Ecology

Seigel, R. A. & Ford, N. B. Reproductive ecology in Snakes: Ecology and Evolutionary Biology (eds. Seigel, R. A., Collins, J. T. &. Novak, S. S.). 210–252. (MacMillan Publishing, 1987).Kremen, C., Merenlender, A. M. & Murphy, D. D. Ecological monitoring: A vital need for integrated conservation and development programs in the tropics. Conserv. Biol. 8, 388–397 (1994).
Google Scholar 
Shine, R. & Bonnet, X. Snakes: A new ‘model organism’ in ecological research?. Trends Ecol. Evol. 15, 221–222 (2000).CAS 
PubMed 

Google Scholar 
Vilela, B., Villalobos, F., Rodríguez, M. Á. & Terribile, L. C. Body size, extinction risk and knowledge bias in New World snakes. PLoS ONE 9, e113429 (2014).ADS 
PubMed 
PubMed Central 

Google Scholar 
Mathies, T. Reproductive cycles of tropical snakes. in Reproductive Biology and Phylogeny of Snakes (eds. Sever, D. & Aldridge, R.). 523–562. (CRC Press, 2016).Shine, R., Harlow, P. S. & Keogh, J. S. The allometry of life-history traits: Insights from a study of giant snakes (Python reticulatus). J. Zool. 244, 405–414 (1998).
Google Scholar 
Natusch, D. J., Lyons, J. A., Riyanto, A., Khadiejah, S. & Shine, R. Detailed biological data are informative, but robust trends are needed for informing sustainability of wildlife harvesting: A case study of reptile offtake in Southeast Asia. Biol. Conserv. 233, 83–92 (2019).
Google Scholar 
Freeman, A. & Freeman, A. Habitat use in a large rainforest python (Morelia kinghorni) in the wet tropics of north Queensland, Australia. Herpetol. Conserv. Biol. 4, 252–260 (2009).
Google Scholar 
Smith, S. N., Jones, M. D., Marshall, B. M. & Strine, C. T. Native Burmese pythons exhibit site fidelity and preference for aquatic habitats in an agricultural mosaic. Sci. Rep. 11, 7014 (2021).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kramer, D. L. & Chapman, M. R. Implications of fish home range size and relocation for marine reserve function. Environ. Biol. Fishes 55, 65–79 (1999).
Google Scholar 
Spong, G. Space use in lions, Panthera leo, in the Selous Game Reserve: Social and ecological factors. Behav. Ecol. Sociobiol. 52, 303–307 (2002).
Google Scholar 
Webb, J. K. & Shine, R. A field study of spatial ecology and movements of a threatened snake species, Hoplocephalus bungaroides. Biol. Conserv. 82, 203–217 (1997).
Google Scholar 
Fearn, S. & Sambono, J. A reliable size record for the scrub python Morelia amethistina (Serpentes: Pythonidae) in north east Queensland. Herpetofauna 30, 2–6 (2000).
Google Scholar 
Grow, D., Wheeler, S. & Clark, B. Reproduction of the Amethystine python Python amethystinus kinghorni at the Oklahoma City Zoo. Int. Zoo Year. 27, 241–244 (1988).
Google Scholar 
Feldman, A. & Meiri, S. Length–mass allometry in snakes. Biol. J. Linn. Soc. 108, 161–172 (2013).
Google Scholar 
Harvey, M. B., Barker, D. G., Ammerman, L. K. & Chippindale, P. T. Systematics of pythons of the Morelia amethistina complex (Serpentes: Boidae) with the description of three new species. Herpetol. Monogr. 14, 139–185 (2000).
Google Scholar 
Fearn, S., Schwarzkopf, L. & Shine, R. Giant snakes in tropical forests: A field study of the Australian scrub python, Morelia kinghorni. Wildl. Res. 32, 193–201 (2005).
Google Scholar 
Natusch, D. J. D., Lyons, J. A. & Shine, R. Rainforest pythons flexibly adjust foraging ecology to exploit seasonal concentrations of prey. J. Zool. 313, 114–123 (2021).
Google Scholar 
Martin, R. W. Field observation of predation on Bennett’s tree-kangaroo (Dendrolagus bennettianus) by an amethystine python (Morelia amethistina). Herpetol. Rev. 26, 74–75 (1995).
Google Scholar 
Natusch, D., Lyons, J., Mears, L. A. & Shine, R. Biting off more than you can chew: Attempted predation on a human by a giant snake (Simalia amethistina). Austral. Ecol. 46, 159–162 (2021).
Google Scholar 
Neldner, V. J. & Clarkson, J. R. Vegetation of Cape York Peninsula. (Department of Environment and Heritage, 1995).Bureau of Meteorology. Climate Data Online. http://www.bom.gov.au/climate/data/. Accessed 17 July 2020 (2020).Whitaker, P. B. & Shine, R. A radiotelemetric study of movements and shelter-site selection by free-ranging brownsnakes (Pseudonaja textilis, Elapidae). Herpetol. Monogr. 17, 130–144 (2003).
Google Scholar 
Harris, S. et al. Home-range analysis using radio-tracking data–A review of problems and techniques particularly as applied to the study of mammals. Mamm. Rev. 20, 97–123 (1990).
Google Scholar 
Fearn, S. & Sambono, J. Some ambush predation postures of the Scrub Python Morelia amethistina (Serpentes: Pythonidae) in north east Queensland. Herpetofauna 30, 39–44 (2000).
Google Scholar 
Caswell, H. Theory and models in ecology: A different perspective. Ecol. Model. 43, 33–44 (1988).
Google Scholar 
Silva, I., Crane, M., Marshall, B. M. & Strine, C. T. Reptiles on the wrong track? Moving beyond traditional estimators with dynamic Brownian bridge movement models. Move. Ecol. 8, 43 (2020).
Google Scholar 
Row, J. R. & Blouin-Demers, G. Kernels are not accurate estimators of home-range size for herpetofauna. Copeia 2006, 797–802 (2006).
Google Scholar 
Newman, P., Dwyer, R. G., Belbin, L. & Campbell, H. A. ZoaTrack—An online tool to analyse and share animal location data: User engagement and future perspectives. Aust. Zool. 41, 12–18. https://zoatrack.org/toolkit/doi (2020).Pearson, D. J. & Shine, R. Expulsion of interperitoneally-implanted radiotransmitters by Australian pythons. Herpetol. Rev. 33, 261–263 (2002).
Google Scholar 
Hale, V. L. et al. Radio transmitter implantation and movement in the wild timber rattlesnake (Crotalus horridus). J. Wildl. Dis. 53, 591–595 (2017).PubMed 

