Philippa Kaur

(ECHA), E. C. A. Know more about the effects of the chemicals we use in Europe (ECHA/PR/16/01). https://echa.europa.eu/de/-/know-more-about-the-effects-of-the-chemicals-we-use-in-europe (2016).Liu, W. J., Nie, H. X., Liang, D. P., Bai, Y. & Liu, H. W. Phospholipid imaging of zebrafish exposed to fipronil using atmospheric pressure matrix-assisted laser desorption ionization mass spectrometry. Talanta https://doi.org/10.1016/j.talanta.2019.120357 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Sparvero, L. J. et al. Mapping of phospholipids by MALDI imaging (MALDI-MSI): Realities and expectations. Chem. Phys. Lipid. 165, 545–562. https://doi.org/10.1016/j.chemphyslip.2012.06.001 (2012).CAS 
Article 

Google Scholar 
Koizumi, S. et al. Imaging mass spectrometry revealed the production of lyso-phosphatidylcholine in the injured ischemic rat brain. Neuroscience 168(1), 219–225. https://doi.org/10.1016/j.neuroscience.2010.03.056 (2010).CAS 
Article 
PubMed 

Google Scholar 
Hankin, J. A. et al. MALDI mass spectrometric imaging of lipids in rat brain injury models. J. Am. Soc. Mass Spectrom. 22(6), 1014–1021. https://doi.org/10.1007/s13361-011-0122-z (2011).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Zhao, C. et al. MALDI-MS imaging reveals asymmetric spatial distribution of lipid metabolites from bisphenol s-induced nephrotoxicity. Anal. Chem. 90(5), 3196–3204. https://doi.org/10.1021/acs.analchem.7b04540 (2018).CAS 
Article 
PubMed 

Google Scholar 
Barbacci, D. C. et al. Mass spectrometric imaging of ceramide biomarkers tracks therapeutic response in traumatic brain injury. ACS Chem. Neurosci. 8(10), 2266–2274. https://doi.org/10.1021/acschemneuro.7b00189 (2017).CAS 
Article 
PubMed 

Google Scholar 
Rompp, A. et al. Histology by mass spectrometry: Label-free tissue characterization obtained from high-accuracy bioanalytical imaging. Angew. Chem. Int. Ed. 49, 3834–3838. https://doi.org/10.1002/anie.200905559 (2010).CAS 
Article 

Google Scholar 
Zemski Berry, K. A. et al. MALDI imaging of lipid biochemistry in tissues by mass spectrometry. Chem. Rev. 111, 6491–6512. https://doi.org/10.1021/cr200280p (2011).CAS 
Article 

Google Scholar 
Cornett, D. S., Reyzer, M. L., Chaurand, P. & Caprioli, R. M. MALDI imaging mass spectrometry: Molecular snapshots of biochemical systems. Nat. Methods 4, 828–833. https://doi.org/10.1038/nmeth1094 (2007).CAS 
Article 
PubMed 

Google Scholar 
Römpp, A. & Spengler, B. Mass spectrometry imaging with high resolution in mass and space. Histochem. Cell Biol. 139, 759–783. https://doi.org/10.1007/s00418-013-1097-6 (2013).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Monroe, E. B. et al. SIMS and MALDI MS imaging of the spinal cord. Proteomics 8(18), 3746-3754. https://doi.org/10.1002/pmic.200800127 (2008).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Chaurand, P., Cornett, D. S., Angel, P. M. & Caprioli, R. M. From whole-body sections down to cellular level, multiscale imaging of phospholipids by MALDI mass spectrometry. Mol. Cell. Proteom. https://doi.org/10.1074/mcp.O110.004259 (2011).Article 

Google Scholar 
Lee, H.-B. & Peart, T. E. Determination of bisphenol A in sewage effluent and sludge by solid-phase and supercritical fluid extraction and gas chromatography/mass spectrometry. J. AOAC Int. 83, 290–298. https://doi.org/10.1093/jaoac/83.2.290 (2000).CAS 
Article 
PubMed 

Google Scholar 
Desbenoit, N., Walch, A., Spengler, B., Brunelle, A. & Römpp, A. Correlative mass spectrometry imaging, applying time-of-flight secondary ion mass spectrometry and atmospheric pressure matrix-assisted laser desorption/ionization to a single tissue section. Rapid Commun. Mass Spectrometry 32, 159–166. https://doi.org/10.1002/rcm.8022 (2018).ADS 
CAS 
Article 

Google Scholar 
Meding, S. et al. Tumor classification of six common cancer types based on proteomic profiling by MALDI imaging. J. Proteome Res. 11, 1996–2003. https://doi.org/10.1021/pr200784p (2012).CAS 
Article 
PubMed 

Google Scholar 
Ritschar, S. et al. Classification of target tissues of Eisenia fetida using sequential multimodal chemical analysis and machine learning. Histochem. Cell Biol. https://doi.org/10.1007/s00418-021-02037-1 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Altshuler, I. et al. An integrated multi-disciplinary approach for studying multiple stressors in freshwater ecosystems: Daphnia as a model organism. Integr. Comp. Biol. 51(4), 623–633. https://doi.org/10.1093/icb/icr103 (2011).CAS 
Article 
PubMed 

Google Scholar 
Bambino, K. & Chu, J. in Zebrafish at the Interface of Development and Disease Research Vol. 124 Current Topics in Developmental Biology (ed K. C. Sadler) 331–367 (2017).Seda, J. & Petrusek, A. Daphnia as a model organism in limnology and aquatic biology: Introductory remarks. J. Limnol. 70, 337–344. https://doi.org/10.4081/jlimnol.2011.337 (2011).Article 

Google Scholar 
de Souza Anselmo, C., Sardela, V. F., de Sousa, V. P. & Pereira, H. M. G. Zebrafish (Danio rerio): A valuable tool for predicting the metabolism of xenobiotics in humans? Comp. Biochem. Physiol. Part C: Toxicol. Pharmacol. 212, 34–46. https://doi.org/10.1016/j.cbpc.2018.06.005 (2018).CAS 
Article 

Google Scholar 
Panula, P. et al. The comparative neuroanatomy and neurochemistry of zebrafish CNS systems of relevance to human neuropsychiatric diseases. Neurobiol. Dis. 40, 46–57. https://doi.org/10.1016/j.nbd.2010.05.010 (2010).CAS 
Article 
PubMed 

Google Scholar 
Korn, H. & Faber, D. S. The Mauthner cell half a century later: A neurobiological model for decision-making?. Neuron 47, 13–28. https://doi.org/10.1016/j.neuron.2005.05.019 (2005).CAS 
Article 
PubMed 

Google Scholar 
Schirmer, E., Schuster, S. & Machnik, P. Bisphenols exert detrimental effects on neuronal signaling in mature vertebrate brains. Commun. Biol. https://doi.org/10.1038/s42003-021-01966-w (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Flößner, D. Book review: Cladocera: The genus Daphnia (including Daphniopsis). Int. Rev. Hydrobiol. 90, 637. https://doi.org/10.1002/iroh.200590003 (2005).Article 

Google Scholar 
OECD. Test No. 211: Daphnia magna Reproduction Test. (2012).Muyssen, B. T. A. & Janssen, C. R. Multigeneration zinc acclimation and tolerance in Daphnia magna: Implications for water-quality guidelines and ecological risk assessment. Environ. Toxicol. Chem. 20, 2053–2060. https://doi.org/10.1002/etc.5620200926 (2001).CAS 
Article 
PubMed 

Google Scholar 
Blewett, T. A. et al. Sublethal and reproductive effects of acute and chronic exposure to flowback and produced water from hydraulic fracturing on the water flea Daphnia magna. Environ. Sci. Technol. 51, 3032–3039. https://doi.org/10.1021/acs.est.6b05179 (2017).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Yang, J. H., Kim, H. J., Lee, S. M., Kim, B. M. & Seo, Y. R. Cadmium-induced biomarkers discovery and comparative network analysis in Daphnia magna. Mol. Cell. Toxicol. 13, 327–336. https://doi.org/10.1007/s13273-017-0036-3 (2017).CAS 
Article 

Google Scholar 
Ferain, A. et al. Body lipid composition modulates acute cadmium toxicity in Daphnia magna adults and juveniles. Chemosphere 205, 328–338. https://doi.org/10.1016/j.chemosphere.2018.04.091 (2018).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Ritschar, S., Narayana, V. K. B., Rabus, M. & Laforsch, C. Uncovering the chemistry behind inducible morphological defences in the crustacean Daphniamagna via micro-Raman spectroscopy. Sci. Rep. 10(1), 22408. https://doi.org/10.1038/s41598-020-79755-4 (2020).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Machnik, P., Schirmer, E., Glück, L. & Schuster, S. Recordings in an integrating central neuron provide a quick way for identifying appropriate anaesthetic use in fish. Sci. Rep. 8, 17541. https://doi.org/10.1038/s41598-018-36130-8 (2018).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Luzio, A. et al. Copper induced upregulation of apoptosis related genes in zebrafish (Danio rerio) gill. Aquat. Toxicol. 128, 183–189. https://doi.org/10.1016/j.aquatox.2012.12.018 (2013).CAS 
Article 
PubMed 

Google Scholar 
Macirella, R. & Brunelli, E. Morphofunctional alterations in zebrafish (Danio rerio) gills after exposure to mercury chloride. Int. J. Mol. Sci. https://doi.org/10.3390/ijms18040824 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Mansouri, B. & Johari, S. A. Effects of short-term exposure to sublethal concentrations of silver nanoparticles on histopathology and electron microscope ultrastructure of zebrafish (Danio rerio) gills. IJT 10, 15–20. https://doi.org/10.32598/IJT.10.1.60.4 (2016).CAS 
Article 

Google Scholar 
Perez, C. J., Tata, A., de Campos, M. L., Peng, C. & Ifa, D. R. Monitoring toxic ionic liquids in zebrafish (Danio rerio) with desorption electrospray ionization mass spectrometry imaging (DESI-MSI). J. Am. Soc. Mass Spectrom. 28, 1136–1148. https://doi.org/10.1007/s13361-016-1515-9 (2017).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Stutts, W. L. et al. Methods for cryosectioning and mass spectrometry imaging of whole-body zebrafish. J. Am. Soc. Mass Spectrom. 31, 768–772. https://doi.org/10.1021/jasms.9b00097 (2020).CAS 
Article 
PubMed 

Google Scholar 
Purves, D. & Williams, S. M. Neuroscience. 2nd edition. Vol. Chapter 11, Vision: The Eye (Sinauer Associates, 2001).
Google Scholar 
Strungaru, S. A. et al. Toxicity and chronic effects of deltamethrin exposure on zebrafish (Danio rerio) as a reference model for freshwater fish community. Ecotoxicol. Environ. Saf. 171, 854–862. https://doi.org/10.1016/j.ecoenv.2019.01.057 (2019).CAS 
Article 
PubMed 

Google Scholar 
Mishra, A. & Devi, Y. Histopathological alterations in the brain (optic tectum) of the fresh water teleost Channa punctatus in response to acute and subchronic exposure to the pesticide Chlorpyrifos. Acta Histochem. 116, 176–181. https://doi.org/10.1016/j.acthis.2013.07.001 (2014).CAS 
Article 
PubMed 

Google Scholar 
Jia, W., Mao, L., Zhang, L., Zhang, Y. & Jiang, H. Effects of two strobilurins (azoxystrobin and picoxystrobin) on embryonic development and enzyme activities in juveniles and adult fish livers of zebrafish (Danio rerio). Chemosphere 207, 573–580. https://doi.org/10.1016/j.chemosphere.2018.05.138 (2018).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Seyoum, A., Pradhan, A., Jass, J. & Olsson, P. E. Perfluorinated alkyl substances impede growth, reproduction, lipid metabolism and lifespan in Daphnia magna. Sci. Total Environ. https://doi.org/10.1016/j.scitotenv.2020.139682 (2020).Article 
PubMed 

Google Scholar 
Scanlan, L. D. et al. Gene transcription, metabolite and lipid profiling in eco-indicator Daphnia magna indicate diverse mechanisms of toxicity by legacy and emerging flame-retardants. Environ. Sci. Technol. 49, 7400–7410. https://doi.org/10.1021/acs.est.5b00977 (2015).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Heinlaan, M. et al. Changes in the Daphnia magna midgut upon ingestion of copper oxide nanoparticles: A transmission electron microscopy study. Water Res. 45, 179–190. https://doi.org/10.1016/j.watres.2010.08.026 (2011).CAS 
Article 
PubMed 

