Immigration, species radiation and extinction in a highly diverse songbird lineage: white-eyes on Indian Ocean islands

Molecular phylogenetic hypotheses of species-rich lineages in regions where geological history can be reliably inferred may provide insights into the scale of processes driving diversification. Here we sample all extant or recently extinct white-eye (Zosterops) taxa of the southwest Indian Ocean, combined with samples from all principal continental lineages. Results support a high dispersal capability, with at least two independent continental sources for white-eyes of the region. An early (within 1.8 million years ago) expansion into the Indian Ocean may have originated either from Asia or Africa; the three resulting lineages show a disparate distribution consistent with considerable extinction following their arrival. Africa is supported as the origin of a later expansion into the region (within 1.2 million years ago). On two islands, a pair of Zosterops species derived from independent immigrations into the Indian Ocean co-occur or may have formerly co-occurred, providing strong support for their origin by double-island colonization rather than within-island (sympatric or microallopatric) speciation. On Mauritius and La Reunion, phylogenetic placement of sympatric white-eyes allow us to rule out a scenario in which independent within-island speciation occurred on both islands; one of the species pairs must have arisen by double colonization, while the other pair is likely to have arisen by the same mechanism. Long-distance immigration therefore appears to be responsible for much of the region's white-eye diversity. Independent immigrations into the region have resulted in lineages with mutually exclusive distributions and it seems likely that competition with congeneric species, rather than arrival frequency, may limit present-day diversity.

Crops and cultures in the Pacific: new data and new techniques for the investigation of old questions

Fifty years ago Carl Sauer suggested, controversially and on the basis of theory rather than evidence, that Southeast Asia was the source area for agriculture throughout the Old World, including the Pacific. Since then, the archaeobotanical record (macroscopic and microscopic) from the Pacific islands has increased, leading to suggestions, also still controversial, that Melanesia was a center of origin of agriculture independent of South-east Asia, based on tree fruits and nuts and vegetatively propagated starchy staples. Such crops generally lack morphological markers of domestication, so exploitation, cultivation and domestication cannot easily be distinguished in the archaeological record. Molecular studies involving techniques such as chromosome painting, DNA fingerprinting and DNA sequencing, can potentially complement the archaeological record by suggesting where species which were spread through the Pacific by man originated and by what routes they attained their present distributions. A combination of archaeobotanical and molecular studies should therefore eventually enable the rival claims of Melanesia versus South-east Asia as independent centers of invention of agriculture to be assessed.

DNA variation in a 13-Mb region including the F9 gene: inferring the genealogical history and causal role of a hemophilia B mutation (IVS 5+13 A -> G)

About 5.5% of all UK hemophilia B patients have the base substitution IVS 5+13 A-->G as the only change in their factor (F)IX gene (F9). This generates a novel donor splice site which fits the consensus better than the normal intron 5 donor splice. Use of the novel splice site should result in a missense mutation followed by the abnormal addition of four amino acids to the patients' FIX. In order to explain the prevalence of this mutation, its genealogical history is examined. Analysis of restriction fragment length polymorphism in the 21 reference UK individuals (from different families) with the above mutation showed identical haplotypes in 19 while two differed from the rest and from each other. In order to investigate the history of the mutation and to verify that it had occurred independently more than once, the sequence variation in 1.5-kb segments scattered over a 13-Mb region including F9 was examined in 18 patients and 15 controls. This variation was then analyzed with a recently developed Bayesian approach that reconstructs the genealogy of the gene investigated while providing evidence of independent mutations that contribute disconnected branches to the genealogical tree. The method also provides minimum estimates of the age of the mutation inherited by the members of coherent trees. This revealed that 17 or 18 mutant genes descend from a founder who probably lived 450 years ago, while one patient carries an independent mutation. The independent recurrence of the IVS5+13 A-->G mutation strongly supports the conclusion that it is the cause of these patients' mild hemophilia.

