Philippa Kaur

Odonnell, C. Population dynamics and survivorship in bats. In Ecology and Behavioral Methods for the Study of Bats (eds Kunz, T. H. & Parsons, S.) 158–176 (The Johns University Press, 2009).
Google Scholar 
Lebreton, J.-D., Burnham, K. P., Clobert, J. & Anderson, D. R. Modeling survival and testing biological hypotheses using marked animals: A unified approach with case studies. Ecol. Monogr. 62, 67–118 (1992).Article 

Google Scholar 
Gibbons, J. W. & Andrews, K. M. PIT tagging: Simple technology at its best. Bioscience 54, 447–454 (2004).Article 

Google Scholar 
Ellison, L. E. et al. A comparison of conventional capture versus PIT reader techniques for estimating survival and capture probabilities of big brown bats (Eptesicus fuscus). Acta Chiropterologica 9, 149–160 (2007).Article 

Google Scholar 
van Harten, E. et al. High detectability with low impact: Optimizing large PIT tracking systems for cave-dwelling bats. Ecol. Evol. 9, 10916–10928 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Schorr, R. A., Ellison, L. E. & Lukacs, P. M. Estimating sample size for landscape-scale mark-recapture studies of North American migratory tree bats. Acta Chiropterologica 16, 231–239 (2014).Article 

Google Scholar 
Baker, G. B. et al. The effect of forearm bands on insectivorous bats (Microchiroptera) in Australia. Wildl. Res. 28, 229–237 (2001).Article 

Google Scholar 
O’Shea, T. J., Ellison, L. E. & Stanley, T. R. Survival estimation in bats: Historical overview, critical appraisal, and suggestions for new approaches. In Sampling Rare or Elusive Species: Concepts, Designs, and Techniques for Estimating Population Parameters (ed. Thompson, W. L.) 297–336 (Island Press, 2004).
Google Scholar 
O’Shea, T. J. et al. Recruitment in a Colorado population of big brown bats: Breeding probabilities, litter size, and first-year survival. J. Mammal. 91, 418–428 (2010).Article 

Google Scholar 
O’Shea, T. J., Ellison, L. E. & Stanley, T. R. Adult survival and population growth rate in Colorado big brown bats (Eptesicus fuscus). J. Mammal. 92, 433–443 (2011).Article 

Google Scholar 
Schorr, R. A. & Siemers, J. L. Population dynamics of little brown bats (Myotis lucifugus) at summer roosts: Apparent survival, fidelity, abundance, and the influence of winter conditions. Ecol. Evol. 11, 7427–7438 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
O’Donnell, C. F. J., Edmonds, H. & Hoare, J. M. Survival of PIT-tagged lesser short-tailed bats (Mystacina tuberculata) through a pest control operation using the toxin pindone in bait stations. N. Z. J. Ecol. 35, 291–295 (2011).
Google Scholar 
Edmonds, H., Pryde, M. & O’Donnell, C. Survival of PIT-tagged lesser short-tailed bats (Mystacina tuberculata) through an aerial 1080 pest control operation. N. Z. J. Ecol. 41, 186–192 (2017).
Google Scholar 
Reusch, C. et al. Differences in seasonal survival suggest species-specific reactions to climate change in two sympatric bat species. Ecol. Evol. 9, 7957–7965 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
IUCN. The IUCN red list of threatened species. Version 2020-2. http://www.iucnredlist.org (2020).Lentini, P. E., Bird, T. J., Griffiths, S. R., Godinho, L. N. & Wintle, B. A. A global synthesis of survival estimates for microbats. Biol. Lett. 11, 20150371 (2015).PubMed 
PubMed Central 
Article 

Google Scholar 
Culina, A., Linton, D. M. & Macdonald, D. W. Age, sex, and climate factors show different effects on survival of three different bat species in a woodland bat community. Glob. Ecol. Conserv. 12, 263–271 (2017).Article 

Google Scholar 
Frick, W. F., Reynolds, D. S. & Kunz, T. H. Influence of climate and reproductive timing on demography of little brown myotis Myotis lucifugus. J. Anim. Ecol. 79, 128–136 (2010).PubMed 
Article 

Google Scholar 
Schorcht, W., Bontadina, F. & Schaub, M. Variation of adult survival drives population dynamics in a migrating forest bat. J. Anim. Ecol. 78, 1182–1190 (2009).PubMed 
Article 

Google Scholar 
Sendor, T. & Simon, M. Population dynamics of the pipistrelle bat: Effects of sex, age and winter weather on seasonal survival. J. Anim. Ecol. 72, 308–320 (2003).Article 

Google Scholar 
Sripathi, K., Raghuram, H., Rajasekar, R., Karuppudurai, T. & Abraham, S. G. Population size and survival in the indian false vampire bat Megaderma lyra. Acta Chiropterologica 6, 145–154 (2004).Article 

