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Explosive radiations have been considered one of the most important diversification patterns across the Tree of Life, but the subsequent change, movement and extinction of species makes radiations hard to discern and understand as geological time passes. Here we synthesise phylogenetic and distributional data for an ongoing radiation --- the mega-diverse plant genus Solanum L. --- to show how dispersal events and past climatic changes have interacted to shape diversification. We find that despite the vast diversity of Solanum lineages in the Neotropics, lineages in the Old World are diversifying more rapidly. This recent explosive diversification coincides with a long-distance dispersal event from the Neotropics, at the time when, and to places where, major climatic changes took place. Two different groups of Solanum have migrated and established in Australia, but only the arid-adapted lineages experienced significant increases in their diversification, which is consistent with the continent9s long-term climatic trend and the diversification of other arid-adapted groups. Our findings provide a clear example of how successful colonisation of new areas and niches can -- but do not always -- drive explosive diversifications.

Significance We explore an extended view of the tropical conservatism hypothesis to account for two often-neglected components of climatic stress: drought and the combined effect of seasonal cold and drought—the latter being a common feature of extratropical dry environments. We show that evolutionary diversity of angiosperm assemblages in extratropical dry biomes is even lower than in biomes subject to only one type of climatic stress. We further show that evolutionary diversity in many assemblages from eastern North America is higher or comparable to that of tropical moist forests, suggesting that some extratropical moist biomes have accumulated angiosperm lineages over deep evolutionary timescales with their flora assembled from lineages that represent the entirety of the angiosperm tree of life., The tropical conservatism hypothesis (TCH) posits that the latitudinal gradient in biological diversity arises because most extant clades of animals and plants originated when tropical environments were more widespread and because the colonization of colder and more seasonal temperate environments is limited by the phylogenetically conserved environmental tolerances of these tropical clades. Recent studies have claimed support of the TCH, indicating that temperate plant diversity stems from a few more recently derived lineages that are nested within tropical clades, with the colonization of the temperate zone being associated with key adaptations to survive colder temperatures and regular freezing. Drought, however, is an additional physiological stress that could shape diversity gradients. Here, we evaluate patterns of evolutionary diversity in plant assemblages spanning the full extent of climatic gradients in North and South America. We find that in both hemispheres, extratropical dry biomes house the lowest evolutionary diversity, while tropical moist forests and many temperate mixed forests harbor the highest. Together, our results support a more nuanced view of the TCH, with environments that are radically different from the ancestral niche of angiosperms having limited, phylogenetically clustered diversity relative to environments that show lower levels of deviation from this niche. Thus, we argue that ongoing expansion of arid environments is likely to entail higher loss of evolutionary diversity not just in the wet tropics but in many extratropical moist regions as well.

Background:Vaccination is one of the most effective public health interventions. We investigate the impact of vaccination activities for Haemophilus influenzae type b, hepatitis B, human papillomavirus, Japanese encephalitis, measles, Neisseria meningitidis serogroup A, rotavirus, rubella, Streptococcus pneumoniae, and yellow fever over the years 2000–2030 across 112 countries.Methods:Twenty-one mathematical models estimated disease burden using standardised demographic and immunisation data. Impact was attributed to the year of vaccination through vaccine-activity-stratified impact ratios.Results:We estimate 97 (95%CrI[80, 120]) million deaths would be averted due to vaccination activities over 2000–2030, with 50 (95%CrI[41, 62]) million deaths averted by activities between 2000 and 2019. For children under-5 born between 2000 and 2030, we estimate 52 (95%CrI[41, 69]) million more deaths would occur over their lifetimes without vaccination against these diseases.Conclusions:This study represents the largest assessment of vaccine impact before COVID-19-related disruptions and provides motivation for sustaining and improving global vaccination coverage in the future.Funding:VIMC is jointly funded by Gavi, the Vaccine Alliance, and the Bill and Melinda Gates Foundation (BMGF) (BMGF grant number: OPP1157270 / INV-009125). Funding from Gavi is channelled via VIMC to the Consortium’s modelling groups (VIMC-funded institutions represented in this paper: Imperial College London, London School of Hygiene and Tropical Medicine, Oxford University Clinical Research Unit, Public Health England, Johns Hopkins University, The Pennsylvania State University, Center for Disease Analysis Foundation, Kaiser Permanente Washington, University of Cambridge, University of Notre Dame, Harvard University, Conservatoire National des Arts et Métiers, Emory University, National University of Singapore). Funding from BMGF was used for salaries of the Consortium secretariat (authors represented here: TBH, MJ, XL, SE-L, JT, KW, NMF, KAMG); and channelled via VIMC for travel and subsistence costs of all Consortium members (all authors). We also acknowledge funding from the UK Medical Research Council and Department for International Development, which supported aspects of VIMC's work (MRC grant number: MR/R015600/1).JHH acknowledges funding from National Science Foundation Graduate Research Fellowship; Richard and Peggy Notebaert Premier Fellowship from the University of Notre Dame. BAL acknowledges funding from NIH/NIGMS (grant number R01 GM124280) and NIH/NIAID (grant number R01 AI112970). The Lives Saved Tool (LiST) receives funding support from the Bill and Melinda Gates Foundation.This paper was compiled by all coauthors, including two coauthors from Gavi. Other funders had no role in study design, data collection, data analysis, data interpretation, or writing of the report. All authors had full access to all the data in the study and had final responsibility for the decision to submit for publication.

