Jurassic radiation of large Branchiopoda (Arthropoda: Crustacea) using secondary structure-based phylogeny and relaxed molecular clocks

The phylogenetic relationships of large Branchiopoda have been one of the most controversial issues in the studies of Crustacea. This study attempts to tackle systematic problems concerning “conchostracan” and anostracan evolution, by analyzing ribosomal RNA sequences of both mitochondrial (12S) and nuclear genes (18S). Phylogenetic trees are reconstructed with these data from 27 genera belonging to 18 families, using maximum parsimony procedures, maximum likelihood, and Bayesian analysis coupled with Markov chain Monte Carlo (MCMC) techniques under mixed and doublet models. The results suggest that Diplostraca (Conchostraca+Cladocera) form a monophyletic group, with Spincaudata and Cladoceromorpha being sister groups and Laevicaudata a basal lineage of Diplostraca; Notostraca and Diplostraca together form the monophyletic Phyllopoda. Within Diplostraca, Conchostraca is paraphyletic in contrast to the traditional systematic classification. Relaxed molecular clock analysis, using multiple fossil calibration points, indicates that the conchostracan three genera—Imnadia, Caenestheriella， and Caenestheria, emerged during Jurassic; most anostracan groups, such as Polyartemiinae, Chirocephalinae, Branchinectidae, and Streptocephalidae, experienced an adaptive radiation during Jurassic, and probably related with the fragmentation of the Pangea supercontinent.     

Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae: Sinocyclocheilus)

The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentation with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Sinocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed mo-lecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletic of cave species and the most basal position of S. jii was corroborated. Relaxed diver-gence-time estimation suggested that Sinocyclocheilus originated at the late Miocene, about 11 million years ago (Ma), which is older than what have been assumed.     

Bayesian mixed models and divergence time estimation of Chinese cavefishes （Cyprinidae： Sinocyclocheilus）

The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentaUon with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Slnocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b （cyt b） and NADH dehydrogenase subunlt 4 （ND4） of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed molecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletlc of cave species and the most basal position of S. jii was corroborated. Relaxed divergence-time estimation suggested that Sinocyclocheilus originated at the late Miocene, about 11 million years ago （Ma）, which is older than what have been assumed.     

Revision of the genus Abrestheria (Crustacea: Conchostraca) from the Dabeigou Formation of northern Hebei, China

Re-examination of the type specimens of the conchostracan genus Abrestheria using a scanning electron microscope (SEM) has revealed details of carapace features of important taxonomic value, which have not been described hitherto. The new characteristics include: (1) small-sized reticulations on growth lines near the umbo; (2) serrated lower margins of growth lines; (3) punctae in the even lumina of reticulations; and (4) tubercles at the lower ends of the claviform radial lirae on the growth bands of the lower parts of the carapace. Consequently, the diagnosis of Abrestheria is revised, and a discussion is also made concerning relationships between Abrestheria and closely related genera, such as Eosestheriopsis, Eosestheria and Orthestheria, which have important biostratigraphic implications.     

Revision of the genus Abrestheria (Crustacea: Conchostraca) from the Dabeigou Formation of northern Hebei, China

Re-examination of the type specimens of the conchostracan genus Abrestheria using a scanning electron microscope (SEM) has revealed details of carapace features of important taxonomic value, which have not been described hitherto. The new characteristics include: (1) small-sized reticulations on growth lines near the umbo; (2) serrated lower margins of growth lines; (3) punctae in the even lumina of reticulations; and (4) tubercles at the lower ends of the claviform radial lirae on the growth bands of the lower parts of the carapace. Consequently, the diagnosis of Abrestheria is revised, and a discussion is also made concerning relationships between Abrestheria and closely related genera, such as Eosestheriopsis, Eosestheria and Orthestheria, which have important biostratigraphic implications.     

Discovery of Middle Jurassic palaeontinids from Inner Mongolia, China (Homoptera: Palaeontinidae)

A new genus and three new species of fossil Palaeontinidae， Papilioncossus conchatus sp. nov., P. giganteus sp. nov.　and P. pteroideus sp. nov.， are described. All of them were collected from Middle Jurassic Jiulongshan Formation in Inner Mongolia, China. Based on distal part of forewing broader and longer than basal and Sc usually with branches, the new taxa are attributed to Palaeontinidae of Homoptera and compared with genus Pseudocossus. A key to species of Papilioncossus gen. nov. is provided. All type specimens are deposited in the Capital Normal University.     

