Rupert C. Barneby and Pugillus Astragalorum

Rupert C. Barneby, his monumental contributions to the taxonomy ofAstragalus and his place among American botanists, is discussed. His twenty contributions in the seriesPugillus Astragalorum spanned fifteen years of his botanical development from an interested naturalist to an accomplished taxonomist in this extremely species-rich genus. Barneby’s work onAstragalus culminated in the 1188 pages of theAtlas of North American Astragalus, which treated of 552 taxa and was published in 1964.     

Using progesterone 5β-reductase, a gene encoding a key enzyme in the cardenolide biosynthesis, to infer the phylogeny of the genus Digitalis

Summary The progesterone 5β-reductase (5β-POR), a key enzyme in the cardenolide biosynthesis, was sequenced for 21 species of Digitalis and Isoplexis to infer phylogenetic and biogeographic relationships. This new secondary metabolism molecular marker was compared to the previously applied nuclear ITS and plastid trnL-F sequences. The results from separate analyses show high congruence within the genus Digitalis and support the conclusion that all species of Isoplexis have a common origin and are embedded in Digitalis. The genus Isoplexis therefore should be reduced to sectional rank within the genus Digitalis. The sequence analyses give further evidence that additional sequence data increase support for relationships. It demonstrates that poorly supported relationships in smaller data sets may lead to erroneous conclusions about the evolution of the investigated taxa.     

Phylogenetic position of the monotypic Des Murs’ Wiretail ( Sylviorthorhynchus desmursii , Aves: Furnariidae) based on mitochondrial and nuclear DNA

Parallelisms and paraphyletic assemblages are common among ovenbirds. Molecular markers are therefore the best approach when studying the evolutionary relationships among the members of this unparalleled diversified family. We obtained nucleotide sequence data from mitochondrial (cytochrome b) and nuclear genes (myoglobin and glyceraldehyde-3-phosphodehydrogenase) and used these to deduce the phylogenetic position of a monotypic genus endemic to the austral temperate rainforests of southern South America, the Des Murs’ Wiretail (Sylviorthorhynchus desmursii Des Murs, 1847, Aves: Furnariidae). Phylogenetic analyses based on maximum parsimony, maximum likelihood and Bayesian inference all converged into a congruent topology, with a basal position of Des Murs’ Wiretail within Synallaxinae together with Tit–Spinetails (Leptasthenura). Our data reject the hypothesis of a phylogenetic relationship between Des Murs’ Wiretail and thistletails (Schizoeaca) which exhibit parallelisms in morphology, tail structure and nest architecture. Using a molecular clock based on the myoglobin intron 2 gene, we estimated a divergence time of Des Murs’ Wiretail from Tit-Spinetails of 14–15 Myr, which is associated with the appearance of sclerophyllous forest elements in Chile at the Middle–Upper Miocene. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phylogeny of the genus<Emphasis Type="Italic">Goodyera</Emphasis> (Orchidaceae; Cranichideae) in Korea based on nuclear ribosomal DNA ITS region sequences

We sequenced the nuclear ribosomal internal transcribed spacer (ITS) regions to determined the phylogenetic relationships of the severalGoodyera species in Korea and to measure the extent of their differentiation region. ITS 1 was 238 to 239 bp long while ITS 2 was 258 to 259 bp. The 5.8S coding region was 156 bp long. Sequence divergences among species, calculated by Kimura’s two- parameter method, ranged from 0.0 to 5.4%. The most parsimonious tree, with a consistency index of 0.935 and a retention index of 0.937, was produced with 337 steps. Our ITS sequence results demonstrate the monophyly of KoreanGoodyera and support previous morphological, geographical, and RAPD data analyses.     

