Molecular phylogeny

Background: The forests of the upper Amazon basin harbour some of the world's highest anuran species richness, but to date we have only the sparsest understanding of the distribution of genetic diversity within and among species in this region. To quantify region-wide genealogical patterns and to test for the presence of deep intraspecific divergences that have been documented in some other neotropical anurans, we developed a molecular phylogeny of the widespread terrestrial leaflitter frog Eleutherodactylus ockendeni (Leptodactylidae) from 13 localities throughout its range in Ecuador using data from two mitochondrial genes (16S and cyt b; 1246 base pairs). We examined the relation between divergence of mtDNA and the nuclear genome, as sampled by five speciesspecific microsatellite loci, to evaluate indirectly whether lineages are reproductively isolated where they co-occur. Our extensive phylogeographic survey thus assesses the spatial distribution of E. ockendeni genetic diversity across eastern Ecuador. Results: We identified three distinct and well-supported clades within the Ecuadorean range of E. ockendeni: an uplands clade spanning north to south, a northeastern and central lowlands clade, and a central and southeastern clade, which is basal. Clades are separated by 12% to 15% net corrected p-distance for cytochrome b, with comparatively low sequence divergence within clades. Clades marginally overlap in some geographic areas (e.g., Napo River basin) but are reproductively isolated, evidenced by diagnostic differences in microsatellite PCR amplification profiles or DNA repeat number and coalescent analyses (in MDIV) best modelled without migration. Using Bayesian (BEAST) and net phylogenetic estimates, the Southeastern Clade diverged from the Upland/ Lowland clades in the mid-Miocene or late Oligocene. Lowland and Upland clades speciated more recently, in the early or late Miocene. Conclusion: Our findings uncover previously unsuspected cryptic species diversity within the common leaflitter frog E. ockendeni, with at least three different species in Ecuador. While these clades are clearly geographically circumscribed, they do not coincide with any existing landscape barriers. Divergences are ancient, from the Miocene, before the most dramatic mountain building in the Ecuadorean Andes. Therefore, this diversity is not a product of Pleistocene refuges. Our research coupled with other studies suggests that species richness in the upper Amazon is drastically underestimated by current inventories based on morphospecies.

A typical character of plants is the production and storage of usually complex mixtures of secondary metabolites (SM). The main function of secondary metabolites is defense against herbivores and microbes; some SM are signal compounds to attract pollinating and seed dispersing animals or play a role in the symbiotic relationships with plants and microbes. The distribution of SM in the plant kingdom shows an interesting pattern. A specific SM is often confined to a particular systematic unit, but isolated occurrences can occur in widely unrelated taxonomic groups. This review tries to explain the patchy occurrence of SM in plants. It could be due to convergent evolution, but evidence is provided that the genes that encode the biosynthesis of SM appear to have a much wider distribution than the actual secondary metabolite. It seems to be rather a matter of differential gene regulation whether a pathway is active and expressed in a given taxonomic unit or not. It is speculated that the...

An African or Asian evolutionary origin for human schistosomes? The origin and the evolution of Schistosomatidae species, due to their medical importance (responsible of the second most important human parasitosis after malaria), arouse a great interest. A combination of phylogenetic studies using several molecular markers has provided support for the traditional grouping and evolutionary inferences derived from morphological and biological data. The genus Schistosoma, which comprises all species parasitizing Man, is generally split into four evolutionary lineages (mansoni, haematobium, indicum and japonicum lineages). The group of African schistosomes (including mansoni and haematobium lineages) appears very divergent from the japonicum lineage. Recent phylogenetic studies using partial 28S rDNA sequencing and including Orientobilharzia turkestanicum from Iran, an Asian parasite of livestock, found, unexpectedly, that this species nested among Schistosoma species, thus rendering the latter paraphyletic, and suggested an Asian origin for the Schistosoma genus. The present work re-examines the question of the geographical origin of human schistosomes by analysing a new genomic marker (ITS2) as well as by including the use of O. turkestanicum originating from northeastern China. Our results are in agreement with previous work using 28S, in demonstrating that Schistosoma is not monophyletic. However, O. turkestanicum, whatever the method of analysis used (distance or parsimony), was grouped with members of the japonicum group to the exclusion of African Schistosoma species. Then, our data argue strongly for the need for further phylogenetic study including new taxa and new genomic sequences before definitly concluding either an Asian or African origin for the genus Schistosoma.