Google Scholar 
Papadatou, E., Butlin, R. K., Pradel, R. & Altringham, J. D. Sex-specific roost movements and population dynamics of the vulnerable long-fingered bat, Myotis capaccinii. Biol. Conserv. 142, 280–289 (2009).Article 

Google Scholar 
López-Roig, M. & Serra-Cobo, J. Impact of human disturbance, density, and environmental conditions on the survival probabilities of pipistrelle bat (Pipistrellus pipistrellus). Popul. Ecol. 56, 471–480 (2014).Article 

Google Scholar 
Wilkinson, G. S. & Adams, D. M. Recurrent evolution of extreme longevity in bats. Biol. Lett. 15, 20180860 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
DELWP. National Recovery Plan for the Southern Bent-wing Bat Miniopterus orianae bassanii (2020).Lumsden, L. & Gray, P. Longevity record for a southern bent-wing bat Miniopterus schreibersii bassanii. Australas. Bat Soc. Newsl. 16, 43–44 (2001).
Google Scholar 
Holz, P. H. et al. Virus survey in populations of two subspecies of bent-winged bats (Miniopterus orianae bassanii and oceanensis) in south-eastern Australia reveals a high prevalence of diverse herpesviruses. PLoS ONE 13, e0197625 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Holz, P. H., Lumsden, L. F., Marenda, M. S., Browning, G. F. & Hufschmid, J. Two subspecies of bent-winged bats (Miniopterus orianae bassanii and oceanensis) in southern Australia have diverse fungal skin flora but not Pseudogymnoascus destructans. PLoS ONE 13, e0204282 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Holz, P. H., Lumsden, L. F. & Hufschmid, J. Ectoparasites are unlikely to be a primary cause of population declines of bent-winged bats in south-eastern Australia. Int. J. Parasitol. Parasites Wildl. 7, 423–428 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Holz, P. H., Lumsden, L. F., Legione, A. R. & Hufschmid, J. Polychromophilus melanipherus and haemoplasma infections not associated with clinical signs in southern bent-winged bats (Miniopterus orianae bassanii) and eastern bent-winged bats (Miniopterus orianae oceanensis). Int. J. Parasitol. Parasites Wildl. 8, 10–18 (2019).PubMed 
Article 

Google Scholar 
Holz, P. H., Clark, P., McLelland, D. J., Lumsden, L. F. & Hufschmid, J. Haematology of southern bent-winged bats (Miniopterus orianae bassanii) from the Naracoorte Caves National Park, South Australia. Comp. Clin. Pathol. 29, 231–237 (2020).CAS 
Article 

Google Scholar 
Dwyer, P. D. The population pattern of Miniopterus schreibersii (Chiroptera) in north-eastern New South Wales. Aust. J. Zool. 14, 1073–1137 (1966).Article 

Google Scholar 
Dwyer, P. D. Mortality factors of the bent-winged bat. Vic. Nat. 83, 31–36 (1966).
Google Scholar 
Dwyer, P. D. Seasonal changes in activity and weight of Miniopterus schreibersii blepotis (Chiroptera) in north-eastern NSW. Aust. J. Zool. 12, 52–69 (1964).Article 

Google Scholar 
Bureau of Meteorology. Drought archive. http://www.bom.gov.au/climate/drought/archive.shtml (2019).Dwyer, P. D. Population ranges of Miniopterus schreibersii (Chiroptera) in south-eastern Australia. Aust. J. Zool. 17, 665–686 (1969).Article 

Google Scholar 
Fleischer, T., Gampe, J., Scheuerlein, A. & Kerth, G. Rare catastrophic events drive population dynamics in a bat species with negligible senescence. Sci. Rep. 7, 7370 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Thomas, D. W. Hibernating bats are sensitive to nontactile human disturbance. J. Mammal. 76, 940–946 (1995).Article 

Google Scholar 
Reeder, D. M. et al. Frequent arousal from hibernation linked to severity of infection and mortality in bats with white-nose syndrome. PLoS ONE 7, e38920 (2012).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Turbill, C., Bieber, C. & Ruf, T. Hibernation is associated with increased survival and the evolution of slow life histories among mammals. Proc. R. Soc. B Biol. Sci. 278, 3355–3363 (2011).Article 

Google Scholar 
van Harten, E. Population Dynamics of the Critically Endangered, Southern Bent-Winged Bat Miniopterus orianae bassanii (La Trobe University, 2020).
Google Scholar 
PIRSA. History of the south east drainage system – summary. https://www.pir.sa.gov.au/aghistory/natural_resources/water_resources_ag_dev/history_of_the_south_east_drainage_system_-_summary/history_of_the_south_east_drainage_system_-_summary#_ftnref2 (2017).Harding, C., Herpich, D. & Cranswick, R. H. Examining temporal and spatial changes in surface water hydrology of groundwater dependent ecosystems using WOfS (Water Observations from Space): Southern Border Groundwaters Agreement area, South East South Australia. (2018).Holz, P. H., Lumsden, L. F., Reardon, T., Gray, P. & Hufschmid, J. Does size matter? Morphometrics of southern bent-winged bats (Miniopterus orianae bassanii) and eastern bent-winged bats (Miniopterus orianae oceanensis). Aust. Zool. AZ https://doi.org/10.7882/AZ.2019.019 (2020).Article 

