Genetic diversity in Isoetes yunguiensis, a rare and endangered endemic fern in China

Isoetes yunguiensis is an endangered and endemic fern in China. Field survey indicated that only one population and no more than 50 individuals occur in the wild. The genetic variation of 46 individuals from the population remaining at Pingba (Guizhou Province, China) was assessed by Random Amplified Polymorphic DNA (RAPD) finger-printing. Twelve primers were screened from sixty ten-bp arbitrary primers, and a total of 95 DNA fragments were scored. Of these, 62.1% were polymorphic loci, which indicated that high level genetic variation existed in the natural population. The accumulation of genetic variation in the history of the taxon and the apparent minimal reduction effect on genetic diversity following destruction of habitat might be responsible for the high level genetic diversity presently remaining in the I. yunguiensis population. However, with the continuing decrease of population size, the genetic diversity will gradually be lost. We suggest that the materials from the extant population should be used for re-establishment of the populations. Translated from Journal of Wuhan University (Natural Sciences Edition), 2005, 51(6): 767–770 [译自: 武汉大学学报 (理学版)]     

AFLP analysis of genetic diversity and relationship among some Chinese domestic ducks and wild ducks

The amplified fragment length polymorphic (AFLP) technique was used to analyze the genome DNA polymorphism among 8 breeds of domestic ducks and 2 species of wild ducks. Nine of the 17 selected primers pairs gave reproducible polymorphic DNA amplification bands. The amplified bands ranged from 44 to 83 per primer pair. Of the 513 AFLP markers obtained, 498 were polymorphic. The proportion of polymorphic loci was 97.1%. The genetic distance (D) and similarity coefficients (GS) were calculated based on the polymorphic data. Between domestic ducks D ranged from 0.331 to 0.589, while between domestic ducks and the wild ducks, it ranged from 0.298 to 0.520 (vs. Anas Platyrhynchos) and from 0.316 to 0.522 (vs. A. Poecilorhyncha), respectively. The variance analysis showed no significant difference between the two groups of data, which indicated that both mallard and spot-billed ducks made contributions to domestic duck evolution. A dendrogram was constructed according to the D value. __________ Translated from Journal of Xiamen University (Natural Science), 2005, 44(5): 729–733 [译自: 厦门大学学报 (自然科学版), 2005, 44(5): 729–733]     

Population genetic structure of wild and farmed rusa deer (<Emphasis Type="Italic">Cervus timorensis russa</Emphasis>) in New-Caledonia inferred from polymorphic microsatellite loci

Historical records indicate that 12 rusa deer (Cervus timorensis russa) were introduced in New-Caledonia during the 1870s. We used eight polymorphic microsatellite DNA loci to assess the genetic differentiation and diversity of farmed and wild deer populations. Past genetic bottlenecks were detected in both sub-populations, although higher genetic diversity was maintained in farmed populations, probably due to the regular introduction of reproducers from wild populations and from other farms. The genetic structure of farmed and wild populations differed significantly. There was a significant isolation by distance for wild populations, whereas farmed populations were significantly differentiated between farms independently from their geographical proximity. Wild rusa deer consisted of small populations (with effective population sizes ranging between 7 and 19 individuals depending on the methods used), with a low parent–offspring dispersion range (0.20–2.02 km). Genetic tools and direct observations provided congruent estimates of dispersion and population sizes. We discuss the relevance of our results for management purposes.     

Molecular genetic analysis of Dongzhou-period ancient human of Helingeer in Inner Mongolia, China

The mtDNA hypervariable region I (HVR-I) of 10 ancient individuals from Dongzhou-period ancient human populations in Helingeer county of Inner Mongolia were amplified and sequenced to investigate the genetic structure. The relationships between the ancient population and related extant populations, as well as its possible origin at the molecular level, were also studied. Moreover, phylogenetic analysis and multidimensional scaling analysis were also performed based on the mtDNA data of the ancient population in Helingeer and the related Eurasian population. The results showed that the ancient population in Helingeer were closer to the northern Asian populations than to the other compared populations in matrilineal lineage. Combining the research results of archaeology and anthropology as well as molecular biology, we inferred that they were nomads who migrated from Mongolia plateau and cis-Baikal region to Helingeer in Inner Mongolia, China. __________ Translated from Journal of Jilin University (Science Edition), 2006, 44 (5): 824–828 [译自: 吉林大学学报(理学版)]     