P rotein sequences from bone-derived collagen as old as 68 million years have been detected by using mass spectrometry (1, 2). A BLAST search of the resulting peptide sequences found the highest similarities between the collagen peptides obtained from extracts of Tyrannosaurus rex fossil bone and those of birds (Gallus gallus) and between mastodon (Mammut americanum) and other mammals, including elephant (Loxodonta africana). We performed phylogenetic analyses to infer the evolutionary relationships of the T. rex [Museum of the Rockies (MOR) 1125] and mastodon (MOR 605). The results extend our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization.

Sequences from internal transcribed spacers (ITS) of nuclear ribosomal DNA were determined to examine phylogenetic relationships in the genus Acer. ITS 1 sequences in twenty-eight species of Acer and a species of Diptemnia in the family Aceraceae ranged from 220 to 242 bp and ITS 2 sequences from 215 to 251 bp. The size of the 5.8s coding region was 164 bp for all species examined in the family. Phylogenetic analysis of TTS sequences placed a very robust clade of section Palmata at the base of the tree. Three species of section Parvifora sensu de Jong (1994), A. spkatum, A. distylum and A. nipponicum, did not form a monophyletic clade. Acer spimfum was separated from the robust clade of A. disty/um and A. nipponicum. Molecular tree strongly supports the close relationship among section Plafanoidea, Glabra series Arguta, and section Macrantha. The close relationship between sections Penfaphyla and Trifoliata was also strongly suggested in ITS tree. Sections Rubra and Hyptiocarpa appeared to be closely allied with each other. The average rate of nucleotide substitution was estimated as (8.0f1.9)~10-" substitutions per site per year for ITS 1 and (9.0t-1.6)~10-~ for ITS 2.

During a continuous survey of yeast diversity in Taiwan, an anamorphic yeast, belonging to the genus Cryptococcus was obtained. To determine the species identity, this yeast was analysed morphologically, physiologically, and phylogenetically. Neither ballistoconidia nor sexual reproduction was observed. Sequence analysis of 26S rRNA gene indicates that Cryptococcus zeae, Bullera kunmingensi, Cryptococcus luteolus, Bullera sinensis are the most closely related species, with 96.0 to 96.7% sequence similarity. But they only show low sequence similarity with the yeast obtained in this study in the ITS region (91.2 to 96.2%), and differ physiologically from it in the ability to assimilate creatine, creatinine and imidazole, and to grow in 0.1% cycloheximide. Judging from these comparative analyses, a novel species, Cryptococcus taiwanensis, is proposed, with BCRC 23252 T (= CBS 12180 T ) as the type strain.

Euphrasia includes perennial or annual green parasitic plants, and has a disjunct bipolar distribution except for one transtropical connection across the high mountains of Oceania. The disjunction is coupled with strikingly contrasting patterns of morphological diversity between the southern and northern hemispheres, making it an exciting model to study processes of evolutionary diversification which shaped present floras. We inferred the relationships among 51 species representing 14 of the 15 sections of the genus based on nrDNA ITS and cpDNA trnL intron, trnL-trnF and atpB-rbcL intergenic spacers. Maximum parsimony and Bayesian inference support monophyly of the genus and of several intrageneric groups characterized by morphology, ploidy level, and geographic range. Molecular phylogenetic dating using Bayesian ''relaxed" clock methods suggests that the earliest Euphrasia radiations occurred minimum 11-8 Mya with bipolarity being achieved 7-5 Mya. Biogeographic analyses using explicit modelbased approach inferred Eurasia as an ancestral area for the genus. The most parsimonious reconstruction found by a dispersal-vicariance analysis requires 17 dispersals to account for the current biogeographic pattern and supports Eurasian origin for Euphrasia. Both long-distance dispersal and across land vicariance can be invoked to explain the diversification in the genus, which experienced rapid radiations driven by new ecological opportunities of the late Pliocene and Pleistocene but also retained a set of local endemic or relict species of an earlier origin.

Mutualisms are of fundamental importance in all ecosystems but their very existence poses a series of challenging evolutionary questions. Recently, the application of molecular analyses combined with theoretical advances have transformed our understanding of many specific systems, thereby contributing to the possibility of a more general understanding of the factors that influence mutualisms.

