Evolutionary status of Entamoeba

In addition to its medical importance as parasitic pathogen, Entamoeba has aroused people's interest in its evolutionary status for a long time. Lacking mitochondrion and other intracellular organelles common to typical eukaryotes, Entamoeba and several other amitochondrial protozoans have been recognized as ancient pre-mitochondriate eukaryotes and named "archezoa", the most primitive extant eukaryotes. It was suggested that they might be living fossils that remained in a primitive stage of evolution before acquisition of organelles, lying close to the transition between prokaryotes and eukaryotes. However, recent studies revealed that Entamoeba contained an organelle, "crypton" or "mitosome", which was regarded as specialized or reductive mitochondrion. Relative molecular phylogenetic analyses also indicated the existence or the probable existence of mitochondrion in Entamoeba. Our phylogenetic analysis based on DNA topoisomerase II strongly suggested its divergence after some mitchondriate eukaryotes. Here, all these recent researches are reviewed and the evolutionary status of Entamoeba is discussed.

蛇毒Ⅱ类磷脂酶A2 功能分化的分析研究

研究蛇毒Ⅱ类磷脂酶A2 (PLA2 ) 中D49 PLA2 和K49 PLA2 的功能分化及其功能分化决定位点的鉴定。方法: 运 用序列比较分析, 进化树构建和DIVERGE v1104 软件计算研究D49 PLA2 和K49 PLA2 的功能分化情况及其分化位点。结果: 序列比较分析, 进化树构建和DIVERGE v1104 软件计算结果表明蛇毒Ⅱ类PLA2 中D49 PLA2 和K49 PLA2 的确发生了功能分 化, 对于K49 PLA2 来说, 1S , 7K, 11Q , E12 , R34 , T56 , N88 , L92 , E108 , K116 , K128 可能为功能分化决定位点。对于 D49 PLA2 , L2 , G33 , G35 , F46 和Y118 可能为功能分化决定位点。结论: 我们首次通过序列比较分析, 进化树构建和DI2 VERGE v1104 软件计算鉴定出蛇毒Ⅱ类PLA2 中D49 PLA2 和K49 PLA2 可能的功能分化位点, 为今后通过基因重组和定点突 变方法研究蛇毒Ⅱ类PLA2 结构功能关系提供了线索。

Variation in mitochondrial DNA and phylogeny of six species of pikas (Ochotona)

Phylogenetic relationships of six species of Ochotona were investigated using mitochondrial DNA (mtDNA) restriction-site analysis. The phylogenetic tree constructed using PAUP was based on 62 phylogenetically informative sites with O. erythrotis designated as an outgroup. Two clades were evident. One contained O. curzoniae, O. huangensis, and O. thibetana. in the second, O. daurica was a sister taxon of O. cansus. The five species appear to come from different maternal lineages. The branching structure of the tree and sequence divergence confirm that huangensis and cansus are distinct species, and that mol-osa is a synonym of O. cansus rather than O. thibetana. Divergence time, estimated from genetic distances, indicates that the ancestors of the two maternal lineages diverged ca. 6.5 x 10(6) years ago. O. curzoniae diverged from O. huangensis, and O. daurica diverged from O. cansus, at about the same time (ca. 3.4 x 10(6) years ago). These data suggest a period of rapid radiation of the genus Ochotona in China, perhaps during the late Pliocene. These calculations correspond roughly to tectonic events and environmental changes in China throughout this period, and appear to be substantiated by the fossil record.

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 Gd. 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 in during the late Pliocene (about 2.6 MaBP).

Molecular phylogeny and biogeography of woolly flying squirrel (Rodentia : Sciuridae), inferred from mitochondrial cytochrome b gene sequences

To investigate the genetic diversity between the populations of woolly flying squirrels (Eupetaurus) from the eastern and western extremes of the Himalayas, partial mitochondrial cytochrome b gene sequences (390-810bp) that were determined from the museum specimens were analyzed using maximum parsimony (MP) and maximum likelihood (ML) methods. The molecular data reveal that the two specimens that were collected in northwestern Yunnan (China) are members of the genus Eupetaurus. Reconstructed phylogenetic relationships show that the populations of Eupetaurus in the eastern and western extremes of the Himalayas are two distinct species with significant genetic differences (12%) and diverged about 10.8 million years ago. Eupetaurus is significantly different from Petaurista and Pteromys. The level of estimated pairwise-sequence divergence observed between Eupetaurus and Petaurista or Pteromys is greater than that observed between Eupetaurus and Trogopterus, Belomys, Glaucomys, or Hylopetes. Considering the divergence time of the two Eupetaurus groups, the glaciations and the uplift of the Himalayas and Qinghai-Tibet plateau during the Pliocene-Pleistocene period might be the major factors affecting the present distribution of Eupetaurus along the Himalayas. (C) 2004 Elsevier Inc. All rights reserved.

