Parsing parallel evolution:Ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua

The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex) - from two Great Lakes and two crater lakes in Nicaragua - to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (dC and dN) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution. © 2012 Blackwell Publishing Ltd.

Molecular comparison of Scytalidium thermophilum isolates using RAPD and ITS nucleotide sequence analyses

Scytalidium thermophilum plays an important role in determining selectivity of compost produced for growing Agaricus bisporus. The objective of this study was to characterise S. thermophilum isolates by random amplified polymorphic DNA (RAPD) analysis and sequence analysis of internally transcribed spacer (ITS) regions of the rDNA, to assess the genetic variation exhibited by this species complex and to compare this with existing morphological and thermogravimetric data. RAPD analysis of 34 isolates from various parts of the world revealed two distinct groups, which could be separated on the basis of the differences in the banding patterns produced with five random primers. Nucleotide sequence analysis of the ITS region, which was ca 536 bp in length, revealed only very minor variation among S. thermophilum isolates examined. Several nucleotide base changes within this region demonstrated variation. Genetic distance values among type 1 and 2 S. thermophilum isolates, as determined by ITS sequence analysis, varied by a value of 0.005 %. Molecular analyses carried out in the present study would suggest that isolates within this species complex exhibit genetic differences which correlate well with morphological variation and thermogravimetric data previously determined.

Autoecological Approaches to Resolve Subjective Taxonomic Divisions within Arcellacea

Arcellacea (testate lobose amoebae) are important lacustrine environmental indicators that have been used in paleoclimatic reconstructions, assessing the effectiveness of mine tailings pond reclamation projects and for studying the effects of land use change in rural, industrial and urban settings. Recognition of ecophenotypically significant infra-specific ‘strains’ within arcellacean assemblages has the potential to enhance the utility of the group in characterizing contemporary and paleoenvironments. We present a novel approach which employs statistical tools to investigate the environmental and taxonomic significance of proposed strains. We test this approach on two identified strains: Difflugia protaeiformis Lamarck strain ‘acuminata’ (DPA), characterized by fine grained agglutination, and Difflugia protaeiformis Lamarck strain ‘claviformis’ (DPC), characterized by coarse grained agglutination. Redundancy analysis indicated that both organisms are associated with similar environmental variables. No relationship was observed between substrate particle size and abundance of DPC, indicating that DPC has a size preference for xenosomes during test construction. Thus DPC should not be designated as a distinct strain but rather form a species complex with DPA. This study elucidates the need to justify the designation of strains based on their autecology in addition to morphological stability.

Cryptic species diversity in a widespread bumble bee complex revealed using mitochondrial DNA RFLPs

Cryptic species diversity is thought to be common within the class Insecta, posing problems for basic ecological and population genetic studies and conservation management. Within the temperate bumble bee (Bombus spp.) fauna, members of the subgenus Bombus sensu stricto are amongst the most abundant and widespread. However, their species diversity is controversial due to the extreme difficulty or inability morphologically to identify the majority of individuals to species. Our character-based phylogenetic analyses of partial CO1 (700 bp) from 39 individuals spread across their sympatric European ranges provided unequivocal support for five taxa (3-22 diagnostic DNA base pair sites per species). Inclusion of 20 Irish specimens to the dataset revealed >= 2.3% sequence divergence between taxa and 200 m) whilst B. cryptarum was relatively more abundant at higher altitudes. Bombus magnus was rarely encountered at urban sites. Both B. lucorum and B. terrestris are nowadays reared commercially for pollination and transported globally. Our RFLP approach to identify native fauna can underpin ecological studies of these important cryptic species as well as the impact of commercial bumble bees on them.

In vitro resistance of Burkholderia cepacia complex isolates to reactive oxygen species in relation to catalase and superoxide dismutase production

The Burkholderia cepacia complex comprises groups of genomovars (genotypically distinct strains with very similar phenotypes) that have emerged as important opportunistic pathogens in cystic fibrosis (CF) patients. The inflammatory response against bacteria in the airways of CF individuals is dominated by polymorphonuclear cells and involves the generation of oxidative stress, which leads to further inflammation and tissue damage. Bacterial catalase, catalase-peroxidase and superoxide dismutase activities may contribute to the survival of B. cepacia following exposure to reactive oxygen metabolites generated by host cells in response to infection. In the present study the authors investigated the production of catalase, peroxidase and SOD by isolates belonging to various genomovars of the B. cepacia complex. Production of both catalase and SOD was maximal during late stationary phase in almost all isolates examined. Native PAGE identified 13 catalase electrophoretotypes and two SOD electrophoretotypes (corresponding to an Fe-SOD class) in strains belonging to the six genomovars of the B. cepacia complex. Seven out of 11 strains displaying high-level survival after H(2)O(2) treatment in vitro had a bifunctional catalase/peroxidase, and included all the genomovar III strains examined. These isolates represent most of the epidemic isolates that are often associated with the cepacia syndrome. The majority of the isolates from all the genomovars were resistant to extracellular O(-)(2), while resistance to intracellularly generated O(-)(2)was highly variable and could not be correlated with the detected levels of SOD activity. Altogether the results suggest that resistance to toxic oxygen metabolites from extracellular sources may be a factor involved in the persistence of B. cepacia in the airways of CF individuals.