Google Scholar 
Abe, T., Saito, H., Niikura, Y., Shigeoka, T. & Nakano, Y. Embryonic development assay with Daphnia magna: Application to toxicity of aniline derivatives. Chemosphere 45, 487–495. https://doi.org/10.1016/s0045-6535(01)00049-2 (2001).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Sengupta, N., Gerard, P. D. & Baldwin, W. S. Perturbations in polar lipids, starvation survival and reproduction following exposure to unsaturated fatty acids or environmental toxicants in Daphnia magna. Chemosphere 144, 2302–2311. https://doi.org/10.1016/j.chemosphere.2015.11.015 (2016).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Huber, K. et al. Approaching cellular resolution and reliable identification in mass spectrometry imaging of tryptic peptides. Anal. Bioanal. Chem. 410, 5825–5837. https://doi.org/10.1007/s00216-018-1199-z (2018).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
White, R. M. et al. Transparent adult zebrafish as a tool for in vivo transplantation analysis. Cell Stem Cell 2, 183–189. https://doi.org/10.1016/j.stem.2007.11.002 (2008).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Nagayoshi, S. et al. Insertional mutagenesis by the Tol2 transposon-mediated enhancer trap approach generated mutations in two developmental genes: tcf7 and synembryn-like. Development 135, 159–169. https://doi.org/10.1242/dev.009050 (2008).CAS 
Article 
PubMed 

Google Scholar 
Perciedu Sert, N. et al. The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research. Exp. Physiol. 105, 1459–1466. https://doi.org/10.1113/EP088870 (2020).Article 

Google Scholar 
Elendt, B. P. Selenium deficiency in Crustacea. Protoplasma 154, 25–33. https://doi.org/10.1007/BF01349532 (1990).CAS 
Article 

Google Scholar 
Sud, M. et al. LMSD: LIPID MAPS structure database. Nucleic Acids Res. 35, D527–D532. https://doi.org/10.1093/nar/gkl838 (2007).CAS 
Article 
PubMed 

Google Scholar 
Race, A. M., Styles, I. B. & Bunch, J. Inclusive sharing of mass spectrometry imaging data requires a converter for all. J. Proteom. 75, 5111–5112. https://doi.org/10.1016/j.jprot.2012.05.035 (2012).CAS 
Article 

Google Scholar 
Robichaud, G., Garrard, K. P., Barry, J. A. & Muddiman, D. C. MSiReader: An open-source interface to view and analyze high resolving power MS imaging files on Matlab platform. J. Am. Soc. Mass Spectrom. 24, 718–721. https://doi.org/10.1007/s13361-013-0607-z (2013).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar  More

Ryther, J. H. Photosynthesis and fish production in the sea. Sci. (80-.) 166, 72–76 (1969).ADS 
CAS 
Article 

Google Scholar 
Follows, M. J., Dutkiewicz, S., Grant, S. & Chisholm, S. W. Emergent biogeography of microbial communities in a model ocean. Sci. (80-.). 315, 1843–1846 (2007).ADS 
CAS 
Article 

Google Scholar 
Edwards, K. F., Litchman, E. & Klausmeier, C. A. Functional traits explain phytoplankton community structure and seasonal dynamics in a marine ecosystem. Ecol. Lett. 16, 56–63 (2013).PubMed 
Article 

Google Scholar 
Nemergut, D. R. et al. Patterns and processes of microbial community assembly. Microbiol. Mol. Biol. Rev. 77, 342–356 (2013).PubMed 
PubMed Central 
Article 

Google Scholar 
Villarino, E. et al. Large-scale ocean connectivity and planktonic body size. Nat. Commun. 9, 142 (2018).Collins, S., Rost, B. & Rynearson, T. A. Evolutionary potential of marine phytoplankton under ocean acidification. Evol. Appl. 7, 140–155 (2014).CAS 
PubMed 
Article 

Google Scholar 
Rusch, D. B. et al. The Sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLOS Biol. 5, e77 (2007).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
de Vargas, C. et al. Eukaryotic plankton diversity in the sunlit ocean. Sci. (80-.). 348, 1261605–1/11 (2015).Sunagawa, S. et al. Structure and function of the global ocean microbiome. Sci. (80-.) 348, 1–10 (2015).Article 
CAS 

Google Scholar 
Fuhrman, J. A. et al. A latitudinal diversity gradient in planktonic marine bacteria. Proc. Natl Acad. Sci. 105, 7774–7778 (2008).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Righetti, D., Vogt, M., Gruber, N., Psomas, A. & Zimmermann, N. E. Global pattern of phytoplankton diversity driven by temperature and environmental variability. Sci. Adv. 5, 1–11 (2019).Article 

Google Scholar 
Cermeño, P. et al. The role of nutricline depth in regulating the ocean carbon cycle. PNAS 105, 20344–20349 (2008).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Barton, A. D., Dutkiewicz, S., Flierl, G., Bragg, J. & Follows, M. J. Patterns of diversity in marine phytoplankton. Sci. (80-.) 327, 1509–1511 (2010).ADS 
CAS 
Article 

Google Scholar 
Mantyla, A. W., Venrick, E. L. & Hayward, T. L. Primary production and chlorophyll relationships, derived from ten year of CalCOFI measurements. Calif. Cooperative Ocean. Fish. Investig. Rep. 36, 159–166 (1995).
Google Scholar 
Hayward, T. L. & Venrick, E. L. Nearsurface pattern in the California Current: Coupling between physical and biological structure. Deep. Res. Part II Top. Stud. Oceanogr. https://doi.org/10.1016/S0967-0645(98)80010-6 (1998).Article 

Google Scholar 
Venrick, E. L. Floral patterns in the California Current: The coastal-offshore boundary zone. J. Mar. Res. 67, 89–111 (2009).Article 

Google Scholar 
Powell, J. R. & Ohman, M. D. Covariability of zooplankton gradients with glider-detected density fronts in the Southern California Current System. Deep Sea Res. Part II Top. Stud. Oceanogr. 112, 79–90 (2015).ADS 
CAS 
Article 

Google Scholar 
Taylor, A. G., Landry, M. R., Selph, K. E. & Wokuluk, J. J. Temporal and spatial patterns of microbial community biomass and composition in the Southern California Current Ecosystem. Deep. Res. Part II Top. Stud. Oceanogr. 112, 117–128 (2015).Catlett, D. et al. Diagnosing seasonal to multi-decadal phytoplankton group dynamics in a highly productive coastal ecosystem. Prog. Oceanogr. 197, 102637 (2021).Article 

Google Scholar 
Lilly, L. E. & Ohman, M. D. CCE IV: El Niño-related zooplankton variability in the southern California Current System. Deep. Res. Part I Oceanogr. Res. Pap. 140, 36–51 (2018).ADS 
Article 

Google Scholar 
Richardson, A. J. et al. Using continuous plankton recorder data. Prog. Oceanogr. 68, 27–74 (2006).ADS 
Article 

Google Scholar 
Wang, Z. et al. Microbial communities across nearshore to offshore coastal transects are primarily shaped by distance and temperature. Environ. Microbiol. 1462–2920.14734. https://doi.org/10.1111/1462-2920.14734 (2019).Wang, Y. et al. Patterns and processes of free-living and particle-associated bacterioplankton and archaeaplankton communities in a subtropical river-bay system in South China. Limnol. Oceanogr. 65, S161–S179 (2020).Ibarbalz, F. M. et al. Global Trends in Marine Plankton Diversity across Kingdoms of Life. Cell 1084–1097. https://doi.org/10.1016/j.cell.2019.10.008 (2019).Fuhrman, J. A., Cram, J. A. & Needham, D. M. Marine microbial community dynamics and their ecological interpretation. Nat. Rev. Microbiol. 13, 133–146 (2015).CAS 
PubMed 
Article 

Google Scholar 
Gilbert, J. A. et al. Defining seasonal marine microbial community dynamics. ISME J. 6, 298–308 (2012).CAS 
PubMed 
Article 

Google Scholar 
Karl, D. M. & Lukas, R. The Hawaii Ocean Time-series (HOT) program: background, rationale and field implementation. Deep. Res. Part II Top. Stud. Oceanogr. 43, 129–156 (1996).ADS 
CAS 
Article 

Google Scholar 
Steinberg, D. K. et al. Overview of the US JGOFS Bermuda Atlantic Time-series Study (BATS): A decade-scale look at ocean biology and biogeochemistry Overview of the US JGOFS Bermuda Atlantic Time-series Study (BATS): a decade-scale look at ocean biology and biogeochemistry. Deep. Res. Part II Top. Stud. Oceanogr. 48, 1405–1447 (2015).ADS 
Article 

Google Scholar 
Needham, D. M. & Fuhrman, J. A. Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom. Nat. Microbiol. 1, 16005 (2016).Zhu, Z. et al. Understanding the blob bloom: Warming increases toxicity and abundance of the harmful bloom diatom Pseudo-nitzschia in California coastal waters. Harmful Algae 67, 36–43 (2017).CAS 
PubMed 
Article 

Google Scholar 
Mcclatchie, S. et al. State of the California Current 2015–16: Comparisons with the 1997–98 El Niño. Calif. Cooperative Ocean. Fish. Investig. Rep. 57, (2016).Walker, H. J. Jr et al. Unusual occurrences of fishes in the Southern California Current System during the warm water period of 2014–2018. Estuar. Coast. Shelf Sci. 236, 106634 (2020).Article 

Google Scholar 
Kahru, M., Jacox, M. G. & Ohman, M. D. CCE1: Decrease in the frequency of oceanic fronts and surface chlorophyll concentration in the California Current System during the 2014–2016 northeast Pacific warm anomalies. Deep. Res. Part I Oceanogr. Res. Pap. 140, 4–13 (2018).ADS 
Article 

Google Scholar 
Azam, F. et al. The Ecological Role of Water-Column Microbes in the Sea. Mar. Ecol. Prog. Ser. 10, 257–263 (1983).ADS 
Article 

Google Scholar 
Calbet, A. & Landry, M. R. Phytoplankton growth, microzooplankton grazing, and carbon cycling in marine systems. Limnol. Oceanogr. 49, 51–57 (2004).ADS 
CAS 
Article 

Google Scholar 
Buchan, A., LeCleir, G. R., Gulvik, C. A. & González, J. M. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat. Rev. Microbiol. 12, 686–698 (2014).CAS 
PubMed 
Article 

Google Scholar 
Kohonen, T. Exploration of very large databases by self-organizing maps. IEEE Int. Conf. Neural Networks – Conf. Proc. 1, (1997).Istvánovics, V. Eutrophication of Lakes and Reservoirs. Encycl. Inl. Waters 157–165 https://doi.org/10.1016/B978-012370626-3.00141-1 (2009).Partensky, F., Blanchot, J. & Vaulot, D. Differential distribution and ecology of Prochlorococcus and Synechococcus in oceanic waters: a review. Bull. Oceanogr. Monaco 19, 457–475 (1999).
Google Scholar 
Laws, E. A., Falkowski, P. G., Smith, W. O., Ducklow, H. & McCarthy, J. J. Temperature effects on export production in the open ocean. Global Biogeochem. Cycles 14, (2000).Grover, J. P. Resource Competition in a Variable Environment: Phytoplankton Growing According to Monod’s Model. Am. Nat. 136, 771–789 (1990).Article 

Google Scholar 
Benincá, E. et al. Chaos in a long-term experiment with a plankton community. Nature 451, 822–825 (2008).ADS 
PubMed 
Article 
CAS 

Google Scholar 
Williams, R. G. & Follows, M. J. Ocean Dynamics and the Carbon Cycle: Principles and Mechanisms. Book (2011).Lindegren, M., Checkley, D. M., Ohman, M. D., Koslow, J. A. & Goericke, R. Resilience and stability of a pelagic marine ecosystem. Proc. R. Soc. B Biol. Sci. 283, (2016).Vallina, S. M. et al. Global relationship between phytoplankton diversity and productivity in the ocean. Nat. Commun. 1–10 https://doi.org/10.1038/ncomms5299 (2014).Chase, J. M. & Leibold, M. A. Spatial scale dictates the productivity-biodiversity relationship. Nature 416, 427–430 (2002).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Jacox, M. G., Edwards, C. A., Hazen, E. L. & Bograd, S. J. Coastal Upwelling Revisited: Ekman, Bakun, and Improved Upwelling Indices for the U.S. West Coast. J. Geophys. Res. Ocean. 123, 7332–7350 (2018).ADS 
Article 

