MADS-box genes encode a family of transcription factors. In angiosperms, MADS-box genes play key roles in vegetative growth and reproductive development, and are indispensable for the formation of inflorescences, flowers and fruits. To understand the evolution of MADS-box genes on a relatively small time scale, we conducted comparative genomic studies of a pair of closely related plant species, Arabidopsis thaliana and A. lyrata. A total of 106 and 115 MADS-box genes were identified from the two species, respectively, and phylogenetic analyses suggested that these genes correspond to Types I and II MADS-box genes. Type I genes have been duplicated and lost extensively in the lineages leading to the two species, whereas the number of Type II genes has not changed very much during the same period. Comparisons of the locations of orthologous gene pairs not only detected chromosomal regions that showed clear microsynteny between the two genomes, but also found evidence that most newly gained genes were generated through tandem and dispersed duplications rather than segmental duplication. Molecular evolutionary studies further suggested that different clades of MADS-box genes have experienced significantly different patterns of evolution, with functional constraints being less stringent for Type I genes than for Type II genes. Our results will help better understand the genetic differences between closely related species, and stimulate additional studies on the mechanisms that underlie speciation and biodiversification.

Gene introgression usually results from spontaneous hybridization among closely related exotic and native species, and thus can significantly impact the genetic structure of native species, especially on endangered species. It is believed that no interspecies reproductive barriers exist within Liriodendronspp. The endangered status of Liriodendron chinense in China is compounded by the potential risk of interspecific introgressive hybridization resulting from the frequent introduction ofL. tulipiferaand by the extensive planting of hybrid Liriodendron within the past decade. Here, we report a possible trend of interspecific introgressive hybridization in the genus Liriodendron. We sampled five mixture plantations with L. chinense, L. tulipifera, and hybrid Liriodendron from southeastern China. In each plantation, 19-130 adults and 60-117 naturally regenerated seedlings or open-pollinated progeny were sampled. The mating pattern of Liriodendron was examined using parentage analysis based on 11 EST-SSR loci, and the extent of introgressive hybridization was estimated in terms of an introgression coefficient derived from parentage-offspring regression coefficients of allele frequencies. We found evidence of interspecific introgressive hybridization in all five plantations of Liriodendron, although the orientation and extent of gene introgression differed among plantations. Furthermore, for any species, we found that the extent of gene introgression was positively related to its population size. Herein, we present conservation strategies for Liriodendron chinense in the context of our results.

Spatial autocorrelation analyses have highlighted the importance of clonal growth in shaping the spatial genetic structure in Eremosparton songoricum, a woody rhizomatic clonal shrub distributed in drift sand dunes of the Gurbantunggut Desert of China. Spatial patterns of genetic variation in five populations of E. songoricum found in different community types and habitats were investigated using Inter Simple Sequence Repeat (ISSR) markers. Using GeneAlEx Genetic Analysis Software and the computer program of SAAP 4.3 and the polymorphic bands generated from eight ISSR primers, we calculated an autocorrelation coefficient with a frequency between 0.3 and 0.7. Equal geographic distance was considered when estimating spatial genetic distribution patterns. In this paper, populations B (located in hinterland desert), D (located in hinterland desert) and F (located in east of desert) occurred as a cline pattern, in which individual plants within distances of 7 m, 7 m and 9 m had significant positive correlation, respectively. Our results suggested that the natural properties of clonal reproduction were the main factors influencing the spatial distribution patterns of these three populations. Population G (located in north of desert) occurred as double cline pattern, in which individual plants within 3 m had significant positive correlation, respectively. Seed recruitment was successful in population G, while restricted seed and pollen dispersal, and intervention of human activities were main factors influencing the spatial genetic structure. Population A (located in hinterland desert) exhibited depression pattern. The small size of population A would increase the likelihood of self-fertilization (inbreeding) by pollination among ramets of the same genets, and would induce random genetic drift. Knowledge of spatial genetic structures within populations is crucial for understanding evolutionary processes and ecological adaptations, and provides a baseline for the conservation and management of E. songoricum, especially for ex situ conservation sampling strategies.