Human evolution, nutritional ecology and prebiotics in ancient diet

Modern studies of prebiotic non digestible carbohydrates continue to expand and demonstrate their colonic and systemic benefits. However, virtually nothing is known of their use among ancient populations. In this paper we discuss evidence for prebiotic use in the archaeological record from select areas of the world. It is suggested that members of our genus Homo would have had sufficient ecological opportunity to include prebiotic-bearing plants in diet as early as ~ 2 million years ago, but that significant dietary intake would not have taken place until the advent of technological advances that characterized the Upper Paleolithic of ~40,000 years ago. Throughout human evolution, hominid populations that diversified their diet to include prebiotic-bearing plants would have had a selective advantage over competitors.

Recent highlights in modified oligonucleotide chemistry

The synthesis of modified nucleic acids has been the subject of much study ever since the structure of DNA was elucidated by Watson and Crick at Cambridge and Wilkins and Franklin at King's College over half a century ago. This review describes recent developments in the synthesis and application of these artificial nucleic acids, predominantly the phosphoramidites which allow for easy inclusion into oligonucleotides, and is divided into three separate sections. Firstly, modi. cations to the base portion will be discussed followed secondly by modi. cations to the sugar portion. Finally, changes in the type of nucleic acid linker will be discussed in the third section. Peptide Nucleic Acids ( PNAs) are not discussed in this review as they represent a separate and large area of nucleic acid mimics.

Stability criteria for the contextual emergence of macrostates in neural networks

More than thirty years ago, Amari and colleagues proposed a statistical framework for identifying structurally stable macrostates of neural networks from observations of their microstates. We compare their stochastic stability criterion with a deterministic stability criterion based on the ergodic theory of dynamical systems, recently proposed for the scheme of contextual emergence and applied to particular inter-level relations in neuroscience. Stochastic and deterministic stability criteria for macrostates rely on macro-level contexts, which make them sensitive to differences between different macro-levels.

Multiple-scattering in radar systems: a review

Although extensively studied within the lidar community, the multiple scattering phenomenon has always been considered a rare curiosity by radar meteorologists. Up to few years ago its appearance has only been associated with two- or three-body-scattering features (e.g. hail flares and mirror images) involving highly reflective surfaces. Recent atmospheric research aimed at better understanding of the water cycle and the role played by clouds and precipitation in affecting the Earth's climate has driven the deployment of high frequency radars in space. Examples are the TRMM 13.5 GHz, the CloudSat 94 GHz, the upcoming EarthCARE 94 GHz, and the GPM dual 13-35 GHz radars. These systems are able to detect the vertical distribution of hydrometeors and thus provide crucial feedbacks for radiation and climate studies. The shift towards higher frequencies increases the sensitivity to hydrometeors, improves the spatial resolution and reduces the size and weight of the radar systems. On the other hand, higher frequency radars are affected by stronger extinction, especially in the presence of large precipitating particles (e.g. raindrops or hail particles), which may eventually drive the signal below the minimum detection threshold. In such circumstances the interpretation of the radar equation via the single scattering approximation may be problematic. Errors will be large when the radiation emitted from the radar after interacting more than once with the medium still contributes substantially to the received power. This is the case if the transport mean-free-path becomes comparable with the instrument footprint (determined by the antenna beam-width and the platform altitude). This situation resembles to what has already been experienced in lidar observations, but with a predominance of wide- versus small-angle scattering events. At millimeter wavelengths, hydrometeors diffuse radiation rather isotropically compared to the visible or near infrared region where scattering is predominantly in the forward direction. A complete understanding of radiation transport modeling and data analysis methods under wide-angle multiple scattering conditions is mandatory for a correct interpretation of echoes observed by space-borne millimeter radars. This paper reviews the status of research in this field. Different numerical techniques currently implemented to account for higher order scattering are reviewed and their weaknesses and strengths highlighted. Examples of simulated radar backscattering profiles are provided with particular emphasis given to situations in which the multiple scattering contributions become comparable or overwhelm the single scattering signal. We show evidences of multiple scattering effects from air-borne and from CloudSat observations, i.e. unique signatures which cannot be explained by single scattering theory. Ideas how to identify and tackle the multiple scattering effects are discussed. Finally perspectives and suggestions for future work are outlined. This work represents a reference-guide for studies focused at modeling the radiation transport and at interpreting data from high frequency space-borne radar systems that probe highly opaque scattering media such as thick ice clouds or precipitating clouds.

