Biogeography of soil nematodes

Biogeography is the study of distributions of organisms, plus an attempt to explain the distributions. Two approaches to explanation of biogeographic patterns may be termed ecological biogeography and historical biogeography. Most nematologists have taken the ecological approach, with a goal of determining why a particular species is restricted to certain areas, and not present in nearby areas. Historical biogeography is based on the premise that present-day patterns of taxa result largely from the history of the taxa and of the areas of the earth in which they have lived. Nematologists generally adhere to the classic view of dispersal in which a center of origin is postulated and long-range dispersal over barriers is invoked. The dispersal mechanism is often assumed to be man himself. Challenges to this approach exist in the form of methods which infer the biogeographic history from phylogeny. Vicariance biogeographers postulate fragmentation of widespread ancestral biotas, resulting from geological, climatic or other disjunctions, and further allopatric speciation among descendant biotas. Distributions amenable to general explanation can be distinguished from those which require unique dispersal events. Biogeography of soil nematodes is hampered by present limitations in systematics, including our inability to determine species limits with certainty.     

Comparative genomics: methods and applications

Interpreting the functional content of a given genomic sequence is one of the central challenges of biology today. Perhaps the most promising approach to this problem is based on the comparative method of classic biology in the modern guise of sequence comparison. For instance, protein-coding regions tend to be conserved between species. Hence, a simple method for distinguishing a functional exon from the chance absence of stop codons is to investigate its homologue from closely related species. Predicting regulatory elements is even more difficult than exon prediction, but again, comparisons pinpointing conserved sequence motifs upstream of translation start sites are helping to unravel gene regulatory networks. In addition to interspecific studies, intraspecific sequence comparison yields insights into the evolutionary forces that have acted on a species in the past. Of particular interest here is the identification of selection events such as selective sweeps. Both intra- and interspecific sequence comparisons are based on a variety of computational methods, including alignment, phylogenetic reconstruction, and coalescent theory. This article surveys the biology and the central computational ideas applied in recent comparative genomics projects. We argue that the most fruitful method of understanding the functional content of genomes is to study them in the context of related genomic sequences. In particular, such a study may reveal selection, a fundamental pointer to biological relevance.     

Charles Darwin, beetles and phylogenetics

Here, we review Charles Darwin’s relation to beetles and developments in coleopteran systematics in the last two centuries. Darwin was an enthusiastic beetle collector. He used beetles to illustrate different evolutionary phenomena in his major works, and astonishingly, an entire sub-chapter is dedicated to beetles in “The Descent of Man”. During his voyage on the Beagle, Darwin was impressed by the high diversity of beetles in the tropics, and he remarked that, to his surprise, the majority of species were small and inconspicuous. However, despite his obvious interest in the group, he did not get involved in beetle taxonomy, and his theoretical work had little immediate impact on beetle classification. The development of taxonomy and classification in the late nineteenth and earlier twentieth century was mainly characterised by the exploration of new character systems (e.g. larval features and wing venation). In the mid-twentieth century, Hennig’s new methodology to group lineages by derived characters revolutionised systematics of Coleoptera and other organisms. As envisioned by Darwin and Ernst Haeckel, the new Hennigian approach enabled systematists to establish classifications truly reflecting evolution. Roy A. Crowson and Howard E. Hinton, who both made tremendous contributions to coleopterology, had an ambivalent attitude towards the Hennigian ideas. The Mickoleit school combined detailed anatomical work with a classical Hennigian character evaluation, with stepwise tree building, comparatively few characters and a priori polarity assessment without explicit use of the outgroup comparison method. The rise of cladistic methods in the 1970s had a strong impact on beetle systematics. Cladistic computer programs facilitated parsimony analyses of large data matrices, mostly morphological characters not requiring detailed anatomical investigations. Molecular studies on beetle phylogeny started in the 1990s with modest taxon sampling and limited DNA data. This has changed dramatically. With very large data sets and high throughput sampling, phylogenetic questions can be addressed without prior knowledge of morphological characters. Nevertheless, molecular studies have not lead to the great breakthrough in beetle systematics—yet. Especially the phylogeny of the extremely species rich suborder Polyphaga remains incompletely resolved. Coordinated efforts of molecular workers and of morphologists using innovative techniques may lead to more profound insights in the near future. The final aim is to develop a well-founded phylogeny, which truly reflects the evolution of this immensely species rich group of organisms.     