In order to study the genetic variation of salinity related cotton germplasm, 47 upland cotton accessions including 23 salinity tolerant materials and 24 salinity sensitive materials were explored using 88 simple sequence repeat (SSR) markers. We detected a total of 338 alleles at 88 SSR loci with an average of 3.841 alleles per locus, 333 of these alleles were detected in salinity tolerant germplasm and 312 alleles in salinity sensitive germplasm. Mean polymorphism information content (PIC), the average effective numbers of alleles (Ne) and the average genotype diversity index (H′) were 0.613, 2.929 and 1.083 in salinity tolerant germplasm, and 0.605, 2.883 and 1.071 in salinity sensitive germplasm, respectively. The similarity coefficients were similar between salinity tolerant germplasm and salinity sensitive germplasm. They varied from 0.530 to 0.979 in salinity tolerant germplasm, with a wider range than in salinity tolerant germplasm (from 0.525 to 0.878). The varieties were clustered into one major group and two small groups. The high genetic similarity coefficients we observed in Chinese salinity tolerant germplasm indicated narrow pedigrees within the group. Our results are useful for assessing cotton pedigrees, improving cotton hybrids, and ultimately allowing for the improved utilization of salinity tolerant germplasm.

We studied the genetic variation and differentiation of five wild populations of Macrobrachium hainanense using SRAP markers. Samples were collected from Oujiang River (OJ), Minjiang River (MJ), Pearl River (PR), Wanquan River (WQ) and Changhuajiang River (CH). A total of 255 loci were detected, of which 47.05% were polymorphic. Proportion of polymorphic loci of the five populations ranked in the order: PR (43.92%) = WQ (43.92%) < MJ (46.67%) < CH (47.45%) < OJ (53.33%), while heterozygosity ranked as PR (0.1657) < WQ (0. 1763) < CH (0. 179) < OJ (0. 1839) < MJ (0. 1892), with an average of 0.1790. Shannon index ranked as PR (0.2543) < WQ (0.2658) < CH (0.2746) < MJ (0.2846) < OJ (0.2876), with an average of 0.2734. Analysis of molecular variation (AMOVA) revealed that 17.64% of the variance was among populations, which significantly affected the total variance ( P <0.001). Values of G_st, N_m and genetic distance suggested the genetic divergence among populations was relatively high (P < 0.001).

Using all available taxonomic data, we updated the master list of macrobenthos for the Yellow Sea, analyzed its taxonomic diversities and 95% probability funnels. There have been 1,360 species, belonging to 17 phyla, 35 classes, 91 orders, 368 families and 842 genera of macrobenthos recorded in the Yellow Sea. The value of average taxonomic distinctness for the region was 93.7, and the variation in taxonomic distinctness was 213.6. To explore the efficacy of these two diversity measures for environmental assessment, we superimposed estimates of these two values for some moderately polluted sites in Jiaozhou Bay on the 95% probability funnels, and all of the stations fell significantly below the 95% probability funnel of average taxonomic distinctness. This result shows the good application foregound of taxonomic diversity in marine pollution monitoring.

In order to understand the biological diversity and the stability of intertidal communities in Meizhou Bay, and to conduct assessement on the environmental quality, we investigated the benthic diversity in Meizhou Bay, Fujian Province in November 2005 and April 2006. A total of 225 species of intertidal benthos from shore wetlands in Meizhou Bay was reported. Polychaetes, Molluscs and Crustaceans accounted for 88% of all species. The number of benthic species differed between transects and was greater in spring than autumn. Average biomass and density were 22.91 g/m² and 388 inds./m², respectively. In terms of biomass, Molluscs exhibited the highest and Crustaceans the second, and in terms of density Polychaetes showed highest, followed by Molluscs. Biomass of middle tidal zones was higher than that of high or low tidal zones. Density of benthic invertebrates among tidal zones, ranked from highest to lowest, was as follows: low tidal zone, middle tidal zone, and high tidal zone. Both biomass and density were lowest in the high tidal zone. Both biomass and density were higher in spring than in autumn. Using the ABC (abundance biomass comparison) curve to analyze the structure of the intertidal community in Meizhou Bay, it was found that the overall disturbance is not apparent. The results suggest that this area retains some of its environmental carrying capacity.

