Closure operations in phylogenetics

Closure operations are a useful device in both the theory and practice of tree reconstruction in biology and other areas of classification. These operations take a collection of trees (rooted or unrooted) that classify overlapping sets of objects at their leaves, and infer further tree-like relationships. In this paper we investigate closure operations on phylogenetic trees; both rooted and unrooted; as well as on X-splits, and in a general abstract setting. We derive a number of new results, particularly concerning the completeness (and incompleteness) and complexity of various types of closure rules.     

甲虫群落构建研究进展

甲虫作为节肢动物中一个庞大的类群,具有繁简各异的生活习性,在生态系统中发挥极为重要的作用.甲虫群落构建是群落生态研究的重要内容之一,可揭示不同生态环境下生物多样性的形成与维持机制.现阶段对甲虫群落构建的研究主要通过物种的功能性状,或将系统发育结构与物种功能性状相结合的方法,对群落构建过程进行解析,用以判断主要的驱动因素...     

Plastome-based phylogeny improves community phylogenetics of subtropical forests in China

Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.     

Reflections on higher mammalian phylogenetics

For well over a decade, the higher-level relationships of mammals has been the focus of intensive and broad-ranging investigations. The sources of evidence drawn upon for this purpose are both traditional (e.g., paleontology, skeletal morphology) and newly sampled (e.g., comparative gene sequencing). A basic methodology, nonetheless, pervades this diversity of sampling. Issues that concern all types of data include the assumptions for recognizing homology, the techniques for building trees, the justification of parsimony and weighting, and the means of evaluating and comparing different results. In some areas (e.g., paleontology, molecular comparisons), we have been continual or even explosive expansion of the data base. In other areas (e.g., comparative behavior, physiology, or comparisons involving many aspects of nonskeletal morphology), the expansion has been far less dramatic. Codifying large arrays of characters is no substitute for penetrating studies of comparative form, function, and ontogeny or careful sampling of a diversity of genes. It is hoped that the latter emphases are maintained and nourished. The results of all this recent activity show a mixed profile of resolution for higher-level patterns of phylogeny. Particularly, the higher eutherian mammal radiation still presents many problems. Such challenges, however, have attracted an unprecedented level of synthesis and interaction.     

Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees

Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea. Sequences of the internal transcribed spacer (ITS) region were obtained for 2079 fungal endophytes from three sites and clustered into molecular operational taxonomic units (MOTUs) at 95% similarity. Multivariate analyses suggest that host affinity plays a significant role in structuring endophyte community composition whereas there was no evidence of endophyte spatial pattern at the scale of tens to hundreds of metres. Differences in endophyte communities between sampled trees were weakly correlated with variation in foliar traits but not with tree species relatedness. The dominance of relatively few generalist endophytes and the presence of a large number of rare MOTUs was a consistent observation at three sites separated by hundreds of kilometres and regional turnover was low. Host specificity appears to play a relatively weak but more important role than dispersal limitation in shaping the distribution of fungal endophyte communities in New Guinea forests. Our results suggest that in the absence of strong ecological gradients and host turnover, beta diversity of endophyte communities could be low in large areas of contiguous forest.     

Python phylogenetics: inference from morphology and mitochondrial DNA

We used nucleotide sequences from four mitochondrial genes and structural features of the mitochondrial control region, combined with a revised, previously published, morphological data set to infer phylogenetic relationships among the pythons. We aimed to determine which of two competing hypotheses of relationships of the genera Aspidites and Python best explains the evolutionary and bioegeographical history of the family. All analyses of the combined data recover a set of relationships in which (1) the genus Python is paraphyletic with the two east Asian species, P. reticulatus and P. timoriensis , as the sister lineage to the seven Australo-Papuan python genera. We support recognition of a distinct genus for the P. reticulatus  +  P. timoriensis clade; (2) the remaining species of the genus Python form a clade which is the sister lineage to the remainder of the family; (3) the genus Aspidites is embedded among the Australo-Papuan genera. The seemingly primitive characteristics of Aspidites may be better interpreted as reversals or specializations that have accompanied a switch to burrowing in this genus. Resolution of the relationships among the Australo-Papuan lineages is weak, possibly because of rapid diversification early in the history of the radiation. We assessed the tempo of the Indo-Australian python radiation using a maximum likelihood framework based on the birth–death process. We find strong support for elevated speciation rates during the period when Australia collided with the proto-Indonesian archipelago. The data support an origin for pythons outside Australia, followed by a radiation into Australia during the mid-Tertiary.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 603–619.     

