Region effects influence local tree species diversity

Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species.Ecologists generally agree that large-scale patterns of diversity reflect a balance between regional processes of species production, extinction, and dispersal, on one hand, and within-region sorting of species based on adaptations to physical conditions of the environment, as well as competition among species for limiting resources, on the other hand (1–4). Nonetheless, the spatial scale down to which region effects extend has not been well resolved (5–7), but has wide-ranging implications for understanding the origins of patterns in local species richness. If the species richness of a local assemblage were strictly limited by competition and other local interactions among populations, new species could not be added without others being forced out, and we would expect to find a common relationship between diversity and local environmental conditions across regions (6). However, if unique historical and biogeographic features of each region influenced within-region diversification and extinction (8–10), these region-specific effects might contribute to the global pattern in local species richness. Efforts to disentangle these effects have met with limited success and have led to a long-standing discussion of the relationship between local and regional diversity (6, 11–21).Analyses designed to distinguish local and regional influences on diversity have found strong region effects in some cases (8, 22) and weak or nonexistent region effects in others (15, 23–25). However, most studies that failed to find significant region effects either have addressed large, biologically heterogeneous samples, or they have used local samples (e.g., 0.1-ha “Gentry” plots) that are too small to characterize the diversity of local assemblages adequately (26, 27). Additionally, many large-scale samples have been compiled from maps generated from presence-only museum records or from coarse-scale atlases that document the extent of species occupancy, not actual local occurrence. Such data often undercount local species richness. Moreover, many tests of the diversity–environment relationship have analyzed data on local communities that extend over broad ranges of ecological conditions (e.g., tropical rainforests to arctic tundra and hot deserts; ref. 25) with a range of biomes and vegetation types unevenly represented among regions. These sampling issues have confounded the testing of region effects.In this study, we analyze a dataset of tree species richness from the Center for Tropical Forest Science—Forest Global Earth Observatories (CTFS—ForestGEO; www.forestgeo.si.edu/; ref. 28) to disentangle the influences of local climate and regional factors, i.e., differences between regions resulting from unique histories and geographic settings, on the global biodiversity pattern. The data represent 47 forest dynamics plots distributed worldwide (Fig. 1) with a median size of 25 ha, within which all individual trees equal to or greater than 1 cm diameter at breast height (DBH) were identified and counted (SI Appendix, Table S1). Plots of this size are large enough to include adequate samples of species richness, but small enough to avoid substantial heterogeneity in climate and vegetation structure within them. The CTFS data are complete censuses, and the species richness in each plot is accurate. Many previous studies have been based on data from herbarium records of coarse-scale species range maps, and species richness is generally underestimated, considerably so in some cases. Moreover, the forest plots represent a single vegetation type surveyed over a range of environmental conditions. We assembled for each plot a set of local plot characteristics and climate data, and used generalized linear models to characterize the relationship between number of tree species and local plot variables and to test the additional statistical effect of region on local species richness. Our analyses were repeated for species richness with tree DBH ≥ 1 cm and DBH ≥ 10 cm.Open in a separate windowFig. 1.Global distribution of the 47 CTFS plots. The number associated with each plot is its size in hectares. The base vegetation map is the 2012 MODIS global land cover map (www.landcover.org/data/lc/) with IGBP Land Cover Type Classification.     

Plant extinctions and introductions lead to phylogenetic and taxonomic homogenization of the European flora

Human activities have altered the composition of biotas through two fundamental processes: native extinctions and alien introductions. Both processes affect the taxonomic (i.e., species identity) and phylogenetic (i.e., species evolutionary history) structure of species assemblages. However, it is not known what the relative magnitude of these effects is at large spatial scales. Here we analyze the large-scale effects of plant extinctions and introductions on taxonomic and phylogenetic diversity of floras across Europe, using data from 23 regions. Considering both native losses and alien additions in concert reveals that plant invasions since AD 1500 exceeded extinctions, resulting in (i) increased taxonomic diversity (i.e., species richness) but decreased phylogenetic diversity within European regions, and (ii) increased taxonomic and phylogenetic similarity among European regions. Those extinct species were phylogenetically and taxonomically unique and typical of individual regions, and extinctions usually were not continent-wide and therefore led to differentiation. By contrast, because introduced alien species tended to be closely related to native species, the floristic differentiation due to species extinction was lessened by taxonomic and phylogenetic homogenization effects. This was especially due to species that are alien to a region but native to other parts of Europe. As a result, floras of many European regions have partly lost and will continue to lose their uniqueness. The results suggest that biodiversity needs to be assessed in terms of both species taxonomic and phylogenetic identity, but the latter is rarely used as a metric of the biodiversity dynamics.     

