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    An altered microbiome in urban coyotes mediates relationships between anthropogenic diet and poor health

    1.
    Foley, J. A. et al. Global consequences of land use. Science 309, 570–574 (2005).
    ADS  CAS  PubMed  Article  Google Scholar 
    2.
    Ellis, E. C., Goldewijk, K. K., Siebert, S., Lightman, D. & Ramankutty, N. Anthropogenic transformation of the biomes, 1700 to 2000. Glob. Ecol. Biogeogr. 19, 589–606 (2010).
    Google Scholar 

    3.
    Concepción, E. D., Moretti, M., Altermatt, F., Nobis, M. P. & Obrist, M. K. Impacts of urbanisation on biodiversity: the role of species mobility, degree of specialisation and spatial scale. Oikos 124, 1571–1582 (2015).
    Article  Google Scholar 

    4.
    Lowry, H., Lill, A. & Wong, B. B. M. Behavioural responses of wildlife to urban environments. Biol. Rev. 88, 537–549 (2013).
    PubMed  Article  Google Scholar 

    5.
    Callaghan, C. T. et al. Generalists are the most urban-tolerant of birds: a phylogenetically controlled analysis of ecological and life history traits using a novel continuous measure of bird responses to urbanization. Oikos 128, 845–858 (2019).
    Article  Google Scholar 

    6.
    Ducatez, S., Sayol, F., Sol, D. & Lefebvre, L. Are urban vertebrates city specialists, artificial habitat exploiters, or environmental generalists? Integr. Comp. Biol. 58, 929–938 (2018).
    PubMed  Article  Google Scholar 

    7.
    Murray, M. H. et al. City sicker? A meta-analysis of wildlife health and urbanization. Front. Ecol. Environ. 17, 575–583 (2019).
    Article  Google Scholar 

    8.
    Lyons, J., Mastromonaco, G., Edwards, D. B. & Schulte-Hostedde, A. I. Fat and happy in the city: eastern chipmunks in urban environments. Behav. Ecol. 28, 1464–1471 (2017).
    Article  Google Scholar 

    9.
    Meillère, A. et al. Corticosterone levels in relation to trace element contamination along an urbanization gradient in the common blackbird (Turdus merula). Sci. Total Environ. 566–567, 93–101 (2016).
    ADS  PubMed  Article  CAS  Google Scholar 

    10.
    Soto-Calderón, I., Acevedo-Garcés, Y., Álvarez-Cardona, J., Hernandez, C. & García, G. Physiological and parasitological implications of living in a city: the case of the white-footed tamarin (Saguinus leucopus). Am. J. Primatol. 78, (2016).

    11.
    Sillero-Zubiri, C., Sukumar, R. & Treves, A. Living with wildlife: the roots of conflict and the solutions. In Key Topics in Conservation Biology (eds. MacDonald, D. & Service, K.) 255–272 (2006).

    12.
    Muegge, B. D. et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970–974 (2011).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    13.
    Hanning, I. & Diaz-Sanchez, S. The functionality of the gastrointestinal microbiome in non-human animals. Microbiome 3, 51 (2015).
    PubMed  PubMed Central  Article  Google Scholar 

    14.
    Tremaroli, V. & Bäckhed, F. Functional interactions between the gut microbiota and host metabolism. Nature 489, 242–249 (2012).
    ADS  CAS  PubMed  Article  Google Scholar 

    15.
    Pickard, J. M., Zeng, M. Y., Caruso, R. & Núñez, G. Gut microbiota: role in pathogen colonization, immune responses, and inflammatory disease. Immunol. Rev. 279, 70–89 (2017).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    16.
    Mockler, B. K., Kwong, W. K., Moran, N. A. & Koch, H. Microbiome structure influences infection by the parasite Crithidia bombi in bumble bees. Appl. Environ. Microbiol. 84, e02335-e2417 (2018).
    PubMed  PubMed Central  Article  Google Scholar 

    17.
    Suzuki, T. A. Links between natural variation in the microbiome and host fitness in wild mammals. Integr. Comp. Biol. 57, 756–769 (2017).
    CAS  PubMed  Article  Google Scholar 

    18.
    Kirchoff, N. S., Udell, M. A. & Sharpton, T. J. The gut microbiome correlates with conspecific aggression in a small population of rescued dogs (Canis familiaris). PeerJ 7, e6103 (2019).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    19.
    Walter, J. Ecological role of lactobacilli in the gastrointestinal tract: implications for fundamental and biomedical research. Appl. Environ. Microbiol. 74, 4985–4996 (2008).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    20.
    Teyssier, A. et al. Inside the guts of the city: urban-induced alterations of the gut microbiota in a wild passerine. Sci. Total Environ. 612, 1276–1286 (2018).
    ADS  CAS  PubMed  Article  Google Scholar 

    21.
    Murray, M. H. et al. Gut microbiome shifts with urbanization and potentially facilitates a zoonotic pathogen in a wading bird. PLoS ONE 15, 1–16 (2020).
    Google Scholar 

    22.
    Phillips, J. N., Berlow, M. & Derryberry, E. P. The effects of landscape urbanization on the gut microbiome: an exploration into the gut of urban and rural white-crowned sparrows. Front. Ecol. Evol. 6, 148 (2018).
    Article  Google Scholar 

    23.
    Teyssier, A. et al. Diet contributes to urban-induced alterations in gut microbiota: experimental evidence from a wild passerine. Proc. R. Soc. B Biol. Sci. 287, (2020).

    24.
    Stothart, M. R., Palme, R. & Newman, A. E. M. It’s what’s on the inside that counts: stress physiology and the bacterial microbiome of a wild urban mammal. Proc. R. Soc. B Biol. Sci. 286, (2019).

    25.
    Becker, C. G., Longo, A. V., Haddad, C. F. B. & Zamudio, K. R. Land cover and forest connectivity alter the interactions among host, pathogen and skin microbiome. Proc. R. Soc. B Biol. Sci. 284, 20170582 (2017).
    Article  Google Scholar 

    26.
    Bestion, E. et al. Climate warming reduces gut microbiota diversity in a vertebrate ectotherm. Nat. Ecol. Evol. 1, 0161 (2017).
    Article  Google Scholar 

    27.
    Barelli, C. et al. Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation. Sci. Rep. 5, 14862 (2015).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    28.
    Trevelline, B. K., Fontaine, S. S., Hartup, B. K. & Kohl, K. D. Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices. Proc. R. Soc. B Biol. Sci. 286, (2019).

    29.
    Nelson, T. M., Rogers, T. L., Carlini, A. R. & Brown, M. V. Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals. Environ. Microbiol. 15, 1132–1145 (2013).
    CAS  PubMed  Article  Google Scholar 

    30.
    Wasimuddin, et al. Gut microbiomes of free-ranging and captive Namibian cheetahs: diversity, putative functions and occurrence of potential pathogens. Mol. Ecol. 26, 5515–5527 (2017).
    CAS  PubMed  Article  Google Scholar 

    31.
    Amato, K. R. et al. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J. 13, 576–587 (2019).
    CAS  PubMed  Article  Google Scholar 

    32.
    Gehrt, S. D. & Riley, S. P. D. Coyotes (Canis latrans). in Urban Carnivores: Ecology, Conflict, and Conservation (eds. Gehrt, S. D., Riley, S. P. D. & Cypher, B. L.) 79–95 (2010).

    33.
    Breck, S. W., Poessel, S. A., Mahoney, P. & Young, J. K. The intrepid urban coyote: a comparison of bold and exploratory behavior in coyotes from urban and rural environments. Sci. Rep. 9, 2104 (2019).
    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

    34.
    Gier, H. T. Coyotes in Kansas. (1968).

    35.
    Murray, M. H. et al. Greater consumption of protein-poor anthropogenic food by urban relative to rural coyotes increases diet breadth and potential for human-wildlife conflict. Ecography 38, 001–008 (2015).
    Article  Google Scholar 

    36.
    Massolo, A., Liccioli, S., Budke, C. & Klein, C. Echinococcus multilocularis in North America: the great unknown. Parasite 21, 73 (2014).
    PubMed  PubMed Central  Article  Google Scholar 

    37.
    Murray, M. H., Edwards, M. A., Abercrombie, B. & St. Clair, C. C. Poor health is associated with use of anthropogenic resources in an urban carnivore. Proc. R. Soc. B Biol. Sci. 282, 20150009 (2015).

    38.
    Murray, M. H., Hill, J., Whyte, P. & St. Clair, C. C. Urban compost attracts coyotes, contains toxins, and may promote disease in urban-adapted wildlife. Ecohealth 13, 285–292 (2016).

    39.
    Luong, L. T., Chambers, J. L., Moizis, A., Stock, T. & St. Clair, C. Helminth parasites and zoonotic risk associated with urban coyotes (Canis latrans) in Alberta, Canada. J. Helminthol. 94, e25 (2020).

    40.
    Corbin, E. et al. Spleen mass as a measure of immune strength in mammals. Mamm. Rev. 38, 108–115 (2008).
    Article  Google Scholar 

    41.
    Newsome, S. D., Ralls, K., Van Horn Job, C., Fogel, M. L. & Cypher, B. L. Stable isotopes evaluate exploitation of anthropogenic foods by the endangered San Joaquin kit fox (Vulpes macrotis mutica). J. Mammol. 91, 1313–1321 (2010).

    42.
    Huot, J., Poulle, M. & Crate, M. Evaluation of several indices for assessment of coyote (Canis latrans) body composition. Can. J. Zool. 73, 1620–1624 (1995).
    Article  Google Scholar 

    43.
    Tucker, C. M. et al. A guide to phylogenetic metrics for conservation, community ecology and macroecology. Biol. Rev. 92, 698–715 (2016).
    PubMed  Article  Google Scholar 

    44.
    Reese, A. T. & Dunn, R. R. Drivers of microbiome biodiversity: a review of general rules, feces, and ignorance. MBio 9, e01294-e1318 (2018).
    PubMed  PubMed Central  Article  Google Scholar 

    45.
    Pilla, R. & Suchodolski, J. S. The role of the canine gut microbiome and metabolome in health and gastrointestinal disease. Front. Vet. Sci. 6, 498 (2020).
    PubMed  PubMed Central  Article  Google Scholar 

    46.
    Conlon, M. A. & Bird, A. R. The impact of diet and lifestyle on gut microbiota and human health. Nutrition 7, 17–44 (2015).
    Google Scholar 

    47.
    Makki, K., Deehan, E. C., Walter, J. & Bäckhed, F. The impact of dietary fiber on gut microbiota in host health and disease. Cell Host Microbe 23, 705–715 (2018).
    CAS  PubMed  Article  Google Scholar 

    48.
    Schnorr, S. L. et al. Gut microbiome of the Hadza hunter-gatherers. Nat. Commun. 5, 3654 (2014).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    49.
    Vieco-Saiz, N. et al. Benefits and inputs from lactic acid bacteria and their bacteriocins as alternatives to antibiotic growth promoters during food-animal production. Front. Microbiol. 10, 1–17 (2019).
    Article  Google Scholar 

    50.
    Karasov, W. H. & Douglas, A. E. Comparative digestive physiology. Comp. Physiol. 3, 741–783 (2013).
    Google Scholar 

    51.
    Wang, T. et al. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J. 6, 320–329 (2012).
    CAS  PubMed  Article  Google Scholar 

    52.
    AlShawaqfeh, M. K. et al. A dysbiosis index to assess microbial changes in fecal samples of dogs with chronic inflammatory enteropathy. FEMS Microbiol. Ecol. 93, 1–8 (2017).
    Article  CAS  Google Scholar 

    53.
    Beldomenico, P. M. & Begon, M. Disease spread, susceptibility and infection intensity: vicious circles? Trends Ecol. Evol. 25, 21–27 (2010).
    PubMed  Article  Google Scholar 

    54.
    Newsome, S. D., Garbe, H. M., Wilson, E. C. & Gehrt, S. D. Individual variation in anthropogenic resource use in an urban carnivore. Oecologia 178, 115–128 (2015).
    ADS  PubMed  Article  Google Scholar 

    55.
    Henderson, G. et al. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci. Rep. 5, 14567 (2015).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    56.
    Brennan, C. A. & Garrett, W. S. Fusobacterium nucleatum – symbiont, opportunist and oncobacterium. Nat. Rev. Microbiol. 17, 156–166 (2019).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    57.
    Bermingham, E. N., Maclean, P., Thomas, D. G., Cave, N. J. & Young, W. Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs. PeerJ 5, e3019 (2017).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    58.
    Alessandri, G. et al. Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features. Environ. Microbiol. 21, 1331–1343 (2019).
    CAS  PubMed  Article  Google Scholar 

    59.
    Schmidt, M. et al. The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets. PLoS ONE 13, e0201279 (2018).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    60.
    Sandri, M., Dal Monego, S., Conte, G., Sgorlon, S. & Stefanon, B. Raw meat based diet influences faecal microbiome and end products of fermentation in healthy dogs. BMC Vet. Res. 13, 1–11 (2017).
    Google Scholar 

    61.
    Moon, C. D., Cookson, A. L., Young, W., Maclean, P. H. & Bermingham, E. N. Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats. Microbiologyopen 7, e677 (2018).
    Article  Google Scholar 

    62.
    Wu, X. et al. Analysis and comparison of the wolf microbiome under different environmental factors using three different data of next generation sequencing. Sci. Rep. 7, 11332 (2017).
    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

    63.
    Wang, B. & Wang, X.-L. Species diversity of fecal microbial flora in Canis lupus familiaris infected with canine parvovirus. Vet. Microbiol. 237, 108390 (2019).
    PubMed  Article  Google Scholar 

    64.
    Chen, L. et al. NLRP12 attenuates colon inflammation by maintaining colonic microbial diversity and promoting protective commensal bacterial growth. Nat. Immunol. 18, 541–551 (2017).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    65.
    Martínez, I. et al. Gut microbiome composition is linked to whole grain-induced immunological improvements. ISME J. 7, 269–280 (2013).
    PubMed  Article  CAS  Google Scholar 

    66.
    Liu, Y. et al. Splenectomy leads to amelioration of altered gut microbiota and metabolome in liver cirrhosis patients. Front. Microbiol. 9, 1–13 (2018).
    Article  Google Scholar 

    67.
    Demas, G. E., Zysling, D. A., Beechler, B. R., Muehlenbein, M. P. & French, S. S. Beyond phytohaemagglutinin: assessing vertebrate immune function across ecological contexts. J. Anim. Ecol. 80, 710–730 (2011).
    PubMed  Article  Google Scholar 

    68.
    Sugden, S. A., St. Clair, C. C. & Stein, L. Y. Individual and site-specific variation in a biogeographical profile of the coyote intestinal microbiota. Microb. Ecol. (2020).

