New insights into the mitochondrial phylogeny of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) in the Mediterranean Basin

The whitefly Bemisia tabaci is vector of plant infecting viruses and it is considered as one of the most important agricultural pests around the Mediterranean basin. At present, five biotypes of B. tabaci have been reported in the Mediterranean Basin: B, Q, S, T and M. To establish the phylogeographic relationship of these Mediterranean biotypes with others, 54 samples collected in Europe and Africa were analysed by sequencing the mitochondrial cytochrome oxidase I gene (mtCOI). The phylogeny showed that Spanish samples corresponding to the biotype S were related to the haplotype Uganda 2 of the African clade, associated with recent epidemic upsurges of cassava mosaic virus (CMD) in that country. This phylogeographic relationship gave support to a distinct subgroup revealed within the African clade. Bemisia tabaci collected from Euphorbia plants in Italy (biotype T) formed one of the three distinct subgroups existing within the Southeast/Far East Asian clade, while samples from Turkey (biotype M) clustered together with reference mitochondrial sequences from whiteflies from Pakistan and Thailand. Recent reports indicate that Bemisia populations corresponding to the biotypes S and T are distributed in areas larger than those initially delimited. Other results indicated that samples collected in Sudan grouped within the Mediterranean–North Africa clade together with reference sequences of the biotype Q corresponding to insects collected in Spain and Morocco. Mitochondrial haplotypes of B. tabaci samples collected on sweet potato in Ghana clustered with reference sequences of samples from Cameroon corresponding to one of the five Sub-Saharan subgroups already described in the African clade. These data extends the phylogenetic information of the B. tabaci species complex and present new questions to be investigated.     

Contrasting patterns of population structure in the montane caddisflies Hydropsyche tenuis and Drusus discolor in the Central European highlands

1. In this study, we compared mitochondrial sequence data (cytochrome oxidase I) to infer the population structure of the two montane caddisflies Hydropsyche tenuis and Drusus discolor. The two species are contrasting examples of montane aquatic insects with insular distributions: D. discolor is restricted to altitudes above 600 m, H. tenuis is limited to the same mountain ranges in Central Europe but inhabits lower altitudes. 2. In particular, we ask whether these two species with similar regional distributions show similar patterns of population structure and haplotype diversity, and whether any differences can be attributed to population history and/or autecology. 3. To determine the population structure of both species, we applied conventional population genetics analyses to mitochondrial sequence data. We collected and sampled 121 specimens of H. tenuis from 29 sites in 10 different regions of the Central European highlands and 138 individuals of D. discolor from 40 sites in 11 different regions. 4. Nine unique haplotypes were identified for H. tenuis and 34 for D. discolor. There were eight variable positions in H. tenuis and 41 in D. discolor. The maximum difference between haplotypes was 0.8% (4 bp) for H. tenuis and 4.2% (21 bp) for D. discolor. We observed haplotype overlap between geographic regions for both species. Analysis of molecular variance showed that two‐thirds of the total variance in H. tenuis was found among regions while in D. discolor, a larger portion of variance was found within regions and populations due to a higher number of haplotypes observed within regions. Mantel test showed a significant relationship between genetic and geographic distance in D. discolor, but no significant relationship in H. tenuis. 5. Our analyses show that, despite their very similar overall distribution pattern in Europe, the two species exhibit distinct population structures, which may reflect differences in phylogeographic history, dispersal capabilities, habitat specifity or within‐region geographic occurrence.     

