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    Snake-like limb loss in a Carboniferous amniote

    Caldwell, M. W. “Without a leg to stand on”: on the evolution and development of axial elongation and limblessness in tetrapods. Can. J. Earth Sci. 40, 573–588 (2003).
    Google Scholar 
    Bejder, L. & Hall, B. K. Limbs in whales and limblessness in other vertebrates: mechanisms of evolutionary and developmental transformation and loss. Evol. Dev. 4, 445–458 (2002).PubMed 

    Google Scholar 
    Gans, C. Locomotion and burrowing in limbless vertebrates. Nature 242, 414–415 (1973).
    Google Scholar 
    Gans, C. Tetrapod limblessness: evolution and functional corollaries. Am. Zool. 15, 455–467 (1975).
    Google Scholar 
    Camaiti, M., Evans, A. R., Hipsley, C. A. & Chapple, D. G. A farewell to arms and legs: a review of limb reduction in squamates. Biol. Rev. 96, 1035–1050 (2021).PubMed 

    Google Scholar 
    Brandley, M. C., Huelsenbeck, J. P. & Wiens, J. J. Rates and patterns in the evolution of snake‐like body form in squamate reptiles: evidence for repeated re‐evolution of lost digits and long‐term persistence of intermediate body forms. Evol. Int. J. Org. Evol. 62, 2042–2064 (2008).
    Google Scholar 
    Skinner, A., Lee, M. S. & Hutchinson, M. N. Rapid and repeated limb loss in a clade of scincid lizards. BMC Evol. Biol. 8, 310 (2008).Marjanović, D. & Laurin, M. Phylogeny of Paleozoic limbed vertebrates reassessed through revision and expansion of the largest published relevant data matrix. PeerJ 6, e5565 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    Woltering, J. M. et al. Axial patterning in snakes and caecilians: evidence for an alternative interpretation of the Hox code. Dev. Biol. 332, 82–89 (2009).CAS 
    PubMed 

    Google Scholar 
    Cohn, M. J. & Tickle, C. Developmental basis of limblessness and axial patterning in snakes. Nature 399, 474–479 (1999).CAS 
    PubMed 

    Google Scholar 
    Jaekel, O. Über die klassen der tetrapoden [About the classes of the tetrapods]. Zool. Anz. 34, 193–212 (1909).
    Google Scholar 
    Anderson J. S. in Major Transitions in Vertebrate Evolution (eds Anderson, J. S. & Sues, H.-D.) 182–227 (Indiana Univ. Press, 2007).Cope, E. D. Synopsis of the extinct Batrachia from the Coal Measures. Ohio Geol. Surv. 2, 349–411 (1875).
    Google Scholar 
    Farrell, Ú. Pyritization of soft tissues in the fossil record: an overview. Paleontol. Soc. Pap. 20, 35–58 (2014).
    Google Scholar 
    Mann, A. Cranial ornamentation of a large Brachydectes newberryi (Recumbirostra: Lysorophia) from Linton, Ohio. Vertebr. Anat. Morphol. Palaeontol. 6, 91–96 (2018).
    Google Scholar 
    Mann, A., Pardo, J. D. & Maddin, H. C. Infernovenator steenae, a new serpentine recumbirostran from the ‘Mazon Creek’ Lagerstätte further clarifies lysorophian origins. Zool. J. Linn. Soc. 187, 506–517 (2019).
    Google Scholar 
    Maisano, J. A. A survey of state of ossification in neonatal squamates. Herpetol. Monogr. 15, 135–157 (2001).Maisano, J. A. Terminal fusions of skeletal elements as indicators of maturity in squamates. J. Vertebr. Paleontol. 22, 268–275 (2002).
    Google Scholar 
    Maisano, J. A. Terminal fusions of skeletal elements as indicators of maturity in squamates. J. Vertebr. Paleontol. 22, 268–275 (2002).
    Google Scholar 
    Pardo, J. D. & Anderson, J. S. Cranial morphology of the Carboniferous–Permian tetrapod Brachydectes newberryi (Lepospondyli, Lysorophia): new data from µCT. PLoS ONE 11, e0161823 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    Milner, A. R. Small temnospondyl amphibians from the Middle Pennsylvanian of Illinois. Paleontology 25, 635–664 (1982).
    Google Scholar 
    Godfrey, S. A diminutive temnospondyl amphibian from the Pennsylvanian of Illinois. Can. J. Earth Sci. 40, 507–514 (2003).
    Google Scholar 
    Mann, A. & Maddin, H. C. Diabloroter bolti, a short-bodied recumbirostran ‘microsaur’ from the Francis Creek Shale, Mazon Creek, Illinois. Zool. J. Linn. Soc. 187, 494–505 (2019).
    Google Scholar 
    Mann, A., McDaniel, E. J., McColville, E. R. & Maddin, H. C. Carbonodraco lundi gen et sp. nov., the oldest parareptile, from Linton, Ohio, and new insights into the early radiation of reptiles. R. Soc. Open Sci. 6, 191191 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    Mann, A. & Gee, B. M. Lissamphibian-like toepads in an exceptionally preserved amphibamiform from Mazon Creek. J. Vertebr. Paleontol. 39, e1727490 (2020).
    Google Scholar 
    Wellstead, C. F. Taxonomic revision of the Lysorophia, Permo-Carboniferous lepospondyl amphibians. Bull. Am. Mus. Nat. Hist. 209, 1–90 (1991).
    Google Scholar 
    Sallan, L. C. & Coates, M. I. The long-rostrumed elasmobranch Bandringa Zangerl, 1969, and taphonomy within a Carboniferous shark nursery. J. Vertebr. Paleontol. 34, 22–33 (2014).
    Google Scholar 
    Allison, P. A. & Briggs, D. E. Exceptional fossil record: distribution of soft-tissue preservation through the Phanerozoic. Geology 21, 527–530 (1993).
    Google Scholar 
    Briggs, D. E. The role of decay and mineralization in the preservation of soft-bodied fossils. Annu. Rev. Earth Planet. Sci. 31, 275–301 (2003).CAS 

    Google Scholar 
    Rieppel, O. Studies on skeleton formation in reptiles. V. Patterns of ossification in the skeleton of Alligator mississippiensis Daudin (Reptilia, Crocodylia). Zool. J. Linn. Soc. 109, 301–325 (1993).
    Google Scholar 
    Sheil, C. A. Skeletal development of Macrochelys temminckii (Reptilia: Testudines: Chelydridae). J. Morphol. 263, 71–106 (2005).PubMed 

    Google Scholar 
    Roscito, J. G. & Rodrigues, M. T. Skeletal development in the fossorial gymnophthalmids Calyptommatus sinebrachiatus and Nothobachia ablephara. Zoology 115, 289–301 (2012).PubMed 

    Google Scholar 
    Boisvert, C. A. Vertebral development of modern salamanders provides insights into a unique event of their evolutionary history. J. Exp. Zool. B 312, 1–29 (2009).
    Google Scholar 
    Klembara, J. & Janiga, M. Variation in Discosauriscus austriacus (Makowsky, 1876) from the Lower Permian of the Boskovice Furrow (Czech Republic). Zool. J. Linn. Soc. 108, 247–270 (1993).
    Google Scholar 
    Pardo, J. D., Szostakiwskyj, M., Ahlberg, P. E. & Anderson, J. S. Hidden morphological diversity among early tetrapods. Nature 546, 642–645 (2017).CAS 
    PubMed 

    Google Scholar 
    Mann, A., Calthorpe, A. S. & Maddin, H. C. Joermungandr bolti, an exceptionally preserved ‘microsaur’ from the Mazon Creek Lagerstätte reveals patterns of integumentary evolution in Recumbirostra. R. Soc. Open Sci. 8, 210319 (2021).PubMed 
    PubMed Central 

    Google Scholar 
    Swofford, D. Phylogenetic analysis using parsimony (PAUP) v.4.0b10 (Sinauer Associates, 2002).Cohn, M. J. & Bright, P. E. Molecular control of vertebrate limb development, evolution and congenital malformations. Cell Tissue Res. 296, 3–17 (1999).CAS 
    PubMed 

    Google Scholar 
    Mizuhashi, K. et al. Resting zone of the growth plate houses a unique class of skeletal stem cells. Nature 563, 254–258 (2018).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Marchini, M. & Rolian, C. Artificial selection sheds light on developmental mechanisms of limb elongation. Evolution 72, 825–837 (2018).PubMed 

    Google Scholar 
    Rolian, C. Endochondral ossification and the evolution of limb proportions. WIREs Dev. Biol. 9, e373 (2020).Weir, E. C. et al. Targeted overexpression of parathyroid hormone-related peptide in chondrocytes causes chondrodysplasia and delayed endochondral bone formation. Proc. Natl Acad. Sci. USA 93, 10240–10245 (1996).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Terpstra, L. et al. Reduced chondrocyte proliferation and chondrodysplasia in mice lacking the integrin-linked kinase in chondrocytes. J. Cell Biol. 162, 139–148 (2003).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Marchini, M., Hernandez, E. S. & Rolian, C. Morphology and development of a novel murine skeletal dysplasia. PeerJ 7, e7180 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    Shapiro, M. D., Hanken, J. & Rosenthal, N. Developmental basis of evolutionary digit loss in the Australian lizard Hemiergis. J. Exp. Zool. B 297, 48–56 (2003).
    Google Scholar 
    Leal, F. & Cohn, M. J. Loss and re-emergence of legs in snakes by modular evolution of Sonic hedgehog and HOXD enhancers. Curr. Biol. 26, 2966–2973 (2016).CAS 
    PubMed 

    Google Scholar 
    Leal, F. & Cohn, M. J. Developmental, genetic, and genomic insights into the evolutionary loss of limbs in snakes. Genesis 56, e23077 (2018).Lande, R. Evolutionary mechanisms of limb loss in tetrapods. Evolution 32, 73–92 (1978).PubMed 

    Google Scholar 
    Anderson, J. S. Revision of the aïstopod genus Phlegethontia (Tetrapoda: Lepospondyli). J. Paleontol. 76, 1029–1046 (2002).
    Google Scholar 
    Anderson, J. S. A new aïstopod (Tetrapoda: Lepospondyli) from Mazon Creek, Illinois. J. Vertebr. Paleontol. 23, 79–88 (2003).
    Google Scholar 
    Shapiro, M. D. Developmental morphology of limb reduction in Hemiergis (Squamata: Scincidae): chondrogenesis, osteogenesis, and heterochrony. J. Morphol. 254, 211–231 (2002).PubMed 

    Google Scholar 
    Herbst, E. C. & Hutchinson, J. R. New insights into the morphology of the Carboniferous tetrapod Crassigyrinus scoticus from computed tomography. Earth Environ. Sci. Trans. R. Soc. Edinb. 109, 157–175 (2019).CAS 

    Google Scholar 
    Carroll, R. L. & Gaskill, P. The order Microsauria. Mem. Am. Philos. Soc. 126, 1–211 (1978).
    Google Scholar 
    Tchernov, E., Rieppel, O., Zaher, H., Polcyn, M. J. & Jacobs, L. L. A fossil snake with limbs. Science 287, 2010–2012 (2000).CAS 
    PubMed 

    Google Scholar 
    Zaher, H., Apesteguia, S. & Scanferla, C. A. The anatomy of the Upper Cretaceous snake Najash rionegrina Apesteguía & Zaher, 2006, and the evolution of limblessness in snakes. Zool. J. Linn. Soc. 156, 801–826 (2009).
    Google Scholar 
    Jenkins, F. A., Walsh, D. M. & Carroll, R. L. Anatomy of Eocaecilia micropodia, a limbed caecilian of the Early Jurassic. Bull. Mus. Comp. Zool. 158, 285–365 (2007).
    Google Scholar 
    Camp, C. L. Classification of the lizards. Bull. Am. Mus. Nat. Hist. 48, 289–480 (1923).
    Google Scholar 
    Essex, R. Studies in reptilian degeneration. Proc. Zool. Soc. Lond. 97, 879–945 (1927).
    Google Scholar 
    Sewertzoff, A. N. Studien über die reduktion der organe der wirbeltiere. Zool. Jahrb. Abt. Anat. Ontog. Tiere 53, 611–699 (1931).
    Google Scholar  More

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    Western boundary currents drive sun-coral (Tubastraea spp.) coastal invasion from oil platforms