Fish-Specific Duplicated dmrt2b Contributes to a Divergent Function through Hedgehog Pathway and Maintains Left-Right Asymmetry Establishment Function

Gene duplication is thought to provide raw material for functional divergence and innovation. Fish-specific dmrt2b has been identified as a duplicated gene of the dmrt2a/terra in fish genomes, but its function has remained unclear. Here we reveal that Dmrt2b knockdown zebrafish embryos display a downward tail curvature and have U-shaped somites. Then, we demonstrate that Dmrt2b contributes to a divergent function in somitogenesis through Hedgehog pathway, because Dmrt2b knockdown reduces target gene expression of Hedgehog signaling, and also impairs slow muscle development and neural tube patterning through Hedgehog signaling. Moreover, the Dmrt2b morphants display defects in heart and visceral organ asymmetry, and, some lateral-plate mesoderm (LPM) markers expressed in left side are randomized. Together, these data indicate that fish-specific duplicated dmrt2b contributes to a divergent function in somitogenesis through Hedgehog pathway and maintains the common function for left-right asymmetry establishment.

Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes

We investigated the molecular evolution of duplicated color vision genes (LWS-1 and SWS2) within cyprinid fish, focusing on the most cavefish-rich genus-Sinocyclocheilus. Maximum likelihood-based codon substitution approaches were used to analyze the evolution of vision genes. We found that the duplicated color vision genes had unequal evolutionary rates, which may lead to a related function divergence. Divergence of LWS-1 was strongly influenced by positive selection causing an accelerated rate of substitution in the proportion of pocket-forming residues. The SWS2 pigment experienced divergent selection between lineages, and no positively selected site was found. A duplicate copy of LWS-1 of some cyprinine species had become a pseudogene, but all SWS2 sequences remained intact in the regions examined in the cyprinid fishes examined in this study. The pseudogenization events did not occur randomly in the two copies of LWS-1 within Sinocyclocheilus species. Some cave species of Sinocyclocheilus with numerous morphological specializations that seem to be highly adapted for caves, retain both intact copies of color vision genes in their genome. We found some novel amino acid substitutions at key sites, which might represent interesting target sites for future mutagenesis experiments. Our data add to the increasing evidence that duplicate genes experience lower selective constraints and in some cases positive selection following gene duplication. Some of these observations are unexpected and may provide insights into the effect of caves on the evolution of color vision genes in fishes.

Speciation and Phylogeography of Opsariichthys bidens (Pisces: Cypriniformes: Cyprinidae) in China: Analysis of the Cytochrome b Gene of mtDNA from Diverse Populations

Gao-Yan Li, Xu-Zhen Wang, Ya-Hui Zhao, Jie Zhang, Chun-Guang Zhang, and Shun-Ping He (2009) Speciation and phylogeography of Opsariichthys bidens (Pisces: Cypriniformes: Cyprinidae) in China: analysis of the cytochrome b gene of mtDNA from diverse populations. Zoological Studies 48(4): 569-583. The cyprinid fish Opsariichthys bidens Gunther is distributed in all major river systems of continental East Asia, and represents an attractive model for phylogeographic studies among cyprinid species or within a given species. In this study, we investigated the phylogeographic and demographic history of this species, using partial sequences of the cytochrome (cyt) b gene in mitochondrial (mt)DNA. Fish samples were collected from almost all major river systems where O. bidens is distributed in China. Sequence analysis showed remarkably high polymorphism, with 125 haplotypes in the 234 specimens examined, and with 89.8% of haplotypes occurring in only 1 specimen. A neutrality test indicated that some groups were not at mutation-drift equilibrium, suggesting a past population expansion. These results were supported by a mismatch distribution analysis. Based on our analysis, O. bidens consists of 4 groups belonging to 2 clades. The divergence time of the 2 clades was estimated to be 11.06-8.04 my. This value corresponds to the time of the 2nd uplift of the Qinghai-Tibet Plateau, the emergence of the East Asian monsoon, and the Epoch-6 Event. A two species scheme is proposed. http://zoolstud.sinica.edu.tw/Journals/48.4/569.pdf

