The rates of introgression and barriers to genetic exchange between hybridizing species: sex chromosomes vs autosomes

Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.     

Evading resistance to gene drives

Gene drives offer the possibility of altering and even suppressing wild populations of countless plant and animal species, and CRISPR technology now provides the technical feasibility of engineering them. However, population-suppression gene drives are prone to select resistance, should it arise. Here, we develop mathematical and computational models to identify conditions under which suppression drives will evade resistance, even if resistance is present initially. Previous models assumed resistance is allelic to the drive. We relax this assumption and show that linkage between the resistance and drive loci is critical to the evolution of resistance and that evolution of resistance requires (negative) linkage disequilibrium between the two loci. When the two loci are unlinked or only partially so, a suppression drive that causes limited inviability can evolve to fixation while causing only a minor increase in resistance frequency. Once fixed, the drive allele no longer selects resistance. Our analyses suggest that among gene drives that cause moderate suppression, toxin-antidote systems are less apt to select for resistance than homing drives. Single drives of moderate effect might cause only moderate population suppression, but multiple drives (perhaps delivered sequentially) would allow arbitrary levels of suppression. The most favorable case for evolution of resistance appears to be with suppression homing drives in which resistance is dominant and fully suppresses transmission distortion; partial suppression by resistance heterozygotes or recessive resistance are less prone to resistance evolution. Given that it is now possible to engineer CRISPR-based gene drives capable of circumventing allelic resistance, this design may allow for the engineering of suppression gene drives that are effectively resistance-proof.     

Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo’s law of irreversible loss

Dollo’s law posits that evolutionary losses are irreversible, thereby narrowing the potential paths of evolutionary change. While phenotypic reversals to ancestral states have been observed, little is known about their underlying genetic causes. The genomes of budding yeasts have been shaped by extensive reductive evolution, such as reduced genome sizes and the losses of metabolic capabilities. However, the extent and mechanisms of trait reacquisition after gene loss in yeasts have not been thoroughly studied. Here, through phylogenomic analyses, we reconstructed the evolutionary history of the yeast galactose utilization pathway and observed widespread and repeated losses of the ability to utilize galactose, which occurred concurrently with the losses of GALactose (GAL) utilization genes. Unexpectedly, we detected multiple galactose-utilizing lineages that were deeply embedded within clades that underwent ancient losses of galactose utilization. We show that at least two, and possibly three, lineages reacquired the GAL pathway via yeast-to-yeast horizontal gene transfer. Our results show how trait reacquisition can occur tens of millions of years after an initial loss via horizontal gene transfer from distant relatives. These findings demonstrate that the losses of complex traits and even whole pathways are not always evolutionary dead-ends, highlighting how reversals to ancestral states can occur.     

