TY - JOUR AU - Wright, S. PY - 1931 DA - 1931// TI - Evolution in Mendelian populations JO - Genetics VL - 16 ID - Wright1931 ER - TY - BOOK AU - Kimura, M. PY - 1983 DA - 1983// TI - The neutral theory of molecular evolution PB - Cambridge University Press CY - Cambridge UR - https://doi.org/10.1017/CBO9780511623486 DO - 10.1017/CBO9780511623486 ID - Kimura1983 ER - TY - JOUR AU - Kimura, M. AU - Maruyama, T. PY - 1966 DA - 1966// TI - The mutation load with epistatic gene interactions in fitness JO - Genetics VL - 54 ID - Kimura1966 ER - TY - JOUR AU - Kondrashov, A. S. PY - 1982 DA - 1982// TI - Selection against harmful mutations in large sexual and asexual populations JO - Genet Res Camb VL - 40 UR - https://doi.org/10.1017/S0016672300019194 DO - 10.1017/S0016672300019194 ID - Kondrashov1982 ER - TY - JOUR AU - Kondrashov, A. S. PY - 1988 DA - 1988// TI - Deleterious mutations and the evolution of sexual reproduction JO - Nature VL - 336 UR - https://doi.org/10.1038/336435a0 DO - 10.1038/336435a0 ID - Kondrashov1988 ER - TY - JOUR AU - Charlesworth, B. PY - 1990 DA - 1990// TI - Mutation-selection balance and the evolutionary advantage of sex and recombination JO - Genet Res Camb VL - 55 UR - https://doi.org/10.1017/S0016672300025532 DO - 10.1017/S0016672300025532 ID - Charlesworth1990 ER - TY - JOUR AU - Muller, H. J. PY - 1964 DA - 1964// TI - The relation of recombination to mutational advance JO - Mutat Res VL - 1 UR - https://doi.org/10.1016/0027-5107(64)90047-8 DO - 10.1016/0027-5107(64)90047-8 ID - Muller1964 ER - TY - JOUR AU - Felsenstein, J. PY - 1974 DA - 1974// TI - The evolutionary advantage of recombination JO - Genetics VL - 78 ID - Felsenstein1974 ER - TY - JOUR AU - Li, W. -. H. AU - Tanimura, M. AU - Sharp, P. M. PY - 1987 DA - 1987// TI - An evaluation of the molecular clock hypothesis using mammalian DNA sequences JO - J Mol Evol VL - 25 UR - https://doi.org/10.1007/BF02603118 DO - 10.1007/BF02603118 ID - Li1987 ER - TY - JOUR AU - Ohta, T. PY - 1995 DA - 1995// TI - Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory JO - J Mol Evol VL - 40 UR - https://doi.org/10.1007/BF00166595 DO - 10.1007/BF00166595 ID - Ohta1995 ER - TY - JOUR AU - Eyre-Walker, A. AU - Keightley, P. D. AU - Smith, N. G. S. AU - Gaffney, D. PY - 2002 DA - 2002// TI - Quantifying the slightly deleterious mutation model of molecular evolution JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004039 DO - 10.1093/oxfordjournals.molbev.a004039 ID - Eyre-Walker2002 ER - TY - JOUR AU - Keightley, P. D. AU - Eyre-Walker, A. PY - 2000 DA - 2000// TI - Deleterious Mutations and the Evolution of Sex JO - Science VL - 290 UR - https://doi.org/10.1126/science.290.5490.331 DO - 10.1126/science.290.5490.331 ID - Keightley2000 ER - TY - JOUR AU - Woolfit, M. AU - Bromham, L. PY - 2005 DA - 2005// TI - Population size and molecular evolution on islands JO - Proc R Soc B VL - 272 UR - https://doi.org/10.1098/rspb.2005.3217 DO - 10.1098/rspb.2005.3217 ID - Woolfit2005 ER - TY - JOUR AU - Popadin, K. AU - Polishchuk, L. V. AU - Mamirova, L. AU - Knorre, D. AU - Gunbin, K. PY - 2007 DA - 2007// TI - Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes: the larger the mammal, the worse the genes JO - BMC Evol Biol VL - 7 UR - https://doi.org/10.1186/1471-2148-7-17 DO - 10.1186/1471-2148-7-17 ID - Popadin2007 ER - TY - JOUR AU - Paland, S. AU - Lynch, M. PY - 2006 DA - 2006// TI - Transitions to asexuality result in excess amino acid substitutions JO - Science VL - 311 UR - https://doi.org/10.1126/science.1118152 DO - 10.1126/science.1118152 ID - Paland2006 ER - TY - JOUR AU - Wernegreen, J. J. AU - Moran, N. A. PY - 1999 DA - 1999// TI - Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding genes JO - Mol Biol Evol VL - 16 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026040 DO - 10.1093/oxfordjournals.molbev.a026040 ID - Wernegreen1999 ER - TY - JOUR AU - Wernegreen, J. J. PY - 2002 DA - 2002// TI - Genome evolution in bacterial endosymbionts of insects JO - Nature Reviews Genetics VL - 3 UR - https://doi.org/10.1038/nrg931 DO - 10.1038/nrg931 ID - Wernegreen2002 ER - TY - JOUR AU - Woolfit, M. AU - Bromham, L. PY - 2003 DA - 2003// TI - Increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes JO - Mol Biol Evol VL - 20 UR - https://doi.org/10.1093/molbev/msg167 DO - 10.1093/molbev/msg167 ID - Woolfit2003 ER - TY - JOUR AU - Bachtrog, D. PY - 2005 DA - 2005// TI - Sex chromosome evolution: molecular aspects of Y-chromosome degeneration in Drosophila JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.3543605 DO - 10.1101/gr.3543605 ID - Bachtrog2005 ER - TY - JOUR AU - Birky, C. W. PY - 1995 DA - 1995// TI - Uniparental inheritance of mitochondrial and chloroplast genes: Mechanisms and evolution JO - Proc Nat Acad Sci USA VL - 92 UR - https://doi.org/10.1073/pnas.92.25.11331 DO - 10.1073/pnas.92.25.11331 ID - Birky1995 ER - TY - JOUR AU - Moran, N. A. PY - 1996 DA - 1996// TI - Accelerated evolution and Muller's ratchet in endosymbiotic bacteria JO - Proc Nat Acad Sci USA VL - 93 UR - https://doi.org/10.1073/pnas.93.7.2873 DO - 10.1073/pnas.93.7.2873 ID - Moran1996 ER - TY - JOUR AU - Bordenstein, S. R. AU - Reznikoff, W. S. PY - 2005 DA - 2005// TI - Mobile DNA in obligate intracellular bacteria JO - Nature Reviews/Microbiology VL - 3 ID - Bordenstein2005 ER - TY - CHAP AU - Levin, B. R. PY - 1988 DA - 1988// TI - The evolution of sex in bacteria BT - Evolution of sex: An Examination of Current Ideas PB - Sinauer Associates Inc., U.S CY - Michod, Levin ID - Levin1988 ER - TY - JOUR AU - Thomas, C. M. AU - Nielsen, K. M. PY - 2005 DA - 2005// TI - Mechanisms of, and barriers to, horizontal gene transfer between bacteria JO - Nature reviews microbiology VL - 3 UR - https://doi.org/10.1038/nrmicro1234 DO - 10.1038/nrmicro1234 ID - Thomas2005 ER - TY - JOUR AU - Hickey, D. A. PY - 1982 DA - 1982// TI - Selfish DNA: a sexually – transmitted nuclear parasite JO - Genetics VL - 101 ID - Hickey1982 ER - TY - JOUR AU - Zeyl, C. AU - Bell, G. PY - 1996 DA - 1996// TI - Symbiotic DNA in eukaryotic genomes JO - Trends in Ecology and Evolution VL - 11 UR - https://doi.org/10.1016/0169-5347(96)81058-5 DO - 10.1016/0169-5347(96)81058-5 ID - Zeyl1996 ER - TY - JOUR AU - Burt, A. AU - Trivers, R. PY - 1998 DA - 1998// TI - Selfish DNA and breeding system in flowering plants JO - Proc R Soc Lond B VL - 265 UR - https://doi.org/10.1098/rspb.1998.0275 DO - 10.1098/rspb.1998.0275 ID - Burt1998 ER - TY - JOUR AU - Duret, L. AU - Marais, G. AU - Biemont, C. PY - 2000 DA - 2000// TI - Transposons, but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabiditis elegans JO - Genetics VL - 156 ID - Duret2000 ER - TY - JOUR AU - Arkhipova, I. AU - Meselson, M. PY - 2000 DA - 2000// TI - Transposable elements in sexual and ancient asexual taxa JO - Proc Natl Acad Sci U S A VL - 98 UR - https://doi.org/10.1073/pnas.97.26.14473 DO - 10.1073/pnas.97.26.14473 ID - Arkhipova2000 ER - TY - JOUR AU - Schön, I. AU - Martens, K. PY - 2000 DA - 2000// TI - Transposable elements and asexual reproduction JO - TREE VL - 15 ID - Schön2000 ER - TY - JOUR AU - Schoen, I. AU - Martens, K. PY - 2002 DA - 2002// TI - Are ancient asexuals less burdened? Selfish DNA, transposons and reproductive mode JO - Journal of Natural History VL - 36 UR - https://doi.org/10.1080/00222930110089148 DO - 10.1080/00222930110089148 ID - Schoen2002 ER - TY - JOUR AU - Sullender, B. W. AU - Crease, T. J. PY - 2001 DA - 2001// TI - The behavior of Daphnia pulex transposable elements in cyclically and obligately parthenogenetic populations JO - J Mol Evol VL - 53 ID - Sullender2001 ER - TY - JOUR AU - Nuzhdin, S. V. AU - Petrov, D. A. PY - 2003 DA - 2003// TI - Transposable elements in clonal lineages: lethal hangover from sex JO - Biological Journal of the Linnean Society VL - 79 UR - https://doi.org/10.1046/j.1095-8312.2003.00188.x DO - 10.1046/j.1095-8312.2003.00188.x ID - Nuzhdin2003 ER - TY - BOOK AU - Li, W. -. H. PY - 1997 DA - 1997// TI - Molecular evolution PB - Sinauer Associates Inc., U.S CY - University of Texas, Health Science Center at Houston ID - Li1997 ER - TY - JOUR AU - Wyckoff, G. J. AU - Malcom, C. M. AU - Vallender, E. J. AU - Lahn, B. T. PY - 2005 DA - 2005// TI - A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate JO - Trends in Genetics VL - 21 UR - https://doi.org/10.1016/j.tig.2005.05.005 DO - 10.1016/j.tig.2005.05.005 ID - Wyckoff2005 ER - TY - JOUR AU - Swanson, W. J. AU - Nielsen, R. AU - Yang, Q. PY - 2003 DA - 2003// TI - Pervasive Adaptive Evolution in Mammalian Fertilization Proteins JO - Mol Biol Evol VL - 20 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004233 DO - 10.1093/oxfordjournals.molbev.a004233 ID - Swanson2003 ER - TY - STD TI - Lemay P: Relative entropy (Kullback-Leibler distance). Download date is 05. 11. 2006, [http://tecfa.unige.ch/~lemay/thesis/THX-Doctorat/node159.html] UR - http://tecfa.unige.ch/~lemay/thesis/THX-Doctorat/node159.html ID - ref37 ER - TY - JOUR AU - Nakamura, Y. AU - Gojobori, T. AU - Ikemura, T. PY - 2000 DA - 2000// TI - Codon usage tabulated from the international DNA sequence databases: status for the year 2000 JO - Nucl Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.292 DO - 10.1093/nar/28.1.292 ID - Nakamura2000 ER - TY - STD TI - Carroll J, Fearnley IM, Skehel JM, Shannon RJ, Hirst J, Walker JE: Bovine complex I is a complex of forty-five different subunits. J Biol Chem. ID - ref39 ER - TY - JOUR AU - Yagi, T. PY - 1993 DA - 1993// TI - The bacterial energy-transducing NADH-quinone oxidoreductases JO - Biochim Biophys Acta VL - 1141 UR - https://doi.org/10.1016/0005-2728(93)90182-F DO - 10.1016/0005-2728(93)90182-F ID - Yagi1993 ER - TY - JOUR AU - Fraser, H. B. AU - Wall, D. P. AU - Hirsh, A. E. PY - 2003 DA - 2003// TI - A simple dependence between protein evolution rate and the number of protein-protein interactions JO - BMC Evolutionary Biology VL - 3 UR - https://doi.org/10.1186/1471-2148-3-11 DO - 10.1186/1471-2148-3-11 ID - Fraser2003 ER - TY - JOUR AU - Krakauer, D. C. AU - Mira, A. PY - 1999 DA - 1999// TI - Mitochondria and germ-cell death JO - Nature VL - 400 UR - https://doi.org/10.1038/22026 DO - 10.1038/22026 ID - Krakauer1999 ER - TY - JOUR AU - Perez, G. I. AU - Trbovich, A. M. AU - Gosden, R. G. AU - Tilly, J. L. PY - 2000 DA - 2000// TI - Mitochondria and the death of oocytes JO - Nature VL - 403 UR - https://doi.org/10.1038/35000651 DO - 10.1038/35000651 ID - Perez2000 ER - TY - JOUR AU - Bergstrom, C. T. AU - Pritchard, J. PY - 1998 DA - 1998// TI - Germline bottlenecks and evolutionary maintenance og mitochondrial genomes JO - Genetics VL - 149 ID - Bergstrom1998 ER - TY - JOUR AU - Hirsh, A. E. AU - Fraser, H. B. PY - 2001 DA - 2001// TI - Protein dispensability and rate of evolution JO - Nature VL - 411 UR - https://doi.org/10.1038/35082561 DO - 10.1038/35082561 ID - Hirsh2001 ER - TY - JOUR AU - Pal, C. AU - Papp, B. AU - Hurst, L. D. PY - 2000 DA - 2000// TI - Highly Expressed Genes in Yeast Evolve Slowly JO - Genetics VL - 158 ID - Pal2000 ER - TY - JOUR AU - Hoekstra, R. F. PY - 2000 DA - 2000// TI - Evolutionary origin and consequences of uniparental mitochondrial inheritance JO - Human Reproduction VL - 15 UR - https://doi.org/10.1093/humrep/15.suppl_2.102 DO - 10.1093/humrep/15.suppl_2.102 ID - Hoekstra2000 ER - TY - JOUR AU - Lynch, M. PY - 1996 DA - 1996// TI - Mutation accumulation in transfer RNAs: molecular evidence for Muller's ratchet in mitochondrial genomes JO - Evolution VL - 13 ID - Lynch1996 ER - TY - JOUR AU - Lynch, M. PY - 1997 DA - 1997// TI - Mutation accumulation in nuclear, organelle, and prokaryotic transfer RNA genes JO - Evolution VL - 14 ID - Lynch1997 ER - TY - JOUR AU - Lynch, M. AU - Blanchard, J. L. PY - 1998 DA - 1998// TI - Deleterious mutation accumulation in organelle genomes JO - Genetica VL - 102–103 UR - https://doi.org/10.1023/A:1017022522486 DO - 10.1023/A:1017022522486 ID - Lynch1998 ER - TY - JOUR AU - Haigh, J. PY - 1978 DA - 1978// TI - The accumulation of deleterious genes in a population – Muller's ratchet JO - Theor Popul Biol VL - 14 UR - https://doi.org/10.1016/0040-5809(78)90027-8 DO - 10.1016/0040-5809(78)90027-8 ID - Haigh1978 ER - TY - JOUR AU - Frost, L. S. AU - Leplae, R. AU - Summers, A. O. AU - Toussaint, A. PY - 2005 DA - 2005// TI - Mobile genetic elements: the agents of open source evolution JO - Nature Reviews Microbiology VL - 3 UR - https://doi.org/10.1038/nrmicro1235 DO - 10.1038/nrmicro1235 ID - Frost2005 ER - TY - JOUR AU - Kidwell, M. G. AU - Lisch, D. R. PY - 2000 DA - 2000// TI - Transposable elements and host genome evolution JO - TREE VL - 15 ID - Kidwell2000 ER - TY - STD TI - NCBI. Download date is January 2006, [http://ncbi.nlm.nih.gov/genomes/ORGANELLES/animalabout.html] UR - http://ncbi.nlm.nih.gov/genomes/ORGANELLES/animalabout.html ID - ref54 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - JOUR AU - Katoh, K. AU - Misawa, K. AU - Kuma, K. AU - Miyata, T. PY - 2002 DA - 2002// TI - MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform JO - Nucleic Acids Research VL - 30 UR - https://doi.org/10.1093/nar/gkf436 DO - 10.1093/nar/gkf436 ID - Katoh2002 ER - TY - JOUR AU - Katoh, K. AU - Kuma, K. AU - Toh, H. AU - Miyata, T. PY - 2005 DA - 2005// TI - MAFFT version 5: improvement in accuracy of multiple sequence alignment JO - Nucleic Acids Research VL - 33 UR - https://doi.org/10.1093/nar/gki198 DO - 10.1093/nar/gki198 ID - Katoh2005 ER - TY - JOUR AU - Guindon, S. AU - Gascuel, O. PY - 2003 DA - 2003// TI - A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood JO - Syst Biol VL - 52 UR - https://doi.org/10.1080/10635150390235520 DO - 10.1080/10635150390235520 ID - Guindon2003 ER - TY - JOUR AU - Guindon, S. AU - Lethiec, F. AU - Duroux, P. AU - Gascuel, O. PY - 2005 DA - 2005// TI - PHYML online – a web server for fast maximum likelihood-based phylogenetic inference JO - Nucleic Acids Research VL - 33 UR - https://doi.org/10.1093/nar/gki352 DO - 10.1093/nar/gki352 ID - Guindon2005 ER - TY - JOUR AU - Goldman, N. AU - Yang, Z. PY - 1994 DA - 1994// TI - A codon-based model of nucleotide substitution for protein-coding DNA sequences JO - Molecular Biology and Evolution VL - 11 ID - Goldman1994 ER - TY - JOUR AU - Yang, Z. H. PY - 1997 DA - 1997// TI - PAML: a program package for phylogenetic analysis by maximum likelihood JO - Comput Appl Biosci VL - 13 ID - Yang1997 ER - TY - JOUR AU - Yang, Z. AU - Nielsen, R. PY - 1998 DA - 1998// TI - Synonymous and nonsynonymous rate variation in nuclear genes of mammals JO - J Mol Evol VL - 46 UR - https://doi.org/10.1007/PL00006320 DO - 10.1007/PL00006320 ID - Yang1998 ER - TY - JOUR AU - Yang, Z. AU - Nielsen, R. AU - Goldman, N. AU - Pedersen, A. K. PY - 2000 DA - 2000// TI - Codon-substitution models for heterogeneous selection pressure at amino acid sites JO - Genetics VL - 155 ID - Yang2000 ER - TY - JOUR AU - Yang, Z. AU - Swanson, W. J. PY - 2002 DA - 2002// TI - Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003981 DO - 10.1093/oxfordjournals.molbev.a003981 ID - Yang2002 ER - TY - JOUR AU - Hughes, A. L. AU - Ota, T. AU - Nei, M. PY - 1990 DA - 1990// TI - Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules JO - Mol Biol Evol VL - 7 ID - Hughes1990 ER - TY - JOUR AU - Zhang, J. PY - 2000 DA - 2000// TI - Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes JO - J Mol Evol VL - 50 ID - Zhang2000 ER - TY - JOUR AU - Yang, Z. AU - Goldman, N. AU - Friday, A. E. PY - 1995 DA - 1995// TI - Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem JO - Syst Biol VL - 44 UR - https://doi.org/10.1093/sysbio/44.3.384 DO - 10.1093/sysbio/44.3.384 ID - Yang1995 ER - TY - JOUR AU - Taylor, W. R. PY - 1986 DA - 1986// TI - The classification of amino acid conservation JO - J Theor Biol VL - 119 UR - https://doi.org/10.1016/S0022-5193(86)80075-3 DO - 10.1016/S0022-5193(86)80075-3 ID - Taylor1986 ER - TY - JOUR AU - Peterson, J. D. AU - Umayam, L. A. AU - Dickinson, T. AU - Hickey, E. K. AU - White, O. PY - 2001 DA - 2001// TI - The comprehensive microbial resource JO - Nucleic Acids Res VL - 29 UR - https://doi.org/10.1093/nar/29.1.123 DO - 10.1093/nar/29.1.123 ID - Peterson2001 ER - TY - STD TI - R Development Core Team 2005 R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, [http://www.R-project.org] UR - http://www.R-project.org ID - ref70 ER - TY - BOOK AU - Pinheiro, J. AU - Bates, D. AU - DebRoy, S. AU - Sarkar, D. PY - 2005 DA - 2005// TI - nlme: Linear and nonlinear mixed effects models ID - Pinheiro2005 ER - TY - BOOK AU - Pinheiro, J. C. AU - Bates, D. M. PY - 2000 DA - 2000// TI - Mixed Effects Models in S and S-PLUS (Statistics & Computing S) PB - Springer Verlag CY - New York UR - https://doi.org/10.1007/978-1-4419-0318-1 DO - 10.1007/978-1-4419-0318-1 ID - Pinheiro2000 ER -