The phylogeny ofActaea (Ranunculaceae): A biogeographical approach

Phylogenetic analyses of the genusActaea were performed using morphological, ecological and biogeographical characters. Using solely morphological characters, the relationships of the three identified species-groups remain uncertain. Close biogeographical examination and comparison of the areas with ecological peculiarities as well as climate data gave important insight into the phylogeny ofActaea and the whole tribe. Consequently, the obtained biogeographical data were used for phylogenetic reconstructions. Both, from the point of view of morphological and biogeographical data,A. pachypoda andA. asiatica are the most ancestral species. They grow on the east sides of the continents, mainly in broad-leaved forests. In West Eurasia the apomorphicA. spicata andA. acuminata occur under similar climatic and ecological conditions, but these species are adapted to another climate rhythm. The most advanced species (A. erythrocarpa, A. rubra) are to be found in the boreal forests where they are widely distributed. This biogeographical approach revealed that the evolution of the species led to a gradual widening and shifting of their ecological constitutions.     

The blackburni/murchisona species complex in Australian Pseudotetracha (Coleoptera: Carabidae: Cicindelinae: Megacephalini): evaluating molecular and karyological evidence

Our phylogenetic analysis of three endemic species of the Australian tiger beetle genus Pseudotetracha (Fleutiaux, 1864) from South Australia used sequences of two fragments of the mitochondrial genes 16S rRNA and cytochrome oxidase III. A matrix for each gene and two combined matrices were constructed. We compared these three riparian species, together with data from nine taxa of this genus available in GenBank, using parsimony and Bayesian methods. These molecular results are in agreement with the phylogenetic hypothesis for the blackburni/murchisona species complex previously proposed based on morphology, whereas other recent molecular analyses have questioned the existence of this species complex. In all of our analyses, samples of P. blackburni divided into two statistically supported clades, one of which is more closely related to P. mendacia and P. pulchra than to the other P. blackburni clade. This suggests the existence of a cryptic new species. Additionally, we analysed chromosomes of the second metaphase cells of members of the two clades. The observations showed different karyotypes as blackburni‐1 has two types of second meiotic metaphase cells with 11 and 12 chromosomes, whereas in blackburni‐2, all cells have 12 chromosomes, adding evidence for the putative existence of two species.     

Phytochemical fingerprinting to thwart black cohosh adulteration: a 15 Actaea species analysis

Introduction – The popular use of black cohosh products (Actaea racemosa L., syn. Cimicifuga racemosa L.) is growing as the demand for alternatives to estrogen therapy has increased. Critical to safe use is the assurance of unadulterated, high‐quality products. Questions have been raised about the safety of black cohosh due to cases of liver toxicity in patients who reported taking it; subsequent evaluation found some products to be adulterated with other related herbal species. Correct plant species identification is a key first step for good manufacturing practices of safe black cohosh products. Objectives – To develop analytical methods which distinguish black cohosh from other species (American and Asian) of Actaea increasingly found as adulterants in commercially available black cohosh products. Material and methods – Fifteen species of Actaea were collected from North America and Asia, and the phytochemical fingerprints of these samples were established using HPLC‐PDA and LC‐MS techniques. Results – The HPLC and LC‐MS fingerprints for polyphenols and triterpene glycosides revealed distinct patterns that make black cohosh clearly distinguishable from most other species of Actaea. Two marker compounds, cimifugin and cimiracemoside F, were found to be important to distinguish black cohosh from most Asian species of Actaea. Formononetin was not found from either Asian or American species of Actaea. Conclusions – Phytochemical fingerprinting is a practical, reliable method for authenticating black cohosh and distinguishing it from other species of Actaea increasingly found as adulterants in commercially available black cohosh products. This should facilitate the continued development of high‐quality, unadulterated black cohosh products. Copyright © 2011 John Wiley & Sons, Ltd.     