Google Scholar 
Zaba, K. D. & Rudnick, D. L. The 2014-2015 warming anomaly in the Southern California Current System observed by underwater gliders. Geophys. Res. Lett. 43, 1241–1248 (2016).ADS 
Article 

Google Scholar 
Weber, E. D. et al. State of the California Current 2019–2020: Back to the Future With Marine Heatwaves? Front. Mar. Sci. 8, (2021).Closset, I. et al. Diatom response to alterations in upwelling and nutrient dynamics associated with climate forcing in the California Current System. Limnol. Oceanogr. 1–16. https://doi.org/10.1002/lno.11705 (2021).Kenitz, K. M. et al. Environmental drivers of population variability in colony-forming marine diatoms. Limnol. Oceanogr. 65, 2515–2528 (2020).ADS 
Article 

Google Scholar 
Mullin, M. M. Biomasses of large-celled phytoplankton and their relation to the nitricline and grazing in the California current system off Southern California, 1994–1996. Calif. Cooperative Ocean. Fish. Investig. Rep. 39, 117–123 (1998).
Google Scholar 
Rykaczewski, R. R. & Checkley, D. M. Influence of ocean winds on the pelagic ecosystem in upwelling regions. PNAS 105, 1965–1970 (2007).ADS 
Article 

Google Scholar 
Grzymski, J. J. & Dussaq, A. M. The significance of nitrogen cost minimization in proteomes of marine microorganisms. ISME J. 6, 71–80 (2012).Margalef, R. Life-forms of phytoplankton as survival alternatives in an unstable environment. Ocean. Acta 1, (1978).Falkowski, P. G. & Oliver, M. J. Mix and match: How climate selects phytoplankton. Nat. Rev. Microbiol. 5, 813–819 (2007).Mende, D. R. et al. Environmental drivers of a microbial genomic transition zone in the ocean’s interior. Nat. Microbiol. 2, 1367–1373 (2017).Phoma, B. S. & Makhalanyane, T. P. Depth-dependent variables shape community structure and functionality in the Prince Edward Islands. Microb. Ecol. 81, 396–409 (2021).Kahru, M. & Mitchell, B. G. Seasonal and nonseasonal variability of satellite-derived chlorophyll and colored dissolved organic matter concentration in the California Current. J. Geophys. Res. Ocean. 106, 2517–2529 (2001).ADS 
CAS 
Article 

Google Scholar 
Barth, A., Walter, R. K., Robbins, I. & Pasulka, A. Seasonal and interannual variability of phytoplankton abundance and community composition on the Central Coast of California. Mar. Ecol. Prog. Ser. 637, (2020).Powell, J. R. & Ohman, M. D. Changes in zooplankton habitat, behavior, and acoustic scattering characteristics across glider-resolved fronts in the Southern California Current System. Prog. Oceanogr. 134, 77–92 (2015).ADS 
Article 

Google Scholar 
Taylor, A. G. & Landry, M. R. Phytoplankton biomass and size structure across trophic gradients in the southern California Current and adjacent ocean ecosystems. Mar. Ecol. Prog. Ser. 592, 1–17 (2018).ADS 
CAS 
Article 

Google Scholar 
Dutkiewicz, S., Follows, M. J. & Bragg, J. G. Modeling the coupling of ocean ecology and biogeochemistry. Glob. Biogeochem. Cycles 23, 1–15 (2009).Article 
CAS 

Google Scholar 
D’Ovidio, F., De Monte, S., Alvain, S., Dandonneau, Y. & Lévy, M. Fluid dynamical niches of phytoplankton types. Proc. Natl Acad. Sci. U. S. A. 107, 18366–18370 (2010).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Clayton, S., Dutkiewicz, S., Jahn, O. & Follows, M. J. Dispersal, eddies, and the diversity of marine phytoplankton. Limnol. Oceanogr. Fluids Environ. 3, 182–197 (2013).Article 

Google Scholar 
Moisan, T. A., Rufty, K. M., Moisan, J. R. & Linkswiler, M. A. Satellite observations of phytoplankton functional type spatial distributions, phenology, diversity, and ecotones. Front. Mar. Sci. 4, 1–24 (2017).Article 

Google Scholar 
Combes, V. et al. Cross-shore transport variability in the California Current: Ekman upwelling vs. eddy dynamics. Prog. Oceanogr. 109, 78–89 (2013).ADS 
Article 

Google Scholar 
Chenillat, F., Rivière, P., Capet, X., Franks, P. J. S. & Blanke, B. California coastal upwelling onset variability: cross-shore and bottom-up propagation in the planktonic ecosystem. PLoS ONE 8, (2013).Chenillat, F., Franks, P. J. S. & Combes, V. Biogeochemical properties of eddies in the California Current System. Geophys. Res. Lett. 43, 5812–5820 (2016).ADS 
CAS 
Article 

Google Scholar 
Edwards, K. F., Thomas, M. K., Klausmeier, C. A. & Litchman, E. Allometric scaling and taxonomic variation in nutrient utilization traits and maximum growth rate of phytoplankton. Limnol. Oceanogr. 57, 554–566 (2012).ADS 
Article 

Google Scholar 
Wells, B. K. et al. State of the California Current 2016–17: Still anything but ‘normal’ in the north. Calif. Cooperative Ocean. Fish. Investig. Rep. 58 (2017).Thompson, A. R. et al. State of the California Current 2017–18: Still not quite normal in the north and getting interesting in the south. Calif. Cooperative Ocean. Fish. Investig. Rep. 59 (2018).Ward, C. S. et al. Annual community patterns are driven by seasonal switching between closely related marine bacteria. ISME J. 11, 1412–1422 (2017).Bograd, S. J., Schroeder, I. D. & Jacox, M. G. A water mass history of the Southern California current system. Geophys. Res. Lett. 46, 6690–6698 (2019).ADS 
Article 

Google Scholar 
Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: Assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18 (2016).Amaral-Zettler, L. A., McCliment, E. A., Ducklow, H. W. & Huse, S. M. A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA Genes. PLoS ONE 4, (2009).Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.J. 17, (2011).Callahan, B. J., Mcmurdie, P. J., Rosen, M. J., Han, A. W. & A, A. J. DADA2: High resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Bokulich, N. A. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6 (2018).Pedregosa, F. et al. Scikit-learn: Machine learning in Python. J. Mach. Learn. Res. 12 (2011).Pruesse, E. et al. SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35 (2007).Guillou, L. et al. The Protist Ribosomal Reference database (PR2): A catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41 (2013).McMurdie, P. J. & Holmes, S. Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible. PLoS Comput. Biol. 10 (2014).Gloor, G. B., Wu, J. R., Pawlowsky-Glahn, V. & Egozcue, J. J. It’s all relative: analyzing microbiome data as compositions. Ann. Epidemiol. 26 (2016).Cameron, E. S., Schmidt, P. J., Tremblay, B. J. M., Emelko, M. B. & Müller, K. M. To rarefy or not to rarefy: Enhancing microbial community analysis through next-generation sequencing. bioRxiv. https://doi.org/10.1101/2020.09.09.290049 (2020).Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5-7. (2020).Bowman, J. S., Amaral-zettler, L. A., Rich, J. J., Luria, C. M. & Ducklow, H. W. Bacterial community segmentation facilitates the prediction of ecosystem function along the coast of the western Antarctic Peninsula. Nat. Publ. Gr. 11, 1460–1471 (2017).
Google Scholar 
Boelaert, J., Bendhaiba, L., Olteanu, M. & Villa-Vialaneix, N. SOMbrero: An R package for numeric and non-numeric self-organizing maps. Adv. Intell. Syst. Comput 295, 219–228 (2014).
Google Scholar 
Johnson, J. B. & Omland, K. S. Model selection in ecology and evolution. Trends Ecol. Evol. 19, 101–108 (2004).PubMed 
Article 

Google Scholar 
James, C. C. et al. Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region. https://doi.org/10.5281/zenodo.6359865 (2022).Legendre, P. & Legendre, L. Numerical ecology (Elsevier, 2012). More

The haplotype networks, PCoA analysis and STRUCTURE analysis based on the six nuclear loci confirm that S. longifolium is a hybrid between S. emersum and S. gramineum, providing molecular support for previous morphological analyses5. Furthermore, all individuals with intermediate admixture coefficient (Fig. 2b) and private haplotypes only present in one out of six nuclear loci (Fig. 1) suggest that S. longifolium is most likely a F1 hybrid. We thus hypothesized that S. emersum and S. gramineum could likely maintain their species boundary through the post-zygote reproductive isolation mechanism of F1 generation sterility. This hypothesis is possible based on the observations from hybrids in European Russia. The pollen viability was checked in S. longifolium samples from Vysokovskoe Lake and Sabro Lake, and the vast majority of checked pollens were sterile5. In addition, flowering plants of S. longifolium often do not form seeds, or the seeds are puny and significantly inferior to normal seeds in size5. However, the hypothesis is only based on our limited sampling, which is contrary to the conclusion inferred from morphological characteristics that it is fertile and may backcross with parental species1. Further studies with extensive sampling are necessary to test our hypothesis.The chloroplast DNA fragment trnH-psbA was used to infer the direction of hybridization between S. emersum and S. gramineum because chloroplast DNA is maternal inheritance in Sparganium3,4. The hybrid S. longifolium shared haplotypes with S. emersum and S. gramineum simultaneously (Fig. 1). This finding clearly indicates that bidirectional hybridization exists between S. emersum and S. gramineum. At the same time, the different frequency of these two haplotypes in the hybrid (H1, 19.1% vs. H2, 80.9%) means that the direction of hybridization is asymmetric. A variety of factors can lead to asymmetry in natural hybridization, such as flowering time, preference of pollinators, quality and quantity of pollen, cross incompatibility and the abundance of parent species7,8. Rare species usually act as maternal species relative to abundant species9,10. S. gramineum is confined to oligotrophic lakes and its abundance is obviously lower than that of S. emersum1,11. The relatively scarcity combined with the ecology of S. gramineum make it more often act as maternal species when hybridizing with S. emersum.As described by5, the morphological diversification of S. longifolium was also observed in this study. For example, individuals of S. longifolium with emergent and floating-leaved life forms occur concurrently in Zaozer’ye Lake (Supplementary Fig. S2). However, all individuals had the same haplotype H2 as S. gramineum (Fig. 1), suggesting that the direction of hybridization do not determine life form of S. longifolium. In addition, all individuals of S. longifolium sampled here are likely F1 hybrid. Their variable phenotypes could not be associated with traits segregation due to F2 generation or backcross. Detailed ecological investigation combining with research at the genomic level are essential to find out the potential factors leading to morphological diversification of S. longifolium.Here, using sequences of six nuclear loci and one chloroplast DNA fragment, we confirmed that S. longifolium is the hybrid between S. emersum and S. gramineum. The natural hybridization between S. emersum and S. gramineum is bidirectional but the latter mainly acts as maternal species. We also found that all samples of S. longifolium were F1 generations, indicating that S. emersum and S. gramineum could maintain their species boundary through the post-zygote reproductive isolation mechanism of F1 generation sterility. More

Meropol, S. B., Haupt, A. A. & Debanne, S. M. Incidence and outcomes of infections caused by multidrug-resistant Enterobacteriaceae in Children, 2007–2015. J. Pediatr. Infect. Dis. Soc. 7, 36–45 (2018).Article 

Google Scholar 
Moxon, C. A. & Paulus, S. Beta-lactamases in Enterobacteriaceae infections in children. J. Infect. 72, S41–S49 (2016).PubMed 
Article 

Google Scholar 
Morrissey, I. et al. A review of ten years of the study for monitoring antimicrobial resistance trends (SMART) from 2002 to 2011. Pharmaceuticals 6, 1335–1346 (2013).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Junnila, J. et al. Changing epidemiology of methicillin-resistant Staphylococcus aureus in a low endemicity area—new challenges for MRSA control. Eur. J. Clin. Microbiol. Infect. Dis. 39, 2299–2307 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Milstone, A. M. et al. Methicillin-resistant Staphylococcus aureus colonization and risk of subsequent infection in critically ill children: Importance of preventing nosocomial methicillin-resistant Staphylococcus aureus transmission. Clin. Infect. Dis. 53, 853–859 (2011).PubMed 
PubMed Central 
Article 