Summary Background Childhood immunisation services have been disrupted by the COVID-19 pandemic. WHO recommends considering outbreak risk using epidemiological criteria when deciding whether to conduct preventive vaccination campaigns during the pandemic. Methods We used 2-3 models per infection to estimate the health impact of 50% reduced routine vaccination coverage in 2020 and delay of campaign vaccination from 2020 to 2021 for measles vaccination in Bangladesh, Chad, Ethiopia, Kenya, Nigeria, and South Sudan, for meningococcal A vaccination in Burkina Faso, Chad, Niger, and Nigeria, and for yellow fever vaccination in the Democratic Republic of Congo, Ghana, and Nigeria. Our counterfactual comparative scenario was sustaining immunisation services at coverage projections made prior to COVID-19 (i.e. without any disruption). Findings Reduced routine vaccination coverage in 2020 without catch-up vaccination may lead to an increase in measles and yellow fever disease burden in the modelled countries. Delaying planned campaigns in Ethiopia and Nigeria by a year may significantly increased the risk of measles outbreaks (both countries did complete their SIAS planned for 2020). For yellow fever vaccination, delay in campaigns leads to a potential disease burden rise of >1 death per 100,000 people until the campaigns are implemented. For meningococcal A vaccination, short term disruptions in 2020 are unlikely to have a significant impact due to the persistence of direct and indirect benefits from past introductory campaigns of the 1 to 29-year-old population, bolstered by inclusion of the vaccine into the routine immunisation schedule accompanied by further catch-up campaigns. Interpretation The impact of COVID-19-related disruption to vaccination programs varies between infections and countries. Planning and implementation of campaigns should consider country and infection-specific epidemiological factors and local immunity gaps worsened by the COVID-19 pandemic when prioritising vaccines and strategies for catch-up vaccination. Funding Bill & Melinda Gates Foundation and Gavi, the Vaccine Alliance Research in context Evidence before the study We searched PubMed for (COVID-19 OR coronavirus OR SARS-CoV-2) AND (child health intervention OR vaccin* or immuni*) AND (disruption OR suspension OR reduction) AND (indirect effect OR health impact) on January 14, 2021, with no language restrictions. We found 178 articles of which 13 articles were relevant. Six articles reported some empirical data on immunization disruption in Bangladesh, Japan, Kenya, Nigeria, Pakistan, Saudi Arabia, South Africa, Spain and Italy, and a survey study focussed on immunization disruption in low and middle-income countries. One article proposed using the WHO health systems framework to assess the effects of COVID-19 on immunisation programmes in South Africa, another study on leveraging systems thinking and implementation science to improve immunization system performance in Africa, and two studies were review articles. One modelling study focused on the indirect effects, including reduction in routine immunisation services, of the COVID-19 pandemic on maternal and child mortality in low-income and middle-income countries. Another modelling study focused on a benefit-risk analysis of routine childhood immunisation during the COVID-19 pandemic in Africa. We also found one other study in the grey literature that analysed the impact on SARS-CoV-2 infections as a result of fixed-post and door-to-door vaccination campaigns targeted at children under five years of age in an Ethiopia-like setting. Added value of this study We estimated the increase in cases and deaths caused by the disruption to immunisation services leading to outbreaks for measles, meningococcal A and yellow fever in 10 countries. The reduction in routine immunisation coverage among under-immunised cohorts of children has enhanced the risk of outbreaks which cannot be averted without catch-up vaccination. This can lead to an increase of 9.89% (0.91 additional deaths per 100,000 individuals, or 48,000 in total) across the three diseases from 2020 to 2030 in the countries considered. Results vary by infection and country, but generally most excess deaths are due to measles. Postponing campaign immunisation may not have a detrimental short-term health impact if campaign immunisation is implemented ahead of future outbreaks caused by these immunity gaps. Implications of the available evidence The COVID-19 pandemic has caused significant disruptions to routine services and vaccination campaigns and resulted in immunity gaps with potential to cause outbreaks in the affected populations. The short-term and long-term health impact differ between measles, meningococcal A and yellow fever vaccination and by countries based on the local epidemiological situation. Thereby, catch-up vaccination should be planned by considering the heterogeneity in population susceptibility across different countries to measles, meningococcal A and yellow fever outbreaks and implemented in time to prevent these outbreaks. The study findings can inform risk-benefit trade-off discussions around the timing of campaigns.

