An estimate of divergence time of parazoa and eumetazoa and that of cephalochordata and vertebrata by aldolase and triose phosphate isomerase clocks

Previously we suggested that four proteins including aldolase and triose phosphate isomerase (TPI) evolved with approximately constant rates over long periods covering the whole animal phyla. The constant rates of aldolase and TPI evolution were reexamined based on three different models for estimating evolutionary distances, It was shown that the evolutionary rates remain essentially unchanged in comparisons not only between different classes of vertebrates but also between vertebrates and arthropods and even between animals and plants, irrespective of the models used, Thus these enzymes might be useful molecular clocks for inferring divergence times of animal phyla, To know the divergence time of Parazoa and Eumetazoa and that of Cephalochordata and Vertebrata, the aldolase cDNAs from Ephydatia fluviatilis, a freshwater sponge, and the TPI cDNAs from Ephydatia fluviatilis and Branchiostoma belcheri an amphioxus, have been cloned and sequenced, Comparisons of the deduced amino acid sequences of aldolase and TPI from the freshwater sponge with known sequences revealed that the Parazoa-Eumetazoa split occurred about 940 million years ago (Ma) as determined by the average of two proteins and three models, Similarly, the aldolase and TPI clocks suggest that vertebrates and amphioxus last shared a common ancestor around 700 Ma and they possibly diverged shortly after the divergence of deuterostomes and protostomes.

Topographic changes in nascent and early mesoderm in amphioxus embryos studied by Dil labeling and by in situ hybridization for a Brachyury gene

In amphioxus embryos, the nascent and early mesoderm (including chorda-mesoderm) was visualized by expression of a Brachyury gene (AmBra-2). A band of mesoderm is first detected encircling the earliest (vegetal plate stage) gastrula sub-equatorially. Soon thereafter, the vegetal plate invaginates. resulting in a cap-shaped gastrula with the mesoderm localized at the blastoporal lip and completely encircling the blastopore. As the gastrula stage progresses, DiI (a vital dye) labeling demonstrates that the entire mesoderm is internalized by a slight involution of the epiblast into the hypoblast all around the perimeter of the blastopore. Subsequently. during the early neurula stage, the internalized mesoderm undergoes anterior extension mid-dorsally (as notochord) and dorsolaterally (in paraxial regions when segments will later form). By the late neurula stage, AmBra-2 is no longer transcribed throughout the mesoderm as a whole; instead. expression is detectable only in the posterior mesoderm and in the notochord, but not in par axial mesoderm where definitive somites have formed.

Tectonic Evolution and Dynamics of Deepwater Area of Pearl River Mouth Basin, Northern South China Sea

Quantitative studies on the evolution and dynamics of the deepwater area of Pearl River Mouth basin (PRMB) were carried out based on the latest geological and seismic data. The study area is generally in an extensional state during the Cenozoic. The major extension happened in the earlier syn-rift stages before 23 Ma and the extension after 23 Ma is negligible. Two rapid subsidence periods, 32-23 Ma and 5.3-2.6 Ma, are identified, which are related to the abrupt heat decay during margin breakup and the collision between the Philippine Sea plate and the Eurasian plate, respectively. The strongest crustal thinning in the Baiyun (sic) sag may trigger the syn-rift volcanism along the weak faulted belt around the sag. The Cenozoic tectonic evolution of the study area could be divided into five stages: rifting (similar to 50-40 Ma), rift-drift transition (similar to 40-32 Ma), early post-breakup (similar to 32-23 Ma), thermal subsidence (similar to 23-5.3 Ma) and neotectonic movement (similar to 5.3-0 Ma).

Formation and evolution of the modern warm current system in the East China Sea and the Yellow Sea since the last deglaciation

