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    Predicting potential global and future distributions of the African armyworm (Spodoptera exempta) using species distribution models

    Zeder, M. A. The domestication of animals. J. Anthropol. Res. 68, 161–190 (2012).Article 

    Google Scholar 
    Zohary, D. & Hopf, M. Domestication of Plants in the Old World: The Origin and Spread of Cultivated Plants in West Asia, Europe and the Nile Valley (Oxford University Press, 2000).
    Google Scholar 
    Epanchin-Niell, R., McAusland, C., Liebhold, A., Mwebaze, P. & Springborn, M. R. Biological invasions and international trade: Managing a moving target. Rev. Environ. Econom. Policy 15, 180–190 (2021).Article 

    Google Scholar 
    Gippet, J. M. & Bertelsmeier, C. Invasiveness is linked to greater commercial success in the global pet trade. Proc. Natl. Acad. Sci. 118, e2016337118 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bertelsmeier, C. Globalization and the anthropogenic spread of invasive social insects. Curr. Opin. Insect Sci. 46, 16–23 (2021).PubMed 
    Article 

    Google Scholar 
    Charles, H. & Dukes, J. S. Biological Invasions 217–237 (Springer, 2008).
    Google Scholar 
    Bellard, C., Cassey, P. & Blackburn, T. M. Alien species as a driver of recent extinctions. Biol. Let. 12, 20150623 (2016).Article 

    Google Scholar 
    Bertolino, S. et al. Spatially explicit models as tools for implementing effective management strategies for invasive alien mammals. Mamm. Rev. 50, 187–199 (2020).Article 

    Google Scholar 
    Grimaldi, D., Engel, M. S., Engel, M. S. & Engel, M. S. Evolution of the Insects (Cambridge University Press, 2005).MATH 

    Google Scholar 
    Hill, M. P., Clusella-Trullas, S., Terblanche, J. S. & Richardson, D. M. Vol. 18, 883–891 (Springer, 2016).Sawicka, B. & Egbuna, C. Natural Remedies for Pest, Disease and Weed Control 1–16 (Elsevier, 2020).Book 

    Google Scholar 
    de la Vega, G. J. & Corley, J. C. Drosophila suzukii (Diptera: Drosophilidae) distribution modelling improves our understanding of pest range limits. Int. J. Pest Manag. 65, 217–227 (2019).Article 

    Google Scholar 
    Kriticos, D. J. et al. The potential distribution of invading Helicoverpa armigera in North America: Is it just a matter of time? PLoS ONE 10, e0119618 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Early, R., González-Moreno, P., Murphy, S. T. & Day, R. Forecasting the global extent of invasion of the cereal pest Spodoptera frugiperda, the fall armyworm. NeoBiota 40, 25–50 (2018).Article 

    Google Scholar 
    Day, R. et al. Fall armyworm: Impacts and implications for Africa. Outlooks Pest Manag. 28, 196–201 (2017).Article 

    Google Scholar 
    Rose, D. D. & Page, W. W. The African Armyworm Handbook 304 (Chatham, 2000).
    Google Scholar 
    De Groote, H. et al. Spread and impact of fall armyworm (Spodoptera frugiperda JE Smith) in maize production areas of Kenya. Agric. Ecosyst. Environ. 292, 106804 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Cheke, R. & Tucker, M. An evaluation of potential economic returns from the strategic control approach to the management of African armyworm Spodoptera exempta (Lepidoptera: Noctuidae) populations in eastern Africa. Crop Prot. 14, 91–103 (1995).Article 

    Google Scholar 
    Fox, K. Migrant Lepidoptera in New Zealand 1972–1973. N. Z. Entomol. 5, 268–271 (1973).Article 

    Google Scholar 
    Baker, G. An Outbreak of Spodoptera exempta (Walker) (Lepidoptera: Noctuidae) in the Highlands of Papua New Guinea (1978).Haggis, M. J. Distribution, Frequency of Attack and Seasonal Incidence of the African Armyworm Spodoptera exempta (Walk.) (Lep.: Noctuidae), with Particular Reference to Africa and Southwestern Arabia (Tropical Development and Research Institute, 1984).
    Google Scholar 
    Brown, E. Control of the African armyworm, Spodoptera exempta (Walk.)—An appreciation of the problem. East Afr. Agric. For. J. 35, 237–245 (1970).Article 

    Google Scholar 
    Rose, D. & Rainey, R. C. The significance of low-density populations of the African armyworm Spodoptera exempta (Walk.). Philos. Trans. R. Soc. Lond. B Biol. Sci. 287, 393–402 (1979).ADS 
    Article 

    Google Scholar 
    Tucker, M. & Pedgley, D. Rainfall and outbreaks of the African armyworm, Spodoptera exempta (Walker) (Lepidoptera: Noctuidae). Bull. Entomol. Res. 73, 195–199 (1983).Article 

    Google Scholar 
    Tucker, M. Forecasting the severity of armyworm seasons in East Africa from early season rainfall. Int. J. Trop. Insect Sci. 5, 51–55 (1984).Article 

    Google Scholar 
    Wilson, K. & Gatehouse, A. Seasonal and geographical variation in the migratory potential of outbreak populations of the African armyworm moth, Spodoptera exempta. J. Anim. Ecol. 62, 169–181 (1993).Article 

    Google Scholar 
    Odiyo, P. O. Development of the first outbreaks of the African armyworm, Spodoptera exempta (Walk.), between Kenya and Tanzania during the ‘off-season’ months of July to December. Int. J. Trop. Insect Sci. 1, 305–318 (1981).Article 

    Google Scholar 
    Haggis, M. Forecasting the severity of seasonal outbreaks of African armyworm, Spodoptera exempta (Lepidoptera: Noctuidae) in Kenya from the previous year’s rainfall. Bull. Entomol. Res. 86, 129–136 (1996).Article 

    Google Scholar 
    Harvey, A. & Mallya, G. Predicting the severity of Spodoptera exempta (Lepidoptera: Noctuidae) outbreak seasons in Tanzania. Bull. Entomol. Res. 85, 479–487 (1995).Article 

    Google Scholar 
    Holt, J., Mushobozi, W., Tucker, M. & Venn, J. Workshop on Research Priorities for Migrant Pests of Agriculture in Southern Africa, 151.Matthew Hill, T. C. M. Bloomberg (Online, 2017).Wilson, K. The Conversation (United Kingdom, 2017).Day, R. K. et al. WormBase: A data management and information system for forecasting Spodoptera exempta (Lepidoptera: Noctuidae) in eastern Africa. J. Econ. Entomol. 89, 1–10 (1996).Article 

    Google Scholar 
    Guisan, A. & Thuiller, W. Predicting species distribution: Offering more than simple habitat models. Ecol. Lett. 8, 993–1009 (2005).PubMed 
    Article 

    Google Scholar 
    Elith, J. & Leathwick, J. R. Species distribution models: Ecological explanation and prediction across space and time. Annu. Rev. Ecol. Evol. Syst. 40, 677–697 (2009).Article 

    Google Scholar 
    Bosso, L. et al. The rise and fall of an alien: Why the successful colonizer Littorina saxatilis failed to invade the Mediterranean Sea. Biol. Invas. https://doi.org/10.1007/s10530-022-02838-y (2022).Article 

    Google Scholar 
    Sutherst, R. W. Pest species distribution modelling: Origins and lessons from history. Biol. Invas. 16, 239–256 (2014).Article 

    Google Scholar 
    Méndez-Vázquez, L. J., Lira-Noriega, A., Lasa-Covarrubias, R. & Cerdeira-Estrada, S. Delineation of site-specific management zones for pest control purposes: Exploring precision agriculture and species distribution modeling approaches. Comput. Electron. Agric. 167, 105101 (2019).Article 

    Google Scholar 
    Raffini, F. et al. From nucleotides to satellite imagery: Approaches to identify and manage the invasive pathogen Xylella fastidiosa and its insect vectors in Europe. Sustainability 12, 4508 (2020).CAS 
    Article 

    Google Scholar 
    Araújo, M. B. et al. Standards for distribution models in biodiversity assessments. Sci. Adv. 5, 4858 (2019).ADS 
    Article 

    Google Scholar 
    Hosmer, D. W. Jr., Lemeshow, S. & Sturdivant, R. X. Applied Logistic Regression Vol. 398 (Wiley, 2013).MATH 
    Book 

    Google Scholar 
    Landis, J. R. & Koch, G. G. The measurement of observer agreement for categorical data. Biometrics 33, 159–174 (1977).CAS 
    PubMed 
    MATH 
    Article 

    Google Scholar 
    Kalisa, W. et al. Assessment of climate impact on vegetation dynamics over East Africa from 1982 to 2015. Sci. Rep. 9, 1–20 (2019).ADS 
    CAS 
    Article 

    Google Scholar 
    Beck, H. E. et al. Present and future Köppen-Geiger climate classification maps at 1-km resolution. Sci. Data 5, 1–12 (2018).ADS 
    Article 

    Google Scholar 
    Mayaux, P., Bartholomé, E., Fritz, S. & Belward, A. A new land-cover map of Africa for the year 2000. J. Biogeogr. 31, 861–877 (2004).Article 