Coronavirus disease (COVID-19) in Colombia was first diagnosed in a traveler arriving from Italy on February 26, 2020. However, limited data are available on the origins and number of introductions of COVID-19 into the country. We sequenced the causative agent of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), from 43 clinical samples we collected, along with another 79 genome sequences available from Colombia. We investigated the emergence and importation routes for SARS-CoV-2 into Colombia by using epidemiologic, historical air travel, and phylogenetic observations. Our study provides evidence of multiple introductions, mostly from Europe, and documents >12 lineages. Phylogenetic findings validate the lineage diversity, support multiple importation events, and demonstrate the evolutionary relationship of epidemiologically linked transmission chains. Our results reconstruct the early evolutionary history of SARS-CoV-2 in Colombia and highlight the advantages of genome sequencing to complement COVID-19 outbreak investigations.

Coronavirus disease 2019 (COVID-19) was first diagnosed in Colombia from a traveler arriving from Italy on February 26, 2020. To date, available data on the origins and number or introductions of SARS-CoV-2 into the country are limited. Here, we sequenced SARS-CoV-2 from 43 clinical samples and—together with other 73 genomes sequences available from the country—we investigated the emergence and the routes of importation of COVID-19 into Colombia using epidemiological, historical air travel and phylogenetic observations. Our study provided evidence of multiple introductions, mostly from Europe, with at least 12 lineages being documented. Phylogenetic findings validated the lineage diversity, supported multiple importation events and the evolutionary relationship of epidemiologically-linked transmission chains. Our results reconstruct the early evolutionary history of SARS-CoV-2 in Colombia and highlight the advantages of genome sequencing to complement COVID-19 outbreak investigation.

Aim: Understanding the impact of land use change within assemblages is fundamental to mitigation policies at local and regional scale. Here, we aim to quantify how site-level terrestrial assemblages are responding to land use change in Colombia a mega-diverse country and to project future biodiversity under different scenarios of land use change associated with climate change policies. Location: Colombia (northern South America). Methods: We collated original biodiversity data from 17 publications (285 sites) that examined how human impact affects terrestrial biodiversity in Colombia. From each site we estimated compositional intactness (i.e. compositional similarity to undisturbed sites). We fitted generalized linear mixed-effects models to estimate how these measures of local biodiversity vary across land use habitats. Using space-for-time substitution, we applied our estimates to hindcast biodiversity changes since 1500 and project future changes under climate change policies of the four representative concentration pathways (RCPs). Results: Assemblages in urban, cropland and pasture sites were compositionally very different from those in primary vegetation. We infer that average compositional intactness has been reduced by 18% across Colombia to date, with strong regional variation. The best RCP scenario for future biodiversity is GCAM-RCP4.5, a path that favours the expansion of secondary forests under a strong carbon market; while the worst is MESSAGE-RCP8.5, ‘the business-as-usual’ scenario. Main conclusions: Land use change has driven an increasing change in the composition of ecological assemblages in Colombia. By 2095, the implementation of carbon markets policy of climate change from GCAM-RCP4.5 could mitigate these changes in community composition. In contrast, the business-as-usual scenario MESSAGE-RCP8.5 predicts a steep community change placing the quality of ecosystems at risk.

