Multistress Interplay: Time and Duration of Ocean Acidification Modulate the Toxicity of Mercury and Other Metals.

The current understanding of multistress interplay assumes stresses occur in perfect synchrony, but this assumption is rarely met in the natural marine ecosystem. To understand the interplay between nonperfectly overlapped stresses in the ocean, we manipulated a multigenerational experiment (F0-F3) to explore how different temporal scenarios of ocean acidification will affect mercury toxicity in a marine copepod Pseudodiaptomus annandalei. We found that the scenario of past acidification aggravated mercury toxicity but current and persistent acidification mitigated its toxicity. We specifically performed a proteomics analysis for the copepods of F3. The results indicated that current and persistent acidification initiated the energy compensation for development and mercury efflux, whereas past acidification lacked the barrier of H+ and had dysfunction in the detoxification and efflux system, providing a mechanistic understanding of mercury toxicity under different acidification scenarios. Furthermore, we conducted a meta-analysis on marine animals, demonstrating that different acidification scenarios could alter the toxicity of several other metals, despite evidence from nonsynchronous scenarios remaining limited. Our study thus demonstrates that time and duration of ocean acidification modulate mercury toxicity in marine copepods and suggests that future studies should move beyond the oversimplified scenario of perfect synchrony in understanding multistress interaction.

Parental environmental effects are common and strong, but unpredictable, in Arabidopsis thaliana.

The phenotypes of plants can be influenced by the environmental conditions experienced by their parents. However, there is still much uncertainty about how common and how predictable such parental environmental effects really are. We carried out a comprehensive experimental test for parental effects, subjecting plants of multiple Arabidopsis thaliana genotypes to 24 different biotic or abiotic stresses, or combinations thereof, and comparing their offspring phenotypes in a common environment. The majority of environmental stresses caused significant parental effects, with -35% to +38% changes in offspring fitness. The expression of parental effects was strongly genotype-dependent, and multiple environmental stresses often acted nonadditively when combined. The direction and magnitude of parental effects were unrelated to the direct effects on the parents: Some environmental stresses did not affect the parents but caused substantial effects on offspring, while for others, the situation was reversed. Our study demonstrates that parental environmental effects are common and often strong in A. thaliana, but they are genotype-dependent, act nonadditively, and are difficult to predict. We should thus be cautious with generalizing from simple studies with single plant genotypes and/or only few individual environmental stresses. A thorough and general understanding of parental effects requires large multifactorial experiments.

Asymmetric character displacement in mixed oak stands.

Ecological character displacement (ECD) refers to a pattern of increased divergence at sites where species ranges overlap caused by competition for resources. Although ECD is believed to be common, there are few in-depth studies that clearly establish its existence, especially in plants. Thus, we have compared leaf traits in allopatric and sympatric populations of two East Asian deciduous oaks: Quercus dentata and Quercus aliena. In contrast to previous studies, we define sympatry and allopatry at a local scale, thereby comparing populations that can or cannot directly interact. Using genetic markers, we found greater genetic divergence between the two oak species growing in mixed stands and inferred that long-term gene flow has predominantly occurred asymmetrically from the cold-tolerant species (Q. dentata) to the warm-demanding later colonizing species (Q. aliena). Analysis of leaf traits revealed greater divergence in mixed than in pure oak stands. This was mostly due to the later colonizing species being characterized by more resource-conservative traits in the presence of the other species. Controlling for relevant environmental differences did not alter these conclusions. These results suggest that asymmetric trait divergence can take place where species coexist, possibly due to the imbalance in demographic history of species resulting in asymmetric inter-specific selection pressures.

Multi-omics analyses on Kandelia obovata reveal its response to transplanting and genetic differentiation among populations.