Epidemic disease decimates amphibian abundance,species diversity,and evolutionary history in the highlands of central Panama

Amphibian populations around the world are experiencing unprecedented declines attributed to a chytrid fungal pathogen, Batrachochytrium dendrobatidis. Despite the severity of the crisis, quantitative analyses of the effects of the epidemic on amphibian abundance and diversity have been unavailable as a result of the lack of equivalent data collected before and following disease outbreak. We present a community-level assessment combining long-term field surveys and DNA barcode data describing changes in abundance and evolutionary diversity within the amphibian community of El Copé, Panama, following a disease epidemic and mass-mortality event. The epidemic reduced taxonomic, lineage, and phylogenetic diversity similarly. We discovered that 30 species were lost, including five undescribed species, representing 41% of total amphibian lineage diversity in El Copé. These extirpations represented 33% of the evolutionary history of amphibians within the community, and variation in the degree of population loss and decline among species was random with respect to the community phylogeny. Our approach provides a fast, economical, and informative analysis of loss in a community whether measured by species or phylogenetic diversity.     

Phylogenetic patterns of species loss in Thoreau's woods are driven by climate change

Climate change has led to major changes in the phenology (the timing of seasonal activities, such as flowering) of some species but not others. The extent to which flowering-time response to temperature is shared among closely related species might have important consequences for community-wide patterns of species loss under rapid climate change. Henry David Thoreau initiated a dataset of the Concord, Massachusetts, flora that spans ≈150 years and provides information on changes in species abundance and flowering time. When these data are analyzed in a phylogenetic context, they indicate that change in abundance is strongly correlated with flowering-time response. Species that do not respond to temperature have decreased greatly in abundance, and include among others anemones and buttercups [Ranunculaceae pro parte (p.p.)], asters and campanulas (Asterales), bluets (Rubiaceae p.p.), bladderworts (Lentibulariaceae), dogwoods (Cornaceae), lilies (Liliales), mints (Lamiaceae p.p.), orchids (Orchidaceae), roses (Rosaceae p.p.), saxifrages (Saxifragales), and violets (Malpighiales). Because flowering-time response traits are shared among closely related species, our findings suggest that climate change has affected and will likely continue to shape the phylogenetically biased pattern of species loss in Thoreau's woods.     

Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions

The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens. A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity—the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences.     

新型隐球菌及念珠菌临床分离株对5种抗真菌药物的体外敏感性

目的 了解临床分离的新型隐球和念珠菌对氟康唑、两性霉素B、伊曲康唑、氟胞嘧啶和酮康唑的体外敏感性及临床治疗效果的相关性。方法 采用标准微量稀释法测定了上述5种抗真菌药物对临床分离株的35株新型隐球菌和56株念株菌量的最低抑菌浓度（MIC）。结果 56株念珠菌对5种药物的敏感性（MIC）分别为氟康唑0.125～64ug/ml,94.6%的菌株对氟康唑敏感,1.8%为剂量依赖性敏感,3.6%耐药;伊曲康唑0.03～1ug/ml,57.1%敏感,37.5%剂量依赖性敏感,5.4%耐药;氟咆嘧啶 0.125～32ug/ml,92.8%敏感,3.6%中度敏感,3.6%耐药;两性霉素B0.06～2ug/ml;酮康唑0.03～0.5ug/ml。35株新型隐球菌对5种药物的MIC范围分别为氟康唑2～64ug/ml,伊曲康唑0.25～1ug/ml,两性霉素B0.3～1ug/ml,氟胞嘧啶0.25～64ug/ml,酮康唑0.125～1ug/ml。结论 标准微量稀释法测定酵母菌对抗真菌药物的敏感性其结果具有可重复性和一致性的特点。     