Chromosomal Evolution of Sibling Species of the Drosophila willistoni Group. I. Chromosomal Arm IIR (Muller’s Element B)

The phylogenetic relationships among nine entities of Drosophila belonging to the D. willistoni subgroup were investigated by establishing the homologous chromosomal segments of IIR chromosome, Muller’s element B (equivalent to chromosome 2L of D. melanogaster). The sibling species of the D. willistoni group investigated include D. willistoni, D. tropicalis tropicalis, D. tropicalis cubana, D. equinoxialis, D. insularis and four semispecies of the D. paulistorum complex. The phylogenetic relationships were based on the existence of segments in different triads of species, which could only be produced by overlapping inversions. Polytene banding similarity maps and break points of inversions between species are presented. The implications of the chromosomal data for the phylogeny of the species and comparisons with molecular data are discussed. The aim of this study is to produce phylogenetic trees depicting accurately the sequence of natural events that have occurred in the evolution of these sibling species. Claudia Rohde, Ana Cristina Lauer Garcia: These authors contributed equally to this work     

Floral scent evolution in the section Pseudophrys: pollinator‐mediated selection or phylogenetic constraints?

• Sexually deceptive orchid species from the Mediterranean genus Ophrys usually interact with one or a few pollinator species by means of specific floral scents. In this study, we investigated the respective role of pollinator‐mediated selection and phylogenetic constraints in the evolution of floral scents in the section Pseudophrys.
• We built a phylogenetic tree of 19 Pseudophrys species based on three nuclear loci; we gathered a dataset on their pollination interactions from the literature and from our own field data; and we extracted and analysed their floral scents using solid phase microextraction and gas chromatography‐mass spectrometry. We then quantified the phylogenetic signal carried by floral scents and investigated the link between plant–pollinator interactions and floral scent composition using phylogenetic comparative methods.
• We confirmed the monophyly of the section Pseudophrys and demonstrated the existence of three main clades within this section. We found that floral scent composition is affected by both phylogenetic relationships among Ophrys species and pollination interactions, with some compounds (especially fatty acid esters) carrying a significant phylogenetic signal and some (especially alkenes and alkadienes) generating dissimilarities between closely related Pseudophrys pollinated by different insects.
• Our results show that in the section Pseudophrys, floral scents are shaped both by pollinator‐mediated selection and by phylogenetic constraints, but that the relative importance of these two evolutionary forces differ among compound classes, probably reflecting distinct selective pressures imposed upon behaviourally active and non‐active compounds.

     

Evaluation of the gene encoding translation termination factor eRF3 as a possible phylogenetic marker

The region of the nuclear GSPT2 gene coding for the N and M domains of translation termination factor eRF3b was tested in Rodentia for applicability as a new molecular marker. It cannot be used as a phylogenetic marker at the intrageneric level because of insufficient variability within families and the impossibility of resolving relationships in the family Cricetidae. However, this GSPT2 region allows reliable identification of higher taxa. The phylogenetic relationships among families revealed with the proposed molecular marker is generally in agreement with current concepts. The new marker indicates a close relationship between the genus Acomys and the family Gerbillidae, which is in agreement with other molecular data but contradicts morphological data. Thus, the region of the nuclear GSPT2 gene encoding the N and M domains of eRF3b can serve as an adequate phylogenetic marker in placental mammals at the level of families or higher taxa. It can also be used in solving controversial questions of phylogeny and taxonomy.     

Primate numts and reticulate evolution of capped and golden leaf monkeys (Primates: Colobinae)

A recent phylogenetic study of langurs and leaf monkeys of South Asia suggested a reticulate evolution of capped and golden leaf monkeys through ancient hybridization between Semnopithecus and Trachypithecus. To test this hybridization scenario, I analysed nuclear copies of the mitochondrial cytochrome b gene (numts) from capped, golden and Phayre’s leaf monkeys. These numts were aligned with mitochondrial cytochrome b sequences of various species belonging to the genera Semnopithecus and Trachypithecus. In the phylogenetic tree derived from this alignment, the numts fell into three distinct clades (A, B and C) suggesting three independent integration events. Clade A was basal to Semnopithecus, and clades B and C were basal to Trachypithecus. Among the numts in clades A and C were sequences derived from species not represented in their respective sister mitochondrial groups. This unusual placement of certain numts is taken as additional support for the hybridization scenario. Based on the molecular dating of these integration events, hybridization is estimated to have occurred around 7.1 to 3.4 million years ago. Capped and golden leaf monkeys might have to be assigned to a new genus to reconcile their unique evolutionary history. Additionally, northeast India appears to be a ‘hot spot’ for lineages that might have evolved through reticulate evolution.     

