The genus Micarea was studied for the first time in the Taita Hills, Kenya. Based on new collections and existing data, we reconstructed a phylogeny using ITS, mtSSU and Mcm7 regions, and generated a total of 27 new sequences. Data were analyzed using maximum likelihood and maximum parsimony methods. Based mainly on new collections, we discovered four undescribed well-supported lineages, characterized by molecular and phenotypic features. These lineages are described here as Micarea pumila, M. stellaris, M. taitensis and M. versicolor. Micarea pumila is characterized by a minutely granular thallus, small cream-white or pale brownish apothecia, small ascospores and the production of prasinic acid. Micarea stellaris has a warted-areolate thallus, cream-white apothecia usually darker at the centre, a hymenium of light grey or brownish pigment that dissolves in K, and intense crystalline granules that appear as a belt-like continuum across the lower hymenium when studied in polarized light. Micarea taitensis is characterized by a warted-areolate thallus and cream-white or yellowish apothecia that sometimes produce the Sedifolia-grey pigment. Micarea versicolor is characterized by a warted-areolate, sometimes partly granular thallus and apothecia varying from cream-white to light grey to blackish in colour. This considerable variation in the coloration of its apothecia is caused by an occasional mixture of the Sedifolia-grey pigment in the epihymenium and another purplish brown pigment in the hymenium. Micarea stellaris, M. taitensis and M. versicolor produce methoxymicareic acid. The main distinguishing characters are presented in a species synopsis. Three of the new species are nested in the M. prasina group, and the fourth one (M. taitensis) resolves as a basal taxon to the M. prasina group. The new species inhabit montane cloud forests, which have fragmented dramatically throughout the Eastern Arc Mountains in recent decades.

The genus Acacia Miller is species-rich, and species discrimination is challenging owing to morphological similarities between closely related species. Naming of specimens is particularly difficult in the Middle East, where confusion in taxonomic identification exists within the context of a wider international debate on the generic systematics of Acacia sensu lato. At least five segregate genera for Acacia s.l. have been advocated: Acacia sensu stricto, Vachellia, Senegalia, Acaciella and Mariosousa. Furthermore, identification to species of the only remaining native Acacia s.l. tree in Kuwait is still a matter of controversy. The present study used multilocus chloroplast DNA sequence data analyses following maximum likelihood (ML) and Bayesian approaches to: 1) test the species concepts of Vachellia pachyceras (≡ Acacia pachyceras O.Schwartz) from the Middle East, and Vachellia tortilis (Forssk.) Galasso & Banfi (≡ Acacia tortilis (Forssk.) Hayne) and Vachellia gerrardii (Benth.) P.J.H.Hurter (≡ Acacia gerrardii Benth.) from Kenya, as well as to investigate species divergence times; and 2) identify the only remaining native Acacia s.l. tree in Kuwait (known as the Lonely Tree), as well as other unidentified Acacia s.l. specimens in cultivation. The Bayesian and ML topologies clearly differentiated Vachellia pachyceras, V. tortilis and V. gerrardii, and demonstrated that the three species are distinct. Divergence time estimates using the ML topology suggested that Vachellia gerrardii diverged from a common ancestor no later than the early Pliocene (3.3 Mya), whereas V. pachyceras originated at least 2.0 Mya (Pliocene). The unknown remaining native Acacia s.l. tree in Kuwait and other specimens collected from the nursery were identified as Vachellia pachyceras. These results stress the need to use plastid DNA barcodes complemented by population genetics approaches to address systematic issues in this complex of Acacia s.l. species in the Middle East and the Arabian Peninsula.

Retinitis pigmentosa (RP) comprises several heritable diseases that involve photoreceptor, and ultimately retinal, degeneration. Currently, mutations in over 50 genes have known links to RP. Despite advances in clinical characterization, molecular characterization of RP remains challenging due to the heterogeneous nature of causal genes, mutations, and clinical phenotypes. In this study, we compiled large datasets of two important visual genes associated with RP: rhodopsin, which initiates the phototransduction cascade, and the retinoid isomerase RPE65, which regenerates the visual cycle. We used a comparative evolutionary approach to investigate the relationship between interspecific sequence variation and pathogenic mutations that lead to degenerative retinal disease. Using codon-based likelihood methods, we estimated evolutionary rates (d N/d S) across both genes in a phylogenetic context to investigate differences between pathogenic and nonpathogenic amino acid sites. In both genes, disease-associated sites showed significantly lower evolutionary rates compared to nondisease sites, and were more likely to occur in functionally critical areas of the proteins. The nature of the dataset (e.g., vertebrate or mammalian sequences), as well as selection of pathogenic sites, affected the differences observed between pathogenic and nonpathogenic sites. Our results illustrate that these methods can serve as an intermediate step in understanding protein structure and function in a clinical context, particularly in predicting the relative pathogenicity (i.e., functional impact) of point mutations and their downstream phenotypic effects. Extensions of this approach may also contribute to current methods for predicting the deleterious effects of candidate mutations and to the identification of protein regions under strong constraint where we expect pathogenic mutations to occur.