    Katsanevakis, S. et al. Impacts of invasive alien marine species on ecosystem services and biodiversity: A pan-European review. Aquat. Invasions 9, 391–423 (2014).
    Google Scholar 
    Huxel, G. R. Rapid displacement of native species by invasive species: Effects of hybridization. Biol. Conserv. 89, 143–152 (1999).
    Google Scholar 
    Molnar, J. L., Gamboa, R. L., Revenga, C. & Spalding, M. D. Assessing the global threat of invasive species to marine biodiversity. Front. Ecol. Environ. 6, 485–492 (2008).
    Google Scholar 
    Blackburn, T. M. et al. A proposed unified framework for biological invasions. Trends Ecol. Evol. 26, 333–339 (2011).PubMed 

    Google Scholar 
    Ferreira, C. E. L., Gonçalves, J. E. A. & Coutinho, R. Ship hulls and oil platforms as potential vectors to marine species introduction. J. Coast. Res. SI 39 (Pro), 1341–1346 (2006).
    Google Scholar 
    Glasby, T. M., Connell, S. D., Holloway, M. G. & Hewitt, C. L. Nonindigenous biota on artificial structures: Could habitat creation facilitate biological invasions?. Mar. Biol. 151, 887–895 (2007).
    Google Scholar 
    Hedge, L. H. & Johnston, E. L. Propagule pressure determines recruitment from a commercial shipping pier. Biofouling 28, 73–85 (2012).PubMed 

    Google Scholar 
    Capel, K. C. C., Creed, J., Kitahara, M. V., Chen, C. A. & Zilberberg, C. Multiple introductions and secondary dispersion of Tubastraea spp. in the Southwestern Atlantic. Sci. Rep. 9, 1–11 (2019).CAS 

    Google Scholar 
    De Paula, A. F. & Creed, J. C. Two species of the coral Tubastraea (Cnidaria, Scleractinia) in Brazil: A case of accidental introduction. Bull. Mar. Sci. 74, 175–183 (2004).
    Google Scholar 
    Lages, B. G., Fleury, B. G., Menegola, C. & Creed, J. C. Change in tropical rocky shore communities due to an alien coral invasion. Mar. Ecol. Prog. Ser. 438, 85–96 (2011).ADS 

    Google Scholar 
    Mantelatto, M. C., Creed, J. C., Mourão, G. G., Migotto, A. E. & Lindner, A. Range expansion of the invasive corals Tubastraea coccinea and Tubastraea tagusensis in the Southwest Atlantic. Coral Reefs 30, 397–397 (2011).ADS 

    Google Scholar 
    do Santos, L. A. H., Ribeiro, F. V. & Creed, J. C. Antagonism between invasive pest corals Tubastraea spp. and the native reef-builder Mussismilia hispida in the southwest Atlantic. J. Exp. Mar. Biol. Ecol. 449, 69–76 (2013).
    Google Scholar 
    Miranda, R. J., Cruz, I. C. S. & Barros, F. Effects of the alien coral Tubastraea tagusensis on native coral assemblages in a southwestern Atlantic coral reef. Mar. Biol. 163, 1–12 (2016).CAS 

    Google Scholar 
    Silva, A. G., Lima, R. P., Gomes, A. N., Fleury, B. G. & Creed, J. C. Expansion of the invasive corals Tubastraea coccinea and Tubastraea tagusensis into the tamoios ecological station marine protected area, Brazil. Aquat. Invasions 6, S105–S110 (2011).
    Google Scholar 
    Mizrahi, D., Navarrete, S. A. & Flores, A. A. V. Groups travel further: Pelagic metamorphosis and polyp clustering allow higher dispersal potential in sun coral propagules. Coral Reefs 33, 443–448 (2014).ADS 

    Google Scholar 
    De Paula, A. F., De Oliveira Pires, D. & Creed, J. C. Reproductive strategies of two invasive sun corals (Tubastraea spp.) in the southwestern Atlantic. J. Mar. Biol. Assoc. UK 94, 481–492 (2014).
    Google Scholar 
    Capel, K. C. C. et al. Clone wars: Asexual reproduction dominates in the invasive range of Tubastraea spp. (Anthozoa: Scleractinia) in the South-Atlantic Ocean. PeerJ 2017, 1–21 (2017).
    Google Scholar 
    Luz, B. L. P., Di Domenico, M., Migotto, A. E. & Kitahara, M. V. Life-history traits of Tubastraea coccinea: Reproduction, development, and larval competence. Ecol. Evol. 10, 6223–6238 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    Kitahara, M. V. Species richness and distribution of azooxanthellate scleractinia in Brazil. Bull. Mar. Sci. 81, 497–518 (2007).
    Google Scholar 
    da Silva, A. G., de Paula, A. F., Fleury, B. G. & Creed, J. C. Eleven years of range expansion of two invasive corals (Tubastraea coccinea and Tubastraea tagusensis) through the southwest Atlantic (Brazil). Estuar. Coast. Shelf Sci. 141, 9–16 (2014).ADS 

    Google Scholar 
    Creed, J. C. et al. The invasion of the azooxanthellate coral Tubastraea (Scleractinia: Dendrophylliidae) throughout the world: History, pathways and vectors. Biol. Invasions 19, 283–305 (2017).
    Google Scholar 
    Mantelatto, M. C., Pires, L. M., de Oliveira, G. J. G. & Creed, J. C. A test of the efficacy of wrapping to manage the invasive corals Tubastraea tagusensis and T. coccinea. Manag. Biol. Invasions 6, 367–374 (2015).
    Google Scholar 
    Crivellaro, M. S. et al. Fighting on the edge: Reproductive effort and population structure of the invasive coral Tubastraea coccinea in its southern Atlantic limit of distribution following control activities. Biol. Invasions 23, 811–823 (2021).
    Google Scholar 
    Creed, J. C., Casares, F. A., Oigman-Pszczol, S. S. & Masi, B. P. Multi-site experiments demonstrate that control of invasive corals (Tubastraea spp.) by manual removal is effective. Ocean Coast. Manag. 207, 105616 (2021).
    Google Scholar 
    Sammarco, P. W., Atchison, A. D., Boland, G. S., Sinclair, J. & Lirette, A. Geographic expansion of hermatypic and ahermatypic corals in the Gulf of Mexico, and implications for dispersal and recruitment. J. Exp. Mar. Biol. Ecol. 436–437, 36–49 (2012).
    Google Scholar 
    Sammarco, P. W., Atchison, A. D. & Boland, G. S. Coral settlement on oil/gas platforms in the northern Gulf of Mexico: Preliminary evidence of rarity. Gulf Mex. Sci. 32, 11–23 (2014).
    Google Scholar 
    López, C. et al. Invasive Tubastraea spp. and Oculina patagonica and other introduced scleractinians corals in the Santa Cruz de Tenerife (Canary Islands) harbor: Ecology and potential risks. Reg. Stud. Mar. Sci. 29, 100713 (2019).
    Google Scholar 
    Yeo, D. C. J. et al. Semisubmersible oil platforms: Understudied and potentially major vectors of biofouling-mediated invasions. Biofouling 26, 179–186 (2009).
    Google Scholar 
    Lockwood, J. L., Cassey, P. & Blackburn, T. M. The more you introduce the more you get: The role of colonization pressure and propagule pressure in invasion ecology. Divers. Distrib. 15, 904–910 (2009).
    Google Scholar 
    Sammarco, P. W., Atchison, A. D. & Boland, G. S. Expansion of coral communities within the Northern Gulf of Mexico via offshore oil and gas platforms. Mar. Ecol. Prog. Ser. 280, 129–143 (2004).ADS 

    Google Scholar 
    Macreadie, P. I., Fowler, A. M. & Booth, D. J. Rigs-to-reefs: Will the deep sea benefit from artificial habitat?. Front. Ecol. Environ. 9, 455–461 (2011).
    Google Scholar 
    Bowler, D. E. & Benton, T. G. Causes and consequences of animal dispersal strategies. Biol. Rev. 80, 205–225 (2005).PubMed 

    Google Scholar 
    Cowen, R. K. & Sponaugle, S. Larval dispersal and marine population connectivity. Ann. Rev. Mar. Sci. 1, 443–466 (2009).PubMed 

    Google Scholar 
    Peterson, R. G. & Stramma, L. Upper-level circulation in the South Atlantic Ocean. Prog. Oceanogr. 26, 1–73 (1991).ADS 

    Google Scholar 
    Johns, W. E. et al. Annual cycle and variability of the North Brazil current. J. Phys. Oceanogr. 28, 103–128 (1998).ADS 

    Google Scholar 
    Silveira, I. C. A. et al. Brazil current off the eastern Brazilian coast. Rev. Brasil. Oceanog. 48, 171–183 (2000).
    Google Scholar 
    Soutelino, R. G., Gangopadhyay, A. & da Silveira, I. C. A. The roles of vertical shear and topography on the eddy formation near the site of origin of the Brazil Current. Cont. Shelf Res. 70, 46–60 (2013).ADS 

    Google Scholar 
    D’Agostini, A., Gherardi, D. F. M. & Pezzi, L. P. Connectivity of marine protected areas and its relation with total kinetic energy. PLoS ONE 10, 1–19 (2015).
    Google Scholar 
    Endo, C. A. K., Gherardi, D. F. M., Pezzi, L. P. & Lima, L. N. Low connectivity compromises the conservation of reef fishes by marine protected areas in the tropical South Atlantic. Sci. Rep. 9, 1–11 (2019).
    Google Scholar 
    Hanski, I. Metapopulation dynamics. Nature 396, 41–49 (1998).ADS 
    CAS 

    Google Scholar 
    López-Duarte, P. C. et al. What controls connectivity? An empirical, multi-species approach. Integr. Comp. Biol. 52, 511–524 (2012).PubMed 

    Google Scholar 
    Batista, D. et al. Distribution of the invasive orange cup coral tubastraea coccinea lesson, 1829 in an upwelling area in the South Atlantic Ocean fifteen years after its first record. Aquat. Invasions 12, 23–32 (2017).
    Google Scholar 
    O’Connor, M. I. et al. Temperature control of larval dispersal and the implications for marine ecology, evolution, and conservation. Proc. Natl. Acad. Sci. USA. 104, 1266–1271 (2007).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Cairns, S. Studies on the natural history of the Caribbean region. Stud. Fauna Curaçao other Caribb. … IXl, (2000).De Paula, A. F. & Creed, J. C. Spatial distribution and abundance of nonindigenous coral genus Tubastraea (Cnidaria, Scleractinia) around Ilha Grande, Brazil. Braz. J. Biol. 65, 661–673 (2005).CAS 
    PubMed 

    Google Scholar 
    Papacostas, K. J. et al. Biological mechanisms of marine invasions. Mar. Ecol. Prog. Ser. 565, 251–268 (2017).ADS 

    Google Scholar 
    Loureiro, T. G., Silva Gentil Anastácio, P. M., Souty-Grosset, C., Araujo, P. B. & Pereira Almerão, M. Red swamp crayfish: Biology, ecology and invasion—an overview. Nauplius 23, 1–19 (2015).
    Google Scholar 
    Shanks, A. L., Grantham, B. A. & Carr, M. H. Propagule dispersal distance and the size and spacing of marine reserves. Ecol. Appl. 13, 159–169 (2003).
    Google Scholar 
    Siegel, D. A. et al. The stochastic nature of larval connectivity among nearshore marine populations. Proc. Natl. Acad. Sci. USA. 105, 8974–8979 (2008).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Viard, F., Ellien, C. & Dupont, L. Dispersal ability and invasion success of Crepidula fornicata in a single gulf: Insights from genetic markers and larval-dispersal model. Helgol. Mar. Res. 60, 144–152 (2006).ADS 

    Google Scholar 
    Rodrigues, R. R., Rothstein, L. M. & Wimbush, M. Seasonal variability of the South Equatorial Current bifurcation in the Atlantic Ocean: A numerical study. J. Phys. Oceanogr. 37, 16–30 (2007).ADS 

    Google Scholar 
    Fenner, D. Biogeography of three Caribbean corals (Scleractinia) and the invasion of Tubastraea coccinea into the Gulf of Mexico. Bull. Mar. Sci. 69, 1175–1189 (2001).
    Google Scholar 
    Gouveia, M. B. et al. Persistent meanders and eddies lead to quasi-steady Lagrangian transport patterns in a weak western boundary current. Sci. Rep. 11, 1–18 (2021).
    Google Scholar 
    Campos, E. J., Gonçalves, J. & Ikeda, Y. Water mass characteristics and geostrophic circulation in the South Brazil bight: Summer of 1991. J. Geophys. Res. Oceans 100, 18537–18550. https://doi.org/10.1029/95jc01724 (1995).ADS 
    Article 

