Systematics of the tribe Podalyrieae (Fabaceae) based on DNA, morphological and chemical data

Phylogenetic relationships among nine genera and 28 species of the southern African tribe Podalyrieae were estimated from sequences of the internal transcribed spacer (ITS) of nuclear ribosomal DNA as well as morphological and chemical data. Morphological and ITS sequence data produced cladograms with similar topologies, both supporting the monophyly of Podalyrieae (excluding Hypocalyptus ). The combined data sets indicate that subtribe Xiphothecinae are monophyletic, but embedded within Podalyriinae. The high degree of congruence between previous taxonomic hypotheses and those based on DNA data provides further evidence for the utility of ITS sequences in studying phylogeny.  © 2002 The Linnean Society of London , Botanical Journal of the Linnean Society , 2002, 139 , 159–170.     

A species complex within the isopod genus Haploniscus (Crustacea: Malacostraca: Peracarida) from the Southern Ocean deep sea: a morphological and molecular approach

Seven new species of the genus Haploniscus from the deep Scotia and Weddell Seas are presented, combining morphological and molecular data (mitochondrial 16S rDNA and nuclear 18S rDNA). Haploniscus cassilatus sp. nov. , H. cucullus sp. nov. , H. weddellensis sp. nov. , H. procerus sp. nov. and H. kyrbasia sp. nov. are characterized by a prominent rostral process, the size and shape of which vary among species. The rostrum of H. microkorys sp. nov. is distinctly smaller than that of the former species, while H. nudifrons sp. nov. does not possess a rostrum. The status of the latter as separate species is obvious, owing to the stronger morphological differences. DNA was sequenced from three of the other five species. Genetic distances together with the more subtle morphological variation justify the erection of separate species. Overall morphological variations between these species are small yet noticeable and include, among others, the rostrum, the shape of the pleotelson and setation of pereopods. Our molecular data sets reveal detailed phylogenetic insights within the Haploniscus cucullus complex, supporting the monophyly of all species. We found p -distances of at least 0.0732 (16S rDNA) and 0.0140 (complete 18S rDNA) between pairs of species and show that both genes can be used as a marker for DNA taxonomy.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 655–706.     

On the monophyly of Dactylorhiza Necker ex Nevski (Orchidaceae): is Coeloglossum viride (L.) Hartman a Dactylorhiza?

Previous phylogenetic analyses of Orchidaceae subtribe Orchidinae resulted in the proposal to classify Coeloglossum viride (L.) Hartman within the genus Dactylorhiza in order to maintain its monophyly. In this paper, we report some results that contradict previous studies regarding the monophyly of the traditional Dactylorhiza and its phylogenetic relationship with Coeloglossum. Our results, which combine sequences of the internal and external transcribed spacers of the nuclear ribosomal DNA, support the monophyly of Dactylorhiza , with Coeloglossum being a sister clade. The position of C. viride in the phylogenetic tree, and the considerable morphological differences with respect to Dactylorhiza , incline us to retain both lineages as distinct genera.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 152 , 261–269.     

A revised classification of subtribe Helianthinae (Asteraceae: Heliantheae). I. Basal lineages

Results for nuclear ITS sequences were combined with previously obtained data from cpDNA restriction site studies to provide a comprehensive molecular phylogeny for subtribe Helianthinae. Results from the two molecular data sets were mostly congruent for basally diverging branches of the subtribe. Based on the results, combined with morphological observations, the basally diverging branches are placed in six genera, including one newly described. Bahiopsis is resurrected to accommodate species previously placed in Viguiera subgenus Bahiopsis . Calanticaria is newly proposed for the five species of Viguiera ser. Brevifolieae . Heliomeris is retained for the group sometimes included within Viguiera as sect. Heliomeris . Hymenostephium is revived and enlarged to include a number of species of similar habit and involucre, including members of Viguiera sect. Diplostichis , Haploca-lymma and Garcilassa . Although cpDNA results place the morphologically distinctive Sclerocarpus within the clade including species of Hymenostephium , the ITS data were consistent with morphology in suggesting it to be a distinctive lineage.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 65–76.     

