Community assembly has long been an important issue in community ecology. The study of community phylogenetic structure, which applies phylogeny to community ecology studies, has provided an effective way to disentangle the most important ecological processes that drive community assembly. Studying the phylogenetic structure of a community involves firstly the construction of a supertree representing the species pool of the community, then a calculation of phylogenetic distances between all species within the community, and finally an inference of phylogenetic structure (e.g., clustering, overdispersion) obtained by statistically testing whether the obtained phylogenetic distances are different from those expected under random model, hence revealing key ecological processes involved in community assembly (e.g., habitat filtering, competition exclusion). Community phylogenetic structure is different when studied at different taxonomic, spatial or temporal scales. At small spatial scales, community phylogenetic pattern tends to change from clustering to overdispersion with decreasing taxonomical scale or increasing tree age class, while the pattern tends to be tighter clustering at larger spatial scales. Phylogenetic information also indicates the influence of environmental factors and studying community phylogeny at the metacommunity level helps to understand regional ecological processes. In addition, phylogenetic structure can help to explore neutral theory, density-dependent hypothesis and other theories in ecology, and even to predict community dynamics and evolution under disturbance. The future application of phylogenetic structure to disclosing underlying causes of community assembly demands the joint analysis of ecological traits and environment factors and, the consideration of both local processes (e.g., microenviroment, biological interactions) and regional processes (e.g., geological history, speciation). In terms of methodological aspects, to construct a phylogenetic tree, appropriate gene segments should be used and the tree needs to be corrected using ecological traits in order to reflect more exact phylogenetic distances among species. Furthermore, more effective statistical models and indices are needed to increase statistical power.

There is a dynamic interplay between ecology and evolution within community ecology. Phylogenetic community ecology describes the intraspecific and interspecific relationships within a community, aiming to reveal the processes driving community assembly at multiple scales. Previous research has highlighted the role of phylogenetic and historical biogeographical data in explaining current patterns of global biodiversity. The success of using DNA barcoding in the construction of tropical forest community phylogenies highlights the usefulness and challenges of long-term research on community ecology and phylogenetics based on forest dynamic plots. In this paper, we illustrate the feasibility of a synthesis between community ecology and evolutionary biology in order to resolve particular ecological issues on community phylogenetic structure, community niche structure, biogeography, and trait evolution. We summarize progress on the development of a plant DNA barcoding system, and introduce the usage of a combination of DNA markers (rbcL+matK+trnH-psbA) for fast species discrimination and community phylogenetic reconstruction. We also explore the utilization of well-resolved phylogenies to understand community ecology. We discuss the limitations of core plant DNA barcodes (rbcL+matK) when identifying congeners, and propose an improved sequencing strategy suitable for studies at the community level. We expect that plant DNA barcodes will prove very useful for the study of species diversity, mechanisms of biodiversity maintenance, phylogenetic beta diversity and functional trait evolution.

The principle of maximum entropy (MaxEnt) was originally studied in information theory and statistical mechanics, and was widely employed in a variety of contexts. MaxEnt provides a statistical inference of unknown distributions on the basis of partial knowledge without taking into any unknown information. Recently there has been growing interest in the use of MaxEnt in ecology. In this review, to provide an intuitive understanding of this principle, we firstly employ an example of dice throwing to demonstrate the underlying basis of MaxEnt, and list the steps one should take when applying this principle. Then we focus on its applications in some fields of ecology and biodiversity, including the predicting of species relative abundances using community aggregated traits (CATs), the MaxEnt niche model of biogeography based on environmental factors, the studying of macroecology patterns such as species abundance distribution (SAD) and species-area relationship (SAR), inferences of species interactions using species abundance matrix or merely occurrence (presence/absence) data, and the predicting of food web degree distributions. We also highlight the main debates about these applications and some recent tests of these models' strengths and limitations. We conclude with the discussion of some matters of attention ecologists should keep in mind when using MaxEnt.

