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1.
New Phytol ; 241(3): 1088-1099, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37991013

ABSTRACT

Stoichiometric rules may explain the allometric scaling among biological traits and body size, a fundamental law of nature. However, testing the scaling of elemental stoichiometry and growth to size over the course of plant ontogeny is challenging. Here, we used a fast-growing bamboo species to examine how the concentrations and contents of carbon (C), nitrogen (N) and phosphorus (P), relative growth rate (G), and nutrient productivity scale with whole-plant mass (M) at the culm elongation and maturation stages. The whole-plant C content vs M and N content vs P content scaled isometrically, and the N or P content vs M scaled as a general 3/4 power function across both growth stages. The scaling exponents of G vs M and N (and P) productivity in newly grown mass vs M relationships across the whole growth stages decreased as a -1 power function. These findings reveal the previously undocumented generality of stoichiometric allometries over the course of plant ontogeny and provide new insights for understanding the origin of ubiquitous quarter-power scaling laws in the biosphere.


Subject(s)
Phosphorus , Plants , Plant Development , Body Size , Nitrogen
2.
Article in English | MEDLINE | ID: mdl-38777778

ABSTRACT

BACKGROUND: Aristolochic acid nephropathy (AAN) is a rapidly progressive interstitial nephropathy caused by Aristolochic acid (AA). AAN is associated with the development of nephropathy and urothelial carcinoma. It is estimated that more than 100 million people worldwide are at risk of developing AAN. However, the underlying mechanisms driving renal deterioration in AAN remain poorly understood, and the treatment options are limited. METHODS: We obtained GSE27168 and GSE136276 series matrix data from the Gene Expression Omnibus (GEO) related to AAN. Using the R Studio environment, we applied the limma package and WGCNA package to identify co-differently expressed genes (co-DEGs). By GO/KEGG/GSVA analysis, we revealed common biological pathways. Subsequently, co-DEGs were subjected to the String database to construct a protein-protein interaction (PPI) network. The MCC algorithms implemented in the Cytohubba plugin were employed to identify hub genes. The hub genes were cross-referenced with the transcription factor (TF) database to identify hub TFs. Immune infiltration analysis was performed to identify key immune cell groups by utilizing CIBERSORT. The expressions of AAN-associated hub TFs were verified in vivo and in vitro. Finally, siRNA intervention was performed on the two TFs to verify their regulatory effect in AAN. RESULTS: Our analysis identified 88 co-DEGs through the "limma" and "WGCNA" R packages. A PPI network comprising 53 nodes and 34 edges was constructed with a confidence level >0.4. ATF3 and c-JUN were identified as hub TFs potentially linked to AAN. Additionally, expressions of ATF3 and c-JUN positively correlated with monocytes, basophils, and vessels, and negatively correlated with eosinophils and endothelial cells. We observed a significant increase in protein and mRNA levels of these two hub TFs. Furthermore, it was found that siRNA intervention targeting ATF3, but not c-JUN, alleviated cell damage induced by AA. The knockdown of ATF3 protects against oxidative stress and inflammation in the AAN cell model. CONCLUSION: This study provides novel insights into the role of ATF3 in AAN. The comprehensive analysis sheds light on the molecular mechanisms and identifies potential biomarkers and drug targets for AAN treatment.


Subject(s)
Aristolochic Acids , Kidney Diseases , Transcription Factors , Aristolochic Acids/toxicity , Transcription Factors/genetics , Transcription Factors/metabolism , Kidney Diseases/chemically induced , Kidney Diseases/genetics , Animals , Mice , Humans , Activating Transcription Factor 3/genetics , Activating Transcription Factor 3/metabolism , Protein Interaction Maps
3.
Planta ; 257(3): 56, 2023 Feb 15.
Article in English | MEDLINE | ID: mdl-36790514

