Advances in the phylogenesis of Agaricales and its higher ranks and strategies for establishing phylogenetic hypotheses

We present an overview of previous research results on the molecular phylogenetic analyses in Agaricales and its higher ranks （Agaricomycetes/Agaricomycotina/Basidiomycota） along with the most recent treatments of taxonomic systems in these taxa. Establishing phylogenetic hypotheses using DNA sequences, from which an understanding of the natural evolutionary relationships amongst clades may be derived, requires a robust dataset. It has been recognized that single-gene phylogenies may not truly represent organismal phylogenies, but the concordant phylogenetic genealogies from multiple-gene datasets can resolve this problem. The genes commonly used in mushroom phylogenetic research are summarized.     

内蒙古棘豆属植物分支分类的初步探讨

本文以内蒙古棘豆属植物为对象，应用分支分类的方法，对豆科棘豆属的植物系统演化关系做了初步的探讨．根据文献和标本按外类群比较，和谐性分析等原则确定了性状极性，利用最大同步法对棘豆属植物进行了分支分析，得出了分支分类支序图，并编写了检索表．     

Phylogenetic studies of the core Alismatales inferred from morphology and rbcL sequences

The phylogeny of Alismatales remains an area of deep uncertainty, with different arrangements being found in studies that examined various subsets of genes and taxa. Herein we conducted separate and combined analyses of 103 morphological characters and 52 rbcL sequences to explore the controversial phylogenies of the families. Congruence between the two data sets was explored by computing several indices. Morphological data sets contain poor phylogenetic signals. The homology of morphological characters was tested based on the total evidence of phylogeny. The incongruence between DNA and morphological results; the hypothesis of the ‘Cymodoceaceae complex’; the relationships between Najadaceae and Hydrocharitaceae; the intergeneric relationships of Hydrocharitaceae; and the evolutionary convergence of morphological characters were analyzed and discussed.     

Studies on the osteology of the bagrid catfishes from the Jialing River（IV）：an approach to the phyloge－neti

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A general integrative model for scaling plant growth, carbon flux, and functional trait spectra

Linking functional traits to plant growth is critical for scaling attributes of organisms to the dynamics of ecosystems and for understanding how selection shapes integrated botanical phenotypes. However, a general mechanistic theory showing how traits specifically influence carbon and biomass flux within and across plants is needed. Building on foundational work on relative growth rate, recent work on functional trait spectra, and metabolic scaling theory, here we derive a generalized trait-based model of plant growth. In agreement with a wide variety of empirical data, our model uniquely predicts how key functional traits interact to regulate variation in relative growth rate, the allometric growth normalizations for both angiosperms and gymnosperms, and the quantitative form of several functional trait spectra relationships. The model also provides a general quantitative framework to incorporate additional leaf-level trait scaling relationships and hence to unite functional trait spectra with theories of relative growth rate, and metabolic scaling. We apply the model to calculate carbon use efficiency. This often ignored trait, which may influence variation in relative growth rate, appears to vary directionally across geographic gradients. Together, our results show how both quantitative plant traits and the geometry of vascular transport networks can be merged into a common scaling theory. Our model provides a framework for predicting not only how traits covary within an integrated allometric phenotype but also how trait variation mechanistically influences plant growth and carbon flux within and across diverse ecosystems.     

Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms

The conflict between the Mendelian theory of particulate inheritance and the observation of continuous variation for most traits in nature was resolved in the early 1900s by the concept that quantitative traits can result from segregation of multiple genes, modified by environmental effects. Although pioneering experiments showed that linkage could occasionally be detected to such quantitative trait loci (QTLs), accurate and systematic mapping of QTLs has not been possible because the inheritance of an entire genome could not be studied with genetic markers. The use of restriction fragment length polymorphisms (RFLPs) has made such investigations possible, at least in principle. Here, we report the first use of a complete RFLP linkage map to resolve quantitative traits into discrete Mendelian factors, in an interspecific back-cross of tomato. Applying new analytical methods, we mapped at least six QTLs controlling fruit mass, four QTLs for the concentration of soluble solids and five QTLs for fruit pH. This approach is broadly applicable to the genetic dissection of quantitative inheritance of physiological, morphological and behavioural traits in any higher plant or animal.     

基于RAPD标记的15种嵩草属(Kobresia Willd.)植物遗传关系

嵩草属(Kobresia Willd.)植物由于其形态结构的多样性及种内变异式样的复杂性,至今仍被认为是分类学上的"困难属".因此,对于该属系统学其他方面的证据,尤其分子方面的研究则显得极为重要和迫切.本文选用21个RAPD随机引物调查了15种嵩草属植物的遗传关系.结果表明:15种嵩草属植物聚为3类,认为嵩草组和异穗嵩草组的建立是比较自然的,而单穗嵩草组的划分并不自然.此外,分子结论并不支持前人发表的K.maquensis为独立新种,建议降为K.setschwanensis的异名.     