BACKGROUND: Restoration through planting is the dominant strategy to conserve mangrove ecosystems. However, many of the plantations fail to survive. Site and seeding selection matters for planting. The process of afforestation, where individuals were planted in a novel environment, is essentially human-controlled transplanting events. Trying to deepen and expand the understanding of the effects of transplanting on plants, we have performed a seven-year-long reciprocal transplant experiment on Kandelia obovata along a latitudinal gradient. RESULTS: Combined phenotypic analyses and next-generation sequencing, we found phenotypic discrepancies among individuals from different populations in the common garden and genetic differentiation among populations. The central population with abundant genetic diversity and high phenotypic plasticity had a wide plantable range. But its biomass was reduced after being transferred to other latitudes. The suppressed expression of lignin biosynthesis genes revealed by RNA-seq was responsible for the biomass reduction. Moreover, using whole-genome bisulfite sequencing, we observed modification of DNA methylation in MADS-box genes that involved in the regulation of flowering time, which might contribute to the adaptation to new environments. CONCLUSIONS: Taking advantage of classical ecological experiments as well as multi-omics analyses, our work observed morphology differences and genetic differentiation among different populations of K. obovata, offering scientific advice for the development of restoration strategy with long-term efficacy, also explored phenotypic, transcript, and epigenetic responses of plants to transplanting events between latitudes.

Adaptive transgenerational effects remain significant.

The comment by Sánchez-Tójar et al. (2020, Ecol Lett) questioned the methodology, transparency and conclusion of our study (Ecol Lett, 22, 2019, 1976). The comment has overlooked important evolutionary assumptions in their reanalysis, and the issues raised were in fact dealt with through the peer-review process. Far from being biased, the key conclusion of our meta-analysis still stands; transgenerational effects are largely adaptive.

A Bayesian multi-risks survival (MRS) model in the presence of double censorings.

Semi-competing risks data include the time to a nonterminating event and the time to a terminating event, while competing risks data include the time to more than one terminating event. Our work is motivated by a prostate cancer study, which has one nonterminating event and two terminating events with both semi-competing risks and competing risks present as well as two censoring times. In this paper, we propose a new multi-risks survival (MRS) model for this type of data. In addition, the proposed MRS model can accommodate noninformative right-censoring times for nonterminating and terminating events. Properties of the proposed MRS model are examined in detail. Theoretical and empirical results show that the estimates of the cumulative incidence function for a nonterminating event may be biased if the information on a terminating event is ignored. A Markov chain Monte Carlo sampling algorithm is also developed. Our methodology is further assessed using simulations and also an analysis of the real data from a prostate cancer study. As a result, a prostate-specific antigen velocity greater than 2.0 ng/mL per year and higher biopsy Gleason scores are positively associated with a shorter time to death due to prostate cancer.

Transgenerational effects benefit offspring across diverse environments: a meta-analysis in plants and animals.

The adaptive value of transgenerational effects (the ancestor environmental effects on offspring) in changing environments has received much attention in recent years, but the related empirical evidence remains equivocal. Here, we conducted a meta-analysis summarising 139 experimental studies in plants and animals with 1170 effect sizes to investigate the generality of transgenerational effects across taxa, traits, and environmental contexts. It was found that transgenerational effects generally enhanced offspring performance in response to both stressful and benign conditions. The strongest effects are in annual plants and invertebrates, whereas vertebrates appear to benefit mostly under benign conditions, and perennial plants show hardly any transgenerational responses at all. These differences among taxonomic/life-history groups possibly reflect that vertebrates can avoid stressful conditions through their mobility, and longer-lived plants have alternative strategies. In addition to environmental contexts and taxonomic/life-history groups, transgenerational effects also varied among traits and developmental stages of ancestors and offspring, but the effects were similarly strong across three generations of offspring. By way of a more comprehensive data set and a different effect size, our results differ from those of a recent meta-analysis, suggesting that transgenerational effects are widespread, strong and persistent and can substantially impact the responses of plants and animals to changing environments.

Genetic admixture accelerates invasion via provisioning rapid adaptive evolution.

