Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic

Distinguishing whether pathogens are novel or endemic is critical for controlling emerging infectious diseases, an increasing threat to wildlife and human health. To test the endemic vs. novel pathogen hypothesis, we present a unique analysis of intraspecific host-pathogen phylogenetic concordance of tiger salamanders and an emerging Ranavirus throughout Western North America. There is significant non-concordance of host and virus gene trees, suggesting pathogen novelty. However, non-concordance has likely resulted from virus introductions by human movement of infected salamanders. When human-associated viral introductions are excluded, host and virus gene trees are identical, strongly supporting coevolution and endemism. A laboratory experiment showed an introduced virus strain is significantly more virulent than endemic strains, likely due to artificial selection for high virulence. Thus, our analysis of intraspecific phylogenetic concordance revealed that human introduction of viruses is the mechanism underlying tree non-concordance and possibly disease emergence via artificial selection.     

1980—2005年中国东北木本植物物候特征及其对气温的响应

基于25年物候观测数据,分析了东北地区木本植物物候的时空变化特征,阐述了近25年来东北地区气候变暖对植物物候的影响,结果表明:1980—2005年,东北地区木本植物展叶初期主要呈提前趋势,提前幅度为0.23d·a-1,枯黄初期主要表现为推后趋势,平均推后0.19d·a-1,生长季延长,平均延长幅度为0.30d·a-1;东北地区广泛分布的5种木本植物(旱柳、杏树、小叶杨、榆树和紫丁香)物候在地理空间上存在显著差异:纬度平均每增加1°,展叶初期推后3d,枯黄初期提前1.35d,生长季长度缩短4.41d;东北地区植物展叶初期与2、3、4月的气温显著负相关(P0.05),其中,4月气温对植物展叶提前的影响最大,展叶提前趋势平均为2.35d·℃-1;2月气温的影响最小,平均趋势为1.18d·℃-1。     

农田防护林的可持续经营管理

林带更新的时空布局对持续发挥林网的防护效益具有重要意义。本文提出用拟法正林思想经营农田防扩林,以行政村为组织经营单位,通过逐步更新调整组织经营单位管理的林带,使整个林网体系形成自幼龄到成熟龄各龄级林带条数基本相等,空间上均匀配置的格局,从而确保时间上农田防护林生态服务的稳定和持续发挥。     

在种与属两个级别评价太子河硅藻群落与环境因子的关系

2009年8—9月,对辽宁省太子河流域67个点位进行采样调查,以硅藻群落为研究对象,比较硅藻属级水平与种级水平相对多度、物种丰富度以及生物多样性指数间的相关性,并比较硅藻属级与种级属性与环境因子的相关性。实验结果表明,太子河流域硅藻属级水平的相对多度、丰富度和多样性指数与硅藻种级水平都极显著相关。Pearson相关性分析表明,硅藻属级水平的丰富度与环境显著相关的因子与种级水平丰富度与环境显著相关的因子相一致。Mantel-Test相关性分析表明,硅藻属级水平的相对多度与环境因子的相关性弱于种级水平与环境因子相关性。典范对应分析结果显示,影响硅藻属级和种级群落结构分布的主要环境因子均为悬浮物。基于硅藻生物评价指数的流域健康评价结果表明,应用硅藻属级和种级属性对太子河流域进行健康评价,其评价结果相一致。     

