Morphological and phylogenetic analyses of <Emphasis Type="Italic">Uromyces appendiculatus</Emphasis> and <Emphasis Type="Italic">U. vignae</Emphasis> on legumes in Japan

Uromyces appendiculatus, inclusive of three varieties, is distinguished from U. vignae primarily by the position of urediniospore germ pores and putative host specificity. However, opinions concerning these morphological and physiological features as taxonomic characters have varied greatly, and distinction of these species has often been confused. To clarify the taxonomy of these two species, morphological features of urediniospores and teliospores of 225 rust fungus specimens on species of Phaseolus, Vigna, Apios, Lablab, and Dunbaria were examined by light microscopy and scanning electron microscopy. Forty-five specimens were subjected to molecular phylogenetic analyses. As a result, the position of germ pores in urediniospores and the teliospore-wall thickness were considered as good characters to separate three morphological groups. In molecular analyses, the specimens fell into two and three clades based on the nucleotide sequence at D1/D2 domain of LSU rDNA and ITS regions, respectively. One of the D1/D2 clades corresponded to one morphological group whereas another D1/D2 clade included two other morphological groups. In contrast, each of the three ITS clades corresponded to a separate morphological group. Neither morphological groups nor molecular clades were host limited. It is suggested that the three morphological groups that corresponded to three distinct ITS clades constitute distinct species.Contribution no. 186 from the Laboratory of Plant Parasitic Mycology, Institute of Agriculture and Forestry, University of Tsukuba, Japan     

Floral morph composition and pollen limitation in the seed set of <Emphasis Type="Italic">Nymphoides indica</Emphasis> populations

We investigated the floral morph composition and seed set of the populations in a heterostylous aquatic plant, Nymphoides indica O. Kuntze (Menyanthaceae). The bias of floral morph ratio in the populations was negatively correlated with the seed set. In the populations with biased floral morph ratio, the pollen on the stigma of the common morphs were dominated by pollen of the same morph, resulting in reduced seed set. The addition of pollen of the opposite morph on the stigmas of the common morph resulted in an increase of fruit and seed set rates. The intermorph pollination rate and the fruit and seed set rates of Nymphoides indica were highest when two floral morphs were close in the populations. Various insect species including Lepidoptera, Diptera and Hymenoptera visited the flowers. However, geitonogamous pollination was common because of the short flying distance of the pollinators. These results indicate that the seed set of Nymphoides indica is limited by the shortage of compatible pollens and that the success of intermorph pollination is influenced by spatial distribution of the two floral morphs. As Nymphoides indica is endangered, conservation of the populations with high fecundity is proposed by us.     

Using multilocus approach to uncover cryptic diversity within Pseudotrapelus lizards from Saudi Arabia

The agamid Pseudotrapelus lizards inhabit the mountainous areas of the Arabian Peninsula and eastern North Africa. Currently six Pseudotrapelus species are recognised, though diagnostic morphological characters are still lacking, creating great difficulty in describing new species. Recently, two specimens of Pseudotrapelus were collected from the vicinity of Riyadh in central Saudi Arabia, an area that was not sampled in previous phylogenetic studies. In here we used both mitochondrial and nuclear data to investigate the phylogenetic position of the new samples, and assess their phylogenetic relationships with the other recognised species of Pseudotrapelus from across the distribution range of the genus. We used a multilocus approach of haplotype networks, concatenated datasets and species trees, performed mitochondrial and nuclear species delimitation analyses, and estimated divergence times. In general, our results support previous molecular studies and uncover the presence of cryptic diversity within Pseudotrapelus. The phylogenetic structure of the genus is of two major clades and within them seven distinct, delimited phylogenetic groups belonging to the six recognised species and the seventh to the individuals from Riyadh. The Riyadh specimens were distinct in all analyses performed. We suggest that the new specimens from the Riyadh area are a distinct lineage, forming a clade with their phylogenetic relatives, P. sinaitus and P. chlodnickii. The clade formed by these three species diverged during the Late Miocene around 6.4 Ma, with cladogenesis possibly facilitated by vicariance and isolation caused due to climatic fluctuations and the progression of sandy areas. Our results suggest further morphological research is necessary to revise the taxonomic status of this lineage and of the entire genus.     