牛磺酸上调基因1(TUG1)对肝纤维化的作用及其机制*

目的:探讨牛磺酸上调基因1(TUG1)在肝纤维化中的作用机制。方法:按照文献建立TGF-β1(5 ng/ml)刺激的活化肝星状细胞模型和经典的1%DMN(1 ml/kg/d)致大鼠肝纤维化模型,将肝纤维化大鼠和活化肝星状细胞(HSC)均分为模型对照组、阴性对照组(沉默TUG1阴性对照)、siRNA干扰组(TUG1基因沉默组)。实验结束后利用苏木精-伊红(HE)染色检测大鼠肝脏组织病理变化;采用逆转录-聚合酶链反应(RT-PCR)法、蛋白免疫印记(Western blot)分别测定大鼠肝组织及活化肝星状细胞中α-平滑肌肌动蛋白(α-SMA)、TUG1、I型胶原蛋白(collagenI)、基质金属蛋白酶-2(MMP-2)、金属蛋白酶组织抑制因子(TIMP-1)、Smad2、Smad3表达水平。结果:肝组织病理学检查显示,沉默TUG1能够明显缓解肝脏纤维化病理改变,Western blot结果显示,沉默TUG1能够显著降低大鼠肝组织和活化肝星状细胞中TUG1、α-SMA、collagenI、MMP-2、TIMP-1、Smad2、Smad3基因与蛋白表达水平(P＜0.05)。与模型对照组相比,阴性对照组的TUG1、α-SMA的蛋白与基因水平明显升高(P＜0.05)。与模型对照组和阴性对照组相比,siRNA干扰组中TUG1, α-SMA, collagenI, MMP-2, TIMP-1, Smad2 and Smad3的蛋白和基因水平显著降低(P＜0.05),而在模型对照组和阴性对照组中TUG1, α-SMA, collagenI, MMP-2, TIMP-1, Smad2 and Smad3的蛋白和基因表达水平之间差异无显著性。结论:TUG1在肝纤维化组织和活化的肝星状细胞中显著上调,沉默TUG1可能通过抑制转化生长因子-β1(TGF-β1)/Smad信号通路改善1%DMN致大鼠肝纤维化病理损伤,降低活化肝星状细胞中纤维化相关蛋白水平,发挥抗肝纤维化的作用。     

既主内政, 又辖外交——以PHR为中心的基因网络调控植物-菌根真菌的共生

磷是植物生长发育必需的大量矿质营养元素, 但自然界大部分土壤都存在严重缺磷的问题。为了适应这一营养逆境, 植物演化出一系列低磷胁迫应答反应。通过改变基因的转录水平调控低磷胁迫应答反应, 而转录因子PHR1在调控植物对低磷胁迫的转录响应中起关键作用。此外, 大部分陆生植物还能与丛枝菌根真菌建立共生关系, 通过丛枝菌根真菌更有效地从土壤中获取磷元素。最近, 中国科学院分子植物科学卓越创新中心王二涛研究组发现, 以PHR为中心的转录调控网络控制植物-丛枝菌根真菌共生的建立。因此, PHR不但在维持植物细胞自身的磷稳态中发挥作用, 而且参与植物与外界微生物的相互作用, 为植物有效地从环境中获得磷元素提供了另外一条途径。     

Evolution and diversity of axon guidance Robo receptor family genes

The diversity of axon guidance (AG) receptors reflects gains in complexity of the animal nervous system during evolution. Members of the Roundabout (Robo) family of receptors interact with Slit proteins and play important roles in many developmental processes, including AG and neural crest cell migration. There are four members of the Robo gene family. However, the evolutionary history of Robo family genes remain obscure. We analyzed the distribution of Robo family members in metazoan species ranging in complexity from hydras to humans. We undertook a phylogenetic analysis in metazoans, synteny analysis, and ancestral chromosome mapping in vertebrates, and detected selection pressure and functional divergence among four mammalian Robo paralogs. Based on our analysis, we proposed that the ancestral Robo gene could have undergone a tandem duplication in the vertebrate ancestor; then one round of whole genome duplication events occurred before the divergence of ancestral lamprey and gnathostome, generating four paralogs in early vertebrates. Robo4 paralog underwent segmental loss in the following evolutionary process. Our results showed that Robo3 paralog is under more powerful purifying selection pressure compared with other three paralogs, which could correlate with its unique expression pattern and function. Furthermore, we found four sites under positive selection pressure on the Ig1‐2 domains of Robo4 that might interfere with its binding to Slits ligand. Diverge analysis at the amino acid level showed that Robo4 paralog have relatively greater functional diversifications than other Robo paralogs. This coincides with the fact that Robo4 predominantly functions in vascular endothelial cells but not the nervous system.     

