志贺菌基因组进化研究进展

志贺菌属(Shigella)是引起全球范围内细菌性痢疾的重要病原菌.近年来,多重耐药型和新血清型志贺菌的不断出现给志贺菌的监测和防控带来了新的挑战.基因组学的快速发展为深入了解志贺菌的进化来源、变异机制及传播规律等提供了极大的帮助,对控制细菌性痢疾的蔓延具有重要的科学意义.本文首先从遗传来源角度探讨志贺菌与大肠杆菌的进化关系及其可能的分子机制,随后对福氏、宋内和1型痢疾志贺菌的基因组进化进展进行了总结,详细描述了它们的时空分布特点以及耐药基因变异在进化中所发挥的作用,以期为志贺菌的研究和防控提供参考.     

The impact of rate heterogeneity on inference of phylogenetic models of trait evolution

Rates of trait evolution are known to vary across phylogenies; however, standard evolutionary models assume a homogeneous process of trait change. These simple methods are widely applied in small‐scale phylogenetic studies, whereas models of rate heterogeneity are not, so the prevalence and patterns of potential rate variation in groups up to hundreds of species remain unclear. The extent to which trait evolution is modelled accurately on a given phylogeny is also largely unknown because studies typically lack absolute model fit tests. We investigated these issues by applying both rate‐static and variable‐rates methods on (i) body mass data for 88 avian clades of 10–318 species, and (ii) data simulated under a range of rate‐heterogeneity scenarios. Our results show that rate heterogeneity is present across small‐scaled avian clades, and consequently applying only standard single‐process models prompts inaccurate inferences about the generating evolutionary process. Specifically, these approaches underestimate rate variation, and systematically mislabel temporal trends in trait evolution. Conversely, variable‐rates approaches have superior relative fit (they are the best model) and absolute fit (they describe the data well). We show that rate changes such as single internal branch variations, rate decreases and early bursts are hard to detect, even by variable‐rates models. We also use recently developed absolute adequacy tests to highlight misleading conclusions based on relative fit alone (e.g. a consistent preference for constrained evolution when isolated terminal branch rate increases are present). This work highlights the potential for robust inferences about trait evolution when fitting flexible models in conjunction with tests for absolute model fit.     

呼吸窘迫综合征早产儿血清VA、PCT、TNF-α及CRP水平的表达及临床意义

目的:探讨呼吸窘迫综合征(RDS)早产儿血清维生素A(VA)、降钙素原(PCT)、肿瘤坏死因子-α(TNF-α)及C反应蛋白(CRP)水平的表达及临床意义。方法:选取2015年2月～2018年5月期间青岛市妇女儿童医院收治的90例RDS早产儿纳入观察组,根据RDS分级将观察组分为轻度组48例,中重度组42例。另选取同期于本院出生的非RDS早产儿35例作为对照组。根据血清VA水平将125例早产儿分为VA缺乏组(n=72),亚临床VA缺乏组(n=36),正常组(n=17)。比较观察组与对照组、轻度组与中重度组早产儿血清VA、PCT、TNF-α及CRP水平,比较不同血清VA水平早产儿的RDS发病情况,分析观察组早产儿血清VA与PCT、TNF-α及CRP水平的相关性。结果:观察组早产儿血清VA水平明显低于对照组(P0.05),而观察组早产儿血清PCT、TNF-α、CRP明显高于对照组(P0.05)。中重度组早产儿血清VA水平与轻度组比较差异无统计学意义(P0.05),而中重度组早产儿血清PCT、TNF-α、CRP水平明显高于轻度组(P0.05)。随着血清VA水平的升高,RDS发病率逐渐降低,组间比较差异有统计学意义(P0.05)。Pearson相关性分析显示,观察组早产儿血清VA与PCT、TNF-α及CRP水平无显著相关性(P0.05)。结论:RDS早产儿血清VA与PCT、TNF-α及CRP水平均存在明显异常,但四者无明显相关性,血清VA相对较低者更易发生RDS,临床可通过及时干预VA水平以降低RDS的发生风险。     