    Google Scholar 
    Silveira, I. C. A. et al. Is the meander growth in the Brazil Current system off Southeast Brazil due to baroclinic instability?. Dyn. Atmos. Ocean. 45, 187–207 (2008).ADS 

    Google Scholar 
    Lima, L. S. et al. Potential changes in the connectivity of marine protected areas driven by extreme ocean warming. Sci. Rep. 11, 1–12 (2021).
    Google Scholar 
    Thompson, D. M. et al. Variability in oceanographic barriers to coral larval dispersal: Do currents shape biodiversity?. Progr. Oceanogr. 165, 110–122 (2018).ADS 

    Google Scholar 
    Ellien, C., Thiébaut, E., Dumas, F., Salomon, J. C. & Nival, P. A modelling study of the respective role of hydrodynamic processes and larval mortality on larval dispersal and recruitment of benthic invertebrates: Example of Pectinaria koreni (Annelida: Polychaeta) in the Bay of Seine (English Channel). J. Plankton Res. 26, 117–132 (2004).
    Google Scholar 
    Leão, Z. M. A. N., Kikuchi, R. K. P. & Testa, V. Corals and coral reefs of Brazil. In Latin American Coral Reefs (ed. Cortés, J.) 9–52 (Elsevier Science, 2003).
    Google Scholar 
    Dutra, G. F., Allen, G. R., Werner, T., et al. A rapid marine biodiversity assessment of the Abrolhos Bank, Bahia, Brazil. In RAP Bull. Mar. Biol. Assessment, Vol. 38 (Conservation International, 2005).Costa, T. J. F. et al. Expansion of an invasive coral species over Abrolhos Bank, Southwestern Atlantic. Mar. Pollut. Bull. 85, 252–253 (2014).CAS 
    PubMed 

    Google Scholar 
    Moura, R. L. et al. An extensive reef system at the Amazon River mouth. Sci. Adv. 2, 1–12 (2016).
    Google Scholar 
    Soares, M. O., Davis, M. & de Macêdo Carneiro, P. B. Northward range expansion of the invasive coral (Tubastraea tagusensis) in the southwestern Atlantic. Mar. Biodivers. 48, 1651–1654 (2018).
    Google Scholar 
    Rocha, L. A. & Rosa, I. L. Baseline assessment of reef fish assemblages of Parcel Manuel Luiz Marine State Park, Maranhão, north-east Brazil. J. Fish Biol. 58, 985–998 (2001).
    Google Scholar 
    Luz, B. L. P. & Kitahara, M. V. Could the invasive scleractinians Tubastraea coccinea and T. tagusensis replace the dominant zoantharian Palythoa caribaeorum in the Brazilian subtidal?. Coral Reefs 36, 875 (2017).ADS 

    Google Scholar 
    Cordeiro, C. A. M. M. et al. Conservation status of the southernmost reef of the Amazon Reef System: The Parcel de Manuel Luís. Coral Reefs 40, 165–185 (2021).
    Google Scholar 
    Rocha, L. A. Patterns of distribution and processes of speciation in Brazilian reef fishes. J. Biogeogr. 30, 1161–1171 (2003).
    Google Scholar 
    Cruz, R. et al. Life cycle and connectivity of the spiny lobster, Panulirus spp.: Case studies from Brazil and the Wider Caribbean (Decapoda, Achelata). Crustaceana 94, 603–645 (2021).
    Google Scholar 
    Castro, B. D., Lorenzzetti, J., Silveira, I. D. & Miranda, L. D. Estrutura termohalina e circulação na região entre o cabo de são tomé (rj) eo chuí (rs). O ambiente oceanográfco da plataforma continental e do talude na região sudeste-sul do Brasil 1, 11–120 (2006).
    Google Scholar 
    Dias, D. F., Pezzi, L. P., Gherardi, D. F. M. & Camargo, R. Modeling the spawning strategies and larval survival of the Brazilian sardine (Sardinella brasiliensis). Prog. Oceanogr. 123, 38–53 (2014).ADS 

    Google Scholar 
    Nickols, K. J., Wilson White, J., Largier, J. L. & Gaylord, B. Marine population connectivity: Reconciling large-scale dispersal and high self-retention. Am. Nat. 185, 196–211 (2015).PubMed 

    Google Scholar 
    Vinagre, C. et al. Food web organization following the invasion of habitat-modifying Tubastraea spp. corals appears to favour the invasive borer bivalve Leiosolenus aristatus. Ecol. Indic. 85, 1204–1209 (2018).
    Google Scholar 
    Capel, K. C. C., Creed, J. C. & Kitahara, M. V. Invasive corals trigger seascape changes in the southwestern Atlantic. Bull. Mar. Sci. 96, 217–218 (2020).
    Google Scholar 
    Silva, R. et al. Sun coral invasion of shallow rocky reefs: Effects on mobile invertebrate assemblages in Southeastern Brazil. Biol. Invasions 21, 1339–1350 (2019).
    Google Scholar 
    Creed, J. C. & De Paula, A. F. Substratum preference during recruitment of two invasive alien corals onto shallow-subtidal tropical rocky shores. Mar. Ecol. Prog. Ser. 330, 101–111 (2007).ADS 

    Google Scholar 
    Glynn, P. W. et al. Reproductive ecology of the azooxanthellate coral Tubastraea coccinea in the Equatorial Eastern Pacific: Part V. Dendrophylliidae. Mar. Biol. 153, 529–544 (2008).
    Google Scholar 
    Eckman, J. E. Closing the larval loop: Linking larval ecology to the population dynamics of marine benthic invertebrates. J. Exp. Mar. Biol. Ecol. 200, 207–237 (1996).
    Google Scholar 
    Cairns, S. D. & Zibrowius, H. Azooxanthellate Scleractinia from the Philippines and Indonesian regions. Mémoires du Muséum national d’Histoire naturelle, Vol. 172, (1997).Saura, S., Bodin, Ö. & Fortin, M. J. EDITOR’S CHOICE: Stepping stones are crucial for species’ long-distance dispersal and range expansion through habitat networks. J. Appl. Ecol. 51, 171–182 (2014).
    Google Scholar 
    Faria, L. C. & Kitahara, M. V. Invasive corals hitchhiking in the Southwestern Atlantic. Ecology 101, 1–3 (2020).
    Google Scholar 
    Mantelatto, M. C., Póvoa, A. A., Skinner, L. F., de Araujo, F. V. & Creed, J. C. Marine litter and wood debris as habitat and vector for the range expansion of invasive corals (Tubastraea spp.). Mar. Pollut. Bull. 160, 111659 (2020).CAS 
    PubMed 

    Google Scholar 
    Braga, M. D. A. et al. Retirement risks: Invasive coral on old oil platform on the Brazilian equatorial continental shelf. Mar. Pollut. Bull. 165, 112156 (2021).CAS 
    PubMed 

    Google Scholar 
    IMO. Anti-fouling systems. Online (2019). https://www.imo.org/en/OurWork/Environment/Pages/Anti-fouling.aspx. (Accessed 01 May 2021).Vander Zanden, M. J., Hansen, G. J. A., Higgins, S. N. & Kornis, M. S. A pound of prevention, plus a pound of cure: Early detection and eradication of invasive species in the Laurentian Great Lakes. J. Great Lakes Res. 36, 199–205 (2010).
    Google Scholar 
    Pimentel, D. et al. Economic and environmental threats of alien plant, animal, and microbe invasions. Agric. Ecosyst. Environ. 84(1), 1–20 (2001).
    Google Scholar 
    Shchepetkin, A. F. & McWilliams, J. C. The regional oceanic modeling system (ROMS): A split-explicit, free-surface, topography-following-coordinate oceanic model. Ocean Model 9, 347–404 (2005).ADS 

    Google Scholar 
    Shchepetkin, A. F. & McWilliams, J. C. Correction and commentary for “ocean forecasting in terrain-following coordinates: Formulation and skill assessment of the regional ocean modeling system” by haidvogel et al., j. comp. phys. 227, pp. 3595–3624. J. Comput. Phys. 228, 8985–9000 (2009).ADS 
    MathSciNet 
    MATH 

    Google Scholar 
    Lett, C. et al. A Lagrangian tool for modelling ichthyoplankton dynamics. Environ. Model. Sofw. 23, 1210–1214 (2008).
    Google Scholar 
    Gouveia, M. B., Gherardi, D. F. M., Lentini, C. A. D., Dias, D. F. & Campos, P. C. Do the Brazilian sardine commercial landings respond to local ocean circulation?. PLoS ONE 12, 1–19 (2017).
    Google Scholar 
    Saha, S. et al. The NCEP climate forecast system reanalysis. Bull. Am. Meteorol. Soc. 91, 1015–1057 (2010).ADS 

    Google Scholar 
    Carton, J. A., Chepurin, G. A. & Chen, L. SODA3: A new ocean climate reanalysis. J. Clim. 31, 6967–6983 (2018).ADS 

    Google Scholar 
    Flather, R. A. A tidal model of the northeast pacific. Atmos. Ocean 25, 22–45 (1987).
    Google Scholar 
    Chapman, D. C. Numerical treatment of cross-shelf open boundaries in a barotropic coastal ocean model. J. Phys. Oceanogr. 15(8), 1060–1075 (1985).ADS 

    Google Scholar 
    Marchesiello, P., McWilliams, J. C. & Shchepetkin, A. Open boundary conditions for long-term integration of regional oceanic models. Ocean Model 3, 1–20 (2001).ADS 

    Google Scholar 
    Egbert, G. D. & Erofeeva, S. Y. Efficient inverse modeling of barotropic ocean tides. J. Atmos. Ocean. Technol. 19, 183–204 (2002).ADS 

    Google Scholar 
    Marchesiello, P., McWilliams, J. C. & Shchepetkin, A. Equilibrium structure and dynamics of the California current system. J. Phys. Oceanogr. 33, 753–783 (2003).ADS 

    Google Scholar 
    Mizrahi, D., Navarrete, S. A. & Flores, A. A. V. Uneven abundance of the invasive sun coral over habitat patches of different orientation: An outcome of larval or later benthic processes?. J. Exp. Mar. Biol. Ecol. 452, 22–30 (2014).
    Google Scholar 
    Silverman, B. W. Density Estimation for Statistics and Data Analysis (Chapman and Hall, 1986).MATH 

    Google Scholar  More

  • in

    Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection

    Poirel, L. et al. Tn125-related acquisition of blaNDM-like genes in Acinetobacter baumannii. Antimicrob. Agents Chemother. 56, 1087–1089 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wang, R. et al. The global distribution and spread of the mobilized colistin resistance gene mcr-1. Nat. Commun. 9, 1179 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    Clark, N. C., Weigel, L. M., Patel, J. B. & Tenover, F. C. Comparison of Tn1546-like elements in vancomycin-resistant Staphylococcus aureus isolates from Michigan and Pennsylvania. Antimicrob. Agents Chemother. 49, 470–472 (2005).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Partridge, S. R., Kwong, S. M., Firth, N. & Jensen, S. O. Mobile genetic elements associated with antimicrobial resistance. Clin. Microbiol. Rev. 31, e00088-17 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    Stokes, H. W. & Gillings, M. R. Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens. FEMS Microbiol. Rev. 35, 790–819 (2011).CAS 

    Google Scholar 
    Ghaly, T. M. & Gillings, M. R. Mobile DNAs as ecologically and evolutionarily independent units of life. Trends Microbiol. 26, 904–912 (2018).CAS 

    Google Scholar 
    Modi, S. R., Lee, H. H., Spina, C. S. & Collins, J. J. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499, 219–222 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Brown-Jaque, M., Calero-Cáceres, W. & Muniesa, M. Transfer of antibiotic-resistance genes via phage-related mobile elements. Plasmid https://doi.org/10.1016/j.plasmid.2015.01.001 (2015).Frantzeskakis, L. et al. Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen. BMC Genomics 19, 381 (2018).Scott, K. P. The role of conjugative transposons in spreading antibiotic resistance between bacteria that inhabit the gastrointestinal tract. Cell. Mol. Life Sci. 59, 2071–2082 (2002).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Pezzella, C., Ricci, A., DiGiannatale, E., Luzzi, I. & Carattoli, A. Tetracycline and streptomycin resistance genes, transposons, and plasmids in Salmonella enterica isolates from animals in Italy. Antimicrob. Agents Chemother. 48, 903–908 (2004).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bengtsson-Palme, J., Boulund, F., Fick, J., Kristiansson, E. & Larsson, D. G. Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Front. Microbiol. 5, 648 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    Imchen, M. & Kumavath, R. Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment. FEMS Microbiol. Ecol. 96, fiaa173 (2020).CAS 

