中国特有诸葛菜复合群的系统发育关系

利用5．8S核糖体DNA全长间隔序列（ITS／5．8S）和叶绿体基因mat K对中国原产诸葛菜复合群的系统发育关系进行了分析研究。ITS序列结果支持中国诸葛菜复合群分为两支：一支由湖北诸葛菜和太白诸葛菜组成;另一支由诸葛菜和铺散诸葛菜组成。mat K的序列分析结果表明,在中国诸葛菜复合群的系统发育树中,铺散诸葛菜和诸葛菜处于基部位置。结合以前的核型分析和本文的研究结果,我们不支持将湖北诸葛菜和太白诸葛菜归隶于诸葛菜,而支持我们之前提出的两种可能的原始细胞型的进化假说。另外,根据生物地理学分析,推测从长江中下游到秦岭地区是中国原产诸葛菜的近代分化中心。     

A "Total Evidence" Analysis of the Phylogenetic Relationships among the Photosynthetic Stramenopiles

Phylogenetic relationships among the nine major autotrophic stramenopile taxa were inferred in a combined analysis of the rbcL, SSU rDNA, partial LSU rRNA, carotenoid, and ultrastructural data sets. The structure of the shortest combined tree is: (Outgroup, ((((Bacillariophyceae, (Pelagophyceae, Dictyochophyceae)),((Phaeophyceae, Xanthophyceae), Raphidophyceae)), Eustigmatophyceae),(Chrysophyceae, Synurophyceae))). The Synurophyceae/Chrysophyceae is the best supported group followed by the Phaeophyceae/Xanthophyceae and the Pelagophyceae/Dictyochophyceae clades. The monophyletic groups composed of Bacillariophyceae/Pelagophyceae/Dictyochophyceae and Phaeophyceae/Xanthophyceae/Raphidophyceae received the lowest Bremer support values. The optimal combined tree suggests that the diatom frustule is derived from the siliceous "skeleton" in Dictyochophyceae, that the reduced flagellar apparatus arose once in the Bacillariophyceae/Dictyochophyceae/Pelagophyceae clade, and that the specific photoreceptor-eyespot apparatus in Chrysophyceae and the Phaeophyceae/Xantophyceae clade originated independently within the autotrophic stramenopiles. Despite conflicts in tree structure between the most-parsimonious combined phylogeny and the optimal tree(s) of each data partition, it cannot be concluded that extensive incongruence exists between the data sets.     

A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data

Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this complex information. We present a Bayesian method for inferring the phylogenetic relationship among related organisms found within metagenomic samples. Our approach exploits variation in the frequency of taxa among samples to simultaneously infer each lineage haplotype, the phylogenetic tree connecting them, and their frequency within each sample. Applications of the algorithm to simulated data show that our method can recover a substantial fraction of the phylogenetic structure even in the presence of high rates of migration among sample sites. We provide examples of the method applied to data from green sulfur bacteria recovered from an Antarctic lake, plastids from mixed Plasmodium falciparum infections, and virulent Neisseria meningitidis samples.     

Stimulated rejuvenation of dormant Aulacoseira granulata (Bacillariophyta) by Gloeocystis planctonica (Chlorophyta) in a eutrophic river

The abundance of Aulacoseira granulata (Ehrenburg) Simonsen and Gloeocystis planctonica (West & G.S.West) Lemmermann was assessed during the summers of 2005 and 2010 in the eutrophic Fox River, Wisconsin, USA. In both years, a mid‐summer bloom of G. planctonica was followed by the rapid growth of A. granulata. Laboratory experiments in which A. granulata was grown in cell‐free filtrate of a G. planctonica culture revealed that the growth of A. granulata was stimulated in the G. planctonica‐treated medium relative to controls. This effect was detected when dormant A. granulata cells were used as the source culture for the experiment but not when actively growing cells were used. Dormant A. granulata also grew more rapidly in river water collected after the 2010 G. planctonica bloom relative to river water collected before the bloom. These results suggest that the summer bloom of A. granulata in the river was stimulated by G. planctonica. This relationship can be described as stimulated rejuvenation, an interaction where the transition of an algal resting stage into active growth is triggered by exposure to another species.     