Recently, a molecular phylogeny based on four mtDNA gene regions has been estimated for 17 species and subspecies of Aegla freshwater crabs from Chile. With this phylogenetic hypothesis and information on geographic distribution, environmental conditions, habitat requirements, and population abundance, Chilean aeglids were assessed for conservation status based on the criteria included in the IUCN Red List Categories (2001). Aegla concepcionensis and Aegla expansa qualify as ''Extinct in the Wild'' and nine other taxa fall within the threatened category: three as ''Critically Endangered'' (A. laevis laevis, A. papudo and A. spectabilis) and six as ''Vulnerable'' (A. alacalufi, A. bahamondei, A. cholchol, A. hueicollensis, A. laevis talcahuano and A. manni). Six hydrographic regions within temperate Chile were ranked for conservation priority using species richness, and phylogenetic and genetic diversity indices. The hydrographic region made up of the Tucapel, Imperial, and Tolte´n Basins was found to rank highest in terms of conservation priorities. Conservation of this region and the regions ranging between the Aconcagua and Mataquito Basins, and the Valdivia and Maullı´n Basins, would preserve almost all the Aegla diversity present in Chile.

Pigment analysis performed on 30 Prasinophy- ceae strains revealed two main groups: the prasinoxanthin-containing and prasinoxanthin- less Prasinophyceae. Prasinoxanthin-containing Prasinophyceae comprised the orders Mamiellales, Pseudoscourfieldiales (Pycnococcaceae), and Prasi- nococcales. For this group, classification with pig- ment composition showed a good agreement with molecular phylogeny. Mamiellales, except Crustomastix stigmatica, accumulated uriolide, mi- cromonal, dihydrolutein, and the pigment Uniden- tified M1 as

When phylogenetic trees constructed from morphological and molecular evidence disagree (i.e. are incongruent) it has been suggested that the differences are spurious or that the molecular results should be preferred a priori. Comparing trees can increase confidence (congruence), or demonstrate that at least one tree is incorrect (incongruence). Statistical analyses of 181 molecular and 49 morphological trees shows that incongruence is greater between than within the morphological and molecular partitions, and this difference is significant for the molecular partition. Because the level of incongruence between a pair of trees gives a minimum bound on how much error is present in the two trees, our results indicate that the level of error may be underestimated by congruence within partitions. Thus comparisons between morphological and molecular trees are particularly useful for detecting this incongruence (spurious or otherwise). Molecular trees have higher average congruence than morphological trees, but the difference is not significant, and both within-and between-partition incongruence is much lower than expected by chance alone. Our results suggest that both molecular and morphological trees are, in general, useful approximations of a common underlying phylogeny and thus, when molecules and morphology clash, molecular phylogenies should not be considered more reliable a priori.

Penaeoidea is a diverse group of economically important marine shrimps. Attention to the evolutionary history of the penaeoids has been raised since studies using mitochondrial DNA markers and sperm ultrastructure contradict classification of the penaeoid families based on morphology and hence challenge the long standing taxonomy of this superfamily. In this study, DNA sequences of two nuclear protein-coding genes, phosphoenolpyruvate carboxykinase and sodium-potassium ATPase alpha-subunit, were determined from 37 penaeoid genera to reconstruct the evolutionary relationships and to estimate divergence ages of the penaeoid shrimps. Phylogenetic analyses using maximum likelihood and Bayesian approaches strongly support the monophyly of Solenoceridae, Aristeidae and Benthesicymidae, but find Sicyoniidae nested within Penaeidae, making this family paraphyletic. Penaeoidea comprises two lineages: the former three families in one while the latter two in another. The diversification of the...

Podosphaera is a genus of the powdery mildew fungi belonging to the tribe Cystotheceae of the Erysipha ceae. Among the host plants of Podosphaera, 86 % of hosts of the section Podosphaera and 57 % hosts of the subsection Sphaerotheca belong to the Rosaceae. In order to reconstruct the phylogeny of Podosphaera and to determine evolutionary relationships between Podosphaera and its host plants, we used 152 ITS sequences and 69 28S rDNA sequences of Podosphaera for phylogenetic analyses. As a result, Podosphaera was divided into two large clades: clade 1, consisting of the section Podosphaera on Prunus (P. tridactyla s.l.) and subsection Magnicel lulatae; and clade 2, composed of the remaining member of section Podosphaera and subsection Sphaerotheca. Because section Podosphaera takes a basal position in both clades, section Podosphaera may be ancestral in the genus Podosphaera, and the subsections Sphaerotheca and Magnicellulatae may have evolved from section Podosphaera independently. Podosphaera isolates from the respective subfamilies of Rosaceae each formed different groups in the trees, suggesting a close evolutionary relationship between Podosphaera spp. and their rosaceous hosts. However, tree topology comparison and molecular clock calibration did not support the possibility of co-speciation between Podosphaera and Rosaceae. Molecular phylogeny did not support species delimitation of P. aphanis, P. clandestina, P. ferruginea, P. spiraeae and P. tridactyla in their current circumscriptions, which suggests the need for revision of these species.

