2010 Vol. 31, No. 4
Sequencing and Analysis of the Complete Mitochondrial Genome of Pseudopodoces humilis (Aves, Paridae)
2010, 31(4): 333-344. doi: 10.3724/SP.J.1141.2010.04333
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The complete sequence of Pseudopodoces humilis mitochondrial genome was determined by using long PCR and conserved primers walking approaches. The results showed that the entire mitochondrial genome of Pseudopodoces humilis was 16 809 bp in length with 52.9% A+T content, and the 37 genes had the same gene order with that of Gallus gallus. All protein coding genes of the Pseudopodoces humilis mitochondrial genome started with ATG codon, except for COIwith GTG. For terminate codon usage, most of genes terminate with codons TAA or TAG, ND1 and ND5 were AGA, COII was AGG, and the COIII and ND4 genes had an incomplete termination codon (T). The secondary structures of 22 tRNA were predicted, all tRNA can form typical secondary structure, except tRNASer ( AGN ) with an absence of DHU arm, and tRNAPhe with an extra nucleotide inserted in the TψC arm. The predicted secondary structures of 12S rRNA and 16S rRNA exhibit 47 helics in 3 structural domains and 60 helics in 6 domains, respectively. The control region of Pseudopodoces humilis located between tRNAGlu and tRNAPhe with 1 240 bp in length, and has structure domains found in that of the other birds.
COI-based DNA Barcoding in Tapetinae Species (Mollusca, Bivalvia, Veneridae) along the Coast of CHINA
2010, 31(4): 345-352. doi: 10.3724/SP.J.1141.2010.04345
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DNA barcoding has exhibited charming effectiveness in species diagnosis, but some studies suggested the proportion of taxa that cannot be barcode-distinguished was still high. In the present study, the efficiency of the DNA barcoding for delimiting species of subfamily Tapetinae along the coast of China was tested. Fifty one original COI sequences of 11 species in five genera were analyzed. Among these sequences, 43 haplotypes were identified. Saturation plots generated for DNA barcode revealed that transitions became saturated after 10% to 15% sequence divergence. However, transversions were not saturated. Excluding Ruditapes variegata haplotype Hap33 that might be the result of a hybridization event, our finding showed that K2P-distances between conspeci?c sequences varied from 0% to 2.02% (0.46% on average), distances between congeneric sequences were from 17.21% to 32.24% (24.96% on average), and all conspeci?cs clustered together in the phylogentic trees. The proportion of individuals that can be distinguished by DNA barcoding was approximately 98% among 51 individuals analyzed in this study. Thus, the results evidenced that subfamily Tapetidae species can be efficiently identified through the use of DNA barcoding.
Validity and Systematic Position of Rana altaica (Rana: Ranidae): Results of a Phylogenetic Analysis
2010, 31(4): 353-360. doi: 10.3724/SP.J.1141.2010.04353
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In order to evaluate the phylogenetic position and validity of Rana altaica, we investigated the phylogeny of brown frogs in Eurasia by Bayesian Inference and Maximum Parsimony analyses of a fragment from the mitochondrial DNA gene Cytochrome b. Both analyses resolved R. altaica as nesting deeply within R. arvalis. Most samples of the nominal R. altaica from the Altai region and specimens from Central Siberia shared a haplotype with R. arvalis. The matrilineal relationships suggested that R. altaica should be considered as a junior synonym of R. arvalis. Furthermore, our study suggested that the species group division of Chinese brown frogs should be re-evaluated within a phylogenetic context.
A 838 bp fragment of mtDNA ND4-tRNALeu gene was sequenced for 66 individuals from five populations (DB: Dabancheng, TU: Turpan, SS: Shanshan, HL: Liushuquan, HD: East district of Hami) of Phrynocephalus axillaris distributed in east of Xinjiang Uygur Autonomous Region. Seventeen haplotypes were identified from 29 nucleotide polymorphic sites in the aligned 838 bp sequence. Excluding DB, there were relatively high haplotype diversity (0.600±0.113) ≤ h ≤0（.922±0.012) and low nucleotide diversity (0.00082±0.00020) ≤ π≤（0.00917±0.00037) in the whole and the rest four populations. The result of phylogenetic analysis showed that the haplotypes from five populations formed cladeⅠ(DB+TU+SS) and cladeⅡ (HL+HD). Network analysis further revealed the phylogeographical structure of these five populations. Analysis of molecular variance (AMOVA) indicated that the significant genetic divergence (81.67%, P<0.01) existed among populations, which was not obviously correlated with the geographic distances between populations inferred from isolation-with-distance analysis (r=0.5324, P=0.1196). The demography analysis implied that TU and HL might have experienced the recent population expansion; SS and HD might be relatively stable. With extremely low genetic diversity, DB might be influenced by the special environment and be experiencing the bottleneck effect. It followed that the significant genetic differentiation among the five populations of P. axillaris might be the consequence of habitat changes resulting from the geological events and climate oscillation since Pleistocene and genetic drift.
