On the information content of characters in comparative morphology and molecular systematics

A review of the fundamental difference between single molecular-sequence positions, or numerical characters, and complex morphological characters is the subject of this study. It has been found that transformation series of single complex structures contain enough information to allow a priori determination of character order and that rooting of a dendrogram is possible without out-group comparison, while trees based on less-informative characters can usually only be rooted with out-group comparison. Furthermore, the quality of total information used is decisive in discriminating between hypotheses of relationships. Numerical methods for the inference of phylogenies have been found to be useful for high numbers of characters that have only a low information content, while the Hennigian procedure seems to be preferable for complex characters.     

On the information content of characters in comparative morphology and molecular systematics

A review of the fundamental difference between single molecular-sequence positions, or numerical characters, and complex morphological characters is the subject of this study. It has been found that transformation series of single complex structures contain enough information to allow a priori determination of character order and that rooting of a dendrogram is possible without out-group comparison, while trees based on less-informative characters can usually only be rooted with out-group comparison. Furthermore, the quality of total information used is decisive in discriminating between hypotheses of relationships. Numerical methods for the inference of phylogenies have been found to be useful for high numbers of characters that have only a low information content, while the Hennigian procedure seems to be preferable for complex characters.

Zusammenfassung

Ein fundamentaler Unterschied zwischen der einzelnen Sequenzposition oder auch numerischen Merkmalen und komplexen morphologischen Merkmalen ist ihr Informationsgehalt. Merkmalsreihen komplexer Strukturen enthalten meist genügend Information, um a priori die Bestimmung der Lesrichtung zu ermöglichen. Die Feststellung des Ursprunges eines Dendrogramms ist somit ohne kladistischen Außengruppenvergleich möglich, während Bäume (Topologien), die auf wenig informativen Merkmalen beruhen, allgemein nur mit dem kladistischen Außengruppenvergleich 'gewurzelt' werden können. Die Qualität der insgesamt verwendeten Information ist entscheidend für die Wahl zwischen alternativen Verwandtschaftshypothesen. Numerische Methoden der Rekonstruktion der Phylogenese sind nützlich bei Verwendung einer gro β en Zahl informationsarmer Merkmale; das Hennigsche Verfahren ist für komplexe Merkmale vorzuziehen.     

The performance of phylogenetic algorithms in estimating haplotype genealogies with migration

Genealogies estimated from haplotypic genetic data play a prominent role in various biological disciplines in general and in phylogenetics, population genetics and phylogeography in particular. Several software packages have specifically been developed for the purpose of reconstructing genealogies from closely related, and hence, highly similar haplotype sequence data. Here, we use simulated data sets to test the performance of traditional phylogenetic algorithms, neighbour-joining, maximum parsimony and maximum likelihood in estimating genealogies from nonrecombining haplotypic genetic data. We demonstrate that these methods are suitable for constructing genealogies from sets of closely related DNA sequences with or without migration. As genealogies based on phylogenetic reconstructions are fully resolved, but not necessarily bifurcating, and without reticulations, these approaches outperform widespread 'network' constructing methods. In our simulations of coalescent scenarios involving panmictic, symmetric and asymmetric migration, we found that phylogenetic reconstruction methods performed well, while the statistical parsimony approach as implemented in TCS performed poorly. Overall, parsimony as implemented in the PHYLIP package performed slightly better than other methods. We further point out that we are not making the case that widespread 'network' constructing methods are bad, but that traditional phylogenetic tree finding methods are applicable to haplotypic data and exhibit reasonable performance with respect to accuracy and robustness. We also discuss some of the problems of converting a tree to a haplotype genealogy, in particular that it is nonunique.     

Circularity,evolution, systematics … and circularity

Many have argued strongly that incorporation of evolutionary theory into systematics is dangerously circular, while others have maintained that such an integrated approach increases the accuracy of phylogenetic inference. Here, it is demonstrated that such blanket statements regarding exclusion or inclusion of evolutionary principles in systematics fail to distinguish between two very different types of principles. ‘Phylogeny-neutral’ evolutionary principles are those inferred without any recourse to specific phylogenetic hypotheses (e.g. via developmental genetics, biomechanics). In contrast, ‘phylogeny-dependent’ principles are those which can only be inferred on the basis of specific phylogenetic hypotheses (e.g. character associations detected via ‘comparative methods’). Inclusion of phylogeny-neutral principles in systematic studies as a priori assumptions can be justified, since these principles have (often strong) external empirical support from other spheres of investigation. However, inclusion of phylogeny-dependent principles in systematic studies is circular, since such principles have no external empirical support but are themselves derived from systematic studies. Advocating inclusion or exclusion of all (or as many as possible) evolutionary principles from phylogenetic analysis is therefore misguided. Rather, phylogeny-neutral principles are independently supported and can be included, while phylogeny-dependent principles are unjustified assumptions and should be excluded to avoid circularity. However, integration of complex phylogeny-neutral principles in systematics can create operational problems, even though there are no methodological reasons against their inclusion.     