To reconstruct the formation and evolution process of the warm current system within the East China Sea (ECS) and the Yellow Sea (YS) since the last deglaciation, the paleoceangraphic records in core DGKS9603, core CSH1 and core YSDP102, which were retrieved from the mainstream of the Kuroshio Current (KC), the edge of the modern Tsushima Warm Current (TWC) and muddy region under cold waters accreted with the Yellow Sea Warm Current (YSWC) respectively, were synthetically analyzed. The results indicate that the formation and evolution of the modern warm current system in the ECS and the YS has been accompanied by the development of the KC and impulse rising of the sea level since the last deglaciation. The influence of the KC on the Okinawa Trough had enhanced since 16 cal kyr BP, and synchronously the modern TWC began to develop with the rising of sea level and finally formed at about 8.5 cal kyr BP. The KC had experienced two weakening process during the Heinrich event 1 and the Younger Drays event from 16 to 8.5 cal kyr BP. The period of 7-6 cal kyr BP was the strongest stage of the KC and the TWC since the last deglaciation. The YSWC has appeared at about 6.4 cal kyr BP. Thus, the warm current system of the ECS and the YS has ultimately formed. The weakness of the KC, indicated by the occurrence of Pulleniatina minimum event (PME) during the period from 5.3 to 2.8 cal kyr BP, caused the main stream of the TWC to shift eastward to the Pacific Ocean around about 3 cal kyr BP. The process resulted in the intruding of continent shelf cold water mass with rich nutrients. Synchronously, the strength of the YSWC was relatively weak and the related cold water body was active at the early-mid stage of its appearance against the PME background, which resulted in the quick formation of muddy deposit system in the southeastern YS. The strength of the warm current system in the ECS and the YS has enhanced evidently, and approached to the modern condition gradually since 3 cal kyr BP.

Mesozoic-Cenozoic tectonic evolution of the Zhuanghai area, Bohai-Bay Basin, east China: the application of balanced cross-sections

The technique of balancing cross-sections, an important method for studying the tectonic history of sedimentary basins, has many applications. It enables one to compile charts for petroleum exploration and development, and growth sections of ancient structures can be restored so that the structural growth history can be studied. In order to study tectonic evolution in the Zhuanghai area of the Bohai-Bay basin, we selected two seismic profiles and compiled two structural growth sections. Based on the two balanced cross-sections, the evolution can be divided into four phases: the Triassic-Middle Jurassic phase, Late Jurassic - Cretaceous phase, Palaeogene extension phase, and Late Palaeogene-to-present phase. The whole area was uplifted during the Triassic-Middle Jurassic phase because of intense extrusion stress related to the Indo-China movement. During the Late Jurassic and Early Cretaceous, intense extension occurred in east China, and the whole area rifted, leading to the deposition of a thick sedimentary sequence. In the Late Cretaceous, the area suffered uplift and compression associated with the sinistral strike slip of the Tanlu fault. In the Palaeogene, a rifting basin developed in the area. Finally, it became stable and was placed in its present position by dextral strike-slip motion. In addition, some problems associated with compiling balanced cross-sections are discussed.

Evolution and variability of the East Asian summer monsoon during the Pliocene: Evidence from clay mineral records of the South China Sea

The Late Pliocene is thought to be characterized by the simultaneous intensification of both the East Asian winter monsoon (EAWM) and East Asian summer monsoon (EASM). However, the evolution of the EASM during the Pliocene remains still controversial and only little is known about the dynamics of the EASM during the Pliocene on orbital time scales. Here we use clay mineral assemblages in sediments from Ocean Drilling Program (ODP) Site 1143 in the southern South China Sea (SCS) to obtain proxy records of past changes in the EASM climate during the Pliocene. Provenance analysis suggests that illite, chlorite and kaolinite originated mainly from the Mekong River drainage area. Smectite was derived mainly from the Indonesian islands. The kaolinite/illite ratio and the chemical index of alteration (CIA) of siliciclastic sediments allowed us to reconstruct the history of chemical weathering and physical erosion of the Mekong River drainage area and thus, the evolution of,the EASM during the Pliocene. Our clay minerals proxy data suggests a stronger EASM during the Early Pliocene than during the Late Pliocene. We propose that the long-term evolution of the EASM has been driven by global cooling rather than the uplift of the Tibetan Plateau. Spectral analysis of kaolinite/ illite ratio displays a set of strong periodicities at 100 ka, 30 ka, 28 ka, 25 ka, and 22 ka. with no clear obliquityrelated signal. Our study suggests that the Pliocene EASM intensity on orbital time scales is not only controlled by the Northern Hemisphere summer insolation, but also strongly influenced by equatorial Pacific ENSO-like ocean atmosphere dynamics. (C) 2010 Elsevier B.V. All rights reserved.

