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1.
Proc Natl Acad Sci U S A ; 117(11): 5949-5954, 2020 Mar 17.
Artículo en Inglés | MEDLINE | ID: mdl-32123088

RESUMEN

The live poultry trade is thought to play an important role in the spread and maintenance of highly pathogenic avian influenza A viruses (HP AIVs) in Asia. Despite an abundance of small-scale observational studies, the role of the poultry trade in disseminating AIV over large geographic areas is still unclear, especially for developing countries with complex poultry production systems. Here we combine virus genomes and reconstructed poultry transportation data to measure and compare the spatial spread in China of three key subtypes of AIV: H5N1, H7N9, and H5N6. Although it is difficult to disentangle the contribution of confounding factors, such as bird migration and spatial distance, we find evidence that the dissemination of these subtypes among domestic poultry is geographically continuous and likely associated with the intensity of the live poultry trade in China. Using two independent data sources and network analysis methods, we report a regional-scale community structure in China that might explain the spread of AIV subtypes in the country. The identification of this structure has the potential to inform more targeted strategies for the prevention and control of AIV in China.

2.
Proc Natl Acad Sci U S A ; 117(8): 4234-4242, 2020 Feb 25.
Artículo en Inglés | MEDLINE | ID: mdl-32029592

RESUMEN

Continual evolution describes the unceasing evolution of at least one trait involving at least one organism. The Red Queen Hypothesis is a specific case in which continual evolution results from coevolution of at least two species. While microevolutionary studies have described examples in which evolution does not cease, understanding which general conditions lead to continual evolution or to stasis remains a major challenge. In many cases, it is unclear which experimental features or model assumptions are necessary for the observed continual evolution to emerge, and whether the described behavior is robust to variations in the given setup. Here, we aim to find the minimal set of conditions under which continual evolution occurs. To this end, we present a theoretical framework that does not assume any specific functional form and, therefore, can be applied to a wide variety of systems. Our framework is also general enough to make predictions about both monomorphic and polymorphic populations. We show that the combination of a fast positive and a slow negative feedback between environment, population, and evolving traits causes continual evolution to emerge even from the evolution of a single evolving trait, provided that the ecological timescale is sufficiently faster than the timescales of mutation and the negative feedback. Our approach and results thus contribute to a deeper understanding of the evolutionary dynamics resulting from biotic interactions.

3.
Proc Natl Acad Sci U S A ; 117(8): 4273-4280, 2020 Feb 25.
Artículo en Inglés | MEDLINE | ID: mdl-32054783

RESUMEN

Bacillus anthracis, the etiological agent of anthrax, is a well-established model organism. For B. anthracis and most other infectious diseases, knowledge regarding transmission and infection parameters in natural systems, in large part, comprises data gathered from closely controlled laboratory experiments. Fatal, natural anthrax infections transmit the bacterium through new host-pathogen contacts at carcass sites, which can occur years after death of the previous host. For the period between contact and death, all of our knowledge is based upon experimental data from domestic livestock and laboratory animals. Here we use a noninvasive method to explore the dynamics of anthrax infections, by evaluating the terminal diversity of B. anthracis in anthrax carcasses. We present an application of population genetics theory, specifically, coalescence modeling, to intrainfection populations of B. anthracis to derive estimates for the duration of the acute phase of the infection and effective population size converted to the number of colony-forming units establishing infection in wild plains zebra (Equus quagga). Founding populations are small, a few colony-forming units, and infections are rapid, lasting roughly between 1 d and 3 d in the wild. Our results closely reflect experimental data, showing that small founding populations progress acutely, killing the host within days. We believe this method is amendable to other bacterial diseases from wild, domestic, and human systems.

