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Zoological Research    2013, 34 (3): 139-248.   DOI:
Abstract ( 479 )   PDF (11188KB) (12014)
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A review on the bioinformatics pipelines for metagenomic research
YE Dan-Dan, FAN Meng-Meng, GUAN Qiong, CHEN Hong-Ju, MA Zhan-Shan
ZOOLOGICAL RESEARCH    2012, 33 (6): 574-585.   DOI: 10.3724/SP.J.1141.2012.06574
Abstract ( 4074 )   PDF (1013KB) (9512)

Metagenome, a term first dubbed by Handelsman in 1998 as “the genomes of the total microbiota found in nature”, refers to sequence data directly sampled from the environment (which may be any habitat in which microbes live, such as the guts of humans and animals, milk, soil, lakes, glaciers, and oceans). Metagenomic technologies originated from environmental microbiology studies and their wide application has been greatly facilitated by next-generation high throughput sequencing technologies. Like genomics studies, the bottle neck of metagenomic research is how to effectively and efficiently analyze the gigantic amount of metagenomic sequence data using the bioinformatics pipelines to obtain meaningful biological insights. In this article, we briefly review the state-of-the-art bioinformatics software tools in metagenomic research. Due to the differences between the metagenomic data obtained from whole genome sequencing (i.e., shotgun metagenomics) and amplicon sequencing (i.e., 16S-rRNA and gene-targeted metagenomics) methods, there are significant differences between the corresponding bioinformatics tools for these data; accordingly, we review the computational pipelines separately for these two types of data.

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ZOOLOGICAL RESEARCH Volume 33, Issues E5-6, December 2012,CONTENTS (PDF)
ZOOLOGICAL RESEARCH    2012, 33 (E5-6): 0-0.   DOI:
Abstract ( 580 )   PDF (11094KB) (6854)
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Special  Issue for Animal Model of Hunman Diseases
Zoological Research    2011, 32 (1): 1-114.   DOI:
Abstract ( 1048 )   PDF (20734KB) (6524)
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Morphological and molecular studies on Garra imberba and its related species in China
Wei-Ying WANG, Wei ZHOU, Jun-Xing YANG, Xiao-Yong CHEN
ZOOLOGICAL RESEARCH    2014, 35 (1): 20-32.   DOI: 10.11813/j.issn.0254-5853.2014.1.020
Abstract ( 743 )   PDF (17425KB) (6405)
Garra imberba is widely distributed in China. At the moment, both Garra yiliangensis and G. hainanensis are treated as valid species, but they were initially named as a subspecies of G. pingi, a junior synonym of G. imberba. Garra alticorpora and G. nujiangensis also have similar morphological characters to G. imberba, but the taxonomic statuses and phylogenetic relationships of these species with G. imberba remains uncertain. In this study, 128 samples from the Jinshajiang, Red, Nanpanjiang, Lancangjiang, Nujiang Rivers as well as Hainan Island were measured while 1 mitochondrial gene and 1 nuclear intron of 24 samples were sequenced to explore the phylogenetic relationship of these five species. The results showed that G. hainanensis, G. yiliangensis, G. alticorpora and G. imberba are the same species with G. imberba being the valid species name, while G. nujiangensis is a valid species in and of itself.
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ZOOLOGICAL RESEARCH    2013, 34 (2): 0-0.   DOI:
Abstract ( 760 )   PDF (13222KB) (5493)
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Fish Production, Water Quality and Bacteriological Parameters of Koi Carp Ponds Under Live-food and Manure Based Management Regimes
Prithwiraj Jha,Sudip Barat,Chitta R. Nayak
ZOOLOGICAL RESEARCH    2008, 29 (2): 165-173.   DOI: 10.3724/SP.J.1141.2008.02165
Abstract ( 2627 )   PDF (151KB) (5311)