    Google Scholar 
    Zhang, T., Zhang, X.-X. & Ye, L. Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge. PLoS ONE 6, e26041 (2011).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hu, H. et al. Novel plasmid and its variant harboring both a blaNDM-1 gene and type IV secretion system in clinical isolates of Acinetobacter lwoffii. Antimicrob. Agents Chemother. 56, 1698–1702 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Smet, A. et al. Complete nucleotide sequence of CTX-M-15-plasmids from clinical Escherichia coli isolates: insertional events of transposons and insertion sequences. PLoS ONE 5, e11202 (2010).PubMed 
    PubMed Central 

    Google Scholar 
    Revilla, C. et al. Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids. Antimicrob. Agents Chemother. 52, 1472–1480 (2008).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Poirel, L., Dortet, L., Bernabeu, S. & Nordmann, P. Genetic features of blaNDM-1-positive Enterobacteriaceae. Antimicrob. Agents Chemother. 55, 5403–5407 (2011).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Toleman, M. A., Spencer, J., Jones, L. & Walsh, T. R. blaNDM-1 is a chimera likely constructed in Acinetobacter baumannii. Antimicrob. Agents Chemother. 56, 2773–2776 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bonnin, R. A., Poirel, L. & Nordmann, P. New Delhi metallo-β-lactamase-producing Acinetobacter baumannii: a novel paradigm for spreading antibiotic resistance genes. Future Microbiol. 9, 33–41 (2014).CAS 

    Google Scholar 
    Waterman, P. E. et al. Bacterial peritonitis due to Acinetobacter baumannii sequence type 25 with plasmid-borne New Delhi metallo-β-lactamase in Honduras. Antimicrob. Agents Chemother. 57, 4584–4586 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    McGann, P. et al. Detection of New Delhi metallo-β-lactamase (encoded by blaNDM-1) in Acinetobacter schindleri during routine surveillance. J. Clin. Microbiol. 51, 1942–1944 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Forsberg, K. J. et al. The shared antibiotic resistome of soil bacteria and human pathogens. Science 337, 1107–1111 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jiang, X. et al. Dissemination of antibiotic resistance genes from antibiotic producers to pathogens. Nat. Commun. 8, 15784 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Spanogiannopoulos, P., Waglechner, N., Koteva, K. & Wright, G. D. A rifamycin inactivating phosphotransferase family shared by environmental and pathogenic bacteria. Proc. Natl Acad. Sci. USA 111, 7102–7107 (2014).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Yang, J. et al. Marine sediment bacteria harbor antibiotic resistance genes highly similar to those found in human pathogens. Microb. Ecol. 65, 975–981 (2013).CAS 

    Google Scholar 
    D’Costa, V. M. et al. Antibiotic resistance is ancient. Nature 477, 457–461 (2011).PubMed 
    PubMed Central 

    Google Scholar 
    Van Goethem, M. W. et al. A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils. Microbiome 6, 40 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    Mindlin, S., Soina, V. S., Petrova, M. A. & Gorlenko, Zh. M. Isolation of antibiotic resistance bacterial strains from Eastern Siberia permafrost sediments. Genetika 44, 36–44 (2008).CAS 

    Google Scholar 
    Cohen, S. N. Transposable genetic elements and plasmid evolution. Nature 263, 731–738 (1976).CAS 

    Google Scholar 
    Wright, G. D. Environmental and clinical antibiotic resistomes, same only different. Curr. Opin. Microbiol. 51, 57–63 (2019).CAS 

    Google Scholar 
    von Wintersdorff, C. J. et al. Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Front. Microbiol. 7, 173 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    Rankin, D. J., Rocha, E. P. C. & Brown, S. P. What traits are carried on mobile genetic elements, and why? Heredity (Edinb) https://doi.org/10.1038/hdy.2010.24 (2011).Kottara, A., Hall, J. P., Harrison, E. & Brockhurst, M. A. Variable plasmid fitness effects and mobile genetic element dynamics across Pseudomonas species. FEMS Microbiol. Ecol. 94, fix172 (2018).
    Google Scholar 
    Hall, J. P., Wood, A. J., Harrison, E. & Brockhurst, M. A. Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities. Proc. Natl Acad. Sci. USA 113, 8260–8265 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hall, J. P. J., Williams, D., Paterson, S., Harrison, E. & Brockhurst, M. A. Positive selection inhibits gene mobilisation and transfer in soil bacterial communities. Nat. Ecol. Evol. 1, 1348–1353 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    Naumann, T. A. & Reznikoff, W. S. Tn5 transposase with an altered specificity for transposon ends. J. Bacteriol. 184, 233–240 (2002).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wang, H. et al. Increased plasmid copy number is essential for Yersinia T3SS function and virulence. Science 353, 492–495 (2016).CAS 

    Google Scholar 
    Sandegren, L. & Andersson, D. I. Bacterial gene amplification: implications for the evolution of antibiotic resistance. Nat. Rev. Microbiol. 7, 578–588 (2009).CAS 

    Google Scholar 
    Dimitriu, T., Mathews, A. C. & Buckling, A. Increased copy number couples the evolution of plasmid horizontal transmission and plasmid-encoded antibiotic resistance. Proc. Natl Acad. Sci. USA 118, e2107818118 (2021).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    De Lorenzo, V., Herrero, M., Jakubzik, U. & Timmis, K. N. Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria. J. Bacteriol. 172, 6568–6572 (1990).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lichtenstein, C. & Brenner, S. Site-specific properties of Tn7 transposition into the E. coli chromosome. Mol. Gen. Genet. 183, 380–387 (1981).CAS 

    Google Scholar 
    Bethke, J. H. et al. Environmental and genetic determinants of plasmid mobility in pathogenic Escherichia coli. Sci. Adv. 6, eaax3173 (2020).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Mahillon, J. & Chandler, M. Insertion sequences. Microbiol. Mol. Biol. Rev. 62, 725–774 (1998).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Siguier, P., Perochon, J., Lestrade, L., Mahillon, J. & Chandler, M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 34, D32–D36 (2006).CAS 

    Google Scholar 
    Seelke, R. W., Kline, B. C., Trawick, J. D. & Ritts, G. D. Genetic studies of F plasmid maintenance genes involved in copy number control, incompatability, and partitioning. Plasmid 7, 163–179 (1982).CAS 

    Google Scholar 
    Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008 (2006).PubMed 
    PubMed Central 

    Google Scholar 
    Watve, M. M., Dahanukar, N. & Watve, M. G. Sociobiological control of plasmid copy number in bacteria. PLoS ONE 5, e9328 (2010).PubMed 
    PubMed Central 

    Google Scholar 
    Lehtinen, S. et al. Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae. Sci. Adv. 6, eaaz6137 (2020).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ubeda, C. et al. Antibiotic-induced SOS response promotes horizontal dissemination of pathogenicity island-encoded virulence factors in staphylococci. Mol. Microbiol. 56, 836–844 (2005).CAS 

    Google Scholar 
    Beaber, J. W., Hochhut, B. & Waldor, M. K. SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature 427, 72–74 (2004).CAS 

    Google Scholar 
    al‐Masaudi, S. B., Day, M. & Russell, A. D. Effect of some antibiotics and biocides on plasmid transfer in Staphylococcus aureus. J. Appl. Bacteriol. 71, 239–243 (1991).
    Google Scholar 
    Nichols, B. P. & Guay, G. G. Gene amplification contributes to sulfonamide resistance in Escherichia coli. Antimicrob. Agents Chemother. 33, 2042–2048 (1989).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Normark, S., Edlund, T., Grundström, T., Bergström, S. & Wolf-Watz, H. Escherichia coli K-12 mutants hyperproducing chromosomal beta-lactamase by gene repetitions. J. Bacteriol. 132, 912–922 (1977).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zienkiewicz, M., Kern-Zdanowicz, I., Carattoli, A., Gniadkowski, M. & Cegłowski, P. Tandem multiplication of the IS 26-flanked amplicon with the blaSHV-5 gene within plasmid p1658/97. FEMS Microbiol. Lett. 341, 27–36 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Matthews, P. R. & Stewart, P. R. Amplification of a section of chromosomal DNA in methicillin-resistant Staphylococcus aureus following growth in high concentrations of methicillin. J. Gen. Microbiol. 134, 1455–1464 (1988).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sun, S., Berg, O. G., Roth, J. R. & Andersson, D. I. Contribution of gene amplification to evolution of increased antibiotic resistance in Salmonella typhimurium. Genetics 182, 1183–1195 (2009).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Andersson, D. I. & Hughes, D. Gene amplification and adaptive evolution in bacteria. Annu. Rev. Genet. 43, 167–195 (2009).CAS 

    Google Scholar 
    Nicoloff, H., Perreten, V. & Levy, S. B. Increased genome instability in Escherichia coli lon mutants: relation to emergence of multiple-antibiotic-resistant (Mar) mutants caused by insertion sequence elements and large tandem genomic amplifications. Antimicrob. Agents Chemother. 51, 1293–1303 (2007).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bertini, A. et al. Multicopy blaOXA-58 gene as a source of high-level resistance to carbapenems in Acinetobacter baumannii. Antimicrob. Agents Chemother. 51, 2324–2328 (2007).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Knapp, C. W. et al. Indirect evidence of transposon-mediated selection of antibiotic resistance genes in aquatic systems at low-level oxytetracycline exposures. Environ. Sci. Technol. 42, 5348–5353 (2008).CAS 

    Google Scholar 
    San Millan, A., Escudero, J. A., Gifford, D. R., Mazel, D. & MacLean, R. C. Multicopy plasmids potentiate the evolution of antibiotic resistance in bacteria. Nat. Ecol. Evol. 1, 10 (2016).
    Google Scholar 
    Rodriguez-Beltran, J. et al. Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation. Nat. Ecol. Evol. 2, 873–881 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    Rodríguez-Beltrán, J., DelaFuente, J., León-Sampedro, R., MacLean, R. C. & San Millán, Á. Beyond horizontal gene transfer: the role of plasmids in bacterial evolution. Nat. Rev. Microbiol. 19, 347–359 (2021).
    Google Scholar 
    Frost, L. S., Leplae, R., Summers, A. O. & Toussaint, A. Mobile genetic elements: the agents of open source evolution. Nat. Rev. Microbiol. 3, 722–732 (2005).CAS 

    Google Scholar 
    You, L., Hoonlor, A. & Yin, J. Modeling biological systems using Dynetica—a simulator of dynamic networks. Bioinformatics 19, 435–436 (2003).CAS 

    Google Scholar 
    Afgan, E. et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 46, W537–W544 (2018).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wingett, S. W. & Andrews, S. FastQ Screen: a tool for multi-genome mapping and quality control. F1000Res. 7, 1338 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    Blankenberg, D. et al. Manipulation of FASTQ data with Galaxy. Bioinformatics 26, 1783–1785 (2010).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).PubMed 
    PubMed Central 

    Google Scholar 
    Smith, T., Heger, A. & Sudbery, I. UMI-tools: modeling sequencing errors in unique molecular identifiers to improve quantification accuracy. Genome Res. 27, 491–499 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).CAS 
    PubMed 
    PubMed Central 

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

    Google Scholar  More

  • in

    Squid adjust their body color according to substrate

    Endler, J. A. Interactions between predators and prey. In Behavioural Ecology: An Evolutionary Approach 3rd edn (eds Krebs, J. R. & Davies, N. B.) 169–196 (Blackwell, 1991).
    Google Scholar 
    Stevens, M. & Merilaita, S. Animal camouflage: Current issues and new perspectives. Philos. Trans. R Soc. Lond. B 364, 423–427 (2009).
    Google Scholar 
    Stevens, M. & Merilaita, S. Animal camouflage: Function and mechanisms. In Animal Camouflage: Mechanisms and Function (eds Stevens, M. & Merilaita, S.) 1–17 (Cambridge University Press, 2011).
    Google Scholar 
    Reiter, S. & Laurent, G. Visual perception and cuttlefish camouflage. Curr. Opin. Neurobiol. 260, 47–54 (2020).
    Google Scholar 
    Cott, H. B. Adaptive Coloration in Animals (Methuen, 1940).
    Google Scholar 
    Cloney, R. A. & Florey, E. Ultrastructure of cephalopod chromatophore organs. Z. Zellforsch. Mikrosk. Anat. 89, 250–280 (1968).CAS 
    PubMed 