    Google Scholar 
    Marchant, R. et al. Drivers and trajectories of land cover change in East Africa: Human and environmental interactions from 6000 years ago to present. Earth Sci. Rev. 178, 322–378 (2018).ADS 
    Article 

    Google Scholar 
    Elith, J., Kearney, M. & Phillips, S. The art of modelling range-shifting species. Methods Ecol. Evol. 1, 330–342 (2010).Article 

    Google Scholar 
    Pemberton, C. E. Highlights in the history of entomology in Hawaii 1778–1963. Pac. Insects 6, 689–729 (1964).
    Google Scholar 
    Andow, D. A. Vegetational diversity and arthropod population response. Annu. Rev. Entomol. 36, 561–586 (1991).Article 

    Google Scholar 
    Andow, D. The extent of monoculture and its effects on insect pest populations with particular reference to wheat and cotton. Agr. Ecosyst. Environ. 9, 25–35 (1983).Article 

    Google Scholar 
    Oliveira, C., Auad, A., Mendes, S. & Frizzas, M. Crop losses and the economic impact of insect pests on Brazilian agriculture. Crop Prot. 56, 50–54 (2014).Article 

    Google Scholar 
    Furlong, M. J., Wright, D. J. & Dosdall, L. M. Diamondback moth ecology and management: Problems, progress, and prospects. Annu. Rev. Entomol. 58, 517–541 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    Howse, M. W., Haywood, J. & Lester, P. J. Bioclimatic modelling identifies suitable habitat for the establishment of the invasive European paper wasp (Hymenoptera: Vespidae) across the southern hemisphere. Insects 11, 784 (2020).PubMed Central 
    Article 

    Google Scholar 
    Rose, D., Dewhurst, C., Page, W. & Fishpool, L. The role of migration in the life system of the African armyworm Spodoptera exempta. Int. J. Trop. Insect Sci. 8, 561–569 (1987).Article 

    Google Scholar 
    Dewhurst, C. F., Page, W. W. & Rose, D. J. The relationship between outbreaks, rainfall and low density populations of the African armyworm, Spodoptera exempta, Kenya. Entomol. Exp. et Appl. 98, 285–294 (2001).Article 

    Google Scholar 
    Aguilon, D. J. & Velasco, L. R. Effects of larval rearing temperature and host plant condition on the development, survival, and coloration of African armyworm, Spodoptera exempta Walker (Lepidoptera: Noctuidae). J. Environ. Sci. Manag. 18, 54 (2015).Article 

    Google Scholar 
    David, W. & Ellaby, S. The viability of the eggs of the African army-worm, Spodoptera exempta in laboratory cultures. Entomol. Exp. Appl. 18, 269–280 (1975).Article 

    Google Scholar 
    He, L., Zhao, S., Ali, A., Ge, S. & Wu, K. Ambient humidity affects development, survival, and reproduction of the invasive fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), China. J. Econ. Entomol. 114, 1145–1158 (2021).PubMed 
    Article 

    Google Scholar 
    Janssen, J. Effects of the mineral composition and water content of intact plants on the fitness of the African armyworm. Oecologia 95, 401–409 (1993).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Shahzad, M. S. et al. Modelling population dynamics of army worm (Spodoptera litura F.) (Lepidoptera: Noctuiidae) in relation to meteorological factors in Multan, Punjab, Pakistan. Int. J. Agron. Agric. Res. 5, 39–45 (2014).
    Google Scholar 
    Garcia, A. G., Ferreira, C. P., Godoy, W. A. & Meagher, R. L. A computational model to predict the population dynamics of Spodoptera frugiperda. J. Pest. Sci. 92, 429–441 (2019).Article 

    Google Scholar 
    Hickling, R., Roy, D. B., Hill, J. K., Fox, R. & Thomas, C. D. The distributions of a wide range of taxonomic groups are expanding polewards. Glob. Change Biol. 12, 450–455 (2006).ADS 
    Article 

    Google Scholar 
    Vanhanen, H., Veteli, T. O., Paivinen, S., Kellomaki, S. & Niemela, P. Climate change and range shifts in two insect defoliators: Gypsy moth and nun moth-a model study. Silva Fennica 41, 621 (2007).Article 

    Google Scholar 
    Falk, W. & Hempelmann, N. Species favourability shift in Europe due to climate change: A case study for Fagus sylvatica L. and Picea abies (L.) Karst. based on an ensemble of climate models. J. Climatol. 2013, 1–18 (2013).Article 

    Google Scholar 
    Arora, R. & Dhawan, A. Climate Change and Insect Pest Management. Integrated Pest Management 44–60 (Scientific Publisher, 2013).
    Google Scholar 
    Andrew, N. R. & Hill, S. J. Effect of climate change on insect pest management. In Environmental Pest Management: Challenges for Agronomists, Ecologists, Economists and Policymakers, 197 (2017).De Boer, J. G. & Harvey, J. A. Range-expansion in processionary moths and biological control. Insects 11, 267 (2020).PubMed Central 
    Article 

    Google Scholar 
    Bras, A. et al. A complex invasion story underlies the fast spread of the invasive box tree moth (Cydalima perspectalis) across Europe. J. Pest. Sci. 92, 1187–1202 (2019).Article 

    Google Scholar 
    Araújo, M. B. et al. Heat freezes niche evolution. Ecol. Lett. 16, 1206–1219 (2013).PubMed 
    Article 

    Google Scholar 
    Barford, E. Crop pests advancing with global warming. Nature 10, 13644 (2013).
    Google Scholar 
    Bebber, D. P., Ramotowski, M. A. & Gurr, S. J. Crop pests and pathogens move polewards in a warming world. Nat. Clim. Change 3, 985–988 (2013).ADS 
    Article 

    Google Scholar 
    Rubenstein, D. I. The greenhouse effect and changes in animal behavior: Effects on social structure and life-history strategies. In Global Warming and Biological Diversity, 180–192 (1992).Karuppaiah, V. & Sujayanad, G. Impact of climate change on population dynamics of insect pests. World J. Agric. Sci. 8, 240–246 (2012).
    Google Scholar 
    Jakhar, B. et al. Influence of climate change on Helicoverpa armigera (Hubner) in pigeonpea. J. Agric. Ecol. 2, 25–31 (2016).
    Google Scholar 
    Akbar, S. M., Pavani, T., Nagaraja, T. & Sharma, H. Influence of CO 2 and temperature on metabolism and development of Helicoverpa armigera (Noctuidae: Lepidoptera). Environ. Entomol. 45, 229–236 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Magandana, T. P., Hassen, A. & Tesfamariam, E. H. Seasonal herbaceous structure and biomass production response to rainfall reduction and resting period in the semi-arid grassland area of South Africa. Agronomy 10, 1807 (2020).CAS 
    Article 

    Google Scholar 
    Gherardi, L. A. & Sala, O. E. Enhanced precipitation variability decreases grass-and increases shrub-productivity. Proc. Natl. Acad. Sci. 112, 12735–12740 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Scheiter, S. & Higgins, S. I. Impacts of climate change on the vegetation of Africa: An adaptive dynamic vegetation modelling approach. Glob. Change Biol. 15, 2224–2246 (2009).ADS 
    Article 

    Google Scholar 
    Hernandez, P. A., Graham, C. H., Master, L. L. & Albert, D. L. The effect of sample size and species characteristics on performance of different species distribution modeling methods. Ecography 29, 773–785 (2006).Article 

    Google Scholar 
    Jiménez-Valverde, A., Lobo, J. & Hortal, J. The effect of prevalence and its interaction with sample size on the reliability of species distribution models. Community Ecol. 10, 196–205 (2009).Article 

    Google Scholar 
    Renault, D., Laparie, M., McCauley, S. J. & Bonte, D. Environmental adaptations, ecological filtering, and dispersal central to insect invasions. Annu. Rev. Entomol. 63, 345–368 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Ellis, S. New pest response guidelines: Spodoptera. USDA/APHIS/PPQ/PDMP (2004).Waage, J. & Mumford, J. D. Agricultural biosecurity. Philos. Trans. R. Soc. B Biol. Sci. 363, 863–876 (2008).CAS 
    Article 

    Google Scholar 
    Anand, M. A systems approach to agricultural biosecurity. Health Secur. 16, 58–68 (2018).PubMed 
    Article 

    Google Scholar 
    MacLeod, A., Pautasso, M., Jeger, M. J. & Haines-Young, R. Evolution of the international regulation of plant pests and challenges for future plant health. Food Secur. 2, 49–70 (2010).Article 

    Google Scholar 
    Jiménez-Valverde, A. et al. Use of niche models in invasive species risk assessments. Biol. Invas. 13, 2785–2797 (2011).Article 

    Google Scholar 
    Oluwole, F. A., Sambo, J. M. & Sikhalazo, D. Long-term effects of different burning frequencies on the dry savannah grassland in South Africa. Afr. J. Agric. Res. 3, 147–153 (2008).
    Google Scholar 
    Kalleshwaraswamy, C. et al. First Report of the Fall Armyworm, Spodoptera frugiperda (JE Smith) (Lepidoptera: Noctuidae), an Alien Invasive Pest on Maize in India (2018).Bentivenha, J., Baldin, E., Hunt, T., Paula-Moraes, S. & Blankenship, E. Intraguild competition of three noctuid maize pests. Environ. Entomol. 45, 999–1008 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Chapman, J. W. et al. Fitness consequences of cannibalism in the fall armyworm, Spodoptera frugiperda. Behav. Ecol. 10, 298–303 (1999).Article 