    69.
    David, L. A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559–563 (2014).
    ADS  CAS  PubMed  Article  Google Scholar 

    70.
    Leung, J. M., Graham, A. L. & Knowles, S. C. L. Parasite-microbiota interactions with the vertebrate gut: synthesis through an ecological lens. Front. Microbiol. 9, 843 (2018).
    PubMed  PubMed Central  Article  Google Scholar 

    71.
    Ezenwa, V. O., Gerardo, N. M., Inouye, D. W., Medina, M. & Xavier, J. B. Animal behavior and the microbiome. Science 338, 198–199 (2012).
    ADS  CAS  PubMed  Article  Google Scholar 

    72.
    Stewart, R. E. A., Stewart, B. E., Stirling, I. & Street, E. Counts of growth layer groups in cementum and dentine in ringed seals. Mar. Mammal Sci. 12, 383–401 (1996).
    Article  Google Scholar 

    73.
    Linhart, S. B. & Knowlton, F. F. Determining age of coyotes by tooth cementum layers. J. Wildl. Manage. 31, 362–365 (1967).
    Article  Google Scholar 

    74.
    Jahren, A. H. & Kraft, R. A. Carbon and nitrogen stable isotopes in fast food: signatures of corn and confinement. Proc. Natl. Acad. Sci. 105, 17855–17860 (2008).
    ADS  CAS  PubMed  Article  Google Scholar 

    75.
    Parnell, A. C. simmr: a stable isotope mixing model. (2019).

    76.
    Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. 108, 4516–4522 (2011).
    ADS  CAS  PubMed  Article  Google Scholar 

    77.
    Hsieh, T. C., Ma, K. H. & Chao, A. iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods Ecol. Evol. 7, 1451–1456 (2016).
    Article  Google Scholar 

    78.
    Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A. & Callahan, B. J. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome 6, 226 (2018).
    PubMed  PubMed Central  Article  Google Scholar 

    79.
    Trachsel, D., Deplazes, P. & Mathis, A. Identification of taeniid eggs in the faeces from carnivores based on multiplex PCR using targets in mitochondrial DNA. Parasitology 134, 911–920 (2007).
    CAS  PubMed  Article  Google Scholar 

    80.
    R Core Team. R: A language and environment for statistical computing. (2019).

    81.
    Chao, A. et al. Rarefaction and extrapolation of phylogenetic diversity. Methods Ecol. Evol. 6, 380–388 (2015).
    Article  Google Scholar 

    82.
    Kembel, S. et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26, 1463–1464 (2010).
    CAS  Article  Google Scholar 

    83.
    Giam, X. & Olden, J. D. Quantifying variable importance in a multimodel inference framework. Methods Ecol. Evol. 7, 388–397 (2016).
    Article  Google Scholar 

    84.
    Cade, B. S. Model averaging and muddled multimodel inferences. Ecology 96, 2370–2382 (2015).
    PubMed  Article  Google Scholar 

    85.
    Fernandes, A., Macklaim, J. M., Linn, T., Reid, G. & Gloor, G. B. ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq. PLoS ONE 8, e67019 (2013).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar  More

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    2000 Year-old Bogong moth (Agrotis infusa) Aboriginal food remains, Australia

    Ethnographic accounts from around the world have reported the widespread use of insects as food by people1,2,3. In some cases, such as among the Shoshone and other Great Basin tribes of the U.S., swarms of grasshoppers and crickets were driven into pits and blankets4, while among the Paiute the larvae of Pandora moths (Coloradia pandora lindseyi) were smoked out of trees to fall into prepared trenches, where they would be cooked5. Across the world, insects could be mass-harvested, often seasonally, offering high nutritional value especially in fat, protein and vitamins6. The harvesting of insects in the past has ranged from opportunities to feed large communal gatherings during times of plenty, to more individualistic economic pursuits such as in the search for delicacies or the exploitation of low-ranked resources when other foods were scarce or depleted7,8,9. Irrespective of the catch, insects often represented an important component of the diet, and of the reliability and thus dependability of locales as resource zones, with implications for social scheduling and cultural practice. However, a paucity of archaeological studies of insect food remains has resulted in a downplay or omission of the use of insects from archaeological narratives and deep-time community histories10.
    In Australia, a wide range of insects is known to have been eaten by Aboriginal groups, in particular the larvae (‘witchetty grubs’) of cossid moths (especially Endoxyla leucomochla) in arid and semi-arid areas11,12,13. Of particular interest to archaeologists and behavioural ecologists has been the seasonal consumption of Bogong moths by mass gatherings of Aboriginal groups in the southern portions of the Eastern Uplands14 (Fig. 1). However, no conclusive archaeological evidence has ever been reported for the processing or use of Bogong moths.
    Figure 1

    (A) Bogong moth, Agrotis infusa (photo: Ajay Narendra). (B) Thousands of moths per square metre aestivating on a rock surface (photo: Eric Warrant).

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    The Cloggs Cave grindstone
    Cloggs Cave is located 72 m above sea level in the southern foothills of the Australian Alps, in the lands of the Krauatungalung clan of the GunaiKurnai Aboriginal peoples of southeastern Australia (Fig. 2). The cave is a small, 12 m long × 5 m wide × 6.8 m high limestone karst formation that is today entered through a walk-through opening on the side of a cliff (Fig. 3). Indirect sunlight dimly illuminates the cave for much of the day (Supplementary Fig. S1).
    Figure 2

    Location of Cloggs Cave and the area of the GunaiKurnai Land and Waters Aboriginal Corporation, at the southern foothills of the Australian Alps. Esri ArcMap 10.5 (https://desktop.arcgis.com/en/arcmap/) and Adobe Illustrator CC 2017 (21.0) (https://helpx.adobe.com/au/illustrator/release-note/illustrator-cc-2017-21-0-release-notes.html) were used by CartoGIS Services, College of Asia and the Pacific at the Australian National University, to create the map.

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    Figure 3

    Cloggs Cave cliffline above the Buchan River flood plain, showing location of cave entrance (white rectangle) (photo: Bruno David).

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    Archaeological excavations were first undertaken in 1971–197214, followed by a new program of excavations in 2019–2020, initiated by the GunaiKurnai Land and Waters Aboriginal Corporation and directed by Bruno David. The new excavations were aimed at better determining the site’s stratigraphy and the antiquity of Aboriginal occupation (Supplementary Fig. S2). An intensive dating programme showed that the oldest excavated evidence for human activity dates to between 19,330–19,730 cal BP (median age of 19,530 cal BP; cal BP = before AD1950) and 20,590–23,530 cal BP (median age of 21,690 cal BP) (all calibrated radiocarbon ages in the text are presented at 95.4% probability range. See “Methods”; Supplementary Fig. S3)15,16,17.
    During the 2019 excavations, a small, flat grindstone was found. The finely stratified hearth layers of stratigraphic unit (SU) 2 in which it was found were radiocarbon-dated to 1567–1696 cal BP at their top (uncalibrated: 1724 ± 16 BP; median age of 1632 cal BP) and 2002–2117 cal BP at their base (uncalibrated: 2091 ± 16 BP; median age of 2062 cal BP). The grindstone therefore dates to between 1600 and 2100 years ago (see “Methods”; Supplementary Figs. S3 and S4)17. No other grindstone has been found at Cloggs Cave.
    The grindstone is a tabular fragment of sandstone with two flat and parallel ground surfaces (Surfaces A and B), in the form of a flat dish (Fig. 4). It measures 10.5 cm long × 8.3 cm wide × 2.2 cm thick and weighs 304 g. The outer, intact margin is elliptical in plan view; the other three margins indicate old breaks that have been subsequently worn from use. Therefore, prior to its deposition at Cloggs Cave, the grindstone had been used in its current form.
    Figure 4

    The Cloggs Cave grindstone. (A) Surface A, with the accretion that formed across parts of the surface after its use. (B) Surface B. (C) Margin A. (D) Margin B. (E) Narrow end. The numbers in circles are the residue sample numbers; the ‘control’ samples are in areas where grinding did not take place (photos: Richard Fullagar).

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    To understand how the grindstone was used, we undertook use-wear and residue analyses (see “Methods”). The central area of both its surfaces contain fine unidirectional striations (Supplementary Figs. S5A and S5B), a lowered but not levelled topography, and areas of missing or ripped quartz grains (Supplementary Figs. S5C and S5D). Its use to shape ground stone axes is an unlikely function because the Cloggs Cave grindstone surfaces are relatively flat with only very slight concavities, and the lowered surface topography (Fig. 4) lacks broad grooves typical of axe grinding.
    When viewed at lower (up to 5 ×) magnification under a stereozoom microscope with a point source of light, each surface appears relatively rough compared with grindstones used for processing seeds, which, in Australia, tend to be highly smoothed and polished18,19. There are numerous ‘pits’ where sand grains have been plucked from the surface during use (Supplementary Fig. S5D). The presence of a lowered surface topography (Supplementary Fig. S5C) with a lack of smooth, developed polish suggests that the stone was not used to process siliceous plants.
    The repeated mechanical action of grinding has been shown to force residues into the voids and interstitial spaces of ground surfaces, where they become trapped20,21,22. Residue analyses conducted on grindstones worldwide have relied on microscopic observations of individual residue morphologies. However, visually diagnostic features can be altered by the mechanical forces of grinding, heat, and contact with water and various environmental factors, which can cause residues to swell or become amorphous21,22,23,24. The distinctiveness of residue identifications can be enhanced significantly with the introduction of biochemical staining that can be observed under high-power microscopy and is best used in conjunction with microscopic use-wear analysis and identification of residue morphologies22.
    We extracted nine samples, or ‘lifts’, for residue analysis from across Surface A and Surface B of the Cloggs Cave grindstone, including a control sample from an unworked part of each surface (Fig. 4; see “Methods”). These samples were analysed using a recently developed biochemical staining technique that enables residues to be identified from colorimetric changes occurring at a cellular level, rather than relying solely on structural features (see “Methods”)22. We used the collagen stain Picrosirius Red (PSR) to differentiate between plant and animal residues (see “Methods”). When PSR comes into contact with collagen (a protein unique to animals), it reacts to produce clear and distinctive staining and enhanced birefringence in cross-polarised light22,25.
    Residues extracted from the grindstone
    A range of residues were identified in the lifts, including amorphous collagen, collagen fibres, collagen structures, partially woven collagen, possible bone-like fragments, moth wing segments, a possible moth hind leg, amorphous cellulose, wood-like structures with pits, carbonised material, bordered pits and minerals (see below).
    We found collagenous residues in mid-range densities across Samples 1 and 4 from Surface B and across Sample 5 from Surface A (Supplementary Fig. S6). These extractions were taken from central areas across each modified surface. In all cases, the frequency of the collagenous residues was approximately three times greater than the collagenous residues associated with the control samples. Residues include damaged collagen fibres of varying thicknesses, including some reticular fibres.
    Woven collagen structures clearly show birefringence in cross-polarised light across Sample 1. Woven collagen, which forms quickly, is mechanically weak and usually associated with immature bone. Although woven collagen may persist as tendon and ligament attachments to bone, it is generally replaced by organised parallel collagen fibre bundles at skeleton maturity26. Collagen fibrils are found in the connective tissues of vertebrates as well as in invertebrates such as insects27, and may be present as individual strands, woven structures or parallel bundles, including among the Lepidoptera (moths and butterflies)28.
    The density and combination of collagenous residues on the Cloggs Cave grindstone indicates that it was used to process fauna. A variety of collagenous materials (including woven collagen) were found in association with carbonised residues across Sample 2, which was extracted from a crystalline layer. The residues present on Samples 1 and 2 suggest that an insect or immature vertebrate was prepared and cooked using the grindstone.
    We identified a moderate density of carbonised plant residues across Sample 2, in particular, wood-like structures with pits. These ranged from being partially to completely carbonised. Partially carbonised residues were also seen across Sample 4. In addition, bordered pits in small clusters were identified, along with pits within the carbonised structures. Bordered pits are cavities that are essential components in the water-transport system of higher-order plants and are found in the lignified cell walls of xylem conduits (vessels and tracheids). The pit membrane allows water to pass between xylem conduits, but limits the spread of embolism and vascular pathogens in the xylem29. Small quantities of lignin were also present (see “Methods”). Lignin is found in the cell walls of vascular plants (especially in wood and bark) and is responsible for the rigidity of plant structures.
    The residues identified via biochemical staining are consistent with the use of twigs and bark as fuel for fires such as those of the microstratified ashy layers in which the grindstone was found (see Supplementary Fig. S3)17. Partially carbonised wood-like material was also noted across Sample 5. The density and distribution of carbonised residues varies across extractions. Our observations suggest either that: (a) the stone has been placed in or near fires; or (b) ash, embers or fires of varying heat were placed or lit across the stone, for varied durations of time.
    We identified especially high densities (frequency of residue particles per unit volume of sample) of amorphous cellulose across Samples 1, 2, 4 and 5 (Supplementary Fig. S7). The presence of partially carbonised amorphous cellulose indicates that the plant residues were associated with fire. While the high density is indicative of a plant-processing event, there is no evidence of combinations of plant residues normally expected from plant processing. In particular, no starch grain or phytolith was seen in any of the extractions. While low heat can damage starch and cause its structure to be disrupted and its characteristic extinction-cross to be lost, low heat does not completely destroy starch visibility30. Similarly, phytoliths can be reshaped but not destroyed by fire31. The presence of animal and mineral residues but absence of starches and phytoliths is thus interpreted as a true absence of plant processing activities rather than a taphonomic effect of environmental factors negatively impacting their preservation.
    We found a high density of variably carbonised insect wings in Sample 6 (Surface A), and lower densities in Samples 2 and 4. These wing fragments contain regular patterning or structure and exhibit distinct birefringence in cross-polarised light. A portion of proteinaceous material was associated with a ‘tangle’ of these structures (Fig. 5). To assess whether the insect remains were those of the Bogong moth, we compared the residues on Samples 2, 4 and 6 with a comparative reference sample (see “Methods”). All 26 cases of wing segments from the grindstone matched the metrical and morphological characteristics of those from Bogong moths in the reference material. The recorded damage on the archaeological wing segments, such as ripped wing structures, small rectangular wing fragments and tearing in various states of carbonisation, is what would be expected from ethnohistoric accounts of Bogong moth processing. Aboriginal people from across the region are known to have cooked Bogong moths on heated earth during the early and mid-nineteenth century. The moths were stirred during cooking, causing the wings and legs to be broken off by friction and heat. Some of the moths were pounded and ground into a paste which could then be smoked to preserve the food for weeks1,2.
    Figure 5

    Examples of Bogong moth segments from lifted samples (all at × 400 magnification). (A) Partially carbonised wing structures from Sample 2 (pp). (B) Partially carbonised wing structure and carbonised material from Sample 2 (pp). (C) Partially carbonised moth wing segment from Sample 4 (pp). (D–E) Damaged moth wing segment from Sample 6 (D pp; E xp). (F–G) Damaged moth wing segment from Sample 6 (F pp; G xp). (H) Damaged moth wing segment with proteinaceous material, from Sample 6 (pp). (I) Unburnt moth wing segment from Sample 4 (pp). (J) Damaged moth wing segment with attachment, from Sample 6 (pp). (K) Damaged moth wing segments from Sample 6 (pp). (L–M) Probable moth hind leg from Sample 6 (L pp; M xp). (N) Damaged moth wing segment from Sample 6 (pp). (O) Damaged moth wing segment with attachment, from Sample 6 (pp). Light source = plane (pp), part polarised (part pol) and cross-polarised (xp) (photos: Birgitta Stephenson).

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    Low oxygen levels caused by Noctiluca scintillans bloom kills corals in Gulf of Mannar, India

    Though the time and place of the origin of this bloom is unknown, the presumable causes of it were high temperatures, abundant nutrients, low tidal amplitude, and little current. According to fishermen, these bioluminescent blooms were first seen about 15 nautical miles offshore of the Mandapam coast between India and Sri Lanka on 6th September, and subsequently moved towards the shore (Fig. 2). Bloom of N. scintillans in 2008 was reported to affect all the marine organisms including corals in GoM12. On 14th September, our preliminary assessment revealed that corals in Shingle and Krusadai islands were possibly affected by the bloom. A great multitude of N. scintillans cells were found settled on corals and other benthic organisms in the affected areas. A greenish settlement was observable on live coral colonies and other benthic organisms including macro algae, coralline algae and sponges etc.(Fig. S2). Settling of N. scintillans on benthic organisms has been reported to cause significant damage to the reef organisms through asphyxiation12. At Shingle Island, the area of significant impact was about 8.1 hectares on the shoreward side of the Island (79°14′14.38″E, 9°14′44.23″N) at depths between 1 and 3 m (Fig. 3). At Krusadai Island, an area of 2.1 hectares in the shoreward side was found affected by the bloom (79°13′20.78″E, 9°15′00.88″N) at depths between 1 and 2 m. The rest of the reef areas in both of these islands were healthy without any impact. The settled cells of N. scintillans were found to be washed ashore during subsequent surveys. In addition to dead fishes, a multitude of benthic communities such as crustaceans, mollusks and echinoderms were also found dead on the bottom in the impacted areas. Surveys between 15 and 18th September 2019 confirmed that corals in other islands (Pullivasal, Poomarichan, Manoliputti, Manoli and Hare) were in good health, and without any noticeable impact due to the bloom. Shingle and Krusadai islands occur closest to the mainland, and the concentrated bloom appeared to get trapped by currents between the mainland shore and islands.
    Figure 2

    (a) Green tide of Noctiluca scintillans in the Gulf of Mannar; (b) image of N.scintillans cells; size of the grid is 1 mm2 (N. scintillans exhibits bioluminescence when disturbed).

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    Figure 3

    Map showing the affected islands in the Mandapam group shown in Fig. 1. Base map was prepared by digitizing the georeferred Toposheet of Survey of India (http://www.surveyofindia.gov.in/) and field data using Open source GIS software (QGIS 3.10.6; https://qgis.org/en/site/forusers/download.html).