Two distinct P element subfamilies, designated M-type and O-type, reside in the genome of D. bifasciata. PCRscreening of 65 Drosophila species revealed that only D. bifasciata and its closest relative D. imaii possess O-type elements. Outside the genus, O-type elements were detected in Scaptomyzapallida. Restriction analyses show that the general structure of the O-type elements from S. pallida and D. bifasciata is the same. Sequence divergence turned out to be extremely low (0.43%). These results suggest that the O-type subfamily of D. bifasciata has been received by horizontal transfer from an external source, most probably from the genus Scaptomyza, as has been previously suspected for the M-type family. Since the sequence divergence between M-type elements from S. paUida and D. bifasciata is eighteenfold higher than that between O-type elements, two independent intergeneric transfer events have to be postulated. In order to re-examine the taxonomic status of S. pallida, a partial sequence (489 bp) of the Adh gene was analysed. The data clearly prove that S. pallida has to be placed far outside the D. obscura group.

The evolutionary history of three out of four birds traditionally classified into the genus Rhodopechys birds has been studied by comparing their mitochondrial cytochrome b DNA sequence with that of greenfinches and other genus Carduelis finches. The desert finch (Rhodopechys obsoleta) or a sister extinct species seems to have existed about 6 million years ago in Asian and perhaps African desert-like areas. This bird has no molecular relationship with other Rhodopechys birds and seems to have given rise to the greenfinches radiation, probably by allopatry of marginal or isolated groups; the latter would have evolved to green plumage colours and more simple song modulations (i.e., greenfinches). The possible role of assortative mating and the newly postulated acquired phenotypic characters in greenfinches speciation are discussed.

The phylogenetic relationships of the moss genus Pleurochaete was investigated using evidence from chloroplast and nuclear ribosomal DNA sequences (atpB-abcL spacer, rps4+rps4-trnS IGS, trnL-trnF region, and ITS1-5.8S-ITS2 region). Monophyly of Pleurochaete is confirmed, but the genus is nested within Tortella. Five highly supported clades, including Chionoloma, Pseudosymblepharis and Trichostomum tenuirostre, were found, partially corresponding to phytogeographic areas. However, denser sampling is needed to resolve subgeneric relationships. Within Pleurochaete three monophyletic clades were recovered: neotropical Pleurochaete luteola, European Pleurochaete squarrosa, and North American P. squarrosa. The relationships between and taxonomic status of these clades are not resolved. Our results point to two hypotheses to explain the current situation: (1) an ancient, wide distribution of P. squarrosa on the Laurasian continent, with a subsequent split into two genetically isolated clades and sympatric ecological isolation of P. luteola; and (2) a neotropical origin of the genus, followed by long-distance dispersal of P. squarrosa into Eurasia. In contrast to previous molecular studies on transatlantic bryophytes, no evidence was found of recent intercontinental gene flow in P. squarrosa. Consequently, the two genetically isolated but morphologically indistinguishable clades of P. squarrosa may represent a further example for either lineage sorting or cryptic speciation in mosses.

As currently defined, the 24 species of Schoenocaulon occur in three disjunct areas: north central Florida (one species, S. dubium), southern Peru (portion of the range of S. officinale), and the region from southeastern New Mexico-Texas south to Venezuela; the 20 species endemic to Mexico are geographically restricted. Species delimitations, often based on tepal morphology, have been problematic. Our analyses of ITS sequence data for all 27 species and infraspecific taxa support recognition of two new species and recircumscription and placement of elements of the polyphyletic S. ghiesbreghtii and S. mortonii complexes. For taxa with adequate sampling, our data also indicate 11-12 cladospecies and 3-6 metaspecies according to the apomorphic species concept. The resolved phylogeny, correlated with geography and morphology, allows insight into biogeographical diversification and the evolution of some unusual morphological characters within the genus, such as nectary differentiation and tepal margin type.

