Porcine linkage and cytogenetic maps integrated by regional mapping of 100 microsatellites on somatic cell hybrid panel

Recently two main genetic maps [Rohrer et al. Genetics 136, 231 (1994); Archibald et al. Mamm. Genome 6, 157 (1995)] and a cytogenetic map [Yerle et al. Mamm. Genome 6, 175 (1995)] for the porcine genome were reported. As only a very few microsatellites are located on the cytogenetic map, it appears to be important to increase the relationships between the genetic and cytogenetic maps. This document describes the regional mapping of 100 genetic markers with a somatic cell hybrid panel. Among the markers, 91 correspond to new localizations. Our study enabled the localization of 14 new markers found on both maps, of 54 found on the USDA map, and of 23 found on the PiGMaP map. Now 21% and 43% of the markers on the USDA and PiGMaP linkage maps respectively are physically mapped. This new cytogenetic information was then integrated within the framework of each genetic map. The cytogenetic orientation of the USDA linkage maps for Chromosomes (Chrs) 3, 8, 9, and 16 and of PiGMaP for Chr 8 was determined. USDA and PiGMaP linkage maps are now oriented for all chromosomes, except for Chrs 17 and 18. Moreover, the linkage group ``R' from the USDA linkage map was assigned to Chr 6. Received: 21 September 1995 / Accepted: 19 January 1996     

县区生态系统服务分布图编制——以北京市延庆区土壤保持服务为例

地图是直观展示生态系统服务空间分布格局的手段,是确定重要生态保护目标和区域的主要方法。结合制图学理论方法及国家、行业相关制图规范,探讨生态系统服务分布图编制的目标、原则、流程和制图方法。以编制北京市延庆区1 ： 25万土壤保持服务分布图为例,分析了地理基础确定、地理要素取舍以及土壤保持服务分级等关键制图方法,提出了土壤保持服务分布图的编制规范。研究结果表明,编制的图件能够详尽的展示土壤保持服务的分布特征,精细的反映生态系统服务与自然、人文要素的关系。通过详实的图面信息可进一步判别土壤保持服务分布重要区域,这将为区域生态环境保护规划提供重要技术手段。     

Integration of the PiGMaP and USD A maps for porcine chromosome 14

In order to align two previously published genetic linkage maps, a set of four of the United States Department of Agriculture (USDA) microsatellite linkage markers was mapped in the International Pig Gene Mapping Project (PiGMaP) reference families. Two-point linkage analysis was used between these USDA markers and the set of genes and markers previously mapped on the PiGMaP chromosome 14 map-Markers with threshold lod scores of three or greater were used for multipoint map construction. The USDA and PigGMaP linkage maps of chromosome 14 were aligned using the four USDA microsatellite markers along with three markers that are common to both maps. The PiGMaP genetic linkage map order for chromosome 14 was confirmed and the map was expanded to 193 cM with addition of the new markers.     

土壤动物的分子分类预测策略评估

土壤动物类群包含庞大的生物多样性, 由于传统的形态学鉴定技术很难满足该类群多样性调查和监测的巨大需求, 基于DNA等遗传物质的分子层面的鉴定技术(分子分类预测)逐渐登上舞台。然而, 分子分类预测能否在参考分子序列严重匮乏的土壤动物分类研究中实现有效鉴定、如何利用分子分类预测更为准确高效地获取土壤动物的分类信息, 是当下分子分类预测在土壤动物应用中的两大难题。为探究这两大难题, 本文基于宏条形码技术, 对5款常用的分子分类预测软件(VSEARCH、HS-BLASTN、EPA-NG、RAPPAS和APPLES; 前两款基于相似度算法, 其余基于系统发育位置算法)进行了准确性(科和属阶元)、运行速度和内存占用等性能的比较和评估。其中, 预测准确性的评估基于4类土壤动物(弹尾纲, 蜱螨亚纲, 环带纲和色矛纲)和3种分子标记(COI、16S和18S)展开。结果表明: EPA-NG在大部分场合下准确性最高, 尤其是在使用COI标记时, 准确性远高于其他工具。VSEARCH和HS-BLASTN准确性也较高, 基于16S和18S标记时, 它们的准确性和EPA-NG相当。此外, VSEARCH在所有软件中运行速度最快且内存占用最小, 这使得它在16S和18S的应用中比EPA-NG更具竞争力。RAPPAS和APPLES具有较低的假阳性, 但假阴性很高, 相对保守的算法使得它们无法将一些物种鉴定到低阶元。总体来说, 即使是在参考数据库缺少目标物种且小部分物种在分类上存在界定争议的前提下, 5款分子分类预测软件都能极为准确地将土壤动物预测至科级阶元, 因此分子分类预测在土壤动物应用中前景远大。COI标记在土壤动物科、属和种阶元上的覆盖度最广且能有效实现分子鉴定, 在目前最适合作为土壤动物尤其是土壤节肢动物的分子标记。在应用COI标记且参考数据库规模不大时, EPA-NG是分子分类预测的最佳选择; 而在应用16S、18S标记或参考数据库规模较大时, 更推荐使用VSEARCH。     

