线粒体控制区在鱼类种内遗传分化中的意义

线粒体DNA（mtDNA）作为分子标记已被广泛应用于各物种系统发生的研究。mtDNA控制区序列（D-Loop）以其较高的突变积累对于研究物种种内的遗传分化具有重要价值。鱼类是脊椎动物中最原始但在种属数量上又最占优势的类群,其物种繁多,分布广泛,起源复杂,研究其系统发生历来是令人饶有兴趣的课题。D-Loop在研究鱼类种内遗传分化中具有多方面的重要意义。近年来,已有越来越多的研究工作将D-Loop作为分子标记来探讨各种鱼类的种内遗传分化,并且获得了许多有启发性的结果。青海湖是我国内陆最大的咸水湖,湖中主要鱼类为青海湖裸鲤（Gymnocypris przewalskii）,D-Loop分析初步结果显示青海湖及其周围河流中的裸鲤似乎没有新的种内遗传分化现象。      

分子标记在雀形目鸟类研究中的应用

雀形目鸟类一直以来都是动物学工作者研究的热点。目前,针对雀形目鸟类研究的标记主要有2部分：一部分是线粒体DNA中12SrRNA、细胞色素b序列、ND2基因和ZENK等基因序列;另一部分是基因组DNA中的c-myc、RAG-1、肌球素基因和核β-纤维蛋白厚基因等DNA序列以及微卫星DNA和单核苷酸多态性（SNP）等。本文概述了这些分子遗传标记在雀形目鸟类中的应用和研究状况。     

DNA 序列在蕨类分子系统学研究中的应用

在分子系统学研究中, 目的基因或者基因片段的选择是最关键的一步, 由于进化速率的差异, 不同的DNA序列适用于不同分类阶元的系统发育研究。本文综述了目前蕨类分子系统发育研究中常用的DNA序列分析, 它们分别来自叶绿体基因组、核基因组和线粒体基因组, 着重阐明叶绿体基因在蕨类分子系统学研究中的应用。本文还简要介绍了分子系统学研究中常见的问题及解决方法(如内类群和外类群的选择, 适宜DNA片段的选择策略), 总结了目前蕨类植物分子系统学研究所取得的进展和研究现状, 展望了当今国际蕨类分子系统学的研究趋势。     

中国鸟类的DNA分类及系统发育研究概述

鸟类分类是鸟类学其他研究领域的基础,近年来分子技术的发展,以及计算机技术的应用为鸟类分类学和鸟类系统演化研究提供了新的研究手段,给传统的系统分类研究带来了新的机遇.Tautz等于2002年首先提出运用DNA序列作为生物分类系统的主要平台,即DNA分类学(DNA Taxonomy).而Hebert等于2003年则首次提出了DNA条形码(DNA Barcoding)的概念,并对其物种分类和鉴定意义予以肯定,建议利用线粒体细胞色素C氧化酶亚单位Ⅰ(COI)的特定区段来做DNA条形编码的基础.在鸟类DNA分类方面,国内学者应用线粒体基因Cut b,COI,c-mos,c-myc,12s rRNA,16s rRNA,ND2,ND3,CR,RAG-1以及核基因myoglobin introⅡ等不同片段对很多类群进行了分类探讨和系统发育研究.但是主要集中在鸡形目及雀形目鸟类.中国是鸟类多样性极其丰富的国家,近年来很多亚种、种及以上分类阶元依然存在问题,因此,中国鸟类物种的分类地位、系统发育与演化关系等依然有很多问题等待深入研究.目前国内基于COI的鸟类分类及系统发育研究有了一些报道,但是真正的DNA条形码工作尚需继续、深入地开展.     

DNA序列在蕨类分子系统学研究中的应用

在分子系统学研究中,目的基因或者基因片段的选择是最关键的一步,由于进化速率的差异,不同的DNA序列适用于不同分类阶元的系统发育研究.本文综述了目前蕨类分子系统发育研究中常用的DNA序列分析,它们分别来自叶绿体基因组、核基因组和线粒体基因组,着重阐明叶绿体基因在蕨类分子系统学研究中的应用.本文还简要介绍了分子系统学研究中常见的问题及解决方法(如内类群和外类群的选择.适宜DNA片段的选择策略),总结了目前蕨类植物分子系统学研究所取得的进展和研究现状,展望了当今国际蕨类分子系统学的研究趋势.     