桑黄Zn(II)2Cys6锌簇蛋白转录因子及其在不同碳氮源条件下的表达

Zn(II)2Cys6锌簇蛋白转录因子（C6 zinc）在真菌次生代谢产物合成中发挥重要作用。本研究首先利用本地BLAST,从桑黄Sanghuangporus sanghuang全基因组中获得Zn(II)2Cys6锌簇蛋白转录因子编码基因,并利用生物信息学手段分析编码蛋白保守结构域、一级结构及二级结构,构建蛋白系统发育树,最后利用半定量PCR对它们在不同碳源和氮源培养条件下的表达情况进行检测。结果显示:从桑黄基因组中分析获得的11个Zn(II)2Cys6锌簇蛋白均具有Cy6型锌指基序,属于GAL4型锌簇蛋白转录因子;它们均为不稳定亲水性蛋白,具磷酸化修饰位点,糖基化修饰位点较少或没有,定位于细胞核中;其二级结构主要以无规卷曲和α螺旋为主;系统发育树分析结果显示,桑黄Zn(II)2Cys6锌簇蛋白分为2个大分支,其中Ⅰ类分支转录因子的保守结构域分布于蛋白N-端,Ⅱ类分支转录因子的保守结构域则分布于蛋白C-端;11个桑黄Zn(II)2Cys6锌簇蛋白转录因子在不同培养基培养的菌丝体中呈现差异化表达,其中,肌醇培养基和乳糖培养基能够有效促进大部分锌簇蛋白转录因子的表达;另外,基因簇分析显示桑黄锌簇蛋白SHCZ4可能是NRPS-PKS杂合基因簇体系的途经特异性转录因子。该结果将为桑黄次生代谢产物合成调控相关转录因子的研究以及潜在次生代谢相关基因簇的挖掘提供参考依据。     

子宫内膜癌组织残疾基因同源物2、核连蛋白-2、黏蛋白4的表达及与预后的关系研究

目的:研究子宫内膜癌组织残疾基因同源物2(DAB2)、核连蛋白-2(nucleobindin-2)、黏蛋白4(MUC4)的表达及与预后的关系。方法:将我院从2015年1月2017年1月收治的子宫内膜癌患者82例纳入研究。分别采集所有患者的子宫内膜癌组织以及癌旁正常组织,以免疫组化法检测不同子宫内膜组织中的DAB2、nucleobindin-2、MUC4表达情况并进行对比。分析子宫内膜癌组织DAB2、nucleobindin-2、MUC4阳性率与临床病理特征的关系。此外,通过Kaplan-Merier生存曲线分析上述蛋白表达与预后的关系,并以Cox比例风险回归模型分析子宫内膜癌患者预后的影响因素。结果:子宫内膜癌组织DAB2阳性率低于癌旁正常组织,而nucleobindin-2、MUC4阳性率均高于癌旁正常组织(均P<0.05)。TNM分期ⅢⅣ期、淋巴结转移子宫内膜癌患者的DAB2阳性率低于TNM分期ⅠⅡ期、无淋巴结转移患者,而nucleobindin-2、MUC4阳性率均高于TNM分期ⅠⅡ期、无淋巴结转移患者(均P<0.05)。所有患者均进行时长360个月的随访,中位随访时间为31个月,至随访结束,DAB2蛋白阳性患者的无进展生存率分别为66.67%(20/30),明显高于DAB2蛋白阴性患者的19.23%(10/52);而nucleobindin-2、MUC4蛋白阳性患者的无进展生存率分别为22.95%(14/61)、24.56%(14/57),明显低于nucleobindin-2、MUC4蛋白阴性患者的76.19%(16/21)、64.00%(16/25),差异均有统计学意义(均P<0.05)。Cox比例风险回归模型分析结果可得:TNM分期、淋巴结转移以及DAB2蛋白阴性、nucleobindin-2蛋白阳性、MUC4蛋白阳性均是子宫内膜癌患者预后的影响因素(均P<0.05)。结论:子宫内膜癌组织DAB2存在异常低表达,而nucleobindin-2、MUC4均存在异常高表达,联合检测上述三项蛋白表达情况可能有助于子宫内膜癌的诊断和预后评估。