Naphthenic acid extraction and speciation from Doba crude oil using carbonate-based ionic liquids

A number of tetraalkylammonium methylcarbonate and hydrogencarbonate based ionic liquids are shown to be capable of reacting with the naphthenic acids contained in Doba crude oil via a neutralisation reaction. Spectral studies show that the ionic liquids neutralisation mechanism involves the formation of an ionic liquid-naphthenate complex, liberating methanol and carbon dioxide. Extraction of the neutralised complex into a separate methanol phase and subsequent regeneration using aqueous carbonic acid results in ∼70% of the ionic liquid being recovered for recycle. Isolation of the naphthenic acids shows that these make up to 0.85 wt% of the crude oil. Speciation of the naphthenic acids shows a mixture of monocyclic, through to tetracyclic structures with carbon numbers in the range C₁₂-C₄₀.

Assessing the Legacy of Red Mud Pollution in a Shallow Freshwater Lake: Arsenic Accumulation and Speciation in Macrophytes

Little is known about long-term ecological responses in lakes following red mud pollution. Among red mud contaminants, arsenic (As) is of considerable concern. Determination of the species of As accumulated in aquatic organisms provides important information about the biogeochemical cycling of the element and transfer through the aquatic food-web to higher organisms. We used coupled ion chromatography and inductively coupled plasma mass spectrometry (ICP-MS) to assess As speciation in tissues of five macrophyte taxa in Kinghorn Loch, UK, 30 years following the diversion of red mud pollution from the lake. Toxic inorganic As was the dominant species in the studied macrophytes, with As species concentrations varying with macrophyte taxon and tissue type. The highest As content measured in roots of Persicaria amphibia (L.) Gray (87.2 mg kg-1) greatly exceeded the 3 - 10 mg kg-1 range suggested as a potential phytotoxic level. Accumulation of toxic As species by plants suggested toxicological risk to higher organisms known to utilise macrophytes as a food source.

Identification of three novel Phyllomedusa sauvagei dermaseptins (sVI-sVIII) by cloning from a skin secretion-derived cDNA library

The defensive skin secretions of many amphibians contain a wide spectrum of biologically active compounds, particularly antimicrobial peptides that act as a first line of defence against bacterial infection. Here we describe for the first time the identification of three novel dermaseptin-related peptides (dermaseptins sVI–sVIII) whose primary structures were deduced from cDNAs cloned from a library constructed from lyophilised skin secretion of the South American hylid frog, Phyllomedusa sauvagei. The molecular masses of each were subsequently confirmed by interrogation of archived LC/MS files of fractionated skin secretion followed by automated Edman degradation sequencing. The heterogeneity of primary structures encountered in amphibian skin antimicrobial peptides may in part be explained by individual variation—a factor essential for selective functional molecular evolution and perhaps, ultimately in speciation.

DNA from pollen: principles and potential

This paper describes our recent extraction of ancient DNA (aDNA) from Holocene pollen and discusses the potential of the technique for elucidating timescales of evolutionary change. We show that plastid DNA is recoverable and usable from pollen grains of Scots pine Pinus sylvestris from 10 ka and 100 years ago. Comparison of the ancient sequences with modern sequences, obtained from an extant population, establish a first genetic link between modern and fossil samples of Scots pine, providing a genetic continuity through time. One common haplotype is present in each of the three periods investigated, suggesting that it persisted near the lake throughout the postglacial. The retrieval of aDNA from pollen has major implications for palaeoecology by allowing (i) investigation of population level dynamics in time and space, and (ii) tracing ancestry of populations and developing phylogenetic trees that include extinct as well as extant taxa. The method should work over the last glacial oscillation, thus giving access to ancestry of populations over a crucial period of time for the understanding of the relationship between speciation and climate change.

Marine micro and macro algal species as biosorbents for heavy metals

This paper reviews some practical aspects of the application of algal biomass for the biosorption of heavy metals from wastewater. The ability of different algal species to remove metals varies with algal group and morphology, with the speciation of specific metals and their competition with others in wastewater, and with environmental or process factors. The scattered literature on the uptake of heavy metals by both living and dead algal biomass - both macroalgae and immobilized microalgae - has been reviewed, and the uptake capacity and efficiency of different species, as well as what is known about the mechanisms of biosorption, are presented. Data on metal uptake have commonly been fitted to equilibrium models, such as the Langmuir and Freundlich isotherm models, and the parameters of these models permit the uptake capacity of different algal species under different process conditions to be compared. Higher uptake capacities have been found for brown algae than for red and green algae. Kelps and fucoids are the most important groups of algae used for biosorption of heavy metals, probably because of their abundant cell wall polysacchrides and extracellular polymers. Another important practical aspect is the possibility of re-using algal biomass in several adsorption/desorption cycles (up to 10 have been used with Sargassum spp), and the influence of morphology and environmental conditions on the re-usability of algal tissue is also considered.