A revision of the assassin spiders of the Eriauchenius gracilicollis group, a clade of spiders endemic to Madagascar (Araneae: Archaeidae)

An endemic group of Malagasy spiders (Araneae: Archaeidae: Eriauchenius ) called the gracilicollis group is revised. The monophyly and phylogenetic relationships of the gracilicollis group are tested based on morphological characters. Archaeid spiders of Madagascar have evolved varying degrees of elongation in the cephalic area. Historically, it was believed that the extremely elongated cephalic area had evolved only once. These morphological data support the monophyly of the gracilicollis group and suggest that the elongated cephalic area has evolved more than once. All 14 species from the gracilicollis group are described and keyed, of which nine are new species: Eriauchenius ambre sp. nov. , Eriauchenius anabohazo sp. nov. , Eriauchenius borimontsina sp. nov. , Eriauchenius griswoldi sp. nov. , Eriauchenius halambohitra sp. nov. , Eriauchenius lavatenda sp. nov. , Eriauchenius namoroka sp. nov. , Eriauchenius spiceri sp. nov. and Eriauchenius voronakely sp. nov . The morphology of the gracilicollis group is examined in detail and figures of the male and female genitalia are presented. The distributions of the gracilicollis group species are presented and discussed and higher species group relationships within the Archaeidae are discussed.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 255–296.     

Molecular phylogenetic interrelationships of the south Asian cyprinid genera Danio, Devario and Microrasbora (Teleostei, Cyprinidae, Danioninae)

Molecular analysis of mitochondrial cytochrome b sequences from 159 species of the family Cyprinidae supports the subfamily Danioninae, of which Rasborinae is shown to be a junior synonym. Analysis of combined cytochrome b and a fragment of the nuclear rhodopsin gene from 68 species, including 43 species representing the subfamily Danioninae, supports phylogenetic distinctness of Danio and Devario. In the combined molecular analysis Microrasbora rubescens, Chela, Laubuca, Devario, and Inlecypris form a clade with M. gatesi , M. nana and M. kubotai being in sister group position to the rest. The sister group of this Devario clade is Danio . Inlecypris is synonymized with Devario. Microdevario, new genus, is proposed for M. gatesi , M. nana and M. kubotai , supported by morphological characters. In the cytochrome b analysis, M. rubescens falls outside Devario , and there is no morphological support for including M. rubescens in Devario . In the cytochrome b analysis Esomus  +  Danionella is the sister group of Danio and Devario clades, whereas in individual rhodopsin and combined analyses Esomus is the sister group of Danio , and of Danio and the Devario clade, respectively. Sundadanio presents at least one strong morphological synapomorphy with Danio , but is positioned in molecular trees either as a member of the Cyprininae or as sister group of the remaining Danioninae. In the morphological analysis, small-sized species grouped together based on shared reductions that are not necessarily synapomorphies. In the molecular analysis, small-sized species such as Danionella and Sundadanio possess long branches and their position varies, but they did not group together. This suggests morphological homoplasy, but phylogenetic positions are not well supported in the molecular analyses     

Phylogenetic analysis of non-stereotyped behavioural sequences with a successive event-pairing method

A new method is proposed which uses transitions among acts in non-stereotyped behavioural sequences as phylogenetic characters. This method is derived from the event-pairing method designed for the phylogenetic study of developmental sequences and from ethological analyses of transition matrices. It is applied to study the phylogenetic relationships within a well-known group, the presocial Zetoborinae cockroaches. The analysis is carried out with three data sets: a behavioural data set with transitions among acts in behavioural dyadic sequences, together with morphological and molecular data sets. Non-stereotyped behaviour proved to be phylogenetically informative and to display low homoplasy. This new method opens an avenue for studying the evolution of behaviour in the framework of phylogenetic analysis, which was restricted until now to the study of stereotyped sequences and/or isolated features involved in courting or building activities.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 853–867.     

