Significance of palynology for phylogeny ofAnnonaceae: Experiments with removal of pollen characters

Phylogenetic analyses based on morphology placeAnaxagorea and other taxa with granular monosulcate pollen, as in otherMagnoliales, at the base ofAnnonaceae. Taxa with columellar tetrads, granular tetrads, and inaperturate monads form a derived clade. To test the systematic importance of palynology, we analyzed the data set with pollen characters removed. The result was lower resolution and a different rooting of the family, betweenUvariopsis and other groups with columellar tetrads.Anaxagorea and other monosulcates are higher in the tree, implying that granular monosulcate pollen, laminar stamens, and irregular endosperm ruminations are reversals. This rooting is highly unparsimonious when pollen characters are included, and only weakly supported over theAnaxagorea rooting when pollen is excluded. Together with preliminary molecular analyses, these experiments confirm the special value of palynology in systematics ofAnnonaceae. This paper is dedicated to emer. Univ.-Prof. DrFriedrich Ehrendorfer on the occasion of his 70th birthday     

A preliminary phylogeny for the NeotropicalRubiaceae

The sequence of subfamilies,Cinchonoideae, Antirheoideae andRubioideae, attemps to show their natural affinities and phylogeny. The subfamilies are those ofVerdcourt, and the order in which they are presented is that ofBremekamp. A list is presented of the subfamilies, tribes and genera of theRubiaceae to be utilized in the Catálogo Ilustrado de las plantas de Cundinamarca, Colombia.     

Therps16 intron and the phylogeny of theRubioideae (Rubiaceae)

The phylogeny of the subfamilyRubioideae (Rubiaceae) was estimated from sequence variation in therps16 intron (cpDNA) in 143 ingroup and 5 outgroup taxa. The analysis largely confirms a recent one based onrbcL sequences, but branch support is often much stronger. Three of the traditional subfamilies are supported,Rubioideae, Cinchonoideae s. str., andIxoroideae s. l. while there is no support forAntirheoideae. TheRubioideae are the sister group of all otherRubiaceae and comprise the tribesAnthospermeae, Coccocypseleae, Cruckshanksieae, Coussareeae, Gaertnereae, Hedyotideae, Knoxieae, Morindeae, Ophiorrhizeae, Paederieae, Pauridiantheae, Perameae, Psychotrieae, Rubieae, Spermacoceae, Theligoneae, andUrophylleae. TheHamelieae andHillieae belong to theCinchonoideae. Rachicallis andSiemensia should be transferred from theHedyotideae to theCinchonoideae. ThePauridiantheae, Urophylleae, Ophiorrhizeae, andRaritebe form the basalmost subclade of theRubioideae. The second basalmost clade consists of the generaLasianthus andPerama. The third basalmost clade consists of the tribesCoussareeae, Coccocypseleae andCruckshanksieae, and the generaDeclieuxia andHindsia. The tribesKnoxieae, Anthospermeae, Argostemmateae, Paederieae, Theligoneae, Rubieae, Hedyotideae, andSpermacoceae are members of one clade. TheKnoxieae are monophyletic ifOtiophora, Otomeria, andPentas are included. The tribeAnthospermeae is supported as monophyletic, but its subtribes are not. ThePaederieae, together withTheligonum, form a paraphyletic grade basal to theRubieae. TheHedyotideae, includingSchismatoclada, form a grade at the base of theSpermacoceae. TheGaertnereae are monophyletic and distinct from thePsychotrieae. TheMorindeae are monophyletic and includeDamnacanthus andMitchella. Schradera is the sister group of theMorindeae. ThePsychotrieae are monophyletic when theGaertnereae, Lasianthus, andDeclieuxia are excluded. The recognition of a subtribeHydnophytineae leaves the rest of thePsychotrieae paraphyletic.Psychotria is paraphyletic with respect to all other genera of the tribe. Approximately 50 genera are here classified for the first time based on molecular data.     

Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa

Recent discoveries of new fossil hominid species have been accompanied by several phylogenetic hypotheses. All of these hypotheses are based on a consideration of hominid craniodental morphology. However, Collard and Wood (2000) suggested that cladograms derived from craniodental data are inconsistent with the prevailing hypothesis of ape phylogeny based on molecular data. The implication of their study is that craniodental characters are unreliable indicators of phylogeny in hominoids and fossil hominids but, notably, their analysis did not include extinct species. We report here on a cladistic analysis designed to test whether the inclusion of fossil taxa affects the ability of morphological characters to recover the molecular ape phylogeny. In the process of doing so, the study tests both Collard and Wood's (2000) hypothesis of character reliability, and the several recently proposed hypotheses of early hominid phylogeny. One hundred and ninety-eight craniodental characters were examined, including 109 traits that traditionally have been of interest in prior studies of hominoid and early hominid phylogeny, and 89 craniometric traits that represent size-corrected linear dimensions measured between standard cranial landmarks. The characters were partitioned into two data sets. One set contained all of the characters, and the other omitted the craniometric characters. Six parsimony analyses were performed; each data set was analyzed three times, once using an ingroup that consisted only of extant hominoids, a second time using an ingroup of extant hominoids and extinct early hominids, and a third time excluding Kenyanthropus platyops. Results suggest that the inclusion of fossil taxa can play a significant role in phylogenetic analysis. Analyses that examined only extant taxa produced most parsimonious cladograms that were inconsistent with the ape molecular tree. In contrast, analyses that included fossil hominids were consistent with that tree. This consistency refutes the basis for the hypothesis that craniodental characters are unreliable for reconstructing phylogenetic relationships. Regarding early hominids, the relationships of Sahelanthropus tchadensis and Ardipithecus ramidus were relatively unstable. However, there is tentative support for the hypotheses that S. tchadensis is the sister taxon of all other hominids. There is support for the hypothesis that A. anamensis is the sister taxon of all hominids except S. tchadensis and Ar. ramidus. There is no compelling support for the hypothesis that Kenyanthropus platyops shares especially close affinities with Homo rudolfensis. Rather, K. platyops is nested within the Homo + Paranthropus + Australopithecus africanus clade. If K. platyops is a valid species, these relationships suggest that Homo and Paranthropus are likely to have diverged from other hominids much earlier than previously supposed. There is no support for the hypothesis that A. garhi is either the sister taxon or direct ancestor of the genus Homo. Phylogenetic relationships indicate that Australopithecus is paraphyletic. Thus, A. anamensis and A. garhi should be allocated to new genera.     

The Freshwater Animal Diversity Assessment: an overview of the results

The geographic genetic structure of two common encrusting sponges, Hymeniacidon sinapium and Hymeniacidon flavia (family Halichondriidae), was investigated using two DNA markers, Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA and NADH dehydrogenase subunit 5 (nad5) of mitochondrial DNA. In the ITS analyses, multiple sequence types were identified within each species. Geographic distribution patterns of sequence types showed higher diversity in the western than eastern areas in both species. However, intraspecific genetic diversity of the two species in Japan differed markedly. Hymeniacidon flavia had far more diverse sequence types, and several genetic differentiations between localities were detected. In contrast, H. sinapium had only four sequence types in Japan, and two Atlantic Hymeniacidon species had sequence types similar to this species. In comparison to ITS, nad5 showed very low genetic diversity in both species, with two haplotypes identified in each species. In H. flavia, frequency of haplotype changed gradually from north to south. In H. sinapium, one haplotype was predominant in most regions, and another haplotype was minor and distributed only in the Korean and Tsushima populations. Based on the unique distribution patterns of sequence types around Shikoku and Kyushu, geographical history and ocean currents were assumed to affect the generation of genetic structure. The geographic genetic structure of H. flavia suggests low dispersal ability of pelagic larvae, whereas higher larval dispersal ability and a far broader distribution range are suggested in H. sinapium. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: C. Sturmbauer     

The phylogeny ofActaea (Ranunculaceae): A biogeographical approach

Phylogenetic analyses of the genusActaea were performed using morphological, ecological and biogeographical characters. Using solely morphological characters, the relationships of the three identified species-groups remain uncertain. Close biogeographical examination and comparison of the areas with ecological peculiarities as well as climate data gave important insight into the phylogeny ofActaea and the whole tribe. Consequently, the obtained biogeographical data were used for phylogenetic reconstructions. Both, from the point of view of morphological and biogeographical data,A. pachypoda andA. asiatica are the most ancestral species. They grow on the east sides of the continents, mainly in broad-leaved forests. In West Eurasia the apomorphicA. spicata andA. acuminata occur under similar climatic and ecological conditions, but these species are adapted to another climate rhythm. The most advanced species (A. erythrocarpa, A. rubra) are to be found in the boreal forests where they are widely distributed. This biogeographical approach revealed that the evolution of the species led to a gradual widening and shifting of their ecological constitutions.     