4.
Genome Biol Evol ; 12(2): 3832-3849, 2020 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-31971556

RESUMEN

The great gerbil (Rhombomys opimus) is a social rodent living in permanent, complex burrow systems distributed throughout Central Asia, where it serves as the main host of several important vector-borne infectious pathogens including the well-known plague bacterium (Yersinia pestis). Here, we present a continuous annotated genome assembly of the great gerbil, covering over 96% of the estimated 2.47-Gb genome. Taking advantage of the recent genome assemblies of the sand rat (Psammomys obesus) and the Mongolian gerbil (Meriones unguiculatus), comparative immunogenomic analyses reveal shared gene losses within TLR gene families (i.e., TLR8, TLR10, and the entire TLR11-subfamily) for Gerbillinae, accompanied with signs of diversifying selection of TLR7 and TLR9. Most notably, we find a great gerbil-specific duplication of the MHCII DRB locus. In silico analyses suggest that the duplicated gene provides high peptide binding affinity for Yersiniae epitopes as well as Leishmania and Leptospira epitopes, putatively leading to increased capability to withstand infections by these pathogens. Our study demonstrates the power of whole-genome sequencing combined with comparative genomic analyses to gain deeper insight into the immunogenomic landscape of the great gerbil and its close relatives.

5.
BMC Ecol ; 20(1): 5, 2020 01 28.
Artículo en Inglés | MEDLINE | ID: mdl-31992270

RESUMEN

BACKGROUND: The availability of preferred habitats determines the spatial and temporal distribution of herbivores in savanna ecosystems. Understanding habitat preference of a targeted wildlife species is crucial for developing effective conservation strategies. Habitat preference of large grazers in connection to grass height and post-fire effect has been debated for the last century. Here, we examined the effects of season, grass height and burning on the habitat preference on Swayne's hartebeest (Alcelaphus buselaphus swaynei) in Maze National Park. Data for seasonal habitat selection were collected using both direct observation along established transect lines and pellet counting using permanently established plots. Every month, we measured grass height commonly preferred by Swayne's hartebeest in grassland habitat. Starting from the first week of burning, we recorded the abundance of Swayne's hartebeest in both burned and unburned grassland patches. RESULTS: From detected pellets, 94.3% were recorded in the grassland habitat indicating that other habitat types are less used despite their extensive cover > 50% of the Park. During wet and early dry seasons, Swayne's hartebeest exclusively preferred grassland habitat. We found that 85.2% (n = 1079) and 85.3% (n = 593) of individuals observed in areas with a grass height below 30 cm during wet and early-dry seasons, respectively; while 70.9% (n = 2288) preferred grass height below 30 cm during the dry season. The density of Swayne's hartebeest in burned grassland area was higher than unburned grassland areas up to 150 days since burning. However, in unburned grassland areas, the density was initially low but showed increasing trend for consecutive days, reaching similar density with burned areas after 150 days since burning. CONCLUSION: Swayne's hartebeest exclusively preferred grassland habitat, particularly during wet and early-dry seasons, shortest available grass height in all seasons and were attracted to burned grassland areas. Our results suggested that fire played an important role in maintaining habitat quality in grassland, and that management should continue using controlled burning as a tool for the conservation of Swayne's hartebeest. However, we remain cautious of our findings given the paucity of information regarding other confounding factors and the absence of long-term data on fire disturbance.


Asunto(s)
Antílopes , Ecosistema , Animales , Etiopía , Pradera , Parques Recreativos , Estaciones del Año
6.
Nat Commun ; 11(1): 281, 2020 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-31941912

RESUMEN

Yersinia pestis is transmitted from fleas to rodents when the bacterium develops an extensive biofilm in the foregut of a flea, starving it into a feeding frenzy, or, alternatively, during a brief period directly after feeding on a bacteremic host. These two transmission modes are in a trade-off regulated by the amount of biofilm produced by the bacterium. Here by investigating 446 global isolated Y. pestis genomes, including 78 newly sequenced isolates sampled over 40 years from a plague focus in China, we provide evidence for strong selection pressures on the RNA polymerase ω-subunit encoding gene rpoZ. We demonstrate that rpoZ variants have an increased rate of biofilm production in vitro, and that they evolve in the ecosystem during colder and drier periods. Our results support the notion that the bacterium is constantly adapting-through extended phenotype changes in the fleas-in response to climate-driven changes in the niche.


