115 resultados para Nuclear genes
em Chinese Academy of Sciences Institutional Repositories Grid Portal
Resumo:
Bat flight poses intriguing questions about how flight independently developed in mammals. Flight is among the most energy-consuming activities. Thus, we deduced that changes in energy metabolism must be a primary factor in the origin of flight in bats. The respiratory chain of the mitochondrial produces 95% of the adenosine triphosphate (ATP) needed for locomotion. Because the respiratory chain has a dual genetic foundation, with genes encoded by both the mitochondrial and nuclear genomes, we examined both genomes to gain insights into the evolution of flight within mammals. Evidence for positive selection was detected in 23.08% of the mitochondrial-encoded and 4.90% of nuclear-encoded oxidative phosphorylation (OXPHOS) genes, but in only 2.25% of the nuclear-encoded nonrespiratory genes that function in mitochondria or 1.005% of other nuclear genes in bats. To address the caveat that the two available bat genomes are of only draft quality, we resequenced 77 OXPHOS genes from four species of bats. The analysis of the resequenced gene data are in agreement with our conclusion that a significantly higher proportion of genes involved in energy metabolism, compared with background genes, show evidence of adaptive evolution specific on the common ancestral bat lineage. Both mitochondrial and nuclear-encoded OXPHOS genes display evidence of adaptive evolution along the common ancestral branch of bats, supporting our hypothesis that genes involved in energy metabolism were targets of natural selection and allowed adaptation to the huge change in energy demand that were required during the origin of flight.
Resumo:
稻属Oryza隶属禾本科Poaceae,包括20多个野生种和2个栽培种(亚洲栽培稻O. sativa L和非洲栽培稻O. glaberrima Steud) ,广泛分布于全球热带和亚热带。稻属物种可划分为10个基因组(又称染色体组)类型:A, B, C, BC, CD, E, F, G, HJ 和 HK。栽培稻所属的A基因组是稻属中物种数目最多、地理分布最广的基因组类型,由8个种组成。由于栽培稻属于A基因组,故A基因组物种是栽培稻遗传改良的巨大基因源。数十年来,国际上许多学者对A基因组类群开展了大量涉及形态、细胞、同工酶和分子标记方面的研究,但由于A基因组物种间遗传关系十分接近,形态上差异小且地理分布重叠,使得A基因组物种的系统发育、物种起源和生物地理学等方面存在诸多悬而未决的问题,是稻属中分类和鉴定困难较多的类群。本文利用核基因内含子序列,结合转座子插入分析,重建了A基因组的系统发育,估测了各类群的分化时间;与此同时,基于多克隆测序和基因谱系分析,探讨了O. rufipogon和O. nivara遗传关系以及亚洲栽培稻起源。主要研究结果如下: 1. A基因组的系统发育 在水稻全基因组数据库搜索的基础上,测定了4个单拷贝核基因(Adh1 及3个未注释基因)的内含子序列,构建了稻属A基因组8个种的系统发育关系。基于最大简约法和贝叶斯法的系统发育分析表明:1)澳大利亚的O. meridionalis为A基因组的基部类群;2)亚洲栽培稻两个亚种O. sativa ssp. japonica 和 O. sativa ssp. indica分别和不同的野生类群聚为独立的两个分支,支持japonica 和 indica为多次起源;3)O. rufipogon和O. nivara在系统发育树上完全混在一起,显示出二者间不存在遗传分化;4)非洲一年生野生种O. barthii是非洲栽培稻O. glaberrima的祖先,而非洲多年生野生种O. longistaminata与O. glaberrima/O. barthii.亲缘关系较远;5)分子钟方法估测A基因组类群约在2百万年前(2.0MYA)开始分化,亚洲栽培稻和非洲栽培稻,以及亚洲栽培稻的两个亚种则分别在0.7和 0.4 MYA左右开始分化。此外,通过核基因内含子序列与其它常用片段如ITS,matK等对比分析表明,进化速率相对较快的核基因内含子序列可以有效地用于近缘类群的系统发育研究。 2. Oryza rufipogon 和O. nivara群体遗传研究及亚洲栽培稻起源 对于亚洲野生类群O. rufipogon和O. nivara是合并为一个种还是处理为两个独立的种一直存在争议。