in

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 


  • Source: Ecology - nature.com

    Waste slag benefits for correction of soil acidity

    Honey bees save energy in honey processing by dehydrating nectar before returning to the nest