叶蝉科昆虫分子系统发育的研究进展

从基因组DNA的提取、研究的基因片段、PCR引物选用、扩增条件以及叶蝉科不同阶元的分子系统发育分析等方面,综述叶蝉科(半翅目:叶蝉科)昆虫分子系统发育的研究进展。目前角顶叶蝉类的研究成果相对较多,大叶蝉亚科次之,其余类群的研究较少或无。线粒体基因与核基因序列联合分析以及线粒体全序列分析以及基因序列与形态数据相结合分析,分子鉴定叶蝉与共生菌之间的协同进化的研究,将是叶蝉分子系统学未来发展的主要研究手段。     

蝗虫分子系统学研究进展

本文从遗传多样性、近缘种鉴别以及分子进化和系统发育重建 3个方面综述了蝗虫分子系统学的研究进展。     

分子系统学原理及其在林木上的应用

综述了林木分子系统学的是新研究进展,分析了现代分子生物学方法的不断改进给林木系统学研究带来的革命性进展,阐述了RAPD,cpDNA,rDNA等在林木分子系统学研究中的应用及取得的成果,评述了各种不同分子标记的适用范围以及对相关基因进化规律的认识,同时提出了这些分子标记在分子系统学研究中应注意的一些问题。     

A phylogenetic reanalysis of allozyme variation among populations of Galapagos finches

We reanalysed Yang & Pattern's allozyme data, published in Auk in 1981, of Darwin's finches with a variety of distance and cladistic methods to estimate the phylogeny of the group. Different methods yielded different results, nevertheless there was widespread agreement among the distance methods on several groupings. First, the two species of Camarhynchus grouped near one another, but not always as a monophyletic group. Second, Cactospiza pallida and Platyspiza crassirostris formed a monophyletic group. Finally, all the methods (including parsimony) supported the monophyly of the ground finches. The three distance methods also found close relationships generally between each of two populations of Geospiza scandens, G. difficilis and G. conirostris. There is evidence for inconstancy of evolutionary rates among species. Results from distance methods allowing for rate variation among lineages suggest three conclusions which differ from Yang and Patton's findings. First, the monophyletic ground finches arose from the paraphyletic tree finches. Yang and Patton found that the ground finches and tree finches were sister monophyletic taxa. Second, Geospiza scandens appears to be a recently derived species, and not the most basal ground finch. Third, G. fuliginosa is not a recently derived species of ground finch, but was derived from an older split from the remaining ground finches. Most of these conclusions should be considered tentative both because the parsimony trees disagreed sharply with the distance trees and because no clades were strongly supported by the results of bootstrapping and statistical tests of alternative hypotheses. Absence of strong support for clades was probably due to insufficient data. Future phylogenetic studies, preferably using DNA sequence data from several unlinked loci, should sample several populations of each species, and should attempt to assess the importance of hybridization in species phylogeny.     

核糖体DNA ITS区序列在植物分子系统学研究中的价值

本文就近年来国内外有关被子植物核糖体ＤＮＡ中的内转录间隔区（ＩＴＳ）序列在植物属内,近缘属间乃至科内系统发育研究中的应用,结合作者在中国姜科山姜属（Ａｌｐｉｎｉａ Ｒｏｘｂ．）上的研究,对ＩＴＳ区序列在植物分子系统学研究中的价值作一简要综述,对其应用前景也进行了讨论。     

Biochemical systematics of the viviparous fish family Goodeidae

The systematic relationships of the freshwater teleost family Goodeidae inferred from a distance Wagner analysis of allozyme data are mainly consistent with previous systematic hypotheses, including some of those based on karyology. However, a recently proposed hypothesis based on bony anatomy of the mouth is not supported. Branching patterns of species within genera were 100% supported based on a jack knife consensus test except for Xenotoca , which is apparently a polyphyletic lineage. A fossil goodeid of Miocene age was used to calibrate the molecular clock for goodeids at Nei D = 1.0 = 11.3 million years.     