核基因在鸟类分子系统发育学研究中的应用

核基因作为一种新的遗传标记,近年来被广泛应用于鸟类分子系统发育研究中.核基因与线粒体基因位于不同的遗传载体上,因此被引入到系统发育学研究中为物种树的重建提供独立的证据.常用的外显子标记为重组激活基因1(RAG-1),重组激活基因2(RAG-2),癌基因c-myc,原癌基因c-mos,它们由于缓慢的进化速率而被用于鸟类高级分类阶元的系统学研究中.常用的内含子标记是β纤维蛋白原基因内含子7(β-fibrinogen intron7,β-fibint7),肌红蛋白基因内含子Ⅱ(myoglobin intionⅡ).内含子标记通常与线粒体序列联合使用,形成具有互补系统发育信号的数据集,应用于各种分类阶元的系统学研究中.     

线粒体DNA序列在半翅目异翅亚目昆虫分子系统学上的应用

随着PCR技术的发展以及大量DNA序列的累积,昆虫分子系统学近年来快速发展。线粒体DNA(mtDNA)序列相对于核内DNA序列进化速率较快,常被用于昆虫的系统发育研究。本文综述了国内外学者利用各种线粒体DNA序列来研究半翅目异翅亚目昆虫系统发育的研究概况。总结发现,COⅠ、COⅡ、12S rDNA、16S rDNA、Cytb、ND1、ND2和ND5等线粒体区段被用于半翅目异翅亚目系统发育的研究,其中以COI、COⅡ、16S rDNA和Cytb应用最广泛,但目前尚缺乏不同分子标记间的联合分析。进一步的研究最好在选定半翅目异翅亚目昆虫的分类阶元(如科间、亚科间、科内属间、种间或种内)后,集中测定线粒体某几个区段的DNA序列,然后进行单一分析和联合分析,并与传统形态学研究结果进行比较,可望全面分析半翅目异翅亚目昆虫的系统发育关系。     

线粒体DNA序列特点与昆虫系统学研究

昆虫线粒体DNA是昆虫分子系统学研究中应用最为广泛的遗传物质之一。线粒体DNA具有进化速率较核DNA快 ,遗传过程不发生基因重组、倒位、易位等突变 ,并且遵守严格的母系遗传方式等特点。本文概述了mtDNA中的rRNA、tRNA、蛋白编码基因和非编码区的一般属性 ,分析了它们在昆虫分子系统学研究中的应用价值 ,以及应用DNA序列数据来推导分类阶 (单 )元的系统发育关系时 ,基因或DNA片段选择的重要性     

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.     

DNA分析与基因组序列和植物系统学研究

从DNA杂交、RFLP分析、DNA的限制酶图谱分析等方面描述DNA分析技术在植物学研究中的应用,讨论了DNA分析技术与植物系统学的关系及分子数据的分析方法。并以高等植物为对象,从核DNA、叶绿体DNA和线粒体DNA三方面对植物分子系统学进行了论述。     

Rates and Patterns of Scndna and Mtdna Divergence within the Drosophila Melanogaster Subgroup

Levels of DNA divergence among the eight species of the Drosophila melanogaster subgroup and D. takahashii have been determined using the technique of DNA-DNA hybridization. Two types of DNA were used: single-copy nuclear DNA (scnDNA) and mitochondrial DNA (mtDNA). The major findings are: (1) A phylogeny has been derived for the group based on scnDNA which is congruent with chromosomal data, morphology, and behavior. The three homosequential species, simulans, sechellia, and mauritiana, are very closely related; the scnDNA divergence indicate the two island species are a monophyletic group. (2) The rates of change of scnDNA and mtDNA are not greatly different; if anything scnDNA evolves faster than mtDNA. (3) The rates of scnDNA evolution are not closely correlated to chromosomal (inversion) evolution. (4) The Drosophila genome appears to consist of two distinct classes of scnDNA with respect to rate of evolutionary change, a very rapidly evolving fraction and a relatively conservative fraction. (5) The absolute rate of change was estimated to be at least 1.7% nucleotide substitution per one million years. (6) DNA distance estimates based on restriction site variation are correlated with distances based on DNA-DNA hybridization, although the correlation is not very strong.     