From introduction to equilibrium: reconstructing the invasive pathways of the Argentine ant in a Mediterranean region

Determining the geographical range of invasive species is an important component of formulating effective management strategies. In the absence of detailed distributional data, species distribution models can provide estimates of an invasion range and increase our understanding of the ecological processes acting at various spatial scales. We used two complementary approaches to evaluate the influence of historical and environmental factors in shaping the distribution of the Argentine ant ( Linepithema humile ), a widespread, highly invasive species native to South America. Occurrence data were combined with environmental data at incremental spatial scales (extent and resolution) to predict the suitable range of the ant invasion using ecological niche models. In addition, we also used a spread model that simulated the jump dispersal of the species to identify the most plausible scenarios of arrival of L. humile in the NE Iberian Peninsula at local scales. Based on the results of both modelling practices, we suggest that L. humile might have reached its maximum geographic range at regional scales in the NE Iberian Peninsula. However, the species does not appear in equilibrium with the environment at small spatial scales, and further expansions are expected along coastal and inland localities of the Costa Brava. Long-distance jumps are ultimately responsible for the spread of the Argentine ant in the area. Overall, our study shows the utility of combining niche based models with spread models to understand the dynamics of species' invasions.     

Spatial patterns of genetic structure among populations of a stone‐cased caddis (Trichoptera: Tasimiidae) in south‐east Queensland,Australia

1. Gene flow and dispersal among populations of a stone‐cased caddis (Tasimiidae: Tasimia palpata) were estimated indirectly using a 460 bp region of the cytochrome oxidase I gene of mitochondrial DNA. 2. There was no significant differentiation at the largest spatial scale (between catchments) and no correlation between genetic distance and geographic distance. These results are consistent with widespread adult dispersal. 3. Conversely, significant genetic differentiation was detected at the smallest spatial scale examined (among reaches within streams). This pattern was primarily because of significant F_ST values in a single stream (Bundaroo Creek). 4. Bundaroo Creek also had the lowest mean number of haplotypes per population (n = 7) suggesting that a limited number of females may be responsible for recruitment at these sites. Significant F_ST's at the reach scale may be a result of this ‘patchy’ recruitment. However, additional evidence regarding the long‐range dispersal ability and fecundity of T. palpata females is needed to test this hypothesis fully.     

Molecular systematics of the Chrysoperla carnea group (Neuroptera: Chrysopidae) in Europe

The green lacewing Chrysoperla carnea is a complex of cryptic species whose differentiation has been so far based upon morphology, ecophysiology, behaviour and preliminary mitochondrial DNA data using cytochrome oxidase subunit II (COII) and NADH dehydrogenase subunit II. In this work we extended the DNA data by screening nucleotide sequences of COII, cytochrome oxidase I, cytochrome b and the large ribosomal subunit of the mtDNA. These new data suggest that C. carnea s.s. is a well-supported, separate taxon, but that other taxa of the complex are not consistently differentiated by the current DNA data.     

Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism

The structure of Mycobacterium tuberculosis dUTP nucleotidohydrolase (dUTPase) has been determined at 1.3 Angstrom resolution in complex with magnesium ion and the non-hydrolyzable substrate analog, alpha,beta-imido dUTP. dUTPase is an enzyme essential for depleting potentially toxic concentrations of dUTP in the cell. Given the importance of its biological role, it has been proposed that inhibiting M.tuberculosis dUTPase might be an effective means to treat tuberculosis infection in humans. The crystal structure presented here offers some insight into the potential for designing a specific inhibitor of the M.tuberculosis dUTPase enzyme. The structure also offers new insights into the mechanism of dUTP hydrolysis by providing an accurate representation of the enzyme-substrate complex in which both the metal ion and dUTP analog are included. The structure suggests that inclusion of a magnesium ion is important for stabilizing the position of the alpha-phosphorus for an in-line nucleophilic attack. In the absence of magnesium, the alpha-phosphate of dUTP can have either of the two positions which differ by 4.5 Angstrom. A transiently ordered C-terminal loop further assists catalysis by shielding the general base, Asp83, from solvent thus elevating its pK(a) so that it might in turn activate a tightly bound water molecule for nucleophilic attack. The metal ion coordinates alpha, beta, and gamma phosphate groups with tridentate geometry identical with that observed in the crystal structure of DNA polymerase beta complexed with magnesium and dNTP analog, revealing some common features in catalytic mechanism.     