Origin and evolution of the RIG-I like RNA helicase gene family

Background: The DExD/H domain containing RNA helicases such as retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) are key cytosolic pattern recognition receptors (PRRs) for detecting nucleotide pathogen associated molecular patterns (PAMPs) of invading viruses. The RIG-I and MDA5 proteins differentially recognise conserved PAMPs in double stranded or single stranded viral RNA molecules, leading to activation of the interferon system in vertebrates. They share three core protein domains including a RNA helicase domain near the C terminus (HELICc), one or more caspase activation and recruitment domains (CARDs) and an ATP dependent DExD/H domain. The RIG-I/MDA5 directed interferon response is negatively regulated by laboratory of genetics and physiology 2 (LGP2) and is believed to be controlled by the mitochondria antiviral signalling protein (MAVS), a CARD containing protein associated with mitochondria. Results: The DExD/H containing RNA helicases including RIG-I, MDA5 and LGP2 were analysed in silico in a wide spectrum of invertebrate and vertebrate genomes. The gene synteny of MDA5 and LGP2 is well conserved among vertebrates whilst conservation of the gene synteny of RIG-I is less apparent. Invertebrate homologues had a closer phylogenetic relationship with the vertebrate RIG-Is than the MDA5/LGP2 molecules, suggesting the RIG-I homologues may have emerged earlier in evolution, possibly prior to the appearance of vertebrates. Our data suggest that the RIG-I like helicases possibly originated from three distinct genes coding for the core domains including the HELICc, CARD and ATP dependent DExD/H domains through gene fusion and gene/domain duplication. Furthermore, presence of domains similar to a prokaryotic DNA restriction enzyme III domain (Res III), and a zinc finger domain of transcription factor (TF) IIS have been detected by bioinformatic analysis. Conclusion: The RIG-I/MDA5 viral surveillance system is conserved in vertebrates. The RIG-I like helicase family appears to have evolved from a common ancestor that originated from genes encoding different core functional domains. Diversification of core functional domains might be fundamental to their functional divergence in terms of recognition of different viral PAMPs.

The complete mitochondrial DNA sequence and the phylogenetic position of Achalinus meiguensis (Reptilia: Squamata)

The mitochondrial genome complete sequence of Achalinus meiguensis was reported for the first time in the present study. The complete mitochondrial genome of A. meiguensis is 17239 bp in length and contains 13 protein-coding genes, 22 tRNA, 2 rRNA, and 2 non-coding regions (Control regions). On the basis of comparison with the other complete mitochondrial sequences reported, we explored the characteristic of structure and evolution. For example, duplication control regions independently occurred in the evolutionary history of reptiles; the pseudo-tRNA of snakes occurred in the Caenophidia; snake is shorter than other vertebrates in the length of tRNA because of the truncations of T psi C arm (less than 5 bp) and "DHU" arm. The phylogenic analysis by MP and BI analysis showed that the phylogenetic position of A. meiguensis was placed in Caenophidia as a sister group to other advanced snakes with the exclusion of Acrochordus granulatus which was rooted in the Caenophidia. Therefore we suggested that the subfamily Xenodermatinae, which contains A. meiguensis, should be raised to a family rank or higher rank. At the same time, based on the phylogenic statistic test, the tree of Bayesian was used for estimating the divergence time. The results showed that the divergence time between Henophidia and Caenophidia was 109.50 Mya; 106.18 Mya for divergence between Acrochordus granulatus and the other snakes of the Caenophidia; the divergence time of A. meiguensis was 103 Mya, and Viperidae diverged from the unilateral of Elapidae and Colubridae was 96.06 Mya.

Molecular systematics of medusae in the genus Craspedacusta (Cnidaria: Hydrozoa: Limnomedusae) in China with the reference to the identity of species

The objective of this study was to illustrate the phylogenetic relationship of the species in the genus Craspedacusta in China. The medusae samples were collected at 28 localities in China representing seven described species with their entire ITS region (the contiguous sequences of ITS-1, 5.8S and ITS-2 rDNA) rDNA sequences cloned. Among the 28 samples, the range of sequence variation in the complete ITS and 5.8S region was between 0 and 36.2%. Three main clades were revealed by both maximum likelihood and neighbour-joining trees, with sequence difference of 0-0.9, 0-3.7 and 0.1-1.5% in the three clades. The nesting of C. xinyangensis representatives within C. sowerbii, C. brevinema within C. sinensis and C. sichuanensis within C. kiatingi is strongly supported, with interspecific sequence divergence of 0-0.9, 0.1-1.4 and 0.0-0.4%, respectively. Thus, it is suggested that C. xinyangensis should be the synonym of C. sowerbii, C. sichuanensis the synonym of C. kiatingi and C. brevinema the synonym of C. sinensis. However, the taxonomic status of C. ziguiensis is still uncertain. According to the tree topology, C. kiatingi was closer to C. sowerbii than to C. sinensis. Craspedacusta sinensis was the most genetically distinct from distance matrix values, and located at the base of the phylogenetic trees, so it can be speculated that the C. sinensis may be the ancestral form in the genus Craspedacusta.