To test the effectiveness of introducing live zooplankton against direct manuring in ornamental fish ponds upon their survival and production, larvae of koi carp, Cyprinus carpio L., were cultured for 11 weeks in earthen ponds maintained according to four management regimes: (1) live zooplankton fed to carp larvae (LF); (2) direct fertilization with poultry manure (PM); (3) direct fertilization with cowdung (CD); and (4) a control treatment (C). There were three replicates for each treatment. The growth of heterotrophic bacteria and pathogenic microorganisms like Aeromonas sp. and Pseudomonas sp. were also examined in response to pond management. Values of dissolved oxygen were significantly higher (P<0.05) in the water of LF ponds, compared to other treatments, while the PM and CD treatments recorded were significantly higher (P<0.05) values of PO4 – P, NH4 – N, NO3 – N, NO2 – N, specific conductivity, alkalinity, and BOD, compared to the LF and C treatments. The percentages of organic carbon and total nitrogen in the bottom sediments were higher in the PM and CD treatments compared to LF (P<0.05). Average counts of heterotrophic bacteria in the water of PM and CD ponds were significantly higher than other treatments (P<0.05). The development of Aeromonas sp. and Pseudomonas sp. were significantly higher (P<0.05) in the PM and CD treatments. Weight gain of koi carp stocked in LF was significantly higher (P<0.05) than that of fish in the other treatments. There was a significant difference in the survival rate of koi carp among the treatments ranging from 67.21% in C to 90.11% in LF. The results suggest that raising koi carp larvae in ponds and feeding them exogenously with zooplankton would support high rates of survival and production through maintenance of better water quality and greater abundance of zooplankton in the system. Significantly lower abundance of Aeromonas sp. and Pseudomonas sp. in the LF treatment considerably lowered any possibility of occurrence of bacterial disease.

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ZOOLOGICAL RESEARCH    2012, 33 (5): 426-546.   DOI:
Abstract ( 568 )   PDF (4456KB) (5074)
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ZOOLOGICAL RESEARCH Volume 35, Issues 4, 18 July 2014 CONTENTS
Zoological Research    2014, 35 (4): 249-352.   DOI:
Abstract ( 193 )   PDF (30995KB) (4733)
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New Year Address of Zoological Research
Wai-Yee Chan, Yong-Gang Yao
ZOOLOGICAL RESEARCH    2017, 38 (1): 1-1.   DOI: 10.13918/j.issn.2095-8137.2017.001
Abstract ( 172 )   PDF (131KB) (4580)
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Zoological Research    2013, 34 (6): 531-701.   DOI:
Abstract ( 446 )   PDF (7256KB) (4570)
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ZOOLOGICAL RESEARCH Volume 35, Issues 1, 18 January 2014
Zoological Research    2014, 35 (1): 1-80.   DOI:
Abstract ( 455 )   PDF (28488KB) (4408)
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Experimental infection of tree shrews(Tupaia belangeri) with Coxsackie virus A16
Jian-Ping LI, Yun LIAO, Ying ZHANG, Jing-Jing WANG, Li-Chun WANG, Kai FENG, Qi-Han LI, Long-Ding LIU
ZOOLOGICAL RESEARCH    2014, 35 (6): 485-491.   DOI: 10.13918/j.issn.2095-8137.2014.6.485
Abstract ( 507 )   HTML   PDF (28150KB) (4306)

Coxsackie virus A16 (CA16) is commonly recognized as one of the main human pathogens of hand-foot-mouth disease (HFMD). The clinical manifestations of HFMD include vesicles of hand, foot and mouth in young children and severe inflammatory CNS lesions. In this study, experimentally CA16 infected tree shrews(Tupaia belangeri) were used to investigate CA16 pathogenesis. The results showed that both the body temperature and the percentages of blood neutrophilic granulocytes / monocytes of CA16 infected tree shrews increased at 4-7 days post infection. Dynamic distributions of CA16 in different tissues and stools were found at different infection stages. Moreover, the pathological changes in CNS and other organs were also observed. These findings indicate that tree shrews can be used as a viable animal model to study CA16 infection.

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《Zoological Research 》vol.33,no.2,2012 PDF
ZOOLOGICAL RESEARCH    2012, 33 (2): 118-240.   DOI:
Abstract ( 648 )   PDF (13246KB) (4157)
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ZOOLOGICAL RESEARCH Volume 35, Issues 3, 18 May 2014
Zoological Research    2014, 35 (3): 161-248.   DOI:
Abstract ( 287 )   PDF (12810KB) (3979)
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Zoological Research    2013, 34 (4): 251-436.   DOI:
Abstract ( 598 )   PDF (15391KB) (3878)
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Bird Diversity and Seasonality in Urban Parks of Guangzhou
LI Hui,HONG Yong-mi,ZOU Fa-sheng,ZHANG Qiang,HUANG Jun-hui
ZOOLOGICAL RESEARCH    2008, 29 (2): 203-211.   DOI: 10.3724/SP.J.1141.2008.02203
Abstract ( 2987 )   PDF (538KB) (3849)

