Phylogeny of the Apodan Holothurians (Echinodermata) inferred from morphology

The Apodida is an order of littoral to deep-sea, largely infaunal sea cucumbers with about 270 extant species in 32 genera and three families, Synaptidae, Chiridotidae and Myriotrochidae. In this study, I perform the first phylogenetic test of the taxonomic and palaeontological hypotheses about evolutionary relationships within Apodida by using cladistic analyses of 34 morphological characters. I introduce several previously unconsidered synapomorphic characters, examine the relationships between all recognized suprageneric taxonomic groups and assess the assumptions of monophyly for each family. Maximum-parsimony analyses of type species from 14 genera and use of three rooting methods recovered identical topologies at the subordinal level and subfamily level within Synaptidae. Overall, the current higher-level classification of Apodida was well corroborated. Within Synaptidae, the relationships (Synaptinae, (Leptosynaptinae, Rynkatorpinae)) are well supported. The monophyly of Chiridotidae was not supported and appears paraphyletic at the subfamily level. Calibrating the phylogenetic hypothesis of Apodida against the fossil record indicated that most higher-level divergences occurred within the Palaeozoic, unlike that of extant non-holothuroid echinoderms, which radiated in the early Mesozoic. Synaptidae appears to have radiated during the Lower Cretaceous. Alternatively, and if one discounts the considerable ghost lineage duration that this hypothesis requires, they may have radiated during the Eocene.     

Adapting generalized frequency coding to use colour spectra in the determination of phylogenetic relationships: an example with hummingbirds

We introduce a methodology to perform phylogenetic analyses on bird taxa using parsimony based on plumage colour characters obtained as spectra. The generalized frequency coding method was adapted to transform continuous colour spectral data into discrete variables. As an example of the application of the methodology, we analysed two species of the hummingbird genus Campylopterus and all species of the genera Anthracothorax and Eulampis , which occur in South and Central America and the Caribbean islands. The genus Topaza was used as an outgroup because of its basal position within the hummingbirds. The results were mostly in accordance with both traditional morphological as well as molecular analyses indicating that there is phylogenetic information in plumage colours measured in an integral and objective way and that the new method is appropriate for phylogenetic analyses at this lower taxonomic level.     

盔唇瓢虫族(鞘翅目：瓢虫科)系统分类研究进展

盔唇瓢虫族昆虫是瓢虫科中一类重要的捕食性天敌,主要捕食介壳虫,是该类害虫的重要生物防治天敌。盔唇瓢虫族昆虫研究历史悠久,目前世界盔唇瓢虫族包括22属超过280种,其中有9属42种分布在中国。该族许多属建立时间早,鉴别特征的原始描述不够详细,导致属间界定模糊,属的地位时常受到质疑且变动频繁。一些种类丰富,形态多变、且分布广泛的属如盔唇瓢虫属、光缘瓢虫属仍缺少世界性的订正研究。随着瓢虫科分子系统发育研究的开展,瓢虫科经典分类系统受到了较大的挑战,而盔唇瓢虫亚科已被证实为非单系起源的类群。目前,将盔唇瓢虫族归入瓢虫亚科得到绝大多数瓢虫科分子系统发育研究的支持,但与其它类群的亲缘关系仍存争议。尽管已有研究对盔唇瓢虫族现存所有属的系统发育关系进行了分析,但部分类群缺少分子数据,导致这些类群在该族系统发育关系中的位置并不明确。本文回顾了国内外盔唇瓢虫族的分类历史,记述了目前该族在瓢虫科的分类地位以及族下系统发育关系进展,最后对盔唇瓢虫族分类研究存在的问题及未来研究进行了展望。     

Morphology, anatomy and histochemistry of Salicornioideae (Chenopodiaceae) fruits and seeds