高通量测序技术研究辽河真核浮游藻类的群落结构特征

真核浮游藻类在河流生态系统中发挥着重要生态功能,本研究对辽河水环境样本的18S rRNA基因的V4可变区进行454焦磷酸测序,对获得的OTU代表性序列进行物种注释.比较注释后的生物种类信息与光学显微镜观察结果的异同,并将OTUs的代表性序列与NCBI中真核浮游藻类的18S rRNA基因序列进行系统发育分析,此外研究了真核浮游藻类群落结构特征及其环境影响指标.研究共获得约167 901条18S rRNA基因V4可变区的高质量序列,注释为424个OTUs,涵盖了134种真核浮游藻类OTUs.与光学显微镜鉴别结果类似,高通量测序结果以硅藻门和绿藻门为优势类群,此外检测到轮藻门、隐藻门、定鞭藻门和金藻纲等显微镜观察结果中未有的类群.系统发育分析可在门这一分类阶元对隐藻门和甲藻门聚类,并将隐藻门在属水平进行聚类和区分,甲藻门可以在部分科或属水平聚类和区分.RDA结果显示,氨氮、活性磷和硝态氮是影响真核浮游藻类群落结构特征最重要的环境因子.本研究为认识辽河水环境中真核浮游藻类的多样性、群落结构及其环境影响因子提供了新的视角,同时也预示着高通量测序技术在辽河流域浮游植物监测和水环境质量指示中的应用潜力.     

广东省蛭态轮虫物种多样性及其系统发育研究

为了解广东省蛭态轮虫物种多样性,采集广东省不同水陆生境样品98份,记录蛭态轮虫3目4科12属66种（含亚种）.陆生环境中鉴定出蛭态轮虫56种,其中苔藓生境42种、落叶生境40种、地衣生境12种,水生生境蛭态轮虫15种,陆生生境的蛭态轮虫种类明显多于水生生境蛭态轮虫.为验证形态鉴定的准确性,获取蛭态轮虫COⅠ基因序列4属16种37条,种间遗传距离8.59%~23.17%,其中楔足盘网轮虫（Adineta cuneata）和迅捷旋轮虫（Philodina rapida）的COⅠ基因序列为全球首次报道.COI基因序列中腺嘌呤（A）与胸腺嘧啶（T）的总含量（71.2%）远大于鸟嘌呤（G）与胞嘧啶（C）（28.8%）的含量.系统发育树的聚类结果与形态学物种鉴定结果一致;同属形态相近的物种,具有较高的同源性.研究结果表明,形态学鉴定与DNA条形码技术相结合,有助于提高蛭态轮虫种类鉴定的准确性和探究蛭态轮虫各属的发育地位,促进蛭态轮虫物种多样性和生态学研究.     

Genetic Analysis of Norovirus Strains that Caused Gastroenteritis Outbreaks Among River Rafters in the Grand Canyon,Arizona

Toilet solid waste samples collected from five outbreaks among rafters in the Grand Canyon were subjected to sequencing analysis of norovirus partial capsid gene. The results revealed that a GI.3 strain was associated with one outbreak, whereas the other outbreaks were caused by GII.5 whose sequences shared >98.9% homology.     

Prenatal and presymptomatic diagnosis of the marfan syndrome using fluorescence pcr and an automated sequencer

The Marfan syndrome (MFS) is a heritable connective tissue disorder characterized by skeletal, ocular, and cardiovascular abnormalities. Defects in fibrillin, an elastin-associated microfibrillar protein, are now known to cause MFS. Since the discovery of fibrillin as the gene responsible for MFS, requests for prenatal and presymptomatic diagnosis have become common-place. Here we report the use of the polymerase chain reaction (PCR), using fluorescence labelled primers and an automated sequencer, to establish linkage data for “molecular diagnosis”. The mistaken clinical diagnosis of MFS based on the appearance of a common cardiovascular manifestation, mitral valve prolapse, and a positive family history is also discussed.     

No evidence for an afrotherian-like delayed dental eruption in South American notoungulates

The fossil South American ungulates are of great interest relative to the new phylogenetic framework elaborated for living placental mammals. In particular, studies on these endemic taxa can allow for testing congruence between southern placental phylogeny and plate tectonics, beyond what has already been suggested in the Atlantogenata hypothesis based on extant afrotherians and xenarthrans. The presence of delayed dental eruption relative to skull growth is one feature characterizing the extant afrotherians and possibly the xenarthrans. Late dental eruption has been mentioned previously in South American notoungulates, thus suggesting possible resemblance with afrotherians and perhaps xenarthrans. We provide here a detailed study of the dental eruption pattern relative to the skull growth in the notoungulates. In contrast to previous statements, our results demonstrate that there is currently no evidence for an afrotherian-like delayed dental eruption in this group. For now, the inferred absence of a delayed dental eruption in notoungulates does not support atlantogenatan/afrotherian affinities for the Notoungulata, but other atlantogenatan/afrotherian characteristics remain to be explored in more detail in this group and other South American ungulates.     