Google Scholar 
Lakhundi, S. & Zhang, K. Methicillin-resistant Staphylococcus aureus: Molecular characterization, evolution, and epidemiology. Clin. Microbiol. Rev. 31, e00020-18 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Schlesinger, Y. et al. Methicillin-resistant nasal colonization in children in Jerusalem: Community vs. chronic care institutions. Isr. Med. Assoc. J. 5, 847–851 (2003).PubMed 

Google Scholar 
Liang, B. et al. Active surveillance, drug resistance, and genotypic profiling of Staphylococcus aureus among school-age children in China. Front. Med. 8, 701494 (2021).Article 

Google Scholar 
Del Rosal, T. et al. Staphylococcus aureus nasal colonization in Spanish children. The COSACO Nationwide Surveillance Study. Infect. Drug Resist. 13, 4643–4651 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Feudtner, C., Feinstein, J. A., Zhong, W., Hall, M. & Dai, D. Pediatric complex chronic conditions classification system version 2: Updated for ICD-10 and complex medical technology dependence and transplantation. BMC Pediatr. 14, 199 (2014).PubMed 
PubMed Central 
Article 

Google Scholar 
Climent Alcalá, F. J., García Fernández de Villalta, M., Escosa García, L., Rodríguez Alonso, A. & Albajara Velasco, L. A. Unidad de niños con patología crónica compleja. Un modelo necesario en nuestros hospitales. Anales de Pediatría 88, 12–18 (2018).PubMed 
Article 

Google Scholar 
Gesualdo, F. et al. Methicillin-resistant Staphylococcus aureus nasal colonization in a department of pediatrics: A cross-sectional study. Ital. J. Pediatr. 40, 3 (2014).PubMed 
PubMed Central 
Article 

Google Scholar 
Yamamoto, M. et al. Effective surveillance to identify the surgical patients carrying methicillin-resistant Staphylococcus aureus on admission in a pediatric ward. Osaka City Med. J. 62, 1–9 (2016).PubMed 

Google Scholar 
Lukac, P. J., Bonomo, R. A. & Logan, L. K. Extended-spectrum-lactamase-producing Enterobacteriaceae in children: Old foe, emerging threat. Clin. Infect. Dis. https://doi.org/10.1093/cid/civ020 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
Fedler, K. A., Biedenbach, D. J. & Jones, R. N. Assessment of pathogen frequency and resistance patterns among pediatric patient isolates: Report from the 2004 SENTRY Antimicrobial Surveillance Program on 3 continents. Diagn. Microbiol. Infect. Dis. 56, 427–436 (2006).CAS 
PubMed 
Article 

Google Scholar 
Caselli, D. et al. Incidence of colonization and bloodstream infection with carbapenem-resistant Enterobacteriaceae in children receiving antineoplastic chemotherapy in Italy. Infect. Dis. 48, 152–155 (2016).Article 

Google Scholar 
Logan, L. K. et al. Multidrug- and Carbapenem-Resistant Pseudomonas aeruginosa in Children, United States, 1999–2012. JPIDSJ piw064 (2016) https://doi.org/10.1093/jpids/piw064.Flokas, M. E., Alevizakos, M., Shehadeh, F., Andreatos, N. & Mylonakis, E. Extended-spectrum β-lactamase-producing Enterobacteriaceae colonisation in long-term care facilities: A systematic review and meta-analysis. Int. J. Antimicrob. Agents 50, 649–656 (2017).CAS 
PubMed 
Article 

Google Scholar 
Bharadwaj, R. et al. Drug-resistant Enterobacteriaceae colonization is associated with healthcare utilization and antimicrobial use among inpatients in Pune, India. BMC Infect. Dis. 18, 504 (2018).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Logan, L. K. Carbapenem-resistant Enterobacteriaceae: An emerging problem in children. Clin. Infect. Dis. 55, 852–859 (2012).CAS 
PubMed 
Article 

Google Scholar 
Badal, R. E. et al. Etiology, extended-spectrum β-lactamase rates and antimicrobial susceptibility of gram-negative bacilli causing intra-abdominal infections in patients in general pediatric and pediatric intensive care units—global data from the Study for Monitoring Antimicrobial Resistance Trends 2008 to 2010. Pediatr. Infect. Dis. J. 32, 636–640 (2013).PubMed 
Article 

Google Scholar 
Wang, Q. et al. Risk factors and clinical outcomes for carbapenem-resistant Enterobacteriaceae nosocomial infections. Eur. J. Clin. Microbiol. Infect. Dis. 35, 1679–1689 (2016).CAS 
PubMed 
Article 

Google Scholar 
Sahbudak Bal, Z. et al. The prospective evaluation of risk factors and clinical influence of carbapenem resistance in children with gram-negative bacteria infection. Am. J. Infect. Control 46, 147–153 (2018).CAS 
PubMed 
Article 

Google Scholar 
Simon, T. D. et al. Pediatric medical complexity algorithm: A new method to stratify children by medical complexity. Pediatrics 133, e1647–e1654 (2014).PubMed 
PubMed Central 
Article 

Google Scholar 
Román, F. et al. Characterization of methicillin-resistant Staphylococcus aureus strains colonizing the nostrils of Spanish children. MicrobiologyOpen 10, e1235 (2021).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
EUCAST. European committee on antimicrobial susceptibility testing breakpoint tables for interpretation of MICs and zone diameters. The European Committee on Antimicrobial Susceptibility Testing. (2018).Oteo, J. et al. Prospective multicenter study of carbapenemase-producing Enterobacteriaceae from 83 hospitals in Spain reveals high in vitro susceptibility to colistin and meropenem. Antimicrob. Agents Chemother. 59, 3406–3412 (2015).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Maseda, E. et al. Risk factors for colonization by carbapenemase-producing enterobacteria at admission to a Surgical ICU: A retrospective study. Enferm. Infecc. Microbiol. Clin. 35, 333–337 (2017).PubMed 
Article 

Google Scholar 
Bassetti, M., Nicco, E. & Mikulska, M. Why is community-associated MRSA spreading across the world and how will it change clinical practice?. Int. J. Antimicrob. Agents 34, S15–S19 (2009).CAS 
PubMed 
Article 

Google Scholar 
El Cheikh, M. R., Barbosa, J. M., Caixêta, J. A. S. & Avelino, M. A. G. Microbiology of tracheal secretions: What to expect with children and adolescents with tracheostomies. Int. Arch. Otorhinolaryngol. 22, 50–54 (2018).PubMed 
Article 

Google Scholar 
González-Del Castillo, J. et al. BAHNG score: Predictive model for detection of subjects with the oropharynx colonized by uncommon microorganisms. Rev. Esp Quimioter. 30, 422–428 (2017).PubMed 

Google Scholar 
Hu, X. et al. Risk factors for methicillin-resistant Staphylococcus aureus colonization and infection in patients with human immunodeficiency virus infection: A systematic review and meta-analysis. J. Int. Med. Res. 50, 3000605211063019 (2022).CAS 
PubMed 

Google Scholar 
Gleeson, A., Larkin, P., Walsh, C. & O’Sullivan, N. Methicillin-resistant Staphylococcus aureus: Prevalence, incidence, risk factors, and effects on survival of patients in a specialist palliative care unit: A prospective observational study. Palliat. Med. 30, 374–381 (2016).PubMed 
Article 

Google Scholar 
Hogardt, M. et al. Current prevalence of multidrug-resistant organisms in long-term care facilities in the Rhine-Main district, Germany, 2013. Euro Surveill. 20, 21171 (2015).PubMed 
Article 

Google Scholar 
Warren, D. K. et al. Epidemiology of methicillin-resistant Staphylococcus aureus colonization in a surgical intensive care unit. Infect. Control Hosp. Epidemiol. 27, 1032–1040 (2006).PubMed 
Article 

Google Scholar 
Folgori, L. et al. Healthcare-associated infections in pediatric and neonatal intensive care units: Impact of underlying risk factors and antimicrobial resistance on 30-day case-fatality in Italy and Brazil. Infect. Control Hosp. Epidemiol. 37, 1302–1309 (2016).PubMed 
Article 

Google Scholar 
Béranger, A. et al. Early bacterial infections after pediatric liver transplantation in the era of multidrug-resistant bacteria: Nine-year single-center retrospective experience. Pediatr. Infect. Dis. J. 39, e169–e175 (2020).PubMed 
Article 

Google Scholar 
Bouras, D. et al. Staphylococcus aureus osteoarticular infections in children: An 8-year review of molecular microbiology, antibiotic resistance and clinical characteristics. J. Med. Microbiol. 67, 1753–1760 (2018).MathSciNet 
CAS 
PubMed 
Article 

Google Scholar 
Rodriguez, M., Hogan, P. G., Krauss, M., Warren, D. K. & Fritz, S. A. Measurement and impact of Staphylococcus aureus colonization pressure in households. J. Pediatr. Infect. Dis. Soc. 2, 147–154 (2013).Article 

Google Scholar 
Messina, N. L., Williamson, D. A., Robins-Browne, R., Bryant, P. A. & Curtis, N. Risk factors for carriage of antibiotic-resistant bacteria in healthy children in the community: A systematic review. Pediatr. Infect. Dis. J. 39, 397–405 (2020).PubMed 
Article 

Google Scholar 
Dualleh, N. et al. Colonization with multiresistant bacteria in acute hospital care: The association of prior antibiotic consumption as a risk factor. J. Antimicrob. Chemother. 75, 3675–3681 (2020).CAS 
PubMed 
Article 

Google Scholar 
Daskalaki, M. et al. Panton-Valentine leukocidin-positive Staphylococcus aureus skin and soft tissue infections among children in an emergency department in Madrid, Spain. Clin. Microbiol. Infect. 16, 74–77 (2010).CAS 
PubMed 
Article 

Google Scholar 
Aguilera-Alonso, D., Escosa-García, L., Saavedra-Lozano, J., Cercenado, E. & Baquero-Artigao, F. Carbapenem-resistant gram-negative bacterial infections in children. Antimicrob. Agents Chemother. 64, e02183-e2219 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Phichaphop, C. et al. High prevalence of multidrug-resistant gram-negative bacterial infection following pediatric liver transplantation. Medicine 99, e23169 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Tacconelli, E. et al. ESCMID guidelines for the management of the infection control measures to reduce transmission of multidrug-resistant Gram-negative bacteria in hospitalized patients. Clin. Microbiol. Infect. 20, 1–55 (2014).PubMed 
Article 

Google Scholar 
McConville, T. H., Sullivan, S. B., Gomez-Simmonds, A., Whittier, S. & Uhlemann, A.-C. Carbapenem-resistant Enterobacteriaceae colonization (CRE) and subsequent risk of infection and 90-day mortality in critically ill patients, an observational study. PLoS ONE 12, e0186195 (2017).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Tamma, P. D. et al. The likelihood of developing a carbapenem-resistant Enterobacteriaceae Infection during a hospital stay. Antimicrob. Agents Chemother. 63, e00757-e819 (2019).CAS 
PubMed 
PubMed Central 

Google Scholar 
Detsis, M., Karanika, S. & Mylonakis, E. ICU acquisition rate, risk factors, and clinical significance of digestive tract colonization with extended-spectrum beta-lactamase-producing Enterobacteriaceae: A systematic review and meta-analysis. Crit. Care Med. 45, 705–714 (2017).PubMed 
Article 

Google Scholar  More

Schimel, J. P., Bennett, J. & Fierer, N. Microbial community composition and soil nitrogen cycling: is there really a connection? In Biological Diversity and Function in Soils Ecological Reviews (eds Bardgett, R. et al.) 171–188 (Cambridge University Press, 2005).
Google Scholar 
Hatzenpichler, R. Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl. Environ. Microbiol. 78, 7501–7510 (2012).CAS 
PubMed 
PubMed Central 

Google Scholar 
Kowalchuk, G. A. & Stephen, J. R. Ammonia-oxidizing bacteria: A model for molecular microbial ecology. Annu. Rev. Microbiol. 55, 485–529 (2001).CAS 
PubMed 