    Google Scholar 
    Borrelli, L., Gherardi, F. & Fiorito, G. A. Catalogue of Body Patterning in Cephalopoda (Firenze University Press, 2006).
    Google Scholar 
    Reiter, S. et al. Elucidating the control and development of skin patterning in cuttlefish. Nature 562, 361–366 (2018).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Barbosa, A., Allen, J. J., Mäthger, L. M. & Hanlon, R. T. Cuttlefish use visual cues to determine arm postures for camouflage. Proc. R Soc. B Biol. Sci. 279, 84–90 (2012).
    Google Scholar 
    Hanlon, R. T. Cephalopod dynamic camouflage. Curr. Biol. 17, R400-404 (2007).CAS 
    PubMed 

    Google Scholar 
    Hill, A. V. & Solandt, D. Y. Myograms from the chromatophores of Sepia. J. Physiol. Lond. 83, 13–14 (1935).
    Google Scholar 
    Williams, T. L. et al. Dynamic pigmentary and structural coloration within cephalopod chromatophore organs. Nat. Commun. 10, 1–5 (2019).
    Google Scholar 
    Hanlon, R. T. et al. Rapid adaptive camouflage in cephalopods. In Animal Camouflage: Mechanisms and Functions (eds Stevens, M. & Merilaita, S.) 145–163 (Cambridge Univ Press, 2011).
    Google Scholar 
    Hanlon, R. T. & Messenger, J. B. Adaptive coloration in young cuttlefish (Sepia officinalis L.): The morphology and development of body patterns and their relation to behavior. Philos. Trans. R Soc. Lond. B 320, 437–487 (1988).ADS 

    Google Scholar 
    Ferguson, G., Messenger, J. B. & Budelmann, B. Gravity and light influence the countershading reflexes of the cuttlefish Sepia officinalis. J. Exp. Biol. 191, 247–256 (1994).CAS 
    PubMed 

    Google Scholar 
    Shohet, A. J., Baddeley, R. J., Anderson, J. C., Kelman, E. J. & Osorio, D. Cuttlefish responses to visual orientation of substrates, water flow and a model of motion camouflage. J. Exp. Biol. 209, 4717–4723 (2006).CAS 
    PubMed 

    Google Scholar 
    Barbosa, A. et al. Disruptive coloration in cuttlefish: A visual perception mechanism that regulates ontogenetic adjustment of skin patterning. J. Exp. Biol. 210, 1139–1147 (2007).PubMed 

    Google Scholar 
    Chiao, C. C., Chubb, C. & Hanlon, R. T. Interactive effects of size, contrast, intensity and configuration of background objects in evoking disruptive camouflage in cuttlefish. Vis. Res. 47, 2223–2235 (2007).PubMed 

    Google Scholar 
    Nakajima, R. & Ikeda, Y. A catalog of the chromatic, postural, and locomotor behaviors of the pharaoh cuttlefish (Sepia pharaonis) from Okinawa Island, Japan. Mar. Biodivers. 47, 735–753 (2017).
    Google Scholar 
    Packard, A. Chromatophore fields in the skin of the octopus. J. Physiol. 238, 38–40 (1974).
    Google Scholar 
    Caldwell, R. L., Ross, R., Rodaniche, A. F. & Huffard, C. L. Behavior and body patterns of the larger pacific striped octopus. PLoS ONE 10, e0134152 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    Gutnick, T., Shomrat, T., Mather, J. A. & Kuba, M. J. The cephalopod brain: Motion control, learning, and cognition. In Physiology of Molluscs: A Collection of Selected Reviews Vol. 2 (eds Salleudin, S. & Mukai, S.) 139–177 (Apple Academic Press, 2016).
    Google Scholar 
    Hanlon, R. T. & Messenger, J. B. Cephalopod Behaviour 2nd edn. (Cambridge University Press, 2018).
    Google Scholar 
    Cloney, R. & Brocco, S. Chromatophore organs, reflector cells, iridocytes, and leucophores. Am. Zool. 23, 581–592 (1983).
    Google Scholar 
    Mäthger, L. M. & Hanlon, R. T. Malleable skin coloration in cephalopods: Selective reflectance, transmission and absorbance of light by chromatophores and iridophores. Cell Tissue Res. 329, 179 (2007).PubMed 

    Google Scholar 
    Josef, N., Berenshtein, I., Fiorito, G., Sykes, A. V. & Shashar, N. Camouflage during movement in the European cuttlefish (Sepia officinalis). J. Exp. Biol. 218, 3391–3398 (2015).PubMed 

    Google Scholar 
    Josef, N. et al. Size matters: Observed and modeled camouflage response of European Cuttlefish (Sepia officinalis) to different substrate patch sizes during movement. Front. Physiol. 7, 671 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    Poulton, E. B. The Colours of Animals: Their Meaning and Use, Especially Considered in the Case of Insects (D. Appleton, 1890).
    Google Scholar 
    Zhang, Y. & Richardson, J. S. Unidirectional prey–predator facilitation: Apparent prey enhance predators’ foraging success on cryptic prey. Biol. Lett. 3, 348–351 (2007).PubMed 
    PubMed Central 

    Google Scholar 
    Troscianko, T., Benton, C. P., Lovell, P. G., Tolhurst, D. J. & Pizlo, Z. Camouflage and visual perception. Philos. Trans. R Soc. B 364, 449–461 (2009).
    Google Scholar 
    Land, M. F. & Nilsson, D. E. Animal Eyes (Oxford University Press, 2012).
    Google Scholar 
    Cronin, T. W., Johnsen, S., Marshall, N. J. & Warrant, E. J. Visual Ecology (Princeton University Press, 2014).
    Google Scholar 
    Hanlon, R. T. & Messenger, J. B. Cephalopod Behaviour (Cambridge University Press, 1996).
    Google Scholar 
    Staudinger, M. D., Hanlon, R. T. & Juanes, F. Primary and secondary defences of squid to cruising and ambush fish predators: Variable tactics and their survival value. Anim. Behav. 81, 585–594 (2011).
    Google Scholar 
    Ferguson, G. P. & Messenger, J. B. A countershading reflex in cephalopods. Proc. R. Soc. B 243, 63–67 (1991).ADS 

    Google Scholar 
    Zylinski, S. & Johnsen, S. Mesopelagic cephalopods switch between transparency and pigmentation to optimize camouflage in the deep. Curr. Biol. 21, 1937–1941 (2011).CAS 
    PubMed 

    Google Scholar 
    Young, R. E. & Roper, C. F. E. Bioluminescent countershading in mid water animals: Evidence from living squid. Science 191, 1046–1048 (1976).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Jereb, P. & Roper, C. F. E. Cephalopods of the World. An Annotated and Illustrated Catalogue of Cephalopod Species Known to Date. Myopsid and Oegopsid Squids Vol. 2 (FAO, 2010).
    Google Scholar 
    Okutani, T. Life history of the oval squid, Sepioteuthis lessoniana. Saibai Giken 13, 69–75 (1984) ((in Japanese)).
    Google Scholar 
    Segawa, S. Food consumption, food conversion and growth rates of the oval squid Sepioteuthis lessoniana by laboratory experiments. Nippon Suisan Gakkai Shi 56, 217–222 (1990).
    Google Scholar 
    Izuka, T., Segawa, S., Okutani, T. & Numachi, K. Evidence on the existence of three species in the oval squid Sepioteuthis lessoniana complex in Ishigaki Island, Okinawa, southwestern Japan, by isozyme analyses. Venus Jpn. J. Malacol/Kairuigaku Zasshi 53, 217–228 (1994).
    Google Scholar 
    Izuka, T. Biochemical study of the population heterogeneity and distribution of the oval squid Sepioteuthis lessoniana complex in southwestern Japan. Am. Malac. Bull. 12, 129–135 (1996).
    Google Scholar 
    Imai, H., & Aoki, M. Genetic diversity and genetic heterogeneity of bigfin reef squid “Sepioteuthis lessoniana” species complex in northwestern Pacific Ocean. in Analysis of Genetic Variation in Animals (Caliskan, M. ed). 151–166. (InTech, 2012).Cheng, S. H. et al. Molecular evidence for co-occurring cryptic lineages within the Sepioteuthis cf. lessoniana species complex in the Indian and Indo-West Pacific Oceans. Hydrobiologia 725, 165–188 (2014).CAS 

    Google Scholar 
    Tomano, S. et al. Contribution of Sepioteuthis sp. 1 and Sepioteuthis sp. 2 to oval squid fishery stocks in western Japan. Fish Sci 82, 585–596 (2016).CAS 

    Google Scholar 
    Okutani, T. Past, present and future studies on cephalopod diversity in tropical west Pacific. Phuket Mar. Biol. Center Res. Bull. 66, 39–50 (2005).
    Google Scholar 
    Lee, P. G., Turk, P. E., Yang, W. T. & Hanlon, R. T. Biological characteristics and biomedical applications of the squid Sepioteuthis lessoniana cultured through multiple generations. Biol. Bull. 186, 328–341 (1994).CAS 
    PubMed 

    Google Scholar 
    Nabhitabhata, J. & Ikeda, Y. Sepioteuthis lessoniana. In Cephalopod Culture (eds Iglesias, J. et al.) 315–347 (Springer, 2014).
    Google Scholar 
    Lajbner, Z. et al. Captive breeding of the oval squid (Aori-ika; Sepioteuthis sp.). in Cephalopod International Advisory Council Conference 2018, Book of Abstracts, St. Petersburg. 152. (2018)Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, i01 (2015).
    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing. http://www.R-project.org (R Foundation for Statistical Computing, 2019).RStudio Team. RStudio: Integrated Development for R. http://www.rstudio.com (RStudio, Inc., 2019)Kenward, M. & Roger, J. Small sample inference for fixed effects from restricted maximum likelihood. Biometrics 53, 983–997 (1997).CAS 
    PubMed 
    MATH 

    Google Scholar 
    Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lin, C. Y., Tsai, Y. C. & Chiao, C. C. Quantitative analysis of dynamic body patterning reveals the grammar of visual signals during the reproductive behavior of the oval squid Sepioteuthis lessoniana. Front. Ecol. Evol. 5, 30 (2017).
    Google Scholar 
    Chung, W. S., Kurniawan, N. D. & Marshall, N. J. Toward an MRI-based mesoscale connectome of the squid brain. Iscience 23, 100816 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Messenger, J. B. Cephalopod chromatophores: Neurobiology and natural history. Biol. Rev. Camb. Philos. Soc. 76, 473–528 (2001).CAS 
    PubMed 

    Google Scholar 
    York, C. A. & Bartol, I. K. Anti-predator behavior of squid throughout ontogeny. J. Exp. Mar. Biol. Ecol. 480, 26–35 (2016).
    Google Scholar 
    Suzuki, M., Kimura, T., Ogawa, H., Hotta, K. & Oka, K. Chromatophore activity during natural pattern expression by the squid Sepioteuthis lessoniana: Contributions of miniature oscillation. PLoS ONE 6, e18244 (2011).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Liu, Y.C., Wang, W.C., & Grasse, B. Electrical coupling between chromatophore muscle fibers allows for versatile control of chromatophore expansion in squid. bioRxiv 2020.02.17.951715 (2020).Hadjisolomou, S. P., El-Haddad, R. W., Kloskowski, K., Chavarga, A. & Abramov, I. Quantifying the speed of chromatophore activity at the single-organ level in response to a visual startle stimulus in living, intact squid. Front. Physiol. 12, 675252. https://doi.org/10.3389/fphys.2021.675252 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar  More

  • in

    Up for crabs: making a home for red-clawed crustaceans in Taiwan

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    This picture was taken at night in the coastal community of Dakenggu in Yilan County, which is just southeast of Taipei in Taiwan. I’m on the left, working with two other researchers to measure the body size of a red-clawed crab (Chiromantes haematocheir).An old man from the local community told me that years ago, during the breeding season, you could barely cross the road because of all the crabs. He said nobody knows where they all went. They’re an important memory for the local people, and part of the culture here.Habitat loss — especially resulting from the widespread use of concrete — seems to be driving the decline. I’m working with local people to create rocky microhabitats and artificial wetlands for the red-clawed crabs to live in. They’re important scavengers — eating dead animals and other organic matter, breaking it down and playing a key part in the nutrient cycle.Small organisms need our help — they can’t stand up for themselves. But in Taiwan, a lot of people think a coastal villa is more important than a few crabs. Corporations want to build luxury developments in our national parks, and authorities often approve them. I’ve seen so many intact habitats destroyed or covered in concrete.Crabs caught my interest because they were frequent visitors to my dormitory. National Sun Yat-sen University in Kaohsiung sits in a coastal buffer zone between a mountain and the ocean, and land hermit crabs (Coenobita cavipes) have to scurry through it on their way to breed.After watching habitat after habitat destroyed by overdevelopment, I’ve realized that just doing the science is not enough. It doesn’t matter how many papers you publish: you need to connect with people through education and communication. That’s why I decided to do my PhD in social science. And it’s why I believe conservation will be my life’s work.