Challenges and opportunities facing contractors in Ghana

The main aim of this study was to ascertain and discuss the current challenges and opportunities facing construction contractors in Ghana. This involved a review of the economic, legal and political environments in which contractors in Ghana operate; a review of published studies on construction in developing countries generally and Ghana specifically; and in-depth interviews and discussions with seven building and civil engineering contractors in Ghana in 2009 and 2010. Six road contractors were also interviewed. The findings indicate significant challenges relating mainly to financing for projects and a harsh business environment. However, most contractors interviewed admitted to significant problems in their own organisations. It is clear that the contracting environment in Ghana is harsh particularly for local contractors who are often not paid on time and without compensation for late payment. However, local construction firms in Ghana who want to breakthrough ought to formulate the right strategic plans, develop innovative business strategies, develop professionalism, and merge with local firms with similar organisational values and characteristics. In short, local or indigenous Ghanaian contractors ought to face up to the reality of competition and the dynamics of modern business in order to survive, grow and become major players in the construction industry in Ghana.

The role of 80K/MARCKS, a specific substrate of protein kinase C, in cell growth and tumour progression

Since its discovery more than a decade ago [Wu et al., 1982; Rozengurt et al., 1983], the 80-87 kDa myristoylated a lanine-rich C-kinase substrate (80K/MARCKS) protein has attracted a great deal of attention from researchers interested in cell growth and tumour progression. However, despite its ubiquitous distribution, a definitive functional role for 80K/MARCKS has not been found. The purpose of this review is to describe the properties, distribution and regulation of 80K/MARCKS and to discuss some of the most recent findings, both from our laboratory and from others, that have suggested a functional role for this protein in modulating cell growth and tumour progression. Furthermore, I will present data from our laboratory that implicates 80K/MARCKS as a novel tumour suppressor in cells of melanocyte origin.

The domestication of water: water management in the ancient world and its prehistoric origins in the Jordan Valley

The ancient civilizations were dependent upon sophisticated systems of water management. The hydraulic engineering works found in ancient Angkor (ninth to thirteenth century AD), the Aztec city of Tenochtitlan (thirteenth to fifteenth century AD), Byzantine Constantinople (fourth to sixth century AD) and Nabatean Petra (sixth century BC to AD 106) are particularly striking because each of these is in localities of the world that are once again facing a water crisis. Without water management, such ancient cities would never have emerged, nor would the urban communities and towns from which they developed. Indeed, the ‘domestication’ of water marked a key turning point in the cultural trajectory of each region of the world where state societies developed. This is illustrated by examining the prehistory of water management in the Jordan Valley, identifying the later Neolithic (approx. 8300–6500 years ago) as a key period when significant investment in water management occurred, laying the foundation for the development of the first urban communities of the Early Bronze Age.

Transport in the middle atmosphere

An overview is provided of the current understanding of transport in the middle atmosphere. Over the past quarter century this subject has evolved from a basic recognition of the Brewer-Dobson circulation to a detailed appreciation of many key features of transport such as the stratospheric surf zone, mixing barriers and the dynamics of filamentation. Whilst the elegant theoretical framework for middle atmosphere transport that emerged roughly twenty years ago never fulfilled its promise, useful phenomenological models have been developed together with innovative diagnostic methods. These advances were made possible by the advent of plenty of satellite and aircraft observations of long-lived chemical species together with developments in data assimilation and numerical modeling, and have been driven in large measure by the problem of stratospheric ozone depletion. This review is primarily focused on the stratosphere, where both the interest and the knowledge are the greatest, but a few remarks are also made on the mesosphere.

The role of rainfall intensity and soil in determining rates of flow through cryoturbated chalk

The effects of different water application rates (3, 10, 15 and 30 mm/h) and of topsoil removal on the rate of downward water movement through the cryoturbated chalk zone in southern England were investigated in situ. During and after each application of water, changes in water content and matric potential of the profile were monitored and percolate was collected in troughs. The measured water breakthrough time showed that water moved to 1.2 m depth quickly (in 8.2 h) even with application rate as low as 3 mm/h and that the time was only 3 h when water was applied at a rate of 15 mm/ h. These breakthrough times were about 150 and 422 fold shorter, respectively, than those expected if the water had been conducted by the matrix alone. Percolate was collected in troughs within 3.5 h at 1.2 m depth when water was applied at 30 mm/h and the quantity collected indicated that a significant amount of the surface applied water moved downward through inter-aggregate pores. The small increase in volumetric water content (about 3%) in excess of matrix water content resulted in a large increase in pore water velocities, from 0.20 to 5.3 m/d. The presence of soil layer had effect on the time taken for water to travel through the cryoturbated chalk layer and in the soil layer, water took about 1-2 h to pass thorough, depending on the intensity.

