Genomic blot hybridization as a tool of phylogenetic analysis: Evolutionary divergence in the genusDrosophila

Summary Comparative, quantitative Southern analysis of genomic DNA, using single-copy sequence probes, potentially is valuable for phylogenetic analysis. We have examined 27Drosophila species, belonging to two subgenera, seven species groups, and ten subgroups, using a variety of cloned and characterized probes: twelve cloned sequences fromD. melanogaster, two fromD. pseudoobscura, and two fromD. grimshawi. The data are generally congruent with accepted phylogenetic relationships inDrosophila, and confirm or clarify some previously uncertain relationships. The potential and limitations of the method are discussed.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986     

Generic delimitation and phylogenetic relationships within the subtribe Chironiinae (Chironieae: Gentianaceae), with special reference to Centaurium: evidence from nrDNA and cpDNA sequences

To better understand the evolutionary history of the genus Centaurium and its relationship to other genera of the subtribe Chironiinae (Gentianaceae: Chironieae), molecular analyses were performed using 80 nuclear ribosomal ITS and 76 chloroplast trnLF (both the trnL UAA intron and the trnL-F spacer) sequences. In addition, morphological, palynological, and phytochemical characters were included to a combined data matrix to detect possible non-molecular synapomorphies. Phylogenetic reconstructions support the monophyly of the Chironiinae and an age estimate of ca. 22 million years for the subtribe. Conversely, both molecular data sets reveal a polyphyletic Centaurium, with four well-supported main clades hereafter treated as separate genera. The primarily Mediterranean Centaurium s.s. is closely related to southern African endemics Chironia and Orphium, and to the Chilean species Centaurium cachanlahuen. The resurrected Mexican and Central American genus Gyrandra is closely related to Sabatia (from eastern North America). Lastly, the monospecific genus Exaculum (Mediterranean) forms a monophyletic group together with the two new genera: Schenkia (Mediterranean and Australian species) and Zeltnera (all other indigenous American centauries). Several biogeographical patterns can be inferred for this group, supporting a Mediterranean origin followed by dispersals to (1) North America, Central America, and South America, (2) southern Africa (including the Cape region), and (3) Australia and Pacific Islands.     

Resolving the systematic and phylogenetic position of isolated ovules: a case study on a new genus from the Permian of China

Isolated ovules occur in many fossil plant assemblages, where they provide important insights into seed‐plant diversity and evolution. However, in many cases, the ovules cannot be attributed to individual groups of seed plants, restricting systematic and evolutionary assessments that can be made from otherwise well‐characterized fossil taxa. In the present paper, we describe a new kind of ovule discovered in tuffaceous sediments from the Permian‐aged Xuanwei Formation in Guizhou Province, China. This ovule has 180° rotational symmetry and an integument comprising a variably thick sarcotesta, a uniformly thick sclerotesta and a uniformly thin endotesta. The nucellus is attached to the integument at least basally and contains a collapsed seed megaspore; a nucellar apex is absent. Both the integument and nucellus are vascularized by paired bundles in the major plane of the ovule; the integumentary bundles are considerably larger than the nucellar bundles and the nucellar bundles emerge from a conical vascular pad. Generation of a three‐dimensional reconstruction based on serial peels revealed the gross morphology and organization of the ovule and highlighted the presence of features consistent with cardiocarpalean‐type ovules (ovule shape, histological features of the integument) and also features more typical of lagenostomalean‐ and trigonocarpalean‐type ovules (large integumentary bundles, presence of nucellar bundles). To assess the affinity and evolutionary significance of the ovule, it has been included in a cladistic matrix of cardiocarpalean‐, lagenostomalean‐ and trigonocarpalean‐type ovules. Results place the ovule within the cardiocarpalean group of ovules known to have been produced by several plant groups, including cordaitean coniferophytes, pteridosperms and Palaeozoic conifers. The cladistic topology supports generic level distinction of the present species, requiring the establishment of Muricosperma guizhouensis Seyfullah & J.Hilton gen. & sp. nov . Lagenostomalean ovules produced by hydrasperman pteridosperms form a basal paraphyletic grade, whereas trigonocarpalean ovules produced by medullosan pteridosperms form a monophyletic group in which Stephanospermum is paraphyletic with respect to Rhynchosperma and Pachytesta. The results also place the Mississippian ovule Mitrospermum bulbosum apart from all of the Pennsylvanian species of Mitrospermum that form a strongly supported clade. Consequently, M. bulbosum is transferred to the new genus Whitaddera Seyfullah & J.Hilton as W. bulbosa (Long) Seyfullah & J.Hilton. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 84–108.     

