Nitrous oxide emissions during establishment of eight alternative cellulosic bioenergy cropping systems in the North Central United States

Greenhouse gas (GHG) emissions from soils are a key sustainability metric of cropping systems. During crop establishment, disruptive land‐use change is known to be a critical, but under reported period, for determining GHG emissions. We measured soil N₂O emissions and potential environmental drivers of these fluxes from a three‐year establishment‐phase bioenergy cropping systems experiment replicated in southcentral Wisconsin (ARL) and southwestern Michigan (KBS). Cropping systems treatments were annual monocultures (continuous corn, corn–soybean–canola rotation), perennial monocultures (switchgrass, miscanthus, and poplar), and perennial polycultures (native grass mixture, early successional community, and restored prairie) all grown using best management practices specific to the system. Cumulative three‐year N₂O emissions from annuals were 142% higher than from perennials, with fertilized perennials 190% higher than unfertilized perennials. Emissions ranged from 3.1 to 19.1 kg N₂O‐N ha^?1 yr^?1 for the annuals with continuous corn > corn–soybean–canola rotation and 1.1 to 6.3 kg N₂O‐N ha^?1 yr^?1 for perennials. Nitrous oxide peak fluxes typically were associated with precipitation events that closely followed fertilization. Bayesian modeling of N₂O fluxes based on measured environmental factors explained 33% of variability across all systems. Models trained on single systems performed well in most monocultures (e.g., R² = 0.52 for poplar) but notably worse in polycultures (e.g., R² = 0.17 for early successional, R² = 0.06 for restored prairie), indicating that simulation models that include N₂O emissions should be parameterized specific to particular plant communities. Our results indicate that perennial bioenergy crops in their establishment phase emit less N₂O than annual crops, especially when not fertilized. These findings should be considered further alongside yield and other metrics contributing to important ecosystem services.     

Experimental evolution of the grain of metabolic specialization in yeast

Adaptation to any given environment may be accompanied by a cost in terms of reduced growth in the ancestral or some alternative environment. Ecologists explain the cost of adaptation through the concept of a trade‐off, by which gaining a new trait involves losing another trait. Two mechanisms have been invoked to explain the evolution of trade‐offs in ecological systems, mutational degradation, and functional interference. Mutational degradation occurs when a gene coding a specific trait is not under selection in the resident environment; therefore, it may be degraded through the accumulation of mutations that are neutral in the resident environment but deleterious in an alternative environment. Functional interference evolves if the gene or a set of genes have antagonistic effects in two or more ecologically different traits. Both mechanisms pertain to a situation where the selection and the alternative environments are ecologically different. To test this hypothesis, we conducted an experiment in which 12 experimental populations of wild yeast were each grown in a minimal medium supplemented with a single substrate. We chose 12 different carbon substrates that were metabolized through similar and different pathways in order to represent a wide range of ecological conditions. We found no evidence for trade‐offs between substrates on the same pathway. The indirect response of substrates on other pathways, however, was consistently negative, with little correlation between the direct and indirect responses. We conclude that the grain of specialization in this case is the metabolic pathway and that specialization appears to evolve through mutational degradation.     

Putative local adaptations modulate the interactions of the carnivorous plant Drosera uniflora Willd (1809) (Droseraceae) with cushion and shrub nurse plants

Cushion and shrub plants are typical high mountain nurse plants. In Magellanic tundras of the Cordillera del Sarao on the coast of Chile, the carnivorous plant Drosera uniflora grows in association with cushions of Donatia fascicularis and the shrubs Chusquea montana var. nigricans and Lepidothamnus fonkii. The different microhabitats for recruitment, in addition to the limited gene flow of D. uniflora, enable us to hypothesise that this plant manifests putative local adaptations, expressed in seed germination and population abundance. Our aim was to evaluate the local adaptation of D. uniflora to cushion and shrub microhabitats by estimating germination and abundance. Local adaptation of seed germination was determined by means of reciprocal transplant experiments. Abundance was determined in small plots located inside, on the edge and outside the nurse plants. Seed origin and growth substrate play a decisive role in D. uniflora germination. Seeds that originate from cushions plant habitat and germinate in the same substrate do so in greater numbers than when those which originate from shrubby habitats. Conversely, seeds that originate from shrubby habitat and germinate in the same substrate do not exhibit significant differences. Abundance was always greater inside than outside of the nurse plants. We concluded that availability and quality of different microhabitats for seed germination and recruitment, together with a limited gene flow, would trigger putative local adaptations in D. uniflora, modulating a long history of interactions with the plants that act as nurse plants.     