Molecular phylogeny of an endemic radiation of Cuban toads (Bufonidae: Peltophryne) based on mitochondrial and nuclear genes

Aim In this study we present a molecular phylogenetic and phylogeographical analysis of Peltophryne (Anura: Bufonidae), an endemic genus of Antillean toads, to investigate the spatial and temporal origins of the genus, with particular focus on the eight Cuban species. Location Greater Antilles, with extensive sampling of the Cuban archipelago. Methods We obtained DNA sequence data from two mitochondrial genes, cytochrome c oxidase subunit I (COI) and ribosomal RNA (16S), for 124 toads representing all eight Cuban species, and combined this with published data from Hispaniola (one of three species) and Puerto Rico (one of one species) to establish a molecular phylogeny for Peltophryne. In addition, we explored the phylogeographical structure of widespread Cuban species. For a subset of 42 toads we also obtained DNA sequence data from two nuclear genes, recombination activator‐1 (RAG‐1) and chemokine receptor 4 (CXCR‐4). We combined our molecular data with published DNA sequences from a global sample of bufonid toads to place the spatial and temporal origins of Peltophryne in the Caribbean within a fuller geographical and phylogenetic context. Results All phylogenetic analyses supported the monophyly of West Indian toads. The ancestor of Peltophyrne diverged from its mainland source around the Eocene–Oligocene boundary, with a subsequent radiation across the Caribbean islands taking place during the Miocene. Cuban species are monophyletic with a basal split in the early–middle Miocene that separates extant small‐bodied from large‐bodied species. Extensive mitochondrial DNA (mtDNA) sampling within widespread Cuban species revealed contrasting phylogeographical patterns. Peltophryne taladai and P. empusa showed deeply divergent lineages, whereas no geographical structure was observed in the widespread P. peltocephala. Main conclusions Our timeline for Peltophryne diversification is consistent with a biogeographical model requiring no long‐distance overwater dispersal. Although confidence intervals on divergence time estimates are wide, the stem age of Peltophyrne coincides with the hypothesized GAARlandia landspan or archipelago, which may have connected South America briefly with the Antilles. The ages of Peltophryne for Puerto Rico, Hispaniola and Cuba are consistent with a recently proposed vicariance scenario for the region. Our molecular results support the recognition of all eight species in Cuba, and provide evidence of possible cryptic species.     

The phylogenetic systematics of blue‐tailed skinks (Plestiodon) and the family Scincidae

Blue‐tailed skinks (genus Plestiodon) are a common component of the terrestrial herpetofauna throughout their range in eastern Eurasia and North and Middle America. Plestiodon species are also frequent subjects of ecological and evolutionary research, yet a comprehensive, well‐supported phylogenetic framework does not yet exist for this genus. We construct a comprehensive molecular phylogeny of Plestiodon using Bayesian phylogenetic analyses of a nine‐locus data set comprising 8308 base pairs of DNA, sampled from 38 of the 43 species in the genus. We evaluate potential gene tree/species tree discordance by conducting phylogenetic analyses of the concatenated and individual locus data sets, as well as employing coalescent‐based methods. Specifically, we address the placement of Plestiodon within the evolutionary tree of Scincidae, as well as the phylogenetic relationships between Plestiodon species, and their taxonomy. Given our sampling of major Scincidae lineages, we also re‐evaluate ‘deep’ relationships within the family, with the goal of resolving relationships that have been ambiguous in recent molecular phylogenetic analyses. We infer strong support for several scincid relationships, including a major clade of ‘scincines’ and the inter‐relationships of major Mediterranean and southern African genera. Although we could not estimate the precise phylogenetic affinities of Plestiodon with statistically significant support, we nonetheless infer significant support for its inclusion in a large ‘scincine’ clade exclusive of Acontinae, Lygosominae, Brachymeles, and Ophiomorus. Plestiodon comprises three major geographically cohesive clades. One of these clades is composed of mostly large‐bodied species inhabiting northern Indochina, south‐eastern China (including Taiwan), and the southern Ryukyu Islands of Japan. The second clade comprises species inhabiting central China (including Taiwan) and the entire Japanese archipelago. The third clade exclusively inhabits North and Middle America and the island of Bermuda. A vast majority of interspecific relationships are strongly supported in the concatenated data analysis, but there is nonetheless significant conflict amongst the individual gene trees. Coalescent‐based gene tree/species tree analyses indicate that incongruence amongst the nuclear loci may severely obscure the phylogenetic inter‐relationships of the primarily small‐bodied Plestiodon species that inhabit the central Mexican highlands. These same analyses do support the sister relationship between Plestiodon marginatus Hallowell, 1861 and Plestiodon stimpsonii (Thompson, 1912), and differ with the mitochondrial DNA analysis that supports Plestiodon elegans (Boulenger, 1887) + P. stimpsonii. Finally, because the existing Plestiodon taxonomy is a poor representation of evolutionary relationships, we replace the existing supraspecific taxonomy with one congruent with our phylogenetic results. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 163–189.     