Because birds are important indicators of biodiversity, and useful for Ecological Impact Assessment (EcIA), scientists have monitored the abundance, richness and distribution of bird species for >100 years throughout the world. In this paper, we reviewed the history and status of land bird monitoring, particularly some well-known long-term monitoring programs such as the Breeding Bird Survey (BBS) in the UK, and the Breeding Bird Survey (BBS) and Christmas Bird Count (CBC) in North America. We also evaluated the status of large-scale bird monitoring programs in China, and propose a monitoring program called the Chinese Breeding Bird Survey (Chinese BBS) based on methodology of BBS in the UK. We suggest the following: (1) the Chinese BBS could initially be administered by relevant government departments with support from academia, with responsibility gradually transitioned to non-government organizations to implement the monitoring scheme and organize professionals, amateurs and volunteers to conduct field surveys; (2) survey squares could be randomly selected after stratification by volunteer density, and surveyed for birds using line and point transect surveys; (3) the results of all bird surveys should be recorded using a standard data format and could be edited and submitted via the Internet through a system named the Chinese BBS information sharing platform; (4) relevant governmental departments and academic organizations should actively promote the development of local bird watching societies, and implement the Chinese BBS with support from volunteer surveyors.

Among the candidate DNA barcoding loci suggested for land plants, only rbcL and trnH-psbA are available for barcoding bryophytes. However, both loci have limitations in discriminating among species. The present study evaluated the feasibility of using the cpDNA rps4 locus as an additional marker to complement other candidate barcodes for bryophytes. We analyzed 3,365 rps4 sequences retrieved from GenBank using pair-wise distance and phylogenetic methods. Our results demonstrated the universality of rps4 in bryophytes; the locus covers 96% of moss families and 88% of liverwort families. The rps4 locus resolved 73.0% of the species we tested. The discriminatory ability of rps4 is better than that of rbcL-a in each of the six bryophyte genera (i.e. Plagiochila, Tortula, Plagiomnium, Pyrrhobryum, Pogonatum, Grimmia) most commonly represented in the database. Moreover, large numbers of rps4 sequences from individuals of known bryophyte identities have been compiled in GenBank, thereby providing a reference for species identification. Therefore, we propose rps4 as an additional barcode, especially when rbcL and trnH-psbA do not perform well in certain bryophyte taxa.

The “3E” principle has been used to determine priorities for preservation of genetic resources in conservation and research projects. The three “E”s refer to Endangered, Endemic, and Economic. Here, we applied this principle to explore wild gymnosperm genetic resources (or germplasm resources) at the species (varieties) level occurring in Yunnan, and to determine their priority for preservation, research and management. There are 107 species and varieties of gymnosperms in Yunnan belonging to 10 families and 29 genera. Among them, 72 species were attributed to “3E” genetic resources. According to the “3E” principle, 9 species were defined as “highest priority” and should be urgently collected and preserved, i.e. Cephalotaxus lanceolata, Cycas revoluta, Podocarpus forrestii, Cycas debaoensis, Juniperus baimashanensis, Pinus squamata, Cycas hongheensis, Juniperus chengii, and Pinus wangii. Forty species were classified as “priority” for collection and preservation, e.g. Abies ferreana, Picea brachytyla, Abies nukiangensis, Cycas tonkinensis, etc. There are a multitude of in situ and ex situ conservation and cultivation methods that can help to conserve these genetic resources. Finally, we discussed the contents and merits of the “3E” principle, and concluded that the principle is a scientific and rational way in which to evaluate the genetic resources contained within this group of gymnosperms. The principle can be adopted in efforts for the collection, conservation and sustainable use of genetic resources.

Secondary birch (Betula spp.) forest is an important vegetation type in western Sichuan, China. These forests have naturally regenerated from primary fir (Abies spp.) forests after clear-cutting. However, little is known about ground bryophyte species composition and community structure during this succession sequence. In our study, we sampled three plots in 9-, 22-, and 42-year old secondary forests, and a primary fir forest, respectively, in Jinchuan County. We found that bryophyte coverage in different aged secondary forests was similar, but communities in the individual forests differed in dominant species composition. Compared with the primary forest, the secondary forests had lower coverage but higher species richness. As for the secondary forests, 9- and 22-year old forests had higher species richness than the 42-year old forest. Similarity coefficients among secondary forests ranged between 0.24-0.50. In contrast, 22- and 42-year old secondary forests exhibited lower similarity coefficients when compared with the primary forest. There were 25 bryophyte species shared by the primary forest and secondary forests, accounting for 71% of the species occurring in the primary fir forest. Our results indicated that naturally regenerated birch forests can harbor more bryophyte species than the spruce plantation. However, there was about 29% bryophyte species failed to recover in the natural recovery process.

