表遗传学推动新一轮遗传学的发展

科学的发展孕育着突破,表遗传学研究推动着新一轮的遗传学的发展。表遗传学是研究没有DNA序列变化的、可遗传的表达改变。表遗传学不仅对医学和农业有重要的实践意义,而且还提供了理解遗传和进化的新观点。研究表明,人类基因组含有两类遗传信息,遗传学信息提供了合成生命所必需蛋白质的模板,而表遗传学信息提供了何时、何地和怎样地应用遗传学信息的指令;遗传学和表遗传学的关系有如“阴阳”,它们既相区别又协同参与调节生命活动。同时还讨论了基因的概念、进化和epigenetics的中文译名等问题。表遗传学研究应引起国内学术界的关注。Abstract: Scientific development is pregnant with a breakthrough, epigenetic studies are pushing the genetics forward. Epigenetics is the study of heritable changes in gene expression that occurs without a change in DNA sequence. Epigenetics not only has practical significance for medicine and agriculture, but also provides new views on understanding heredity and evolution. Human genome contains information in two forms: the genetic information provides the blueprint for the manufacture of all the proteins necessary to create a living thing while the epigenetic information provides instructions on how, where, and when the genetic information should be used. The interrelationship of genetics and epigenetics is like a yin-yan, they are different from each other, and cooperatively take part in regulation of a variety of living activities. In this paper concept of gene and problems of evolution has been also discussed according to epigenetic viewpoints.     

黑素皮质素受体1——哺乳动物黑色素形成中的关键基因MC1R——the Key Gene in Mammalian Melanin Synthesis

黑色素的形成与产生在动物的生长发育过程中受到许多基因的调控。本文综述了近年来被广泛研究的哺乳动物黑色素形成调控中的一个关键基因——黑素皮质素受体1（melanocortin-1-receptor, MC1R）基因的作用机制、DNA序列变异与黑色素性状之间的关系,并且对另一重要的脊椎动物类群——鸟类中MC1R基因的确定与突变情况作以概述,此外对乌骨鸡富含黑色素的原因和鸟类的黑色素形成机制也进行了探讨。Abstract: The study of the molecular regulation mechanism of melanin synthesis during animal development has become a new focus recently .The synthesis and production of melanin during animal development are regulated by many genes. This paper summarized the molecular function mechanism of melanocortin-1-receptor (MC1R) gene and the relationship between the consequences of polymorphic variation of the gene and melanin traits, in addition to summarized the identification and mutation of MC1R gene in birds. Furthermore, the reason of abundant melanin in silkies and melanin synthesis mechanism in birds are all also discussed here.     

Study on fibroin heavy chain of the silkworm Bombyx mori by fluorescence in situ hybridization (FISH)

The sericulture industry plays a very important role in our national economy. Silkworm (Bombyx mori) is always regarded as a model animal and biological reactor. There have been detailed studies on the structure, expression and control and molecular evolution of silk genes. However, few, if any, reports are available on the localization of structural genes in silkworm by molecular cytogenetics. The present experiment has tentatively localized the Fib-H gene at the distal end of the 25th linkage group, namely at the 25-0.0 position, and verified that Fib-H has only one locus, thus providing a temporary solution to the problem about its localization.     

Intercontinental and intracontinental biogeography patterns and methods

The study of biogeography has benefited from the exponential increase of DNA sequence data from recent molecular systematic studies, the development of analytical methods in the last decade concerning divergence time estimation and geographic area analyses, and the availability of large-scale distributiofi data of species in many groups of organisms. The underlying principle of divergence time estimation from DNA and protein data is that sequence divergence depends on the product of evolutionary rate and time. With their molecular clock hypothesis, Zuckerkandl and Pauling （1965） separated rates of molecular evolution from time by incorporating fossil evidence. Originally,     