Bird diversity was surveyed in five urban parks of Guangzhou from January 1999 to April 2000, and from July 2006 to June 2007, using a transect line method. A total of sixty-four bird species were recorded. Japanese White-eye (Zosterops japonica), Chinese Bulbul (Pycnonotus sinensis), and Black-crowned Night Heron (Nycticorax nyctinorax) were dominant species. Residents, winter visitors and summer visitors accounted for 64.1%, 26.6% and 7.8% of recorded bird species, respectively. The greatest number of species was recorded in September (31), the least was recorded in July (20) and November (20). The mean encounter rates of birds was 65±;5 ind./h (±SE), with the highest in March (98±29 ind./h) and lowest in January (35±11 ind./h). There was fluctuation, but it did not differ significantly between months (F 11,48=1.35, P= 0.226). There were a greater number of migratory species in April, September and December. Encounter rates of migratory birds significantly differed between months (F 11,48=3.098,P=0.003). Bird richness differed among the five parks and significantly and positively correlated with the park area (R=0.905, P=0.035), with S=11.02 A0.28 (S:bird species richness, A:park area). This meant that a greater number of bird species occurred in larger parks. Parks with an area of about 65 hm2 were better for avian diversity conservation and land use in Guangzhou.

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Zoological Research    2011, 32 (2): 114-242.   DOI:
Abstract ( 583 )   PDF (33894KB) (3842)
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Expression of Human Semenogelin I-52 and Antibacterial Activity Investigation of Recombinant Peptide
ZHAO Hui,LIU Xiao-dong,GAO Zhen-hua,ZHANG Jian-hua,LI Hong,ZHANG Yun,LEE
ZOOLOGICAL RESEARCH    2008, 29 (2): 139-144.   DOI: 10.3724/SP.J.1141.2008.02139
Abstract ( 2778 )   PDF (422KB) (3814)

Nucleotide sequence coding for SgI-52 with amino acid residues of 85-136 form mature human semenogelin I was amplified by PCR technique from the cDNA of a human seminal vesicle. The obtained PCR products were inserted into vector pMAL-p2X. The constructed expression vector of pMAL-p2X/SgI-52 was transformed into Escherichia coli DH5α. Fusion protein was expressed in the periplasma of the E. coli DH5αafter IPTG inducement. Recombinant SgI-52 was purified after factor X cleavage and a ultrafiltering process. MALDI-TOF- MS results indicated that the purified recombinant SgI-52 was the target peptide. Recombinant SgI-52 showed antibacterial activities on E. coli ATCC 25922 and E. coli ML-35P with MIC values of 32.45 and 46.30 &#61549;μg/mL, respectively. Our results and other relevant works suggested that different human semenogelin I degradation fragments during the liquefaction might have various biological functions and deserve to be investigated further.

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Expression of the Ghrelin in Sheep Ooctyes and Pre-implantation Embryos Produced in vivo
DU Chen-guang,YANG Yan-yan,LI Hai-jun,BAO Qing-jiang
ZOOLOGICAL RESEARCH    2008, 29 (2): 134-138.   DOI: 10.3724/SP.J.1141.2008.02134
Abstract ( 2922 )   PDF (386KB) (3701)

The possibility of ghrelin expressed in sheep oocytes and pre-implantation embryos produced in vivo was investigated in this study. The observed ghrelin immunoreactivity of oocytes and embryos at all stages was predominantly in the cytoplasm. Relative real-time reverse-transciptase (RT)-PCR experiments confirmed that the ghrelin mRNA levels varied depending on the developmental stage, with the highest expression in the blastocyst, metaphase II (MII) oocytes, 2- and 8-cell stages had a significantly higher expression in the germinal vesicle (GV) oocytes, 4-stage and morula. Dynamic changes and the persistent presence of the ghrelin signaling system within oocytes and pre-implantation embryos opens up the possibility of a potential regulatory role of this novel molecule during oocyte maturation and embryonic development.

