Menispermaceae, a dioecious, largely pantropical family of vines and lianas, consists of approximately 70 genera. In this paper, we present phylogenies (derived using maximum parsimony, maximum likelihood, and Bayesian inference) based on chloroplast atpB and rbcL sequence data for 42 Menispermaceae genera (60 species) and 15 outgroup genera representing all families in the Ranunculales. Results of this work confirm that a clade consisting of Berberidaceae and Ranunculaceae is sister to the Menispermaceae and that Menispermaceae is highly supported as monophyletic. Within Menispermaceae, Menispermum and Sinomenium, two genera with distributions in the Northern Hemisphere, are weakly to moderately supported as sister to all remaining Menispermaceae. Many of the tribes as described by previous workers are not monophyletic. To expand both the data and sampling, we combined our atpB and rbcL data with previously published ndhF data for two additional analyses: 1) for matching species and 2) for all genera available, including those with either atpB/rbcL or ndhF missing (22% missing data). All trees produced from our three analyses were highly congruent, especially where branch support was high. Four major clades were recovered from all analyses and are informally named. Superimposing our geographical distributions on our atpB/rbcL phylogeny indicates that many well supported clades have distributions on multiple continents, probably due to both vicariance and dispersal. Several previous hypotheses regarding trends in character evolution are tested; our phylogenies suggest that the following are all derived character states within the family: arborescent habit; acrodromous, peltate, compound, or lobed leaves; absence of condyle and endosperm; smooth endosperm; fused stamens; and tricolpate pollen.

These phylogenetic results do not agree with any previous classifications of the genus. Molecular data also suggest that the endemic Macaronesian species B. salicifolium is a neoendemic, as the sequence divergence between the populations in Madeira and Canary Islands, and closer mainland relatives in north-west Africa is small. All endemic north-west African taxa are included in a single unresolved but well-supported clade, and the low nucleotide variation of ITS suggests a recent radiation within this group. The only southern hemisphere species, B. mundii (southern Africa), is shown to be a neoendemic, apparently closely related to B. falcatum, a Eurasian species.

Several fruit characters differentiate major clades, and further synapomorphies are diagnostic of various subclades. Fruit characters that can be inferred as ancestral in the family are basal or subbasal stylar scars, endocarps with dorsoventral curvature, endocarp walls woody or bony, presence of a condyle, locule without ribs, sublateral vascular traces, presence of endosperm, and foliaceous or subterete cotyledons.

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Many Streptomyces strains are known to produce valinomycin (VLM) antibiotic and the VLM biosynthetic gene cluster (vlm) has been characterized in two independent isolates. Here we report the phylogenetic relationships of these strains using both parsimony and likelihood methods, and discuss whether the vlm gene cluster shows evidence of horizontal transmission common in natural product biosynthetic genes. Eight Streptomyces strains from around the world were obtained and sequenced for three regions of the two large nonribosomal peptide synthetase genes (vlm1 and vlm2) involved in VLM biosynthesis. The DNA sequences representing the vlm gene cluster are highly conserved among all eight environmental strains. The geographic distribution pattern of these strains and the strict congruence between the trees of the two vlm genes and the housekeeping genes, 16S rDNA and trpB, suggest vertical transmission of the vlm gene cluster in Streptomyces with no evidence of horizontal gene transfer. We also explored the relationship of the sequence of vlm genes to that of the cereulide biosynthetic genes (ces) found in Bacillus cereus and found them highly divergent from each other at DNA level (genetic distance values≥95.6%). It is possible that the vlm gene cluster and the ces gene cluster may share a relatively distant common ancestor but these two gene clusters have since evolved independently.

HighlightsDesulfovibrio gigas genome encodes two HcpR paralogs, HcpR1 and HcpR2.Cells lacking HcpR1 are less tolerant to NO.HcpR1 regulates the expression of several genes related to nitrogen metabolism.Phylogenetic analyses indicate that the presence of HcpR paralogs is a common finding among Desulfovibrio species.

No abstract

DNA sequences are important sources of data for phylogenetic analysis. Nowadays, DNA sequencing is a routine technique in molecular biology laboratories. However, there are specific questions associated with project design and sequencing of plant samples for phylogenetic analysis, which may not be familiar to researchers starting in the field. This chapter gives an overview of methods and protocols involved in the sequencing of plant samples, including general recommendations on the selection of species/taxa and DNA regions to be sequenced, and field collection of plant samples. Protocols of plant sample preparation, DNA extraction, PCR and cloning, which are critical to the success of molecular phylogenetic projects, are described in detail. Common problems of sequencing (using the Sanger method) are also addressed. Possible applications of second-generation sequencing techniques in plant phylogenetics are briefly discussed. Finally, orientation on the preparation of sequence data for phylogenetic analyses and submission to public databases is also given.