The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species

The evolution of the RecA protein was analyzed using molecular phylogenetic techniques. Phylogenetic trees of all currently available complete RecA proteins were inferred using multiple maximum parsimony and distance matrix methods. Comparison and analysis of the trees reveal that the inferred relationships among these proteins are highly robust. The RecA trees show consistent subdivisions corresponding to many of the major bacterial groups found in trees of other molecules including the , , , , proteobacteria, cyanobacteria, high-GC gram-positives, and the Deinococcus-Thermus group. However, there are interesting differences between the RecA trees and these other trees. For example, in all the RecA trees the proteins from gram-positive species are not monophyletic. In addition, the RecAs of the cyanobacteria consistently group with those of the high-GC gram-positives. To evaluate possible causes and implications of these and other differences phylogenetic trees were generated for small-subunit rRNA sequences from the same (or closely related) species as represented in the RecA analysis. The trees of the two molecules using these equivalent species-sets are highly congruent and have similar resolving power for close, medium, and deep branches in the history of bacteria. The implications of the particular similarities and differences between the trees are discussed. Some of the features that make RecA useful for molecular systematics and for studies of protein evolution are also discussed.     

A new look at geographic and phylogenetic relationships within the species group surrounding Octopus vulgaris (Mollusca, Cephalopoda): indications of very wide distribution from mitochondrial DNA sequences

The distribution of Octopus vulgaris has not yet been completely clarified. For a long time, a cosmopolitan distribution with unknown distribution limits had been assumed. This assumption has recently been questioned and it has been postulated that the distribution is restricted to the Mediterranean and the northeastern Atlantic. However, as our previous studies show, the existence of O. vulgaris can be confirmed for the Mediterranean and the whole eastern Atlantic, and evidence is provided for its occurrence in the western Atlantic. The aim of the present work is to extend our previous data matrix and to clarify whether O. vulgaris exists in the northwestern Pacific. Therefore, the sequence variation in ostensible O. vulgaris from 13 localities in the Mediterranean (France), the Atlantic Ocean [Lanzarote, Senegal, South Africa (Atlantic, Indian Ocean), Tristan da Cunha, north, middle and south Brazil], the Caribbean Sea (Venezuela) and the Pacific Ocean (Taiwan, Japan and Costa Rica) was examined using the mitochondrial genes coding for the 16S rRNA and cytochrome oxidase subunit III (COIII). Sequence divergence was relatively low between populations of O. vulgaris from the Mediterranean, the eastern and western Atlantic (except north Brazil), Venezuela, Taiwan and Japan compared with other species of the genus Octopus . Trees constructed by using maximum likelihood, neighbour joining and maximum parsimony algorithms (PAUP) show the above-mentioned populations from the Mediterranean, the western and eastern Atlantic, Venezuela and the northwestern Pacific (Japan and Taiwan) as a monophyletic cluster. Thus, even if the Octopus vulgaris -like octopus from north Brazil should turn out a cryptic species, the data of this work not only support our hypothesis of the distribution of O. vulgaris in the Mediterranean, the eastern and western Atlantic but also show that O. vulgaris is present in the northwestern Pacific, namely in the waters of Taiwan and Japan.     