索科线虫分子系统学研究进展

昆虫病原索科线虫是一类宝贵的昆虫天敌资源,对农、林及卫生害虫的综合治理、环境保护以及实现农田生物多样性,都具有重要的学术和实用价值。其分子系统学研究涉及RAPD技术、SAFLP技术和基因分子标记技术对索科线虫种属间的亲缘关系探究,以及其线粒体全基因组分析等。     

Utility of rbcS gene as a novel target DNA region for brown algal molecular systematics

The usefulness of molecular phylogenetic studies has increased remarkably as the quantity and quality of available DNA sequences has increased. When compared with the progress that has occurred in angiosperms and animals, there have been relatively few target DNA regions identified for use in taxonomic studies of brown algae. Therefore, in this study, we developed a new set of primers to amplify Rubisco small subunit (rbcS) gene sequences and determined the rbcS gene sequences of various species of brown algae including those belonging to Dictyotales, Ectocarpales, Fucales and Sphacelariales. The level of sequence variations in the rbcS gene varied according to the brown algal lineages. When focusing on the relationship of species within the genus Sargassum, the rbcS gene sequences provided useful information regarding the phylogenetic relationship among sections of the subgenus Bactrophycus. Based on the broad applicability and phylogenetic utility of the rbcS gene, we suggest that the sequence be used as a new target region for the molecular systematics of brown algae.     

Phylogenetic relationships in Bulbostylis (Abildgaardieae: Cyperaceae) inferred from nuclear and plastid DNA sequence data

Previous molecular phylogenetic analyses of the family Cyperaceae based on rbcL sequences showed Bulbostylis as paraphyletic, with B. atrosanguinea and B. hispidula forming a clade with Nemum spadiceum. On the contrary, phylogenetic analyses of the tribe Abildgaardieae based on nuclear (ITS ribosomal region) and plastid sequences (trnL-F region) showed Bulbostylis as monophyletic, although they only incorporated four species of Bulbostylis and none of Nemum. In this work, we presented a phylogenetic hypothesis of Bulbostylis based on a comprehensive sampling, including species from different continents for the first time. New sequences of Abildgaardia, Crosslandia, Fimbristylis, and Nemum were included to test the monophyly of Bulbostylis. In total, 84 sequences of both ITS and trnL regions were generated. Analyses were performed using Bayesian inference, maximum likelihood, and parsimony. Ancestral state reconstruction was performed using ML, MCMC, and parsimony methods. In all analyses, Bulbostylis resulted paraphyletic as Nemum atracuminatum is nested within it. Most American species of Bulbostylis grouped together, but relationships amongst them appeared poorly resolved. Ancestral state reconstructions of native distribution suggest an African ancestor of Bulbostylis, with at least three introduction independent events of the species in America. Morphological diagnostic characters such as the ‘style base permanence or detachment from the ripe achene’, and the ‘micromorphological patterns of the achene surface’ are homoplastic in this phylogenetic context, and therefore unsuitable to propose infrageneric groupings within the Bulbostylis.     

Molecular phylogeny of the Forcipulatacea (Asteroidea: Echinodermata): systematics and biogeography

We present a comprehensively sampled three‐gene phylogeny of the monophyletic Forcipulatacea, one of three major lineages within the crown‐group Asteroidea. We present substantially more Southern Hemisphere and deep‐sea taxa than were sampled in previous molecular studies of this group. Morphologically distinct groups, such as the Brisingida and the Zoroasteridae, are upheld as monophyletic. Brisingida is supported as the derived sister group to the Asteriidae (restricted), rather than as a basal taxon. The Asteriidae is paraphyletic, and is broken up into the Stichasteridae and four primary asteriid clades: (1) a highly diverse boreal clade, containing members from the Arctic and sub‐Arctic in the Northern Hemisphere; (2) the genus Sclerasterias; (3) and (4) two sister clades that contain asteriids from the Antarctic and pantropical regions. The Stichasteridae, which was regarded as a synonym of the Asteriidae, is resurrected by our results, and represents the most diverse Southern Hemisphere forcipulatacean clade (although two deep‐sea stichasterid genera occur in the Northern Hemisphere). The Labidiasteridae is artificial, and should be synonymized into the Heliasteridae. The Pedicellasteridae is paraphyletic, with three separate clades containing pedicellasterid taxa emerging among the basal Forcipulatacea. Fossils and timing estimates from species‐level phylogeographic studies are consistent with prior phylogenetic hypotheses for the Forcipulatacea, suggesting diversification of basal taxa in the early Mesozoic, with some evidence for more widely distributed ranges from Cretacous taxa. Our analysis suggests a hypothesis of an older fauna present in the Antarctic during the Eocene, which was succeeded by a modern Antarctic fauna that is represented by the recently derived Antarctic Asteriidae and other forcipulatacean lineages. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 646–660.     