Asunto(s)
Proteínas Bacterianas/genética , Peste/microbiología , Siphonaptera/microbiología , Yersinia pestis/fisiología , Animales , Biopelículas , Evolución Biológica , China , Clima , ARN Polimerasas Dirigidas por ADN/genética , Reservorios de Enfermedades , Ecosistema , Infestaciones por Pulgas , Variación Genética , Genoma Bacteriano , Interacciones Huésped-Parásitos , Interacciones Huésped-Patógeno , Marmota/parasitología , Fenotipo , Filogenia , Sciuridae/parasitología , Selección Genética , Siphonaptera/fisiología , Yersinia pestis/genética
7.
Proc Natl Acad Sci U S A ; 117(6): 3026-3033, 2020 02 11.
Artículo en Inglés | MEDLINE | ID: mdl-31988125

RESUMEN

The Arctic climate was warmer than today at the last interglacial and the Holocene thermal optimum. To reveal the impact of past climate-warming events on the demographic history of an Arctic specialist, we examined both mitochondrial and nuclear genomic variation in the collared lemming (Dicrostonyx torquatus, Pallas), a keystone species in tundra communities, across its entire distribution in northern Eurasia. The ancestral phylogenetic position of the West Beringian group and divergence time estimates support the hypothesis of continental range contraction to a single refugial area located in West Beringia during high-magnitude warming of the last interglacial, followed by westward recolonization of northern Eurasia in the last glacial period. The West Beringian group harbors the highest mitogenome diversity and its inferred demography indicates a constantly large effective population size over the Late Pleistocene to Holocene. This suggests that northward forest expansion during recent warming of the Holocene thermal optimum did not affect the gene pool of the collared lemming in West Beringia but reduced genomic diversity and effective population size in all other regions of the Eurasian Arctic. Demographic inference from genomic diversity was corroborated by species distribution modeling showing reduction in species distribution during past climate warming. These conclusions are supported by recent paleoecological evidence suggesting smaller temperature increases and moderate northward forest advances in the extreme northeast of Eurasia during the Late Pleistocene-to-Holocene warming events. This study emphasizes the importance of West Beringia as a potential refugium for cold-adapted Arctic species under ongoing climate warming.


Asunto(s)
Arvicolinae/genética , Variación Genética/genética , Calentamiento Global/historia , Animales , Regiones Árticas , Asia , Europa (Continente) , Genoma/genética , Genoma Mitocondrial/genética , Genómica , Historia Antigua , Refugio de Fauna , Tundra
8.
Proc Natl Acad Sci U S A ; 117(1): 29-36, 2020 01 07.
Artículo en Inglés | MEDLINE | ID: mdl-31871172

RESUMEN

CO2 emissions are of global concern because of climate change. China has become the largest CO2 emitter in the world and presently accounts for 30% of global emissions. Here, we analyze the major drivers of energy-related CO2 emissions in China from 1978 when the reform and opening-up policy was launched. We find that 1) there has been a 6-fold increase in energy-related CO2 emissions, which was driven primarily (176%) by economic growth followed by population growth (16%), while the effects of energy intensity (-79%) and carbon intensity (-13%) slowed the growth of carbon emissions over most of this period; 2) energy-related CO2 emissions are positively related to per capita gross domestic product (GDP), population growth rate, carbon intensity, and energy intensity; and 3) a portfolio of command-and-control policies affecting the drivers has altered the total emission trend. However, given the major role of China in global climate change mitigation, significant future reductions in China's CO2 emissions will require transformation toward low-carbon energy systems.