在系统发育研究基础上,我们选取4个核基因内含子或5’-UTR区(Waxy, LHS,CatA和1个未注释基因),对采自整个分布区的群体样品进行了多克隆测序,结果表明:1)检测到O. rufipogon和O. nivara均有较高的核苷酸多态性,4个位点上π值和θw值平均分别为0.011和0.014;2)且二者在遗传上没有明显分化,两个类群在4个核基因位点上均检测到大量共享多态(shared polymorphism),未发现固有差异(fixed difference),表明它们历史上可能属于一个大群体,支持将二者作为种内不同生态型或亚种处理;3)基因谱系树表明亚洲栽培稻的两个亚种indica和japonica分别和不同的O. rufipogon (包括O. nivara)群体聚在一起,进一步从基因谱系角度支持亚洲栽培稻多次起源假说。 3.转座子在群体遗传与系统发育研究中的应用 鉴于目前植物谱系地理学研究中缺乏具有足够信息量的分子标记用于检测种内遗传变异,我们选取3个核基因中的转座子,通过对取自O. rufipogon和O. nivara整个分布区的37份样品的克隆测序,探讨了进化速率快、信息含量丰富的转座子序列在群体遗传上的应用。结果表明:1)无论在物种水平还是群体水平,转座子能检测到比包括内含子在内的其它DNA区域高得多的遗传变异;2)在物种水平上,异交多年生的O. rufipogon和自交一年生的O. nivara多样性均较高,且2个种间相差很小,二者在3个位点上平均核苷酸多样性π值均为0.013,差别主要表现在O. rufipogon杂合位点比例(46.1%)明显高于O. nivara(9.1%),说明交配系统不同并不一定和物种多样性水平相关;3)是否发生转座子序列插入是有价值的系统发育信息,发生在不同染色体上3个基因中的转座子插入进一步证实A基因组基部类群是O. meridionalis;通过叶绿体中3个转座子的插入现象推断了稻族一些四倍体物种,如稻属BC基因组的一些类群的母本来源。
Resumo:
Carnivora; Caniformia; Feliformia; Phylogenetic tree; Mitochondrial DNA; Nuclear genes; 【摘要】 追溯生物界不同生物类型的起源及进化关系,即重建生物类群的系统发育树是进化生物学领域中一个十分重要的内容。食肉目哺乳动物位于食物链顶端,很多成员不仅在我国野生动物保护工作中占有重要地位,而且还是研究动物适应性进化遗传机制的重要模式生物。因而,食肉目物种作为物种资源中的一个重要类群,其系统发育学一直是国内外研究的热门课题。构建可靠的食肉目分子系统树,无疑将具有重要的进化理论意义和保护生物学价值。鉴于目前食肉目各科间系统发育关系仍然处于“广泛争论”的状态,本文将针对食肉目科水平上的系统发育学研究进展,包括来自于形态学特征、细胞学及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。这对今后食肉目系统发育方面的进一步研究工作具有指导意义,并为以该类群作为模式生物开展适应性进化研究奠定基础
Resumo:
Nectogaline shrews are a major component of the small mammalian fauna of Europe and Asia, and are notable for their diverse ecology, including utilization of aquatic habitats. So far, molecular phylogenetic analyses including nectogaline species have been unable to infer a well-resolved, well-supported phylogeny, thus limiting the power of comparative evolutionary and ecological analyses of the group. Here, we employ Bayesian phylogenetic analyses of eight mitochondrial and three nuclear genes to infer the phylogenetic relationships of nectogaline shrews. We subsequently use this phylogeny to assess the genetic diversity within the genus Episoriculus, and determine whether adaptation to aquatic habitats evolved independently multiple times. Moreover, we both analyze the fossil record and employ Bayesian relaxed clock divergence dating analyses of DNA to assess the impact of historical global climate change on the biogeography of Nectogalini. We infer strong support for the polyphyly of the genus Episoriculus. We also find strong evidence that the ability to heavily utilize aquatic habitats evolved independently in both Neomys and Chimarrogale + Nectogale lineages. Our Bayesian molecular divergence analysis suggests that the early history of Nectogalini is characterized by a rapid radiation at the Miocene/Pliocene boundary, thus potentially explaining the lack of resolution at the base of the tree. Finally, we find evidence that nectogalines once inhabited northern latitudes, but the global cooling and desiccating events at the Miocene/Pliocene and Pliocene/Pleistocene boundaries and Pleistocene glaciation resulted in the migration of most Nectogalini lineages to their present day southern distribution. (C) 2010 Elsevier Inc. All rights reserved.