Genetic admixture, the intraspecific hybridization among divergent introduced sources, can immediately facilitate colonization via hybrid vigor and profoundly enhance invasion via contributing novel genetic variation to adaption. As hybrid vigor is short-lived, provisioning adaptation is anticipated to be the dominant and long-term profit of genetic admixture, but the evidence for this is rare. We employed the 30 years' geographic-scale invasion of the salt marsh grass, Spartina alterniflora, as an evolutionary experiment and evaluated the consequences of genetic admixture by combining the reciprocal transplant experiment with quantitative and population genetic surveys. Consistent with the documentation, we found that the invasive populations in China had multiple origins from the southern Atlantic coast and the Gulf of Mexico in the US. Interbreeding among these multiple sources generated a "hybrid swarm" that spread throughout the coast of China. In the northern and mid-latitude China, natural selection greatly enhanced fecundity, plant height and shoot regeneration compared to the native populations. Furthermore, genetic admixture appeared to have broken the negative correlation between plant height and shoot regeneration, which was genetically-based in the native range, and have facilitated the evolution of super competitive genotypes in the invasive range. In contrast to the evolved northern and mid-latitude populations, the southern invasive populations showed slight increase of plant height and shoot regeneration compared to the native populations, possibly reflecting the heterotic effect of the intraspecific hybridization. Therefore, our study suggests a critical role of genetic admixture in accelerating the geographic invasion via provisioning rapid adaptive evolution.

Understanding the evolutionary potential of epigenetic variation: a comparison of heritable phenotypic variation in epiRILs, RILs, and natural ecotypes of Arabidopsis thaliana.

Increasing evidence for epigenetic variation within and among natural plant populations has led to much speculation about its role in the evolution of plant phenotypes. However, we still have a very limited understanding of the evolutionary potential of epigenetic variation, in particular in comparison to DNA sequence-based variation. To address this question, we compared the magnitudes of heritable phenotypic variation in epigenetic recombinant inbred lines (epiRILs) of Arabidopsis thaliana-lines that mainly differ in DNA methylation but only very little in DNA sequence-with other types of A. thaliana lines that differ strongly also in DNA sequence. We grew subsets of two epiRIL populations with subsets of two genetic RIL populations, of natural ecotype collections, and of lines from a natural population in a common environment and assessed their heritable variation in growth, phenology, and fitness. Among-line phenotypic variation and broad-sense heritabilities tended to be largest in natural ecotypes, but for some traits the variation among epiRILs was comparable to that among RILs and natural ecotypes. Within-line phenotypic variation was generally similar in epiRILs, RILs, and ecotypes. Provided that phenotypic variation in epiRILs is mainly caused by epigenetic differences, whereas in RILs and natural lines it is largely driven by sequence variation, our results indicate that epigenetic variation has the potential to create phenotypic variation that is stable and substantial, and thus of evolutionary significance.

Bayesian path specific frailty models for multi-state survival data with applications.

Multi-state models can be viewed as generalizations of both the standard and competing risks models for survival data. Models for multi-state data have been the theme of many recent published works. Motivated by bone marrow transplant data, we propose a Bayesian model using the gap times between two successive events in a path of events experienced by a subject. Path specific frailties are introduced to capture the dependence structure of the gap times in the paths with two or more states. Under improper prior distributions for the parameters, we establish propriety of the posterior distribution. An efficient Gibbs sampling algorithm is developed for drawing samples from the posterior distribution. An extensive simulation study is carried out to examine the empirical performance of the proposed approach. A bone marrow transplant data set is analyzed in detail to further demonstrate the proposed methodology.

Bayesian gamma frailty models for survival data with semi-competing risks and treatment switching.

Motivated from a colorectal cancer study, we propose a class of frailty semi-competing risks survival models to account for the dependence between disease progression time, survival time, and treatment switching. Properties of the proposed models are examined and an efficient Gibbs sampling algorithm using the collapsed Gibbs technique is developed. A Bayesian procedure for assessing the treatment effect is also proposed. The deviance information criterion (DIC) with an appropriate deviance function and Logarithm of the pseudomarginal likelihood (LPML) are constructed for model comparison. A simulation study is conducted to examine the empirical performance of DIC and LPML and as well as the posterior estimates. The proposed method is further applied to analyze data from a colorectal cancer study.