Phylogenetic Relationships among Some Chinese Genera of Phoridae Based on Mitochondrial 12S and 16S rRNA Gene Sequences
2010, 31(4): 370-374. doi: 10.3724/SP.J.1141.2010.04370
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The phylogenetic relationships among 14 Chinese genera of Phoridae were reconstructed based on concatenated sequences of the mitochondrial 12S and 16S rRNA genes using maximum parsimony, maximum likelihood and Bayesian methods. The alignment of the concatenated sequences spanned 819 sites including 277 variable sites, of which 200 were parsimony-informative. The sequences showed a 77.7% A+T bias. The phylogenetic analysis showed that the Phoridae was monophyletic. It was shown that the involved genera in the study clustered into monophyletic Phorinae and Metopininae. The genera Diplonevra and Dohrniphora were closely related to each other. The relationships among Anevrina, Conicera and Spiniphora were also closer. The genera Metopina and Puliciphora proved to be reciprocal sister group and the cluster analysis showed the close relationship between Gymnophora and Phalacrotophora.
2010, 31(4): 375-380. doi: 10.3724/SP.J.1141.2010.04375
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Amphioxus (lancelet) is an important model animal in the field of Evo-Devo study. However, the specimens for laboratorial experiments are usually sampled directly from the field. Thus, it is necessary to correctly identify species and evaluate the genetic diversity of geographic populations. In the present investigation, we amplified and sequenced COX Ι gene of amphioxus collected from various localities of the West Pacific Ocean and downloaded all available sequences of the gene from NCBI. Based on those sequences data, we constructed NJ tree to decide the taxonomic status of those amphioxus and performed AMOVA analysis to estimate genetic diversities among geographic populations and individuals. The current results supported the validity of the three amphioxus species, Branchiostoma malayanum, B. belcheri and B. japonicum. We also proposed that some amphioxus species names recorded in NCBI sequence database might be inaccurate. Genetic analysis on the geographic populations of amphioxus species suggested that each examined amphioxus species have a high level of genetic diversity. However, the genetic divergences among geographic populations of the same species are indetectable, indicating a frequent gene flow among them.
Preliminary Classification and Phylogenetic Relationship Among Onchidiidae in China Inferred from 18S rRNA Partial Sequence
2010, 31(4): 381-386. doi: 10.3724/SP.J.1141.2010.04381
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As a nutritious mollusk living in the intertidal zone, Onchidiidae has a significant value for biological research. Nine populations were collected from the costal areas such as Chongming (Shanghai), Ningde (Fujian), Haikou (Hainan) in this study. Through the study of anatomy and other methods to investigate the major category characteristics, the nine populations were preliminary classified. By sequencing segments of 18S rRNA gene and constructing phylogenetic trees using these nine populations and four other 18S rRNA gene sequences from GenBank, with Siphonaria as an outgroup, we analyzed the phylogeny of Onchidiidae in mainland China. The trees were used for discussing the relationship between the populations of the Onchidiidae in this study. The results showed that the southern coast has more populations than the northern coast in China. Besides two known species, Onchidium struma (JZH) and O. verruculatum (FJZ & HNZ), five new recorded species may exist: Onchidium(1), Platevindex(2), one Peronia(1) and Paraoncidium(1). The phylogenetic trees indicated that the nine populations can be divided into four subgroups, Peronia, Onchidium, Platevindex and Paraoncidium, and Peronia has the highest confidence level in clustering. Onchidium verruculatum (FJZ & HNZ) should be Peronia verruculata.
Identification and Characterization of Myostatin Gene in Rough-skinned Sculp, Trachidermus fasciatus
2010, 31(4): 387-394. doi: 10.3724/SP.J.1141.2010.04387
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Myostatin is a member of the TGF-β superfamily and acts as a negative regulator of skeletal muscle growth. The characterization of the myostatin gene and its expression in Trachidermus fasciatus was reported in the current study. A full-length of 2 568 bp myostatin cDNA sequence in T. fasciats was cloned by 5' and 3' RACE, which included a 1 128 bp complete ORF encoding a 375 amino acid peptide, a 106 bp long 5'-UTR and a 1134 bp long 3′UTR. As other MSTN, the putative peptide contains a 22 amino acids long signal peptide, a conserved RXXR proteolytic processing site, and 10 conserved cysteine residues in the C terminal of the protein. The Trachidermus fasciatus MSTN has high homology with Umbrina cirrosa, Morone saxatilis, Morone americana, Morone chrysops myostatin while has low homology with mammalian and birds myostatin. The phylogenetic analysis showed that the T. fasciatus myostatin had the closest relationship with U. cirrosa. In the four examined tissues, the myostatin gene was highly expressed in muscle and intestine and weakly expressed in brain and liver. These results suggested that the fish myostatin gene might not only play roles in muscle development but also contribute to other biological functions.