The order Decapoda represents a species-rich group of crustaceans. Numerous economically important and morphologically diverse members of this group have been studied extensively for many decades, in part to understand their phylogeny. There are several competing hypotheses concerning relationships among the major lineages of Decapoda. Our laboratories are estimating a robust decapod phylogeny based on molecular and morphological data in an attempt to resolve relationships among major lineages. The order includes roughly 175 families and more than 15,000 described species (extant and extinct). Interpretations are complicated by the estimated 437 million years since origin of the Decapoda, with all the major lineages likely established by 325 million years ago. Constructing a molecular phylogeny across such a timescale requires markers with enough variation to infer relationships at the fi ne scale (at and within the family level) but which are conservative enough to refl ect deeper divergences across infraorders. Here we present a molecular phylogeny for the order Decapoda, combining nuclear and mitochondrial sequences, to investigate relationships among nine pleocyemate infraorders, one dendrobranchiate superfamily, 56 families, 113 genera, and 128 species. New and available sequence data are assembled to build the most extensive decapod phylogeny to date both in terms of taxon representation and genetic coverage. We discuss current and new hypotheses of decapod relationships and suggest a plan for the movement towards a consensus of decapod evolution.

In Chapter 1, the literature relating to rabies virus and the rabies like lyssaviruses is reviewed. In Chapter 2, data are presented from 1170 diagnostic submissions for ABLV testing by fluorescent antibody test (Centocor FAT). All 27 non-bat submissions were ABLV-...

We present Wrst insights into the molecular phylogeny of the grayling genus Thymallus (Salmonidae) using sequences from the mitochondrial control region and ATPase6 genes. A suite of analytical approaches were applied for each gene separately and for the combined data. The ATPase6 gene is shown to have a mean divergence rate across the genus of 2.46 times faster than the complete control region. Based on the combined data, four major (internal) clades, presumably originating in the Pliocene, were resolved with high support in all analyses and represented two distinct lineages in the Amur basin, one lineage in all remaining Siberian and Mongolian drainages, and one lineage corresponding to European grayling Thymallus thymallus. The resolution of multiple lineages, from both additional internal and terminal clades, within each major drainage basin underscores the complexity and eVects that Pleistocene hydrological dynamics have had on the distribution of biodiversity in Siberia. 

The effect of meta-topolin (mT) and meta-topolin riboside (mTR) on the micropropagation of 'Williams' Cavendish banana was studied in comparison with benzyladenine (BA). In vitro cultures of Williams' banana, at third sub-culture level, were purchased from African Biotechnologies (Pty) Ltd South Africa. These were then sub-cultured on Murashige and Skoog media containing 15, 22.2 and 30 µM of BA, mT and mTR and supplemented with 2 mg/l indole-3-acetic acid (IAA), 3% sucrose, 0.2 g/l adenine sulphate, 0.38 g/l sodium dihydrogen orthophosphate and solidified with 2 g/l gelrite. Results recorded after six weeks of growth demonstrated that there were statistically significant differences in the number of shoots and roots between the treatments at 22.2 µM concentration. This concentration was previously reported to be optimum for banana micropropagation. At 15 µM there was excessive vegetative growth of individual plants with little or no multiplication. The 30 µM concentration on the other hand resulted in the growth of a mass of undifferentiated tissue. At 22.2 µM, mTR gave the highest multiplication rate (5.3 shoots per explant). BA-treated plants rooted better in the multiplication medium (contrary to our previous finding on Aloe polyphylla) and mTR-treated plants produced the least number of roots. mT treatment gave intermediate results in both shoot and root numbers. There was no significant difference in shoot length between the treatment means compared to the control. The effect of mT and mTR on somaclonal variation is being further investigated.

Species composition and systematic placement within the order Plagiorchiida has been controversial. Species number in Glypthelmins Stafford, 1905, a genus of cosmopolitan parasites of anurans, has varied between 19 and 28 species, depending on the taxonomic treatment. The present study performs a phylogenetic analysis using partial lsrDNA sequences to test the monophyly of the genus, and compares new sequences obtained with those published for different plagiorchiids to clarify the systematic position of Glypthelmins within the order Plagiorchiida. Maximum parsimony (MP) and maximum likelihood (ML) analyses result in identical tree topology. The single MP tree (L ¼ 1587, CI ¼ 0.40, RI ¼ 0.76) includes several clades with high bootstrap and Bremer support values. Glypthelmins sensu lato as traditionally classified is paraphyletic.

