A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages

The aims of the work were (1) to develop statistical tests to identify whether substitution takes place under a covariotide model in sequences used for phylogenetic inference and (2) to determine the influence of covariotide substitution on phylogenetic trees inferred for photosynthetic and other organisms. (Covariotide and covarion models are ones in which sites that are variable in some parts of the underlying tree are invariable in others and vice versa.) Two tests were developed. The first was a contingency test, and the second was an inequality test comparing the expected number of variable sites in two groups with the observed number. Application of these tests to 16S rDNA and tufA sequences from a range of nonphotosynthetic prokaryotes and oxygenic photosynthetic prokaryotes and eukaryotes suggests the occurrence of a covariotide mechanism. The degree of support for partitioning of taxa in reconstructed trees involving these organisms was determined in the presence or absence of sites showing particular substitution patterns. This analysis showed that the support for splits between (1) photosynthetic eukaryotes and prokaryotes and (2) photosynthetic and nonphotosynthetic organisms could be accounted for by patterns arising from covariotide substitution. We show that the additional problem of compositional bias in sequence data needs to be considered in the context of patterns of covariotide/covarion substitution. We argue that while covariotide or covarion substitution may give rise to phylogenetically informative patterns in sequence data, this may not always be so.      

禾木科植物染色体消除型远缘杂交的研究进展

植物远缘杂交是作物育种中广泛应用的技术。除了核型稳定的种间杂交可以获得杂种以外,还可以利用核型不稳定的种间杂交后父本染色体消除的现象,通过胚培养和染色体加倍处理获得加倍单倍体(     

Soil respiration in a Mediterranean oak forest at different developmental stages after coppicing

To assess the variation of soil respiration at different forest stages we measured it in a coppiced oak (Quercus cerris L.) chronosequence in central Italy during two campaigns, spanning 2 successive years, in four stands at different stages of the rotation: 1 year (S1), 5 years (S5), 10 years (S10) and 17 years (S17) after coppicing. The contribution of the different components of soil respiration flux (aboveground litter, belowground decomposition soil organic matter and root respiration) was estimated by a paired comparison of manipulative experiments between the recently coppiced stand (S1) and mature stand (S17). Ninety percent of soil respiration values were between 1.7 and 7.8 μmol m^?2 s^?1, with an overall mean (±SD) of 4.0±2.7 μmol m^?2 s^?1. Spatial variation of soil respiration was high (CV=44.9%), with a mean range (i.e. patch size) of 4.8±2.7 m, as estimated from a semivariance analysis. In the absence of limitation by soil moisture, soil respiration was related to soil temperature with the exponential Q₁₀ model (average Q₁₀=2.25). During summer, soil moisture constrained soil respiration and masked its dependence on soil temperature. Soil respiration declined over the years after coppicing. Assuming a linear decline with stand age, we estimated a reduction of 24% over a 20‐year‐rotation cycle. The response of soil respiration to temperature also changed with age of the stands: the Q₁₀ was estimated to decrease from 2.90 in S1 to 2.42 in S17, suggesting that different components or processes may be involved at different developmental stages. The contribution of heterotrophic respiration to total soil respiration flux was relatively larger in the young S1 stand than in the mature S17 stand.     

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic

Metagenomic data sets were generated from samples collected along a coastal to open ocean transect between Southern California Bight and California Current waters during a seasonal upwelling event, providing an opportunity to examine the impact of episodic pulses of cold nutrient-rich water into surface ocean microbial communities. The data set consists of ∼5.8 million predicted proteins across seven sites, from three different size classes: 0.1–0.8, 0.8–3.0 and 3.0–200.0 μm. Taxonomic and metabolic analyses suggest that sequences from the 0.1–0.8 μm size class correlated with their position along the upwelling mosaic. However, taxonomic profiles of bacteria from the larger size classes (0.8–200 μm) were less constrained by habitat and characterized by an increase in Cyanobacteria, Bacteroidetes, Flavobacteria and double-stranded DNA viral sequences. Functional annotation of transmembrane proteins indicate that sites comprised of organisms with small genomes have an enrichment of transporters with substrate specificities for amino acids, iron and cadmium, whereas organisms with larger genomes have a higher percentage of transporters for ammonium and potassium. Eukaryotic-type glutamine synthetase (GS) II proteins were identified and taxonomically classified as viral, most closely related to the GSII in Mimivirus, suggesting that marine Mimivirus-like particles may have played a role in the transfer of GSII gene functions. Additionally, a Planctomycete bloom was sampled from one upwelling site providing a rare opportunity to assess the genomic composition of a marine Planctomycete population. The significant correlations observed between genomic properties, community structure and nutrient availability provide insights into habitat-driven dynamics among oligotrophic versus upwelled marine waters adjoining each other spatially.