莲科系统位置评述

莲科含1属1种2亚种,以具有最古老的有活力的种子而著称。形态学研究显示,莲不仅具有双子叶植物特征,而且又具有单子叶植物的某些性状。因此,对研究被子植物(有花植物)的起源与演化以及单子叶植物的起源具有重要价值。被子植物(有花植物)的起源与辐射一直是植物学家关注的热点,有关莲科的系统位置存在争议。该文对该科系统位置的研究历史与现状进行评述。     

腺齿木科系统位置评述

腺齿木科(Trimeniaceae)含2属5种。形态学研究显示腺齿木科具有许多原始性状。最新的分子系统发育研究显示,腺齿木科是现存被子植物的重要基部类群之一。但有关腺齿木科的系统位置存在争议。被子植物(有花植物)的起源与辐射一直是植物系统学家关注的热点。对该科系统位置的研究历史与现状进行评述。     

Angiosperm classification and phylogeny: a criticism

This is a criticism of Dahlgren's recent classification of angiosperms (1980) and his basic diagram of angiosperm phylogeny. The first is shown to include unnatural orders and super-orders; the second is accordingly as questionable. Basic factors for phylogenetic taxonomy in the angiosperms are considered. Leptocauly leads to parallel evolution and specific multiplication. Nomenclatural artifices for taxonomic equivalence are exposed; the name 'pseudon' is suggested for a conjectural taxon.     

Angiosperm classification and phylogeny: a rectifying comment

A commentary is given on the criticism of Dahlgren's recent classification of angiosperms by Corner ( Botanical Journal of the Linnean Society, 82: 81–87 (1981)). In his dissatisfaction with the current, (almost) generally accepted nomenclatural concepts he has chosen to use my classification as a target. It is agreed that nomenclature is not 'fair' to plant groups playing the most important role in building up the biosphere, and that nomenclatural constructions do not reflect the consideration given to various parts of the plant. Corner does not seem to be familiar with the fact that his so-called 'pseudons' are common to all current systems of classification, nor that the termination '-florae' has been used by Thorne (1968) and in a number of publications since. This suffix does not imply that the botanists using it neglect vegetative characters, nor characters from fruits and seeds. Other misunderstandings are also pointed out. In no case has it been satisfactorily demonstrated by Corner that my orders or superorders are unnatural entities (even though a number of them most likely are).     

Using phylogeny and functional traits for assessing community assembly along environmental gradients: A deterministic process driven by elevation

Community assembly processes is the primary focus of community ecology. Using phylogenetic‐based and functional trait‐based methods jointly to explore these processes along environmental gradients are useful ways to explain the change of assembly mechanisms under changing world. Our study combined these methods to test assembly processes in wide range gradients of elevation and other habitat environmental factors. We collected our data at 40 plots in Taibai Mountain, China, with more than 2,300 m altitude difference in study area and then measured traits and environmental factors. Variance partitioning was used to distinguish the main environment factors leading to phylogeny and traits change among 40 plots. Principal component analysis (PCA) was applied to colligate other environment factors. Community assembly patterns along environmental gradients based on phylogenetic and functional methods were studied for exploring assembly mechanisms. Phylogenetic signal was calculated for each community along environmental gradients in order to detect the variation of trait performance on phylogeny. Elevation showed a better explanatory power than other environment factors for phylogenetic and most traits’ variance. Phylogenetic and several functional structure clustered at high elevation while some conserved traits overdispersed. Convergent tendency which might be caused by filtering or competition along elevation was detected based on functional traits. Leaf dry matter content (LDMC) and leaf nitrogen content along PCA 1 axis showed conflicting patterns comparing to patterns showed on elevation. LDMC exhibited the strongest phylogenetic signal. Only the phylogenetic signal of maximum plant height showed explicable change along environmental gradients. Synthesis. Elevation is the best environment factors for predicting phylogeny and traits change. Plant's phylogenetic and some functional structures show environmental filtering in alpine region while it shows different assembly processes in middle‐ and low‐altitude region by different trait/phylogeny. The results highlight deterministic processes dominate community assembly in large‐scale environmental gradients. Performance of phylogeny and traits along gradients may be independent with each other. The novel method for calculating functional structure which we used in this study and the focus of phylogenetic signal change along gradients may provide more useful ways to detect community assembly mechanisms.     

