dna dna11 DNA Consequence of the H-W principle: if the assumptions of the H-W population hold true, polymorphism can be maintained solely by random mating and Mendelian inheritance BUT! real populations usually differ from the model: population size finite mating may be nonrandom migration selection emergence of new alleles by mutation File:Jaguar head shot.jpg File:Black jaguar.jpg mutation (incl. transposition) recombination migration (gene flow) nonrandom mating natural selection random genetic drift (incl. bottleneck, founder effect) (molecular drive) MAIN MICROEVOLUTIONARY MECHANISMS: spontaneous ´ induced in germ cells ´ somatic according to their deleterious/beneficial effect: beneficial (positive) deleterious (lethal, negative) neutral File:Portulaca grandiflora mutant1.jpg File:Pyrene adduct.jpg substitutions (transitions, transversions) According to effect point (gene) chromosomal genome Point mutations: TsTv synonymous nonsynonymous missense nonsense GTC ® GTA Val ® Val GTC ® TTC Val ® Phe AAG ® TAG Lys ® ochre (stop) indels ® shift of reading frame } Þ change of allele frequencies by mutations very slow insertions ACGGT ® ACAGGT delections ACGGT ® AGGT back mutations: generally 10-times lower frequencies recurrent mutations ® mutation pressure: eg. when allele frequency A = 0,5; 2N = 2000: after 1st generation ® N = 1001 Þ increase to 0,5005 after 100 generations ® 0,55 ... inversions pericentric paracentric Chromosomal mutations (chr. rearrangements) inverze Rb fusions and dissociations (Robertsonian translocations) Rb translocations Mus1 Mus2 house mouse http://www.naturephoto-cz.com/photos/andera/house-mouse-xxx1235.jpg http://images.slideplayer.com/2/685195/slides/slide_64.jpg fusions and dissociations whole-arm reciprocal translocations (WART) Rb translocations house mouse http://www.naturephoto-cz.com/photos/andera/house-mouse-xxx1235.jpg deletions duplications insertions Types-of-mutation Types-of-mutation Genome mutations -somies (monosomies, trisomies) mostly incompatible with life monosomies: the only viable = X0 (Turner syndrom) trisomies: imbalance in gene dosage (increased expression of the trisomic pair) viable trisomies : XXY, XXX, XYY, Patau syndrom (chr. 13), Edwards s. (chr. 18), Down s. (chr. 21) -ploidies (polyploidy) especially plants in animals less frequent (invertebrates, fishes, amphibians) during the vertebrate evolution 2 rounds of whole genome duplications (2R-hypothesis) polyploid individuals usually bigger (increased cell volume) odd multiples of the genome ® problems in meiosis Þ reproductive barrier (not always – eg. triploid frogs) autopolyploidy: combination of two identical genomes fusion of cells endoreplication abortive cell cycle allopolyploidy: combination of two different genomes fusion of diploid gametes polyspermy Randomness and mutation rate (m) mutation effects random, position and rate nonrandom transitions > transversions mutation „hotspots“: CpG in animals (methylated C ® T); TpT in Procaryota „SOS reactions“ in Bacteria, minisatellites (VNTR), microsatellites (STR) mtDNA > nuclear DNA sex chromosomes > autosomes influence of proximity of the replication start, centromeres, telomeres, repetitive sequences, intensity of transcriptions cold-blooded animals: > temperature Þ > m RNA viruses (HIV) parasites antigens, immunoglobulins > m of somatic mutations males > females: humans 6x, rodents, fox: 2x … more cell divisions in germ cells Adaptive (directed) mutations? Max Delbrück, Salvador Luria (1943): fluctuation test File:Max Delbruck.jpg File:Salvador E. Luria teaching at MIT.jpg directed mutations random mutations mutations ® new alleles recombinations ® new genotypes (exception = intragenomic recombination) Vytvoření zlomu na jednom chromozomu. Invaze řetězce do homologního chromozomu. Spojení řetězců homologních chromozomů. Holidayův spoj Migrace Holidayova spoje. Vytvoření heteroduplexu. Štěpení Holidayova spoje Heteroduplex in many organisms crossing-over important for right meiosis (at least 1 c-o per chromosome, otherwise aneuploidies) women with > c-o ® > children children of older women ® > recombinations differences in various parts of chromosome (near centromeres and telomeres etc., differences among organisms) small