9.
Am J Primatol ; : e23074, 2019 Dec 03.
Artículo en Inglés | MEDLINE | ID: mdl-31793676

RESUMEN

Primates inhabiting human-modified landscapes often exploit matrix habitat to supplement their diet with cultivated foods, at times resulting in economic losses and conflict with local people. Understanding human-nonhuman primate interactions and the attitudes and perceptions of local people towards crop feeding species are crucial to designing effective species-based management plans. Over a 12-month period, we used scan sampling to study the consumption of cultivated foods and matrix use patterns by two habituated groups of Bale monkeys (Chlorocebus djamdjamensis), Ethiopian-endemic bamboo specialists, in two forest fragments (Kokosa and Afursa) set amidst human settlements and farmland in the southern Ethiopian Highlands. Further, we conducted interviews with local people to document their attitudes and perceptions towards Bale monkeys at the two sites. We found that Bale monkeys at Kokosa, a more degraded habitat by most measures, consumed significantly more cultivated foods than their counterparts at Afursa. Moreover, Bale monkeys at Kokosa spent significantly more time in the matrix than in the forest habitat, while monkeys at Afursa spent significantly less time in the matrix than in the forest habitat. Not surprisingly, local people displayed a more negative attitude towards monkeys inhabiting Kokosa than those inhabiting Afursa. The differences in Bale monkey cultivated food consumption and matrix use patterns-as well as in local people's attitudes and perceptions towards Bale monkeys-between Kokosa and Afursa are probably associated with differences in habitat structure, degree of habitat alteration, and land-use practices between the sites. We conclude that to ensure long-term coexistence between Bale monkeys and local people in human-modified landscapes, it is vital to incorporate nearby matrix habitats into management plans and to work closely with local communities to develop effective nonlethal crop protection strategies, thereby reducing the likelihood of negative interactions between Bale monkeys and humans.

10.
Proc Natl Acad Sci U S A ; 116(38): 19001-19008, 2019 Sep 17.
Artículo en Inglés | MEDLINE | ID: mdl-31481618

RESUMEN

Accelerated anthropogenic impacts and climatic changes are widely considered to be responsible for unprecedented species extinction. However, determining their effects on extinction is challenging owing to the lack of long-term data with high spatial and temporal resolution. In this study, using historical occurrence records of 11 medium- to large-sized mammal species or groups of species in China from 905 BC to AD 2006, we quantified the distinctive associations of anthropogenic stressors (represented by cropland coverage and human population density) and climatic stressors (represented by air temperature) with the local extinction of these mammals. We found that both intensified human disturbances and extreme climate change were associated with the increased local extinction of the study mammals. In the cold phase (the premodern period of China), climate cooling was positively associated with increased local extinction, while in the warm phase (the modern period) global warming was associated with increased local extinction. Interactive effects between human disturbance and temperature change with the local extinction of elephants, rhinos, pandas, and water deer were found. Large-sized mammals, such as elephants, rhinos, and pandas, showed earlier and larger population declines than small-sized ones. The local extinction sensitivities of these mammals to the human population density and standardized temperature were estimated during 1700 to 2000. The quantitative evidence for anthropogenic and climatic associations with mammalian extinction provided insights into the driving processes of species extinction, which has important implications for biodiversity conservation under accelerating global changes.

11.
PLoS Negl Trop Dis ; 13(9): e0007757, 2019 09.
Artículo en Inglés | MEDLINE | ID: mdl-31545808

RESUMEN

Seoul hantavirus (SEOV) has recently raised concern by causing geographic range expansion of hemorrhagic fever with renal syndrome (HFRS). SEOV infections in humans are significantly underestimated worldwide and epidemic dynamics of SEOV-related HFRS are poorly understood because of a lack of field data and empirically validated models. Here, we use mathematical models to examine both intrinsic and extrinsic drivers of disease transmission from animal (the Norway rat) to humans in a SEOV-endemic area in China. We found that rat eradication schemes and vaccination campaigns, but below the local elimination threshold, could diminish the amplitude of the HFRS epidemic but did not modify its seasonality. Models demonstrate population dynamics of the rodent host were insensitive to climate variations in urban settings, while relative humidity had a negative effect on the seasonality in transmission. Our study contributes to a better understanding of the epidemiology of SEOV-related HFRS, demonstrates asynchronies between rodent population dynamics and transmission rate, and identifies potential drivers of the SEOV seasonality.


