Phylogenetic relationships in Magnoliaceae subfam. Magnolioideae: a morphological cladistic analysis

Relationships within Magnolioideae have been the subject of persistent debate; the main point at issue mostly being the disposition of tribes, genera and sections. A morphological cladistic analysis of the subfamily using Liriodendron as the out-group showed that Magnolioideae consisted of a large basal polytomy, but with five resolved and variously supported clades. Manglietia constituted a clade with sect. Rytidospermum of Magnolia subg. Magnolia. Kmeria and Woonyoungia formed a pair. Pachylarnax, Parakmeria and Manglietiastrum were grouped together, and sect. Splendentes and Dugandiodendron also formed a pair. The largest and best supported clade consisted of Magnolia subg. Magnolia sects. Oyama and Maingola, Magnolia subg. Yulania, Michelia, Aromadendron, Alcimandra, Elmerrillia, Paramichelia and Tsoongiodendron, with sect. Oyama of Magnolia subg. Magnolia is sister to the remainder. Although Magnolia sect. Maingola, Aromadendron, Alcimandra and Elmerrillia constituted a poorly resolved subclade, Aromadendron formed a monophyletic clade with Alcimandra. Within the Michelia/Magnolia subgen. Yulania subclade, Paramichelia was sister to Tsoongiodendron. These results are supported by similar placement of taxa within various molecular analyses of the family, but the low level of resolution indicates that more morphological data are needed to improve phylogenetic signal. Our results support the molecular analyses in suggesting that Magnolia is best considered to be a large and diverse genus, but that the relationships between the taxa within it require more detailed clarification, with more extensive sampling and a combined molecular and morphological approach being needed.     

Phylogenetic relationships of Lecythidaceae: a cladistic analysis using rbcL sequence and morphological data

This study examined in detail the rbcL sequence and morphological support for subfamilial relationships and monophyly of Lecythidaceae. Initially we needed to establish relationships of Lecythidaceae among other dicot families. To complete this we examined 47 rbcL sequences of 25 families along with molecular observations from several large analyses of rbcL data. All analyses strongly support the monophyly of the asterid III grouping. This analysis revealed Lecythidaceae to be paraphyletic and indicated potential outgroup relationships with Sapotaceae. Once relationships had been evaluated using molecular data we then concentrated on analyzing separate and combined morphological and molecular databases. The topology of the morphological data set was similar to the rbcL sequence and combined data sets except for the positioning of Napoleonaeoideae, Grias, Gustavia, and Oubanguia. According to the combined results, Planchonioideae, Lecythidoideae. and Foetidioideae are monophyletic, whereas the subfamily Napoleonaeoideae are paraphyletic. Nested within Napolconaeoideae, we found Asteronthos forms a strongly supported clade with Oubanguia (Scytopetalaceae). Foetidia, the only genus of Foetidioideae, is sister to Planchonioideae, and this clade is sister to Lecythidoideae. The [(Planchonioideae, Foetidioideae) Lecythidoideae are sister to Asteranthos/Oubanguia. Napoleonaeoideae are sister to the rest of Lecythidaceae.     

螟黄足盘绒茧蜂复合群支序系统学研究（膜翅目：茧蜂科：小腹茧蜂亚科）

对螟黄足盘绒茧蜂复合群Cotesia flavipes complex (膜翅目：茧蜂科：小腹茧蜂亚科)分布全世界的5个种和外群侧沟茧蜂Microplitis 及荻茧蜂Diolcogaster 的25个性状,以及复合群5个种和外群螟蛉盘绒茧蜂Cotesia ruficrus、粘虫盘绒茧蜂Cotesia kariyai、粉蝶盘绒茧蜂Cotesia glomerata 的24个性状,分别进行比较研究,并运用支序分析的方法探讨该复合群内5个种种间的系统发育关系。支序分析表明螟黄足盘绒茧蜂复合群是一单系群,二化螟盘绒茧蜂C. chilonis 和大螟盘绒茧蜂C. sesamiae 近缘,芦螟盘绒茧蜂C. chiloluteelli 和汉寿盘绒茧蜂C. hanshouensis 近缘,螟黄足盘绒茧蜂C. flavipes相对独立。 以上研究表明无论是以近缘属作外群还是以同属其它种作外群,所得结果基本上都能反映螟黄足盘绒茧蜂复合群各种之间的分类地位。     