Google Scholar 
Daims, H. et al. Complete nitrification by Nitrospira bacteria. Nature 528, 504–509 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
Shi, X. et al. Niche separation of comammox Nitrospira and canonical ammonia oxidizers in an acidic subtropical forest soil under long-term nitrogen deposition. Soil Biol. Biochem. 126, 114–122 (2018).CAS 

Google Scholar 
van Kessel, M. A. H. J. et al. Complete nitrification by a single microorganism. Nature 528, 555–559 (2015).PubMed 
PubMed Central 

Google Scholar 
Wang, X. et al. Comammox bacterial abundance, activity, and contribution in agricultural rhizosphere soils. Sci. Total Environ. 727, 138563 (2020).CAS 
PubMed 

Google Scholar 
Wang, F., Liang, X., Ma, S., Liu, L. & Wang, J. Ammonia-oxidizing archaea are dominant over comammox in soil nitrification under long-term nitrogen fertilization. J. Soils Sediments 21, 1800–1814 (2021).CAS 

Google Scholar 
Rotthauwe, J.-H., Witzel, K.-P. & Liesack, W. The ammonia monooxygenase structural gene amoA as a functional marker: Molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63, 4704–4712 (1997).CAS 
PubMed 
PubMed Central 

Google Scholar 
Spang, A. et al. Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol. 18, 331–340 (2010).CAS 
PubMed 

Google Scholar 
Schleper, C. & Nicol, G. W. Ammonia-oxidising archaea—Physiology, ecology and evolution. Adv. Microb. Physiol. 57, 1–41 (2010).CAS 
PubMed 

Google Scholar 
Prosser, J. I. & Nicol, G. W. Archaeal and bacterial ammonia-oxidisers in soil: The quest for niche specialisation and differentiation. Trends Microbiol. 20, 523–531 (2012).CAS 
PubMed 

Google Scholar 
Amin, S. A. et al. Copper requirements of the ammonia-oxidizing archaeon Nitrosopumilus maritimus SCM1 and implications for nitrification in the marine environment. Limnol. Oceanogr. 58, 2037–2045 (2013).CAS 

Google Scholar 
Jenkins, S. N., Murphy, D. V., Waite, I. S., Rushton, S. P. & O’Donnell, A. G. Ancient landscapes and the relationship with microbial nitrification. Sci. Rep. 6, 30733 (2016).CAS 
PubMed 
PubMed Central 

Google Scholar 
Gubry-Rangin, C. et al. Niche specialization of terrestrial archaeal ammonia oxidizers. Proc. Natl. Acad. Sci. U.S.A. 108, 21206–21211 (2011).CAS 
PubMed 
PubMed Central 

Google Scholar 
Lehtovirta-Morley, L. E., Stoecker, K., Vilcinskas, A., Prosser, J. I. & Nicol, G. W. Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc. Natl. Acad. Sci. U.S.A. 108, 15892–15897 (2011).CAS 
PubMed 
PubMed Central 

Google Scholar 
Banning, N. C., Maccarone, L. D., Fisk, L. M. & Murphy, D. V. Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil. Sci. Rep. 5, 11146 (2015).PubMed 
PubMed Central 

Google Scholar 
Di, H. J. et al. Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions. FEMS Microbiol. Ecol. 72, 386–394 (2010).CAS 
PubMed 

Google Scholar 
Wang, J., Wang, J., Rhodes, G., He, J. Z. & Ge, Y. Adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations: Implications for the relative contributions of different ammonia oxidizers to soil nitrogen cycling. Sci. Total Environ. 668, 224–233 (2019).CAS 
PubMed 

Google Scholar 
Ouyang, Y., Evans, S. E., Friesen, M. L. & Tiemann, L. K. Effect of nitrogen fertilization on the abundance of nitrogen cycling genes in agricultural soils: A meta-analysis of field studies. Soil Biol. Biochem. 127, 71–78 (2018).CAS 

Google Scholar 
Verhamme, D. T., Prosser, J. I. & Nicol, G. W. Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms. ISME J. 5, 1067–1071 (2011).CAS 
PubMed 
PubMed Central 

Google Scholar 
Wardle, D. A. Controls of temporal variability of the soil microbial biomass: A global-scale synthesis. Soil Biol. Biochem. 30, 1627–1637 (1998).CAS 

Google Scholar 
Adair, K. L. & Schwartz, E. Evidence that ammonia-oxidizing archaea are more abundant than ammonia-oxidizing bacteria in semiarid soils of northern Arizona, USA. Microb. Ecol. 56, 420–426 (2008).CAS 
PubMed 

Google Scholar 
Taylor, A. E., Zeglin, L. H., Wanzek, T. A., Myrold, D. D. & Bottomley, P. J. Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials. ISME J. 6, 2024–2032 (2012).CAS 
PubMed 
PubMed Central 

Google Scholar 
Hayatsu, M., Katsuyama, C. & Tago, K. Overview of recent researches on nitrifying microorganisms in soil. Soil Sci. Plant Nutr. 67, 1–14 (2021).
Google Scholar 
Sher, Y., Zaady, E. & Nejidat, A. Spatial and temporal diversity and abundance of ammonia oxidizers in semi-arid and arid soils: Indications for a differential seasonal effect on archaeal and bacterial ammonia oxidizers. FEMS Microbiol. Ecol 86, 544–556 (2013).CAS 
PubMed 

Google Scholar 
Stopnišek, N. et al. Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonium amendment. Appl. Environ. Microbiol. 76, 7626–7634 (2010).PubMed 
PubMed Central 

Google Scholar 
Habteselassie, M. Y., Xu, L. & Norton, J. M. Ammonia-oxidizer communities in an agricultural soil treated with contrasting nitrogen sources. Front. Microbiol. 4, 326 (2013).PubMed 
PubMed Central 

Google Scholar 
Wang, C. et al. Climate change amplifies gross nitrogen turnover in montane grasslands of Central Europe in both summer and winter seasons. Glob. Change Biol. 22, 2963–2978 (2016).
Google Scholar 
Wessén, E., Nyberg, K., Jansson, J. K. & Hallin, S. Responses of bacterial and archaeal ammonia oxidizers to soil organic and fertilizer amendments under long-term management. Appl. Soil Ecol. 45, 193–200 (2010).
Google Scholar 
Kong, A. Y. Y., Hristova, K., Scow, K. M. & Six, J. Impacts of different N management regimes on nitrifier and denitrifier communities and N cycling in soil microenvironments. Soil Biol. Biochem. 42, 1523–1533 (2010).CAS 
PubMed 
PubMed Central 

Google Scholar 
Harrison, P. & Pearce, F. AAAS Atlas of Population & Environment 204 (University of California Press, 2000).
Google Scholar 
Reynolds, J. F., Maestre, F. T., Kemp, P. R., Smith, D. M. S. & Lambin, E. F. Natural and human dimensions of land degradation in drylands: Causes and consequences. In Terrestrial Ecosystems in a Changing World Global Change—The IGBP Series (eds Canadell, J. G. et al.) 247–258 (Springer, 2007).
Google Scholar 
McArthur, W. M. Reference Soils of South-Western Australia 2nd edn. (Department of Agriculture, 2004).
Google Scholar 
Barton, L., Murphy, D. V. & Butterbach-Bahl, K. Influence of crop rotation and liming on greenhouse gas emissions from a semi-arid soil. Agric. Ecosyst. Environ. 167, 23–32 (2013).CAS 

Google Scholar 
Barton, L., Hoyle, F. C., Stefanova, K. T. & Murphy, D. V. Incorporating organic matter alters soil greenhouse gas emissions and increases grain yield in a semi-arid climate. Agric. Ecosyst. Environ. 231, 320–330 (2016).CAS 

Google Scholar 
Gubry-Rangin, C., Nicol, G. W. & Prosser, J. I. Archaea rather than bacteria control nitrification in two agricultural acidic soils. FEMS Microbiol. Ecol. 74, 566–574 (2010).CAS 
PubMed 

Google Scholar 
Gleeson, D. B. et al. Response of ammonia oxidizing archaea and bacteria to changing water filled pore space. Soil Biol. Biochem. 42, 1888–1891 (2010).CAS 

Google Scholar 
O’Sullivan, C. A., Wakelin, S. A., Fillery, I. R. P. & Roper, M. M. Factors affecting ammonia-oxidising microorganisms and potential nitrification rates in southern Australian agricultural soils. Soil Res. 51, 240–252 (2013).
Google Scholar 
Zhang, L.-M., Hu, H.-W., Shen, J.-P. & He, J.-Z. Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils. ISME J. 6, 1032–1045 (2012).CAS 
PubMed 

Google Scholar 
Wang, F. et al. Responses of soil ammonia-oxidizing bacteria and archaea to short-term warming and nitrogen input in a semi-arid grassland on the Loess Plateau. Eur. J. Soil Biol. 102, 103267 (2021).CAS 

Google Scholar 
Bolland, M. D. A. & Brennan, R. F. Phosphorus, copper and zinc requirements of no-till wheat crops and methods of collecting soil samples for soil testing. Aust. J. Exp. Agric. 46, 1051–1059 (2006).CAS 

Google Scholar 
Gilkes, B., Lee, S. & Singh, B. The imprinting of aridity upon a lateritic landscape: An illustration from southwestern Australia. C. R. Geosci. 335, 1207–1218 (2003).
Google Scholar 
Hoyle, F. C. & Murphy, D. V. Influence of organic residues and soil incorporation on temporal measures of microbial biomass and plant available nitrogen. Plant Soil 347, 53–64 (2011).CAS 

Google Scholar 
Noy-Meir, I. Desert ecosystems: Environment and producers. Annu. Rev. Ecol. Syst. 4, 25–51 (1973).
Google Scholar 
Petersen, D. G. et al. Abundance of microbial genes associated with nitrogen cycling as indices of biogeochemical process rates across a vegetation gradient in Alaska. Environ. Microbiol. 14, 993–1008 (2012).CAS 
PubMed 

Google Scholar 
Fisk, L. M., Barton, L., Jones, D. L., Glanville, H. C. & Murphy, D. V. Root exudate carbon mitigates nitrogen loss in a semi-arid soil. Soil Biol. Biochem. 88, 380–389 (2015).CAS 

Google Scholar 
Murphy, D. V., Sparling, G. P., Fillery, I. R. P., McNeill, A. M. & Braunberger, P. Mineralisation of soil organic nitrogen and microbial respiration after simulated summer rainfall events in an agricultural soil. Aust. J. Soil Res. 36, 231–246 (1998).
Google Scholar 
Anderson, G. C., Fillery, I. R. P., Dunin, F. X., Dolling, P. J. & Asseng, S. Nitrogen and water flows under pasture–wheat and lupin–wheat rotations in deep sands in Western Australia 2. Drainage and nitrate leaching. Aust. J. Agric. Res. 49, 345–361 (1998).CAS 

Google Scholar 
Nicholls, N. Local and remote causes of the southern Australian autumn-winter rainfall decline, 1958–2007. Clim. Dyn. 34, 835–845 (2010).
Google Scholar 
Delworth, T. L. & Zeng, F. Regional rainfall decline in Australia attributed to anthropogenic greenhouse gases and ozone levels. Nat. Geosci. 7, 583 (2014).CAS 

Google Scholar 
Alexander, L. V. et al. Trends in Australia’s climate means and extremes: A global context. Aust. Meteorol. Mag. 56, 1–18 (2007).
Google Scholar 
Austin, A. T. et al. Water pulses and biogeochemical cycles in arid and semiarid ecosystems. Oecologia 141, 221–235 (2004).PubMed 

Google Scholar 
Isbell, R. F. The Australian Soil Classification 2nd edn. (CSIRO Publishing, 2002).
Google Scholar 
IUSS Working Group WRB. World Reference Base for Soil Resources 2006, First Update 2007 203 (FAO, 2007).
Google Scholar 
Brookes, P. C., Landman, A., Pruden, G. & Jenkinson, D. S. Chloroform fumigation and the release of soil nitrogen: A rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biol. Biochem. 17, 837–842 (1985).CAS 

Google Scholar 
Wu, J., Joergensen, R. G., Pommerening, B., Chaussod, R. & Brookes, P. C. Measurement of soil microbial biomass C by fumigation-extraction—An automated procedure. Soil Biol. Biochem. 22, 1167–1169 (1990).CAS 

