More stories

  • in

    Climatic limit for agriculture in Brazil

    1.Brazil. USDA Foreign Agricultural Service https://www.fas.usda.gov/regions/brazil (2019).2.Planilha do PIB do Agronegócio Brasileiro de 1996 a 2018 (Centro de Estudos Avançados em Economia Aplicada, 2018); https://www.cepea.esalq.usp.br/br/pib-do-agronegocio-brasileiro.aspx3.Boletim da Safra de Grãos. Companhia Nacional de Abastecimento https://www.conab.gov.br/info-agro/safras/graos/boletim-da-safra-de-graos (2020).4.Projeções do Agronegócio: Brasil 2017/18 a 2027/28 Projeções de Longo Prazo (Ministério da Agricultura, Pecuária e Abastecimento, 2018).5.Atlas Irrigação: Uso da Água na Agricultura Irrigada (Agência Nacional de Águas, 2017).6.Costa, M. H. et al. Climate risks to Amazon agriculture suggest a rationale to conserve local ecosystems. Front. Ecol. Environ. 17, 584–590 (2019).
    Google Scholar 
    7.Fu, R. et al. Increased dry-season length over southern Amazonia in recent decades and its implication for future climate projection. Proc. Natl Acad. Sci. USA 110, 18110–18115 (2013).CAS 

    Google Scholar 
    8.Spera, S. A., Galford, G. L., Coe, M. T., Macedo, M. N. & Mustard, J. F. Land-use change affects water recycling in Brazil’s last agricultural frontier. Glob. Change Biol. 22, 3405–3413 (2016).
    Google Scholar 
    9.Abrahão, G. M. & Costa, M. H. Evolution of rain and photoperiod limitations on the soybean growing season in Brazil: the rise (and possible fall) of double-cropping systems. Agric. Meteorol. 256–257, 32–45 (2018).
    Google Scholar 
    10.Silvério, D. V. et al. Agricultural expansion dominates climate changes in southeastern Amazonia: the overlooked non-GHG forcing. Environ. Res. Lett. 10, 104015 (2015).
    Google Scholar 
    11.Barkhordarian, A., Saatchi, S. S., Behrangi, A., Loikith, P. C. & Mechoso, C. R. A recent systematic increase in vapor pressure deficit over tropical South America. Sci. Rep. 9, 15331 (2019).
    Google Scholar 
    12.Barkhordarian, A., von Storch, H., Zorita, E., Loikith, P. C. & Mechoso, C. R. Observed warming over northern South America has an anthropogenic origin. Clim. Dyn. 51, 1901–1914 (2018).
    Google Scholar 
    13.Leite‐Filho, A. T., Costa, M. H. & Fu, R. The southern Amazon rainy season: the role of deforestation and its interactions with large‐scale mechanisms. Int. J. Climatol. 40, 2328–2341 (2020).
    Google Scholar 
    14.FAOSTAT (Food and Agriculture Organization of the United Nations, 2020); http://www.fao.org/faostat/en/#data/QC15.Presidência da República Secretaria-Geral Subchefia para Assuntos Jurídicos (Ministério da Agricultura, 2015).16.Rashid, M. A. et al. Impact of heat-wave at high and low VPD on photosynthetic components of wheat and their recovery. Environ. Exp. Bot. 147, 138–146 (2018).CAS 

    Google Scholar 
    17.Lobell, D. B. et al. Greater sensitivity to drought accompanies maize yield increase in the U.S. Midwest. Science 344, 516–519 (2014).CAS 

    Google Scholar 
    18.Fletcher, A. L., Sinclair, T. R. & Allen, L. H. Transpiration responses to vapor pressure deficit in well watered ‘slow-wilting’ and commercial soybean. Environ. Exp. Bot. 61, 145–151 (2007).CAS 

    Google Scholar 
    19.Bunce, J. A. Comparative responses of leaf conductance to humidity in single attached leaves. J. Exp. Bot. 32, 629–634 (1981).
    Google Scholar 
    20.Kiniry, J. et al. Radiation-use efficiency response to vapor pressure deficit for maize and sorghum. Field Crops Res. 56, 265–270 (1998).
    Google Scholar 
    21.Spera, S. A. et al. Recent cropping frequency, expansion, and abandonment in Mato Grosso, Brazil had selective land characteristics. Environ. Res. Lett. 9, 064010 (2014).
    Google Scholar 
    22.Dias, L. C. P., Pimenta, F. M., Santos, A. B., Costa, M. H. & Ladle, R. J. Patterns of land use, extensification, and intensification of Brazilian agriculture. Glob. Change Biol. 22, 2887–2903 (2016).
    Google Scholar 
    23.Cohn, A. S., Vanwey, L. K., Spera, S. A. & Mustard, J. F. Cropping frequency and area response to climate variability can exceed yield response. Nat. Clim. Change 6, 601–604 (2016).
    Google Scholar 
    24.Morton, D. C. et al. Reevaluating suitability estimates based on dynamics of cropland expansion in the Brazilian Amazon. Glob. Environ. Change 37, 92–101 (2016).
    Google Scholar 
    25.Duursma, R. A. et al. The peaked response of transpiration rate to vapour pressure deficit in field conditions can be explained by the temperature optimum of photosynthesis. Agric. Meteorol. 189–190, 2–10 (2014).
    Google Scholar 
    26.Spera, S. A., Winter, J. M. & Partridge, T. F. Brazilian maize yields negatively affected by climate after land clearing. Nat. Sustain. 3, 845–852 (2020).
    Google Scholar 
    27.Cirino, P. H., Féres, J. G., Braga, M. J. & Reis, E. Assessing the impacts of ENSO-related weather effects on the Brazilian agriculture. Proc. Econ. Financ. 24, 146–155 (2015).
    Google Scholar 
    28.Pereira, P. A. A., Martha, G. B., Santana, C. A. & Alves, E. The development of Brazilian agriculture: future technological challenges and opportunities. Agric. Food Secur. 1, 4 (2012).
    Google Scholar 
    29.Marengo, J. A. & Bernasconi, M. Regional differences in aridity/drought conditions over Northeast Brazil: present state and future projections. Climatic Change 129, 103–115 (2015).
    Google Scholar 
    30.Naylor, R. L. Energy and resource constraints on intensive agricultural production. Annu. Rev. Energy Environ. 21, 99–123 (1996).
    Google Scholar 
    31.Getirana, A. Extreme water deficit in Brazil detected from space. J. Hydrometeorol. 17, 591–599 (2016).
    Google Scholar 
    32.Lathuillière, M. J., Coe, M. T. & Johnson, M. S. A review of green- and blue-water resources and their trade-offs for future agricultural production in the Amazon Basin: what could irrigated agriculture mean for Amazonia? Hydrol. Earth Syst. Sci. 20, 2179–2194 (2016).
    Google Scholar 
    33.Dobrovolski, R. & Rattis, L. Water collapse in Brazil: the danger of relying on what you neglect. Nat. Conserv. 13, 80–83 (2015).
    Google Scholar 
    34.da Silva, A. L. et al. Water appropriation on the agricultural frontier in western Bahia and its contribution to streamflow reduction: revisiting the debate in the Brazilian Cerrado. Water 13, 1054 (2021).
    Google Scholar 
    35.Pousa, R. et al. Climate change and intense irrigation growth in western Bahia, Brazil: the urgent need for hydroclimatic monitoring. Water 11, 933 (2019).
    Google Scholar 
    36.Ort, D. R. & Long, S. P. Limits on yields in the corn belt. Science 344, 484–485 (2014).CAS 

    Google Scholar 
    37.de Bossoreille de Ribou, S., Douam, F., Hamant, O., Frohlich, M. W. & Negrutiu, I. Plant science and agricultural productivity: why are we hitting the yield ceiling? Plant Sci. 210, 159–176 (2013).
    Google Scholar 
    38.Long, S. P. & Ort, D. R. More than taking the heat: crops and global change. Curr. Opin. Plant Biol. 13, 240–247 (2010).
    Google Scholar 
    39.Pommer, C. V. & Barbosa, W. The impact of breeding on fruit production in warm climates of Brazil. Rev. Bras. Frutic. 31, 612–634 (2009).
    Google Scholar 
    40.Lenka, N. K. et al. Carbon dioxide and temperature elevation effects on crop evapotranspiration and water use efficiency in soybean as affected by different nitrogen levels. Agric. Water Manag. 230, 105936 (2020).
    Google Scholar 
    41.Soares, W. R., Marengo, J. A. & Nobre, C. A. Assessment of warming projections and probabilities for Brazil in Climate Change Risks in Brazil (eds Nobre, C. et al.) 7–30 (Springer, 2019); https://doi.org/10.1007/978-3-319-92881-4_242.Schwalm, C. R., Glendon, S. & Duffy, P. B. RCP8.5 tracks cumulative CO2 emissions. Proc. Natl Acad. Sci. USA 117, 19656–19657 (2020).CAS 

    Google Scholar 
    43.Schwalm, C. R., Glendon, S. & Duffy, P. B. Reply to Hausfather and Peters: RCP8.5 is neither problematic nor misleading. Proc. Natl Acad. Sci. USA 117, 27793–27794 (2020).CAS 

    Google Scholar 
    44.Sistematização das Informações sobre Recursos Naturais—Mapa de Biomas do Brasil (Instituto Brasileiro de Geografia e Estatística, 2006); https://www.ibge.gov.br/geociencias/cartas-e-mapas/informacoes-ambientais/15842-biomas.html?=&t=downloads45.Base Cartográfica Continua Do Brasil, Escala 1:250.000—BC250 (Instituto Brasileiro de Geografia e Estatística, 2019); https://geoftp.ibge.gov.br/cartas_e_mapas/bases_cartograficas_continuas/bc250/versao2019/informacoes_tecnicas/Documentacao_bc250_v2019.pdf46.Campos, J., de, O. & Chaves, H. M. L. Tendências e variabilidades nas séries históricas de precipitação mensal e anual no bioma Cerrado no período 1977–2010. Rev. Bras. Meteorol. 35, 157–169 (2020).
    Google Scholar 
    47.Debortoli, N. S. et al. Rainfall patterns in the southern Amazon: a chronological perspective (1971–2010). Climatic Change 132, 251–264 (2015).
    Google Scholar 
    48.Oliveira, P. T. S. et al. Trends in water balance components across the Brazilian Cerrado. Water Resour. Res. 50, 7100–7114 (2014).
    Google Scholar 
    49.Panisset, J. S. et al. Contrasting patterns of the extreme drought episodes of 2005, 2010 and 2015 in the Amazon Basin. Int. J. Climatol. 38, 1096–1104 (2018).
    Google Scholar 
    50.Cai, W. et al. Increasing frequency of extreme El Niño events due to greenhouse warming. Nat. Clim. Change 4, 111–116 (2014).
    Google Scholar 
    51.Jiménez-Muñoz, J. C. et al. Record-breaking warming and extreme drought in the Amazon rainforest during the course of El Niño 2015–2016. Sci. Rep. 6, 33130 (2016).
    Google Scholar 
    52.Marengo, J. A. & Espinoza, J. C. Extreme seasonal droughts and floods in Amazonia: causes, trends and impacts. Int. J. Climatol. 36, 1033–1050 (2016).
    Google Scholar 
    53.Funk, C. et al. The climate hazards infrared precipitation with stations—a new environmental record for monitoring extremes. Sci. Data 2, 150066 (2015).
    Google Scholar 
    54.Abatzoglou, J. T., Dobrowski, S. Z., Parks, S. A. & Hegewisch, K. C. TerraClimate, a high-resolution global dataset of monthly climate and climatic water balance from 1958–2015. Sci. Data 5, 170191 (2018).
    Google Scholar 
    55.Harris, I., Osborn, T. J., Jones, P. & Lister, D. Version 4 of the CRU TS monthly high-resolution gridded multivariate climate dataset. Sci. Data 7, 109 (2020).
    Google Scholar 
    56.Gorelick, N. et al. Google Earth Engine: planetary-scale geospatial analysis for everyone. Remote Sens. Environ. 202, 18–27 (2017).
    Google Scholar 
    57.R Core Team R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2019).58.Challinor, A. J. & Wheeler, T. R. Crop yield reduction in the tropics under climate change: processes and uncertainties. Agric. Meteorol. 148, 343–356 (2008).
    Google Scholar 
    59.Bates, D. et al. lme4. R package version (2012).60.Barton, K. MuMIn: Multi-model inference. R package version 1.0.0 (2009).61.Arvor, D., Dubreuil, V., Ronchail, J., Simões, M. & Funatsu, B. M. Spatial patterns of rainfall regimes related to levels of double cropping agriculture systems in Mato Grosso (Brazil). Int. J. Climatol. 34, 2622–2633 (2014).
    Google Scholar 
    62.Hengl, T. et al. SoilGrids250m: global gridded soil information based on machine learning. PLoS ONE 12, e0169748 (2017).
    Google Scholar 
    63.Brill, F., Passuni Pineda, S., Espichán Cuya, B. & Kreibich, H. A data-mining approach towards damage modelling for El Niño events in Peru. Geomat. Nat. Hazards Risk 11, 1966–1990 (2020).
    Google Scholar 
    64.Rattis, L. ludmilarattis/effect-of-climate-on–agriculture: Rattis_etal_NCC_2021. Zenodo https://zenodo.org/badge/latestdoi/271879616 (2021).65.Malhi, Y. et al. Exploring the likelihood and mechanism of a climate-change-induced dieback of the Amazon rainforest. Proc. Natl Acad. Sci. USA 106, 20610–20615 (2009).CAS 

    Google Scholar 
    66.Castanho, A. D. A. et al. Potential shifts in the aboveground biomass and physiognomy of a seasonally dry tropical forest in a changing climate. Environ. Res. Lett. 15, 034053 (2020).
    Google Scholar 
    67.Allen, R. G. et al. The ASCE Standardized Reference Evapotranspiration Equation (American Society of Civil Engineers, 2005).68.IPCC Climate Change 2014: Synthesis Report (eds Core Writing Team, Pachauri, R. K. & Meyer, L. A.) (IPCC, 2014).69.Koutroulis, A. G., Grillakis, M. G., Tsanis, I. K. & Papadimitriou, L. Evaluation of precipitation and temperature simulation performance of the CMIP3 and CMIP5 historical experiments. Clim. Dyn. 47, 1881–1898 (2016).
    Google Scholar 
    70.Análise Territorial para o Desenvolvimento da Agricultura Irrigada no Brasil (Ministério da Integração Nacional, 2014). More

  • in

    Decreased resting and nursing in short-finned pilot whales when exposed to louder petrol engine noise of a hybrid whale-watch vessel

    1.O’Connor. Whale Watching Worldwide: Tourism Numbers, Expenditures and Expanding Economic Benefits. A special report from the International Fund for Animal Welfare Yarmouth, USA. Prepared by Economists at Large. www.ecolarge.com (2009). Accessed 15 Apr 2021.2.Cisneros-Montemayor, A. M., Sumaila, U. R., Kaschner, K. & Pauly, D. The global potential for whale watching. Mar. Policy 34, 1273–1278 (2010).Article 

    Google Scholar 
    3.Parsons, E. C. M. The negative impacts of whale-watching. J. Mar. Biol. 2012, 1–9 (2012).ADS 
    Article 

    Google Scholar 
    4.Hoyt, E. & Hvenegaard, G. T. A review of whale-watching and whaling. Coast. Manag. 30, 381–399 (2002).Article 

    Google Scholar 
    5.Cunningham, P. A., Huijbens, E. H. & Wearing, S. L. From whaling to whale watching: Examining sustainability and cultural rhetoric. J. Sustain. Tour. 20, 143–161 (2012).Article 

    Google Scholar 
    6.Senigaglia, V. et al. Meta-analyses of whale-watching impact studies: Comparisons of cetacean responses to disturbance. Mar. Ecol. Prog. Ser. 542, 251–263 (2016).ADS 
    CAS 
    Article 

    Google Scholar 
    7.Bejder, L. et al. Decline in relative abundance of bottlenose dolphins exposed to long-term disturbance. Conserv. Biol. 20, 1791–1798 (2006).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    8.Lusseau, D., Slooten, L. & Currey, R. J. C. Unsustainable dolphin-watching tourism in Fiordland, New Zealand. Tour. Mar. Environ. 3, 173–178 (2006).Article 

    Google Scholar 
    9.Erbe, C. Underwater noise of whale-watching boats and potential effects on killer whales (Orcinus orca), based on an acoustic impact model. Mar. Mamm. Sci. 18, 394–418 (2002).Article 

    Google Scholar 
    10.Sprogis, K. R., Videsen, S. & Madsen, P. T. Vessel noise levels drive behavioural responses of humpback whales with implications for whale-watching. Elife 9, 1–17 (2020).Article 

    Google Scholar 
    11.Au, W. W. L. The Sonar of Dolphins (Springer, 1993).Book 

    Google Scholar 
    12.Tyack, P. L. & Clark, C. W. Communication and acoustic behavior of dolphins and whales. In Hearing by Whales and Dolphins (eds. Au, W. W. L., Fay, R. R. & Popper, A. N.) 156–224 (Springer, 2000). https://doi.org/10.1007/978-1-4612-1150-1_4.13.Lesage, V., Barrette, C., Kingsley, M. C. S. & Sjare, B. The effect of vessel noise on the vocal behavior of belugas in the St. Lawrence River estuary, Canada. Mar. Mamm. Sci. 15, 65–84 (1999).Article 

    Google Scholar 
    14.Jensen, F. H. et al. Vessel noise effects on delphinid communication. Mar. Ecol. Prog. Ser. 395, 161–175 (2009).ADS 
    Article 

    Google Scholar 
    15.Pirotta, E. et al. Vessel noise affects beaked whale behavior: Results of a dedicated acoustic response study. PLoS One 7, e42535 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    16.Slabbekoorn, H. et al. A noisy spring: The impact of globally rising underwater sound levels on fish. Trends Ecol. Evol. 25, 419–427 (2010).PubMed 
    Article 

    Google Scholar 
    17.Andrew, R. K., Howe, B. M. & Mercer, J. A. Long-time trends in ship traffic noise for four sites off the North American West Coast. J. Acoust. Soc. Am. 129, 642–651 (2011).ADS 
    PubMed 
    Article 

    Google Scholar 
    18.Miksis-Olds, J. L. & Nichols, S. M. Is low frequency ocean sound increasing globally?. J. Acoust. Soc. Am. 139, 501–511 (2016).ADS 
    PubMed 
    Article 

