Species, clusters and the ‘Tree of life’: A graph-theoretic perspective

A hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more recent quest for a ‘Tree of Life’. In this paper we use an approach based on discrete mathematics to address a basic question: could one delineate this hierarchical structure in nature purely by reference to the ‘genealogy’ of present-day individuals, which describes how they are related with one another by ancestry through a continuous line of descent? We describe several mathematically precise ways by which one can naturally define collections of subsets of present day individuals so that these subsets are nested (and so form a tree) based purely on the directed graph that describes the ancestry of these individuals. We also explore the relationship between these and related clustering constructions.     

稻鸭共作及其它控草措施对稻田杂草群落的影响

运用群落生态学方法研究了稻鸭共作、人工除草、化学除草3种控草措施对稻田杂草群落特征的影响及其对田间杂草的控制作用.结果表明,稻鸭共作显著降低了田间杂草的发生密度,对稻田主要杂草鸭舌草(Monochoriavaginalis)、异型莎草(Cyperusdifformis)、矮慈姑(Sagittariapygmaea)的防效均达到95%以上,总体控草效果显著优于化学除草和人工除草.稻鸭共作使稻田杂草群落的物种丰富度及Shannon-Wiener多样性指数略有降低,但Pielou均匀度指数显著提高,表明群落物种组成有了很大的改变,降低了原来优势杂草的发生危害.在不同控草措施作用下,稻田杂草群落的结构组成也发生了一定的变化,稻鸭共作区群落组成为陌上菜(Linderniaprocumbens)+异型莎草+水虱草(Fimbristylismiliacea),Whittaker群落指数显著高于化学除草、人工除草及对照区,表明稻鸭共作对田间杂草群落结构影响较大.从Sorensen群落相似性指数及以其为距离测度指标的聚类分析结果中也可得到同样的结论.     

新疆博格达山地面生苔藓植物物种多样性研究

采用相似性系数和物种多样性指数对新疆博格达山地面生苔藓植物的物种多样性进行了研究．结果表明,博格达山地区苔藓植物区系具有丰富性和复杂性的特点,共有地面生苔藓植物32科73属186种(含变种、变型);山地荒漠带和山地草原带苔藓植物物种相似性最高,为0．6809,山地森林带和高山垫状植被带相似性最低,仅为0．1342;山地森林带苔藓植物在整个博格达山地面生苔藓植物群落中占据优势地位;山地森林带苔藓植物物种多样性最为丰富,为该山地苔藓植物多样性的分布中心,是苔藓植物多样性保护的关键地区．     

广东南岭自然保护区堇菜属植物垂直分布格局的研究

在南岭自然保护区核心区选择海拔高度为500—600m、600—800m、800—1000m、1000—1200m、1200—1400m、1400—1600m、1600—1800m、1800—1902m共8个连续的海拔梯度,分别对植物群落中的堇菜属植物进行普查。结果表明,随着海拔升高,各海拔段有堇菜属植物5、8、9、10、9、7、3、1种,以中海拔段的物种多样性较高。两海拔段间距离越近,物种相似性系数越大;距离越远,相似性系数越小。在中海拔段,堇菜属植物种类的多度最大,两端较小。南岭自然保护区堇菜属植物的垂直分布格局呈“中间膨胀型”或“单峰型”,与普遍的木本植物一致,这种格局可能是与沿海拔水热梯度的变化相关。     

