Phylogenetic analysis of the Malvadendrina clade (Malvaceae s.l.) based on plastid DNA sequences

Phylogenetic relationships within Malvaceae s.l., a clade that includes the traditional families Bombacaceae, Malvaceae s.str., Sterculiaceae, and Tiliaceae, have become greatly clarified thanks to recent molecular systematic research. In this paper, we use DNA sequences of four plastid regions (atpB, matK, ndhF, and rbcL) to study relationships within Malvadendrina, one of the two major clades of Malvaceae s.l. The four data sets were generally in agreement, but five terminal taxa manifested highly unexpected affinities in the rbcL partition, and the non-coding sequences of the trnK intron were found to provide limited phylogenetic information for resolving relationships at the base of Malvadendrina. The remaining data strongly support the existence of six major clades within Malvadendrina: Brownlowioideae, Dombeyoideae, Helicteroideae, Malvatheca (comprising Bombacoideae and Malvoideae), Sterculioideae, and Tilioideae. These data also resolve the placement of two problematic taxa: Nesogordonia (in Dombeyoideae) and Mortoniodendron (in Tilioideae). The relationships among the six clades are not definitively resolved, but the best-supported topology has Dombeyoideae as sister to the remainder of Malvadendrina (posterior probability PP=80%) and Sterculioideae as sister to Malvatheca (PP=86%). This early branching position of Dombeyoideae is supported by similarities in floral characters between members of that clade and outgroup taxa in Byttnerioideae. Similarly, the sister-group relationship of Sterculioideae and Malvatheca receives support from androecial characteristics, like subsessile or sessile anthers and an absence of staminodes, shared by these two clades.     

Phylogeny of the core Malvales: evidence from ndhF sequence data

The monophyly of the group comprising the core malvalean families, Bombacaceae, Malvaceae, Sterculiaceae, and Tiliaceae, was recently confirmed by molecular studies, but the internal structure of this clade is poorly understood. In this study, we examined sequences of the chloroplast ndhF gene (aligned length 2226 bp) from 70 exemplars representing 35 of the 39 putative tribes of core Malvales. The monophyly of one traditional family, the Malvaceae, was supported in the trees resulting from these data, but the other three families, as traditionally circumscribed, are nonmonophyletic. In addition, the following relationships were well supported: (1) a clade, /Malvatheca, consisting of traditional Malvaceae and Bombacaceae (except some members of tribe Durioneae), plus Fremontodendron and Chiranthodendron, which are usually treated as Sterculiaceae; (2) a clade, /Malvadendrina, supported by a unique 21-bp (base pair) deletion and consisting of /Malvatheca, plus five additional subclades, including representatives of Sterculiaceae and Tiliaceae, and Durionieae; (3) a clade, /Byttneriina, with genera traditionally assigned to several tribes of Tiliaceae, plus exemplars of tribes Byttnerieae, Hermannieae, and Lasiopetaleae of Sterculiaceae. The most striking departures from traditional classifications are the following: Durio and relatives appear to be more closely related to Helicteres and Reevesia (Sterculiaceae) than to Bombacaceae; several genera traditionally considered as Bombacaceae (Camptostemon, Matisia, Phragmotheca, and Quararibea) or Sterculiaceae (Chiranthodendron and Fremontodendron) appear as sister lineages to the traditional Malvaceae; the traditional tribe Helictereae (Sterculiaceae) is polyphyletic; and Sterculiaceae and Tiliaceae, as traditionally circumscribed, represent polyphyletic groups that cannot sensibly be maintained with their traditional limits for purposes of classification. We discuss morphological characters and conclude that there has been extensive homoplasy in characters previously used to delineate major taxonomic groups in core Malvales. The topologies here also suggest that /Malvatheca do not have as a synapormophy monothecate anthers, as has been previously supposed but, instead, may be united by dithecate, transversely septate (polysporangiate) anthers, as found in basal members of both /Bombacoideae and /Malvoideae. Thus, “monothecate” anthers may have been derived at least twice, independently, within the /Bombacoideae (core Bombacaceae) and /Malvoideae (traditional Malvaceae).     

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.     