Antarctica is a continent locked in ice, with almost 99.7% of current terrain covered by permanent ice and snow, and clear evidence that, as recently as the Last Glacial Maximum (LGM), ice sheets were both thicker and much more extensive than they are now. Ice sheet modelling of both the LGM and estimated previous ice maxima across the continent give broad support to the concept that most if not all currently ice-free ground would have been overridden during previous glaciations. This has given rise to a widely held perception that all Mesozoic (pre-glacial) terrestrial life of Antarctica was wiped out by successive and deepening glacial events. The implicit conclusion of such destruction is that most, possibly all, contemporary terrestrial life has colonised the continent during subsequent periods of glacial retreat. However, several recently emerged and complementary strands of biological and geological research cannot be reconciled comfortably with the current reconstruction of Antarctic glacial history, and therefore provide a fundamental challenge to the existing paradigms. Here, we summarise and synthesise evidence across these lines of research. The emerging fundamental insights corroborate substantial elements of the contemporary Antarctic terrestrial biota being continuously isolated in situ on a multi-million year, even pre-Gondwana break-up timescale. This new and complex terrestrial Antarctic biogeography parallels recent work suggesting greater regionalisation and evolutionary isolation than previously suspected in the circum-Antarctic marine fauna. These findings both require the adoption of a new biological paradigm within Antarctica and challenge current understanding of Antarctic glacial history. This has major implications for our understanding of the key role of Antarctica in the Earth System.

Phylogenetic relationships among the 10 nominate taxa of Japanese brown frogs (Rana pirica, R. dybowskii, R. omativentris, R. japonica, R. tagoi tagoi, R. t. yakushimensis, R. t. okiensis, R. sakuraii, R. tsushimensis and R. okinavana) are assessed using sequences of 456 base pairs of the mitochondrial cytochrome b genes. The resultant phylogenetic trees indicate that a presumptive common ancester of R. tagoi and R. sakuraii, both with distinct breeding habits, differentiated earliest, followed by that of R. tsushimensis and R. okinavana, both isolated on small islands. Considerable genetic differentiation is found between subspecies of R. tagoi and between two populations of R. okinavana. Rana pirica, R. dybowskii and R. ornativentris, all with 2n= 24 chromosomes, form e monophyletic group, and appear to be derived from a 26-chromosome ancestor.

The morphological based taxonomy of highly derived parasite groups is likely to poorly reflect their evolutionary relationships. The taxonomy of the monogenean family Capsalidae, which comprises approximately 180 species of flatworm parasites that predominantly attach to external surfaces of chondrichthyan and teleost fishes, is based mainly on six morphological characters. The phylogenetic history of the family is largely unknown. We reconstructed the phylogenetic relationships of 47 species in 20 genera from eight of the nine subfamilies, from nucleotide sequences of three unlinked nuclear genes, 28S ribosomal RNA, Histone 3 and Elongation Factor 1 a. Our phylogeny was well corroborated, with 75% of branches receiving strong support from both Bayesian posterior probabilities and maximum likelihood bootstrap proportions and all nodes showed positive partitioned likelihood support for each of the three genes. We found that the family was monophyletic, with the Gyrodactylidae and Udonellidae forming the sister group. The Capsalinae was monophyletic, however, our data do not support monophyly for the Benedeniinae, Entobdellinae and Trochopodinae. Monophyly was supported for Capsala, Entobdella, Listrocephalos, Neobenedenia and Tristoma, but Benedenia and Neoentobdella were polyphyletic. Comparisons of the distribution of character states for the small number of morphological characters on the molecular phylogeny show a high frequency of apparent homoplasy. Consequently the current morphological classification shows little correspondence with the phylogenetic relationships within the family.

We sequenced a part of the mitochondrial cytochrome-b gene from the seven treecreeper species, including 18 subspecies, to reconstruct the phylogeny of the genus Certhia . Species status of all seven species could be affirmed. Certhia discolor , C. himalayana , C . nipalensis , and C . tianquanensis , the species with relatively small distribution ranges in southeast Asia and simple territorial song, are found at the base of all phylogenetic trees, although without good support. A comparatively recent sister species of C. tianquanensis is C. nipalensis , replacing C. discolor as closest relative. Certhia familiaris , C. brachydactyla and C. americana form a derived set of species (again only weak support). The closest relative of C. americana is C. brachydactyla . The C. familiaris subtree is deeply split into two well-defined population groups: a Eurasian group including populations in northern China (Qinling range northward and all Eurasia) and a Sino-Himalayan group (Himalayas and China excluding northern China). In accordance with acoustic characters, the three subspecies hodgsoni , mandellii and khamensis of the Sino-Himalayan group are combined and elevated to species rank: Certhia hodgsoni . Certhia discolor manipurensis is deeply split from nominate discolor as well, and is also promoted to species level. Within C. brachydactyla (western palearctic) and within C. hodgsoni (Himalayas, China) several populations form well-supported separate lineages that diverged quite recently and represent subspecies level. In all other species, moleculargenetic and vocal characters support traditional species delimitation. . List of proposed species and superspecies in Certhia including the taxonomic changes.