    Google Scholar 
    Divya, J., Kalleshwaraswamy, C., Mallikarjuna, H. & Deshmukh, S. Does recently invaded fall armyworm, Spodoptera frugiperda displace native lepidopteran pests of maize in India? Curr. Sci. 120, 1358 (2021).Article 

    Google Scholar 
    Hailu, G. et al. Could fall armyworm, Spodoptera frugiperda (JE Smith) invasion in Africa contribute to the displacement of cereal stemborers in maize and sorghum cropping systems. Int. J. Trop. Insect Sci. 41, 1753–1762 (2021).Article 

    Google Scholar 
    Srivastava, V., Lafond, V. & Griess, V. C. Species distribution models (SDM): Applications, benefits and challenges in invasive species management. CAB Rev. 14, 1–13 (2019).Article 

    Google Scholar 
    Fick, S. E. & Hijmans, R. J. WorldClim 2: New 1-km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302–4315 (2017).Article 

    Google Scholar 
    Eyring, V. et al. Overview of the coupled model intercomparison project phase 6 (CMIP6) experimental design and organization. Geosci. Model Dev. 9, 1937–1958 (2016).ADS 
    Article 

    Google Scholar 
    Wu, T. et al. The Beijing Climate Center climate system model (BCC-CSM): The main progress from CMIP5 to CMIP6. Geosci. Model Dev. 12, 1573–1600 (2019).ADS 
    Article 

    Google Scholar 
    O’Neill, B. C. et al. The roads ahead: Narratives for shared socioeconomic pathways describing world futures in the 21st century. Glob. Environ. Change 42, 169–180 (2017).Article 

    Google Scholar 
    Petitpierre, B., Broennimann, O., Kueffer, C., Daehler, C. & Guisan, A. Selecting predictors to maximize the transferability of species distribution models: Lessons from cross-continental plant invasions. Glob. Ecol. Biogeogr. 26, 275–287 (2017).Article 

    Google Scholar 
    Cano, J. et al. Modelling the spatial distribution of aquatic insects (Order Hemiptera) potentially involved in the transmission of Mycobacterium ulcerans in Africa. Parasit. Vectors 11, 1–16 (2018).Article 

    Google Scholar 
    Gómez-Undiano, I. Modelos y patrones de distribución geográfica de especies de Culicidae (Culex pipiens, Mansonia africana y Mansonia uniformis) vectores de filariasis linfática en ámbitos urbanos y periurbanos del África subsahariana. Máster en Zoología thesis, Universidad Complutense de Madrid (2018).R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2020).Phillips, S. J. et al. Sample selection bias and presence-only distribution models: Implications for background and pseudo-absence data. Ecol. Appl. 19, 181–197 (2009).PubMed 
    Article 

    Google Scholar 
    Elith, J. et al. Novel methods improve prediction of species’ distributions from occurrence data. Ecography 29, 129–151 (2006).Article 

    Google Scholar 
    Barbet-Massin, M., Jiguet, F., Albert, C. H. & Thuiller, W. Selecting pseudo-absences for species distribution models: How, where and how many? Methods Ecol. Evol. 3, 327–338 (2012).Article 

    Google Scholar 
    Thuiller, W., Lafourcade, B., Engler, R. & Araújo, M. B. BIOMOD—A platform for ensemble forecasting of species distributions. Ecography 32, 369–373 (2009).Article 

    Google Scholar 
    Thuiller, W. et al. Package ‘biomod2’. Species Distribution Modeling Within an Ensemble Forecasting Framework (2016).Acevedo, P., Jiménez-Valverde, A., Lobo, J. M. & Real, R. Delimiting the geographical background in species distribution modelling. J. Biogeogr. 39, 1383–1390 (2012).Article 

    Google Scholar 
    VanDerWal, J., Shoo, L. P., Graham, C. & Williams, S. E. Selecting pseudo-absence data for presence-only distribution modeling: How far should you stray from what you know? Ecol. Model. 220, 589–594 (2009).Article 

    Google Scholar 
    Hijmans, R., Phillips, S., Leathwick, J. & Elith, J. (2012).Araújo, M. B. & New, M. Ensemble forecasting of species distributions. Trends Ecol. Evol. 22, 42–47 (2007).PubMed 
    Article 

    Google Scholar 
    Gama, M., Crespo, D., Dolbeth, M. & Anastácio, P. M. Ensemble forecasting of Corbicula fluminea worldwide distribution: Projections of the impact of climate change. Aquat. Conserv. Mar. Freshw. Ecosyst. 27, 675–684 (2017).Article 

    Google Scholar 
    Liu, C., White, M., Newell, G. & Griffioen, P. Species distribution modelling for conservation planning in Victoria, Australia. Ecol. Model. 249, 68–74 (2013).Article 

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    How a COVID lockdown changed bird behaviour

    Sightings of some common bird species increased during the UK’s 2020 lockdown.Credit: Tolga Akmen/AFP via Getty

    People weren’t the only ones who changed their ways during the COVID-19 pandemic — birds did, too. Four out of five of the most commonly observed birds in the United Kingdom altered their behaviour during the nation’s first lockdown of 2020, although they did so in different ways depending on the species, according to an analysis.The study, published in Proceedings of the Royal Society B on 21 September1, is one of several that used the disruptions brought about by the pandemic — from a reduction in the number of cars on the roads to the closure of some national parks — to quantify the impact that humanity has on the natural world. Although some research has found that lockdowns had a largely positive effect on wildlife2, the latest data from the United Kingdom provide a much more nuanced picture (see Bird Behaviour).

    Credit: Warrington et al/Proceedings of the Royal Society B

    “People didn’t disappear during the lockdown,” says co-author Miyako Warrington, a behavioural ecologist at the University of Manitoba in Winnipeg, Canada. “We changed our behaviour, and wildlife responded.”Rare experimentIn the early months of the pandemic, social media was abuzz with reports of wild animals being seen in unusual places. These claims were partially validated when Warrington and her colleagues reported that, in 2020, many bird species in the United States and Canada were spotted moving into spaces usually occupied by people2.To see how a COVID-19 lockdown affected birds in the United Kingdom, Warrington and her colleagues tallied sightings of the 25 most common birds between March and July 2020 — during the country’s first lockdown — and compared their data set with data from previous years. In total, the study included around 870,000 observations.The team then compared this information to data showing how people split their time between home, essential shops and parks: three places people in the United Kingdom were allowed to be during the lockdown.Because people spent more time at home and in parks than before March 2020, the analysis found that 20 of the 25 bird species examined behaved differently during lockdown. Parks — which were flooded with visitors — saw an an uptick in the numbers of corvids and gulls, whereas smaller birds, such as Eurasian blue tits (Cyanistes caeruleus) and house sparrows (Passer domesticus), were spotted less frequently than in previous years. And because people spent more time at home, the number of avian species that visited domestic gardens also dropped, by around one-quarter, compared with previous years.Other species, including rock pigeons (Columba livia), didn’t react to the lockdown at all. Warrington found this surprising, because pigeons are city dwellers, so she thought they would be affected by the changes in people’s behaviour. “But they don’t give a crap about what we do,” she says.Adapting to changeThe birds that altered their habits during the lockdown were probably responding to changes in human behaviour, says Warrington. Tits and other birds whose numbers dipped might have fled when people and their pets started spending more time in parks and gardens. The reverse could be true for scavengers, such as gulls and corvids, which might have benefited from park visitors leaving behind rubbish for them to feed on.When combined with the results of other studies, the behaviour of British birds reveals the complex ways in which wildlife was affected by lockdowns and underlines the importance of reducing the disturbance of animals by people, says Raoul Manenti, a conservation zoologist at the University of Milan in Italy.For Warrington, that means acknowledging that lockdowns were not universally good for wildlife. “Our relationship with nature is complicated,” she says. By developing a better understanding of this relationship, “we know we can affect positive change as long as we do it in a thoughtful manner”. More

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    Spatial distribution and interactions between mosquitoes (Diptera: Culicidae) and climatic factors in the Amazon, with emphasis on the tribe Mansoniini