Subterranean archipelago in the Australian arid zone: mitochondrial DNA phylogeography of amphipods from central Western Australia

In 1998, a unique subterranean ecosystem was discovered in numerous isolated calcrete (carbonate) aquifers in the arid Yilgarn region of Western Australia. Previous morphological and genetic analyses of a subterranean water beetle fauna suggest that calcrete aquifers are equivalent to closed island habitats that have been isolated for millions of years. We tested this hypothesis further by phylogeographic analyses of subterranean amphipods (Crangonyctoidea: Paramelitidae and Hyalidae) using mitochondrial DNA sequence data derived from the cytochrome oxidase I gene. Phylogenetic analyses and population genetic analyses (samova) provided strong evidence for the existence of at least 16 crangonyctoid and six hyalid divergent mitochondrial lineages, each restricted in their distribution to a single calcrete aquifer, in support of the 'subterranean island (archipelago) hypothesis' and extending its scope to include entirely water respiring invertebrates. Sequence divergence estimates between proximate calcrete populations suggest that calcretes have been isolated at least since the Pliocene, coinciding with a major aridity phase that led to the intermittent drying of surface water. The distribution of calcretes along palaeodrainage channels and on either side of drainage divides, have had less influence on the overall phylogeographic structure of populations, with evidence that ancestral crangonyctoid and hyalid species moved between catchments multiple times prior to their isolation within calcretes. At least two potential modes of evolution may account for the diversity of subterranean amphipod populations: dispersal/vicariance of stygobitic species or colonization of calcretes by surface species and independent evolution of stygobitic characteristics.     

Incongruence of morphology and genetic markers in Hyles tithymali (Lepidoptera: Sphingidae) from the Canary Islands

Hyles t. tithymali on the Canary Islands has been observed to occur in two larval morphotypes, connected by intermediate forms along a geographical cline from east to west. In this study, it was tested whether this distribution of phenotypes reflects a genealogical division of the population. mtDNA sequence data (COI + II, tRNA-leu) and genomic fingerprints from intersimple sequence repeat (ISSR)-PCR data were used. The sequence data had low variation (max. 0.4%), and phylogenetic analyses did not reveal groups that correlated with the morphotype. The samples did not group according to their island of origin and the most common haplotype was shared among all islands. Although nine haplotypes occurred only on the westernmost islands, the data showed little phylogeographical structure. The population of H. t. tithymali appears to reflect a comparatively rapid and recent colonization event of the Canary Islands. The ISSR-PCR data were very variable and did not reveal patterns corresponding to morphological variation or geographical distribution. Although the two morphs observed may represent the first stage of differentiation between two lineages, the recent origin of H. t. tithymali provided insufficient time for complete lineage sorting of ancestral polymorphism. Hence, the population of Hyles t. tithymali on the Canary Islands appears genetically more homogeneous than that was expected from the phenotypic distribution of the two morphotypes in the population.     

Long-term fire frequency variability in the eastern Canadian boreal forest: the influences of climate vs. local factors

The influence of climatic and local nonclimatic factors on the fire regime of the eastern Canadian boreal forest over the last 8000 years is investigated by examining charred particles preserved in four lacustrine deposits. Herein, we compare the distribution of fire-free intervals (FFIs) and the synchronicity of fire events among sites, using Ripley's K -function to determine the extent of the role of local-scale vs. large-scale processes with respect to fire control. Between 8000 and 5800 cal. bp (calibrated years before present) the climatic and ecological conditions were less conducive to fire events than after this date. After 5800 cal. bp , the number of fires per 1000 years (fire frequency) progressively increased, reaching a maximum ca. 3400 cal. bp . There was a sharp decrease in fire frequency during the last 800 years. Between 8000 and 4000 cal. bp , comparable FFIs and synchronous fire episodes were determined for the study sites. During this period, the fire frequency was predominantly controlled by climate. After 4000 cal. bp , two sites displayed independent fire histories (different FFI distributions or asynchronous fire events), underlining the important influence of local factors, including short-term fuel wetness, characteristics of the watershed and landscape connectivity, in determining fire occurrence. We conclude that climatic changes occurred during the last 4000 years that induced a rise in the water table; this may explain the high spatial heterogeneity in fire history. Current and projected global climatic changes may cause similar spatial variability in fire frequency.     