ABSTRACT

MAIN CONCLUSION: We developed a more realistic modeling framework by integrating stem photosynthesis into the canopy carbon assimilation model to compare the photosynthetic productivity between the stem and leaf of Eucalyptus urophylla plantations. Stems of Eucalyptus species with smooth outer bark have photosynthetic green tissue that can recycle internal stem CO2. However, the potential contribution of stem photosynthesis to forest productivity has not previously been adequately quantified, and we also do not know how it compares to leaf photosynthetic productivity. To assist in addressing this knowledge gap, we conducted field surveys in Eucalyptus urophylla plantations of different ages and developed a more realistic modeling framework by integrating stem photosynthesis into the existing canopy carbon assimilation model. We calculated the proportion of tree stems shaded by neighboring tree trunks based on Poisson spatial point process. Under the stand density of 2000 trees per hectare, the light absorption area of tree trunks of 2-year-old and 7-year-old E. urophylla plantations were 0.11 (± 0.15) and 0.35 (± 0.12) m2 stem m-2 land, the stem photosynthetic productivity (GPPstem) was 0.72 (± 0.45) and 1.81 (± 1.12) mol C m-2 month-1, and the ratios of GPPstem to leaf photosynthetic productivity (GPPleaf) were 5.10 and 8.17% for 2- and 7-year-old plantations, respectively. Overall, this study presents the feasibility of incorporating stem photosynthesis into the productivity prediction of E. urophylla plantations by developing the stem light absorption model.


Subject(s)
Eucalyptus , Photosynthesis , Trees , Plant Leaves , Carbon
4.
Glob Chang Biol ; 29(18): 5321-5333, 2023 09.
Article in English | MEDLINE | ID: mdl-36970888

ABSTRACT

Carbon-focused climate mitigation strategies are becoming increasingly important in forests. However, with ongoing biodiversity declines we require better knowledge of how much such strategies account for biodiversity. We particularly lack information across multiple trophic levels and on established forests, where the interplay between carbon stocks, stand age, and tree diversity might influence carbon-biodiversity relationships. Using a large dataset (>4600 heterotrophic species of 23 taxonomic groups) from secondary, subtropical forests, we tested how multitrophic diversity and diversity within trophic groups relate to aboveground, belowground, and total carbon stocks at different levels of tree species richness and stand age. Our study revealed that aboveground carbon, the key component of climate-based management, was largely unrelated to multitrophic diversity. By contrast, total carbon stocks-that is, including belowground carbon-emerged as a significant predictor of multitrophic diversity. Relationships were nonlinear and strongest for lower trophic levels, but nonsignificant for higher trophic level diversity. Tree species richness and stand age moderated these relationships, suggesting long-term regeneration of forests may be particularly effective in reconciling carbon and biodiversity targets. Our findings highlight that biodiversity benefits of climate-oriented management need to be evaluated carefully, and only maximizing aboveground carbon may fail to account for biodiversity conservation requirements.


Subject(s)
Forests , Trees , Biodiversity , Carbon , Climate
5.
Gynecol Oncol ; 168: 17-22, 2023 01.
Article in English | MEDLINE | ID: mdl-36368128

ABSTRACT

OBJECTIVE: The GOG 281/LOGS trial found that trametinib prolonged progression-free survival (PFS) in patients with recurrent low-grade serous ovarian cancer (LGSOC), compared with standard of care (SOC). The current study aimed to evaluate the cost-effectiveness of trametinib versus standard of care for recurrent LGSOC from the US payer perspective. METHODS: A Markov model was adopted to compare the cost and effectiveness of trametinib and standard of care group in patients with recurrent LGSOC. Life years (LYs), quality-adjusted LYs (QALYs), lifetime costs, and incremental cost-effectiveness ratios (ICERs) were calculated. One-way, and probabilistic sensitivity analyses were performed to explore the model robustness. RESULT: Trametinib group provided an additional 0.58 QALYs (1.14 LYs) and an incremental cost of $248,214 compared with the SOC group. The incremental cost-effectiveness ratio was $424,097 per QALY. The results of one-way sensitivity analyses suggested that our model was sensitive to the hazard ratio of OS and PFS between trametinib and SOC group, utility of PFS and the cycle cost of trametinib. Probabilistic sensitivity analyses revealed that there was 6% probability of the trametinib group being cost-effective at a willingness-to-pay (WTP) threshold of $150,000 per QALY. CONCLUSIONS: From the US payer perspective, trametinib is not cost-effective for patients with recurrent LGSOC at the assumed WTP threshold of $150,000 per QALY. Based on the value standpoint, price reduction of trametinib is expected to improve the cost-effectiveness of trametinib in patients with recurrent LGSOC.