分子人类学与现代人的起源*

1953年Watson & Crick 对于DNA双螺旋结构模型的提出及对其遗传机理的解释,标志着现代分子生物学的诞生。其后短短50年的时间里,分子生物学在各个学科之间广泛渗透,相互促进,不断深入和发展。在以研究人类的起源和进化为首要任务的人类学领域,由于现代分子生物学理论和方法的应用,诞生了分子人类学这一全新的结合型分支学科,为人类学的发展提供了科学可信的研究方法和具发展前景的研究方向。系统地介绍了分子人类学的发展历史、研究方法及原理;另外,结合分子人类学在古人类学研究中的应用,讨论了关于现代人起源的“非洲起源说”和“多地区连续演化说”。Abstract: Since Watson & Crick put forward the double-helix model of DNA structure and hereditary mechanism in 1953, it is generally accepted that this event marks the birth of modern molecular biology. This new field of biology has experienced a flourishing development in the past 50 years. On one hand, the development of molecular biology has been deeply influencing many relative fields; on the other hand, its own proceeding pace has been accelerated by the reaction from the other fields. Anthropology is one of the fields most deeply impacted by the theory and method of molecular biology. Most importantly, molecular anthropology was born as a result of combination of molecular biology, anthropology as well as paleoanthropology. This new branch provides reliable method and vital direction for paleoanthropology. This paper systematically reviews the history, principle and method of molecular anthropology. Two hypotheses on the origin of modern human, which include “out-of-African theory” and “theory of multiregional evolution” are also discussed for the purpose of showing how molecular anthropology is applied in paleoanthropology.     

Special Issue on “Plant Genomics”

正We are very pleased to announce a special issue,to be published in the spring of 2019,on"Plant Genomics"in the journal Genomics,ProteomicsBioinformatics(GPB).The development of genomics has greatly accelerated and even renovated the plant research.The sequencing of plant genomes has greatly facilitated the research on gene functions.The multiple released genomes further promote the research on genome evolution and its functional     

Special Issue on “Plant Genomics”

正We are very pleased to announce a special issue,to be published in the spring of 2019,on‘‘Plant Genomics’’in the journal Genomics,ProteomicsBioinformatics(GPB).The development of genomics has greatly accelerated and even renovated the plant research.The sequencing of plant genomes has greatly facilitated the research on gene functions.The multiple released genomes further promote the research on genome evolution and its functional     

Special Issue on “Plant Genomics”

正We are very pleased to announce a special issue,to be published in the fall of 2018,on‘‘Plant Genomics’’in the journal Genomics,ProteomicsBioinformatics(GPB).The development of genomics has greatly accelerated and even renovated the plant research.The sequencing of plant genomes has greatly facilitated the research on gene functions.The multiple released genomes further promote the research on genome evolution and its functional     

Special Issue on ‘‘Plant Genomics”

正We are very pleased to announce a special issue, to be published in the summer of 2019,on ‘‘Plant Genomics’’ in the journal Genomics, ProteomicsBioinformatics (GPB).The development of genomics has greatly accelerated and even renovated the plant research.The sequencing of plant genomes has greatly facilitated the research on gene functions. The multiple released genomes further promote the research on genome evolution and its functional     

Special Issue on “Plant Genomics”

正We are very pleased to announce a special issue,to be published in Summer 2018,on "Plant Genomics" in the journal Genomics,ProteomicsBioinformatics(GPB).The development of genomics has greatly accelerated and even renovated the plant research.The sequencing of plant genomes has greatly facilitated the research on gene functions.The multiple released genomes further promote the research on genome evolution and its functional     

蚕类昆虫线粒体DNA研究及其在起源与进化研究中的应用

线粒体DNA(mtDNA)属母系遗传,进化速率较核基因快且基因组结构相对简单,已作为理想的分子标记广泛应用于昆虫群体遗传学及分子系统学等研究。本文对蚕类昆虫线粒体DNA在分子水平上的最新研究进展进行了较详细的阐述,重点介绍了蚕类昆虫线粒体基因组的组成及特征、mtDNA克隆与多态性及在蚕类昆虫分子系统学研究中的应用等。     

DNA在鸟类分子系统发育研究中的应用

鸟类分子系统发育研究中常用的DNA技术有DNA杂交、RFLP和DNA序列分析等。DNA杂交技术曾在鸟类中有过大规模的应用,并由此诞生了一套新的鸟类分类系统。在鸟类的RFLP分析中,用的最多的靶序列是线粒体DNA。DNA序列分析技术被认为是进行分子系统发育研究最有效、最可靠的方法。在DNA序列分析中,线粒体基因应用最广泛,但由于其自身的一些不足,近年来,不少学者把目光投向了核基因,将线粒体基因和核基因结合起来进行系统发育研究。目前在鸟类分子系统发育中,应用较多的核基因是scnDNA,其内含子可以用于中等阶元水平的系统研究,而外显子主要用于高等阶元的系统研究。除了分子标记自身的问题之外,鸟类分子系统发育研究中还存在着方法上的问题,包括分子标记的选择,样本数量以及数据处理等。今后鸟类分子系统发育研究应该更加注重方法的标准化。     