Systematics and biogeography of the New World species of Trichadenotecnum Enderlein (Insecta: Psocodea: 'Psocoptera': Psocidae)

The taxonomy of the New World species of the genus Trichadenotecnum is revised. A total of 44 species, including 29 new species, were treated. These species are classified into 12 monophyletic species groups, eight of them newly proposed here. Two species previously assigned to Trichadenotecnum , T. pichincha New & Thornton and T. sylvaticum Turner, are recognized as not belonging to this genus. Phylogenetic relationships among 16 previously and presently proposed species groups are estimated based on a data matrix of 58 morphological characters. Trees from these analyses support monophyly of Trichadenotecnum and the proposed species groups. The New World species were divided into three major clades. Based on the phylogenetic hypothesis and distributional pattern of the species groups, the biogeographical history of the New World Trichadenotecnum is discussed.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 651–723.     

Systematics and evolutionary relationships of the mountain lizard Liolaemus monticola (Liolaemini): how morphological and molecular evidence contributes to reveal hidden species diversity

The delimitation of species is a major issue in systematic biology and has been a re-emerging discipline in the last decade. A number of studies have shown that the use of multiple data sets is critical for the identification of cryptic species, particularly in groups with complex evolutionary histories. Liolaemus monticola is a montane lizard species distributed in central Chile (32°–42°S), with four described subspecies in a latitudinal gradient from north to south: L. m. monticola , L. m. chillanensis , L. monticola ssp. and L. m. villaricensis . In order to test the systematic status and phylogenetic relationships of the taxa included in the L. monticola group, we analysed morphological (morphometric and meristic) and molecular (allozyme and mitochondrial DNA) data sets. The results of the morphological analyses showed that meristic variables correctly assigned individuals with higher accuracy than did morphometric characters. The results of the analyses of allozyme data revealed eight diagnostic loci that are evidence for significant differences among the four L. monticola subspecies. Phylogenetic analyses with mitochondrial DNA data, including additional species, showed that the L. monticola group is polyphyletic. We postulate that the four current subspecies represent independent evolutionary lineages and must be raised to the specific level as L. monticola , L. chillanensis and L. villaricensis . The taxonomic status of the unnamed L. monticola ssp. remains unresolved, although we provide a preliminary proposal.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 635–650.     

Adaptive modifications of carapace outlines in the Cytheroidea (Ostracoda: Crustacea)

Shell outlines of 202 extant cytheroidean ostracods were analysed in dorsal, lateral, and posterior views by elliptic Fourier analysis. The results obtained confirm that the exterior morphology is related to ecological factors as well as phylogenetic constraints. Phytal species living on tall seagrass and benthic species burrowing in sediments are characterized and differentiated from the species crawling on sediments by the presence of slender shells with tapered venters. With reference to reconstruction of ancestral state of outline traits on the molecular phylogeny, the hypothetical ancestor of cytheroidean ostracods is presumed to have had an average-shaped shell. Morphological plasticity of the shell outline was observed in many families. The phytal species living on tall seagrass appear to have evolved convergently with species from other habitats, acquiring slim shell outlines during the Cenozoic period. The present analysis also reveals the phylogenetic constraints on the morphological evolution of the Trachyleberididae in their adaptation to a burrowing habit.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 810–821.     

Phylogenetic relationships of thorny catfishes (Siluriformes: Doradidae) inferred from molecular and morphological data

Doradidae is a putatively monophyletic group of South American freshwater catfishes containing 30 extant genera and 72 valid species. Only one study to date has attempted to estimate phylogenetic relationships among doradids. This morphological analysis partitioned species into two basal genera ( Wertheimeria and Francisodoras ) and a crown group of three subfamilies (Platydoradinae, Astrodoradinae and Doradinae) whose relationships were unresolved. No subsequent work has been done to resolve the subfamilial trichotomy or to assess whether postulated intergeneric relationships are accurate. We address this problem with complete sequences (2.5 kilobases, kb) of mitochondrial 12S and 16S rRNA genes and partial (1.3 kb) sequences of the nuclear elongation factor-1 alpha (EF1α) gene from representatives of 23 doradid genera (43 species) and 13 outgroups from additional siluriform families. Phylogenetic analysis of these data yields strong support for the monophyly of Doradidae and Astrodoradinae (as well as other relationships), but otherwise shows significant conflict with morphological results. A partial re-examination of published morphological data indicates that many characters may have been incorrectly polarized and many taxa have incorrect state assignments. Our results provide a framework for ongoing efforts to describe the species-level diversity of this poorly understood neotropical family.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 551–575.     