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    On 14th September, coral mortality was not observed in the affected areas though the colonies were observed to be disturbed by the settling N. scintillans cells. Low dissolved oxygen levels have been reported to be the primary cause of benthic mortality during algal blooms22. Dissolved oxygen levels were 1.48 mg l−1 at Shingle Island and 2.02 mg l−1 at Krusadai Island in the affected areas. This compares to ‘normal’ levels for coral reefs of 5–8 mg l−1, and Haas et al.11 found that dissolved oxygen content less than 4 mg l−1 is detrimental to acroporid corals. Moreover, branching coral forms have been reported to be more susceptible to hypoxic episodes than spherical or massive forms5. Corals are routinely exposed to fluctuations in oxygen levels at the tissue level due to photosynthesis and respiration processes of endosymbionts7, but are negatively impacted when (sub-) lethal thresholds of hypoxia exposure are exceeded1,5,11. Lethal hypoxia thresholds appear to differ considerably between coral species, ranging between 0.5 and 4 mg O2 l−11,5,11, while sub-lethal hypoxia thresholds for corals are almost entirely unknown5.
    Seawater temperature can significantly impact dissolved oxygen levels23,24. Water temperature was 29.9 and 29.8º C (Table 1) at Shingle and Krusadai islands respectively and these levels are marginally higher than the normal levels for this particular time of the year. Apart from the summer months (April to June), temperature levels in GoM do not go higher than 29º C20. The concentration of N. scintillans was 43.4 × 105 and 27.3 × 105 cells l−1 at Shingle and Krusadai Islands respectively; pH and TDS were also high in the affected area (Table 1). Dissolved oxygen levels in other sites of these two islands and in other five islands were higher than 5 mg l−1.
    Table 1 Environmental characterization at the affected sites in Shingle and Krusadai Islands.
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    During the next assessment on 17th of September 2019, severe coral mortality was observed at the affected sites. At Shingle Island, overall coral colony density was 134.25 (SE ± 3.28) no.100 m−2 (n = 537) within ten 20 m belt transects which is dominated by Acropora (64%) followed by Montipora (15%). Out of total 537 colonies, 33.52% (n = 180) were found dead (Fig. 4), which include 34.5 (SE ± 1.05) no.100 m−2 (n = 138) of Acropora, 7.75 (SE ± 0.75) no.100 m−2 (n = 31) of Montipora and 2.75 (SE ± 0.35) no.100 m−2 (n = 11) of Pocillopora. The death of coral colonies was so rapid that the coral tissue was intact on the colony surface and still had its natural colour (Fig. 5). When wafted with water by hand or with scuba air, the tissue peeled off exposing the skeleton (Supplementary video). Other observed genera such as Dipsastraea, Favites, Porites, Hydnophora, Goniastrea, Echinopora, Turbinaria, Platygyra, Goniopora and Symphyllia in the same site were all alive (Fig. S3), though with excess mucus production. This may be explained by differential lethal thresholds for oxygen levels at species and growth form levels5,19. At Krusadai Island, the overall coral density on 17th September was 66 (SE ± 2.54) no.100 m−2 (n = 132), dominated by Acropora. Among the counted colonies, 6 (SE ± 1.03) no.100 m−2 of Acropora were found recently dead while mortality was not observed in other available genera such as Montipora, Pocillopora, Dipsastraea, Favites, Porites and Turbinaria. Dissolved oxygen levels had increased to 3.78 mg l−1 at Shingle Island and to 4.02 mg l−1 at Krusadai Island at the affected sites and the water had started to become clear. The concentration of N. scintillans had reduced to 1.63 × 103 cells l−1 and 0.88 × 103 cells l−1 at Shingle and Krusadai Islands, respectively (Table 1).
    Figure 4

    Density of live and dead colonies of affected coral genera (Acropora, Montipora and Pocillopora) in Shingle Island, by date; the green line indicates the drastic decline of Acropora density between 17.09.2019 and 27.09.2019.

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    Figure 5

    Rapid mortality of corals presumably due to low oxygen levels caused by Noctiluca scintillans; (a, b) Acropora; (c) Montipora; (d) Pocillopora.

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    Assessment on 27th September 2019 at the impacted area in Shingle Island, showed that the overall density of coral colonies within ten 20 m transects was 135.75 (SE ± 2.82) no.100 m−2 (n = 543) and of them 70.35% (n = 382) of colonies belonging to Acropora, Montipora and Pocillopora were found dead revealing that the impact of algal bloom was more severe than expected (Fig. 4). It was almost two weeks since the corals had died and hence secondary algae had started colonizing the dead colonies. On the same day at the impacted area of Krusadai Island, overall coral density within five belt transects was 65.5 (SE ± 1.83) no.100 m−2 (n = 131), of which 9.09% (n = 12) of colonies belonging to Acropora were found dead. By 27th September, dissolved oxygen levels had increased to 6.02 and 5.73 mg l−1 respectively at the affected areas of Shingle and Krusadai islands (Table 1). N. scintillans cells were absent in all the sites indicating the end of bloom. On 04th October 2019, the overall coral colony density within 20 m belt transects was 138 (SE ± 2.08) no.100 m−2 (n = 552) and of them 71.23% (n = 393) colonies belonging to Acropora, Montipora and Pocillopora were found dead at the area of impact in Shingle Island (Fig. 4). No further mortality was witnessed in the affected area of Krusadai Island. Secondary algae have completely overgrown the dead coral colonies making the reef look green (Fig. S4). Dissolved oxygen levels were reasonably high at 7.13 and 7.24 mg l−1 respectively at Shingle and Krusadai Islands during this time (Table 1).
    Coral mortality due to algal bloom and consequent hypoxia has rarely been reported12,13,25. The present study reports that the impact of blooms can be severe on corals. Different coral species respond differently to low oxygen levels according to their respiration and photosynthesis5,26. Thus, low oxygen levels can orchestrate the coral mortality by affecting coral’s productivity and respiration7. Further, fast growing corals such as Acropora and Pocillopora have been reported to be more susceptible to low oxygen levels11,13,27. Fast growing coral species have faster metabolism rates28 and hence metabolic oxygen requirements are higher11,29. Thus, the mortality of fast growing species in the present study was presumably due to the low oxygen levels induced by N.scintillans bloom.
    Bleaching episodes in 2010 and 2016 had also caused significant mortality to these fast growing species in GoM19,20. Corals in GoM start to bleach when water temperature exceeds 30º C and the temperature levels during this bloom period ranged between 28.4 and 29.9º C. Though bleaching was not observed, heat stress might also have played its role in coral mortality along with low oxygen levels as the temperature level almost reached 30º C. Similar temperature levels were reported during the bloom of N. scintillans in 2008 in GoM12.
    Corals in Gulf of Mannnar are still recovering from the 2016 bleaching episode20 and hence the present decline is significant. Phase shifts on coral reefs are predominantly associated with shifts from hard coral-dominated communities to macroalgae-dominated ones30. Space competition between corals and other organisms such as algae and sponges has been reported to negatively impact the corals of GoM after the 2016 bleaching event20,31. At present, secondary algae have completely occupied the dead coral colonies, which will affect the coral recovery by hindering the attachment of new coral recruits during the next spawning season32. Recent studies suggest hypoxia increases coral susceptibility to bleaching27, and may increase disease prevalence and algal proliferation7. Thus algal blooms add to the existing array of threats to corals of GoM that needs to be understood more with further focused research.
    On account of the problems related to climate change, there has been a steady and severe decline of coral reefs in the past two decades. Bleaching and diseases have been reported to cause mass coral mortalities within a very short time. The observations of the present study alert us to possible mass mortality due to short-term hypoxic condition caused by algal blooms. Algal blooms and hypoxic conditions are predicted to occur more frequently in the future due to climate change14. Hence, it is likely that shallow water coral reefs will be affected more frequently by temporary low oxygen levels caused by algal blooms. More studies are, however, required to understand the mechanism of coral mortality due to algal blooms, impacts on community composition and the potential for subsequent recovery. More

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    Endophytic fungi protect tomato and nightshade plants against Tuta absoluta (Lepidoptera: Gelechiidae) through a hidden friendship and cryptic battle

    1.
    Ekesi, S., Chabi-Olaye, A., Subramanian, S. & Borgemeister, C. Horticultural pest management and the African economy: successes, challenges and opportunities in a changing global environment. Acta Hortic. 911, 165–183 (2011).
    Article  Google Scholar 
    2.
    Pratt, C. F., Constantine, K. L. & Murphy, S. T. Economic impacts of invasive alien species on African smallholder livelihoods. Glob. Food Secur. 14, 31–37 (2017).
    Article  Google Scholar 

    3.
    Desneux, N., Luna, M. G., Guillemaud, T. & Urbaneja, A. The invasive South American tomato pinworm, Tuta absoluta, continues to spread in Afro-Eurasia and beyond: the new threat to tomato world production. J. Pest Sci. 84, 403–408 (2011).
    Article  Google Scholar 

    4.
    Idriss, G. E. A. et al. Host range and effects of plant species on preference and fitness of Tuta absoluta (Lepidoptera: Gelechiidae). J. Econ. Entomol. https://doi.org/10.1093/jee/toaa002 (2020).
    Article  PubMed  Google Scholar 

    5.
    Aigbedion-Atalor, P. O. et al. The South America tomato leafminer, Tuta absoluta (Lepidoptera: Gelechiidae), spreads its wings in Eastern Africa: distribution and socioeconomic impacts. J. Econ. Entomol. 112, 2797–2807 (2019).
    PubMed  Article  Google Scholar 

    6.
    Biondi, A., Guedes, R. N. C., Wan, F.-H. & Desneux, N. Ecology, worldwide spread, and management of the invasive South American tomato pinworm, Tuta absoluta: past, present, and future. Annu. Rev. Entomol. 63, 239–258 (2018).
    CAS  PubMed  Article  Google Scholar 

    7.
    Desneux, N. et al. Biological invasion of European tomato crops by Tuta absoluta: ecology, geographic expansion and prospects for biological control. J. Pest Sci. 83, 197–215 (2010).
    Article  Google Scholar 

    8.
    Guedes, R. N. C. C. et al. Insecticide resistance in the tomato pinworm Tuta absoluta: patterns, spread, mechanisms, management and outlook. J. Pest Sci. 92, 1329–1342 (2019).
    Article  Google Scholar 

    9.
    Dimbi, S., Maniania, N. K. & Ekesi, S. Horizontal transmission of Metarhizium anisopliae in fruit flies and effect of fungal infection on egg laying and fertility. Insects 4, 206–216 (2013).
    PubMed  PubMed Central  Article  Google Scholar 

    10.
    Maniania, N. K., Ekesi, S. & Dolinski, C. Entomopathogens routinely used in pest control strategies: orchards in tropical climate. In Microbial Control of Insect and Mite Pests: From Theory to Practice (Elsevier Inc., 2016). https://doi.org/10.1016/B978-0-12-803527-6.00018-4.

    11.
    Mweke, A. et al. Evaluation of the entomopathogenic fungi Metarhizium anisopliae, Beauveria bassiana and Isaria sp. for the management of Aphis craccivora (Hemiptera: Aphididdae). J. Econ. Entomol. 111, 1587–1594 (2018).
    ADS  CAS  PubMed  Article  Google Scholar 

    12.
    Akutse, K. S. et al. Ovicidal effects of entomopathogenic fungal isolates on the invasive Fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae). J. Appl. Entomol. 143, 626–634 (2019).
    CAS  Article  Google Scholar 

    13.
    Akutse, K. S., Subramanian, S., Khamis, F. M., Ekesi, S. & Mohamed, S. A. Entomopathogenic fungus isolates for adult Tuta absoluta (Lepidoptera: Gelechiidae) management and their compatibility with Tuta pheromone. J. Appl. Entomol. https://doi.org/10.1111/jen.12812 (2020).
    Article  Google Scholar 

    14.
    Inglis, G. D., Goettel, M. S., Butt, T. M. & Strasser, H. Use of hyphomycetous fungi for managing insect pests. In Fungi as Biocontrol Agents: Progress, Problems and Potential (eds. Butt, T. M. & Magan, M.) 23–69 (2001). https://doi.org/10.1079/9780851993560.0023.

    15.
    Behie, S. W. & Bidochka, M. J. Ubiquity of insect-derived nitrogen transfer to plants by endophytic insect-pathogenic fungi: an additional branch of the soil nitrogen cycle. Appl. Environ. Microbiol. 80, 1553–1560 (2014).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    16.
    Akutse, K. S., Khamis, F. M., Ekesi, S., Wekesa, S. & Subramanian, S. Effect of endophytically-colonized tomato and nightshade host plants on life-history parameters of Tuta absoluta (Lepidoptera: Gelechiidae). (International Congress on Invertebrate Pathology and Microbial Control and 52nd Annual Meeting of the Society for Invertebrate Pathology & 17th Meeting of the IOBC‐WPRS Working Group “Microbial and Nematode Control of Invertebrate Pests”, 2019).

    17.
    Wilson, D. Endophyte: the evolution of a term, and clarification of its use and definition. Oikos 73, 274–276 (1995).
    Article  Google Scholar 

    18.
    Quesada-Moraga, E., Muñoz-Ledesma, F. J. & Santiago-Álvarez, C. Systemic protection of Papaver somniferum L. against Iraella luteipes (Hymenoptera: Cynipidae) by an endophytic strain of Beauveria bassiana (Ascomycota: Hypocreales). Environ. Entomol. 38, 723–730 (2009).
    CAS  PubMed  Article  Google Scholar 

    19.
    Barelli, L., Moonjely, S., Behie, S. W. & Bidochka, M. J. Fungi with multifunctional lifestyles: endophytic insect pathogenic fungi. Plant Mol. Biol. 90, 657–664 (2016).
    CAS  PubMed  Article  Google Scholar 

    20.
    Latz, M. A. C., Jensen, B., Collinge, D. B. & Jørgensen, H. J. L. Endophytic fungi as biocontrol agents: elucidating mechanisms in disease suppression. Plant Ecol. Divers. 11, 555–567 (2018).
    Article  Google Scholar 

    21.
    Ownley, B. H. et al. Beauveria bassiana: endophytic colonization and plant disease control. J. Invertebr. Pathol. 98, 267–270 (2008).
    CAS  PubMed  Article  Google Scholar 

    22.
    Akello, J. & Sikora, R. Systemic acropedal influence of endophyte seed treatment on Acyrthosiphon pisum and Aphis fabae offspring development and reproductive fitness. Biol. Control 61, 215–221 (2012).
    Article  Google Scholar 

    23.
    Akutse, K. S., Maniania, N. K., Fiaboe, K. K. M., Van den Berg, J. & Ekesi, S. Endophytic colonization of Vicia faba and Phaseolus vulgaris (Fabaceae) by fungal pathogens and their effects on the life-history parameters of Liriomyza huidobrensis (Diptera: Agromyzidae). Fungal Ecol. 6, 293–301 (2013).
    Article  Google Scholar 

    24.
    Russo, M. L. et al. Endophytic effects of Beauveria bassiana on Corn (Zea mays) and its herbivore, Rachiplusia nu (Lepidoptera: Noctuidae). Insects 10, 2–9 (2019).
    Article  Google Scholar 

    25.
    Lahrmann, U. et al. Host-related metabolic cues affect colonization strategies of a root endophyte. Proc. Natl. Acad. Sci. USA 110, 13965–13970 (2013).
    ADS  CAS  PubMed  Article  Google Scholar 

    26.
    Fadiji, A. E. & Babalola, O. O. Elucidating mechanisms of endophytes used in plant protection and other bioactivities with multifunctional prospects. Front. Bioeng. Biotechnol. 8, 1–20 (2020).
    Article  Google Scholar 

    27.
    Gathage, J. W. et al. Prospects of fungal endophytes in the control of Liriomyza leafminer flies in common bean Phaseolus vulgaris under field conditions. Biocontrol 61, 741–753 (2016).
    Article  Google Scholar 

    28.
    Muvea, A. M. et al. Colonization of onions by endophytic fungi and their impacts on the biology of Thrips tabaci. PLoS ONE 9, 1–7 (2014).
    Article  CAS  Google Scholar 

    29.
    Powell, W. A., Klingeman, W. E., Ownley, B. H. & Gwinn, K. D. Evidence of endophytic Beauveria bassiana in seed-treated tomato plants acting as a systemic entomopathogen to larval Helicoverpa zea (Lepidoptera: Noctuidae). J. Entomol. Sci. 44, 391–396 (2009).
    Article  Google Scholar 

    30.
    Klieber, J. & Reineke, A. The entomopathogen Beauveria bassiana has epiphytic and endophytic activity against the tomato leaf miner Tuta absoluta. J. Appl. Entomol. 140, 580–589 (2016).
    CAS  Article  Google Scholar 

    31.
    Resquín-romero, G., Garrido-jurado, I., Delso, C., Ríos-moreno, A. & Quesada-moraga, E. Transient endophytic colonizations of plants improve the outcome of foliar applications of mycoinsecticides against chewing insects. J. Invertebr. Pathol. 136, 23–31 (2016).
    PubMed  Article  CAS  Google Scholar 