Fukinolic acid and cimicifugic acids: a review

During the last decades, the research on the biological activities of extracts from Cimicifuga/Actaea species and Petasites japonicus as well as their active ingredients has been intensified. Besides terpenoids as dominant natural product group, hydroxycinnamic acid esters such as fukinolic acid and several cimicifugic acids have been isolated from Actaea and Petasites species and their chemical structures have been elucidated. Investigations on the biological properties of these hydroxycinnamic acid esters are currently undertaken and some compounds might be promising therapeutic tools. In this review, we have gathered information on the genera Actaea and Petasites, the occurrence of cimicifugic and fukinolic acids and some aspects of their biosynthesis. Furthermore, we have summarized the medicinal aspects of fukinolic acid and cimicifugic acids. In connection with the biological activities of these compounds, structural features of the hydroxycinnamic acid derivatives move into the focus. The position of the hydroxyl group at the aromatic rings and the introduction of an electron-donating moiety may be important for anti-inflammatory, antiviral, cytotoxic and vasoactive effects of these compounds.

     

Integration of mitogenomic and morphological data disentangles the systematics of Pollenia and establishes a revised phylogenetic hypothesis for the Polleniidae

The Polleniidae (Diptera) are a family of flies best known for species of the genus Pollenia, which overwinter inside human dwellings. Previously divided across the Calliphoridae, Tachinidae and Rhinophoridae, the polleniid genera have only recently been united. Several studies have utilized molecular data to analyse polleniid phylogenetic relationships, although all have suffered from low taxon sampling or insufficient phylogenetic signal in molecular markers. To alleviate these problems, we utilized two automated organellar genome extraction software, GetOrganelle and MitoFinder, to assemble mitogenomes from genome skimming data from 22 representatives of the polleniid genera: Dexopollenia, Melanodexia, Morinia, Pollenia and Xanthotryxus. From these analyses, we provide 14 new mitogenomes for the Polleniidae and perform phylogenetic analyses of 13 protein-coding mitochondrial genes using both maximum likelihood and Bayesian inference. Subfamilial phylogenetic relationships within the Polleniidae are interrogated and Pollenia is found to form a monophyletic clade sister to Melanodexia, Morinia and Dexopollenia, providing no evidence for the synonymisation of any of these genera. Our topology conflicts with previous morphology-based cladistic interpretations, with the amentaria, griseotomentosa, semicinerea and viatica species-groups resolving as non-monophyletic. We provide support for our topology through analysis of adult morphology and male and female terminalia, while identifying new diagnostic characters for some of the clades of the Pollenia. To test the validity of the current diagnostic morphology in the Polleniidae, newly assembled cytochrome C oxidase subunit 1 (COI) data are combined with a polleniid COI barcode reference library and analysed using the species delimitation software ASAP. COI barcodes support the current morphologically defined species within the Pollenia.     