Relative patterns and rates of evolution in heron nuclear and mitochondrial DNA

Mitochondrial cytochrome b sequence data from 15 species of herons (Aves: Ardeidae), representing 13 genera, were compared with DNA hybridization data of single-copy nuclear DNA (scnDNA) from the same species in a taxonomic congruence assessment of heron phylogeny. The two data sets produced a partially resolved, completely congruent estimate of phylogeny with the following basic structure: (Tigrisoma, Cochlearius, (((Zebrilus, (Ixobrychus, Botaurus)), (((Ardea, Casmerodius), Bubulcus), ((Egretta thula, Egretta caerulea, Egretta tricolor), Syrigma), Butorides, Nycticorax, Nyctanassa)))). Because congruence indicated similar phylogenetic information in the two data sets, we used the relatively unsaturated DNA hybridization distances as surrogates of time to examine graphically the patterns and rates of change in cytochrome b distances. Cytochrome b distances were computed either from whole sequences or from partitioned sequences consisting of transitions, transversions, specific codon site positions, or specific protein-coding regions. These graphical comparisons indicated that unpartitioned cytochrome b has evolved at 5-10 times the rate of scnDNA. Third-position transversions appeared to offer the most useful sequence partition for phylogenetic analysis because of their relatively fast rate of substitution (two times that of scnDNA) and negligible saturation. We also examined lineage-based rates of evolution by comparing branch length patterns between the nuclear and cytochrome b trees. The degree of correlation in corresponding branch lengths between cytochrome b and DNA hybridization trees depended on DNA sequence partitioning. When cytochrome b sequences were not partitioned, branch lengths in the cytochrome b and DNA hybridization trees were not correlated. However, when cytochrome b sequences were reduced to third-position transversions (i.e., unsaturated, relatively fast changing data), branch lengths were correlated. This finding suggests that lineage-based rates of DNA evolution in nuclear and mitochondrial genomes are influenced by common causes.     

Multiple nuclear-gene phylogenies: application to pinnipeds and comparison with a mitochondrial DNA gene phylogeny

Phylogenetic analyses of closely related species should use information from multiple, independent genes with relatively high rates of sequence evolution. To investigate species for which there are few prior sequence data for single-copy nuclear (scnDNA) genes, primers for gene amplification can be designed to highly conserved regions of exons in order to amplify both coding (exons) and noncoding (introns) sequences. We have explored this approach in a phylogenetic analysis of six species of pinnipeds that, together with terrestrial carnivore outgroups, encompass divergence times < or = 40-50 Mya. We sequenced one intron from each of the aldolase A (ALD-A), aldolase C (ALD-C), and histone H2AF genes; one exon from the major-histocompatibility-complex DQA gene; a H2AF processed pseudogene (psi H2AF); and, for comparison with the nuclear genes, the 5' portion of the mitochondrial DNA (mtDNA) control region. The pinniped psi H2AF genes were found to be of limited use because they were paralogous with the gene in the outgroup. The rate of silent substitution in scnDNA (primarily introns) was 5-10-fold lower than that for mtDNA control region I, and scnDNA sequence divergence increased linearly with time < or = 40-50 Mya. Alleles at three polymorphic scnDNA loci (ALD-A, H2AF, and DQA) in the southern elephant seal were paraphyletic with respect to the allele from the closely related northern elephant seal, while the more numerous mtDNA alleles were monophyletic. This we attribute to the consequences of a higher mutation rate rather than to a lower effective population size of mtDNA compared with scnDNA. Within the short (i.e., < 500-bp) sequences of individual scnDNA sequences, phylogenetically informative variation was insufficient to obtain robust phylogenies. However, the combined scnDNA sequences produced a well-supported phylogeny congruent with that derived from mtDNA. This analysis illustrates the high resolution of mtDNA sequences compared with a similar length of scnDNA sequence, but it also demonstrates the utility of combining information from multiple short scnDNA sequences obtained using broadly applicable primers.      

