Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.

BACKGROUND: The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. RESULTS: Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n=80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. CONCLUSIONS: Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.

Evolution of networks and sequences in eukaryotic cell cycle control.

The molecular networks regulating the G1-S transition in budding yeast and mammals are strikingly similar in network structure. However, many of the individual proteins performing similar network roles appear to have unrelated amino acid sequences, suggesting either extremely rapid sequence evolution, or true polyphyly of proteins carrying out identical network roles. A yeast/mammal comparison suggests that network topology, and its associated dynamic properties, rather than regulatory proteins themselves may be the most important elements conserved through evolution. However, recent deep phylogenetic studies show that fungal and animal lineages are relatively closely related in the opisthokont branch of eukaryotes. The presence in plants of cell cycle regulators such as Rb, E2F and cyclins A and D, that appear lost in yeast, suggests cell cycle control in the last common ancestor of the eukaryotes was implemented with this set of regulatory proteins. Forward genetics in non-opisthokonts, such as plants or their green algal relatives, will provide direct information on cell cycle control in these organisms, and may elucidate the potentially more complex cell cycle control network of the last common eukaryotic ancestor.

Evolution of Marine Organisms under Climate Change at Different Levels of Biological Organisation

Research to date has suggested that both individual marine species and ecological processes are expected to exhibit diverse responses to the environmental effects of climate change. Evolutionary responses can occur on rapid (ecological) timescales, and yet studies typically do not consider the role that adaptive evolution will play in modulating biological responses to climate change. Investigations into such responses have typically been focused at particular biological levels (e.g., cellular, population, community), often lacking interactions among levels. Since all levels of biological organisation are sensitive to global climate change, there is a need to elucidate how different processes and hierarchical interactions will influence species fitness. Therefore, predicting the responses of communities and populations to global change will require multidisciplinary efforts across multiple levels of hierarchy, from the genetic and cellular to communities and ecosystems. Eventually, this may allow us to establish the role that acclimatisation and adaptation will play in determining marine community structures in future scenarios.

The origin and evolution of synaptic proteins - choanoflagellates lead the way.

The origin of neurons was a key event in evolution, allowing metazoans to evolve rapid behavioral responses to environmental cues. Reconstructing the origin of synaptic proteins promises to reveal their ancestral functions and might shed light on the evolution of the first neuron-like cells in metazoans. By analyzing the genomes of diverse metazoans and their closest relatives, the evolutionary history of diverse presynaptic and postsynaptic proteins has been reconstructed. These analyses revealed that choanoflagellates, the closest relatives of metazoans, possess diverse synaptic protein homologs. Recent studies have now begun to investigate their ancestral functions. A primordial neurosecretory apparatus in choanoflagellates was identified and it was found that the mechanism, by which presynaptic proteins required for secretion of neurotransmitters interact, is conserved in choanoflagellates and metazoans. Moreover, studies on the postsynaptic protein homolog Homer revealed unexpected localization patterns in choanoflagellates and new binding partners, both which are conserved in metazoans. These findings demonstrate that the study of choanoflagellates can uncover ancient and previously undescribed functions of synaptic proteins.

Hydrochemical and isotopic tracing of mixing dynamics and water quality evolution under pumping conditions in the mine shaft of the abandoned Frances Colliery, Scotland.

Since 1995, when pumps were withdrawn from deep mines in East Fife (Scotland), mine waters have been rebounding throughout the coalfield. Recently, it has become necessary to pump and treat these waters to prevent their uncontrolled emergence at the surface. However, even relatively shallow pumping to surface treatment lagoons of the initially chemically-stratified mine water from a shaft in the coastal Frances Colliery during two dynamic step-drawdown tests to establish the hydraulic characteristics of the system resulted in rapid breakdown of the stratification within 24 h and a poor pumped water quality with high dissolved Fe loading. Further, data are presented here of hydrochemical and isotopic sampling of the extended pump testing lasting up to several weeks. The use in particular of the environmental isotopes d18O, d2H, d34S, 3H, 13C and 14C alongside hydrochemical and hydraulic pump test data allowed characterisation of the Frances system dynamics, mixing patterns and water quality sources feeding into this mineshaft under continuously pumped conditions. The pumped water quality reflects three significant components of mixing: shallow freshwater, seawater, and leakage from the surface treatment lagoons. In spite of the early impact of recirculating lagoon waters on the hydrochemistries, the highest Fe loadings in the longer-term pumped waters are identified with a mixed freshwater–seawater component affected by pyrite oxidation/melanterite dissolution in the subsurface system.

