The population dynamics of transposable elements

This paper describes analytical and simulation models of the population dynamics of transposable elements in randomly mating populations. The models assume a finite number of chromosomal sites that are occupable by members of a given family of elements. Element frequencies can change as a result of replicative transposition, loss of elements from occupied sites, selection on copy number per individual, and genetic drift. It is shown that, in an infinite population, an equilibrium can be set up such that not all sites in all individuals are occupied, allowing variation between individuals in both copy number and identity of occupied sites, as has been observed for several element families in Drosophila melanogaster . Such an equilibrium requires either regulation of transposition rate in response to copy number per genome, a sufficiently strongly downwardly curved dependence of individual fitness on copy number, or both. The probability distributions of element frequencies, generated by the effects of finite population size, are derived on the assumption of independence between different loci, and compared with simulation results. Despite some discrepancies due to violation of the independence assumption, the general pattern seen in the simulations agrees quite well with theory. Data from Drosophila population studies are compared with the theoretical models, and methods of estimating the relevant parameters are discussed.

[1]  J. B. S. Haldane,et al.  The Effect of Variation of Fitness , 1937, The American Naturalist.

[2]  B. Mcclintock,et al.  Controlling elements and the gene. , 1956, Cold Spring Harbor symposia on quantitative biology.

[3]  R. Lewontin,et al.  Estimation of the Number of Different Classes in a Population , 1956 .

[4]  M. Kimura,et al.  An introduction to population genetics theory , 1971 .

[5]  R. Lewontin,et al.  Is the gene the unit of selection? , 1970, Genetics.

[6]  T. Ohta,et al.  Theoretical aspects of population genetics. , 1972, Monographs in population biology.

[7]  R. Lewontin,et al.  The Genetic Basis of Evolutionary Change , 2022 .

[8]  J. Felsenstein.  The theoretical population genetics of variable selection and migration. , 1976, Annual review of genetics.

[9]  Population Genetics and Ecology. , 1976 .

[10]  W. G. Hill.  Non-Random Association of Neutral Linked Genes in Finite Populations , 1976 .

[11]  M. G. Kidwell,et al.  Hybrid Dysgenesis in DROSOPHILA MELANOGASTER: A Syndrome of Aberrant Traits Including Mutation, Sterility and Male Recombination. , 1977, Genetics.

[12]  J. Crow,et al.  Mutations affecting fitness in Drosophila populations. , 1977, Annual review of genetics.

[13]  G. Dover.  DNA conservation and speciation: adaptive or accidental? , 1978, Nature.

[14]  M. W. Young,et al.  Middle repetitive DNA: a fluid component of the Drosophila genome. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[15]  G. Rubin,et al.  Polymorphisms in the chromosomal locations of elements of the 412, copia and 297 dispersed repeated gene families in drosophila , 1979, Cell.

[16]  W. Ewens.  Mathematical Population Genetics , 1980 .

[17]  G. Rubin,et al.  Transposition of elements of the 412, copia and 297 dispersed repeated gene families in drosophila , 1979, Cell.

[18]  W. Doolittle,et al.  Selfish genes, the phenotype paradigm and genome evolution , 1980, Nature.

[19]  M. M. Green.  Transposable elements in Drosophila and other Diptera. , 1980, Annual review of genetics.

[20]  M. Bulmer.  The Mathematical Theory of Quantitative Genetics , 1981 .

[21]  F. Crick,et al.  Selfish DNA: the ultimate parasite , 1980, Nature.

[22]  M. G. Kidwell,et al.  Rapid unidirectional change of hybrid dysgenesis potential in Drosophila. , 1981, The Journal of heredity.

[23]  Transpositions, mutable genes, and the dispersed gene family Dm225 in Drosophila melanogaster. , 1981, Cold Spring Harbor symposia on quantitative biology.

[24]  K. Block,et al.  Derivation-dependent distribution of insertion sites for a Drosophila transposon. , 1981, Cold Spring Harbor symposia on quantitative biology.

[25]  W. Engels.  Hybrid dysgenesis in Drosophila and the Stochastic loss hypothesis. , 1981, Cold Spring Harbor symposia on quantitative biology.

[26]  T. Ohta.  Population genetics of selfish DNA , 1981, Nature.

[27]  N. Kleckner,et al.  Transposable elements in prokaryotes. , 1981, Annual review of genetics.

[28]  T. Ohta,et al.  Some calculations on the amount of selfish DNA. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[29]  K. Skryabin,et al.  General properties of mobile dispersed genetic elements in Drosophila melanogaster. , 1981, Cold Spring Harbor symposia on quantitative biology.

[30]  G. Dover,et al.  Molecular drive: a cohesive mode of species evolution , 1982, Nature.

[31]  G. Rubin,et al.  The molecular basis of P-M hybrid dysgenesis: The role of the P element, a P-strain-specific transposon family , 1982, Cell.

[32]  G. Rubin,et al.  The molecular basis of P-M hybrid dysgenesis: The nature of induced mutations , 1982, Cell.

[33]  Nucleotide sequence of gamma delta resolvase gene and demonstration that its gene product acts as a repressor of transcription. , 1982, Nature.

[34]  J. Brookfield.  Interspersed repetitive DNA sequences are unlikely to be parasitic. , 1982, Journal of theoretical biology.

[35]  D. Hickey.  Selfish DNA: a sexually-transmitted nuclear parasite. , 1982, Genetics.

[36]  P. Kitts,et al.  Inter-replicon transposition of Tn1/3 occurs in two sequential genetically separable steps , 1982, Nature.

[37]  T. Ohta.  Theoretical study on the accumulation of selfish DNA. , 1983, Genetical research.

[38]  J. Brookfield,et al.  Transposable Elements in Mendelian Populations. III. Statistical Results. , 1983, Genetics.

[39]  J. Brookfield,et al.  Transposable elements in mendelian populations. I. A theory. , 1983, Genetics.

[40]  C. Langley,et al.  Transposable Elements in Mendelian Populations. II. Distribution of Three COPIA-like Elements in a Natural Population of DROSOPHILA MELANOGASTER. , 1983, Genetics.

[41]  J. Brookfield,et al.  The effect of homozygosity of selective differences between sites of transposable elements. , 1983, Theoretical population biology.