线粒体DNA及其提取方法

线粒体是存在于绝大多数真核细胞内的一种基本的重要的细胞器,其具有相对独立的遗传系统。线粒体基因在真核生物具有高保守性,线粒体DNA(mtDNA)已被广泛应用于发病机理、临床诊断、遗传变异、生物进化等多方面的研究。1981年,Anderson用氯化铯密度梯度分离得到线粒体DNA(mtDNA),进行了全序列分析。此后,mtDNA的研究日益得到重视。已有的mtDNA提取方法概括起来可分为密度梯度离心法、酶消化法、柱层析法、氯化铯超速离心法、碱变性法和改进高盐沉淀法等,通过对以上方法的比较,发现改进高盐沉淀法具有简便、经济、易重复等优点。     

Congruent Avian Phylogenies Inferred from Mitochondrial and Nuclear DNA Sequences

Recent molecular studies addressing the phylogenetic relationships of avian orders have had conflicting results. While studies using nuclear DNA sequences tend to support traditional taxonomic views, also supported by morphological data [(paleognaths (galloanseres (all other birds)))], with songbirds forming a clade within Neoaves (all other birds), analyses with complete mtDNA genomes have resulted in topologies that place songbirds as one of the earliest-diverging avian lineages. Considering that over half of the extant bird species are songbirds, these different results have very different implications for our understanding of avian evolution. We analyzed data sets comprising nearly 4 kb of mitochondrial DNA (mtDNA) (complete 12S, ND1, ND2, and cytochrome b) plus 600 bp of the nuclear gene c-mos for 15 birds that were chosen to represent all major avian clades and to minimize potential long-branch attraction problems; we used a partition-specific maximum likelihood approach. Our results show congruence with respect to the ingroup among phylogenies obtained with mtDNA and the nuclear gene c-mos, separately or combined. The data sets support a traditional avian taxonomy, with paleognaths (ratites and tinamous) occupying a basal position and with songbirds more derived and forming a monophyletic group. We also show that, for mtDNA studies, turtles may be a better outgroup for birds than crocodilians because of their slower rate of sequence evolution.     

GLOBAL MITOCHONDRIAL DNA PHYLOGEOGRAPHY OF HOLARCTIC BREEDING DUNLINS (CALIDRIS ALPINA)

Comparison of mitochondrial DNA (mtDNA) control-region sequences of 155 dunlins from 15 breeding populations confirmed the existence of five major phylogeographic groups in the circumpolar breeding range of this migratory shorebird species. Time estimates of the origin of groups, based on sequence divergences and a molecular clock for birds, suggest a scenario of repeated fragmentation of populations in isolated tundra refugia during the late Pleistocene. The distribution of about three-quarters of all detected molecular variance between phylogeographic groups attests to the strongly subdivided genetic population structure in dunlins that is being maintained by natal philopatry. Each mtDNA phylogeographic group can be related to a morphometrically defined subspecies, but several other recognized subspecies are not supported by monophyletic mtDNA lineages within their purported ranges. More detailed analysis of several European populations reveals low amounts of gene flow and the partitioning of a substantial fraction of molecular variance between them. This ongoing evolution of population-genetic structuring within the European phylogeographic group most likely started with the last retreat of the ice sheets some 10,000 years ago. Dunlins thus provide one of the clearest examples of the linkage between historical and contemporary components of mtDNA phylogeographic structuring in birds.     

蜜蜂线粒体DNA在遗传分析中的应用

线粒体DNA是动物细胞核外唯一的遗传物质,具有结构简单、进化速度快、母系遗传和基因重组率小等特点。文章在介绍蜜蜂线粒体DNA的结构大小及其多态性的研究的基础上,对其在蜜蜂的种间多态性、亚种间及亚种内多态性、起源进化、群体遗传结构及基因流动、亚种及类型的分类等方面的研究应用进行阐述。     