Homology as a relation of correspondence between parts of individuals

The recognition of correspondences has long been a fundamental activity among systematists. Advocates ofNaturphilosophie, such as Lorenz Oken, drew far-fetched analogies between taxonomic groups and all sorts of other things, including the Persons of the Trinity. They treated change through time either as analogous to an ontogeny or as the product of divinely instituted laws of nature. Darwin changed things by making the taxonomic units strictly historical, implying that they are not classes but rather individuals in a broad metaphysical sense. That means that taxa are concrete, particular things, or wholes made up of parts which are themselves individuals, and that there are no laws of nature for them. Homology is a relationship of correspondence between parts of organisms that are also parts of populations and lineages. It is not a relationship of similarity, and unlike similarity it is transitive. Analogy is a relationship of correspondence between parts of organisms that are members of classes, and is not necessarily due to function. Taxa, like other individuals, can change indefinitely, and the only thing that they must share is a common ancestor. They do not share an essence, Platonic Idea orBauplan, although “conservative characters” may be widespread in them. Iterative homology likewise is a relationship of correspondence, but the nature of that correspondence remains unclear. The difficulties of the homology concept can be overcome by treating phylogenetics and comparative biology in general as historical narrative. From the 46th “Phylogenetisches Symposium”, Jena, Germany, November 20–21, 2004. Theme of the symposium: “Evolutionary developmental biology—new challenges to the homology concept”.     

Metatarsal robusticity in primates and a few other plantigrade mammals

By using a new technique for determining relative metatarsal robusticity, the distribution of the 1+5 pattern (in which M5 is the second most robust metatarsal after M1) and 15 pattern (in which M5 is the least robust of all metatarsals) was established in primates and a few other plantigrade mammals. The first pattern is associated with a terrestrial and the second with an arboreal substrate. Robusticity formulae are not connected with specific locomotor patterns, but a total robusticity quotient is associated with these patterns and substrate preference as well. Changes in substrate preference are accompanied by changes of total robusticity, an increased number of permutations and ultimately a change of the robusticity pattern. Intermetatarsal robusticity gradients are related to the direction and intensity of muscular activity. A combined analysis of all factors can reveal a great deal of the locomotor history of a taxon.Also ofThe Institute of Applied Biology, New York.     

Studies on chlorophyll biosynthesis and other things

Our research on chlorophyll biosynthesis, over a period of approximately twenty years, has been described, emphasizing those areas in which our laboratory made significant and timely contributions. References to some of our most important articles are included. Portions of the chlorophyll biosynthetic pathway, in which our own laboratory was not involved, for example, the reduction of protochlorophyllide to chlorophyllide and the phytylation of the latter to yield chlorophyll a, have not been covered in this article. Those events which preceded my involvement with chlorophyll biosynthesis, but which contributed to the formation of my own scientific personality, are mentioned briefly in the Introduction. My non-scientific avocations have been included at the request of the reviewers and Govindjee.     

Notes on theorizing racism and other things

ABSTRACT

In the spirit of ‘furthering debate and reflection’ in this response to Theories of Race and Ethnicity, we consider here the pertinence of the theme of resistance that occupies particular chapters within the collection and that has been central to key works within the wider race critical scholarship. Yet, when the larger field of contemporary race study is considered, we also note that other contiguous concerns – including capitalism, religion, nation, and war – are key factors in thinking through racism. Here, we further elaborate on how future theorizations of race and ethnicity must engage with these domains.     

云南西北部地区地表甲虫的物种多样性

共调查了云南西北部地区的中甸大雪山、中甸碧塔海、德钦白芒雪山、丽江石鼓镇、玉龙雪山保护区和永胜县6个小区域。采用巴氏罐诱法研究不同生境下地表甲虫物种多样性的变化。其结果：①共采集甲虫标本2852号,分属16个科,以隐翅虫数量最多,占41.3%;步甲次之,占25.9%;金龟、象甲、拟步甲的数量各占5％以上;其他11科合计占13％;②甲虫群落的物种多样性分析表明：农业活动频繁的永胜县,个体数量和丰富度较低;游牧业和旅游业频繁的中甸碧塔海多样性指数和丰富度较低;其他4个区域多样性指数、均量和丰富度较低;游牧业和旅游业频繁的中甸碧塔海多样性指数和丰富度较低;其他4个区域多样性指数、均匀度指数、丰富度以及个体数量比较均匀。除永胜县外,其他地区甲虫群落间相似性系数随空间距离的增大而降低。③比较针叶林、阔叶林、混交林、灌丛和草甸等5种生境,所有甲虫、步甲、金龟数量在针叶林和草甸生境内较高;隐翅虫数量在针叶林和阔叶林内较高;象甲在阔叶林内数量较高;拟步甲在灌丛内数量较高;但只有步甲和隐翅虫差异显著。④物种的个体数量、丰富度和多样性指数随海拔高度不同,其变化趋势相似。在1500－2000m呈下降趋势;在2500－3000m和3500－4000m分别形成2个峰值。均匀度指数的变化趋势则与之相反。以上结果表明,空间距离和生境类型影响云南西北部地区地表甲虫群落的物种多样性和相似性,频繁的农牧业和旅游业活动,对保持地表甲虫物种多样性的自然分布规律产生一定影响。     