一株祁连野生羊肚菌多基因联合分子鉴定及其生物地理分析

【背景】青海野生羊肚菌野生资源丰富,但物种识别度低,相关研究滞后。【目的】鉴定识别采集自青海祁连的野生羊肚菌并分析其生物地理。【方法】利用形态学、多基因谱系一致性系统发育学物种识别法与多基因分子系统学相结合的方法,鉴定野生羊肚菌并分析该物种分化时间和重建祖先区域。【结果】野生羊肚菌菌株MQL-1子实体菌盖呈黄褐色,圆顶,菌柄呈白色、中空,形似羊肚菌,孢子大小为（21.17±4.33）μm×（14.26±3.25）μm,菌丝直径（13.95±3.19）μm。系统发育分析结果表明分离到的菌株MQL-1与羊肚菌属中的黄色羊肚菌类群的内转录间隔区（internal transcribed spacer,ITS）序列相似性高达99%,多基因谱系一致性系统发育学物种识别法将MQL-1识别为粗柄羊肚菌（Morchella crassipes）。分化时间估算和祖先重建结果表明青海祁连粗柄羊肚菌MQL-1与云南M.crassipes M10的分化时间12.75 Mya （百万年前）,其重建的最可能的祖先区域为印度（52.49%）。【结论】本研究得到了一株青海祁连地区粗柄羊肚菌菌株并确定了其正确的科学命名,丰富了青海省羊肚菌资源信息数据库,为后续的工作奠定了基础,也为真菌研究提供新思路。     

Effects of woody plant species richness on mammal species richness in southern Africa

Aim To determine the relationship between the species richness of woody plants and that of mammals after accounting for the effect of environmental variables. Location Southern Africa, including Namibia, South Africa, Lesotho, Swaziland, Botswana, Zimbabwe, and part of Mozambique. Methods We used a comprehensive dataset including the species richness of mammals and of woody plants and environmental variables for 118 quadrats (each of 25,000 km²) across southern Africa, and used structural equation models (SEMs) and spatial regressions to examine the relationship between the species richness of woody plants and of mammal trophic guilds (herbivores, insectivores, carni/omnivores) and habitat guilds (aquatic/fossorial, ground‐living, climbers, aerial), after controlling for environment. We compared the results of SEMs with those of single‐predictor regressions (without controlling for environment) and of spatial regressions (controlling for both environment and residual spatial autocorrelation). Results The geographical variation of mammal species richness in southern Africa was strongly and positively related to that of woody plant species richness, and this relationship held for most mammal guilds even when the influence of environment and spatial autocorrelation had been accounted for. However, the effect of woody plant species richness on the richness of aquatic/fossorial species almost disappeared after controlling for environment, suggesting that the congruence in species richness patterns between these two groups results from similar responses to the same environmental variables. For many mammal guilds, the relative role of environmental predictors as measured by standardized partial regression coefficients changed depending on whether non‐spatial single‐predictor regressions, non‐spatial SEMs, or spatial regressions were used. Main conclusions Woody plants are important determinants of the species richness of most mammal guilds in southern Africa, even when controlling for environment and residual spatial autocorrelation. Environmental correlates with animal species richness as measured by simple correlations or single‐predictor regressions might not always reflect direct effects; they might, at least to some degree, result from indirect effects via woody plants. Interpretations of the strength of the effect of environmental variables on mammal species richness in southern Africa depend largely on whether spatial or non‐spatial models are used. We therefore stress the need for caution when interpreting environmental ‘effects’ on broad‐scale patterns of species richness if spatial and non‐spatial methods yield contrasting results.     

Miocene divergence,phenotypically cryptic lineages,and contrasting distribution patterns in common lichen‐forming fungi (Ascomycota: Parmeliaceae)

Despite the recent advancements in recognizing diversity in lichen‐forming fungi, assessing the timing of diversification remains largely unexplored in these important fungal symbionts. To better understand the evolutionary processes driving diversification in common lichen‐forming fungi, we investigated the phylogeny and biogeography of the broadly distributed Melanelixia fuliginosa/M. glabratula group, using molecular data from six nuclear markers. Phylogenetic analyses of individual gene alignments and combined data provide strong evidence for five species‐level lineages within this species complex. Three of these lineages correspond to the previously described species M. fuliginosa, M. glabratula, and M. subaurifera. The remaining two lineages, ‘M. sp. 1’ and ‘M. sp. 2’, merit species recognition based on genealogical concordance. Both M. glabratula and M. subaurifera had broad intercontinental distributions, sharing identical haplotypes among intercontinental populations. Based on the current sampling, M. fuliginosa s.s. was represented exclusively by European material and was not collected in North America. ‘M. sp. 1’ was represented by collections from Scotland and Spain; and ‘M. sp. 2’ was represented by collections in California, USA. Environmental factors driving the contrasting distribution patterns in this group remain unknown. Divergence times estimated using a coalescence‐based multilocus species‐tree approach suggest that diversification within the M. fuliginosa/M. glabratula group occurred exclusively during the Miocene. The results of the present study indicate that phenotypically cryptic lichen‐forming fungal species‐level lineages may be relatively ancient and do not necessarily reflect recent divergence events. Furthermore, diagnosable phenotypic differences may be absent even millions of years after the initial divergence. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ●●, ●●–●●.     