DNA barcodes provide new evidence of a recent radiation in the genus Sporophila (Aves: Passeriformes)

The capuchinos are a group of birds in the genus Sporophila that has apparently radiated recently, as evidenced by their lack of mitochondrial genetic diversity. We obtained cytochrome c oxidase I (COI) sequences (or DNA barcodes) for the 11 species of the group and various outgroups. We compared the patterns of COI variability of the capuchinos with those of the largest barcode data set from neotropical birds currently available (500 species representing 51% of avian richness in Argentina), and subjected COI sequences to neighbour-joining, maximum parsimony and Bayesian phylogenetic analyses as well as statistical parsimony network analysis. A clade within the capuchinos, the southern capuchinos, showed higher intraspecific and lower interspecific divergence than the remaining Argentine species. As most of the southern capuchinos shared COI haplotypes and pairwise distances within species were in many cases higher than distances between them, the phylogenetic affinities within the group remained unresolved. The observed genetic pattern is consistent with both incomplete lineage sorting and gene flow between species. The southern capuchinos constitute the only large group of species among the neotropical birds barcoded so far that are inseparable when using DNA barcodes, and one of few multispecies avian groups known to lack reciprocal monophyly. Extending the analysis to rapidly evolving nuclear and mitochondrial markers will be crucial to understanding this radiation. Apart from giving insights into the evolution of the capuchinos, this study shows how DNA barcoding can rapidly flag species or groups of species worthy of deeper study.     

Genetic variation and phylogeny of Scandinavian species of Grania (Annelida: Clitellata: Enchytraeidae), with the discovery of a cryptic species

Individuals of five nominal species of Grania (Annelida: Clitellata: Enchytraeidae) were collected from locations in Sweden, Norway and France, for studies on the intraspecific variation at the Cytochrome Oxidase I (COI) locus of mitochondrial DNA and internal transcribed spacer (ITS) region of nuclear DNA. It was found that the previously described morphospecies in general contain low variation compared to the between‐species variation in both loci. In one instance, however, an individual morphologically indistinguishable from G. ovitheca was found to be deviant and instead cluster with G. postclitellochaeta both by COI and ITS. We describe this individual as a new species: G. occulta sp.n. Furthermore, phylogenetic analyses were conducted, showing a close relationship between G. variochaeta, G. occulta, G. ovitheca and G. postclitellochaeta, as well as between G. pusilla and G. maricola. Using the results from the phylogenetic analyses, we discuss the evolution of morphological characters in Scandinavian species of Grania.     

Application of multiplex PCR approaches for shark molecular identification: feasibility and applications for fisheries management and conservation in the Eastern Tropical Pacific

Here we describe the application of new and existing multiplex PCR methodologies for shark species molecular identification. Four multiplex systems (group ID, thresher sharks, hammerhead sharks and miscellaneous shark) were employed with primers previously described and some designed in this study, which allow for species identification after running PCR products through an agarose gel. This system was implemented for samples (bodies and fins) collected from unidentified sharks landed in the port of Buenaventura and from confiscated tissues obtained from illegal fishing around the Malpelo Island Marine Protected Area, Pacific Coast of Colombia. This method has allowed reliable identification, to date, of 407 samples to the genus and/or species levels, most of them (380) identified as the pelagic thresher shark (Alopias pelagicus). Another seven samples were identified as scalloped hammerhead sharks (Sphyrna lewini). This is an easy-to-implement and reliable identification method that could even be used locally to monitor shark captures in the main fishing ports of developed and developing countries.     

