Grain-filling, an important trait that contributes greatly to grain weight, is regulated by quantitative trait loci and is associated with crop domestication syndrome. However, the genes and underlying molecular mechanisms controlling crop grain-filling remain elusive. Here we report the isolation and functional analysis of the rice GIF1 (GRAIN INCOMPLETE FILLING 1) gene that encodes a cell-wall invertase required for carbon partitioning during early grain-filling. The cultivated GIF1 gene shows a restricted expression pattern during grain-filling compared to the wild rice allele, probably a result of accumulated mutations in the gene's regulatory sequence through domestication. Fine mapping with introgression lines revealed that the wild rice GIF1 is responsible for grain weight reduction. Ectopic expression of the cultivated GIF1 gene with the 35S or rice Waxy promoter resulted in smaller grains, whereas overexpression of GIF1 driven by its native promoter increased grain production. These findings, together with the domestication signature that we identified by comparing nucleotide diversity of the GIF1 loci between cultivated and wild rice, strongly suggest that GIF1 is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement.

Increasing evidence has emerged for non-random spatial distributions of microbes, but knowledge of the processes that cause variation in microbial assemblage among ecosystems is lacking. For instance, some studies showed that deterministic processes such as habitat specialization are important, while other studies hold that bacterial communities are assembled by stochastic forces. Here we examine the relative influence of deterministic and stochastic processes for bacterial communities from subsurface environments, stream biofilm, lake water, lake sediment and soil using pyrosequencing of the 16S ribosomal RNA gene. We show that there is a general pattern in phylogenetic signal in species ecological niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among-habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within-habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups. For three sample groups, spatial distance reflected unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial Mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat associations that have likely emerged through evolutionary adaptation.

Aim: The number of studies investigating the nestedness and turnover components of beta diversity has increased substantially, but our general understanding of the drivers of turnover and nestedness remains elusive. Here, we examined the effects of species traits, spatial extent, latitude and ecosystem type on the nestedness and turnover components of beta diversity. Location: Global.Time period: 1968-2017.Major taxa studied: From bacteria to mammals. Methods:From the 99 studies that partition total beta diversity into its turnover and nestedness components, we assembled 269 and 259 data points for the pairwise and multiple site betadiversity metrics, respectively. Our data covered a broad variation in species dispersal type, body size and trophic position. The data were from freshwater, marine and terrestrial realms, and encompassed geographical areas from the tropics to near polar regions. We used linear modelling as a meta-regression tool to analyse the data.Results: Pairwise turnover, multiple site turnover and total beta diversity all decreased significantly with latitude. In contrast, multiple site nestedness showed a positive relationship with latitude. Beta-diversity components did not generally differ among the realms. The turnover component and total beta diversity increased with spatial extent, whereas nestedness was scale invariant for pairwise metrics. Multiple site beta-diversity components did not vary with spatial extent. Surprisingly, passively dispersed organisms had lower turnover and total beta diversity than flying organisms. Body size showed a relatively weak relationship with beta diversity but had important interactions with trophic position, thus also affecting beta diversity via interactive effects. Producers had significantly higher average pairwise turnover and total beta diversity than carnivores. Main conclusions:The present results provide evidence that species turnover, being consistently the larger component of total beta diversity, and nestedness are related to the latitude of the study area and intrinsic organismal features. We showed that two beta-diversity components had generally opposing patterns with regard to latitude. We highlight that beta-diversity partition may give additional insights into the underlying causes of spatial variability in biotic communities compared with total beta diversity alone. K E Y W O R D Sbiodiversity, body size, dispersal, global, macroecology, meta-analysis, nestedness, turnover 96 |

Accurate climate projections require an understanding of the effects of warming on ecological communities and the underlying mechanisms that drive them 1-3 . However, little is known about the effects of climate warming on the succession of microbial communities 4,5 . Here we examined the temporal succession of soil microbes in a long-term climate change experiment at a tall-grass prairie ecosystem. Experimental warming was found to significantly alter the community structure of bacteria and fungi. By determining the time-decay relationships and the paired differences of microbial communities under warming and ambient conditions, experimental warming was shown to lead to increasingly divergent succession of the soil microbial communities, with possibly higher impacts on fungi than bacteria. Variation partition-and null model-based analyses indicate that stochastic processes played larger roles than deterministic ones in explaining microbial community taxonomic and phylogenetic compositions. However, in warmed soils, the relative importance of stochastic processes decreased over time, indicating a potential deterministic environmental filtering elicited by warming. Although successional trajectories of microbial communities are difficult to predict under future climate change scenarios, their composition and structure are projected to be less variable due to warming-driven selection.

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Climate effects and human impacts, that is, nutrient enrichment, simultaneously drive spatial biodiversity patterns. However, there is little consensus about their independent effects on biodiversity. Here we manipulate nutrient enrichment in aquatic microcosms in subtropical and subarctic regions (China and Norway, respectively) to show clear segregation of bacterial species along temperature gradients, and decreasing alpha and gamma diversity toward higher nutrients. The temperature dependence of species richness is greatest at extreme nutrient levels, whereas the nutrient dependence of species richness is strongest at intermediate temperatures. For species turnover rates, temperature effects are strongest at intermediate and two extreme ends of nutrient gradients in subtropical and subarctic regions, respectively. Species turnover rates caused by nutrients do not increase toward higher temperatures. These findings illustrate direct effects of temperature and nutrients on biodiversity, and indirect effects via primary productivity, thus providing insights into how nutrient enrichment could alter biodiversity under future climate scenarios.

DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and evaluate the applicability of using the COI gene for the identification of fish at the species level. A total of 284 mitochondrial COI barcode sequences were obtained from 85 genera, 38 families and 12 orders of fishes. The mean length of the sequences was 655 base pairs. The average Kimura two parameter (K2P) distances within species, genera, families, orders and classes were 0.21%, 6.50%, 23.70% and 25.60%, respectively. The mean interspecific distance was 31-fold higher than the mean intraspecific distance. The K2P neighbor-joining trees based on the sequence generally clustered species in accordance with their taxonomic classifications. High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species.

Although elevational gradients in microbial biodiversity have attracted increasing attention recently, the generality in the patterns and underlying mechanisms are still poorly resolved. Further, previous studies focused mostly on species richness, while left understudied evenness, another important aspect of biodiversity. Here, we studied the elevational patterns in species richness and evenness of stream biofilm bacteria and diatoms in six mountains in Asia and Europe. We also reviewed published results for elevational richness patterns for soil and stream microbes in a literature analysis. Our results revealed that even within the same ecosystem type (that is, stream) or geographical region, bacteria and diatoms showed contrasting patterns in diversity. Stream microbes, including present stream data, tend to show significantly increasing or decreasing elevational patterns in richness, contrasting the findings for soil microbes that typically showed nonsignificant or significantly decreasing patterns. In all six mountains for bacteria and in four mountains for diatoms, species richness and evenness were positively correlated. The variation in bacteria and diatom richness and evenness were substantially explained by anthropogenic driven factors, such as total phosphorus (TP). However, diatom richness and evenness were also related to different main drivers as richness was mostly related to pH, while evenness was most explained by TP. Our results highlight the lack of consistent elevational biodiversity patterns of microbes and further indicate that the two facets of biodiversity may respond differently to environmental gradients.