Interobserver concordance in the assessment of features used for the diagnosis of cervical atypical squamous cells and squamous intraepithelial lesions (ASC‐US,ASC‐H,LSIL and HSIL)

G. Bigras, J. Wilson, L. Russell, G. Johnson, D. Morel and M. Saddik
Interobserver concordance in the assessment of features used for the diagnosis of cervical atypical squamous cells and squamous intraepithelial lesions (ASC‐US, ASC‐H, LSIL and HSIL) Objectives: Given the well‐known poor reproducibility of cervical cytology diagnosis, especially for atypical squamous cells of undetermined significance (ASC‐US) and low‐grade squamous intraepithelial lesion (LSIL), this study surveyed reproducibility in the assessment of individual cytomorphological features. Methods: One hundred and fifty cells or groups of cells, with a variety of morphological appearances, including normal cells, high‐grade squamous intraepithelial lesion (HSIL), LSIL, ASC‐US and ASC cannot exclude HSIL (ASC‐H), were precisely marked on 150 different liquid‐based cytological preparations. They were analysed by 17 observers who assessed 17 cytological features including nuclear features (chromatin texture, nuclear outline, nuclear shape, etc.), cytoplasmic features (cell shape, cytoplasmic staining, cytoplasmic clearing, etc.) and group characteristics (nuclear polarity, cellular density, etc.). A total of 43 350 data scores were collected in a database using a web‐based survey. Kendall’s W and relative entropy indexes were utilized to compute concordance indexes of respectively ordinal and nominal variables. Results: Nuclear features have significantly lower reproducibility (0.46) compared with other cytological features (0.59). The feature with least agreement is assessment of chromatin texture. A small but significant difference in concordance was found between two subsets of observers with different levels of experience. Conclusion: Most previous studies assessing reproducibility of cytological diagnoses show, at best, moderate reproducibility among observers. This study focused on agreement regarding the presence of constituent morphological features used to recognize dyskaryosis and various grades of squamous intraepithelial lesions. A map of reproducibility indexes is presented that highlights, for daily practice or teaching, the robustness of features used for cytological assessment, recognizing that diagnosis is always based on a combination of features.     

Evidence against the use of surrogates for biomonitoring of Neotropical floodplains

1. Community concordance measures the level of association between the compositional patterns shown by two groups of organisms. If strong community concordance occurs, one group could be used as a surrogate for another in conservation planning and biodiversity monitoring. In this study, we evaluated the variability in the strength of community concordance, the likely mechanisms underlying community concordance and the degree to which one community can predict another in a set of Neotropical floodplain lakes (Upper Paraná River floodplain, Brazil). 2. We used a data set including six aquatic communities: fish, macrophytes, benthic macroinvertebrates, zooplankton, phytoplankton and periphyton. We used Mantel and PROTEST approaches to evaluate the levels of community concordance in up to four sampling periods. Also, we used partial Mantel test and information about biotic interactions to investigate reasons for observed patterns of concordance. Finally, we used co‐correspondence analysis to evaluate the performance of one taxonomic group in predicting the structures of other communities. 3. The levels of community concordance varied over time for almost all cross‐taxa comparisons. Concordance between phytoplankton and periphyton probably resulted from similar responses to environmental gradients, whereas other patterns of concordance were likely generated by interactions among groups. However, the levels of predictability were low, and no particular taxonomic group significantly predicted all other groups. 4. The low and temporally variable levels of community concordance cast doubts on the use of surrogate groups for biodiversity management in Neotropical floodplains.