Late Holocene methane rise caused by orbitally controlled increase in tropical sources

Considerable debate surrounds the source of the apparently ‘anomalous’1 increase of atmospheric methane concentrations since the mid-Holocene (5,000 years ago) compared to previous interglacial periods as recorded in polar ice core records2. Proposed mechanisms for the rise in methane concentrations relate either to methane emissions from anthropogenic early rice cultivation1, 3 or an increase in natural wetland emissions from tropical4 or boreal sources5, 6. Here we show that our climate and wetland simulations of the global methane cycle over the last glacial cycle (the past 130,000 years) recreate the ice core record and capture the late Holocene increase in methane concentrations. Our analyses indicate that the late Holocene increase results from natural changes in the Earth's orbital configuration, with enhanced emissions in the Southern Hemisphere tropics linked to precession-induced modification of seasonal precipitation. Critically, our simulations capture the declining trend in methane concentrations at the end of the last interglacial period (115,000–130,000 years ago) that was used to diagnose the Holocene methane rise as unique. The difference between the two time periods results from differences in the size and rate of regional insolation changes and the lack of glacial inception in the Holocene. Our findings also suggest that no early agricultural sources are required to account for the increase in methane concentrations in the 5,000 years before the industrial era.

Comparative genomics suggests that an ancestral polyploidy event leads to enhanced root nodule symbiosis in the Papilionoideae

Root nodule symbiosis (RNS) is one of the most efficient biological systems for nitrogen fixation and it occurs in 90% of genera in the Papilionoideae, the largest subfamily of legumes. Most papilionoid species show evidence of a polyploidy event occurred approximately 58 million years ago. Although polyploidy is considered to be an important evolutionary force in plants, the role of this papilionoid polyploidy event, especially its association with RNS, is not understood. In this study, we explored this role using an integrated comparative genomic approach and conducted gene expression comparisons and gene ontology enrichment analyses. The results show the following: (1) approximately a quarter of the papilionoid-polyploidy-derived duplicate genes are retained; (2) there is a striking divergence in the level of expression of gene duplicate pairs derived from the polyploidy event; and (3) the retained duplicates are frequently involved in the processes crucial for RNS establishment, such as symbiotic signalling, nodule organogenesis, rhizobial infection and nutrient exchange and transport. Thus, we conclude that the papilionoid polyploidy event might have further refined RNS and induced a more robust and enhanced symbiotic system. This conclusion partly explains the widespread occurrence of the Papilionoideae.

Quantification of UV-B flux through time using UV-B-absorbing compounds contained in fossil Pinus sporopollenin

• UV-B radiation currently represents c. 1.5% of incoming solar radiation. However, significant changes are known to have occurred in the amount of incoming radiation both on recent and on geological timescales. Until now it has not been possible to reconstruct a detailed measure of UV-B radiation beyond c. 150 yr ago. • Here, we studied the suitability of fossil Pinus spp. pollen to record variations in UV-B flux through time. In view of the large size of the grain and its long fossil history, we hypothesized that this grain could provide a good proxy for recording past variations in UV-B flux. • Two key objectives were addressed: to determine whether there was, similar to other studied species, a clear relationship between UV-B-absorbing compounds in the sporopollenin of extant pollen and the magnitude of UV-B radiation to which it had been exposed; and to determine whether these compounds could be extracted from a small enough sample size of fossil pollen to make reconstruction of a continuous record through time a realistic prospect. • Preliminary results indicate the excellent potential of this species for providing a quantitative record of UV-B through time. Using this technique, we present the first record of UV-B flux during the last 9500 yr from a site near Bergen, Norway.