Phylogeny of <Emphasis Type="Italic">Litsea</Emphasis> and related genera (Laureae-Lauraceae) based on analysis of <Emphasis Type="Italic">rpb2</Emphasis> gene sequences

The relationship between Litsea and related genera is currently unclear. Previous molecular studies on these taxa using cpDNA and nrITS were unable to produce well-resolved phylogenetic trees. In this study, we explored the potential of the rpb2 gene as a source of molecular information to better resolve the phylogenetic analysis. Although rpb2 was believed to be a single-copy gene, our cloning results showed that most species examined possessed several copies of these sequences. However, the genetic distance among copies from any one species was low, and these copies always formed monophyletic groups in our molecular trees. Our phylogenetic analyses of rpb2 data resulted in better resolved tree topologies compared to those based on cpDNA or nrITS data. Our results show that monophyly of the genus Litsea is supported only for section Litsea. As a genus, Litsea was shown to be polyphyletic. The genera Actinodaphne and Neolitsea were resolved as monophyletic groups in all analyses. They were also shown to be sisters and closer to the genus Lindera than to the genus Litsea. Our results also revealed that the genus Lindera is not a monophyletic group.     

Phylogeny of Impatiens (Balsaminaceae): integrating molecular and morphological evidence into a new classification

Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty‐six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB‐rbcL and trnL‐F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum‐parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three‐colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well‐supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.     

Phylogeny of Veneridae (Bivalvia) based on mitochondrial genomes

Veneridae is one of the most diverse families of bivalve molluscs. However, their phylogenetic relationships among subfamilies have been debated for years. To explore phylogenetic relationships of Veneridae, we sequenced 13 complete mitochondrial genome sequences from eight subfamilies and compared with available complete mitochondrial genome of other Veneridae taxa (18 previously reported sequences). Phylogenetic analyses using probabilistic methods recovered two highly supported clades. In addition, the protein‐coding gene order revealed a highly conserved pattern among the same subclade lineages. According to our molecular analyses, Tapetinae should be recognized as a valid subfamily, but the genera formed para‐polyphyletic clades. Chioninae was recovered not monophyletic that differs from a previously molecular phylogeny. Furthermore, the reconstructed chronogram calibrated with fossils recovered the Veneridae have originated during the early Permian (about 290 million years ago). Noticeably, programmed frameshift was found in the nad4 gene of Leukoma jedoensis, Anomalodiscus squamosus and Antigona lamellaris and cob gene of L. jedoensis. This is the first time that the presence of the programmed frameshift has been found in the protein‐coding genes of Heterodonta species. Our results improved the phylogenetic resolution within Veneridae, and a more taxonomic sampling analysis of the subfamily Chioninae is supposed to construct.     

Molecular systematics of the Philippine forest skinks (Squamata: Scincidae: Sphenomorphus): testing morphological hypotheses of interspecific relationships

Skinks of the genus Sphenomorphus are the most diverse clade of squamates in the Philippine Archipelago. Morphological examination of these species has defined six phenotypic groups that are commonly used in characterizations of taxonomic hypotheses. We used a molecular phylogeny based on four mitochondrial and two nuclear genes to assess the group's biogeographical history in the archipelago and examine the phylogenetic validity of the currently recognized Philippine species groups. We re‐examined traditional characters used to define species groups and used multivariate statistics to quantitatively evaluate group structure in morphometric space. Clustering analyses of phenotypic similarity indicate that some (but not all) members of previously defined species groups are phenotypically most similar to other members of the same group. However, when species group membership was mapped on our partitioned Bayesian phylogenetic hypothesis, only one species group corresponds to a clade; all other species group arrangements are strongly rejected by our phylogeny. Our results demonstrate that (1) previously recognized species group relationships were misled by phenotypic convergence; (2) Sphenomorphus is widely paraphyletic; and (3) multiple lineages have independently invaded the Philippines. Based on this new perspective on the phylogenetic relationships of Philippine Sphenomorphus, we revise the archipelago's diverse assemblage of species at the generic level, and resurrect and/or expand four previously recognized genera, and describe two new genera to accommodate the diversity of Philippine skinks of the Sphenomorphus group. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 1217–1243.     