Google Scholar 
Krom, M. D. Spectrophotometric determination of ammonia: A study of a modified Berthelot reaction using salicylate and dichloroisocyanurate. Analyst 105, 305–316 (1980).CAS 

Google Scholar 
Kamphake, L. J., Hannah, S. A. & Cohen, J. M. Automated analysis for nitrate by hydrazine reduction. Water Res. 1, 205–216 (1967).CAS 

Google Scholar 
Keeney, D. R. & Bremner, J. M. Comparison and evaluation of laboratory methods of obtaining an index of soil nitrogen availability. Agron. J. 58, 498–503 (1966).CAS 

Google Scholar 
Waring, S. A. & Bremner, J. M. Ammonium production in soil under waterlogged conditions as an index of nitrogen availability. Nature 201, 951–952 (1964).CAS 

Google Scholar 
Griffiths, R. I., Whiteley, A. S., O’Donnell, A. G. & Bailey, M. J. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl. Environ. Microbiol. 66, 5488–5491 (2000).CAS 
PubMed 
PubMed Central 

Google Scholar 
Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E. & Oakley, B. B. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc. Natl. Acad. Sci. U.S.A. 102, 14683–14688 (2005).CAS 
PubMed 
PubMed Central 

Google Scholar 
Barton, L., Gleeson, D. B., Maccarone, L. D., Zúñiga, L. P. & Murphy, D. V. Is liming soil a strategy for mitigating nitrous oxide emissions from semi-arid soils? Soil Biol. Biochem. 62, 28–35 (2013).CAS 

Google Scholar 
Akaike, H. Likelihood of a model and information criteria. J. Econom. 16, 3–14 (1981).MATH 

Google Scholar 
Cresswell, H. P. & Hamilton, G. J. Bulk density and pore space relations. In Soil Physical Measurement and Interpretation for Land Evaluation (eds McKenzie, N. et al.) 35–58 (CSIRO Publishing, 2002).
Google Scholar 
Rayment, G. E. & Lyons, D. J. Soil Chemical Methods—Australasia 495 (CSIRO Publishing, 2011).
Google Scholar  More

Miyata, T., Miyazawa, S. & Yasunaga, T. Two types of amino acid substitutions in protein evolution. J. Mol. Evol. 12, 219–236 (1979).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Li, W.-H., Wu, C.-I. & Luo, C.-C. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2, 150–174 (1985).PubMed 

Google Scholar 
Bielawski, J. P. & Yang, Z. Positive and negative selection in the DAZ gene family. Mol. Biol. Evol. 18, 523–529 (2001).CAS 
PubMed 
Article 

Google Scholar 
Ohta, T. Slightly deleterious mutant substitutions in evolution. Nature 246, 96–98 (1973).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Ohta, T. The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Evol. Syst. 23, 263–286 (1992).Article 

Google Scholar 
Johnson, K. P. & Seger, J. Elevated rates of nonsynonymous substitution in island birds. Mol. Biol. Evol. 18, 874–881 (2001).CAS 
PubMed 
Article 

Google Scholar 
Woolfit, M. & Bromham, L. Population size and molecular evolution on islands. Proc. Biol. Sci. 272, 2277–2282 (2005).CAS 
PubMed 
PubMed Central 

Google Scholar 
Ross, L., Hardy, N. B., Okusu, A. & Normark, B. B. Large population size predicts the distribution of asexuality in scale insects. Evolution 67, 196–206 (2013).PubMed 
Article 

Google Scholar 
Weber, C. C., Nabholz, B., Romiguier, J. & Ellegren, H. Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biol. 15, 542 (2014).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Brandt, A. et al. Effective purifying selection in ancient asexual oribatid mites. Nat. Commun. 8, 873 (2017).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Figuet, E. et al. Life history traits, protein evolution, and the nearly neutral theory in amniotes. Mol. Biol. Evol. 33(6), 1517–1527 (2016).CAS 
PubMed 
Article 

Google Scholar 
Saclier, N. et al. Life history traits impact the nuclear rate of substitution but not the mitochondrial rate in isopods. Mol. Biol. Evol. 35, 2900–2912 (2018).CAS 
PubMed 
Article 

Google Scholar 
Hebert, P. D. The Daphnia of North America: An Illustrated Fauna (on CD-ROM) (CyberNatural Software, Guelph, 1995).
Google Scholar 
Colbourne, J. K. et al. Phylogenetics and evolution of a circumarctic species complex (Cladocera: Daphnia pulex). Biol. J. Linn. Soc. 65, 347–365 (1998).
Google Scholar 
Crease, T. J., Omilian, A. R., Costanzo, K. S. & Taylor, D. J. Transcontinental phylogeography of the Daphnia pulex species complex. PLoS ONE 7, e46620 (2012).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Mergeay, J., Verschuren, D. & De Meester, L. Cryptic invasion and dispersal of an American Daphnia in East Africa. Limnol. Oceanogr. 50, 1278–1283 (2005).ADS 
CAS 
Article 

Google Scholar 
Ma, X. et al. Lineage diversity and reproductive modes of the Daphnia pulex group in Chinese lakes and reservoirs. Mol. Phylogenet. Evol. 130, 424–433 (2019).PubMed 
Article 

Google Scholar 
So, M. et al. Invasion and molecular evolution of Daphnia pulex in Japan. Limnol. Oceanogr. 60, 1129–1138 (2015).ADS 
Article 

Google Scholar 
Duggan, I. C. et al. Identifying invertebrate invasions using morphological and molecular analyses: North American Daphnia ‘pulex’ in New Zealand fresh waters. Aquat. Invasions 7, 585–590 (2012).Article 

Google Scholar 
Ye, Z. et al. The rapid, mass invasion of New Zealand by North American Daphnia “pulex”. Limnol. Oceanogr. 66, 2673–2683 (2021).ADS 
Article 

Google Scholar 
Paland, S., Colbourne, J. K. & Lynch, M. Evolutionary history of contagious asexuality in Daphnia pulex. Evolution 59, 800–813 (2005).CAS 
PubMed 
Article 

Google Scholar 
Muller, H. J. The relation of recombination to mutational advance. Mutat. Res. 106, 2–9 (1964).CAS 
PubMed 
Article 

Google Scholar 
Felsenstein, J. The evolutionary advantage of recombination. Genetics 78, 737–756 (1974).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Paland, S. & Lynch, M. Transitions to asexuality result in excess amino acid substitutions. Science 311, 990–992 (2006).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Johnson, S. G. & Howard, R. S. Contrasting patterns of synonymous and nonsynonymous sequence evolution in asexual and sexual freshwater snail lineages. Evolution 61, 2728–2735 (2007).PubMed 
Article 

Google Scholar 
Neiman, M. et al. Accelerated mutation accumulation in asexual lineages of a freshwater snail. Mol. Biol. Evol. 27, 954–963 (2010).CAS 
PubMed 
Article 

Google Scholar 
Henry, L., Schwander, T. & Crespi, B. J. Deleterious mutation accumulation in asexual Timema stick insects. Mol. Biol. Evol. 29, 401–408 (2012).CAS 
PubMed 
Article 

Google Scholar 
Tucker, A. E. et al. Population-genomic insights into the evolutionary origin and fate of obligately asexual Daphnia pulex. Proc. Natl. Acad. Sci. 110, 15740–15745 (2013).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Colbourne, J. K. et al. The ecoresponsive genome of Daphnia pulex. Science 331, 555–561 (2011).ADS 
CAS 
PubMed 
PubMed Central 
Article 

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

Google Scholar 
Ye, Z. et al. A new reference genome assembly for the microcrustacean Daphnia pulex. G3 (Bethesda) 7, 1405–1416 (2017).CAS 
Article 

Google Scholar 
Keith, N. et al. High mutational rates of large-scale duplication and deletion in Daphnia pulex. Genome Res. 26, 60–69 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Hall, D. J. An experimental approach to the dynamics of a natural population of Daphnia galeata mendotae. Ecology 45, 94–112 (1964).Article 

Google Scholar 
McCauley, E., Murdoch, W. W. & Nisbet, R. M. Growth, reproduction, and mortality of Daphnia pulex Leydig: Life at low food. Ecology 4, 505–514 (1990).
Google Scholar 
Xu, S. et al. High mutation rates in the mitochondrial genomes of Daphnia pulex. Mol. Biol. Evol. 29, 763–769 (2012).CAS 
PubMed 
Article 

Google Scholar 
Zheng, Y., Peng, R., Kuro-o, M. & Zeng, X. Exploring patterns and extent of bias in estimating divergence time from mitochondrial DNA sequence data in a particular lineage: A case study of salamanders (Order Caudata). Mol. Biol. Evol. 28, 2521–2535 (2011).CAS 
PubMed 
Article 

Google Scholar 
Zaret, T. M. Predation and Freshwater Communities (Yale University Press, New Haven, 1980).
Google Scholar 
Lynch, M. Predation, competition, and zooplankton community structure: An experimental study. Limnol. Oceanogr. 24, 253–272 (1979).ADS 
Article 

Google Scholar 
Mills, E. L. & Forney, J. L. Impact on Daphnia pulex of predation by young yellow perch in Oneida Lake, New York. Trans. Am. Fish. Soc. 112(2A), 154–161 (1983).Article 

Google Scholar 
Craddock, D. R. Effects of increased water temperature on Daphnia pulex. Fish. Bull. 74, 403–408 (1976).
Google Scholar 
Maruoka, N. & Urabe, J. Inter and intraspecific competitive abilities and the distribution ranges of two Daphnia species in Eurasian continental islands. Popul. Ecol. 62, 353–363 (2020).Article 

Google Scholar 
Dodson, S. I. & Hanazato, T. Commentary on effects of anthropogenic and natural organic chemicals on development, swimming behavior, and reproduction of Daphnia, a key member of aquatic ecosystems. Environ. Health Perspect. 103(Suppl 4), 7–11 (1995).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Claska, M. E. & Gilbert, J. J. The effect of temperature on the response of Daphnia to toxic cyanobacteria. Freshw. Biol. 39, 221–232 (1998).Article 

Google Scholar 
Bast, J. et al. Consequences of asexuality in natural populations: Insights from stick insects. Mol. Biol. Evol. 35, 1668–1677 (2018).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Hartfield, M. Evolutionary genetic consequences of facultative sex and outcrossing. J Evol Biol 29, 5–22 (2016).CAS 
PubMed 
Article 

Google Scholar 
Hörandl, E. et al. Genome evolution of asexual organisms and the paradox of sex in eukaryotes. In Evolutionary Biology—A Transdisciplinary Approach (ed. Pontarotti, P.) (Springer, Cham, 2020). https://doi.org/10.1007/978-3-030-57246-4_7.Chapter 

Google Scholar 
Lynch, M., Bürger, R., Butcher, D. & Gabriel, W. The mutational meltdown in asexual populations. J. Hered. 84, 339–344 (1993).CAS 
PubMed 
Article 

Google Scholar 
Gordo, I. & Charlesworth, B. The degeneration of asexual haploid populations and the speed of Muller’s ratchet. Genetics 154, 1379–1387 (2000).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Downing, J. A. et al. The global abundance and size distribution of lakes, ponds, and impoundments. Limnol. Oceanogr. 51, 2388–2397 (2006).ADS 
Article 

Google Scholar 
McDonald, C. P., Rover, J. A., Stets, E. G. & Striegl, R. G. The regional abundance and size distribution of lakes and reservoirs in the United States and implications for estimates of global lake extent. Limnol. Oceanogr. 57, 597–606 (2012).ADS 
Article 

Google Scholar 
De Meester, L., Góme, A., Okamura, B. & Schwenk, K. The monopolization hypothesis and the dispersal-gene flow paradox in aquatic organisms. Acta Oecol. 23, 121–135 (2002).ADS 
Article 

Google Scholar 
Fukami, T., Bezemer, T. M., Mortimer, S. R. & Van Der Putten, W. H. Species divergence and trait convergence in experimental plant community assembly. Ecol. Lett. 8, 1283–1290 (2005).Article 

Google Scholar 
Makino, T. & Kawata, M. Invasive invertebrates associated with highly duplicated gene content. Mol. Ecol. 28, 1652–1663 (2019).CAS 
PubMed 
Article 