Molecular Phylogenies in Dolichopoda Cave Crickets and mtDNA Rate Calibration

Five species of Dolichopoda cave crickets have been studied by means of mtDNA RFLPs. The phylogenetic relationships among them were previously inferred from two different molecular measures: allozyme polymorphisms and DNA-DNA hybridization. mtDNA data generate a phylogeny exactly matching those obtained from the other two genetic markers. This is not always the case for other organisms studied so far. This result is discussed in respect of the performance of the three molecular approaches and the population biology of these cave dwelling insects. A tentative calibration of mtDNA rate for Dolichopoda produces an estimate of about 2%/lineage/Myr. The comparison between mtDNA and scnDNA divergence estimates suggests that in these crickets changes accumulate approximately 2-3 times faster in mitochondrial than single copy nuclear sequences.     

GEOGRAPHIC DISTRIBUTION OF MOLECULAR VARIANCE WITHIN THE BLUE MARLIN (MAKAIRA NIGRICANS): A HIERARCHICAL ANALYSIS OF ALLOZYME,SINGLE-COPY NUCLEAR DNA,AND MITOCHONDRIAL DNA MARKERS

This study presents a comparative hierarchical analysis of variance applied to three classes of molecular markers within the blue marlin (Makaira nigricans). Results are reported from analyses of four polymorphic allozyme loci, four polymorphic anonymously chosen single-copy nuclear DNA (scnDNA) loci, and previously reported restriction fragment length polymorphisms (RFLPs) of mitochondrial DNA (mtDNA). Samples were collected within and among the Atlantic and Pacific Oceans over a period of several years. Although moderate levels of genetic variation were detected at both polymorphic allozyme (H = 0.30) and scnDNA loci (H = 0.37), mtDNA markers were much more diverse (h = 0.85). Allele frequencies were significantly different between Atlantic and Pacific Ocean samples at three of four allozyme loci and three of four scnDNA loci. Estimates of allozyme genetic differentiation (θ_O) ranged from 0.00 to 0.15, with a mean of 0.08. The θ_O values for scnDNA loci were similar to those of allozymes, ranging from 0.00 to 0.12 with a mean of 0.09. MtDNA RFLP divergence between oceans (θ_O = 0.39) was significantly greater than divergence detected at nuclear loci (95% nuclear confidence interval = 0.04–0.11). The fourfold smaller effective population size of mtDNA and male-mediated gene flow may account for the difference observed between nuclear and mitochondrial divergence estimates.     

Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans)

Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within approximately 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single-copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter-ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neu varied by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions of FST are expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex-biased dispersal. Furthermore, divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci.     

The problems of molecular phylogenetics with the example of squamate reptiles: Mitochondrial DNA markers

The review considers the current problems of molecular phylogenetics based on mitochondrial and chromosomal DNA sequences. The emphasis is placed on mtDNA markers, which are widely employed in reconstructing molecular evolution, but often without a critical analysis of the physiological and biochemical features of mitochondria that affect the adequacy and reliability of the results. In addition to the factors that make mtDNA-based phylogenies difficult to interpret (unrecognized hybridization and introgression events, ancestral polymorphism, and nuclear paralogs of mtDNA sequences), attention is paid to the nonneutrality and unequal mutation rates of mtDNA genes and their fragments, violations of uniparental inheritance of mitochondria, recombination events, natural heteroplasmy, and mtDNA haplotypic diversity. These factors may influence the congruence of phylogenetic inferences and trees constructed for the same organisms with different mtDNA markers or with mitochondrial and nuclear markers. The review supports the viewpoint that mitochondrial genes and their fragments fail to provide reliable evolutionary markers when considered without a thorough study of the environmental conditions and life of the taxa. The influence of external conditions on the metabolism and physiology of mitochondria cannot be taken into account in full nor modeled well enough for phylogenetic applications. It is assumed that mtDNA is valuable as a phylogenetic marker primarily because its complete sequence may be analyzed to identify the apomorphic and synmorphic properties of a taxon and to search for informative nuclear paralogs of mtDNA for phylogeographical studies and estimations of relative evolution times.     