    Changes in temperature and extreme environmental conditions can affect the dynamics of vector-borne pathogens. These include leishmaniasis, transmitted by phlebotomine sandflies, as well as mosquitoes that spread arboviruses like dengue, encephalitis, yellow fever, West Nile fever, and lymphatic filariasis19,20,21.The CCA analysis showed that maximum temperature significantly influenced the abundance of mosquito populations in the study area. In addition, the NMDS showed two different groupings that consisted of samples collected during the rainy and dry seasons. Accordingly, Refs.22,23 report that changes in temperature and relative humidity determine the abundance of mosquitoes, which can disappear entirely during the dry season. Moreover, Refs.22,24,25 note that certain species of mosquitoes increase proportionally with the regional rainfall regime. This is consistent with Ref.10, who find alternating patterns in tropical and temperate climates in some Brazilian regions.As shown by the geometric regression, there is a positive correlation between cumulative rainfall in the days before collection and the number of species found in the study period. Likewise, Ref.26 reported that under the conditions observed in the Serra do Mar State Park, climate variables directly influenced the abundance of Cq. chrysonotum and Cq. venezuelensis, favoring the occurrence of culicids during the more warm, wet, and rainy months.The current climate scenario and future projections about climate, environmental, demographic, and meteorological factors directly influence the distribution and abundance of mosquito vectors and/or diseases27,28,29,30. Environmental temperature alters mosquito population dynamics, thereby affecting the development of immature stages as well as reproduction31. While temperature has an important effect on population dynamics, rainfall and drought also affect the density and dispersal of mosquitoes in temperate and tropical regions32.To be sure, environmental changes other than climate can modify the behavior of vector insects and, subsequently, the mechanism of transmission of parasites20. Specifically, human impacts on the environment can result in drastically different disease transmission cycles in and around inhabited areas33.A previous study34 reported that changes in land use influence the mosquito communities with potential implications for the emergence of arboviruses. Another study35 noted that environmental changes negatively affect natural ecosystems with accelerated biodiversity loss. This is due to the modification and loss of natural habitat and unsustainable land use, which leads to the spread of pathogens and disease vectors.Hence, understanding the relationship between humans and the environment becomes increasingly critical, given the way in which climate changes can lead to alterations in the epidemiology of diseases such as dengue in areas considered free of the disease, as well as in endemic areas36.We found that the abundance and diversity of Mansoniini were directly influenced by the effect of the rainy season and other climatic factors. The rainfall regime has been shown to affect the development of immature forms12,37; explaining the greater frequency of these specimens in the warmer and wetter months38,39,40. According to Ref.41, stable ecosystems such as forests contain great species diversity. On the other hand, diversity tends to be reduced in biotic communities suffering from stress.Studies of insect populations in natural areas are important because they allow a direct analysis of how environmental factors influence phenomena such as the choice of breeding sites by females for oviposition, hematophagous behavior, and the distribution of species along a vegetation gradient12,26,42,43.Throughout the experimental period of the present study, we observed that Shannon light traps are an effective method for catching mosquitoes from the Mansoniini tribe. Interestingly, Ref.44 reported a species richness pattern strongly influenced by Coquillettidia fasciolata (Lynch Arribálzaga, 1891) on mosquito samples from different capture points by using CDC and Shannon light traps as sampling methods. In contrast to the results of Ref.44, where the highest population density of mosquitoes was captured with CDC traps, we observed that these traps were not effective at capturing specimens of Mansoniini in spite of being used in large numbers in the present study. Moreover, Ref.45 conducted another study on faunal diversity in an Atlantic Forest remnant of the state of Rio de Janeiro and observed the highest abundance of Cq. chrysonotum (Peryassú, 1922) and Cq. venezuelensis by using Shannon light traps, while the numbers of captures of Ma. titillans were very similar using CDC and Shannon traps.The results of this study indicate that the makeup of culicid fauna remains quite similar throughout the year, despite seasonal variations in abundance, though there was a lower variability of fauna in the dry season. Therefore, although the seasonality did not affect the temporal variation of the faunal composition in a generalized way, it was possible to detect a partial effect of the seasonality on fauna abundance.
    Reference46 report that the incidence peaks of mosquitoes in the warmer and wetter months, as well as mosquito populations remaining between tolerance limits for most of the year, indicate the sensitivity of some species to the local climate.The elevated abundance and diversity of species of Mansoniini in the study area were influenced by the favorable maintenance of breeding sites, including specific water accumulations with emerging vegetation that remain present throughout the year and the well-defined rainy season in the region. In addition, the representatives of Mansoniini, which prefer breeding sites containing macrophytes, made up nearly all of the species collected7.Besides providing a greater awareness of mosquito populations’ ecological and biological aspects, research carried out in wild areas also provides information on the relationship between species diversity and the area in which they are found. Considering that wild insects may become potential vectors of diseases, research in wild areas also provides helpful information for understanding relevant epidemiological aspects. These studies facilitate the identification, monitoring, and control of mosquito populations following environmental changes caused by direct human action, which can lead to major epidemics26.We observed considerable heterogeneity among Mansoniini fauna, and the months with the highest rainfall directly influence the structure of the communities and contribute to the increase in mosquito diversity and abundance, possibly due to variations in the availability of habitat for their immature forms. More

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    Save the world’s forest giants from infernos

    Gigantic trees occur in only a few regions on Earth. Some of the world’s largest eucalypts, for example, are on the island of Tasmania, off southeastern Australia. As wildfires increase in severity and frequency as a result of climate change, we urge the authorities to protect these trees by adopting measures similar to those applied to safeguard California’s redwood forests.
    Competing Interests
    The authors declare no competing interests. More

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    Signals of local bioclimate-driven ecomorphological changes in wild birds

