Identification of novel loci influencing refractive error in East Asian populations using an extreme phenotype design

The global “myopia boom” has raised significant international concerns. Despite a higher myopia prevalence in Asia, previous large-scale genome-wide association studies (GWASs) were mostly based on European descendants. Here, we report a GWAS of spherical equivalent (SE) in 1852 Chinese Han individuals with extreme SE from Guangzhou (631 < ?6.00D and 574 > 0.00D) and Wenzhou (593 < ?6.00D and 54 > ?1.75D), followed by a replication study in two independent cohorts with totaling 3538 East Asian individuals. The discovery GWAS and meta-analysis identify three novel loci, which show genome-wide significant associations with SE, including 1q25.2 FAM163A, 10p11.22 NRP1/PRAD3, and 10p11.21 ANKRD30A/MTRNR2L7, together explaining 3.34% of SE variance. 10p11.21 is successfully replicated. The allele frequencies of all three loci show significant differences between major continental groups (P < 0.001). The SE reducing (more myopic) allele of rs10913877 (1q25.2 FAM163A) demonstrates the highest frequency in East Asians and much lower frequencies in Europeans and Africans (EAS = 0.60, EUR = 0.20, and AFR = 0.18). The gene-based analysis additionally identifies three novel genes associated with SE, including EI24, LHX5, and ARPP19. These results provide new insights into myopia pathogenesis and indicate the role of genetic heterogeneity in myopia epidemiology among different ethnicities.     

Two stochastic processes shape diverse senescence patterns in a single‐cell organism

Despite advances in aging research, a multitude of aging models, and empirical evidence for diverse senescence patterns, understanding of the biological processes that shape senescence is lacking. We show that senescence of an isogenic Escherichia coli bacterial population results from two stochastic processes. The first process is a random deterioration process within the cell, such as generated by random accumulation of damage. This primary process leads to an exponential increase in mortality early in life followed by a late age mortality plateau. The second process relates to the stochastic asymmetric transmission at cell fission of an unknown factor that influences mortality. This secondary process explains the difference between the classical mortality plateaus detected for young mothers’ offspring and the near nonsenescence of old mothers’ offspring as well as the lack of a mother–offspring correlation in age at death. We observed that lifespan is predominantly determined by underlying stochastic stage dynamics. Surprisingly, our findings support models developed for metazoans that base their arguments on stage‐specific actions of alleles to understand the evolution of senescence. We call for exploration of similar stochastic influences that shape aging patterns beyond simple organisms.     

Le site Paléolithique supérieur de Yudinovo : résultats des recherches archéologiques des années 2004–2016

The Upper Palaeolithic site of Yudinovo is one of the reference sites, located in the Desna River Basin. Multidisciplinary field studies, organized by the Desna mission (MAE RAS) and conducted between 2004 and 2016, have changed the vision existed so far on the structure and character of the Yudinovo site as well as on the duration of its occupations. The researchers found an ancient ford used by mammoths and other big mammals to cross the river, and a water source was one of the main factors in explaining the location of the Yudinovo site. The site has been occupied in a cyclical way for stays of varied duration. It was frequented by Prehistoric Men during the different seasons, and periods of occupation were apparently of different duration. The stratigraphy of the Yudinovo site reveals two major episodes in the evolution of the site. The dating of the lower archaeological layer dates back to 15,000–13,500 BC. J.C., while the upper layer is attributed to the period of 12,500–12,000 BC. The lower layer, which was formed during the major episode of occupation of the site, is rather thin and shows the complex stratigraphic structure. Various areas of activities, evacuation structures, storage areas with mammoth bones are discovered. Some elements of the lower archaeological layer are perfectly correlated with different episodes of sporadic occupation.     

Double-exponential kinetics of binding and redistribution of the fluorescent dyes in cell membranes witness for the existence of lipid microdomains

New technique of detecting lateral heterogeneity of the plasma membrane of living cells by means of membrane-binding fluorescent dyes is proposed. The kinetics of dye incorporation into the membrane or its lateral diffusion inside the membrane is measured and decomposed into exponential components by means of the Maximum Entropy Method. Two distinct exponential components are obtained consistently in all cases for several fluorescent dyes, two different cell lines and in different types of experiments including spectroscopy, flow cytometry and fluorescence recovery after photobleaching. These components are attributed to the liquid-ordered and disordered phases in the plasma membrane of studied cells in their dynamic equilibrium.     

Effect of detection heterogeneity in occupancy‐detection models: an experimental test of time‐to‐first‐detection methods

Imperfect detection can bias estimates of site occupancy in ecological surveys but can be corrected by estimating detection probability. Time‐to‐first‐detection (TTD) occupancy models have been proposed as a cost–effective survey method that allows detection probability to be estimated from single site visits. Nevertheless, few studies have validated the performance of occupancy‐detection models by creating a situation where occupancy is known, and model outputs can be compared with the truth. We tested the performance of TTD occupancy models in the face of detection heterogeneity using an experiment based on standard survey methods to monitor koala Phascolarctos cinereus populations in Australia. Known numbers of koala faecal pellets were placed under trees, and observers, uninformed as to which trees had pellets under them, carried out a TTD survey. We fitted five TTD occupancy models to the survey data, each making different assumptions about detectability, to evaluate how well each estimated the true occupancy status. Relative to the truth, all five models produced strongly biased estimates, overestimating detection probability and underestimating the number of occupied trees. Despite this, goodness‐of‐fit tests indicated that some models fitted the data well, with no evidence of model misfit. Hence, TTD occupancy models that appear to perform well with respect to the available data may be performing poorly. The reason for poor model performance was unaccounted for heterogeneity in detection probability, which is known to bias occupancy‐detection models. This poses a problem because unaccounted for heterogeneity could not be detected using goodness‐of‐fit tests and was only revealed because we knew the experimentally determined outcome. A challenge for occupancy‐detection models is to find ways to identify and mitigate the impacts of unobserved heterogeneity, which could unknowingly bias many models.     