Resurrection in Carapa (Meliaceae): a reassessment of morphological variation and species boundaries using multivariate methods in a phylogenetic context

The taxonomy of the amphi‐Atlantic tree genus Carapa (Meliaceae) has long been controversial. Of the three species currently recognized in the genus, two are known to present substantial morphological variation that has been used in the past to distinguish several taxa, most of which are currently placed in synonymy. Here, a combination of field observations, univariate analyses of leaf, floral and seed characters and principal coordinate analyses of floral characters in the context of a molecular phylogenetic analysis was used to investigate the patterns of variation and delimit morphological species anew in the genus. These results support the recognition of 27 species in Carapa, of which 16 are previously described and 11 are new. In general, phylogenetically related species occurred in the same geographical area, but were morphologically distinct. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 186–221.     

石山苣苔属(苦苣苔科)花形态演化及分类学意义

石山苣苔属(苦苣苔科)约30种,主要分布于我国南部的石灰岩地区.目前该属已知物种数虽少但花形态极其多样,是该科中分类最为困难的类群之一.基于分子证据,其它8个属中花形态迥异的一些物种被并入石山苣苔属.然而,该属花形态的演化趋势缺乏系统性的研究,传统分类对属的界定与分子系统学研究结果相矛盾的原因,以及是否有形态特征支持新界定的石山苣苔属还不清楚.该研究中,总共编码了19种石山苣苔属植物和9种报春苣苔属植物的35个形态特征,其中包括26个花部形态特征,在分子系统树上追踪了它们的演化路径.结果表明:无论属内还是属间,多数花部形态特征,尤其以往属的分类界定特征,在演化过程中变化频繁且发生了高度同塑性演化,这是导致传统形态分类不自然的关键因素.此外,在观察研究的所有特征中,花丝和柱头的差异可能在石山苣苔属植物共同祖先中经历了演变,或可用于区分石山苣苔属与其姐妹报春苣苔属的大多数种类.因此,在苦苣苔科植物的分类学研究中应当慎用这些花部性状作为分类依据,而且应对形态特征进行广泛地观察研究,在密集的取样和分辨率更高、更可靠的系统树上追踪它们的演化规律.更为重要的是,需要进一步研究导致复杂形态性状演化的内在分子调控机理和外在的自然选择动力,最终更加深入地理解石山苣苔属等典型喀斯特植物的演化过程和机理.     

SPECIES BOUNDARIES IN THE TOXIC DINOFLAGELLATE PROROCENTRUM LIMA (DINOPHYCEAE,PROROCENTRALES), BASED ON MORPHOLOGICAL AND PHYLOGENETIC CHARACTERS1

Wild and cultured specimens of Prorocentrum lima (Ehrenb.) F. Stein from 26 widely different areas in 13 countries were examined in order to determine consistent characters for delimiting species boundaries in this taxon. The morphological characters valve shape, valve size, valve ornamentation, number and shape of valve pores, number and shape of marginal pores, and periflagellar platelets were observed using LM and SEM, and two molecular genetic regions were sequenced. We identified stable morphological characters that were consistent among wild specimens and all cultures, which were valve shape, valve ornamentation, and number and arrangement of periflagellar platelets. All cultures of P. lima identified by these characters formed a monophyletic group in phylogenetic analyses based on the two genes, which, however, included the species Prorocentrum arenarium. P. arenarium was determined to be within the range of morphological variation of P. lima, and therefore we synonymize the two taxa. Within this monophyletic group, P. lima was divided into several subclades in the all phylogenetic analyses. There were no morphological characters specifically related to any one subclade. The subclades appeared to correlate broadly to sample collection regions, suggesting that geographically separated populations may have become genetically distinct within this epi‐benthic species. We have emended species boundaries in P. lima.     

Molecules,morphology, missing data and the phylogenetic position of a recently extinct madtom catfish (Actinopterygii: Ictaluridae)

Taxa missing large amounts of data pose challenges that may hinder the recovery of a well‐resolved, accurate phylogeny and leave questions surrounding their phylogenetic position. Systematists commonly have to contend with one or two species in a group for which there is little or no material available suitable for recovering molecular data. It is unclear whether these taxa can be better placed using analyses based on morphological data only, or should be included in broader analyses based on both morphological and molecular data. The extinct madtom catfish Noturus trautmani is known from few specimens for which molecular data are unavailable. We included this taxon in parsimony and Bayesian analyses of relationships of madtom catfishes based on a combination of morphological and molecular data. Results indicate that using a combination of morphological and molecular data does a better job at providing a phylogenetic placement for N. trautmani than morphology alone, even though it is missing all of its molecular characters. We provide a novel hypothesis of relationships among Noturus species and recommendations for classification within the group. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 60–75.     