The wild fruit-tree forest on the north slope of the Ili Valley is a living testament to the vegetative history of the Tianshan region. It is a type of broad-leaved forest appearing in the desert region. However, little is known about interspecific relationships among the major woody species or their process of succession. In 2009, we sampled 10 typical communities and investigated the abundance, height and coverage of woody plants as well as the topographical and soil conditions within each quadrat (20 m×20 m quadrats for trees, 10 m×10 m for shrubs). Interspecific associations were analyzed using continuity corrected χ² test, Pearson correlation and Spearman rank correlation. DCCA (detrended canonical correspondence analysis) was used to identify topographical and soil factors that affected woody plant distributions. The network diagram based on Pearson’s and Spearman’s rank correlation coefficients displayed interspecific relationships clearly. There were negative associations among overall tree or shrub species, indicating a strong independent relationship between species. However, correlation coefficients of most species pairs were insignificant, a fact that may be related to the community’s developmental stage (the early succession stage) and the species’ ecological traits. Positive correlations among the abundance of dominant species were likely due to similar ecological tolerances. This assertion is also supported by our analyses of woody plant distributions and environmental factors. DCCA analysis showed that elevation was the most dominant factor affecting the plant distribution, followed by aspect, soil moisture, organic matter, total nitrogen.

Understanding the distribution of suitable habitat of target species and their relationship with environment are critical to formulating effective protective measures. The Qinling Mountains contain important habitat for Ursus thibetanus. A predictive habitat distribution map of this species was estimated using the Maximum Entropy (MAXENT) model with a total of 68 recorded points of known bear occurrence and 34 environmental factors. The distribution of potential habitat and its relationship with major environmental factors were analyzed and a gap analysis was carried out in light of existing nature reserves. Habitat corridor networks were also planned using resistance surface and least-cost analysis. Results showed that human interference and landuse type were the main factors influencing habitat choice of U. thibetanus. Three variables including residential density, distance to grassland and distance to cultivated land had the greatest effect on habitat selection, with a contribution of 21.4%, 17.5% and 15.9% respectively, followed by the distance to broad-leaf forest and distance to water. Estimated suitable habitat for U. thibetanus was distributed mainly in the middle and western portions of the Qinling Mountains and occupied 19.23% of the Mountains’ total area. Gap analysis showed that approximately 23.49% of the bear’s predicted suitable habitat was protected within the nature reserves, but that 8,480 km² of suitable habitat was outside these reserves. In order to protect U. thibetanus and its habitat more effectively, suggestions for the construction of 12 habitat corridors and a systematic conservation planning process integrating other species’ needs were proposed.

Mites form one of the most important and complex communities of arthropods in tea plantations. We examined the responses of mite communities in terms of species composition, structure and diversity in tea plantations subjected to two types of intercropping. Samples were collected between March 2006 and April 2008 from tea canopies using both knock-down and pruning methods, and from ground litter in four different treatments in tea plantations in the Wuyi Mountains. Results from both canopy and litter samples showed that tea plantations intercropped with Paspalum notatum or Cassia rotundifolia had significantly higher species richness (S), effective diversity index (e^H′), number of individuals (N), and absolute abundance ($\bar{n}$) of predatory mites than in control tea plantations with natural vegetation. Plantations intercropped with P. notatum or C. rotundifolia displayed a significantly higher number of individuals (N) of Anystis baccarum, a common predatory species, for both canopy and litter samples versus the tea plantation with natural ground cover and on bare ground. Species richness, number of individuals, and diversity indices of both phytophagous and saprophagous mite communities collected from tea canopies and of saprophagous mite communities in litter were not different among the various intercropping treatments. Seasonal dynamics in mite species richness (S) and number of individuals (N) were apparent for all treatments. Czekanowski similarity indices suggested that these communities were highly similar to each other. For the tea plantation intercropped with P. notatum or C. rotundifolia, or with natural ground cover, the total number of mites in tea canopies was positively associated with the total number of mites in the litter. We suggest that diversifying tea agroecosystems by using intercrops can bolster predatory mite densities, thus providing a viable strategy for pest management and promoting the environmentally benign production of tea products.

