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1.
核基因序列在昆虫分子系统学上的应用 总被引:16,自引:2,他引:14
核基因中含有更加丰富的生物学信息,运用核基因序列或将核基因序列与线粒体基因序列相结合研究昆虫的系统发育正成为分子系统学领域的一种发展趋势.核糖体基因中18S rDNA、28S rDNA、ITS已在昆虫分子系统学中得到了广泛的应用.与核糖体基因相比,虽然编码蛋白的核基因应用于昆虫分子系统学的种类不少,但大部分都是应用于双翅目和鳞翅目昆虫的分子系统学研究中,能够成功地普遍用于多个目昆虫的系统学研究的核基因并不多.本文简要介绍了应用于昆虫分子系统学的核中核糖体基因和编码蛋白的核基因,并分析了核基因序列在分子系统学应用上的局限性和应用前景. 相似文献
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线粒体DNA序列特点与昆虫系统学研究 总被引:50,自引:9,他引:41
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 相似文献
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ITS序列的特点及其在昆虫学研究中的应用 总被引:1,自引:0,他引:1
随着PCR技术和DNA测序技术的成熟及广泛应用,分子数据的分析和利用逐渐成为生物学研究的重要手段。基因组中含有丰富的遗传信息,运用核基因序列或将核基因与线粒体基因序列相结合作为遗传标记,研究昆虫的系统发育,已成为分子系统学领域的发展趋势。由于长度适中、易于扩增、进化速度快、变异性高等优点,核糖体基因中内转录间隔区(ITS)已在昆虫系统学研究中得到广泛的应用。本文介绍了ITS序列的结构特点,重点对ITS序列在近缘种及种型快速鉴定、属及属上高级阶元系统学研究、谱系生物地理学及与其它基因联合分析昆虫系统进化关系等研究中的应用及前景进行了综述。 相似文献
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植物分子系统学近五年的研究进展概况 总被引:52,自引:3,他引:52
本文综述了与分子系统学发展密切相关的4个因素:1.分子生物学方法的不断改进;2.基因组的全序列测定;3.用于分子系统学研究的基因种类不断增加,对这些基因进化规律的认识不断深入;4.化石DNA的研究。本文还阐述了核基因及叶绿体基因在系统学研究中的应用,例举了rbcL、matk、18s rDNA和ITS序列分析在植物系统发育研究中取得的重要成果,同时提出了分子系统学研究中应注意的一些问题。 相似文献
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核基因在两栖爬行动物分子系统学中的研究进展 总被引:1,自引:0,他引:1
从DNA水平探索生物进化的理论、生物类群的演化历史具有重要的意义,应用DNA序列研究生物的系统发育和进化规律成为当前分子系统学研究的热点,与线粒体DNA相比,核基因由于包含有更加丰富的生物学信息,运用核基因序列或将核基因序列与线粒体基因序列相结合研究两栖爬行动物的系统发育,正成为分子系统学领域的新的发展趋势.Rag-1、Rag-2、tyrosinase、rhodopsin、C-mos等核基因已在两栖爬行动物分子系统学中得到了广泛的应用.由于目前的技术手段等诸多因素,限制了更多的核基因用于两栖爬行动物分子系统学研究.为此简要介绍了目前核基因在两栖爬行动物分子系统学方面的研究进展,并分析了核基因序列在分子系统学应用上面临的问题和应用前景. 相似文献
9.
分子系统学已被广泛用于解决物种之间的亲缘关系。迄今为止,被子植物分子系统学大都采用叶绿体和线粒体基因。但叶绿体和线粒体多数采用单亲遗传方式,不能完全记录物种的进化历史。而且叶绿体和线粒体基因相对保守,可用于系统发育重建的信息有限,很难用来解决科以下类群之间的亲缘关系。相反,核基因遵守双亲遗传方式并能提供大量信息位点,但却没有得到广泛运用。本文以十字花科为例,从17种十字花科植物中得到了5个编码蛋白的单拷贝核基因序列,采用最大简约法、最大似然法和贝叶斯法重建它们之间的亲缘关系。结果表明,和目前常用的基因相比,这些基因能提供更多的信息位点,由此得到的系统发育树具有很高的支持,利用最大简约法得到的5个核基因的系统树中各分支均得到了100%的自展支持率。结果表明,我们选取的核基因可以用来进行科、属及种间的系统发育重建。因此,这5个基因可以用来解决被子植物其它科内的亲缘关系,而且也可以作为DNA条形码研究的有效分子标记。 相似文献
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分子系统学已被广泛用于解决物种之间的亲缘关系.迄今为止,被子植物分子系统学大都采用叶绿体和线粒体基因.但叶绿体和线粒体多数采用单亲遗传方式,不能完全记录物种的进化历史.而且叶绿体和线粒体基因相对保守,可用于系统发育重建的信息有限,很难用来解决科以下类群之间的亲缘关系.相反,核基因遵守双亲遗传方式并能提供大量信息位点,但却没有得到广泛运用.本文以十字花科为例,从17种十字花科植物中得到了5个编码蛋白的单拷贝核基因序列,采用最大简约法、最大似然法和贝叶斯法重建它们之间的亲缘关系.结果表明,和目前常用的基因相比,这些基因能提供更多的信息位点,由此得到的系统发育树具有很高的支持,利用最大简约法得到的5个核基因的系统树中各分支均得到了100%的自展支持率.结果表明,我们选取的核基因可以用来进行科、属及种间的系统发育重建.因此,这5个基因可以用来解决被子植物其它科内的亲缘关系,而且也可以作为DNA条形码研究的有效分子标记. 相似文献
11.