Google Scholar 
Rashid, M. M. & Beecham, S. Characterization of meteorological droughts across South Australia. Meteorol. Appl. 26, 556–568 (2019).Article 

Google Scholar 
Culina, A., Linton, D. M., Pradel, R., Bouwhuis, S. & Macdonald, D. W. Live fast, don’t die young: Survival–reproduction trade-offs in long-lived income breeders. J. Anim. Ecol. 88, 746–756 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Kunz, T. H., Whitaker, J. O. & Wadanoli, M. D. Dietary energetics of the insectivorous Mexican free-tailed bat (Tadarida brasiliensis) during pregnancy and lactation. Oecologia 101, 407–415 (1995).CAS 
PubMed 
Article 

Google Scholar 
Adams, R. A. & Hayes, M. A. Water availability and successful lactation by bats as related to climate change in arid regions of western North America. J. Anim. Ecol. 77, 1115–1121 (2008).PubMed 
Article 

Google Scholar 
Henry, M., Thomas, D. W., Vaudry, R. & Carrier, M. Foraging distances and home range of pregnant and lactating little brown bats (Myotis lucifugus). J. Mammal. 83, 767–774 (2002).Article 

Google Scholar 
Lučan, R. & Radil, J. Variability of foraging and roosting activities in adult females of Daubenton’s bat (Myotis daubentonii) in different seasons. Biologia (Bratisl.) 65 (2010).Amorim, F., Jorge, I., Beja, P. & Rebelo, H. Following the water? Landscape-scale temporal changes in bat spatial distribution in relation to Mediterranean summer drought. Ecol. Evol. 8, 5801–5814 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
O’Donnell, C. F. J. Timing of breeding, productivity and survival of long-tailed bats Chalinolobus tuberculatus (Chiroptera: Vespertilionidae) in cold-temperate rainforest in New Zealand. J. Zool. 257, 311–323 (2002).Article 

Google Scholar 
Holz, P. H., Stent, A., Lumsden, L. F. & Hufschmid, J. Trauma found to be a significant cause of death in a pathological investigation of bent-winged bats (Miniopterus orianae). J. Zoo Wildl. Med. 50, 966–971 (2020).PubMed 
Article 

Google Scholar 
Hughes, P. M., Rayner, J. M. V. & Jonesg, G. Ontogeny of ‘true’ flight and other aspects of growth in the bat Pipistrellus pipistrellus. J. Zool. 236, 291–318 (1995).Article 

Google Scholar 
Wund, M. A. Learning and the development of habitat-specific bat echolocation. Anim. Behav. 70, 441–450 (2005).Article 

Google Scholar 
McGuire, L. P. et al. Common condition indices are no more effective than body mass for estimating fat stores in insectivorous bats. J. Mammal. 99, 1065–1071 (2018).Article 

Google Scholar 
Mispagel, C. et al. DDT and metabolites residues in the southern bent-wing bat (Miniopterus schreibersii bassanii) of south-eastern Australia. Chemosphere 55, 997–1003 (2004).CAS 
PubMed 
Article 

Google Scholar 
Allinson, G. et al. Organochlorine and trace metal residues in adult southern bent-wing bat (Miniopterus schreibersii bassanii) in southeastern Australia. Chemosphere 64, 1464–1471 (2006).CAS 
PubMed 
Article 

Google Scholar 
Kolkert, H., Andrew, R., Smith, R., Rader, R. & Reid, N. Insectivorous bats selectively source moths and eat mostly pest insects on dryland and irrigated cotton farms. Ecol. Evol. https://doi.org/10.1002/ece3.5901 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Sherwin, H. A., Montgomery, W. I. & Lundy, M. G. The impact and implications of climate change for bats. Mammal Rev. 43, 171–182 (2013).Article 

Google Scholar 
O’Shea, T. J., Cryan, P. M., Hayman, D. T. S., Plowright, R. K. & Streicker, D. G. Multiple mortality events in bats: A global review. Mammal Rev. 46, 175–190 (2016).Article 

Google Scholar 
Mundinger, C., Scheuerlein, A. & Kerth, G. Long-term study shows that increasing body size in response to warmer summers is associated with a higher mortality risk in a long-lived bat species. Proc. R. Soc. B Biol. Sci. 288, 20210508 (2021).Article 