The phylogenetic relationships and evolution of the Canarian laurel forest endemicIxanthus viscosus (Aiton) Griseb. (Gentianaceae): Evidence frommatK and ITS sequences, and floral morphology and anatomy

The phylogenetic relationships of the Canarian laurel forest endemicIxanthus viscosus (Aiton) Griseb. (Gentianaceae) are investigated through a cladistic analysis of sequence variation of parts of the chloroplast genematK and the ITS region of nuclear ribosomal DNA. The floral anatomical and morphological characteristics ofIxanthus based on paraffin sections and SEM studies are also discussed. In the molecular analysesIxanthus is part of a clade of mostly temperate Erythraeinae and Chironiinae sensu Gilg, in which it is sister to the mostly Mediterranean annualBlackstonia. This relationship is supported by farreaching similarities in flower morphology and anatomy, and the shared possession of at least some perfoliate leaves. This finding contradicts most former classifications in whichIxanthus was placed either in subtribe Gentianinae which never includedBlackstonia, or in a subtribe of its own which was suggested to connect woody tropical with herbaceous temperate taxa. The phylogenetic relationships found here show that 1) the sister group ofIxanthus is distributed in the Mediterranean area, and that 2) its habit as a basally woody suffrutescent herb is best interpreted as an advanced character state.     

利用叶绿体基因组数据解析锦葵科梧桐亚科的系统位置和属间关系

分子系统学研究将传统梧桐科与锦葵科、木棉科和椴树科合并为广义锦葵科,并进一步分为9个亚科.然而,9个亚科之间的关系尚未完全明确,且梧桐亚科内的属间关系也未得到解决.为了明确梧桐亚科在锦葵科中的系统发育位置,厘清梧桐亚科内部属间系统发育关系,该研究对锦葵科8个亚科进行取样,共选取55个样本,基于叶绿体基因组数据,采用最大...     

First molecular phylogenetic insights into the evolution of Eriocaulon (Eriocaulaceae,Poales)

Eriocaulon is a genus of c. 470 aquatic and wetland species of the monocot plant family Eriocaulaceae. It is widely distributed in Africa, Asia and America, with centres of species richness in the tropics. Most species of Eriocaulon grow in wetlands although some inhabit shallow rivers and streams with an apparent adaptive morphology of elongated submerged stems. In a previous molecular phylogenetic hypothesis, Eriocaulon was recovered as sister of the African endemic genus Mesanthemum. Several regional infrageneric classifications have been proposed for Eriocaulon. This study aims to critically assess the existing infrageneric classifications through phylogenetic reconstruction of infrageneric relationships, based on DNA sequence data of four chloroplast markers and one nuclear marker. There is little congruence between our molecular results and previous morphology-based infrageneric classifications. However, some similarities can be found, including Fyson’s sect. Leucantherae and Zhang’s sect. Apoda. Further phylogenetic studies, particularly focusing on less well sampled regions such as the Neotropics, will help provide a more global overview of the relationships in Eriocaulon and may enable suggesting the first global infrageneric classification.

     

ALG11--a new variable DNA marker for sponge phylogeny: comparison of phylogenetic performances with the 18S rDNA and the COI gene

Phylogenetic relationships within sponge classes are highly debated. The low phylogenetic signal observed with some current molecular data can be attributed to the use of few markers, usually slowly-evolving, such as the nuclear rDNA genes and the mitochondrial COI gene. In this study, we conducted a bioinformatics search for a new molecular marker. We sought a marker that (1) is likely to have no paralogs; (2) evolves under a fast evolutionary rate; (3) is part of a continuous exonic region; and (4) is flanked by conserved regions. Our search suggested the nuclear ALG11 as a potential suitable marker. We next demonstrated that this marker can indeed be used for solving phylogenetic relationships within sponges. Specifically, we successfully amplified the ALG11 gene from DNA samples of representatives from all four sponge classes as well as from several cnidarian classes. We also amplified the 18S rDNA and the COI gene for these species. Finally, we analyzed the phylogenetic performance of ALG11 to solve sponge relationships compared to and in combination with the nuclear 18S rDNA and the COI mtDNA genes. Interestingly, the ALG11 marker seems to be superior to the widely-used COI marker. Our work thus indicates that the ALG11 marker is a relevant marker which can complement and corroborate the phylogenetic inferences observed with nuclear ribosomal genes. This marker is also expected to contribute to resolving evolutionary relationships of other apparently slow-evolving animal phyla, such as cnidarians.     