To kill or not to kill—Practitioners’ opinions on invasive alien species management as a step towards enhancing control of biological invasions

The spread of invasive alien species (IAS) has become an increasingly important environmental, social and economic issue in almost all regions of the world. To have the capacity to effectively counter the effects of invasions, besides basic research on invasion processes and the ecological impacts of IAS, there is a need to get an information and better understanding of the effectiveness of biological control and its social acceptability. Conservation practitioners are a particular group of stakeholders as they act in the first line to undertake control actions again IAS spread. Yet, not many research was done to deliver quantitative, comprehensive information on practitioners’ knowledge and attitudes towards IAS. In this paper, we present a study from Poland—a country with relatively well preserved nature, yet currently facing the problem of biological invasions in the terrestrial and aquatic environments. We investigated nature conservation practitioners’ knowledge of biological invasions, their views on the principles and methods of IAS control, and their degree of acceptance of control methods. We conducted a survey among people professionally involved in nature conservation in Poland and collected 916 questionnaires (out of 3330 sent). Overall, we find that conservation practitioners in Poland accept the use of radical methods of control, yet they differ about the use of various types of control method, and about the various control methods application to various systematic groups. Also, the level of practitioners’ knowledge is rather limited—both in relation to correct identification of IAS, as well as to knowledge on legal regulations. We also highlight significant differences between decision-makers and professionals not perceiving themselves as decisive over IAS management. We show examples suggesting that nature conservation practitioners may not hold well-formed opinions on the principles and methods of dealing with alien species. This is surely an important deficit to overcome to enhance the effectiveness of IAS control.     

Lesch—Nyhan syndrome: Carrier and prenatal diagnosis

We report the results of carrier and prenatal diagnosis for hypoxanthine guanine phosphoribosyltransferase (HPRT) deficiency, Lesch—Nyhan syndrome, by carrier testing of 83 women and prenatal analysis of 26 pregnancies. Our diagnostic methodologies include mutation detection and linkage analysis for probands and their families and biochemical measurement of HPRT enzyme activity for at-risk pregnancies. Identification of the mutation in the index case of each family permits precise carrier diagnosis using polymerase chain reaction (PCR) amplification of HPRT gene sequences and automated DNA sequencing. We demonstrate 100 per cent sensitivity for the detection of mutations in the HPRT gene of affected males and highly efficient carrier testing of at-risk females. Two other molecular methods proven to have high utility include PCR-based dosage analysis and linkage analysis by PCR amplification of a short tandem repeat (STR) in intron 3 of the HPRT gene. As a result, 45 at-risk women, 56 per cent of those tested, were identified not to be carriers of their family's HPRT gene mutation. Seven of these women were the mothers of affected males and prenatal testing for future pregnancies was recommended because of the possibility of gonadal mosaicism. Thirty-eight of these women were more distant relatives of affected males, thereby eliminating the need for future prenatal procedures. These studies illustrate the utility and precision of molecular methodologies for carrier and prenatal diagnosis of Lesch—Nyhan syndrome. These studies also illustrate that molecular diagnostic studies of affected males and carrier testing prior to pregnancy can clarify genetic risk predictions and eliminate unnecessary prenatal procedures.     

环境DNA宏条形码技术在蓝藻群落监测中的应用

全球气候变化下的蓝藻水华大规模暴发成为重要的环境问题,对蓝藻准确、高效和实时的监测是蓝藻水华防控的关键.近年来,环境DNA（environmental DNA,eDNA）宏条形码技术开始应用于蓝藻群落监测,弥补了显微镜镜检法物种鉴定难和受主观经验影响大的缺点.eDNA宏条形码为快速和大规模蓝藻群落监测提供了可能,其应用尚处于初步探索阶段,数据处理方法尚不成熟,因此有必要从引物选择、序列聚类、注释方法和绝对定量4个层面系统综述eDNA宏条形码技术在蓝藻群落监测中的研究进展,以推进eDNA宏条形码在蓝藻群落监测中的应用.引物选择应针对目标蓝藻类群,16S rRNA基因数据库涵盖蓝藻物种范围广,是最常用的eDNA宏条形码,但16S-23S rRNA基因间隔区域（internal transcribed spacer,ITS）和功能基因在属内物种间具有较好的区分效果,为eDNA宏条形码在蓝藻物种水平注释提供可能.序列聚类一般通过设定物种间分类阈值进行OTUs聚类,但可能丢失序列相似度高于分类阈值的不同物种;序列差异低至单核苷酸变异方法的应用进一步区分了隐蔽的物种和生态型,产生的序列具有生物学意义,可以实现跨数据集间的比较分析.在注释方法上,基于数据库参考序列距离相似度的注释方法,注释结果的分辨率和准确度不高;基于系统进化位置的注释方法,提升了注释结果的准确度,反映了物种间的进化关系.加入外源DNA的内标法,以及基于细胞体积和基因拷贝数目关系的细胞体积校正系数法为eDNA宏条形码物种丰度的绝对定量提供了可能.      

