Scholar 
    Krishnamurthy SR, Janowski AB, Zhao G, Barouch D, Wang D. Hyperexpansion of RNA bacteriophage diversity. PLOS Biol. 2016;14:e1002409.PubMed 
    PubMed Central 

    Google Scholar 
    Hillman BI, Cai G. The family Narnaviridae. Simplest of RNA viruses. Adv Virus Res. 2013;86:149–76.
    Google Scholar 
    Obbard DJ, Shi M, Roberts KE, Longdon B, Dennis AB. A new lineage of segmented RNA viruses infecting animals. Virus Evol. 2020;6:61.
    Google Scholar 
    Xu X, Bei J, Xuan Y, Chen J, Chen D, Barker SC, et al. Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data. BMC Genom. 2020;21:1–8.
    Google Scholar 
    Roossinck MJ. The good viruses: viral mutualistic symbioses. Nat Rev Microbiol. 2011;9:99–108. Nature Publishing Group.CAS 
    PubMed 

    Google Scholar 
    Milgroom MG, Cortesi P. Biological control of chestnut blight with hypovirulence: a critical analysis. Annu Rev Phytopathol. 2004;42:311–38. Annual ReviewsCAS 
    PubMed 

    Google Scholar 
    Zell R, Delwart E, Gorbalenya AE, Hovi T, King AMQ, Knowles NJ, et al. ICTV virus taxonomy profile: Picornaviridae. J Gen Virol. 2017;98:2421–2.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Valles SM, Chen Y, Firth AE, Guérin DMA, Hashimoto Y, Herrero S, et al. ICTV virus taxonomy profile: Dicistroviridae. J Gen Virol. 2017;98:355–6.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Barrios E. Soil biota, ecosystem services and land productivity. Ecol Econ. 2007;64:269–85.
    Google Scholar 
    Vainio EJ, Chiba S, Ghabrial SA, Maiss E, Roossinck M, Sabanadzovic S, et al. ICTV virus taxonomy profile: Partitiviridae. J Gen Virol. 2018;99:17–18.CAS 
    PubMed 

    Google Scholar 
    Yong CY, Yeap SK, Omar AR, Tan WS. Advances in the study of nodavirus. PeerJ. 2017;2017:e3841.
    Google Scholar 
    Schmitt AP, Lamb RA. Escaping from the cell: assembly and budding of negative-strand RNA viruses. In: Kawaoka Y (ed). Biology of negative-strand RNA viruses: the power of reverse genetics. 2004. (Springer Berlin Heidelberg, Berlin, Heidelberg, pp 145–96.Käfer S, Paraskevopoulou S, Zirkel F, Wieseke N, Donath A, Petersen M, et al. Re-assessing the diversity of negative-strand RNA viruses in insects. PLoS Pathog. 2019;15:e1008224.PubMed 
    PubMed Central 

    Google Scholar 
    Bejerman N, Debat H, Dietzgen, RG. The plant negative-sense RNA virosphere: virus discovery through new eyes. Front. Microbiol. 2020;11:588427.PubMed 
    PubMed Central 

    Google Scholar 
    Wolf YI, Silas S, Wang Y, Wu S, Bocek M, Kazlauskas D, et al. Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome. Nat Microbiol. 2020;5:1262–70.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Adriaenssens EM, Kramer R, van Goethem MW, Makhalanyane TP, Hogg I, Cowan DA. Environmental drivers of viral community composition in Antarctic soils identified by viromics. Microbiome. 2017;5:1–14.
    Google Scholar 
    Mahmoud H, Jose L. Phage and nucleocytoplasmic large viral sequences dominate coral viromes from the Arabian Gulf. Front Microbiol. 2017;8:2063.PubMed 
    PubMed Central 

    Google Scholar 
    Koyama A, Steinweg JM, Haddix ML, Dukes JS, Wallenstein MD. Soil bacterial community responses to altered precipitation and temperature regimes in an old field grassland are mediated by plants. FEMS Microbiol Ecol. 2018;94:fix156.
    Google Scholar 
    Hurwitz BL, Hallam SJ, Sullivan MB. Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome Biol. 2013;14:R123.PubMed 
    PubMed Central 

    Google Scholar  More