Google Scholar 
Adams, R. A. & Hayes, M. A. Assemblage-level analysis of sex-ratios in Coloradan bats in relation to climate variables: A model for future expectations. Glob. Ecol. Conserv. 14, e00379 (2018).Article 

Google Scholar 
Crichton, E. G., Seamark, R. F. & Krutzsch, P. H. The status of the corpus luteum during pregnancy in Miniopterus schreibersii (Chiroptera: Vespertilionidae) with emphasis on its role in developmental delay. Cell Tissue Res. 258, 183–201 (1989).CAS 
PubMed 
Article 

Google Scholar 
Olsen, I. C. The analysis of continuous mark-recapture data (Norwegian University of Science and Technology, 2006).
Google Scholar 
Barbour, A. B., Ponciano, J. M. & Lorenzen, K. Apparent survival estimation from continuous mark-recapture/resighting data. Methods Ecol. Evol. 4, 846–853 (2013).Article 

Google Scholar 
van Harten, E. et al. Recovery of southern bent-winged bats (Miniopterus orianae bassanii) after PIT-tagging and the use of surgical adhesive. Aust. Mammal. 42, 216–219 (2020).Article 

Google Scholar 
McDonald, T. L., Amstrup, S. C. & Manly, B. F. Tag loss can bias Jolly-Seber capture-recapture estimates. Wildl. Soc. Bull. 31, 814–822 (2003).
Google Scholar 
van Harten, E. et al. Low rates of PIT-tag loss in an insectivorous bat species. J. Wildl. Manag. 85, 1739–1743 (2021).Article 

Google Scholar 
Lebl, K. & Ruf, T. An easy way to reduce PIT-tag loss in rodents. Ecol. Res. 25, 251–253 (2010).Article 

Google Scholar 
Rigby, E. L., Aegerter, J., Brash, M. & Altringham, J. D. Impact of PIT tagging on recapture rates, body condition and reproductive success of wild Daubenton’s bats (Myotis daubentonii). Vet. Rec. 170, 101 (2012).CAS 
PubMed 
Article 

Google Scholar 
Locatelli, A. G., Ciuti, S., Presetnik, P., Toffoli, R. & Teeling, E. Long-term monitoring of the effects of weather and marking techniques on body condition in the Kuhl’s pipistrelle bat, Pipistrellus kuhlii. Acta Chiropterologica 21, 87–102 (2019).Article 

Google Scholar 
Paniw, M. et al. The myriad of complex demographic responses of terrestrial mammals to climate change and gaps of knowledge: A global analysis. J. Anim. Ecol. 90, 1398–1407 (2021).PubMed 
Article 

Google Scholar 
Frick, W. F., Kingston, T. & Flanders, J. A review of the major threats and challenges to global bat conservation. Ann. N. Y. Acad. Sci. 1469, 5–25 (2020).PubMed 
Article 

Google Scholar 
Brunet-Rossinni, A. K. & Wilkinson, G. S. Methods for age estimation and the study of senescence in bats. In Ecological and Behavioral Methods for the Study of Bats (eds Kunz, T. H. & Parsons, S.) 315–325 (Johns Hopkins University Press, 2009).
Google Scholar 
Churchill, S. Australian Bats (Allen and Unwin, 2008).
Google Scholar 
Laake, J. L. RMark: An R interface for analysis of capture-recapture data with MARK. 25 (2013).Burnham, K. P. & Anderson, D. R. Model Selection and Multimodel Inference (Springer, 2002). https://doi.org/10.1007/b97636.Book 
MATH 

Google Scholar 
Caswell, H. Matrix population models. In Encyclopedia of Environmetrics (eds El-Shaarawi, A. H. & Piegorsch, W. W.) (Wiley, Berlin, 2006). https://doi.org/10.1002/9780470057339.vam006m.Chapter 

Google Scholar 
Dwyer, P. D. The breeding biology of Miniopterus schreibersii blepotis (Termminck) (Chiroptera) in north-eastern NSW. Aust. J. Zool. 11, 219–240 (1963).Article 

Google Scholar 
Richardson, E. G. The biology and evolution of the reproductive cycle of Miniopterus schreibersii and M. australis (Chiroptera: Vespertilionidae). J. Zool. 183, 353–375 (1977).Article 

Google Scholar  More

Water samples were filtered twice (see Methods), first through a large filter (0.45 µm, LF or “Large Filter”) and then the filtrate was passed through a small filter (0.05 µm, UF or “Ultrafine Fraction”). Using whole genome shotgun metagenomics from four water samples (LF92 and UF92 from the 92 m depth, LF99 and UF99 from the 99 m depth) as well as one sediment sample, we provide the first comprehensive whole genome shotgun metagenomics investigation of this section of the lake and highlight both the taxonomic composition and potential metabolic strategies for survival, as well as identify areas for deeper investigation.Cell counts and dissolved nutrientsIn order to determine the habitability of the anoxic basin, the cell counts were measured in the oxycline (75 m depth) and the anoxic region (92 and 99 m depth), where oxygen content is  More