Google Scholar 
Martin, A. E., Jørgensen, D. & Gates, C. C. Costs and benefits of straight versus tortuous migration paths for Prairie Rattlesnakes (Crotalus viridis viridis) in seminatural and human-dominated landscapes. Can. J. Zool. 95, 921–928 (2017).
Google Scholar 
Glaudas, X., Rice, S. E., Clark, R. W. & Alexander, G. J. Male energy reserves, mate-searching activities, and reproductive success: Alternative resource use strategies in a presumed capital breeder. Oecologia 194, 415–425 (2020).ADS 
PubMed 

Google Scholar 
Glaudas, X., Rice, S. E., Clark, R. W. & Alexander, G. J. The intensity of sexual selection, body size and reproductive success in a mating system with male–male combat: is bigger better?. Oikos 129, 998–1011 (2020).
Google Scholar 
Gannon, V. P. J. & Secoy, D. M. Seasonal and daily activity patterns in a Canadian population of the prairie rattlesnake, Crotalus viridus viridis. Can. J. Zool. 63, 86–91 (1985).
Google Scholar 
Heard, G. W., Black, D. & Robertson, P. Habitat use by the inland carpet python (Morelia spilota metcalfei: Pythonidae): Seasonal relationships with habitat structure and prey distribution in a rural landscape. Austral. Ecol. 29, 446–460 (2004).
Google Scholar 
Madsen, T. & Shine, R. Seasonal migration of predators and prey—A study of pythons and rats in tropical Australia. Ecology 77, 149–156 (1996).
Google Scholar 
Graves, B. M. & Duvall, D. Reproduction, rookery use, and thermoregulation in free-ranging, pregnant Crotalus v. viridis. J. Herpetol. 27, 33–41 (1993).
Google Scholar 
Chiaraviglio, M. The effects of reproductive condition on thermoregulation in the Argentina boa constrictor (Boa constrictor occidentalis) (Boidae). Herpetol. Monogr. 20, 172–177 (2006).
Google Scholar 
Smith, C. F., Schuett, G. W., Earley, R. L. & Schwenk, K. The spatial and reproductive ecology of the copperhead (Agkistrodon contortrix) at the northeastern extreme of its range. Herpetol. Monogr. 23, 45–73 (2009).
Google Scholar 
Shine, R. & Fitzgerald, M. Large snakes in a mosaic rural landscape: The ecology of carpet pythons Morelia spilota (Serpentes: Pythonidae) in coastal eastern Australia. Biol. Conserv. 76, 113–122 (1996).
Google Scholar 
Heard, G. W. et al. Canid predation: A potentially significant threat to relic populations of the Inland Carpet Python ‘Morelia spilota metcalfei’ (Pythonidae) in Victoria. Vic. Nat. 123, 68–74 (2006).
Google Scholar 
Downes, S. & Shine, R. Sedentary snakes and gullible geckos: Predator–prey coevolution in nocturnal rock-dwelling reptiles. Anim. Behav. 55, 1373–1385 (1998).CAS 
PubMed 