    Google Scholar 
    19.Payne, R. & Webb, D. Orientation by means of long range acoustic signaling in Baleen whales. Ann. N. Y. Acad. Sci. 188, 110–141 (1971).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    20.Melcón, M. L. et al. Blue whales respond to anthropogenic noise. PLoS One 7, e32681 (2012).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    21.Romagosa, M. et al. Underwater ambient noise in a baleen whale migratory habitat off the Azores. Front. Mar. Sci. 4, 1–14 (2017).Article 

    Google Scholar 
    22.Aguilar Soto, N. et al. Does intense ship noise disrupt foraging in deep-diving cuvier’s beaked whales (Ziphius cavirostris)?. Mar. Mamm. Sci. 22, 690–699 (2006).Article 

    Google Scholar 
    23.Wisniewska, D. M. et al. High rates of vessel noise disrupt foraging in wild harbour porpoises (Phocoena phocoena). Proc. R. Soc. B Biol. Sci. 285, 20172314 (2018).Article 

    Google Scholar 
    24.Hermannsen, L., Beedholm, K., Tougaard, J. & Madsen, P. T. High frequency components of ship noise in shallow water with a discussion of implications for harbor porpoises (Phocoena phocoena). J. Acoust. Soc. Am. 136, 1640–1653 (2014).ADS 
    PubMed 
    Article 

    Google Scholar 
    25.Wladichuk, J., Hannay, D. E., MacGillivray, A. O., Li, Z. & Thornton, S. J. Systematic source level measurements of whale watching vessels and other small boats. J. Ocean Technol. 14, 108–126 (2019).
    Google Scholar 
    26.Arranz, P., Aguilar de Soto, N., Madsen, P. T. & Sprogis, K. R. Whale-watch vessel noise levels with applications to whale-watching guidelines and conservation. Mar. Policy 134, 104776 (2021).Article 

    Google Scholar 
    27.Higham, J., Bejder, L. & Williams, R. Whale-Watching: Sustainable Tourism and Ecological Management (Cambridge University Press, 2014).Book 

    Google Scholar 
    28.Montero, R. & Arechavaleta, M. Distribution patterns: Relationships between depths, sea surface temperature, and habitat use of Short-finned pilot whales south-west of Tenerife. Eur. Res. Cetaceans 10, 193–198 (1996).
    Google Scholar 
    29.Servidio, A. et al. Site fidelity and movement patterns of short-finned pilot whales within the Canary Islands: Evidence for resident and transient populations. Aquat. Conserv. Mar. Freshw. Ecosyst. 29, 227–241 (2019).Article 

    Google Scholar 
    30.Würsig, B. Ethology and Behavioral Ecology of Odontocetes (Springer, 2019). https://doi.org/10.1007/978-3-030-16663-2_23.Book 

    Google Scholar 
    31.Sequeira, M. et al. Review of whalewatching activities in mainland Portugal, the Azores, Madeira and Canary archipelagos and the Strait of Gibraltar. J. Cetacean Res. Manag. SC61/WW11, 1–40 (2009).
    32.IWC whale-watching handbook. https://wwhandbook.iwc.int/es/case-studies/canary-islands-spain#Accessed 15 Apr 2021.33.Hoyt, E. Tourism. In Encyclopedia of Marine Mammals 1010–1014 (2018). https://doi.org/10.1016/B978-0-12-804327-1.00262-4.
    34.Kasuya, T. & Matsui, S. Age determination and growth of the short-finned pilot whale off the Pacific coast of Japan. Sci. Rep. Whales Res. Inst. 35, 57–91 (1984).
    Google Scholar 
    35.Reddy, M., Kamolnick, T., Skaar, D., Curry, C. & Ridgway, S. Bottlenose dolphins: Energy consumption during pregnancy, lactation, and growth. Int. Mar. Mammal Trainers Assoc. Conf. Proc. 30–37 (1991).36.Srinivasan, M., Swannack, T. M., Grant, W. E., Rajan, J. & Würsig, B. To feed or not to feed? Bioenergetic impacts of fear-driven behaviors in lactating dolphins. Ecol. Evol. 8, 1384–1398 (2018).PubMed 
    Article 

    Google Scholar 
    37.Marsh, H. & Kasuya, T. Changes in the role of a female pilot whale with age. In Dolphin Societies (eds. Pryor, K. & Norris, K.S.) 281–286 (University of California Press, 1991).38.Augusto, J. F., Frasier, T. R. & Whitehead, H. Characterizing alloparental care in the pilot whale (Globicephala melas) population that summers off Cape Breton, Nova Scotia, Canada. Mar. Mamm. Sci. 33, 440–456 (2017).Article 

    Google Scholar 
    39.Quick, N., Scott-hayward, L., Sadykova, D., Nowacek, D. & Read, A. Effects of a scientific echo sounder on the behavior of short-finned pilot whales (Globicephala macrorhynchus). Can. J. Fish. Aquat. Sci. 74, 716–726 (2017).Article 

    Google Scholar 
    40.Würsig, B. & Jefferson, T. A. Methods of photo-identification for small cetaceans. Report of the International Whaling Commission (1990).41.Greenhow, D. R., Brodsky, M. C., Lingenfelser, R. G. & Mann, D. A. Hearing threshold measurements of five stranded short-finned pilot whales (Globicephala macrorhynchus). J. Acoust. Soc. Am. 135, 531–536 (2014).ADS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    42.Tougaard, J. & Beedholm, K. Practical implementation of auditory time and frequency weighting in marine bioacoustics. Appl. Acoust. 145, 137–143 (2019).Article 

    Google Scholar 
    43.Pérez, J. M., Jensen, F. H., Rojano-Doñate, L. & Aguilar de Soto, N. Different modes of acoustic communication in deep-diving short-finned pilot whales (Globicephala macrorhynchus). Mar. Mamm. Sci. 33, 59–79 (2017).Article 

    Google Scholar 
    44.Pacini, A. F. et al. Audiogram of a formerly stranded long-finned pilot whale (Globicephala melas) measured using auditory evoked potentials. J. Exp. Biol. 213, 3138–3143 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    45.Christiansen, F., Rojano-Doñate, L., Madsen, P. T. & Bejder, L. Noise levels of multi-rotor unmanned aerial vehicles with implications for potential underwater impacts on marine mammals. Front. Mar. Sci. 3, 1–9 (2016).Article 

    Google Scholar 
    46.Christiansen, F., Nielsen, M. L. K., Charlton, C., Bejder, L. & Madsen, P. T. Southern right whales show no behavioral response to low noise levels from a nearby unmanned aerial vehicle. Mar. Mamm. Sci. 36, 953–963 (2020).Article 

    Google Scholar 
    47.Giles, A. B. et al. Responses of bottlenose dolphins (Tursiops spp.) to small drones. Aquat. Conserv. Mar. Freshw. Ecosyst. 31, 677–684 (2021).Article 

    Google Scholar 
    48.Nielsen, M. L. K., Sprogis, K. R., Bejder, L., Madsen, P. T. & Christiansen, F. Behavioural development in southern right whale calves. Mar. Ecol. Prog. Ser. 629, 219–234 (2019).ADS 
    Article 

    Google Scholar 
    49.Hofmann, B., Scheer, M. & Behr, I. P. Underwater behaviors of short-finned pilot whales (Globicephala macrorhynchus) off Tenerife. Mammalia 68, 221–224 (2004).Article 

    Google Scholar 
    50.Lockyer, C. All creatures great and smaller: A study in cetacean life history energetics. J. Mar. Biol. Assoc. U. K. 87, 1035–1045 (2007).Article 

    Google Scholar 
    51.Hin, V., Harwood, J. & de Roos, A. M. Bio-energetic modeling of medium-sized cetaceans shows high sensitivity to disturbance in seasons of low resource supply. Ecol. Appl. 29, 1–19 (2019).Article 

    Google Scholar 
    52.Christiansen, F., Rasmussen, M. H. & Lusseau, D. Inferring energy expenditure from respiration rates in minke whales to measure the effects of whale watching boat interactions. J. Exp. Mar. Biol. Ecol. 459, 96–104 (2014).Article 

    Google Scholar 
    53.Mann, J., Connor, R. C., Tyack, P. L. & Whitehead, H. Cetacean Societies: Field Studies of Dolphins and Whales (The University of Chicago Press, 2000).
    Google Scholar 
    54.Zuur, A. F., Ieno, E. N. & Elphick, C. S. A protocol for data exploration to avoid common statistical problems. Methods Ecol. Evol. 1, 3–14 (2010).Article 

    Google Scholar 
    55.R Development Core Team. R: A Language and Environment for Statistical Computing. (2018).56.National Marine Fisheries Service. Technical guidance for assessing the effects of anthropogenic sound on marine mammal hearing underwater acoustic thresholds for onset of permanent and temporary threshold shifts. NOAA Technical Memorandum NMFS-OPR-55. (2016).57.Heimlich-Boran, J. R. Social Organisation of the Short-finned Pilot Whale, Globicephala macrorhynchus, with Special Reference to the Comparative Social Ecology of Delphinids (University of Cambridge, 1993).
    Google Scholar 
    58.Hastie, G. D., Wilson, B., Tufft, L. H. & Thompson, P. M. Bottlenose dolphins increase breathing synchrony in response to boat traffic. Mar. Mamm. Sci. 19, 74–084 (2003).Article 

    Google Scholar 
    59.Williams, R. & Noren, D. P. Swimming speed, respiration rate, and estimated cost of transport in adult killer whales. Mar. Mamm. Sci. 25, 327–350 (2009).Article 

    Google Scholar 
    60.Senigaglia, V. & Whitehead, H. Synchronous breathing by pilot whales. Mar. Mamm. Sci. 28, 213–219 (2012).Article 

    Google Scholar 
    61.Aguilar Soto, N. et al. Cheetahs of the deep sea: Deep foraging sprints in short-finned pilot whales off Tenerife (Canary Islands). J. Anim. Ecol. 77, 936–947 (2008).PubMed 
    Article 

    Google Scholar 
    62.Ariza, A. et al. Vertical distribution, composition and migratory patterns of acoustic scattering layers in the Canary Islands. J. Mar. Syst. 157, 82–91 (2016).Article 

    Google Scholar 
    63.Owen, K., Andrews, R. D., Baird, R. W., Schorr, G. S. & Webster, D. L. Lunar cycles influence the diving behavior and habitat use of short-finned pilot whales around the main Hawaiian Islands. Mar. Ecol. Prog. Ser. 629, 193–206 (2019).ADS 
    Article 

    Google Scholar 
    64.Kasuya, T. & Marsh, H. Life history and reproductive biology of the short-finned pilot whale, Globicephala macrorhynchus, off the Pacific coast of Japan. Rep. Int. Whal. Commun. Spec. Iss. 6, 259–310 (1984).
    Google Scholar 
    65.Barton, E. et al. The transition zone of the canary current upwelling region. Prog. Ocean. 41, 455–504 (1998).Article 

    Google Scholar 
    66.Olson, P. A. Pilot Whales: Globicephala melas and G. macrorhynchus. In Encyclopedia of Marine Mammals, 3rd ed (eds. Würsig, B., Thewissen, J. G. M. & Kovacs, K. M.) 701–705 (Academic Press, 2018). https://doi.org/10.1016/B978-0-12-804327-1.00194-1.67.Puig-Lozano, R. et al. Retrospective study of fishery interactions in stranded cetaceans, Canary Islands. Front. Vet. Sci. 7, 1–15 (2020).Article 

    Google Scholar 
    68.Almunia, J., Delponti, P. & Rosa, F. Using automatic identification system (AIS) data to estimate whale watching effort. Front. Mar. Sci. 8, 827 (2021).Article 

    Google Scholar 
    69.Schlundt, C. E. et al. Auditory evoked potentials in two short-finned pilot whales (Globicephala macrorhynchus). J. Acoust. Soc. Am. 129, 1111–1116 (2011).ADS 
    PubMed 
    Article 

    Google Scholar 
    70.Visser, F. et al. Risso’s dolphins alter daily resting pattern in response to whale watching at the Azores. Mar. Mamm. Sci. 27, 366–381 (2011).Article 

    Google Scholar 
    71.Constantine, R., Brunton, D. H. & Dennis, T. Dolphin-watching tour boats change bottlenose dolphin (Tursiops truncatus) behaviour. Biol. Conserv. 117, 299–307 (2004).Article 

    Google Scholar 
    72.Stensland, E. & Berggren, P. Behavioural changes in female Indo-Pacific bottlenose dolphins in response to boat-based tourism. Mar. Ecol. Prog. Ser. 332, 225–234 (2007).ADS 
    Article 

    Google Scholar 
    73.Jensen, F. H., Perez, J. M., Johnson, M., Soto, N. A. & Madsen, P. T. Calling under pressure: Short-finned pilot whales make social calls during deep foraging dives. Proc. R. Soc. B Biol. Sci. 278, 3017–3025 (2011).Article 

    Google Scholar 
    74.Kiszka, J. J., Caputo, M., Méndez-Fernandez, P. & Fielding, R. Feeding ecology of elusive Caribbean killer whales inferred from bayesian stable isotope mixing models and whalers’ ecological knowledge. Front. Mar. Sci. 8, 1–11 (2021).Article 

    Google Scholar 
    75.Whitehead, H. Babysitting, dive synchrony, and indications of alloparental care in sperm whales. Behav. Ecol. Sociobiol. 38, 237–244 (1996).Article 

    Google Scholar 
    76.Konrad, C. M. Kinship in Sperm Whale Society: Effects on Association, Alloparental Care and Vocalization (Dalhousie University, 2017).
    Google Scholar 
    77.Leung, E. S., Vergara, V. & Barrett-Lennard, L. G. Allonursing in captive belugas (Delphinapterus leucas). Zoo Biol. 29, 633–637 (2010).PubMed 
    Article 

    Google Scholar 
    78.Houston, A. I. & Carbone, C. The optimal allocation of time during the diving cycle. Behav. Ecol. 3, 255–265 (1992).Article 

    Google Scholar 
    79.Thompson, D. & Fedak, M. A. How long should a dive last? A simple model of foraging decisions by breath-hold divers in a patchy environment. Anim. Behav. 61, 287–296 (2001).Article 

    Google Scholar 
    80.Aoki, K., Sato, K., Isojunno, S., Narazaki, T. & Miller, P. J. O. High diving metabolic rate indicated by high-speed transit to depth in negatively buoyant long-finned pilot whales. J. Exp. Biol. 220, 3802–3811 (2017).PubMed 
    Article 

    Google Scholar 
    81.New, L. F. et al. The modelling and assessment of whale-watching impacts. Ocean Coast. Manag. 115, 10–16 (2015).Article 

    Google Scholar 
    82.Parsons, M. J. G., Duncan, A. J., Parsons, S. K. & Erbe, C. Reducing vessel noise: An example of a solar-electric passenger ferry. J. Acoust. Soc. Am. 147, 3575–3583 (2020).ADS 
    PubMed 
    Article 

    Google Scholar 
    83.Dale, S. J., Hebner, R. E. & Sulligoi, G. Electric ship technologies. Proc. IEEE 103, 2225–2228 (2015).Article 

    Google Scholar 
    84.Anwar, S., Zia, M. Y. I., Rashid, M., De Rubens, G. Z. & Enevoldsen, P. Towards ferry electrification in the maritime sector. Energies 13, 1–22 (2020).Article 
    CAS 

    Google Scholar 
    85.Filby, N. E., Christiansen, F., Scarpaci, C. & Stockin, K. A. Effects of swim-with-dolphin tourism on the behaviour of a threatened species, the Burrunan dolphin Tursiops Australis. Endanger. Species Res. 32, 479–490 (2017).Article 

    Google Scholar 
    86.Sprogis, K. R., Bejder, L., Hanf, D. & Christiansen, F. Behavioural responses of migrating humpback whales to swim-with-whale activities in the Ningaloo Marine Park, Western Australia. J. Exp. Mar. Bio. Ecol. 522, 151254 (2020).Article 

    Google Scholar  More

  • in

    Indigenous sex-selective salmon harvesting demonstrates pre-contact marine resource management in Burrard Inlet, British Columbia, Canada

    1.Drucker, P. Indians of the Northwest Coast (McGraw-Hill, 1955).Book 

    Google Scholar 
    2.Kroeber, A. Culture and natural areas of Native North America (University of California Press, 1939).
    Google Scholar 
    3.Introduction, S. W. In Handbook of North American Indians volume 7: Northwest Coast (ed. Suttles, W.) 1–15 (Smithsonian Institution, 1990).
    Google Scholar 
    4.Suttles, W. Coping with abundance: subsistence on the Northwest Coast. In Coast Salish Essays (ed. Suttles, W.) (Talon Books, 1987).
    Google Scholar 
    5.Barnett, H. G. The Coast Salish of British Columbia (University of Oregon Press, 1955).
    Google Scholar 
    6.Ames, K. The Northwest Coast: Complex hunter-gatherers, ecology, and social evolution. Annu. Rev. Anthropol. 23, 209–229 (1994).Article 

    Google Scholar 
    7.Carlson, R. L., Szpak, P. & Richards, M. The Pender Canal site and the beginnings of the Northwest Coast cultural system. Can. J. Archaeol. 41, 1–29 (2017).
    Google Scholar 
    8.Cannon, A. & Yang, D. Y. Early storage and sedentism on the Pacific Northwest Coast: ancient DNA analysis of salmon remains from Namu, British Columbia. Am. Antiquity 71, 123–140 (2006).Article 

    Google Scholar 
    9.Matson, R. G. The evolution of Northwest Coast subsistence. In Research in Economic Anthropology Supplement 6: Long-Term Subsistence Change in Prehistoric North America (eds Croes, D. et al.) 366–428 (JAI Press Inc., 1992).
    Google Scholar 
    10.Caldwell, M. et al. A bird’s eye view of northern Coast Salish intertidal resource management features, southern British Columbia. J. Island Coast. Archaeol. 7, 219–233 (2012).Article 

    Google Scholar 
    11.Caldwell, M. & Lepofsky, D. Indigenous marine resource management on the Northwest Coast of North America. Ecol. Process. 2(1), 12 (2013).
    Google Scholar 
    12.Croes, D. R. (ed.). The Qwu?gwes Archaeological Site and Fish Trap (45TN240), and Tested Homestead (45TN396), Eleven-year South Puget Sound Community College Summer Field School Investigations with the Squaxin Island Tribe—Final Report. Report on file, Washington State Department of Archaeology and Historic Preservation, Olympia (2013).13.Lepofsky, D. et al. Shellfish mariculture on the Northwest Coast of North America. Am. Antiq. 80, 236–259 (2015).Article 