Alignment of the PiGMaP and USDA linkage maps of porcine chromosomes 2 and 5

The PiGMaP and USDA porcine linkage maps for chromosomes 2 and 5 have been aligned by typing five USDA microsatellite markers from chromosomes 2 and 4 from chromosome 5 on the PiGMaP reference families. The markers in the two maps can be successfully aligned except for Sw395 on chromosome 2, which is the end-most marker in the USDA map 22 cM remote from the next marker, but which maps to a more central location and in the same position as Sw776 in the PiGMaP families. The mapping of four additional chromosome 5 markers has enabled amalgamation of the two previously separate PiGMaP linkage groups assigned to chromosome 5 and has more than doubled the length of its map. The USDA map of chromosome 5 is considerably shorter than the revised PiGMaP version, particularly between DAGK and Sw1071 , where the corresponding lengths are 9 cM versus 33 cM.     

A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.     

中国植物分类学者姓名拼写的讨论与建议

在汉语拼音方案未正式推行前, 近代较早的文献书籍里对中国植物分类学者姓名的记载以威妥玛拼音为主, 同时混杂其他拼音形式, 另外存在诸多以缩写方式记录人名的情况。在进行近当代中国植物学的文献阅读、资料查询以及文献引证时, 多样化的人名拼写与缩写方式在一定程度上造成了困扰与混乱。本文简述了中国植物分类学发展初期主要用于人名地名的拼写系统, 以近当代中国植物学相关研究者的姓名索引为基础数据, 结合国内外的植物学相关网站及数据库, 整理出了较完整的早期中国植物分类学家姓名拼写的信息对照表。基于历史数据和当下应用实例, 归纳了中国植物分类学者姓名拼写多样现象的类型及其原因。过去及当代国内外在拼写中国人名上存在的问题有: (1)历史记载中写法不规范现象; (2)不同拼音形式的识别与使用混乱现象; (3)现代拼写在姓与名的顺序、拼音大小写、双名连接以及缩写上不统一现象。最后, 我们提出了关于中国植物分类学者姓名拼写与引用的建议。     

UniEuk: Time to Speak a Common Language in Protistology!

Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho‐taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental ‘‐omics’ surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta‐omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist ‐omics age to the fragile, centuries‐old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community‐based and expert‐driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL‐EBI, ensuring its broad use and long‐term preservation as a reference taxonomy for eukaryotes.     

Correlations in one-dimensional fully developed chaos

Correlations in the baker map and the tent map as examples of one-dimensional, fully developed chaos are considered. It is shown, utilizing symbolic dynamical systems derived from these maps, that the vanishing second-order correlation function is not sufficient to guarantee uncorrelatedness. Importance of the higher-order, especially third-order, correlation functions is emphasized for chaotic systems. In search of the quantities that grasp correlational behaviors as a whole in chaotic systems, it is proposed to use the fixed-separation correlation integral, which is a modified quantity of the usual correlation integral devised to calculate the fractal dimension of strange attractors, for these maps. It is shown that the new quantity contains all the even-number orders of autocorrelation function that are commonly considered.     

异质景观条件下江汉平原土壤的空间分异

景观异质与土壤分异息息相关。以DEM数据为基础,以海拔50m、100m为界,将江汉平原划分为平原湖区景观、平缓岗地景观及起伏丘陵景观3种类型。在ArcG IS 10支持下,将江汉平原土壤图与景观类型图进行叠置分析,提取不同景观类型片区各土壤亚类斑块周长、面积等信息,计算了各景观类型片区各土壤亚类的分维数、平均斑块面积、稳定度等信息,定量分析了江汉平原各景观类型片区土壤空间分异特征,结论如下:(1)不同景观类型区各土壤亚类分布差异明显,起伏丘陵景观区主要以红壤和黄棕壤地带性土壤为主;平原湖区潮土和水稻土等耕作土非常发育;平缓岗地区地带性土壤和耕作土壤平分秋色。(2)连片性较好的土壤亚类呈现不同的景观选择性:耕作土集中分布于平原湖区景观片区;地带性土壤多集中分布于丘陵和岗地景观片区。(3)平原湖区面积很大,各类土壤都有发育的空间,土壤亚类之间分维数和稳定度差别比较大;平缓岗地景观区由于面积非常局限,土壤亚类发生发育受到空间的限制,边界破碎化,分维数平均都比较大,斑块镶嵌结构均比较复杂,稳定度差别较小。(4)主要土壤亚类的分维数和稳定性指数值一定程度地反映了各主要土壤亚类的最匹配的景观类型,即能够提供其发生发育的最佳条件。研究有利于深入认识土壤形成和演化规律,为土壤资源的合理利用及定向培育服务。     