Free from mitochondrial DNA: Nuclear genes and the inference of species trees among closely related darter lineages (Teleostei: Percidae: Etheostomatinae)

Investigations into the phylogenetics of closely related animal species are dominated by the use of mitochondrial DNA (mtDNA) sequence data. However, the near-ubiquitous use of mtDNA to infer phylogeny among closely related animal lineages is tempered by an increasing number of studies that document high rates of transfer of mtDNA genomes among closely related species through hybridization, leading to substantial discordance between phylogenies inferred from mtDNA and nuclear gene sequences. In addition, the recent development of methods that simultaneously infer a species phylogeny and estimate divergence times, while accounting for incongruence among individual gene trees, has ushered in a new era in the investigation of phylogeny among closely related species. In this study we assess if DNA sequence data sampled from a modest number of nuclear genes can resolve relationships of a species-rich clade of North American freshwater teleost fishes, the darters. We articulate and expand on a recently introduced method to infer a time-calibrated multi-species coalescent phylogeny using the computer program ^*BEAST. Our analyses result in well-resolved and strongly supported time-calibrated darter species tree. Contrary to the expectation that mtDNA will provide greater phylogenetic resolution than nuclear gene data; the darter species tree inferred exclusively from nuclear genes exhibits a higher frequency of strongly supported nodes than the mtDNA time-calibrated gene tree.     

Molecular markers and modern phylogenetics of mammals

Application of modern molecular techniques such as molecular cloning, sequences and polymerase chain reaction of DNA resulted in the increasing of resolution of the phylogenetic analysis and enhanced the role of molecular markers in the evolutionary and taxonomic studies. However, certain properties of the molecular markers are to be taken into consideration when results of the molecular phylogenetic analyses are discussed. This survey reviews the advantages and shortages of different molecular markers (mtDNA and nDNA genes, satellite sequences, long and short retroposons) at the various taxonomic levels. The most part of new phylogenetic reconstructions are established on the results of mtDNA analysis and must be interpreted cautiously because of non-mendelian inheritance of mitochondrial genome. The extremely rapid rate of nucleotide change in mtDNA as compared with nDNA reinforces the saturation in nucleotide sequence and screens the phylogenetic signal. The analysis of nuclear genomes in constrained by that only truly orthologous genes are suitable for the phylogeny reconstruction. So there is a problem to distinguish genes from pseudogenes. Besides, there are some general problems of gene reconstruction such as nucleotide and amino acid compositional shift, long branch attraction and the choice of outgroup. Short interspersed nuclear elements (SINEs) may provide the most valuable phylogenetic information. The markers of multilocus DNA analysis (RAPD-PCR, IS-PCR, RELP, ISSR-PCR), their advantages and shortages are also discussed. A brief survey of the recent studies of molecular phylogeny of mammals for the period of about ten years is presented. The results based on the combined analysis of the mitochondrial and nuclear genes reject the reliability of some previously recognized supraordinal Eutherian taxa in favour of independent range of four main super-order clades: Afrotheria, Xenarthra, Euarchontoglires, and Laurasiatheria. Within these clades, monophyly of some of traditionally recognized orders was proved by molecular data. The recent advances of molecular phylogenetics are very encouraging. However, its future developments are full off serious difficulties. The problem of accumulation of the data turns into the problem of their correct analysis that is more difficult from the methodological point of view. The careful analysis of the conformities and contradictions between different data sets and looking for congruent conclusions deduced from different characters are the most fruitful way of further phylogenetic development.     

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.