Prediction,dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses

Human seasonal influenza viruses evolve rapidly, enabling the virus population to evade immunity and reinfect previously infected individuals. Antigenic properties are largely determined by the surface glycoprotein hemagglutinin (HA), and amino acid substitutions at exposed epitope sites in HA mediate loss of recognition by antibodies. Here, we show that antigenic differences measured through serological assay data are well described by a sum of antigenic changes along the path connecting viruses in a phylogenetic tree. This mapping onto the tree allows prediction of antigenicity from HA sequence data alone. The mapping can further be used to make predictions about the makeup of the future A(H3N2) seasonal influenza virus population, and we compare predictions between models with serological and sequence data. To make timely model output readily available, we developed a web browser-based application that visualizes antigenic data on a continuously updated phylogeny.Seasonal influenza viruses evade immunity in the human population through frequent amino acid substitutions in their hemagglutinin (HA) and neuraminidase (NA) surface glycoproteins (1). To maintain efficacy, vaccines against seasonal influenza viruses need to be updated frequently to match the antigenic properties of the circulating viruses. To facilitate informed vaccine strain selection, the genotypes and antigenic properties of circulating viruses are continuously monitored by the World Health Organization (WHO) Global Influenza Surveillance and Response System (GISRS), with a substantial portion of the virological characterizations being performed by the WHO influenza Collaborating Centers (WHO CCs) (2).Antigenic properties of influenza viruses are measured in hemagglutination inhibition (HI) assays (3) that record the minimal antiserum concentration (titer) necessary to prevent crosslinking of red blood cells by a standardized amount of virus based on hemagglutinating units. An antiserum is typically obtained from a single ferret infected with a particular reference virus. For a panel of test viruses, the HI titer is determined by a series of twofold dilutions of each antiserum. An antiserum is typically potent against the homologous virus (the reference virus used to produce the antiserum), but higher concentrations (and hence lower titers) are frequently required to prevent hemagglutination by other (heterologous) test viruses. HI titers typically decrease with increasing genetic distance between reference and test viruses (1).Given multiple antisera raised against different reference viruses and a panel of test viruses, WHO CCs routinely measure the HI titers T_aβ of all combinations of test viruses a and sera β, resulting in a matrix of HI titers (see Fig. 1A). The HI titer of a test virus a using antiserum β raised against the reference virus b is typically standardized as H_aβ = log₂(T_bβ) ? log₂(T_aβ), i.e., the difference in the number of twofold dilutions between homologous and heterologous titer. Standardized log₂ titers from many HI assays can be visualized in two dimensions via multidimensional scaling—an approach termed “antigenic cartography” (4). Although standard cartography does not use sequence information, sequences have been used as priors for positions in a Bayesian version of multidimensional scaling (5). To infer contributions of individual amino acid substitutions to antigenic evolution, Harvey et al. and Sun et al. (6, 7) have used models that predict HI titer differences by comparing sequences of reference and test viruses.Open in a separate windowFig. 1.Antigenic data and models for HI titers. (A) A typical table reporting HI titer data. Each number in the table is the maximum dilution at which the antiserum (column) inhibited hemagglutination of red blood cells by a virus (row). The red numbers on the diagonal indicate homologous titers. A typical HI assay consists of all reciprocal measurements of the available antisera and reference viruses, and a number of test viruses that are measured against all antisera, but for which no homologous antiserum exists. To make measurements using different antisera comparable, we define standardized log-transformed titers H_aβ relative to the homologous titer. (B) Each HI titer between antiserum α and virus b can be associated with a path on the tree connecting the reference and test viruses a and b, respectively, indicated as a thick line. The tree model seeks to explain the antigenic differences as additive contributions of branches. (C) In the substitution model, the sum over branches on the tree is replaced by a sum of contributions of amino acid substitutions.Here, we show that antigenic properties of seasonal influenza viruses are accurately described by a model based on the phylogenetic tree structure of their HA sequences. We use the model to show that HI titers have a largely symmetric and tree-like structure that can be used to define an antigenic distance between viruses. We show that large-effect substitutions account for about half of the total antigenic change and that the effect of specific substitutions is dependent on the genetic background in which they occur. We further investigate the ability of HI measurements to predict dominant clades in the next influenza season. To visualize antigenic properties on the phylogenetic tree, we have integrated the models of antigenic distances and the raw HI titer data into nextflu.org—an interactive real-time tracking tool for influenza virus evolution (8).This comprehensive summary of HA sequences from past and current influenza viruses linked to their antigenic properties has the potential to inform vaccine strain selections and facilitate efforts to predict successful influenza lineages (9–13).     

Niche and neutral models predict asymptotically equivalent species abundance distributions in high-diversity ecological communities

A fundamental challenge in ecology is to understand the mechanisms that govern patterns of relative species abundance. Previous numerical simulations have suggested that complex niche-structured models produce species abundance distributions (SADs) that are qualitatively similar to those of very simple neutral models that ignore differences between species. However, in the absence of an analytical treatment of niche models, one cannot tell whether the two classes of model produce the same patterns via similar or different mechanisms. We present an analytical proof that, in the limit as diversity becomes large, a strong niche model give rises to exactly the same asymptotic form of SAD as the neutral model, and we verify the analytical predictions for a Panamanian tropical forest data set. Our results strongly suggest that neutral processes drive patterns of relative species abundance in high-diversity ecological communities, even when strong niche structure exists. However, neutral theory cannot explain what generates high diversity in the first place, and it may not be valid in low-diversity communities. Our results also confirm that neutral theory cannot be used to infer an absence of niche structure or to explain ecosystem function.     