Homology and hominid phylogeny: Problems and potential solutions

This paper addresses the problem of how to reconstruct accurately the hominid evolutionary tree from skeletal remains. Few would disagree that DNA is generally better than bone as a source of data for assessing phylogenetic relationships. To be sure, DNA base pairs present their own special headaches for phylogenetic reconstruction,¹ not the least of which is that only four possible characters exist at any locus. But base pairs satisfy all the criteria for good phylogenetic data (see Box 1): By definition, they are discrete, heritable, quantifiable, and natural units of phylogenetic information that pass directly from ancestor to descendant. © 1999 Wiley-Liss, Inc.     

A preliminary phylogeny of the Pterasteridae (Echinodermata,Asteroidea) and the first fossil record: Late Cretaceous of Germany and Belgium

The Pterasteridae comprises a diversified group of extant largely deep-sea starfishes. Generic diagnoses have been based classically on soft tissue characters and skeletal architecture. A preliminary phylogeny of sixteen extant species is here worked out by cladistic analysis. The resulting tree suggests monophyly of extant genera and the validity of dissociated plates for identification of genera. Fossil remains of Pterasteridae are here described for the first time. By comparison with extant species, all the skeletal remains from the lower Upper Campanian of Belgium and from the lower Maastrichtian of Germany are tentatively assigned to the genusPteraster. The fossil record of starfishes is poor, but the present Late Cretaceous pterasterids provide one more piece of evidence of the high diversity of starfishes during the Mesozoic. Known Late Cretaceous and Paleogene fossils are broadly similar, which suggests the end-Cretaceous extinction event did not cause major turnover in asteroid faunal composition. As suggested for other starfish groups, both the fossil record of deep-sea Pterasteridae in shelf settings and tree topology imply an onshore-offshore evolutionary trend.      

水螨群总科阶元系统发育的支序分析 (蜱螨亚纲：水螨群)

对水螨群9总科进行了系统发育分析,支序分析选用了23个形态学特征和3个生物学特征。据分析结果所揭示的9总科间的系统发育关系和姐妹群关系,将水螨群9总科划分为5类：拟水螨类,含冥绒螨总科;始水螨类,含溪螨总科;真水螨类,含古水螨类和新水螨类;古水螨类,含水螨总科、盾水螨总科和皱喙螨总科;新水螨类,含刺触螨总科、腺水螨总科、湿螨总科和雄尾螨总科。类间姐妹群关系为：拟水螨类与始水螨类+真水螨类为姐妹群,始水螨类与真水螨类(古水螨类+新水螨类)为姐妹群,古水螨类与新水螨类为姐妹群。该文还就所提出的水螨群5类9总科的阶元排列建议与已有的观点进行了比较。     

A phylogeny of the Platyhelminthes: towards a total-evidence solution

We advocate a total-evidence approach for the reconstruction of working phylogenies for the Turbellaria and the phylum Platyhelminthes. Few morphology-based character matrices are available in the systematic literature concerning flatworms, and molecular-based phylogenies are rapidly providing the only means by which we can estimate phylogenies cladistically. Character matrices based on gross morphology and ultrastructure are required and should be internally consistent, i.e. character coding should follow a set of a priori guidelines and character duplication and contradiction is avoided. In order to test our molecular phylogenies we need complementary data sets from morphology. To understand morphological homology we need phylogenetic evidence from independent (e.g. molecular) data. Fully complementary morphological and molecular data sets enable us to validate phylogenetic hypotheses and the combination of these sets in phylogenetic reconstruction utilises all statements of homology. Working phylogenies which include all phylogenetic information not only shed light on individual character evolution, but form a strong basis for comparative studies investigating the origin and evolutionary radiation of the taxonomic group under scrutiny. This revised version was published online in July 2006 with corrections to the Cover Date.     