Phylogenetic Relationships Among Treeshrews (Scandentia): A Review and Critique of the Morphological Evidence

Although the supraordinal relationships of Scandentia (treeshrews) have been studied in great detail from both morphological and molecular perspectives, the phylogenetic relationships among treeshrews have been largely ignored. Here we review several published studies of qualitative morphological variation among living treeshrews and their contribution to our understanding of intraordinal phylogenetic relationships. Reanalysis of the data from each of these studies demonstrates that none of the trees in the original publications represents the most parsimonious interpretation. In addition to performing new analyses, we argue that all such studies to date suffer from one or more fundamental shortcomings, notably the failure to include reference to nonscandentian outgroups and the a priori assumption of generic monophyly of the relatively speciose genus Tupaia. Parsimony analyses of these data sets fail to resolve either intergeneric or interspecific relationships. Finally, several inconsistencies and conflicts with respect to character coding both within and between published studies are discussed. We conclude that a more rigorous investigation of morphological character state variation is sorely needed, one that explicitly identifies voucher specimens and does not make any assumptions of generic monophyly. This is necessary not only for the purpose of resolving phylogenetic relationships, but also for inference of ancestral states in a group that continues to figure prominently in studies of placental mammal diversification.     

A Total Evidence Phylogeny of the Arctoidea (Carnivora: Mammalia): Relationships Among Basal Taxa

A total evidence phylogenetic analysis was performed for 14 extant and 18 fossil caniform genera using a data matrix of 5.6 kbp of concatenated sequence data from six independent loci and 80 morphological characters from the cranium and dentition. Maximum parsimony analysis recovered a single most parsimonious cladogram (MPC). The topology of the extant taxa in the MPC agreed with previous molecular phylogenies. Phylogenetic positions for fossil taxa indicate that several taxa previously described as early members of extant families (e.g., Bathygale and Plesictis) are likely stem taxa at the base of the Arctoidea. Taxa in the “Paleomustelidae” were found to be paraphyletic, but a monophyletic Oligobuninae was recovered within this set of taxa. This clade was closely related to the extant genera Gulo and Martes, therefore, nested within the extant radiation of the family Mustelidae. This analysis provides a resolution to several discrepancies between phylogenies considering either fossil taxa or extant taxa separately, and provides a framework for incorporating fossil and extant taxa into comprehensive combined evidence analyses.     

Phylogenetic Relationships within the Excavating Hadromerida (Porifera), with a Systematic Revision

This study was performed to ascertain the relationships among clionid and spirastrellid species from the Mediterranean Sea, based on phylogenetic criteria. A matrix of 34 taxa and 20 characters was analysed. Cladistic analysis using PAUP produced 12 equally parsimonious trees of 54 steps (CI=0.648, RI=0.865). Resolution was high in all parts of the strict consensus tree except in those which involved relationships among the most characteristic clionid species: those having only tylostyles as megascleres and, if microscleres are present, these being spirasters. Six monophyletic groups, three of them represented by monospecific clades, appear in the totally resolved part of the trees, which supports their separation into different genera. On the basis of the results obtained, the species at present within the genus Cliona have been allocated to five different genera: Scantilletta, Pione, Volzia, Bernatia and Cliona , while Dotona and Cliothosa are maintained as separate genera. Scantilletta and Pione are genera erected by de Laubenfels (1936 Pap. Tortugas Lab. 30 , 1–225) and Gray (1867 Proc. Zool. Soc. Lond. XXXII , 492–558) respectively, and whose diagnoses are amended here. Volzia and Bernatia are proposed as new genera to include Cliona albicans and Cliona rovignensis , and Cliona vermifera , respectively. Thus, the genus Cliona clearly appears in our analysis as a polyphyletic group. It is only maintained provisionally to harbour species whose position cannot be clearly ascertained from the information at hand. Skeletal characters such as spicule types and skeletal arrangement have proven to be useful in discriminating some genera and families but they do not completely resolve the phylogeny of this group of species. Biochemical, genetic, cytological or reproductive information, when available, may help in the resolution of the phylogenetic tree.     