Sampling strategy for wild soybean (Glycine soja) populations based on their genetic diversity and fine-scale spatial genetic structure

A total of 892 individuals sampled from a wild soybean population in a natural reserve near the Yellow River estuary located in Kenli of Shandong Province (China) were investigated.Seventeen SSR (simple sequence repeat) primer pairs from cultivated soybeans were used to estimate the genetic diversity of the population and its variation pattern versus changes of the sample size (sub-samples),in addition to investigating the fine-scale spatial genetic structure within the population.The results showed relatively high genetic diversity of the population with the mean value of allele number (A) being 2.88,expected heterozygosity (He) 0.431,Shannon diversity index (/) 0.699,and percentage of polymorphic loci (P) 100%.Sub-samples of different sizes (ten groups) were randomly drawn from the population and their genetic diversity was calculated by computer simulation.The regression model of the four diversity indexes with the change of sample sizes was computed.As a result,27-52 individuals can reach 95% of total genetic variability of the population.Spatial autocorrelation analysis revealed that the genetic patch size of this wild soybean population is about 18 m.The study provided a scientific basis for the sampling strategy of wild soybean populations.     

Biological characteristics of wild Cycas fairylakea population in Guangdong Province, China

There are five wild populations of Cycas fairylakea in Guangdong Province, China, three of which are newly found. A study of the biological characteristics of C. fairylakea populations showed that this species had a narrow colonization area within 300 hm², and an island pattern of distribution. Because of the overexploitation, urbanization, environment pollution, plant diseases, and insect pests, the wild populations and individuals of C. fairylakea decreased markedly in the past decades. All five populations have an opposite pyramid age structure, few coning plants, few seed production, and low level of seed germination rate or sterility. In conclusion, C. fairylakea in Guangdong Province was threatened seriously and an urgent need to take effective efforts to protect the plants and habitats in its location sites was required. __________ Translated from Acta Scientiarum Naturalium Universitatis Sunyatseni, 2005, 44(6): 97–100 [译自: 中山大学学报 (自然科学版), 2006, 44(6): 97–100]     

A preliminary study on designing ecological corridors in Xishuangbanna National Nature Reserve with 3S techniques

This paper is based on the fieldwork in Xishuangbanna Natioanl Nature Reserve in Yunnan Province of China. GPS data of Asian elephants were collected and analyzed with the remote sensing satellite photos of the region to estimate the landform physiognomy of different colors. We also analyzed a series of ecological factors including altitude, landform, relief, villages and roads which affected the distribution and movement of Asian elephants. The results suggested the possibility of designing and establishing corridors in Xishuangbanna National Nature Reserve to protect the population of wild elephants in the region. __________ Translated from Journal of Beijing Normal University (Natural Science) 2006, 42(4): 405-C409 [译自: 北京师范大学学报 (自然科学版)]     

Differentiation of Indica-Japonica rice revealed by insertion/deletion (InDel) fragments obtained from the comparative genomic study of DNA sequences between 93-11 ( Indica ) and Nipponbare ( Japonica )

DNA polymorphisms from nucleotide insertion/deletions (InDels) in genomic sequences are the basis for developing InDel molecular markers. To validate the InDel primer pairs on the basis of the comparative genomic study on DNA sequences between an Indica rice 93-11 and a Japonica rice Nipponbare for identifying Indica and Japonica rice varieties and studying wild Oryza species, we studied 49 Indica, 43 Japonica, and 24 wild rice accessions collected from ten Asian countries using 45 InDel primer pairs. Results indicated that of the 45 InDel primer pairs, 41 can accurately identify Indica and Japonica rice varieties with a reliability of over 80%. The scatter plotting data of the principal component analysis (PCA) indicated that: (i) the InDel primer pairs can easily distinguish Indica from Japonica rice varieties, in addition to revealing their genetic differentiation; (ii) the AA-genome wild rice species showed a relatively close genetic relationship with the Indica rice varieties; and (iii) the non-AA genome wild rice species did not show evident differentiation into the Indica and Japonica types. It is concluded from the study that most of the InDel primer pairs obtained from DNA sequences of 93-11 and Nipponbare can be used for identifying Indica and Japonica rice varieties, and for studying genetic relationships of wild rice species, particularly in terms of the Indica-Japonica differentiation. Translated from Journal of Fudan University (Natural Science), 2006, 45(3): 309–315 [译自: 复旦学报(自然科学版)]     