Partial mitochondrial cytochrome c oxidase subunit I (mt COI) sequences were generated from: Toxoplasma gondii (strains CTG, GTI, MAS, ME49, PTG, TgCatBr5, TgCat, Br64, TgCgCal, TgToucan); Neospora caninum (Strain NC1); Hammondia hammondi (Strain H.H–20); H. heydorni; H. cf. triffittae; Cystoisospora felis; C. suis; C. canis; C. rivolta; C. cf. ohioensis; Caryospora bigenetica; Sarcocystis rileyi; and S. neurona. Nuclear 18S rDNA sequences were generated for H. heydorni, H. hammondi, C. suis, C. canis, C. felis, C. rivolta, C. cf. ohioensis, S. neurona, and S. rileyi. Aligned, concatenated 18S rDNA and COI sequences were Bayesian analysed using partitioned nucleotide substitution models [HKY + I + G for 18S; GTR + I + G codon (code = metmt) for COI]. Phylogenetic hypotheses supported a monophyletic Sarcocystidae and its subfamilie with two major clades within the Toxoplasmatinae: (1) a monophyletic clade of Cystoisospora spp. with Nephroisospora eptesici; and (2) a clade of Toxoplasma, Neospora and Hammondia. Within the latter, Hammondia was shown to be paraphyletic; H. heydorni and H. triffittae were monophyletic with N. caninum [canine definitive hosts (DHs)], whereas H. hammondi was monophyletic with T. gondii (feline DHs). A new genus is erected to resolve the paraphyly of the genus Hammondia confirmed using mt COI and combined 18S/COI sequence datasets.

The monospecific hexactinellid sponge genus Symplectella endemic to New Zealand waters was originally assigned to family Rossellidae within the order Lyssacinosida (subclass Hexasterophora), although affinities to family Euplectellidae were also noted. Seventy-eight years later, the genus was transferred to Euplectellidae (subfamily Corbitellinae) on rather subjective grounds. Here, I test these two competing taxonomic hypotheses with molecular phylogenetic methods and demonstrate that Symplectella rowi is indeed a rossellid, as was originally suggested. The genus is officially transferred back to Rossellidae (subfamily Rossellinae), which represents another small step towards a more natural classification system of glass sponges.

The delimitation of two morphologically similar and not easily separable Vulpicida species, V. juniperinus and V. tubulosus, is analyzed using nuclear ITS and Mcm7, and mitochondrial SSU DNA sequences. Seventy-nine Vulpicida specimens, most from the two focal taxa, are included in the three-locus gene tree. The results from Bayesian and parsimony analyses are presented. There are strong conflicts between the single locus gene trees. Vulpicida juniperinus and V. tubulosus are divided into two clearly distinguished groups in the ITS and concatenated B/MCMC tree. However, these species are mixed in both clades, appearing polyphyletic. Currently accepted V. juniperinus and V. tubulosus are not distinct according to the loci studied. Vulpicida pinastri appears monophyletic based on the available sequences.

This study focuses on European Usnea species with sorediate shrubby thalli, with the aim to evaluate the morphological and chemical separation of species in the light of molecular data. Twenty-two Usnea species, including widely distributed taxa such as U. diplotypus, U. fulvoreagens, U. glabrescens, U. lapponica, U. subfloridana, U. substerilis and U. wasmuthii, were included in the study using Bayesian and maximum parsimony analyses of nuclear ITS and beta-tubulin sequences. The analyses showed that: 1) most taxa that are morphologically well delimited are also distinct by means of molecular characters, 2) shrubby taxa in the section Usnea that are difficult to determine by traditional characters form a group of closely related but still genetically distinct entities, except U. diplotypus and U. substerilis which appear to be polyphyletic. The branch lengths differed largely between two parts of the ITS tree (sections Usnea and Ceratinae). Usnea intermedia is proposed as the sexually reproducing counterpart for the sorediate U. lapponica. Additionally, some new chemotypes of Usnea species were determined.