Subject(s)
Cost-Effectiveness Analysis , Ovarian Neoplasms , Humans , Female , Cost-Benefit Analysis , Pyridones/therapeutic use , Ovarian Neoplasms/drug therapy , Quality-Adjusted Life Years
6.
Microb Ecol ; 85(2): 628-641, 2023 Feb.
Article in English | MEDLINE | ID: mdl-35083529

ABSTRACT

Microorganisms inhabit the entire soil profile and play important roles in nutrient cycling and soil formation. Recent studies have found that soil bacterial diversity and composition differ significantly among soil layers. However, little is known about the vertical variation in soil bacterial communities and how it may change along an elevation gradient. In this study, we collected soil samples from 5 forest types along an elevation gradient in Taibai Mountain to characterize the bacterial communities and their vertical patterns and variations across soil profiles. The richness and Shannon index of soil bacterial communities decreased from surface soils to deep soils in three forest types, and were comparable among soil layers in the other two forests at the medium elevation. The composition of soil bacterial communities differed significantly between soil layers in all forest types, and was primarily affected by soil C availability. Oligotrophic members of the bacterial taxa, such as Chloroflexi, Gemmatimonadetes, Nitrospirae, and AD3, were more abundant in the deep layers. The assembly of soil bacterial communities within each soil profile was mainly governed by deterministic processes based on environmental heterogeneity. The vertical variations in soil bacterial communities differed among forest types, and the soil bacterial communities in the Betula albo-sinensis forest at the medium elevation had the lowest vertical variation. The vertical variation was negatively correlated with mean annual precipitation (MAP), weighted rock content, and weighted sand particle content in soils, among which MAP had the highest explanatory power. These results indicated that the vertical mobilization of microbes with preferential and matrix flows likely enhanced bacterial homogeneity. Overall, our results suggest that the vertical variations in soil bacterial communities differ along the elevation gradient and potentially affect soil biological processes across soil profiles.


Subject(s)
Chloroflexi , Soil , Soil Microbiology , Forests , Bacteria
7.
Proc Natl Acad Sci U S A ; 115(16): 4021-4026, 2018 04 17.
Article in English | MEDLINE | ID: mdl-29666314

ABSTRACT

China's terrestrial ecosystems have functioned as important carbon sinks. However, previous estimates of carbon budgets have included large uncertainties owing to the limitations of sample size, multiple data sources, and inconsistent methodologies. In this study, we conducted an intensive field campaign involving 14,371 field plots to investigate all sectors of carbon stocks in China's forests, shrublands, grasslands, and croplands to better estimate the regional and national carbon pools and to explore the biogeographical patterns and potential drivers of these pools. The total carbon pool in these four ecosystems was 79.24 ± 2.42 Pg C, of which 82.9% was stored in soil (to a depth of 1 m), 16.5% in biomass, and 0.60% in litter. Forests, shrublands, grasslands, and croplands contained 30.83 ± 1.57 Pg C, 6.69 ± 0.32 Pg C, 25.40 ± 1.49 Pg C, and 16.32 ± 0.41 Pg C, respectively. When all terrestrial ecosystems are taken into account, the country's total carbon pool is 89.27 ± 1.05 Pg C. The carbon density of the forests, shrublands, and grasslands exhibited a strong correlation with climate: it decreased with increasing temperature but increased with increasing precipitation. Our analysis also suggests a significant sequestration potential of 1.9-3.4 Pg C in forest biomass in the next 10-20 years assuming no removals, mainly because of forest growth. Our results update the estimates of carbon pools in China's terrestrial ecosystems based on direct field measurements, and these estimates are essential to the validation and parameterization of carbon models in China and globally.


Subject(s)
Carbon Sequestration , Carbon/analysis , Ecosystem , Biomass , China , Conservation of Natural Resources/legislation & jurisprudence , Conservation of Natural Resources/statistics & numerical data , Farms , Forests , Grassland , Human Activities , Humans , Plant Dispersal , Plants/chemistry , Rain , Research Report , Soil/chemistry , Specimen Handling , Surveys and Questionnaires , Temperature
8.
Proc Natl Acad Sci U S A ; 115(16): 4033-4038, 2018 04 17.
Article in English | MEDLINE | ID: mdl-29666316