Nuclear DNA and salmonid phylogenetics

There are many unresolved problems in salmonid systematics, both at the interspecific and sub-specific levels. Some of the major systematic problems in the subfamily Salmoninae are briefly reviewed along with the available molecular methods for their analysis. Nuclear DNA markers available for use in molecular systematics include localized and dispersed highly repetitive DNA sequences, moderately repetitive sequences such as the ribosomal RNA genes (rDNA), and single copy DNA sequences. Both coding and non-coding sequences can be examined in the rDNA and single copy DNA. The rDNA is especially suitable for use in phylogenetic analysis, since different regions evolve at different rates and can be used for comparisons at different taxonomic levels. Comparison of restriction maps of the entire rDNA repeating unit in 17 salmonid species from Hucho. Sahelinus, Salmo and Oncorhynchus has shown that the transcribed spacer regions are the most informative for interspecific comparisons and that the intergenic spacer has potential for use in intraspecific comparisons. Our current approach is to amplify selected regions from each of these spacers for analysis by DNA sequencing. DNA sequence analysis of the internal transcribed spacers should be very informative in elucidating interspecific relationships in Salvelinus and Oncorhynchus . Analysis of a hypervariable region in the intergenic spacer has potential for identification of geographically separated stocks. The relative utility of different types of nuclear DNA sequences for identification of stocks and subspecies is examined.     

Comparing primate communities: a multivariate approach

Although there have been many studies of the ecology of primates in communities throughout the world, there have been few attempts to compare community ecology within and among continents. In this study the ecological characteristics of the sympatric primate species at eight localities—two from each of the major biogeographic areas inhabited by primates today—South America, Africa, Madagascar, and Asia—were compared using a multivariate technique (principal components analysis of the correlation matrix) to summarize the ten dimensional ecological niche space. The most striking clustering of species in ecological multivariate space is according to phylogeny with closely related species showing similar ecological features. Likewise, the ecological characteristics of individual communities are determined by phylogenetic groups present at each locality or biogeographic region. As a result, communities within any biogeographical region are more similar ecologically to one another than to communities from other continental areas. In several measures of ecological diversity among the species comprising each community, the neotropical communities show lower overall diversity than do communities from other continents.     

暖湿化气候情景下喀斯特木本植物群落构建机制

云南喀斯特区域是滇桂黔岩溶石漠化重点治理区之一,探讨气候暖湿化下植物群落演替阶段的构建特征是生态恢复和森林管理可持续的关键。以气候暖湿化为背景,将喀斯特天坑作为天然“开顶式气室”,天坑南坡地下森林为群落演替顶极。联合系统发育和功能性状探讨演替序列(坑外针阔混交林,坑外常绿阔叶林,坑内常绿阔叶林)的群落构建机制。结果发现：(1)演替前期植物性状的系统发育信号较弱,叶长宽比、叶面积、叶厚度和比叶面积的系统发育信号显著,但功能性状的保守性较弱;演替后期植物性状转为趋同进化,系统发育信号均不显著。(2)演替阶段植物群落的系统发育多样性逐渐降低,并与物种丰富度显著正相关。(3)系统发育指数NRI(净亲缘指数)和NTI(最近种间亲缘指数)由小于0转为大于0,功能性状结构指数TraitSESMPD(标准化平均配对性状距离指数)和TraitSESMNTD(标准化平均最近相邻性状距离指数)均大于0。演替阶段的群落构建过程由生境过滤和物种间相互作用所主导。(4)系统发育和功能性状结构指数主要与土壤含水量、全磷和速效钾含量显著负相关。演替阶段下土壤水分和养分受限时群落趋于聚集,群落构建过程支持生态位假说。研...     

