单细胞生物进化研究的进步

20世纪60年代,生物大致分为5界的谱系图,　经历了几次翻新,开始提出了线粒体和叶绿体的内共生学说。 由于分子生物学的发展,首先将各种生物的蛋白质的分子进行比较,构建成蛋白质的分子系统树。再转向核糖核酸,将核糖体的小亚单位,作为区别生命类型之间亲缘关系的指标。发现有些嗜极端条件的细菌,它们不同于原核生物也不同于真核生物,是第三种类型的生命形式。因此,在 80年代为生命建立了细菌、古细菌和真核生物三界的系统树。对许许多多单个基因的系统树的分析,又使人们认识到,古细菌与细菌和真核微生物之间以及各个物种之间,显然皆发生过大量的基因交换。对单细胞进化来说,基因除垂直传递外,横向的或叫侧向的基因转移也十分繁多。在一张完全的系统图中,要同时表现几千个不同的基因家族的超联结的种系型式才符合实际。因而,最新版本的系统树是分枝交缠、无主干的。Abstract:In 1960s,kimgdoms of organisms were charted generally in a five branching form.Later,the endosymbiont hypothesis for the mitochondria and the chloroplast was proposed.The life-form is divided into two forms,the prokaryotes (bacteria) and the eukaryotes.The study of the molecular biology made the progress faster.In 1980s,Woese,CR.asserted that two-domain view of life was no longer true,a three-domain construct,the Bacteria,the Archaea,and the Eukaryotes had to take its place.At first,phylogeny trees based on differences in the amino acid sequences,then among ribosomal RNAs and also nuclear gene from hundreds of microbial species were depicted and many mini phylogenetic trees grouped the species according to their differences in the sequences.It was found that they shared genes between their contemporaries and across the species barriers.At the root of the phylogeny tree,there was not a single common cell,it was replaced by a common ancestral community of primitive cells.Genes transfered rather freely as the transposons swapping between those cells.There was no last universal common ancestor of single cell that could be found in the revised Tree of Life,It was not easy to represent the genealogical patterns of thousands of different families of genes,in one systematic map,therefor there was no trunk at all.     

Towards a phylogeny of chitons (Mollusca, Polyplacophora) based on combined analysis of five molecular loci

This study represents the first phylogenetic analysis of the molluscan class Polyplacophora using DNA sequence data. We employed DNA from a nuclear protein-coding gene (histone H3), two nuclear ribosomal genes (18S rRNA and the D3 expansion fragment of 28S rRNA), one mitochondrial protein-coding gene (cytochrome c oxidase subunit I), and one mitochondrial ribosomal gene (16S rRNA). A series of analyses were performed on independent and combined data sets. All these analyses were executed using direct optimization with parsimony as the optimality criterion, and analyses were repeated for nine combinations of parameters affecting indel and transversion/transition cost ratios. Maximum likelihood was also explored for the combined molecular data set, also using the direct optimization method, with a model equivalent to GTR + I + Γ that accommodates gaps. The results of all nine parameter sets for the combined parsimony analysis of all molecular data (as well as ribosomal data) and the maximum-likelihood analysis of all molecular data support monophyly of Polyplacophora. The resulting topologies mostly agree with a division of Polyplacophora into two major lineages: Lepidopleuridae and Chitonida (sensu Sirenko 1993). In our analyses the genus Callochiton is positioned as the sister group to Lepidopleuridae, and not as sister group to the remaining Chitonida (sensu Buckland-Nicks & Hodgson 2000), nor as the sister group to the remaining Chitonina (sensu Buckland-Nicks 1995). Chitonida (excluding Callochiton) is monophyletic, but conventional subgroupings of Chitonida are not supported. Acanthochitonina (sensu Sirenko 1993) is paraphyletic, or alternatively monophyletic, and is split into two clades, both with abanal gills only and cupules in the egg hull, but one has simple cupules whereas the other has more strongly hexagonal cupules. Sister to the Acanthochitonina clades is Chitonina, including taxa with adanal gills and a spiny egg hull. Schizochiton, the only genus with adanal gills that has an egg hull with cupules, is the sister-taxon to one of the Acanthochitonina clades plus Chitonina, or alternatively basal to Chitonina. Support values for either position are low, leaving this relationship unsettled. Our results refute several aspects of conventional classifications of chitons that are based primarily on shell characters, reinforcing the idea that chiton classification should be revised using additional characters.     

Root of the Eukaryota tree as inferred from combined maximum likelihood analyses of multiple molecular sequence data

Extensive studies aiming to establish the structure and root of the Eukaryota tree by phylogenetic analyses of molecular sequences have thus far not resulted in a generally accepted tree. To re-examine the eukaryotic phylogeny using alternative genes, and to obtain a more robust inference for the root of the tree as well as the relationship among major eukaryotic groups, we sequenced the genes encoding isoleucyl-tRNA and valyl-tRNA synthetases, cytosolic-type heat shock protein 90, and the largest subunit of RNA polymerase II from several protists. Combined maximum likelihood analyses of 22 protein-coding genes including the above four genes clearly demonstrated that Diplomonadida and Parabasala shared a common ancestor in the rooted tree of Eukaryota, but only when the fast-evolving sites were excluded from the original data sets. The combined analyses, together with recent findings on the distribution of a fused dihydrofolate reductase-thymidylate synthetase gene, narrowed the possible position of the root of the Eukaryota tree on the branch leading to Opisthokonta or to the common ancestor of Diplomonadida/Parabasala. However, the analyses did not agree with the position of the root located on the common ancestor of Opisthokonta and Amoebozoa, which was argued by Stechmann and Cavalier-Smith [Curr. Biol. 13:R665-666, 2003] based on the presence or absence of a three-gene fusion of the pyrimidine biosynthetic pathway: carbamoyl-phosphate synthetase II, dihydroorotase, and aspartate carbamoyltransferase. The presence of the three-gene fusion recently found in the Cyanidioschyzon merolae (Rhodophyta) genome sequence data supported our analyses against the Stechmann and Cavalier-Smith-rooting in 2003.     

Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias

The inference of population divergence times and branching patterns is of fundamental importance in many population genetic analyses. Many methods have been developed for estimating population divergence times, and recently, there has been particular attention towards genome-wide single-nucleotide polymorphisms (SNP) data. However, most SNP data have been affected by an ascertainment bias caused by the SNP selection and discovery protocols. Here, we present a modification of an existing maximum likelihood method that will allow approximately unbiased inferences when ascertainment is based on a set of outgroup populations. We also present a method for estimating trees from the asymmetric dissimilarity measures arising from pairwise divergence time estimation in population genetics. We evaluate the methods by simulations and by applying them to a large SNP data set of seven East Asian populations.     

The influence of phylogenetic uncertainty on the detection of positive Darwinian selection

The power of maximum likelihood tests of positive selection on protein-coding genes depends heavily on detecting and accounting for potential biases in the studied data set. Although the influence of transition:transversion and codon biases have been investigated in detail, little is known about how inaccuracy in the phylogeny used during the calculations affects the performance of these tests. In this study, 3 empirical data sets are analyzed using sets of simulated topologies corresponding to low, intermediate, and high levels of phylogenetic uncertainty. The detection of positive selection was largely unaffected by errors in the underlying phylogeny. However, the number of sites identified as being under positive selection tended to be overestimated.