Revision of Phymatolithon purpureum (Hapalidiales,Rhodophyta) based on ultrastructural and molecular data

ABSTRACT

To elucidate the taxonomy and phylogeny of Phymatolithon purpureum (P. Crouan & H. Crouan) Woelkerling & L.M. Irvine, we observed the type specimens and fresh samples using SEM (ultra-morphology) and analysed DNA sequences. Phymatolithon purpureum was originally described as Lithothamnion purpureum P. Crouan & H. Crouan from Mingant, Brittany, France. Our molecular phylogenetic analyses using psbA and COI–5P regions placed our collections from Ireland, UK and France in a clade with ‘P. borealis W.H. Adey, J.J. Hernandez-Kantun & P.W. Gabrielson (MH252286)’ from Iceland and ‘uncultured Corallinales (GQ917711 and GQ917512)’ from Roscoff, Brittany, France, near the type locality of P. purpureum. We show that P. purpureum is conspecific with P. borealis and P. polymorphum f. papillatum (Foslie) Foslie based on morphology and molecular data. Also, although P. purpureum has been often confused with P. laevigatum (Foslie) Foslie because of their similar morphology (e.g. smooth surface and sunken tetra/bisporangial conceptacles), our molecular phylogenetic analyses indicate that P. purpureum and P. laevigatum are sister taxa. Our sequences from lectotype material of P. laevigatum and syntype material of Lithothamnion emboloides Heydrich are identical.     

Mitochondrial rate variation among lineages of passerine birds

The order Passeriformes comprises the majority of extant avian species. Analyses of molecular data have provided important insights into the evolution of this diverse order. However, molecular estimates of the evolutionary and demographic timescales of passerine species have been hindered by a lack of reliable calibrations. This has led to a reliance on the application of standard substitution rates to mitochondrial DNA data, particularly rates estimated from analyses of the gene encoding cytochrome b (CYTB). To investigate patterns of rate variation across passerine lineages, we used a Bayesian phylogenetic approach to analyse the protein‐coding genes of 183 mitochondrial genomes. We found that the most commonly used mitochondrial marker, CYTB, has low variation in rates across passerine lineages. This lends support to its widespread use as a molecular clock in birds. However, we also found that the patterns of among‐lineage rate variation in CYTB are only weakly related to the evolutionary rate of the mitochondrial genome as a whole. Our analyses confirmed the presence of mutational saturation at third codon positions across the protein‐coding genes of the mitochondrial genome, reinforcing the view that these sites should be excluded in studies of deep passerine relationships. The results of our analyses have provided information that will be useful for molecular‐clock studies of passerine evolution.     

Species delimitation and phylogeography of Abies delavayi complex: Inferred from morphological,molecular, and climatic data

The species delimitation within Abies delavayi complex, consisting of A. delavayi Franch., A. fabri (Mast.) Craib, A. nukiangensis W. C. Cheng & L. K. Fu, and A. delavayi subsp. fansipanensis (Q. P. Xiang, L. K. Fu & Nan Li) Rushforth, has been a subject of long‐term dispute. We combined different lines of evidence, including morphological characters, population‐based mitochondrial DNA and chloroplast DNA sequences, and plastome data to assess its species delimitation. These four independent datasets revealed a consistent result that the four taxa of A. delavayi complex were hardly separated and could be regarded as one species. Our results further suggested that these four taxa might have experienced rapid morphological diversification, following a common expansion triggered by climate oscillations during the Pleistocene. In addition, we surveyed the phylogeographical history of A. delavayi complex as a whole based on ecological niche models and molecular data. These results consistently revealed that this high‐mountain fir complex had experienced glacial expansion and interglacial contraction. Therefore, we propose that A. delavayi complex probably has undergone the phalanx expansion model in response to climate change during the Quaternary. Such expansion patterns demand consideration when establishing conservation strategies for threatened fir species.     

An Orphan Protist Quadricilia rotundata Finally Finds Its Phylogenetic Home in Cercozoa

Quadricilia rotundata is a heterotrophic flagellate with four flagella. However, because this species has no clear morphological characteristics or molecular data affiliating it with any known group, Q. rotundata has been treated as a protist incertae sedis, for a long time. Here, we established a clonal culture of Q. rotundata and sequenced its 18S rDNA sequence. Molecular phylogenetic analysis successfully placed Q. rotundata in an environmental clade within Cercozoa, which contributes to expand the morphological and species diversity within Cercozoa. We also discuss morphological evolution within Cercozoa based on this finding.     