Complex sociogenetic organization and reproductive skew in a primitively eusocial sweat bee, Lasioglossum malachurum, as revealed by microsatellites

The sweat bees (Family Halictidae) are a socially diverse taxon in which eusociality has arisen independently numerous times. The obligate, primitively eusocial Lasioglossum malachurum, distributed widely throughout Europe, has been considered the zenith of sociality within halictids. A single queen heads a colony of smaller daughter workers which, by mid-summer, produce new sexuals (males and gynes), of which only the mated gynes overwinter to found new colonies the following spring. We excavated successfully 18 nests during the worker- and gyne-producing phases of the colony cycle and analysed each nest's queen and either all workers or all gynes using highly variable microsatellite loci developed specifically for this species. Three important points arise from our analyses. First, queens are facultatively polyandrous (queen effective mating frequency: range 1–3, harmonic mean 1.13). Second, queens may head colonies containing unrelated individuals (n = 6 of 18 nests), most probably a consequence of colony usurpation during the early phase of the colony cycle before worker emergence. Third, nonqueen's workers may, but the queen's own workers do not, lay fertilized eggs in the presence of the queen that successfully develop into gynes, in agreement with so-called 'concession' models of reproductive skew

Species distribution and coordination of uranyl chloro complexes in acetonitrile

The complex formation of the uranyl ion, UO22+, with chloride ions in acetonitrile has been investigated by factor analysis of UV-vis absorption and U L-3 edge EXAFS (extended X-ray absorption fine structure) spectra. As a function of increasing [Cl-]/[UO22+] ratio, the five monomeric species [UO2(H2O)(5)](2+), [UO2Cl(H2O)(2)(MeCN)(2)](+), [UO2Cl2(H2O)(MeCN)(2)], [UO2Cl3(MeCN)(2)](-), and [UO2Cl4](2-) have been observed. The distances determined in the first coordination sphere are: U-O-ax = 1.77 angstrom, U-O-H2O = 2.43 angstrom, U-N-MeCN = 2.53 angstrom, and U-Cl = 2.68 angstrom. A crystalline material has been obtained from the intermediate solution with the [Cl-]/[UO22+] ratio of similar to 2, where [UO2Cl2(H2O)(MeCN)(2)] is the dominating species. The crystal structure analysis of this material revealed a tetrameric complex, [(UO2)(4)(mu(2)-Cl)(4)(mu(3)-O)(2)(H2O)(2)(CH3CN)(4)]center dot(CH3CN). The crystal data are: monoclinic, space group P2(1)/n, a 10.6388(5) angstrom, b = 14.8441(5) angstrom, c = 10.8521(5) angstrom, beta = 109.164(5)degrees, and Z = 2. The U(VI) coordination of the solution species [UO2Cl2(H2O)(MeCN)(2)] changes during the crystallization by replacing one MeCN molecule with a bridging mu(3)-O atom in the tetramer.

Invader-invader interactions in relation to environmental heterogeneity leads to zonation of two invasive amphipods, Dikerogammarus villosus (Sowinsky) and Gammarus tigrinus Sexton: amphipod pilot species project (AMPIS) report 6

As biological invasions continue, interactions occur not only between invaders and natives, but increasingly new invaders come into contact with previous invaders. Whilst this can lead to species replacements, co-existence may occur, but we lack knowledge of processes driving such patterns. Since environmental heterogeneity can determine species richness and co-existence, the present study examines habitat use and its mediation of the predatory interaction between invasive aquatic amphipods, the Ponto-Caspian Dikerogammarus villosus and the N. American Gammarus tigrinus. In the Dutch Lake IJsselmeer, we found broad segregation of D. villosus and G. tigrinus by habitat type, the former predominating in the boulder zone and the latter in the soft sediment. However, the two species co-exist in the boulder zone, both on the short and longer terms. We used an experimental simulation of habitat heterogeneity and show that both species utilize crevices, different sized holes in a plastic grid, non-randomly. These amphipods appear to optimise the use of holes with respect to their 'C-shape' body size. When placed together, D. villosus adults preyed on G. tigrinus adults and juveniles, while G. tigrinus adults preyed on D. villosus juveniles. Juveniles were also predators and both species were cannibalistic. However, the impact on G. tigrinus of the superior intraguild predator, D. villosus, was significantly reduced where experimental grids were present as compared to absent. This mitigation of intraguild predation between the two species in complex habitats may explain the co-existence of these two invasive species.

