Simulating the mitochondrial DNA inheritance

Summary Analysing the current mitochondrial DNA patterns biologists have concluded that we all descend from the same mitochondrial Eve, who is postulated to have lived around 200.000 years ago. Such a result is in agreement with the coalescence theory. Here we represent the mitochondrial DNAs as bitstrings that are maternally transmitted with mutations, and that may also participate in the selection process for survival together with the nuclear DNAs. We end up with the same common ancestor, whose mitochondrial DNA can be traced back from the current population, despite the mitochondrial mutations considered. For a given mutation rate, the degree of confidence of this tracing-back process increases even further when the selection mechanism is included.     

The Bayesian "star paradox" persists for long finite sequences

The "star paradox" in phylogenetics is the tendency for a particular resolved tree to be sometimes strongly supported even when the data is generated by an unresolved ("star") tree. There have been contrary claims as to whether this phenomenon persists when very long sequences are considered. This note settles one aspect of this debate by proving mathematically that the chance that a resolved tree could be strongly supported stays above some strictly positive number, even as the length of the sequences becomes very large.     

古DNA的新发现支持现代人东亚起源说

1983年,科学家们根据线粒体DNA（mtDNA）系统发育树构建了首个现代人起源的分子模型,认为现代人起源于亚洲,但1987年非洲起源说的提出取代了这一亚洲起源说。非洲起源说所依赖的无限多位点假说以及分子钟假说后来被普遍认为是错误的且不切实际的。我们近几年提出了一个新的分子进化模式,即遗传多样性上限理论,重新构建了一个新的人类起源模型。这一模型与多地区起源说基本吻合, 重新把现代人类起源地定位在了东亚。非洲说与东亚说在线粒体进化树上的主要区别是单倍型N和R的关系,非洲起源说认为N是R的祖先,东亚说则反之。本研究引用了已发表的古代人群mtDNA数据,重点分析了线粒体单倍群N和R的关系。结果显示,三个最古老的人类（一个距今45000年,其他两个约40000年）都属于单倍群R;在距今39500到30000年前的人类样本中,绝大部分属于单倍群R下游的亚单倍群U,只有两例为单倍群N（Oase1距今39500年,Salkhit距今34425年）。这两例所属单倍型位于单倍群N下游最基本的未分化亚型,不属于今天存在的任何N下游单倍型,所以可能靠近单倍群N的根部。这些古DNA数据揭示单倍群R比单倍群N古老大约5000年,进一步证实了亚洲起源说的正确性,非洲说的依据不足。     

Reconstructing the evolutionary history of polyploids from multilabeled trees

In recent studies, phylogenetic networks have been derived from so-called multilabeled trees in order to understand the origins of certain polyploids. Although the trees used in these studies were constructed using sophisticated techniques in phylogenetic analysis, the presented networks were inferred using ad hoc arguments that cannot be easily extended to larger, more complicated examples. In this paper, we present a general method for constructing such networks, which takes as input a multilabeled phylogenetic tree and outputs a phylogenetic network with certain desirable properties. To illustrate the applicability of our method, we discuss its use in reconstructing the evolutionary history of plant allopolyploids. We conclude with a discussion concerning possible future directions. The network construction method has been implemented and is freely available for use from http://www.uea.ac.uk/ approximately a043878/padre.html.     

Species Delimitation--a Geneious plugin for the exploration of species boundaries

Species Delimitation is a plugin to the Geneious software to support the exploration of species boundaries in a gene tree. The user assigns taxa to putative species and the plugin computes statistics relating to the probability of the observed monophyly or exclusivity having occurred by chance in a coalescent process. It also assesses the within and between species genetic distances to infer the probability with which members of a putative species might be identified successfully with tree-based methods.     

Phylogenetic relationships among Malagasy lemurs as revealed by mitochondrial DNA sequence analysis

Systematics and evolution of Malagasy lemurs has been analyzed using morphological characters, fossil evidence, ecological/ethological data, and chromosomal banding patterns. Recent developments in DNA technology have provided evolutionary biologists with additional and powerful tools for making phylogenetic inference. In the last years several studies concerning highly repeated DNA sequences (hrDNA) provided new insights about the systematic relationships among the different species of Lemuridae and Cheirogaleidae. Here, a reconstruction of molecular phylogeny of extant Malagasy lemurs based on the comparison of cytochrome-b mitochondrial DNA sequences is presented. With the Polymerase Chain Reaction (PCR) and direct sequencing of amplified DNA fragments, both the phylogenetic range and resolving power of comparative analysis can be extended. These techniques allow to gather sequence data useful to evaluate the pattern of molecular evolution offering opportunities for phylogenetic purposes. A 290-bp fragment of cytochrome-b gene has been amplified and sequenced from the following species:Tupaia glis, Galago alleni, Daubentonia madagascariensis, Indri indri, Varecia variegata, Eulemur fulvus, Eulemur coronatus, Eulemur rubriventer, Eulemur mongoz, Eulemur macaco, Lemur catta, andHapalemur griseus griseus. The phylogenetic trees obtained show the relationships among the Eulemur species and confirm the karyological and hrDNA results of a separated clade forL. catta/Hapalemur. The separation ofVarecia variegata from the other genus of the family Lemuridae is discussed.     