    32.
    Mutune, B. et al. Fungal endophytes as promising tools for the management of bean stem maggot Ophiomyia phaseoli on beans Phaseolus vulgaris. J. Pest Sci. 89, 993–1001 (2016).
    Article  Google Scholar 

    33.
    Posada, F., Aime, M. C., Peterson, S. W., Rehner, S. A. & Vega, F. E. Inoculation of coffee plants with the fungal entomopathogen Beauveria bassiana (Ascomycota: Hypocreales). Mycol. Res. 111, 748–757 (2007).
    CAS  PubMed  Article  Google Scholar 

    34.
    Bing, L. A. & Lewis, L. C. Suppression of Ostrinia nubilalis (Hübner) (Lepidoptera: Pyralidae) by endophytic Beauveria bassiana (Balsamo) Vuillemin. Environ. Entomol. 20, 1207–1211 (1991).
    Article  Google Scholar 

    35.
    Behie, S. W., Jones, S. J., Bidochka, M. J. & Hyde, K. Plant tissue localization of the endophytic insect pathogenic fungi Metarhizium and Beauveria. Fungal Ecol. 13, 112–119 (2015).
    Article  Google Scholar 

    36.
    Akello, J. et al. Beauveria bassiana (Balsamo) Vuillemin as an endophyte in tissue culture banana (Musa spp.). J. Invertebr. Pathol. 96, 34–42 (2007).
    PubMed  Article  Google Scholar 

    37.
    Posada, F. J. & Vega, F. E. A new method to evaluate the biocontrol potential of single spore isolates of fungal entomopathogens. J. Insect Sci. 5, 1–10 (2005).
    Article  Google Scholar 

    38.
    Demers, J. E., Gugino, B. K. & del Jiménez-Gasco, M. Highly diverse endophytic and soil Fusarium oxysporum populations associated with field-grown tomato plants. Appl. Environ. Microbiol. 81, 81–90 (2015).
    PubMed  Article  CAS  Google Scholar 

    39.
    Bogner, C. W. et al. Fungal root endophytes of tomato from Kenya and their nematode biocontrol potential. Mycol. Prog. 15, 1–17 (2016).
    Article  Google Scholar 

    40.
    Hardoim, P. R. et al. The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol. Mol. Biol. Rev. 79, 293–320 (2015).
    PubMed  PubMed Central  Article  Google Scholar 

    41.
    Martin, J. T. Role of cuticle in the defense against plant disease. Annu. Rev. Phytopathol. 2, 81–100 (1964).
    Article  Google Scholar 

    42.
    Jensen, R. E., Enkegaard, A. & Steenberg, T. Increased fecundity of Aphis fabae on Vicia faba plants following seed or leaf inoculation with the entomopathogenic fungus Beauveria bassiana. PLoS ONE 14, 1–12 (2019).
    Google Scholar 

    43.
    Landa, B. B. et al. In-planta detection and monitorization of endophytic colonization by a Beauveria bassiana strain using a new-developed nested and quantitative PCR-based assay and confocal laser scanning microscopy. J. Invertebr. Pathol. 114, 128–138 (2013).
    CAS  PubMed  Article  Google Scholar 

    44.
    Bing, L. A. & Lewis, L. C. Endophytic Beauveria bassiana (Balsamo) Vuillemin in corn: The influence of the plant growth stage and Ostrinia nubilalis (Hubner). Biocontrol Sci. Technol. 2, 39–47 (1992).
    Article  Google Scholar 

    45.
    Greenfield, M. et al. Beauveria bassiana and Metarhizium anisopliae endophytically colonize cassava roots following soil drench inoculation. Biol. Control 95, 40–48 (2016).
    PubMed  PubMed Central  Article  Google Scholar 

    46.
    Card, S., Johnson, L., Teasdale, S. & Caradus, J. Deciphering endophyte behaviour: the link between endophyte biology and efficacious biological control agents. FEMS Microbiol. Ecol. 92, 1–19 (2016).
    Article  CAS  Google Scholar 

    47.
    Philippot, L., Raaijmakers, J. M., Lemanceau, P. & Van Der Putten, W. H. Going back to the roots: the microbial ecology of the rhizosphere. Nat. Publ. Gr. 11, 789–799 (2013).
    CAS  Google Scholar 

    48.
    Tumuhaise, V. et al. Pathogenicity and performance of two candidate isolates of Metarhizium anisopliae and Beauveria bassiana (Hypocreales: Clavicipitaceae) in four liquid culture media for the management of the legume pod borer Maruca vitrata (Lepidoptera: Crambidae). Int. J. Trop. Insect Sci. 35, 34–47 (2015).
    Article  Google Scholar 

    49.
    Branine, M., Bazzicalupo, A. & Branco, S. Biology and applications of endophytic insect-pathogenic fungi. PLoS Pathog. 15, 1–7 (2019).
    Article  CAS  Google Scholar 

    50.
    Barelli, L., Moreira, C. C. & Bidochka, M. J. Initial stages of endophytic colonization by Metarhizium involves rhizoplane colonization. Microbiology 164, 1531–1540 (2018).
    CAS  PubMed  Article  Google Scholar 

    51.
    Wyrebek, M., Huber, C., Sasan, R. K. & Bidochka, M. J. Three sympatrically occurring species of Metarhizium show plant rhizosphere specificity. Microbiology 157, 2904–2911 (2011).
    CAS  PubMed  Article  Google Scholar 

    52.
    Muvea, A. M. et al. Behavioral responses of Thrips tabaci Lindeman to endophyte-inoculated onion plants. J. Pest Sci. 88, 555–562 (2015).
    Article  Google Scholar 

    53.
    Slansky, F. Jr. Insect nutrition: an adaptationist’s perspective. Florida Entomol. 65, 45–71 (1982).
    Article  Google Scholar 

    54.
    Carroll, G. Fungal endophytes in stems and leaves: from latent pathogen to mutualistic symbiont. Ecology 69, 2–9 (1988).
    Article  Google Scholar 

    55.
    Allegrucci, N., Velazquez, M. S., Russo, M. L., Perez, E. & Scorsetti, A. C. Endophytic colonisation of tomato by the entomopathogenic fungus Beauveria bassiana: the use of different inoculation techniques and their effects on the tomato leafminer Tuta absoluta (Lepidoptera : Gelechiidae). J. Plant Prot. Res. 54, 331–337 (2017).
    Google Scholar 

    56.
    Barta, M. In planta bioassay on the effects of endophytic Beauveria strains against larvae of horse-chestnut leaf miner (Cameraria ohridella). Biol. Control 121, 88–98 (2018).
    Article  Google Scholar 

    57.
    Russo, M. L. et al. Effect of endophytic entomopathogenic fungi on soybean Glycine max (L.) Merr. growth and yield. J. King Saud Univ. Sci. 31, 728–736 (2018).
    Article  Google Scholar 

    58.
    Contreras-cornejo, H. A., Macías-rodríguez, L. & Larsen, J. The root endophytic fungus Trichoderma atroviride induces foliar herbivory resistance in maize plants. Appl. Soil Ecol. 124, 45–53 (2017).
    Article  Google Scholar 

    59.
    Contreras-Cornejo, H. A., Macías-Rodríguez, L., Del Val, E. & Larsen, J. Ecological functions of Trichoderma spp. and their secondary metabolites in the rhizosphere: interactions with plants. FEMS Microbiol. Ecol. 92, 1–17 (2016).
    Article  CAS  Google Scholar 

    60.
    Coppola, M. et al. Trichoderma harzianum enhances tomato indirect defense against aphids. Insect Sci. 24, 1025–1033 (2017).
    CAS  PubMed  Article  Google Scholar 

    61.
    Meera, M. S., Shivanna, M. B., Kageyama, K. & Hyakumachi, M. Persistence of induced systemic resistance in cucumber in relation to root colonization by plant growth promoting fungal isolates. Crop Prot. 14, 123–130 (1995).
    Article  Google Scholar 

    62.
    Lewis, L. C., Berry, E. C., Obrycki, J. J. & Bing, L. A. Aptness of insecticides (Bacillus thuringiensis and carbofuran ) with endophytic Beauveria bassiana, in suppressing larval populations of the European corn borer. Agric. Ecosyst. Environ. 57, 27–34 (1996).
    Article  Google Scholar 

    63.
    Qayyum, M. A., Wakil, W., Arif, M. J., Sahi, S. T. & Dunlap, C. A. Infection of Helicoverpa armigera by endophytic Beauveria bassiana colonizing tomato plants. Biol. Control 90, 200–207 (2015).
    Article  Google Scholar 

    64.
    Jallow, M. F. A., Dugassa-Gobena, D. & Vidal, S. Influence of an endophytic fungus on host plant selection by a polyphagous moth via volatile spectrum changes. Arthropod. Plant. Interact. 2, 53–62 (2008).
    Article  Google Scholar 

    65.
    Jaber, L. R. & Vidal, S. Fungal endophyte negative effects on herbivory are enhanced on intact plants and maintained in a subsequent generation. Ecol. Entomol. 35, 25–36 (2010).
    Article  Google Scholar 

    66.
    Davis, T. S., Crippen, T. L., Hofstetter, R. W. & Tomberlin, J. K. Microbial volatile emissions as insect semiochemicals. J. Chem. Ecol. 39, 840–859 (2013).
    CAS  PubMed  Article  Google Scholar 

    67.
    Silva, D. B., Bueno, V. H. P., Lins, J. C. & Van Lenteren, J. C. Life history data and population growth of Tuta absoluta at constant and alternating temperatures on two tomato lines. Bull. Insectol. 68, 223–232 (2015).
    Google Scholar 

    68.
    Pereyra, P. C. & Sánchez, N. E. Effect of two solanaceous plants on developmental and population parameters of the tomato leaf miner, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae). Neotrop. Entomol. 35, 671–676 (2006).
    PubMed  Article  Google Scholar 

    69.
    Dash, C. K. et al. Endophytic entomopathogenic fungi enhance the growth of Phaseolus vulgaris L. (Fabaceae) and negatively affect the development and reproduction of Tetranychus urticae Koch (Acari: Tetranychidae). Microb. Pathog. 125, 385–392 (2018).
    PubMed  Article  Google Scholar 

    70.
    Akello, J., Dubois, T., Coyne, D. & Kyamanywa, S. Endophytic Beauveria bassiana in banana (Musa spp.) reduces banana weevil (Cosmopolites sordidus) fitness and damage. Crop Prot. 27, 1437–1441 (2008).
    Article  Google Scholar 

    71.
    Golo, P. S. et al. Production of destruxins from Metarhizium spp. fungi in artificial medium and in endophytically colonized cowpea plants. PLoS ONE 9, 1–9 (2014).
    Article  CAS  Google Scholar 

    72.
    Goettel, M. S. & Inglis, D. G. Fungi: Hyphomycetes. Manual of Techniques in Insect Pathology (1997). https://doi.org/10.1016/B978-012432555-5/50013-0.

    73.
    Schulz, B., Guske, S., Dammann, U. & Boyle, C. Endophyte-host interactions. II. Defining symbiosis of the endophyte–host interaction. Symbiosis 25, 213–227 (1998).
    Google Scholar 

    74.
    Inglis, G. D., Enkerli, J. & Goettel, M. S. Laboratory Techniques Used for Entomopathogenic Fungi. Hypocreales. Manual of Techniques in Invertebrate Pathology (Elsevier, New York, 2012). https://doi.org/10.1016/B978-0-12-386899-2.00007-5
    Google Scholar 

    75.
    Petrini, O. & Fisher, P. J. Fungal endophytes in Salicornia perennis. Trans. Br. Mycol. Soc. 87, 647–651 (1986).
    Article  Google Scholar 

    76.
    Aigbedion-Atalor, P. O. et al. Host stage preference and performance of Dolichogenidea gelechiidivoris (Hymenoptera: Braconidae), a candidate for classical biological control of Tuta absoluta in Africa. Biol. Control 144, 1–8 (2020).
    Article  CAS  Google Scholar 

    77.
    Oliveira, F. A., da Silva, D. J. H., Leite, G. L. D., Jham, G. N. & Picanço, M. Resistance of 57 greenhouse-grown accessions of Lycopersicon esculentum and three cultivars to Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae). Sci. Hortic. (Amsterdam) 119, 182–187 (2009).
    CAS  Article  Google Scholar 

    78.
    Shapiro, S. S. & Wilk, M. B. An analysis of variance test for normality (complete samples). Biometrika 52, 591–611 (1965).
    MathSciNet  MATH  Article  Google Scholar 

    79.
    De Mendiburu, F. agricolae: statistical procedures for agricultural research. R package version 1.3–2 https://CRAN.R-project.org/package=agricolae (2020).

    80.
    Therneau, T. A Package for Survival Analysis in R. R package version 3.1-12, https://CRAN.R-project.org/package=survival. (2020).

    81.
    Crawley, M. J. The R Book (Wiley, New York, 2007). https://doi.org/10.1002/9780470515075.
    Google Scholar 

    82.
    R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, 2019).
    Google Scholar  More

  • in

    Antler cannibalism in reindeer

    1.
    McKintosh, E., Tabrizi, S. J. & Collinge, J. Prion diseases. J. Neuro. Virol. 9, 183–193 (2003).
    CAS  Google Scholar 
    2.
    Chen, C. & Dong, X. P. Epidemiological characteristics of human prion diseases. Infect. Dis. Poverty 5, 47 (2016).
    Article  Google Scholar 

    3.
    Huor, A. et al. The emergence of classical BSE from atypical/Nor98 scrapie. PNAS 116, 26853–26862 (2019).
    CAS  Article  Google Scholar 

    4.
    Prusiner, S. B. Prion diseases and the BSE crisis. Science 278, 245–251 (1997).
    CAS  Article  Google Scholar 

    5.
    Wadsworth, J. D. F. et al. The origin of the prion agent of kuru: molecular and biological strain typing. Philos. Trans. R. Soc. Lond. B Biol. Sci. 363, 3747–3753 (2008).
    CAS  Article  Google Scholar 

    6.
    Liberski, P. P., Gajos, A., Sikorska, B. & Lindenbaum, S. Kuru, the first human prion disease. Viruses 11, 232 (2019).
    Article  Google Scholar 

    7.
    Haley, N. J. & Hoover, E. A. Chronic Wasting Disease of cervids: current knowledge and future perspectives. Annu. Rev. Anim. Biosci. 3, 305–325 (2015).
    CAS  Article  Google Scholar 

    8.
    Benestad, S. L., Mitchell, G., Simmons, M., Ytrehus, B. & Vikøren, T. First case of chronic wasting disease in Europe in a Norwegian free-ranging reindeer. Vet. Res. 47, 88 (2016).
    Article  Google Scholar 

    9.
    Becker, R. Deadly animal prion disease appears in Europe. Nature https://doi.org/10.1038/nature.2016.19759 (2016).
    Article  PubMed  PubMed Central  Google Scholar 

    10.
    Stokstad, E. Norway seeks to stamp out prion disease. Science 356, 12 (2017).
    ADS  CAS  Article  Google Scholar 

    11.
    Sutherland, W. J. et al. A 2018 horizon scan of emerging issues for global conservation and biological diversity. Trends Ecol. Evol. 33, 47–58 (2018).
    Article  Google Scholar 

    12.
    Nonno, R., Di Bari, M. A., Pirisinu, L., et al. Studies in bank voles reveal strain differences between chronic wasting disease prions from Norway and North America. Proc Natl Acad Sci USA in press, (2020).