Farmers at a Great Green Wall site in Niger. Researchers have found that the project is not always benefiting the most vulnerable people.Credit: Boureima Hama/AFP/Getty

It’s now 15 years since the African Union gave its blessing to Africa’s Great Green Wall, one of the world’s most ambitious ecological-restoration schemes. The project is intended to combat desertification across the width of Africa, and spans some 8,000 kilometres, from Senegal to Djibouti. Its ambition is staggering: it aims to restore 100 million hectares of degraded land by 2030, capturing 250 million tonnes of carbon dioxide and creating 10 million jobs in the process. But it continues to struggle.An assessment two years ago by independent experts commissioned by the United Nations stated that somewhere between 4% and 20% of the restoration target had been achieved (go.nature.com/39zqgkr). That figure has not changed, according to the latest edition of Global Land Outlook (go.nature.com/3kdjtw5) from the UN Convention to Combat Desertification (UNCCD), out last week. Equally concerning is the fact that funding for the project continues to lag. Africa’s governments and international donors need to find around US$30 billion to reach the 100-million-hectare target. So far, $19 billion has been raised.A pandemic — and now a cost-of-living crisis — has placed demands on all governments, and that means countries might be expected to reduce their green-wall commitments. But the project continues to be weighed down by other difficulties, including the complex system through which it is funded and governed, as well as how its success is measured. These problems can and must be fixed, otherwise it will struggle to achieve its goals.One potential solution — improved metrics — comes from an analysis published last year by Matthew Turner at the University of Wisconsin–Madison and his colleagues (M. D. Turner et al. Land Use Policy 111, 105750; 2021). The researchers explored limitations in the Great Green Wall project metrics by assessing the impact of World Bank funding from 2006 to 2020. As their work indicates, definitions of success depend on which measure is used.In Niger, for example, green-wall projects could be said to be succeeding if measured by the area of eroded soil that has been recovered or by the number of trees that have been planted. But the authors report that these gains were not necessarily benefiting the most vulnerable people. In places, women were being excluded from employment in green-wall projects, and in some cases, local administrations looked to privatize restored land that might instead have been owned by everyone in a community.Broader problems with metrics are highlighted in the UN’s latest land-degradation report. This estimates that nearly half of the land that has been pledged for restoration worldwide will be planted predominantly with fast-growing trees and plants. This will provide only a fraction of the ecosystem services produced by forests that are allowed to naturally regenerate, including significantly less carbon storage, groundwater recharge and wildlife habitat.The Great Green Wall project also needs more predictable funding and more transparent governance. The project was conceived by Africa’s leaders for the benefit of the continent’s people, on the basis of warnings from scientists about the risks of desertification and land degradation. The original idea was not brought to Africa by international donors, as is often the case in international science-based development projects. But it still relies on donor financing, and lots of it — and that brings other problems, among them coordination challenges.The project is the responsibility of an organization set up by the African Union called the Pan African Agency of the Great Green Wall, based in Nouakchott, Mauritania. But some donors, such as the European Union and the World Bank, are not providing most of their Great Green Wall funding through this agency. Instead, they often deal directly with individual governments, because this gives them more control over how their money is spent. It is unfair to expect the Pan African Agency to coordinate a raft of donors doing one-on-one deals with individual countries. Bypassing the Pan African Agency also creates a problem for transparency, because it makes it harder for the African Union to determine precisely who is funding what.In January 2021, at an international biodiversity summit hosted by France, Emmanuel Macron, the French president, announced that the Great Green Wall would receive an extra $14 billion in funding for 5 years. He also said that a new body, called the Great Green Wall Accelerator, based in Bonn, Germany, would be responsible for pulling together funding pledges and tracking progress against targets. This is well-intentioned, but the accelerator needs to coordinate its work with the Pan African Agency. It is not yet clear how this will happen.A potentially more transformative solution was proposed two years ago by a group of UN-appointed experts. They recommended that a single trust fund be set up that all donors could contribute to and through which they could decide funding priorities together. Regrettably, this has not happened, and observers say it is not likely to happen in the current climate.This month, the international community will come together in Abidjan, Côte d’Ivoire, for the 15th conference of the parties to the UNCCD. The green wall’s funders and participating countries will all be there. If a single trust fund is off the table, they must work together to find a better way to coordinate their green-wall project activities. It is also essential that they study the findings of Turner and colleagues’ review. Along with a focus on existing metrics, the Great Green Wall needs evaluation criteria that take better account of the needs of all people in participating countries, particularly the most vulnerable. More

Kollas, C., Körner, C. & Randin, C. F. Spring frost and growing season length co-control the cold range limits of broad-leaved trees. J. Biogeogr. 41, 773–783 (2014).Article 