中国斑翅蝗科(直翅目:蝗总科)11属的系统发育关系支序分析

在比较形态学研究的基础上，本文选择了25个性状，利用Hennig86程序包，以支序分析探讨了中国斑翅蝗科11属昆虫间的系统发育关系，结果表明：斑翅蝗科11属昆虫可分为3支：由小车蝗属(11)与车蝗属(4)和飞蝗属(5)这一对姐妹群组成第1支，相互间关系不明确的尖翅蝗属(9)和绿纹蝗属(10)组成第2支，剩余的赤翅蝗属(12)、束颈蝗属(14)、疣蝗属(13)、异痴蝗属(6)、痴蝗属(7)及皱膝蝗属(8)6属构成第3支，其中痴蝗属与皱膝蝗属为1对姐妹群，它俩的最近共同祖先与异痴蝗属构成姐妹群关系，然后依次与疣蝗属、束颈蝗属、赤翅蝗属分别构成关系上渐远的单系群，它们的亲缘关系可表示为：((11(4，5))(9，10(12(14(13(6(7，8)))))))。     

Primate facial allometry and interpretations of australopithecine variation.

Pilbeam and Gould have discussed African Plio-Pleistocene hominid evolution in the context of allometry (size-dependent morphological change). These authors demonstrate that some general aspects of australopithecine morphology (tooth, brain and body size) support the hypothesis that certain early African hominids were merely scaled variations of each other at different sizes. They also speculate that the methods applied to these very broad anatomical categories can be extended to more specific and detailed traits, especially in the face and cranium. Such traits underlie most taxonomic and phylogenetic discussions of the early African Hominidae, so it is useful to follow Pilbeam and Gould's lead, as we do here, and investigate the structural differences in the australopithecine face and cranimum in a quantificiable fashion.     

三肠亚目(扁形动物门:涡虫纲:序列目)涡虫系统发育研究进展

比较分析了基于形态特征和分子序列数据的三肠亚目涡虫的系统发育关系,总结出现今大家公认的该亚目的系统发生关系:Tricladida是一个亚目级阶元,即三肠亚目,隶属于扁形动物门、涡虫纲、序列目.该亚目下分4个次目:海栖次目、陆栖次目、沼栖次目和穴居次目,其中海栖次目是一个单系,为亚目内较原始的类群;沼栖次目是一个并系,其内的三角涡虫科和陆栖次目有最近共同祖先;陆栖次目为单系起源.三肠亚目涡虫的演化路线是由海生到淡水再到陆生,之后又有逆转现象,即个别类群(如Spathula、Romankenkius)又返回淡水生活.文中还对未来该亚目系统发育研究的焦点进行了展望和预测.     

基于线粒体ND4基因探讨水龟组系统发生关系

水龟组由旧大陆潮龟科的拟水龟属、眼斑龟属和新大陆龟科的水龟属组成,这三个属以前一直被认为是同属的,但没有得到形态学和染色体等方面的认同.本文测定了四眼斑水龟和黄喉拟水龟线粒体基因组的ND4基因,用部分ND4基因及相邻tRNA基因共985bp的序列(包含简约信息位点235bp)讨论了它们的系统进化关系.MP树和ML树显示:在水龟属中,牟氏水龟和木雕水龟亲缘关系最近,与星点水龟亲缘关系次之,石纹水龟位于水龟属的基部,与水龟属其它物种的亲缘关系较远.拟水龟属与眼斑龟属在潮龟科是姐妹群关系,但与龟科水电属亲缘关系较远.本文结果支持潮龟科和龟科的单系起源,二者为非姐妹群.     

Investigations into the perplexing interrelationship of the Genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae)

The phylogenetic relationships within the genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodonti- dae) remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this ge- nus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsi- mony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that (1) the genus Takifugu is a monophyletic assemblage; (2) the genus is divided into 6 subgroups based on the mo- lecular data; and (3) there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our re- sults also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data.     

雏蝗属五种蝗虫雄性外生殖器的比较(直翅目:网翅蝗科)

利用显微观察并描述了直翅目网翅蝗科雏蝗属青藏雏蝗Chorthippus qingzangensis、小翅雏蝗C．fallax、东方雏蝗C．intermedius、红胫雏蝗C．rufitibis、白纹雏蝗C．albonemus共五种雏蝗雄性外生殖器的形态特征。结果表明：五种雏蝗雄性外生殖器发生变化最为明显的部位是冠突、前突、侧板、桥和色带连片及阳茎基瓣，在种间存在明显差异。通过对雄性外生殖器的形态结构比较，在探讨蝗总科分类和系统发育上均具有重要意义，并为雏蝗属种类鉴定提供了新的分类依据。     

中国三北地区部分野生小鼠形态分类学分析

对中国并部地区１０个捕鼠地捕获的野生小鼠（鼷鼠）进行了分类学分析和形态特征调查,主要对３００只野生小鼠和３０只实验品系小鼠的体重、头体长、尾长、后脚长及耳长等体征进行了测量和形态特征描述。同时应用统计学分析了不同区域野生小鼠之间、相同捕鼠地雌雄野生小鼠之间及野生小鼠与实验近交系小鼠之间形态特征差异,这些实量指标和形态学特征可望成为识别不同地区野生小鼠资源的重要标志。     

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.     