Phylogenetic relationships among the phyllotini (rodentia: Sigmodontinae) using morphological characters

Thirty-three species representing all 14 genera of the South American rodent tribe Phyllotini and 5 problematic genera are surveyed for 96 multistate and binary dental, cranial, skeletal, external, and male reproductive tract characters. Wagner parsimony analysis confirmsCalomys as the most basal phyllotine genus, and as currently constituted it is likely paraphyletic. The results are consistent with the exclusion ofPseudoryzomys from the phyllotines and the separation ofReithrodon andNeotomys fromHolochilus at the tribal level. Several highly differentiated generic groups that include a radiation of altiplano endemics centered onAuliscomys and the largely southern Andean/PatagonianReithrodon group appear to form a clade. AGraomys generic group that includesAndalgalomys andEligmodontia is also apparent, but its relationships to other phyllotines are obscured by poorly resolved internal nodes in the more species-rich and probably paraphyletic genusPhyllotis. The significance and consequences of more intensive taxonomic sampling are discussed. The taxonomic consequences of the phylogeny are presented.     

Suprageneric relationships of galliform birds (Aves, Galliformes): a cladistic analysis of morphological characters

Of the basal clades of extant birds (Neornithes) the 'landfowl' or galliforms (Aves, Galliformes) are the most speciose. Cladistic analysis of more than 100 morphological characters coded at the generic level for most putative galliform genera confirms that the megapodes ('mound builders'; Megapodiidae) are the most basal clade within the order. They are followed successively by the curassows, guans and chachalacas (Cracidae), which comprise the sister-group to all other extant Galliformes (i.e. Phasianoidea). Within this large 'phasianoid' clade, analyses suggest that the guineafowl (Numididae) are the most basal taxon, although monophyly of this 'family' is not strictly supported on the basis of the morphological characters employed. An additional major clade within the phasianoid Galliformes is recovered by this analysis, comprising the traditional groupings of New World quails (Odontophoridae) and Old World quails ('Perdicini'), yet only monophyly of the former is supported unambiguously by morphological characters. Relationships within the remainder of the phasianoid taxa, including the grouse (Tetraonidae), turkeys (i.e. Meleagris / Agriocharus spp.) as well as other 'pavonine' galliforms (i.e. peafowl; Pavo , Afropavo , Rheinardia , Argusianus and Polyplectron spp.) remain largely unresolved on the basis of morphological characters, yet monophyly of the major subdivisions is supported here. Although there are a number of important differences, especially with regard to relationships within the nonquail phasianoids, the results of this morphological phylogenetic (cladistic) analysis are broadly congruent both with traditional classifications and existing molecular hypotheses of galliform phylogenetic relationships.     

The systematic relationships of glucosinolate-producing plants and related families: a cladistic investigation based on morphological and molecular characters

A cladistic analysis is performed using 94 morphological and biochemical characters for 42 genera to compare a phylogeny based on morphological data with those obtained using different genes ( rbc L, atp B, 18S RNA, mat K) or their combination with morphological data, and to understand the floral evolution within the expanded Brassicales (Capparales) relative to Sapindales and Malvales. The tree produced with morphological data is congruent with those obtained from macromolecular studies in obtaining a well-supported glucosinolate-producing clade and an expanded Sapindales. The combined analysis of the morphological and molecular characters is generally well resolved with support for many of the relationships. The inclusion of the fossil taxon Dressiantha demonstrates the value of inserting fossil evidence in phylogenetic analyses. However, the fossil appears to be related to the Anacardiaceae and not to the Brassicales. The core Brassicales are well supported by a number of synapomorphies, although the internal position of Tovariaceae and Pentadiplandraceae is not well resolved. Emblingiaceae appears to be related to Bataceae and Salvadoraceae. Several significant morphological characters are mapped on the combined trees and their evolutionary significance is discussed. Within Brassicales and Sapindales several well supported clades can be recognized which merit ordinal or subordinal status, putting the present orders at a higher level; these include: Tropaeolales, Setchellanthales, Batidales, Brassicales (Brassiciflorae), Burserales, Sapindales and Rutales (Sapindiflorae). The present scheme of affinities within the Brassicales corresponds well with a gradual morphological evolution in the order.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 453–494.     