Integrating paper-based habitat mapping with mobile electronic field recording procedures

A hybrid method of ecological habitat survey and mapping is presented, bridging paper-based methods and mobile electronic procedures. The hybrid approach uses a hand-held PDA with real-time dGPS to map habitats and record habitat attributes. It retains paper field maps to facilitate ecological decisions and to overcome the need for field surveyors to operate a fully functional mobile GIS system. The transition from paper records to a full GIS implementation is bridged by secondary digitisation in which a GIS specialist, trained in field survey procedures, interacts routinely with the field surveyors, throughout the field season to assure data quality standards. The methodology is practical and affordable, particularly if there are multiple field surveyors.     

Dendritic Targeting in the Leg Neuropil of Drosophila: The Role of Midline Signalling Molecules in Generating a Myotopic Map

Neural maps are emergent, highly ordered structures that are essential for organizing and presenting synaptic information. Within the embryonic nervous system of Drosophila motoneuron dendrites are organized topographically as a myotopic map that reflects their pattern of innervation in the muscle field. Here we reveal that this fundamental organizational principle exists in adult Drosophila, where the dendrites of leg motoneurons also generate a myotopic map. A single postembryonic neuroblast sequentially generates different leg motoneuron subtypes, starting with those innervating proximal targets and medial neuropil regions and producing progeny that innervate distal muscle targets and lateral neuropil later in the lineage. Thus the cellular distinctions in peripheral targets and central dendritic domains, which make up the myotopic map, are linked to the birth-order of these motoneurons. Our developmental analysis of dendrite growth reveals that this myotopic map is generated by targeting. We demonstrate that the medio-lateral positioning of motoneuron dendrites in the leg neuropil is controlled by the midline signalling systems Slit-Robo and Netrin-Fra. These results reveal that dendritic targeting plays a major role in the formation of myotopic maps and suggests that the coordinate spatial control of both pre- and postsynaptic elements by global neuropilar signals may be an important mechanism for establishing the specificity of synaptic connections.     

Overview of the taxonomy of zooxanthellate Scleractinia

Coral taxonomy has entered a historical phase where nomenclatorial uncertainty is rapidly increasing. The fundamental cause is mandatory adherence to historical monographs that lack essential information of all sorts, and also to type specimens, if they exist at all, that are commonly unrecognizable fragments or are uncharacteristic of the species they are believed to represent. Historical problems, including incorrect subsequent type species designations, also create uncertainty for many well‐established genera. The advent of in situ studies in the 1970s revealed these issues; now molecular technology is again changing the taxonomic landscape. The competing methodologies involved must be seen in context if they are to avoid becoming an additional basis for continuing nomenclatorial instability. To prevent this happening, the International Commission on Zoological Nomenclature (ICZN) will need to focus on rules that consolidate well‐established nomenclature and allow for the designation of new type specimens that are unambiguous, and which include both skeletal material and soft tissue for molecular study. Taxonomic and biogeographic findings have now become linked, with molecular methodologies providing the capacity to re‐visit past taxonomic decisions, and to extend both taxonomy and biogeography into the realm of evolutionary theory. It is proposed that most species will ultimately be seen as operational taxonomic units that are human rather than natural constructs, which in consequence will always have fuzzy morphological, genetic, and distribution boundaries. The pathway ahead calls for the integration of morphological and molecular taxonomies, and for website delivery of information that crosses current discipline boundaries. © 2013 The Author. Zoological Journal of the Linnean Society published by John Wiley & Sons Ltd. on behalf of The Linnean Society of London     

Estimating soil carbon fluxes following land-cover change: a test of some critical assumptions for a region in Costa Rica