The Chishui River is an important part of the Rare and Endemic Fishes Nature Reserve in the upper reaches of the Yangtze River. We surveyed the Chishui River between April and October of 2007 to assess the current status of fish assemblages it contains. We sampled 51 sites in the river basin and identified a total of 119 species belonging to 5 orders, 16 families and 75 genera. Among them, 25 species were new records for the Chishui River basin and 34 species were endemic to the upper reaches of the Yangtze River. Sinocrossocheilus labiatus was present only in the Chishui River. There were 36, 61 and 100 fish species found in the upper, middle and lower reaches of the river, respectively. Zacco platypus, Spinibarbus sinensis,Pelteobagrus nitidus, Hemiculter tchangi andSaurogobio dabryi were the main commercially-important species captured of the Chishui River, but the components of fishery catches varied significantly among reaches. We offer recommendations for the protection of the diminishing fish resources of the Chishui River.

To explore the status of fish assemblage characteristics and historical changes, investigations on fish assemblage were carried out in the mainstream of the Yellow River in spring (May-June) and autumn (September-November) of 2008. A total of 54 fish species were collected, belonging to 13 families and 7 orders, among which 4 species were endemic to the river basin. Cypriniformes were dominant, accounting for 68.5% of the total species captured. Fish assemblages in the upper section were relative simple, while those in the middle and lower sections were much more complex. Species richness increased from upper to lower sections. The ecological guilds of fishes in the Yellow River showed great variety in migration, feeding, spawning and inhabit. Although the catch composition was different from section to section, the dominant groups were all small fishes, including Pelteobagrusspp., Silurus asotus,Carassius auratus, Gobioninae and so on and fishes showed miniaturization significantly. Compared with historical data, fish abundance and diversity in our samples were dramatically lower and the loss of endemic species was severe. Over exploitation of water resources, construction of hydraulic engineering infrastructure, water pollution and the unreasonable utilization of resource are potential underlying reasons for observed shifts in the fish assemblages.

Arbuscular mycorrhizal (AM) fungi can improve vigor and reduce susceptibility of hosts challenged by root pathogens. Salvia miltiorrhiza, native to China and Japan, is highly valued for its roots in traditional Chinese medicine. To elucidate species composition and diversity of AM fungi associated withS.miltiorrhiza, we collected soil samples from the rhizosphere of S. miltiorrhiza in Shatou, Zhongzhijidi, Qicun, and Qizhou in Anguo City of Hebei Province in August 2008 and 2009. A total of 24 AM fungal species belonging to four genera were isolated, of which 16 belonged to Glomus, 5 belonged to Acaulospora, 2 were Scutellosporaunique to Qizhou, and 1 belonged to Entrophospora only found in Shatou. Glomuswas the dominant genus with a frequency of 100% occurrence and a relative abundance of 76.4% in the four sites. Glomus aggregatum was the dominant species. Maximum spore density was 77.55 degrees per soil sample and maximum colonization rate was 72.72%. In Zhongzhijidi spore density and species richness decreased with soil available P and N, organic matter and increasing pH. We found a significant difference in AM fungal composition between Zhongzhijidi and other sites. Shannon-Wiener indices at the four sites listed in descending order were: Qicun, Qizhou, Shatou and Zhongzhijidi. Our results provide some of the first descriptions of the abundant AM fungal species associated withS. miltiorrhiza.

Endophytic bacteria can directly stimulate plant growth in several ways, including production of plant hormones such as indole-3-acetic acid (IAA). We investigated the diversity of IAA-producing endophytic bacteria in the roots of Cymbidium goeringii using culture-dependent approaches. A total of 57 IAA-producing strains were obtained from 256 strains isolated from the interior roots of C. goeringii. Based on amplified ribosomal DNA restriction analyses (ARDRA) and 16S rDNA sequences, these 57 strains were divided into 25 groups. The IAA-producing endophytic bacteria were grouped into six phyla, i.e., Alphaproteobacteria (35.1%), Firmicutes (33.3%), Gammaproteobacteria (14.0%), Betaproteobacteria (8.8%), Actinobacteria (7.0%) and Bacteroidetes (1.8%). The dominant groups were Alphaproteobacteria and Firmicutes, and the dominant genus, Paenibacillus, produced relatively high levels of IAA. In addition, four potential novel taxonomic units were found. Our results revealed diverse and abundant communities of IAA-producing endophytic bacteria in the roots of C. goeringii and highlight the microbial resources represented by plant growth-promoting bacteria.