    13.
    Sutcliffe, A. J. Similarity of bones and antlers gnawed by deer to human artefacts. Nature 246, 428–430 (1973).
    ADS  CAS  Article  Google Scholar 

    14.
    Gambín, P., Ceacero, F., Garcia, A. J., Landete-Castillejos, T. & Gallego, L. Patterns of antler consumption reveal osteophagia as a natural mineral resource in key periods for red deer (Cervus elaphus). Eur. J. Wildl. Res. 63, 39 (2017).
    Article  Google Scholar 

    15.
    Klaus, G. & Schmid, B. Geophagy at natural licks and mammal ecology: a review. Mammalia 62, 481–497 (1999).
    Google Scholar 

    16.
    Mahaney, W. C. & Krishnamani, R. Understanding geophagy in animals: standard procedures for sampling soils. J. Chem. Ecol. 29, 1503–1523 (2003).
    CAS  Article  Google Scholar 

    17.
    Bazely, D. R. Carnivorous herbivores: mineral nutrition and the balanced diet. Trends Ecol. Evol. 4, 155–156 (1989).
    Article  Google Scholar 

    18.
    Loe, L. E. et al. Antler growth as a cost of reproduction in female reindeer. Oecologia 189, 601–609 (2019).
    ADS  Article  Google Scholar 

    19.
    Clutton-Brock, T. H., Albon, S. D. & Harvey, P. H. Antlers, body size and breeding group size in the Cervidae. Nature 285, 565–567 (1980).
    ADS  Article  Google Scholar 

    20.
    Schaefer, J. A. & Mahoney, S. P. Antlers on female caribou: biogeography of the bones of contention. Ecology 82, 3556–3560 (2001).
    Article  Google Scholar 

    21.
    Angers, R. C. et al. Chronic wasting disease prions in elk antler velvet. Emerg. Infect. Dis. 15, 696–703 (2009).
    CAS  Article  Google Scholar 

    22.
    Nieto-Diaz, M. et al. Deer antler innervation and regeneration. Front Biosci. 17, 1389–1401 (2012).
    CAS  Article  Google Scholar 

    23.
    Guiroy, D. C. et al. Neuronal degeneration and neurofilament accumulation in the trigeminal ganglia in creutzfeldt-jakob disease. Ann Neurol. 25, 102–106 (1989).
    CAS  Article  Google Scholar 

    24.
    Rolf, H. J. & Enderle, A. Hard fallow deer antler: a living bone till antler casting?. Anat. Rec. 255, 69–77 (1999).
    CAS  Article  Google Scholar 

    25.
    Huor, A. et al. Infectivity in bone marrow from sporadic CJD patients. J. Pathol. 243, 273–278 (2017).
    Article  Google Scholar 

    26.
    Davenport, K. A. et al. PrPC expression and prion seeding activity in the alimentary tract and lymphoid tissue of deer. PLoS ONE 12, e0183927 (2017).
    Article  Google Scholar 

    27.
    Mysterud, A. et al. The demographic pattern of infection with chronic wasting disease in reindeer at an early epidemic stage. Ecosphere 10, e02931 (2019).
    Article  Google Scholar 

    28.
    Pirisinu, L. et al. A novel type of Chronic Wasting Disease detected in European moose (Alces alces) in Norway. Emerg. Infect. Dis. 24, 2210–2218 (2018).
    CAS  Article  Google Scholar 

    29.
    Vikøren, T. et al. First detection of Chronic Wasting Disease in a wild red deer (Cervus elaphus) in Europe. J. Wildl. Dis. 55, 970–972 (2019).
    Article  Google Scholar 

    30.
    Buschmann, A. et al. Atypical BSE in Germany – Proof of transmissibility and biochemical characterization. Vet. Microbiol. 117, 103–116 (2006).
    CAS  Article  Google Scholar 

    31.
    Benestad, S. L. et al. Cases of scrapie with unusal features in Norway and designation of a new type, Nor98. Vet. Rec. 153, 2002–2008 (2003).
    Article  Google Scholar 

    32.
    Estevez, J. A., Landete-Castillejos, T., García, A. J., Ceacero, F. & Gallego, L. Population management and bone structural effects in composition and radio-opacity of iberian red deer (Cervus elaphus hispanicus) antlers. Eur. J. Wildl. Res. 54, 215–223 (2008).
    Article  Google Scholar 

    33.
    Norman, G. Likert scales, levels of measurement and the “laws” of statistics. Adv. Health. Sci. Educ. 15, 625–632 (2019).
    Article  Google Scholar 

    34.
    Collinge, J. & Clarke, A. R. A general model of prion strains and their pathogenicity. Science 318, 930 (2007).
    ADS  CAS  Article  Google Scholar 

    35.
    Marion, M. S. et al. Experimental oral transmission of atypical scrapie to sheep. Emerg. Infect. Dis. 17, 848 (2011).
    Article  Google Scholar 

    36.
    Angers, R. C. et al. Prion strain mutation determined by prion protein conformational compatibility and primary structure. Science 328, 1154 (2010).
    ADS  CAS  Article  Google Scholar 

    37.
    Igel-Egalon, A., Béringue, V., Rezaei, H. & Sibille, P. Prion strains and transmission barrier phenomena. Pathogens 7, (2018).

    38.
    Le Dur, A. et al. Divergent prion strain evolution driven by PrPC expression level in transgenic mice. Nat. Commun. 8, 14170 (2017).
    ADS  Article  Google Scholar  More

  • in

    Picophytoplankton dynamics in a large temperate estuary and impacts of extreme storm events

    1.
    Johnson, P. W. & Sieburth, J. M. Chroococcoid cyanobacteria in the sea: A ubiquitous and diverse phototrophic biomass1. Limnol. Oceanogr. 24, 928–935 (1979).
    ADS  Article  Google Scholar 
    2.
    Waterbury, J. B., Watson, S. W., Guillard, R. L. & Brand, L. E. Widespread occurrence of a unicellular, marine, planktonic, cyanobacterium. Nature 277, 293–294 (1979).
    ADS  Article  Google Scholar 

    3.
    Stockner, J. G. & Antia, N. J. Algal picoplankton from marine and freshwater ecosystems: A multidisciplinary perspective. Can. J. Fish. Aquat. Sci. 43, 2472–2503 (1986).
    Article  Google Scholar 

    4.
    Partensky, F., Blanchot, J. & Vaulot, D. Differential distribution and ecology of Prochlorococcus and Synechococcus in oceanic waters: A review. Bull. l’Institut Oceanogr. Monaco Spec. 19, 457–475 (1999).
    Google Scholar 

    5.
    Stal, L. J. & Staal, M. Nutrient control of cyanobacterial blooms in the Baltic Sea. Aquat. Microb. Ecol. 18, 165–173 (1999).
    Article  Google Scholar 

    6.
    Paczkowska, J. et al. Allochthonous matter: An important factor shaping the phytoplankton community in the Baltic Sea. J. Plankton Res. 39, 23–34 (2017).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    7.
    Gaulke, A. K., Wetz, M. S. & Paerl, H. W. Picophytoplankton: A major contributor to planktonic biomass and primary production in a eutrophic, river-dominated estuary. Estuar. Coast. Shelf Sci. 90, 45–54 (2010).
    ADS  CAS  Article  Google Scholar 

    8.
    Wang, K., Wommack, K. E. & Chen, F. Abundance and distribution of Synechococcus spp. and cyanophages in the Chesapeake Bay. Appl. Environ. Microbiol. 77, 7459–7468 (2011).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    9.
    Olson, R. J., Zettler, E. R. & DuRand, M. D. Phytoplankton analysis using flow cytometry. In Handbook of Methods in Aquatic Microbial Ecology 175–186 (Lewis Publishers, Boca Raton, 1993).

    10.
    Li, W. K. W. Cytometric diversity in marine ultraphytoplankton. Limnol. Oceanogr. 42, 874–880 (1997).
    ADS  CAS  Article  Google Scholar 

    11.
    Collier, J. L. Flow cytometry and the single cell in phycology. J. Phycol. 36, 628–644 (2000).
    PubMed  Article  PubMed Central  Google Scholar 

    12.
    Liu, H., Jing, H., Wong, T. H. C. & Chen, B. Co-occurrence of phycocyanin- and phycoerythrin-rich Synechococcus in subtropical estuarine and coastal waters of Hong Kong. Environ. Microbiol. Rep. 6, 90–99 (2013).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    13.
    Rajaneesh, K. M. & Mitbavkar, S. Factors controlling the temporal and spatial variations in Synechococcus abundance in a monsoonal estuary. Mar. Environ. Res. 92, 133–143 (2013).
    Article  CAS  Google Scholar 

    14.
    Albrecht, M., Pröschold, T. & Schumann, R. Identification of cyanobacteria in a eutrophic coastal lagoon on the southern Baltic coast. Front. Microbiol. 8, 923 (2017).
    PubMed  PubMed Central  Article  Google Scholar 

    15.
    Caroppo, C. Ecology and biodiversity of picoplanktonic cyanobacteria in coastal and brackish environments. Biodivers. Conserv. 24, 949–971 (2015).
    Article  Google Scholar 

    16.
    Murrell, M. C. & Lores, E. M. Phytoplankton and zooplankton seasonal dynamics in a subtropical estuary: Importance of cyanobacteria. J. Plankton Res. 26, 371–382 (2004).
    Article  Google Scholar 

    17.
    Xia, X., Guo, W., Tan, S. & Liu, H. Synechococcus assemblages across the salinity gradient in a salt wedge estuary. Front. Microbiol. 8, 1254 (2017).
    PubMed  PubMed Central  Article  Google Scholar 

    18.
    Phlips, E. J., Badylak, S. & Lynch, T. C. Blooms of the picoplanktonic cyanobacterium Synechococcus in Florida Bay, a subtropical inner-shelf lagoon. Limnol. Ocean. 44, 1166–1175 (1999).
    Article  Google Scholar 

    19.
    Weisse, T. Dynamics of autotrophic picoplankton in marine and freshwater ecosystems. In Advances in Microbial Ecology, vol 13 (ed. Jones, J. G.) 327–370 (Springer US, New York, 1993).

    20.
    Tomas, C. R. Identifying marine phytoplankton (Academic Press, New York, 1997).
    Google Scholar 

    21.
    Gobler, C. J., Renaghan, M. J. & Buck, N. J. Impacts of nutrients and grazing mortality on the abundance of Aureococcus anophagefferens during a New York brown tide bloom. Limnol. Oceanogr. 47, 129–141 (2002).
    ADS  Article  Google Scholar 

    22.
    Vaquer, A., Troussellier, M., Courties, C. & Bibent, B. Standing stock and dynamics of picophytoplankton in the Thau Lagoon (northwest Mediterranean coast). Limnol. Oceanogr. 41, 1821–1828 (1996).
    ADS  Article  Google Scholar 

    23.
    Calvo-Diaz, A. & Moran, X. A. G. Seasonal dynamics of picoplankton in shelf waters of the southern Bay of Biscay. Aquat. Microb. Ecol. 42, 159–174 (2006).
    Article  Google Scholar 

    24.
    Worden, A. Z., Nolan, J. K. & Palenik, B. Assessing the dynamics and ecology of marine picophytoplankton: The importance of the eukaryotic component. Limnol. Ocean. 49, 168–179 (2004).
    CAS  Article  Google Scholar 

    25.
    O’Kelly, C. J., Sieracki, M. E., Thier, E. C. & Hobson, I. C. A transient bloom of Ostreococcus (Chlorophyta, Prasinophyceae) in West Neck Bay, Long Island, New York. J. Phycol. 39, 850–854 (2003).
    Article  Google Scholar 

    26.
    Péquin, B., Mohit, V., Poisot, T., Tremblay, R. & Lovejoy, C. Wind drives microbial eukaryote communities in a temperate closed lagoon. Aquat. Microb. Ecol. 78, 187–200 (2017).
    Article  Google Scholar 

    27.
    Bec, B. et al. Distribution of picophytoplankton and nanophytoplankton along an anthropogenic eutrophication gradient in French Mediterranean coastal lagoons. Aquat. Microb. Ecol. 63, 29–45 (2011).
    Article  Google Scholar 

    28.
    Stal, L. J. et al. BASIC: Baltic Sea cyanobacteria. An investigation of the structure and dynamics of water blooms of cyanobacteria in the Baltic Sea–-responses to a changing environment. Cont. Shelf Res. 23, 1695–1714 (2003).
    ADS  Article  Google Scholar 

    29.
    Chen, F., Wang, K., Kan, J., Suzuki, M. T. & Wommack, K. E. Diverse and unique picocyanobacteria in Chesapeake Bay, revealed by 16S–23S rRNA internal transcribed spacer sequences. Appl. Environ. Microbiol. 72, 2239–2243 (2006).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    30.
    Paerl, H. W., Pinckney, J. L., Fear, J. M. & Peierls, B. L. Ecosystem responses to internal and watershed organic matter loading: Consequences for hypoxia in the eutrophying Neuse River Estuary, North Carolina, USA. Mar. Ecol. Prog. Ser. 166, 17–25 (1998).
    ADS  CAS  Article  Google Scholar 

    31.
    Peierls, B. L., Hall, N. S. & Paerl, H. W. Non-monotonic responses of phytoplankton biomass accumulation to hydrologic variability: A comparison of two coastal plain north carolina estuaries. Estuar. Coasts 35, 1376–1392 (2012).
    Article  Google Scholar 

    32.
    Paerl, H. W. et al. Two decades of tropical cyclone impacts on North Carolina’s estuarine carbon, nutrient and phytoplankton dynamics: Implications for biogeochemical cycling and water quality in a stormier world. Biogeochemistry 141, 307–332 (2018).
    ADS  CAS  Article  Google Scholar 

    33.
    Wetz, M. S., Paerl, H. W., Taylor, J. C. & Leonard, J. A. Environmental controls upon picophytoplankton growth and biomass in a eutrophic estuary. Aquat. Microb. Ecol. 63, 133–143 (2011).
    Article  Google Scholar 

    34.
    Apple, J. K., Strom, S. L., Palenik, B. & Brahamsha, B. Variability in protist grazing and growth on different marine Synechococcus isolates. Appl. Environ. Microbiol. 77, 3074–3084 (2011).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    35.
    Zwirglmaier, K., Spence, E. D., Zubkov, M. V., Scanlan, D. J. & Mann, N. H. Differential grazing of two heterotrophic nanoflagellates on marine Synechococcus strains. Environ. Microbiol. 11, 1767–1776 (2009).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    36.
    Paz-Yepes, J., Brahamsha, B. & Palenik, B. Role of a microcin-C-like biosynthetic gene cluster in allelopathic interactions in marine Synechococcus. Proc. Natl. Acad. Sci. 110, 12030–12035 (2013).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    37.
    Wall, C., Rodgers, B., Gobler, C. & Peterson, B. Responses of loggerhead sponges Spechiospongia vesparium during harmful cyanobacterial blooms in a sub-tropical lagoon. Mar. Ecol. Prog. Ser. 451, 31–43 (2012).
    ADS  Article  Google Scholar 

    38.
    Hamilton, T. J., Paz-Yepes, J., Morrison, R. A., Palenik, B. & Tresguerres, M. Exposure to bloom-like concentrations of two marine Synechococcus cyanobacteria (strains CC9311 and CC9902) differentially alters fish behaviour. Conserv. Physiol. 2, cuo020 (2014).
    Article  Google Scholar 

    39.
    Bales, J. D. Effects of Hurricane Floyd inland flooding, September–October 1999, on tributaries to Pamlico Sound, North Carolina. Estuaries 26, 1319–1328 (2003).
    Article  Google Scholar 

    40.
    Paerl, H. W. et al. Recent increase in catastrophic tropical cyclone flooding in coastal North Carolina, USA: Long-term observations suggest a regime shift. Sci. Rep. 9, 10620 (2019).
    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

    41.
    Osburn, C. L., Rudolph, J. C., Paerl, H. W., Hounshell, A. G. & Van Dam, B. R. Lingering carbon cycle effects of Hurricane Matthew in North Carolina’s coastal waters. Geophys. Res. Lett. 46, 2654–2661 (2019).
    ADS  CAS  Article  Google Scholar 

    42.
    Paerl, H. W., Rossignol, K. L., Hall, S. N., Peierls, B. L. & Wetz, M. S. Phytoplankton community indicators of short- and long-term ecological change in the anthropogenically and climatically impacted neuse river estuary, North Carolina, USA. Estuar. Coasts 33, 485–497 (2010).
    CAS  Article  Google Scholar 

    43.
    Six, C., Sherrard, R., Lionard, M., Roy, S. & Campbell, D. A. Photosystem II and pigment dynamics among ecotypes of the green alga Ostreococcus. Plant Physiol. 151, 379–390 (2009).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    44.
    Bec, B., Husseini-Ratrema, J., Collos, Y., Souchu, P. & Vaquer, A. Phytoplankton seasonal dynamics in a Mediterranean coastal lagoon: Emphasis on the picoeukaryote community. J. Plankton Res. 27, 881–894 (2005).
    CAS  Article  Google Scholar 

    45.
    Mohan, A. P., Jyothibabu, R., Jagadeesan, L., Lallu, K. R. & Karnan, C. Summer monsoon onset-induced changes of autotrophic pico-and nanoplankton in the largest monsoonal estuary along the west coast of India. Environ. Monit. Assess. 188, 93 (2016).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    46.
    Paerl, H. W. et al. Microbial indicators of aquatic ecosystem change: Current applications to eutrophication studies. In FEMS Microbiology Ecology 46, 233–246 (Elsevier, Amsterdam, 2003).

    47.
    NC Weather Forecast Office Newport/Morehead City. Post Tropical Cyclone Report—Hurricane Florence. National Weather Service (2018).