The incomplete natural history of mitochondria

Mitochondrial DNA (mtDNA) has been used to study molecular ecology and phylogeography for 25 years. Much important information has been gained in this way, but it is time to reflect on the biology of the mitochondrion itself and consider opportunities for evolutionary studies of the organelle itself and its ecology, biochemistry and physiology. This review has four sections. First, we review aspects of the natural history of mitochondria and their DNA to show that it is a unique molecule with specific characteristics that differ from nuclear DNA. We do not attempt to cover the plethora of differences between mitochondrial and nuclear DNA; rather we spotlight differences that can cause significant bias when inferring demographic properties of populations and/or the evolutionary history of species. We focus on recombination, effective population size and mutation rate. Second, we explore some of the difficulties in interpreting phylogeographical data from mtDNA data alone and suggest a broader use of multiple nuclear markers. We argue that mtDNA is not a sufficient marker for phylogeographical studies if the focus of the investigation is the species and not the organelle. We focus on the potential bias caused by introgression. Third, we show that it is not safe to assume a priori that mtDNA evolves as a strictly neutral marker because both direct and indirect selection influence mitochondria. We outline some of the statistical tests of neutrality that can, and should, be applied to mtDNA sequence data prior to making any global statements concerning the history of the organism. We conclude with a critical examination of the neglected biology of mitochondria and point out several surprising gaps in the state of our knowledge about this important organelle. Here we limelight mitochondrial ecology, sexually antagonistic selection, life-history evolution including ageing and disease, and the evolution of mitochondrial inheritance.     

Genetic analysis of early holocene skeletal remains from Alaska and its implications for the settlement of the Americas

Mitochondrial and Y-chromosome DNA were analyzed from 10,300-year-old human remains excavated from On Your Knees Cave on Prince of Wales Island, Alaska (Site 49-PET-408). This individual's mitochondrial DNA (mtDNA) represents the founder haplotype of an additional subhaplogroup of haplogroup D that was brought to the Americas, demonstrating that widely held assumptions about the genetic composition of the earliest Americans are incorrect. The amount of diversity that has accumulated in the subhaplogroup over the past 10,300 years suggests that previous calibrations of the mtDNA clock may have underestimated the rate of molecular evolution. If substantiated, the dates of events based on these previous estimates are too old, which may explain the discordance between inferences based on genetic and archaeological evidence regarding the timing of the settlement of the Americas. In addition, this individual's Y-chromosome belongs to haplogroup Q-M3*, placing a minimum date of 10,300 years ago for the emergence of this haplogroup.     

Phylogeography of Aglais urticae (Lepidoptera) based on DNA sequences of the mitochondrial COI gene and control region

Mitochondrial DNA (mtDNA) sequences of the COI gene and the control region were used to examine the genetic population structure of Aglais urticae L. (Lepidoptera) over its entire geographic range, i.e., the Palaearctic. The phylogenetic relationships within and between A. urticae subspecies were determined and patterns of mtDNA divergence and ecological differentiation were compared. High gene flow together with a recent and sudden population expansion characterise the genetic population structure of this species. No geographically induced differentiation was observed, nor were subspecies identified as separate evolutionary units. The discrepancy between the genetic and ecological variation is most likely due to the slower rate of mtDNA evolution compared to ecological differentiation. The control region proved to be a less useful molecular marker for the population genetics and the phylogenetic reconstruction of closely related taxa in A. urticae than it has for other species. The extreme bias in adenine and thymine content (A+T=90.91%) probably renders this region highly susceptible to homoplasy, resulting in a less informative molecular marker.     

Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts

Mitochondrial DNA (mtDNA) has been a marker of choice for reconstructing historical patterns of population demography, admixture, biogeography and speciation. However, it has recently been suggested that the pervasive nature of direct and indirect selection on this molecule renders any conclusion derived from it ambiguous. We review here the evidence for indirect selection on mtDNA in arthropods arising from linkage disequilibrium with maternally inherited symbionts. We note first that these symbionts are very common in arthropods and then review studies that reveal the extent to which they shape mtDNA evolution. mtDNA diversity patterns are compatible with neutral expectations for an uninfected population in only 2 of 19 cases. The remaining 17 studies revealed cases of symbiont-driven reduction in mtDNA diversity, symbiont-driven increases in diversity, symbiont-driven changes in mtDNA variation over space and symbiont-associated paraphyly of mtDNA. We therefore conclude that these elements often confound the inference of an organism's evolutionary history from mtDNA data and that mtDNA on its own is an unsuitable marker for the study of recent historical events in arthropods. We also discuss the impact of these studies on the current programme of taxonomy based on DNA bar-coding.