Neotropical nymphoides (Menyanthaceae): Meso-American and west indian species

Studies ofNymphoides (Menyanthaceae) in Mexico, Central America, and the West Indies indicate that three species are present in this region, all of which are members of theNymphoides indica complex. White-flowered plants of Meso-America, the Antilles, and South America traditionally have been referred toN. humboldtiana but are identical to the otherwise Old WorldN. indica and must be called by the latter name. The Mexican and GuatemalanNymphoides fallax, described in this paper, differs fromN. indica in having winged yellow petals with a stipitate basal tuft of hairs, consistently yellow anthers, larger seeds, and higher altitudinal occurrence. Yellow-flowered plants of the Bahamas and Cuba are considered to represent a third species,N. grayana, which resembles plants of southern Brazil and southern Africa in flower color and morphology. However, because of the geographic distribution and unique ultraviolet-light emittance characters ofN. grayana and the still uncertain relationships of the Brazilian and African populations, this third taxon is provisionally retained at the specific level pending further study of those populations.     

Nomimoscolex suspectus n. sp. (Eucestoda: Proteocephalidea: Zygobothriinae) with morphological and molecular phylogenetic analyses of the genus

We describe a new species of Nomimoscolex from the Amazon siluriform fishes Brachyplatystoma filamentosum, B. flavicans and B. vaillanti. It differs from N. piraeeba in a lower mean number of testes, the paramuscular position of the vitelline follicles, the ovarian width/proglottis width ratio and the cirrus-pouch length/proglottis width ratio. Protein electrophoresis assays performed for 25 enzymatic systems showed that specimens of N. suspectus n. sp. from the three host species form a homogenous population which was genetically isolated from N. piraeeba and N. dorad. Moreover, the latter two species, synonymised by Rego (1991) because of their close morphological similarity, could be separated at eight loci. We thus restore N. dorad as a valid species. We finally examined the composition of the genus Nomimoscolex using DNA sequences from the 5.8S rRNA, ITS-2 and 28S rRNA nuclear ribosomal genes and a matrix of 24 morphological characters. Phylogenetic relationships were inferred for nine species of the genus, five members of other monticelliid genera and two outgroup species. The results of the phylogenetic analyses performed on morphological and molecular characters converged with those from allozyme studies and showed that N. suspectus, N. piraeeba and N. dorad clustered in a distinct clade that excluded other members of the genus. We therefore recognised them as an aggregate of species to reflect an isolation supported by both morphological and genetic data. Because relationships among the remaining Nomimoscolex representatives and other genera were generally poorly resolved, regardless of the database analysed, no action was taken to reorganise them into alternative groupings.     

The comparative osteology and phylogenetic relationships of African and South American lungfishes (Sarcopterygii: Dipnoi)

Lepidosirenidae is a clade of freshwater lungfishes that include the extant South American Lepidosiren paradoxa Fitzinger, 1837 and African species of the genus Protopterus. These genera have been geographically separated since the break‐up of Gondwana in the Early Cretaceous, but they display similar biology and morphology. Species were distinguished by a combination of features such as head‐to‐body ratios, the number of pairs of ribs, and the presence of external gills, but no discrete skeletal characters were identified, and no comparative studies including all extant species have been published. I used computed tomography (CT), X‐ray photography, and specimens from museum collections to describe the skeletal morphology of all species of lepidosirenid in a comparative context. I digitally disarticulated the bones in each specimen to compile a comparative atlas of the cranial and pectoral elements of all extant lungfishes, which has the potential to increase the correct identifications of specimens in museum collections. The morphology of the frontoparietal, parasphenoid, supraorbital, and suboperculum differ between species. I used those characters, along with molecular sequence data from the ribosomal RNA gene 16S, to run combined morphological and molecular phylogenetic analyses. Lepidosirenidae is monophyletic in all analyses, but the interrelationships of the species of Protopterus vary with the different sources of character data. © 2015 The Linnean Society of London     

Parasenecio chenopodiifolius (Compositae–Senecioneae) is a Synotis and conspecific with S. otophylla based on evidence from morphology,cytology and ITS/ETS sequence data

Observations on living plants and herbarium specimens have convinced us that Synotis otophylla (Compositae–Senecioneae) from south Xizang (Tibet), China, must be merged with the Himalayan Parasenecio chenopodiifolius. However, is the plant a Synotis or a Parasenecio? We have examined floral micro‐morphological and cytological characters of P. chenopodiifolius, and performed molecular phylogenetic analyses based on ITS and ETS sequence data. The anther collar of this taxon is balusterform, and the endothecial tissue cell wall thickenings are radial. These conform to the floral micro‐characters of Synotis but differ from those of Parasenecio, which has subcylindrical anther collars, and polarized endothecial tissue cell wall thickenings. Chromosome counts indicate the taxon has 2n = 40, a number common in Synotis, whereas Parasenecio has 2n = 60. Our phylogenetic analyses based on ITS/ETS sequences also place P. chenopodiifolius in Synotis. We make the new combination S. chenopodiifolia and synonymize S. otophylla.     