An invasive aster (Ageratina adenophora) invades and dominates forest understories in China: altered soil microbial communities facilitate the invader and inhibit natives

Exotic plant invasion may alter underground microbial communities, and invasion-induced changes of soil biota may also affect the interaction between invasive plants and resident native species. Increasing evidence suggests that feedback of soil biota to invasive and native plants leads to successful exotic plant invasion. To examine this possible underlying invasion mechanism, soil microbial communities were studied where Ageratina adenophora was invading a native forest community. The plant–soil biota feedback experiments were designed to assess the effect of invasion-induced changes of soil biota on plant growth, and interactions between A. adenophora and three native plant species. Soil analysis showed that nitrate nitrogen (NO₃⁻-N), ammonium nitrogen (NH₄⁺-N), and available P and K content were significantly higher in a heavily invaded site than in a newly invaded site. The structure of the soil microbial community was clearly different in all four sites. Ageratina adenophora invasion strongly increased the abundance of soil VAM (vesicular-arbuscular mycorrhizal fungi) and the fungi/bacteria ratio. A greenhouse experiment indicated that the soil biota in the heavily invaded site had a greater inhibitory effect on native plant species than on A. adenophora and that soil biota in the native plant site inhibited the growth of native plant species, but not of A. adenophora. Soil biota in all four sites increased A. adenophora relative dominance compared with each of the three native plant species and soil biota in the heavily invaded site had greater beneficial effects on A. adenophora relative dominance index (20% higher on average) than soil biota in the non-invaded site. Our results suggest that A. adenophora is more positively affected by the soil community associated with native communities than are resident natives, and once the invader becomes established it further alters the soil community in a way that favors itself and inhibits natives, helping to promote the invasion. Soil biota alteration after A. adenophora establishment may be an important part of its invasion process to facilitate itself and inhibit native plants.     

From introduction to fishery dominance: the initial impacts of the invasive carp Cyprinus carpio in Lake Naivasha, Kenya, 1999 to 2006

Following the accidental introduction of the carp Cyprinus carpio into Lake Naivasha during 1999, a sustainable population became rapidly established and in early 2004 became the principal species exploited in the commercial fishery. Over 9000 kg of carp were harvested from the lake between October 2005 and 2006, when fish were captured between fork lengths ( L _F) 200 and 800 mm (>8 kg). Diet of carp <100 mm L _F was dominated by zooplankton, >100 mm L _F there was a shift to benthic macro-invertebrates, with these carp feeding principally upon food resources previously unexploited by the fish community. Contrary to predictions and despite the increasing carp abundance, there has been macrophyte regeneration in littoral areas since 2004. There have been substantial increases in areal cover, with coverage in 2006 at levels not observed since the late 1980s, and significant increases in species richness. Possible reasons for this, and the significance of this carp introduction, are discussed.     

Identifying the most noxious invasive plants in China: role of geographical origin, life form and means of introduction

In a heterogenous world, invasive plants often differ in noxiousness and nature of impacts, and there is a difference between strong and weak invaders. That knowing which invaders are most noxious and their nature of impacts is of great value to invasive ecology and management. Here we show that in China the most notorious invasive plants are with a perennial life cycle, clonal growth ability and from the American continent. They often form monocultural populations in land and water, replacing almost all other plants, and are mainly distributed in Central and South China. Following are some accidentally introduced annuals. Annuals from the American continent are often common, dominant or in monocultural populations in ruderal and agricultural habitats whereas those from Eurasia are highly noxious only in agricultural habitats. Annuals are not restricted in distribution and could spread fast to all of the country. There are also two perennial grasses from Europe and Mediterranean area and four intentionally introduced annuals from South America that were identified in this study. Factors that may account for these patterns include relatedness between invasives and natives, vegetative propagation, and plant strategies. The invasive plants identified in this study have caused significant negative impacts to native biodiversity, environment, economics and agriculture, with different groups being different in their extent and nature of impacts.     