Temperature dependence, spatial scale, and tree species diversity in eastern Asia and North America

The increase of biodiversity from poles to equator is one of the most pervasive features of nature. For 2 centuries since von Humboldt, Wallace, and Darwin, biogeographers and ecologists have investigated the environmental and historical factors that determine the latitudinal gradient of species diversity, but the underlying mechanisms remain poorly understood. The recently proposed metabolic theory of ecology (MTE) aims to explain ecological patterns and processes, including geographical patterns of species richness, in terms of the effects of temperature and body size on the metabolism of organisms. Here we use 2 comparable databases of tree distributions in eastern Asia and North America to investigate the roles of environmental temperature and spatial scale in shaping geographical patterns of species diversity. We find that number of species increases exponentially with environmental temperature as predicted by the MTE, and so does the rate of spatial turnover in species composition (slope of the species-area relationship). The magnitude of temperature dependence of species richness increases with spatial scale. Moreover, the relationship between species richness and temperature is much steeper in eastern Asia than in North America: in cold climates at high latitudes there are more tree species in North America, but the reverse is true in warmer climates at lower latitudes. These patterns provide evidence that the kinetics of ecological and evolutionary processes play a major role in the latitudinal pattern of biodiversity.     

Predicting potential drop-out and future commitment for first-time donors based on first 1.5-year donation patterns: the case in Hong Kong Chinese donors

BACKGROUND AND OBJECTIVES: Adequate blood supply is crucial to the health-care system. To maintain a stable donor pool, donation-promotion strategies should not only be targeted in recruitment but also focus on retaining donors to give blood regularly. A study using statistical modelling is conducted to understand the first 4-year donation patterns for drop-out and committed first-time blood donors and to build model for the donor-type identification based on their first 1.5-year donation patterns. SUBJECTS AND METHODS: First-time whole blood (n= 20 631) adult donors recruited in year 2000 and 2001 in Hong Kong were observed for more than 4 years. Cluster analysis was first applied to group donor type by their similarities in donation behaviour under the surveillance period. A decision tree model based on a shorter surveillance period (1.5 years) is then built to predict the donor type. RESULTS: Three donation patterns - one-time, drop-out, and committed donor behaviour - were identified in cluster analysis. Three variables - donation frequencies in the first-year and in the half-year period after first year, and the number of donation centre visits in the following half year after first year, were able to predict drop-out donors with potential to become committed and committed donors with relatively lower donation frequency. CONCLUSIONS: The present statistical modelling is able to identify those donors with potential to become committed donors and those committed donors who can donate more frequently. This information is useful for development of targeted donor retention strategies.     

人源隐孢子虫分离株种类鉴定与种系发育关系分析

目的确定郑州某医院分离到1株隐孢子虫(PRHN)所属种/基因型。方法用PCR对该分离株18S rRNA、HSP70、Cpn60和AOX进行PCR扩增,并对扩增产物进行测序,扩增序列经用DNAstar和ClustalX与GenBank参考序列比对,用PAUP4.0构建种系发育进化树,以确定该分离株与其他隐孢子虫虫种之间的亲缘关系。结果通过18S rRNA、HSP70基因分析该分离株与Cryptosporidium parvum(C.parvum)鼠基因型同源性最高,分别为99.9%和99.2%,在种系发育树上,PRHN均与C.parvum鼠基因型亲缘关系最近;对Chaperponin 60(Cpn60)和Alternative oxidase(AOX)进行序列分析时,该分离株与本实验室分离到的猪隐孢子虫(C.suis)亲缘关系最近。结论该分离株为C.parvum鼠基因型。     

肥胖症的药物治疗现状与展望

肥胖是一个严重的公众健康问题，人们迫切希望能有安全、有效的减肥药物。目前用于减肥的药物主要有两类：即西布曲明和赛尼可，前者主要抑制食物的摄取，后者抑制脂肪的吸收。由于对复杂的体重调节机制的认识越来越深入，很多新的减肥药物正在研制过程之中。目前正在研究的具有较大潜力的减肥药物共有30余种，其中研究较多的有瘦素、黑皮质素受体激动剂、神经肽Y拮抗剂、β3肾上腺素能受体激动剂、胰高血糖素样肽－1激动剂以及激活或增加解偶联蛋白表达的药物。     

Dipetalonema viteae infection in three species of rodents: species specific patterns of the antibody response

Groups of jirds (Meriones unguiculatus), multimammate rats (Mastomys natalensis) and golden hamsters (Mesocricetus auratus) were infected with third stage larvae (L3) of Dipetaloneam viteae and the course of infection was followed until 20 weeks post infection. Worm growth was best and microfilaraemia was high and long lasting in jirds and in multimammate rats, whereas golden hamsters were poor hosts as measured by these parameters. The IgG and IgM antibody responses of the species were compared by immunoblotting and ELISA using proteins of D. viteae, separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The levels of antibodies against most proteins of high molecular weight declined during infection in jirds and in multimammate rats, whereas an increase was observed in golden hamsters. In contrast, several antigens of low molecular weight induced increasing antibody levels in all species. Species specific antigen recognition was observed for a number of protein bands of L3, microfilariae and female worms. The data suggest that susceptibility to immunesuppression and the species specific pattern of antigen recognition might determine the qualities of a rodent species as host for D. viteae.     