Relationships, classification and evolution of Scleranthus (Caryophyllaceae) as inferred from analysis of morphological characters

Study of floral anatomy, micromorphology, palynology and onotogeny has revealed new characters for phylogenetic analysis in the genus Scleranthus . Cladistic analysis of these characters, along with those previously available, suggests that the genus consists of Eurasian/Mediterranean and Australasian sister clades. Gynoecial morphology and development are closely similar in all species, suggesting the genus is monophyletic despite its disjunct northern and southern hemisphere distribution. Variation in pollen:ovule ratios and their implications for the evolution of Scleranthus species are also discussed and it is concluded that a range of breeding strategies intermediate between autogamy and xenogamy exists in the genus. Single-stamened species of Scleranthus are likely to be obligate autogams, despite their comparatively high pollen:ovule ratios in relation to autogamic species of other genera.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 15–29.     

Evolution of metatherian and eutherian (mammalian) characters: a review based on cladistic methodology

Cladistic methodology is used to test the hypothesis that three major monophyletic groups exist among living mammals–the oviparous monotremes (Prototheria), and the viviparous marsupials (Metatheria) and placentals (Eutheria). Evaluation is made of the polarity (i.e. the direction of change in a primitive-to-derived sequence) of numerous characters which distinguish some or all of these groups, and of the usefulness of these characters in phylogenetic inference. An attempt is made to establish the state of these characters in the common Late Jurassic-Early Cretaceous therian ancestor of marsupials and placentals.
It is concluded that the most basic division of the Mammalia is the dichotomy into the subclasses Prototheria (including Monotremata, Multituberculata, Triconodonta, Docodonta) and Theria (including Metatheria, Eutheria, Pantotheria and Symmetrodonta). Two major groups exist among living viviparous mammals, the Metatheria and Eutheria; in a cladistic framework these are sister-groups. It is demonstrated that there is no special (sister-group) relationship between monotremes and marsupials, and there is no justification for placing them in a group Marsupionta.     

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.     

A cladistic analysis of Asarum (Aristolochiaceae) and implications for the evolution of herkogamy

A cladistic analysis of Asarum was conducted to examine relationships among species within the genus and to test the monophyly of several groups of taxa that have often been treated as segregate genera. Thirty-two species were drawn from throughout the range of the genus, representing a broad sample of sections and all segregate genera. The data matrix included 37 characters derived from various aspects of vegetative and floral morphology. A strict consensus of all most parsimonious trees suggests that Asarum s.l. is monophyletic and consists of two main clades: an Asarum clade, which is characterized by connate styles and inferior ovaries, and an Asiasarum-Hexastylis-Heterotropa clade, which is characterized by ridges on the inner perianth surface, dorsal stigmas, and bifid style extensions. The latter is a large and morphologically diverse clade that includes the North American segregate Hexastylis and two Asiatic segregates. Examination of pollination mechanisms in the context of this phylogeny supports the conclusion that herkogamy, and thus obligate insect pollination, is derived from a plesiomorphic condition of autonomous self-pollination. Associated with herkogamy are characters such as glandular trichomes and other ornamentation of the surface of the calyx that probably represent increased specialization to attract insect pollinators. This study also indicates that chromosomal evolution has occurred via aneuploid decrease from an ancestral chromosome number of 2n = 26 to 2n = 24 in Heterotropa. The recognition of two subgenera, subgenus Asarum and subgenus Heterotropa, corresponding to the two clades in the cladistic analysis, is recommended.     

Macrodasyida (Gastrotricha): a cladistic analysis of morphology

Abstract. A cladistic analysis based on 33 morphological characters was performed for the 31 genera currently assigned to the order Macrodasyida (Gastrotricha). Outgroup analysis indicated that the order is monophyletic and that it is defined by the structure of the pharynx and the complex distribution of duo-gland adhesive organs. Of the 6 currently recognized families in Macrodasyida, our analysis confirmed that 4 families are monophyletic: Dactylopodolidae, Macrodasyidae, Thaumastodermatidae and Turbanellidae. Dactylopodolidae was further confirmed as the most basal family within the order based on the retention of several plesiomorphies. The other three families have well-defined autapomorphies but will require further investigation to increase inter- and intrafamilial phylogenetic resolution. Planodasyidae appeared to be a paraphyletic taxon with no obvious autapomorphies; genera clustered among members of a polyphyletic family, Lepidodasyidae. We recommend that future research on macrodasyidan phylogeny focus on issues of comparative morphology and ultrastructure in lesser-known taxa such as the Dactylopodolidae, and on the taxa Lepidodasyidae and Planodasyidae.     

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.     