Genetic differentiation of Arthrobacter population from heavy metal-contaminated environment

Six samples containing extremely high concentration of Pb, Zn, and Cd were obtained from the layers of 5–10 cm and 25–30 cm three tailing piles, with ages of about 10, 20 and more than 80 years, respectively. Then, 48 bacterial strains were obtained from these samples, and subsequently their phylogenetic positions were determined by analysis on the partial sequence of 16S rRNA gene (fragment length ranging from 474 to 708 bp). These isolates were members of the Arthrobacter genus, phylogenetically close to A. keyseri and A. ureafaciens, with sequence ranging from 99.1% to 100%. Furthermore, genetic variation between subpopulations from different samples was revealed by analysis on their randomly amplified polymorphic DNA profile. Nei genetic distance showed that the greatest differentiation occurred between subpopulation A and C. Notably, either genetic distance between subpopulations from the layers of 5–10 cm and 25–30 cm of each tailing pile or between same layers of different tailing pile increased with the history of tailings. Moreover, correlation analysis showed that soluble Pb has a significantly negative relationship with Nei’ gene diversity of subpopulation. It was assumed that soluble Pb may be responsible for the reduced genetic diversity of the Arthrobacter population. Our data provided evidence that genetic differentiation of microbial populations was consistent with the changes of environmental factors, particularly heavy metals. Translated from Acta Ecologica Sinica, 2005, 25(10): 2569–2573 [译自: 生态学报]     

Postglacial population expansion of Dacrydium pectinatum (Podocarpaceae) in Hainan, southem China, based on cpDNA trnL-F nocoding sequence data

This study determined the sequences of chloroplast DNA (cpDNA) trnL-F non-coding regions of individuals of a tropical coniferous species, Dacrydium pectinatum, collected from 12 natural populations located in Hainan Province, southern China. Sequence length varied from 868 bp to 876 bp, indicating length polymorphism. Base composition in the sequences was high in A+T content between 64.17% and 64.95%, and no recombination event occurred (Rm = 0). Thirty haplotypes were identified based on statistical parsimony algorithm by running the TCS program. Populations of D. pectinatum in Hainan were lacking genetic differentiation. Such a deduction was supported by the observed F _ST values (0.00), AMOVA (24.17% of molecular variance attributed to difference among populations, P>0.05), high values of Nm (ranging from 1.92 to 2.50) and the branching structure in neighbor-joining (NJ) tree constructed from haplotypes. A ‘star-like’ pattern was exhibited in the TCS network of trnL-F haplotypes, and majority of the haplotypes coalesced near the tips in NJ tree. Gene genealogies of cpDNA haplotypes proposed a recent population expansion of D. pectinatum in Hainan, which was further supported by the results from Tajima’s D test and mismatch distribution analysis. Our data, in conjunction with geological and palynological evidences, showed that in the Holocene, due to global warming, refugee populations of D. pectinatum in Hainan might experience a range expansion. __________ Translated from Acta Scientiarum Naturalium Universitatis Sunyatseni, 2005, 44(5): 70–74 [译自: 中山大学学报 (自然科学版), 2005, 44(5): 70–74]     

Proteomic approach for acute-phase proteins of hemolymph and muscles in Scylla serrata challenged by a pathogenic bacterium

Acute-phase response is documented to be a significant mechanism of innate immunity in vertebrates and invertebrates. In this study, proteomic methodologies were applied for different protein expressions in hemolymph of Scylla serrata challenged by Vibrio parahaemolyticus after immunization, and in muscles of the crabs separately challenged by V. parahaemolyticus, V. anguillarum and Aeromonas hydrophila. Up-regulated cryptocyanin is documented in the hemolymph and up-regulated calexcitin, wingless (fragment) and tachykinin-related peptide in the muscle as acute-phase proteins. All the four altered proteins were responsible for bacterial stress, but cryptocyanin seemed to be a memory response protein against the challenge by a live bacterium after immunization of the live cells. These up-regulated proteins can be indicative of an understanding of immunity of a crab. __________ Translated from Journal of Xiamen University (Natural Science), 2005, 44(4): 559–562, 44(Sup.): 191–194 [译自: 厦门大学学报(自然科学版), 2005, 44(4): 559–562, 44(增刊): 191–194]     