Google Scholar 
Lenz, A., Hoch, G., Körner, C. & Vitasse, Y. Convergence of leaf-out towards minimum risk of freezing damage in temperate trees. Funct. Ecol. 30, 1480–1490 (2016).Article 

Google Scholar 
Körner, C. et al. Where, why and how? Explaining the low-temperature range limits of temperate tree species. J. Ecol. 104, 1076–1088 (2016).Article 
CAS 

Google Scholar 
Körner, C. Plant adaptation to cold climates. F1000Research 5, 2769 (2016).Article 

Google Scholar 
Vitra, A., Lenz, A. & Vitasse, Y. Frost hardening and dehardening potential intemperate trees from winter to budburst. New Phytol. 216, 113–123 (2017).PubMed 
Article 

Google Scholar 
Dy, G. & Payette, S. Frost hollows of the boreal forest as extreme environments for black spruce tree growth. Can. J. For. Res. 37, 492–504 (2007).Article 

Google Scholar 
Marquis, B., Bergeron, Y., Simard, M. & Tremblay, F. Growing-season frost is a better predictor of tree growth than mean annual temperature in boreal mixedwood forest plantations. Glob. Change Biol. 26, 6537–6554 (2020).ADS 
Article 

Google Scholar 
Hufkens, K. et al. Ecological impacts of a widespread frost event following early spring leaf-out. Glob. Change Biol. 18, 2365–2377 (2012).ADS 
Article 

Google Scholar 
Guo, X., Khare, S., Silvestro, R. & Rossi, S. Minimum spring temperatures at the provenance origin drive leaf phenology in sugar maple populations. Tree Physiol. 40, 1639–1647 (2020).CAS 
PubMed 
Article 

Google Scholar 
Marquis, B., Bergeron, Y., Simard, M. & Tremblay, F. Probability of spring frosts, not growing degree-days, drives onset of spruce bud burst in plantations at the boreal-temperate forest ecotone. Front. Plant Sci. 11, 1031 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Mahony, C. R., Cannon, A. J., Wang, T. & Aitken, S. N. A closer look at novel climates: New methods and insights at continental to landscape scales. Glob. Change Biol. 23, 3934–3955 (2017).ADS 
Article 

Google Scholar 
Roman-Palacios, C. & Wiens, J. Recent responses to climate change reveal the drivers of species extinction and survival. Proc. Natl. Acad. Sci. U.S.A. 117, 4211–4217 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Chuine, I. A unified model for budburst of trees. J. Theor. Biol. 207, 337–347 (2000).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Horvath, P. et al. Improving the representation of high-latitude vegetation distribution in dynamic global vegetation models. Biogeosciences 18, 95–112 (2021).ADS 
CAS 
Article 

Google Scholar 
Wullschleger, S. D. et al. Plant functional types in Earth system models: Past experiences and future directions for application of dynamic vegetation models in high-latitude ecosystems. Ann. Bot. Lond. 114, 1–16 (2014).CAS 
Article 

Google Scholar 
Deser, C. et al. Insights from earth system model initial-condition large ensembles and future prospects. Nat. Clim. Change 10, 277–286 (2020).ADS 
Article 

Google Scholar 
Machete, R. L. & Smith, L. A. Demonstrating the value of larger ensembles in forecasting physical systems. Tellus A Dyn. Meteorol. Oceanogr. 68, 28393 (2016).Article 

Google Scholar 
Deser, C., Phillips, A., Bourdette, V. & Teng, H. Uncertainty in climate change projections: The role of internal variability. Clim. Dyn. 38, 527–546 (2012).Article 

Google Scholar 
Leduc, M. et al. The ClimEx project: A 50-member ensemble of climate change projections at 12-km resolution over Europe and Northeastern North America with the Canadian regional climate model (CRM5). J. Appl. Meteor. Climatol. 58, 663–693 (2019).ADS 
Article 

Google Scholar 
Innocenti, S., Mailhot, A., Leduc, M., Cannon, A. J. & Frigon, A. Projected changes in the probability distributions, seasonality, and spatiotemporal scaling of daily and subdaily extreme precipitation simulated by a 50-member ensemble over Northeastern North America. J. Geophys. Res. Atmos. 124, 19 (2019).Article 

Google Scholar 
Kay, J. E. et al. The community earth system model (CESM) large ensemble project: A community resource for studying climate change in the presence of internal climate variability. Bull. Am. Meteor. Soc. 96, 1333–1349 (2015).ADS 
Article 

Google Scholar 
Thompson, D. W. J., Barnes, E. A., Deser, C., Foust, W. E. & Phillips, A. S. Quantifying the role of internal climate variability in future climate trends. J. Clim. 28, 6443–6456 (2015).ADS 
Article 

Google Scholar 
Kumar, D. & Ganguly, A. R. Intercomparison of model response and internal variability across climate model ensembles. Clim. Dyn. 51, 207–219 (2018).Article 