基于地理信息技术的树种分布知识的挖掘与发现——以四川省石棉县为例

论文以四川省石棉县为例,对空间数据库支持下的树种分布知识的发现进行了研究。利用GIS技术建立相关空间数据库,主要有森林资源二类调查GIS数据库、树种GIS数据库,以及10 m分辨率的DEM、多年平均大于10 ℃的年积温和多年平均年降雨量等栅格数据库。利用GIS的叠加统计分析等方法,发现了各树种分布的的海拔、年平均大于10 ℃的积温、年平均降雨量等带谱知识。利用GIS的拓扑空间分析方法,挖掘了各树种间的空间配置知识。该知识可用于退耕还林、造林绿化中,因地制宜地选择树种,以及配置树种。该知识对于辅助数据协同下的各树种遥感识别也具有重要意义。此外,对其他区域也有示范意义。     

Juvenile morphology in baleen whale phylogeny

Phylogenetic reconstructions are sensitive to the influence of ontogeny on morphology. Here, we use foetal/neonatal specimens of known species of living baleen whales (Cetacea: Mysticeti) to show how juvenile morphology of extant species affects phylogenetic placement of the species. In one clade (sei whale, Balaenopteridae), the juvenile is distant from the usual phylogenetic position of adults, but in the other clade (pygmy right whale, Cetotheriidae), the juvenile is close to the adult. Different heterochronic processes at work in the studied species have different influences on juvenile morphology and on phylogenetic placement. This study helps to understand the relationship between evolutionary processes and phylogenetic patterns in baleen whale evolution and, more in general, between phylogeny and ontogeny; likewise, this study provides a proxy how to interpret the phylogeny when fossils that are immature individuals are included. Juvenile individuals in the peramorphic acceleration clades would produce misleading phylogenies, whereas juvenile individuals in the paedomorphic neoteny clades should still provide reliable phylogenetic signals.     

农村外出务工人员承包地处置方式的区域差异与影响因素——基于社会融入视角

我国农村外出务工人员保有相当规模的承包地,如何高效集约利用是农业现代化的基础。利用流动人口卫生计生动态监测数据,在分析省域承包地处置方式差异的基础上,以其社会融入水平为切入点,分析其承包地处置决策的影响因素。研究发现：（1）粮食主产区承包地流转已具一定规模,但撂荒在全国也有相当比例,显性撂荒呈“西南高、东北低”的空间格局,农村外出务工人员承包地处置方式的集聚特征与其流动目的地社会融入水平存在一定程度的关联性;（2）社会融入水平的提升会显著降低农村外出务工人员的自耕意愿,易于形成亲朋耕种、流转等承包地处置决策,但是,撂荒的概率也会随之增加;（3）地方土地流转政策尚不足以将农村外出务工人员转移经营权的意愿完全转化为亲朋耕种、流转等行为,依然有较高概率显性或隐性撂荒。针对这些问题,流出地与流动目的地的政策应统筹考虑。一方面提升社会服务水平,降低农村外出务工人员生计风险;另一方面应积极引导其将承包地流转,避免撂荒造成耕地资源浪费。     

生物效应比(BER)技术预测我国水生生物基准探讨

基于中国与美国间生物敏感性的差异,对生物效应比(BER)技术预测我国水生生物基准值进行了研究.首先,对中美共有的且急性生物毒性数据符合3门8科的污染物进行筛选,然后,依据两国物种的敏感性与代表性建立基于不同生物组合的BER技术,最后,对不同生物组合BER技术预测水生生物急性基准值与实测基准值进行比较与分析,筛选出预测效果较好的BER技术.结果表明:共筛选出9个中美共有且毒性数据丰富的污染物(As(III)、Cr(VI)、Hg、Cu、Zn、Pb、对硫磷、毒死蜱和三丁基锡),依据本土生物毒性数据推导出该9种污染物的我国水生生物急性基准值分别为201.72、2.64、0.74、1.32、55.83、92.25、0.12、0.36和0.38μg/L.此外,在对7种生物组合方式BER技术的预测效果进行分析比较的基础上,初步提出基于同属或科的生物组合方式的BER技术可较好地对9种污染物的本土水生生物急性基准值进行预测.研究结果可为在本土生物毒性数据缺乏时充分利用现有毒性数据或进行少量毒性试验的基础上对我国水生生物急性基准值的预测提供帮助.     