    Google Scholar 
    14.Mathews, D. L. & Turner, N. J. Ocean cultures: northwest coast ecosystems and indigenous management systems. In Conservation for the Anthropocene Ocean: Interdisciplinary Science in Support of Nature and People (eds Levin, P. S. & Poe, M. R.) 169–201 (Academic Press, 2017).Chapter 

    Google Scholar 
    15.Williams, J. Clam gardens: aboriginal mariculture on Canada’s West Coast (New Star Books, 2006).
    Google Scholar 
    16.Campbell, S. & Butler, V. Archaeological evidence for resilience of Pacific Northwest salmon populations and the socioecological system over the last~7,500 years. Ecol. Soc. 15(1), 17 (2000).Article 

    Google Scholar 
    17.Thornton, T., Deur, D. & Kitka, H. Cultivation of salmon and other marine resources on the Northwest Coast of North America. Hum. Ecol. 43, 189–199 (2015).Article 

    Google Scholar 
    18.Thornton, T. The ideology and practice of Pacific Herring cultivation among the Tlingit and Haida. Hum. Ecol. 43, 213–223 (2015).Article 

    Google Scholar 
    19.Petersen, J. R. et al. Use of the traditional halibut hook of the Makah Tribe, the čibu⋅d, reduces bycatch in recreational halibut fisheries. PeerJ 8, e9288 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    20.Ritchie, M. & Angelbeck, B. “Coyote broke the dams”: Power, reciprocity, and conflict in fish weir narratives and implications for traditional and contemporary fisheries. Ethnohistory 67(2), 191–220 (2020).Article 

    Google Scholar 
    21.Royle, T. C. A. et al. An efficient and reliable DNA-based sex identification method for archaeological Pacific salmonid (Oncorhynchus spp.) remains. PLoS ONE 13(3), e0193212 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    22.Royle, T. C. A. et al. Investigating the sex-selectivity of a Middle Ontario Iroquoian Atlantic salmon (Salmo salar) and lake trout (Salvelinus namaycush) fishery through ancient DNA analysis. J. Archaeol. Sci. Rep. 31, 102301 (2020).
    Google Scholar 
    23.George, G. National Energy Board Hearing Order OH-001-2014. Trans Mountain Pipeline ULC. Trans Mountain Expansion Project. Volume 6 (2014).24.Morin, J. Tsleil-Waututh Nation’s History, Culture and Aboriginal Interests in Eastern Burrard Inlet. Report on file, Gowlings, Lafleur, Henderson LLP, Vancouver (2015).25.Suttles, W. Central Coast Salish. In Handbook of North American Indians Volume 7: Northwest Coast (ed. Suttles, W.) 453–475 (Smithsonian Institution, 1990).26.Hancock, M. J. & Marshall, D.E. Catalogue of Salmon Streams and Spawning Escapements of Statistical Area 28 Howe Sound-Burrard Inlet. Canadian Data Report of Fisheries and Aquatic Sciences No. 557 (1986).27.Harris, G. The salmon and trout streams of Vancouver. Waters J. Vanc. Aquar. 3, 4–23 (1978).
    Google Scholar 
    28.Ricker, W. E. Effects of the Fishery and of Obstacles to Migration on the Abundance of Fraser River Sockeye Salmon (Oncorhynchus nerka). Canadian Technical Report of Fisheries and Aquatic Sciences No. 1522 (1987).29.Charlton, A. S. The Belcarra Park Site. (Department of Archaeology, Simon Fraser University, 1980).30.Lepofsky, D., Trost, D. & Morin, J. Coast Salish interaction: a view from the inlets. Can. J. Archaeol. 31, 190–223 (2007).
    Google Scholar 
    31.Morin, J., Lepofsky, D., Ritchie, M., Porcic, M. & Edinborough, K. Assessing continuity in the ancestral territory of the Tsleil-Waututh-Coast Salish, southwest British Columbia, Canada. J. Anthropol. Archaeol. 51, 77–87 (2018).Article 

    Google Scholar 
    32.Morin, J., Muir, B., Ritchie, M. & Sellers, I. Tsleil-Waututh and Simon Fraser University Archaeological Investigations at Port Moody (Reed Point, Shoreline Park, Old Orchard Park, Slaughterhouse Creek, Carraholly Point, and Barnet Beach). Permit 2014–344. Report on file, British Columbia Archaeology Branch, Victoria (2020).33.Harris, C. Voices of disaster: smallpox around the Strait of Georgia in 1782. Ethnohistory 41, 591–626 (1994).Article 

    Google Scholar 
    34.Chisholm, B. S. Reconstructions of Prehistoric Diet in British Columbia Using Stable-Carbon Isotopic Analysis. PhD dissertation. (Simon Fraser University, 1986).35.Hanson, D. K. Late Prehistoric Subsistence in the Strait of Georgia Region of the Northwest Coast. Master’s thesis. (Simon Fraser University, 1991).36.Trost, T. Forgotten Waters: A Zooarchaeological Analysis of the Cove Cliff Site (DhRr 18), Indian Arm, British Columbia. Master’s thesis. (Simon Fraser University, 2005).37.Pierson, N. Bridging Troubled Waters: Zooarchaeology and Marine Conservation on Burrard Inlet, Southwest British Columbia. Master’s thesis. (Simon Fraser University, 2011).38.Morin, J. et al. DNA-based species identification of ancient salmonid remains provides new insight into pre-contact Coast Salish salmon fisheries in Burrard Inlet, British Columbia, Canada. J. Archaeol. Sci. Rep. 37, 102956 (2021).
    Google Scholar 
    39.Sproat, G. June 15, 1877. Copy of minute of decision, Joint Indian Reserve Commission. Signed by Dominion Commissioner Alex Anderson, Provincial Commissioner Arch. McKinley and Joint Commissioner G.M. Sproat. Federal set of JIRC’s Minutes and plans, surveyor’s copy. Aboriginal and Northern Affairs Canada, BC Regional Office Specific Claims Branch, Resource Library, Vancouver. AAND Lands and Trusts registration #15215. Also LAC, RG10, Volume 3612, File 3756-23, Reel C10106 (1877).40.Mortimer, H. & George, D. You Call Me Chief: Impressions of the Life of Dan George (Doubleday, 1981).
    Google Scholar 
    41.Talbot, M. Old Legends and Customs of the British Columbia Coast Indians. s.n., New Westminster (1952).42.Thornton, M. Indian Lives and Legends (Mitchell Press, 1966).
    Google Scholar 
    43.MacDonald, C., Drake, D., Doerksen, J. & Cotton, M. Between Forest and Sea: Memories of Belcarra (Belcarra Historical Group, 1998).
    Google Scholar 
    44.Romanoff, S. Fraser Lillooet Fishing. In A Complex Culture of the British Columbia Plateau, Vancouver (ed. Hayden, B.) 222–265 (University of British Columbia Press, 1992).
    Google Scholar 
    45.Kennedy, D. & Bouchard, R. Sliammon Life, Sliammon Lands (Talonbooks, 1983).
    Google Scholar 
    46.Mathisen, O. A. The effect of altered sex ratios on the spawning of red salmon. In Studies of Alaska Red Salmon (ed. Koo, T.) 137–246 (University of Washington Press, 1962).
    Google Scholar 
    47.Reed, W. J. Sex-selective harvesting of Pacific salmon: a theoretically optimal solution. Ecol. Model. 14, 261–271 (1982).Article 

    Google Scholar 
    48.Salo, E. O. Life history of chum salmon (Oncorhynchus keta). In Pacific Salmon Life Histories (eds Margolis Groot, C. & Margolis, L.) 231–310 (UBC Press, 1991).
    Google Scholar 
    49.Jenness, D. The Faith of a Coast Salish Indian (British Columbia Provincial Museum, 1955).50.Richling, B. (ed.) The W̲SÁNEĆ and Their Neighbours: Diamond Jenness on the Coast Salish of Vancouver Island, 1935 (Rock’s Mills Press, 2016).51.Dale, C. & Natcher, D. C. What is old is new again: the reintroduction of Indigenous fishing technologies in British Columbia. Local Environ. 20(11), 1309–1321 (2015).Article 

    Google Scholar 
    52.Ritchie, M. P. & Springer, C. Harrison River Chum Fishery: The Ethnographic and Archaeological Perspective. Report on file, Sts′ailes, Agassiz (2010).53.Simeone, W. E. & Valentine, E. M. Ahtna Knowledge of Long-Term Changes in Salmon runs in the Upper Copper River Drainage, Alaska (Alaska Department of Fish and Game, Division of Subsistence, 2007).54.Langdon, S. J. Traditional Knowledge and Harvesting of Salmon by Huna and Hinyaa Tlingit. (U.S. Fish and Wildlife Service, Office of Subsistence Management, Fisheries Resource Monitoring Program, 2006).55.Ratner, N. C. et al. Local Knowledge, Customary Practices, and Harvest of Sockeye salmon from the Klawock and Sarkar Rivers, Prince of Wales Island, Alaska (Alaska Department of Fish and Game, Division of Subsistence, 2006)56.Curtis, E. The North American Indian: being a series of volumes picturing and describing the Indians of the United States, the Dominion of Canada, and Alaska, Vol. 13 (Plimpton Press, 1924).
    Google Scholar 
    57.Kennedy, D. & Bouchard, R. Stl’atl’imx fishing. In A Complex Culture of the British Columbia Plateau (ed. Hayden, B.) 266–354 (UBC Press, 1992).
    Google Scholar 
    58.Yang, D. Y. & Watt, K. Contamination controls when preparing archaeological remains for ancient DNA analysis. J. Archaeol. Sci. 32(3), 331–336 (2005).Article 

    Google Scholar 
    59.Speller, C. F. et al. High potential for using DNA from ancient herring bones to inform modern fisheries management and conservation. PLoS ONE 7, e51122 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    60.Yang, D. Y., Eng, B., Waye, J. S., Dudar, J. C. & Saunders, S. R. Technical note: improved DNA extraction from ancient bones using silica-based spin columns. Am. J. Phys. Anthropol. 105(4), 539–543 (1998).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    61.Yang, D. Y., Liu, L., Chen, X. & Speller, C. F. Wild or domesticated: DNA analysis of ancient water buffalo remains from North China. J. Archaeol. Sci. 35(10), 2778–2785 (2008).Article 

    Google Scholar 
    62.Bertho, S. et al. The unusual rainbow trout sex determination gene hijacked the canonical vertebrate gonadal differentiation pathway. Proc. Natl. Acad. Sci. U.S.A. 115(50), 12781–12786 (2008).Article 
    CAS 

    Google Scholar 
    63.Yano, A. et al. An immune-related gene evolved into the master sex-determining gene in rainbow trout, Oncorhynchus mykiss. Curr. Biol. 22(15), 1423–1428 (2012).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    64.Yano, A. et al. The sexually dimorphic on the Y-chromosome gene (sdY) is a conserved male-specific Y-chromosome sequence in many salmonids. Evol. Appl. 6(3), 486–496 (2013).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    65.Yang, D., Cannon, A. & Sanders, S. R. DNA species identification of archaeological salmon bone from the Pacific Northwest Coast of North America. J. Archaeol. Sci. 31, 619–631 (2004).Article 

    Google Scholar 
    66.R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2019).67.Kim, K. et al. A real-time PCR-based amelogenin Y allele dropout assessment model in gender typing of degraded DNA samples. Int. J. Legal Med. 127, 55–61 (2013).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    68.Sinding, M. et al. Sex determination of baleen whale artefacts: Implications for ancient DNA use in zooarchaeology. J. Archaeol. Sci. Rep. 10, 345–349 (2016).
    Google Scholar 
    69.Cooper, A. & Poinar, H. Ancient DNA: do it right or not at all. Science 289(5482), 1139 (2000).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    70.McKechnie, I. Investigating the complexities of sustainable fishing at a prehistoric village on western Vancouver Island, British Columbia, Canada. J. Nat. Conserv. 15(3), 208–222 (2007).Article 

    Google Scholar 
    71.Cannon, A., Yang, D. Y. & Speller, C. Site-specific salmon fisheries on the central coast of British Columbia. In The Archaeology of North Pacific Fisheries (eds Moss, M. & Cannon, A.) 57–74 (University of Alaska Press, 2011).
    Google Scholar 
    72.McKechnie, I. & Moss, M. Meta-analysis in zooarchaeology expands perspectives on Indigenous fisheries of the Northwest Coast of North America. J. Archaeol. Sci. Rep. 8, 470–485 (2016).
    Google Scholar 
    73.Orchard, T. J. & Szpak, P. Zooarchaeological and isotopic insights into locally variable economic patterns: a case study from late Holocene southern Haida Gwaii, British Columbia. BC Stud. 187, 107–147 (2015).
    Google Scholar 
    74.Rodrigues, A. T., McKechnie, I. & Yang, D. Y. Ancient DNA analysis of indigenous rockfish use on the Pacific Coast: implications for marine conservation areas and fisheries management. PLoS ONE 13(2), e0192716 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    75.McGregor, D. Coming full circle: Indigenous knowledge, environment, and our future. Am. Indian Q. 28(3), 385–410 (2004).Article 

    Google Scholar 
    76.Suttles, W. Economic Life of the Coast Salish of Hario and Rosario Straits. PhD Dissertation. (University of Washington, 1951).77.Caldwell, M. E. Northern Coast Salish Marine Resource Management. PhD dissertation. (University of Alberta, 2015).78.Deur, D. Tending the garden, making the soil: Northwest Coast estuarine gardens as engineered environments. In Keeping It Living: Traditions of Plant Use and Cultivation on the Northwest Coast of North America (eds Deur, D. & Turner, N.) (UBC Press, 2005).
    Google Scholar 
    79.Hoffmann, T. et al. Engineered feature used to enhance gardening at a 3800-year-old site on the Pacific Northwest coast. Sci. Adv. 2(12), e1601282 (2016).PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    80.Lepofsky, D. et al. Documenting pre-contact plant management on the Northwest Coast: an example of prescribed burning in the Central and Upper Fraser Valley, British Columbia. In Keeping It Living: Traditions of Plant Use and Cultivation on the Northwest Coast of North America (eds Deur, D. & Turner, N.) 218–239 (UBC Press, 2005).
    Google Scholar 
    81.Turner, N. J., Deur, D. & Lepofsky, D. Plant management systems of British Columbia’s First Peoples. BC Stud. 179, 107–133 (2013).
    Google Scholar 
    82.Turner, N. J., Smith, R. & Jones, J. A fine line between two nations: ownership patterns for plant resources among Northwest Coast indigenous peoples. In Keeping It Living: Traditions of Plant Use and Cultivation on the Northwest Coast of North America (eds Deur, D. & Turner, N. J.) 151–180 (UBC Press, 2005).
    Google Scholar 
    83.Turner, N. J. & Peacock, S. Solving the perennial paradox: ethnobotanical evidence for plant resource management on the Northwest Coast. In Keeping It Living: Traditions of Plant Use and Cultivation on the Northwest Coast of North America (eds Deur, D. & Turner, N. J.) 101–151 (UBC Press, 2005).
    Google Scholar 
    84.Limburg, K. E., Walther, Y., Hong, B., Olson, C. & Stora, J. Prehistoric versus modern Baltic Sea cod fisheries: selectivity across the millennia. Proc. R. Soc. B 275, 2659–2665 (2008).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    85.Sanchez, G. Indigenous stewardship of marine and estuarine fisheries? Reconstructing the ancient size of Pacific herring through linear regression models. J. Archaeol. Sci. Rep. 29, 102061 (2020).
    Google Scholar 
    86.Slaney, T. L., Hyatt, K. D., Northcote, T. G. & Fielden, R. J. Status of anadromous salmon and trout in British Columbia and Yukon. Fisheries 21(10), 20–35 (1996).Article 

    Google Scholar 
    87.Kope, R. & Wainwright, T. Trends in the status of Pacific salmon populations in Washington, Oregon, California, and Idaho. N. Pac. Anadr. Fish Comm. Bull. 1, 1–12 (1998).
    Google Scholar 
    88.Gustafson, R. G. et al. Pacific salmon extinctions: Quantifying lost and remaining diversity. Conserv. Biol. 21(4), 1009–1020 (2007).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    89.Price, M. H., English, K. K., Rosenberger, A. G., MacDuffee, M. & Reynolds, J. D. Canada’s wild salmon policy: an assessment of conservation progress in British Columbia. Can. J. Fish. Aquat. Sci. 74(10), 1507–1518 (2017).Article 

    Google Scholar 
    90.Gayeski, N. J. et al. The failure of wild salmon management: need for a place-based conceptual foundation. Fisheries 43(7), 303–309 (2018).Article 

    Google Scholar 
    91.Morales, Q. E., Lepofsky, D. & Berkes, F. Ethnobiology and fisheries: Learning from the past for the present. J. Ethnobiol. 37(3), 369–379 (2017).Article 

    Google Scholar 
    92.Reid, A. J. et al. Two-eyed seeing: an Indigenous framework to transform fisheries research and management. Fish Fish. 00, 1–19 (2020).
    Google Scholar 
    93.Atlas, W. I. et al. Indigenous systems of management for culturally and ecologically resilient Pacific salmon (Oncorhynchus spp.) fisheries. Bioscience 71(2), 1–19 (2021).Article 

    Google Scholar  More

  • in

    Spatial regulation of cell motility and its fitness effect in a surface-attached bacterial community

    1.Flemming H-C, Wingender J, Szewzyk U, Steinberg P, Rice SA, Kjelleberg S. Biofilms: an emergent form of bacterial life. Nat Rev Microbiol. 2016;14:563–75.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    2.Nadell CD, Xavier JB, Foster KR. The sociobiology of biofilms. FEMS Microbiol Rev. 2009;33:206–24.CAS 
    PubMed 

    Google Scholar 
    3.Rumbaugh KP, Sauer K. Biofilm dispersion. Nat Rev Microbiol. 2020;18:571–86.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    4.Costerton JW, Stewart PS, Greenberg EP. Bacterial biofilms: a common cause of persistent infections. Science. 1999;284:1318–22.CAS 
    PubMed 

    Google Scholar 
    5.Drenkard E, Ausubel FM. Pseudomonas biofilm formation and antibiotic resistance are linked to phenotypic variation. Nature. 2002;416:740–3.CAS 
    PubMed 

    Google Scholar 
    6.de Carvalho CCCR. Marine biofilms: a successful microbial strategy with economic implications. Front Mar Sci. 2018;5:126.7.McDougald D, Rice SA, Barraud N, Steinberg PD, Kjelleberg S. Should we stay or should we go: mechanisms and ecological consequences for biofilm dispersal. Nat Rev Microbiol. 2012;10:39–50.CAS 