Google Scholar 
Miller, A. K., Maritz, B., McKay, S., Glaudas, X. & Alexander, G. J. An ambusher’s arsenal: chemical crypsis in the puff adder (Bitis arietans). Proc. R. Soc. B 282, 20152182 (2015).PubMed 
PubMed Central 

Google Scholar 
Maritz, B. & Alexander, G. J. Dwarfs on the move: Spatial ecology of the world’s smallest viper, Bitis schneideri. Copeia 2012, 115–120 (2012).
Google Scholar 
Stirrat, S. C. Seasonal changes in home-range area and habitat use by the agile wallaby (Macropus agilis). Wildl. Res. 30, 593–600 (2003).
Google Scholar 
Ayers, D. Y. & Shine, R. Thermal influences on foraging ability: Body size, posture and cooling rate of an ambush predator, the python Morelia spilota. Funct. Ecol. 11, 342–347 (1997).
Google Scholar 
Pearson, D., Shine, R. & Williams, A. Spatial ecology of a threatened python (Morelia spilota imbricata) and the effects of anthropogenic habitat change. Austral. Ecol. 30, 261–274 (2005).
Google Scholar 
Freeman, A. A study in power and grace: The amethystine python. Wildl. Aust. 53, 27–29 (2016).
Google Scholar 
Silva, I., Crane, M., Suwanwaree, P., Strine, C. & Goode, M. Using dynamic Brownian bridge movement models to identify home range size and movement patterns in king cobras. PLoS ONE 13, e0203449 (2018).PubMed 
PubMed Central 

Google Scholar 
Marshall, B. M. et al. Space fit for a king: Spatial ecology of king cobras (Ophiophagus hannah) in Sakaerat Biosphere Reserve, Northeastern Thailand. Amphibia-Reptilia 40, 163–178 (2019).
Google Scholar 
Udyawer, V., Simpfendorfer, C. A., Heupel, M. R. & Clark, T. D. Temporal and spatial activity-associated energy partitioning in free-swimming sea snakes. Funct. Ecol. 31, 1739–1749 (2017).
Google Scholar 
Smaniotto, N. P., Moreira, L. F., Rivas, J. A. & Strüssmann, C. Home range size, movement, and habitat use of yellow anacondas (Eunectes notaeus). Salamandra 56, 159–167 (2020).
Google Scholar 
Low, M. R. Rescue, rehabilitation and release of reticulated pythons in Singapore. in Global Reintroduction Perspectives: 2018. Case Studies from Around the Globe (ed. Soorae, P. S.) 78–81 (IUCN/SSC Reintroduction Specialist Group, 2018).Alexander, G. J. & Maritz, B. Sampling interval affects the estimation of movement parameters in four species of African snakes. J. Zool. 297, 309–318 (2015).
Google Scholar 
Smith, B. J. et al. Betrayal: Radio-tagged Burmese pythons reveal locations of conspecifics in Everglades National Park. Biol. Invasions 18, 3239–3250 (2016).
Google Scholar  More

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

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

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

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

Download PDF

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

Related Articles

The ancient whale from my Egyptian home town

A partridge in hand on the Spanish steppe

‘I have to use a torch and watch my step’: netting seabirds at night

Subjects

Careers

Ecology

Environmental sciences

Latest on:

Careers

Afghanistan’s girls’ schools can — and must — stay open. There is no alternative
Editorial 28 MAR 22

The marine biologist whose photography pastime became a profession
Career Column 25 MAR 22

How the career path to principal investigator is narrowing
Career News 24 MAR 22

Ecology

The marine biologist whose photography pastime became a profession
Career Column 25 MAR 22

Subaqueous foraging among carnivorous dinosaurs
Article 23 MAR 22

Where are Earth’s oldest trees? Far from prying eyes
Research Highlight 22 MAR 22

Environmental sciences

The size of the land carbon sink in China
Matters Arising 16 MAR 22

Are there limits to economic growth? It’s time to call time on a 50-year argument
Editorial 16 MAR 22

Landmark treaty on plastic pollution must put scientific evidence front and centre
Editorial 08 MAR 22

Jobs

Postdoctoral position in decision-making in aging and Alzheimer’s disease

University of Minnesota (UMN)
Minneapolis, MN, United States

Postdoctoral Fellowship (Translational Cardiovascular Medicine)

University of Alberta (U of A)
Edmonton, Alberta, Canada

Higher Scientific Officer – Protein production, purification and biophysics

Institute of Cancer Research (ICR)
London, United Kingdom

POSTDOCTORAL FELLOWSHIPS on Neurobiology of Overgrowth syndromes

Inserm-Université Paris Cité
Paris, France More

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

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