Evolutionary relationships of euthyneuran gastropods (Mollusca): a cladistic re-evaluation of morphological characters

Morphological characters of the Euthyneura available from the literature were re-evaluated in terms of terminology and primary homology. A total of 77 characters and 75 taxa were retained in a data matrix. Several assumptions on character weights and types were tested. In the cladistic analyses, it appeared that the data matrix was highly homoplastic, and only robust nodes (those which were little modified by variations in weight and coding of characters) were retained in a concensus tree. The evolutionary histories of all characters and monophylies of higher euthyneuran taxa were discussed. The following interrelationships of the taxa were obtained in a consensus tree: the clade Heterobranchia includes paraphyletic allogastropod taxa which emerge basally, and the clade Euthyneura. The latter includes the clade Pulmonata and at least 10 opisthobranch clades of unresolved relationship (Thecosomata, Gymnosomata, Acochlidioidea, Pyramidelloidea, Runcinoidea, Cephalaspidea, Sacoglossa, Umbraculoidea, Pleurobranchoidea, Nudibranchia). The Pulmonata include basommatophoran paraphyletic taxa and the clade Geophila (Onchidiidae, Soleolifera, Stylommatophora). The position of the Sacoglossa and the monophyly of the Notaspidea are also discussed.  © 2002 The Linnean Society of London, Zoological Journal of the Linnean Society , 2002, 135 , 403–470.     

老鸦瓣属(百合科)的恢复: 以形态性状的分支分析为依据

老鸦瓣群(Amana群)是百合科中的一个东亚特有类群,仅分布在中国中东部、日本和朝鲜半岛。该类群在形态上与广义郁金香属Tulipa L.相似,但也具有与子房近等长的花柱以及2-3(-4)个苞片等与郁金香属不同的形态特征。有关该类群是否应置于郁金香属中或是否应独立为属的问题长期以来存在争议。为了澄清该问题,我们对产于中国的Amana群进行了广泛的标本室和野外形态观察,并采用分支系统学方法,对该类群3个种以及郁金香属的其他15种植物(包括土耳其的3个种)的28个形态性状数据进行了分支分析。结果表明广义郁金香属并非是一个单系类群。Amana群与广义郁金香属的其他4个组sect. Orithyia、sect. Eriostemones、sect. Leiostemones、sect. Tulipanum以及Lloydia属的两个种共同构成一个大支的3个分支。我们对广义郁金香属5个组共19种植物的ITS以及trnL-F分子序列综合分析的结果也表明：sect. Tulipanum、sect. Leiostemones、sect. Eriostemones和sect. Orithyia构成一大支,Amana群和猪牙花属的Erythronium sibiricum构成另一大支。因此,我们认为Amana群应从广义郁金香属中独立出来,恢复其老鸦瓣属Amana Honda作为属的分类地位。     

Phylogenetic relationships of Microdontinae (Diptera: Syrphidae) based on molecular and morphological characters

The intrasubfamilial classification of Microdontinae Rondani (Diptera: Syrphidae) has been a challenge: until recently more than 300 out of more than 400 valid species names were classified in Microdon Meigen. We present phylogenetic analyses of molecular and morphological characters (both separate and combined) of Microdontinae. The morphological dataset contains 174 characters, scored for 189 taxa (9 outgroup), representing all 43 presently recognized genera and several subgenera and species groups. The molecular dataset, representing 90 ingroup species of 28 genera, comprises sequences of five partitions in total from the mitochondrial gene COI and the nuclear ribosomal genes 18S and 28S. We test the sister‐group relationship of Spheginobaccha with the other Microdontinae, attempt to elucidate phylogenetic relationships within the Microdontinae and discuss uncertainties in the classification of Microdontinae. Trees based on molecular characters alone are poorly resolved, but combined data are better resolved. Support for many deeper nodes is low, and placement of such nodes differs between parsimony and Bayesian analyses. However, Spheginobaccha is recovered as highly supported sister group in both. Both analyses agree on the early branching of Mixogaster, Schizoceratomyia, Afromicrodon and Paramicrodon. The taxonomical rank in relation to the other Syrphidae is discussed briefly. An additional analysis based on morphological characters only, including all 189 taxa, used implied weighting. A range of weighting strengths (k‐values) is applied, chosen such that values of character fit of the resulting trees are divided into regular intervals. Results of this analysis are used for discussing the phylogenetic relationships of genera unrepresented in the molecular dataset.     