ISSR primer screening and preliminary evaluation of genetic diversity in wild populations of Gycyrrhiza uralensis

Fourteen efficient inter-simple sequence repeat (ISSR) primers were screened and optimized for detecting the genetic diversity in wild populations of Glycyrrhiza uralensis Fisch. By using these primers, 249 polymorphic bands out of a total of 270 (92.2 %) were generated from 70 individuals of 4 wild G. uralensis populations sampled from Inner Mongolia Province of China. Nei’s gene diversity (h) and Shannon index (I) calculated from the data matrix of the ISSR phenotypes revealed a high level of genetic diversity with h = 0.268 and I = 0.415 within this plant. Analysis of molecular variation (AMOVA) showed that most of the genetic variation (81 %) occurred within the populations, whereas the variance among populations was only 19 %. The UPGMA tree based on Nei’s unbiased genetic diversity illustrated that populations from Bulage and Bayanwusu were genetically close related, while the population from Shanghaimiao was found to be the most diverse from the other three. The high genetic diversity implies that the wild resources of this species could be restored soon if an appropriate and efficient protection strategy was employed. Our results also provided an optimized method for evaluating genetic diversity of G. uralensis using ISSR markers which was useful for further investigation.     

Analysis of nutrient components of food for Asian elephants in the wild and in captivity

Thirty-seven wild plants as food for Asian elephants in the field in Simao, Yunnan province, China and five cultivated plants as food for captive elephants in the Beijing Zoo were collected and analyzed for their main nutrient components. Protein, fat, fiber, dry material, ash as well as major microelements: calcium, kalium, zincum, sodium in the food were analyzed by standard methodology. No significant differences were found between the wild plants taken in the field and forage provided in captivity. However, the calcium content in the forage is significantly less than the average of those in the wild plants. It is suggested that the increase in calcium intake may contribute to the relief of low plasma calcium diseases of elephants in captivity. Translated from Journal of Beijing Normal University (Natural Science), 2006, 42(2): 184–188 [译自: 北京师范大学学报 (自然科学版)]     

Genetic assessment of captive elephant (Elephas maximus) populations in Thailand

The genetic diversity and population structure of 136 captive Thai elephants (Elephas maximus) with known region of origin were investigated by analysis of 14 highly polymorphic microsatellite loci. We did not detect significant indications of inbreeding and only a low differentiation of elephants from different regions. This is probably explained by the combined effects of isolation by distance and exchange between different regions or between captive and wild elephant populations. Estimates of effective population sizes were in the range of 90–240 individuals, which emphasizes the necessity to guard against inbreeding as caused by the current use of a restricted number of breeding bulls.     

The degree of parasitism of the bumblebee (Bombus terrestris) by cuckoo bumblebees (Bombus (Psithyrus) vestalis)

Host–parasite systems are characterised by coevolutionary arms races between host and parasite. Parasites are often the driving force, as they replicate much faster than their hosts and have shorter generation times and larger population sizes, resulting in higher mutation rates per time interval. This scenario does not fit all host–parasite systems. Socially parasitic cuckoo bumblebees (Bombus (Psithyrus) vestalis) parasitise colonies of Bombus terrestris share most life history characteristics with their hosts. As they parasitise only a subset of all available colonies, their population size should be lower than that of their hosts. This might have strong negative effects on the genetic diversity of B. vestalis and their adaptability. Here, we study for the first time the population structure of a Bombus/Bombus (Psithyrus) system. Highly polymorphic DNA markers were used to reconstruct sibships from individuals collected in the wild. The analysis of the host and parasite populations revealed a rate of parasitism of about 42% (range 33–50%). The population size of B. vestalis was lower compared to their hosts, which was also reflected in low within-group genetic distance. An analysis of the reconstructed queen genotypes revealed more supersisters amongst the B. vestalis queens when compared to the B. terrestris host. The data suggest that B. vestalis females and males do not disperse over long distances. This shows a potential for local adaptation to their hosts.     