ABSTRACT

Plant nitrogen (N) and phosphorus (P) content regulate productivity and carbon (C) sequestration in terrestrial ecosystems. Estimates of the allocation of N and P content in plant tissues and the relationship between nutrient content and photosynthetic capacity are critical to predicting future ecosystem C sequestration under global change. In this study, by investigating the nutrient concentrations of plant leaves, stems, and roots across China's terrestrial biomes, we document large-scale patterns of community-level concentrations of C, N, and P. We also examine the possible correlation between nutrient content and plant production as indicated by vegetation gross primary productivity (GPP). The nationally averaged community concentrations of C, N, and P were 436.8, 14.14, and 1.11 mg·g-1 for leaves; 448.3, 3.04 and 0.31 mg·g-1 for stems; and 418.2, 4.85, and 0.47 mg·g-1 for roots, respectively. The nationally averaged leaf N and P productivity was 249.5 g C GPP·g-1 N·y-1 and 3,157.9 g C GPP·g-1 P·y-1, respectively. The N and P concentrations in stems and roots were generally more sensitive to the abiotic environment than those in leaves. There were strong power-law relationships between N (or P) content in different tissues for all biomes, which were closely coupled with vegetation GPP. These findings not only provide key parameters to develop empirical models to scale the responses of plants to global change from a single tissue to the whole community but also offer large-scale evidence of biome-dependent regulation of C sequestration by nutrients.


Subject(s)
Carbon Sequestration , Carbon/analysis , Ecosystem , Nitrogen/analysis , Phosphorus/analysis , Plants/chemistry , Atmosphere/chemistry , Biomass , China , Climate , Farms , Forests , Grassland , Humans , Organ Specificity , Plant Dispersal , Plant Leaves/chemistry , Plant Roots/chemistry , Plant Stems/chemistry , Soil/chemistry , Species Specificity
9.
Proc Natl Acad Sci U S A ; 115(16): 4027-4032, 2018 04 17.
Article in English | MEDLINE | ID: mdl-29666315

ABSTRACT

Despite evidence from experimental grasslands that plant diversity increases biomass production and soil organic carbon (SOC) storage, it remains unclear whether this is true in natural ecosystems, especially under climatic variations and human disturbances. Based on field observations from 6,098 forest, shrubland, and grassland sites across China and predictions from an integrative model combining multiple theories, we systematically examined the direct effects of climate, soils, and human impacts on SOC storage versus the indirect effects mediated by species richness (SR), aboveground net primary productivity (ANPP), and belowground biomass (BB). We found that favorable climates (high temperature and precipitation) had a consistent negative effect on SOC storage in forests and shrublands, but not in grasslands. Climate favorability, particularly high precipitation, was associated with both higher SR and higher BB, which had consistent positive effects on SOC storage, thus offsetting the direct negative effect of favorable climate on SOC. The indirect effects of climate on SOC storage depended on the relationships of SR with ANPP and BB, which were consistently positive in all biome types. In addition, human disturbance and soil pH had both direct and indirect effects on SOC storage, with the indirect effects mediated by changes in SR, ANPP, and BB. High soil pH had a consistently negative effect on SOC storage. Our findings have important implications for improving global carbon cycling models and ecosystem management: Maintaining high levels of diversity can enhance soil carbon sequestration and help sustain the benefits of plant diversity and productivity.


Subject(s)
Biodiversity , Carbon Sequestration , Carbon/analysis , Ecosystem , Plants/metabolism , Soil/chemistry , Biomass , China , Conservation of Natural Resources , Datasets as Topic , Farms , Forests , Grassland , Human Activities , Humans , Hydrogen-Ion Concentration , Nitrogen/analysis , Plant Dispersal , Plants/chemistry , Plants/classification , Rain , Temperature
10.
Proc Natl Acad Sci U S A ; 115(16): 4039-4044, 2018 04 17.
Article in English | MEDLINE | ID: mdl-29666317

ABSTRACT

The long-term stressful utilization of forests and grasslands has led to ecosystem degradation and C loss. Since the late 1970s China has launched six key national ecological restoration projects to protect its environment and restore degraded ecosystems. Here, we conducted a large-scale field investigation and a literature survey of biomass and soil C in China's forest, shrubland, and grassland ecosystems across the regions where the six projects were implemented (∼16% of the country's land area). We investigated the changes in the C stocks of these ecosystems to evaluate the contributions of the projects to the country's C sink between 2001 and 2010. Over this decade, we estimated that the total annual C sink in the project region was 132 Tg C per y (1 Tg = 1012 g), over half of which (74 Tg C per y, 56%) was attributed to the implementation of the projects. Our results demonstrate that these restoration projects have substantially contributed to CO2 mitigation in China.