基因序列在蚤蝇科分子系统学研究中的应用

概述基因序列在双翅目蚤蝇科分子系统学研究中的应用。对蚤蝇科已测序的分类单元和基因序列进行了总结,12S rDNA和16S rDNA应用最广泛,涉及蚤蝇科17个属;获得基因序列最多的是Melaloncha属。蚤蝇科分子系统学研究内容为高级阶元系统发育分析、物种鉴定和隐存种发现。今后蚤蝇科分子系统学研究应增加蚤蝇标本的种类与数量,选择标准化基因。     

基因序列在金龟总科(Scarabaeoidea)分子系统学研究中的应用

基因序列分析是揭示金龟总科系统发育关系的重要工具。统计了应用于金龟总科中13个科的线粒体和核基因序列,综述了COⅠ、16S rRNA、28S rRNA、18S rRNA等基因序列在金龟总科分子系统学研究的新进展,探讨了不同基因序列在分类鉴定、隐存种发现、系统发育关系重建等方面的作用,对未来研究趋势进行了展望,为进一步阐明金龟总科系统发育机制奠定基础。     

A multidisciplinary approach to the fine-systematics within Tisbe - an evaluation of morphological and molecular methods

Six species from the species-rich taxon Tisbe (Copepoda, Harpacticoida) were selected that could be reared in the laboratory as mass cultures. Phylogenetic relationships among these species were assessed by morphological studies of adults and larvae, DNA restriction site polymorphisms, allozymic, immunological distance, and lipid composition. Limits of scope and practicability of these analyses became apparent, as well as their potential and importance for future work in zoological systematics.     

A molecular approach to the phylogenetic relationships of the western palaearctic Helicoidea (Gastropoda: Stylommatophora)

Molecular phylogenetic relationships among 45 members of the Helicoidea (Gastropoda: Stylommatophora) were examined using partial mitochondrial 16S rRNA sequences. Phylogenetic relationships were inferred using maximum parsimony, maximum likelihood and Bayesian methods. The reconstructed phylogenies showed a good degree of support for more recent branches, but gave little support to deeper nodes. Mitochondrial rDNA data further confirmed monophyletic status of helicids, recognized monachine hygromiid and bradybaenid clades and resolved a number of relationships in the helicelline hygromiids. With the respect to the latter assemblage, most of the anatomically based groups are confirmed, corroborating the diagnostic value of the dart-sac complex and a close affinity between Ichnusomunda sacchii and species of the genus Cernuella . Nevertheless, some well resolved branches challenge previous systematic arrangements, grouping species previously placed in different arrangements. In particular, support was not found for the monophyly of helicelline hygromiids with pedal penial innervation. Possible explanations for these incongruencies are suggested. 16S sequence data are appropriate for studies of relationships within the different species groups and less so for recovery of more ancient radiations in the Helicoidea. It will be valuable to combine the 16S data with other gene sequences to estimate basal relationships.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 501–512.     

线粒体DNA序列特点与昆虫系统学研究

昆虫线粒体DNA是昆虫分子系统学研究中应用最为广泛的遗传物质之一。线粒体DNA具有进化速率较核DNA快 ,遗传过程不发生基因重组、倒位、易位等突变 ,并且遵守严格的母系遗传方式等特点。本文概述了mtDNA中的rRNA、tRNA、蛋白编码基因和非编码区的一般属性 ,分析了它们在昆虫分子系统学研究中的应用价值 ,以及应用DNA序列数据来推导分类阶 (单 )元的系统发育关系时 ,基因或DNA片段选择的重要性     

The phylogenetic position of the Aeolosomatidae and Parergodrilidae, two enigmatic oligochaete-like taxa of the 'Polychaeta', based on molecular data from 18S rDNA sequences

The Aeolosomatidae and the Parergodrilidae are meiofaunal Annelida showing different combinations of clitellate‐like and non‐clitellate character states. Their phylogenetic positions and their systematic status within the Annelida are still in debate. Here we attempt to infer their systematic position using 18S rDNA sequences of the aeolosomatid Aeolosoma sp. and the parergodrilid Stygocapitella subterranea and several other meiofaunal taxa such as the Dinophilidae, Polygordiidae and Saccocirridae. The data matrix was complemented by sequences from several annelid, arthropod and molluscan species. After evaluation of the phylogenetic signal the data set was analysed with maximum‐parsimony, distance and maximum‐likelihood algorithms. Sequences from selected arthropods or molluscs were chosen for outgroup comparison. The resolution of the resulting phylogenies is discussed in comparison to previous studies. The results do not unequivocally support a sister‐group relationship of Aeolosoma sp. and the Clitellata. Instead, depending on the algorithms applied, Aeolosoma clusters in various clades within the polychaetes, for instance, together with eunicidan species, the Dinophilidae, Harmothoë impar or Nereis limbata. The position of Aeolosoma sp. thus cannot be resolved on the basis of the data available. S. subterranea always falls close to a cluster comprising Scoloplos armiger, Questa paucibranchiata and Magelona mirabilis, all of which were resolved as not closely related to both Aeolosoma sp. and the Clitellata. Therefore, convergent evolution of clitellate‐like characters in S. subterranea and hence in the Parergodrilidae is suggested by our phylogenetic analysis. Moreover, the Clitellata form a monophyletic clade within the paraphyletic polychaetes.