Modern humans in Sarawak, Malaysian Borneo, during Oxygen Isotope Stage 3: palaeoenvironmental evidence from the Great Cave of Niah

During recent reinvestigations in the Great Cave of Niah in Borneo, the ‘Hell Trench’ sedimentary sequence seen by earlier excavators was re-exposed. Early excavations here yielded the earliest anatomically-modern human remains in island Southeast Asia. Calibrated radiocarbon dates, pollen, algal microfossils, palynofacies, granulometry and geochemistry of the ‘Hell Trench’ sequence provide information about environmental and vegetational changes, elements of geomorphic history and information about human activity. The ‘Hell’ sediments were laid down episodically in an ephemeral stream or pool. The pollen suggests cyclically changing vegetation with forest habitats alternating with more open environments; indicating that phases with both temperatures and precipitation reduced compared with the present. These events can be correlated with global climate change sequences to produce a provisional dating framework. During some forest phases, high counts of Justicia, a plant which today colonises recently burnt forest areas, point to fire in the landscape. This may be evidence for biomass burning by humans, presumably to maintain forest-edge habitats. There is evidence from palynofacies for fire on the cave floor in the ‘Hell’ area. Since the area sampled is beyond the limit of plant growth, this is evidence for human activity. The first such evidence is during an episode with significant grassland indicators, suggesting that people may have reached the site during a climatic phase characterised by relatively open habitats ~50 ka. Thereafter, people were able to maintain a relatively consistent presence at Niah. The human use of the ‘Hell’ area seems to have intensified through time, probably because changes in the local hydrological regime made the area dryer and more suitable for human use.

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.

Algal epiphytes of Zostera marina: Variation in assemblage structure from individual leaves to regional scale

Data from a hierarchical study of four Zostera marina beds in Wales were used to identify the spatial scales of variation in epiphyte assemblages. There were significant within and among bed differences in assemblage structure. The differences in assemblage structure with spatial scale generally persisted when species identifications were aggregated into functional groups. There was also significant within and among bed variability in Zostera density and average length. Local variations in Zostera canopy variables at the quadrat scale (total leaf length, average leaf length and leaf density per quadrat) were not related to epiphyte species richness nor to the structure of the assemblage. In contrast, individual leaf length was significantly related to species richness in two of the beds and the structure of epiphyte assemblages was always related to individual leaf lengths. The absence of links between quadrat scale measurements of canopy variables and assemblage structure may reflect the high turnover of individual Zostera leaves. Experimental work is required to discriminate further between the potential causes of epiphyte assemblage variation within and between beds. No bed represented a refuge where a rare species was abundant. If a species was uncommon at the bed scale, it was also uncommon in beds where it occurred. The heterogeneous assemblages found in this study suggest that a precautionary approach to conservation is advisable.

Kinetic model for the hydrolysis of lignocellulosic biomass in the ionic liquid, 1-ethyl-3-methyl-imidazolium chloride†

The kinetics of the acid-catalysed hydrolysis of cellobiose in the ionic liquid 1-ethyl-3-methylimidazolium chloride, [C(2)mim]Cl, was studied as a model for general lignocellulosic biomass hydrolysis in ionic liquid systems. The results show that the rate of the two competing reactions, polysaccharide hydrolysis and sugar decomposition, vary with acid strength, and that for acids with an aqueous pK(a) below approximately zero, the hydrolysis reaction is significantly faster than the degradation of glucose, thus allowing hydrolysis to be performed with a high selectivity in glucose. In tests with soluble cellulose, hemicellulose (xylan), and lignocellulosic biomass (Miscanthus grass), comparable hydrolysis rates were observed with bond scission occurring randomly along the biopolymer chains, in contrast to end-group hydrolysis observed with aqueous acids.