Phylogenetic relationships within the turacos (Musophagidae)

Cytochrome b sequences were used to investigate both the systematic position of the Musophagidae and the species relationships within the family. Phylogenetic analyses (neighbour-joining, maximum likelihood and maximum parsimony) supported the hypothesis that the Musophagidae are more closely related to the cuckoos, parrots and the Hoatzin than the gamebirds. Within the family, three major clades are evident that correspond to the three subfamilies generally recognized. The 'grey turacos' and the turacin-bearing turacos form two separate monophyletic groups. Corythaixoides leucogaster appears to be basal within the subfamily Criniferinae (the 'grey turacos'). This analysis yields a hypothesis for the controversy surrounding the position of Gallirex porphyreolophus and Tauraco johnstoni, which appear to be closely related and basal to the other turacin-bearing turacos. The Musophaga species are placed within the Tauraco clade and appear to be specialized forms of typical turacos. The superspecies persa forms a monophyletic group, within which T. hartlaubi falls. This is an association that has not been suggested previously.     

Phylogenetic Relationships of the Suborders of Coleoptera (Insecta)

One hundred seven external and internal characters of larval and adult representatives of 28 genera of the coleopteran suborders were analyzed cladistically. Four groups of Neuropterida were introduced as outgroup. The analysis yielded 18 trees with a minimum of 194 steps (CI 0.691). All trees support the monophyly of all four suborders and a branching pattern (Archostemata + (Adephaga + (Myxophaga + Polyphaga))). The presence of elytra with meso- and metathoracic locking devices, the specific hind-wing folding, the close connection of exposed sclerites, the absence of the mera, the absence of eight thoracic muscles, the reduced abdominal sternite I, and the invagination of terminal segments are autapomorphies of Coleoptera. The monophyly of Coleoptera excl. Archostemata is supported by further transformations of the thoracic sclerites such as absence of the mesothoracic discriminal line and katepisternal joint, by an internalized or absent metathoracic trochantin, by the presence of a bending zone in the hind-wing, and by eight further muscle losses. Fusion of tibia and tarsus and presence of a single claw are larval synapomorphies of Myxophaga and Polyphaga. Adults are characterized by fusion of protrochantin and propleura and by the rigid connection of the meso- and metathoracic ventrites. The eucinetoid lineage of Polyphaga is characterized by the secondary absence of the bending zone of the alae. This results in a distinctly simplified wing folding mechanism. The monophyly of Cucujiformia (+ Bostrichoidea) is supported by the presence of cryptonephric Malpighian tubules. Transformations of fore-and hind-wings, reinforcement and simplification of the thoracic exoskeleton, and an efficient use of a distinctly reduced set of thoracic muscles play an important role in the early evolution of Coleoptera. Many different larval character transformations take place in the earlier Mesozoic within the suborders.     

Phylogenetic Relationships among the True Porpoises (Cetacea: Phocoenidae)

Portions of the cytochrome b gene and control region of the mitochondrial DNA molecule were sequenced to investigate systematic relationships among the six extant species of true porpoises, (Cetacea: Phocoenidae). Phylogenetic analyses of mitochondrial cytochrome b sequences support a close relationship between Burmeister′s porpoise, Phocoena spinipinnis, and the vaquita, Phocoena sinus, and the association of these two species with the spectacled porpoise, Australophocaena dioptrica. The latter result is not in concordance with a recent morphological reclassification which groups A. dioptrica with Dall′s porpoise, Phocoenoides dalli, in the subfamily Phocoenoidinae. The molecular analysis found no support for this grouping. A dioptrica was originally described as a member of the genus Phocoena, and our results support returning it to that genus at this time. Finally, the data suggest that the tropical species Neophocaena phocaenoides, the finless porpoise, may represent the most basal member of the family. The control region sequences corroborated the relationships among the closely related taxa P. sinus, P. spinipinnis, and A. dioptrica, but were unable to resolve the deeper branches of the tree, probably as a result of a high level of saturation of these sequences.     

A Floral Ontogenetic Approach to Questions of Homology within the Cyperoideae (Cyperaceae)

Within the Cyperoideae, which comprise all Cyperaceae except the Mapanioideae, several questions of homology are discussed and reinterpreted based on results of our SEM and LM floral ontogenetic studies. In all species studied, spikelets are interpreted as being indeterminate, with spirally to distichously arranged glumes, each subtending (or not) a flower. Floral development starts with the formation of two lateral stamen primordia, simultaneously with, or followed by the formation of a third, abaxial stamen primordium. Perianth parts, if present, originate only after the formation of the androecium, simultaneously with the appearance of an annular ovary primordium, surrounding a central ovule primordium. Perianth parts vary in number and morphology, and, where present, perianth development follows a general pattern. Three (or two) stigma primordia are formed on the top of the rising ovary wall. In dimerous gynoecia, stigma primordia originate either dorsiventrally, resulting in a laterally flattened ovary/nutlet, or laterally, resulting in a dorsiventrally flattened ovary/nutlet. We conclude that in all species studied the spikelet and floral development occurs according to a general, scirpoid, ontogenetic pattern, which we illustrate using new spikelet and floral ontogenetic results in Eleocharis palustris and other species. Spikelet and floral ontogeny in species with apparently deviating morphologies, can be traced back to the general ontogenetic pattern.