Balanced cross section for restoration of tectonic evolution in the southwest Okinawa Trough

On the basis of the multi-channel seismic data and the other data, using 2DMove software, the tectonic evolution in three seismic profiles was restored since Pliocene. The tectonic restoration results show that: (1) the initial active center lay in the west slope and then was transferred to east and south via trough center during the evolution process; (2) several main normal faults controlled the evolution of the southern Okinawa Trough; (3) since Late Pliocene, the southern Okinawa Trough has experienced two spreading stages. The early is depression in Early-Middle Pleistocene and the late is back-are spreading in Late Pleistocene and Holocene, which is in primary oceanic crust spreading stage.

Observation of the seasonal evolution of the Yellow Sea Cold Water Mass in 1996-1998

We use the hydrographic data obtained during the joint survey of the Yellow Sea by the First Institute of Oceanography, China and the Korea Ocean Research and Development Institute, Korea, to quantify the spatial structures and temporal evolution of the southern Yellow Sea Cold Water Mass (YSCWM). It is indicated that the southern YSCWM is a water mass that develops in summer and decays in fall. In winter, due to the intrusion of the Yellow Sea Warm Current (YSWC), the central area (approximately between 34 degrees N and 35 degrees N, 122 degrees E and 124 degrees E) of the Yellow Sea is mainly occupied by relatively high temperature water (T > 10 degrees C). By contrast, from early summer to fall, under the seasonal thermocline, the central area of Yellow Sea is occupied by cold water (T < 10 degrees C). In summer, the southern YSCWM has two cold cores. One is formed locally southeast of Shandong Peninsula, and the other one has a tongue-like feature occupying the area approximately between 34 degrees N and 37 degrees N, 123 degrees E and 126 degrees E. The bottom layer temperature anomalies from February to July in the cold tongue region, along with the trajectories of the bottom floaters, suggest that the cold water mass in the northeast region has a displacement from the north to the central area of the Yellow Sea during the summer. (c) 2007 Elsevier Ltd. All rights reserved.

Evolution of freshwater plumes and salinity fronts in the northern Bay of Bengal

[1] The evolution of freshwater plumes and the associated salinity fronts in the northern Bay of Bengal ( henceforth the bay) is studied using rotated empirical orthogonal function (REOF) analysis and extended associate pattern analysis (EAPA). The results show that sea surface salinity distribution is featured by eastern-bay and western-bay plumes in the northern bay during different seasons. The western-bay plume begins in early July, peaks in late August, and then turns into a bay-shaped plume with the two plumes in either side of the bay, which peaks in late October. The southward extension of the western-bay plume can be explained by the southwestward geostrophic flow associated with the cyclonic gyre in the northern bay, which counters the northeastward Ekman drift driven by wind stress. The offshore expansion of the western-bay plume is induced by the offshore Ekman drift which also produces a salinity front near the east coast of India. The bay-shaped plume appears when the cyclonic gyre shifts westward and a weak anticyclonic gyre occupies the northeastern bay. As the season advances, the western part of the bay-shaped plume decays while the eastern part persists until the following June, which is believed to be associated with the anticyclonic gyre in the northern bay. The evolution of the plumes except the eastern part of the bay-shaped plume in fall can be partly explained by the seasonal variation of mass transport associated with the Sverdrup balance. The fact that the western-bay (eastern-bay) plume appears when surface freshwater flux in the northeastern bay increases ( decreases) dramatically suggests that the plumes are not produced directly by surface freshwater flux. River discharge seems to be the freshwater source for the plumes and has little to do with the evolution of the plumes.