Multiple nuclear-gene phylogenies: application to pinnipeds and comparison with a mitochondrial DNA gene phylogeny 总被引:8,自引:1,他引:7
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.
相似文献
12.
DNA在鸟类分子系统发育研究中的应用 总被引:1,自引:0,他引:1
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。 相似文献
13.
Rates and Patterns of Scndna and Mtdna Divergence within the Drosophila Melanogaster Subgroup 总被引:12,自引:5,他引:7
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. 相似文献
14.
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. 相似文献
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Vincent P. Buonaccorsi Kimberly S. Reece Lee W. Morgan John E. Graves 《Evolution; international journal of organic evolution》1999,53(2):568-579
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 (θO) ranged from 0.00 to 0.15, with a mean of 0.08. The θO 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 (θO = 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. 相似文献
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To examine Holarctic snake dispersal, we inferred a phylogenetic tree from four mtDNA genes and one scnDNA gene for most species of the Old World (OW) and New World (NW) colubrid group known as ratsnakes. Ancestral area distributions are estimated for various clades using divergence-vicariance analysis and maximum likelihood on trees produced using Bayesian inference. Dates of divergence for the same clades are estimated using penalized likelihood with statistically crosschecked calibration references obtained from the Miocene fossil record. With ancestral areas and associated dates estimated, various hypotheses concerning the age and environment associated with the origin of ratsnakes and the dispersal of NW taxa from OW ancestors were tested. Results suggest that the ratsnakes originated in tropical Asia in the late Eocene and subsequently dispersed to the Western and Eastern Palearctic by the early Oligocene. These analyses also suggest that the monophyletic NW ratsnakes (the Lampropeltini) diverged from OW ratsnakes and dispersed through Beringia in the late Oligocene/early Miocene when this land bridge was mostly composed of deciduous and coniferous forests. 相似文献
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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. 相似文献
18.
Crawford AJ 《Journal of molecular evolution》2003,57(6):636-641
Accurate estimation of relative mutation rates of mitochondrial DNA (mtDNA) and single-copy nuclear DNA (scnDNA) within lineages contributes to a general understanding of molecular evolutionary processes and facilitates making demographic inferences from population genetic data. The rate of divergence at synonymous sites (Ks) may be used as a surrogate for mutation rate. Such data are available for few organisms and no amphibians. Relative to mammals and birds, amphibian mtDNA is thought to evolve slowly, and the Ks ratio of mtDNA to scnDNA would be expected to be low as well. Relative Ks was estimated from a mitochondrial gene, ND2, and a nuclear gene, c-myc, using both approximate and likelihood methods. Three lineages of congeneric frogs were studied and this ratio was found to be approximately 16, the highest of previously reported ratios. No evidence of a low Ks in the nuclear gene was found: c-myc codon usage was not biased, the Ks was double the intron divergence rate, and the absolute Ks was similar to estimates obtained here for other genes from other frog species. A high Ks in mitochondrial vs. nuclear genes was unexpected in light of previous reports of a slow rate of mtDNA evolution in amphibians. These results highlight the need for further investigation of the effects of life history on mutation rates.
Current address (Andrew J. Crawford): Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Ancon, Republic of Panama 相似文献
19.
High molecular weight poly(A)+ RNA (26–35 S) from chicken embryo trunks which is enriched for collagen mRNA was iodinated and hybridized to DNA under conditions of R-loop formation. The R-loops were separated in Cs2SO4 gradients from the bulk of DNA yielding double stranded DNA enriched for collagen genes. 相似文献
20.
Noncoding regions from the genes encoding aromatase cytochrome P450 and lactoferrin have been sequenced in ten bovine and one cervid species for an investigation of the evolutionary relationships within the tribe Bovini. The evolutionary rate of DNA-nucleotide alterations along the ancestral bovine lineage amounts to 0.38% per million years, as estimated from this combined 0.478-kb-single copy nuclear (scn) DNA sequence data set. Whereas rate homogenity is apparent within the Bovini, the relative rate test suggests that the boselaphine lineage (as represented by Boselaphus) has evolved at only about one third of the rate found within the Bovini. Consistent with other results, the scnDNA data provide evidence for (i) a monophyletic origin of the Bovini, (ii) a sister group position of the Boselaphini, and (iii) two different clades within the Bovini, the buffaloes (Bubalus and Syncerus) and the cattle (Bos/Bibos and Bison). Surprisingly, the results indicate very clearly that the enigmatic dwarf buffalo of Sulawesi Island (Anoa depressicornis) is most closely related to Boselaphus and that the divergence from the true Bovini occurred close to the base of bovine cladogenesis in the Middle Miocene (≈ 14—12 million years ago). 相似文献