    48.
    Welschmeyer, N. A. Fluorometric analysis of chlorophyll a in the presence of chlorophyll b and pheopigments. Limnol. Oceanogr. 39, 1985–1992 (1994).
    ADS  CAS  Article  Google Scholar 

    49.
    Schlitzer, R. Ocean Data View. (2020).

    50.
    Mangiafico, S. S. Summary and analysis of extension program evaluation in R, version 1.15. 0. Rutgers Coop. Extension, New Brunswick, NJ https//rcompanion. org/handbook/.[Google Sch. (2016).

    51.
    Siegel, A. F. Robust regression using repeated medians. Biometrika 69, 242–244 (1982).
    MATH  Article  Google Scholar 

    52.
    R Core Team. R: A language and environment for statistical computing. R Found. Stat. Comput. Vienna, Austria. http://www.R-project.org/. R Foundation for Statistical Computing (2014).

    53.
    Oksanen, J. et al. Package vegan. R Packag ver 254, (2013).

    54.
    Dray, S. et al. Community ecology in the age of multivariate multiscale spatial analysis. Ecol. Monogr. 82, 257–275 (2012).
    Article  Google Scholar 

    55.
    Simpson, G. L. ggvegan: ‘ggplot2’ Plots for the ‘vegan’ Package. (2015).

    56.
    Rudolph, J. C., Arendt, C. A., Hounshell, A. G., Paerl, H. W. & Osburn, C. L. Use of geospatial, hydrologic, and geochemical modeling to determine the influence of wetland-derived organic matter in coastal waters in response to extreme weather events. Front. Mar. Sci. 7, (2020). https://doi.org/10.3389/fmars.2020.00018

    57.
    Ray, R. T., Haas, L. W. & Sieracki, M. E. Autotrophic picoplankton dynamics in a Chesapeake Bay sub-estuary. Mar. Ecol. Prog. Ser. 52, 273–285 (1989).
    ADS  Article  Google Scholar 

    58.
    Marshall, H. G. & Nesius, K. K. Seasonal relationships between phytoplankton composition, abundance, and primary productivity in three tidal rivers of the lower Chesapeake Bay. J. Elisha Mitchell Sci. Soc. 109, 141–151 (1993).
    Google Scholar 

    59.
    Larsson, J. et al. Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea. ISME J. 8, 1892–1903 (2014).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    60.
    Berry, D. L. et al. Shifts in Cyanobacterial strain dominance during the onset of harmful algal blooms in Florida Bay, USA. Microb. Ecol. 70, 361–371 (2015).
    PubMed  Article  PubMed Central  Google Scholar 

    61.
    DeLong, J. P., Okie, J. G., Moses, M. E., Sibly, R. M. & Brown, J. H. Shifts in metabolic scaling, production, and efficiency across major evolutionary transitions of life. Proc. Natl. Acad. Sci. U. S. A. 107, 12941–12945 (2010).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    62.
    Cabello-Yeves, P. J. et al. Novel Synechococcus genomes reconstructed from freshwater reservoirs. Front. Microbiol. 8, 1151 (2017).
    PubMed  PubMed Central  Article  Google Scholar 

    63.
    Grébert, T. et al. Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria. Proc. Natl. Acad. Sci. U. S. A. 115, E2010–E2019 (2018).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    64.
    Stomp, M. et al. Colourful coexistence of red and green picocyanobacteria in lakes and seas. Ecol. Lett. 10, 290–298 (2007).
    PubMed  Article  PubMed Central  Google Scholar 

    65.
    Marsan, D., Place, A., Fucich, D. & Chen, F. Toxin-antitoxin systems in estuarine Synechococcus strain CB0101 and their transcriptomic responses to environmental stressors. Front. Microbiol. 8, 1213 (2017).
    PubMed  PubMed Central  Article  Google Scholar 

    66.
    Zborowsky, S. & Lindell, D. Resistance in marine cyanobacteria differs against specialist and generalist cyanophages. Proc. Natl. Acad. Sci. U. S. A. 116, 16899–16908 (2019).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    67.
    Paerl, H. W., Hall, N. S., Peierls, B. L., Rossignol, K. L. & Joyner, A. R. Hydrologic variability and its control of phytoplankton community structure and function in two shallow, coastal, lagoonal ecosystems: The Neuse and New River estuaries, North Carolina, USA. Estuar. Coasts 37, 31–45 (2014).
    Article  Google Scholar 

    68.
    Rae, B. D., Förster, B., Badger, M. R. & Price, G. D. The CO2-concentrating mechanism of Synechococcus WH5701 is composed of native and horizontally-acquired components. Photosynth. Res. 109, 59–72 (2011).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    69.
    Cabello-Yeves, P. J. et al. Ecological and genomic features of two widespread freshwater picocyanobacteria. Environ. Microbiol. 20, 3757–3771 (2018).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    70.
    Vörös, L., Callieri, C., V-Balogh, K. & Bertoni, R. Freshwater picocyanobacteria along a trophic gradient and light quality range. Hydrobiologia 369–370, 117–125 (1998).
    Article  Google Scholar 

    71.
    Osburn, C. L. et al. Optical proxies for terrestrial dissolved organic matter in estuaries and coastal waters. Front. Mar. Sci. 2, 127 (2016).
    MathSciNet  Article  Google Scholar 

    72.
    Kirk, J. T. O. Light and Photosynthesis in Aquatic Ecosystems (Cambridge University Press, Cambridge, 2010).
    Google Scholar 

    73.
    Anderson, S. R., Diou-Cass, Q. P. & Harvey, E. L. Short-term estimates of phytoplankton growth and mortality in a tidal estuary. Limnol. Oceanogr. 63, 2411–2422 (2018).
    ADS  Article  Google Scholar 

    74.
    Brand, L. E., Sunda, W. G. & Guillard, R. R. L. Reduction of marine phytoplankton reproduction rates by copper and cadmium. J. Exp. Mar. Biol. Ecol. 96, 225–250 (1986).
    CAS  Article  Google Scholar 

    75.
    Bianchi, T. S. Biogeochemistry of Estuaries (Oxford University Press, Oxford, 2007).
    Google Scholar 

    76.
    Coclet, C. et al. Trace metal contamination as a toxic and structuring factor impacting ultraphytoplankton communities in a multicontaminated Mediterranean coastal area. Prog. Oceanogr. 163, 196–213 (2018).
    Article  Google Scholar 

    77.
    Delpy, F. et al. Pico- and nanophytoplankton dynamics in two coupled but contrasting coastal bays in the NW Mediterranean Sea (France). Estuar. Coasts 41, 2039–2055 (2018).
    CAS  Article  Google Scholar 

    78.
    CDM Smith. City of Raleigh—Neuse River Water Quality Sampling Report. (2014).

    79.
    Fuller, N. J. et al. Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the red sea. Appl. Environ. Microbiol. 69, 2430–2443 (2003).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    80.
    Mackey, K. R. M. et al. Seasonal succession and spatial patterns of Synechococcus microdiversity in a salt marsh estuary revealed through 16S rRNA gene oligotyping. Front. Microbiol. 8, 1496 (2017).
    PubMed  PubMed Central  Article  Google Scholar 

    81.
    Gong, W. et al. Molecular insights into a dinoflagellate bloom. ISME J. 11, 439–452 (2017).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    82.
    Ning, X., Cloern, J. E. & Cole, B. E. Spatial and temporal variability of picocyanobacteria Synechococcus sp. San Francisco Bay. Limnol. Oceanogr. 45, 695–702 (2000).
    ADS  CAS  Article  Google Scholar 

    83.
    Li, W. K. W. Primary production of prochlorophytes, cyanobacteria, and eucaryotic ultraphytoplankton: measurements from flow cytometric sorting. Limnol. Ocean. 39, 169–175 (1994).
    CAS  Article  Google Scholar 

    84.
    Jardillier, L., Zubkov, M. V., Pearman, J. & Scanlan, D. J. Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean. ISME J. 4, 1180–1192 (2010).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    85.
    Morán, X. A. G. Annual cycle of picophytoplankton photosynthesis and growth rates in a temperate coastal ecosystem: A major contribution to carbon fluxes. Aquat. Microb. Ecol. 49, 267–279 (2007).
    Article  Google Scholar 

    86.
    Christaki, U., Vázquez-Domínguez, E., Courties, C. & Lebaron, P. Grazing impact of different heterotrophic nanoflagellates on eukaryotic (Ostreococcus tauri) and prokaryotic picoautotrophs (Prochlorococcus and Synechococcus). Environ. Microbiol. 7, 1200–1210 (2005).
    PubMed  Article  PubMed Central  Google Scholar 

    87.
    Gobler, C. J., Lonsdale, D. J. & Boyer, G. L. A Review of the causes, effects, and potential management of harmful brown tide blooms caused by Aureococcus anophagefferens (Hargraves et Sieburth). Estuaries 28, 726–749 (2005).
    Article  Google Scholar 

    88.
    Schoemann, V., Becquevort, S., Stefels, J., Rousseau, V. & Lancelot, C. Phaeocystis blooms in the global ocean and their controlling mechanisms: A review. J. Sea Res. 53, 43–66 (2005).
    ADS  CAS  Article  Google Scholar 

    89.
    Vaulot, D., Eikrem, W., Viprey, M. & Moreau, H. The diversity of small eukaryotic phytoplankton (≤ 3 μm) in marine ecosystems. FEMS Microbiol. Rev. 32, 795–820 (2008).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    90.
    Worden, A. Z. & Not, F. Ecology and diversity of picoeukaryotes. Microb. Ecol. Ocean. 2, 159–205 (2008).
    Article  Google Scholar 

    91.
    Paerl, R. W., Bertrand, E. M., Allen, A. E., Palenik, B. & Azam, F. Vitamin B1 ecophysiology of marine picoeukaryotic algae: Strain-specific differences and a new role for bacteria in vitamin cycling. Limnol. Oceanogr. 60, 215–228 (2015).
    ADS  CAS  Article  Google Scholar 

    92.
    Lovejoy, C. et al. Distribution, phylogeny, and growth of cold-adapted picoprasinophytes in Arctic seas. J. Phycol. 43, 78–89 (2007).
    CAS  Article  Google Scholar 

    93.
    McKie-Krisberg, Z. M. & Sanders, R. W. Phagotrophy by the picoeukaryotic green alga Micromonas: Implications for Arctic Oceans. ISME J. 8, 1953–1961 (2014).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    94.
    Botebol, H. et al. Acclimation of a low iron adapted Ostreococcus strain to iron limitation through cell biomass lowering. Sci. Rep. 7, 327 (2017).
    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

    95.
    Rodríguez, F. et al. Ecotype diversity in the marine picoeukaryote Ostreococcus (Chlorophyta, Prasinophyceae). Environ. Microbiol. 7, 853–859 (2005).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    96.
    Valdes-Weaver, L. M. et al. Long-term temporal and spatial trends in phytoplankton biomass and class-level taxonomic composition in the hydrologically variable Neuse-Pamlico estuarine continuum, North Carolina, USA. Limnol. Oceanogr. 51, 1410–1420 (2006).
    ADS  Article  Google Scholar 

    97.
    Wetz, M. S. & Paerl, H. W. Estuarine phytoplankton responses to hurricanes and tropical storms with different characteristics (trajectory, rainfall, winds). Estuar. Coasts 31, 419–429 (2008).
    CAS  Article  Google Scholar 

    98.
    Mojica, K. D. A., Huisman, J., Wilhelm, S. W. & Brussaard, C. P. D. Latitudinal variation in virus-induced mortality of phytoplankton across the North Atlantic Ocean. ISME J. 10, 500–513 (2016).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    99.
    Wang, K. & Chen, F. Prevalence of highly host-specific cyanophages in the estuarine environment. Environ. Microbiol. 10, 300–312 (2008).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    100.
    Waterbury, J. B. & Valois, F. W. Resistance to co-occurring phages enables marine Synechococcus communities to coexist with cyanophages abundant in seawater. Appl. Environ. Microbiol. 59, 3393–3399 (1993).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    101.
    Brussaard, C. P. D. Viral control of phytoplankton Ppopulations—a review. J. Eukaryot. Microbiol. 51, 125–138 (2004).
    PubMed  Article  PubMed Central  Google Scholar 

    102.
    Moore, L. R., Post, A. F., Rocap, G. & Chisholm, S. W. Utilization of different nitrogen sources by the marine cyanobacteria Prochlorococcus and Synechococcus. Limnol. Oceanogr. 47, 989–996 (2002).
    ADS  CAS  Article  Google Scholar 

    103.
    Moore, L. R., Ostrowski, M., Scanlan, D. J., Feren, K. & Sweetsir, T. Ecotypic variation in phosphorus-acquisition mechanisms within marine picocyanobacteria. Aquat. Microb. Ecol. 39, 257–269 (2005).
    Article  Google Scholar 

    104.
    Scanlan, D. J. et al. Ecological genomics of marine picocyanobacteria. Microbiol. Mol. Biol. Rev. 73, 249–299 (2009).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    105.
    Berg, G. M. B. M., Repeta, D. J. & LaRoche, J. The role of the picoeukaryote Aureococcus anophagefferens in cycling of marine high—molecular weight dissolved organic nitrogen. Limnol. Oceanogr. 48, 1825–1830 (2003).
    ADS  CAS  Article  Google Scholar 

    106.
    Martins, R., Fernandez, N., Beiras, R. & Vasconcelos, V. Toxicity assessment of crude and partially purified extracts of marine Synechocystis and Synechococcus cyanobacterial strains in marine invertebrates. Toxicon 50, 791–799 (2007).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    107.
    Gobler, C. J. et al. Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. Proc. Natl. Acad. Sci. U. S. A. 108, 4352–4357 (2011).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    108.
    Waterbury, J. B. Biological and ecological characterization of the marine unicellular cyanobacterium Synechococcus. Photosynth. Picoplankt. 71–120 (1986).

    109.
    Easterling, D. R. et al. Precipitation change in the United States. (2017).

    110.
    Kossin, J. P. et al. Extreme storms. In Climate Science Special Report: Fourth National Climate Assessment, Volume I (eds. Wuebbles, D. J. et al.) 257–276 (U.S. Global Change Research Program, Washington, DC, 2017).

    111.
    Wuebbles, D. et al. CMIP5 climate model analyses: Climate extremes in the United States. Bull. Am. Meteorol. Soc. 95, 571–583 (2014).
    ADS  Article  Google Scholar 

    112.
    Kunkel, K. E. et al. North Carolina Climate Science Report. (2020).

    113.
    Yeo, S. K., Huggett, M. J., Eiler, A. & Rappé, M. S. Coastal bacterioplankton community dynamics in response to a natural disturbance. PLoS ONE 8, e56207 (2013).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    114.
    Montagna, P. A., Hu, X., Palmer, T. A. & Wetz, M. Effect of hydrological variability on the biogeochemistry of estuaries across a regional climatic gradient. Limnol. Oceanogr. 63, 2465–2478 (2018).
    ADS  CAS  Article  Google Scholar 

    115.
    Ares, Á. et al. Extreme storms cause rapid but short-lived shifts in nearshore subtropical bacterial communities. Environ. Microbiol. 22, 4571–4588 (2020).
    CAS  Article  Google Scholar 

    116.
    Marshall, H. G. Autotrophic picoplankton: their presence and significance in marine and freshwater ecosystems. Va. J. Sci. 53, (2002).

