A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae

Background: The Galliformes is a well-known and widely distributed Order in Aves. The phylogenetic relationships of galliform birds, especially the turkeys, grouse, chickens, quails, and pheasants, have been studied intensively, likely because of their close association with humans. Despite extensive studies, convergent morphological evolution and rapid radiation have resulted in conflicting hypotheses of phylogenetic relationships. Many internal nodes have remained ambiguous. Results: We analyzed the complete mitochondrial (mt) genomes from 34 galliform species, including 14 new mt genomes and 20 published mt genomes, and obtained a single, robust tree. Most of the internal branches were relatively short and the terminal branches long suggesting an ancient, rapid radiation. The Megapodiidae formed the sister group to all other galliforms, followed in sequence by the Cracidae, Odontophoridae and Numididae. The remaining clade included the Phasianidae, Tetraonidae and Meleagrididae. The genus Arborophila was the sister group of the remaining taxa followed by Polyplectron. This was followed by two major clades: ((((Gallus, Bambusicola) Francolinus) (Coturnix, Alectoris)) Pavo) and (((((((Chrysolophus, Phasianus) Lophura) Syrmaticus) Perdix) Pucrasia) (Meleagris, Bonasa)) ((Lophophorus, Tetraophasis) Tragopan))). Conclusions: The traditional hypothesis of monophyletic lineages of pheasants, partridges, peafowls and tragopans was not supported in this study. Mitogenomic analyses recovered robust phylogenetic relationships and suggested that the Galliformes formed a model group for the study of morphological and behavioral evolution.

Reconstructing the evolutionary history of China: A caveat about inferences drawn from ancient DNA

The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modem data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (similar to 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modem populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.

High rate of chimeric gene origination by retroposition in plant genomes

Retroposition is widely found to play essential roles in origination of new mammalian and other animal genes. However, the scarcity of retrogenes in plants has led to the assumption that plant genomes rarely evolve new gene duplicates by retroposition, de

Anti-HIV-1 activities of extracts from the medicinal plant Rhus chinensis

Rhus chinensis, a species used in folk medicine by Chinese native people, the anti-HIV-1 activities of the petroleum ether, ethyl acetate, butanol and aqueous extract of Rhus chinensis, named as RC-1, RC-2, RC-3 and RC-4, respectively, was evaluated. The

Anti-HIV-1 activities of compounds isolated from the medicinal plant Rhus chinensis

Aim of the study: Previously, we reported that the petroleum ether fraction, RC-1, and EtOAc fraction, RC-2, of the medicinal plant Rhus chinensis showed potent anti-HIV-1 activities. To address anti-HIV-1 constituents of RC-1 and RC-2, 17 compounds were

Seasonal variations in the activity budget of Nomascus concolor jingdongensis at Mt. Wuliang, Central Yunnan, China: Effects of diet and temperature

We studied seasonal variation in the activity budget of a habituated group of Nomascus concolor jingdongensis at Mt. Wuliang, Central Yunnan, China from March 2005 to April 2006 via scan sampling at 5-min intervals. The study site is near the northern extreme of the distribution of hylobatids, at high altitude with extreme seasonality of temperature and rainfall. During the day, feeding manifested a bimodal pattern of high activity levels in mid-morning and mid-afternoon, whereas resting reached a peak at midday, with proportionally less time used for traveling. Annually, the group spent an average of 40.0% of the time resting, 35.1% feeding, 19.9% traveling, 2.6% singing, 1.2% playing, and 1.3% in other activities. The proportion of time allocated to activities showed significant monthly variations and was influenced by the diet and temperature. Gibbons increased traveling and playing time and decreased feeding time when they ate more fruit, and they decreased traveling, singing, and playing time and increased feeding time when they ate more leaves. Moreover, when the temperature was low, the gibbons decreased time traveling and increased time resting. In summary, black-crested gibbons employed high-effort activities when they ate more fruit and energy-conservation patterns when they ate more leaves and in low temperature. Behavioral data from the site are particularly useful in understanding gibbon behavioral adaptations to different sets of ecological conditions.

Interactions between a cyanobacterial bloom (Microcystis) and the submerged aquatic plant Ceratophyllum oryzetorum Kom.

In aquatic ecosystems, macrophytes and phytoplankton are main primary producers, in which macrophyte plays an important role in maintaining clear water state, while phytoplankton often dominates in turbid waterbodies. In the present study, the growth and photosynthetic activity of the submerged aquatic plant Ceratophyllum oryzetorum Kom. in different cell densities of cyanobacterial bloom are studied. The results show that the plant length and fresh mass of C. oryzetorum are promoted by low cyanobacterial cell densities. Medium and high cyanobacterial cell densities, on the contrary, act as inhibitory. Furthermore, the photosynthetic activity of C. oryzetorum is strongly inhibited by high cyanobacterial cell densities. To a certain extent, the growth of cyanobacteria is inhibited by C. oryzetorum, but no significant effect is found in this study.