Stingless bees (Meliponini) constitute a diverse group of highly eusocial insects that occur throughout tropical regions around the world. The meliponine genus Melipona is restricted to the New World tropics and has over 50 described species. Melipona, like Apis, possesses the remarkable ability to use representational communication to indicate the location of foraging patches. Although Melipona has been the subject of numerous behavioral, ecological, and genetic studies, the evolutionary history of this genus remains largely unexplored. Here, we implement a multigene phylogenetic approach based on nuclear, mitochondrial, and ribosomal loci, coupled with molecular clock methods, to elucidate the phylogenetic relationships and antiquity of subgenera and species of Melipona. Our phylogenetic analysis resolves the relationship among subgenera and tends to agree with morphology-based classification hypotheses. Our molecular clock analysis indicates that the genus Melipona shared a most recent common ancestor at least $14-17 million years (My) ago. These results provide the groundwork for future comparative analyses aimed at understanding the evolution of complex communication mechanisms in eusocial Apidae.

Species of Diaporthe are important plant pathogens of a wide range of hosts worldwide. In the present study the species causing melanose and stem end rot diseases of Citrus spp. are revised. Three species of Diaporthe occurring on Citrus are characterised, including D. citri, D. cytosporella and D. foeniculina. Morphology and phylogenetic analyses of the complete nuclear ribosomal internal transcribed spacer regions and partial sequences of actin, beta-tubulin, calmodulin and translation elongation factor 1-alpha were used to resolve species on Citrus and related Diaporthe species. Diaporthe citri occurs on Citrus throughout the Citrus-growing regions of the world. Diaporthe cytosporella is found on Citrus in Europe and California (USA). Diaporthe foeniculina, including the synonym D. neotheicola, is recognised as a species with an extensive host range including Citrus. Diaporthe medusaea, a name widely used for D. citri, was determined to be a synonym of D. rudis, a species with a broad host range. Diaporthe citri is delimited based on molecular phylogenetic analysis with the inclusion of the conserved ex-type and additional collections from different geographic locations worldwide. D. cytosporella, D. foeniculina and D. rudis are epitypified, fully described and illustrated with a review of all synonyms based on molecular data and morphological studies. Newly designed primers are introduced to optimise the amplification and sequencing of calmodulin and actin genes in Diaporthe. A discussion is provided of the utility of genes and the need for multi-gene phylogenies when distinguishing species of Diaporthe or describing new species.

A new species of Tetraselmis, T. indica Arora & Anil, was isolated from nanoplankton collected from salt pans in Goa (India) and is described based on morphological, ultrastructural, 18S rRNA gene sequence, and genome size data. The species is characterized by a distinct eyespot, rectangular nucleus, a large number of Golgi bodies, two types of flagellar pit hairs and a characteristic type of cell division. In nature, the species was found in a wide range of temperatures (48°C down to 28°C) and salinities, from hypersaline (up to 350 psu) down to marine (c. 35 psu) conditions. Phylogenetic analysis based on 18S rDNA sequence data showed that T. indica is most closely related to unidentified Tetraselmis strains from a salt lake in North America.

The aerial parts of 54 accessions representing 41 Linum species and four species of related genera were analysed for lignans by means of HPLC-ESI/MS-MS-UV/DAD. In total, 64 different lignans of the aryltetralin-, arylnaphthalene-, aryldihydronaphthalene-, dibenzylbutyrolactone-, and furofuran type were identified. According to their lignan profile, the Linum species can be divided in two groups accumulating as major lignan types either cyclolignans of the aryltetralin-series on one hand, or aryldihydronaphthalenes/ arylnaphthalenes, on the other. Five of the investigated Linum species did not contain any detectable amounts of these lignans under the chosen analytical conditions. Furthermore, none of the lignans identified in Linum species was detectable in representatives of three related genera, namely, Reinwardtia (Linaceae, Linoideae), Hugonia and Indorouchera (Linaceae, Hugonioideae).