SummaryExplosive radiations have been considered one of the most intriguing diversification patterns across the Tree of Life, but the subsequent change, movement and extinction of the constituent species makes radiations hard to discern or understand as geological time passes.We synthesised phylogenetic and distributional data for an ongoing radiation — the mega-diverse plant genus Solanum L. — to show how dispersal events and past climatic changes have interacted to shape diversification.We found that despite the vast diversity of Solanum lineages in the Neotropics, lineages in the Old World are diversifying more rapidly. This recent explosive diversification coincides with a long-distance dispersal event from the Neotropics, at the time when, and to places where, major climatic changes took place. Two different groups of Solanum have migrated and established in Australia, but only the arid-adapted lineages experienced significant increases in their diversification, which is consistent with adaptation to the continent’s long-term climatic trend and the diversification of other arid-adapted groups.Our findings provide a clear example of how successful colonisation of new areas and niches can – but do not always – drive explosive radiations.

Human activities, especially conversion and degradation of habitats, are causing global biodiversity declines. How local ecological assemblages are responding is less clear—a concern given their importance for many ecosystem functions and services. We analysed a terrestrial assemblage database of unprecedented geographic and taxonomic coverage to quantify local biodiversity responses to land use and related changes. Here we show that in the worst-affected habitats, these pressures reduce within-sample species richness by an average of 76.5%, total abundance by 39.5% and rarefaction-based richness by 40.3%. We estimate that, globally, these pressures have already slightly reduced average within-sample richness (by 13.6%), total abundance (10.7%) and rarefaction-based richness (8.1%), with changes showing marked spatial variation. Rapid further losses are predicted under a business-as-usual land-use scenario; within-sample richness is projected to fall by a further 3.4% globally by 2100, with losses concentrated in biodiverse but economically poor countries. Strong mitigation can deliver much more positive biodiversity changes (up to a 1.9% average increase) that are less strongly related to countries' socioeconomic status. Fil: Newbold, Tim. United Nations Environment Programme World Conservation Monitoring Centre; Reino Unido Fil: Hudson, Lawrence N.. Natural History Museum. Department of Life Sciences; Reino Unido Fil: Hill, Samantha L. L.. United Nations Environment Programme World Conservation Monitoring Centre; Reino Unido Fil: Contu, Sara. Natural History Museum. Department of Life Sciences; Reino Unido Fil: Lysenko, Igor. Imperial College London. Department of Life Sciences; Reino Unido Fil: Diaz, Sandra Myrna. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina Fil: Harrison, Michelle L. K.. Imperial College London. Department of Life Sciences; Reino Unido Fil: Alhusseini, Tamera. Imperial College London. Department of Life Sciences; Reino Unido Fil: Ingram, Daniel J.. Imperial College London. Department of Life Sciences; Reino Unido Fil: Itescu, Yuval. Tel-Aviv University. Faculty of Life Sciences. Deptartment of Zoology; Israel Fil: Kattge, Jens. Max Planck Institute for Biogeochemistry; Alemania. German Centre for Integrative Biodiversity Research; Alemania Fil: Kirkpatrick, Lucinda. Imperial College London. Department of Life Sciences,; Reino Unido Fil: Kleyer, Michael. University of Oldenburg. Institute of Biology and Environmental Sciences. Landscape Ecology Group; Alemania Fil: Pinto Correia, David Laginha. Natural History Museum. Department of Life Sciences; Reino Unido Fil: Martin, Callum D.. Imperial College London. Department of Life Sciences; Reino Unido Fil: Meiri, Shai. Tel-Aviv University. Faculty of Life Sciences. Deptartment of Zoology; Israel Fil: Novosolov, Maria. Tel-Aviv University. Faculty of Life Sciences. Deptartment of Zoology; Israel Fil: Pan, Yuan. Imperial College London. Department of Life Sciences; Reino Unido Fil: Phillips, Helen R. P.. Natural History Museum. Department of Life Sciences; Reino Unido. Imperial College London. Department of Life Sciences; Reino Unido Fil: Purves, Drew W.. Microsoft Research Cambridge. Computational Science Laboratory, ; Reino Unido Fil: Robinson, Alexandra. Imperial College London. Department of Life Sciences; Reino Unido Fil: Simpson, Jake. Imperial College London. Department of Life Sciences; Reino Unido Fil: Tuck, Sean L.. University of Oxford, Department of Plant Sciences; Reino Unido Fil: Weiher, Evan. University of Wisconsin–Eau Claire. Biology Department; Estados Unidos Fil: White, Hannah J.. Imperial College London. Department of Life Sciences; Reino Unido Fil: Ewers, Robert M.. Imperial College London. Department of Life Sciences; Reino Unido Fil: Mace, Georgina M.. University College London. Centre for Biodiversity and Environment Research. Department of Genetics, Evolution and Environment; Reino Unido Fil: Scharlemann, Jörn P. W.. United Nations Environment Programme World Conservation Monitoring Centre; Reino Unido Fil: Purvis, Andy. Natural History Museum. Department of Life Sciences; Reino Unido. Imperial College London. Department of Life Sciences; Reino Unido