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Zoological Research    2013, 34 (5): 437-530.   DOI:
Abstract ( 456 )   PDF (4055KB) (3664)
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Systematics of Perca Species Based on Multivariate Morphometrics and Mitochondrial Cytochrome b Gene Variation Analysis
HAI Sa,LI Jia-le,FENG Jian-bin,Mulati
ZOOLOGICAL RESEARCH    2008, 29 (2): 113-120.   DOI: 10.3724/SP.J.1141.2008.02113
Abstract ( 2102 )   PDF (659KB) (3617)

This paper investigated the classification of the genus Perca based on the 32 multivariate morphometrics and the 1 134 bp sequences of mitochondrial cytochrome b (Cyt b) gene. The result of multivariate morphometric analyses showed that the distance between P. fluviatilis and P. schrenki, between P. schrenki and P. flavescens, between P. fluviatilis and P. flavescens was 0.15, 0.14, 0.09, respectively. Perca fluviatilis and P. flavescens were much more similar in morphology, and there was a remarkable difference between P. schrenki and the two other species. In the scatter-plot figure based on principal components 1 to 2, there was an overlapping section between P. fluviatilis and P. flavescens, but there was no overlapping section between P. schrenki and the two others. In the analysis of mitochondrial cytchrome b gene, the percentage nucleotide sequence divergence between P. fluviatilis and P. schrenki, between P. schrenki and P. flavescens, between P. fluviatilis and P. flavescens was 13.08%, 10.68%, 11.47% respectively. The sequence divergences among the three Perca species were within interspecific divergence. Molecular phylogenetic trees were constructed based on the sequences of 20 samples with maximum parsimony (MP), neighbor-joining (NJ) and Maximum likelihood methods. The topological structures of the three trees were consistent, and they all showed that the relationship between the P. schrenki and P. flavescens was much closer than that between P. fluviatilis and P. flavescens. From the genetic divergence of the Cyt b gene and the isolation in geographic distribution, we further concluded that P. fluviatilis and P. flavescens were different species. The genus Perca therefore, includes three species, P. fluviatilis, P.schrenki and P. flavescens.

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Detecting Natural Selection at the DNA Level
ZOOLOGICAL RESEARCH    2004, 25 (1): 73-80.   DOI:
Abstract ( 1804 )   PDF (359KB) (3588)
In the 1960s,the neutral theory proposed by Kimura caused an unprecedented challenge to the classical Darwin s theory of natural selection.However,recent advances in evolutionary genetics have provided a great deal of evidence on the role played by natural selection at the DNA level.These progresses have been stemmed from the appearance of enormous DNA sequence data of populations and genomes as well as the development of theoretical population genetics.There are mainly two kinds of approaches to detect selection at the DNA level:intraspecific polymorphism tests and interspecific divergence tests.The former one is represented by Tajima s (1989) D test while the latter one is based on the principle that the intraspecific polymorphism should be consistent with the interspecific divergence under neutrality.These methods are usually called "neutrality tests" because the neutrality hypothesis is taken as the null hypothesis in the tests.They are important tools not only in solving the basic theoretical questions in evolutionary biology but also in interpreting data and results obtained in the studies of human genetics and bioinformatics.In this paper,we shall review the progresses in detecting natural selection at the DNA sequence level and introduce the basis and application of several widely used tests.
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Humanized SCID Mouse:A Small Animal Model for HIV Research
ZHANG Gao-hong,CHEN Ya-li,TANG Hong,ZHENG Yong-tang
ZOOLOGICAL RESEARCH    2004, 25 (4): 356-362.   DOI:
Abstract ( 1957 )   PDF (344KB) (3523)
A limitation in advancing the study of HIV-1 is the lack of a suitable small animal model system that allows for HIV-1 infection to be monitored.A mouse model of AIDS would be very useful because of it practicality and the ready availability of knowledge,reagents and immunogenetics.SCID-hu (Thy/Liv) mouse model,in which human fetal thymus and liver tissue are co-implanted into severe combined immunodeficient mice and resulting in a functional human hematopoietic organ (Thy/Liv),recapitulates the effects of HIV-1 infection in the human thymus.SCID-hu (Thy/Liv) mice are attractive and well-established small animal models for the study of HIV-1 infection in vivo.The humanized SCID mouse model would be served as valuable tools for in vivo studying pathogenesis of HIV,analysis of candidate anti-HIV drugs and vaccines prior to their clinical evaluation in human.
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Genetic Variation and Diversity of Phrynocephalus vlangalii hongyuanensis in Zoige Wetland Inferred from ND4-tRNAleu Gene
LIU Li,GUO Xian-guang,WANG Yue-zhao
ZOOLOGICAL RESEARCH    2008, 29 (2): 121-126.   DOI: 10.3724/SP.J.1141.2008.04353
Abstract ( 2767 )   PDF (281KB) (3512)