Molecular phylogeny of the specialized schizothoracine fishes （Teleostei： Cyprinidae）,with their implications for the uplift of the Qinghai-Tibetan Plateau

Molecular phylogeny of three genera containing nine species and subspecies of the specialized schizothoracine fishes are investigated based on the complete nucleotide sequence of mitochondrial cytochrome b gene. Meantime relationships between the main cladogenetic events of the specialized schizothoracine fishes and the stepwise uplift of the Qinghai-Tibetan Plateau are also conducted using the molecular clock, which is calibrated by geological isolated events between the upper reaches of the Yellow River and the Qinghai Lake. Results indicated that the specialized schizothoracine fishes are not a monophyly. Five species and subspecies of Ptychobarbus form a monophyly. But three species of Gymnodiptychus do not form a monophyly. Gd.integrigymnatus is a sister taxon of the highly specialized schizothoracine fishes while Gdo pachycheilus has a close relation with Gd. dybowskii, and both of them are as a sister group of Diptychus maculatus. The specialized schizothoracines fishes might have originated during the Miocene(about 10 MaBP), and then the divergence of three genera happened during late Miocene (about 8 MaBP). Their main specialization occurred during the late Pliocene and Pleistocene (3.54-0.42 MaBP). The main cladogenetic events of the specialized schizothoracine fishes are mostly correlated with the geological tectonic events and intensive climate shift happened at 8, 3.6, 2.5 and 1.7 MaBP of the late Cenozoic.Molecular clock data do not support the hypothesis that the Qinghai-Tibetan Plateau uplifted to near present or even higher elevations during the Oligocene or Miocene, and neither in agreement with the view that the plateau uplifting reached only to an altitude of 2000 m during the late Pliocene(about 2.6 MaBP).     

Jurassic and Cretaceous Cupedomorpha (Insecta: Coleoptera) faunas of China

Widespread non-marine Mesozoic deposits in China often contain abundant cupedomorpha fossils with significance for correlation. Based on the composition and characteristics of the cupedomorphs, at present, seven cupedid and ommatid assemblages are recognized from the Jurassic-Cretaceous rocks, of which three cupedid and two ommatid assemblages were recovered from North and northeast China: Middle Jurassic Tetrocupes-Hebeicupes cupedid assemblage from northern Hebei and Inner Mongolia (Yanliao fauna); Late Jurassic or Early Cretaceous Ovatocupes-Priacma cupedid and Amblomma-Sinocupes ommatid assemblages from western Liaoning (Jehol fauna); Early Cretaceous Lupicupes-Diluticupes cupedid and Monticupes ommatid assemblages from Beijing and adjacent areas. Both the Ovatocupes-Priacma and AmblommaSinocupes assemblages are important elements of the Jehol entomofauna. Remaining are the Late Jurassic or Early Cretaceous MesotricupesGansucupes cupedid assemblage from Jiuquan Basin, Gansu Province, NW China and the ForticupesPicticupes ommatid assemblage from Shandong Province. In southern China only one poorly preserved ommatid specimen, Zygadenia (=Notocupes) sp. occurs.     

New fossil elaterids （Insect： Coleoptera： Polyphaga： Elateridae） from the Middle Jurassic of Inner Mongolia, China

A new genus with a new species of fossil elaterid, Paraprotagrypnus superbus gen. et sp. nov., from the Middle Jurassic Jiulongshan Formation in Daohugou Village (N41°18.979′, E119°14.318′), Shantou Township, Ningcheng County, Inner Mongolia, China is described and illustrated. The genus Paraprotagrypnus belongs to the family of Elateridae, subfamily of Protagrypninae and tribe of Protagrypnini. Some primitive characters of the new genus and new species shed light on the ages between the Jiulongshan Formation in Inner Mongolia and the Yixian Formation in the western Liaoning Province of China. The habitat of the new species is briefly discussed.     

Jurassic and Cretaceous Cupedomorpha (Insecta: Coleoptera) faunas of China

Widespread non-marine Mesozoic deposits in China often contain abundant cupedomorpha fossils with significance for correlation. Based on the composition and characteristics of the cupedomorphs, at present, seven cupedid and ommatid assemblages are recognized from the Jurassic-Cretaceous rocks, of which three cupedid and two ommatid assemblages were recovered from North and northeast China: Middle Jurassic Tetrocupes-Hebeicupes cupedid assemblage from northern Hebei and Inner Mongolia (Yanliao fauna); Late Jurassic or Early Cretaceous Ovatocupes-Priacma cupedid and Amblomma-Sinocupes ommatid assemblages from western Liaoning (Jehol fauna); Early Cretaceous Lupicupes-Diluticupes cupedid and Monticupes ommatid assemblages from Beijing and adjacent areas. Both the Ovatocupes-Priacma and AmblommaSinocupes assemblages are important elements of the Jehol entomofauna. Remaining are the Late Jurassic or Early Cretaceous MesotricupesGansucupes cupedid assemblage from Jiuquan Basin, Gansu Province, NW China and the ForticupesPicticupes ommatid assemblage from Shandong Province. In southern China only one poorly preserved ommatid specimen, Zygadenia (=Notocupes) sp. occurs.     