    Google Scholar 
    8.Nathan R, Getz WM, Revilla E, Holyoak M, Kadmon R, Saltz D, et al. A movement ecology paradigm for unifying organismal movement research. Proc Natl Acad Sci USA. 2008;105:19052–9.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    9.Yan J, Monaco H, Xavier JB. The ultimate guide to bacterial swarming: an experimental model to study the evolution of cooperative behavior. Annu Rev Microbiol. 2019;73:293–312.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    10.Gokhale S, Conwill A, Ranjan T, Gore J. Migration alters oscillatory dynamics and promotes survival in connected bacterial populations. Nat Commun. 2018;9:5273.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    11.Hallatschek O, Fisher DS. Acceleration of evolutionary spread by long-range dispersal. Proc Natl Acad Sci USA. 2014;111:E4911–9.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    12.Birzu G, Hallatschek O, Korolev KS. Fluctuations uncover a distinct class of traveling waves. Proc Natl Acad Sci USA. 2018;115:E3645–54.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    13.Ping D, Wang T, Fraebel DT, Maslov S, Sneppen K, Kuehn S. Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations. ISME J. 2020;14:2007–18.PubMed 
    PubMed Central 

    Google Scholar 
    14.Chen L, Noorbakhsh J, Adams RM, Samaniego-Evans J, Agollah G, Nevozhay D, et al. Two-dimensionality of yeast colony expansion accompanied by pattern formation. PLoS Comput Biol. 2014;10:e1003979.PubMed 
    PubMed Central 

    Google Scholar 
    15.Patra P, Kissoon K, Cornejo I, Kaplan HB, Igoshin OA. Colony expansion of socially motile Myxococcus xanthus cells is driven by growth, motility, and exopolysaccharide production. PLoS Comput Biol. 2016;12:e1005010.PubMed 
    PubMed Central 

    Google Scholar 
    16.Chapman BB, Brönmark C, Nilsson J-Å, Hansson L-A. The ecology and evolution of partial migration. Oikos. 2011;120:1764–75.
    Google Scholar 
    17.Lundberg P. Partial bird migration and evolutionarily stable strategies. J Theor Biol. 1987;125:351–60.
    Google Scholar 
    18.Kokko H. Directions in modelling partial migration: how adaptation can cause a population decline and why the rules of territory acquisition matter. Oikos. 2011;120:1826–37.
    Google Scholar 
    19.Singh NJ, Leonardsson K. Partial migration and transient coexistence of migrants and residents in animal populations. PloS One. 2014;9:e94750.PubMed 
    PubMed Central 

    Google Scholar 
    20.Armbruster CE, Mobley HLT. Merging mythology and morphology: the multifaceted lifestyle of Proteus mirabilis. Nat Rev Microbiol. 2012;10:743.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    21.Schaffer JN, Pearson MM. Proteus mirabilis and urinary tract infections. Microbiol Spectr. 2015;3. https://doi.org/10.1128/microbiolspec.UTI-0017-2013.22.Jones BV, Young R, Mahenthiralingam E, Stickler DJ. Ultrastructure of Proteus mirabilis swarmer cell rafts and role of swarming in catheter-associated urinary tract infection. Infect Immun. 2004;72:3941–50.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    23.Li X, Zhao H, Lockatell CV, Drachenberg CB, Johnson DE, Mobley HL. Visualization of Proteus mirabilis within the matrix of urease-induced bladder stones during experimental urinary tract infection. Infect Immun. 2002;70:389–94.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    24.Stickler DJ. Bacterial biofilms in patients with indwelling urinary catheters. Nat Clin Pr Urol. 2008;5:598–608.CAS 

    Google Scholar 
    25.Jacobsen SM, Stickler DJ, Mobley HLT, Shirtliff ME. Complicated catheter-associated urinary tract infections due to Escherichia coli and Proteus mirabilis. Clin Microbiol Rev. 2008;21:26–59.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    26.Harshey RM. Bacterial motility on a surface: many ways to a common goal. Annu Rev Microbiol. 2003;57:249–73.CAS 
    PubMed 

    Google Scholar 
    27.Verstraeten N, Braeken K, Debkumari B, Fauvart M, Fransaer J, Vermant J, et al. Living on a surface: swarming and biofilm formation. Trends Microbiol. 2008;16:496–506.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    28.Kearns DB. A field guide to bacterial swarming motility. Nat Rev Microbiol. 2010;8:634–44.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    29.Wu Y, Jiang Y, Kaiser AD, Alber M. Self-organization in bacterial swarming: lessons from myxobacteria. Phys Biol. 2011;8:055003.PubMed 

    Google Scholar 
    30.Howery KE, Şimşek E, Kim M, Rather PN. Positive autoregulation of the flhDC operon in Proteus mirabilis. Res Microbiol. 2018;169:199–204.CAS 
    PubMed 

    Google Scholar 
    31.Little K, Austerman J, Zheng J, Gibbs KA. Cell shape and population migration are distinct steps of Proteus mirabilis swarming that are decoupled on high-percentage agar. J Bacteriol. 2019;201:e00726–18.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    32.Furness RB, Fraser GM, Hay NA, Hughes C. Negative feedback from a Proteus class II flagellum export defect to the flhDC master operon controlling cell division and flagellum assembly. J Bacteriol. 1997;179:5585–8.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    33.Claret L, Hughes C. Functions of the subunits in the FlhD(2)C(2) transcriptional master regulator of bacterial flagellum biogenesis and swarming. J Mol Biol. 2000;303:467–78.CAS 
    PubMed 

    Google Scholar 
    34.Deegan RD, Bakajin O, Dupont TF, Huber G, Nagel SR, Witten TA. Capillary flow as the cause of ring stains from dried liquid drops. Nature. 1997;389:827–9.CAS 

    Google Scholar 
    35.Andac T, Weigmann P, Velu SKP, Pinçe E, Volpe G, Volpe G, et al. Active matter alters the growth dynamics of coffee rings. Soft Matter. 2019;15:1488–96.CAS 
    PubMed 

    Google Scholar 
    36.Nellimoottil TT, Rao PN, Ghosh SS, Chattopadhyay A. Evaporation-induced patterns from droplets containing motile and nonmotile bacteria. Langmuir. 2007;23:8655–8.CAS 
    PubMed 

    Google Scholar 
    37.Clemmer KM, Rather PN. Regulation of flhDC expression in Proteus mirabilis. Res Microbiol. 2007;158:295–302.CAS 
    PubMed 

    Google Scholar 
    38.Howery KE, Clemmer KM, Rather PN. The Rcs regulon in Proteus mirabilis: implications for motility, biofilm formation, and virulence. Curr Genet. 2016;62:775–89.CAS 
    PubMed 

    Google Scholar 
    39.Howery KE, Clemmer KM, Şimşek E, Kim M, Rather PN. Regulation of the min cell division inhibition complex by the Rcs phosphorelay in Proteus mirabilis. J Bacteriol. 2015;197:2499–507.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    40.Wang Q, Zhao Y, McClelland M, Harshey RM. The RcsCDB signaling system and swarming motility in Salmonella enterica Serovar Typhimurium: dual regulation of flagellar and SPI-2 virulence genes. J Bacteriol. 2007;189:8447–57.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    41.Samanta P, Clark ER, Knutson K, Horne SM, Prüß BM. OmpR and RcsB abolish temporal and spatial changes in expression of flhD in Escherichia coli biofilm. BMC Microbiol. 2013;13:182.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    42.Girgis HS, Liu Y, Ryu WS, Tavazoie S. A comprehensive genetic characterization of bacterial motility. PLoS Genet. 2007;3:e154.PubMed Central 

    Google Scholar 
    43.Francez-Charlot A, Laugel B, Van Gemert A, Dubarry N, Wiorowski F, Castanié-Cornet MP, et al. RcsCDB His-Asp phosphorelay system negatively regulates the flhDC operon in Escherichia coli. Mol Microbiol. 2003;49:823–32.CAS 
    PubMed 

    Google Scholar 
    44.Rieck VT, Palumbo SA, Witter LD. Glucose availability and the growth rate of colonies of Pseudomonas fluorescens. J Gen Microbiol. 1973;74:1–8.CAS 
    PubMed 

    Google Scholar 
    45.Shao X, Mugler A, Kim J, Jeong HJ, Levin BR, Nemenman I. Growth of bacteria in 3-d colonies. PLoS Comput Biol. 2017;13:e1005679.PubMed 
    PubMed Central 

    Google Scholar 
    46.Warren MR, Sun H, Yan Y, Cremer J, Li B, Hwa T. Spatiotemporal establishment of dense bacterial colonies growing on hard agar. Elife. 2019;8:e41093.PubMed 
    PubMed Central 

    Google Scholar 
    47.Lavrentovich MO, Koschwanez JH, Nelson DR. Nutrient shielding in clusters of cells. Phys Rev E Stat Nonlin Soft Matter Phys. 2013;87:062703. -PubMed 
    PubMed Central 

    Google Scholar 
    48.Dal Co A, van Vliet S, Ackermann M. Emergent microscale gradients give rise to metabolic cross-feeding and antibiotic tolerance in clonal bacterial populations. Philos Trans R Soc Lond B Biol Sci. 2019;374:20190080.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    49.Huang YH, Ferrières L, Clarke DJ. The role of the Rcs phosphorelay in Enterobacteriaceae. Res Microbiol. 2006;157:206–12.CAS 
    PubMed 

    Google Scholar 
    50.Majdalani N, Gottesman S. The Rcs phosphorelay: a complex signal transduction system. Annu Rev Microbiol. 2005;59:379–405.CAS 
    PubMed 

    Google Scholar 
    51.Fraebel DT, Mickalide H, Schnitkey D, Merritt J, Kuhlman TE, Kuehn S. Environment determines evolutionary trajectory in a constrained phenotypic space. Elife. 2017;6:e24669.PubMed 
    PubMed Central 

    Google Scholar 
    52.Yi X, Dean AM. Phenotypic plasticity as an adaptation to a functional trade-off. Elife. 2016;5:e19307.PubMed 
    PubMed Central 

    Google Scholar 
    53.van Ditmarsch D, Boyle KE, Sakhtah H, Oyler JE, Nadell CD, Déziel É, et al. Convergent evolution of hyperswarming leads to impaired biofilm formation in pathogenic bacteria. Cell Rep. 2013;4:697–708.PubMed 
    PubMed Central 

    Google Scholar 
    54.Auer GK, Oliver PM, Rajendram M, Lin T-Y, Yao Q, Jensen GJ, et al. Bacterial swarming reduces Proteus mirabilis and Vibrio parahaemolyticus cell stiffness and increases β-Lactam susceptibility. mBio. 2019;10:e00210–19.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    55.Kaiser D. Bacterial swarming: a re-examination of cell-movement patterns. Curr Biol. 2007;17:R561–R70.CAS 
    PubMed 

    Google Scholar 
    56.Inoue T, Shingaki R, Hirose S, Waki K, Mori H, Fukui K. Genome-wide screening of genes required for swarming motility in Escherichia coli K-12. J Bacteriol. 2007;189:950–7.CAS 
    PubMed 

    Google Scholar 
    57.Dong T, Joyce C, Schellhorn H. The role of RpoS in bacterial adaptation. In: El-Sharoud W, editor. Bacterial physiology. Heidelberg: Springer, Berlin; 2008. pp 313-37.58.Phaiboun A, Zhang Y, Park B, Kim M. Survival kinetics of starving bacteria is biphasic and density-dependent. PLoS Comput Biol. 2015;11:e1004198.PubMed 
    PubMed Central 

    Google Scholar 
    59.Majdalani N, Hernandez D, Gottesman S. Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Mol Microbiol. 2002;46:813–26.CAS 
    PubMed 

    Google Scholar 
    60.Peterson CN, Carabetta VJ, Chowdhury T, Silhavy TJ. LrhA regulates rpoS translation in response to the Rcs phosphorelay system in Escherichia coli. J Bacteriol. 2006;188:3175–81.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    61.Lok T, Overdijk O, Piersma T. The cost of migration: spoonbills suffer higher mortality during trans-Saharan spring migrations only. Biol Lett. 2015;11:20140944.PubMed 
    PubMed Central 

    Google Scholar 
    62.Flack A, Fiedler W, Blas J, Pokrovsky I, Kaatz M, Mitropolsky M, et al. Costs of migratory decisions: a comparison across eight white stork populations. Sci Adv. 2016;2:e1500931.PubMed 
    PubMed Central 

    Google Scholar 
    63.Rankin MA, Burchsted JCA. The cost of migration in insects. Annu Rev Entomol. 1992;37:533–59.
    Google Scholar 
    64.Ni B, Colin R, Link H, Endres RG, Sourjik V. Growth-rate dependent resource investment in bacterial motile behavior quantitatively follows potential benefit of chemotaxis. Proc Natl Acad Sci USA. 2020;117:595–601.CAS 
    PubMed 

    Google Scholar 
    65.Amsler CD, Cho M, Matsumura P. Multiple factors underlying the maximum motility of Escherichia coli as cultures enter post-exponential growth. J Bacteriol. 1993;175:6238–44.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    66.Yokota T, Gots JS. Requirement of adenosine 3’, 5’-cyclic phosphate for flagella formation in Escherichia coli and Salmonella typhimurium. J Bacteriol. 1970;103:513–6.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    67.Soutourina O, Kolb A, Krin E, Laurent-Winter C, Rimsky S, Danchin A, et al. Multiple control of flagellum biosynthesis in Escherichia coli: role of H-NS protein and the cyclic AMP-catabolite activator protein complex in transcription of the flhDC master operon. J Bacteriol. 1999;181:7500–8.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    68.Silverman M, Simon M. Characterization of Escherichia coli flagellar mutants that are insensitive to catabolite repression. J Bacteriol. 1974;120:1196–203.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    69.Mitrophanov AY, Groisman EA. Positive feedback in cellular control systems. Bioessays. 2008;30:542–55.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    70.Raj A, van Oudenaarden A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell. 2008;135:216–26.71.Ferrières L, Clarke DJ. The RcsC sensor kinase is required for normal biofilm formation in Escherichia coli K-12 and controls the expression of a regulon in response to growth on a solid surface. Mol Microbiol. 2003;50:1665–82.PubMed 

    Google Scholar 
    72.Guttenplan SB, Kearns DB. Regulation of flagellar motility during biofilm formation. FEMS Microbiol Rev. 2013;37:849–71.CAS 

    Google Scholar  More

  • in

    Microbial diversity in extreme environments

    1.Rothschild, L. J. & Mancinelli, R. L. Life in extreme environments. Nature 409, 1092–1101 (2001).CAS 
    PubMed 

    Google Scholar 
    2.Schmid, A. K., Allers, T. & DiRuggiero, J. Snapshot: microbial extremophiles. Cell 180, 818–818.e1 (2020).CAS 
    PubMed 

    Google Scholar 
    3.Denef, V. J., Mueller, R. S. & Banfield, J. F. AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J. 4, 599–610 (2010).PubMed 

    Google Scholar 
    4.Inskeep, W. P. et al. The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem. Front. Microbiol. 4, 67 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    5.Oren, A. Halophilic microbial communities and their environments. Curr. Opin. Microbiol. 33, 119–124 (2015).CAS 

    Google Scholar 
    6.Reysenbach, A. L., Wickham, G. S. & Pace, N. R. Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park. Appl. Environ. Microbiol. 60, 2113–2119 (1994).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    7.Bond, P. L., Smriga, S. P. & Banfield, J. F. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl. Environ. Microbiol. 66, 3842–3849 (2000).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    8.Huber, J. A. et al. Microbial population structures in the deep marine biosphere. Science 318, 97–100 (2007).CAS 
    PubMed 

    Google Scholar 
    9.Kuang, J. L. et al. Contemporary environmental variation determines microbial diversity patterns in acid mine drainage. ISME J. 7, 1038–1050 (2013).CAS 
    PubMed 

    Google Scholar 
    10.Power, J. F. et al. Microbial biogeography of 925 geothermal springs in New Zealand. Nat. Commun. 9, 2876 (2018). Extensive sampling and high-throughput 16S rRNA gene sequencing have provided deeper insights into the patterns and ecological drivers of microbial communities inhabiting geothermal springs.PubMed 
    PubMed Central 

    Google Scholar 
    11.Podell, S. et al. Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J. 8, 979–990 (2014).CAS 
    PubMed 

    Google Scholar 
    12.Chen, L. X. et al. Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage. ISME J. 9, 1579–1592 (2015).PubMed 

    Google Scholar 
    13.Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013).CAS 
    PubMed 

    Google Scholar 
    14.Brown, C. T. et al. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523, 208–211 (2015).CAS 
    PubMed 

    Google Scholar 
    15.Castelle, C. J. et al. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr. Biol. 25, 690–701 (2015). The cultivation-independent reconstruction of the first complete genomes for members of the DPANN archaea allowed confident prediction of incomplete or absent pathways for these enigmatic organisms.CAS 
    PubMed 

    Google Scholar 
    16.Sharp, C. E. et al. Humboldt’s spa: microbial diversity is controlled by temperature in geothermal environments. ISME J. 8, 1166–1174 (2014).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    17.Hedlund, B. P. et al. Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’. Curr. Opin. Microbiol. 25, 136–145 (2015).CAS 
    PubMed 

    Google Scholar 
    18.Hua, Z. S. et al. Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. ISME J. 9, 1280–1294 (2015).CAS 
    PubMed 

    Google Scholar 
    19.Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37–43 (2004). This is the first shotgun metagenomic sequencing study that enabled reconstruction of near-complete microbial genomes directly (without cultivation) from a natural community.CAS 
    PubMed 

    Google Scholar 
    20.Castelle, C. J. & Banfield, J. F. Major new microbial groups expand diversity and alter our understanding of the tree of life. Cell 172, 1181–1197 (2018).CAS 
    PubMed 

    Google Scholar 
    21.Chen, L. X. et al. Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota. ISME J. 12, 756–775 (2018).CAS 
    PubMed 

    Google Scholar 
    22.Baker, B. J. et al. Enigmatic, ultrasmall, uncultivated Archaea. Proc. Natl Acad. Sci. USA 107, 8806–8811 (2010).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    23.Narasingarao, P. et al. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J. 6, 81–93 (2012).CAS 
    PubMed 

    Google Scholar 
    24.Brock, T. D. Life at high temperatures. Science 158, 1012–1019 (1967).CAS 
    PubMed 

    Google Scholar 
    25.Cole, J. K. et al. Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities. ISME J. 7, 718–729 (2013).CAS 
    PubMed 

    Google Scholar 
    26.Colman, D. R. et al. Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs. FEMS Microbiol. Ecol. 92, fiw137 (2016).PubMed 