Landscape dynamics and diversification of the megadiverse South American freshwater fish fauna

Landscape dynamics are widely thought to govern the tempo and mode of continental radiations, yet the effects of river network rearrangements on dispersal and lineage diversification remain poorly understood. We integrated an unprecedented occurrence dataset of 4,967 species with a newly compiled, time-calibrated phylogeny of South American freshwater fishes—the most species-rich continental vertebrate fauna on Earth—to track the evolutionary processes associated with hydrogeographic events over 100 Ma. Net lineage diversification was heterogeneous through time, across space, and among clades. Five abrupt shifts in net diversification rates occurred during the Paleogene and Miocene (between 30 and 7 Ma) in association with major landscape evolution events. Net diversification accelerated from the Miocene to the Recent (c. 20 to 0 Ma), with Western Amazonia having the highest rates of in situ diversification, which led to it being an important source of species dispersing to other regions. All regional biotic interchanges were associated with documented hydrogeographic events and the formation of biogeographic corridors, including the Early Miocene (c. 23 to 16 Ma) uplift of the Serra do Mar and Serra da Mantiqueira and the Late Miocene (c. 10 Ma) uplift of the Northern Andes and associated formation of the modern transcontinental Amazon River. The combination of high diversification rates and extensive biotic interchange associated with Western Amazonia yielded its extraordinary contemporary richness and phylogenetic endemism. Our results support the hypothesis that landscape dynamics, which shaped the history of drainage basin connections, strongly affected the assembly and diversification of basin-wide fish faunas.