Pericarp structure and phylogeny of theLamiaceae-Verbenaceae-complex

Pericarp structure was investigated in 158 species of the familiesLamiaceae andVerbenaceae. Data from 221 out of 262 genera ofLamiaceae s.l. and a few ofVerbenaceae s.str. were collected in a table. A cladistic analysis was performed on the basis of pericarp characters only. The abandonment of subfam.Pogostemonoideae as a taxonomic unit is considered. Examples of groups given additional support by similarities in pericarp characters are: (1) the gynobasic-styled labiates (subfamiliesPogostemonoideae, Lamioideae, Nepetoideae); (2) aLamioideae-Pogostemonoideae-group; (3)Nepetoideae; (4) aWestringia-Hemigenia-Hemiandra-Microcorys group (in subfam.Chloranthoideae); (5) aLepechinia-Chaunostoma-group (inNepetoideae); (6) aPrunella-Cleonia-group (inNepetoideae).     

Taxonomy and phylogeny of the tribePlucheeae (Asteraceae)

The tribePlucheeae (Benth.)A. Anderb., has been analysed cladistically by means of a computerized parsimony program (Hennig 86), using theArctotideae as outgroup. The results of the analysis are presented in a consensus tree and one cladogram. Four major monophyletic subgroups can be recognized: TheColeocoma group (3 genera), thePterocaulon group (3 genera), theLaggera group (6 genera), and thePluchea group (12 genera). All recognized genera are described and most genera are supplied with taxonomical notes including comments on their taxonomic status. Genera such asBlumea, Pluchea, andEpaltes are demonstrated to be unnatural assemblages.Monarrhenus andTessaria are both closely related to thePluchea complex. The old generic nameLitogyne Harv. has been taken up for one species ofEpaltes, the genusRhodogeron is reduced to a synonym ofSachsia, and the following new combinations are made;Litogyne gariepina (DC.)A. Anderb., andSachsia coronopifolia (Griseb.)A. Anderb.     

Molecular phylogeny ofCheirolophus (Asteraceae:Cardueae-Centaureinae) based on ITS sequences of nuclear ribosomal DNA

The genusCheirolophus has an interesting western Mediterranean and Macaronesian distribution. Here we investigate the delimitation of the genus and its exclusion from the large genusCentaurea, the systematic position of the related genusPaleocyanus, the delimitation of some species and the phylogeny of the group. We have carried out a phylogenetic analysis of the PCR-generated sequences of the internal transcribed spacers (ITS-1 and ITS-2) of the nuclear ribosomal DNA. The results suggest that the genus, includingPaleocyanus crassifolius is monophyletic; thus, a new combination of this species underCheirolophus is proposed. The Macaronesian group of species is also monophyletic, indicating a single colonization of the archipelago. The poor resolution of microspecies in the Macaronesian group reinforces the hypothesis of a very recent differentiation of the group.     

The grand game of metazoan phylogeny: rules and strategies

Many cladistic analyses of animal phylogeny have been published by authors arguing that their results are well supported. Comparison of these analyses indicates that there can be as yet no general consensus about the evolution of the animal phyla. We show that the various cladistic studies published to date differ significantly in methods of character selection, character coding, scoring and weighting, ground-pattern reconstructions, and taxa selection. These methodological differences are seldom made explicit, which hinders comparison of different studies and makes it impossible to assess a particular phylogeny outside its own scope. The effects of these methodological differences must be considered before we can hope to reach a morphological reference framework needed for effective comparison and combination with the evidence obtained from molecular and developmental genetic studies.     