Integration, individuality and species concepts

Integration (interaction among parts of an entity) is suggested to be necessary for individuality (contra, Metaphysics and the Origin of Species). A synchronic species is an integrated individual that can evolve as a unified whole; a diachronic lineage is a non-integrated historical entity that cannot evolve. Synchronic species and diachronic lineages are consequently suggested to be ontologically distinct entities, rather than alternative perspectives of the same underlying entity (contra Baum (1998), Syst. Biol. 47, 641–653; de Queiroz (1995), Endless Forms: Species and Speciation, pp. 57–75; Genes, Categories and Species). Species concepts usually refer to either one or the other entity; for instance, the Biological Species Concept refers to synchronic species, whereas the Cladistic Species Concept refers to diachronic lineages. The debate over species concepts has often failed to recognise this distinction, resulting in invalid comparisons between definitions that attempt to delineate fundamentally different entities. This revised version was published online in July 2006 with corrections to the Cover Date.     

广东省自然保护区尺度陆生脊椎动物物种多样性与高级分类单元的关系

利用广东省自然保护区陆生脊椎动物名录,分析保护区尺度上物种与高级分类单元在数量上的关系.结果表明,属、科在数量上都随着物种数的增加而增加,且具有相似的增长趋势.物种-属、物种-科在数量上呈现出极显著相关关系(P<0.01,r>0.8),在乘幂模型、线性模型、指数模型和对数模型拟合中,乘幂模型拟合最好.结果显示了,保护区...     

阿拉善干旱荒漠区不同植被类型土壤种子库研究

[1]兰州大学草地农业科技学院,兰州730020 [2]甘肃草原生态研究所,兰州730020 [3]内蒙古阿拉善盟草原站,巴彦浩特750360     

Synthesis, characterisation and natural abundance Os NMR spectroscopy of hydride bridged triosmium clusters with chiral diphosphine ligands

Treatment of [Os₃(μ-H)₂(CO)₁₀] with the chiral diphosphines BINAP, tolBINAP [(R)-2,2′-bis(di-4-tolylphosphino)-1,1′-binaphthyl], DIOP [(4R,5R)-(−)-O-isopropenylidene-2,3-dihydroxy-1,4-bis(diphenylphosphino)butane] affords [Os₃(μ-H)₂(CO)₈(μ-L)] (L = BINAP (1), tolBINAP (2), DIOP (4)) in high yield. The X-ray structures for 1, 2 and 4 are reported, and structural and spectroscopic comparisons are made between these clusters and [Os₃(μ-H)₂(CO)₈(μ-L)] (L = dppm (5), dppe (6), dppp (7)) which were synthesised similarly. Compounds 5 to 7 were previously synthesised by hydrogenation of 1,2-[Os₃(CO)₁₀(μ-L)] but the route from [Os₃(μ-H)₂(CO)₁₀] is preferable. The H-bridged Os?Os distances are similar in 1, 2 and 4 indicating that these species are formally unsaturated 46-electron clusters. The P?P distances vary from 4.24 to 4.30 Å in 1 and 2, respectively, to 4.53 Å in 4 and there are related changes in the angles associated with the ligand set around the H-bridged osmium atoms. Introduction of the diphosphine ligands completely suppresses the ability to add CO, to insert acetylene to form a μ-η¹,η²-vinyl compound, and to exchange hydride ligands with styrene-d₈, which are reactions characteristic of [Os₃(μ-H)₂(CO)₁₀]. Clusters 2 and 5-7 were also used to examine the potential of natural abundance ¹⁸⁷Os NMR spectroscopy through techniques based on inverse detection by HMQC, HSQC and HMBC spectroscopy.     