    Study areaWe conducted field studies in both regions from August to March, each year from 2012 to 2016. In north India, we selected the two traditional breeding colonies of the Painted Storks, viz., the Delhi Zoo (28° 36′ N 77° 14′ E) and Keoladeo National Park (KNP) (27° 17′ N 77° 52′ E), Bharatpur, Rajasthan (Fig. 1). In the Delhi Zoo, close to the river Yamuna, the Painted Storks nest in the traditional heronries with other colonial nesters, Little Cormorant, Indian Cormorant, Black-headed Ibis, and Night Heron38. The KNP, a Ramsar site spread over 29 km2, situated at the confluence of the rivers Gambhir and Banganga on the western edge of the Gangetic basin, supports diverse fauna, flora, and a mosaic of habitats, wetlands, woodlands, scrub forests, grasslands, and heronries39. In 2013, we recorded 680 adults and 310 nests in the Delhi Zoo and 1584 adults and 430 nests of Painted Storks in the KNP.We selected the Vedanthangal Bird Sanctuary (VBS), the nesting colonies at Melmaruvathur Lake, and Koonthankulam Bird Sanctuary (KBS). The KBS & VBS are the newly declared Ramsar sites in Tamil Nadu, south India. The VBS (12° 32′ 02″ N and 79° 52′ 29″ E) is a 40.3-hectare community reserve effectively protected by the state Forest Department, Tamil Nadu, and Vedanthangal villagers40. It is the oldest breeding waterbird reserve in south India, located 85 km southwest of Chennai. More than 40 species of waterbirds, both residents and migrants, live here. Along with the other 17 heronry species, the Painted Storks build nests every year from November to April during its breeding season. The Painted Stork nesting colonies at Melmaruvathur Lake (12° 25′ 53″ N and 79° 49′ 36″ E) are about 20 km away from the VBS. Here, the Painted Storks build nests at 1.8–5 m above the water level, on trees of Acacia nilotica and Barringtonia acutangula on mounds surrounded by water41. In 2012, we recorded a total of 3185 nests in the VBS, with a maximum number of nests belonging to Spot-billed Pelican (1050 nests) followed by Painted Stork (550 nests), Asian Open-bill (770 nests), and others.Birds have been breeding in Melmaruvathur Lake since 2013, and we counted 80 nests of Spot-billed pelican, 45 nests of Oriental White Ibis, and 56 nests of Painted Stork during the winter of the year 2014. The Lake is spread over 0.19 km2 with islets (mounds) with four clusters of Acacia nilotica and Barringtonia acutangula trees. Rainwater and domestic sewage from the neighboring residential complex are the primary water source, and recreational boating attracts a large crowd visiting the Melmaruvathur temple41. KBS (8° 29′ 44″ N and 77° 45′ 30″ E) is about a 1.3 km2 protected area, declared a bird sanctuary in 1994 and an Important Bird Area40. It comprises Koonthankulam and Kadankulam irrigation tanks actively protected and managed by the local community. We noticed the frequent failures of breeding events due to water shortages related to monsoon failures in VBS and KBS. In 2015, we also observed Painted Storks’ breeding failure across northern India for unknown reasons; therefore, data could not be collected for those periods.Bioclimatic variablesWe obtained the bioclimatic variable, particularly temperature at 2 m height for all the four study sites, from the National Aeronautics and Space Administration (NASA) Langley Research Center (LaRC) Prediction of Worldwide Energy Resource (POWER) Project funded through the NASA Earth Science/Applied Science Program. The monthly average data from 2010 to 2020 was downloaded from the POWER Project’s Hourly 2.0.0 version on 2022/01/04.Digital images of Painted Storks collected under field conditionsUsing Binoculars (Olympus 10X50), Digital Cameras (Canon 5D Mark III and Sony handy-cam), we monitored and recorded all active nests with juveniles and adult Painted Storks twice a week. The nests were on trees, 3–7 m in height, and chicks and adults were visible, which aided the photography. Nests were numbered for our records by taking note of tree branching patterns, the nest’s position on the tree, and other local identification marks. Numbering the nests helped us identify the individuals associated with a given nest and avoided re-recording the same individual (pseudoreplication). Storks show site fidelity42,43, and hence we assumed the same breeding pairs occupied the same nesting site.During the initial months of the breeding seasons, pairing and copulations of the breeding pairs could be readily noticeable. We took consecutive photographs when they were copulating at the nest. After disengagement following the copulation, the birds (male and female) standing side by side at the nest were also photographed. The first author noted all the relevant spatial orientations of males and females during each copulation event in the field notes. Thus nearly 100 copulations involving different individuals of the Painted Storks pair were photographed. To minimize measurement errors, we selected for further analysis only the images of males and females standing parallel and close to each other, perpendicular to the camera. Since we used the digital images of the free-living Storks, we did not have the freedom to choose all morphological features resulting in some missing values. Therefore, we selected a hundred and forty-eight individuals for the analysis from nearly 1500 localized adults. The technique has an efficiency of less than 10% of the population, more efficient than the traditional capture, measure, and release of individuals. Though many individuals were recorded, only a few were subjected to the analyses. Moreover from the digital images, not all the morphological characters of the individuals were measured. The birds’ orientation towards the camera assumes importance because the correct direction ensures maximum exposure of body parts in the picture. In many pictures, correct orientation was missing as the birds were behind other individuals or branches of the trees or leaves. Therefore, selecting the right digital image becomes crucial. Keeping all the above criteria, we filtered images that were later included in the analysis.Calibrations of subject-distance using Exif MetadataWe extracted the EXIF metadata from each JPEG image of Painted Stork. EXIF metadata includes the filename, type, date, and time of the image captured, image width and height in pixels, camera model, lens information, field of view, focal length, and subject-distance. The subject-distance (Painted Stork distance from the camera) being a critical variable and its Exif metadata were standardized with the following equation.$${text{Subject{-}distance}} = 0.7864 times {text{(EXIF subject{-}distance)}}^{{1.0301}}$$
    (1)
    Using the Eq. (1) derived from an earlier study5, we regressed actual subject-distance with the Exif subject-distance from the images. Then multiplying with the field of view, available as Exif metadata (angle of view) with standardized subject-distance (Eq. 1), the total image size (length and width) in metric units was estimated. We excluded the cropped or manipulated images because Image (size) estimation is possible only for the images coming straight from the camera with EXIF tags. The methodological details for calibration and estimation of in-situ measurements of the morphological variables are given in Mahendiran et al.5.Measurements of the morphological variablesWe created a TPS file for JPEG images of Painted Storks with the TPSUtility Program44. Using the TPS file in the TPSDig (v. 2.17) program44, we measured the selected characters (morphological variables) in pixels. Later, it was used along with the total image size to estimate the size of the specific morphological features in metric units, following Mahendiran et al.5. Ten different morphological variables were measured: Bill length (upper and lower mandible), tibia & tarsus length of both legs, distances among the ear, nostril and corners of the mouth, and body length. We estimated the dimensions of the rigid body parts, viz., bill length, tibia, and tarsus using the given methodology13,15,21. Bill length is the distance from the tip of the upper mandible to the beginning of skin corners near nostrils, the proximal end of the beak (marked as ‘a’ in Fig. 3); Tibia length is the distance from the joint of the tibia-tarsus to the feathers (marked as ‘b’ in Fig. 3); Tarsus length is the distance between the tibia-tarsus joint and foot (marked as ‘c’ in Fig. 3). We took measurements of each individual’s right and left legs and other characters, viz., inter-distances among the nostril, corner of the eye, corner of the mouth on each side (marked as ‘d’, ‘e’, ‘f’ in Fig. 3). Body depth is the distance from the base of the neck near the breast to the tip of the tail (marked as ‘g’ in Fig. 3).Data analysisWe performed the statistical analysis in R45, primarily through the nlme, ggbiplot, nnet, tidyverse, devtools packages. We did not have the freedom to measure a few morphological variables due to the problems mentioned above, which led to missing values in the datasets. We filled the missing values with the impute function using the R Core team45 through mice & VIM packages. When the missing values are high in numbers, we discard the data rather than use the impute function. Since almost about 70% of the lower mandible values were missing, we discarded them and ended up having only nine morphological variables in the final analysis. Moreover, the lower mandible is movable, with the mouth being open and closed, producing a considerable variation in measurements.We designed the matrix (Individuals × Region × Sex) representing the intraspecific variations concerning the region and sexes of Painted Storks46. The individuals are in rows (R), their region in column (C1), and sex in column (C2). We considered the regional variations as a sequence of the latitudinal gradient of the study sites. The values of the individuals (R) were the selected morphological variables. This matrix helped us investigate the critical questions relating to eco-geographic variations and sexual dimorphism.To determine whether temperature varied between study sites, we conducted a two-way ANOVA to analyse the effect of study sites (between North India (DZ & KNP) and South India (VBS & KBS)) and months of the year on the temperature at 2 m. For each character, Dimorphism Index (DI) was calculated as a mean value of female divided by the mean male, multiplied by 100, following the method of Urfi and Kalam15. We estimated the general body size of Painted Storks from the selected morphological variables through Principal Component Analysis (PCA) and tested hypotheses on Eco-geographic variations (Bergmann’s or Allen’s rules)2,47 and the sexual dimorphism15,48. The dimension reduction through PCA was carried out after the imputation as there were a few missing values. Body depth was omitted only for the principal component analysis due to many missing values. However, the values of all the characters are presented in the summary statistics in Table 1. The first principal component is characterized as a measure of size, and subsequent components describe various aspects of shape; therefore, it is considered a measure of general body size15,48,49. The PC1 indicated the body size variation, and PC2 revealed leg length variation (tibia and tarsus). We used nested ANOVA to test their body size variation between regions and sexes. The sexes nested within the region explained the eco-geographic rules and sexual selection patterns.Using a multinomial logistic regression model, we compared the Painted Storks’ northern male (NM), southern male (SM), and female (SF) with the reference category, northern female (NF). Then, we classified the data through multinomial log-linear and feed-forward neural network models. We predicted the Painted Stork’s region and sex using the Machine Learning (ML) algorithms through open-source software Waikato Environment for Knowledge Analysis (WEKA.3.9.5) implemented in Java50. WEKA has standard Machine learning/data-mining algorithms with pre-processing tools generating insightful knowledge from the Painted Storks’ morphological data.Using the R and Python interfaces, we used different ML software frameworks, libraries, and computer programs, viz., TensorFlow and Keras, and extensively explored the WEKA workbench environment to predict the sex and region of the Painted Stork. We used the k-fold cross-validation (k = 10) to avoid overlapping test sets, including splitting the data into k subsets of equal size, using each subset for testing and the remainder for training. We analyzed using the WEKA on a Lenovo ThinkPad P53s Mobile Workstation with the 8th Gen Intel® Core i7 @ 1.80 GHz processor, 48 GB DDR4 Memory, NVIDIA® Quadro® P520 with 2 GB GDDR5 Graphics. The performance criteria for all the eight models were assessed by using the Precision (TP/(TP + FP)), Recall (TP/(TP + FN)), Area under Curve (AUC) = (Sensitivity + Specificity)/2, Accuracy = (TP + TN)/(TP + TN + FP + FN), where TP, TN, FN and FP are the acronyms of true positive, true negative, false negative and false positive, respectively. We used the WEKA experimenter environment to test the statistical significance of the selected Machine Learning algorithms. We performed the Paired T-tester based on the number of correctly classified instances and areas under the curve. More

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    From the archive: ancient poisonous honey, and museum photography

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    Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades

    Morens, D. M. et al. The origin of COVID-19 and why it matters. Am. J. Trop. Med. Hyg. 103, 955–959 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pierson, T. C. & Diamond, M. S. The emergence of Zika virus and its new clinical syndromes. Nature 560, 573–581 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Gates, B. The next epidemic—Lessons from Ebola., https://doi.org/10.1056/NEJMp1502918 (2015).World Health Organization. Lassa fever research and development (R&D) roadmap. https://www.who.int/publications/m/item/lassa-fever-research-and-development-(r-d)-roadmap (2018).World Health Organization. Prioritizing diseases for research and development in emergency contexts. https://www.who.int/activities/prioritizing-diseases-for-research-and-development-in-emergency-contexts.Akpede, G. O. et al. Caseload and case fatality of Lassa fever in Nigeria, 2001–2018: A specialist center’s experience and its implications. Front. Public Health 7, https://doi.org/10.3389/fpubh.2019.00170 (2019).Eberhardt, K. A. et al. Ribavirin for the treatment of Lassa fever: A systematic review and meta-analysis. Int. J. Infect. Dis. 87, 15–20 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Lukashevich, I. S., Paessler, S. & de la Torre, J. C. Lassa virus diversity and feasibility for universal prophylactic vaccine. F1000Res 8, https://doi.org/10.12688/f1000research.16989.1 (2019).Purushotham, J., Lambe, T. & Gilbert, S. C. Vaccine platforms for the prevention of Lassa fever. Immunol. Lett. 215, 1–11 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Mateo, M. et al. A single-shot Lassa vaccine induces long-term immunity and protects cynomolgus monkeys against heterologous strains. Sci. Transl. Med. 13, eabf6348 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    McCormick, J. B. et al. Lassa Fever. N. Engl. J. Med. 314, 20–26 (1986).CAS 
    PubMed 
    Article 

