Phylogeny of the green lacewing Chrysoperla nipponensis species‐complex (Neuroptera: Chrysopidae) in China,based on mitochondrial sequences and AFLP data

Abstract Several studies have indicated that the green lacewing, Chrysoperla nipponensis (Neuroptera: Chrysopidae) may include more than one valid species. We investigated the phylogenetic status of Chrysoperla nipponensis s.l. in China and Japan using mitochondrial sequences and AFLP data. The molecular phylogenetic analyses based on mitochondrial genes showed that the C. nipponensis species‐complex comprises four clades, each having high support values. In addition, the phylogenetic tree based on AFLP data indicates that the species‐complex comprises three groups. These results confirm that C. nipponensis s.l. comprises at least three genetically distinct clades and suggests that two of these clades may be closely related to populations of C. nipponensis in Japan. However, these clades cannot be recognized as species until analysis of their courtship songs has been completed.     

肥厚型心肌病的致病分子机制研究进展

肥厚型心肌病(Hypertrophic cardiomyopathy,HCM)是以左心室及室间隔不对称肥厚为基本特征的原发性心肌病,其发病率约为0.2%,是青少年和运动员心源性猝死的最常见原因。HCM的发病年龄、发病程度和猝死风险等临床表型具有多样性,通常呈常染色体显性遗传。目前已报道的HCM相关突变超过900种,主要定位在β肌球蛋白重链基因、肌球蛋白结合蛋白C基因、心脏肌钙蛋白T基因等13个心脏肌节蛋白基因;另一方面,越来越多的研究显示线粒体基因突变与HCM发生相关。文章在简单介绍HCM形态学特征及临床表型的基础上,着重综述了HCM的致病分子机制及其最新研究进展。     

Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles

Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation–extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings.     

基因序列在小蜂总科分子系统发育研究中的应用

总结了线粒体基因和核基因在膜翅目小蜂总科分子系统发育研究中的应用.核基因中,28S rDNA序列应用最广泛,探讨的问题从种级到科级不等;其次是ITS序列,主要用于探讨种及种级以下阶元问题;18S rDNA适于探讨科级以上高级阶元的问题.线粒体基因中,16S rDNA和3个蛋白编码基因COⅠ、COⅡ和Cytb,主要用于属种级系统发育关系研究.核基因间、线粒体基因间、核基因和线粒体基因间以及分子数据和形态数据间进行的联合分析,在解决不同层次的问题中均有应用.建议对更多的小蜂类群测定线粒体基因和核基因的序列,不断寻找新的基因对小蜂分子系统发育研究进行充实和拓展.     

The role of vicariance vs. dispersal in shaping genetic patterns in ocellated lizard species in the western Mediterranean

The schism between North Africa and Southern Europe caused by the opening of the Strait of Gibraltar and the consequent refilling of the Mediterranean basin at the end of Messinian salinity crisis (MSC), 5.33 million years ago, has been advocated as the main event shaping biogeographical patterns in the western Mediterranean as exemplified by the distribution of species and subspecies and genetic variation within the ocellated lizard group. To reassess the role of the MSC, partial sequences of three mitochondrial DNA genes (cytochrome b , 12S and 16S ribosomal RNA) and two nuclear genes (β-fibrinogen and C-mos) from species of the ocellated lizard group were analysed. Three alternative hypotheses were tested: that divergence was initiated (i) by post-MSC vicariance as the basin filled, (ii) when separate populations established either side of the strait by pre-MSC overseas dispersal, and (iii) by post-MSC overseas dispersal. The pattern and level of divergence detected clearly refute the post-MSC vicariance hypothesis, and support a model of divergence initiated by earlier overseas dispersal. Indeed, our best estimate is that the basal Euro-African divergence predates the MSC event by several million years. The estimated divergence times among the populations in former Miocene Mediterranean islands, the current Betic and Rifian mountains, from adjacent mainland populations suggest overseas dispersal for the former and overland dispersal, or perhaps vicariance, for the latter. These results suggest that the MSC may have played a much less important role in shaping the current western Mediterranean biogeographical patterns than might have been anticipated from the dramatic nature of the episode.     