Landscapes of kingship in early medieval Ireland, AD 400–1150

This thesis explores the evolution of kingship in early medieval Ireland (AD 400–1150) through a kingdom based and multi-scalar approach to royal landscapes. Through exploring the role of place and landscape in the construction of early medieval Irish kingship, this study will assess the relationship between the social, economic and ideological roles of the king in Irish society. Kingship in Ireland was vested in places, such that royal landscapes were the pre-eminent symbol of regality and authority. As such, an interdisciplinary study of kingship grounded in archaeological methodologies has a unique potential to contribute to our knowledge of the practice of kingship. Consequently, this research considers the material apparatus of different scales of kingships and explores the role of landscape in the construction of kingship and the evolution of kingdoms. It takes two major case studies; (i) Cashel, Munster and the Éoganachta federation; and (ii) the Uí Néill, Tara and the Síl nÁedo Sláine kingdom of Brega. Through interdisciplinary methodologies it charts the genesis and development of political federations, focusing specifically on the role that royal landscapes’ played in their evolution. Similarly, this thesis engages critically with the nature of assembly places and practices in Ireland, and focuses specifically on issues pertaining to the nature of assembly and the archaeological manifestation of such practices. It includes a list of 115 landscapes identified as assembly places, and through the analysis of this material, this thesis examines the ways in which different types of royal sites articulated together to create royal landscapes implicated in the exercise of kingship, and the construction and maintenance of authority. Moreover, through the analysis of assembly places within the context of the development of kingdoms, and structures of jurisdiction and administration, it also investigates the evolution of supra-regional scales of identity and community associated with the emergence of major political federations in early medieval Ireland.

The ecology of the Irish stoat

The Irish stoat, Mustela erminea hibernica (Thomas and Barrett-Hamilton), has been regarded as an intermediate between the British stoat and the weasel. In this study Irish stoats, mainly from road casualties, were collected and studied. A small number were also live-trapped and radio-tracked. Thus information was gathered on the stoat’s ecology, in particular its form (size and coat colours), reproduction, food habits, parasites, habitat utilisation mortality and predation. The Irish stoats studied were clearly not intermediate in size between British stoats and weasels. They showed considerable size overlap with British stoats, and marked size variation within Ireland. It is argued that size of stoats is determined by food supply early in life. The ventral coat pattern of Irish stoats is apparently unique in the Palaearctic, being similar to that of some stoats found on the west coast of North America. It is argued that this is an example of parallel evolution resulting from adaptation to similar climatic conditions. The stoats were reproductively active in spring and summer. Food consisted mainly of rabbits, but rats, birds, shrews mice and voles were also consumed. Mites were the most numerous ectoparasites, followed by lice, ticks and fleas. Damage by the parasitic nematode Skrjabingylus nasicola was found more frequently in female stoat skulls. Stoats were frequently found in a variety of habitats, both open and wooded. Some of the radio-tracked stoats climbed trees. Dens used were often rat holes. Only one home range, that of a breeding female, was considered to have been accurately measured. It was 22 ha. in size. Mortality is known to have been caused by road accidents and domestic carnivores. It is argued that predation by raptorial birds is important to stoat populations. Results of this study are compared with information available from elsewhere.

Newly resolved relationships in an early land plant lineage: Bryophyta class Sphagnopsida (peat mosses).

UNLABELLED: PREMISE OF THE STUDY: The Sphagnopsida, an early-diverging lineage of mosses (phylum Bryophyta), are morphologically and ecologically unique and have profound impacts on global climate. The Sphagnopsida are currently classified in two genera, Sphagnum (peat mosses) with some 350-500 species and Ambuchanania with one species. An analysis of phylogenetic relationships among species and genera in the Sphagnopsida were conducted to resolve major lineages and relationships among species within the Sphagnopsida. • METHODS: Phylogenetic analyses of nucleotide sequences from the nuclear, plastid, and mitochondrial genomes (11 704 nucleotides total) were conducted and analyzed using maximum likelihood and Bayesian inference employing seven different substitution models of varying complexity. • KEY RESULTS: Phylogenetic analyses resolved three lineages within the Sphagnopsida: (1) Sphagnum sericeum, (2) S. inretortum plus Ambuchanania leucobryoides, and (3) all remaining species of Sphagnum. Sister group relationships among these three clades could not be resolved, but the phylogenetic results indicate that the highly divergent morphology of A. leucobryoides is derived within the Sphagnopsida rather than plesiomorphic. A new classification is proposed for class Sphagnopsida, with one order (Sphagnales), three families, and four genera. • CONCLUSIONS: The Sphagnopsida are an old lineage within the phylum Bryophyta, but the extant species of Sphagnum represent a relatively recent radiation. It is likely that additional species critical to understanding the evolution of peat mosses await discovery, especially in the southern hemisphere.

Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing.