Cytotaxonomy and phylogeny in certain species ofTaxodiaceae

Various species ofTaxodiaceae were selected for chromosome studies to indicate cytotaxonomic and phylogenetic relationships. Point dispersal patterns of diagrammatic presentations of the species' karyotypes, rather than marker chromosomes, were found to be the most significant cytotaxonomic characteristic in indicating phylogenetic relationships. Karyotypic evolution inTaxodiaceae appears to occur by unequal reciprocal translocations followed by pericentric and paracentric inversions. Cytotaxonomic relationships among species generally correspond to the phylogenetic relationships withinTaxodiaceae indicated by classical taxonomic classification. Presence and types of marker chromosomes may have the potential to indicate relationships between different coniferous families.     

Characterization of 22 microsatellite marker loci in the Madagascar rousette (Rousettus madagascariensis)

Twenty-two nuclear microsatellite loci were isolated from a genomic DNA library derived from Madagascar’s Rousettus madagascariensis. Marker characteristics were determined from a single population (37 individuals) from Fort Dauphin (southeastern Madagascar). Sixteen of the 22 loci were within Hardy–Weinberg expectations. These loci are highly informative with polymorphic information content values ranging between 0.757 and 0.916. These loci will provide valuable information for the study of population genetics and gene flow within this species of bats. Due to the dramatic reduction and alteration of their habitat, data generated utilizing this marker suite will potentially provide additional information for the effective long-term management of this near-threatened bat species.     

Effects of ethylene and 1-MCP (1-methylcyclopropene) on bud and flower drop in mini <Emphasis Type="Italic">Phalaenopsis</Emphasis> cultivars

Phalaenopsis frequently exhibits bud drop during production and in response to adverse postharvest conditions. The effect of exogenous ethylene on bud drop of mini Phalaenopsis was studied and ethylene sensitivity of four cultivars was compared. Water content, membrane permeability and ABA (abscisic acid) content in floral buds and flowers were determined after ethylene treatment. Exogenous ethylene induced flower bud drop in all tested Phalaenopsis cultivars and the different cultivars showed distinct differences in ethylene sensitivity. The cultivar Sogo ‘Vivien’ exhibited the highest bud drop, water loss and change in membrane permeability in floral petals, while Sogo ‘Berry’ showed the lowest sensitivity. The ethylene inhibitor 1-MCP (1-methylcyclopropene) reduced ethylene-induced floral bud drop in the cultivar Sogo ‘Yenlin’. ABA content in floral buds was increased in response to ethylene and 1-MCP pretreatment inhibited the ethylene-induced increase in ABA levels efficiently. This finding suggests that the observed increase in ABA content during bud drop was mediated by ethylene. The interaction between ABA and ethylene is discussed.     

Revisiting the phylogeny of papilionoid legumes: New insights from comprehensively sampled early-branching lineages

• Premise of study: Phylogenetic relationships of the papilionoid legumes (Papilionoideae) reveal that the early branches are more highly diverse in floral morphology than are other clades of Papilionoideae. This study attempts for the first time to comprehensively sample the early-branching clades of this economically and ecologically important legume subfamily and thus to resolve relationships among them. • Methods: Parsimony and Bayesian phylogenetic analyses of the plastid matK and trnL intron sequences included 29 genera not yet sampled in matK phylogenies of the Papilionoideae, 11 of which were sampled for DNA sequence data for the first time. • Key results: The comprehensively sampled matK phylogeny better resolved the deep-branching relationships and increased support for many clades within Papilionoideae. The potentially earliest-branching papilionoid clade does not include any genus traditionally assigned to tribe Swartzieae. Dipterygeae is monophyletic with the inclusion of Monopteryx. The genera Aldina and Amphimas represent two of the nine main but as yet unresolved lineages comprising the large 50-kb inversion clade within papilionoids. The quinolizidine-alkaloid-accumulating genistoid clade is expanded to include a strongly supported subclade containing Ormosia and the previously unplaced Clathrotropis s.s., Panurea, and Spirotropis. Camoensia is the first-branching genus of the core genistoids. • Conclusions: The well-resolved phylogeny of the earliest-branching papilionoids generated in this study will greatly facilitate the efforts to redefine and stabilize the classification of this legume subfamily. Many key floral traits did not often predict phylogenetic relationships, so comparative studies on floral evolution and plant–animal interactions, for example, should also benefit from this study.     