Effects of intercropping with persimmon on the rhizosphere environment of tea

The rhizosphere environment of tea (Camellia sinensis Kuntze) intercropped with persimmon (Diospyros kaki) differs from monocultures of tea. A trial was conducted to determine the effects of intercropping with persimmon on root exudates and soil nutrient condition of tea. Amino acid exuded in intercropping was three times higher than that in monoculture. Phenol, phenol/amino acid ration, dissolved sugar, and total organic acid were also lower in intercropping. The value of pH in soil was higher, and soil nutrient condition of rhizosphere, especially available nutrient, was not as well in intercropping as that in tea grown alone. While soil nutrient of non-rhizosphere was better than that in monoculture, tea quality and soil nutrient condition were better in intercropping ecosystem. __________ Translated from Journal of Southwest China Normal University (Natural Science), 2005, 30(4): 715–718 [译自: 西南师范大学学报 (自然科学版), 2005, 30(4): 715–718]     

Role of magpie in bird community formation in secondary forest

We analyzed a bird community in a secondary forest and the results show that the magpie was one of the key groups in the secondary forest. The key group is identified based on the nests used by other birds at a rate of 25%–40.17%. The size of the community is different and the number of these key groups is not certain. __________ Translated from Journal of Northeast Normal University (Natural Science Edition), 2006, 38 (3): 644-651 [译自: 东北师大学报(自然科 学版)]     

Application of petG-trnP sequence to systematic study of Chinese Cupressus species

Chinese Cupressus L. includes five species. The molecular phylogenetic relationship of the Cupressus species and Chamaecyparis L. were determined by comparing 417–479 bp of chloroplast petG-trnP intergenic spacer sequence. In PAUP^* analysis, Platycladus orientalis was used as the functional out group. By using the maximum likelihood method 1 077 trees were examined and the result showed that one tree had a best score of -Ln=2 232.47. The phylogenetic tree clearly showed that Chamaecyparis nootkatensis was diverged from other Chamaecyparis species. Based on the results, together with evidences from other aspects, we consider that Cupressus funebris and Chamaecyparis nootkatensis should be placed in the genus Cupressus. The use of cpDNA intergenic spacer petG-trnP in Cupressus was also discussed. __________ Translated from Journal of Sichuan University (Natural Science Edition), 2005, 42(5): 1033–1037 [译自: 四川大学学报 (自然科学版) 2005, 42(5): 1033–1037]     

Wild genetic diversity preservation in a small-sized first generation breeding population of <Emphasis Type="Italic">Allanblackia floribunda</Emphasis> (Clusiaceae)

Founder group size is of prime importance in tree breeding programs. We determined whether sampling 20-plus trees for breeding in Allanblackia floribunda, a tropical forest tree species that has been recently enrolled in tree improvement program for fruit and seed production, would affect neutral genetic diversity and inbreeding level in both breeding and production populations. Using eight informative microsatellite loci, we: (a) assessed the nuclear genetic diversity of ten natural populations, and of the breeding population in the humid forest zone of Cameroon; (b) investigated temporal effective-size fluctuations in A. floribunda natural populations, with a view to identifying the role of past demographic events in the genetic structure of the studied species; and (c) tested the hypothesis that genetic diversity in a founder group of 20 individuals is not different from that existing in the wild. The eight loci were variable. High levels of genetic diversity (A = 4.96; H _E = 0.59) and moderate differentiation (R _ST = 0.061) were found within and among populations in wild stands. High genetic distances existed between populations ( \textaverage chord distance = 0.\text2769 ±0.00\text554 ) \left( {{\text{average chord distance}} = 0.{\text{2769}} \pm 0.00{\text{554}}} \right) . Eight of the ten surveyed populations showed signs of deviation from mutation-drift equilibrium, suggesting Pleistocene population bottlenecks and fluctuations in effective population size. Mantel tests did not reveal any relationships between genetic and geographic distances. A neighbor-joining dendrogram showed a population structure that could be explained by historical factors. The hypothesis tested has been accepted. However, a slight increase in inbreeding was observed in the breeding population.     

Analysis of sparteines in the seeds of Ammopiptanthus mongolica

Seven alkaloids were isolated from the seeds of Ammopiptanthus mongolica by thin layer chromatography and silica gel column chromatography, and the chemical structures of five alkaloids, 17-oxosparteine, β-isosparteine, 3α-hydroxysparteine, sparteine, and 3β-hydroxysparteine were identified by ¹H nuclear magnetic resonance (NMR) and electron ionization mass spectrum (EIMS). __________ Translated from Journal of Lanzhou University (Natural Sciences), 2007, 43(2): 43–46 [译自: 兰州大学学报(自然科学版)]