Mapping the evolution of optically generated rotational wave packets in a room-temperature ensemble of D2

A coherent superposition of rotational states in D2 has been excited by nonresonant, ultrafast (12 fs), intense (2×1014 W cm-2) 800 nm laser pulses, leading to impulsive dynamic alignment. Field-free evolution of this rotational wave packet has been mapped to high temporal resolution by a time-delayed pulse, initiating rapid double ionization, which is highly sensitive to the angle of orientation of the molecular axis with respect to the polarization direction, . The detailed fractional revivals of the neutral D2 wave packet as a function of and evolution time have been observed and modeled theoretically.

The VLT-FLAMES Survey of massive stars: Rotation and nitrogen enrichment as the key to understanding massive star evolution

Rotation has become an important element in evolutionary models of massive stars, specifically via the prediction of rotational mixing. Here we study a sample of stars, including rapid rotators, to constrain such models and use nitrogen enrichments as a probe of the mixing process. Chemical compositions (C, N, O, Mg, and Si) have been estimated for 135 early B-type stars in the Large Magellanic Cloud with projected rotational velocities up to similar to 300 km s(-1) using a non-LTE TLUSTY model atmosphere grid. Evolutionary models, including rotational mixing, have been generated attempting to reproduce these observations by adjusting the overshooting and rotational mixing parameters and produce reasonable agreement with 60% of our core hydrogen burning sample. We find (excluding known binaries) a significant population of highly nitrogen-enriched intrinsic slow rotators (nu sin i less than or similar to 50 km s(-1)) incompatible with our models (similar to 20% of the sample). Furthermore, while we find fast rotators with enrichments in agreement with the models, the observation of evolved (dex) fast rotators (log g < 3.7 dex) that are relatively unenriched (a further similar to 20% of the sample) challenges the concept of rotational mixing. We also find that 70% of our blue supergiant sample cannot have evolved directly from the hydrogen-burning main sequence. We are left with a picture where invoking binarity and perhaps fossil magnetic fields is required to understand the surface properties of a population of massive main- sequence stars.

Rapid change in energy status in fighting animals: causes and effects of strategic decisions

Energetic costs of fighting, such as high lactate or low glucose, have been shown in a range of species to correlate with the decisions made by each opponent, particularly the decision by one opponent, the 'loser', to end the fight by 'giving up'. Studies based on complete fights of differing duration, however, do not provide information on the changes in the physiological correlates of fighting that may take place during the course of the encounter, or how these changes may influence the capability and decisions of the contestants. We interrupted fights between hermit crabs, Pagurus bernhardus, at specific points, and related energy status to the preceding activities. Costs rose quickly with a rapid accumulation of lactic acid in attackers and declining muscular glycogen in defenders. Changes in physiological status appeared much earlier than the changes in behaviour that they may have caused. Furthermore, some physiological changes might have been an effect, rather than the cause, of fight decisions. (c) 2005 The Association for the Study of Animal Behaviour Published by Elsevier Ltd. All rights reserved.

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.

A rapid PCR-based assay for identification of cryptic Myotis spp (Myotis mystacinus, Myotis brandtii and Myotis alcathoe).

The development of a quick PCR-based method to distinguish European cryptic Myotis spp., Myotis mystacinus, Myotis brandtii and Myotis alcathoe is described. Primers were designed around species-specific single nucleotide polymorphisms (SNP’s) in the ND1 mitochondrial gene, and a pair of control primers was designed in the 12S mitochondrial gene. A multiplex of seven primer combinations produces clear species-specific bands using gel electrophoresis. Robustness of the method was tested on 33 M. mystacinus, 16 M. brandtii and 15 M. alcathoe samples from across the European range of these species. The method worked well on faecal samples collected from maternity roosts of M. mystacinus. The test is intended to aid collection of data on these species through a rapid and easy identification method with the ability to use DNA obtained from a range of sources including faecal matter.

Evolution of Organisational Structure and Capabilities in Internationalising Banks: The CEE Operations of UniCredit's Vienna Office

Cross-border integration is the central management issue for banks that expand internationally, and this is especially true in Central and Eastern Europe, where the pace of internationalisation through mergers and acquisitions has been rapid. A critical challenge in cross-border integration is aligning a multinational company's formal organizational structure with the distribution of capabilities across its subsidiary units, and this issue is explored by tracking the co-evolution of organizational structure and capabilities during the internationalisation of a large banking network into this region. Our focus is the Vienna head office of Bank Austria Creditanstalt, which was acquired first by HypoVereinsbank (Germany) and then UniCredit (Italy). Despite its formal role being downgraded during these changes, the unit continued to develop its distinctive capabilities. The key insight our article offers is that managing cross-border integration is not simply about recognizing the value of the distinctive capabilities of individual units and designing formal structures that successfully align with them. It is also about understanding the need for dynamic interaction between formal corporate structure and individual units' desires to retain power and influence, which have significant implications for the development of their organizational capabilities.