Google Scholar 
Gu, L. et al. The contribution of internal climate variability to climate change impacts on droughts. Sci. Total Environ. 684, 229–246 (2019).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Mittermeier, M., Braun, M., Hofstätter, M., Wang, Y. & Ludwig, R. Detecting climate change effects on Vb cyclones in a 50-member single-model ensemble using machine learning. Geophys. Res. Lett. 46, 14653–14661 (2019).ADS 
Article 

Google Scholar 
Fyfe, J. C. et al. Large near-term projected snowpack loss over the western United States. Nat. Commun. 8, 14996 (2017).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).MATH 
Book 

Google Scholar 
Liu, Q. et al. Extension of the growing season increases vegetation exposure to frost. Nat. Commun. 9, 426 (2018).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Zohner, C. M. et al. Late-spring frost risk between 1959 and 2017 decreased in North America but increased in Europe and Asia. Proc. Natl. Acad. Sci. U.S.A. 117, 12192–12200 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ma, Q., Huang, J.-G., Hänninen, H. & Berninger, F. Divergent trends in the risk of spring frost damage to trees in Europe with recent warming. Glob. Change Biol. 25, 351–360 (2018).ADS 
Article 

Google Scholar 
Cannell, M. G. R. & Smith, R. I. Climatic warming, spring budburst and forest damage on trees. J. Appl. Ecol. 23, 177–191 (1986).Article 

Google Scholar 
Morin, X. & Chuine, I. Will tree species experience increased frost damage due to climate change because of changes in leaf phenology? Can. J. For. Res. 44, 1555–1565 (2014).Article 

Google Scholar 
Fu, Y. et al. Progress in plant phenology modeling under global climate change. Sci. China Earth Sci. 63, 1237 (2020).ADS 
Article 

Google Scholar 
Gill, A. L. et al. Changes in autumn senescence in northern hemisphere deciduous trees: A meta-analysis of autumn phenology studies. Ann Bot. 116, 875–888 (2015).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Perrin, M., Rossi, S. & Isabel, S. N. Synchronisms between bud and cambium phenology in black spruce: Early-flushing provenances exhibit early xylem formation. Tree Physiol. 37, 593–603 (2017).PubMed 
Article 

Google Scholar 
Guo, X. et al. Common-garden experiment reveals clinical trends of bud phenology in black spruce populations from a latitudinal gradient in the boreal forest. J. Ecol. https://doi.org/10.1111/1365-2745.13582 (2021).Article 

Google Scholar 
Usmani, A. et al. Ecotypic differentiation of black spruce populations: Temperature triggers bud burst but not bud set. Trees 34, 1313–1321 (2020).Article 

Google Scholar 
Buttò, V., Rozenberg, P., Deslauriers, A., Rossi, S. & Morin, H. Environmental and developmental factors driving xylem anatomy and micro-density in black spruce. New Phytol. 230, 957. https://doi.org/10.1111/nph.17223 (2021).CAS 
Article 
PubMed 

Google Scholar 
Keenan, T. F. & Richardson, A. D. The timing of autumn senescence is affected by the timing of spring phenology: Implications for predictive models. Glob. Change Biol. 21, 2634–2641 (2015).ADS 
Article 

Google Scholar 
Zani, D., Crowther, T. W., Mo, L., Renner, S. S. & Zohner, C. M. Increased growing-season productivity drives earlier autumn leaf senescence in temperate trees. Science 370, 1066–1071 (2020).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Silvestro, R. et al. From phenology to forest management: Ecotypes selection can avoid early or late frosts, but not both. For. Ecol. Manage. 436, 21–26 (2019).Article 

Google Scholar 
D’Orangeville, L. et al. Beneficial effects of climate warming on boreal tree growth may be transitory. Nat. Commun. 9, 3213 (2018).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Menezes-Silva, P. E. et al. Different ways to die in a changing world: Consequences of climate change for tree species performance and survival through an ecophysiological perspective. Ecol. Evol. 9, 11979–11999 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Schwarz, J. A., Saha, S. & Bauhus, J. Potential of forest thinning to mitigate drought stress: A meta-analysis. For. Ecol. Manage. 380, 261–273 (2016).Article 

Google Scholar 
Marquis, B., Bergeron, Y., Simard, M. & Tremblay, F. Disentangling the effect of topography and microtopography on near-ground growing-season frosts at the boreal-temperate forest ecotone (Québec, Canada). New For. https://doi.org/10.1007/s11056-021-09840-7 (2021).Article 

Google Scholar 
Marquis, B. growth stagnation of planted spruce in boreal mixedwoods: Importance of landscape, microsite, and growing-season frosts. For. Ecol. Manage. 479, 118533 (2021).Article 