Subject(s)
Carbon Sequestration , Carbon/analysis , Conservation of Natural Resources , Ecosystem , Biomass , China , Conservation of Natural Resources/legislation & jurisprudence , Conservation of Natural Resources/statistics & numerical data , Forests , Grassland , Humans , Plants/chemistry , Program Evaluation , Soil/chemistry , Water Movements
11.
Ecol Lett ; 23(6): 1003-1013, 2020 Jun.
Article in English | MEDLINE | ID: mdl-32249502

ABSTRACT

A key challenge in ecology is to understand the relationships between organismal traits and ecosystem processes. Here, with a novel dataset of leaf length and width for 10 480 woody dicots in China and 2374 in North America, we show that the variation in community mean leaf size is highly correlated with the variation in climate and ecosystem primary productivity, independent of plant life form. These relationships likely reflect how natural selection modifies leaf size across varying climates in conjunction with how climate influences canopy total leaf area. We find that the leaf size-primary productivity functions based on the Chinese dataset can predict productivity in North America and vice-versa. In addition to advancing understanding of the relationship between a climate-driven trait and ecosystem functioning, our findings suggest that leaf size can also be a promising tool in palaeoecology for scaling from fossil leaves to palaeo-primary productivity of woody ecosystems.


Subject(s)
Ecosystem , Magnoliopsida , China , North America , Plant Leaves
12.
Ecology ; 100(3): e02624, 2019 03.
Article in English | MEDLINE | ID: mdl-30644535

ABSTRACT

Positive biodiversity-ecosystem-functioning (BEF) relationships are commonly found in experimental and observational studies, but how they vary in different environmental contexts and under the influence of coexisting life forms is still controversial. Investigating these variations is important for making predictions regarding the dynamics of plant communities and carbon pools under global change. We conducted this study across 433 shrubland sites in northern China. We fitted structural equation models (SEMs) to analyze the variation in the species-richness-biomass relationships of shrubs and herbs along a wetness gradient and general liner models (GLMs) to analyze how shrub or herb biomass affected the species-richness-biomass relationship of the other life form. We found that the positive species-richness-biomass relationships for both shrubs and herbs became weaker or even negative with higher water availability, likely indicating stronger interspecific competition within life forms under more benign conditions. After accounting for variation in environmental contexts using residual regression, we found that the benign effect of greater facilitation by a larger shrub biomass reduced the positive species-richness-biomass relationships of herbs, causing them to become nonsignificant. Different levels of herb biomass, however, did not change the species-richness-biomass relationship of shrubs, possibly because greater herb biomass did not alter the stress level for shrubs. We conclude that biodiversity in the studied plant communities is particularly important for plant biomass production under arid conditions and that it might be possible to use shrubs as nurse plants to facilitate understory herb establishment in ecological restoration.


Subject(s)
Ecosystem , Water , Biodiversity , Biomass , China
13.
Proc Biol Sci ; 285(1885)2018 08 22.
Article in English | MEDLINE | ID: mdl-30135164

ABSTRACT

Forest ecosystems are an integral component of the global carbon cycle as they take up and release large amounts of C over short time periods (C flux) or accumulate it over longer time periods (C stock). However, there remains uncertainty about whether and in which direction C fluxes and in particular C stocks may differ between forests of high versus low species richness. Based on a comprehensive dataset derived from field-based measurements, we tested the effect of species richness (3-20 tree species) and stand age (22-116 years) on six compartments of above- and below-ground C stocks and four components of C fluxes in subtropical forests in southeast China. Across forest stands, total C stock was 149 ± 12 Mg ha-1 with richness explaining 28.5% and age explaining 29.4% of variation in this measure. Species-rich stands had higher C stocks and fluxes than stands with low richness; and, in addition, old stands had higher C stocks than young ones. Overall, for each additional tree species, the total C stock increased by 6.4%. Our results provide comprehensive evidence for diversity-mediated above- and below-ground C sequestration in species-rich subtropical forests in southeast China. Therefore, afforestation policies in this region and elsewhere should consider a change from the current focus on monocultures to multi-species plantations to increase C fixation and thus slow increasing atmospheric CO2 concentrations and global warming.


