http://www.nature.com/ncomms/2014/140219/ncomms4311/images/ncomms4311-f2.jpg https://onliving.files.wordpress.com/2013/05/chromosome.jpg http://ngs-expert.com/wp-content/uploads/2014/03/god.jpg http://discovermagazine.com/~/media/Images/Issues/2013/November/gender-ratios.jpg http://census.gov.ph/sites/default/files/hsd/2_14.gif 33_12_07_11_4_08_44.jpeg EVOLUTION OF THE GENOME Genome size and C-value: C-value = amount of DNA in haploid genome (pg, bp) Prokaryotes: 6´105 – 107 bp (20-fold span) smalles: Mycoplasma genitalium 525 genes, the smallest fuctional artificially synthesized genome » 473 genů (modified from M. mycoides) largest: some G+ bacteria, cyanobacteria http://upload.wikimedia.org/wikipedia/commons/8/80/Genome_Sizes.png Eukaryotes: 8,8´106 – 6,9´1011 bp (80 000-fold span!) http://upload.wikimedia.org/wikipedia/commons/8/80/Genome_Sizes.png no relation between genome size and organismal complexity or number of genes large differences even in related organisms: Paramecium caudatum (8 600 000 kb) ´ P. aurelia (190 000 kb) human: ca. 6´109 bp (~ 6,5 pg DNA) ´ Amoeba proteus: 2,9´1011 bp Polychaos dubium (Amoeba dubia): 6,7´1011 bp Þ C-value paradox (C-value enigma) marbled lungfish: > 40´ larger than human almost 200´ larger than human closely related species! C-value paradox: large genomes include large amount of non-coding DNA large genomes Þ large cells Þ influence on: cell division speed metabolism efficiency rate of ions/proteins exchange body size the larger the genome, the larger the cell G-value paradox: despite diversity of organismal complexity, metazoans tend to have similar numbers of protein-coding genes (G-value) No dependency on the total number of genes but on complexity of gene regulation networks – organisms with similar number of genes may have very different patterns of gene regulation networks How many coding genes are in the human genome? before 2001 (draft version of the genome) estimates from 50 000 till > 140 000 (max. 212 278) genes Int. Human Genome Sequencing Consortium (IHGSC) 2001: 30 000–40 000 protein coding genes IHGSC 2004: 20 000–25 000 protein coding genes Ensembl – May 2012: 21 065 coding genes Ensembl – January 2013: 20 848 coding genes Ensembl – February 2014: 20 805 coding genes Ensembl – December 2014: 20 364 coding genes whole genome sequence Repetitive DNA: 1.Highly repetitive = satellite 2.Moderately repetitive = minisatellites, microsatellites 3.Transposable elements, retroelements (SINE, LINE) Why does repetitive DNA exist? Cavalier-Smith (1978): there must be some function Doolittle and Sapienza, Orgel and Crick (1980): repetitive DNA is „selfish“ Susumu Ohno (1972): „junk DNA“ „junk“ ¹ „garbage“ Þ in future it may gain some function http://www.nap.edu/books/0309084768/xhtml/images/p20005c54g234001.jpg Výsledek obrázku pro evolutionary tinkering image EVOLUTION OF SEX sex = meiosis, recombination amphimixis http://phenomena.nationalgeographic.com/files/2012/12/Bacteria_conjugation.jpg „sex“ in Prokaryotes: conjugation transformation transduction conjugation in E.coli: http://www.evolution-textbook.org/content/free/figures/23_EVOW_Art/06_EVOW_CH23.jpg no division in haploid stage facultative sex most of life in haploid phase sex at the end of life cycle sex triggered by starving (shortage of N2) http://www.evolution-textbook.org/content/free/figures/23_EVOW_Art/09_EVOW_CH23.jpg phylogenetic position of asexual taxa: mostly recent lineages taxa scattered Taraxacum%20officinale most asexual lineages arised recently from sexual; eg. dandelion Taraxacum officinale: non-functional stamina, yellow colour T. officinale exceptions: Bdelloidea rotifers: fossils in amber 35-40 MY existency ~100 MY ostracods: asexual ~100 MY ´ recently males found 10_EVOW_CH23 Philodina roseola Macrotrachela quadricornifera 10_EVOW_CH23 http://www.evolution-textbook.org/content/free/figures/23_EVOW_Art/08_EVOW_CH23.jpg eggs Darwinula stevensoni time and energy necessary for finding a partner (finding itself may be a problem), further effort before copulation increased risk of predation or parasitation, transmission of venereal diseases susceptibility to extinction at low Ne lower capability of colonization complex meiotic molecular machinery meiosis: 10-100 h ´ mitosis: 15 min – 4 h impact of sexual selection on males ® reduction of population fitness eg. Soay sheep (St. Kilda): males die during the first winter ´ females and castrated males several years Disadvantages of sexual