A densely sampled ITS phylogeny of the Cape flagship genus Erica L. suggests numerous shifts in floral macro-morphology

Erica L. is the largest of the ‘Cape’ clades that together comprise around half of the disproportionately high species richness of the Cape Floristic Region (CFR) of South Africa. Around 840 species of Erica are currently recognised, C.680 of which are found in the CFR, the rest distributed across the rest of Southern Africa, the highlands of Tropical Africa and Madagascar, and Europe. Erica is taxonomically well documented, but very little is known about species-level relationships. We present the first densely sampled phylogenetic analysis of Erica, using nuclear ribosomal DNA sequences (internal transcribed spacers; ITS) of c. 45% of the species from across the full geographic range of the genus, both Calluna and Daboecia (Ericeae; monotypic genera and putative sister groups of Erica), and further Ericoideae outgroups. Our results show both morphological and geographic coherence of some clades, but numerous shifts in floral macro-morphology as represented by variation in individual morphological characters and pollination syndromes. European Ericeae is a paraphyletic grade subtending a monophyletic African/Malagasy Erica. Given the limited resolution of this single gene tree, more data are needed for further conclusions. Clades are identified that will serve as an effective guide for targeted sampling from multiple linkage groups.     

Hidden biodiversity: total evidence phylogenetics and evolution of morphological traits in a highly diverse lineage of endogean ground beetles,Typhlocharis Dieck, 1869 (Carabidae,Trechinae, Anillini)

Typhlocharis is the most diverse eyeless endogean ground beetle genus known to date, with 62 species all endemic to the West Mediterranean region. The lineage is characterized by a conservative and singular body plan within Carabidae that contrasts with a high morphological diversity in many traits. We provide an exhaustive phylogeny of the lineage through the study of 92 morphological characters from all 62 described species and 45 potential new species from 70 additional populations, and the combination of morphological and available molecular data, in the first total evidence phylogenetic approach for a highly diverse endogean lineage. We tracked the evolution of morphological traits over the obtained phylogenies. Results suggest eight morphologically distinct clades, which do not correspond to the species groups proposed formerly. Ancestral state reconstructions and phylogenetic signal analyses of morphological traits revealed that some of the previously key characters to the classification of Typhlocharis, such as the umbilicate series or the apical denticles of elytra, are highly homoplasic, whereas other characters show stronger phylogenetic signal, including structures in the antennae, gula, pronotum and last abdominal ventrite. This evidence supports the split of Typhlocharis into three genera: Lusotyphlus gen. nov. ; Typhlocharis Dieck, 1869 and Microcharidius Coiffait, 1969 (revalidated), forming the subtribe Typhlocharina Jeanne, 1973.     

Time of diversification in the Cape fauna endemisms,inferred by phylogenetic studies of the genus Iselma (Coleoptera: Meloidae: Eleticinae)

The endemic diversification of the Cape zone fauna and the phylogenetic relationships among the 30 species of the blister beetle genus Iselma are investigated. We analysed morphological, molecular (mtDNA 16S) and combined datasets of characters using a number of approaches (maximum parsimony, maximum likelihood, Bayesian inference analyses). We propose hypotheses of diversification times among taxa from molecular clock analyses. Morphological and molecular analyses produced similar results. According to maximum likelihood molecular studies, radiation within the genus Iselma occurred during the Pliocene and Pleistocene, roughly contemporaneously with the shift in African climate, vegetation and faunal assemblages. Two main lineages, one Namibian and one South African, separated c. 4.9 Ma. Within the South African lineage we identify two groups of endemic species, one in Little Karoo and one that extend towards southern Namaqualand. The remaining South African groups of species are spread through Namaqualand and the southwestern Cape area. These include several endemisms, with different times of diversification during the Pleistocene, probably related in part to glacial cycles. These endemisms are distributed in small areas of the following ecosystems: coastal Strandveld, Succulent Karoo and particularly Fynbos.     

Molecular study of the genus Astraeus

The aim of the present work was to determine phylogenetic relationships among Astraeus species and to support macroscopic and microscopic characters of Astraeus with analysis of the ITS rDNA region. Collections of Astraeus basidiomes were made from different geographical areas in Thailand and compared with existing collections made worldwide. The marriage of observations on morphological features, including basidiospore ornamentation and molecular data demonstrated the presence of several Astraeus species. Sequences for 41 Astraeus collections were compared and the phylogenetic analyses grouped Thai Astraeus collections into two distinct groups. One contained A. odoratus and an Asian species described herein as A. asiaticus. There are at least two additional species: A. pteridis, and one so far un-named from North America. Our results show that molecular data can be used in combination with traditional morphological characteristics to resolve taxonomic uncertainties in the genus Astraeus.     