The spatial correlation network structure and its formation mechanism of urban high-quality economic development: a comparative analysis from the Yangtze River Economic Belt and the Yellow River Basin in China.

In the context of regional integration, it is more than crucial to compare and analyze the spatial correlation network structure and formation mechanism of high-quality economic development in the Yangtze River Economic Belt and the Yellow River Basin urban cities as an attempt to strengthen collaborative work on high-quality economic development in both river basins. The paper measured high-quality economic development of the Yangtze River Economic Belt and the Yellow River Basin from 2010 to 2021. Then, it employed social network analysis and the QAP method to study the network structure's characteristics and formation mechanism. The conclusion of the research illustrates a few points clearly that first, the high-quality economic development of the two rivers presents a complex and multithreaded network structure. Although the network structure is hold at a comparatively stable state, the correlation degree needs improvement. Second, cities such as Chongqing, Wuhan, Hefei, Nanjing, Hangzhou, Shanghai, and Changsha and cities like Zhengzhou, Xi'an, Luoyang, Yulin, Hulunbuir, Ordos, and Nanyang are at the very central as well as central position of the network. The spatial correlation networks of the Yangtze River Economic Belt and the Yellow River Basin can be divided into four plates: "agent plate," "main outflow plate," "bidirectional spillover plate," and "main inflow plate." Third, reverse geographical distance and differences in the digital economy attach great significance to the spatial correlation networks of the two basins. The difference in urbanization level makes significant impacts only on the spatial correlation network of the Yangtze River Economic Belt, while the difference in environmental regulation and material capital accumulation only significantly influences the spatial correlation network of the Yellow River Basin.

New genes helped acorn barnacles adapt to a sessile lifestyle.

Barnacles are the only sessile lineages among crustaceans, and their sessile life begins with the settlement of swimming larvae (cyprids) and the formation of protective shells. These processes are crucial for adaptation to a sessile lifestyle, but the underlying molecular mechanisms remain poorly understood. While investigating these mechanisms in the acorn barnacle, Amphibalanus amphitrite, we discovered a new gene, bcs-6, which is involved in the energy metabolism of cyprid settlement and originated from a transposon by acquiring the promoter and cis-regulatory element. Unlike mollusks, the barnacle shell comprises alternate layers of chitin and calcite and requires another new gene, bsf, which generates silk-like fibers that efficiently bind chitin and aggregate calcite in the aquatic environment. Our findings highlight the importance of exploring new genes in unique adaptative scenarios, and the results will provide important insights into gene origin and material development.

Environment-induced heritable variations are common in Arabidopsis thaliana.

Parental or ancestral environments can induce heritable phenotypic changes, but whether such environment-induced heritable changes are a common phenomenon remains unexplored. Here, we subject 14 genotypes of Arabidopsis thaliana to 10 different environmental treatments and observe phenotypic and genome-wide gene expression changes over four successive generations. We find that all treatments caused heritable phenotypic and gene expression changes, with a substantial proportion stably transmitted over all observed generations. Intriguingly, the susceptibility of a genotype to environmental inductions could be predicted based on the transposon abundance in the genome. Our study thus challenges the classic view that the environment only participates in the selection of heritable variation and suggests that the environment can play a significant role in generating of heritable variations.

Dipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests.

Dipterocarpoideae species form the emergent layer of Asian rainforests. They are the indicator species for Asian rainforest distribution, but they are severely threatened. Here, to understand their adaptation and population decline, we assemble high-quality genomes of seven Dipterocarpoideae species including two autotetraploid species. We estimate the divergence time between Dipterocarpoideae and Malvaceae and within Dipterocarpoideae to be 108.2 (97.8‒118.2) and 88.4 (77.7‒102.9) million years ago, and we identify a whole genome duplication event preceding dipterocarp lineage diversification. We find several genes that showed a signature of selection, likely associated with the adaptation to Asian rainforests. By resequencing of two endangered species, we detect an expansion of effective population size after the last glacial period and a recent sharp decline coinciding with the history of local human activities. Our findings contribute to understanding the diversification and adaptation of dipterocarps and highlight anthropogenic disturbances as a major factor in their endangered status.