reproduction Disadvantages of sexual reproduction: break-up of advantageous allele combinations by recombination Eg.: A1 (dominant) = large claws, A2 (recessive) = small claws B1 (dominant) = agressive, B2 (recessive) = meek advantageous combinations disadvantageous combinations advantageous combinations Disadvantages of sexual reproduction: action of selfish elements (conflict of genes) ® reduction of population fitness (B chromosomes, transposons) from the sexual female´s point of view disadvantage, because the offspring have only 1/2 of her genes 2N 2N 2N 2N N N N N diploid asexual females diploid offspring diploid sexual females haploid gametes F ´ M ¯ F ´ M F ´ M ¯ ¯ F ´ M F ´ M F ´ M F ´ M F ¯ F F F F ¯ ¯ ¯ ¯ F F F F F F F F F F F F F F F F 1/3 1/2 2/3 frekvence asexuálů J. Maynard Smith: What is the fate of sexual and asexual population? assumptions: way of reproduction has no effect on 1. number of descendants (eg. when males take care of offspring) 2. probability of offspring survival if sexual individuals prevail in the population the number of asexual females is rougly doubled in each generation Þ twofold cost of sex, ie. 50% selective disadvantage of sex (not for isogamy! ® so rather cost of males) ad 2) effect of environment experiment with Tribolium castaneum: competition, insecticide, reproductive advantage of „asexuals“ at first prevalence of asexuals, eventually fixation of sexuals faster at higher insecticide concentrations offspring of sexuals have higher fitness Þ assumption 2 is not valid 0 0.5 1.0 1 ppm 3 ppm 5 ppm 10 ppm konc. malathionu 0.5 1.0 0 1 ppm 3 ppm 5 ppm 10 ppm konc. malathionu 0.5 1.0 0 1 ppm 3 ppm 5 ppm 10 ppm konc. malathionu 0.5 1.0 0 1 ppm 3 ppm 5 ppm 10 ppm konc. malathionu sexual simulation of asexuality Advantages of sexual reproduction Fisher-Muller argument: Rekombinace čas advantageous alleles A, B a C arise in 3 different individuals individuals AB arise only when mutation B emerges in individuals A recombination combines various advantageous alleles which can arise simultaneously in the population Effects of recombination: 1 locus ® max. 2 variants of gametes (heterozygote) 2 loci ® 4 variants: gametes AB/ab ® ab, aB, Ab, AB 10 loci ® 210 = 1024 different gametes and 2n-1(2n+1) = 524 800 diploid genotypes for population genetics the only consequence of sex is linkage equilibrium – when it is reached sex loses sense every model explaining advantage of sex must include a mechanism which eliminates some gene combinations (LD arises), and explain why genes causing LD are favoured by selection Sexual reproduction increases variation and hence rate of evolution but this advantage mostly in long-term perspective, asexuality in the short-term more advantageous Eg.: yeast Saccharomyces cerevisiae favourable environment: abundance of glucose, optimal temperature ® no difference unfavourable environment: shortage of glucose, high temperature The only way how to escape from deleterious mutations either back mutation, or mutation which invalidate effect of the previous mutation 1. Elimination of deleterious mutations I. Muller’s ratchet: http://upload.wikimedia.org/wikipedia/commons/thumb/b/b7/Ratchet_Drawing.svg/387px-Ratchet_Drawing. svg.png pawl gear ratchet base 0 1 2 3 4 5 6 7 8 9 10 0 1 2 3 4 5 6 7 8 9 10 0 1 2 3 4 5 6 7 8 9 10 Počet mutací accumulation of deleterious mutations small population Þ role of drift (stochastic process) with sex chance to avoid „ratchet“ with increase of genotype frequencies without deleterious mutations spread of genes responsible for sex best when mutations are only slightly deleterious „ratchet“ Andersson and Hughes (1996) - Salmonella typhimurium 444 experimental cultures, each from 1 individual ® growth overnight repetition Þ repeated drift, total of 1700 generations comparison with a free-living strain ® 5 cultures (1%) with significantly reduced fitness, none with higher Lambert and Moran (1998) – comparison of fitness of bacteria living within insect cells with free-living species 9 species of bacteria living only in insect cells each species had its free-living relative counterpart thermal stability of rRNA genes did endosymbionts accumulated deleterious mutations? ® in all cases rRNA of endosymbionts by 15 - 25% less stable http://www.food.dtu.dk/~/media/Institutter/Foedevareinstituttet/Nyheder/Billeder/F%C3%B8devaresikke rhed/Salmonella-typhimurium-2000x950.ashx 0 1 2 3 4 5 6 T a) 0 1 2 3 4 5 6 T Pohlavní b) 0 1 2 3 4 5 6 T Nepohlavní