Morphological evolution in the variable resin-producing Detarieae (Fabaceae): do morphological characters retain a phylogenetic signal?

Background and Aims

Previous molecular phylogenetic studies disagree with the informal generic-level taxonomic groups based on morphology. In this study morphological characters in the caesalpinioid clade Detarieae are evaluated within a phylogenetic framework as a means of better understanding phylogenetic relationships and morphological evolution.

Methods

Morphological characters were observed and scored for representative species of Detarieae focusing on the resin-producing genera. Phylogenetic analyses were carried out with morphological characters alone and then combined with DNA sequences.

Key Results

Despite a high level of homoplasy, morphological data support several clades corresponding to those recovered in molecular phylogenetic analyses. The more strongly supported clades are each defined by at least one morphological synapomorphy. Several characters (e.g. apetaly) previously used to define informal generic groups evolved several times independently, leading to the differences observed with the molecular phylogenetic analyses. Although floral evolution is complex in Detarieae some patterns are recovered.

Conclusions

New informal taxonomic groupings are proposed based on the present findings. Floral evolution in the diverse Detarieae clade is characterized by a repeated tendency toward zygomorphy through the reduction of lateral petals and toward complete loss of petals.Key words: Caesalpinioideae, Detarieae, floral evolution, Leguminosae, morphology, phylogeny, resins, taxonomy     

Renewed sampling of inland aquatic habitats in southern Africa yields two novel freshwater crab species (Decapoda: Potamonautidae: Potamonautes)

A recent survey of the freshwater streams of the Mecula and Yao mountains in the Niassa province of Mozambique resulted in the discovery of a new freshwater crab species. This species is genetically and morphologically distinct from described species from Mozambique or its neighbouring countries, and is described as P otamonautes bellarussus sp. nov. In addition, a new semi‐terrestrial burrowing freshwater crab P otamonautes flavusjo sp. nov. from the Highveld of the Mpumalanga province in South Africa is described based on unique genetic and morphological characters. The phylogenetic affinities of the two new species in relation to the described eastern and southern African Potamonautes species is determined and the biogeographic implications are discussed. © 2014 The Linnean Society of London     

Molecular phylogeny and species delimitation of Stachyuraceae: Advocating a herbarium specimen‐based phylogenomic approach in resolving species boundaries

Species concept and delimitation are fundamental to taxonomic and evolutionary studies. Both inadequate informative sites in the molecular data and limited taxon sampling have often led to poor phylogenetic resolution and incorrect species delineation. Recently, the whole chloroplast genome sequences from extensive herbarium specimen samples have been shown to be effective to amend the problem. Stachyuraceae are a small family consisting of only one genus Stachyurus of six to 16 species. However, species delimitation in Stachyurus has been highly controversial because of few and generally unstable morphological characters used for classification. In this study, we sampled 69 individuals of seven species (each with at least three individuals) covering the entire taxonomic diversity, geographic range, and morphological variation of Stachyurus from herbarium specimens for genome‐wide plastid gene sequencing to address species delineation in the genus. We obtained high‐quality DNAs from specimens using a recently developed DNA reconstruction technique. We first assembled four whole chloroplast genome sequences. Based on the chloroplast genome and one nuclear ribosomal DNA sequence of Stachyurus, we designed primers for multiplex polymerase chain reaction and high throughput sequencing of 44 plastid loci for species of Stachyurus. Data of these chloroplast DNA and nuclear ribosomal DNA internal transcribed spacer sequences were used for phylogenetic analyses. The phylogenetic results showed that the Japanese species Stachyurus praecox Siebold & Zucc. was sister to the rest in mainland China, which indicated a typical Sino‐Japanese distribution pattern. Based on diagnostic morphological characters, distinct distributional range, and monophyly of each clade, we redefined seven species for Stachyurus following an integrative species concept, and revised the taxonomy of the family based on previous reports and specimens, in particular the type specimens. Furthermore, our divergence time estimation results suggested that Stachyuraceae split from its sister group Crossosomataceae from the New World at ca. 54.29 Mya, but extant species of Stachyuraceae started their diversification only recently at ca. 6.85 Mya. Diversification time of Stachyurus in mainland China was estimated to be ca. 4.45 Mya. This research has provided an example of using the herbarium specimen‐based phylogenomic approach in resolving species boundaries in a taxonomically difficult genus.