Epigenetic variation creates potential for evolution of plant phenotypic plasticity.

Heritable variation in plant phenotypes, and thus potential for evolutionary change, can in principle not only be caused by variation in DNA sequence, but also by underlying epigenetic variation. However, the potential scope of such phenotypic effects and their evolutionary significance are largely unexplored. Here, we conducted a glasshouse experiment in which we tested the response of a large number of epigenetic recombinant inbred lines (epiRILs) of Arabidopsis thaliana--lines that are nearly isogenic but highly variable at the level of DNA methylation--to drought and increased nutrient conditions. We found significant heritable variation among epiRILs both in the means of several ecologically important plant traits and in their plasticities to drought and nutrients. Significant selection gradients, that is, fitness correlations, of several mean traits and plasticities suggest that selection could act on this epigenetically based phenotypic variation. Our study provides evidence that variation in DNA methylation can cause substantial heritable variation of ecologically important plant traits, including root allocation, drought tolerance and nutrient plasticity, and that rapid evolution based on epigenetic variation alone should thus be possible.

The effectiveness of artificial microbial community selection: a conceptual framework and a meta-analysis.

The potential for artificial selection at the community level to improve ecosystem functions has received much attention in applied microbiology. However, we do not yet understand what conditions in general allow for successful artificial community selection. Here we propose six hypotheses about factors that determine the effectiveness of artificial microbial community selection, based on previous studies in this field and those on multilevel selection. In particular, we emphasize selection strategies that increase the variance among communities. We then report a meta-analysis of published artificial microbial community selection experiments. The reported responses to community selection were highly variable among experiments; and the overall effect size was not significantly different from zero. The effectiveness of artificial community selection was greater when there was no migration among communities, and when the number of replicated communities subjected to selection was larger. The meta-analysis also suggests that the success of artificial community selection may be contingent on multiple necessary conditions. We argue that artificial community selection can be a promising approach, and suggest some strategies for improving the performance of artificial community selection programs.

Physiological and transcriptomic responses to cold waves of the most cold-tolerant mangrove, Kandelia obovata.

Mangrove forests inhabit tropical or subtropical intertidal zones and have remarkable abilities in coastline protection. Kandelia obovata is considered the most cold-tolerant mangrove species and has been widely transplanted to the north subtropical zone of China for ecological restoration. However, the physiological and molecular mechanisms of K. obovata under colder climate was still unclear. Here, we manipulated the typical climate of cold waves in the north subtropical zone with cycles of cold/recovery and analyzed the physiological and transcriptomic responses of seedlings. We found that both physiological traits and gene expression profiles differed between the first and later cold waves, indicating K. obovata seedlings were acclimated by the first cold experience and prepared for latter cold waves. 1,135 cold acclimation-related genes (CARGs) were revealed, related to calcium signaling, cell wall modification, and post-translational modifications of ubiquitination pathways. We identified the roles of CBFs and CBF-independent transcription factors (ZATs and CZF1s) in regulating the expression of CARGs, suggesting both CBF-dependent and CBF- independent pathways functioned in the cold acclimation of K. obovata. Finally, we proposed a molecular mechanism of K. obovata cold acclimation with several key CARGs and transcriptional factors involved. Our experiments reveal strategies of K. obovata coping with cold environments and provide prospects for mangrove rehabilitation and management.

Updated results of magnetic resonance imaging guided partial prostate brachytherapy for favorable risk prostate cancer: implications for focal therapy.