    Google Scholar 
    27.Ward, D. M. et al. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345, 63–65 (1990).CAS 
    PubMed 

    Google Scholar 
    28.Miller, S. R. et al. Bar-coded pyrosequencing reveals shared bacterial community properties along the temperature gradients of two alkaline hot springs in Yellowstone National Park. Appl. Environ. Microbiol. 75, 4565–4572 (2009).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    29.Ward, L. et al. Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring. ISME J. 11, 1158–1167 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    30.Barns, S. M., Fundyga, R. E., Jeffries, M. W. & Pace, N. R. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl Acad. Sci. USA 91, 1609–1613 (1994).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    31.Takai, K. & Yoshihiko, S. A molecular view of archaeal diversity in marine and terrestrial hot water environments. FEMS Microbiol. Ecol. 28, 177–188 (1999).CAS 

    Google Scholar 
    32.Elkins, J. G. et al. A korarchaeal genome reveals insights into the evolution of the Archaea. Proc. Natl Acad. Sci. USA 105, 8102–8107 (2008).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    33.Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    34.Nunoura, T. et al. Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments. Environ. Microbiol. 7, 1967–1984 (2005).CAS 
    PubMed 

    Google Scholar 
    35.Nunoura, T. et al. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res. 39, 3204–3223 (2011).CAS 
    PubMed 

    Google Scholar 
    36.Beam, J. P. et al. Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous ‘streamer’ community. ISME J. 10, 210–224 (2016).CAS 
    PubMed 

    Google Scholar 
    37.Hua, Z. S. et al. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat. Commun. 9, 2832 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    38.Takami, H. et al. A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem. PLoS ONE 7, e30559 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    39.Colman, D. R. et al. Novel, deep-branching heterotrophic bacterial populations recovered from thermal spring metagenomes. Front. Microbiol. 7, 304 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    40.Nobu, M. et al. Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics. ISME J. 10, 273–286 (2016).CAS 
    PubMed 

    Google Scholar 
    41.Hugenholtz, P., Pitulle, C., Hershberger, K. L. & Pace, N. R. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180, 366–376 (1998).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    42.Orcutt, B. N., Sylvan, J. B., Knab, N. J. & Edwards, K. J. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol. Mol. Biol. Rev. 75, 361–422 (2011).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    43.Eloe-Fadrosh, E. A. et al. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat. Commun. 7, 10476 (2016). This is a good example of how analysis of the increasing wealth of metagenomic data collected from diverse environments may lead to the discovery of novel major lineages.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    44.Kelley, D. S., Baross, J. A. & Delaney, J. R. Volcanoes, fluids, and life at Mid-Ocean Ridge spreading centers. Annu. Rev. Earth Planet. Sci. 30, 385–491 (2002).CAS 

    Google Scholar 
    45.Perner, M. et al. In situ chemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from Irina II in the Logatchev field. Environ. Microbiol. 15, 1551–1560 (2013).CAS 
    PubMed 

    Google Scholar 
    46.Flores, G. E. et al. Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge. Environ. Microbiol. 13, 2158–2171 (2011).CAS 
    PubMed 

    Google Scholar 
    47.Dick, G. J. et al. The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally. Nat. Rev. Microbiol. 17, 271–283 (2019).CAS 
    PubMed 

    Google Scholar 
    48.Campbell, B. J., Summers Engel, A., Porter, M. L. & Takai, K. The versatile ε-proteobacteria: key players in sulphidic habitats. Nat. Rev. Microbiol. 4, 458–468 (2006).CAS 
    PubMed 

    Google Scholar 
    49.Reysenbach, A. L., Longnecker, K. & Kirshtein, J. Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a Mid-Atlantic Ridge hydrothermal vent. Appl. Environ. Microbiol. 66, 3798–3806 (2000).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    50.Takai, K., Komatsu, T., Inagaki, F. & Horikoshi, K. Distribution of archaea in a black smoker chimney structure. Appl. Environ. Microbiol. 67, 3618–3629 (2001).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    51.Schrenk, M. O., Kelley, D. S., Bolton, S. A. & Baross, J. A. Low archaeal diversity linked to subseafloor geochemical processes at the Lost City Hydrothermal Field, Mid-Atlantic Ridge. Environ. Microbiol. 6, 1086–1095 (2004).CAS 
    PubMed 

    Google Scholar 
    52.Brazelton, W. J., Schrenk, M. O., Kelley, D. S. & Baross, J. A. Methane- and sulfur-metabolizing microbial communities dominate the Lost City Hydrothermal Field ecosystem. Appl. Environ. Microbiol. 72, 6257–6270 (2006).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    53.Reveillaud, J. et al. Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise. Environ. Microbiol. 18, 1970–1987 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    54.Brazelton, W. J. et al. Archaea and bacteria with surprising micro-diversity show shifts in dominance over 1000-year time scales in hydrothermal chimneys. Proc. Natl Acad. Sci. USA 107, 1612–1617 (2010).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    55.Huber, H. et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63–67 (2002).CAS 
    PubMed 

    Google Scholar 
    56.Waters, E. et al. The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc. Natl Acad. Sci. USA 100, 12984–12988 (2003).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    57.Casanueva, A. et al. Nanoarchaeal 16S rRNA gene sequences are widely dispersed in hyperthermophilic and mesophilic halophilic environments. Extremophiles 12, 651–656 (2008).CAS 
    PubMed 

    Google Scholar 
    58.Wurch, L. et al. Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment. Nat. Commun. 7, 12115 (2016). This is an interesting study demonstrating that insights from genomic studies may help develop effective cultivation strategies for the isolation of novel microbial species.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    59.Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015). The discovery and genomic characterization of Lokiarchaeota have unveiled insights into eukaryogenesis.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    60.Seitz, K. W., Lazar, C. S., Hinrichs, K. U., Teske, A. P. & Baker, B. J. Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. ISME J. 10, 1696–1705 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    61.Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017).CAS 
    PubMed 

    Google Scholar 
    62.Imachi, H. et al. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature 577, 519–525 (2020). This study reports the isolation of the first member of the superphylum Asgard, confirming the existence of these archaea and their close phylogenetic relatedness to eukaryotes.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    63.Margesin, R. & Collins, T. Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge. Appl. Microbiol. Biotechnol. 103, 2537–2549 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    64.Boetius, A., Anesio, A. M., Deming, J. W., Mikucki, J. A. & Rapp, J. Z. Microbial ecology of the cryosphere: sea ice and glacial habitats. Nat. Rev. Microbiol. 13, 677–690 (2015).CAS 
    PubMed 

    Google Scholar 
    65.Hoham, R. W. & Duval, B. in Snow Ecology (eds Jones, H. et al.) 168–228 (Cambridge Univ. Press, 2001).66.Edwards, A. et al. Coupled cryoconite ecosystem structure-function relationships are revealed by comparing bacterial communities in alpine and Arctic glaciers. FEMS Microbiol. Ecol. 89, 222–237 (2014).CAS 
    PubMed 

    Google Scholar 
    67.Jungblut, A. D., Lovejoy, C. & Vincent, W. F. Global distribution of cyanobacterial ecotypes in the cold biosphere. ISME J. 4, 191–202 (2010).CAS 
    PubMed 

    Google Scholar 
    68.Franzetti, A. et al. Temporal variability of bacterial communities in cryoconite on an alpine glacier. Environ. Microbiol. Rep. 9, 71–78 (2017).CAS 
    PubMed 

    Google Scholar 
    69.Anesio, A. M., Hodson, A. J., Fritz, A., Psenner, R. & Sattler, B. High microbial activity on glaciers: importance to the global carbon cycle. Glob. Chang. Biol. 15, 955–960 (2009).
    Google Scholar 
    70.Christner, B. C. et al. A microbial ecosystem beneath the West Antarctic ice sheet. Nature 512, 310–313 (2014).CAS 
    PubMed 

    Google Scholar 
    71.Hultman, J. et al. Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521, 208–212 (2015).CAS 
    PubMed 

    Google Scholar 
    72.Mackelprang, R. et al. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480, 368–371 (2011).CAS 
    PubMed 

    Google Scholar 
    73.Frey, B. et al. Microbial diversity in European alpine permafrost and active layers. FEMS Microbiol. Ecol. 92, fiw018 (2016).PubMed 

    Google Scholar 
    74.Fernández, A. B. et al. Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics. FEMS Microbiol. Ecol. 88, 623–635 (2014).PubMed 

    Google Scholar 
    75.Ventosa, A. et al. Microbial diversity of hypersaline environments: a metagenomic approach. Curr. Opin. Microbiol. 25, 80–87 (2015).CAS 
    PubMed 

    Google Scholar 
    76.Emerson, J. B. et al. Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia. Archaea 2013, 370871 (2013).PubMed 
    PubMed Central 

    Google Scholar 
    77.Ley, R. E. et al. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl. Environ. Microbiol. 72, 3685–3695 (2006).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    78.Harris, J. K. et al. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME J. 7, 50–60 (2013). This study retrieves an unprecedented number of nearly full length 16S rRNA gene sequences from the microbial mats of the Guerrero Negro hypersaline environment, Mexico, demonstrating them to be among the most diverse, complex and novel microbial ecosystems known.PubMed 

    Google Scholar 
    79.Vavourakis, C. D. et al. Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines. Front. Microbiol. 7, 211 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    80.Hamm, J. N. et al. Unexpected host dependency of Antarctic Nanohaloarchaeota. Proc. Natl Acad. Sci. USA. 116, 14661–14670 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    81.Nigro, L. M., Hyde, A. S., MacGregor, B. J. & Teske, A. Phylogeography, salinity adaptations and metabolic potential of the candidate division KB1 bacteria based on a partial single cell genome. Front. Microbiol. 7, 1266 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    82.Vavourakis, C. D. et al. A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. Microbiome 6, 168 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    83.Edwards, K. J., Becker, K. & Colwell, F. The deep, dark energy biosphere: intraterrestrial life on Earth. Annu. Rev. Earth Planet. Sci. 40, 551–568 (2012).CAS 

    Google Scholar 
    84.Parkes, R. J. et al. A review of prokaryotic populations and processes in sub-seafloor sediments, including biosphere: geosphere interactions. Mar. Geol. 352, 409–425 (2014).CAS 

    Google Scholar 
    85.Starnawski, P. et al. Microbial community assembly and evolution in subseafloor sediment. Proc. Natl Acad. Sci. USA 114, 2940–2945 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    86.Ciobanu, M. C. et al. Microorganisms persist at record depths in the subseafloor of the Canterbury Basin. ISME J. 8, 1370–1380 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    87.Inagaki, F. et al. Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor. Science 349, 420–424 (2015).CAS 
    PubMed 

    Google Scholar 
    88.D’Hondt, S., Pockalny, R., Fulfer, V. M. & Spivack, A. J. Subseafloor life and its biogeochemical impacts. Nat. Commun. 10, 3519 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    89.Petro, C., Starnawski, P., Schramm, A. & Kjeldsen, K. U. Microbial community assembly in marine sediments. Aquat. Microb. Ecol. 79, 177–195 (2017).
    Google Scholar 
    90.Teske, A. & Sørensen, K. B. Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J. 2, 3–18 (2008).CAS 
    PubMed 

    Google Scholar 
    91.Orsi, W. D. Ecology and evolution of seafloor and subseafloor microbial communities. Nat. Rev. Microbiol. 16, 671–683 (2018).CAS 
    PubMed 

    Google Scholar 
    92.Sørensen, K. B. & Teske, A. Stratified communities of active Archaea in deep marine subsurface sediments. Appl. Environ. Microbiol. 72, 4596–4603 (2006).PubMed 
    PubMed Central 

    Google Scholar 
    93.Walsh, E. A. et al. Relationship of bacterial richness to organic degradation rate and sediment age in subseafloor sediment. Appl. Environ. Microbiol. 82, 4994–4999 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    94.Petro, C. et al. Marine deep biosphere microbial communities assemble in near-surface sediments in Aarhus Bay. Front. Microbiol. 10, 758 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    95.Jorgensen, S. L. et al. Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. Proc. Natl Acad. Sci. USA 109, E2846–E2855 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    96.Edwards, K. J., Wheat, C. G. & Sylvan, J. B. Under the sea: microbial life in volcanic oceanic crust. Nat. Rev. Microbiol. 9, 703–712 (2011).CAS 
    PubMed 

    Google Scholar 
    97.Li, J. et al. Recycling and metabolic flexibility dictate life in the lower oceanic crust. Nature 579, 250–255 (2020). This is a multiple-approach exploration to provide the first insights into the ultralow-biomass microbial assemblages inhabiting the lithified lower oceanic crust.CAS 
    PubMed 

    Google Scholar 
    98.Bar-On, Y. M., Phillips, R. & Milo, R. The biomass distribution on Earth. Proc. Natl Acad. Sci. USA 115, 6506–6511 (2018).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    99.Nyyssönen, M. et al. Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield. ISME J. 8, 126–138 (2014).PubMed 

    Google Scholar 
    100.Lin, X., Kennedy, D., Fredrickson, J., Bjornstad, B. & Konopka, A. Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site. Environ. Microbiol. 14, 414–425 (2012).CAS 
    PubMed 

    Google Scholar 
    101.Osburn, M. R. et al. Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA. Front. Microbiol. 5, 610 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    102.Magnabosco, C. et al. The biomass and biodiversity of the continental subsurface. Nat. Geosci. 11, 707–717 (2018).CAS 

    Google Scholar 
    103.Navarro-Noya, Y. E. et al. Pyrosequencing analysis of the bacterial community in drinking water wells. Microb. Ecol. 66, 19–29 (2013).PubMed 

    Google Scholar 
    104.Wrighton, K. C. et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 337, 1661–1665 (2012).CAS 
    PubMed 

    Google Scholar 
    105.Bagnoud, A. et al. Reconstructing a hydrogen driven microbial metabolic network in Opalinus Clay rock. Nat. Commun. 7, 12770 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    106.Magnabosco, C. et al. A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust. ISME J. 10, 730–741 (2016).CAS 
    PubMed 

    Google Scholar 
    107.Hernsdorf, A. W. et al. Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. ISME J. 11, 1915–1929 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    108.Anantharaman, K. et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat. Commun. 7, 13219 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    109.Kantor, R. S. et al. Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. mBio 4, e00708–e00713 (2013).PubMed 
    PubMed Central 

    Google Scholar 
    110.Wrighton, K. C. et al. Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer. ISME J. 8, 1452–1463 (2014).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    111.Hallberg, K. B., Coupland, K., Kimura, S. & Johnson, D. B. Macroscopic streamer growths in acidic, metal-rich mine waters in north Wales consist of novel and remarkably simple bacterial communities. Appl. Environ. Microbiol. 72, 2022–2030 (2006).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    112.Belnap, C. P. et al. Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions. ISME J. 5, 1152–1161 (2011).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    113.Edwards, K. J. et al. Seasonal variations in microbial populations and environmental conditions in an extreme acid mine drainage environment. Appl. Environ. Microbiol. 65, 3627–3632 (1999).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    114.Liu, J. et al. Correlating microbial diversity patterns with geochemistry in an extreme and heterogeneous environment of mine tailings. Appl. Environ. Microbiol. 80, 3677–3686 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    115.Golyshina, O. V. et al. ‘ARMAN’ archaea depend on association with euryarchaeal host in culture and in situ. Nat. Commun. 8, 60 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    116.Antony, C. P. et al. Microbiology of Lonar Lake and other soda lakes. ISME J. 7, 468–476 (2013).PubMed 

    Google Scholar 
    117.Sorokin, D. Y. et al. Microbial diversity and biogeochemical cycling in soda lakes. Extremophiles 18, 791–809 (2014).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    118.Reynolds, J. F. et al. Global desertification: building a science for dryland development. Science 316, 847–851 (2007).CAS 
    PubMed 

    Google Scholar 
    119.Maestre, F. T. et al. Increasing aridity reduces soil microbial diversity and abundance in global drylands. Proc. Natl Acad. Sci. USA. 112, 15684–15689 (2015).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    120.Makhalanyane, T. P. et al. Microbial ecology of hot desert edaphic systems. FEMS Microbiol. Rev. 39, 203–221 (2015).CAS 
    PubMed 

    Google Scholar 
    121.Reinthaler, T. et al. Prokaryotic respiration and production in the meso- and bathypelagic realm of the eastern and western North Atlantic basin. Limnol. Oceanogr. 51, 1262–1273 (2006).CAS 

    Google Scholar 
    122.Hewson, I., Steele, J. A., Capone, D. G. & Fuhrman, J. A. Remarkable heterogeneity in meso- and bathypelagic bacterioplankton assemblage composition. Limnol. Oceanogr. 51, 1274–1283 (2006).
    Google Scholar 
    123.DeLong, E. F. et al. Community genomics among stratified microbial assemblages in the ocean’s interior. Science 311, 496–503 (2006).CAS 
    PubMed 

    Google Scholar 
    124.Pham, V. D., Konstantinidis, K. T., Palden, T. & DeLong, E. F. Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre. Environ. Microbiol. 10, 2313–2330 (2008).CAS 
    PubMed 

    Google Scholar 
    125.Karner, M. B., DeLong, E. F. & Karl, D. M. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409, 507–510 (2001).CAS 
    PubMed 

    Google Scholar 
    126.Ziegler, S. et al. Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria. ISME J. 7, 1725–1737 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    127.Méndez-García, C. et al. Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage. ISME J. 8, 1259–1274 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    128.Klatt, C. G. et al. Temporal metatranscriptomic patterning in phototrophic Chloroflexi inhabiting a microbial mat in a geothermal spring. ISME J. 7, 1775–1789 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    129.Klatt, C. G. et al. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Front. Microbiol. 4, 106 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    130.Inskeep, W. P. et al. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PLoS ONE 5, e9773 (2010).PubMed 
    PubMed Central 

    Google Scholar 
    131.Swingley, W. D. et al. Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem. PLoS ONE 7, e38108 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    132.Liu, Z. et al. Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat. ISME J. 5, 1279–1290 (2011).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    133.Woodcroft, B. J. et al. Genome-centric view of carbon processing in thawing permafrost. Nature 560, 49–54 (2018).CAS 
    PubMed 

    Google Scholar 
    134.Ghai, R. et al. New abundant microbial groups in aquatic hypersaline environments. Sci. Rep. 1, 135 (2011).PubMed 
    PubMed Central 

    Google Scholar 
    135.Uritskiy, G. et al. Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert. ISME J. 13, 2737–2749 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    136.Uritskiy, G. et al. Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community. Environ. Microbiol. 23, 3401–3417 (2021).CAS 
    PubMed 