This study constitutes the first evolutionary investigation of the snake family Psammophiidae-the most widespread, most clearly defined, yet perhaps the taxonomically most problematic of Africa's familylevel snake lineages. Little is known of psammophiid evolutionary relationships, and the type genus Psammophis is one of the largest and taxonomically most complex of the African snake genera. Our aims were to reconstruct psammophiid phylogenetic relationships and to improve characterisation of species boundaries in problematic Psammophis species complexes. We used approximately 2500 bases of DNA sequence from the mitochondrial and nuclear genomes, and 114 terminals covering all psammophiid genera and incorporating approximately 75% of recognised species and subspecies. Phylogenetic reconstructions were conducted primarily in a Bayesian framework and we used the Wiens/Penkrot protocol to aid species delimitation. Rhamphiophis is diphyletic, with Rhamphiophis acutus emerging sister to Psammophylax. Consequently we transfer the three subspecies of Rhamphiophis acutus to the genus Psammophylax. The monotypic genus Dipsina is sister to Psammophis. The two species of Dromophis occupy divergent positions deeply nested within Psammophis, and we therefore relegate Dromophis to the synonymy of Psammophis. Our results allow division of the taxonomically problematic Psammophis 'sibilans' species complex into two monophyletic entities, provisionally named the 'phillipsii' and 'subtaeniatus' complexes. Within these two clades we found support for the status of many existing species, but not for a distinction between P.p. phillipsii and P. mossambicus. Additionally, P. cf. phillipsii occidentalis deserves species status as the sister taxon of P. brevirostris.

The family Callichthyidae comprises eight genera of fishes widely distributed across the Neotropical region. In the present study, sequences of the mitochondrial genes 12S rRNA, 16S rRNA, ND4, tRNA His , and tRNA Ser were obtained from 28 callichthyid specimens. The sample included 12 species of Corydoras, three species of Aspidoras, two species of Brochis, Dianema, Lepthoplosternum, and Megalechis, and two local populations of Callichthys and Hoplosternum. Sequences of Nematogenys inermis (Nematogenyidae), Trichomycterus areolatus, and Henonemus punctatus (Trichomycteridae), Astroblepus sp. (Astroblepidae), and Neoplecostomus paranensis, Delturus parahybae, and Hemipsilichthys nimius (Loricariidae) were included as the outgroup. Phylogenetic analyses were performed by using the methods of maximum parsimony and maximum likelihood. The results of almost all analyses were very similar. The family Callichthyidae is monophyletic and comprises two natural groups: the subfamilies Corydoradinae (Aspidoras, Brochis, and Corydoras) and Callichthyinae (Callichthys, Dianema, Hoplosternum, Lepthoplosternum, and Megalechis), as previously demonstrated by morphological studies. The relationships observed within these subfamilies are in several ways different from those previously proposed on the basis of morphological data. Molecular results were compared with the morphologic and cytogenetic data available on the family.

Cockatoos are the distinctive family Cacatuidae, a major lineage of the order of parrots (Psittaciformes) and distributed throughout the Australasian region of the world. However, the evolutionary history of cockatoos is not well understood. We investigated the phylogeny of cockatoos based on three mitochon- drial and three nuclear DNA genes obtained from 16 of 21 species of Cacatuidae. In addition, five novel mitochondrial genomes were used to estimate time of divergence and our estimates indicate Cacatuidae diverged from Psittacidae approximately 40.7 million years ago (95% CI 51.6–30.3 Ma) during the Eocene. Our data shows Cacatuidae began to diversify approximately 27.9 Ma (95% CI 38.1–18.3 Ma) during the Oligocene. The early to middle Miocene (20–10 Ma) was a significant period in the evolution of modern Australian environments and vegetation, in which a transformation from mainly mesic to xeric habitats (e.g., fire-adapted sclerophyll vegetation and grasslands) occurred. We hypothesize that this environmen- tal transformation was a driving force behind the diversification of cockatoos. A detailed multi-locus molecular phylogeny enabled us to resolve the phylogenetic placements of the Palm Cockatoo (Probosciger aterrimus), Galah (Eolophus roseicapillus), Gang-gang Cockatoo (Callocephalon fimbriatum) and Cockatiel (Nymphicus hollandicus), which have historically been difficult to place within Cacatuidae. When the molecular evidence is analysed in concert with morphology, it is clear that many of the cockatoo species’ diagnostic phenotypic traits such as plumage colour, body size, wing shape and bill morphology have evolved in parallel or convergently across lineages.