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.     

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。     

Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genes

Plastid genomes (plastomes) have a quadripartite structure, but some species have drastically reduced or lost inverted repeat (IR) regions. IR regions are important for genome stability and the evolution rate. In the evolutionary process of gymnosperms, the typical IRs of conifers were lost, possibly affecting the evolutionary rate and selection pressure of genomic protein‐coding genes. In this study, we selected 78 gymnosperm species (51 genera, 13 families) for evolutionary analysis. The selection pressure analysis results showed that negative selection effects were detected in all 50 common genes. Among them, six genes in conifers had higher ω values than non‐conifers, and 12 genes had lower ω values. The evolutionary rate analysis results showed that 9 of 50 common genes differed between conifers and non‐conifers. It is more obvious that in non‐conifers, the rates of psbA (trst, trsv, ratio, dN, dS, and ω) were 2.6‐ to 3.1‐fold of conifers. In conifers, trsv, ratio, dN, dS, and ω of ycf2 were 1.2‐ to 3.6‐fold of non‐conifers. In addition, the evolution rate of ycf2 in the IR was significantly reduced. psbA is undergoing dynamic change, with an abnormally high evolution rate as a small portion of it enters the IR region. Although conifers have lost the typical IR regions, we detected no change in the substitution rate or selection pressure of most protein‐coding genes due to gene function, plant habitat, or newly acquired IRs.     

单细胞基因组测序技术新进展及其在生物医学中的应用

随着单细胞基因组测序技术的建立与发展,对细胞基因组特征的分析进入了单细胞水平.单细胞的基因组分辨率不但使研究人员能够在单细胞尺度上分析肿瘤细胞的异质性,也使得传统上难以检测的稀有细胞的基因组研究成为可能.这些稀有细胞往往具有重要的生物学意义或临床价值,如癌症患者血液中循环肿瘤细胞(circulating tumor c...     

基于单细胞转录组的视网膜母细胞瘤进展特征分析

视网膜母细胞瘤（retinoblastoma,RB）是婴幼儿最常见的眼内恶性肿瘤。在RB进展过程中的关键致病因素目前尚不十分清楚。因此,识别与RB进展密切相关的基因能为病情诊断及基因治疗提供重要信息。然而,肿瘤组织具有很强的细胞异质性,不同病理状态下的细胞,其功能及基因表达都可能呈现显著的差异。本研究从公共基因表达数据库（gene expression omnibus,GEO）下载了1例4个月肿瘤患者和1例2年患者的肿瘤及癌旁组织的单细胞转录组测序数据,从单细胞水平解析不同患病时长的RB肿瘤转录图谱,鉴定与RB进展有潜在关联的细胞亚群及基因集。结果显示,肿瘤组织与癌旁组织在单细胞转录图谱上具有整体的一致性,但视锥前体G1期细胞群、G2期细胞群以及小胶质细胞群在肿瘤与癌旁组织中的分布比例存在明显差异。进一步分析了这3种细胞群在RB肿瘤进展过程中的作用。研究发现,在RB肿瘤的早期阶段,视锥前体细胞在G1期异常增殖,随着RB肿瘤的进展,视锥前体G2期细胞比例显著增加。同时,RB进展过程的小胶质细胞群差异分析结果显示,主要参与免疫应答的关键基因包括RPL23、B2M、HLA家族基因。本研究可为RB发病机制及进展研究提供更多新视角和数据资源。     

Chemical characterization of rat cholecystokinin-58

Cholecystokinin-58 (CCK-58) was purified from rat intestines using an extraction method that yields large amounts of this peptide. Greater than 30% of total CCK immunoreactivity eluted before CCK-39 upon gel permeation chromatography (Sephadex G-50) if extracts were loaded onto Sep Pak cartridges before freezing. If the extracts were frozen and stored at −70°C for six weeks, only 20% of the material eluted in this region and total immunoreactivity was reduced by 50%, suggesting that proteases were active under these storage conditions. This early eluting peak was purified by reverse phase and ion-exchange HPLC to a single absorbance peak. Microsequence analysis of this peak detected AVLRPDSEP which is the amino terminus of rat CCK-58 predicted from the rat preprocholecystokinin cDNA. Because degradation of CCK-58 occurred in these extracts, it is possible that CCK-58 is the predominant molecule form in the rat small intestine.     

A flexible summary statistics-based colocalization method with application to the mucin cystic fibrosis lung disease modifier locus

Mucus obstruction is a central feature in the cystic fibrosis (CF) airways. A genome-wide association study (GWAS) of lung disease by the CF Gene Modifier Consortium (CFGMC) identified a significant locus containing two mucin genes, MUC20 and MUC4. Expression quantitative trait locus (eQTL) analysis using human nasal epithelia (HNE) from 94 CF-affected Canadians in the CFGMC demonstrated MUC4 eQTLs that mirrored the lung association pattern in the region, suggesting that MUC4 expression may mediate CF lung disease. Complications arose, however, with colocalization testing using existing methods: the locus is complex and the associated SNPs span a 0.2 Mb region with high linkage disequilibrium (LD) and evidence of allelic heterogeneity. We previously developed the Simple Sum (SS), a powerful colocalization test in regions with allelic heterogeneity, but SS assumed eQTLs to be present to achieve type I error control. Here we propose a two-stage SS (SS2) colocalization test that avoids a priori eQTL assumptions, accounts for multiple hypothesis testing and the composite null hypothesis, and enables meta-analysis. We compare SS2 to published approaches through simulation and demonstrate type I error control for all settings with the greatest power in the presence of high LD and allelic heterogeneity. Applying SS2 to the MUC20/MUC4 CF lung disease locus with eQTLs from CF HNE revealed significant colocalization with MUC4 (p = 1.31 × 10^?5) rather than with MUC20. The SS2 is a powerful method to inform the responsible gene(s) at a locus and guide future functional studies. SS2 has been implemented in the application LocusFocus.