Asunto(s)
Fiebre Hemorrágica con Síndrome Renal/epidemiología , Fiebre Hemorrágica con Síndrome Renal/transmisión , Animales , China/epidemiología , Ciudades , Clima , Fiebre Hemorrágica con Síndrome Renal/prevención & control , Humanos , Modelos Teóricos , Control de Roedores , Roedores/virología , Estaciones del Año , Virus Seoul , Vacunación
12.
R Soc Open Sci ; 6(6): 190216, 2019 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-31312490

RESUMEN

Plague remains a threat to public health and is considered as a re-emerging infectious disease today. Rodents play an important role as major hosts in plague persistence and driving plague outbreaks in natural foci; however, few studies have tested the association between host diversity in ecosystems and human plague risk. Here we use zero-inflated generalized additive models to examine the association of species richness with human plague presence (where plague outbreaks could occur) and intensity (the average number of annual human cases when they occurred) in China during the Third Pandemic. We also account for transportation network density, annual precipitation levels and human population size. We found rodent species richness, particularly of rodent plague hosts, is positively associated with the presence of human plague. Further investigation shows that species richness of both wild and commensal rodent plague hosts are positively correlated with the presence, but only the latter correlated with the intensity. Our results indicated a positive relationship between rodent diversity and human plague, which may provide suggestions for the plague surveillance system.

14.
15.
Nat Commun ; 10(1): 2836, 2019 06 27.
Artículo en Inglés | MEDLINE | ID: mdl-31249288

RESUMEN

Conservation efforts and management decisions on the living environment of our planet often rely on the results from statistical models. Yet, these models are imperfect and quantification of risk associated with the estimate of management-relevant quantities becomes crucial in providing robust advice. Here we demonstrate that estimates of risk themselves could be substantially biased but by combining data fitting with an extensive simulation-estimation procedure, one can back-calculate the correct values. We apply the method to 627 time series of population abundance across four taxa using the Gompertz state-space model as an example. We find that the risk of large bias in population status estimate increases with the species' growth rate, population variability, weaker density dependence, and shorter time series, across taxa. We urge scientists dealing with conservation and management to adopt a similar approach to ensure a more accurate estimate of risk measures and contribute towards a precautionary approach to management.


Asunto(s)
Conservación de los Recursos Naturales , Medición de Riesgo/métodos , Animales , Ecología , Humanos , Modelos Estadísticos , Densidad de Población , Dinámica Poblacional
16.
Proc Natl Acad Sci U S A ; 116(19): 9155-9163, 2019 May 07.
Artículo en Inglés | MEDLINE | ID: mdl-31061115

RESUMEN

Zoonoses, such as plague, are primarily animal diseases that spill over into human populations. While the goal of eradicating such diseases is enticing, historical experience validates abandoning eradication in favor of ecologically based control strategies (which reduce morbidity and mortality to a locally accepted risk level). During the 20th century, one of the most extensive plague-eradication efforts in recorded history was undertaken to enable large-scale changes in land use in the former Soviet Union (including vast areas of central Asia). Despite expending tremendous resources in its attempt to eradicate plague, the Soviet antiplague response gradually abandoned the goal of eradication in favor of plague control linked with developing basic knowledge of plague ecology. Drawing from this experience, we combine new gray-literature sources, historical and recent research, and fieldwork to outline best practices for the control of spillover from zoonoses while minimally disrupting wildlife ecosystems, and we briefly compare the Soviet case with that of endemic plague in the western United States. We argue for the allocation of sufficient resources to maintain ongoing local surveillance, education, and targeted control measures; to incorporate novel technologies selectively; and to use ecological research to inform developing landscape-based models for transmission interruption. We conclude that living with emergent and reemergent zoonotic diseases-switching to control-opens wider possibilities for interrupting spillover while preserving natural ecosystems, encouraging adaptation to local conditions, and using technological tools judiciously and in a cost-effective way.