    Google Scholar 
    137.Herrmann, M. et al. Large fractions of CO2-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds. Appl. Environ. Microbiol. 81, 2384–2394 (2015).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    138.Probst, A. J. et al. Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nat. Microbiol. 3, 328–336 (2018).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    139.Mueller, R. S. et al. Ecological distribution and population physiology defined by proteomics in a natural microbial community. Mol. Syst. Biol. 6, 374 (2010).PubMed 
    PubMed Central 

    Google Scholar 
    140.Chen, L. X. et al. Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings. Environ. Microbiol. 15, 2431–2444 (2013).CAS 
    PubMed 

    Google Scholar 
    141.Mueller, R. S. et al. Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community. Environ. Microbiol. 13, 2279–2292 (2011).CAS 
    PubMed 

    Google Scholar 
    142.Mosier, A. C. et al. Elevated temperature alters proteomic responses of individual organisms within a biofilm community. ISME J. 9, 180–194 (2015).CAS 
    PubMed 

    Google Scholar 
    143.Papke, R. T., Koenig, J. E., Rodriguez-Valera, F. & Doolittle, W. F. Frequent recombination in a saltern population of Halorubrum. Science 306, 1928–1929 (2004).CAS 
    PubMed 

    Google Scholar 
    144.Whitaker, R. J., Grogan, D. W. & Taylor, J. W. Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Mol. Biol. Evol. 22, 2354–2361 (2005).CAS 
    PubMed 

    Google Scholar 
    145.Naor, A., Lapierre, P., Mevarech, M., Papke, R. T. & Gophna, U. Low species barriers in halophilic archaea and the formation of recombinant hybrids. Curr. Biol. 22, 1444–1448 (2012).CAS 
    PubMed 

    Google Scholar 
    146.Reno, M. L., Held, N. L., Fields, C. J., Burke, P. V. & Whitaker, R. J. Biogeography of the Sulfolobus islandicus pan-genome. Proc. Natl Acad. Sci. USA 106, 8605–8610 (2009).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    147.Mongodin, E. F. et al. The genome of Salinibacter Ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc. Natl Acad. Sci. USA 102, 18147–18152 (2005).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    148.Nelson-Sathi, S. et al. Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proc. Natl Acad. Sci. USA 109, 20537–20542 (2012). Comparative genomics provides evidence that massive amounts of gene influx from bacterial sources may have led to the drastic change in lifestyle in the extremely salt tolerant Haloarchaea.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    149.Wolf, Y. I., Makarova, K. S., Yutin, N. & Koonin, E. V. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol. Direct 7, 46 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    150.Nelson-Sathi, S. et al. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517, 77–80 (2015).CAS 
    PubMed 

    Google Scholar 
    151.Simmons, S. L. et al. Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol. 6, e177 (2008).PubMed 
    PubMed Central 

    Google Scholar 
    152.Lo, I. et al. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446, 537–541 (2007).CAS 
    PubMed 

    Google Scholar 
    153.Denef, V. J. et al. Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ. Microbiol. 11, 313–325 (2009).CAS 
    PubMed 

    Google Scholar 
    154.Denef, V. J. et al. Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc. Natl Acad. Sci. USA 107, 2383–2390 (2010).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    155.Denef, V. J. & Banfield, J. F. In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids. Science 336, 462–466 (2012). This study provides a time-series population metagenomic analysis of microorganisms in exceptionally low diversity AMD biofilms, allowing for the first time measurement of evolutionary rates for wild populations.CAS 
    PubMed 

    Google Scholar 
    156.Brochier-Armanet, C., Boussau, B., Gribaldo, S. & Forterre, P. Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol. 6, 245–252 (2008).CAS 
    PubMed 

    Google Scholar 
    157.Kelly, S., Wickstead, B. & Gull, K. Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes. Proc. Biol. Sci. 278, 1009–1018 (2011).CAS 
    PubMed 

    Google Scholar 
    158.Sorokin, D. Y. et al. Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis. Nat. Microbiol. 2, 17081 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    159.Baker, B. J. et al. Diversity, ecology and evolution of archaea. Nat. Microbiol. 5, 887–900 (2020).CAS 
    PubMed 

    Google Scholar 
    160.Paul, B. G. et al. Targeted diversity generation by intraterrestrial archaea and archaeal viruses. Nat. Commun. 6, 6585 (2015).CAS 
    PubMed 

    Google Scholar 
    161.Paul, B. G. et al. Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea. Nat. Microbiol. 2, 17045 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    162.Burstein, D. et al. New CRISPR-Cas systems from uncultivated microbes. Nature 542, 237–241 (2017).CAS 
    PubMed 

    Google Scholar 
    163.Anderson, R. E. et al. Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents. Nat. Commun. 8, 1114 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    164.Brazelton, W. J. & Baross, J. A. Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J. 3, 1420–1424 (2009).CAS 
    PubMed 

    Google Scholar 
    165.Jansson, J. K. & Taş, N. The microbial ecology of permafrost. Nat. Rev. Microbiol. 12, 414–425 (2014).CAS 
    PubMed 

    Google Scholar 
    166.Kuang, J. et al. Predicting taxonomic and functional structure of microbial communities in acid mine drainage. ISME J. 10, 1527–1539 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    167.Clark, D. R. et al. Biogeography at the limits of life: do extremophilic microbial communities show biogeographical regionalization? Glob. Ecol. Biogeogr. 26, 1435–1446 (2017).
    Google Scholar 
    168.Atanasova, N. S., Roine, E., Oren, A., Bamford, D. H. & Oksanen, H. M. Global network of specific virus-host interactions in hypersaline environments. Environ. Microbiol. 14, 426–440 (2012).CAS 
    PubMed 

    Google Scholar 
    169.Wilkins, D. et al. Key microbial drivers in Antarctic aquatic environments. FEMS Microbiol. Rev. 37, 303–335 (2013).CAS 
    PubMed 

    Google Scholar 
    170.Cavicchioli, R. Microbial ecology of Antarctic aquatic systems. Nat. Rev. Microbiol. 13, 691–706 (2015).CAS 
    PubMed 

    Google Scholar 
    171.López-Bueno, A. et al. High diversity of the viral community from an Antarctic lake. Science 326, 858–861 (2009).PubMed 

    Google Scholar 
    172.Aguirre de Cárcer, D., López-Bueno, A., Pearce, D. A. & Alcamí, A. Biodiversity and distribution of polar freshwater DNA viruses. Sci. Adv. 1, e1400127 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    173.Yau, S. et al. Virophage control of Antarctic algal host–virus dynamics. Proc. Natl Acad. Sci. USA 108, 6163–6168 (2011). This is the first study to reveal the important ecological roles of virophages and their regulation of host–virus interactions.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    174.Al-Shayeb, B. et al. Clades of huge phages from across Earth’s ecosystems. Nature 578, 425–431 (2020). Analysis of massive metagenomic datasets revealed clades of huge phages from diverse habitats, including extreme environments.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    175.Tschitschko, B. et al. Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation. ISME J. 9, 2094–2107 (2015).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    176.Mosier, A. C. et al. Fungi contribute critical but spatially varying roles in nitrogen and carbon cycling in acid mine drainage. Front. Microbiol. 7, 238 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    177.Quemener, M. et al. Meta-omics highlights the diversity, activity and adaptations of fungi in deep oceanic crust. Environ. Microbiol. 22, 3950–3967 (2020).CAS 
    PubMed 

    Google Scholar 
    178.Fredrickson, J. K. Ecological communities by design. Science 348, 1425–1427 (2015).CAS 
    PubMed 

    Google Scholar 
    179.Fuhrman, J. A. et al. Annually reoccurring bacterial communities are predictable from ocean conditions. Proc. Natl Acad. Sci. USA 103, 13104–13109 (2006).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    180.Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).PubMed 

    Google Scholar 
    181.Lozupone, C. A. & Knight, R. Global patterns in bacterial diversity. Proc. Natl Acad. Sci. USA 104, 11436–11440 (2007).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    182.Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl Acad. Sci. USA 103, 626–631 (2006).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    183.López-Pérez, M., Haro-Moreno, J. M., Coutinho, F. H., Martinez-Garcia, M. & Rodriguez-Valera, F. The evolutionary success of the marine bacterium SAR11 analyzed through a metagenomic perspective. mSystems 5, e00605-20 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    184.Altshuler, I., Goordial, J. & Whyte, L. G. in Psychrophiles: From Biodiversity to Biotechnology (ed. Margesin, R.) 153–180 (Springer International Publishing, 2017).185.Huang, L. N., Kuang, J. L. & Shu, W. S. Microbial ecology and evolution in the acid mine drainage model system. Trends Microbiol. 24, 581–593 (2016).CAS 
    PubMed 

    Google Scholar 
    186.Klatt, C. G. et al. Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. ISME J. 5, 1262–1278 (2011).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    187.Menzel, P. et al. Comparative metagenomics of eight geographically remote terrestrial hot springs. Microb. Ecol. 70, 411–424 (2015).PubMed 

    Google Scholar 
    188.Stokke, R. et al. Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm. Environ. Microbiol. 17, 4063–4077 (2015).CAS 
    PubMed 

    Google Scholar 
    189.Zeng, Y. et al. Potential rhodopsin- and bacteriochlorophyll-based dual phototrophy in a High Arctic glacier. mBio 11, e02641–20 (2020).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    190.Simon, C., Wiezer, A., Strittmatter, A. W. & Daniel, R. Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome. Appl. Environ. Microbiol. 75, 7519–7526 (2009).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    191.Lipson, D. A. et al. Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile. PLoS ONE 8, e64659 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    192.Podell, S. et al. Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS ONE 8, e61692 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    193.DeMaere, M. Z. et al. High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proc. Natl Acad. Sci. USA. 110, 16939–16944 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    194.Smith, A. R. et al. Carbon fixation and energy metabolisms of a subseafloor olivine biofilm. ISME J. 13, 1737–1749 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    195.Zhao, R. et al. Geochemical transition zone powering microbial growth in subsurface sediments. Proc. Natl Acad. Sci. USA. 117, 32617–32626 (2020).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    196.Luo, Z. H. et al. Diversity and genomic characterization of a novel Parvarchaeota family in acid mine drainage sediments. Front. Microbiol. 11, 612257 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    197.Lewin, A., Wentzel, A. & Valla, S. Metagenomics of microbial life in extreme temperature environments. Curr. Opin. Biotechnol. 24, 516–525 (2013).CAS 
    PubMed 

    Google Scholar 
    198.Schlesinger, M. J. Heat-shock proteins. J. Biol. Chem. 265, 12111–12114 (1990).CAS 
    PubMed 

    Google Scholar 
    199.D’Amico, S., Collins, T., Marx, J.-C., Feller, G. & Gerday, C. Psychrophilic microorganisms: challenges for life. EMBO Rep. 7, 385–389 (2006).PubMed 
    PubMed Central 

    Google Scholar 
    200.Bakermans, C., Bergholz, P. W., Ayala-del-Río, H. & Tiedje, J. in Permafrost Soils (ed. Margesin, R.) 159–168 (Springer, 2009).201.Gunde-Cimerman, N., Plemenitaš, A. & Oren, A. Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations. FEMS Microbiol. Rev. 42, 353–375 (2018).CAS 
    PubMed 

    Google Scholar 
    202.Baker-Austin, C. & Dopson, M. Life in acid: pH homeostasis in acidophiles. Trends Microbiol. 15, 165–171 (2007).CAS 
    PubMed 

    Google Scholar 
    203.Dopson, M., Baker-Austin, C., Koppineedi, P. R. & Bond, P. L. Growth in sulfidic mineral environments: metal resistance mechanisms in acidophilic micro-organisms. Microbiology 149, 1959–1970 (2003).CAS 
    PubMed 

    Google Scholar 
    204.Dopson, M., Ossandon, F. J., Lövgren, L. & Holmes, D. S. Metal resistance or tolerance? Acidophiles confront high metal loads via both abiotic and biotic mechanisms. Front. Microbiol. 5, 157 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    205.Allen, E. E. & Banfield, J. F. Community genomics in microbial ecology and evolution. Nat. Rev. Microbiol. 3, 489–498 (2005).CAS 
    PubMed 

    Google Scholar 
    206.Sakowski, E. et al. Current state of and future opportunities for prediction in microbiome research: report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019. mSystems 4, e00392–19 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    207.Lima-Mendez, G. et al. Determinants of community structure in the global plankton interactome. Science 348, 1262073 (2015).PubMed 

    Google Scholar  More

  • in

    Water column structure influences long-distance latitudinal migration patterns and habitat use of bumphead sunfish Mola alexandrini in the Pacific Ocean

    1.Sims, D. W., Queiroz, N., Doyle, T. K., Houghton, J. D. R. & Hays, G. C. Satellite tracking of the world’s largest bony fish, the ocean sunfish (Mola mola L.) in the North East Atlantic. J. Exp. Mar. Biol. Ecol. 370, 127–133 (2009a)2.Sims, D. W., Queiroz, N., Humphries, N. E., Lima, F. P. & Hays, G. C. Long-term GPS tracking of ocean sunfish Mola mola offers a new direction in fish monitoring. PLoS ONE 4, e7351 (2009b).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    3.Dewar, H. et al. Satellite tracking the world’s largest jelly predator, the ocean sunfish, Mola mola, in the Western Pacific. J. Exp. Mar. Biol. Ecol. 393, 32–42 (2010).Article 

    Google Scholar 
    4.Thys, T. M. et al. Ecology of the ocean sunfish, Mola mola, in the southern California current system. J. Exp. Mar. Biol. Ecol. 471, 64–76 (2015).Article 

    Google Scholar 
    5.Sousa, L. L., Queiroz, N., Mucientes, G., Humphries, N. E. & Sims, D. W. Environmental influence on the seasonal movements of satellite-tracked ocean sunfish Mola mola in the north-east Atlantic. Anim. Biotelemetry 4, 7 (2016a).Article 

    Google Scholar 
    6.Sousa, L. L. et al. Integrated monitoring of Mola mola behaviour in space and time. PLoS ONE 11, e0160404 (2016b).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    7.Chang, C. T. et al. Horizontal and vertical movement patterns of sunfish off eastern Taiwan. Deep-Sea Res. Part II Top. Stud. Oceanogr. 175, 104683 (2020).8.Sawai, E., Yamanoue, Y., Yoshita, Y., Sakai, Y. & Hashimoto, H. Seasonal occurrence patterns of Mola sunfishes (Mola spp. A and B; Molidae) in waters off the Sanriku region, eastern Japan. Japan. J. Ichthyol. 58, 181–187 (2011).
    Google Scholar 
    9.Thys, T. M., Ryan, J. P., Weng, K. C., Erdmann, M. & Tresnati, J. Tracking a marine ecotourism star: Movements of the short ocean sunfish Mola ramsayi in Nusa Penida, Bali, Indonesia. J. Mar. Biol. 2016, 8750193 (2016).Article 

    Google Scholar 
    10.Thys, T. M., Hearn, A. R., Weng, K. C., Ryan, J. P. & Peñaherrera-Palma, C. Satellite tracking and site fidelity of short ocean sunfish, Mola ramsayi, in the Galapagos Islands. J. Mar. Biol. 2017, 7097965 (2017).Article 

    Google Scholar 
    11.Aspillaga, E. et al. Thermal stratification drives movement of a coastal apex predator. Sci. Rep. 7, 526 (2017).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    12.Gaube, P. et al. Mesoscale eddies influence the movements of mature female white sharks in the Gulf Stream and Sargasso Sea. Sci. Rep. 8, 7363 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    13.Nakamura, I., Goto, Y. & Sato, K. Ocean sunfish rewarm at the surface at the surface after deep excursion to forage for siphonophores. J. Anim. Ecol. 84, 590–603 (2015).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    14.Tolotti, M. et al. Fine-scale vertical movements of oceanic whitetip sharks (Carcharhinus longimanus). Fish. Bull. 115, 380–395 (2017).Article 

    Google Scholar 
    15.Musyl, M. K. et al. Postrelease survival, vertical and horizontal movements, and thermal habitats of five species of pelagic sharks in the central Pacific Ocean. Fish. Bull. 109, 341–368 (2011).
    Google Scholar 
    16.Furukawa, S. et al. Vertical movements of Pacific bluefin tuna (Thunnus orientalis) and dolphinfish (Coryphaena hippurus) relative to the thermocline in the northern East China Sea. Fish. Res. 149, 86–91 (2014).Article 

    Google Scholar 
    17.Gaube, P. et al. The use of mesoscale eddies by juvenile loggerhead sea turtles (Caretta caretta) in the southwestern Atlantic. PloS ONE 12, e0172839 (2017).18.Braun, C. D., Gaube, P., Sinclair-Taylor, T. H., Skomal, G. B. & Thorrold, S. R. Mesoscale eddies release pelagic sharks from thermal constraints to foraging in the ocean twilight zone. PNAS 116, 17187–17192 (2019).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    19.Sawai, E., Yamanoue, Y., Nyegaard, M. & Sakai, Y. Redescription of the bump-head sunfish Mola alexandrini (Ranzani 1839), senior synonym of Mola ramsayi (Giglioli 1883), with designation of a neotype for Mola mola (Linnaeus 1758) (Tetraodontiformes: Molidae). Ichthyol. Res. 65, 142–160 (2018).Article 

    Google Scholar 
    20.Sawai, E. & Yamada, M. Bump-head sunfish Mola alexandrini photographed in the north-west Pacific Ocean mesopelagic zone. J. Fish Biol. 96, 278–280 (2020).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    21.Kiyofuji, H. et al. Northward migration dynamics of skipjack tuna (Katsuwonus pelamis) associated with the lower thermal limit in the western Pacific Ocean. Progr. Oceanogr. 175, 55–67 (2019).ADS 
    Article 

    Google Scholar 
    22.Fujioka, K. et al. Spatial and temporal variability in the trans-Pacific migration of Pacific bluefin tuna (Thunnus orientalis) revealed by archival tags. Progr. Oceanogr. 162, 52–65 (2018).23.Kobari, T. et al. Variability in taxonomic composition, standing stock, and productivity of the plankton community in the Kuroshio and its neighboring waters in Kuroshio Current: Physical, Biogeochemical, and Ecosystem Dynamics (ed. Nagai, T., Saito, H., Suzuki, K., Takahashi, M.) 223–243 (Hoboken, 2019).24.Queiroz, N., Humphries, N. E., Noble, L. R., Santos, A. M. & Sims, D. W. Short-term movements and diving behaviour of satellite-tracked blue sharks Prionace glauca in the northeastern Atlantic Ocean. Mar. Ecol. Progress Ser. 406, 265–279 (2010).ADS 
    Article 