In situ study on effect of food competition on diet shifts and growth of silver and bighead carps in large biomanipulation fish pens in Meiliang Bay, Lake Taihu

Silver and bighead carps were cultured in large fish pens to reduce the risks of cyanobacterial bloom outbreaks in Meiliang Bay, Lake Tauhu in 2004 and 2005. Diet compositions and growth rates of the carps were studied from April to November each year. Both carp species fed mainly on zooplankton (> 50% in diet) in 2004 when competition was low, but selected more phytoplankton in 2005 when competition was high. Silver carp had a broader diet breadth than did bighead carp. Higher densities and fewer food resources increased diet breadths but decreased the diet overlap in both types of carps. It can be predicted that silver and bighead carps would be released from diet competition and shift to feed mainly on zooplankton at low densities, decreasing the efficiency of controlling cyanobacterial blooms. Conclusively, when silver and bighead carps are used to control cyanobacterial blooms, a sufficiently high stocking density is very important for a successful practice.

Seasonal variations of estrogenic compounds and their estrogenicities in influent and effluent from a municipal sewage treatment plant in China

The seasonal variations of estrogenic compounds and the estrogenicities of influent and effluent were investigated by OF chemical analysis and in vitro assay in a municipal sewage treatment plant in Wuhan (China). The levels of eight estrogenic compounds, including 17 beta-estradiol (E-2) estrone (E-1), estriol (E-3) diethylstilbestrol (DES), 17 alpha-ethinylestradiol, nonylphenol (NP), 4-tert-octylphenol (OP), and bisphenol A (BPA), were measured by gas chromatography-mass spectrometry. Total estrogenic activity of sewage was quantitatively assessed using primary cultured hepatocytes of male Megalobrama amblycephala Yih using vitellogenin as a biomarker. The E-2 equivalents (EEQs) obtained from the chemical analysis were consistent with those measured by bioassay. The natural (E-1, E-2, and E-3) and synthetic (DES) estrogens, as well as NP, were the main contributors of the total EEQs of influent and effluent in the present study. The levels of natural estrogens E-1 and E-3 in the influent and effluent were higher in winter than in summer, whereas the situation for NP and OP was the reverse. The levels of E-2, DES, and BPA varied little among different seasons. 17 alpha-Ethinylestradiol was not detected in the influent and effluent. The estrogenicities of the influent and of the primary and secondary effluents were all higher in summer than in winter. Estrogenic activities in winter mainly originated from natural (E-1, E-2, and E-3) and synthetic (DES) estrogens, whereas the increase of EEQs in summer was contributed by NP The results from chemical analysis and bioassay demonstrate that estrogenic compounds cannot be entirely removed by the existing sewage treatment process, which should be further improved to protect aquatic ecosystems and human health.

Diet overlap between the endemic fish Anablariflus grahami(Cyprinidae) and the exotic noodlefish Neosalanx taihuensis (Salangidae) in lake Fuxian, China

We studied diet composition and overlap of the exotic noodlefish (Neosalanx taihuensis) and the endemic fish Anaborilius grahami in a deep, oligotrophic lake in the Yunnan Plateau. A. grahami dominated the fish community in Lake Fuxian before the invasion of N. taihuensis in 1982, but it is now in the process of extinction, corresponding with an explosive increase in N. taihuensis population. Schoener's index (alpha=0.773) indicate that N. taihuensis and A. grahami have significant diet overlap, with both fish feeding mainly on zooplankton. An increased proportion of littoral prey, such as Procladius spp., Coleoptera, and epiphytes, in the diet of A. grahami indicated that this endemic fish shifted its main habitat from the off-shore zone in the late 1980s to the littoral zone at the present. A difference in reproduction between the two fishes, along with the overfishing, may have exacerbated the occupation of A. grahami's pelagic niche by N. taihuensis. The endemic species has shown large competitive disadvantage for food and space in the presence of N. taihuensis.