BACKGROUND AND AIMS: The subfamily Salicornioideae (Chenopodiaceae) are a taxonomically difficult group largely due to the lack of diagnostic characters available to delineate tribal- and generic-level boundaries; a consequence of their reduced floral and vegetative features. This study examined the variation in fruits and seeds across both tribes of the Salicornioideae to assess if characters support traditional taxonomic sections. METHODS: Light microscopy, environmental scanning electron microscopy and anatomical ultra-thin sectioning were employed to examine variation in fruits and seeds. Sixty-eight representatives across 14 of the 15 genera currently recognized within the tribes Halopeplideae and Salicornieae were examined to determine whether characters support current taxonomic groups. KEY RESULTS: Characters such as seed coat structure, embryo shape, seed orientation, the forms of seed storage proteins and carbohydrates show variation within the Salicornioideae and may be phylogenetically useful. The campylotropous ovule typical of the Chenopodiaceae generally results in a curved embryo; however, many Halosarcia and Sclerostegia species have straight embryos and in Salicornia and Sarcocornia the large peripheral embryo appears bent rather than curved. Seed coat ornamentation of Microcnemum and Arthrocnemum is distinct from other Salicornioideae as the elongated epidermal cells of the exotesta have convex walls. Histochemical stains of anatomical sections of cotyledon cells showed protein bodies were variable in shape, and starch grains were present in some species, namely Salicornia bigelovii, S. europaea and Allenrolfea occidentalis. CONCLUSIONS: While fruits and seeds were found to be variable within the subfamily, no synapomorphic characters support the tribe Halopeplideae as these genera have crustaceous seed coats, curved embryos and abundant perisperm; features characteristic of many of the tribe Salicornieae. The endemic Australian genera are closely related and few seed and fruit characters are diagnostic at the generic level. Nineteen characters identified as being potentially informative will be included in future phylogenetic analyses of the subfamily.     

Molecular taxonomy and phylogenetic relationships among Australian Nasutitermes and Tumulitermes genera (Isoptera, Nasutitermitinae) inferred from mitochondrial COII and 16S sequences

The subfamily Nasutitermitinae Hare (1937) is a tropical and subtropical group, generally considered as the most specialised subfamily of Termitidae. To highlight some taxonomic inconsistencies, the phylogenetic relationships among seven Australian species, morphologically ascribed to the genera Nasutitermes and Tumulitermes, were studied through the analyses of the mitochondrial markers cytochrome oxidase II and 16S ribosomal RNA genes. In our trees, N. longipennis samples clearly pertain to two different specific entities with an apparently parapatric distribution. Further, the phylogenetic analysis performed on separated and combined data sets shows the placement of Tumulitermes species within a clade grouping Nasutitermes ones, and vice versa. Tests for alternative topologies do not support the monophyly of the genera Nasutitermes and Tumulitermes. Our results confirm the hypothesis that the morphological features used to establish relationships among these species are not phylogenetically decisive.     

Utility of the white gene in estimating phylogenetic relationships among mosquitoes (Diptera: Culicidae)

The utility of a nuclear protein-coding gene for reconstructing phylogenetic relationships within the family Culicidae was explored. Relationships among 13 species representing three subfamilies and nine genera of Culicidae were analyzed using a 762-bp fragment of coding sequence from the eye color gene, white. Outgroups for the study were two species from the sister group Chaoboridae. Sequences were determined from clone PCR products amplified from genomic DNA, and aligned following conceptual intron splicing and amino acid translation. Third codon positions were characterized by high levels of divergence and biased nucleotide composition, the intensity and direction of which varied among taxa. Equal weighting of all characters resulted in parsimony and neighboring-joining trees at odds with the generally accepted phylogenetic hypothesis based on morphology and rDNA sequences. The application of differential weighting schemes recovered the traditional hypothesis, in which the subfamily Anophelinae formed the basal clade. The subfamily Toxorhynchitinae occupied an intermediate position, and was a sister group to the subfamily Culicinae. Within Culicinae, the genera Sabethes and Tripteroides formed an ancestral clade, while the Culex-Deinocerites and Aedes- Haemagogus clades occupied increasingly derived positions in the molecular phylogeny. An intron present in the Culicinae- Toxorhynchitinae lineage and one outgroup taxon was absent in the basal Anophelinae lineage and the second outgroup taxon, suggesting that intron insertions or deletions may not always be reliable systematic characters.      