Two Novel Closure Rules for Constructing Phylogenetic Super-Networks

A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection ℘ of partial trees (leaf-labeled trees whose leaves are bijectively labeled by species or, more generally, taxa, each supported by, e.g., a gene) into an overall parental structure that displays all trees in ℘. This already difficult problem is complicated by the fact that the trees in ℘ regularly support conflicting phylogenetic relationships and are not on the same but only overlapping taxa sets. A desirable requirement on the sought after parental structure, therefore, is that it can accommodate the observed conflicts. Phylogenetic networks are a popular tool capable of doing precisely this. However, not much is known about how to construct such networks from partial trees, a notable exception being the Z-closure super-network approach, which is based on the Z-closure rule, and the Q-imputation approach. Although attractive approaches, they both suffer from the fact that the generated networks tend to be multidimensional making it necessary to apply some kind of filter to reduce their complexity. To avoid having to resort to a filter, we follow a different line of attack in this paper and develop closure rules for generating circular phylogenetic networks which have the attractive property that they can be represented in the plane. In particular, we introduce the novel Y-(closure) rule and show that this rule on its own or in combination with one of Meacham’s closure rules (which we call the M-rule) has some very desirable theoretical properties. In addition, we present a case study based on Rivera et al. “ring of life” to explore the reconstructive power of the M- and Y-rule and also reanalyze an Arabidopsis thaliana data set.     

Phylotranscriptomics of Swertiinae (Gentianaceae) reveals that key floral traits are not phylogenetically correlated

Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on Earth. Floral traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic groups. The subtribe Swertiinae (Gentianaceae) comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nectaries. Here we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu, representing the range of floral diversity, using data from the nuclear and plastid genomes. Extensive topological conflicts were present between the nuclear and plastome trees. Three of the 15 genera represented by multiple species are polyphyletic in both trees. Key floral traits including corolla type, absence or presence of lobe scales, nectary type, nectary position, and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic correlation. We also revealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral traits. These results highlight the complex evolutionary history of this subtribe. The phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversification and floral diversity.     

A plastid gene phylogeny of the non-photosynthetic parasitic <Emphasis Type="Italic">Orobanche</Emphasis> (Orobanchaceae) and related genera

The phylogenetic relationships of the non-photosynthetic Orobanche sensu lato (Orobanchaceae), which includes some of the economically most important parasitic weeds, remain insufficiently understood and controversial. This concerns both the phylogenetic relationships within the genus, in particular its monophyly or lack thereof, and the relationships to other holoparasitic genera such as Cistanche or Conopholis. Here we present the first comprehensive phylogenetic study of this group based on a region from the plastid genome (rps2 gene). Although substitution rates appear to be elevated compared to the photosynthetic members of Orobanchaceae, relationships among the major lineages Cistanche, Conopholis plus Epifagus, Boschniakia rossica (Cham. & Schltdl.) B. Fedtsch., B. himalaica Hook. f. & Thomson, B. hookeri Walp. plus B. strobilacea A. Gray, and Orobanche s. l. remain unresolved. Resolution within Orobanche, however, is much better. In agreement with morphological, cytological and other molecular phylogenetic evidence, five lineages, corresponding to the four traditionally recognised sections (Gymnocaulis, Myzorrhiza, Orobanche, Trionychon) and O. latisquama Reut. ex Boiss. (of sect. Orobanche), can be distinguished. A combined analysis of plastid rps2 and nuclear ITS sequences of the holoparasitic genera results in more resolved and better supported trees, although the relationships among Orobanche s. l., Cistanche, and the clade including the remaining genera is unresolved. Therefore, rps2 is a marker from the plastid genome that is well-suited to be used in combination with other already established nuclear markers for resolving generic relationships of Orobanche and related genera.