Calibrated tree priors for relaxed phylogenetics and divergence time estimation

The use of fossil evidence to calibrate divergence time estimation has a long history. More recently, Bayesian Markov chain Monte Carlo has become the dominant method of divergence time estimation, and fossil evidence has been reinterpreted as the specification of prior distributions on the divergence times of calibration nodes. These so-called "soft calibrations" have become widely used but the statistical properties of calibrated tree priors in a Bayesian setting hashave not been carefully investigated. Here, we clarify that calibration densities, such as those defined in BEAST 1.5, do not represent the marginal prior distribution of the calibration node. We illustrate this with a number of analytical results on small trees. We also describe an alternative construction for a calibrated Yule prior on trees that allows direct specification of the marginal prior distribution of the calibrated divergence time, with or without the restriction of monophyly. This method requires the computation of the Yule prior conditional on the height of the divergence being calibrated. Unfortunately, a practical solution for multiple calibrations remains elusive. Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis.     

New gene-derived simple sequence repeat markers for common bean (Phaseolus vulgaris L.)

Common bean is an important and diverse crop legume with several wild relatives that are all part of the Phaseoleae tribe of tropical crop legumes. Sequence databases have been a good source of sequences to mine for simple sequence repeats (SSRs). The objective of this research was to evaluate 14 sequence collections from common bean for SSRs and to evaluate the diversity of the polymorphic microsatellites derived from these collections. SSRs were found in 10 of the GenBank sequence collections with an average of 11.3% of sequences containing microsatellite motifs. The most common motifs were based on tri- and dinucleotides. In a marker development programme, primers were designed for 125 microsatellites which were tested on a panel of 18 common bean genotypes. The markers were named as part of the bean microsatellite-database (BMd) series, and the average polymorphism information content was 0.404 for polymorphic markers and predicted well the genepool structure of common beans and the status of the wild and cultivated accessions that were included in the study. Therefore, the BMd series of microsatellites is useful for multiple studies of genetic relatedness and as anchor markers in future mapping of wide crosses in the species.     

被子植物起源研究中几种观点的思考

对被子植物起源研究中的几种观点进行了讨论。(1)由于被子植物存在着一组共同的性状,它们不可能是从不同祖先起源的,而是有着共同的祖先。被子植物是一个单源起源的类群。现存被子植物分类系统是依据包括形态学(广义)、分子系统学、古植物学和植物地理学等的综合性状建立的,只能表示出现存类群的亲缘关系并且追溯到它们最近的祖先。人们现在还不可能建立一个包括全部已绝灭的类群和现代生存类群的谱系发生系统。因此,现存被子植物分类系统只能看作是“亲缘”系统。(2)分析了用于推测被子植物起源时间的分子、化石和地理分布证据。我们认为,要确定被子植物起源时间,植物化石是一类重要证据,但化石只能说是植物本身可保存部分和当时当地所提供的化石条件的综合反映,它们不可能就是植物类群或种的起源时间。人们还必须考虑到化石本身的演化历史。应用分子钟也是一种手段,但误差比较大。如果我们除了利用上述两种资料之外,根据植物类群的现代分布格局及其形成,把植物的演化同地球的历史和板块运动联系起来,以推断它们起源的时间,这无疑会增加其可信度。通过对56个种子植物不同演化水平的重要科属地理分布的研究结果,我们曾提出被子植物的起源时间可能要追溯到早侏罗世,甚至晚三叠世。(3)分析了基于分子证据所提出的被子植物基部类群——ANITA成员(包括无油樟科Amborellaceae、睡莲科Nymphaeaceae、八角目Illiciales、早落瓣科Trimeniaceae、木兰藤科Austrobaileyaceae)的性质,讨论了ANITA成员在现代几个被子植物分类系统中的系统位置的不同观点,评价了它们的形态学(广义)性状。指出ANITA的成员由于包含大量的祖征,是属于原始的类群。但由于它们的共有衍征很少,如花粉球形,说明它们在被子植物演化早期就分道扬镳了,沿着不同的传代线分化。因此ANITA是一个源于不同传代线的复合群。