Esta tercera entrega del reporte anual de la biodiversidad en Colombia profundiza en la linea editorial iniciada el ano 2014 mediante nuevas propuestas analiticas y graficas, con la intencion de garantizar que la informacion llegue a todos los publicos y pueda ser discutida de manera amena sin sacrificio de calidad. La apuesta comunicativa sigue siendo central en el proyecto institucional y los nuevos lenguajes con los que estamos aprendiendo a conversar con la sociedad y las instituciones son un experimento que esperamos sea cada vez mas satisfactorio: ya estamos construyendo la version 2017 con el apoyo de las nuevas tecnologias digitales de manera que la potencia de la conexion vital colombiana se exprese en toda su capacidad. Por los contenidos es evidente que aun distamos mucho de tener una capacidad de seguimiento sistematico para la mayoria de temas relativos a la gestion de la biodiversidad y los servicios ecosistemicos, la unica manera de evaluar si las medidas de politica y las inversiones que realiza la sociedad estan teniendo los efectos deseados. De hecho, parte de las limitaciones reconocidas por robustamente los cambios positivos o negativos que afectan los diferentes niveles de organizacion de la vida planetaria, por lo cual las mismas metas de Aichi, nuestra carta de navegacion global, estan pendientes de verificacion. Un proposito adicional de este proceso es la invitacion a todos los colombianos para contribuir con la construccion y alimentacion de los indicadores basicos de seguimiento a la gestion, ya que es imposible identificar las tendencias de largo plazo en que estan inmersas la flora y fauna colombianas sin el apoyo de las instituciones, los investigadores y los ciudadanos: en el pais de la megadiversidad, el reto es inmenso. Por este motivo, este reporte ira abriendo sus paginas a expertos, incluso indigenas o de comunidades locales, para que presenten de manera sistematica y documentada sus perspectivas del cambio ambiental y sus efectos en la biodiversidad, con el animo de promover el compromiso de todos en su gestion. La unica manera de superar el riesgo de extincion es mediante un activo proceso de aprendizajes sociales que haga que todos los sectores asuman una parte de la compleja responsabilidad que significa proteger todas las formas de vida del pais, una decima parte mal contada de las planetarias. Agradezco a las decenas de personas que contribuyeron con este reporte, a quienes nos han apoyado en todas las etapas de produccion y a sus lectores y usuarios, quienes son en ultimo termino los jueces de su utilidad.

Panbiogeography represents an evolutionary approach to biogeography, using rational cost-efficient methods to reduce initial complexity to locality data, and depict general distribution patterns. However, few quantitative, and automated panbiogeographic methods exist. In this study, we propose a new algorithm, within a quantitative, geometrical framework, to perform panbiogeographical analyses as an alternative to more traditional methods. The algorithm first calculates a minimum spanning tree, an individual track for each species in a panbiogeographic context. Then the spatial congruence among segments of the minimum spanning trees is calculated using five congruence parameters, producing a general distribution pattern. In addition, the algorithm removes the ambiguity, and subjectivity often present in a manual panbiogeographic analysis. Results from two empirical examples using 61 species of the genus Bomarea (2340 records), and 1031 genera of both plants and animals (100118 records) distributed across the Northern Andes, demonstrated that a geometrical approach to panbiogeography is a feasible quantitative method to determine general distribution patterns for taxa, reducing complexity, and the time needed for managing large data sets.