Plumage evolution in relation to light environment in a novel clade of Neotropical tanagers

Molecular phylogenetic analyses have greatly changed Neotropical avian systematics in the past couple of decades. These new phylogenies provide the necessary framework to study the ecology and natural history of species in the region in an evolutionary context. This study addresses the systematics of Poospiza, Compsospiza, Hemispingus, Thlypopsis, and eight monotypic genera, which form a strongly supported and novel clade within the tanagers. We find Poospiza, Hemispingus, and Thlypopsis to be polyphyletic, confirm or reject relationships proposed based on morphology and life history, and describe novel relationships among these and the monotypic genera. The diversity of plumage, habitat, and geography throughout the clade allows us to test hypotheses of plumage evolution in relation to light environment. We find that overall plumage brightness best fits a model that includes selective regimes based on open versus closed habitats and foraging strata, while plumage measures describing color diversity and chroma best fit a model that only includes selective regimes based on open and closed habitats.     

Multilocus phylogeny reveals unexpected diversification patterns in Asian wolf snakes (genus Lycodon)

The diverse group of Asian wolf snakes of the genus Lycodon represents one of many poorly understood radiations of advanced snakes in the superfamily Colubroidea. Outside of three species having previously been represented in higher‐level phylogenetic analyses, nothing is known of the relationships among species in this unique, moderately diverse, group. The genus occurs widely from central to Southeast Asia, and contains both widespread species to forms that are endemic to small islands. One‐third of the diversity is found in the Philippine archipelago. Both morphological similarity and highly variable diagnostic characters have contributed to confusion over species‐level diversity. Additionally, the placement of the genus among genera in the subfamily Colubrinae remains uncertain, although previous studies have supported a close relationship with the genus Dinodon. In this study, we provide the first estimate of phylogenetic relationships within the genus Lycodon using a new multi‐locus data set. We provide statistical tests of monophyly based on biogeographic, morphological and taxonomic hypotheses. With few exceptions, we are able to reject many of these hypotheses, indicating a need for taxonomic revisions and a reconsideration of the group's biogeography. Mapping of color patterns on our preferred phylogenetic tree suggests that banded and blotched types have evolved on multiple occasions in the history of the genus, whereas the solid‐color (and possibly speckled) morphotype color patterns evolved only once. Our results reveal that the colubrid genus Dinodon is nested within Lycodon—a clear finding that necessitates the placing of the former genus in synonymy with the latter.     

Phylogenetic relationships among microgastrine braconid wasp genera based on data from the 16S, COI and 28S genes and morphology

Abstract Phylogenetic relationships among the genera of the large braconid wasp subfamily Microgastrinae were explored using DNA sequence data from the mitochondrial large ribosomal subunit (16S), nuclear large ribosomal subunit (28S) and mitochondrial cytochrome oxidase (COI) genes, along with morphological characters, both new and from previous studies. The taxonomic history of this group of wasps is reviewed, along with a critique of previous phylogenetic studies on the group. Molecular data were sampled from forty-six species representing twenty-six genera of microgastrines, plus three species representing the close outgroup taxa Cardiochilinae and Miracinae. Some 2300 base pairs of aligned sequence were obtained per taxon from the three genes. In addition, fifty-three morphological characters were coded for all known genera, including two undescribed genera, except Semionis Nixon (known from only a single male type specimen). Relationships among several groups of genera are clarified and challenge some major assumptions made in earlier classifications. In particular, it is clear that dependence on one or a few major morphological character systems oversimplifies relationships, and can lead to misleading results. Despite the large amount of data analysed, basal divergences within the subfamily remain poorly resolved and essentially unsupported in any rigorous statistical sense.     