Subject(s)
Biodiversity , Carbon Sequestration , Forests , Trees/physiology , China , Time Factors
14.
Proc Natl Acad Sci U S A ; 112(7): 2281-6, 2015 Feb 17.
Article in English | MEDLINE | ID: mdl-25646423

ABSTRACT

Lakes are widely distributed on the Mongolian Plateau and, as critical water sources, have sustained Mongolian pastures for hundreds of years. However, the plateau has experienced significant lake shrinkage and grassland degradation during the past several decades. To quantify the changes in all of the lakes on the plateau and the associated driving factors, we performed a satellite-based survey using multitemporal Landsat images from the 1970s to 2000s, combined with ground-based censuses. Our results document a rapid loss of lakes on the plateau in the past decades: the number of lakes with a water surface area >1 km(2) decreased from 785 in the late 1980s to 577 in 2010, with a greater rate of decrease (34.0%) in Inner Mongolia of China than in Mongolia (17.6%). This decrease has been particularly pronounced since the late 1990s in Inner Mongolia and the number of lakes >10 km(2) has declined by 30.0%. The statistical analyses suggested that in Mongolia precipitation was the dominant driver for the lake changes, and in Inner Mongolia coal mining was most important in its grassland area and irrigation was the leading factor in its cultivated area. The deterioration of lakes is expected to continue in the following decades not only because of changing climate but also increasing exploitation of underground mineral and groundwater resources on the plateau. To protect grasslands and the indigenous nomads, effective action is urgently required to save these valuable lakes from further deterioration.


Subject(s)
Lakes , Mongolia , Satellite Imagery
15.
Ann Bot ; 120(6): 937-942, 2017 Nov 28.
Article in English | MEDLINE | ID: mdl-29028870

ABSTRACT

BACKGROUND AND AIMS: The nitrogen (N) to phosphorus (P) ratio (N:P) has been widely used as a threshold for identifying nutrient limitations in terrestrial plants; however, the associated reliability has not been well assessed. METHODS: The uncertainty of nutrient limitations caused by the N:P threshold was evaluated using two approaches: fertilization experiments synthesized across multiple ecosystems; and random sampling simulation of the impacts of different nutrient sufficiencies and deficiencies. KEY RESULTS: The fertilization experiment data indicated that the types of nutrient limitation determined via N:P thresholds were partly inconsistent with the growth responses observed under N and P additions, i.e. under N:P thresholds of 14 and 16 (or 10 and 20), 32.5 % (or 16.2 %) of the data were inconsistent between these two. The random sampling simulation suggested that N:P thresholds may indicate N (or P) limitations when leaf N (or P) content is sufficient, whereas these thresholds may not indicate N (or P) limitations when leaf N (or P) content is deficient. The error risks calculated from the sampling simulation presented large fluctuations at small sample sizes and decreased as the thresholds of nutrient content sufficiency (or deficiency) increased (or decreased). The N:P thresholds of 10 and 20 showed lower error risks than the thresholds of 14 and 16. CONCLUSIONS: These findings highlight that canonical N:P thresholds have the potential to introduce a large uncertainty when used to detect plant nutrient limitations, suggesting that the error risks should be cautioned in future studies.


Subject(s)
Botany/methods , Nitrogen/metabolism , Phosphorus/metabolism , Plant Physiological Phenomena , Ecosystem , Fertilizers , Reproducibility of Results , Uncertainty
16.
BMC Evol Biol ; 15: 182, 2015 Sep 03.
Article in English | MEDLINE | ID: mdl-26334527

ABSTRACT

BACKGROUND: The rice genus (Oryza) contains many wild genetic resources that are vital to the well-being of humans. However, little is known about the process by which the genus diversified or the factors that drove its speciation. Here, we integrated the phylogenetic, molecular dating and biogeographic methods to investigate the spatial-temporal patterns of Oryza diversification, and used a series of model tests to examine whether intercontinental migrations and/or key innovations were associated with significant changes in diversification rates in the genus. RESULTS: Oryza became differentiated in tropical Asia in the Miocene. There were two migrations from the ancestral area into Africa and Australia during the Miocene. We inferred at least 10 migration events out of tropical Asia since the Pleistocene, mainly involving the species adapting open habitat. A rapid increase in diversification rates of the whole Oryza occurred during the Pleistocene. Intercontinental migrations from tropical Asia to other tropical regions were positively correlated with shift in habitat, but not with changes in life history. A habitat preference shift from shade tolerant to open habitat predated the burst in diversification rates. CONCLUSIONS: Rice species may have been pre-adapted to invade open habitat. Significant increase in diversification rates occurred during the Pleistocene and is associated with range expansion and habitat shift, but not with life history. The rice genus provides an excellent case supporting the idea that range expansion and invasion of novel habitats can drive the diversification of a group.