To evaluate the potential role of an urban wetland park in conserving biodiversity during urbanization, we studied ground beetle (Carabidae) diversity using pitfall traps in five vegetation types, i.e., poplar, cypress, mixed forest, barberry scrub, and reed beds, within a newly-built urban wetland park, Cuihu Wetland Park in Beijing, for three years. A total of 441 individuals representing 30 species and 18 genera of carabid beetles were captured. Carabid species richness and abundance both sharply increased with park age. For each of the five vegetation types, approximately 25% of their carabid species (3-4 species) were unique and were not detected in other types. Poplar forest exhibited the highest abundance and richness of carabid species and showed the strongest increasing trend through time. Our results suggested a significant role of urban wetland parks in the conservation of carabid beetle diversity in the process of urbanization. In order to maximize their conservation value, they should be revegetated by a diversity of plants while using poplars as pioneers.

To better understand the role that fertilization systems play in soil fertility buildup and evolution, we employed denaturing gradient gel electrophoresis (DGGE) and restriction fragment length polymorphism (RFLP) to determine the influence of different fertilization treatments on archaeal community structure in calcareous purplish paddy soil under rice/wheat rotations. The eight fertilization treatments were as follows: manure only (M), nitrogen plus manure (NM), nitrogen and phosphorus plus manure (NPM), nitrogen, phosphorus and potassium plus manure (NPKM), without fertilization (CK), mineral nitrogen (N), nitrogen-phosphorus (NP) and nitrogen, and phosphorus and potassium (NPK). Our results showed that long-term fertilization significantly affected soil archaeal community structure; the richness and diversity of archaeal community under NM, NP and NPKM were lower than those under the other fertilization treatments (M, NPM, CK, N, and NPK). Based on the DGGE patterns, two soil DNA samples isolated from the NPK-amended soil were used for RFLP analysis of archaea. Phylogenetic analyses showed that archaea in the calcareous purplish paddy soil was highly diverse, and the sequences were closely related to those archaeal sequences isolated from various soils and water environment. Cluster analysis of the DGGE profiles showed that archaeal communities under the eight fertilization treatments clustered into three groups. In soil from paddies currently under rice cultivation, the archaeal communities in the soil amended with M and NPK grouped into the first cluster, while NP was in the second group, and NPKM, NM, CK, N and NPM were in the third. In the soil with wheat cultivation, NP-treated archaeal communities clustered into a cluster, NPKM and M were in the second cluster, and N, NPK, NM, NPM and CK soil communities comprised the third cluster. The cluster analysis showed that crop type impacts the community structure of soil archaea.

Salix psammophila is an excellent sand-fixation plant that can not only thrive in arid desert environment, but also can fix sand and promote desert management by maintaining the balance and stability of desert ecosystems. To understand the species diversity and ecological distribution of AM fungi associated with S. psammophila, we collected soil samples (0-50 cm deep) from the rhizosphere of S. psammophila at three different sites (Heichengzi, Zhenglanqi and Yuanshangdu) in Inner Mongolia in May, August and October 2009. A total of 37 AM fungal species belonging to four genera were isolated. Of these, 23 species belong to Glomus, 10 to Acaulospora, 3 to Scutellospora, and 1 to Gigaspora. Glomus reticulatum was the dominant species at all three sites, Scutellospora was found only in Heichengzi and Zhenglanqi, and Gigaspora decipiens only in Zhenglanqi. Generally, species richness, evenness, Shannon diversity and Simpson diversity indices showed the following trend across sites: Zhenglanqi > Heichengzi > Yuanshangdu. Species diversity of AM fungi in Yuanshangdu was significantly lower than that at the other sites. Species richness and Shannon diversity index of AM fungi were higher in August and October than in May. Species richness, evenness, and diversity indices first increased and then decreased with increasing levels of soil available N. Our results suggest that the subtle complexities present in the symbiotic relationship between S. psammophila and AM fungi in desert ecosystems.