    Google Scholar 
    25.McMahon, C. R. & Hays, G. C. Thermal niche, large-scale movements and implications of climate change for a critically endangered marine vertebrate. Glob. Change Biol. 12, 1330–1338 (2006).ADS 
    Article 

    Google Scholar 
    26.Nakatsubo, T., Kawachi, M., Mano, N. & Hirose, H. Spawning period of ocean sunfish Mola mola in waters of the eastern Kanto region, Japan. Aquacult. Sci. 55, 613–618 (2007).
    Google Scholar 
    27.Ashida, H., Suzuki, N., Tanabe, T., Suzuki, N. & Aonuma, Y. Reproductive condition, batch fecundity, and spawning fraction of large Pacific bluefin tuna Thunnus orientalis landed at Ishigaki Island, Okinawa, Japan. Environ. Biol. Fish. 98, 1173–1183 (2015).Article 

    Google Scholar 
    28.Watai, M. et al. Comparative analysis of the early growth history of Pacific bluefin tuna Thunnus orientalis from different spawning grounds. Mar. Ecol. Progress Ser. 607, 207–220 (2018).ADS 
    Article 

    Google Scholar 
    29.Stevens, J. D., Bradford, R. W. & West, G. J. Satellite tagging of blue sharks (Prionace glauca) and other pelagic sharks off eastern Australia: Depth behaviour, temperature experience and movements. Mar. Biol. 157, 575–591 (2010).Article 

    Google Scholar 
    30.Musyl, M. K. et al. Vertical movements of bigeye tuna (Thunnus obesus) associated with islands, buoys, and seamounts near the main Hawaiian Islands from archival tagging data. Fish. Oceanogr. 12, 152–169 (2003).Article 

    Google Scholar 
    31.Lin, S. J. et al. Vertical and horizontal movements of bigeye tuna (Thunnus obesus) in southeastern Taiwan. Mar. Freshw. Behav. Physiol. 54, 1–21 (2021).Article 

    Google Scholar 
    32.Yasuda, I. & Kitagawa, D. Locations of early fishing grounds of saury in the northwestern Pacific. Fish. Oceanogr. 5, 63–69 (1996).Article 

    Google Scholar 
    33.Godø, O. R. et al. Mesoscale eddies are oases for higher trophic marine life. PloS ONE 7, e30161 (2012). 34.Polovina, J. J. et al. Forage and migration habitat of loggerhead (Caretta caretta) and olive ridley (Lepidochelys olivacea) sea turtles in the central North Pacific Ocean. Fish. Oceanogr. 13, 36–51 (2004).Article 

    Google Scholar 
    35.Sbragaglia, V. et al. Annual rhythms of temporal niche partitioning in the Sparidae family are correlated to different environmental variables. Sci. Rep. 9, 1708 (2019).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    36.Nakamura, I., Mastumoto, R. & Sato, K. Body temperature stability in the whale shark, the world’s largest fish. J. Exp. Biol. 223, jeb210286 (2020).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    37.Brill, R. W., Bigelow, K. A., Musyl, M. K., Fritsches, K. A. & Warrant, E. J. Bigeye tuna (Thunnus obesus) behavior and physiology and their relevance to stock assessments and fishery biology. Col. Vol. Sci. Pap. ICCAT 57, 142–161 (2005).
    Google Scholar 
    38.Stramma, L. et al. Expansion of oxygen minimum zones may reduce available habitat for tropical pelagic fishes. Nat. Clim. Change 2, 33–37 (2012).ADS 
    CAS 
    Article 

    Google Scholar 
    39.Brill, R. W. A review of temperature and oxygen tolerance studies of tunas pertinent to fisheries oceanography, movement models and stock assessments. Fish. Oceanogr. 3, 204–216 (1994).Article 

    Google Scholar 
    40.Lam, C. H., Kiefer, D. A. & Domeier, M. L. Habitat characterization for striped marlin in the Pacific Ocean. Fish. Res. 166, 80–91 (2015).Article 

    Google Scholar 
    41.Carlisle, A. B. et al. Influence of temperature and oxygen on the distribution of blue marlin (Makaira nigricans) in the Central Pacific. Fish. Oceanogr. 26, 34–48 (2017).Article 

    Google Scholar 
    42.Madigan D. J. et al. Water column structure defines vertical habitat of twelve pelagic predators in the South Atlantic. ICES J. Mar. Sci. 78, 867–883 (2021).Article 

    Google Scholar 
    43.Schlitzer, R. Export production in the equatorial and North Pacific derived from dissolved oxygen, nutrient and carbon data. J. Oceanogr. 60, 53–62 (2004).CAS 
    Article 

    Google Scholar 
    44.Thomsen, S. et al. The formation of a subsurface anticyclonic eddy in the Peru-Chile Undercurrent and its impact on the near-coastal salinity, oxygen, and nutrient distributions. J. Geophys. Res. 121, 476–501 (2016).ADS 
    Article 

    Google Scholar 
    45.Nakamura, I. & Sato, K. Ontogenetic shift in foraging habit of ocean sunfish Mola mola from dietary and behavioral studies. Mar. Biol. 161, 1263–1273 (2014).Article 

    Google Scholar 
    46.QGIS Development Team. Quantum GIS geographic information system. Open Source Geospatial Foundation Project. http://www.qgis.org/en/site/ (2016).47.Chelton, D. B., Gaube, P., Schlax, M. G., Early, J. J. & Samelson, R. M. The influence of nonlinear mesoscale eddies on near-surface oceanic chlorophyll. Science 334, 328–332 (2011).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    48.Fiedler, P. C. Comparison of objective descriptions of the thermocline. Limnol. Oceanogr. Methods 8, 313–325 (2010).Article 

    Google Scholar 
    49.Zar, J. H. Biostatistical Analysis 4th edn. (Prentice Hall, 1999).
    Google Scholar 
    50.Clarke, K. R., & Gorley, R. N. PRIMER v6: User manual/tutorial. PRIMER-E, Plymouth.51.Wood, S. N. On p-values for smooth components of an extended generalized additive model. Biometrika 100, 221–228 (2013).MathSciNet 
    MATH 
    Article 

    Google Scholar  More

  • in

    Pheromones that correlate with reproductive success in competitive conditions

    Reproductive successThe production of urinary pheromones correlated with male but not female reproductive success (RS; defined in “Materials and methods” section). The most important predictors of male RS were total urinary protein concentration (75%) and social status (69%; Table 1; based on conditional model average sum of weights). The relative importance of age, creatinine, and mass ranged from 23 to 39%; PC ratio (protein:creatinine concentration) was excluded from the model due to collinearity (VIF = 6.97). Total urinary protein concentration during the enclosure phase was positively correlated with RS for males (Spearman R = 0.52, p = 0.01; Fig. 1a), but not females (Fig. 1b). This correlation is explained by the low protein concentration in the urine of non-reproductive males, as it is no longer significant after removing these males from the analysis (R = 0.12, p = 0.62; Supplementary Fig. S2). The median total urinary protein concentration was 5512 µg mL−1 and 5028 µg mL−1 for reproductive and non-reproductive males, respectively (Wilcoxon rank sum test W = 5, p  More

  • in

    Description of five new species of the Madagascan flagship plant genus Ravenala (Strelitziaceae)