Phylogenetic relationships within Maldanidae (Capitellida,Annelida), based on morphological characters

The Maldanidae annelid worms are reviewed and the phylogenetic relationships of their subgroups provided, based on Hennigian principles and maximum parsimony. Characters were coded as binary and multistate (transformation series). We used 33 terminal taxa (species), and 50 characters. Characters were treated as unordered and of equal weight, and analysis was run in TNT. Three equally most-parsimonious trees were obtained with heuristic searches, with lengths of 64 steps; CI = 0.95, and RI = 0.98. The monophyly of Maldanidae was supported with 100% of bootstrap and jackknife values. As a result of our analysis, Arenicolidae remains the sister-group of Maldanidae, and both should be referred to Maldanomorpha. Maldanidae was supported by the following synapomorphies: dorsal prostomium; prostomium keel-shaped and fused to peristomium; torus globose behind median chaetigers; median chaetigers greatly elongated; number of pre-anal segments reduced. The subfamily Bogueinae was not monophyletic; Boguea and Boguella were included within Rhodininae. Clymenura, previously included in the Clymenurinae, was included within Euclymeninae. The taxa Notoproctinae, Maldaninae, Nicomachinae and Euclymeninae were grouped in the Maldanoplaca, a new taxon. Eight further new clades have been found, but were not named.     

Phylogenetic analysis of Eurytominae (Chalcidoidea: Eurytomidae) based on morphological characters

A phylogenetic study of the Eurytominae (Hymenoptera: Chalcidoidea) treating 178 taxa and based on 150 morphological characters is given. Several cladograms using the complete species sample, but obtained with different weightings, are presented. Local studies were also carried out to provide possible alternate topologies. The deep nodes of the trees were unstable and were never supported, but most of the superficial nodes were stable and robust. The results therefore provide support for a generic classification of the subfamily. The large genus Eurytoma– which includes about half of the described species of the subfamily – proved to be polyphyletic, and is redefined in a narrowed sense using putative synapomorphies. Bruchophagus and Prodecatoma were similarly redefined. The genera Philolema and Aximopsis are reconsidered and defined in a broader concept. A number of the species presently included in Eurytoma were transferred to these genera. Finally, 22 new generic synonymies are proposed and 33 species are transferred. The study also demonstrates that the Eurytomidae are polyphyletic. The results strongly support a sister‐group relationship between the Heimbrinae and the Chalcididae. The Rileyinae consist of two groups of unrelated taxa. A redefinition of the subfamily in a more restricted sense is supported by our results. The remaining group, consisting of the traditional Rileyinae, is included in the subfamily Buresiinae. Considered in this way they comprise the genera Buresium and Macrorileya, the latter being a senior synonym of Archirileya. The Buresiinae appear as the sister group of the Eurytominae. We propose to restrict the family Eurytomidae to these two taxa. This sister‐group relationship provides evidence to polarize the biological habits within Eurytominae. The common ancestor of Buresiinae is presumed to parasitize insects (mostly at the egg stage) living in grass stems. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 151 , 441–510.     

