Evolution of DNA damage in irradiated cells

Ionizing radiation damage to a mammalian genome is modeled using continuous time Markov chains. Models are given for the initial infliction of DNA double strand breaks by radiation and for the enzymatic processing of this initial damage. Damage processing pathways include DNA double strand break repair and chromosome exchanges. Linear, saturable, or inducible repair is considered, competing kinetically with pairwise interactions of the DNA double strand breaks. As endpoints, both chromosome aberrations and the inability of cells to form clones are analyzed. For the post-irradiation behavior, using the discrete time Markov chain embedded at transitions gives the ultimate distribution of damage more simply than does integrating the Kolmogorov forward equations. In a representative special case explicit expressions for the probability distribution of damage at large times are given in the form used for numerical computations and comparisons with experiments on human lymphocytes. A principle of branching ratios, that late assays can only measure appropriate ratios of repair and interaction functions, not the functions themselves, is derived and discussed.This work was supported in # DMS-9025103     

The main regulatory region of mammalian mitochondrial DNA: Structure-function model and evolutionary pattern

Summary The evolution of the main regulatory region (D-loop) of the mammalian mitochondrial genome was analyzed by comparing the sequences of eight mammalian species: human, common chimpanzee, pygmy chimpanzee, dolphin, cow, rat, mouse, and rabbit. The best alignment of the sequences was obtained by optimization of the sequence similarities common to all these species.The two peripheral left and right D-loop domains, which contain the main regulatory elements so far discovered, evolved rapidly in a species-specific manner generating heterogeneity in both length and base composition. They are prone to the insertion and deletion of elements and to the generation of short repeats by replication slippage. However, the preservation of some sequence blocks and similar cloverleaf-like structures in these regions, indicates a basic similarity in the regulatory mechanisms of the mitochondrial genome in all mammalian species.We found, particularly in the right domain, significant similarities to the telomeric sequences of the mitochondrial (mt) and nuclear DNA ofTetrahymena thermophila. These sequences may be interpreted as relics of telomeres present in ancestral linear forms of mtDNA or may simply represent efficient templates of RNA primase-like enzymes.Due to their peculiar evolution, the two peripheral domains cannot be used to estimate in a quantitative way the genetic distances between mammalian species. On the other hand the central domain, highly conserved during evolution, behaves as a good molecular clock.Reliable estimates of the times of divergence between closely and distantly related species were obtained from the central domain using a Markov model and assuming nonhomogeneous evolution of nucleotide sites.     

突变质体随细胞分裂而传递的性质和规律初探

设一初始细胞中共有ｍ个质体,其中ｉ个是突变的,我们研究了它们随细胞分裂而分裂并在细胞间进行随机分配的过程中,一细胞分配ｍ个突变质体的概率。令ｘ（ｔ）＝１表示在第ｔ次分裂时,一细胞只含突变质体这一随机事件,ｘ（ｔ）＝０为其对立事件。我们得到了随机过程｛ｘ（ｔ）,ｔ∈Ｔ｝的一些性质、证明了该过程为一马尔可夫链,给出了细胞质内质体杂化（含突变与非突变两类质体）与质体纯化（仅含一类质体）两种状态之间的转移概率矩阵,揭示了突变质体随细胞分裂而传递的若干规律。     

生态网络中物质、能量流动的时间链分析

本文以Ｍａｒｋｏｖ过程理论为基础,利用转移矩阵对生态网络中物质、能量流动和随机行为进行的描述;将输入的物质、能量在生态网络中宏观分布随时间的变化定义为物质、能量流动的时间链,并给一般生态网络中物质、能量流动时间链的分析方法。两个稳态生态网络中物质、能量流动的时间链分析表明,时间链直观地反映了物质、能量在流动中流失或耗散的宏观行为,由于物质再循机普遍存在,使得物质流动的时间链与能量流动的时间链有着质     

Markov models and initial floristic composition in heathland vegetation dynamics

A simple Markov model is used to test the hypothesis that the floristic composition of vegetation colonizing bare ground immediately after burning is the major factor influencing post-fire development in heathland vegetation. Data are taken from stands of different ages at time of burning in a species-rich Calluna-Arctostaphylos heath in NE Scotland. It is shown that variation in the initial floristic composition of the stands is not, in itself, sufficient to produce model simulations which match observed trends, although altering the probabilities of transition from bare ground to other states allows more successful simulations. The model supports the hypothesis that stand age before burning influences the post-fire development through the process of colonization of bare ground. After a very severe fire post-fire development may initially depend on the formation of a moss cover, although this requires further study. It is concluded that simple Markov models can provide the basis for examining successional processes when used in a comparative way.Nomenclature follows Tutin et al. (1964–80) for vascular plants and Smith (1978) for mosses.We thank Prof. C. H. Gimingham for comments on the draft, and J. M. M. Humphrey, P. Marren and the Nature Conservancy Council for permission to work on the Muir of Dinnet.     

One step beyond lethal equivalents: characterization of deleterious loci in the rapid cycling Brassica rapa L. base population

The total number of lethal equivalents as defined by Morton, Crow and Muller (1956) is a function of three parameters: M, the number of loci at which deleterious mutations can occur, q, the frequency of the deleterious alleles at each locus, and s, their selective value. A new approach based on multi‐generation inbreeding data is outlined and used to infer these three parameters as well as the dominance coefficient, h, in a self‐incompatible species, Brassica rapa L. Germination and flowering data from thirty bud‐selfed lines of fast‐cycling B.rapa were assessed over three generations. Germination and flowering were significantly postponed by inbreeding but germination and flowering success were not so strongly decreased. Estimates of the average s values were obtained but it was not possible to get separate estimates of M and q. For both characters, the average dominance coefficient was particularly low. The number of lethal equivalents at the zygotic level was around two for germination and three for flowering, which, owing to the self‐incompatibility of B.rapa, is an unexpectedly low value. These results may be explained by past biparental inbreeding which in turn may have increased self‐compatibility thus allowing the purging of more deleterious alleles than under strict self‐incompatibility. This revised version was published online in July 2006 with corrections to the Cover Date.     

MEASURING EVOLUTIONARY CONSTRAINTS: A MARKOV MODEL FOR PHYLOGENETIC TRANSITIONS AMONG SEED DISPERSAL SYNDROMES

I introduce a Markov probabilistic model of transitions among discrete morphological states as a method for describing and testing nonrandom patterns of evolutionary change. The Markov model assumes one-generational dependency, i.e., that the future direction of evolutionary change depends on the current morphology of a species, not on any history of changes. This model is very flexible, allowing for any number of discrete states to describe morphology, yet permit rigorous testing of even complex evolutionary hypotheses. I apply this model to changes in seed dispersal mechanisms within 571 genera of Neotropical plants, using cladistic methods to infer the ancestral and derived states within each genus. I then test a series of progressively more complex hypotheses about the constraints that might shape the patterns of observed evolutionary transitions: 1) no transition constraints; 2) all dispersal mechanisms are equally labile evolutionarily; 3) the probability of particular evolutionary transitions among dispersal mechanisms depends on the descendant state but not on the ancestral state; 4) transition probabilities differ among pairs of dispersal mechanisms, but are reciprocal within such pairs. More complex hypotheses matched the data significantly better than did simpler hypotheses. However, only one of the hypotheses (reciprocal transitions) fit the observed data and then only for the most cautious interpretation of the frequencies of transitions within genera. These results suggest that evolutionary transitions among major adaptive syndromes are indeed ordered, and the observed patterns of transitions suggest possible reasons for such macroevolutionary structure.