Molecular phylogeny and biogeography of the highly specialized grade schizothoracine fishes （Teleostei： Cyprinidae） inferred from cytochrome b sequences

We recovered the phylogenetic relationships among 23 species and subspecies of the highly special-ized grade schizothoracine fishes distributing at 36 geographical sites in the Tibetan Plateau and its surrounding regions by analyzing sequences of cytochrome b genes. Furthermore, we estimated the possible divergent times among lineages based on a historical geological isolation event in the Tibetan Plateau. The molecular data revealed that the highly specialized grade schizothoracine fishes were not a monophyletic group, but were the same as genera Gymnocypris and Schizogypsis. Our results indi-cated that the molecular phylogenetic relationships apparently reflected their geographical and historical associations with drainages, namely species from the same and adjacent drainages clustered together and had close relationships. The divergence times of different lineages were well consistent with the rapid uplift phases of the Tibetan Plateau in the late Cenozoic, suggesting that the origin and evolution of schizothoracine fishes were strongly influenced by environment changes resulting from the upheaval of the Tibetan Plateau.     

Combining docking and comparative molecular similarity indices analysis （COMSIA） to predict estrogen activity and probe molecular mechanisms of estrogen activity for estrogen compounds

Estrogen compounds are suspected of disrupting endocrine functions by mimicking natural hormones, and such compounds may pose a serious threat to the health of humans and wildlife. Close attention has been paid to the prediction and molecular mechanisms of estrogen activity for estrogen com- pounds. In this article, estrogen receptor a subtype （ERa） -based comparative molecular similarity indices analysis （COMSIA） was performed on 44 estrogen compounds with structural diversity to find out the structural relationship with the activity and to predict the activity. The model with the significant correlation and the best predictive power （R^2= 0.965, Q^2 LOO： 0.599, R^2 pred ： 0.825） was achieved. The COMSIA and docking results revealed the structural features for estrogen activity and key amino acid residues in binding pocket, and provided an insight into the interaction between the ligands and these amino acid residues.     

猪抑胃肽/葡萄糖依赖性促胰岛素释放肽(GIP)基因的克隆与组织表达分析

本研究采用RT-PCR方法,克隆长白猪(Landrace)GIP基因全长cDNA序列,并对其在家猪组织中的表达情况进行分析.结果显示:长白猪GIP(pGIP)cDNA全长435bp,编码144个氨基酸GIP的前体蛋白;该前体蛋白含有信号肽序列,经蛋白酶水解后产生GIP成熟肽.与人、小鼠GIP表达图谱类似,GIP mRNA也在长白猪小肠及肾脏中有较高水平表达.     

Remote sensing of spatial patterns of urban renewal using linear spectral mixture analysis: A case of central urban area of Shanghai (1997―2000)

It is very important to integrate remote sensing with urban geography that the spectral mixture analysis technique is applied to urban land cover evolvement and its eco-environmental effect. Urban land cover is mainly composed of complicated artificial materials, which is the key factor to limit the development of the spectral mixture analysis technique. There are two main aspects in which the technique of spectral mixture analysis is applied to urban geography： one is to calculate vegetation fraction; the other is to build quantitative model of the urban impervious surface obtained from the combination between high albedo fraction and low albedo fraction. The technique of spectral mixture analysis is firstly applied to study urban renewal pattern, scale and mode which happened in Shanghai City from 1997 to 2000,     

Molecular phylogenetics of Gymnocypris （Teleostei：Cyprinidae） in Lake Qinghai and adjacent drainages

149 complete mitochondrial DNA (mtDNA) cytochrome b (Cyt b) genes (1140 bp) of Gymnocypris przewaiskii, Gymnocypris eckloni and Gymnocypris scolistomus from the Lake Qinghai, Yellow River and Qaidam Basin were sequenced and analyzed. Consistent dendrogram indicated that the samples collected from the same species do not constitute a separate monophyletic group and all the samples were grouped into three highly divergent lineages (A, B and C). Among them, Lineage A contained all samples of G.przewaiskii from the Lake Qinghai and partial samples of the G. eckloni from the Yellow River. Lineage B contained the remaining samples of G. eckloni from the Yellow River.Lineage C was composed of a monophyletic group by G. eckloni from the Qaidam Basin. Analysis of molecular variance (AMOVA) indicated that most of genetic variations were detected within these three mtDNA lineages (93.12%), suggesting that there are three different lineages of Gymnocypris in this region. Our Cyt b sequence data showed that G.przewaiskii was not a polytypic species, and G. scolistomus was neither an independent species nor a subspecies of G.eckloni. The divergent mtDNA lineages of G. eckloni from theYellow River suggested that gene flow between the different populations was restricted to a certain extent by several gorges on the upper reach of the Yellow River. Lineage B of G. eckloni might be the genetic effect from the ancestor which was incorporated with the endemic schizothoracinefishes when the headward erosion of the Yellow Riverreached to its current headwaters of late. The G. eckloni from Basin Qaldam was a monophyletic group (lineage C) and Fst values within G. eckloni from the Yellow River were higher than 0.98, suggesting that the gene flow has been interrupted for a long time and the G. eckloni from Basin Qaidam might have been evolved into different species by ecology segregation. The correlation between the rakers number of Gymnocypris and population genetic variation was not significant.All Gymnocypris populations exhibited a low nucleotide diversity (n=0.00096-0.00485). Therefore the Gymnocypris populations from Basin Qaidam could have experienced severe bottleneck effect in history. Our result suggested Gymnocypris populations of Basin Qaidam should give a high priority in conservation programs.