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Resumen  Varias preguntas sobre homología para las Cyperoideae, que incluyen todas las Cyperaceae excepto las Mapanioideae, se discuten e interpretan con base en estudios de ontogenia floral realizados con SEM y LM. En todas las especies estudiadas, las espiguillas son indeterminadas con glumas arregladas en espiral o dicotomicamente, cada una sosteniendo (o no) una flor. El desarrollo floral comienza con la formación de dos primordios estaminales laterales, simultáneamente con o seguido por la formación del tercer primordio estaminal abaxial. Si se desarrollan las partes del perianto, se originan solo después de la formación del androceo, simultáneamente con el desarrollo del primordio anular del ovario que envuelve al primordio central del óvulo. Cuando están presentes las partes del perianto, varían en número y morfología y el desarrollo sigue un patrón general. Se forman tres (o dos) primordios del estigma en el ápice de la pared del ovario en desarrollo. En gineceos dímeros, los primordios de los estigmas se originan dorsiventralmente resultando en una nuececilla/ovario comprimido lateralmente, o se originan lateralmente, resultando en una nuececilla/ovario comprimido dorsiventralmente. Concluimos que, tanto el desarrollo floral, como el de las espiguillas en todas las especies estudiadas, siguen un patrón ontogenético general scirpoide que se ilustra con los resultados obtenidos para Eleocharis palustris y otros especies. La ontogenia floral y de las espiguillas en especies con morfologías aparentemente atípicas, puede estar reducida al patrón ontogenetico general.

     

星肋小环藻的一新变种

作者在进行四川、云南硅藻分类研究中,发现了星肋小环藻的一新变种,定名为星肋小环藻线纹变种(Cyclotella asterocoaata var.striata),为编写《中国硅藻志》提供资料。       

The Phylogenetic Relationships of Eucynodontia (Amniota: Synapsida)

The phylogeny of Eucynodontia is an important topic in vertebrate paleontology and is the foundation for understanding the origin of mammals. However, consensus on the phylogeny of Eucynodontia remains elusive. To clarify their interrelationships, a cladistic analysis, based on 145 characters and 31 species, and intergrating most prior works, was performed. The monophyly of Eucynodontia is confirmed, although the results slightly differ from those of previous analyses with respect to the composition of both Cynognathia and Probainognathia. This is also the first numerical cladistic analysis to recover a monophyletic Traversodontidae. Brasilodon is the plesiomorphic sister taxon of Mammalia, although it is younger than the oldest mammals and is specialized in some characters. A monophyletic Prozostrodontia, including tritheledontids, tritylodontids, and mammals, is well supported by many characters. Pruning highly incomplete taxa generally has little effect on the inferred pattern of relationships among the more complete taxa, although exceptions sometimes occur when basal fragmentary taxa are removed. Taxon sampling of the current data matrix shows that taxon sampling was poor in some previous studies, implying that their results are not reliable. Two major unresolved questions in cynodont phylogenetics are whether tritylodontids are more closely related to mammals or to traversodontids, and whether tritylodontids or tritheledontids are closer to mammals. Analyses of possible synapomorphies support a relatively close relationship between mammals and tritylodontids, to the exclusion of traversodontids, but do not clearly indicate whether or not tritheledontids are closer to mammals than are tritylodontids.     