Ecological differentiation and diploid superiority across a moving ploidy contact zone

Plant polyploid complexes provide useful model systems for distinguishing between adaptive and nonadaptive causes of parapatric distributions in closely related lineages. Polyploidy often gives rise to morphological and physiological changes, which may be adaptive to different environments, but separate distributions may also be maintained by reproductive interference caused by postzygotic reproductive isolation. Here, we test the hypothesis that diploid and descendent polyploid races of the wind-pollinated herb Mercurialis annua , which are found in parapatry over an environmental gradient in northeast Spain, are differentiated in their ecophysiology and life history. We also ask whether any such differences represent adaptations to their different natural environments. On the basis of a series of reciprocal transplant experiments in the field, and experiments under controlled conditions, we found that diploid and polyploid populations of M. annua are ecologically differentiated, but that they do not show local adaptation; rather, the diploids have higher fitness than the polyploids across both diploid- and polyploid-occupied regions. In fact, diploids are currently displacing polyploids by advancing south on two separate fronts in Spain, and previous work has shown that this displacement is being driven to a large extent by asymmetrical pollen swamping. Our results here suggest that ecophysiological superiority of the diploids may also be contributing to their expansion.     

花部重金属积累对植物-传粉昆虫互惠关系影响的研究进展

传粉昆虫急剧下降是当前全球生态学家最为关注的热点问题之一,全球气候变化、土地利用改变、生境破碎化以及工农业生产带来的有害物质如杀虫剂等均有重要影响。相比而言,土壤重金属污染对传粉昆虫的潜在影响缺乏深入评价。土壤重金属会进入植物组织如花部,在传粉过程中传递到传粉者体内,并通过影响传粉者行为改变植物雌雄适合度,全面梳理相关研究进展和存在的问题,有助于提升对重金属污染带来的生态后果的全面认识,了解动植物相互关系对环境变化的响应。本文结合前期的研究成果,从重金属在植物花部中的积累模式、花部重金属积累对植物雌雄适合度的影响、经花部报酬介导的重金属积累对蜂类传粉者传粉行为、生活史关键环节的影响等进行综述,以期为理解花部重金属积累对植物与传粉昆虫互惠关系的影响,进而拓展关于土壤重金属污染与传粉昆虫数量减少之间的内在联系的科学认识。     

Maladaptation beyond a geographic range limit driven by antagonistic and mutualistic biotic interactions across an abiotic gradient

Species’ geographic range limits often result from maladaptation to the novel environments beyond the range margin. However, we rarely know which aspects of the n‐dimensional environment are driving this maladaptation. Especially of interest is the influence of abiotic versus biotic factors in delimiting species’ distributions. We conducted a 2‐year reciprocal transplant experiment involving manipulations of the biotic environment to explore how spatiotemporal gradients in precipitation, fatal mammalian herbivory, and pollination affected lifetime fitness within and beyond the range of the California annual plant, Clarkia xantiana ssp. xantiana. In the first, drier year of the experiment, fitness outside the range edge was limited mainly by low precipitation, and there was some evidence for local adaptation within the range. In the second, wetter year, we did not observe abiotic limitations to plant fitness outside the range; instead biotic interactions, especially herbivory, limited fitness outside the range. Together, protection from herbivory and supplementation of pollen resulted in three‐ to sevenfold increases in lifetime fitness outside the range margin in the abiotically benign year. Overall, our work demonstrates the importance of biotic interactions, particularly as they interact with the abiotic environment, in determining fitness beyond geographic range boundaries.     