    117.
    Buitenhuis, E. T. et al. Picophytoplankton biomass distribution in the global ocean. Earth Syst. Sci. Data 4, 37–46 (2012).
    ADS  Article  Google Scholar 

    118.
    Stockner, J. G. Phototrophic picoplankton: An overview from marine and freshwater ecosystems. Limnol. Oceanogr. 33, 765–775 (1988).
    ADS  CAS  Google Scholar 

    119.
    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 

    120.
    Flombaum, P. et al. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc. Natl. Acad. Sci. 110, 9824–9829 (2013).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    121.
    Hunter-Cevera, K. R. et al. Physiological and ecological drivers of early spring blooms of a coastal phytoplankter. Science 354, 326–329 (2016).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    122.
    Agusti, S., Lubián, L. M., Moreno-Ostos, E., Estrada, M. & Duarte, C. M. Projected changes in photosynthetic picoplankton in a warmer subtropical ocean. Front. Mar. Sci. 5, 506 (2019).
    Article  Google Scholar 

    123.
    Cloern, J. E. et al. Human activities and climate variability drive fast-paced change across the world’s estuarine-coastal ecosystems. Glob. Change Biol. 22, 513–529 (2016).
    ADS  Article  Google Scholar  More

  • in

    More than one million barriers fragment Europe’s rivers

    1.
    Reid, A. J. et al. Emerging threats and persistent conservation challenges for freshwater biodiversity. Biol. Rev. Camb. Phil. Soc. 94, 849–873 (2019).
    Google Scholar 
    2.
    Grizzetti, B. et al. Relationship between ecological condition and ecosystem services in European rivers, lakes and coastal waters. Sci. Total Environ. 671, 452–465 (2019).
    ADS  CAS  PubMed  PubMed Central  Google Scholar 

    3.
    Grill, G. et al. Mapping the world’s free-flowing rivers. Nature 569, 215–221 (2019).
    ADS  CAS  PubMed  Google Scholar 

    4.
    Vannote, R. L., Minshall, G. W., Cummins, K. W., Sedell, J. R. & Cushing, C. E. The river continuum concept. Can. J. Fish. Aquat. Sci. 37, 130–137 (1980).
    Google Scholar 

    5.
    Vitousek, P. M., Mooney, H. A., Lubchenco, J. & Melillo, J. M. Human domination of Earth’s ecosystems. Science 277, 494–499 (1997).
    CAS  Google Scholar 

    6.
    Carpenter, S. R., Stanley, E. H. & Zanden, M. J. V. State of the world’s freshwater ecosystems: physical, chemical, and biological changes. Annu. Rev. Environ. Resour. 36, 75–99 (2011).
    Google Scholar 

    7.
    Fuller, M. R., Doyle, M. W. & Strayer, D. L. Causes and consequences of habitat fragmentation in river networks: river fragmentation. Ann. NY Acad. Sci. 1355, 31–51 (2015).
    ADS  PubMed  PubMed Central  Google Scholar 

    8.
    Van Looy, K., Tormos, T. & Souchon, Y. Disentangling dam impacts in river networks. Ecol. Indic. 37, 10–20 (2014).
    Google Scholar 

    9.
    Kemp, P. & O’Hanley, J. Procedures for evaluating and prioritising the removal of fish passage barriers: a synthesis. Fish. Manag. Ecol. 17, 297–322 (2010).
    Google Scholar 

    10.
    Lehner, B. et al. High-resolution mapping of the world’s reservoirs and dams for sustainable river-flow management. Front. Ecol. Environ. 9, 494–502 (2011).
    Google Scholar 

    11.
    Lehner, B. et al. Global Reservoir and Dam Database version 1 (GRanDv1) https://doi.org/10.7927/H4N877QK (NASA Socioeconomic Data and Applications Center, 2011).

    12.
    Mulligan, M., Soesbergen, A. V. & Sáenz, L. GOODD, a global dataset of more than 38,000 georeferenced dams. Sci. Data 7, 31 (2020).
    PubMed  PubMed Central  Google Scholar 

    13.
    Garcia de Leaniz, C., Berkhuysen, A. & Belletti, B. Beware small dams, they can do damage too. Nature 570, 164 (2019).
    ADS  Google Scholar 

    14.
    Mantel, S. K., Rivers-Moore, N. & Ramulifho, P. Small dams need consideration in riverscape conservation assessments: small dams and riverscape conservation. Aqua. Conserv. Mar. Freshw. Ecosyst. 27, 748–754 (2017).
    Google Scholar 

    15.
    Lucas, M. C., Bubb, D. H., Jang, M.-H., Ha, K. & Masters, J. E. G. Availability of and access to critical habitats in regulated rivers: effects of low-head barriers on threatened lampreys. Freshw. Biol. 54, 621–634 (2009).
    Google Scholar 

    16.
    Birnie-Gauvin, K., Aarestrup, K., Riis, T. M. O., Jepsen, N. & Koed, A. Shining a light on the loss of rheophilic fish habitat in lowland rivers as a forgotten consequence of barriers, and its implications for management. Aqua. Conserv. Mar. Freshw. Ecosyst. 27, 1345–1349 (2017).
    Google Scholar 

    17.
    Magilligan, F. J., Nislow, K. H. & Renshaw, C. E. in Treatise on Geomorphology (ed. Shroder, J. F.) 794–808 (Academic Press, 2013).

    18.
    Petts, G. E. & Gurnell, A. M. Dams and geomorphology: research progress and future directions. Geomorphology 71, 27–47 (2005).
    ADS  Google Scholar 

    19.
    Bizzi, S. et al. On the control of riverbed incision induced by run-of-river power plant. Wat. Resour. Res. 51, 5023–5040 (2015).
    ADS  Google Scholar 

    20.
    Jones, P. E., Consuegra, S., Börger, L., Jones, J. & Garcia de Leaniz, C. Impacts of artificial barriers on the connectivity and dispersal of vascular macrophytes in rivers: a critical review. Freshw. Biol. 65, 1165–1180 (2020).
    Google Scholar 

    21.
    Carpenter-Bundhoo, L. et al. Effects of a low-head weir on multi-scaled movement and behavior of three riverine fish species. Sci. Rep. 10, 6817 (2020).
    ADS  CAS  PubMed  PubMed Central  Google Scholar 

    22.
    Graf, W. L. Dam nation: a geographic census of American dams and their large-scale hydrologic impacts. Wat. Resour. Res. 35, 1305–1311 (1999).
    ADS  Google Scholar 

    23.
    Jones, J. et al. A comprehensive assessment of stream fragmentation in Great Britain. Sci. Total Environ. 673, 756–762 (2019).
    ADS  CAS  PubMed  PubMed Central  Google Scholar 

    24.
    Grizzetti, B. et al. Human pressures and ecological status of European rivers. Sci. Rep. 7, 205 (2017).
    ADS  CAS  PubMed  PubMed Central  Google Scholar 

    25.
    Mauch, C. & Zeller, T. (eds) Rivers in History: Perspectives on Waterways in Europe and North America (Univ. of Pittsburgh Press, 2008).

    26.
    Petts, G. E., Möller, H. & Roux, A. L. Historical Change of Large Alluvial Rivers: Western Europe 355 (John Wiley and Sons, 1989).

    27.
    Kemp, P. S. in Freshwater Fisheries Ecology (ed. Craig, J. F.) 717–769 (Wiley, 2015).

    28.
    European Environment Agency in European Waters—Assessment of Status and Pressures 85 (EEA, 2018).

    29.
    Garcia de Leaniz, C. et al. in From Sea to Source v2. Protection and Restoration of Fish Migration in Rivers Worldwide (eds Brink, K. et al.) 142–145 (World Fish Migration Foundation, 2018).

    30.
    Pistocchi, A. et al. Assessment of the Effectiveness of Reported Water Framework Directive Programmes of Measures. Part II—Development of a System of Europe-wide Pressure Indicators. Report No. EUR 28412 EN (Joint Research Centre, 2017).

    31.
    Garcia de Leaniz, C. Weir removal in salmonid streams: implications, challenges and practicalities. Hydrobiologia 609, 83–96 (2008).
    Google Scholar 

    32.
    Downward, S. & Skinner, K. Working rivers: the geomorphological legacy of English freshwater mills. Area 37, 138–147 (2005).
    Google Scholar 

    33.
    Sun, J., Galib, S. M. & Lucas, M. C. Are national barrier inventories fit for stream connectivity restoration needs? A test of two catchments. Wat. Environ. J. https://doi.org/10.1111/wej.12578 (2020).

    34.
    Atkinson, S. et al. An inspection-based assessment of obstacles to salmon, trout, eel and lamprey migration and river channel connectivity in Ireland. Sci. Total Environ. 719, 137215 (2020).
    ADS  CAS  PubMed  PubMed Central  Google Scholar 

    35.
    European Environment Agency European Catchments and Rivers Network System (ECRINS) (EEA, 2012).

    36.
    Kristensen, P. & Globevnik, L. European small water bodies. Biol. Environ. 114B, 281–287 (2014).
    Google Scholar 

    37.
    Ferreira, T., Globevnik, L. & Schinegger, R. in Multiple Stressors in River Ecosystems 139–155 (Elsevier, 2019).

    38.
    Schwarz, U. Hydropower Pressure on European Rivers 36 (WWF, 2019).

    39.
    Schiemer, F. et al. The Vjosa River corridor: a model of natural hydro-morphodynamics and a hotspot of highly threatened ecosystems of European significance. Land. Ecol. 35, 953–968 (2020).
    Google Scholar 

    40.
    Duflo, E. & Pande, R. Dams. Q. J. Econ. 122, 601–646 (2007).
    Google Scholar 

    41.
    Grill, G., Ouellet Dallaire, C., Fluet Chouinard, E., Sindorf, N. & Lehner, B. Development of new indicators to evaluate river fragmentation and flow regulation at large scales: a case study for the Mekong River Basin. Ecol. Indic. 45, 148–159 (2014).
    Google Scholar 

    42.
    Zarfl, C., Lumsdon, A. E., Berlekamp, J., Tydecks, L. & Tockner, K. A global boom in hydropower dam construction. Aquat. Sci. 77, 161–170 (2015).
    Google Scholar 

    43.
    Tilt, B., Braun, Y. & He, D. Social impacts of large dam projects: a comparison of international case studies and implications for best practice. J. Environ. Manage. 90, S249–S257 (2009).
    PubMed  PubMed Central  Google Scholar 

    44.
    Schmitt, R. J. P., Bizzi, S., Castelletti, A. & Kondolf, G. M. Improved trade-offs of hydropower and sand connectivity by strategic dam planning in the Mekong. Nature Sust. 1, 96–104 (2018).
    Google Scholar 

    45.
    Weibel, D. & Peter, A. Effectiveness of different types of block ramps for fish upstream movement. Aquat. Sci. 75, 251–260 (2013).
    Google Scholar 

    46.
    Cote, D., Kehler, D. G., Bourne, C. & Wiersma, Y. F. A new measure of longitudinal connectivity for stream networks. Landsc. Ecol. 24, 101–113 (2009).
    Google Scholar 

    47.
    Tickner, D. et al. Bending the curve of global freshwater biodiversity loss: an emergency recovery plan. BioScience 70, 330–342 (2020).
    PubMed  PubMed Central  Google Scholar 

    48.
    Bódis, K., Monforti, F. & Szabó, S. Could Europe have more mini hydro sites? A suitability analysis based on continentally harmonized geographical and hydrological data. Renew. Sust. Energy Rev. 37, 794–808 (2014).
    Google Scholar 

    49.
    Huđek, H., Žganec, K. & Pusch, M. T. A review of hydropower dams in Southeast Europe—distribution, trends and availability of monitoring data using the example of a multinational Danube catchment subarea. Renew. Sust. Energy Rev. 117, 109434 (2020).
    Google Scholar 

    50.
    European Union Bringing Nature Back Into Our Lives. EU 2030 Biodiversity Strategy. https://eur-lex.europa.eu/legal-content/EN/TXT/?qid=1590574123338&uri=CELEX:52020DC0380 (European Commission, 2020).

    51.
    Wohl, E. Connectivity in rivers. Progr. Phys. Geog. Earth. Env. 41, 345–362 (2017).
    Google Scholar 

    52.
    Belletti, B. et al. Datasets for the AMBER Barrier Atlas of Europe. Table S1. Details of test rivers showing number of barriers present in current inventories (Atlas) and those encountered in the field. Table S3. Barrier Database sources. figshare https://doi.org/10.6084/m9.figshare.12629051 (2020).

    53.
    Jones, J. et al. Quantifying river fragmentation from local to continental scales: data management and modelling methods. Preprint at https://doi.org/10.22541/au.159612917.72148332 (2020).

    54.
    QGIS Geographic Information System https://qgis.org/en/site/ (Open Source Geospatial Foundation Project, 2010).

    55.
    Chao, A., Wang, Y. T. & Jost, L. Entropy and the species accumulation curve: a novel entropy estimator via discovery rates of new species. Methods Ecol. Evol. 4, 1091–1100 (2013).
    Google Scholar 

    56.
    Strahler, A. N. Quantitative analysis of watershed geomorphology. Trans. AGU 38, 913–920 (1957).
    Google Scholar 

    57.
    R: A Language And Environment For Statistical Computing Version 4.0.0 (2020-04-24) https://www.r-project.org/ (R Foundation for Statistical Computing, 2020).

    58.
    Signorell, A. et al. DescTools: tools for descriptive statistics. R package version 0.99.37 https://andrisignorell.github.io/DescTools/ (2020).

    59.
    Januchowski-Hartley, S. R. et al. Restoring aquatic ecosystem connectivity requires expanding inventories of both dams and road crossings. Front. Ecol. Environ. 11, 211–217 (2013).
    Google Scholar 

    60.
    Schmutz, S. & Moog, O. in Riverine Ecosystem Management 111–127 (Springer, 2018).

    61.
    European Environment Agency CORINE Land Cover (CLC) Version 20 https://www.eea.europa.eu/data-and-maps/data/copernicus-land-monitoring-service-corine (2012).

    62.
    European Commission Global Human Settlement—GHS Population Grid https://ghsl.jrc.ec.europa.eu/ghs_pop.php (2015).

    63.
    European Environment Agency EU-DEM v1.1, https://land.copernicus.eu/imagery-in-situ/eu-dem/eu-dem-v1.1 (Copernicus Land Monitoring Service, 2016).

    64.
    Meijer, J. R., Huijbregts, M. A. J., Schotten, K. C. G. J. & Schipper, A. M. Global patterns of current and future road infrastructure. Environ. Res. Lett. 13, 064006 (2018).
    ADS  Google Scholar 

    65.
    Louppe, G., Wehenkel, L., Sutera, A. & Geurts, P. in Advances in Neural Information Processing Systems (eds Burges, C. J. C. et al.) 431–439 (Neural Information Processing Systems Foundation, 2013).

    66.
    National Inventory of Dams http://nid.usace.army.mil/ (2018).

    67.
    Yoshimura, C., Omura, T., Furumai, H. & Tockner, K. Present state of rivers and streams in Japan. River Res. Appl. 21, 93–112 (2005).
    Google Scholar 

    68.
    Brazil Dams Safety Report http://www.snisb.gov.br/portal/snisb/relatorio-anual-de-seguranca-de-barragem/2019/rsb19-v0.pdf (National Water Agency (ANA), Brazil, 2020).

    69.
    World Commission on Dams Dams and Development: A New Framework for Decision Making https://pubs.iied.org/pdfs/9126IIED.pdf (Earthscan Publications, 2000).

    70.
    International Rivers. The True Cost of Hydropower in China. https://www.internationalrivers.org/wp-content/uploads/sites/86/2020/06/truecostofhydro_en_small.pdf (2014).

    71.
    Lehner, B., Verdin, K. & Jarvis, A. New global hydrography derived from spaceborne elevation data. Trans. AGU 89, 93–94 (2008).
    ADS  Google Scholar  More

  • in

    Ecological niche partitioning in a fragmented landscape between two highly specialized avian flush-pursuit foragers in the Andean zone of sympatry

    1.
    Patterson, B. D., Stotz, D. F., Solari, S., Fitzpatrick, J. W. & Pacheco, V. Contrasting patterns of elevational zonation for birds and mammals in the Andes of southeastern Peru. J. Biogeogr. 25, 593–607 (1998).
    Article  Google Scholar 
    2.
    Cadena, C. D. et al. Latitude, elevational climatic zonation and speciation in New World vertebrates. Proc. R. Soc. B 279, 194–201 (2012).
    PubMed  Article  PubMed Central  Google Scholar 

    3.
    Diamond, J. M. Distributional ecology of New Guinea birds: recent ecological and biogeographical theories can be tested on the bird communities of New Guinea. Science 179, 759–769 (1973).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    4.
    Terborgh, J. & Weske, J. S. The role of competition in the distribution of Andean birds. Ecology 56, 562–576 (1975).
    Article  Google Scholar 

    5.
    Garcia-Moreno, J., Arctander, P. & Fjeldsa, J. Strong diversification at the treeline among Metallura hummingbirds. Auk 116, 702–711 (1999).
    Article  Google Scholar 

    6.
    Freeman, B. G. Competitive interactions upon secondary contact drive elevational divergence in tropical birds. Am. Nat. 186, 470–479 (2015).
    PubMed  Article  PubMed Central  Google Scholar 

    7.
    Cadena, C. D. Testing the role of interspecific competition in the evolutionary origin of elevational zonation: an example with Buarremon Brush-finches (Aves, Emberizidae) in the neotropical mountains. Evolution 61, 1120–1136 (2007).
    PubMed  Article  PubMed Central  Google Scholar 

    8.
    Curson, J. & de Juana, E. Spectacled redstart (Myioborus melanocephalus), version 1.0. In Birds of the World (eds del Hoyo, J. et al.) (Cornell Lab of Ornithology, Ithaca, 2020). https://doi.org/10.2173/bow.spered1.01.
    Google Scholar 

    9.
    Harrod, W. D. & Mumme, R. L. Slate-throated redstart (Myioborus miniatus), version 1.0. In Birds of the World (ed. Schulenberg, T. S.) (Cornell Lab of Ornithology, Ithaca, 2020). https://doi.org/10.2173/bow.sltred.01.
    Google Scholar 

    10.
    Remsen, J. V. Jr. & Robinson, S. K. A classification scheme for foraging behavior of birds in terrestrial habitats. Stud. Avian Biol. 13, 144–160 (1990).
    Google Scholar 

    11.
    Jimenez, D. A bird forages through a tree. Elevation: 2263 m. Movie clip at https://macaulaylibrary.org/asset/201110671, added to IBC (Internet Bird Collection) on June 23, 2019; accessed on 26 July, 2020 through Slate-throated Redstart (Myioborus miniatus), version 1.0. (Harrod, W. D. & Mumme R. L.) in Birds of the World (ed. Schulenberg, T. S.); https://doi.org/10.2173/bow.sltred.01 (Cornell Lab of Ornithology, 2016)

    12.
    Jimenez, D. Bird looking for food. Elevation: 2663 m. Movie clip at IBC (Internet Bird Collection (https://macaulaylibrary.org/asset/201955691); Added to IBC on 23 June, 2016; accessed on 26 July, 2020 through Slate-throated Redstart (Myioborus miniatus), version 1.0. (Harrod, W. D. & Mumme R. L.) in Birds of the World (ed. Schulenberg, T. S.); https://doi.org/10.2173/bow.sltred.01 (Cornell Lab of Ornithology, 2016).