Phylogenetic relationships among the baleen whales based on maternally and paternally inherited characters

Phylogenetic relationships in the Cetacean suborder Mysticeti (baleen whales) have recently been the focus of increased attention. Here, we examine the evolutionary history of this group by comparing genealogies derived from Y chromosome and mitochondrial DNA sequences. We generated topologies based on paternally and maternally inherited characters for males from nine baleen whale species, including representatives of three families (Balaenidae, Eschrichtiidae, and Balaenopteridae) and four genera (Balaena, Eschrichtius, Balaenoptera, and Megaptera). Divergence among species was fifteen times greater for mtDNA than for Y-specific DNA. Both mtDNA and yDNA topologies revealed the family Balaenopteridae to be paraphyletic, but this relationship was neither strongly supported nor consistent across phylogenetic analysis methodologies. Humpback and fin whales, representing different genera, were reciprocally monophyletic sister species according to mtDNA. Although the monophyly of fin whales decayed for yDNA, a close relationship between fin and humpback whales was retained in yDNA trees. The paraphyly of fin whales and the long branch leading to humpback whales for the yDNA marker may suggest life history differences between these species. Specifically, male humpback whales showed higher than average divergence from other baleen whales at yDNA, although not at mtDNA, suggesting a potential for smaller effective population sizes among male humpbacks on an evolutionary timescale. The observation that those species that have been found to hybridize in nature (blue/fin and blue/humpback) do not reveal evidence for paraphyly for either maternal or paternal markers suggests that introgressive hybridization has not historically been extensive and thus may not represent a substantial source of phylogenetic error for Mysticeti.     

Phylogenetic relationships of ascomycetes and basidiomycetes based on comparative genomics analysis

The relationship between ascomycetes and basidiomycetes, the two main phyla of non-flagellated fungi, has rarely been investigated. In this study, we performed a comparative genomics analysis of genome sequences of 55 ascomycetes and 26 basidiomycetes species and detected 81 universal markers, 875 homologous genes and a conserved contig in the glucose-regulated protein gene. In dendrograms based on simple sequence repeat markers and homologous genes, ascomycetes and basidiomycetes formed distinct clusters, with each set of taxa having a high coefficient of relatedness. Ascomycetes and basidiomycetes also constituted distinct groups in a phylogenetic tree based on a conserved contig in the glucose-regulated protein gene. These results provide evidence that basidiomycetes may be derived from ascomycetes but are definitely genetically differentiated at the genomic level. The phylogenetic relationships of ascomycetes and basidiomycetes uncovered in this study provide new insights for future research related to fungal classification and evolution.     

Phylogenetic analysis of Anacaenini (Coleoptera: Hydrophilidae: Hydrophilinae) based on morphological characters of adults

Abstract.  The skeletal features of adults of fifty species of Anacaenini (Coleoptera: Hydrophilidae) and six outgroup taxa belonging to Hydrophilini and Laccobiini were examined. Eighty-one characters were selected and analysed cladistically. The resulting trees confirm the sister group relationship of Anacaenini and Laccobiini. Paracymus forms a clade within Laccobiini, as sister group of Oocyclus . Paranacaena is highly polyphyletic and, like Hebauerina , Grodum and Enigmata deeply nested within a complex formed mainly by Anacaena species ( Anacaena complex). The position of Gentilina remains ambiguous, but is also likely to be nested within this group. Notionotus is also part of this clade and clearly is monophyletic. Phelea , Crenitis and Notohydrus are distinctive groups which split off successively at the base of the Anacaena complex. On the basis of our results Enigmata Hansen ( syn.n. ), Gentilina Hebauer ( syn.n. ), Grodum Hansen ( syn.n. ) and Hebauerina Gentili ( syn.n. ) are synonymized with Anacaena Thomson.     

Phylogenetic relationships of the monozoic tapeworms (Eucestoda: Caryophyllidea) inferred from morphological characters

Phylogenetic relationships of all genera of the order Caryophyllidea, possibly the earliest branching group of true tapeworms (Platyhelminthes: Eucestoda) and the only one that is monozoic, have been assessed for the first time. Results of this cladistic analysis, inferred from 30 unweighted morphological characters, are only partly congruent with the existing classification, which consists of four families based on the position of the inner longitudinal muscles in relation to the internal genital organs. Whereas all but five genera of the Caryophyllaeidae form a monophyletic clade, members of the Capingentidae are split, occurring within six unrelated groups. The Lytocestidae is also paraphyletic, as some genera appear in four unrelated clades. Archigetes appears in a derived clade, indicating that its direct (monoxenous) life-cycle involving only tubificid oligochaetes is secondarily derived and not plesiomorphic among the Eucestoda, as postulated by some authors.     

