The complete mitochondrial genomes of two common shrimps (Litopenaeus vannamei and Fenneropenaeus chinensis) and their phylogenomic considerations

Complete mitochondrial genomes have proven extremely valuable in helping to understand the evolutionary relationships among metazoans. However, uneven taxon sampling may lead to unclear or even erroneous phylogenetic topologies. The decapod crustaceans are relatively well-sampled, but sampling is still uneven within this group. We have sequenced the mitochondrial genomes of two shrimps Litopenaeus vannamei and Fenneropenaeus chinensis. As seen in other metazoans, the genomes contain a standard set of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and an AT-rich non-coding region. The gene arrangements are consistent with the pancrustacean ground pattern. Both the pattern of gene rearrangements and phylogenomic analyses using concatenated nucleic acid and amino acid sequences of the 13 mitochondrial protein-coding genes strengthened the support that Caridea and Palinura are primitive members of Pleocyemata. These sequences, in combination with two previously published penaeid mitochondrial genomes, suggest that genera within the family Penaeidae have the following relationship: (((Penaeits + Fenneropenaett.) + Litopeiiaelts) + Marsupenaeus). The analyses of nucleic acid and amino acid sequences of the mitochondrial genomes also strongly support the monophyly of Penaeidae, Brachyura and Pleocyemata. In addition, the analyses of the average Ka/Ks in the 13 mitochondrial protein-coding genes of penaeid shrimps indicated a strong purifying selection within this group.

EAWM-related air-sea-land interaction and the Asian summer monsoon circulation

Based on the data analysis, this study further explores the characteristics of East Asian winter monsoon (hereafter, EAWM, for brevity) as well as the related air-sea-land system, and illustrates how and to what degree anomalous signals of the subsequent Asian summer monsoon are rooted in the preceding EAWM activity. We identified an important air-sea coupled mode, i.e., the EAWM mode illustrated in Section 3. In cold seasons, strong EAWM-related air-sea two-way interaction is responsible for the development and persistence of the SSTA pattern of EAWM mode. As a consequence, the key regions, i.e., the western Pacific and South China Sea (hereafter, SCS, for brevity), are dominated by such an SSTA pattern from the winter to the following summer. In the strong EAWM years, the deficient snow cover dominates eastern Tibetan Plateau in winter, and in spring, this anomaly pattern is further strengthened and extended to the northwestern side of Tibetan Plateau. Thus, the combined effect of strong EAWM-related SSTA and Tibetan snow cover constitutes an important factor in modulating the Asian monsoon circulation. The active role of the EAWM activity as well as the related air-sea-land interaction would, in the subsequent seasons, lead to: 1) the enhancement of SCS monsoon and related stronger rainfall; 2) the northward displacement of subtropical high during Meiyu period and the related deficient rainfall over Meiyu rainband; 3) above-normal precipitation over the regions from northern Japan to northeastern China in summer; 4) more rainfall over the Arabian Sea and Northeast India, while less rainfall over southwest India and the Bay of Bengal. The strong EAWM-related air-sea interaction shows, to some degree, precursory signals to the following Asian summer monsoon. However, the mechanism for the variability of Indian summer monsoon subsequent to the strong EAWM years remains uncertain.

Analysis on suspended sediment deposition rate for muddy coast of reclaimed land

A new expression for calculating suspended fine-sediment deposition rate is developed based on theoretic analysis and experiments. The resulting equation is applied to simulation of fine sediment deposition in the reclaimed land in the Hangzhou Bay, China. The hydrodynamic environment in this area is solved by use of a long wave model, which gives the 2D-velocity field and considers bathymetric changes due to fine sediment deposition. The expression is proved convenient to use in engineering practice, and the predicted deposition rate agrees with the annual data available from field measurements from the first year to the third year after the construction of the long groin as a reclaiming method.

Classification of common oysters from North China

Oysters are commonly found on rocky shores along China's northern coast, although there is considerable confusion as to what species they are. To determine the taxonomic status of these oysters, we collected specimens from nine locations north of the Yangtze River and conducted genetic identification using DNA sequences. Fragments from three genes, mitochondrial 165 rRNA, mitochondria! cytochrome oxidase I (COI), and nuclear 285 rRNA, were sequenced in six oysters from each of the nine sites. Phylogenetic analysis of all three gene fragments clearly demonstrated that the small oysters commonly found on intertidal rocks in north China are Crassostrea gigas (Thunberg, 1793), not C. plicatula (the zhe oyster) as widely assumed. Their small size and irregular shell characteristics are reflections of the stressful intertidal environment they live in and not reliable characters for classification. Our study confirms that the oysters from Weifang, referred to as Jinjiang oysters or C. rivularis (Gould, 1861), are C. ariakensis (Wakiya, 1929). We found no evidence for the existence of C. talienwhanensis (Crosse, 1862) and other Crassostrea species in north China. Our study highlights the need for reclassifying oysters of China with molecular data.

Dissection of rye B chromosomes, and nondisjunction properties of the dissected segments in a common wheat background

The rye B chromosome is a supernumerary chromosome that increases in number in its host by directed postmeiotic drive. Two types of rye B chromosomes that had been introduced into common wheat were dissected into separate segments by the gametocidal system to produce a number of rearranged B chromosomes, such as telosomes, terminal deletions and translocations with wheat chromosomes. A total of 13 dissected B chromosomes were isolated in common wheat, and were investigated for their nondisjunction. properties. Rearranged B chromosomes, separated from their B-specific repetitive sequences on the distal part of the long arm, did not undergo nondisjunction, and neither did a translocated wheat chromosome carrying a long-arm distal segment containing the B-specific repetitive sequences. However, such rearranged B chromosomes, missing their B-specific sequences could undergo nondisjunction when they coexisted with the standard B chromosome or a wheat chromosome carrying the B-specific sequences. Deficiencies of the short arm did not completely abolish the nondisjunction properties of the B chromosome, but did reduce the frequency of nondisjunction. These results confirmed previous suggestions that the directed nondisjunction of the rye B chromosome is controlled by two elements, pericentromeric sticking sites and a trans-acting element carried at the distal region of the long arm of the B chromosome. Additionally, it is now shown that the distal region of the long arm of the B chromosome which provides this function is that which carries the B-specific repetitive sequences.