Investisations into the perplexing interrelationship of the Genus Takifugu Abe, 1949 （Tetraodontiformes,Tetraodontidae）

The phylogenetic relationships within the genus Takifugu Abe, 1949 （Tetraodontiformes, Tetraodontidae） remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this genus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsi- mony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that （1） the genus Takifugu is a monophyletic assemblage; （2） the genus is divided into 6 subgroups based on the moecular data; and （3） there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our results also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data.     

中国斑腿蝗科线粒体基因的分子系统学研究(英文)

使用线粒体基因COⅠ,COⅡ,Cytb分析并建立中国斑腿蝗科部分种属的系统发育关系,其中对7个新种(Apalacris eminifronta,Caryanda pseudodentata,Caryanda bannaensis,Caryanda ruiliensis,Longchuanacris fui,Longchuanacris xiaoheis-hanensis,Podismodes dabieshanensis)的归属从分子角度也做了讨论。本研究将实验所获得的56条序列与NCBI中所收录的斑腿蝗科序列进行联合分析,采用最大似然法、贝叶斯推论等系统分析方法并综合P距离进行分析,最终得出以下几点结论:①龙川蝗属Longchuanaceis Zheng et Fu划归卵翅蝗亚科Caryandinae;②蹦蝗属Sinopodisma Chang、云秃蝗属Yunnanacris Chang均为华秃蝗属Podismodes Ramme的同物异名;③不支持Storozhenko将豫蝗属Yupodisma Zhang et Xia并入安秃蝗属AnapodismaDovnar-Zapolskii,从本研究所建的系统发育树来看,豫蝗属仍应作为秃蝗亚科Podisminae的一个独立属;④前人利用形态特征鉴定的七个新种与分子系统发育分析结果一致,新种独立有效。     

Primate eta-globin DNA sequences and man's place among the great apes

Molecular studies indicate that chimpanzee and gorilla are the closest relatives of man (refs 1-7 and refs therein). The small molecular distances found point to late ancestral separations, with the most recent being between chimpanzee and man, as judged by DNA hybridization. Kluge and Schwartz contest these conclusions: morphological characters group a chimpanzee-gorilla clade with the Asian ape orang-utan in Kluge's cladistic study and with an orang-utan-human clade in Schwartz's study. Clearly, extensive sequencing of nuclear DNA is needed to resolve by cladistic analysis the branching order within Hominoidea. Towards this goal, we are sequencing orthologues of the primate psi eta-globin locus. Here, we compare the newly completed sequences of orang-utan and rhesus monkey with human, chimpanzee, gorilla, owl monkey, lemur and goat orthologues. Our findings substantially increase the evidence indicative of a human-chimpanzee-gorilla clade with ancestral separations around 8 to 6 Myr ago. We also verify that neutral hominoid DNA evolved at markedly retarded rates.     

鸟类分子系统学新进展

由于鸟类经历了一个古老而快速的分化,且以往的分类学研究多以形态学和化石记录为基础,分类学家对其系统发育了解很少.最近的分子系统发育研究表明:鸟类进化树上只有古颚总目和今颚总目之间的分化、鸡雁小纲和新鸟下纲的分化2个节点始终得到分子和形态证据的一致支持;分子研究支持新鸟下纲的白垩纪起源,反对化石记录支持新生代起源.但在最新的系统发育树中,大部分鸟类目之间的亲缘关系仍有待确定.今后应该增强鸟类分子进化的研究,并与形态学、古生物学研究相整合,以期完善鸟类的系统学.     

Nonindependence of mammalian dental characters

Studies of mammalian evolution frequently use data derived from the dentition. Dental characters are particularly central for inferring phylogenetic relationships of fossil taxa, of which teeth are often the only recovered part. The use of different aspects of dental morphology as phylogenetic signals implies the independence of dental characters from each other. Here we report, however, that, at least developmentally, most dental characters may be nonindependent. We investigated how three different levels of the cell signalling protein ectodysplasin (Eda) changed dental characters in mouse. We found that with increasing expression levels of this one gene, the number of cusps increases, cusp shapes and positions change, longitudinal crests form, and number of teeth increases. The consistent modification of characters related to lateral placement of cusps can be traced to a small difference in the formation of an early signalling centre at the onset of tooth crown formation. Our results suggest that most aspects of tooth shape have the developmental potential for correlated changes during evolution which may, if not taken into account, obscure phylogenetic history.