Phylogenetic analysis of the genus Thricops Rondani (Diptera: Muscidae) based on molecular and morphological characters

Abstract. The muscid genus Thricops Rondani comprises forty‐four species and two subspecies restricted to the northern hemisphere. A species‐level phylogenetic analysis of Thricops was conducted using forty‐four morphological characters, 426 bp of the nuclear gene white and 523 bp spanning the 5′ end of the cytochrome c oxidase subunit I (COI), the tRNA leucine gene (L2 region) and the 3′ end of the cytochrome c oxidase subunit II (COII). Thirty‐nine species and two subspecies of Thricops were included in the analysis. Two species of Azelia Robineau‐Desvoidy and one species of Hydrotaea Robineau‐Desvoidy were used as outgroups. Morphological characters were coded for all included species, the mitochondrial gene fragment (COI + II) was sequenced for a subset of seventeen species of Thricops and three outgroup species, and white for twelve of those seventeen Thricops species and two outgroup species. Six separate maximum parsimony analyses were performed on three taxon sets of different sizes (n = 14, n = 20, n = 44). Results from the partition homogeneity test indicated no significant incongruence between data partitions, and four combined maximum parsimony analyses were conducted (DNA + morphology for n = 14; COI + II + morphology for n = 20; DNA + morphology for n = 20; DNA + morphology for n = 44). The relative contribution of each data partition to individual nodes was assessed using partitioned Bremer support. Strict consensus trees resulting from the unweighted analyses of each dataset are presented. Combination of datasets increased resolution for the small taxon set (n = 14), but not for the larger ones (n = 20, n = 44), most probably due to increasing amounts of missing data in the larger taxon sets. Results from both individual and combined analyses of the smaller taxon sets (n = 14, n = 20) provided support for the monophyly of Thricops and a complete division of the genus into two monophyletic subgroups. The strict consensus cladograms resulting from the analysis of the morphological data alone and the combined data for the large taxa set (n = 44) both supported the monophyly of the genus, but placed the species Thricops foveolatus (Zetterstedt) and Thricops bukowskii (Ringdahl) at the base of the ingroup, in a polytomy with a relatively well‐resolved branch comprising all remaining species of the genus. The basal position of these two species, included in the morphological taxon set but absent in the others, illustrates the potential pitfalls of taxon sampling and missing data in phylogenetic analyses. The synonymy of Alloeostylus with Thricops as proposed by previous authors was supported by our results. Relative contributions of different data partitions is discussed, with the mitochondrial sequence generally providing finer resolution and better branch support than white.     

Phylogenetic relationships of the Wolbachia of nematodes and arthropods

Wolbachia are well known as bacterial symbionts of arthropods, where they are reproductive parasites, but have also been described from nematode hosts, where the symbiotic interaction has features of mutualism. The majority of arthropod Wolbachia belong to clades A and B, while nematode Wolbachia mostly belong to clades C and D, but these relationships have been based on analysis of a small number of genes. To investigate the evolution and relationships of Wolbachia symbionts we have sequenced over 70 kb of the genome of wOvo, a Wolbachia from the human-parasitic nematode Onchocerca volvulus, and compared the genes identified to orthologues in other sequenced Wolbachia genomes. In comparisons of conserved local synteny, we find that wBm, from the nematode Brugia malayi, and wMel, from Drosophila melanogaster, are more similar to each other than either is to wOvo. Phylogenetic analysis of the protein-coding and ribosomal RNA genes on the sequenced fragments supports reciprocal monophyly of nematode and arthropod Wolbachia. The nematode Wolbachia did not arise from within the A clade of arthropod Wolbachia, and the root of the Wolbachia clade lies between the nematode and arthropod symbionts. Using the wOvo sequence, we identified a lateral transfer event whereby segments of the Wolbachia genome were inserted into the Onchocerca nuclear genome. This event predated the separation of the human parasite O. volvulus from its cattle-parasitic sister species, O. ochengi. The long association between filarial nematodes and Wolbachia symbionts may permit more frequent genetic exchange between their genomes.