Two new basal crocodylomorph archosaurs from the Lower Jurassic and the monophyly of the Sphenosuchia

We report on and name two new taxa of basal crocodylomorph archosaurs from the Lower Jurassic, Litargosuchus leptorhynchus gen. et sp. nov. , from the upper Elliot Formation (Stormberg Group) of South Africa, and Kayentasuchus walkeri gen. et sp. nov. , from the Kayenta Formation (Glen Canyon Group) of Arizona, USA. Examination of this material led to a reconsideration of basal crocodylomorph interrelationships. A phylogenetic analysis found no support for the monophyly of Sphenosuchia.  © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society , 2002, 136 , 77–95.     

Phylogenetic relationships, taxonomy, character evolution and biogeography of the lacertid lizards of the genus Takydromus (Reptilia: Squamata): a molecular perspective

Historical relationships were inferred for the oriental lizards of the genus Takydromus Daudin 1802 (Lacertidae) on the basis of DNA sequences. Of the 17 species currently recognized for the genus, 13 species represented by 42 specimens from 29 localities were examined. Maximum-likelihood and maximum-parsimony analyses of data for 829 aligned sites from parts of the mitochondrial 12S and 16S rRNA genes yielded relationships that, while showing no substantial discrepancy with each other, were strikingly different from a currently prevailing phylogenetic hypothesis from a parsimony analysis of morphological characters. Based on the results of these molecular analyses, supplemented by results of the morphological analysis that offered robust evidence for positions of two additional species ( T. khasiensis and T. sylvaticus ), the following interrelationships were hypothesized as the most preferred phylogeny: ( kuehnei ( sexlineatus khasiensis ))( tachydromoides (( smaragdinus ( sauteri ( dorsalis sylvaticus ))) ( amurensis ((( formosanus wolteri ) hsuehshanensis )( toyamai ( septentrionalis stejnegeri )))))). These interrelationships indicate: (1) invalidity of Platyplacopus Boulenger 1917 , which was recently resurrected as a subgenus of Takydromus on the basis of the morphological analysis; (2) homoplasy in states of some morphological characters, such as green dorsal coloration, that were considered as synapomorphs of certain nodes in the morphological analysis; and (3) involvement of the genus in a series of vicariances in both the continental and insular parts of eastern Eurasia. Due to the paucity of available samples, phylogenetic status of T. intermedius and T. haughtonianus remain to be examined in future studies.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 76 , 493–509.     

Monophyly and phylogenetic placement of the spider genus Labulla Simon, 1884 (Araneae, Linyphiidae) and description of the new genus Pecado

The genus Labulla Simon is circumscribed in phylogenetic terms to include the species Labulla thoracica (Wider), L. flahaulti Simon and L. machadoi sp. nov. The genital anatomy of the genus is described in detail and the taxonomy of the genus is reviewed. The monophyly of Labulla is supported by numerous morphological apomorphies of the male palp and female epigynum. Based on a cladistic analysis, a new genus, Pecado gen. nov. , is erected to place Labulla impudica Denis, from Northern Africa. Lepthyphantes insularis Saito and ' Labulla ' nepula Tikader, both formerly included in Labulla , are not congeneric with the type species of Labulla .  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 359–404.     

Phylogenetic relationships of Danio within the order Cypriniformes: a framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.     

Phylogeny and biogeography of African Biomphalaria (Gastropoda: Planorbidae), with emphasis on endemic species of the great East African lakes

The pulmonate snails of the genus Biomphalaria are widely distributed in the tropics, and they are intermediate hosts of the digenean trematode Schistosoma mansoni that causes intestinal schistosomiasis in humans. Recent molecular evidence suggests that Biomphalaria originated in South America, and following a recent transatlantic migration colonized Africa, where it radiated into the currently recognized 12 species. In the present study we further investigate the internal phylogenetic relationships of African Biomphalaria with emphasis on the dispersal and speciation on the continent, especially in the Great Lakes in East Africa. Our results, based on 16S ribosomal DNA, cytochrome oxidase subunit I (COI), and ribosomal internal transcribed spacer I (ITS1), support the monophyly of an African clade with two separate lineages ( Biomphalaria pfeifferi / Biomphalaria camerunensis and the Nilotic species complex/ Biomphalaria angulosa ). Following the initial colonization of Africa, Biomphalaria spread towards the east where a later radiation occurred in the Lake Victoria basin and the Albertine Rift Valley Lakes. With further dispersal along the River Nile, additional speciation took place giving origin to the North-east African species Biomphalaria alexandrina . Our results present almost no support of the species groups of Mandahl-Barth (except for the pfeifferi group), which is in accordance with other molecular appraisals. Our results suggest that Biomphalaria stanleyi , which is endemic to Lake Albert, is not an ecophenotype of the continental B. pfeifferi as previously suggested by other molecular studies. B. angulosa is sequenced for the first time and it is inferred to have an important phylogenetic position as sister group to the Albertine Rift/Lake Victoria basin radiation.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 151 , 337–349.     