An enzyme-linked immunosorbent assay for rare minnow (Gobiocypris rarus) vitellogenin and comparison of vitellogenin responses in rare minnow and zebrafish (Danio rerio)

A competitive enzyme-linked immunosorbent assay (ELISA) was developed to determine vitellogenin (Vtg) in rare minnow (Gobiocypris rarus) based on the separation and purification of rare minnow Vtg (r-Vtg) as well as the production of polyclonal antibody against r-Vtg in rabbits. Three different ELISAs for measuring r-Vtg were then compared: (1) indirect ELISA with the antibody against carp (Cyprinus carpio) Vtg (c-Vtg) (IC-ELISA); (2) competitive ELISA with the antibody against c-Vtg, and using r-Vtg for coating the plates and preparing standard curve (CC-ELISA); (3) competitive ELISA with the antibody against r-Vtg, and using r-Vtg for coating the plates and preparing standard curve (CR-ELISA). The result showed that the homologous CR-ELISA was the most sensitive among the three assays for quantifying r-Vtg. The sensitivities to 17 alpha-ethinylestradiol (EE2) Of rare minnow and zebrafish (Danio rerio) were compared upon the establishment of homologous competitive ELISA. The lowest observed effect concentrations (LOECs) to induce Vtg were found to be 0.8 ng EE2 l(-1) for rare minnow and 4 ng EE2 l(-1) for zebrafish respectively. Afterwards, CR-ELISA was applied to measure Vtg concentration in whole body homogenate (WBH) of juvenile rare minnow fed by three diets (tubifex from wastewater treatment plant, Artemia nauplii and commercial pellet food), and the agreements between bioassay and GC-MS analysis demonstrated that rare minnow was a sensitive fish model for assessing estrogenic effects of endocrine disrupting compounds in aquatic environment. (c) 2006 Elsevier B.V. All rights reserved.

Effect of plant architecture on the structure of epiphytic macro invertebrate communities in a Chinese lake

We examined the effect of different plant architecture types on epiphytic macroinvertebrates of a shallow macrophyte-dominated lake in China. Macroinvertebrates were sampled from four dominant submersed macrophytes in the lake - two dissected plants (Myriophyllum spicatum L. and Ceratophyllum demersum L.) and two undissected plants (Potamogeton maackianus A. Benn. and Vallisneria spiralis L.). Macro invertebrate richness showed significant differences among four submersed macrophyte habitats, and higher density per g of dry plant were associated with dissected plants than undissected plants. The average abundance in dissected plants was as three-six times as in undissected plants. The biodiversity of epiphytic macroinvertebrates was higher in dissected plants than undissected plants. Our results suggest that dissected plants provide different habitat for macroinvertebrates than dissected plant, and this concurs with the hypothesis that the former could support more epiphytic macroinvertebrates than the latter.

Species richness in a riparian plant community along the banks of the Xiangxi River, the Three Gorges region

The distribution of vascular plant species richness along an altitudinal gradient and their relationships with environmental variables, including slope, aspect, bank (flooding) height, and river width of the Xiangxi River, Hubei Province, were examined. Total vascular plant species richness changed with elevation: it increased at lower elevations, reached a maximum in the midreaches and decreased thereafter. In particular, tree and herbaceous species richness were related to altitude. Correlation analysis (Kendall's tau) between species richness and environmental variables indicated that the change in species richness in the riparian zone was determined by riparian environmental factors and characteristics of regional vegetation distribution along the altitudinal gradient. The low species richness at lower elevations resulted from seasonal flooding and human activities - agriculture and fuel collection - and the higher. Species richness ill (he midreaches reflected transitional zones ill natural vegetation types that had had little disturbance. These results oil species distribution in the riparian community could he utilized as a reference for restoration efforts to improve water quality of the emerging reservoir resulting from the Three Gorges Hydroelectric Dam project.

Biomarker responses and reproductive toxicity of the effluent from a Chinese large sewage treatment plant in Japanese medaka (Oryzias latipes)

The present study was conducted to assess the potential toxicity of the effluent from a large sewage treatment plant (GBD-STP) in Beijing. Japanese medakas (Oryzias latipes) at reproduction active period were exposed to a serial of graded concentrations of the effluent or 100 ng l(-1) of 17-alpha-ethinylestradiol (EE2, positive control). Growth, gonadosomatic index (GSI), hepatosomatic index (HSI), reproductive success, induction potency of vitellogenin (VTG) in male fish and that of 7-ethoxyresorufin-o-deethylase activity (EROD) in male fish liver were used as test endpoints. The growth suppression of fish was observed in a dose-dependent manner, resulting in significant differences in both body length and body weight of medaka above 5% effluent. This effluent can inhibit the growth of gonad of medakas and are more sensitive to male than to female. At exposure concentration of 40% and higher, there was an unexpected decrease of HSI values, which may be resulted from sub-lethal toxicity of effluent to fish liver. VTG of plasma in males were induced in all exposure concentration levels, but not in a dose-dependent manner. The concentration of 5% effluent would be the lowest observed adverse effect level (LOAEL) affecting reproductive success when examining fertile individuals, fecundity and fertilization rate. The overt CYP1A response and higher reproductive toxicity may be indicative of low process efficiency of this STP. (c) 2004 Elsevier Ltd. All rights reserved.