Trends in cation, nitrogen, sulfate and hydrogen ion concentrations in precipitation in the United States and Europe from 1978 to 2010: a new look at an old problem

Industrial emissions of SO₂ and NO_x, resulting in the formation and deposition of sulfuric and nitric acids, affect the health of both terrestrial and aquatic ecosystems. Since the mid-late 20th century, legislation to control acid rain precursors in both Europe and the US has led to significant declines in both SO₄–S and H⁺ in precipitation and streams. However, several authors noted that declines in streamwater SO₄–S did not result in stoichiometric reductions in stream H⁺, and suggested that observed reductions in base cation inputs in precipitation could lessen the effect of air pollution control on improving stream pH. We examined long-term precipitation chemistry (1978–2010) from nearly 30 sites in the US and Europe that are variably affected by acid deposition and that have a variety of industrial and land-use histories to (1) quantify trends in SO₄–S, H⁺, NH₄–N, Ca, and NO₃–N, (2) assess stoichiometry between H⁺ and SO₄–S before and after 1990, and (3) examine regional synchrony of trends. We expected that although the overall efforts of developed countries to reduce air pollution and acid rain by the mid-late 20th century would tend to synchronize precipitation chemistry among regions, geographically varied patterns of fossil fuel use and pollution control measures would produce important asynchronies among European countries and the United States. We also expected that control of particulate versus gaseous emission, along with trends in NH₃ emissions, would be the two most significant factors affecting the stoichiometry between SO₄–S and H⁺. Relationships among H⁺, SO₄–S, NH₄–N, and cations differed markedly between the US and Europe. Controlling for SO₄–S levels, H⁺ in precipitation was significantly lower in Europe than in the US, because (1) alkaline dust loading from the Sahara/Sahel was greater in Europe than the US, and (2) emission of NH₃, which neutralizes acidity upon conversion to NH₄ ⁺, is generally significantly higher in Europe than in the US. Trends in SO₄–S and H⁺ in precipitation were close to stoichometric in the US throughout the period of record, but not in Europe, especially eastern Europe. Ca in precipitation declined significantly before, but not after 1990 in most of the US, but Ca declined in eastern Europe even after 1990. SO₄–S in precipitation was only weakly related to fossil fuel consumption. The stoichiometry of SO₄–S and H⁺ may be explained in part by emission controls, which varied over time and among regions. Control of particulate emissions reduces alkaline particles that neutralize acid precursors as well as S-containing particulates, reducing SO₄–S and Ca more steeply than H⁺, consistent with trends in the northeastern US and Europe before 1990. In contrast, control of gaseous SO₂ emissions results in a stoichiometric relationship between SO₄–S and H⁺, consistent with trends in the US and many western European countries, especially after 1991. However, in many European countries, declining NH₃ emissions contributed to the lack of stoichiometry between SO₄–S and H⁺.Recent reductions in NO_x emissions have also contributed to declines in H⁺ in precipitation. Future changes in precipitation acidity are likely to depend on multiple factors including trends in NO_x and NH₃ emission controls, naturally occurring dust, and fossil fuel use, with significant implications for the health of both terrestrial and aquatic ecosystems.     

Limnonectins: a new class of antimicrobial peptides from the skin secretion of the Fujian large-headed frog (Limnonectes fujianensis)