In 2002, a jellyfish bloom occurred throughout the Gulf of Oman and the Persian Gulf causing decreased catch in artisanal and industrial fisheries, damage to fishing gear, interrupted operation of desalination plants, and damage to the seawater cooling systems of coastal power plants. The cause and source of the bloom and the species of medusa were unknown. Here, the temporal and spatial distribution of the medusa are described using data from incidental catches in Iranian fisheries surveys, and morphological and molecular evidence are used to identify the medusa as Crambionella orsini (Vanhöffen). This species is endemic to the western Indian Ocean and adjacent basins which dismisses species introduction as the cause of this bloom. Furthermore, because the bloom was geographically widespread, it probably was not caused by local coastal degradation. Although human activities with large-scale effects cannot be ruled out, large-scale oceanographic or ecosystem conditions, perhaps part of natural climate cycles, that yielded moderate sea surface temperatures (in terms of the annual mean monthly anomaly for each year since 1982) were the most likely causes of the bloom of this endemic jellyfish.

Until recently the genus Didymocarpus Wall. (Gesneriaceae) was used in an unwarrantably wide sense and included more than 180 species. It has now been remodelled and restricted to around 70 species. Of these, 18 species and one variety are known to occur in Thailand. To clarify the relationships among Thai species of Didymocarpus we sequenced the internal transcribed spacers (ITS) of nuclear ribosomal DNA (nrDNA) from a sample of 23 taxa, including 15 from Thailand, four from China, three from Malaysia and one from Bhutan. Seventeen morphological characters were coded for all 23 taxa and optimized onto a retention index (RI) reweighted maximum parsimony (MP) tree. The phylogenetic analyses suggested that Didymocarpus taxa formed a strongly supported monophyletic clade, with several supported subclades. The combination of molecular phylogeny and optimization of morphological characters suggests the presence of three distinct groups: the first, corresponding to Didymocarpus sect. Elati Ridl., includes plants with tall stems, yellow or white flowers and one-celled conoid or two-celled headed pigment glands; the other two groups, which represent Didymocarpus sect. Didymocarpus, both contain plants with dwarfed stems and violet or purple flowers, but are distinguished by the presence of both four-celled conoid or onecelled globose glands in one, and the absence in the other. Optimization of geographical locality onto the phylogeny led us to propose the hypothesis that, based on this sample, the geographical origin of Didymocarpus is the Malay Peninsula, and the ancestral corolla colour is white/yellow. Subsequent dispersal northward through southern and northern Thailand to China and Bhutan was accompanied by the evolution of a purple/violet corolla colour.

Molecular clocks based on sequence change in mitochondrial (mt) DNA have been useful for placing molecular phytogenies in their historical context, thereby enhancing evolutionary insight. Nonetheless, despite their importance to phylogeographers, the methodology is controversial. Here we report on two mitochondrial clocks for the butterfly genus Danaus based on sequences from the cytochrome c oxidase subunit I (COI) and small subunit 12S rRNA (12S) genes. Both clocks are, within the context of Danaus, reliable time-keepers, mutually consistent and, respectively, in agreement with a crustacean COI clock and a molluscan 12S clock. Though we have no fossils with which directly to calibrate sequence divergence rates for Danaus, the 12S molluscan and COI crustacean clocks chosen for comparison were calibrated to radiometrically dated geomorphological events. Our results indicate that the Danaus COI clock evolves approximately four times faster than the 12S clock. Differences between rates of sequence change in terminal sister-taxa are small and likelihood ratio tests do not reject a hypothesis that evolution has been clock-like. The species Danaus chrysippus is paraphyletic and, therefore, invalid. Danaus probably split from its sister-genus Tirumala around 4.9 ± 0.3 million years ago in the early Pliocene.

PCR amplification of 16S rDNA was used to determine the diversity of bacteria associated with 3 strains of sheep scab mite, Psoroptes ovis. Eight species of bacteria were identified by phylogenetic analysis of the PCR product sequences. Seven of these species are previously unreported in association with sheep scab mites. Five species were matched to Serratia marcesens, Proponibacteium acnes, Phyllobacterium rubiacearum, Pantoea agglomerans, Curacaobacter baltica, whereas the remaining 3 sequences matched unclassified sequences belonging to the gamma proteobacteria, pseudomonads and streptococci. Bacterial diversity of the in vivo cultured strain was very low and did not match the diversity of the 2 wild collected isolates. The diversity of the bacteria in relation to the disease of sheep scab and the possible importance of these bacteria in the diet of the mites are discussed.