2010, 31(4): 395-400. doi: 10.3724/SP.J.1141.2010.04395
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Using seven pairs of microsatellite markers we studied the relationship between the size of the the candidate groups and the microsatellite paternity testing accuracy by separate breed or the microsatellite paternity appraisal ability by mixed breed. By computer software analysis, the appraisal ability decreased with the candidate groups increase. For the 81 putative parents the microsatellite paternity testing accuracy was 80% and the microsatellite paternity appraisal ability was 78.9%; for the 9 putative parents, the testing accuracy was 93.3% and the appraisal ability was 92.2%. The results indicated that the microsatellite DNA markers can be used for the parentage determination of Hucho taimen Pallas.
2010, 31(4): 401-407. doi: 10.3724/SP.J.1141.2010.04401
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Microsatellite polymorphisms were analyzed in F5, F6 and F7 WHBE rabbits (Oryctolagus cuniculus) to monitor inbreeding. Out of 21 microsatellite loci, 11 were successfully amplified and showed polymorphic. For the F5 WHBE rabbits, the number of alleles per locus (Na) ranged from 3 to 9 and the mean effective number of alleles (Ne) was 1.81. The mean value of observed heterozygosity (Ho) and polymorphism information content (PIC) of the 11 polymorphic loci were 0.381 and 0.524, respectively. The power of cumulative discrimination (CDP) was 1.0. The value of cumulative exclusion probability of the 11 polymorphic loci in the absence (CPE-1) or in the presence of genetic information on the first parent (CPE-2) was 0.926 and 0.993, respectively. For the F6 WHBE rabbits, Na per locus ranged from 3 to 8 and the mean value of Ne was 1.68. The mean value of Ho, PIC, CDP, CPE-1, CPE-2 of the 11 polymorphic loci were 0.356, 0.548, 1.0, 0.931, 0.994 respectively. For the F7 WHBE rabbits, Na per locus ranged from 2 to 6 and the mean value of Ne was 1.51. The mean value of Ho, PIC, CDP, CPE-1, CPE-2 of the 11 polymorphic loci were 0.287, 0.498, 1.0, 0.891, 0.986 respectively. The average number of effective alleles and the average observed heterozygosity were decreasing continuously in F 5, F6 and F7, suggesting that the purity of WHBE rabbits was increasing continuously.
Observation on the Embryo Development of Lutraria sieboldii Reeve(A Unique New Type of Cleavage — Fusion Cleavage)
2010, 31(4): 408-414. doi: 10.3724/SP.J.1141.2010.04408
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The embryonic development process of Lutraria sieboldii Reeve was observed. The results showed that：(1) Like other bivalves, its embryonic development could be divided into 5 phases: cleavage, blastula, gastrula, trochophore and veliger. (2) In cleavage phase, the cleavage mode for Lutraria sieboldii Reeve was completely different from other animals. Although the ova of L. sieboldii Reeve obtained the ability to fertilize before they developed into the prophase of meiosis I (prior to the breakage of blastocyst), the release of polar bodies was not observed posterior to fertilization of ova, instead multi-nuclear fertilized ova were found. In later cleavage, longitudinal or latitudinal cleavages with the fertilized eggs did not occur as in other animals. A more unique and intricate type of cleavage, we called it fusion cleavage, was observed, viz., before 2-cell, 4-cell, 8-cell blastomeres entered into next division, nuclei disappeared gradually, blastomere fused gradually into one cell. After some time, in the centre of the cell appeared gradually nuclei that had been doubled in number. The nuclei gradually moved outward, and finally number-doubled blastomeres were cleaved out at one time.
2010, 31(4): 415-420. doi: 10.3724/SP.J.1141.2010.04415
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An effective algorithm for detecting pupil size based on image processing was established. Three features reflecting differences between opiate addicts and normal subjects in pupillary light reflex were extracted by applying this algorithm, including absolute amplitude of contraction (AAC), relative amplitude of contraction (RAC) and slope of contraction velocity (SCV). Effects of addiction, sex, myopia, aging, sleep deprivation on the three features were studied. None of three features was found significant differences between sexes, myopia, sleep deprived and normal subjects. Only RAC increased significantly in aging subjects in comparison to opiate addicts, The features of pupillary light reflex in opiate addicts decreased significantly not only comparing with normal subjects, but the subjects with potential facts that may alter their pattern of pupil light reflex as well. Our study provided basic data for future establishment of a rapid, non-contact method in distinguishing opiate addicts from other subjects based on pupillary light reflex.