Google Scholar 
Kondrashov, F. A. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc. R. Soc. Lond. B Biol. Sci. 279, 5048–5057 (2012).
Google Scholar 
Barrick, J. E. & Lenski, R. E. Genome dynamics during experimental evolution. Nat. Rev. Genet. 14, 827–839 (2013).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Rocha, E. P. C. Neutral theory, microbial practice: Challenges in bacterial population genetics. Mol. Biol. Evol. 35, 1338–1347 (2018).CAS 
PubMed 
Article 

Google Scholar 
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Tanabe, A. S. Kakusan4 and Aminosan: Two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data. Mol. Ecol. Resour. 11, 914–921 (2011).PubMed 
Article 

Google Scholar 
Stamatakis, A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Tian, X., Ohtsuki, H. & Urabe, J. Evolution of asexual Daphnia pulex in Japan: Variations and covariations of the digestive, morphological and life history traits. BMC Evol. Biol. 19, 122 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Chen, Y. et al. SOAPnuke: A MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience 7, 1–6 (2018).ADS 
PubMed 
PubMed Central 

Google Scholar 
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2019).Article 
CAS 

Google Scholar 
Lee, T. H. et al. SNPhylo: A pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics 15, 162 (2014).PubMed 
PubMed Central 
Article 

Google Scholar 
R Core Team, R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, Austria, 2019). https://www.R-project.org/ More

Cooke, S. J. et al. Knowledge co-production: A pathway to effective fisheries management, conservation, and governance. Fisheries 46, 89–97 (2021).Article 

Google Scholar 
Kobluk, H. M. et al. Indigenous knowledge of key ecological processes confers resilience to a small-scale kelp fishery. People Nat. 3, 723–739 (2021).Article 

Google Scholar 
Lee, L. C. et al. Drawing on indigenous governance and stewardship to build resilient coastal fisheries: People and abalone along Canada’s northwest coast. Mar. Policy 109, 103701 (2019).Article 

Google Scholar 
Reid, A. J. et al. “Two-Eyed Seeing”: An Indigenous framework to transform fisheries research and management. Fish. Fish. 22, 243–261 (2021).Article 

Google Scholar 
Toniello, G., Lepofsky, D., Lertzman-Lepofsky, G., Salomon, A. K. & Rowell, K. 11,500 y of human–clam relationships provide long-term context for intertidal management in the Salish Sea, British Columbia. Proc. Natl Acad. Sci. 116, 22106–22114 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ahn, J. E. & Ronan, A. D. Development of a model to assess coastal ecosystem health using oysters as the indicator species. Estuar., Coast. Shelf Sci. 233, 106528 (2020).CAS 
Article 

Google Scholar 
Skilbeck, C. G., Heap, A. D. & Woodroffe, C. D. Geology and sedimentary history of modern estuaries. in Applications of Paleoenvironmental Techniques in Estuarine Studies (eds. Weckström, K., Saunders, K. M., Gell, P. A. & Skilbeck, C. G.) 45–74 (Springer Netherlands, 2017). https://doi.org/10.1007/978-94-024-0990-1_3.Durham, S. R., Gillikin, D. P., Goodwin, D. H. & Dietl, G. P. Rapid determination of oyster lifespans and growth rates using LA-ICP-MS line scans of shell Mg/Ca ratios. Palaeogeogr., Palaeoclimatol., Palaeoecol. 485, 201–209 (2017).Article 

Google Scholar 
Lockwood, R. & Mann, R. A conservation palaeobiological perspective on Chesapeake Bay oysters. Philos. Trans. R. Soc. B 374, 20190209 (2019).CAS 
Article 

Google Scholar 
Rick, T. C. et al. Millennial-scale sustainability of the Chesapeake Bay native American oyster fishery. Proc. Natl Acad. Sci. 113, 6568–6573 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Thompson, V. D. et al. Ecosystem stability and Native American oyster harvesting along the Atlantic Coast of the United States. Sci. Adv. 6, eaba9652 (2020).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zimmt, J. B., Lockwood, R., Andrus, C. F. T. & Herbert, G. S. Sclerochronological basis for growth band counting: A reliable technique for life-span determination of Crassostrea virginica from the mid-Atlantic United States. Palaeogeogr. Palaeoclimatol. Palaeoecol. 516, 54–63 (2019).Article 

Google Scholar 
Alleway, H. K. & Connell, S. D. Loss of an ecological baseline through the eradication of oyster reefs from coastal ecosystems and human memory. Conserv Biol. 29, 795–804 (2015).PubMed 
Article 

Google Scholar 
Beck, M. W. et al. Oyster reefs at risk and recommendations for conservation, restoration, and management. Bioscience 61, 107–116 (2011).Article 

Google Scholar 
Kirby, M. X. Fishing down the coast: Historical expansion and collapse of oyster fisheries along continental margins. Proc. Natl Acad. Sci. 101, 13096 (2004).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Lotze, H. K. et al. Depletion, degradation, and recovery potential of estuaries and coastal seas. Science 312, 1806 (2006).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Zu Ermgassen, P. S. et al. Historical ecology with real numbers: Past and present extent and biomass of an imperilled estuarine habitat. Proc. R. Soc. B: Biol. Sci. 279, 3393–3400 (2012).Article 

Google Scholar 
Carranza, A., Defeo, O. & Beck, M. Diversity, conservation status and threats to native oysters (Ostreidae) around the Atlantic and Caribbean coasts of South America. Aquat. Conserv.: Mar. Freshw. Ecosyst. 19, 344–353 (2009).Article 

Google Scholar 
Pluckhahn, T. J. & Thompson, V. D. Woodland-period mound building as historical tradition: Dating the mounds and monuments at Crystal River (8CI1). J. Archaeological Sci.: Rep. 15, 73–94 (2017).Article 

Google Scholar 
Waselkov, G. A. Shellfish gathering and shell midden archaeology. Adv. Archaeol. Method Theory 10, 93–210 (1987).Article 

Google Scholar 
McNiven, I. J. Ritualized middening practices. J. Archaeol. Method Theory 20, 552–587 (2013).Article 

Google Scholar 
Hawkes, A. D. et al. Relative sea-level change in northeastern Florida (USA) during the last ~8.0 ka. Quat. Sci. Rev. 142, 90–101 (2016).ADS 
Article 

Google Scholar 
Kelley, J. T., Belknap, D. F. & Claesson, S. Drowned coastal deposits with associated archaeological remains from a sea-level “slowstand”: Northwestern Gulf of Maine, USA. Geology 38, 695–698 (2010).ADS 
Article 

Google Scholar 
Khan, N. S. et al. Drivers of Holocene sea-level change in the Caribbean. Quat. Sci. Rev. 155, 13–36 (2017).ADS 
Article 

Google Scholar 
Love, R. et al. The contribution of glacial isostatic adjustment to projections of sea-level change along the Atlantic and Gulf coasts of North America. Earth’s Future 4, 440–464 (2016).ADS 
Article 

Google Scholar 
Shugar, D. H. et al. Post-glacial sea-level change along the Pacific coast of North America. Quat. Sci. Rev. 97, 170–192 (2014).ADS 
Article 

Google Scholar 
Dougherty, A. J. et al. Redating the earliest evidence of the mid-Holocene relative sea-level highstand in Australia and implications for global sea-level rise. PLoS ONE. 14, e0218430 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Bailey, G. N. The role of molluscs in coastal economies: The results of midden analysis in Australia. J. Archaeol. Sci. 2, 45–62 (1975).Article 

Google Scholar 
Habu, J., Matsui, A., Yamamoto, N. & Kanno, T. Shell midden archaeology in Japan: Aquatic food acquisition and long-term change in the Jomon culture. Quat. Int. 239, 19–27 (2011).Article 

Google Scholar 
Hale, J. C. et al. Submerged landscapes, marine transgression and underwater shell middens: Comparative analysis of site formation and taphonomy in Europe and North America. Quat. Sci. Rev. 258, 106867 (2021).Article 

Google Scholar 
Erlandson, J. M. et al. Shellfish, geophytes, and sedentism on Early Holocene Santa Rosa Island, Alta California, USA. J. Isl. Coast. Archaeol. 15, 504–524 (2020).Article 

Google Scholar 
Rick, T. C. Early to Middle Holocene estuarine shellfish collecting on the islands and mainland coast of the Santa Barbara Channel, California, USA. Open Quaternary 6, 9 (2020).Sanger, D. & Sanger, M. J. Boom and bust on the river: The story of the Damariscotta oyster shell heaps. Archaeol. East. North Am. 14, 65–78 (1986).
Google Scholar 
Moss, M. L. Shellfish gender, and status on the Northwest Coast: Reconciling archaeological, ethnographic, and ethnohistoric records of the Tlingit. Am. Anthropologist 95, 631–652 (1993).Article 

Google Scholar 
Cannon, A., Burchell, M. & Bathurst, R. Trends and strategies in shellfish gathering on the Pacific Northwest Coast of North America. in Early Human Impact on Megamolluscs (eds. Antczak, A. & Cipriani, R.) 7–22 (Archaeopress, 2008).Grier, C., Angelbeck, B. & McLay, E. Terraforming and monumentality as long-term social practice in the Salish Sea region of the Northwest Coast of North America. Hunt. Gatherer Res. 3, 107–132 (2017).Article 

Google Scholar 
Pluckhahn, T. J. & Thompson, V. D. New Histories of Village Life at Crystal River. (University Press of Florida, 2018).Thompson, V. D. et al. Ancient engineering of fish capture and storage in southwest Florida. Proc. Natl Acad. Sci. 117, 8374–8381 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Sassaman, K. E. Complex hunter–gatherers in evolution and history: A North American perspective. J. Archaeol. Res. 12, 227–280 (2004).Article 

Google Scholar 
Luby, E. M. & Gruber, M. F. The dead must be fed: Symbolic meanings of the shellmounds of the San Francisco Bay area. Camb. Archaeol. J. 9, 95–108 (1999).Article 

Google Scholar 
Lightfoot, K. G. & Luby, E. M. Mound building by California hunter-gatherers. in The Oxford Handbook of North American Archaeology (ed. Pauketat, T.) 212–223 (Oxford University Press, 2012).Smith, A. D. T. Archaeological expressions of Holocene cultural and environmental change in coastal Southeast Queensland. (The University of Queensland, 2016).Reeder-Myers, L., Rick, T., Lowery, D., Wah, J. & Henkes, G. Human ecology and coastal foraging at Fishing Bay, Maryland, USA. J. Ethnobiol. 36, 595–616 (2016).Article 

Google Scholar 
Petrie, C. C. Tom Petrie’s reminiscences of Early Queensland (dating from 1837). (Watson, Ferguson & Company, 1904).Eipper, C. Statement of the Origin, Condition and Prospects, of the German Mission to the Aborigines at Moreton Bay, etc. (James Reading, 1841).Watkins, G. Notes on the Aboriginals of Stradbroke and Moreton Islands. Proc. R. Soc. Qld. 8, 40–50 (1891).
Google Scholar 
Ross, A. & with members of the Quandamooka Aboriginal Land Council. Aboriginal approaches to cultural heritage management: A Quandamooka case study. in Australian Archaeology ’95: Proceedings of the 1995 Australian Archaeological Association Annual Conference (eds. Ulm, S., Lilley, I. & Ross, A.) vol. Tempus 6 107–112 (Anthropology Museum, University of Queensland, 1996).Jenkins, J. A. & Gallivan, M. D. Shell on earth: Oyster harvesting, consumption, and deposition practices in the Powhatan Chesapeake. J. Isl. Coast. Archaeol. 15, 384–406 (2020).Article 

