Phylogenetic structure and formation mechanism of shrub communities in arid and semiarid areas of the Mongolian Plateau

The mechanisms of species coexistence within a community have always been the focus in ecological research. Community phylogenetic structure reflects the relationship of historical processes, regional environments, and interactions between species, and studying it is imperative to understand the formation and maintenance mechanisms of community composition and biodiversity. We studied the phylogenetic structure of the shrub communities in arid and semiarid areas of the Mongolian Plateau. First, the phylogenetic signals of four plant traits (height, canopy, leaf length, and leaf width) of shrubs and subshrubs were measured to determine the phylogenetic conservation of these traits. Then, the net relatedness index (NRI) of shrub communities was calculated to characterize their phylogenetic structure. Finally, the relationship between the NRI and current climate and paleoclimate (since the Last Glacial Maximum, LGM) factors was analyzed to understand the formation and maintenance mechanisms of these plant communities. We found that desert shrub communities showed a trend toward phylogenetic overdispersion; that is, limiting similarity was predominant in arid and semiarid areas of the Mongolian Plateau despite the phylogenetic structure and formation mechanisms differing across habitats. The typical desert and sandy shrub communities showed a significant phylogenetic overdispersion, while the steppified desert shrub communities showed a weak phylogenetic clustering. It was found that mean winter temperature (i.e., in the driest quarter) was the major factor limiting steppified desert shrub phylogeny distribution. Both cold and drought (despite having opposite consequences) differentiated the typical desert to steppified desert shrub communities. The increase in temperature since the LGM is conducive to the invasion of shrub plants into steppe grassland, and this process may be intensified by global warming

Spanning Trees and bootstrap reliability estimation in correlation based networks

We introduce a new technique to associate a spanning tree to the average linkage cluster analysis. We term this tree as the Average Linkage Minimum Spanning Tree. We also introduce a technique to associate a value of reliability to links of correlation based graphs by using bootstrap replicas of data. Both techniques are applied to the portfolio of the 300 most capitalized stocks traded at New York Stock Exchange during the time period 2001-2003. We show that the Average Linkage Minimum Spanning Tree recognizes economic sectors and sub-sectors as communities in the network slightly better than the Minimum Spanning Tree does. We also show that the average reliability of links in the Minimum Spanning Tree is slightly greater than the average reliability of links in the Average Linkage Minimum Spanning Tree.Comment: 17 pages, 3 figure

DM-PhyClus: A Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

Background. Conventional phylogenetic clustering approaches rely on arbitrary cutpoints applied a posteriori to phylogenetic estimates. Although in practice, Bayesian and bootstrap-based clustering tend to lead to similar estimates, they often produce conflicting measures of confidence in clusters. The current study proposes a new Bayesian phylogenetic clustering algorithm, which we refer to as DM-PhyClus, that identifies sets of sequences resulting from quick transmission chains, thus yielding easily-interpretable clusters, without using any ad hoc distance or confidence requirement. Results. Simulations reveal that DM-PhyClus can outperform conventional clustering methods, as well as the Gap procedure, a pure distance-based algorithm, in terms of mean cluster recovery. We apply DM-PhyClus to a sample of real HIV-1 sequences, producing a set of clusters whose inference is in line with the conclusions of a previous thorough analysis. Conclusions. DM-PhyClus, by eliminating the need for cutpoints and producing sensible inference for cluster configurations, can facilitate transmission cluster detection. Future efforts to reduce incidence of infectious diseases, like HIV-1, will need reliable estimates of transmission clusters. It follows that algorithms like DM-PhyClus could serve to better inform public health strategies

Phylogenetic mixtures: Concentration of measure in the large-tree limit

The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories, often make it necessary to model molecular data as originating from a mixture of phylogenies. Such mixed models play an increasingly important role in practice. Using concentration of measure techniques, we show that mixtures of large trees are typically identifiable. We also derive sequence-length requirements for high-probability reconstruction.Comment: Published in at http://dx.doi.org/10.1214/11-AAP837 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

Dissecting the genome-wide evolution and function of R2R3-MYB transcription factor family in Rosa chinensis

Rosa chinensis, an important ancestor species of Rosa hybrida, the most popular ornamental plant species worldwide, produces flowers with diverse colors and fragrances. The R2R3-MYB transcription factor family controls a wide variety of plant-specific metabolic processes, especially phenylpropanoid metabolism. Despite their importance for the ornamental value of flowers, the evolution of R2R3-MYB genes in plants has not been comprehensively characterized. In this study, 121 predicted R2R3-MYB gene sequences were identified in the rose genome. Additionally, a phylogenomic synteny network (synnet) was applied for the R2R3-MYB gene families in 35 complete plant genomes. We also analyzed the R2R3-MYB genes regarding their genomic locations, Ka/Ks ratio, encoded conserved motifs, and spatiotemporal expression. Our results indicated that R2R3-MYBs have multiple synteny clusters. The RcMYB114a gene was included in the Rosaceae-specific Cluster 54, with independent evolutionary patterns. On the basis of these results and an analysis of RcMYB114a-overexpressing tobacco leaf samples, we predicted that RcMYB114a functions in the phenylpropanoid pathway. We clarified the relationship between R2R3-MYB gene evolution and function from a new perspective. Our study data may be relevant for elucidating the regulation of floral metabolism in roses at the transcript level

Macroecology of methane-oxidizing bacteria: the β-diversity of pmoA genotypes in tropical and subtropical rice paddies

Studies addressing microbial biogeography have increased during the past decade, but research on microbial distribution patterns is still in its infancies, and many aspects are only poorly understood. Here, we compared the methanotroph community in paddy soils sampled in Indonesia, Vietnam, China and Italy, focusing on the distance-decay relationship. We used the pmoA gene as marker for methanotroph diversity in terminal restriction fragment length polymorphism, microarray and pyrosequencing approaches. We could observe a significant increase of -diversity with geographical distance across continents (12000km). Measured environmental parameters explained only a small amount of data variation, and we found no evidence for dispersal limitation. Thus, we propose historical contingencies being responsible for the observed patterns. Furthermore, we performed an in-depth analysis of type II methanotroph pmoA distribution at the sequence level. We used ordination analysis to project sequence dissimilarities into a three-dimensional space (multidimensional scaling). The ordination suggests that type II methanotrophs in paddy fields can be divided into five major groups. However, these groups were found to be distributed in all soils independent of the geographic origin. By including tropical field sites (Indonesia and Vietnam) into the analysis, we further observed the first paddy fields harbouring a methanotroph community depleted in type II methanotrophs