Habitat Selection and Use of François's Langurs (Trachypithecus francoisi) in Guangxi Province, Fusui Area
2010, 31(4): 421-427. doi: 10.3724/SP.J.1141.2010.04421
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To explore the influence of habitat fragmentation on the ecology of the François's langur (Trachypithecus francoisi), data on habitat use were collected from a group of François's langurs living in an isolated hill in the Fusui Rare Animal Nature Reserve, Guangxi Province, from March to December 2001. To identify the effect of human activities on vegetation, 10 vegetation quadrats were sampled in the habitat, including 5 on the slopes with more human disturbance, and 5 on the hill-tops with less human disturbance. Because of human destruction, not only the number of plant species, diversity and density, but also the densities of preferred foods for François's langurs were less on the slope than those on the hill-top. Analyses of habitat use indicated that the langurs showed preference for the hill-top with abundant food resources and less human disturbance, and avoided to use the slope with more human disturbance. In the rainy seasons, langurs spent significantly more time on the hill-top rather than on the cliff. Therefore, habitat selection and use of the species may be resulted from the balance of feeding benefit and human disturbance. François's langurs used the platforms and caves on the cliffs as sleeping sites. They reused some sleeping sites, and tend to use the same caves on consecutive nights.
Aggressive Behavior Comparisons of TibetanMacaques from Mt. Huangshan, China (Macaca thibetana) According to Their Age and Sex
2010, 31(4): 428-434. doi: 10.3724/SP.J.1141.2010.04428
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To investigate the relationship between monkey-human aggressive behaviors and age/sex classes of monkey (initiator) and human (recipient)，by using all-occurrence sampling and continuous recording, we evaluated the monkey-human aggressive behaviors between macaques (Macaca thibetana) and tourists at Mt. Huangshan in two periods (Nov. − Dec.2008 and Apr. − May 2009). After we divide the aggression into three types according to the dangerous level to tourists, some significant patterns were observed.Our observations indicate that Tibetan macaques respond differently to human according to the age/sex classes involved. On one hand, We found that the adult male monkeys tend to be more aggressive than expected (P<0.01), while the adult female monkeys and immature monkeys participated in AGⅢ behaviors (threat) less than expected (P<0.01); On the other hand, The adult male human received more aggressive behaviors than expected ( P< 0.01), while the adult female human and child received less aggressive in AGⅢ behaviors (threat) (P<0.01). Our results provide not only a scientific basis for the management advice that adult male monkeys and adult male human should be given special attention, but also a good management model of Huangshan for other primate tourist exploring places.
2010, 31(4): 435-443. doi: 10.3724/SP.J.1141.2010.04435
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The morphometrical variability of six natural populations of Difflugia tuberspinifera was investigated using the statistic methods based on 374 samples from Yangtze River and Pearl River valleys. The size frequency distribution analysis indicated that D. tuberspinifera is a size-monomorphic species with normal distribution of shell height, shell diameter and aperture diameter. The size of spine length, collar height, foreside length and number of conical spines are the most variable. The correlation analysis showed that most characters are inter-correlated with P＜0.05. The shell height, shell diameter, aperture diameter, spine length, collar height, rear end length, foreside length, number of aperture tooth-like structures and number of conical spines differed significantly between different populations (P＜0.0001), but principal component analysis (PCA) did not clearly distinguish the six populations based on the morphometric data. However, the cluster analysis separated the six populations into two groups, the Pearl River-Yangtze River group and the Yangtze River group. Further, the populations with different shell characters can coexist within the same river valley. Thus, there is a high morphological variability or diversity within the populations of D. tuberspinifera which is related with local environmental conditions.
2010, 31(4): 444-445. doi: 10.3724/SP.J.1141.2010.04444
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One specimen was collected from Lancangjiang River in Jinghong, China on August 1st, 2006. It is identified as Anguilla bicolor McClelland, 1844, a new record of Anguillidae species occurring in Lancangjiang River in China. It could be distinguished from other Anguilla species by the character as: dorsal-fin origin located above vent vertically. It is an active nocturnal forager, feeding largely on a diet of crustaceans and mollusks.
2010, 31(4): 446-452. doi: 10.3724/SP.J.1141.2010.04446
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Protandry refers the earlier arrival at breeding sites or reproductive stages of males than females. Focusing on the general phenomenon of males arriving at breeding sites earlier than females in migratory birds, we introduced six hypotheses for explaining the protandrous arrival, including rank advantage, susceptibility, constraint, mate opportunity, waiting cost, and mate choice hypothesis. We also discussed the applicability of these hypotheses to explain the protandry in migratory birds. In addition, we put forward the issues which might be important in the future research, including 1) occurrences of protandry in species of sexually homomorphism, 2) effects of global warming on protandry, and 3) effects of intrasexual competition on protandry.