    Google Scholar 
    Bell-Kareem, A. R. & Smither, A. R. Epidemiology of Lassa fever. in 1–23 (Springer, 2021). https://doi.org/10.1007/82_2021_234.Nigeria Centre for Disease Control. https://ncdc.gov.ng/diseases/sitreps/?cat=5&name=An%20update%20of%20Lassa%20fever%20outbreak%20in%20Nigeria.Manning, J. T., Forrester, N. & Paessler, S. Lassa virus isolates from Mali and the Ivory Coast represent an emerging fifth lineage. Front. Microbiol. 6, https://doi.org/10.3389/fmicb.2015.01037 (2015).Dzotsi, E. K. et al. The first cases of Lassa fever in Ghana. Ghana. Med. J. 46, 166–170 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Patassi, A. A. et al. Emergence of Lassa fever disease in northern Togo: Report of two cases in Oti District in 2016. Case Rep. Infect. Dis. 2017, 8242313 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    Yadouleton, A. et al. Lassa fever in Benin: Description of the 2014 and 2016 epidemics and genetic characterization of a new Lassa virus. Emerg. Microbes Infect. 9, 1761–1770 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    McCormick, J. B. & Fisher-Hoch, S. P. Lassa fever. Curr. Top. Microbiol. Immunol. 262, 75–109 (2002).CAS 
    PubMed 

    Google Scholar 
    Monath, T. P., Newhouse, V. F., Kemp, G. E., Setzer, H. W. & Cacciapuoti, A. Lassa virus isolation from Mastomys natalensis rodents during an epidemic in Sierra Leone. Science 185, 263–265 (1974).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Stephenson, E. H., Larson, E. W. & Dominik, J. W. Effect of environmental factors on aerosol-induced Lassa virus infection. J. Med. Virol. 14, 295–303 (1984).CAS 
    PubMed 
    Article 

    Google Scholar 
    Wozniak, D. M. et al. Inoculation route-dependent Lassa virus dissemination and shedding dynamics in the natural reservoir – Mastomys natalensis. Emerg. Microbes Infect. 10, 2313–2325 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ter Meulen, J. et al. Hunting of peridomestic rodents and consumption of their meat as possible risk factors for rodent-to-human transmission of Lassa virus in the Republic of Guinea. Am. J. Trop. Med. Hyg. 55, 661–666 (1996).PubMed 
    Article 

    Google Scholar 
    Downs, I. L. et al. Natural history of aerosol induced Lassa fever in non-human primates. Viruses 12, 593 (2020).CAS 
    PubMed Central 
    Article 

    Google Scholar 
    Lecompte, E. et al. Mastomys natalensis and Lassa Fever, West Africa. Emerg. Infect. Dis. 12, 1971–1974 (2006).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Smither, A. R. & Bell-Kareem, A. R. Ecology of Lassa Virus. in 1–20 (Springer, 2021). https://doi.org/10.1007/82_2020_231.Ogbu, O., Ajuluchukwu, E. & Uneke, C. J. Lassa fever in West African sub-region: An overview. J. Vector Borne Dis. 44, 1–11 (2007).CAS 
    PubMed 

    Google Scholar 
    Fichet-Calvet, E. et al. Fluctuation of abundance and Lassa virus prevalence in Mastomys natalensis in Guinea, West Africa. Vector Borne Zoonotic Dis. 7, 119–128 (2007).PubMed 
    Article 

    Google Scholar 
    Fichet-Calvet, E., Becker-Ziaja, B., Koivogui, L. & Günther, S. Lassa serology in natural populations of rodents and horizontal transmission. Vector Borne Zoonotic Dis. 14, 665–674 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lo Iacono, G. et al. Using modelling to disentangle the relative contributions of zoonotic and anthroponotic transmission: The case of Lassa fever. PLoS Negl. Trop. Dis. 9, e3398 (2015).Siddle, K. J. et al. Genomic analysis of Lassa virus during an increase in cases in Nigeria in 2018. N. Engl. J. Med. 379, 1745–1753 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kafetzopoulou, L. E. et al. Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak. Science 363, 74–77 (2019).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Andersen, K. G. et al. Clinical sequencing uncovers origins and evolution of Lassa virus. Cell 162, 738–750 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lalis, A. & Wirth, T. Mice and men: An evolutionary history of Lassa fever. in Biodiversity and Evolution (eds. Grandcolas, P. & Maurel, M.-C.) 189–212, https://doi.org/10.1016/B978-1-78548-277-9.50011-5 (Elsevier, 2018).Mylne, A. Q. N. et al. Mapping the zoonotic niche of Lassa fever in Africa. Trans. R. Soc. Trop. Med. Hyg. 109, 483–492 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Colangelo, P. et al. A mitochondrial phylogeographic scenario for the most widespread African rodent, Mastomys natalensis. Biol. J. Linn. Soc. 108, 901–916 (2013).Article 

    Google Scholar 
    Gryseels, S. et al. When viruses don’t go viral: The importance of host phylogeographic structure in the spatial spread of arenaviruses. PLoS Path 13, e1006073 (2017).Article 

    Google Scholar 
    Cuypers, L. N. et al. Three arenaviruses in three subspecific natal multimammate mouse taxa in Tanzania: Same host specificity, but different spatial genetic structure? Virus Evol. https://doi.org/10.1093/ve/veaa039 (2020).Vazeille, M., Gaborit, P., Mousson, L., Girod, R. & Failloux, A.-B. Competitive advantage of a dengue 4 virus when co-infecting the mosquito Aedes aegypti with a dengue 1 virus. BMC Infect. Dis. 16, 318 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Chan, K. F. et al. Investigating viral interference between influenza A virus and human respiratory syncytial virus in a ferret model of infection. J. Infect. Dis. 218, 406–417 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Meunier, D. Y., McCormick, J. B., Georges, A. J., Georges, M. C. & Gonzalez, J. P. Comparison of Lassa, Mobala, and Ippy virus reactions by immunofluorescence test. Lancet 1, 873–874 (1985).CAS 
    PubMed 
    Article 

    Google Scholar 
    Howard, C. R. Antigenic diversity among the Arenaviruses. in The Arenaviridae (ed. Salvato, M. S.) 37–49, https://doi.org/10.1007/978-1-4615-3028-2_3 (Springer US, 1993).Bhattacharyya, S., Gesteland, P. H., Korgenski, K., Bjørnstad, O. N. & Adler, F. R. Cross-immunity between strains explains the dynamical pattern of paramyxoviruses. Proc. Natl Acad. Sci. U. S. A. 112, 13396–13400 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Luis, A. D., Douglass, R. J., Mills, J. N. & Bjørnstad, O. N. Environmental fluctuations lead to predictability in Sin Nombre hantavirus outbreaks. Ecology 96, 1691–1701 (2015).Article 

    Google Scholar 
    Anderson, R. M., Jackson, H. C., May, R. M. & Smith, A. M. Population dynamics of fox rabies in Europe. Nature 289, 765–771 (1981).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Tian, H. et al. Anthropogenically driven environmental changes shift the ecological dynamics of hemorrhagic fever with renal syndrome. PLoS Pathog. 13, e1006198 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Redding, D. W., Moses, L. M., Cunningham, A. A., Wood, J. & Jones, K. E. Environmental-mechanistic modelling of the impact of global change on human zoonotic disease emergence: a case study of Lassa fever. Methods Ecol. Evol. 7, 646–655 (2016).Article 

    Google Scholar 
    Peterson, A. T., Moses, L. M. & Bausch, D. G. Mapping transmission risk of Lassa fever in West Africa: the importance of quality control, sampling bias, and error weighting. PLoS One 9, e100711 (2014).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Fichet-Calvet, E. & Rogers, D. J. Risk maps of Lassa fever in West Africa. PLoS. Negl. Trop. Dis. 3, e388 (2009).Basinski, A. J. et al. Bridging the gap: Using reservoir ecology and human serosurveys to estimate Lassa virus spillover in West Africa. PLoS Comput. Biol. 17, e1008811 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Iacono, G. L. et al. A unified framework for the infection dynamics of zoonotic spillover and spread. PLoS Negl. Trop. Dis. 10, e0004957 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Coumou, D. & Rahmstorf, S. A decade of weather extremes. Nat. Clim. Change 2, 491–496 (2012).ADS 
    Article 

    Google Scholar 
    Coumou, D., Robinson, A. & Rahmstorf, S. Global increase in record-breaking monthly-mean temperatures. Clim. Change 118, 771–782 (2013).ADS 
    Article 

    Google Scholar 
    Bathiany, S., Dakos, V., Scheffer, M. & Lenton, T. M. Climate models predict increasing temperature variability in poor countries. Sci. Adv. 4, eaar5809 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Arneth, A. Uncertain future for vegetation cover. Nature 524, 44–45 (2015).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Brandt, M. et al. Human population growth offsets climate-driven increase in woody vegetation in sub-Saharan Africa. Nat. Ecol. Evol. 1, 81 (2017).PubMed 
    Article 

    Google Scholar 
    Herrmann, S. M., Brandt, M., Rasmussen, K. & Fensholt, R. Accelerating land cover change in West Africa over four decades as population pressure increased. Com. Earth Envir 1, 1–10 (2020).
    Google Scholar 
    Gibb, R., Moses, L. M., Redding, D. W. & Jones, K. E. Understanding the cryptic nature of Lassa fever in West Africa. Pathog. Glob. Health 111, 276–288 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Elith, J., Leathwick, J. R. & Hastie, T. A working guide to boosted regression trees. J. Anim. Ecol. 77, 802–813 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Frieler, K. et al. Assessing the impacts of 1.5 °C global warming—simulation protocol of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP2b). Geosci. Model Dev. 10, 4321–4345 (2017).ADS 
    Article 