    Generic nameRavenala Adans.1 (1763: 67). (equiv) Urania Schreb.22 (1789: 212). –Ravenala Scop.23, nom. illeg. (1777: 96) as “Ravenalla Adans”.Type species Ravenala madagascariensis Sonn.24.Note: Dorr & Parkinson25 proposed to conserve the spelling Ravenala Scop. (and correct Scopoli’s original orthography “Ravenalla”) against Ravenala Adans. on the basis that Adanson’s generic names (using a uninominal nomenclature for species) were invalid. Brummitt26 rejected this proposal and considered that Adanson’s generic names were valid27 and thus that there was no need to use Scopoli’s Ravenala (Ravenalla). Moreover, the exact wording in Scopoli23 (1777: 96) is “Ravenalla Adans.”, citing Adanson explicitly, but with an incorrect spelling for the generic name (the double “l”).Typification and emended descriptionRavenala madagascariensis Sonn. (1782: 2[ed. qto.]: 223, tt. 124–126).(equiv) Ravenala madagascariensis J.F.Gmel.28 (1791: 567). (equiv) Urania madagascariensis (Sonn.) Schreb. ex Forsyth f.29 (1794: 212). (equiv) Heliconia ravenala Willemet30 (1796: 22). (equiv) Urania speciosa Willdenow31 (1799: 7). (equiv) Urania ravenalia (Willemet) A.Rich.32 (1831: 19). –Ravenala madagascariensis Adans.1 (1763: 597), nomen invalid., appearing on page 597, abbreviated in the final index of Adanson’s book as “Ravenala madag. 67”, which can also be construed as referring to Madagascar as a locality.Type Lectotype, here designated: The plate numbered 126, representing the typical lax mature infructescence, in Sonnerat24 (1782: plate 126). Epitype, here designated: MADAGASCAR (bullet) Fort-Dauphin, Forêt de Manantantely, [24°58′ 59.988″S, 46°55′0.012″E, calc. from label], 60–300 m elev., 15 September 1928, H. Humbert 5730 (Epitype: MNHN-P-P02234599!, Isoepitypes: MNHN-P-P02234602!, MNHN-P-P02234604!, MNHN-P-P02234605!).Additional specimen examined: MADAGASCAR (bullet) Toamasina: Foulpointe, Analalava Forest, plant growing close to the main forest station, 17°42.3′S, 49°27.38′E, 50 m elev., 20 March 2016, T.Haevermans, M. Vorontsova, S. Dransfield & J. Razanatsoa 821 (TAN!, P!, K !) (bullet) X. Aubriot et al. 45 (P00696168!, P00696167!, P00685124!, TAN!) (bullet) Along Route #5 from Fenerive to Maroantsetra, disturbed areas along road, 100 m elev., 28 February 1975, T. B. Croat 32540 (L-WAG.1111446!, L-WAG.1111447!, MO-358490!, MO-358491!, MO-358523!) (bullet) Toalagnaro, Ebakika, District de Fort-Dauphin, 12 July 1932, R. Decary 10107 (P02234596!) (bullet) Vondrozo (commune de Farafangana), 16 September 1926, R. Decary 5428 (P02234588!, P02234591!, P02234592!) (bullet) 2 km E of Ranomafana towards Brickaville, 18.965° S, 48.8564° E, 4 March 1992, J. Kress et al. 92-3412 (US00424302!, US00424299!, US00424300!, US00424301!, US00424303!) (bullet) 18 km E of Ranomafana, 25 km W of Brickaville, 18.9453° S, 48.9664° E, 4 March 1992, J. Kress et al. 92-3414 (US00424312!, US00424309!, US00424310!, US00424311!, US00424313!). MAURITIUS (bullet) Isle de France, s.dat., Commerson s.n. (P02234587!, P-JU!, P-LAM!).Identity of Ravenala madagascariensis Sonn. —Figs. 2d, 3d, 4d, 5d— In the absence of a specimen undoubtedly collected or seen by Sonnerat (Commerson’s specimens, collected in Mauritius and preserved in both Jussieu’s and Lamarck’s herbaria at the Paris herbarium (P-JU and P-LAM), might actually be part of original material), we decided to lectotypify from plates 124, 125 and 126 of the protologue in Sonnerat’s valid publication24 of the species. On page 225, Sonnerat24 mentions that the plant originated from Madagascar but was transported and established in Mauritius (known at the time as Isle de France) at the “Jardin des Pamplemousses”. We observed plants growing in this garden as well as naturalized plants occurring in the wild in Mauritius; all the plants we saw suckered and possessed the characteristic pointed conical fruits also observed in the Fort-Dauphin population. Sonnerat also specified that the original plant grew in marshy areas, which corresponds exactly to the coastal populations that can be found on the eastern coast of Madagascar (i.e. the “Horonorona” variant of Blanc et al.13). Plate 126 shows the typical mature infructescence of the species, with the space between bracts increasing before releasing the seeds (unlike other species of Ravenala). However, the “tree” pictured on plate 124 is a non-suckering plant, which in our opinion can be explained as artistic license on the part of the illustrator, as all the plants observed in Mauritius consistently sucker, like the plants growing in the south-eastern marshy areas. We also decided to designate an epitype with a documented locality in Madagascar (the material in P-JU and P-LAM does not bear a precise indication of locality) to fix the application of the name R. madagascariensis to the populations occurring in the marshy areas surrounding Fort-Dauphin, where only one morphotype is known.Figure 3Comparison of petiole bases. (a) R. agatheae. (b) R. blancii. (c) R. grandis. (d) R. madagascariensis. (e) R. menahirana. (f) R. hladikorum. Photographs Thomas Haevermans©.Full size imageFigure 4Comparison of inflorescences. (a) R. agatheae. (b) R. blancii. (c) R. grandis. (d) R. madagascariensis. (e) R. menahirana. (f) R. hladikorum. Photographs Thomas Haevermans©.Full size imageFigure 5Species of Ravenala in their natural habitat. (a) R. agatheae. (b) R. blancii. (c) R. grandis. (d) R. madagascariensis. (e) R. menahirana. (f) R. hladikorum. Photographs Thomas Haevermans©.Full size imageEmended description Plants suckering, 6–12 meters tall (adult), trunk circumference (d.b.h.) 20–30 cm, juvenile and adult laminae distributed in a perfect fan, 14–25 leaves simultaneously alive on the adult plant, 1–3 leaves between inflorescences. Leaves adult petiole 380–440 cm long, greenish-yellow, slightly waxy, sheath margin undeveloped to moderately developed (0–9 mm), entire, not drying, slightly splitting when aged (Fig. 3d), petiole/lamina ratio 1.9–(2.2)–2.3, adult lamina (200 times 100) cm, light green, juvenile lamina base non-decurrent. Inflorescences 4–6 live lateral inflorescences at a time, (100 times 100) cm (peduncle excluded), 8–16 bracts per inflorescence, bracts 200–(450 times 50)–100 mm, with some wax to very waxy, margin uniformly green (Fig. 4d), cincinnii of ca. 10 flowers per bract, flowering sequentially, bracteoles without a colored stripe. Flowers 240–280 mm long (ovary included), inferior ovary 40–50 mm long, perianth yellowish, sepals narrowly triangular 240–250 (times 10)–12 mm, sheathing (fused) petals narrowly triangular 220–230(times)ca. 10 mm, free petal acicular 180–190 (times 5) mm, slightly smaller than the remaining perianth with mean free petal/mean fused petal length ratio = 0.8, petal blotches absent, stamens (roughly) the same size as the perianth, 200–210 mm long, style 200–230 mm long, stigma 15–20 mm long, oblong ovoid with a basal constriction. Infructescences lax (bract bases not imbricate at maturity), stiff and coriaceous persisting bracts, old infructescences deciduous, 4–8 fruits per bract. Fruits 70–120 (times 30)–35 mm, trilocular septifragal capsule, apices conical (Fig. 2d), seeds 6–(8.5)–(11 times 5)–(6.4)–8 mm, shiny, dark brown, mostly globose, varying in shape according to their distribution in the capsule, ultramarine blue aril.Ecology Ravenala madagascariensis is a low-altitude species restricted to swampy areas of the eastern coast of Madagascar. Populations outside of Madagascar on nearby islands are reputedly non-indigenous24.Preliminary IUCN assessments We propose a Least Concern status for R. madagascariensis, having an E.O.O ( > 20,000) km2 and an A.O.O. ( > 2,000) km2 (criterion B)33.Note This emended description for R. madagascariensis was drawn up from our own observations and collections, and was made comparable point by point to the descriptions of the five new species presented below, along with a dichotomous identification key to all six species.New species descriptions
    Ravenala agatheae Haev. & Razanats. sp. nov.—Figs. 2a, 3a, 4a, 5a, 6
    Type MADAGASCAR (bullet) Antsiranana: Ambanja District, along R.N.6 road to Ankaramibe, 13°45′54.8″S, 48°21′27.7″E, 30 m elev., on degraded lateritic slopes, 28 October 2018, T. Haevermans, A. Haevermans & J. Razanatsoa 830 (Holotype: TAN!, Isotypes: K!, MO!, P!).Figure 6Ravenala agatheae. (a) young infructescence. (b) adult plant habit showing the suckers at the base and the persistent petioles and old infructescences. (c) fruit with a conical apex. (d) infructescence with remains of dried flowers and dried bracts. (e) style apex. (f) inflorescence with open flowers. (g) open flower. Ink drawings on (75 , upmu) polyester tracing paper by Agathe Haevermans© from specimen Haevermans et al. 830, and observations in-situ.Full size imageParatypes MADAGASCAR (bullet) Antsiranana: 57–58 km N of Ambanja, 13°22′59.9″S, 48°48′E, 22 May 1974, A.H. Gentry 11878 (L-WAG.1111448!, L-WAG.1111449!, MO-358489!, TAN) (bullet) Ampasindava, forêts d’Ambilanivy et Rangoty, 13°48′36″S, 48°10′48″E, 29 November 2007, L. Nusbaumer 2658 (G334213/1!, MO!, TAN) (bullet) Mahajanga: Morafenobe, Beravy, 15 km from Beravy, near the road from Orombato to Beravy, 18°3′50″S, 44°31′46″E, 09 June 2016, F. Rakotonasolo et al. 2772 (K, P00782931!, TAN).Diagnosis Similar to Ravenala madagascariensis but differs in its dark green narrower laminae, tricolor petioles with very developed dryish petiole sheath margins, very waxy petioles, the persistence of older infructescences for several years, a purple stripe on the bract margin, longer bracts, a whitish perianth, brown blotches on its mature fused petals, the bracteole apex tinged with pink, an ovoid pointed stigma, dense infructescences, smaller inflorescences, the free petal much shorter than the fused petals, and an end of year flowering period.Distribution Plants restricted to Madagascar, growing in the north-western part of the island. We observed it growing from the southern part of the Diego Suarez area (on the hills along the road leading to Tsingy Rouge and the city of Sadjoavato) in the north to the western part of the Mahajanga province down to the Melaky region, with most observations around Ambanja34. We also observed that the species was cultivated on Nosy Be.Preliminary IUCN assessments We propose a Least Concern status for R. agatheae, having an E.O.O ( > 20,000) km2 and an A.O.O. ( > 2,000) km2 (criterion B)33.Ecology This species is adapted to seasonally dry and warm coastal habitats, growing on slopes at low elevations in north-western coastal areas of Madagascar, from Antsiranana (Diego-Suarez) down to the Melaky region in the Mahajanga province.Etymology This species is named after to the first author’s wife, Agathe Haevermans, a botanical illustrator at the Muséum National d’Histoire Naturelle, who helped discover this species in the field with the collecting team and who contributes greatly to botany by producing illustrations of new taxa from biodiversity hotspots such as Madagascar.Description Plants suckering, 6–10 meters tall (adult), trunk circumference (d.b.h.) 20–30 cm, juvenile and adult laminae distributed like a regular fan, 9–22 leaves simultaneously alive on the adult plant, 1–3 leaves between inflorescences. Leaves adult petiole 300–460 cm long, tricolor (dark green with a waxy white strip and red petiole sheath margin subsequently drying out, Fig. 3a), very waxy, sheath margin very developed (10 mm and more), entire, dryish-papyraceous and protruding at 90 degrees, petiole/lamina ratio 1.7–(1.95)–2.2, adult lamina 174–(210 times 72)–86 cm, dark green, juvenile lamina base non-decurrent. Inflorescences 4–6 live lateral inflorescences at a time, 70–(90 times 90)–100 cm (peduncle excluded), 10–14 bracts per inflorescence, bracts 450–500 (times 80)– 90 mm, with some waxiness (Fig. 4a), margin bearing a purple stripe, cincinnii of 8–10 flowers per bract, flowering sequentially, some pink tinge at the apex of bracteoles. Flowers 260–310 mm long (ovary included), inferior ovary 40–60 mm long, perianth whitish, sepals narrowly triangular 220–250(times)ca. 10 mm, sheathing (fused) petals narrowly triangular 200–(220times)ca. 10 mm, free petal acicular 130–(140 times 5) mm, much smaller than the remaining perianth with a mean free petal / mean fused petal length ratio = 0.6, petal blotches present, stamens (roughly) the same size as the perianth, 210–220 mm long, style 220 mm long, stigma 15 mm long, ovoid-pointed with basal constriction. Infructescences compact (bracts bases imbricate at all stages of maturity), stiff and coriaceous persisting bracts on mature infructescence, persistence of old infructescences, 4–10 fruits per bract. Fruits 90–110 (times) 30–45 mm, trilocular septifragal capsule, apices conical (Fig. 2a), seeds shiny, dark brown, mostly globose, varying in shape according to their distribution in the capsule, ultramarine blue aril.
    Ravenala blancii Haev., V. Jeannoda & A. Hladik sp. nov. —Figs. 2b, 3b, 4b, 5b, 7
    Type MADAGASCAR (bullet) Andasibe; 18°56′00″S, 48°25′06″E; 940 m elev.; 01 December 2002; A. Hladik & C.-M. Hladik 6760 (Holotype: TAN!, Isotypes: K!, MO!, P!).Paratypes MADAGASCAR (bullet) Andasibe; 18°56′00″S, 48°25′06″E; 940 m elev., 23 Aug. 1998, A. Hladik & al. 6239 (P!, fruits) (bullet) June 2001, A. Hladik & al. 6650 (P!, leaves, fruits, bracts) (bullet) Andasibe-Mantadia area, Vakôna, Kalonora; 18°53′17.3″S, 48°25′51.3″E, 08 November 2018, 934 m elev., T. Haevermans & al. 832 (K!, MO!, P!, TAN!).Diagnosis Similar to Ravenala madagascariensis but differs in its non-suckering habit, decurrent juvenile lamina bases, toroidal distribution of juvenile laminae, smaller number of leaves simultaneously alive on the adult plant, dark green lamina and green non waxy petiole, smaller leaves, smaller number of live inflorescences, smaller number of bracts in an inflorescence, non-waxy bracts, sub-simultaneous flowering, smaller flowers, smaller inflorescences, non-persistence of entire bracts on dry infructescences, October/November flowering period.Distribution Andasibe-Mantadia, Ranomafana21. Restricted to Madagascar.Preliminary IUCN assessments We propose a Data Deficient status for R. blancii; further fieldwork is required to understand its precise distribution and the status of its populations33.Ecology High-elevation species found in eastern rainforests at elevations between 600 and 1,100 m. The species seems to favor cool tropical humid and shady conditions.Etymology This species is named after Dr. Patrick Blanc, world renowned botanist, plant ecologist and street artist, inventor of the planted vertical walls known as “Mur Végétal” and who first recognized the sheer originality of the juvenile phases of this peculiar taxon.Description Plants solitary (never suckering), 10–15 meters tall (adult), trunk circumference (d.b.h.) 20–30 cm, juvenile laminae distributed in a toroidal shape, adult laminae arranged in a regular fan, 9–16 leaves simultaneously alive on the adult plant, 2–4 leaves between inflorescences. Leaves adult petiole 240–310 cm long, green, not waxy, sheath margin undeveloped, entire, not drying, smooth with a worn-out irregular aspect (Fig. 3b), petiole/lamina ratio 1.8–(2.0)–2.2, adult lamina 120–160 (times) 90–104 cm, dark green, juvenile lamina base decurrent. Inflorescences 2–3 live lateral inflorescences at a time, (60 times 70) cm (peduncle excluded), 4–6 bracts per inflorescence, bracts 160–350 (times) 50–90 mm, no waxiness (Fig. 4b), margin color uniformly green, cincinnii of 5–14 flowers per bract, flowering sub-simultaneously, bracteoles sometimes pink colored. Flowers 165–280 mm long (ovary included), inferior ovary 40–50 mm long, perianth whitish-yellowish, sepals narrowly triangular 125–231 (times) 10–12 mm, sheathing (fused) petals narrowly triangular 105–190 (times 10) mm, free petal acicular 105–178 (times 3)–5 mm, free petal and fused petals of sub-equal size with a mean free petal / mean fused petal length ratio = 1.0, petal blotches absent or present, stamens (roughly) the same size as the perianth, 115–186 mm long, style 132–220 mm long, stigma 20-25 mm long, ovoid to ovoid-pointed with a basal constriction. Infructescences compact (bract bases imbricate at all stages of maturity), torn and degraded bracts on mature infructescence, old infructescences deciduous, 5–14 fruits per bract. Fruits 80–120 (times) 32–45 mm, trilocular septifragal capsule, apices conical (Fig. 2b), seeds 6–10 (times) 3.2–6 mm, shiny, dark brown, mostly globose, varying in shape according to their distribution in the capsule, ultramarine blue aril.Note The strong leaf dimorphism between juvenile and adult forms is characteristic of this species13, a phenomenon which is not present in the other taxa. The base of the juvenile plant usually grows buried in the leaf litter due to the action of traction roots13, its decurrent leaves (Fig. 7) giving it the aspect of a bird’s nest fern.Figure 7Ravenala blancii. (a) juvenile plant habit with roots. (b) juvenile plant showing the arrangement of laminae. (c) adult plant habit. (d) mature infructescence segment. (e) juvenile leaf showing the attenuate base of the lamina. (f) inflorescence with sub-simultaneous opening of the flowers. (g) young infructescence with already degraded bracts. (h) seeds with arilla. (i) open flower. (j) details of the stigma. (k) style. Ink drawings on (75 , upmu) polyester tracing paper by Agathe Haevermans© from specimens Hladik 6790, 6239, 6650, Haevermans et al. 832, and observations in-situ.Full size image
    Ravenala grandis Haev., Razanats., A. Hladik & P. Blanc sp. nov.—Figs. 2c, 3c, 4c, 5cType. MADAGASCAR (bullet) Ampasimbe Commune, Maromaniry Fokontany, along Route Nationale, 18°57′41.8″S, 48°42′41.4″E, 258 m elev., 08 November 2018, T. Haevermans, A. Haevermans & J. Razanatsoa 831 (Holotype: TAN!, Isotypes: K!, MO!, P!).Paratypes MADAGASCAR (bullet) Varifoana, près d’Ambohimahasoa-sud, 15 May 1964, R. Capuron 26014SF (P02234597!) (bullet) Soanierana-Antasibe[Andasibe], 350 m elev., 10 December 1938, H.J. Lam & A.D.J. Meeuse 5867 (L-WAG.1111450!, L-WAG.1111451!, L-WAG.1111452!, L-WAG.1111453!, L-L.1477714!, L-L.1477715!).Diagnosis Similar to Ravenala madagascariensis but differs in its non-suckering habit, much larger dimensions, very thick leathery laminae, very waxy dark green-yellowish petioles, much larger bracts and overall dimensions, whitish/pure white perianth, strong reddish-pink stripes on its bracteoles, cylindrical stigma without basal constriction, stamens much shorter than perianth, and fruit with a truncated apex.Distribution Eastern rainforests at around 200–500 m elevation in Madagascar13,20.Preliminary IUCN assessments We propose a Data Deficient status for R. grandis; further fieldwork is required to understand its precise distribution and the status of its populations33.Ecology This species seems to favor growing in low discontinuous forests on inselbergs12 and thrives in secondary degraded vegetation on the slopes of eastern rain forests.Etymology The name of this species is in reference to its stature and habit, the most robust species of Ravenala known.Description Plants solitary (never suckering), 20–30 meters tall (adult), trunk circumference (d.b.h.) 30 cm, juvenile and adult laminae distributed in a perfect fan, 15–30 leaves simultaneously alive on the adult plant, usually 3 leaves between inflorescences. Leaves adult petiole 390–440 cm long, dark green/light green-yellowish, very waxy (Fig. 3c), sheath margin moderately developed to undeveloped (0–9 mm), entire on young leaves, splitting and dryish when old, petiole/lamina ratio 1.8–(2.2)–2.6, adult lamina 170–230 (times) 94–120 cm, light green, juvenile lamina base non-decurrent. Inflorescences 4–6 live lateral inflorescences at a time, 100–120 (times) 80–100 cm (peduncle excluded), 10–20 bracts per inflorescence, bracts 440–540 (times) 140–170 mm, some waxiness (Fig. 4c), margin color uniformly green, cincinnii of ca. 20 flowers per bract, flowering sequentially, bracteoles with a strong reddish-pink stripe. Flowers 300 mm long (ovary included), inferior ovary 50–70 mm long, perianth whitish/pure white, sepals narrowly triangular 220–240 (times) 10–15 mm, sheathing (fused) petals narrowly triangular 210–220 (times) 10–12 mm, free petal acicular 150–170 (times 3) mm, slightly smaller than the rest of the perianth with a mean free petal / mean fused petal length ratio = 0.8, petal blotches absent, stamens much shorter than the perianth, 180–200 mm long, style 180–210 mm long, stigma 14–16 mm long, oblong without basal constriction (almost indistinguishable from style). Infructescences lax (bract bases not imbricate at some stages of maturity), stiff and coriaceous persisting bracts on mature infructescence, old infructescences deciduous, 5–18 fruits per bract. Fruits 100–120 (times) 35–40 mm, trilocular septifragal capsule, apices truncate (Fig. 2c), seeds shiny, dark brown, mostly globose, varying in shape according to their distribution in the capsule, ultramarine blue aril.Note The leaves of this species are the most robust and tough of all Ravenala species, with a thick leathery texture, making it the material of choice for building roofs35.
    Ravenala hladikorum Haev., Razanats., V. Jeannoda & P. Blanc sp. nov. — Figs. 2f, 3f, 4f, 5fType MADAGASCAR (bullet) Andasibe; 18°56′00″S, 48°25′06″E; 940 m elev.; 05 February 2004; A. Hladik & C.-M. Hladik 6842 (Holotype: TAN!, Isotype: P!). Paratypes. MADAGASCAR (bullet) Andasibe; 18°56′00″S, 48°25′06″E; 940 m elev.; 23 August 1998; A. Hladik & al. 6240 (fruit with seeds: P!). (bullet) Andasibe-Mantadia area, Vakôna, Kalonora; 18°53′17.3″S, 48°25′51.3″E; 934 m elev., 08 November 2018; T. Haevermans & al. 833 (TAN!, P!, K!, MO!).Diagnosis Similar to Ravenala madagascariensis but differs in its non-suckering habit, the alternate positioning of its adult laminae, its dark green leaves, non-waxy petioles with their very papyraceous petiole sheath margins, more than 1 cm long, smaller lamina dimensions, smaller number of simultaneously live inflorescences, purple stripe on bracts and on bracteoles, non-waxy inflorescences, smaller inflorescences, dense infructescences, truncated fruit apices, and short flowering period from November to December.Distribution Andasibe, Mantady, Ranomafana21. Restricted to Madagascar.Preliminary IUCN assessments We propose a Data Deficient status for R. hladikorum; further fieldwork is required to understand its precise distribution and the status of its populations33.Ecology High-elevation species found in eastern rainforests at elevations between 600 and 1100 m. The species seems to favor cool tropical humid and shady conditions.Etymology This species is named in honor of Annette and Claude-Marcel Hladik from the Muséum National d’Histoire Naturelle in Paris, who dedicated their lives to the study of Madagascan biodiversity and contributed greatly to the discovery of this species.Description Plants solitary (never suckering), 10–15 meters tall (adult), trunk circumference (d.b.h.) 20–30 cm, juvenile laminae distributed like a fan, adult laminae arranged in an irregular fan, 9–18 leaves simultaneously alive on the adult plant, 1–3 leaves between inflorescences. Leaves adult petiole 280–440 cm long, greenish-yellow, not waxy (Fig. 3f), sheath margin very developed (10 mm and more), split, very papyraceous with min. 1 cm brown dry expansions, petiole/lamina ratio 2.1–(2.42)–2.8, adult lamina 120–160 (times) 102–116 cm, dark green, juvenile lamina base non-decurrent. Inflorescences 2–3 live lateral inflorescences at a time, (60 times 90) cm (peduncle excluded), 4–7 bracts per inflorescence, bracts 150–510 (times) 64–100 mm, no waxiness (Fig. 4f), margin green with a purple stripe, cincinnii of 5–14 flowers per bract, sequentially flowering, bracteoles with a dark purple colored stripe. Flowers 240–320 mm long (ovary included), inferior ovary 40–60 mm long, perianth whitish, sepals narrowly triangular 210–265(times)ca. 10 mm, sheathing (fused) petals narrowly triangular 190–240(times)ca. 10 mm , free petal acicular 135–220 (times) 5 mm, almost the same size as the fused petals with a mean free petal / mean fused petal length ratio = 0.9, petal blotches unknown, stamens (roughly) the same size as the perianth, 170–230 mm long, style 187–250 mm long, stigma 20–25 mm long, ovoid with a basal constriction. Infructescences compact (bract bases imbricate at all stages of maturity), stiff and coriaceous persistent bracts on mature infructescences, old infructescences deciduous, 5–14 fruits per bract. Fruits 82–108 (times) 34–48 mm, trilocular septifragal capsule, apices truncate (Fig. 2f), seeds 4–9 (times) 3–6 mm, shiny, dark brown, mostly globose, varying in shape according to their distribution in the capsule, ultramarine blue aril.
    Ravenala menahirana Haev. & Razanats. sp. nov.—Figs. 2e, 3e, 4e, 5eType MADAGASCAR (bullet) Foulpointe, Analalava Forest; 17°42.3′S, 49°27.38′E; 50 m elev.; 20 March 2016; T.Haevermans, M. Vorontsova, S. Dransfield & J. Razanatsoa 826 (Holotype: TAN!, Isotypes: P!, K !, MO!).Diagnosis Similar to Ravenala madagascariensis but differs in its non-suckering habit, the alternate dark green laminae tending not to form a perfect fan (Fig. 5e), dark red petioles with a zigzagging well developed dryish sheath margin, more strongly obovoid laminae, smaller number of simultaneously live inflorescences, smaller inflorescences tinged with red, pure white/whitish perianth, smaller flowers, dense infructescences, the fruit apices truncate with a mucro, and subequal free and fused petals.Distribution Appears to be restricted to the east coast in the area around Analalava-Foulpointe up to the Mananara-Avaratra area. Two human observations from Marojejy (North-East) and Tampolo (Masoala) seem also to be this species. Restricted to Madagascar.Preliminary IUCN assessments We propose a Data Deficient status for R. menahirana; further fieldwork is required to understand its precise distribution and the status of its populations33.Ecology This coastal forest-dwelling species favors low-elevation tropical humid conditions in the Analalava-Foulpointe area, extending north to Mananara-Avaratra area, and maybe up to Marojejy.Etymology The name of this species is in reference to one of its local names “menahirana”, given to the species in the Analalava-Foulpointe area and meaning “red ravenala”.Description Plants solitary (never suckering), 6–10 meters tall (adult), trunk circumference (d.b.h.) 20–30 cm, juvenile laminae distributed like a fan, adult laminae arranged in an irregular to regular fan, 12–18 leaves simultaneously alive on the adult plant, 3 leaves between inflorescences. Leaves adult petiole 200–230 cm long, dark red, slightly to very waxy, sheath margin very developed (10 mm and more), red, entire, forming a three dimensional zigzag pattern (Fig. 3e), then splitting and drying on old leaves, petiole/lamina ratio 1.4–(1.7)–1.9, adult lamina (350 times 120) cm, lamina color dark green, juvenile lamina base non-decurrent. Inflorescences 1–2 live lateral inflorescences at a time, (60 times 70) cm (peduncle excluded), 10–12 bracts per inflorescence, bracts 260–360 (times) 50–80 mm, very waxy (Fig. 4e), margin color uniformly reddish-green, cincinnii of 8–12 flowers per bract, flowering sequentially, no colored stripe on bracteoles (apices sometimes suffused with pink). Flowers 220–250 mm long (ovary included), inferior ovary 40–60 mm long, perianth pure white to whitish, sepals narrowly triangular 180–230 (times) 12–16 mm, sheathing (fused) petals narrowly triangular 160–180 (times) 5 mm, free petal acicular 160–170 (times) 5 mm, free petal the same size as the remaining perianth with a mean free petal / mean fused petal length ratio = 1.0, petal blotches absent, stamens the same size (roughly) as the perianth, stamen 150–160 mm long, style 150–200 mm long, stigma 10 mm long, oblong with a basal constriction. Infructescences compact (bract bases imbricate at all stages of maturity), stiff and coriaceous persisting bracts on mature infructescences, old infructescences deciduous, 8–12 fruits per bract. Fruits 80–100 (times) 30–35 mm, trilocular septifragal capsule, apices truncate with a mucro (Fig. 2e), seeds shiny, dark brown, mostly globose, varying in shape according to their distribution in the capsule, ultramarine blue aril.Note This species is similar to R. hladikorum but is easily distinguished by, in addition to its petioles and its ecology, its truncate mucronate fruit apices, the shape of the synflorescence bracts and the absence of a red stripe on the cyme bracteoles.Identification key to the species of genus Ravenala More