Species boundaries and phylogenetic relationships within the green algal genus Codium (Bryopsidales) based on plastid DNA sequences

Despite the potential model role of the green algal genus Codium for studies of marine speciation and evolution, there have been difficulties with species delimitation and a molecular phylogenetic framework was lacking. In the present study, 74 evolutionarily significant units (ESUs) are delimited using 227 rbcL exon 1 sequences obtained from specimens collected throughout the genus' range. Several morpho-species were shown to be poorly defined, with some clearly in need of lumping and others containing pseudo-cryptic diversity. A phylogenetic hypothesis of 72 Codium ESUs is inferred from rbcL exon 1 and rps3-rp/16 sequence data using a conventional nucleotide substitution model (GTR + Gamma + I), a codon position model and a covariotide (covarion) model, and the fit of a multitude of substitution models and alignment partitioning strategies to the sequence data is reported. Molecular clock tree rooting was carried out because out-group rooting was probably affected by phylogenetic bias. Several aspects of the evolution of morphological features of Codium are discussed and the inferred phylogenetic hypothesis is used as a framework to study the biogeography of the genus, both at a global scale and within the Indian Ocean. (c) 2007 Elsevier Inc. All rights reserved.

Structure and solvation in ionic liquids

This Account describes experimental data used to understand the structure of ionic liquids and solute-solvent interactions of both molecular solutes and dissolved metal complexes. In general, the structures of the ionic liquids determined from experimental data show good agreement with both simulated structures and solid-state structures. For all ionic liquids studied, strong charge ordering is found leading to long-range order even in the presence of a solute. For dissolved metal complexes, the ionic liquid is not innocent and a clear dependence on the speciation is observed with variations in both the cation and anion.

Phenotype-environment correlations in a putative whitefish adaptive radiation

1. The adaptive radiation of fishes into benthic (littoral) and pelagic (lentic) morphs in post-glaciallakes has become an important model system for speciation. Although these systems are well stud-ied, there is little evidence of the existence of morphs that have diverged to utilize resources in theremaining principal lake habitat, the profundal zone.
2. Here, we tested phenotype-environment correlations of three whitefish (Coregonus lavaretus)morphs that have radiated into littoral, pelagic and profundal niches in northern Scandinavianlakes. We hypothesized that morphs in such trimorphic systems would have a morphology adaptedto one of the principal lake habitats (littoral, pelagic or profundal niches). Most whitefish popula-tions in the study area are formed by a single (monomorphic) whitefish morph, and we furtherhypothesized that these populations should display intermediate morphotypes and niche utiliza-tion. We used a combination of traditional (stomach content, habitat use, gill raker counts) andmore recently developed (stable isotopes, geometric morphometrics) techniques to evaluate pheno-type-environment correlations in two lakes with trimorphic and two lakes with monomorphicwhitefish.
3. Distinct phenotype-environment correlations were evident for each principal niche in whitefishmorphs inhabiting trimorphic lakes. Monomorphic whitefish exploited multiple habitats, hadintermediate morphology, displayed increased variance in gillraker-counts, and relied significantlyon zooplankton, most likely due to relaxed resource competition.
4. We suggest that the ecological processes acting in the trimorphic lakes are similar to each other,and are driving the adaptive evolution of whitefish morphs, possibly leading to the formation ofnew species.

Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times

Background: After a volcano erupts, a lake may form in the cooled crater and become an isolated aquatic ecosystem. This makes fishes in crater lakes informative for understanding sympatric evolution and ecological diversification in barren environments. From a geological and limnological perspective, such research offers insight about the process of crater lake ecosystem establishment and speciation. In the present study we use genetic and coalescence approaches to infer the colonization history of Midas cichlid fishes (Amphilophus cf. citrinellus) that inhabit a very young crater lake in Nicaragua-the ca. 1800 year-old Lake Apoyeque. This lake holds two sympatric, endemic morphs of Midas cichlid: one with large, hypertrophied lips (~20% of the total population) and another with thin lips. Here we test the associated ecological, morphological and genetic diversification of these two morphs and their potential to represent incipient speciation.
Results: Gene coalescence analyses [11 microsatellite loci and mitochondrial DNA (mtDNA) sequences] suggest that crater lake Apoyeque was colonized in a single event from the large neighbouring great lake Managua only about 100 years ago. This founding in historic times is also reflected in the extremely low nuclear and mitochondrial genetic diversity in Apoyeque. We found that sympatric adult thin- and thick-lipped fishes occupy distinct ecological trophic niches. Diet, body shape, head width, pharyngeal jaw size and shape and stable isotope values all differ significantly between the two lip-morphs. The eco-morphological features pharyngeal jaw shape, body shape, stomach contents and stable isotopes (d15N) all show a bimodal distribution of traits, which is compatible with the expectations of an initial stage of ecological speciation under disruptive selection. Genetic differentiation between the thin- and thick-lipped population is weak at mtDNA sequence (FST = 0.018) and absent at nuclear microsatellite loci (FST < 0.001).
Conclusions: This study provides empirical evidence of eco-morphological differentiation occurring very quickly after the colonization of a new and vacant habitat. Exceptionally low levels of neutral genetic diversity and inference from coalescence indicates that the Midas cichlid population in Apoyeque is much younger (ca. 100 years or generations old) than the crater itself (ca. 1 800 years old). This suggests either that the crater remained empty for many hundreds of years after its formation or that remnant volcanic activity prevented the establishment of a stable fish population during the early life of the crater lake. Based on our findings of eco-morphological variation in the Apoyeque Midas cichlids, and known patterns of adaptation in Midas cichlids in general, we suggest that this population may be in a very early stage of speciation (incipient species), promoted by disruptive selection and ecological diversification.

Parasite diversity, patterns of MHC II variation and olfactory based mate choice in diverging three-spined stickleback ecotypes

Ecological speciation has been the subject of intense research in evolutionary biology but the genetic basis of the actual mechanism driving reproductive isolation has rarely been identified. The extreme polymorphism of the major histocompatibility complex (MHC), probably maintained by parasite-mediated selection, has been proposed as a potential driver of population divergence. We performed an integrative field and experimental study using three-spined stickleback river and lake ecotypes. We characterized their parasite load and variation at MHC class II loci. Fish from lakes and rivers harbor contrasting parasite communities and populations possess different MHC allele pools that could be the result of a combined action of genetic drift and parasite-mediated selection. We show that individual MHC class II diversity varies among populations and is lower in river ecotypes. Our results suggest the action of homogenizing selection within habitat type and diverging selection between habitat types. Finally, reproductive isolation was suggested by experimental evidence: in a flow channel design females preferred assortatively the odor of their sympatric male. This demonstrates the role of olfactory cues in maintaining reproductive isolation between diverging fish ecotypes.

An explanatory model for food-web structure and evolution

Food webs are networks describing who is eating whom in an ecological community. By now it is clear that many aspects of food-web structure are reproducible across diverse habitats, yet little is known about the driving force behind this structure. Evolutionary and population dynamical mechanisms have been considered. We propose a model for the evolutionary dynamics of food-web topology and show that it accurately reproduces observed food-web characteristics in the steady state. It is based on the observation that most consumers are larger than their resource species and the hypothesis that speciation and extinction rates decrease with increasing body mass. Results give strong support to the evolutionary hypothesis. (C) 2005 Elsevier B.V. All rights reserved.

Chlorometallate(III) ionic liquids as Lewis acidic catalysts - a quantitative study of acceptor properties

The Gutmann Acceptor Number (AN), which is a quantitative measure of Lewis acidity, has been estimated using the P-31 NMR chemical shift of a probe molecule, triethylphosphine oxide, for a range of chlorometallate(III) ionic liquids, based on Group 13 metals (aluminium(III), gallium(III) and indium(III)) and the 1-octyl-3-methylimidazolium cation, at different compositions. The results were interpreted in terms of extant speciation studies of chlorometallate(III) ionic liquids, and compared with a range of standard molecular solvents and acids. The value of these data were illustrated in terms of the selection of appropriate ionic liquids for specific applications.