c) prahová hodnota T Alexey S. Kondrashov (1988) assumption that deleterious mutations act synergically ® epistasis „truncation selection“ (deterministic process) since in sexuals proportion of deleterious mutations exceeding T value is higher than in asexuals, elimination of these mutations is faster in the former (recombination combines them) question if frequencies of deleterious mutations are sufficiently high (at least 1/generation/genome) model proven in E. coli and S. cerevisiae 2. Elimination of deleterious mutations II. Kondrashov´s model: biotope divided into local sites to which descendants randomly „distributed“ ® only best adapted ones survive, parents cannot know a priori which of them will do analogy with purchase of a lottery ticket 3. Unpredictable environment – lotery model, elm-oyster model http://www.ceskestudny.cz/wp-content/uploads/2013/08/lipa2.jpg http://tribkcpq.files.wordpress.com/2014/01/lotto.jpg http://extension.entm.purdue.edu/eseries3/images/articles/medium_E-217-W_amg18.jpg Eg. aphids: http://www.sphere.be/media/3006/download/shutterstock_93554776.jpg Eg. Daphnia: new predator, dearth of food, pond drying up Þ transition to sexual reproduction Problem: models 3 and 4 are valid only for organisms with high fertility assumption that in heterogenous and homogenous biotopes genotypes can differ in usage of limited sources competition among siblings ® more descendants of sexual parents can coexist at the same site because competition of asexual offspring is more intense 4. Unpredictable environment – elbow room model Fluctuation of environment: itself does not maintain sex ® fluctuation of epistasis necessary eg. 2 loci: alternatio of association cold-wet and warm-dry « cold-dry and warm-wet this model can work eg. in parasite-host interaction http://peaceaware.com/seam/RedQueen.jpg William D. Hamilton based on the Red Queen hypothesis (Leigh Van Valen) File:W D Hamilton.jpg P1010022 L. Van Valen W.D. Hamilton http://2.bp.blogspot.com/_efcyhZxKKGc/TOd_o2PkQgI/AAAAAAAAABE/11pzsdY2Qpg/s1600/Red-Queen-733517.jp g 5. Red Queen hypothesis fluctuation of epistasis fitness and gene frequencies cycles coevolution of parasite and host Þ arms races multilocus „gene-for-gene“ relation oscillation of gene frequencies higher in asexual individuals Populace hostitele Rezistence vůči parazitovi s genotypem I Populace hostitele Rezistence vůči parazitovi s genotypem I Populace hostitele Rezistence vůči parazitovi s genotypem I I II I II I II Populace parazita http://www.antonine-education.co.uk/Salters/MUS/images/Making3.jpg asexual sexual model assumption: in heterogonous organisms (changing of sexual and asexual reproduction) and organisms with facultative sexuality sexual reproduction more frequent in case of increased parasitation extinction Curtis Lively (1992): freshwater gastropod Potamopyrgus antipodarum New Zealand lakes and rivers both sexual and asexual females http://www.spxdaily.com/images-lg/snail-potamopyrgus-antipodarum-lg.jpg http://nomadnarratives.files.wordpress.com/2011/01/ralexandrinaimgp9544.jpg >12 parasitic trematode species (host castration Þ strong selection) 66 lakes number of males as indicator of sexual reproduction Lake Alexandria, South Island, New Zealand Potamopyrgus antipodarum correlation with number of parasites Lively et al. (1992): 0.00 0.01 0.05 0.10 0.15 0.20 0.30 0.40 Počet parazitů number of parasites EVOLUTION OF SEX RATIO sex ratio often 1:1 ® why to waste for males? R. A. Fisher (1930) frequency-dependent selection condition for validity of Fisher´s argument: 1. random mating 2. same costs of both sexes ad 1) Local mating competition: mites Adactylidium, Pyemotes ventricosus, Acarophenax tribolii parasitoid wasps (eg. Nasonia vitripennis) Nasonia vitripennis acaro%20Pediculoides%20ventricosus%20Pyemotes%20tritici Pyemotes ventricosus http://www.pressan.is/ImageHandler.ashx?ID=4eaeb1a2-221f-4d84-a363-d320360f7d09&type=originals Acarophenax tribolii skenovat0001 čím méně vajíček 2. matky než 1. matky, tím větší zastoupení synů 2. matky theoretical prediction: with increasing number of egg laying females percentage of sons increases ad 2) Trivers-Willard hypothesis: Robert L. Trivers, Dan Willard investment in sex ensuring higher fitness in next generation dominant mother ® investment in sons and vice versa sex ratio bias or unequal parental investment Eg.: deers dew sex ratio 1 D. Willard Trivers_2 R.L. Trivers sons of dominant mothers have higher fitness deer2