    13.
    Jablonski, P. G. A rare predator exploits prey escape behavior: the role of tail fanning and plumage contrast in foraging of the painted redstart (Myioborus pictus). Behav. Ecol. 10, 7–14 (1999).
    Article  Google Scholar 

    14.
    Jablonski, P. G. Searching for conspicuous versus cryptic prey: search rates of flush-pursuing versus substrate-gleaning birds. Condor 104, 657–661 (2002).
    Article  Google Scholar 

    15.
    Jablonski, P. G. et al. Habitat-specific sensory-exploitative signals in birds: propensity of dipteran prey to cause evolution of plumage variation in flush-pursuit birds. Evolution 60, 2633–2642 (2006).
    PubMed  Article  PubMed Central  Google Scholar 

    16.
    Jablonski, P. G., Lee, S. D. & Jerzak, L. Innate plasticity of a predatory behavior: nonlearned context dependence of avian flush-displays. Behav. Ecol. 6, 925–932 (2006).
    Article  Google Scholar 

    17.
    Mumme, R. L. Scare tactics in a Neotropical warbler: white tail feathers enhance flush-pursuit foraging performance in the Slate-throated redstart (Myioborus miniatus). Auk 119, 1024–1035 (2002).
    Google Scholar 

    18.
    Mumme, R. L., Galatowitsch, M. L., Jablonski, P. G., Stawarczyk, T. M. & Cygan, J. P. Evolutionary significance of geographic variation in a plumage-based foraging adaptation: an experimental test in the Slate-throated redstart (Myioborus miniatus). Evolution 60, 1086–1097 (2006).
    PubMed  Article  PubMed Central  Google Scholar 

    19.
    Perez-Eman, J. L., Mumme, R. L. & Jablonski, P. G. Phylogeography and adaptive plumage evolution in Central American subspecies of the slate-throated redstart (Myioborus miniatus). Ornithol. Monogr. 67, 90–102 (2010).
    Article  Google Scholar 

    20.
    Dawkins, R. The Extended Phenotype (Oxford University Press, Oxford, 1983).
    Google Scholar 

    21.
    Jablonski, P. G. & Lee, S. D. Effects of visual stimuli, substrate borne vibrations and air current stimuli on escape reactions in insect prey of flush-pursuing birds and their implications for evolution of flush-pursuers. Behaviour 143, 303–324 (2006).
    Article  Google Scholar 

    22.
    Jablonski, P. G. & Strausfeld, N. J. Exploitation by a recent avian predator of an ancient arthropod escape circuit: prey sensitivity and elements of the displays by predators. Brain Behav. Evol. 56, 94–106 (2000).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    23.
    Jablonski, P. G. & Strausfeld, N. J. Exploitation of an ancient escape circuit by an avian predator: relationships between taxon-specific prey escape circuits and the sensitivity to visual cues from the predator. Brain Behav. Evol. 58, 218–240 (2001).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    24.
    Boles, W. Black fantail (Rhipidura atra), version 1.0. In Birds of the World (eds del Hoyo, J. et al.) (Cornell Lab of Ornithology, Ithaca, 2020). https://doi.org/10.2173/bow.blafan1.01.
    Google Scholar 

    25.
    Boles, W. Dimorphic fantail (Rhipidura brachyrhyncha), version 1.0. In Birds of the World (eds del Hoyo, J. et al.) (Cornell Lab of Ornithology, Ithaca, 2020). https://doi.org/10.2173/bow.dimfan1.01.
    Google Scholar 

    26.
    Moeliker, K. Blue-headed crested-flycatcher (Trochocercus nitens), version 1.0. In Birds of the World (eds del Hoyo, J. et al.) (Cornell Lab of Ornithology, Ithaca, 2020). https://doi.org/10.2173/bow.bhcfly1.01.
    Google Scholar 

    27.
    Clement, P. African blue flycatcher (Elminia longicauda), version 1.0. In Birds of the World (eds del Hoyo, J. et al.) (Cornell Lab of Ornithology, Ithaca, 2020). https://doi.org/10.2173/bow.afbfly1.01.
    Google Scholar 

    28.
    Horak, D. et al. Forest structure determines spatial changes in avian communities along an elevational gradient in tropical Africa. J. Biogeogr. 46, 2466–2478 (2019).
    Article  Google Scholar 

    29.
    Curson, J., Quinn, D. & Beadle, D. New World Warblers (Christopher Helm, London, 1994).
    Google Scholar 

    30.
    Perez-Eman, J. L. Molecular phylogenetics and biogeography of the Neotropical redstarts (Myioborus, Aves, Parulidae). Mol. Phylogen. Evol. 37, 511–528 (2005).
    CAS  Article  Google Scholar 

    31.
    Ridgely, R. S. & Tudor, G. Birds of South America: Passerines (Christopher Helm, London, 2009).
    Google Scholar 

    32.
    Hilbie, C. & Block, N. L. Collared redstart (Myioborus torquatus), version 1.0. In Birds of the World (ed. Schulenberg, T. S.) (Cornell Lab of Ornithology, Ithaca, 2020). https://doi.org/10.2173/bow.colred1.01.
    Google Scholar 

    33.
    Curson, J., del Hoyo, J., Bonan, A., Collar, N. & Kirwan, G. M. Golden-fronted redstart (Myioborus ornatus), version 1.0. In Birds of the World (eds Billerman, S. M. et al.) (Cornell Lab of Ornithology, Ithaca, 2020). https://doi.org/10.2173/bow.gofred1.01.
    Google Scholar 

    34.
    Curson, J. White-fronted redstart (Myioborus albifrons), version 1.0. In Birds of the World (eds del Hoyo, J. et al.) (Cornell Lab of Ornithology, Ithaca, 2020). https://doi.org/10.2173/bow.whfred2.01.
    Google Scholar 

    35.
    Price, T. Speciation in Birds (Roberts and Company, Greenwood Village, 2008).
    Google Scholar 

    36.
    Cadena, C. D. & Loiselle, B. A. Limits to elevational distributions in two species of emberizine finches: disentangling the role of interspecific competition, autoecology, and geographic variation in the environment. Ecography 30, 491–504 (2007).
    Article  Google Scholar 

    37.
    Bussman, R. W. The montane forests of Reserva Biologica San Francisco (Zamora-Chinchipe, Ecuador) Vegetation zonation and natural regeneration. Erde 132, 9–25 (2001).
    Google Scholar 

    38.
    Bussman, R. W. The vegetation of reserva biologica San Francisco, Zamora-Chinchipe, Southern Ecuador—a phytosociological synthesis. In Conservacion de Bioriversidad an los Andes y la Amazonia. Conservation of Biodiversity in the Andes and the Amazon, Cusco, 24–28.09.2001. Memorias del Congreso—Congress Proceedings (eds Bussmann, R. W. & Lange, S.) 71–175 (INKA Cusco, Cuzco, 2002).
    Google Scholar 

    39.
    Ridgely, R. S. & Greenfield, P. J. The Birds of Ecuador (Cornell Univ. Press, Ithaca, 2001).
    Google Scholar 

    40.
    Google. Cascadas de Nambillo by Brian Driscoll. Google Street View, Jul 2018. Accessed 6 August 2020. https://goo.gl/maps/cTv5Cf34LvZV33yTA (2018).

    41.
    Google. Cabanas San Isidro by Daniel Zurita Arthos. Google Street View, Sep 2018.Accessed 6 August 2020. https://goo.gl/maps/NHqLxRMsngRwDbto8 (2018).

    42.
    Google. Milagrosa Waterfall by Elizabeth Clark. Google Street View, Mar 2018. Accessed 6 August 2020. https://goo.gl/maps/SfTW8J8xDVDnpBCC6 (2018).

    43.
    Shopland, J. M. Facultative following of mixed species flocks by two species of neotropical warbler. PhD Dissertation. University of Chicago (1985).

    44.
    Stiles, F. G. & Skutch, A. F. A Guide to the Birds of Costa Rica (Cornell Univ. Press, Ithaca, 1989).
    Google Scholar 

    45.
    Schulenberg, T. S., Stotz, D. F., Lane, D. F., O’Neill, J. P. & Parker, T. A. Birds of Peru (Princeton Univ. Press, Ithaca, 2010).
    Google Scholar 

    46.
    Sullivan, B. L. et al. eBird: a citizen-based bird observation network in the biological sciences. Biol. Conserv. 142, 2282–2292 (2009).
    Article  Google Scholar 

    47.
    eBird. eBird: An online database of bird distribution and abundance [web application]. eBird, Cornell Lab of Ornithology, Ithaca, New York. Available: http://www.ebird.org. Accessed 24 July 2020 (2017).

    48.
    Greeney, H. F. et al. Nesting ecology of the Spectacled Whitestart in Ecuador. Ornitol. Neotrop. 19, 335–344 (2008).
    Google Scholar 

    49.
    Merkord, C. L. Seasonality and Elevational Migration in an ANDEAN BIRD COMMUNITY. PhD Thesis, University of Missouri-Columbia, pp. 154 (2010)

    50.
    Nitta, B. Altitudinal Distribution and Niche Partitioning of Two Redstart Species in Monteverde (Parulidae). Digital Collections > Tropical Ecology Collection [Monteverde Institute], https://digital.lib.usf.edu/?m39.519 (2009).

    51.
    Shopland, J. M. Facultative following of mixed species flocks by two species of Neotropical warbler. Ph.D. Thesis, University of Chicago, Chicago (1985)

    52.
    Brehm, G., Sussenbach, D. & Fiedler, K. Unique elevational diversity patterns of geometrid moths in an Andean montane forest. Ecography 26, 456–466 (2003).
    Article  Google Scholar 

    53.
    Pyrcz, T. W., Wojtusiak, J. & Garlacz, R. Diversity and distribution patterns of Pronophilina butterflies (Lepidoptera: Nymphaliae: Satyrinae) along an altitudinal transect in North-Western Ecuador. Neotrop. Entomol. 38, 716–726 (2009).
    PubMed  Article  PubMed Central  Google Scholar 

    54.
    Brehm, G. & Fiedler, K. Diversity and community structure of geometrid moths of disturbed habitat in a montane area in the Ecuadorian Andes. J. Res. Lepidoptera 38, 1–14 (2005).
    Google Scholar 

    55.
    Janzen, D. H. Sweep samples of tropical foliage insects: effects of seasons, vegetation types, elevation, time of day, and insularity. Ecology 54, 687–708 (1973).
    Article  Google Scholar 

    56.
    Hilt, N. & Fiedler, K. Diversity and composition of Arctiidae moth ensembles along a successional gradient in the Ecuadorian Andes. Divers. Distrib. 11, 387–398 (2005).
    Article  Google Scholar 

    57.
    Harmackova, L., Remesova, E. & Remes, V. Specialization and niche overlap across spatial scales: revealing ecological factors shaping species richness and coexistence in Australian songbirs. J. Anim. Ecol. 88, 1766–1776 (2019).
    PubMed  Article  PubMed Central  Google Scholar 

    58.
    Freeman, B. G., Class Freeman, A. M. & Hochachka, W. M. Asymmetric interspecific aggression in New Guinean songbirds that replace one another along an elevational gradient. Ibis 158, 726–737 (2016).
    Article  Google Scholar 

    59.
    Pyrcz, T. W. & Wojtusiak, J. The vertical distribution of pronophilinae butterflies (Nymphalidae, Satyrinae) along an elevational transect in Monte Zerpa (Cordillera de Merida, Venezuela) with remarks on their diversity and parapatric distribution. Glob. Ecol. Biogeogr. 11, 211–221 (2002).
    Article  Google Scholar 

    60.
    Brehm, G., Zeuss, D. & Colwell, R. K. Moth body size increases with elevation along a complete tropical elevational gradient for two hyperdiverse clades. Ecography 42, 632–642 (2019).
    Article  Google Scholar 

    61.
    Robbins, M. B. et al. Abra Maruncunca, dpto. Puno, Peru, revisited: vegetation cover and avifauna changes over a 30-year period. Bull. B.O.C 133, 31–51 (2013).
    Google Scholar 

    62.
    Pouds, J. A., Fogden, M. P. L. & Campbell, J. H. Biological response to climate change on a tropical mountain. Nature 398, 611–615 (1999).
    ADS  Article  CAS  Google Scholar 

    63.
    Swenson, J. J. et al. Plant and animal endemism in the eastern Andean slope: challenges to conservation. BMC Ecol. 12, 1. https://doi.org/10.1186/1472-6785-12-1 (2012).
    Article  PubMed  PubMed Central  Google Scholar 

    64.
    Valencia, R. Composition and structure of an Andean forest fragment in eastern Ecuador. In Biodiversity and Conservation of Neotropical Montane Forests (eds Churchill, S. et al.) 239–249 (New York Botanical Garden, New York, 1995).
    Google Scholar 

    65.
    Pollard, J. H. On distance estimators of density in randomly distributed forest. Biometrics 27, 991–1002 (1971).
    Article  Google Scholar 

    66.
    Levins, R. Evolution in Changing Environment (Princeton University Press, Princeton, 1968).
    Google Scholar 

    67.
    Pianka, E. R. Niche overlap and diffuse competition. Proc. Nat. Acad. Sci. U.S.A. 71, 2142–2145 (1974).
    ADS  Article  Google Scholar 

    68.
    Sokal, R. R. & Rohlf, F. J. Biometry (Freeman and Co., New York, 1997).
    Google Scholar 

    69.
    McLachlan, G. Discriminant Analysis and Statistical Pattern Recognition (Wiley, Hobolken, 2004).
    Google Scholar 

    70.
    StatSoft Inc. Electronic Statistics Textbook. http://www.statsoft.com/textbook/ (Tulsa, OK: StatSoft. WEB, 2013).

    71.
    Molga, M. Meteorologia rolnicza. PWRiL, Warszawa [in Polish; English translation: Agricultural meteorology. Warszawa: Centralny Instytut Informacji Naukowo-Technicznej i Ekonomicznej, translated by M. Widymski and L. Widymski. OCLC Number: 641437878, 1962], (1986).

    72.
    Nowakowski, J. J. Long-term variability of phenotypic traits in the Sedge Warbler (Acrocephalus schoenobaenus) population in the Biebrza Marshes—Adaptation to the changing environment [in Polish]. Dissertation and Monographs 168, 1–294 (Publishing House of the University of Warmia and Mazury, Olsztyn, 2011).

    73.
    Holm, S. A simple sequential rejective method procedure. Scand. J. Stat. 6, 65–70 (1979).
    MATH  Google Scholar 

    74.
    Nakagawa, S. A farewell to Bonferroni: the problems of low statistical power and publication bias. Behav. Ecol. 15, 1044–1045 (2004).
    Article  Google Scholar 

    75.
    Akaike, H. Information theory and an extension of the maximum likelihood principle. In 2nd Int Symposium on Information Theory (eds Petrov, B. N. & Csaki, F.) 267–281 (Akademia Kiado, Budapest, 1973).
    Google Scholar 

    76.
    Burnham, K. P. & Anderson, D. R. Model Selection and Inference: A Practical Information-Theoretic Approach (Springer, New York, 1998).
    Google Scholar  More