Current approaches to whole genome phylogenetic analysis

It has long been known that evolutionary trees (phylogenies) can be estimated by comparing the DNA or protein sequences of homologous genes across different organisms. More recently, attempts have been made to estimate phylogenies by comparing entire genomes. These attempts have focused largely on comparisons of gene content and gene order. Many different methods have been proposed for making these comparisons. These include primarily maximum parsimony and distance methods, although more recently maximum likelihood and Bayesian methods are being developed. This paper discusses each of these approaches in turn, including their merits and limitations, and any software which is available to make use of them.     

利用12个血液蛋白和非蛋白标记分析同羊起源及系统地位

采用典型群随机抽样在陕西省白水县抽取同羊样本。采用淀粉凝胶和醋酸纤维薄膜检测12个的结构基因座位的遗传多型性,结果在同羊中发现10个多型座位：运铁蛋白（Tf）、碱性磷酸酶（Alp）、亮氨酸氨肽酶（Lap）、芳基酯酶（Ary-Es）、血红蛋白β（Hb-β）、X-蛋白（X-p）、碳酸酐酶（CA）、过氧化氢酶（Cat）、苹果酸脱氢酶（MDH）和赖氨酸（Ly）;而白蛋白（Al）和后白蛋白（Po）为单态。采用遗传贴近度和系统关系聚类分析两种方法分析同羊起源及系统地位。结果表明两种方法均支持同羊属于蒙古羊系统,同羊起源于蒙古羊,这与同羊的育成史实相符。和聚类分析方法相比,遗传贴近度分析方法可以更为有效地用于中亚以东南绵羊群体的血统判别,可以更有效地反映同羊的育成过程。     

中国貉线粒体DNA多态性及其与亚种分化的关系

本文以８种限制性内切酶对来自７个地区的１４只中国貉进行了ｍｔＤＮＡ的ＲＦＬＰ分析,并构建了貉ｍｔＤＮＡ的限制酶物理图谱。根据各群体间的遗传距离构建ＵＰＧ分子系统树,结合形态、地理分布资料对中国貉的亚种分化进行了探讨。结果表明,中国貉的指名亚种已发生明显的遗传分化;对于分类地位没有确定的华北和陕西群体,建议将它们各自单独定为一个亚种;中国貉最先发生南北分歧,然后发生东西分歧。     

Genetic Relationship of Chinese and Japanese Gamecocks Revealed by mtDNA Sequence Variation

Cockfighting has a very long history dating back to as early as 2500 years ago in China. Cockfighting was intertwined with human cultural traditions, helped disperse chickens across the world, and influenced the subsequent breed selection. Therefore, tracing the origin of gamecocks could mirror the distribution of the cockfighting culture. In this study, we compared the available mtDNA control region sequences in Chinese and Japanese gamecocks to test the recently proposed hypothesis behind the dual origin of the Japanese cockfighting culture (from China and Southeast Asia independently). We assigned gamecock mtDNAs to different matrilineal components (or phylogenetic clades) that emerged from the phylogenetic tree and network profile, and compared the frequency differences between Chinese and Japanese gamecocks. Among the six clades (A–F) identified, Japanese gamecocks were most frequently found in clades C and D (74%, 32/43), whereas more than half of the Chinese gamecock samples (69%, 35/51) were grouped in clades A and B. Haplotypes in Japanese gamecocks assigned to clades A, B, and E were either shared with those of the Chinese samples or differed from the close Chinese types by no more than a three-mutation distance. This genetic pattern is in accordance with the proposed dual origin of Japanese gamecocks but has left room for single origin of Japanese gamecocks from China. The genetic structure of gamecocks in China and Japan might also be influenced by subsequent breed selection and conservation after the initial gamecock introduction.     

Gene's Functional Arrangement as a Measure of thePhylogenetic Relationships of Microorganisms

With the development of genome sequencing more whole genomes of microorganisms were completed, many methods wereintroduced to reconstruct the phylogenetic tree of those microorganismswith the information extracted from the whole genomes through variousways of transforming or mapping the whole genome sequences into otherforms which can describe the evolutionary distance in a new way. We thinkit might be possible that there exists information buried in the wholegenome transferred along lineage, which remains stable and is moreessential than sequence conservation of individual genes or the arrangementof some genes of a selected set. We need to find one measurement that caninvolve as many phylogenetic features as possible that are beyond thegenome sequence itself. We converted each genome sequence of themicroorganisms into another linear sequence to represent the functionalstructure of the sequence, and we used a new information function tocalculate the discrepancy of sequences and to get one distance matrix of thegenomes, and built one phylogenetic tree with a neighbor joining method.The resulting tree shows that the major lineages are consistent with theresult based on their 16srRNA sequences. Our method discovered onephylogenetic feature derived from the genome sequences and the encodedgenes that can rebuild the phylogenetic tree correctly. The mapping of onegenome sequence to its new form representing the relative positions of thefunctional genes provides a new way to measure the phylogeneticrelationships, and with the more specific classification of gene functions theresult could be more sensitive.