A comprehensive examination of the network position hypothesis across multiple river metacommunities

The hierarchical branching nature of river networks can have a strong influence on the assembly of freshwater communities. This unique structure has spurred the development of the network position hypothesis (NPH), which states that the strength of different assembly processes depends on the community position in the river network. Specifically, it predicts that 1) headwater communities should be exclusively controlled by the local environment given that they are more isolated and environmentally heterogeneous relative to downstream reaches. In contrast, 2) downstream communities should be regulated by both environmental and dispersal processes due to increased connectivity given their central position in the riverscape. Although intuitive, the NPH has only been evaluated on a few catchments and it is not yet clear whether its predictions are generalizable. To fill this gap, we tested the NPH on river dwelling fishes using an extensive dataset from 28 French catchments. Stream and climatic variables were assembled to characterize environmental conditions and graph theory was applied on river networks to create spatial variables. We tested both predictions using variation partitioning analyses separately for headwater and downstream sites in each catchment. Only 10 catchments supported both predictions, 11 failed to support at least one of them, while in 7 the NPH was partially supported given that spatial variables were also significant for headwater communities. We then assembled a dataset at the catchment scale (e.g. topography, environmental heterogeneity, network connectivity) and applied a classification tree analysis (CTA) to determine which regional property could explain these results. The CTA showed that the NPH was not supported in catchments with high heterogeneity in connectivity among sites. In more homogeneously connected catchments, the NPH was only supported when headwaters were more environmentally heterogeneous than downstream sites. We conclude that the NPH is context dependent even for taxa dispersing exclusively within streams.     

大兴安岭原麝冬季的生境选择

2005年3～4月和2006年3月,在黑龙江省大兴安岭呼中自然保护区,采用机械布点法随机设置样线,对原麝(Moschus moschiferus)冬季生境选择进行了研究。对海拔、乔木密度、雪深、隐蔽度、食物丰富度、坡度和倒木数量进行2个独立样本的Mann-Whitey U检验,找出生境利用样方与任意样方的生态因子的差异。U检验的结果表明,原麝冬季喜欢活动在相对海拔高、乔木密度小、雪层浅、隐蔽度高、坡度陡且喜食食物丰富的区域;对植被类型、坡位、坡向、距水源距离、距人为干扰距离、动物干扰和碎石坡7个名词性变量采用卡方(Chi-square)统计进行显著性检验,卡方检验的结果表明:原麝冬季偏好远离人为干扰、接近碎石坡、阳坡和其他动物干扰较少的针阔混交林中;对以上14个生态因子进行主成分分析,结果表明,前6个特征值的累计贡献率达到72·318%,可以较好地反映原麝生境特征,根据主成分分析结果,将原麝冬季生境选择影响因子分别命名为空间因子(海拔、坡度、距碎石坡距离)、干扰因子(距人为干扰距离、距水源距离)、坡向因子(坡向、乔木密度)、坡位因子(坡位、动物干扰)、食物因子(食物丰富度、隐蔽度)和倒木因子(倒木数量)。     

同域分布的黑麂和小麂的时空生态位分化

生态位分化是解释物种共存的重要理论。Schonenr认为空间维度对生态位差异形成的影响程度最高,营养维度次之,时间维度则最后被启动。为验证这一假说,我们于2018年12月至2019年11月,在浙江清凉峰国家级自然保护区龙塘山区域采用公里网格法布设52台红外相机,对同域分布且食性相似的黑麂和小麂种群进行监测,计算平均拍摄率,分析不同季节黑麂和小麂对不同植被类型、海拔、坡位、水源距离的选择差异,并运用核密度估计法分析二者日活动节律及重叠程度。结果显示,(1)黑麂和小麂对空间生态位的选择出现分化：黑麂偏好针阔混交林,主要栖息于1 301～1 500 m的高海拔地区,回避下坡位和谷地,在距离水源较近的区域内活动频繁;小麂则偏好落叶阔叶林,主要栖息于901～1 100 m的中海拔地区,偏好中坡位,回避谷地,对水源距离没有明显的选择倾向。(2)黑麂和小麂均为晨昏性活动的昼行性动物,二者全年日活动节律重叠程度较高(Δ4=0.86),仅冬季较低(Δ1=0.65)。上述结果支持Schonenr的假说：首先,空间维度对物种生态位分化的影响大于时间维度,龙塘山区域黑麂和小麂主要通过选择不同的栖息地来增加空间...     

异质性光照条件下匍匐茎草本野草莓的克隆整合

通过盆栽实验,研究了匍匐茎草本野草莓在异质性光照条件下的克隆整合。结果显示克隆整合显著增强了野草莓胁迫分株段的生长,损—益分析表明未受胁迫分株没有显著损耗,整个克隆片段的生长得到显著提高。在局部遮荫处理,克隆整合对克隆形态可塑性的修饰作用没有观察到。最后,讨论了克隆植物对环境的生态适应意义。