According to the distribution of Phrynocephalus vlangalii hongyuanensis in Zoige Wetland,three geographic units: Zoige Xiaman (XM),Hongyuan (HY),both in Sichuan Province and Maqu (MQ) in Gansu Province were defined. We used molecular methods to reveal these unit’s genetic variation and diversity. A 785bp fragment of the mtDNA ND4-tRNAleu was determined from 72 samp1es in seven populations of P. vlangalii hongyuanensis. Seven variable nucleotide sites and nine haplotypes were identified in the 785bp fragments. As a whole,the haplotype diversity was high (0.806±0.024),but the nucleotide diversity was low (0.00231±0.00016). In a single population,MQa,MQb and XMb had very low genetic diversities,and XMc had a much higher one. The Kimura 2-parameter distances among all the populations were small (0.001-0.005),and the distance between MQa and XMa was the greatest. Analysis of molecular variance (AMOVA) showed that the three units were distinctly different (P<0.01),and 62.61% of the total genetic diversity was attributable to variation among units. There were 3 haplotypes shared among XM and HY,and no geographic clustering was observed except MQ from the TCS network. The results from the mismatch distribution analysis and Fu’s Fs test (Fs=-2.21937) implied that there might be a recent population expansion in the XM unit,and this may be the reason why XM had a high haplotype diversity but a low nucleotide diversity. We estimate that the MQ and XMb have lower diversities because of some very recent geographic events,such as the formation of the Yellow river’s upriver and the Zoige Wetland. Although they are distinctly different,not enough time has passed for them to have diverged a great genetic distance.

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Review of mtDNA in molecular evolution studies
CHEN Xing, SHEN Yong-Yi, ZHANG Ya-Ping
ZOOLOGICAL RESEARCH    2012, 33 (6): 566-573.   DOI: 10.3724/SP.J.1141.2012.06566
Abstract ( 1482 )   PDF (368KB) (3509)

Mitochondria are old organelles found in most eukaryotic cells. Due to its rapid mutation ratio, mitochondrial DNA (mtDNA) has been widely used as a DNA marker in molecular studies and has long been suggested to undergo neutral evolution or purifying selection. Mitochondria produces 95% of the adenosine triphosphate (ATP) needed for locomotion, and heat for thermoregulation. Recent studies had found that mitochondria play critical roles in energy metabolism, and proved that functional constraints acting on mitochondria, due to energy metabolism and/or thermoregulation, influence the evolution of mtDNA. This review summarizes mitochondrial genome composition, evolution, and its applications in molecular evolution studies (reconstruction of species phylogenesis, the relationship between biological energy metabolism and mtDNA evolution, and the mtDNA codon reassignment influences the adaptation in different creatures).

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Phylogenetic Relationships of the Pentatomomorpha (Hemiptera: Heteroptera) Inferred from Nuclear 18S rDNA Sequences
LI Hong-mei,DENG Ri-qiang,WANG Xun-zhang ,*
ZOOLOGICAL RESEARCH    2006, 27 (3): 307-316.   DOI:
Abstract ( 2090 )   PDF (696KB) (3397)
Sequences from a region of the nuclear ribosomal 18S rDNA gene of approximately 1 912 base pairs (bp) were used to generate a molecular phylogeny for the Pentatomomorpha based on 53 species representing 21 putative families. Phylogenetic analyses using the most parsimony method (MP), maximum likelihood method (ML), and neighbor joining method (NJ) showed strong support that the Pentatomomorpha lineage is a monophyly and the superfamily Aradoidea is a sister group to the remainder of the Pentatomomorpha (Trichophora). The Trichophora could be divided into two clades: one clade consisted of the monophyletic superfamilies Pentatomoidea and Pyrrhocoroidea; the other was mainly the polyphyletic superfamilies Lygaeoidea, Coreoidea and Idiostoloidea. The superfamilies Lygaeoidea and Coreoidea were both polyphyletic. Within Lygaeoidea, Piesmatidae was sister to Berytidae. They formed a clade locating at the basal of the Trichophora and distantly related to the other two families Lygaeidae and Rhyparochromidae. This research suggested that 18S rDNA was a proper marker to reconstruct the phylogeny of Pentatomomorpha that was accordant to morphological studies and the research of Li et al (2005). The Pyrrhocoroidea was further divided from the Coreoidea (s.lat). It was suggested that the Piesmatidae might be assigned as a superfamily of Pentatomomorpha rather than a family in Lygaeoidea.
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Comparison of Mitochondrial Control Region Sequences Between Chelydridae and Platysternidae
YAN Liang,ZHANG Yan,WANG Ning,ZHANG Li,NIE Liu-wang
ZOOLOGICAL RESEARCH    2008, 29 (2): 127-133.   DOI: 10.3724/SP.J.1141.2008.02127
Abstract ( 2514 )   PDF (622KB) (3287)