Google Scholar 
Hatch, M. B. A. & Wyllie-Echeverria, S. Historic distribution of Ostrea lurida (Olympia oyster) in the San Juan Archipelago. Wash. State Tribal Coll. Univ. Res. J. 1, 38–45 (2016).
Google Scholar 
Swanton, J. R. Social Organization and Social Usages of the Indians of the Creek Confederacy. (Bureau of American Ethnology, 1928).Hening, W. W. The Statutes at Large of Virginia. (1809).Wharton, J. The Bounty of the Chesapeake: Fishing in Colonial Virginia. (Virginia 350th Anniversary Celebration Corporation, 1957).Denys, N. Description géographique et historique des Costes de l’Amérique Septentrionale. Avec l’Histoire naturelle du Pais. (Chez Claude Barbin, 1672).Nicolar, J. The Life and Traditions of the Red Man. (Duke University Press, 2007 Print, 1893).Speck, F. G. Penobscot Man: The Life History of a Forest Tribe in Maine. (University of Pennsylvania Press, 1940).Washburn, K. Passamaquoddy tribe conducts oyster project. Bangor Daily News (1979).Kennedy, V. S. Shifting Baselines in the Chesapeake Bay: An Environmental History. (Johns Hopkins University Press, 2018).de Charlevoix, P. F. X. Journal of a Voyage to North America, Vollume II. Translated by Louise Phelps Kellogg. (The Caxton Club, 1923).Ingersoll, E. The Oyster Industry. (United States Bureau of Fisheries, United States Census Office, Government Printing Office, 1881).Brice, J. J. Report on the fish and fisheries of the coastal waters of Florida. in Report of the Commissioner for the Year Ending June 30, 1896 263–242 (U.S. Commission of Fish and Fisheries, U.S. Government Printing Office, 1896).Blake, B. & Zu Ermgassen, P. S. E. The history and decline of Ostrea lurida in Willapa Bay, Washington. J. Shellfish Res. 34, 273–280 (2015).Article 

Google Scholar 
Thurstan, R. H. et al. Charting two centuries of transformation in a coastal social-ecological system: A mixed methods approach. Global Environmental Change 61, 102058 (2020).Schulte, D. M. History of the Virginia oyster fishery, Chesapeake Bay, USA. Front. Mar. Sci. 4, 127 (2017).Fletcher, M.-S., Hamilton, R., Dressler, W. & Palmer, L. Indigenous knowledge and the shackles of wilderness. Proc. Natl Acad. Sci. 118, e2022218118 (2021).Ross, A., Coghill, S. & Coghill, B. Discarding the evidence: The place of natural resources stewardship in the creation of the Peel Island Lazaret Midden, Moreton Bay, southeast Queensland. Quat. Int. 385, 177–190 (2015).Article 

Google Scholar 
Reeder-Myers, L. A. & Rick, T. C. Kayak surveys in estuarine environments: addressing sea level rise and climate change. Antiquity 93, 1040–1051 (2019).Article 

Google Scholar 
Savarese, M., Walker, K. J., Stingu, S., Marquardt, W. H. & Thompson, V. The effects of shellfish harvesting by aboriginal inhabitants of Southwest Florida (USA) on productivity of the eastern oyster: Implications for estuarine management and restoration. Anthropocene 16, 28–41 (2016).Article 

Google Scholar 
Lulewicz, I. H., Thompson, V. D., Cramb, J. & Tucker, B. Oyster paleoecology and native American subsistence practices on Ossabaw Island, Georgia, USA. J. Archaeol. Sci.: Rep. 15, 282–289 (2017).
Google Scholar 
Hesterberg, S. G. et al. Prehistoric baseline reveals substantial decline of oyster reef condition in a Gulf of Mexico conservation priority area. Biol. Lett. 16, 20190865 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Cannarozzi, N. R. & Kowalewski, M. Seasonal oyster harvesting recorded in a Late Archaic period shell ring. PloS ONE. 14, e0224666 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Cook-Patton, S. C., Weller, D., Rick, T. C. & Parker, J. D. Ancient experiments: Forest biodiversity and soil nutrients enhanced by Native American middens. Landsc. Ecol. 29, 979–987 (2014).Article 

Google Scholar 
Stalter, R. & Kincaid, D. The vascular flora of five Florida shell middens. J. Torre. Botanical Soc. 131, 93–103 (2004).Article 

Google Scholar 
Kirby, M. X. & Miller, H. M. Response of a benthic suspension feeder (Crassostrea virginica Gmelin) to three centuries of anthropogenic eutrophication in Chesapeake Bay. Estuar. Coast. Shelf Sci. 62, 679–689 (2005).ADS 
Article 

Google Scholar 
Suttles, W. Variation in habitat and culture on the Northwest Coast. in Coastal Salish Essays 26–44 (University of Washington Press, 1987).Bliege Bird, R. & Nimmo, D. Restore the lost ecological functions of people. Nat. Ecol. Evolution 2, 1050–1052 (2018).Article 

Google Scholar 
Berkes, F. Indigenous ways of knowing and the study of environmental change. J. R. Soc. N.Z. 39, 151–156 (2009).Article 

Google Scholar 
Tengö, M., Malmer, P., Elmqvist, T. & Brondizio, E. S. A Framework for Connecting Indigenous, Local and Scientific Knowledge Systems. (2012).Ellis, E. C. et al. People have shaped most of terrestrial nature for at least 12,000 years. Proc. Natl Acad. Sci.118, e2023483118 (2021).Roberts, P. et al. Reimagining the relationship between Gondwanan forests and Aboriginal land management in Australia’s “Wet Tropics”. Iscience 24, 102190 (2021).Ogburn, D. M., White, I. & McPhee, D. P. The disappearance of oyster reefs from eastern Australian estuaries—impact of colonial settlement or mudworm invasion? Coast. Manag. 35, 271–287 (2007).Article 

Google Scholar 
Diggles, B. K. Historical epidemiology indicates water quality decline drives loss of oyster (Saccostrea glomerata) reefs in Moreton Bay, Australia. N.Z. J. Mar. Freshw. Res. 47, 561–581 (2013).CAS 
Article 

Google Scholar 
Pritchard, C., Shanks, A., Rimler, R., Oates, M. & Rumrill, S. The Olympia oyster Ostrea lurida: Recent advances in natural history, ecology, and restoration. J. Shellfish Res. 34, 259–271 (2015).Article 

Google Scholar 
Trimble, A. C., Ruesink, J. L. & Dumbauld, B. R. Factors preventing the recovery of a historically overexploited shellfish species, Ostrea lurida Carpenter 1864. J. Shellfish Res. 28, 97–106 (2009).Article 

Google Scholar 
White, J., Ruesink, J. L. & Trimble, A. C. The nearly forgotten oyster: Ostrea lurida Carpenter 1864 (Olympia oyster) history and management in Washington State. J. Shellfish Res. 28, 43–49 (2009).Article 

Google Scholar 
Harding, J. M., Spero, H. J., Mann, R., Herbert, G. S. & Sliko, J. L. Reconstructing early 17th century estuarine drought conditions from Jamestown oysters. Proc. Natl Acad. Sci. 107, 10549–10554 (2010).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Mann, R., Harding, J. M. & Southworth, M. J. Reconstructing pre-colonial oyster demographics in the Chesapeake Bay, USA. Estuar., Coast. Shelf Sci. 85, 217–222 (2009).ADS 
Article 

Google Scholar 
Bayne, B. L. Biology of Oysters. (Elsevier Science & Technology, 2017).Galtsoff, P. S. The American Oyster Crassostrea virginica Gmelin. (United States Government Printing Office, 1964).Kennedy, V. S., Newell, R. I. E. & Eble, A. F. The Eastern Oyster: Crassostrea virginica. (University of Maryland Sea Grant Publications, 1996).Grabowski, J. H., Powers, S. P., Peterson, C. H., Gaskill, D. & Summerson, H. C. Growth and survivorship of non-native (Crassostrea gigas and Crassostrea ariakensis) versus native eastern (Crassostrea virginica) oysters. J. Shellfish Res. 23, 781–793 (2004).
Google Scholar 
Shumway, S. Natural environmental factors. in The eastern oyster Crassostrea virginica (eds. Kennedy, V., Newell, R. & Eble, A.) 467–513 (Maryland Sea Grant, 1996).Lyman, R. L. Paleoenvironmental reconstruction from faunal remains: Ecological basics and analytical assumptions. J. Archaeol. Res. 25, 315–371 (2017).MathSciNet 
Article 

Google Scholar 
Claasen, C. Shells. (Cambridge University Press, 1990).Giovas, C. M. The shell game: Analytic problems in archaeological mollusc quantification. J. Archaeol. Sci. 36, 1557–1564 (2009).Article 

Google Scholar 
Peltier, W. R., Argus, D. F. & Drummond, R. Space geodesy constrains ice age terminal deglaciation: The global ICE-6G_C (VM5a) model: Global Glacial Isostatic Adjustment. J. Geophys. Res.: Solid Earth 120, 450–487 (2015).ADS 
Article 

Google Scholar  More

Argonema gen. nov. Skoupý et Dvořák.Type species: Argonema galeatum.Morphology: Filamentous cyanobacterium, colonies macroscopic, growing in round bulbs and tufts. The filaments are dark green to blue-green, grey-green or brown-green in color. Cells are wider than they are long. Filaments sheathed, sheaths are colorless to light brown, distinct, and variable in length. The filament can protrude from the sheath or the sheath can exceed filament. Trichomes are cylindrical, not attenuated to slightly attenuated towards the end, slightly or not constricted at cell walls. The apical cell can be concave, dark brown, purple-brown to almost black. Cell content often granulated. Necridic cells present, reproduction by hormogonia. The morphological description was based on both culture and fresh material.Etymology: The genus epithet (Argonema) is derived from greek Argo – slow, latent (αργός) and nema – thread (νήμα).A. galeatum sp. nov. Skoupý et Dvořák.Morphology: The cells of A. galeatum are 6.5–9.1 µm (mean 7.81 µm) wide and 1.1–2.5 µm (mean 1.83 µm) long (Figs. 1–5). Filaments are straight, blue-green to gray-green in color. The sheaths are colorless to light brown, distinct, and variable in length. The filament can protrude from the sheath or the sheath can exceed filament. No true branching was observed. Trichomes are cylindrical, not attenuated or slightly attenuated towards the end, slightly or not constricted at cell walls. Some filaments have a concave apical cell that is dark brown, purple-brown to almost black (Fig. 11b). Cell content often granulated. Reproduction by necridic cells and subsequent breaking of the filaments into hormogonia (Fig. 11a,c). The morphological description was based on both culture and fresh material.Figures 1-8Microphotographs of Argonema galeatum (Figs 1–5) and Argonema antarcticum (Figs. 6–8) Trichomes of A. galeatum appear more straight (Fig 2), while trichomes of A. antarcticum form waves (Fig 6) and loops (Fig 7). Scale = 10 µm, wide arrow = necridic cells, arrowhead = granules, asterisk = colored apical cell, circle = empty sheath.Full size imageFigures 9 and 10Histograms of cell dimensions constructed using PAST software. Fig. 9 – Histogram of cell width frequencies in A. galeatum (blue) and A. antarcticum (red). Fig. 10 – Histogram of cell length frequencies in A. galeatum (blue) and A. antarcticum (red).Full size imageHolotype: 38,057, Herbarium of the Department of Botany (OL), Palacký University Olomouc, Czech Republic.Reference strain: Argonema galeatum A003/A1.Type locality: James Ross Island, Western Antarctica, 63.80589S, 57.92147 W.Habitat: Well-developed soil crust.Etymology: Species epithet A. galeatum was derived from latin galea – helmet.A. antarcticum sp. nov. Skoupý et Dvořák.Morphology: The cells are 7.6–9.2 µm (mean 8.52 µm) wide and 1.2–2.8 µm (mean 1.72 µm) long (Figs. 5–8). Filaments are wavy, gray-green to brown-green in color. The sheaths are colorless to light brown, distinct, and variable in length. The filament can protrude from the sheath or the sheath can exceed filament. No true branching was observed. Trichomes are cylindrical, not attenuated or slightly attenuated towards the end with a concave apical cell, slightly or not constricted at cell walls (Fig. 11d). Necridic cells present (Fig. 11e), reproduction by hormogonia. The morphological description was based on both culture and fresh material.Holotype: 38,058, Herbarium of the Department of Botany (OL), Palacký University, Olomouc, Czech Republic.Reference strain: Argonema antarcticum A004/B2.Type locality: James Ross Island, Western Antarctica, 63.89762S, 57.79743 W.Habitat: Well-developed soil crust.Etymology: Species epithet A. antarcticum was derived from the original sampling site.Morphological variabilityWe used light microscopy to assess the morphology of Argonema from soil crust samples and cultured strains. Argonema is morphologically similar to other Oscillatoriales, such as Lyngbya, Phormidium, and Oscillatoria. In culture, the morphology of A. galeatum and A. antarcticum differed slightly. Filaments of A. antarcticum are wider than cells of A. galeatum, averaging at 8.52 µm (A. galeatum – 7.81 µm). The average cell width/length ratio is 4.54 for A.galeatum and 4.89 for A. antarcticum. The cell width was significantly different between the two species (Nested ANOVA, p  More