    Nature 603, 962 (2022)
    doi: https://doi.org/10.1038/d41586-022-00810-3

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    Water shifts the balance of coexistence

    van der Putten, W. H. et al. J. Ecol. 101, 265–276 (2013).Article 

    Google Scholar 
    Smith-Ramesh, L. M. & Reynolds, H. L. J. Veg. Sci. 28, 484–494 (2017).Article 

    Google Scholar 
    De Long, J. R., Fry, E. L., Veen, G. & Kardol, P. Funct. Ecol. 33, 118–128 (2019).Article 

    Google Scholar 
    Pugnaire, F. I. et al. Sci. Adv. 5, eaaz1834 (2019).CAS 
    Article 

    Google Scholar 
    Dudenhöffer, J.-H., Luecke, N. C. & Crawford, K. M. Nat. Ecol. Evol. https://doi.org/10.1038/s41559-022-01700-7 (2022).Article 

    Google Scholar 
    Bever, J. D., Westover, K. M. & Antonovics, J. J. Ecol. 85, 561–573 (1997).Article 

    Google Scholar 
    Crawford, K. M. et al. Ecol. Lett. 22, 1274–1284 (2019).Article 

    Google Scholar 
    Dudenhöffer, J., Ebeling, A., Klein, A., Wagg, C. & Farrer, E. J. Ecol. 106, 230–241 (2018).Article 

    Google Scholar 
    Kandlikar, G. S., Johnson, C. A., Yan, X., Kraft, N. J. B. & Levine, J. M. Ecol. Lett. 22, 1178–1191 (2019).PubMed 

    Google Scholar 
    Nguyen, N. H. et al. Fungal Ecol. 20, 241–248 (2016).Article 

    Google Scholar 
    Rudgers, J. A. et al. Annu. Rev. Ecol. Evol. Syst. 51, 561–586 (2020).Article 

    Google Scholar 
    Ke, P.-J., Zee, P. C. & Fukami, T. New Phytol. 231, 1546–1558 (2021).CAS 
    Article 

    Google Scholar  More

  • in

    DNA barcoding and phylogeography of the Hoplias malabaricus species complex

    Cardoso, Y. P. et al. A continental-wide molecular approach unraveling mtDNA diversity and geographic distribution of the Neotropical genus Hoplias. PLoS ONE 13(8), e0202024. https://doi.org/10.1371/journal.pone.0202024 (2018).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bertollo, L. A. C., Born, G. G., Dergam, J. A., Fenocchio, A. S. & Moreira-Filho, O. A biodiversity approach in the Neotropical Erythrinidae fish, Hoplias malabaricus: Karyotypic survey, geographic distribution of karyomorphs and cytotaxonomic considerations. Chrom. Res. 8(7), 603–613 (2000).CAS 
    Article 

    Google Scholar 
    Oyakawa, O. T. Family Erythrinidae (Trahiras). in Check list of the freshwater fishes of South and Central America (Reis, R. E., Kullander, S. O. & Ferraris, C.). Edipucrs 238–240 (Porto Alegre, 2003).Dagosta, F. C. P. & de Pinna, M. C. C. The fishes of the Amazon: distribution and biogeographical patterns, with a comprehensive list of species. Bull. Am. Museum Nat. Hist. 431, 1–163 (2019).
    Google Scholar 
    Da Rosa, R., Vicari, M. R., Dias, A. L. & Giuliano-Caetano, L. New insights into the biogeographic and Karyotypic Evolution of Hoplias Malabaricus. Zebrafish 11(3), 198–206. https://doi.org/10.1089/zeb.2013.0953 (2014).CAS 
    Article 
    PubMed 

    Google Scholar 
    Santos, U. et al. Molecular and karyotypic phylogeography in the neotropical Hoplias malabaricus (Erythrinidae) fish in eastern Brazil. J. Fish Biol. 75(9), 2326–2343. https://doi.org/10.1111/j.1095-8649.2009.02489.x (2009).CAS 
    Article 
    PubMed 

    Google Scholar 
    Blanco, D. R., Lui, R. L., Bertollo, L. A. C., Diniz, D. & Filho, O. M. Characterization of invasive fish species in a river transposition region: Evolutionary chromosome studies in the genus Hoplias (Characiformes, Erythrinidae). Rev. Fish Biol. Fish. 20(1), 1–8. https://doi.org/10.1007/s11160-009-9116-3 (2010).Article 

    Google Scholar 
    Jacobina, U. P. et al. DNA barcode sheds light on systematics and evolution of neotropical freshwater trahiras. Genetica 146, 505. https://doi.org/10.1007/s10709-018-0043-x (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    Marques, D. F., Santos, F. A., da Silva, S. S., Sampaio, I. & Rodrigues, L. R. R. Cytogenetic and DNA barcoding reveals high divergence within the trahira, Hoplias malabaricus (Characiformes: Erythrinidae) from the lower Amazon River. Neotrop. Ichthyol. 11(2), 459–466. https://doi.org/10.1590/S1679-62252013000200015 (2013).Article 

    Google Scholar 
    Paz, F. P. C., Batista, J. S. & Porto, J. I. R. DNA barcodes of rosy tetras and allied species (Characiformes: Characidae: Hyphessobrycon) from the Brazilian Amazon Basin. PLoS ONE 9(5), e98603. https://doi.org/10.1371/journal.pone.0098603 (2014).ADS 
    CAS 
    Article 

    Google Scholar 
    Guimarães, K. L. A., de Sousa, M. P. A., Ribeiro, F. R. V., Porto, J. I. R. & Rodrigues, L. R. R. DNA barcoding of fish fauna from low order streams of Tapajós River basin. PLoS ONE 13(12), e0209430. https://doi.org/10.1371/journal.pone.0209430 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Machado, V. N. et al. One thousand DNA barcodes of piranhas and pacus reveal geographic structure and unrecognized diversity in the Amazon. Sci. Rep. 8, 8387. https://doi.org/10.1038/s41598-018-26550-x (2018).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hebert, P. D. N., Cywinska, A., Ball, S. L. & Dewaard, J. R. Biological identifications through DNA barcodes. Philos. Trans. R. Soc. B 270(1512), 313–321. https://doi.org/10.1098/rspb.2002.2218 (2003).CAS 
    Article 

    Google Scholar 
    Pugedo, M. L., de Andrade Neto, F. R., Pessali, T. C., Birindelli, J. L. O. & Carvalho, D. C. Integrative taxonomy supports new candidate fish species in a poorly studied neotropical region: the Jequitinhonha River Basin. Genetica 144(3), 1–9. https://doi.org/10.1007/s10709-016-9903-4 (2016).Article 

    Google Scholar 
    Rosso, J. J. et al. Integrative taxonomy reveals a new species of the Hoplias malabaricus species complex (Teleostei: Erythrinidae). Ichthyol. Explor. Freshw. 1, 1–18. https://doi.org/10.23788/IEF-1076 (2018).Article 

    Google Scholar 
    Azpelicueta, M. M., Benítez, M., Aichino, D. & Mendez, C. M. D. A new species of the genus Hoplias (Characiformes, Erythrinidae), a tararira from the lower Paraná River, in Missiones, Argentina. Acta Zool. Lilloana 59(1–2), 71–82 (2015).
    Google Scholar 
    Rosso, J. J. et al. A new species of the Hoplias malabaricus species complex (Characiformes: Erythrinidae) from the La Plata River basin. Cybium 40(3), 199–208 (2016).
    Google Scholar 
    Cardoso, Y. P. & Montoya-Burgos, J. I. Unexpected diversity in the catfish Pseudancistrus brevispinis reveals dispersal routes in a Neotropical center of endemism: The Guyanas Region. Mol. Ecol. 18(5), 947–964. https://doi.org/10.1111/j.1365-294X.2008.04068.x (2009).CAS 
    Article 
    PubMed 

    Google Scholar 
    Hoorn, C., Wesselingh, F. P., Hovikoski, J. & Guerrero, J. The development of the Amazonian mega-wetland (Miocene; Brazil, Colombia, Peru, Bolivia). Amazon. Landsc. Species Evol. https://doi.org/10.1002/9781444306408.ch8 (2010).Article 

    Google Scholar 
    Albert, J. S. & Reis, R. E. Introduction to neotropical freshwaters. In Historical Biogeography of Neotropical Freshwater Fishes (eds Albert, J. S. & Reis, R. E.) 3–19 (University of California Press, 2011).
    Google Scholar 
    Leys, M., Keller, I., Räsänen, K., Gattolliat, J.-L. & Robinson, C. T. Distribution and population genetic variation of cryptic species of the Alpine mayfly Baetis alpinus (Ephemeroptera: Baetidae) in the Central Alps. BMC Evol. Biol. https://doi.org/10.1186/s12862-016-0643-y (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Aljanabi, S. M. & Martinez, I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 25(22), 4692–4693 (1997).CAS 
    Article 

    Google Scholar 
    Vitorino, C. A., Oliveira, R. C. C., Margarido, V. P. & Venere, P. C. Genetic diversity of Arapaima gigas (Schinz, 1822) (Osteoglossiformes: Arapaimidae) in the Araguaia-Tocantins basin estimated by ISSR marker. Neotrop. Ichthyol. 13, 557–568. https://doi.org/10.1590/1982-0224-20150037 (2015).Article 

    Google Scholar 
    Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R. & Hebert, P. D. N. DNA barcoding Australia’s fish species. Philos. Trans. R. Soc. B 359, 1847–1857. https://doi.org/10.1098/srtb.2005.1716 (2005).Article 

    Google Scholar 
    Dunn, I. S. & Blattner, F. R. Sharons 36 to 40: Multienzyme, high capacity, recombination deficient replacement vectors with polylinkers and polystuffers. Nucleic Acids Res. 15, 2677–2698 (1987).CAS 
    Article 

    Google Scholar 
    Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22), 4673–4680 (1994).CAS 
    Article 

    Google Scholar 
    Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552. https://doi.org/10.1093/oxfordjournals.molbev.a026334 (2000).CAS 
    Article 

    Google Scholar 
    Ratnasingham, S. & Hebert, P. D. N. DNA-Based registry for all animal species: The Barcode Index Number (BIN) system. PLoS ONE 8(7), e66213. https://doi.org/10.1371/journal.pone.0066213 (2013).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Pons, J. et al. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst. Biol. 55(4), 595–609. https://doi.org/10.1080/10635150600852011 (2006).Article 
    PubMed 

    Google Scholar 
    Fujisawa, T. & Barraclough, T. G. Delimiting species using single-locus data and the generalized mixed yule coalescent approach: A revised method and evaluation on simulated data sets. Syst. Biol. 62(5), 707–724. https://doi.org/10.1093/sysbio/syt033 (2013).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Puillandre, N., Lambert, A., Brouillet, S. & Achaz, G. ABGD, automatic barcode gap discovery for primary species delimitation. Mol. Ecol. 21(8), 1864–1877. https://doi.org/10.1111/j.1365-294X.2011.05239.x (2012).CAS 
    Article 
    PubMed 

    Google Scholar 
    Drummond, A. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214. https://doi.org/10.1186/1471-2148-7-214 (2007).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Posada, D. jModelTest: Phylogenetic model averaging. Mol. Biol. Evol. 25, 1253–1256. https://doi.org/10.1093/molbev/msn083 (2008).CAS 
    Article 
    PubMed 

    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing. https://www.R-project.org/ (2017).Ezard, T., Fujisawa, T. & Barraclough, T. splits: Species Limits by Threshold Statistics. R package version 1.0–19/r52. https://R-Forge.R-project.org/projects/splits/ (2017).Paradis, E. & Schliep, K. ape 5.0: An environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2018).Article 