Molecular phylogeny of the nutmeg shells (Neogastropoda, Cancellariidae)

Cancellariidae, or nutmeg shells, is a family of marine gastropods that feed on the body fluids and the egg cases of marine animals. The 300 or so living species are distributed worldwide, mostly on soft bottoms, from intertidal to depths of about 1000 m. Although they are a key group for the understanding of neogastropod evolution, they are still poorly known in terms of anatomy, ecology and systematics. This paper reports the first mitochondrial multi-gene phylogenetic hypothesis for the group. Data were collected for 50 morphospecies, representative of 22 genera belonging to the three currently recognized subfamilies. Sequences from three genes (12S, 16S and COI) were analyzed with Maximum Likelihood analysis and Bayesian Inference, both as single gene datasets and in two partitioned concatenated alignment. Largely consistent topologies were obtained and discussed with respect to the traditional subfamilial arrangements. The obtained phylogenetic trees were also used to produce Robinson-Foulds supertrees. Our results confirmed the monophyly of the subfamily Plesiotritoninae, while Admetinae and Cancellariinae, as currently conceived, were retrieved as polyphyletic. Based on our findings we propose changes to the systematic arrangement of these subfamilies. At a lower taxonomic rank, our results highlighted the rampant homoplasy of many characters traditionally used to segregate genera, and thus the need of a critical re-evaluation of the contents of many genera (e.g. Nipponaphera, Merica, Sydaphera, Bivetia), the monophyly of which was not recovered.     

Relationships of the New Guinean songbird genera Amalocichla and Pachycare based on mitochondrial and nuclear DNA sequences

The New Guinean songbird fauna contains numerous enigmatic species and genera whose phylogenetic affinities have been difficult to resolve. Two such genera are ditypic Amalocichla and monotypic Pachycare. Here we obtained DNA sequences of two nuclear gene regions and a mitochondrial gene to ascertain the phylogenetic positions of these genera. Amalocichla was identified as the sister of the Australasian robins (Petroicidae) contrary to most recent classifications, which align it with the New Guinean mouse‐warblers Crateroscelis in the family Acanthizidae. The morphological characters used to place Amalocichla in the Acanthizidae appear to be convergent and linked to ground‐living adaptations. Pachycare was found to be most closely related to the Acanthizidae and not to the Pachycephalidae, corvine assemblage, or Petroicidae, as most commonly assumed. Morphological and behavioural characters support the molecular data in this conclusion. Previous taxonomic placements appear to have been based on superficial similarities in plumage coloration and vocal characterizations.     

Phylogenetic relationships of the genus Dugesia (Platyhelminthes, Tricladida, Paludicola)

A phylogenetic analysis was performed on the genera and subgenera within the freshwater triclad family Dugesiidae, based on 19 terminal taxa and 17 morphological characters. The phylogenetic tree proposed has length of 27 steps and consistency index of 0.66. This phylogenetic hypothesis implies that the current genus Dugesia is paraphyletic and that its subgenera Girardia, Schmidiea and Dugesia S.S. should be elevated to the rank of genus. The genera Cura, Spathula and Neppia are presumed monophyletic by default because the database was unable to provide autapomorphies for any of these genera. The genera Dugesia S.S. and Neppia share sistergroup relationship. Several characters are discussed which were previously considered to be of phylogenetic importance but were not included in the present analysis. It is emphasized that sensory organs form potentially useful set of phylogenetic characters for the Dugesiidae.     

Phylogeny of the parasitic wasp subfamily Charipinae (Hymenoptera, Cynipoidea, Figitidae)

The Charipinae are a major group of hyperparasitoids of Hemiptera. Here, we present the first cladistic analysis of this subfamily's internal relationships, based on 96 morphological characters of adults. The data matrix was analysed using uniformly weighted parsimony. The effects of using alternative weighting schemes were explored by performing additional searches employing implied weights criteria. One of the caveats of implied weights analysis is that it lacks an objective criterion for selecting the value of the concavity function. In the present study, differential weighting was used to explore the sensitivity of our results to the alternative assumptions made in the analysis and to select one of the most parsimonious trees under equal weights, which we regard as being the hypothesis that minimizes the amount of ad hoc assumptions. The validity of the two existing tribes and the monophyly of all the genera of Charipinae were tested, in particular the cosmopolitan and highly species-rich Alloxysta and Phaenoglyphis , which appear repeatedly in ecological and biochemical studies of host–parasitoid associations. The evolution of several major characters and the relationships between genera are discussed. On the basis of the phylogenetic results, we discuss a number of taxonomic issues. A new classification of the subfamily is proposed in which no tribes are maintained, Carvercharips is synonymyzed with Alloxysta , and the creation of a new genus from Nepal is justified. Our analysis points to the need for a world revision of the basal genus Phaenoglyphis , which is shown as paraphyletic.     