Breakpoint mapping of a novel de novo translocation t(X;20)(q11.1;p13) by positional cloning and long read sequencing

Disease associated chromosomal rearrangements often have break points located within disease causing genes or in their vicinity. The purpose of this study is to characterize a balanced reciprocal translocation in a girl with intellectual disability and seizures by positional cloning and whole genome sequencing. The translocation was identification by G- banding and confirmed by WCP FISH. Fine mapping using BAC clones and whole genome sequencing using Oxford nanopore long read sequencing technology for a 1.46 X coverage of the genome was done. The positional cloning showed split signals with BAC RP11-943 J20. Long read sequencing analysis of chimeric reads carrying parts of chromosomes X and 20 helped to identify the breakpoints to be in intron 2 of ARHGEF9 gene on Xp11.1 and on 20p13 between RASSF2 and SLC23A2 genes. This is the first report of translocation which successfully delineated to single base resolution using Nanopore sequencing. The genotype-phenotype correlation is discussed.     

Estimation of the proportion of genetically unbalanced spermatozoa in the semen of boars carrying chromosomal rearrangements using FISH on sperm nuclei

Many chromosomal rearrangements are detected each year in France on young boars candidates for reproduction. The possible use of these animals requires a good knowledge of the potential effect of the rearrangements on the prolificacy of their mates. This effect can be estimated by an accurate determination of the rate of unbalanced spermatozoa in the semen of boars which carry the rearrangements. Indeed, these spermatozoa exhibiting normal fertilizing ability are responsible for an early embryonic mortality, and then, for a decrease of the litter sizes. The "spermFISH" technique, i.e. fluorescent in situ hybridization on decondensed sperm heads, has been used on several occasions in Man, in this perspective. In livestock species, this method was formerly used mainly for semen sexing purposes. We used it, for the first time, to estimate the rates of imbalance in the semen of four boars carrying chromosomal rearrangements: two reciprocal translocations, rcp(3;15)(q27;q13) and rcp(12;14)(q13;q21), as well as two independent cases of trisomy 18 mosaicism. The rates of unbalanced gametes were relatively high for the two reciprocal translocations (47.83% and 24.33%, respectively). These values differed from the apparent effects of the rearrangements estimated using a limited number of litters: a decrease in prolificacy of 23% (estimation obtained using the results of 6 litters) and 39% (57 litters), respectively for the 3/15 and 12/14 translocations. The imbalance rates were much lower for the trisomy mosaics (0.58% and 1.13%), suggesting a very moderate effect of this special kind of chromosomal rearrangement.     

Using flowering times and leaf numbers to model the phases of photoperiod sensitivity in Antirrhinum majus L

A model has been developed that can be used to determine the phases of sensitivity to photoperiod for seedlings subjected to reciprocal transfers at regular intervals between long (LD) and short day (SD) conditions. The novel feature of this approach is that it enables the simultaneous analysis of the time to flower and number of leaves below the inflorescence. A range of antirrhinum cultivars were grown, all of which were shown to be quantitative long-day plants. Seedlings were effectively insensitive to photoperiod when very young (juvenile). However, after the end of the juvenile phase, SD delayed flowering and increased the number of leaves below the inflorescence. Plants transferred from LD to SD showed a sudden hastening of flowering and a decrease in leaf number once sufficient LD had been received for flower commitment. Photoperiod had little effect on the rate of flower development. The analysis clearly identified major cultivar differences in the length of the juvenile phase and the photoperiod-sensitive inductive phase in both LD and SD.     

Bayesian meta-analysis for longitudinal data models using multivariate mixture priors

We propose a class of longitudinal data models with random effects that generalizes currently used models in two important ways. First, the random-effects model is a flexible mixture of multivariate normals, accommodating population heterogeneity, outliers, and nonlinearity in the regression on subject-specific covariates. Second, the model includes a hierarchical extension to allow for meta-analysis over related studies. The random-effects distributions are decomposed into one part that is common across all related studies (common measure), and one part that is specific to each study and that captures the variability intrinsic between patients within the same study. Both the common measure and the study-specific measures are parameterized as mixture-of-normals models. We carry out inference using reversible jump posterior simulation to allow a random number of terms in the mixtures. The sampler takes advantage of the small number of entertained models. The motivating application is the analysis of two studies carried out by the Cancer and Leukemia Group B (CALGB). In both studies, we record for each patient white blood cell counts (WBC) over time to characterize the toxic effects of treatment. The WBCs are modeled through a nonlinear hierarchical model that gathers the information from both studies.