Protective shade, tree diversity and soil properties in coffee agroforestry systems in the Atlantic Rainforest biome

Sustainable production and biodiversity conservation can be mutually supportive in providing multiple ecosystem services to farmers and society. This study aimed to determine the contribution of agroforestry systems, as tested by family farmers in the Brazilian Rainforest region since 1993, to tree biodiversity and evaluated farmers’ criteria for tree species selection. In addition, long-term effects on microclimatic temperature conditions for coffee production and chemical and biological soil characteristics at the field scale were compared to full-sun coffee systems. A floristic inventory of 8 agroforests and 4 reference forest sites identified 231 tree species in total. Seventy-eight percent of the tree species found in agroforests were native. The variation in species composition among agroforests contributed to a greater γ-diversity than α-diversity. Monthly average maximum temperatures were approximately 6 °C higher in full-sun coffee than in agroforests and forests. Total soil organic C, N mineralization and soil microbial activity were higher in forests than in coffee systems, whereas the chemical and biological soil quality in agroforests did not differ significantly from full-sun coffee after 13 years. Given its contribution to the conservation of biodiversity and its capacity to adapt coffee production to future climate change, coffee agroforestry offers a promising strategy for the area.     

Extraction and quantification of "condensed tannins" as a measure of plant anti-herbivore defence? Revisiting an old problem

Contents of phenolic compounds in leaf extracts often serve as a measure of plant anti-herbivore defence. This method suffers from the multifunctionality of phenolics and from problems with their colorimetric quantification. Here we present further evidence for the pertinence of these problems. Contents of condensed tannins (CCT) were spectrophotometrically quantified in leaf extracts of 11 closely related mimosoid species, and Spodoptera littoralis caterpillars were reared on artificial diet containing these extracts. The relationship of CCT with caterpillar growth differed considerably among plant species, since both positive and negative correlations were detected. There was, however, a negative correlation of CCT with fungal spore germination, indicating a role of these compounds in resistance to fungi. Detailed knowledge on the structure and biological function of defensive compounds and on the overall composition of leaves is required to estimate a plant's defensive efficacy against a particular group of enemies.     

Behavioral genomics of honeybee foraging and nest defense

The honeybee has been the most important insect species for study of social behavior. The recently released draft genomic sequence for the bee will accelerate honeybee behavioral genetics. Although we lack sufficient tools to manipulate this genome easily, quantitative trait loci (QTLs) that influence natural variation in behavior have been identified and tested for their effects on correlated behavioral traits. We review what is known about the genetics and physiology of two behavioral traits in honeybees, foraging specialization (pollen versus nectar), and defensive behavior, and present evidence that map-based cloning of genes is more feasible in the bee than in other metazoans. We also present bioinformatic analyses of candidate genes within QTL confidence intervals (CIs). The high recombination rate of the bee made it possible to narrow the search to regions containing only 17–61 predicted peptides for each QTL, although CIs covered large genetic distances. Knowledge of correlated behavioral traits, comparative bioinformatics, and expression assays facilitated evaluation of candidate genes. An overrepresentation of genes involved in ovarian development and insulin-like signaling components within pollen foraging QTL regions suggests that an ancestral reproductive gene network was co-opted during the evolution of foraging specialization. The major QTL influencing defensive/aggressive behavior contains orthologs of genes involved in central nervous system activity and neurogenesis. Candidates at the other two defensive-behavior QTLs include modulators of sensory signaling (Am5HT ₇ serotonin receptor, AmArr4 arrestin, and GABA-B-R1 receptor). These studies are the first step in linking natural variation in honeybee social behavior to the identification of underlying genes.     

2株海洋石油降解细菌的降解能力

为实施海洋石油污染的生物治理,从厦门储油码头油污水中分离得到了2株石油降解菌.它们能够在以柴油、萘或芘为唯一碳源的培养基中生长,并适应于海洋环境的温度、pH和盐度.它们对萘都有很强的降解能力,3d内降解率可达87.53%和84.01%;7 d内对芘降解率分别为8.35%、5.37%.经16S rDNA同源性分析表明2菌株之间及其与施氏假单胞菌的同源性皆为99%;Biolog生化鉴定也表明它们为不同的菌株.通过兼并PCR扩增,序列分析发现2种菌编码完全相同的萘双加氧酶基因,该基因与其它假单胞菌的萘双加氧酶大亚基有98%同源性.