The effect of land management on plant community composition, species diversity, and productivity of alpine Kobersia steppe meadow

Grassland degradation is widespread and severe on the Tibet Plateau. To explore management approaches for sustainable development of degraded and restored ecosystems, we studied the effect of land degradation on species composition, species diversity, and vegetation productivity, and examined the relative influence of various rehabilitation practices (two seeding treatments and a non-seeded natural recovery treatment) on community structure and vegetation productivity in early secondary succession. The results showed: (1) All sedge and grass species of the natural steppe meadow had disappeared from the severely degraded land. The above-ground and root biomass of severely degraded land were only 38 and 14.7%, respectively, of those of the control. So, the original ecosystem has been dramatically altered by land degradation on alpine steppe meadow. (2) Seeding measures may promote above-ground biomass, particularly grass biomass, and ground cover. Except for the grasses seeded, however, other grass and sedge species did not occur after seeding treatments in the sixth year of seeding. Establishment of grasses during natural recovery treatment progressed slowly compared with during seeding treatments. Many annual forbs invaded and established during the 6 years of natural recovery. In addition, there was greater diversity after natural recovery treatment than after seeding treatments. (3) The above-ground biomass after seeding treatment and natural recovery treatment were 114 and 55%, respectively, of that of the control. No significant differences in root biomass occurred among the natural recovery and seeded treatments. Root biomass after rehabilitation treatment was 23-31% that of the control.

The effect of land management on carbon and nitrogen status in plants and soils of alpine meadows on the Tibetan plateau

Large-scale grassland rehabilitation has been carried out on the severely degraded lands of the Tibetan plateau. The grasslands created provide a useful model for evaluating the recovery of ecosystem properties. The purposes of this research were: (1) to examine the relative influence of various rehabilitation practices on carbon and nitrogen in plants and soils in early secondary succession; and (2) to evaluate the degree to which severely degraded grassland altered plant and soil properties relative to the non-disturbed native community. The results showed: (1) The aboveground tissue C and N content in the control were 105-97 g m(-2) and 3.356gm(-2), respectively. The aboveground tissue C content in the mixed seed treatment, the single seed treatment, the natural recovery treatment and the severely degraded treatment was 137 per cent, 98 per cent, 49 per cent and 38 per cent, respectively, of that in the control. The corresponding aboveground tissue N content was 109 per cent, 84 per cent, 60 per cent and 47 per cent, respectively, of that in the control. (2) Root C and N content in 0-20 cm depths of the control had an 2 2 average 1606 gm(-2) and 30-36 gm(-2) respectively. Root C and N content in the rehabilitation treatments were in the range of 26-36 per cent and 35-53 per cent, while those in the severely degraded treatment were only 17 per cent and 26 per cent of that in the control. (3) In the control the average soil C and N content at 0-20 cm was 11307 gm(-2) and 846 gm(-2), respectively. Soil C content in the uppermost 20 cm in the seeded treatments, the natural recovery treatment and the severely degraded treatment was 67 per cent, 73 per cent and 57 per cent, respectively, while soil N content in the uppermost 20cm was 72 per cent, 82 per cent and 79 per cent, respectively, of that in the control. The severely degraded land was a major C source. Restoring the severely degraded lands to perennial vegetation was an alternative approach to sequestering C in former degraded systems. N was a limiting factor in seeding grassland. It is necessary for sustainable utilization of seeding grassland to supply extra N fertilizer to the soil or to add legume species into the seed mix. Copyright (c) 2005 John Wiley & Sons, Ltd.

Dynamic and complex microclimate responses to warming and grazing manipulations

Synthesis efforts that identify patterns of ecosystem response to a suite of warming manipulations can make important contributions to climate change science. However, cross-study comparisons are impeded by the paucity of detailed analyses of how passive warming and other manipulations affect microclimate. Here we document the independent and combined effects of a common passive warming manipulation, open-top chambers (OTCs), and a simulated widespread land use, clipping, on microclimate on the Tibetan Plateau. OTCs consistently elevated growing season averaged mean daily air temperature by 1.0-2.0 degrees C, maximum daily air temperature by 2.1-7.3 degrees C and the diurnal air temperature range by 1.9-6.5 degrees C, with mixed effects on minimum daily air temperature, and mean daily soil temperature and moisture. These OTC effects on microclimate differ from reported effects of a common active warming method, infrared heating, which has more consistent effects on soil than on air temperature. There were significant interannual and intragrowing season differences in OTC effects on microclimate. For example, while OTCs had mixed effects on growing season averaged soil temperatures, OTCs consistently elevated soil temperature by approximately 1.0 degrees C early in the growing season. Nonadditive interactions between OTCs and clipping were also present: OTCs in clipped plots generally elevated air and soil temperatures more than OTCs in nonclipped plots. Moreover, site factors dynamically interacted with microclimate and with the efficacy of the OTC manipulations.These findings highlight the need to understand differential microclimate effects between warming methods, within warming method across ecosystem sites, within warming method crossed with other treatments, and within sites over various timescales. Methods, sites and scales are potential explanatory variables and covariables in climate warming experiments. Consideration of this variability among and between experimental warming studies will lead to greater understanding and better prediction of ecosystem response to anthropogenic climate warming.