    Google Scholar 
    Soberón, J. & Nakamura, M. Niches and distributional areas: Concepts, methods, and assumptions. Proc. Natl Acad. Sci. U. S. A. 106, 19644–19650 (2009).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Moss, R. H. et al. The next generation of scenarios for climate change research and assessment. Nature 463, 747–756 (2010).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Lemey, P., Rambaut, A., Welch, J. J. & Suchard, M. A. Phylogeography takes a relaxed random walk in continuous space and time. Mol. Biol. Evol. 27, 1877–1885 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lukashevich, I. S. Generation of reassortants between African arenaviruses. Virology 188, 600–605 (1992).CAS 
    PubMed 
    Article 

    Google Scholar 
    Vijaykrishna, D., Mukerji, R. & Smith, G. J. D. RNA virus reassortment: an evolutionary mechanism for host jumps and immune evasion. PLoS Path 11, e1004902 (2015).Article 

    Google Scholar 
    Whitmer, S. L. M. et al. New lineage of Lassa Virus, Togo, 2016. Emerg. Infect. Dis. 24, 599 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ehichioya, D. U. et al. Phylogeography of Lassa virus in Nigeria. J. Virol. 93, e00929–19 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Dellicour, S., Rose, R., Faria, N. R., Lemey, P. & Pybus, O. G. SERAPHIM: studying environmental rasters and phylogenetically informed movements. Bioinformatics 32, 3204–3206 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Dellicour, S. et al. Using viral gene sequences to compare and explain the heterogeneous spatial dynamics of virus epidemics. Mol. Biol. Evol. 34, 2563–2571 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Dellicour, S. et al. Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework. Nat. Commun. 11, 5620 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Dijkstra, E. W. A note on two problems in connexion with graphs. Numer. Math. 1, 269–271 (1959).MathSciNet 
    MATH 
    Article 

    Google Scholar 
    Strahler, A. N. Quantitative analysis of watershed geomorphology. Eos, Trans. Am. Geophys. Union 38, 913–920 (1957).Article 

    Google Scholar 
    Kass, R. E. & Raftery, A. E. Bayes factors. J. Am. Stat. Assoc. 90, 773–795 (1995).MathSciNet 
    MATH 
    Article 

    Google Scholar 
    Ehichioya, D. U. et al. Current molecular epidemiology of Lassa virus in Nigeria. J. Clin. Microbiol. 49, 1157 (2011).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Oloniniyi, O. K. et al. Genetic characterization of Lassa virus strains isolated from 2012 to 2016 in southeastern Nigeria. PLoS Negl. Trop. Dis. 12, e0006971 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Olesen, J. E. et al. Uncertainties in projected impacts of climate change on European agriculture and terrestrial ecosystems based on scenarios from regional climate models. Clim. Change 81, 123–143 (2007).Article 

    Google Scholar 
    Simo Tchetgna, H. et al. Molecular characterization of a new highly divergent Mobala related arenavirus isolated from Praomys sp. rodents. Sci. Rep. 11, 10188 (2021).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Olayemi, A. et al. New hosts of the Lassa virus. Sci. Rep. 6, 25280 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zaidi, M. B. et al. Competitive suppression of dengue virus replication occurs in chikungunya and dengue co-infected Mexican infants. Parasit. Vectors 11, 378 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Olayemi, A. et al. Widespread arenavirus occurrence and seroprevalence in small mammals, Nigeria. Parasit. Vectors 11, 416 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Nigeria Centre for Disease Control. https://ncdc.gov.ng/diseases/sitreps/?cat=5&name=An%20update%20of%20Lassa%20fever%20outbreak%20in%20Nigeria.Norris, K. et al. Biodiversity in a forestagriculture mosaic: the changing face of west Africa rainforests. Biol. Conserv. 143, 2341–2350 (2010).Article 

    Google Scholar 
    Stocker, T. F. et al. Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the fifth assessment report of the Intergovernmental Panel on Climate Change. (Cambridge University Press, Cambridge, United Kingdom and New York, 2013).Buba, M. I. et al. Mortality among confirmed Lassa fever cases during the 2015-2016 outbreak in Nigeria. Am. J. Public Health 108, 262–264 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Tobin, E. A. et al. Knowledge of secondary school children in Edo State on Lassa fever and its implications for prevention and control. West. Afr. J. Med. 34, 101–107 (2015).CAS 
    PubMed 

    Google Scholar 
    Saez, A. M. et al. Rodent control to fight Lassa fever: Evaluation and lessons learned from a 4-year study in Upper Guinea. PLoS Negl. Trop. Dis. 12, e0006829 (2018).Article 

    Google Scholar 
    Ejembi, J. et al. Contact tracing in Lassa fever outbreak response, an effective strategy for control? Online J. Public Health Inf. 11, e378 (2019).
    Google Scholar 
    ECHO Flash List. https://erccportal.jrc.ec.europa.eu/ECHO-Flash/ECHO-Flash-List/yy/2018/mm/2.Pigott, D. M. et al. Local, national, and regional viral haemorrhagic fever pandemic potential in Africa: a multistage analysis. Lancet 390, 2662–2672 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kraemer, M. U. G. et al. Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus. Nature Microbiology https://doi.org/10.1038/s41564-019-0376-y (2019).Elith, J. et al. Novel methods improve prediction of species’ distributions from occurrence data. Ecography 29, 129–151 (2006).Article 

    Google Scholar 
    Dhingra, M. S. et al. Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade 2.3.4.4 viruses with spatial cross-validation. eLife 5, e19571 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Phillips, S. J., Anderson, R. P. & Schapire, R. E. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190, 231–259 (2006).Article 

    Google Scholar 
    Elith, J. et al. A statistical explanation of MaxEnt for ecologists. Divers. Distrib. 17, 43–57 (2011).Article 

    Google Scholar 
    Phillips, S. J. et al. Sample selection bias and presence-only distribution models: Implications for background and pseudo-absence data. Ecol. Appl. 19, 181–197 (2009).PubMed 
    Article 

    Google Scholar 
    Valavi, R., Elith, J., Lahoz‐Monfort, J. J. & Guillera‐Arroita, G. blockCV: An r package for generating spatially or environmentally separated folds for k-fold cross-validation of species distribution models. Methods Ecol. Evol. 10, 225–232 (2019).Article 

    Google Scholar 
    Suchard, M. A. et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 4, vey016 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Randin, C. F. et al. Are niche-based species distribution models transferable in space? J. Biogeogr. 33, 1689–1703 (2006).Article 

    Google Scholar 
    Lange, S. Bias correction of surface downwelling longwave and shortwave radiation for the EWEMBI dataset. Earth Syst. Dyn. 9, 627–645 (2018).ADS 
    Article 

    Google Scholar 
    Dunne, J. P. et al. GFDL’s ESM2 global coupled climate–carbon earth system models. Part I: physical formulation and baseline simulation characteristics. J. Clim. 25, 6646–6665 (2012).ADS 
    Article 

    Google Scholar 
    Jones, C. D. et al. The HadGEM2-ES implementation of CMIP5 centennial simulations. Geosci. Model Dev. 4, 543–570 (2011).ADS 
    Article 

    Google Scholar 
    Dufresne, J.-L. et al. Climate change projections using the IPSL-CM5 Earth System Model: from CMIP3 to CMIP5. Clim. Dyn. 40, 2123–2165 (2013).Article 

    Google Scholar 
    Watanabe, M. et al. Improved climate simulation by MIROC5: Mean states, variability, and climate sensitivity. J. Clim. 23, 6312–6335 (2010).ADS 
    Article 

    Google Scholar 
    Taylor, K. E., Stouffer, R. J. & Meehl, G. A. An overview of CMIP5 and the experiment design. Bull. Am. Meteor. Soc. 93, 485–498 (2012).ADS 
    Article 

    Google Scholar 
    Hurtt, G. C. et al. Harmonization of global land-use change and management for the period 850-2100 (LUH2) for CMIP6. Geosci. Model Dev. 1–65 https://doi.org/10.5194/gmd-2019-360 (2020)Jones, B. & O’Neill, B. C. Spatially explicit global population scenarios consistent with the Shared Socioeconomic Pathways. Environ. Res. Lett. 11, 084003 (2016).ADS 
    Article 

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

    Google Scholar 
    Larsson, A. AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30, 3276–3278 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ayres, D. L. et al. BEAGLE 3: Improved performance, scaling, and usability for a high-performance computing library for statistical phylogenetics. Syst. Biol. https://doi.org/10.1093/sysbio/syz020 (2019).Tavaré, S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect. Math. Life Sci. 17, 57–86 (1986).MathSciNet 
    MATH 