Weintrauboa, a new genus of pimoid spiders from Japan and adjacent islands, with comments on the monophyly and diagnosis of the family Pimoidae and the genus Pimoa (Araneoidea, Araneae)

The spider genus Weintrauboa new genus (Araneae, Pimoidae) is described to place two species of pimoids from Japan and adjacent islands that were formerly classified in the linyphiid genus Labulla . Weintrauboa contortipes (Karsch) new comb., the type species, and W. chikunii (Oi) new comb. are redescribed. Parsimony analysis of morphological characters provides robust support for the monophyly of the genus Weintrauboa and corroborates the monophyly of Pimoa , Pimoidae, and the clade Linyphiidae plus Pimoidae. New diagnoses for Pimoa and Pimoidae are provided.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139 , 261–281     

The green-veined white (Pieris napi L.), its Pierine relatives, and the systematics dilemmas of divergent character sets (Lepidoptera, Pieridae)

The butterfly Pieris napi (L.) and relatives exemplify recently evolving taxa, exhibiting variation that makes their evolutionary dynamics interesting, but their systematics difficult. Wing-pattern characters commonly used to distinguish these Holarctic insects display both genetic polymorphism and environmentally-cued polyphenism. Often, these causes of variation are confounded, impairing the characters' phylogenetic usefulness. DNA sequences of four mitochondrial genes offer an independent view of pierine phylogeny. Sampling diverse relatives within family Pieridae assists resolution of the P. napi complex, suggests previous underestimation of clade diversity in subfamily Pierinae, and shows that other genera near Pieris also display confusions of wing-pattern-based phylogenetic inference. The European P. napi is sister to all North American taxa, and is well diverged from them all in sequences. The North American taxa comprise a northern subclade including Pieris oleracea , and questionably distinct Pieris ' angelika ', and a southern subclade including distinct Pieris virginiensis , Pieris marginalis , and Pieris macdunnoughii , and other regional entities yet to be clarified. Weak bootstrap support for some nodes in this group arises from a closeness of sequence identity rather than character conflict; more sequence data and denser geographical sampling may resolve these nodes more clearly. Evidence of reproductive isolation, from other experimental hybridization studies, agrees with the DNA results where these conflict with other divergent character sets. The system offers much promise for a deeper understanding of character evolution in relation to phyletic differentiation.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 413–435.     

Combining molecular, morphological and ecological data to infer species boundaries in a cryptic tropical pitviper

Few operational methods exist for delimiting species boundaries, and these usually require sampling strategies that are unrealistic for widespread organisms that occur at low densities. Here we apply molecular, morphological and ecological species delimitation criteria to a wide-ranging, fragmented group of Asian green pitvipers, the Popeia popeiorum complex. A mitochondrial DNA phylogeny for the group indicates two well-differentiated clades, corresponding mainly to northern and southern parts of its range. Strong phylogeographical structure within each clade suggests isolation in forest refugia during the Pliocene and a southward colonization of the Sunda islands during the Pleistocene. Multivariate analysis of morphological characters reveals a generally conserved pattern of geographical variation, incongruent with the recovered phylogenetic history. We compare groups delineated by mtDNA variation to morphological and ecological divisions in the complex, and discuss the implications of these for the taxonomy of the group. Discordance between species boundaries inferred from different criteria suggests that combining independent sources of data provides the most reliable estimation of species boundaries in organisms that are difficult to sample in large numbers.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 343–364.