On the structure of the aedeagus in shield bugs (Heteroptera, Pentatomidae): II. Subfamily Podopinae

This paper is the second communication in a series of papers that treats the structure of the aedeagus in the family Pentatomidae and its taxonomic applications. Inner structures of the aedeagus were examined in the completely inflated state. The structure of the aedeagus was studied on 25 species. It is impossible to offer a diagnosis of the subfamily Podopinae on the basis of the structure of the aedeagus only, because this structure is very diverse. Nevertheless, some distinguishing characters were found in each of the three tribes, currently recognized within the subfamily. On the basis of the structure of the aedeagus, the tribe Graphosomatini can be subdivided into four groups, partly corresponding to the previously recognized tribes Graphosomatini (sensu Puchkov, 1965), Ancyrosomatini, and Trigonosmatini. Three different types of the structure of the aedeagus were revealed in the tribe Podopini. Special types of the structure of the aedeagus were found in the genera Bolbocoris and Testrica with unclear taxonomic position.     

A molecular phylogeny of the Percidae (Teleostei, Perciformes) based on mitochondrial DNA sequence

The family Percidae is among the most speciose families of northern hemisphere fishes with > 178 178 North American species and 14 Eurasian species. Previous phylogenetic studies have been hampered by a lack of informative characters, inadequate taxonomic sampling, and conflicting data. We estimated phylogenetic relationships among 54 percid species (9 of 10 genera and all but one subgenus of darters) and four outgroup taxa using mitochondrial DNA data from the 12S rRNA and cytochrome b genes. Four primary evolutionary lineages were consistently recovered: Etheostomatinae (Ammocrypta, Crystallaria, Etheostoma, and Percina), Perca, Luciopercinae (Romanichthys, Sander, and Zingel), and Gymnocephalus. Except Etheostoma and Zingel, all polytypic genera were monophyletic. The Etheostoma subgenus Nothonotus failed to resolve with other members of the genus resulting in a paraphyletic Etheostoma. The subfamily Percinae (Gymnocephalus and Perca) was not recovered in phylogenetic analyses with Gymnocephalus sister to Luciopercinae. Etheostomatinae and Romanichthyini were never resolved as sister groups supporting convergent evolution as the cause of small, benthic, stream-inhabiting percids in North American and Eurasian waters.     

Evolution of avian plumage color in a tetrahedral color space: a phylogenetic analysis of new world buntings

We use a tetrahedral color space to describe and analyze male plumage color variation and evolution in a clade of New World buntings--Cyanocompsa and Passerina (Aves: Cardinalidae). The Goldsmith color space models the relative stimulation of the four retinal cones, using the integrals of the product of plumage reflectance spectra and cone sensitivity functions. A color is represented as a vector defined by the relative stimulation of the four cone types--ultraviolet, blue, green, and red. Color vectors are plotted in a tetrahedral, or quaternary, plot with the achromatic point at the origin and the ultraviolet/violet channel along the Z-axis. Each color vector is specified by the spherical coordinates theta, phi, and r. Hue is given by the angles theta and phi. Chroma is given by the magnitude of r, the distance from the achromatic origin. Color vectors of all distinct patches in a plumage characterize the plumage color phenotype. We describe the variation in color space occupancy of male bunting plumages, using various measures of color contrast, hue contrast and diversity, and chroma. Comparative phylogenetic analyses using linear parsimony (in MacClade) and generalized least squares (GLS) models (in CONTINUOUS) with a molecular phylogeny of the group document that plumage color evolution in the clade has been very dynamic. The single best-fit GLS evolutionary model of plumage color variation over the entire clade is a directional change model with no phylogenetic correlation among species. However, phylogenetic innovations in feather color production mechanisms--derived pheomelanin and carotenoid expression in two lineages--created new opportunities to colonize novel areas of color space and fostered the explosive differentiation in plumage color. Comparison of the tetrahedral color space of Goldsmith with that of Endler and Mielke demonstrates that both provide essentially identical results. Evolution of avian ultraviolet/violet opsin sensitivity in relation to chromatic experience is discussed.