Resumo:
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.
Resumo:
The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.
Resumo:
The four species of "river dolphins" are associated with six separate great river systems on three subcontinents and have been grouped for more than a century into a single taxon based on their similar appearance. However, several morphologists recently questioned the monophyly of that group. By using phylogenetic analyses of nucleotide sequences from three mitochondrial and two nuclear genes, we demonstrate with statistical significance that extant river dolphins are not monophyletic and suggest that they are relict species whose adaptation to riverine habitats incidentally insured their survival against major environmental changes in the marine ecosystem or the emergence of Delphinidae.
Resumo:
Phylogenetic relationships among 37 living species of order Carnivora spanning a relatively broad range of divergence times and taxonomic levels were examined using nuclear sequence data from exon1 of the IRBP gene (approximate to1.3 kb) and first intron
Resumo:
The taxomic classification and phylogenetic relationships within the bear family remain argumentative subjects in recent years. Prior investigation has been concentrated on the application of different mitochondrial (mt) sequence data, herein we employ tw
Resumo:
The pantherine lineage of the cat family Felidae (order: Carnivora) includes five big cats of genus Panthera and a great many midsized cats known worldwide. Presumably because of their recent and rapid radiation, the evolutionary relationship among pantherines remains ambiguous. We provide an independent assessment of the evolutionary history of pantherine lineage using two complete mitochondrial (mt) genes (ND2 and ND4) and the nuclear beta-fibrmogen intron 7 gene, whose utility in carnivoran phylogeny was first explored. The available four mt (ND5, cytb, 12S, and 16SrRNA) and two nuclear (IRBP and TTR) sequence loci were also combined to reconstruct phylogeny of 14 closely related cat species. Our analyses of combined mt data (six genes; approximate to 3750 bp) and combined mt and nuclear data (nine genes; approximate to 6500 bp) obtained identical tree topologies, which were well-resolved and strongly supported for almost all nodes. Monophyly of Panthera genus in pantherine lineage was confirmed and interspecific affinities within this genus revealed a novel branching pattern, with P. tigris diverging first in Panthera genus, followed by P. onca, P. leo, and last two sister species P. pardus and P. uncia. In addition, close association of Neofelis nebulosa to Panthera, the phylogenetic redefinition of Otocolobus manil within the domestic cat group, and the relatedness of Acinonyx jubatus and Puma concolor were all important findings in the resulting phylogenies. The potential utilities of nine different genes for phylogenetic resolution of closely related pantherine species were also evaluated, with special interest in that of the novel nuclear beta-fibrinogen intron 7. (c) 2005 Elsevier Inc. All rights reserved.
Resumo:
The phylogenetic relationships among 12 genera of treefrogs (Family, Rhacophoridae), were investigated based on a large sequence data set, including five nuclear (brain-derived neurotrophic factor, proopiomelanocortin, recombination activating gene 1, tyr
Resumo:
Phylogenetic relationships among representative species of the subfamily Raninae were investigated using approximately 2000 base pairs of DNA sequences from two mitochondrial (12S rRNA, 16S rRNA) and two nuclear (tyrosinase, rhodopsin) genes. Phylogenetic