Google Scholar 
Pedlar, J. et al. The implementation of assisted migration in Canadian forests. For. Chron. 87, 766–777 (2011).Article 

Google Scholar 
Marris, E. Planting the forest for the future. Nature 459, 906–908 (2009).CAS 
PubMed 
Article 

Google Scholar 
Klisz, M. et al. Limitations at the limit? Diminishing of genetic effects in Norway spruce provenance trials. Front. Plant Sci. 10, 306 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Pedlar, J. H., McKenney, D. W. & Lu, P. Critical seed transfer distances for selected tree species in eastern North America. J. Ecol. https://doi.org/10.1111/1365-2745.13605 (2021).Article 

Google Scholar 
Prudhomme, G. O. et al. Ecophysiology and growth of white spruce seedlings from various seed sources along a climatic gradient support the need for assisted migration. Front. Plant Sci. 8, 2214 (2017).Article 

Google Scholar 
Girardin, M. P. et al. Annual aboveground carbon uptake enhancements from assisted gene flow in boreal black spruce forests are not long-lasting. Nat. Commun. 12, 1169 (2021).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zohner, C. M., Mo, L., Sebald, V. & Renner, S. S. Leaf-out in northern ecotypes of wide-ranging trees requires less spring warming, enhancing the risk of spring frost damage at cold range limits. Glob. Ecol. Biogeogr. 29, 1065–1072 (2020).Article 

Google Scholar 
Saucier, J.-P., Baldwin, K., Krestov, P. & Jorgenson, T. Boreal forests. In Routledge Handbook of Forest Ecology (eds Peh, K.S.-H. et al.) 7–29 (Routledge, 2015).
Google Scholar 
Hutchinson, M. F. et al. Development and testing of Canada-wide interpolated spatial models of daily minimum-maximum temperature and precipitation for 1961–2003. J. Appl. Meteorol. Climatol. 48, 725–741 (2009).ADS 
Article 

Google Scholar 
Gennaretti, F., Sangelantoni, L. & Grenier, P. Toward daily climate scenarios for Canadian Arctic coastal zones with more realistic temperature-precipitation interdependence. J. Geophys. Res. Atmos. 120, 862–877 (2015).Article 

Google Scholar 
Mpelasoka, F. S. & Chiew, F. H. S. Influence of rainfall scenario construction methods on runoff projections. J. Hydrometeorol. 10, 1168–1183 (2009).ADS 
Article 

Google Scholar 
Giorgi, F. Thirty years of regional climate modeling: Where are we and where are we going next? J. Geophys. Res. 124, 5696–5723 (2019).Article 

Google Scholar 
Laughlin, G. P. & Kalma, J. D. Frost hazard assessment from local weather and terrain data. Agric. For. Meteorol. 40, 1–16 (1987).ADS 
Article 

Google Scholar 
Sørland, S. L., Schar, C., Luthi, D. & Kjellstrom, E. Bias patterns and climate change signals in GCM-RCM model chains. Environ. Res. Lett. 13, 074017 (2018).ADS 
Article 

Google Scholar 
von Trentini, F., Aalbers, E. E., Fischer, E. M. & Ludwig, R. Comparing interannual variability in three regional single-model initial-condition large ensembles (smiles) over Europe. Earth Syst. Dyn. 11, 1013–1031 (2020).ADS 
Article 

Google Scholar 
Hänninen, H. & Pelkonen, H. Effects of temperature on dormancy release in Norway spruce and Scots pine seedlings. Silva Fenn. 22, 5357 (1988).
Google Scholar 
Lechowicz, M. J. Why do temperate deciduous trees leaf out at different times? Adaptation and ecology of forest communities. Am. Nat. 124, 821–842 (1984).Article 

Google Scholar 
Olson, M. S. et al. The adaptive potential of Populus balsamifera L. to phenology requirements in a warmer global climate. Mol. Ecol. 22, 1214–1230 (2013).CAS 
PubMed 
Article 

Google Scholar 
Hawkins, C. D. B. & Dhar, A. Spring bud phenology of 18 Betula papyrifera populations in British Columbia. Scand. J. For. Res. 27, 507–519 (2012).Article 

Google Scholar 
Bronson, D. R., Gower, S. T., Tanner, M. & Van Herk, I. Effect of ecosystem warming on boreal black spruce bud burst and shoot growth. Glob. Change Biol. 15, 1534–1543 (2009).ADS 
Article 

Google Scholar 
Basler, D. Evaluating phenological models for the prediction of leaf-out dates in six temperate tree species across central Europe. Agric. For. Meteorol. 217, 10–21 (2016).ADS 
Article 

Google Scholar 
Man, R., Lu, P. & Dang, Q.-L. Insufficient chilling effects vary among boreal tree species and chilling duration. Front. Plant Sci. https://doi.org/10.3389/fpls.2017.01354 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
R Development Core Team. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2020). http://www.R-project.org. 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

(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

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