Changes in soil carbon storage that accompany land‐cover change may have significant effects on the global carbon cycle. The objective of this work was to examine how assumptions about preconversion soil C storage and the effects of land‐cover change influence estimates of regional soil C storage. We applied three models of land‐cover change effects to two maps of preconversion soil C in a 140 000 ha area of northeastern Costa Rica. One preconversion soil C map was generated using values assigned to tropical wet forest from the literature, the second used values obtained from extensive field sampling. The first model of land‐cover change effects used values that are typically applied in global assessments, the second and third models used field data but differed in how the data were aggregated (one was based on land‐cover transitions and one was based on terrain attributes). Changes in regional soil C storage were estimated for each combination of model and preconversion soil C for three time periods defined by geo‐referenced land‐cover maps. The estimated regional soil C under forest vegetation (to 0.3 m) was higher in the map based on field data (10.03 Tg C) than in the map based on literature data (8.90 Tg C), although the range of values derived from propagating estimation errors was large (7.67–12.40 Tg C). Regional soil C storage declined through time due to forest clearing for pasture and crops. Estimated CO₂ fluxes depended more on the model of land‐cover change effects than on preconversion soil C. Cumulative soil C losses (1950–1996) under the literature model of land‐cover effects exceeded estimates based on field data by factors of 3.8–8.0. In order to better constrain regional and global‐scale assessments of carbon fluxes from soils in the tropics, future research should focus on methods for extrapolating regional‐scale constraints on soil C dynamics to larger spatial and temporal scales.     

中国植物分类学者的历史与现状

中国植物资源丰富, 长期以来被外国人所关注和研究。直到1916年, 中国植物分类学者才开始独立研究本国植物, 并经历了从民国时期开始自立、到1949年后自主完成《中国高等植物图鉴》《中国植物志》等国家级和相对完整的地方植物志以及中外合作完成英文版的国家植物志Flora of China、再到21世纪新一代学者每年更新《中国生物物种名录》并且开始主导国际性植物分类学研究工作等3个主要时期。统计表明, 超过3,000位中国学者参与过植物命名或植物名称处理等命名相关工作, 近些年更是达到每年新增100人左右的新高。但这种繁荣局面与中国植物分类学的衰退状况彼此矛盾。为了解释这个矛盾, 结合对历史回顾的深入分析说明, 真正能够反映分类学发展程度的量化指标应当是“活跃”分类学者数目。这个数目在21世纪停滞不前, 表明当今的分类学人才队伍建设仍存在不少问题, 特别是新分类群的发表与系统学研究脱节, 对分子系统学证据的应用仍有不足, 以及科研评价体系偏重于论文影响因子等。本文因此提出了当今分类学者应该具备的6条技能标准: (1)具有科学精神和全球视野; (2)掌握学科内知识; (3)掌握学科外知识; (4)具备野外工作技能; (5)具备标本馆和实验室工作技能; (6)掌握文献和数据库检索技能。     

川西亚高山针叶林土壤颗粒的分形特征

分形理论为土壤等复杂体系的定量化研究提供了一种有效工具。本文以12个川西亚高山针叶林土壤颗粒组成数据为基础,运用分形模型研究了亚高山针叶林土壤颗粒的分形维数。结果表明,12个川西亚高山针叶林表层土壤颗粒的分形维数D为2.5209~2.7978。通过逐步多元回归分析,土壤颗粒分形维数仅与<0.001 mm颗粒含量的相关系数达极显著。土壤颗粒分形维数与土壤有机质含量、全氮含量和pH相关性不显著,然而土壤有机质含量与全氮含量呈极显著正相关。本研究探讨了利用土壤颗粒粒径分布的分形维数来定量表征川西亚高山针叶林土壤的特征。     

Estimation of soil organic matter by geostatistical methods: Use of auxiliary information in agricultural and environmental assessment

Mapping soil properties such as soil organic matter (SOM), or soil organic carbon (SOC) content represent a problem often arising in agronomic and environmental surveys, since point data must be spatialized with the best interpolation. Deterministic methods (Inverse Distance Weighting, Splines, ecc.) do not account for the error, thus probabilistic methods as geostatistics (e.g. Ordinary Kriging, OK) have been successfully applied for many years. Maps derived from this kind of stochastic interpolation, based only on a recognized autocorrelation among measured points, could not be suitable in representing the reality, since they usually show a smoothed pattern. Hybrid interpolation methods, such as Regression Kriging (RK), combine an interpolation based only on point data and an interpolation based on a regression of the target variable with other continuous variables, spatially related, well known on the whole area.In the Teramo province, central Italy, a set of 250 soil samples, collected from the surface horizon of agricultural soils is available. From these samples the estimation of soil texture, SOC, SOM related to texture and C/N both by OK and RK was performed. The following predictors were used for RK: (i) indexes derived from Landsat TM imagery, (ii) morphometric parameters derived from DEM, (iii) soil subsystems map 1:250,000. The maps obtained by both OK and RK in this survey show substantial agreement, without significant improvement in map accuracy using auxiliary information.