17.
Proc Natl Acad Sci U S A ; 116(24): 11833-11838, 2019 Jun 11.
Artículo en Inglés | MEDLINE | ID: mdl-31138696

RESUMEN

Quantitative knowledge about which natural and anthropogenic factors influence the global spread of plague remains sparse. We estimated the worldwide spreading velocity of plague during the Third Pandemic, using more than 200 years of extensive human plague case records and genomic data, and analyzed the association of spatiotemporal environmental factors with spreading velocity. Here, we show that two lineages, 2.MED and 1.ORI3, spread significantly faster than others, possibly reflecting differences among strains in transmission mechanisms and virulence. Plague spread fastest in regions with low population density and high proportion of pasture- or forestland, findings that should be taken into account for effective plague monitoring and control. Temperature exhibited a nonlinear, U-shaped association with spread speed, with a minimum around 20 °C, while precipitation showed a positive association. Our results suggest that global warming may accelerate plague spread in warm, tropical regions and that the projected increased precipitation in the Northern Hemisphere may increase plague spread in relevant regions.

19.
Artículo en Inglés | MEDLINE | ID: mdl-30884913

RESUMEN

How a disease is transmitted affects our ability to determine R0, the average number of new cases caused by an infectious host at the onset of an epidemic. R0 becomes progressively more difficult to compute as transmission varies from directly transmitted diseases to diseases that are vector-borne to environmentally transmitted diseases. Pathogens responsible for diseases with environmental transmission are typically maintained in environmental reservoirs that exhibit a complex spatial distribution of local infectious zones (LIZs). Understanding host encounters with LIZs and pathogen persistence within LIZs is required for an accurate R0 and modeling these contacts requires an integrated geospatial and dynamical systems approach. Here we review how interactions between host and pathogen populations and environmental reservoirs are driven by landscape-level variables, and synthesize the quantitative framework needed to formulate outbreak response and disease control.


Asunto(s)
Migración Animal , Enfermedades Transmisibles/epidemiología , Modelos Biológicos , Animales , Brotes de Enfermedades , Humanos
20.
Nature ; 567(7749): 516-520, 2019 03.
Artículo en Inglés | MEDLINE | ID: mdl-30818324

RESUMEN

The nitrogen cycle has been radically changed by human activities1. China consumes nearly one third of the world's nitrogen fertilizers. The excessive application of fertilizers2,3 and increased nitrogen discharge from livestock, domestic and industrial sources have resulted in pervasive water pollution. Quantifying a nitrogen 'boundary'4 in heterogeneous environments is important for the effective management of local water quality. Here we use a combination of water-quality observations and simulated nitrogen discharge from agricultural and other sources to estimate spatial patterns of nitrogen discharge into water bodies across China from 1955 to 2014. We find that the critical surface-water quality standard (1.0 milligrams of nitrogen per litre) was being exceeded in most provinces by the mid-1980s, and that current rates of anthropogenic nitrogen discharge (14.5 ± 3.1 megatonnes of nitrogen per year) to fresh water are about 2.7 times the estimated 'safe' nitrogen discharge threshold (5.2 ± 0.7 megatonnes of nitrogen per year). Current efforts to reduce pollution through wastewater treatment and by improving cropland nitrogen management can partially remedy this situation. Domestic wastewater treatment has helped to reduce net discharge by 0.7 ± 0.1 megatonnes in 2014, but at high monetary and energy costs. Improved cropland nitrogen management could remove another 2.3 ± 0.3 megatonnes of nitrogen per year-about 25 per cent of the excess discharge to fresh water. Successfully restoring a clean water environment in China will further require transformational changes to boost the national nutrient recycling rate from its current average of 36 per cent to about 87 per cent, which is a level typical of traditional Chinese agriculture. Although ambitious, such a high level of nitrogen recycling is technologically achievable at an estimated capital cost of approximately 100 billion US dollars and operating costs of 18-29 billion US dollars per year, and could provide co-benefits such as recycled wastewater for crop irrigation and improved environmental quality and ecosystem services.


Asunto(s)
Agricultura/métodos , Fertilizantes/análisis , Fertilizantes/provisión & distribución , Ciclo del Nitrógeno , Nitrógeno/análisis , Nitrógeno/provisión & distribución , Calidad del Agua/normas , Agricultura/estadística & datos numéricos , Animales , China , Ecosistema , Monitoreo del Ambiente , Abastecimiento de Alimentos/métodos , Abastecimiento de Alimentos/estadística & datos numéricos , Humanos , Contaminantes Químicos del Agua/análisis , Contaminación del Agua/análisis
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