Cotylea (Polycladida): a cladistic analysis of morphology

Abstract. Polyclad flatworms are acoelomate bilaterians found in benthic communities worldwide, predominantly in marine environments. Current polyclad systematics is unstable, with two non-concordant classification schemes resulting in a poor understanding of within-group relationships. Here we present the first phylogenetic framework for the suborder Cotylea using a morphological matrix. Representatives of 34 genera distributed among all cotylean families (except four, excluded due to their dubious taxonomic status) were investigated. The number of families included ranges from a conservative eight to a revisionary 11. Outgroup analysis indicated that the suborder is monophyletic and defined by the presence of a ventral adhesive structure, a short posteriorly positioned vagina, and cement glands. Of the eight to 11 families included, we confirmed that three were monophyletic: Boniniidae, Prosthiostomidae, and Pseudocerotidae. Boniniidae was consistently recovered as the sister group to other Cotylea, based on the retention of the plesiomorphic Lang's vesicle. The clade consisting of Anonymus, Marcusia , and Pericelis is sister to the Boniniidae and the rest of the Cotylea. Above this clade there is little resolution at the base of the sister group. The Euryleptidae are found to be paraphyletic and give rise to the Pseudocerotidae. Neither classification scheme received unequivocal support. The intrafamilial relationships of the diverse Pseudocerotidae and Euryleptidae were examined. Color pattern characters (used for species identification) were highly homoplasious but increased cladogram resolution within genera. The monophyly of seven genera within the Pseudocerotidae and Euryleptidae was not supported and many genera showed no autapomorphies, highlighting the need for taxonomic revision of these families.     

Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics

The schizomid genus Mayazomus Reddell & Cockendolpher, 1995, endemic to south‐eastern Mexico, currently comprises seven species. It was originally proposed to accommodate two species, from Chiapas and Tabasco. Recently, five additional species from Chiapas were described. The monophyly of the genus has never been tested using cladistic analysis. We undertook a phylogenetic analysis using the seven described species of Mayazomus as the ingroup, ten exemplar species representing the most similar New World hubbardiids as the outgroup, and one protoschizomid species to root the tree. The analysis was based on 130 morphological characters (continuous and discrete characters). The resulting topologies recovered Mayazomus as paraphyletic, with Heteronochrus estor Armas & Viquez, 2010, from Guatemala nested within the genus; therefore, we formally propose its synonymy herein. Mayazomus appears to be most closely related to Rowlandius Reddell & Cokendolpher, 1995, a South American genus. This contribution also provides new characters derived from the pedipalp setae with important phylogenetic information; as well as the implementation of morphometric ratios, as continuous characters, to partially codify the shape of the male flagellum. The relationships recovered amongst the outgroups used in this contribution are a reliable baseline for future analyses of the phylogeny of the New World schizomids.     

Taxonomic characters of the staminal tube and epicalyx in Brazilian Pavonia (Malvaceae)

This study was based on the analysis of staminal tube and epicalyx morphology of species ofPavonia (Malvaceae) from northeastern and southeastern Brazil. The importance of characters in the infrageneric taxonomy is discussed. In general, the variability in staminal tube and epicalyx characters are useful mainly in separating closely related species and a few sections; these characters, however, cannot be used to separate subgenera.     

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.     

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。     

Perenniporia cinereofusca sp. nov. (Polyporales,Basidiomycota) evidenced by morphological characters and phylogenetic analysis

A new Perenniporia species, P. cinereofusca, is described based on morphological and molecular characters. It is characterized by an annual growth habit, resupinate basidiocarps with gray to pale brown pore surface, tissues becoming black in 5% potassium hydroxide (KOH), a dimitic hyphal system with weakly dextrinoid skeletal hyphae and hyaline to pale yellowish, distinctly thick-walled and indextrinoid basidiospores (6.5–7.7 × 5.3–6.3 μm), and presence of dendrohyphidia and large rhomboid crystals. Both morphological and molecular evidence confirmed the placement of the new species in Perenniporia sensu stricto and showed its relationships with similar species in the genus.     