Pollen,women, war and other things: reflections on the history of palynology

The development of palynology since its recognised launch in 1916 by Lennart von Post is examined in terms of its historiography, the biographies of pollen analysts and the role of those who have influenced the discipline. Emphasis is placed upon research beginnings in Scandinavia (especially Sweden), Great Britain and Ireland. Within an analytical narrative which includes archival and published sources, special consideration is given to a ‘proclamation’ on methodology which appeared in 1909, on a supposed geology/botany dichotomy stemming from von Post’s background, on the forgotten early practitioners in Britain and Ireland and their connections, on the role of women up to the end of the Second World War and on issues related to wartime hostilities. Present day palynology can trace a continuity from von Post and palynologists are part of an extended disciplinary genealogy. Ignorance of these can be seen as a loss of heritage and to represent an intellectual impoverishment.     

安徽省兽类物种多样性及其分布格局

搜集整理安徽省兽类物种分布数据,结合调查数据,通过生境分析,确定兽类物种分布范围。基于GIS技术,以面积约为404.685 km²的425个栅格收集安徽省兽类的二元分布数据,采用多元分析的分层聚类方法,依据地理单元中物种组成和分布型组成的相似程度进行分析,对安徽兽类物种多样性及其分布格局和相关的动物地理学问题进行了探讨。结果表明,山区兽类物种丰富度显著高于平原丘陵区,其中,皖南山区兽类物种丰富度总体高于皖西大别山区,东部的江淮丘陵区略高于皖北的淮北平原。依物种组成进行的聚类分析结果表明,当相似性系数分别为0.647、0.570、0.461和0.399时,将425个地理单元聚为9、5、3 和2 个单元组,分析结果表明兽类分布受地形因素和人为活动的影响较自然地理亚区的界限影响明显。依分布型组成进行聚类分析时,当卡方距离为1.561、1.759、2.521和3.509 时,分别聚为9、5、3 和2 组,分析结果表明分布单元以长江为界分为两组,以古北型物种为主的长江以北地区和以东洋型物种为主的长江以南地区。对9 个分布单元组中的古北型和东洋型物种优势度分析结果表明:古北界和东洋界宏观上的界线大致以长江为界,呈现广阔的过渡区。过渡区的北界沿大别山北麓,经六安、舒城、合肥、定远以至来安一线,南界西起东至县北部、经贵池、青阳、南陵、沿宣城北部至广德一线。     

Theoretical studies on doubly and triply linked polymers of Ge9 clusters

Experimental isolation of singly-bonded polymers of Ge₉, Sn₉ clusters and oligomers of doubly linked Ge₉ clusters encouraged us to explore other possibilities of polymerizing Ge₉ units. The electron counts in the reported oligomers are not consistent with simple ideas of localized intercluster bonding; demanding a detailed theoretical analysis. Band structure calculations suggest delocalized bonding with a charge requirement of 2− per Ge₉ unit for all polymeric doubly linked chains. DFT-based geometry optimization of model doubly linked polymers shows that one of the two possible forms is stable and has a band gap of ≈1.0 eV. A detailed bonding analysis of a theoretical model, Rb₄Ge₁₈, shows that the increased inter-polyhedral bond weakens the intra-polyhedral bonding. Ternary fusions are found to be generally unstable - for triple linkages the intrapolyhedral bonding is still further reduced; the polymers appear to be unstable towards dissociation into individual Ge₉ units.