Geological and climatic events are widely believed to shape the biodiversity of continental biotas (1–3), yet we are only beginning to understand the nuanced ways in which individual geological and climatic events have contributed to evolutionary diversification (speciation minus extinction) across large spatial scales (4–7). South America harbors the most diverse fauna of continental freshwater fishes in the world (~5,750 species), providing unique opportunities to study the effects of geological history and river dynamics on diversification in obligate aquatic taxa (8, 9). Hydrogeographic processes, operating over tens of millions of years, have caused predictable changes in the geometry of river drainage networks, by isolating and merging portions of adjacent river basins and their connections to the sea, and by altering the physiochemical characteristics of water discharge (10, 11). Here, we evaluate the influence of major geological events on diversity patterns of obligate freshwater fishes of South America over the past 100 Ma, the time period over which hydrogeographic events shaped the origins of modern fluvial systems (4, 5, 12). We conducted the most comprehensive assessment of diversification in this group to date, using an extensive dataset on species geographic occurrences and a newly compiled, species-dense phylogeny of South American freshwater fishes (13). This new synthesis afforded us the opportunity to link unique hydrogeographic events with the spatial and temporal diversification and dispersal of individual fish clades.The historical dynamics of South American river basins and aquatic biotas were strongly shaped by four prominent geophysical events (Fig. 1) (11, 14). The first was the final separation of South America from Africa during the Late Cretaceous (c. 100 Ma). Between the Late Cretaceous and Early Paleogene (c. 100 to 55 Ma), river drainage patterns of South America were controlled by the location of the preexisting continental uplands (cratons and shields), ongoing uplift of the Andean cordilleras, super greenhouse climatic conditions characterized by high temperatures and precipitation, and dramatically fluctuating eustatic sea levels. As a result, most low-elevation coastal plains and interior structural basins were covered by nearshore marine habitats, and upland freshwater riverine and riparian habitats were intermittently isolated and connected (4, 15). During the Paleogene (c. 55 to 33 Ma), the Proto-Amazon-Orinoco river basin (Proto-Amazon basin, hereafter) drained the Sub-Andean Foreland basin, including much of northern South America and the northern La Plata region (Fig. 1 A and B; 5, 16).Open in a separate windowFig. 1.Bioregions, principle current landforms and sub-basins, and approximate chronology and location of the principal landscape evolution events that shaped the current drainage basins of South America and influenced the diversification of freshwater fishes. (A) Current river basins and geological formations mentioned in the text and the six bioregions proposed (detailed in SI Appendix). (B–E) Between 100 and 55 Ma, aquatic systems in South America were intermittently connected by multiple marine transgressions and regressions.Thus drainages across the continent during this time were intermittently connected by epicontinental seaways. During this time, the Proto-Amazon basin was the main drainage of northern South America, flowing through the sub-Andean foreland. At the same time, the Paraná and Paraguay basins (La Plata bioregion) represented major aquatic systems in South America (4, 5, 10, 11). Additional information about principal landforms controlling basin connectivity at each time interval and for each bioregion delineation appears in SI Appendix, Table S1.Second, intraplate compression and tectonic subduction along the Pacific margin during the Oligocene (c. 33 to 23 Ma) drove tectonic uplift of the Altiplano and Michicola Arch (c. 30 Ma) associated with formation of the Bolivian Orocline (17). These orogenic deformations intermittently isolated and connected rivers among the Western Amazonian, Upper Madeira, and Upper Paraguay sedimentary basins of the Sub-Andean Foreland, facilitating vicariance and biotic exchanges across their watershed divides (Fig. 1C; 4, 18–20). Third, tectonic reactivation and uplift of Serra do Mar and Serra da Mantiqueira ranges in southeastern Brazil during the Early Miocene (c. 23 to 16 Ma) re-routed some rivers from the La Plata basin directly to the Atlantic (Fig. 1D; 21, 22–24), isolating many terrestrial and aquatic species in the coastal basins of the Atlantic Forest. Also, at about this time (c. 23 to 10 Ma), the Pebas Megawetland extended over large areas of the modern Western Amazonia and Orinoco basins (Fig. 1D; 5, 7, 22–26). Fourth, the uplift of the Northern Andes during the Late Miocene and Pliocene (c. 10 to 4.5 Ma), which profoundly reorganized regional river drainage networks, isolated the modern Amazon, Orinoco, Magdalena, and Maracaibo river basins and connected the modern Western and Eastern Amazon basins, thereby forming the modern transcontinental Amazon River (Fig. 1E; 16, 27).Variation in connectivity and configuration of regional river networks resulting from these four major geological events strongly shaped diversity patterns of the Neotropical freshwater fish fauna (4, 12). In particular, river capture, in which a river drainage system is diverted from its historic bed to a neighboring bed, is a landscape evolution process that exerts a potent influence on diversification in obligate freshwater organisms, because it both severs existing and constructs new corridors of aquatic habitat among portions of adjacent drainage basins (18, 28). Because continental fishes are eco-physiologically restricted to freshwater habitats within drainage basins, watersheds represent natural dispersal barriers, as evidenced by the strong spatial concordance of geographic ranges in freshwater fish species with basin boundaries (28, 29). By isolating and connecting populations of aquatic taxa across watershed divides, river capture exerts complex effects on the diversity of freshwater organisms, for example by elevating extinction risk through geographic-range contraction, promoting speciation by genetic isolation and vicariance, and increasing biotic homogenization by dispersal and gene flow (16, 30–32).Although the role of geological events in shaping the evolution of rivers and freshwater diversity has long been recognized, the relative contributions of particular geological events remain poorly understood. Insights into their contributions can be gained only by studying diversity patterns at appropriate spatial, temporal, and taxonomic scales (28, 33–36). For instance, recent studies identified Western Amazonia as the center of Amazon fish diversity (high species richness, low phylogenetic diversity (PD), and high phylogenetic clustering, compared to Eastern Amazonia), with younger fish lineages dispersing progressively eastward across Amazonia after the formation of the modern transcontinental river c. 10 Ma (37–39). However, this interpretation did not consider the more ancient history of Neotropical fishes in the upland Brazilian and Guianas Shields, the formation of the modern lowland (< 250 m.a.s.l.) fauna in the Proto-Amazon basin, and the phenotypically and taxonomically modern composition of all the known Miocene paleo-ichthyofaunas (4, 40). Taking this deeper history into account, Pliocene and Pleistocene events may have served more as buffers against extinction than as drivers of speciation in the formation of Amazonian fish species diversity (Fig. 2; 15, 41). In fact, the most species-rich clades of Neotropical freshwater fishes are thought to have radiated during the Paleogene (c. 63 to 23 Ma) (4, 42, 43).Open in a separate windowFig. 2.Changes in the rates of net lineage diversification among South American freshwater fishes. Tips represent 2,523 fish species. (A) Branch colors indicate net lineage diversification rate estimated by BAMM, where red indicates highest and blue lowest diversification rates. Significant shifts in diversification rates are shown as pale green circles on the branches. Selected representative clades of Melanorivulus, Orestias, Ancistrini, Hypostomus, and Corydoras species are illustrated. The principal orders are represented by colored columns to the right of the tree tips. The timescale at the bottom is expressed in millions of years ago (Ma). Vertical dashed lines indicate timing of the main principal hydrogeographic events detailed in the inset legend on the left. (B) Rates-through-time plots based on BAMM estimations, considering all bioregions together (see Material and Methods for parametrization details). The shaded areas around the curves correspond to 95% CIs of the estimated rates. Dashed lines indicate the time period when most of shifts in diversification rates were estimated. (C) Rates-through-time plots considering the species present in each bioregion separately. Rates of diversification, speciation, and extinction were estimated mainly within crown taxa. The five photographs: Wikipedia Commons. *Ancistrini species of genera Hopliancistrus, Guyanancistrus, Pseudolithoxus, Lasiancistrus, Pseudancistrus, Panaque, and Pterygoplichthys.In the case of South American freshwater fishes, previous macroevolutionary studies have been hindered by the large number of species (~5,750), remote sampling localities, and logistical difficulties of gathering reliable data (8). Our new data on fish distributions, which we combine with a new, time-calibrated molecular phylogeny, offer powerful resources to study the role of geomorphological events and associated river captures in shaping fish diversity over longer time periods and larger spatial scales than has previously been attempted. In particular, we evaluate the prediction that the high diversity in Western Amazonia was influenced by biogeographical bridges formed across different aquatic systems and time periods, which led to both accelerated diversification rates and a role for Western Amazonia as a principal source of freshwater fish species for all of South America.     