Multiple introductions promote range expansion of the mollusc Cyclope neritea (Nassariidae) in France: evidence from mitochondrial sequence data

Since the 1970s, the nassariid gastropod Cyclope neritea has been extending its range north along the French Atlantic coasts from the Iberian Peninsula. This may be due to natural spread because of the recent warming of the northeastern Atlantic. However, human-mediated introductions related to shellfish culture may also be a probable explanation for this sudden range expansion. To examine these two hypotheses, we carried out a comprehensive study based on mitochondrial gene sequences (cytochrome oxidase I) of the five recently colonized French bays as well as 14 populations located in the recognized native range of the species. From a total of 594 individuals, we observed 29 haplotypes to split into three divergent clades. In the native range, we observed a low molecular diversity, strong genetic structure and agreement between geography and gene genealogies. Along the French coasts, we observed the opposite: high genetic diversity and low genetic structure. Our results show that recurrent human-mediated introductions from several geographical areas in the native range may be a source for the French Atlantic populations. However, despite the low dispersal ability of C. neritea, the isolation-by-distance pattern in France suggested that this gastropod may have been present (although unnoticed) on the French Atlantic coasts before the 1970s. As C. neritea shows characteristics of a cryptogenic species, the classification of Atlantic populations as either native or introduced is not straightforward. Cryptogenic species should be studied further to determine the status of new populations close to their recognized native range.     

Crystal structure of a cAMP-dependent protein kinase mutant at 1.26A: new insights into the catalytic mechanism

The catalytic subunit of cAMP-dependent protein kinase has served as a paradigm for the entire kinase family. In the course of studying the structure-function relationship of the P+1 loop (Leu198-Leu205) of the kinase, we have solved the crystal structure of the Tyr204 to Ala mutant in complexes with Mg.ATP and an inhibitory peptide at 1.26A, with overall structure very similar to that of the wild-type protein. However, at the nucleotide binding site, ATP was found largely hydrolyzed, with the products ADP-PO(4) retained in the structure. High-resolution refinement suggests that 26% of the molecules contain the intact ATP, whereas 74% have the hydrolyzed products. The observation of the substrate and product states in the same structure adds significant information to our understanding of the phosphoryl transfer process. Structural examination of the mutation site substantiates and extends the emerging concept that the hydrophobic core in the large lobe of the kinase might serve as a stable platform for anchoring key segments involved in catalysis. We propose that Tyr204 is critical for anchoring the P+1 loop to the core. Further analysis has highlighted two major connections between the P+1 loop and the catalytic loop (Arg165-Asn171). One emphasizes the hydrophobic packing of Tyr204 and Leu167 mediated through residues from the alphaF-helix, recently recognized as a signal integration motif, which together with the alphaE-helix forms the center of the hydrophobic core network. The other connection is mediated by the hydrogen bond interaction between Thr201 and Asp166, in a substrate-dependent manner. We speculate that the latter interaction may be important for the kinase to sense the presence of substrate and prepare itself for the catalytic reaction. Thus, the P+1 loop is not merely involved in substrate binding; it mediates the communication between substrate and catalytic residues.     

Resurrection of Rabdophaga salicivora Shinji (Diptera: Cecidomyiidae), a Japanese gall midge formerly misidentified as a North American species, Rabdophaga rigidae (Osten Sacken), with observations on the phylogenetic relationships of its populations in Japan and the Russian Far East

Intercontinental biotic connections between Eurasia and North America are common in many gall midge genera (Diptera: Cecidomyiidae), but only a few species have been recorded from both continents. In Japan, four gall midge species had been previously considered to be identical to North American species, but three of these cases have already been disproved. We examined the remaining species, Rabdophaga rigidae, which had been originally described from Japan as Rabdophaga salicivora in 1938, later recorded from the Russian Far East in 1967, and synonymized with a North American species, R. rigidae, in 1982. Morphological features and partial sequence data of the mtDNA cytochrome oxidase subunit I (COI) region suggested that the Japanese species is a distinct species and is identical to the species recorded from the Russian Far East. We therefore apply the original name, R. salicivora, to the Japanese and the Russian species. In addition, on the basis of a molecular phylogenetic analysis, we conclude that R. salicivora possibly came to the Japanese Archipelago through the Korean Peninsula and established itself first in the southern parts of Japan. Then, it expanded its distribution range to northern parts of Honshu, but could not reach Hokkaido, probably because of the Tsugaru Strait between Honshu and Hokkaido.