Estimating the phylogeny in mollusc Littorina saxatilis (Olivi) from enzyme data: methodological considerations

The evolutionary history of 19 populations of Littorina saxatilis (Olivi) was estimated by four different approaches. Three of these operate upon a population by population matrix of genetic distances: average linkage clustering, and two versions of the Fitch-Margoliash method. The fourth method was a maximum likelihood estimate based on differences in allele frequencies between populations. The study aims to assess how well each method estimates the phylogeny by including seven populations of the closely related species L. arcana Hannaford Ellis. The rationale behind this is that a good estimation technique should be able to separate these two monophyletic taxa.The results show that, by our criteria, the maximum likelihood method yields the best estimate and the unconstrained Fitch-Margoliash technique gives reasonable estimates. Both average-linkage clustering and the Fitch-Margoliash method with evolutionary clock perform less well. We argue that this is expected since both these techniques are based on probably unrealistic assumptions such as the overall rate of evolutionary divergence being homogeneous over phyletic lines.     

Diagnosis and phylogeny of the new world streptocephalidae (Branchiopoda: Anostraca)

We present an updated diagnosis of 13Streptocephalus species of North America. Three new species are included. A key to the species is provided.The phylogeny of the group is discussed on the basis of (1) a systematic approach (Maeda-Martinezet al., 1995; this volume), which considers the entire distal antennal outgrowth, the frontal appendage, and the morphology of the ovaries as essential in defining different genetic lineages or species-groups, and (2) a cladistic analysis. We suggest that of nine monophyletic groups, three are represented in both the Old and New World. Thus, contrary to former disparsalist hypotheses, we argue that the New World species represent relict forms of ancestral groups fragmented by continental drift (vicariance model).     

Chloroplast DNA reassociation and grass phylogeny

Sequence variation in chloroplast DNA (cpDNA) as measured by DNA reassociation was examined in 12 grass species to address systematic problems in thePoaceae at the subfamilial and tribal levels. Two species,Petunia (Solanaceae) andGlycine (Leguminosae), were included to determine degrees of sequence divergence in cpDNA between monocots and dicots. The data were analyzed phenetically and phylogenetically. Species were segregated into four major groups that corresponded to the subfamiliesPooideae, Oryzoideae, Chloridoideae, andPanicoideae. Representatives of thePooideae andOryzoideae grouped together as did members of theChloridoideae andPanicoideae. ThePooideae split into two major groups corresponding to the recently recognized supertribesTriticanae andPoanae. Internodes between subfamily branches were short which might indicate a burst of divergence in the family early in its evolution. Sequence similarity values between the monocot grass species and the two dicot taxa ranged from 0.15 to 0.27, representing the highly conserved sequences of the chloroplast genome.     

鸢尾属分子系统发育学研究进展

鸢尾属植物具有重要的观赏价值和经济价值,研究该属属内系统演化关系对该属种质保存、利用和遗传育种具有重要意义.目前,有关鸢尾属各分类单元的系统学关系长期处于争议状态.因此,该文以经典分类系统主要观点为基础,从不同分类单元的系统关系总结了鸢尾属分子系统发育学研究进展.结果表明:现有分子系统发育学研究结果大多支持鸢尾属为并系...     

Journeys through discrete‐character morphospace: synthesizing phylogeny,tempo, and disparity

Palaeontologists have long employed discrete categorical data to capture morphological variation in fossil species, using the resulting character–taxon matrices to measure evolutionary tempo, infer phylogenies and capture morphological disparity. However, to date these have been seen as separate approaches despite a common goal of understanding morphological evolution over deep time. Here I argue that there are clear advantages to considering these three lines of enquiry in a single space: the phylomorphospace. Conceptually these high‐dimensional spaces capture how a phylogenetic tree explores morphospace and allow us to consider important process questions around evolutionary rates, constraints, convergence and directional trends. Currently the literature contains fundamentally different approaches used to generate such spaces, with no direct comparison between them, despite the differing evolutionary histories they imply. Here I directly compare five different phylomorphospace approaches, three with direct literature equivalents and two that are novel. I use a single empirical case study of coelurosaurian theropod dinosaurs (152 taxa, 853 characters) to show that under many analyses the literature‐derived approaches tend to reflect introduced phylogenetic (rather than the intended morphological) signal. The two novel approaches, which produce limited ancestral state estimates prior to ordination, are able to minimize this phylogenetic signal and thus exhibit more realistic amounts of phylogenetic signal, rate heterogeneity, and convergent evolution.