Amphibian skin secretions are rich sources of biologically-active peptides with antimicrobial peptides predominating in many species. Several studies involving molecular cloning of biosynthetic precursor-encoding cDNAs from skin or skin secretions have revealed that these exhibit highly-conserved domain architectures with an unusually high degree of conserved nucleotide and resultant amino acid sequences within the signal peptides. This high degree of nucleotide sequence conservation has permitted the design of primers complementary to such sites facilitating “shotgun” cloning of skin or skin secretion-derived cDNA libraries from hitherto unstudied species. Here we have used such an approach using a skin secretion-derived cDNA library from an unstudied species of Chinese frog - the Fujian large-headed frog, Limnonectes fujianensis - and have discovered two 16-mer peptides of novel primary structures, named limnonectin-1Fa (SFPFFPPGICKRLKRC) and limnonectin-1Fb (SFHVFPPWMCKSLKKC), that represent the prototypes of a new class of amphibian skin antimicrobial peptide. Unusually these limnonectins display activity only against a Gram-negative bacterium (MICs of 35 and 70 μM) and are devoid of haemolytic activity at concentrations up to 160 μM. Thus the “shotgun” cloning approach described can exploit the unusually high degree of nucleotide conservation in signal peptide-encoding domains of amphibian defensive skin secretion peptide precursor-encoding cDNAs to rapidly expedite the discovery of novel and functional defensive peptides in a manner that circumvents specimen sacrifice without compromising robustness of data.     

A new look at an old visual system: structure and development of the compound eyes and optic ganglia of the brine shrimp artemia salina linnaeus, 1758 (branchiopoda,anostraca)

Compared to research carried out on decapod crustaceans, the development of the visual system in representatives of the entomostracan crustaceans is poorly understood. However, the structural evolution of the arthropod visual system is an important topic in the new debate on arthropod relationships, and entomostracan crustaceans play a key role in this discussion. Hence, data on structure and ontogeny of the entomostracan visual system are likely to contribute new aspects to our understanding of arthropod phylogeny. Therefore, we explored the proliferation of neuronal stem cells (in vivo incorporation of bromodeoxyuridine) and the developmental expression of synaptic proteins (immunohistochemistry against synapsins) in the developing optic neuropils of the brine shrimp Artemia salina Linnaeus, 1758 (Crustacea, Entomostraca, Branchiopoda, Anostraca) from hatching to adulthood. The morphology of the adult visual system was examined in serial sections of plastic embedded specimens. Our results indicate that the cellular material that gives rise to the visual system (compound eyes and two optic ganglia) is contributed by the mitotic activity of neuronal stem cells that are arranged in three band‐shaped proliferation zones. Synapsin‐like immunoreactivity in the lamina ganglionaris and the medulla externa initiated only after the anlagen of the compound eyes had already formed, suggesting that the emergence of the two optic neuropils lags behind the proliferative action of these stem cells. Neurogenesis in A. salina is compared to similar processes in malacostracan crustaceans and possible phylogenetic implications are discussed. © 2002 Wiley Periodicals, Inc. J Neurobiol 52: 117–132, 2002     

Morphology and phylogenetic relationships of a new eschrichtiid genus (Cetacea: Mysticeti) from the Early Pliocene of northern Italy

A new eschrichtiid, Eschrichtioides gastaldii gen. nov., comb. nov. , is established based on a specimen previously assigned to Balaenoptera gastaldii Portis, 1885. The holotype is from the Early Pliocene of north-east Italy. It represents a fossil mysticete closely related to the living grey whale, Eschrichtius robustus . Comparative morphology and phylogenetic analysis support the monophyly of Eschrichtiidae and Cetotherium -like mysticetes and a sister group relationship between this clade and Balaenopteridae. Eschrichtiid fossils previously described are all from the Pleistocene and Late Pliocene while Eschrichtioides gastaldii is from the Early Pliocene. The recognition of this new eschrichtiid genus suggests that the Mediterranean trophic web of the Early Pliocene was more complex than at present and that the Neogene mysticete family-level biodiversity of the Mediterranean was higher than that currently observed in this basin.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 161–186.     