分泌性中耳炎患者外周血Th1Th2细胞及T淋巴细胞亚群水平的表达及临床意义

目的:探讨分泌性中耳炎(SOM)患者外周血T辅助细胞1(Th1)、T辅助细胞2(Th2)细胞因子及T淋巴细胞亚群水平的表达及其临床意义。方法:选取我院于2015年1月至2018年1月期间收治的SOM患者135例记为SOM组,根据病程将患者分为急性组(病程14d,49例)、亚急性组(病程14-30d,53例)、慢性组(病程30d,33例)。另外选择同期于我院进行体检的100例健康者为对照组。分别对比SOM组和对照组受试者、不同病程SOM患者外周血Th1细胞因子[干扰素(INF-γ)、白细胞介素-2(IL-2)]、Th2细胞因子[白细胞介素-4(IL-4)、白细胞介素-10(IL-10)]以及T淋巴细胞亚群[CD3~+、CD4~+、CD8~+、CD4~+/CD8~+]水平。采用Pearson相关性分析INF-γ、IL-2、IL-4、IL-10与CD3~+、CD4~+、CD8~+、CD4~+/CD8~+的相关性。结果:SOM组患者外周血INF-γ、IL-2、IL-4、IL-10水平高于对照组(P0.05);急性组患者外周血INF-γ、IL-2、IL-4、IL-10水平低于亚急性组、慢性组,亚急性组患者外周血INF-γ、IL-2、IL-4、IL-10水平低于慢性组(P0.05)。SOM组患者外周血CD3~+、CD4~+、CD4~+/CD8~+水平低于对照组,CD8~+水平高于对照组(P0.05);急性组患者外周血CD3~+、CD4~+、CD4~+/CD8~+水平高于亚急性组、慢性组,CD8~+水平低于亚急性组、慢性组,亚急性组患者外周血CD3~+、CD4~+、CD4~+/CD8~+水平高于慢性组,CD8~+水平低于慢性组(P0.05)。Pearson相关性分析结果显示,SOM患者外周血INF-γ、IL-4与CD8~+呈正相关(P0.05),IL-4与CD3~+、CD4~+呈负相关(P0.05)。结论:SOM患者外周血Th1Th2细胞因子、T淋巴细胞亚群水平均表现异常,且其水平与疾病发生和发展存在一定联系,通过监测Th1Th2细胞因子、T淋巴细胞亚群有助于评估SOM患者病情。     

Polyploidy does not control all: Lineage‐specific average chromosome length constrains genome size evolution in ferns

Recent studies investigating the evolution of genome size diversity in ferns have shown that they have a distinctive genome profile compared with other land plants. Ferns are typically characterized by possessing medium‐sized genomes, although a few lineages have evolved very large genomes. Ferns are different from other vascular plant lineages as they are the only group to show evidence for a correlation between genome size and chromosome number. In this study, we aim to explore whether the evolution of fern genome sizes is not only shaped by chromosome number changes arising from polyploidy but also by constraints on the average amount of DNA per chromosome. We selected the genus Asplenium L. as a model genus to study the question because of the unique combination of a highly conserved base chromosome number and a high frequency of polyploidy. New genome size data for Asplenium taxa were combined with existing data and analyzed within a phylogenetic framework. Genome size varied substantially between diploid species, resulting in overlapping genome sizes among diploid and tetraploid spleenworts. The observed additive pattern indicates the absence of genome downsizing following polyploidy. The genome size of diploids varied non‐randomly and we found evidence for clade‐specific trends towards larger or smaller genomes. The 578‐fold range of fern genome sizes have arisen not only from repeated cycles of polyploidy but also through clade‐specific constraints governing accumulation and/or elimination of DNA.     

Excavating ghost footprints and tangled trees from modern genomes

Due to pervasive gene flow and admixture, simple bifurcating trees often do not provide an accurate representation of relationships among diverging lineages, but limited resolution in the available genomic data and the spatial distribution of samples has hindered detailed insights regarding the evolutionary and demographic history of many species and populations. In this issue of Molecular Ecology, Foote et al. (2019) combine a powerful sampling design with novel analytical methods adopted from human genetics to describe previously unrecognized patterns of recurrent vicariance and admixture among lineages in the globally distributed killer whale (Orcinus orca). Based on sequence data from modern samples alone, they discover clear signatures of ancient admixture with a now extinct “ghost” lineage, providing one of the first accounts of archaic introgression in a nonhominid species. Coupling a cost‐effective sequencing strategy with novel analytical approaches, their paper provides a roadmap for advancing inference of evolutionary history in other nonmodel species, promising exciting times ahead for our field.     

Background selection and FST: Consequences for detecting local adaptation

Background selection is a process whereby recurrent deleterious mutations cause a decrease in the effective population size and genetic diversity at linked loci. Several authors have suggested that variation in the intensity of background selection could cause variation in F_ST across the genome, which could confound signals of local adaptation in genome scans. We performed realistic simulations of DNA sequences, using recombination maps from humans and sticklebacks, to investigate how variation in the intensity of background selection affects F_ST and other statistics of population differentiation in sexual, outcrossing species. We show that, in populations connected by gene flow, Weir and Cockerham's (1984; Evolution, 38 , 1358) estimator of F_ST is largely insensitive to locus‐to‐locus variation in the intensity of background selection. Unlike F_ST, however, d_XY is negatively correlated with background selection. Moreover, background selection does not greatly affect the false‐positive rate in F_ST outlier studies in populations connected by gene flow. Overall, our study indicates that background selection will not greatly interfere with finding the variants responsible for local adaptation.