线粒体疾病与核基因-线粒体基因的表达调控

线粒体与疾病是当前生物医学领域最前沿之一。本文简单介绍线粒体生物医学的基础知识、线粒体疾病的遗传模式,综述了近年来在线粒体DNA（mtDNA）突变和疾病、核基因突变和疾病等领域的研究进展,着重阐明核基因（特别是核修饰基因）调控mtDNA突变致病表达的分子机制。     

食肉目猫科物种的系统发育学研究概述

猫科动物(Felidae)是食肉目中肉食性最强的一科, 其中许多成员是人们最熟悉、最引人注目的动物, 也是各地的顶级食肉动物。目前37个现存猫科物种中有36个已经被列为濒危和稀有对象。食肉目猫科物种的进化历史是一个快速辐射和较近时期发生的物种形成事件, 使得猫科物种之间系统发育关系的重建非常困难, 一直处于广泛争论的状态。构建可靠的猫科系统发育关系, 具有重要的进化理论意义和保护生物学价值。文章对猫科物种的系统发育学研究进展, 包括来自于形态学特征、细胞学和分子生物学方面的证据做简要概述, 并提出目前研究中存在的问题。以期对今后猫科物种的系统发育方面的进一步研究工作具有指导意义, 并为该类群的生物多样性资源保护提供科学依据。     

西藏牦牛mtDNA D-loop区的遗传多样性及其遗传分化

通过测定和分析西藏11个牦牛类群114个个体的mtDNA D-loop区全序列,对西藏牦牛的遗传多样性、类群间的亲缘关系及其遗传分化进行了研究。结果表明:①西藏牦牛mtDNA D-loop区全序列长度为890—896 bp,4种核苷酸T、C、A、G的平均比例分别为28.5%、25.3%、32.4%、13.8%,西藏牦牛mtDNA D-loop区富含碱基A+T,表现出一定的碱基偏好性。②共检测到130个变异位点,占分析总位点数的14.33%;其中单一多态位点85个,占多态位点总数的65.38%,简约信息位点45个,占多态位点总数的34.62%。序列变异中碱基缺失、插入和碱基替换等均有,其中碱基替换变异类型中转换114次,颠换12次,在转换变异类型中以A/G、T/C为主,占95.61%,在颠换变异类型中以A/T为主,占75%。③在114个个体中鉴定出90种单倍型,单倍型多样性为0.981±0.008,核苷酸多样性为0.01056±0.00701,均说明西藏牦牛具有丰富的单倍型类型。④90种单倍型分为2个聚类簇(Ⅰ、Ⅱ),聚类簇Ⅰ包含80种单倍型,占全部单倍型的88.89%,涵盖本研究中所有的西藏牦牛类群;聚类簇Ⅱ中有10种单倍型,占单倍型总数的11.11%,涉及的类群有工布江达、帕里、丁青、巴青、江达、类乌齐、桑桑、桑日、斯布,说明西藏牦牛可能有2个母系起源。⑤西藏牦牛类群间核苷酸分歧度(Dxy)在0.503%—1.416%之间,聚类分析和AMOVA分析显示西藏牦牛可分为两大类,康布牦牛、嘉黎牦牛为一类,其余的牦牛类群为另一类。     

Mammalian genes as molecular clocks?

Summary In analyzing the silent nucleotide substitutions in some mammalian mitochondrial mRNA coding genes, we had found that the frequency of each of the four nucleotides in rat, mouse, and cow, but not in humans, is the same in the silent third codon position (Lanave C, Preparata G, Saccone C, Serio G (1984) J Mol Evol 20:86-93). Because our findings for these three species were compatible with a stationary Markov process for the evolution of nucleotide sequences, we applied such a model to calculate the effective evolutionary silent substitution rate (v_s) and the divergence times among the species. In this paper we have analyzed the first and second codon positions in the same mammalian mitochondrial genes. We found that in the first and second codon positions the human mitochondrial genes satisfy the stationarity conditions. This has allowed us to use the stochastic model mentioned above to calculate the divergence times among mouse, rat, cow, and human. Furthermore, we have analyzed the silent substitution rate in one nuclear gene for these four mammals. We found that in this gene the effective silent substitution rate is about 3 times lower than in mitochondrial genes, and that humans are in this case stationary with respect to the other three mammals in the third codon position as well. Application of our Markov model to this latter gene yields divergence times consistent with our previous determinations.     

Matching loci surveyed to questions asked in phylogeography

Although mitochondrial DNA (mtDNA) has long been used for assessing genetic variation within and between populations, its workhorse role in phylogeography has been criticized owing to its single-locus nature. The only choice for testing mtDNA results is to survey nuclear loci, which brings into contrast the difference in locus effective size and coalescence times. Thus, it remains unclear how erroneous mtDNA-based estimates of species history might be, especially for evolutionary events in the recent past. To test the robustness of mtDNA and nuclear sequences in phylogeography, we provide one of the largest paired comparisons of summary statistics and demographic parameters estimated from mitochondrial, five Z-linked and 10 autosomal genes of 30 avian species co-distributed in the Caucasus and Europe. The results suggest that mtDNA is robust in estimating inter-population divergence but not in intra-population diversity, which is sensitive to population size change. Here, we provide empirical evidence showing that mtDNA was more likely to detect population divergence than any other single locus owing to its smaller N_e and thus faster coalescent time. Therefore, at least in birds, numerous studies that have based their inferences of phylogeographic patterns solely on mtDNA should not be readily dismissed.