A new genus in the tribe Acidoxanthini (Diptera: Tephritidae: Trypetinae) from India,with a discussion of its phylogenetic relationships

Gibbifronta pavoniae David, Hancock and Han, gen. et sp. nov., is described from India. The current status of the subtribe Acidoxanthina is scrutinized based on both morphological characters and DNA barcoding analysis, and this taxon is formally proposed as the tribe Acidoxanthini within the subfamily Trypetinae in order to accommodate the genera Gibbifronta, Acidoxantha Hendel, Craspedoxanthitea Hardy and Acidoxanthopsis Hering. We found that the members of the Acidoxanthini possess a unique characteristic within the family Tephritidae, the short and broadly truncate lateral surstylus with reduced prensisetae and 1–3 pairs of strong dorsal setae on epandrium. Even though comparable information is not available for Acidoxanthopsis, it is retained in Acidoxanthini. Gibbifronta is distinguished from other genera of the tribe by the presence of a high gena and prominent hump-like projection on the frons. Phylogenetic analysis based on DNA barcodes revealed that Gibbifronta is closely related to Acidoxantha and support its placement in Acidoxanthini. COI sequences of Gibbifronta pavoniae, Nitrariomyia lukjanovitshi Rohdendorf, Acidoxantha galibeedu David and Ramani and an undescribed Acidoxantha species have been obtained and reported. A key to the genera of Acidoxanthini is also provided.http://zoobank.org/100D010D-21D3-4F0B-B38E-1F72DC8E9BF3.     

First report of the family Palaeosetidae (Lepidoptera: Hepialoidea) from mainland China,with description of a new Ogygioses species and its phylogenetic position within the genus

The family Palaeosetidae is newly recorded from mainland China. A new species of the genus Ogygioses, O. maoershana sp. nov., is described from Guangxi Province, China. The adults, male and female genitalia, venation, head and legs structures are illustrated. Some ecological information and a key to all species of the genus are also provided. The phylogenetic position of the new species in the genus Ogygioses is inferred as intermediate between primitive O. luangensis Kristensen and other four derived species based on morphological characters and DNA barcodes sequences.www.zoobank.org/urn:lsid:zoobank.org:pub:D1FD6818-500A-4AE1-9F0B-13CB5A6E1ED4.     

Intergeneric phylogenetic relationships in catfishes of the Loricariinae (Siluriformes: Loricariidae), with the description of Fonchiiloricaria nanodon: a new genus and species from Peru

Recent investigations in the upper Río Huallaga in Peru revealed the presence of an intriguing species of the Loricariinae. To characterize and place this species within the evolutionary tree of the subfamily, a molecular phylogeny of this group was inferred based on the 12S and 16S mitochondrial genes and the nuclear gene F-reticulon4. The phylogeny indicated that this distinctive species was a member of the subtribe Loricariina. Given its phylogenetic placement, and its unusual morphology, this species is described as a new genus and new species of Loricariinae: Fonchiiloricaria nanodon. This new taxon is diagnosed by usually possessing one to three premaxillary teeth that are greatly reduced; lips with globular papillae on the surface; the distal margin of lower lip bearing short, triangular filaments; the premaxilla greatly reduced; the abdomen completely covered by plates, with the plates between lateral abdominal plates small and rhombic; a caudal fin with 14 rays; the orbital notch absent; five lateral series of plates; dorsal-fin spinelet absent; preanal plate present, large and solid, and of irregular, polygonal shape, the caudal peduncle becoming more compressed posteriorly for the last seven to 10 plates.     

Jsowerbya, new genus of Muricidae (Mollusca: Gastropoda) from the Eocene of the Paris (France) and Hampshire (England) basins with a phylogenetic assessment of its Ocenebrine versus Ergalataxine affinities

Jsowerbya, nov. gen. (Gastropoda: Muricidae) includes three species from the Eocene of the Paris and Hampshire basins. It increases the number of extinct muricid genera, which curiously represent a very small fraction of the described genera. The species of Jsowerbya, often mistaken for the muricopsine genus Muricopsis, possess a unique combination of characters shared with the subfamilies Ocenebrinae and Ergalataxinae. A cladistic analysis, based on structural homologies of the spiral sculpture, however, suggests that Jsowerbya is closely related to the Ocenebrinae. Thus, Jsowerbya is here regarded as one the most basal Ocenebrinae.