    Google Scholar 
    Bermingham, E., McCafferty, S. S. & Martin, A. P. Fish biogeography and molecular clocks: Perspectives from the Panamanian Isthmus. In Molecular Systematics of Fishes (eds Kocher, T. D. & Stepien, C. A.) 113–128 (Academic Press, 1997).Chapter 

    Google Scholar 
    Thomaz, A. T., Malabarba, L. R., Bonatto, S. L. & Knowles, L. L. Testing the effect of palaeodrainages versus habitat stability on genetic divergence in riverine systems: Study of a Neotropical fish of the Brazilian coastal Atlantic Forest. J. Biogeogr. 42, 2389–2401. https://doi.org/10.1111/jbi.12597 (2015).Article 

    Google Scholar 
    Kimura, M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111–120 (1980).ADS 
    CAS 
    Article 

    Google Scholar 
    Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549. https://doi.org/10.1093/molbev/msy096 (2018).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Guillot, G., Renaud, S., Ledevin, R., Michaux, J. & Claude, J. A unifying model for the analysis of phenotypic, genetic and geograhic data. Syst. Biol. 61(6), 897–911. https://doi.org/10.1093/sysbio/sys038 (2012).Article 
    PubMed 

    Google Scholar 
    Excoffier, L., Laval, G. & Schneider, S. Arlequin: A Software for Population Data Analysis. Version 3.1. http://cmpg.unibe.ch/software/arlequin3 (2007).Wright, S. Evolution and the genetics of populations: Variability within and among natural populations. Univ. Chicago 4, 580 (1978).
    Google Scholar 
    Rozas, J. et al. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol. Biol. Evol. 34, 3299–3302. https://doi.org/10.1093/molbev/msx248 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Bandelt, H. J., Forster, P. & Röhl, A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16(1), 37–48 (1999).CAS 
    Article 

    Google Scholar 
    Leigh, J. W. & Bryant, D. POPART: Full-feature software for haplotype network construction. Methods Ecol. Evol. 6, 1110–1116. https://doi.org/10.1111/2041-210X.12410 (2015).Article 

    Google Scholar 
    Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595 (1989).CAS 
    Article 

    Google Scholar 
    Fu, Y. X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915–925 (1997).CAS 
    Article 

    Google Scholar 
    Austin, M. P. Continuum concept, ordination methods, and niche theory. Annu. Rev. Ecol. Syst. 16(1), 39–61. https://doi.org/10.1146/annurev.es.16.110185.000351 (1985).MathSciNet 
    Article 

    Google Scholar 
    Graham, A., Atkinson, P. & Danson, F. Spatial analysis for epidemiology. Acta Trop. 91(3), 219–225. https://doi.org/10.1016/j.actatropica.2004.05.001 (2004).CAS 
    Article 
    PubMed 

    Google Scholar 
    Phillips, S. J., Anderson, R. P. & Schapire, R. E. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190(3–4), 231–259. https://doi.org/10.1016/j.ecolmodel.2005.03.026 (2006).Article 

    Google Scholar 
    Guimarães, K. L. A., Rosso, J. J., Souza, M. F. B., de Astarloa, J. M. D. & Rodrigues, L. R. R. Integrative taxonomy reveals disjunct distribution and first record of Hoplias misionera (Characiformes: Erythrinidae) in the Amazon River basin: Morphological, DNA barcoding and cytogenetic considerations. Neotrop. Ichthyol. 19(2), e200110. https://doi.org/10.1590/1982-0224-2020-0110 (2021).Article 

    Google Scholar 
    Queiroz, L. J. et al. Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus. Mol. Phylogenet. Evol. 145, 106711. https://doi.org/10.1016/j.ympev.2019.106711 (2020).Article 

    Google Scholar 
    Phillips, J. D., Gillis, D. J. & Hanner, R. H. Incomplete estimates of genetic diversity within species: Implications for DNA barcoding. Ecol. Evol. https://doi.org/10.1002/ece3.4757 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Blaxter, M. L. The promise of a DNA taxonomy. Philos. Trans. R. Soc. B. 359(1444), 669–679. https://doi.org/10.1098/rstb.2003.1447 (2004).CAS 
    Article 

    Google Scholar 
    Nwani, C. D. et al. DNA barcoding discriminates freshwater fishes from southeastern Nigeria and provides river system-level phylogeographic resolution within some species. Mitochondrial DNA 22(1), 43–51. https://doi.org/10.3109/19401736.2010.536537 (2011).CAS 
    Article 
    PubMed 

    Google Scholar 
    Aguirre, W. E., Shervette, V. R., Navarrete, R., Calle, P. & Agorastos, S. Morphological and genetic divergence of Hoplias microlepis (Characiformes: Erythrinidae) in rivers and artificial impoundments of Western Ecuador. Copeia 2013(2), 312–323. https://doi.org/10.1643/ci-12-083 (2013).Article 

    Google Scholar 
    Pires, W. M. M., Barros, M. C. & Fraga, E. C. DNA Barcoding unveils cryptic lineages of Hoplias malabaricus from Northeastern Brazil. Braz. J. Biol. 81(4), 917–927. https://doi.org/10.1590/1519-6984.231598 (2020).Article 

    Google Scholar 
    Souza, F. H. S. et al. interspecific genetic differences and historical demography in South American Arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum). Genes 10(9), 693. https://doi.org/10.3390/genes10090693 (2019).CAS 
    Article 
    PubMed Central 

    Google Scholar 
    Torati, L. S. et al. Genetic diversity and structure in Arapaima gigas populations from Amazon and Araguaia-Tocantins river basins. BMC Genet. https://doi.org/10.1186/s12863-018-0711-y (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lovejoy, N. R. & Araujo, M. L. G. Molecular systematics, biogeography and population structure of Neotropical freshwater needlefishes of the genus Potamorrhaphis. Mol. Ecol. 9(3), 259–268. https://doi.org/10.1046/j.1365-294x.2000.00845.x (2000).CAS 
    Article 
    PubMed 

    Google Scholar 
    Mabesoone, J. M. Sedimentary Basins of Northeast Brazil (Federal University of Pernambuco, 1994).
    Google Scholar 
    Haffer, J. & Prance, G. T. Impulsos climáticos da evolução na Amazônia durante o Cenozóico: Sobre a teoria dos Refúgios da diferenciação biótica. Estudos Avançados USP 46, 175–208. https://doi.org/10.1590/S0103-40142002000300014 (2002).Article 

    Google Scholar 
    Riker, S. R. L., Lima, F. J. C., Motta, M. B. Evidências de glaciação Pleistocênica na Amazônia Brasileira. Anais do 14° Simpósio de Geologia da Amazônia, Sociedade Brasileira de Geologia 15–18 (2015).Albert, J. S., Val, P. & Hoorn, C. The changing course of the Amazon River in the Neogene: Center stage for Neotropical diversification. Neotrop. Ichthyol. 16(3), e180033. https://doi.org/10.1590/1982-0224-20180033 (2018).Article 

    Google Scholar 
    Lundberg, J. G. et al. The stage for Neotropical fish diversification: a history of tropical South American rivers. (eds. Malabarba, L. R., Reis, R. E., Vari, R. P., Lucena, Z. M., Lucena, C. A. S. Phylogeny and classification of Neotropical fishes). Edipucrs 13–48 (1998).Hubert, N. & Renno, J. F. Historical biogeography of South American freshwater fishes. J. Biogeogr. 33(8), 1414–1436. https://doi.org/10.1111/j.1365-2699.2006.01518.x (2006).Article 

    Google Scholar 
    Farias, I. P. & Hrbek, T. Patterns of diversification in the discus fishes (Symphysodon spp. Cichlidae) of the Amazon basin. Mol. Phylogenet. Evol. 49, 32–43. https://doi.org/10.1016/j.ympev.2008.05.033 (2008).CAS 
    Article 
    PubMed 

    Google Scholar 
    Tagliacollo, V. A., Bernt, M. J., Craig, J. M., Oliveira, C. & Albert, J. S. Model-based total evidence phylogeny of Neotropical electric knifefishes (Teleostei, Gymnoti-formes). Mol. Phylogenet. Evol. 95, 20–33. https://doi.org/10.1016/j.ympev.2015.11.007 (2015).Article 
    PubMed 

    Google Scholar 
    Hutchinson, G. E. Concluding remarks. Cold Spring Harbor Symposium. Quant. Biol. 22, 415–427 (1957).Article 

    Google Scholar 
    Wiens, J. J. & Graham, C. H. Niche conservatism: Inte-grating evolution, ecology, and conservation biology. Annu. Rev. Ecol. Evol. Syst. 36, 519–539 (2005).Article 

    Google Scholar 
    McNyset, K. M. Ecological niche conservatism in North American freshwater fishes. Biol. J. Lin. Soc. 96, 282–295 (2009).Article 

    Google Scholar 
    Silva, W. C., Marceniuk, A. P., Sales, J. B. L. & Araripe, J. Early pleistocene lineages of Bagre bagre (Linnaeus, 1766) (Siluriformes: Ariidae), from the Atlantic coast of South America, with insights into the demography and biogeography of the species. Neotrop. Ichthyol. https://doi.org/10.1590/1982-0224-20150184 (2016).Article 

    Google Scholar 
    Lemopoulos, A. & Covain, R. Biogeography of the freshwater fishes of the Guianas using a partitioned parsimony analysis of endemicity with reappraisal of ecoregional boundaries. Cladistics 35(2019), 106–124. https://doi.org/10.1111/cla.12341 (2018).Article 
    PubMed 

    Google Scholar 
    Hoorn, C. Marine incursions and the influence of Andean tectonics on the Miocene depositional history of northwestern Amazonia: Results of a palynostratigraphic study. Palaeogeogr. Palaeoclimatol. Palaeoecol. 105, 267–309. https://doi.org/10.1016/0031-0182(93)90087-Y (1993).Article 

    Google Scholar 
    Hoorn, C., Guerreiro, J. & Sarmiento, G. Andean tectonics as a cause for changing drainage patterns in Miocene Northern South America. Geology 23(3), 237–240. https://doi.org/10.1130/0091-7613(1995)023%3c0237:ATAACF%3e2.3.CO;2 (1995).ADS 
    Article 

    Google Scholar 
    Ribeiro, A. C. Tectonic history and the biogeography of the freshwater fishes from the coastal drainages of eastern Brazil: An example of faunal evolution associated with a divergent continental margin. Neotrop. Ichthyol. 4(2), 225–246. https://doi.org/10.1590/S1679-62252006000200009 (2006).Article 

    Google Scholar 
    Lovejoy, N. R., Albert, J. S. & Crampton, W. G. R. Miocene marine incursions and marine/freshwater transitions: Evidence from Neotropical fishes. J. S. Am. Earth Sci. 21(1–2), 5–13. https://doi.org/10.1016/j.jsames.2005.07.009 (2006).Article 

    Google Scholar  More

  • in

    Reactive nitrogen restructures and weakens microbial controls of soil N2O emissions

    Steffen, W. et al. Planetary boundaries: guiding human development on a changing planet. Science 347, 1259855 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    Kanter, D. R. et al. Nitrogen pollution policy beyond the farm. Nat. Food 1, 27–32 (2020).
    Google Scholar 
    Tian, H. Q. et al. A comprehensive quantification of global nitrous oxide sources and sinks. Nature 586, 248–256 (2020).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Thompson, R. L. et al. Acceleration of global N2O emissions seen from two decades of atmospheric inversion. Nat. Clim. Change 9, 993–998 (2019).CAS 

    Google Scholar 
    Isobe, K., Allison, S. D., Khalili, B., Martiny, A. C. & Martiny, J. B. H. Phylogenetic conservation of bacterial responses to soil nitrogen addition across continents. Nat. Commun. 10, 2499 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    Dai, Z. M. et al. Long-term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro-ecosystems across the globe. Glob. Change Biol. 24, 3452–3461 (2018).
    Google Scholar 
    Wallenstein, M., Myrold, D., Firestone, M. & Voytek, M. Environmental controls on denitrifying communities and denitrification rates: insights from molecular methods. Ecol. Appl 16, 2143–2152 (2006).PubMed 
    PubMed Central 