MEASUREMENT OF SUPEROXIDE FORMATION BY MITOCHONDRIAL COMPLEX I OF YARROWIA LIPOLYTICA

Complex I (NADH: ubiquinone oxidoreductase) is generally regarded as one of the major sources of mitochondrial reactive oxygen species (ROS). Mitochondrial membranes from the obligate aerobic yeast Yarrowia lipolytica, as well as the purified and reconstituted enzyme, can be used to measure complex I-dependent generation of superoxide (O-2(center dot-)). The use of isolated complex I excludes interference with other respiratory chain complexes and matrix enzymes during superoxide dismutase-sensitive reduction of acetylated cytochrome c. Alternately. hydrogen peroxide formation can be measured by the Amplex Red/horseradish peroxidase assay. Both methods allow the determination of complex I-generated ROS, depending on substrates (NADH, artificial ubiquinones), membrane potential, and active/deactive transition. ROS production by Yorrowia complex I in the

Superoxide radical formation by pure complex I (NADH : Ubiquinone oxidoreductase) from Yarrowia lipolytica

Generation of reactive oxygen species (ROS) is increasingly recognized as an important cellular process involved in numerous physiological and pathophysiological processes. Complex I ( NADH: ubiquinone oxidoreductase) is considered as one of the major sources of ROS within mitochondria. Yet, the exact site and mechanism of superoxide production by this large membrane-bound multiprotein complex has remained controversial. Here we show that isolated complex 1 from Yarrowia lipolytica forms superoxide at a rate of 0.15% of the rate measured for catalytic turnover. Superoxide production is not inhibited by ubiquinone analogous inhibitors. Because mutant complex I lacking a detectable iron-sulfur cluster N2 exhibited the same rate of ROS production, this terminal redox center could be excluded as a source of electrons. From the effect of different ubiquinone derivatives and pH on this side reaction of complex I we concluded that oxygen accepts electrons from FMNH2 or FMN semiquinone either directly or via more hydrophilic ubiquinone derivatives.

Solid and liquid charge-transfer complex formation between 1-methylnaphthalene and 1-alkyl-cyanopyridinium bis{(trifluoromethyl)sulfonyl}imide ionic liquids

Liquid charge-transfer (CT) complexes were observed to form on contacting electron-rich aromatics with electron withdrawing group appended 1-alkyl-4-cyanopyridinium ionic liquids (ILs). Cooling below the melting point of the ionic liquid resulted in crystallisation of ionic liquid from the complex for 2-cyano and 3-cyano pyridinium isomers and in the formation of a 1 : 1 IL : aromatic crystalline CT-complex with the 4-cyanopyridinium isomer. The liquid structure of a 1 : 1 mixture of 1-methyl-4-cyanopyridinium bis{(trifluoromethyl)sulfonyl} imide with 1-methylnaphthalene has been probed by neutron diffraction experiments and molecular dynamics simulations. A high degree of correlation between the experimental data and the simulations was found with a significant displacement of the anions from around the cation by the aromatic species and the resulting structure having pi-pi stacks between the cations and the aromatic.

Simplification of structured population dynamics in complex ecological communities

Goldstone's idea of slow dynamics resulting from spontaneously broken symmetries is applied to Hubbell's neutral hypothesis of community dynamics, to efficiently simplify stage-structured multi-species models-introducing the quasi-neutral approximation (QNA). Rather than assuming population-dynamical neutrality in the QNA, deviations from ideal neutrality, thought to be small, drive dynamics. The QNA is systematically derived to first and second order in a two-scale singular perturbation expansion. The total reproductive value of species, as computed from the effective life-history parameters resulting from the non-linear interactions with the surrounding community, emerges as the new dynamic variables in this aggregated description. Using a simple stage-structured community-assembly model, the QNA is demonstrated to accurately reproduce population dynamics in large, complex communities. Further, the utility of the QNA in building intuition for management problems is illustrated by estimating the responses of a fish stock to harvesting and variations in fecundity.