To quantitatively characterize leaf trait variation and the manner that plants adapt to extremely dry climates, we measured four leaf functional traits, i.e., leaf mass per area (LMA), mass- and area-based leaf nitrogen concentration (N_mass, N_area) and leaf dry matter content (LDMC) for 110 plant species in Xinjiang Junggar Basin, NW China. Plant family, plant functional group and climatic factors (plant water availability: α; mean temperature of the warmest month: MTWA) were used as the dependent variables to explain the species-level variation in LDMC, LMA, N _mass, and N_area. The plot-level leaf trait values were related to α and MTWA via stepwise regression. Our results indicated that: (1) the species-level leaf trait variations are to large extent determined by plant family, while the influence of functional group and climatic factor tends to be the second; (2) At the plot-level, LMA increases as the climate becomes drier, while N _mass is positively related to the simultaneous optimization of α and MTWA, i.e., N _masstends to be higher in warm-wet habitats than in cold-dry one. LDMC and N_mass are less relevant to the climatic gradient. Plants in the study area have demonstrated an overall adaptation to the extremely dry climate. However, due to the differences in phylogenic background, different species may take different strategies in the face of the same climatic gradient. It is therefore important to examine the relative importance of plant phylogenic background and the environments on plant trait variation, which may matter for our prediction of plant response to the environmental changes in arid area.

Climbing plants (or climbers) are important components of vegetation. They are often overlooked in ecological research due to difficulties in field identification of species or clones. To explore the diversity of climbing plants in China, we report on their taxonomic composition, floristic element types and climbing methods. A total of 3,073 spermatophyte species belonging to 85 families and 409 genera are climbers, accounting for 11.3% of the spermatophyte flora of China, including 898 vines (3.3%) and 2,175 lianas (8.0%). Tropical floristic elements are common in China, including 87.9% and 79.2% of families and genera containing climber, respectively. Fourteen genera containing climbers are endemic to China. In terms of climbing methods, 56.7% are twining, 22.1% are sprawling, 17.0% are tendrillar and 4.2% are adhesive.

The present study was conducted in subtropical humid forests of Meghalaya to study the distributional pattern of species, floristic composition, community structure and tree population structure. Forest fragments of varying sizes (0.5 ha, 1 ha, 2 ha and 5 ha) were used in the study. All of the forest fragments are distributed within the same altitudinal range, and had similar rainfall and temperature regimes. Four forest fragments were sampled using random quadrats to analyze the impact of fragment size on tree diversity and population structure. Indices were used to compare the dispersion pattern of plant species, species diversity among fragments, and the heterogeneity and homogeneity of the fragments. A total of 45 tree species were recorded from all the fragments and simple correlation showed that the species richness was positively related to fragment size (n = 4, P<0.05). Other measures such as stand density, basal cover, diversity and dominance indices were unrelated to fragment size. Forest canopy was composed mainly ofCastonopsis indica,C. armata,Schima khasiana andEngelhardtia spicata in all of the fragments. A majority of woody tree species were contagiously distributed which made the forest community highly patchy in nature. Low values of Sorensen’s similarity index and high values of Whittaker’s β-diversity index between the fragments suggest marked difference in the species composition among the fragments. The maximum stand density, basal area, Shannon diversity index and Simpson dominance index was recorded in a 5-ha fragment. Trees in lower girth classes (15-55 cm circumference at breast height, CBH) accounted for 52-86% of stand density in all fragments except in 0.5-ha fragments where middle girth class (55-95 cm CBH) accounted for 47% of the total stand density. The overall density of seedlings, saplings and adult trees formed a pyramidal structure, indicating that the period between the sapling and adult stage was a critical stage in tree life cycles, as the maximum mortality occurred during this period. These groves are mildly/highly disturbed by communities using forests for their timber and fuel wood requirements as well as cattle and goat grazing. Tree regeneration was apparently not limited, as was evidenced by high density of saplings. These human activities may have been responsible for a decrease in tree diversity in the smaller fragments. Large fragments that were less disturbed harbored species not present in small fragments.