Rusts (Uredinales) of Triticeae: evolution and extent of coevolution, a cladistic analysis

BAUM, B. R. & SAVILE, D. B. O., 1985. Rusts (Uredinales) of Triticeae: evolution and extent of coevolution, a cladistic analysis. Established evolutionary trends in Uredinales as a whole are reviewed, and primitive and advanced characters are presented. The rusts of all Poaceae arc presented in a table that strongly indicates Bambusoideae to be the oldest and Pooideae the youngest subfamily. The rusts of Triticeae and their ecogeography are outlined; the rusts of Cyperaceae, selected as an out-group, are beiefly summarized; and the available characters and character states for rusts of Triticeae are given. Host alternation complicates the analysis. The aerial host (never a grass) is ecologically associated with the unrelated telial (grass) host. There are no appropriate methods to permit analysis of the combined components: aecial host evolution, telial host evolution, rust evolution, and their coevolution. Also, several aecial hosts are unknown. Consequently it was necessary to omit aecial hosts from the analysis. Cladistic analysis of the rusts of Triticeae was performed using five methods and consisted of cycles of tree analysis and modification of character state trees. A cladogram put together from a Dollo and a Wagner cladogram was used as a basis for the classification of rusts given. Subsequently a cladistic analysis of genera of Triticeae, using presence/absence of rusts as characters (Brooks' approach) was performed. The Triticeae cladogram of Baum (1983) was also analysed. Distances between the cladogram generated by various methods and that of Baum were computed for each possible pair, using the method of Robinson & Foulds, and then the resulting distance matrix was reduced in dimensionality by principal components and non-metric multidimensional scaling. The results are discussed in light of the limitation of the analyses and the data. It is concluded that coevolution is limited and that frequent jumps to ecologically associated hosts explain the parallelism in evolution of rusts on Triticeae.     

Phylogenetic relationships in the tribe Oxyptilini (Lepidoptera,Pterophoridae, Pterophorinae) based on morphological data of adults

The monophyly of the tribe Oxyptilini and phylogenetic relationships of the genera embraced in this tribe were examined using 171 (75 binary and 96 multistate) characters of adult morphology. The study material included 98 species of 30 genera, representing all previously recognized genera of Oxyptilini, together with the genera Sphenarches, Antarches, Diacrotricha, and Cosmoclostis, four species of Oidaematophorini, three species of Platyptiliini, as well as three and two other species belonging to Pterophorini and Exelastini respectively. Two Agdistis species were used as outgroups. The cladistic analysis resulted in six equally parsimonious trees. A majority of the recovered synapomorphic characters have previously been used in the taxonomy of the subfamily. However, 25 novel characters were found. The monophyly of Oxyptilini was supported, although only with homoplastic characters and low amounts of tree confidence; the genera Capperia, Procapperia, Paracapperia, Oxyptilus, Megalorhipida, and Trichoptilus were found to be nonmonophyletic; Sphenarches and Antarches were recovered as members of Oxyptilini; the two genera Cosmoclostis and Diacrotricha were placed out of Oxyptilini, inside the tribe Pterophorini; and close affinity of the genus Dejongia to Stangeia, Stenodacma, Megalorhipida, Trichoptilus, and Buckleria species was revealed. Four new combinations, Cosmoclostis lanceata (Arenberger) comb. nov. , Nippoptilia regulus (Meyrick) comb. nov. , Capperia tadzhica (Zagulajev) comb. nov. , and Buckleria negotiosus (Meyrick) comb. nov. are proposed; Capperia insomnis Townsend was considered as a senior synonym of Procapperia hackeri Arenberger syn. nov. , Buckleria negotiosus (Meyrick) as a senior synonym of Buckleria vanderwolfi Gielis syn. nov. , and Oxyptilus variegatus Meyrick syn. nov. as a junior synonym of Oxyptilus secutor Meyrick. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 484–547.     

The relative lability of floral vs. non-floral characters and a morphological phylogenetic analysis of Cobaea (Polemoniaceae)

The relative levels of lability in floral vs. vegetative characters have been suggested to give insight into the mechanisms of adaptation and speciation. Cobaea (Polemoniaceae) exhibits a remarkable diversity in floral form. A morphology-based phylogeny was constructed and is congruent in most regards with a previously published molecular phylogeny, but significant incongruence was found in the placement of two taxa. A combined analysis was performed, excluding C. aquatoriensis and C. lutea, and was nearly identical to the molecular analysis. The phylogenies are compatible with a recently published classification. Incongruencies between the phylogenies within section Rosenbergia may have profound implications for floral evolution. A simple method for testing the levels of homoplasy, as an indicator of lability between two classes of data, is developed and used to test for differences between floral and non-floral classes of characters. The method is based on repeated randomization of the data into partitions and recalculation of a test statistic defined as the difference between consistency index (CI) values of the data in each partition over a given tree. The null hypothesis that the floral characters are no more homoplasious than the non-floral characters cannot be rejected (P=0.09).