We used ultra-deep sequencing to obtain tens of thousands of HIV-1 sequences from regions targeted by CD8+ T lymphocytes from longitudinal samples from three acutely infected subjects, and modeled viral evolution during the critical first weeks of infection. Previous studies suggested that a single virus established productive infection, but these conclusions were tempered because of limited sampling; now, we have greatly increased our confidence in this observation through modeling the observed earliest sample diversity based on vastly more extensive sampling. Conventional sequencing of HIV-1 from acute/early infection has shown different patterns of escape at different epitopes; we investigated the earliest escapes in exquisite detail. Over 3-6 weeks, ultradeep sequencing revealed that the virus explored an extraordinary array of potential escape routes in the process of evading the earliest CD8 T-lymphocyte responses--using 454 sequencing, we identified over 50 variant forms of each targeted epitope during early immune escape, while only 2-7 variants were detected in the same samples via conventional sequencing. In contrast to the diversity seen within epitopes, non-epitope regions, including the Envelope V3 region, which was sequenced as a control in each subject, displayed very low levels of variation. In early infection, in the regions sequenced, the consensus forms did not have a fitness advantage large enough to trigger reversion to consensus amino acids in the absence of immune pressure. In one subject, a genetic bottleneck was observed, with extensive diversity at the second time point narrowing to two dominant escape forms by the third time point, all within two months of infection. Traces of immune escape were observed in the earliest samples, suggesting that immune pressure is present and effective earlier than previously reported; quantifying the loss rate of the founder virus suggests a direct role for CD8 T-lymphocyte responses in viral containment after peak viremia. Dramatic shifts in the frequencies of epitope variants during the first weeks of infection revealed a complex interplay between viral fitness and immune escape.

The Evolution of the Russian Romance Through the Nineteenth and Twentieth centuries

This performance dissertation traced the evolution of the Russian romance from 1800 to the present. The Russian romance is a relatively unknown and greatly neglected genre of classical art songs. It is commonly believed that the Russian romance began with Dargomizhsky and Glinka proceeding directly to Tchaikovsky and Rachmaninoff. Forgotten are the composers before Dargornizhsky and Glinka, the bridge composers, and the post-Tchaikovsky and post-Rachmaninoff composers. This may be, in part, because of the difficulties in obtaining Russian vocal scores. While most of the musical world is acquainted with the magnificent Russian instrumental music, the "true soul" of the Russian people lies in its romances. I presented examples of the two different schools of composition, reflecting their philosophical differences in thinking that came about in the 1860s: (1) Russian National school, (2) Western European school. Each school's influence on generations of Russian composers and their pupils have been represented in the recital programs. Also represented was the effect of the October Revolution on music and the voice of the Russian people, Anna Akhmatova. The amount of music that could be included in this dissertation greatly exceeds the amount of available performance time and represents a selected portion of the repertoire. The first recital included repertoire from the beginning of the romance in the early nineteenth century to the beginning of the twentieth century and the second recital focused on the music of the twentieth century, pre and post, the October Revolution. Finally, given the status of Anna Akhmatova and her contributions, the third recital was devoted entirely to her poetry. The "Russian soul" is one of deep, heartfelt emotions and sorrow. Happiness and joy are also present, but always with a touch of melancholy. The audience did not simply go through a musical journey, but took a journey through the "Russian soul". With the strong response of the audience to these recitals, my belief that this repertoire deserves a prominent place in recital programming was confirmed.

The evolution of airplanes

The prevailing view is that we cannot witness biological evolution because it occurred on a time scale immensely greater than our lifetime. Here, we show that we can witness evolution in our lifetime by watching the evolution of the flying human-and-machine species: the airplane. We document this evolution, and we also predict it based on a physics principle: the constructal law. We show that the airplanes must obey theoretical allometric rules that unite them with the birds and other animals. For example, the larger airplanes are faster, more efficient as vehicles, and have greater range. The engine mass is proportional to the body size: this scaling is analogous to animal design, where the mass of the motive organs (muscle, heart, lung) is proportional to the body size. Large or small, airplanes exhibit a proportionality between wing span and fuselage length, and between fuel load and body size. The animal-design counterparts of these features are evident. The view that emerges is that the evolution phenomenon is broader than biological evolution. The evolution of technology, river basins, and animal design is one phenomenon, and it belongs in physics. © 2014 AIP Publishing LLC.