The sequences of mitochondrial control region (CR) of Macroclemys temminckii, Chelydra serpentina and Platysternon megacephalum were obtained using PCR and sequencing techniques, with gene-specific primers, based on the CR and its flanking sequences from other species. The CR lengths of the three species were 1089 bp, 1124 bp and 1119 bp respectively, and the base composition of A+T were 68.97%, 69.34% and 69.44% respectively. One fragment of (TA)20 microsatellite was found in M. temminckii; one fragment of (TATAT) 13 direct tandem repeats followed by (TA)15 microsatellites were found in C.serpentina; and one fragment of (AGTATGTTAT)4 direct tandem repeats followed by (GTTGTTATATAACATAT) 13 repeats were found in P. megacephalum. The distribution of mtDNA microsatellites in tortoises was discussed based on the CR sequences of the three species and other six tortoises published in GenBank. The result suggested that all the nine tortoises have microsatellites, and there are obvious differences both at the site and the sequences.

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The Validity of Red Knobby Newt (Tylototriton shanjing) Species Status Based on Mitochondrial Cyt b Gene
ZHANG Ming-wang,RAO Ding-qi,*,YU Guo-hua,YANG Jun-xing,*
ZOOLOGICAL RESEARCH    2007, 28 (4): 430-436.   DOI:
Abstract ( 2971 )   PDF (499KB) (3286)

The delimitation between Tylototriton shanjing and T. verrucosus was not clear. Forty individuals of T. verrucosus and T. shanjing were collected from fourteen localities in Southwest China and 753?bp of partial mitochondrial Cyt b gene sequence were sequenced. Molecular phylogenetic trees of T. verrucosus group were reconstructed using neighbor-joining, maximum parsimony and Bayesian inference methods. Pairwise sequence comparisons to determine the amount of variation were performed using MEGA 3.0 software. According to the results of phylogeny analysis and Kimura 2-parameter distance, the species validities were evaluated. The results showed that: (1) the T. shanjing did not form a monophyletic group; (2) the genetic distance was low between T. shanjing and T. verrucosus, it was only 1.2% on average. Therefore, T. shanjing as a valid species is not supported and can be argued to be a synonym of T. verrucosus. According to our phylogenetic tree, the genetic divergences and geographic distribution, T. verrucosus' distribution in the Yunnan Province can be divided into three geographic groups, i.e. the Pianma group, the Middle and West Yunnan group and the Southeast Yunnan group.

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Review of Satellite Tracking in Bird Migratory Studies
WU He-qi,YANG Xiao-jun,YANG Jun-xing
ZOOLOGICAL RESEARCH    2008, 29 (3): 346-352.   DOI: 10.3724/SP.J.1141.2008.03346
Abstract ( 1864 )   PDF (241KB) (3268)
Satellite tracking, based on the Argos satellite system, has been used in the studies of migratory birds since the 1980’s, and ornithologists have learned a lot using this method. But it is not widely used by Chinese ornithologists. We satellite-tracked several wintering Black-necked Cranes in Yunnan Province, in the winter of 2004, to confirm their migratory routes. We were also able to review the utility, advantage and development of this technology. Recent research has focused on discovering migratory routes and important stopover sites, finding new breeding and wintering areas, evaluating habitat quality and habitat use and discussing migration strategies. We hope this review might promote migratory studies and conservation of birds in China.
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