Herbivory and warming interact in opposing patterns of covariation between arctic shrub species at large and local scales

A major challenge in predicting species’ distributional responses to climate change involves resolving interactions between abiotic and biotic factors in structuring ecological communities. This challenge reflects the classical conceptualization of species’ regional distributions as simultaneously constrained by climatic conditions, while by necessity emerging from local biotic interactions. A ubiquitous pattern in nature illustrates this dichotomy: potentially competing species covary positively at large scales but negatively at local scales. Recent theory poses a resolution to this conundrum by predicting roles of both abiotic and biotic factors in covariation of species at both scales, but empirical tests have lagged such developments. We conducted a 15-y warming and herbivore-exclusion experiment to investigate drivers of opposing patterns of covariation between two codominant arctic shrub species at large and local scales. Climatic conditions and biotic exploitation mediated both positive covariation between these species at the landscape scale and negative covariation between them locally. Furthermore, covariation between the two species conferred resilience in ecosystem carbon uptake. This study thus lends empirical support to developing theoretical solutions to a long-standing ecological puzzle, while highlighting its relevance to understanding community compositional responses to climate change.

A readily observable phenomenon in nature is the tendency for the distributions of potentially competing species to covary positively at large spatial scales but negatively at small scales (1, 2). This scale dependence in patterns of species covariation is a defining phenomenon in ecology (3), and a classic illustration of it derives from MacArthur’s observations of Dendroica sp. warblers in mixed forests of the northeastern United States (1) and related theoretical work (4, 5). However, while opposing patterns of species covariation at large and local scales are ubiquitous, assigning causality to interacting drivers of such patterns in natural systems is challenging. Originally, theory explained this phenomenon as a product of distinct types of drivers of species abundance and distribution at large versus local scales. According to this framework, regional factors, such as climate, determine species’ distributions over large scales, while biotic interactions such as exploitation and interference determine presence, absence, and relative abundances of species at local scales (5–10). Hence, species with similar resource demands should, and often do, overlap spatially (covary positively) at broad scales as their distributions track abiotic niche requirements such as favorable climatic conditions (11). Meanwhile, the same species should, and often do, covary negatively at smaller spatial scales, where local biotic interactions such as competition, interference, niche complementarity, or exploitation by consumers or pathogens promote exclusion or segregation (5, 12–14). More recent theoretical developments have, however, highlighted the potential for roles of both types of drivers in patterns at both scales (7, 15, 16). Understanding whether, and how, climate and biotic interactions simultaneously influence species’ covariation at large and local scales has been repeatedly identified as a key challenge in improving predictions of species’ distributional and biodiversity responses to climate change (15, 17, 18).In contrast to progress in theory, field experimental tests of such potential interactions between biotic and abiotic factors in opposing patterns of species covariation at large and local scales have been lacking (14), in part because of the challenges inherent in conducting sufficiently controlled field experiments over suitably long time scales (19, 20). Consequently, novel empirical support for the role of, for example, biotic interactions in large scale patterns of species covariation has been strictly observational (21). Application of more robust empirical tests of predictions deriving from recent theory on this topic may also improve understanding of the consequences of patterns of species covariation at opposing spatial scales for important aspects of ecosystem function (22), including carbon exchange (23–26). Here, we present results of a 15-y warming and herbivore-exclusion experiment conducted at a remote arctic field site aimed at investigating influences of both drivers on patterns of covariation between two dominant shrub species at local and large spatial scales. The experimental design targets temperature as the abiotic limiting factor and herbivory (and associated ancillary effects) as the biotic limiting factor (Methods).The two focal shrub species in this study, dwarf birch (Betula nana) and gray willow (Salix glauca), hereafter “birch” and “willow,” respectively, are the most abundant plant species at our study site in low-arctic Greenland (27), and their functional role in ecosystem CO₂ exchange far exceeds that of any other vascular plant species at the site (28, 29). Furthermore, the two species are codominant across much of the Arctic (Fig. 1) (30, 31), but some experimental evidence indicates that Betula has the capacity to outcompete Salix at local scales in the Arctic due to its greater developmental plasticity and ability to invest rapidly in stem growth (32). Hence, although annual sampling throughout the duration of our experiment has assessed aboveground dynamics of all components of the plant community (Methods), our focus here is on patterns of covariation between birch and willow. Although birch is generally more common than willow across the study site (SI Appendix), the two species share similar distributions across the site, occur mainly on low to mid elevation slopes and plateaus, and predictably avoid arid steep slopes and stagnant mesic or saturated lowlands and fens (Fig. 1B). Each of the two species readily forms monospecific “shrub islands” at the local scale (Fig. 1C and SI Appendix, Fig. S3).Open in a separate windowFig. 1.(A) Circum-Arctic distributions of the two focal shrub species, dwarf birch (B. nana) and gray willow (S. glauca). Shaded polygons were derived from published range maps (30, 65). Point locations were derived from occurrence records (66–68) and the GBIF data portal (www.gbif.org). (B and C) Landscape and local scale views of patterns of covariation between the two species at the study site near Kangerlussuaq, Greenland. (B) South-facing hillside and lowland plains at the study site illustrating cooccurrence of dwarf birch (B. nana) and gray willow (S. glauca) at the landscape scale. (C) Monospecific shrub islands of each species are evident at smaller plot scales at the study site. In both photographs, birch appears dark or olive green, while willow appears lighter green. Image credit: E.P.     