Phylogenetic relationships within Nephtyidae (Polychaeta,Annelida)

Ravara, A., Wiklund, H., Cunha, M. R. & Pleijel, F. (2010). Phylogenetic relationships within Nephtyidae (Polychaeta, Annelida). —Zoologica Scripta, 39, 394–405. We present the first phylogeny of nephtyids, a common, soft‐bottom living polychaete family comprising five genera and over 100 species. Characters used to distinguish nephtyid genera are a matter of controversy and considerable confusion remains as to the generic delineations. The phylogeny is estimated with molecular data from the mitochondrial genes cytochrome oxidase I and 16S rDNA, the nuclear genes 18S rDNA and 28S rDNA and morphological data. The results reveal two well‐supported major clades, corresponding in part to the two main genera of the family, Aglaophamus and Nephtys. The species Nephtys pulchra and Nephtys australiensis are transferred to Aglaophamus, and new diagnoses for the genera are provided. Dentinephtys is synonymized with Nephtys, and Nephtys cornuta is sister to the remaining nephtyids and is referred to the new genus Bipalponephtys, together with Nephtys danida and Micronephthys neotena. Micronephthys is sister to Nephtys and Inermonephtys is of uncertain position.     

Phylogenetic relationships within laticaudine sea snakes (Elapidae)

The sea snake subfamily Laticaudinae consists of a single genus with eight named species, based on morphological characters. We used microsatellite and mitochondrial DNA (mtDNA) data to clarify the adaptive radiation of these oviparous sea snakes in the South Pacific, with special reference to New Caledonia and Vanuatu. A mitochondrial DNA data set (ND4 gene 793 bp) was obtained from 345 individuals of the five species of Laticauda sp. sea snakes endemic to the region. Maximum likelihood and Bayesian approaches yielded the same optimal tree topology, identifying two major clades (yellow-banded and blue-banded sea snakes). Although all laticaudine sea snakes rely on small islands as oviposition sites, the two lineages differ in their use of marine vs. terrestrial habitats. A highly aquatic species (Laticauda laticaudata) shows a strong pattern of genetic isolation by distance, implying that the patchy distribution of terrestrial habitats has had little impact on gene flow. The more terrestrial clade (Laticauda colubrina, Laticauda frontalis, Laticauda guineai, Laticauda saintgironsi) shows stronger geographic differentiation in allelic frequencies, associated with island groups rather than with geographic distance. Microsatellites and mtDNA suggest that L. frontalis (restricted to Vanuatu) represents a recent founder-induced speciation event, from allopatric migrants of the New Caledonian taxon L. saintgironsi. A major divergence in speciation patterns between the two major clades of laticaudine snakes thus correlates with (and perhaps, is driven by) differences in the importance of terrestrial habitats in the species' ecology.     

Phylogenetic Relationships and Evolution of the Androecia in Ruteae (Rutaceae)

Ruta, which belongs to tribe Ruteae, is the type genus of the subfamily Rutoideae and the family Rutaceae. Molecular systematic studies have shown that the genera in Ruteae are closer related to Aurantioideae than to most other genera of Rutoideae, some of the genera traditionally placed in Ruteae have been shown to be nested within the Aurantioideae clade, but the diagnostic characters for determining new patterns in the relationship are poor. In this study, we investigated the floral development of Boenninghausenia in Ruteae (sensu stricto), Haplophyllum in the basal position of Aurantioideae and Murraya in traditional Aurantioideae using scanning electron microscopy. The androecium of Boenninghausenia is obdiplostemony. As androecia in other genera within Ruteae (s.s.) are also obdiplostemonous, reconstruction of the ancestral state indicates that obdiplostemony is an ancestral character in this clade. Because the androecia of Haplophyllum and Murraya are also obdiplostemonous, obdiplostemony is also an ancestral character in Aurantioideae clade. The ancestral state reconstruction indicates this character can serve as a synapomorphy of the Ruteae-Aurantioideae clade. The results of our work also shed light on the evolution of the androecium in Rutaceae, as the obdiplostemony of this group is clearly derived from haplostemony in the ancestral genera in Rutaceae and has develop into polyandry by increasing antepetalous stamens.     

Phylogenetic Relationships in the Macrobiotidae (Tardigrada: Eutardigrada: Parachela)

Characters of the claws, buccal-pharyngeal apparatus and ultrastructure of the cuticle have been examined to identify phyletic relationships within the Macrobiotidae. Several apomorphies have been identified. The resulting cladogram shows two main phyletic lines within the family, corresponding to the subfamilies Macrobiotinae and Murrayinae. The relationships among the genera of the Murrayinae are resolved, whereas in the Macrobiotinae five main phyletic lines are identified, whose relationships are still unknown. Pseudodiphascon and Macrobiotus appear to be polyphyletic genera.