Subject(s)
Oryza/classification , Phylogeny , Biological Evolution , Ecosystem , Oryza/genetics , Plastids/genetics
17.
Plant Divers ; 46(1): 49-58, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38343596

ABSTRACT

Beta-diversity reflects the spatial changes in community species composition which helps to understand how communities are assembled and biodiversity is formed and maintained. Larch (Larix) forests, which are coniferous forests widely distributed in the mountainous and plateau areas in North and Southwest China, are critical for maintaining the environmental conditions and species diversity. Few studies of larch forests have examined the beta-diversity and its constituent components (species turnover and nestedness-resultant components). Here, we used 483 larch forest plots to determine the total beta-diversity and its components in different life forms (i.e., tree, shrub, and herb) of larch forests in China and to evaluate the main drivers that underlie this beta-diversity. We found that total beta-diversity of larch forests was mainly dependent on the species turnover component. In all life forms, total beta-diversity and the species turnover component increased with increasing geographic, elevational, current climatic, and paleoclimatic distances. In contrast, the nestedness-resultant component decreased across these same distances. Geographic and environmental factors explained 20%-25% of total beta-diversity, 18%-27% of species turnover component, and 4%-16% of nestedness-resultant component. Larch forest types significantly affected total beta-diversity and species turnover component. Taken together, our results indicate that life forms affect beta-diversity patterns of larch forests in China, and that beta-diversity is driven by both niche differentiation and dispersal limitation. Our findings help to greatly understand the mechanisms of community assemblies of larch forests in China.

18.
Chem Sci ; 15(7): 2545-2557, 2024 Feb 14.
Article in English | MEDLINE | ID: mdl-38362424

ABSTRACT

Due to the complex high-order structures and interactions of proteins within an aqueous solution, a majority of chemical functionalizations happen on the hydrophilic sites of protein external surfaces which are naturally exposed to the solution. However, the hydrophobic pockets inside proteins are crucial for ligand binding and function as catalytic centers and transporting tunnels. Herein, we describe a reagent pre-organization and in situ photochemical trifluoromethylation strategy to profile the functional sites inside the hydrophobic pockets of native proteins. Unbiased mass spectrometry profiling was applied for the characterization of trifluoromethylated sites with high sensitivity. Native proteins including myoglobin, trypsin, haloalkane dehalogenase, and human serum albumin have been engaged in this mild photochemical process and substantial hydrophobic site-specific and structure-selective trifluoromethylation substitutes are obtained without significant interference to their bioactivity and structures. Sodium triflinate is the only reagent required to functionalize the unprotected proteins with wide pH-range tolerance and high biocompatibility. This "in-pocket" activation model provides a general strategy to modify the potential binding pockets and gain essential structural insights into the functional hotspots inside protein hydrophobic pockets.

19.
Sci China Life Sci ; 67(4): 817-828, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38217639

ABSTRACT

The Convention on Biological Diversity seeks to conserve at least 30% of global land and water areas by 2030, which is a challenge but also an opportunity to better preserve biodiversity, including flowering plants (angiosperms). Herein, we compiled a large database on distributions of over 300,000 angiosperm species and the key functional traits of 67,024 species. Using this database, we constructed biodiversity-environment models to predict global patterns of taxonomic, phylogenetic, and functional diversity in terrestrial angiosperms and provide a comprehensive mapping of the three diversity facets. We further evaluated the current protection status of the biodiversity centers of these diversity facets. Our results showed that geographical patterns of the three facets of plant diversity exhibited substantial spatial mismatches and nonoverlapping conservation priorities. Idiosyncratic centers of functional diversity, particularly of herbaceous species, were primarily distributed in temperate regions and under weaker protection compared with other biodiversity centers of taxonomic and phylogenetic facets. Our global assessment of multifaceted biodiversity patterns and centers highlights the insufficiency and unbalanced conservation among the three diversity facets and the two growth forms (woody vs. herbaceous), thus providing directions for guiding the future conservation of global plant diversity.


Subject(s)
Magnoliopsida , Phylogeny , Biodiversity , Plants , Ecosystem , Conservation of Natural Resources
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