    Google Scholar 
    Scheer, C., Fuchs, K., Pelster, D. E. & Butterbach-Bahl, K. Estimating global terrestrial denitrification from measured N2O:(N2O + N2) product ratios. Curr. Opin. Enviro 47, 72–80 (2020).
    Google Scholar 
    Inatomi, M., Hajima, T. & Ito, A. Fraction of nitrous oxide production in nitrification and its effect on total soil emission: a meta-analysis and global-scale sensitivity analysis using a process-based model. PLoS One 14, e0219159 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Liang, D. & Robertson, G. P. Nitrification is a minor source of nitrous oxide (N2O) in an agricultural landscape and declines with increasing management intensity. Glob. Change Biol. 27, 5599–5613 (2021).
    Google Scholar 
    Zumft, W. G. Cell biology and molecular basis of denitrification. Microbiol Mol. Biol. R. 61, 533–616 (1997).CAS 

    Google Scholar 
    Graf, D. R. H., Jones, C. M. & Hallin, S. Intergenomic comparisons highlight modularity of the denitrification pathway and underpin the importance of community structure for N2O emissions. PLoS One 9, e114118 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    Lycus, P. et al. Phenotypic and genotypic richness of denitrifiers revealed by a novel isolation strategy. ISME J. 11, 2219–2232 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Roco, C. A., Bergaust, L. L., Bakken, L. R., Yavitt, J. B. & Shapleigh, J. P. Modularity of nitrogen-oxide reducing soil bacteria: linking phenotype to genotype. Environ. Microbiol 19, 2507–2519 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hallin, S., Philippot, L., Loffler, F. E., Sanford, R. A. & Jones, C. M. Genomics and ecology of novel N2O-reducing microorganisms. Trends Microbiol 26, 43–55 (2018).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Philippot, L., Andert, J., Jones, C. M., Bru, D. & Hallin, S. Importance of denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil. Glob. Change Biol. 17, 1497–1504 (2011).
    Google Scholar 
    Domeignoz-Horta, L. A. et al. Non-denitrifying nitrous oxide-reducing bacteria—an effective N2O sink in soil. Soil Biol. Biochem 103, 376–379 (2016).CAS 

    Google Scholar 
    Ramirez, K. S., Craine, J. M. & Fierer, N. Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Glob. Change Biol. 18, 1918–1927 (2012).
    Google Scholar 
    Leff, J. W. et al. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proc. Natl. Acad. Sci. USA 112, 10967–10972 (2015).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Shi, S. et al. The interconnected rhizosphere: high network complexity dominates rhizosphere assemblages. Ecol. Lett. 19, 926–936 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    Huang, R. L. et al. Plant-microbe networks in soil are weakened by century-long use of inorganic fertilizers. Micro. Biotechnol. 12, 1464–1475 (2019).CAS 

    Google Scholar 
    Tylianakis, J. M. & Morris, R. J. Ecological networks across environmental gradients. Annu. Rev. Ecol. Evol. S 48, 25–48 (2017).
    Google Scholar 
    Geisseler, D. & Scow, K. M. Long-term effects of mineral fertilizers on soil microorganisms—a review. Soil Biol. Biochem 75, 54–63 (2014).CAS 

    Google Scholar 
    Simek, M. & Cooper, J. The influence of soil pH on denitrification: progress towards the understanding of this interaction over the last 50 years. Eur. J. Soil Sci. 53, 345–354 (2002).CAS 

    Google Scholar 
    Klemedtsson, L., von Arnold, K., Weslien, P. & Gundersen, P. Soil CN ratio as a scalar parameter to predict nitrous oxide emissions. Glob. Change Biol. 11, 1142–1147 (2005).
    Google Scholar 
    Parn, J. et al. Nitrogen-rich organic soils under warm well-drained conditions are global nitrous oxide emission hotspots. Nat. Commun. 9, 1135 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    Maeda, K. et al. Relative contribution of nirK-and nirS-bacterial denitrifiers as well as fungal denitrifiers to nitrous oxide production from dairy manure compost. Environ. Sci. Technol. 51, 14083–14091 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Coyotzi, S. et al. Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity. Environ. Microbiol 19, 1189–1208 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Nadeau, S. A. et al. Metagenomic analysis reveals distinct patterns of denitrification gene abundance across soil moisture, nitrate gradients. Environ. Microbiol 21, 1255–1266 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Enwall, K., Throbäck, I. N., Stenberg, M., Söderström, M. & Hallin, S. Soil resources influence spatial patterns of denitrifying communities at scales compatible with land management. Appl Environ. Microbiol 76, 2243–2250 (2010).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jones, C. M. & Hallin, S. Ecological and evolutionary factors underlying global and local assembly of denitrifier communities. ISME J. 4, 633–641 (2010).PubMed 

    Google Scholar 
    Silverman, J. D., Washburne, A. D., Mukherjee, S. & David, L. A. A phylogenetic transform enhances analysis of compositional microbiota data. eLife 6, 5721 (2017).
    Google Scholar 
    Magurran, A. E. & Henderson, P. A. Explaining the excess of rare species in natural species abundance distributions. Nature 422, 714–716 (2003).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Dai, Z. et al. Long-term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteriain agro-ecosystems across the globe. Glob. Change Biol. 24, 3452–3461 (2018).
    Google Scholar 
    Fierer, N. et al. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J. 6, 1007–1017 (2011).PubMed 
    PubMed Central 

    Google Scholar 
    Naether, A. et al. Environmental factors affect acidobacterial communities below the subgroup level in grassland and forest soils. Appl Environ. Microbiol. 78, 7398–7406 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Navarrete, A. A. et al. Differential response of Acidobacteria subgroups to forest-to-pasture conversion and their biogeographic patterns in the Western Brazilian Amazon. Front. Microbiol. 6, 1443 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    Jones, C. M., Stres, B., Rosenquist, M. & Hallin, S. Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification. Mol. Biol. Evol. 25, 1955–1966 (2008).CAS 
    PubMed 

    Google Scholar 
    Kuypers, M. M. M., Marchant, H. K. & Kartal, B. The microbial nitrogen-cycling network. Nat. Rev. Microbiol 16, 263–274 (2018).CAS 
    PubMed 

    Google Scholar 
    Zhou, J., Deng, Y., Luo, F., He, Z. & Yang, Y. Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2. MBio 2, e00122-00111–e00122-00111 (2011).
    Google Scholar 
    Huang, R. et al. Plant–microbe networks in soil are weakened by century‐long use of inorganic fertilizers. Micro. Biotechnol. 12, 1464–1475 (2019).CAS 

    Google Scholar 
    Bar-Massada, A. Complex relationships between species niches and environmental heterogeneity affect species co-occurrence patterns in modelled and real communities. Proc. Royal Soc. B 282, 20150927 (2015).
    Google Scholar 
    Boccaletti, S., Latora, V., Moreno, Y., Chavez, M. & Hwang, D. U. Complex networks: structure and dynamics. Phys. Rep. 424, 175–308 (2006).
    Google Scholar 
    Yuan, M. M. et al. Climate warming enhances microbial network complexity and stability. Nat. Clim. Change 11, 343–U100 (2021).
    Google Scholar 
    Freilich, S. et al. The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res. 38, 3857–3868 (2010).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Samad, M. D. S. et al. Phylogenetic and functional potential links pH and N2O emissions in pasture soils. Sci. Rep. 6, 35990 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wang, Y. et al. Soil pH as the chief modifier for regional nitrous oxide emissions: new evidence and implications for global estimates and mitigation. Glob. Change Biol. 24, E617–E626 (2018).
    Google Scholar 
    Jones, C. M. et al. Recently identified microbial guild mediates soil N2O sink capacity. Nat. Clim. Change 4, 801–805 (2014).CAS 

    Google Scholar 
    Dorsch, P., Braker, G. & Bakken, L. R. Community-specific pH response of denitrification: experiments with cells extracted from organic soils. FEMS Microbiol Ecol. 79, 530–541 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Linton, N. F., Machado, P. V. F., Deen, B., Wagner-Riddle, C. & Dunfield, K. E. Long-term diverse rotation alters nitrogen cycling bacterial groups and nitrous oxide emissions after nitrogen fertilization. Soil Biol. Biochem 149, 107917 (2020).CAS 

    Google Scholar 
    Xu, X. Y. et al. nosZ clade II rather than clade I determine in situ N2O emissions with different fertilizer types under simulated climate change and its legacy. Soil Biol. Biochem 150, 107974 (2020).CAS 

    Google Scholar 
    Philippot, L. et al. Loss in microbial diversity affects nitrogen cycling in soil. ISME J. 7, 1609–1619 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Delgado-Baquerizo, M., Grinyer, J., Reich, P. B. & Singh, B. K. Relative importance of soil properties and microbial community for soil functionality: insights from a microbial swap experiment. Funct. Ecol. 30, 1862–1873 (2016).
    Google Scholar 
    Kottek, M., Grieser, J., Beck, C., Rudolf, B. & Rubel, F. World map of the Köppen–Geiger climate classification updated. Meteorol. Z. 15, 259–263 (2006).
    Google Scholar 
    Lu, C. Q. & Tian, H. Q. Global nitrogen and phosphorus fertilizer use for agriculture production in the past half century: shifted hot spots and nutrient imbalance. Earth Syst. Sci. Data 9, 181–192 (2017).
    Google Scholar 
    Van Meter, K. J., Basu, N. B., Veenstra, J. J. & Burras, C. L. The nitrogen legacy: emerging evidence of nitrogen accumulation in anthropogenic landscapes. Environ. Res. Lett. 11, 035014–035013 (2016).
    Google Scholar 
    Takahashi, S., Tomita, J., Nishioka, K., Hisada, T. & Nishijima, M. Development of a prokaryotic universal primer for simultaneous analysis of bacteria and archaea using next-generation sequencing. PLoS One 9, e105592 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: a fast and accurate illumina paired-end reAd mergeR. Bioinformatics 30, 614–620 (2014).CAS 
    PubMed 

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

    Google Scholar 
    Pruesse, E., Peplies, J. & Glöckner, F. O. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823–1829 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ludwig, W. et al. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371 (2004).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Oksanen J. vegan: Community Ecology Package version 1.8–5 (Semantic Scholar, 2007).McMurdie, P. J. & Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8, e61217 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kembel, S. W. et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26, 1463–1464 (2010).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Palarea-Albaladejo, J. & Martin-Fernandez, J. A. zCompositions—R package for multivariate imputation of left-censored data under a compositional approach. Chemom. Intell. Lab 143, 85–96 (2015).CAS 

    Google Scholar 
    Kuznetsova, A., Brockhoff, P. B. & Christensen, R. H. B. lmerTest package: tests in linear mixed effects models. J. Stat. Softw. 82, 1–26 (2017).
    Google Scholar 
    Csardi, G. & Nepusz, T. The igraph software package for complex network research. Int. J. Complex Syst. 1695, 1–9 (2006).
    Google Scholar 
    Menzel, U. RMThreshold: Signal-Noise Separation in Random Matrices by Using Eigenvalue. R Package Version 1.1 edn. https://rdrr.io/cran/RMThreshold/man/RMThreshold-package.html (2016).Gu, Z. G., Gu, L., Eils, R., Schlesner, M. & Brors, B. circlize implements and enhances circular visualization in R. Bioinformatics 30, 2811–2812 (2014).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Goenawan, I. H., Bryan, K. & Lynn, D. J. DyNet: visualization and analysis of dynamic molecular interaction networks. Bioinformatics 32, 2713–2715 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jones, C. M. & Hallin, S. Geospatial variation in co-occurrence networks of nitrifying microbial guilds. Mol. Ecol. 28, 293–306 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Newman, M. E. J. & Girvan, M. Finding and evaluating community structure in networks. Phys. Rev. E 69, 268–215 (2004).
    Google Scholar 
    Deng, Y. et al. Molecular ecological network analyses. BMC Bioinform. 13, 113 (2012).
    Google Scholar 
    Elith, J., Leathwick, J. R. & Hastie, T. A working guide to boosted regression trees. J. Anim. Ecol. 77, 802–813 (2008).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Dormann, C. F. et al. Collinearity: a review of methods to deal with it and a simulation study evaluating their performance. Ecography 36, 27–46 (2012).
    Google Scholar 
    Kuhn, M. Building predictive models in R using the caret package. J. Stat. Softw. 28, 1–26 (2008).
    Google Scholar 
    Greenwell, B. M. & Boehmke, B. C. Variable importance plots-an introduction to the vip package. R. J. 12, 343–366 (2020).
    Google Scholar 
    Molnar, C. iml: An R package for Interpretable. Mach. Learn. J. Open Source Softw. 3, 786 (2018).
    Google Scholar  More