Politics, policy preferences and the evolution of Irish bureaucracy:A framework for analysis

Analysis of the Irish state's administrative system is an unaccountably neglected area of systematic academic inquiry. This is all the more difficult to account for in view of the dynamic relationship between government actors and the public bureaucracy in realizing political goals. This paper identifies some distinguishing institutional features and dominant trends in Irish politico-administrative governance, and suggests avenues for future inquiry. The paper begins with an examination of the literature on administrative system change, with a focus on the New Public Management literature. Following this, the Irish case is profiled, identifying the evolution of ministerial departments and of state agencies by successive Irish governments, including patterns of agency creation and termination over time. Particular attention is given to the period 1989-2010, which has been one of quite rapid and complex organizational change within the state's bureaucratic apparatus. © 2012 Political Studies Association of Ireland.

Rapid magmatic processes accompany arc-continent collision: the Western Bismarck arc, Papua New Guinea

New U-Th-Ra, major and trace element, and Sr-Nd-Pb isotope data are presented for young lavas from the New Britain and Western Bismarck arcs in Papua New Guinea. New Britain is an oceanic arc, whereas the latter is the site of an arc-continent collision. Building on a recent study of the Manus Basin, contrasts between the two arcs are used to evaluate the processes and timescales of magma generation accompanying arc-continent collision and possible slab detachment. All three suites share many attributes characteristic of arc lavas that can be ascribed to the addition of a regionally uniform subduction component derived from the subducting altered oceanic crust and sediment followed by dynamic melting of the modified mantle. However, the Western Bismarck arc lavas diverge from the Pb isotope mixing array formed by the New Britain and the Manus Basin lavas toward elevated Pb-208/Pb-204. We interpret this to reflect a second and subsequent addition of sediment melt at crustal depth during collision. U-238 and Ra-226 excesses are preserved in all of the lavas and are greatest in the Western Bismarck arc. High-Mg andesites with high Sr/Y ratios in the westernmost arc are attributed to recent shallow mantle flux melting at the slab edge. Data for two historical rhyolites are also presented. Although these rhyolites formed in quite different tectonic settings and display different geochemical and isotopic compositions, both formed from mafic parents within millennia.

Within-host evolution of Burkholderia pseudomallei over a twelve-year chronic carriage infection

UNLABELLED: Burkholderia pseudomallei causes the potentially fatal disease melioidosis. It is generally accepted that B. pseudomallei is a noncommensal bacterium and that any culture-positive clinical specimen denotes disease requiring treatment. Over a 23-year study of melioidosis cases in Darwin, Australia, just one patient from 707 survivors has developed persistent asymptomatic B. pseudomallei carriage. To better understand the mechanisms behind this unique scenario, we performed whole-genome analysis of two strains isolated 139 months apart. During this period, B. pseudomallei underwent several adaptive changes. Of 23 point mutations, 78% were nonsynonymous and 43% were predicted to be deleterious to gene function, demonstrating a strong propensity for positive selection. Notably, a nonsense mutation inactivated the universal stress response sigma factor RpoS, with pleiotropic implications. The genome underwent substantial reduction, with four deletions in chromosome 2 resulting in the loss of 221 genes. The deleted loci included genes involved in secondary metabolism, environmental survival, and pathogenesis. Of 14 indels, 11 occurred in coding regions and 9 resulted in frameshift mutations that dramatically affected predicted gene products. Disproportionately, four indels affected lipopolysaccharide biosynthesis and modification. Finally, we identified a frameshift mutation in both P314 isolates within wcbR, an important component of the capsular polysaccharide I locus, suggesting virulence attenuation early in infection. Our study illustrates a unique clinical case that contrasts a high-consequence infectious agent with a long-term commensal infection and provides further insights into bacterial evolution within the human host.

IMPORTANCE: Some bacterial pathogens establish long-term infections that are difficult or impossible to eradicate with current treatments. Rapid advances in genome sequencing technologies provide a powerful tool for understanding bacterial persistence within the human host. Burkholderia pseudomallei is considered a highly pathogenic bacterium because infection is commonly fatal. Here, we document within-host evolution of B. pseudomallei in a unique case of human infection with ongoing chronic carriage. Genomic comparison of isolates obtained 139 months (11.5 years) apart showed a strong signal of adaptation within the human host, including inactivation of virulence and immunogenic factors, and deletion of pathways involved in environmental survival. Two global regulatory genes were mutated in the 139-month isolate, indicating extensive regulatory changes favoring bacterial persistence. Our study provides insights into B. pseudomallei pathogenesis and, more broadly, identifies parallel evolutionary mechanisms that underlie chronic persistence of all bacterial pathogens.