奶粉中混合菌种检验方法的比较研究

目的研究奶粉中混合菌种的检测方法。方法用直接平板分离法和增菌培养法对奶粉中质控菌株进行增菌、分纯,依据细菌生长特性、菌落平板特征、涂片革兰染色镜检结果、生化试验和血清学鉴定结果综合判断。结果奶粉中质控菌株为混合菌种,分别是金黄葡萄球菌、大肠埃希菌O157∶H7。结论做混合菌种样品检测时,平板直接分离法效果较好;BHI肉汤培养诱导鞭毛抗原的方法值得推广使用。     

2014年福建省南平市登革病毒E基因序列分析

目的 测定2014年南平市登革暴发相关登革病毒E基因序列,探讨其输入来源及基因型别.方法 将患者急性期血清接种C6/36细胞,分离登革病毒,通过RT-PCR进行血清型鉴定,扩增全长E基因,测定序列并绘制系统进化树.结果 共分离到4株DENV-1,2株DENV-2,扩增并测序获得E基因全长序列,4株南平地区DENV-1型分离株之间同源性为100%,与D13459(Donguang)分离株同源性也高达99.7%;2株DENV-2型分离株与DENV2/CN/GZ05/2014分离株的同源性均达100%.系统进化分析发现,4株DENV-1病毒株与来自广东及印度的毒株处于同一进化树分支,均为基因Ⅴ型;2株DENV-2病毒株与来自广东及新加坡的毒株处于同一进化树分支,均为基因Ⅳ型.结论 福建省南平市本次登革热本地病例暴发可能是由广东或者东南亚地区的登革热输入病例引起的.     

Evolutionary history and the effect of biodiversity on plant productivity

Loss of biological diversity because of extinction is one of the most pronounced changes to the global environment. For several decades, researchers have tried to understand how changes in biodiversity might impact biomass production by examining how biomass correlates with a number of biodiversity metrics (especially the number of species and functional groups). This body of research has focused on species with the implicit assumption that they are independent entities. However, functional and ecological similarities are shaped by patterns of common ancestry, such that distantly related species might contribute more to production than close relatives, perhaps by increasing niche breadth. Here, we analyze 2 decades of experiments performed in grassland ecosystems throughout the world and examine whether the evolutionary relationships among the species comprising a community predict how biodiversity impacts plant biomass production. We show that the amount of phylogenetic diversity within communities explained significantly more variation in plant community biomass than other measures of diversity, such as the number of species or functional groups. Our results reveal how evolutionary history can provide critical information for understanding, predicting, and potentially ameliorating the effects of biodiversity loss and should serve as an impetus for new biodiversity experiments.     

饶河地区野生动物携带病毒的基因分型及序列特征分析

目的 确定当前饶河地区宿主动物所携带病原体的基因型别,分析其变异情况,对该地区自然宿主动物的感染情况进行监测。方法 使用TRIZOL法提取待测样本RNA,经RT-PCR扩增后对PCR产物进行核苷酸序列测定。应用DNAStar软件包对核苷酸序列进行同源性比较,构建系统进化树和氨基酸序列的比对。结果 在饶河地区,除褐家鼠(Rattus norvegicus)以外,松鼠(Sciurus vulgaris)也携带SEOV。本次从3只褐家鼠和1只松鼠体内分离出汉城型汉坦病毒(Seoul virus, SEOV),4株SEOV的遗传距离范围为0.00~0.01,与黑龙江地区常见SEOV病毒株亲缘关系较近。结论 黑龙江地区的气候和自然地理条件非常适合携带汉坦病毒(HV)宿主动物的生存和繁殖,但是随着人们生活条件的改善,禁止伐木狩猎,家鼠和野鼠与人类交集的逐渐减小,肾综合征出血热(HFRS)在黑龙江省暴发的概率也越来越小。