    Google Scholar 
    Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901–904 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Laenen, L. et al. Spatio-temporal analysis of Nova virus, a divergent hantavirus circulating in the European mole in Belgium. Mol. Ecol. 25, 5994–6008 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Dellicour, S. et al. Landscape genetic analyses of Cervus elaphus and Sus scrofa: comparative study and analytical developments. Heredity 123, 228–241 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Dellicour, S. et al. Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak. Nat. Commun. 9, 2222 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Dellicour, S. et al. Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing. bioRxiv https://doi.org/10.1101/788059 (2020).Dellicour, S., Rose, R. & Pybus, O. G. Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data. BMC Bioinform 17, 1–12 (2016).Article 

    Google Scholar 
    McRae, B. H. Isolation by resistance. Evolution 60, 1551–1561 (2006).PubMed 
    Article 

    Google Scholar 
    Jacquot, M., Nomikou, K., Palmarini, M., Mertens, P. & Biek, R. Bluetongue virus spread in Europe is a consequence of climatic, landscape and vertebrate host factors as revealed by phylogeographic inference. Proc. R. Soc. Lond. B 284, 20170919 (2017).
    Google Scholar 
    Gill, M. S. et al. Improving Bayesian population dynamics inference: A coalescent-based model for multiple loci. Mol. Biol. Evol. 30, 713–724 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    Karcher, M. D., Palacios, J. A., Bedford, T., Suchard, M. A. & Minin, V. N. Quantifying and mitigating the effect of preferential sampling on phylodynamic inference. PLoS Comput. Biol. 12, e1004789 (2016).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar  More

  • in

    Microbacterium kunmingensis sp. nov., an attached bacterium of Microcystis aeruginosa

    Liu LP. Characteristics of blue algal bloom in Dianchi Lake and analysis on its cause. Res Environ Sci. 1999;12:36–37.
    Google Scholar 
    Liu YM, Chen W, Li DH, Shen YW, Liu YD, Song LR. Analysis of paralytic shellfish toxins in Aphanizomenon DC-1 from Lake Dianchi, China. Environ Toxicol. 2006;21:289–95.CAS 
    PubMed 
    Article 

    Google Scholar 
    Dziallas C, Grossart HP. Temperature and biotic factors influence bacterial communities associated with the cyanobacterium Microcystis sp. Environ Microbiol. 2011;13:1632–41.PubMed 
    Article 

    Google Scholar 
    Parveen B, Ravet V, Djediat C, Mary I, Quiblier C, Debroas D, Humbert JF. Bacterial communities associated with Microcystis colonies differ from free-living communities living in the same ecosystem. Environ Microbiol Rep. 2013;5:716–24.CAS 
    PubMed 

    Google Scholar 
    Shi LM, Cai YF, Kong FX, Yu Y. Specific association between bacteria and buoyant Microcystis colonies compared with other bulk bacterial communities in the eutrophic Lake Taihu, China. Environ Microbiol Rep. 2012;4:669–78.CAS 
    PubMed 

    Google Scholar 
    Kouzuma A, Watanabe K. Exploring the potential of algae/bacteria interactions. Curr Opin Biotech. 2015;33:125–9.CAS 
    PubMed 
    Article 

    Google Scholar 
    Cooper MB, Smith AG. Exploring mutualistic interactions between microalgae and bacteria in the omics age. Curr Opin Plant Biol. 2015;26:147–53.PubMed 
    Article 

    Google Scholar 
    Yang L, Xiao L. Outburst, jeopardize and control of cyanobacterial bloom in lakes. Beijing: Science Press; 2011. p. 71–212.
    Google Scholar 
    de-Bashan LE, Antoun H, Bashan Y. Involvement of indole-3-acetic-acid produced by the growth-promoting bacterium Azospirillum spp. in promoting growth of Chlorella vulgaris. J Phycol. 2008;44:938–47.CAS 
    PubMed 
    Article 

    Google Scholar 
    Xiao Y, Wang L, Wang X, Chen M, Chen J, Tian BY, Zhang BH. Nocardioides lacusdianchii sp. nov., an attached bacterium of Microcystis aeruginosa. Antonie van Leeuwenhoek. 2022;115:141–53.PubMed 
    Article 

    Google Scholar 
    Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol. 1966;16:313–40.Article 

    Google Scholar 
    Zhang BH, Chen W, Li HQ, Zhou EM, Hu WY, Duan YQ, Mohamad OA, Gao R, Li WJ. An antialgal compound produced by Streptomyces jiujiangensis JXJ 0074T. Appl Microbiol Biotechnol. 2015;99:7673–83.CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhang BH, Salam N, Cheng J, Xiao M, Li HQ, Yang JY, Zha DM, Li WJ. Citricoccus lacusdiani sp. nov., an actinobacterium promoting Microcystis growth with limited soluble phosphorus. Antonie Van Leeuwenhoek. 2016;109:1457–65.CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhang BH, Salam N, Cheng J, Li HQ, Yang JY, Zha DM, Guo QG, Li WJ. Microbacterium lacusdiani sp. nov., a phosphate–solubilizing novel actinobacterium isolated from mucilaginous sheath of Microcystis. J Antibiot. 2017;70:147–51.Article 

    Google Scholar 
    Smibert RM, Krieg NR. Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR, editors. Methods for general and molecular bacteriology. Washington, DC: American Society for Microbiology; 1994. p. 607–54.Dong XZ, Cai MY. Manual of systematic identification of common bacteria. Beijing: Science Press; 2001. p. p349–89.
    Google Scholar 
    Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol. 1979;47:87–95.CAS 
    Article 

    Google Scholar 
    Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol. 1983;54:31–36.CAS 
    Article 

    Google Scholar 
    Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev. 1972;36:407–77.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Tang SK, Wang Y, Chen Y, Lou K, Cao LL, Xu LH, Li WJ. Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella. Int J Syst Evol Microbiol. 2009;59:2025–32.CAS 
    PubMed 
    Article 

    Google Scholar 
    Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J. Introducing EzBiocloud: a taxonomically united database of 16S rRNA gene sequences and whole–genome assemblies. Int J Syst Evol Microbiol. 2017;67:1613–7.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28:2731–9.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Saitou N, Nei M. The neighbor–joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–42.CAS 
    PubMed 

    Google Scholar 
    Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool. 1971;20:406–16.Article 

    Google Scholar 
    Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17:368–76.CAS 
    PubMed 
    Article 

    Google Scholar 
    Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39:783–91.PubMed 
    Article 

    Google Scholar 
    Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Massouras A, Hens K, Gubelmann C, Uplekar S, Decouttere F, Rougemont J, Cole ST, Deplancke B. Primer-initiated sequence synthesis to detect and assemble structural variants. Nat Methods. 2010;7:485–6.CAS 
    PubMed 
    Article 

    Google Scholar 
    Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.CAS 
    PubMed 
    Article 

    Google Scholar 
    Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P. CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinforma. 2007;8:209.Article 

    Google Scholar 
    Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence–based species delimitation with confidence intervals and improved distance functions. BMC Bioinforma. 2013;14:60.Article 

    Google Scholar 
    Xiao Y, Chen J, Chen M, Deng SJ, Xiong ZQ, Tian BY, Zhang BH. Mycolicibacterium lacusdiani sp. nov., an attached bacterium of Microcystis aeruginosa. Front Microbiol. 2022;13:861291.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Vaz-Moreira I, Lopes AR, Faria C, Spröer C, Schumann P, Nunes OC, Manaia CM. Microbacterium invictum sp. nov., isolated from homemade compost. Int J Syst Evol Microbiol. 2009;59:2036–41.PubMed 
    Article 

    Google Scholar 
    Ohta Y, Ito T, Mori K, Nishi S, Shimane Y, Mikuni K, Hatada Y. Microbacterium saccharophilum sp. nov., isolated from a sucrose-refining factory. Int J Syst Evol Microbiol. 2013;63:2765–9.CAS 
    PubMed 
    Article 

    Google Scholar 
    Kageyama A, Takahashi Y, Ōmura S. Microbacterium deminutum sp. nov., Microbacterium pumilum sp. nov. and Microbacterium aoyamense sp. nov. Int J Syst Evol Microbiol. 2006;56:2113–7.CAS 
    PubMed 
    Article 

    Google Scholar 
    Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today. 2006;33:152–5.
    Google Scholar 
    Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinforma. 2013;14:60.Article 

    Google Scholar 
    Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014;64:346–51.CAS 
    PubMed 
    Article 

    Google Scholar 
    Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol. 2018;68:461–6.CAS 
    PubMed 
    Article 

    Google Scholar 
    Hoke AK, Reynoso G, Smith MR, Gardner MI, Lockwood DJ, Gilbert NE, Wilhelm SW, Becker IR, Brennan GJ, Crider KE, Farnan SR, Mendoza V, Poole AC, Zimmerman ZP, Utz LK, Wurch LL, Steffen MM. Genomic signatures of Lake Erie bacteria suggest interaction in the Microcystis phycosphere. PLoS ONE. 2021;16:e0257017.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zhang BH, Salam N, Cheng J, Li HQ, Yang JY, Zha DM, Zhang YQ, Ai MJ, Hozzein WN, Li WJ. Modestobacter lacusdianchii sp. nov., a phosphate-solubilizing actinobacterium with ability to promote Microcystis growth. PLoS ONE. 2016;11:e0161069.PubMed 
    PubMed Central 
    Article 

    Google Scholar  More