Molecular evidence for the occurrence of the leaf deer <Emphasis Type="Italic">Muntiacus putaoensis</Emphasis> in Arunachal Pradesh,north-east India

The discovery of the leaf deer Muntiacus putaoensis in northern Myanmar has added to the growing list of large mammals recently discovered in remote, unexplored parts of south and south-east Asia. Its subsequent discovery in eastern Arunachal Pradesh, India, based on morphometric analyses of two skulls collected from local hunters, doubled the size of its known east-west range, which is significant for a newly-discovered and poorly understood species. However, ambiguity remained regarding several other partial skulls and dried skin samples collected during subsequent surveys. The sympatric occurrence of the Indian muntjac Muntiacus muntjak further complicates species identification based primarily on morphometry. In this paper, we develop molecular genetic analyses that can unambiguously identify muntjac species. Further, we test and apply our methods to unknown skin samples to confirm the occurrence of the leaf deer in Arunachal Pradesh. Finally, we use our samples and genetic data from three mitochondrial markers to establish phylogenetic affinities between these samples and other extant members of the Muntiacus genus. Our approach, which combines the use of specific primers and phylogenetic analyses, is generally applicable towards the detection of cryptic biodiversity in unexplored and species-rich areas like north-east India.     

GENETIC DIVERSITY AND INTROGRESSION IN TWO CULTIVATED SPECIES (PORPHYRA YEZOENSIS AND PORPHYRA TENERA) AND CLOSELY RELATED WILD SPECIES OF PORPHYRA (BANGIALES,RHODOPHYTA)1

We investigated the genetic variations of the samples that were tentatively identified as two cultivated Porphyra species (Porphyra yezoensis Ueda and Porphyra tenera Kjellm.) from various natural populations in Japan using molecular analyses of plastid and nuclear DNA. From PCR‐RFLP analyses using nuclear internal transcribed spacer (ITS) rDNA and plastid RUBISCO spacer regions and phylogenetic analyses using plastid rbcL and nuclear ITS‐1 rDNA sequences, our samples from natural populations of P. yezoensis and P. tenera showed remarkably higher genetic variations than found in strains that are currently used for cultivation. In addition, it is inferred that our samples contain four wild Porphyra species, and that three of the four species, containing Porphyra kinositae, are closely related to cultivated Porphyra species. Furthermore, our PCR‐RFLP and molecular phylogenetic analyses using both the nuclear and plastid DNA demonstrated the occurrence of plastid introgression from P. yezoensis to P. tenera and suggested the possibility of plastid introgression from cultivated P. yezoensis to wild P. yezoensis. These results imply the importance of collecting and establishing more strains of cultivated Porphyra species and related wild species from natural populations as genetic resources for further improvement of cultivated Porphyra strains.     

Ultrastructure and molecular phylogenetic position of a new marine sand-dwelling dinoflagellate from British Columbia,Canada: Pseudadenoides polypyrenoides sp. nov. (Dinophyceae)

Two monospecific genera of marine benthic dinoflagellates, Adenoides and Pseudadenoides, have unusual thecal tabulation patterns (lack of cingular plates in the former; and no precingular plates and a complete posterior intercalary plate series in the latter) and are thus difficult to place within a phylogenetic framework. Although both genera share morphological similarities, they have not formed sister taxa in previous molecular phylogenetic analyses. We discovered and characterized a new species of Pseudadenoides, P. polypyrenoides sp. nov., at both the ultrastructural and molecular phylogenetic levels. Molecular phylogenetic analyses of SSU and LSU rDNA sequences demonstrated a close relationship between P. polypyrenoides sp. nov. and Pseudadenoides kofoidii, and Adenoides and Pseudadenoides formed sister taxa in phylogenetic trees inferred from LSU rDNA sequences. Comparisons of morphological traits, such as the apical pore complex (APC), demonstrated similarities between Adenoides, Pseudadenoides and several planktonic genera (e.g. Heterocapsa, Azadinium and Amphidoma). Molecular phylogenetic analyses of SSU and LSU rDNA sequences also demonstrated an undescribed species within Adenoides.