Degradation of carbon disulphide (CS2) in soils and groundwater from a CS2 -contaminated site

This study is the first investigation of biodegradation of carbon disulphide (CS₂) in soil that provides estimates of degradation rates and identifies intermediate degradation products and carbon isotope signatures of degradation. Microcosm studies were undertaken under anaerobic conditions using soil and groundwater recovered from CS₂-contaminated sites. Proposed degradation mechanisms were validated using equilibrium speciation modelling of concentrations and carbon isotope ratios. A first-order degradation rate constant of 1.25 × 10-2 h-1 was obtained for biological degradation with soil. Carbonyl sulphide (COS) and hydrogen sulphide (H₂S) were found to be intermediates of degradation, but did not accumulate in vials. A 13C/12C enrichment factor of -7.5 ± 0.8 ‰ was obtained for degradation within microcosms with both soil and groundwater whereas a 13C/12C enrichment factor of -23.0 ± 2.1 ‰ was obtained for degradation with site groundwater alone. It can be concluded that biological degradation of both CS2-contaminated soil and groundwater is likely to occur in the field suggesting that natural attenuation may be an appropriate remedial tool at some sites. The presence of biodegradation by-products including COS and H₂S indicates that biodegradation of CS₂ is occurring and stable carbon isotopes are a promising tool to quantify CS₂ degradation.

Neotropical refugia

Patterns of endemism in the Neotropics have been explained by restriction of forest to ‘refugia’ in arid cold-stages of the Quaternary (Haffer J (1969)
Speciation in Amazonian forest birds. Science 165: 131–137). The palaeoecological record, however, shows no such forest contraction. We review
palaeoecological and phylogenetic data on the response of Neotropical taxa and communities to climatic changes of the Cenozoic. Solar insolation varies
over this period with latitude and geography, including shifts in opposite directions between high and low latitudes. In the Neotropics, distribution and
abundance patterns originate on a wide range of timescales through the Cenozoic, down to the currently dominant precession forcing (20 kyr). In contrast,
distributions and abundances at higher latitudes are controlled by obliquity forcing (40 kyr). The patterns observed by Haffer (1969) are likely derived
from pre-Quaternary radiations and are not inconsistent with palaeoecological findings of continuous forest cover in major areas of the Neotropics
during the Quaternary. The relative proportions of speciation processes have changed through time between predominantly sympatric to predominantly
allopatric depending on the prevailing characteristics of orbitally forced climatic changes. Behaviour of Neotropical organisms and ecosystems on long
timescales may be influenced much more by precessional forcing than by the obliquity forcing that controls high-latitude climate change and glaciations.

Convergent evolutionary processes driven by foraging opportunity in two sympatric morph pairs of Arctic charr with contrasting post-glacial origins

The expression of two or more discrete phenotypes amongst individuals within a species (morphs) provides multiple modes upon which selection can act semi-independently, and thus may be an important stage in speciation. In the present study, we compared two sympatric morph systems aiming to address hypotheses related to their evolutionary origin. Arctic charr in sympatry in Loch Tay, Scotland, exhibit one of two discrete, alternative body size phenotypes at maturity (large or small body size). Arctic charr in Loch Awe segregate into two temporally segregated spawning groups (breeding in either spring or autumn). Mitochondrial DNA restriction fragment length polymorphism analysis showed that the morph pairs in both lakes comprise separate gene pools, although segregation of the Loch Awe morphs is more subtle than that of Loch Tay. We conclude that the Loch Awe morphs diverged in situ (within the lake), whereas Loch Tay morphs most likely arose through multiple invasions by different ancestral groups that segregated before post-glacial invasion (i.e. in allopatry). Both morph pairs showed clear trophic segregation between planktonic and benthic resources (measured by stable isotope analysis) but this was significantly less distinct in Loch Tay than in Loch Awe. By contrast, both inter-morph morphological and life-history differences were more subtle in Loch Awe than in Loch Tay. The strong ecological but relatively weak morphological and life-history divergence of the in situ derived morphs compared to morphs with allopatric origins indicates a strong link between early ecological and subsequent genetic divergence of sympatric origin emerging species pairs. The emergence of parallel specialisms despite distinct genetic origins of these morph pairs suggests that the effect of available foraging opportunities may be at least as important as genetic origin in structuring sympatric divergence in post-glacial fishes with high levels of phenotypic plasticity. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, , .