PURPOSE: We report updated results of magnetic resonance imaging guided partial prostate brachytherapy and propose a definition of biochemical failure following focal therapy. MATERIALS AND METHODS: From 1997 to 2007, 318 men with cT1c, prostate specific antigen less than 15 ng/ml, Gleason 3 + 4 or less prostate cancer received magnetic resonance imaging guided brachytherapy in which only the peripheral zone was targeted. To exclude benign prostate specific antigen increases due to prostatic hyperplasia, we investigated the usefulness of defining prostate specific antigen failure as nadir +2 with prostate specific antigen velocity greater than 0.75 ng/ml per year. Cox regression was used to determine the factors associated with prostate specific antigen failure. RESULTS: Median followup was 5.1 years (maximum 12.1). While 36 patients met the nadir +2 criteria, 16 of 17 biopsy proven local recurrences were among the 26 men who also had a prostate specific antigen velocity greater than 0.75 ng/ml per year (16 of 26 vs 1 of 10, p = 0.008). Using the nadir +2 definition, prostate specific antigen failure-free survival for low risk cases at 5 and 8 years was 95.1% (91.0-97.3) and 80.4% (70.7-87.1), respectively. This rate improved to 95.6% (91.6-97.7) and 90.0% (82.6-94.3) using nadir +2 with prostate specific antigen velocity greater than 0.75 ng/ml per year. For intermediate risk cases survival was 73.0% (55.0-84.8) at 5 years and 66.4% (44.8-81.1) at 8 years (the same values as using nadir +2 with prostate specific antigen velocity greater than 0.75 ng/ml per year). CONCLUSIONS: Requiring a prostate specific antigen velocity greater than 0.75 ng/ml per year in addition to nadir +2 appears to better predict clinical failure after therapies that target less than the whole gland. Further followup will determine whether magnetic resonance imaging guided brachytherapy targeting the peripheral zone produces comparable cancer control to whole gland treatment in men with low risk disease. However, at this time it does not appear adequate for men with even favorable intermediate risk disease.

Patient-reported quality of life during radiation treatment for localized prostate cancer: results from a prospective phase II trial.

UNLABELLED: Study Type--Therapy (cohort) Level of Evidence 2a. What's known on the subject? and What does the study add? Patient-reported quality of life (QoL) in prostate cancer is recognized as an important outcome, and has been shown in multiple studies to capture the incidence and timing of patient symptoms more accurately than physician-graded toxicity reports. Although the long-term QoL after completing radiation therapy (RT) has been previously studied, patient experience during RT is not well described in the literature. The present study collected patient-reported QoL during RT in a prospective phase II clinical trial. The study describes in detail the time course and severity of gastrointestinal and genitourinary symptoms during radiation, providing clinically useful information for patients and physicians considering RT during the treatment decision-making process. OBJECTIVE: • To evaluate data collected from a phase II trial to describe the time course and trajectory of patient-reported acute urinary and bowel symptom development during radiation therapy (RT) for prostate cancer. PATIENTS AND METHODS: • In all, 100 patients with intermediate- or high-risk prostate cancer received 72 Gy of RT to the prostate and seminal vesicles, with 6 months of concurrent androgen deprivation therapy; a rectal balloon was used for prostate immobilization. • Patients completed the validated Prostate Cancer Symptom Indices questionnaire every 1-2 weeks, reporting urinary and bowel symptoms on a four- or five-point Likert scale. • A score of ≥ 3 in a symptom is associated with clinically meaningful distress. Cumulative incidence of each symptom is reported. Bonferroni corrections of P values were used to adjust for multiple comparisons. RESULTS: • Urinary symptoms were frequent at baseline and worsened during treatment. By the end of RT, 28-50% of patients developed clinically meaningful obstructive and irritative urinary symptoms. • Acute bowel symptoms were less frequent. Each bowel symptom increased in frequency by 9-26% from baseline to end of RT. • Urinary incontinence was rare. • Overall, symptom burden at the end of treatment was modest. CONCLUSIONS: • Urinary symptoms were common during RT, and bowel symptoms were less frequent. • These results inform patients and physicians during the decision-making process about potential patient quality of life experiences during RT, and also provide a benchmark for comparative effectiveness studies against newer treatments and technologies.