Dilute acid hydrolysis of Lignocellulosic biomass

The overall aim of this work was to establish the optimum conditions for acid hydrolysis of hemicellulosic biomass in the form of potato peel. The hydrolysis reaction was undertaken in a 1l high pressure pilot batch reactor using dilute phosphoric acid. Analysis of the decomposition rate of hemicellulosic biomass (namely Cellulose, Hemicellulose and lignin) was undertaken using HPLC of the reaction products namely, 5 and 6 carbon sugars. Process parameters investigated included, reactor temperature (from 135 degrees C to 200 degrees C) and acid concentration (from 2.5% (w/w) to 10% (w/w)). Analysis of the reactor products indicated that high conversion of cellulose to glucose was apparent although arabinose conversion was quite low due to thermally un-stability. However, an overall sugar yield is 82.5% was achieved under optimum conditions. This optimum yield was obtained at 135 degrees C and 10% (w/w) acid concentration. 55.2 g sugar/100 g dry potato peel is produced after a time of 8 min. The work indicates that the use of potato peel may be a feasible option as a feed material for the production of sugars for biofuel synthesis, due its low cost and high sugar yields. (C) 2009 Elsevier B.V. All rights reserved.

Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life

Background. The assembly of the tree of life has seen significant progress in recent years but algae and protists have been largely overlooked in this effort. Many groups of algae and protists have ancient roots and it is unclear how much data will be required to resolve their phylogenetic relationships for incorporation in the tree of life. The red algae, a group of primary photosynthetic eukaryotes of more than a billion years old, provide the earliest fossil evidence for eukaryotic multicellularity and sexual reproduction. Despite this evolutionary significance, their phylogenetic relationships are understudied. This study aims to infer a comprehensive red algal tree of life at the family level from a supermatrix containing data mined from GenBank. We aim to locate remaining regions of low support in the topology, evaluate their causes and estimate the amount of data required to resolve them. Results. Phylogenetic analysis of a supermatrix of 14 loci and 98 red algal families yielded the most complete red algal tree of life to date. Visualization of statistical support showed the presence of five poorly supported regions. Causes for low support were identified with statistics about the age of the region, data availability and node density, showing that poor support has different origins in different parts of the tree. Parametric simulation experiments yielded optimistic estimates of how much data will be needed to resolve the poorly supported regions (ca. 103 to ca. 104 nucleotides for the different regions). Nonparametric simulations gave a markedly more pessimistic image, some regions requiring more than 2.8 105 nucleotides or not achieving the desired level of support at all. The discrepancies between parametric and nonparametric simulations are discussed in light of our dataset and known attributes of both approaches. Conclusions. Our study takes the red algae one step closer to meaningful inclusion in the tree of life. In addition to the recovery of stable relationships, the recognition of five regions in need of further study is a significant outcome of this work. Based on our analyses of current availability and future requirements of data, we make clear recommendations for forthcoming research.

Intertidal molluscan and algal species richness around the UK coast

Geographically referenced databases of species records are becoming increasingly available. Doubts over the heterogeneous quality of the underlying data may restrict analyses of such collated databases. We partitioned the spatial variation in species richness of littoral algae and molluscs from the UK National Biodiversity Network database into a smoothed mesoscale component and a local component. Trend surface analysis (TSA) was used to define the mesoscale patterns of species richness, leaving a local residual component that lacked spatial autocorrelation. The analysis was based on 10 km grid squares with 115035 records of littoral algae (729 species) and 66879 records of littoral molluscs (569 species). The TSA identified variation in algal and molluscan species richness with a characteristic length scale of approximately 120 km. Locations of the most species-rich grid squares were consistent with the southern and western bias of species richness in the UK marine flora and fauna. The TSA also identified areas which showed significant changes in the spatial pattern of species richness: breakpoints, which correspond to major headlands along the south coast of England. Patterns of algal and molluscan species richness were broadly congruent. Residual variability was strongly influenced by proxies of collection effort, but local environmental variables including length of the coastline and variability in wave exposure were also important. Relative to the underlying trend, local species richness hotspots occurred on all coasts. While there is some justification for scepticism in analyses of heterogeneous datasets, our results indicate that the analysis of collated datasets can be informative.