Molecular characteristics of Camallanus spp. (Spirurida : Camallanidae) in fishes from China based on its rDNA sequences

In the,paper, we explored the intra- and interspecific evolutionary variation among species of Camallanus collected from different fish species in various regions of China. We determined the internal transcribed spacers of ribosomal DNA (ITS rDNA) sequences of these nematodes. The divergence (uncorrected p-distance) of ITS 1, ITS2, and ITS rDNA data sets confirmed 2 valid species of Camallanus in China, i.e., C. cotti and C. hypophthalmichthys. The 2 species were distinguished not only by their different morphologies and host ranges but also by a letranucleotide microsatellite (TTGC)n present in the ITS I region of C cotti. Phylogenetic analyses of the nematodes disclosed 2 main clades, corresponding to different individuals of C cotti and C. hypophthalmichthys from different fish species in various geographical locations, although the interior nodes of each clade received poor support.

Phylogeny and speciation of the eastern Asian cyprinid genus Sarcocheilichthys

The genus Sarcocheilichthys is a group of small cyprinid fishes comprising 10 species/sub-species widely distributed in East Asia, which represents a valuable model for understanding the speciation of freshwater fishes in East Asia. In the present study, the molecular phylogenetic relationship of the genus Sarcocheilichthys was investigated using a 1140 bp section of the mitochondrial cytochrome b gene. Two different tree-building methods, maximum parsimony (MP) and Bayesian methods, yielded trees with almost the same topology, yielding high bootstrap values or posterior probabilities. The results showed that the genus Sarcocheilichthys consists of two large clades, clades I and II. Clade I contains Sarcocheilichthys lacustris, Sarcocheilichthys sinensis and Sarcocheilichthys parvus, with S. parvus at a basal position. In clade II, Sarcocheilichthys variegatus microoculus is at a basal position; samples of the widespread species, Sarcocheilichthys nigripinnis, form a large subclade containing another valid species Sarcocheilichthys czerskii. Sarcocheilichthys kiangsiensis is retained at an intermediate position. Since S. czerskii is a valid species in the S. nigripinnis clade, remaining samples of S. nigripinnis form a paraphyly. This speciation process is attributed to geographical isolation and special environmental conditions experienced by S. czerskii and stable environments experienced by the other S. nigripinnis populations. This type of speciation process was suggested to be very common. Samples of Sarcocheilichthys sinensis sinensis and Sarcocheilichthys sinensis fukiensis that did not form their own monophyletic groups suggest an early stage of speciation and support their sub-species status. Molecular clock analysis indicates that the two major lineages of the genus Sarcocheilichthys, clades I and II diverged c. 8.89 million years ago (mya). Sarcocheilichthys v. microoculus from Japan probably diverged 4.78 mya from the Chinese group. The northern-southern clades of S. nigripinnis began to diverge c. 2.12 mya, while one lineage of S. nigripinnis evolved into a new species, S. czerski, c. 0.34 mya. (C) 2008 The Authors Journal compilation (C) 2008 The Fisheries Society of the British Isles.

Molecular evolution of connective tissue growth factor in Cyprinidae (Teleostei : Cypriniformes)

Connective tissue growth factor (CTGF) plays an important role in regulation of cell growth, differentiation, apoptosis and individual development in animals. The study of sequences variation and molecular evolution of CTGF gene across various species of the cyprinid could be helpful for understanding of speciation and gene divergence in this kind of fish. In this study, 19 novel sequences of CTGF gene were obtained from the representative species of the family Cyprinidae using PCR amplification, cloning and sequencing. Phylogenetic relationships of Cyprinidae were reconstructed by neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian method. Oryzias latipes from the family Cyprinodontidae was assigned to be the outgroup taxon. Leuciscini and Barbini were clustered into the monophyletic lineages, respectively, with the high nodal supports. The estimation of the ratio of non-synonymous to synonymous substitution (dN/dS) for the various branches indicated that there stood the different evolution rates between the Leuciscini and the Barbini. With the ratio of dN/dS of the Leuciscini being lower than that of the Barbini, species within the Barbini were demonstrated to be subjected to the relatively less selection pressure and under the relaxable evolution background. A 6 by indel (insertion/deletion) was found at the 5' end of CTGF gene of Cyprinidae, and this 6 by deletion only appeared in the Leuciscini, which is a typical characteristic of the Leuciscini and provides evidence for the monophylogeny of the Leuciscini. For the amino acid sequences of CTGF protein, the most variations and indels were distributed in the signal region and IGFBP region of this protein, implying that these variations were correlated with the regulation of the CTGF gene expression and protein activity. (c) 2007 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.