chromosomes > recombination frequencies recombination „hotspots“: humans ~25 000 absent in Drosophila and Caenorhabditis elegans frequent appearance and disappearance demise of 1 point often compensated by increased aktivity of a neighbour point differences in recombination rate between sexes: - Haldane-Huxley rule: if one sex doesn´t recombine, it is the heterogametic sex - if both sexes recombine, mostly in females > recombinations (man 1,7x, mouse 1,3x) differences between species: - species with more small chromosomes ® more recombinations than species with less large chromosomes - correlation with the number of arms: more recombinations in karyotypes with large numbers of chrom. arms (at least 1 c-o/arm to avoid aneuploidies?) Recombination and polymorphism: EVOLUTIONARY CONSEQUENCES OF RECOMBINATION: Rekombinace absence of recombination Þ linkage disequilibrium large populations small populations no recombination recombination positive selection: selective sweep hitchhiking (draft) more frequent appearance of rare alleles negative selection: background selection ® loss of polymorphism EVOLUTIONARY CONSEQUENCES OF RECOMBINATION: Recombination and polymorphism: Migration rate, m = proportion of gene copies appearing in the population by immigration from other populations in the given generation m m gene flow increases variation in the deme gene flow but no migration long-distance migration but no gene flow 1. direct capture-mark-recapture (CMR) finger clipping, special dyes, tattooing, tags, rings, collars, genetic marking METHODS OF GENE FLOW ESTIMATION: http://www.71ranch.com/images/glossary/tag5.jpg http://www.dickinsonlonghorn.net/longhorn_info/management_tips/Images/Branding-CU-1009-033.jpg http://www.photomecan.eu/_data/section-1/1321_b-krouzek.jpg http://www.dosits.org/images/dosits/PilotWhaleinNCwithDTag_Ari_400.jpg http://image.slidesharecdn.com/humberheadcmrtalk-140630165931-phpapp02/95/capturemarkrecapture-cmr- as-a-method-for-species-monitoring-at-a-landscape-scale-3-638.jpg?cb=1404165669 http://image.slidesharecdn.com/humberheadcmrtalk-140630165931-phpapp02/95/capturemarkrecapture-cmr- as-a-method-for-species-monitoring-at-a-landscape-scale-3-638.jpg?cb=1404165669 http://im.novinky.cz/mynews/815/28154-top_foto1-sdyf7.jpg http://conservationmedia.com/wp-content/photo/Telemetry_980px.jpg 1. Direct methods remote tracking – telemetry transmitters, anntenas; GPS systems ... more expensive, time consuming http://www.selmy.cz/data/images/clanky/MarkoInGalichnik01.JPG http://www.spaceoffice.nl/blobs/spaceplaza/upload/images/wolf_with_radiocollar.jpg http://extras.mnginteractive.com/live/media/site36/2011/0801/20110801__animal-wandering~p1.jpg Risk of underestimation of gene flow!! 2. Indirect methods molecular markers gene flow models maximum likelihood and Bayesian programs dispersal: distance between parents and offspring http://www.evolution-textbook.org/content/free/figures/16_EVOW_Art/04_EVOW_CH16.jpg Island model can be also asymmetric: http://media.indiedb.com/images/games/1/11/10298/cycladic-islands-IIa.png A) Island model continent-island model island model S. Wright (F-statistics): FST = 1/(4Nm + 1) Þ Nm = (1/FST ‒ 1)/4 … Nm = number of migrants per generation B) Isolation by distance models discontinuous = stepping stone model http://www.apsnet.org/edcenter/advanced/topics/PopGenetics/Article%20Images/pop_figure_07.jpg 1D stepping-stone model 2D stepping-stone model http://fbcatown.com/filerequest/1631 ital7439 http://www.fla-keys.com/img/footer_floridakeys_500.png Linanthus parryae (Polemoniaceae), Mojave Desert (California) T. Dobzhansky, Sewall Wright L. parryae http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0108/1668.jpeg File:Linanthus demissus 1.jpg http://eolspecies.lifedesks.org/image/view/1686/_original http://eolspecies.lifedesks.org/image/view/1607/_original B) Isolation by distance models continuous Migrace Gene flow consequences: genetic homogenization of subpopulations, preventing their genetic divergence in many species migration severely reduced Eg.: melanic forms of moths in England scalloped hazel (Odontoptera [Gonodontis] bidentata) biston_betularia_ha3_2507_t biston_betularia_hs5_1004_t peppered moth (Biston betularia) Migrace Bez názvu - 1.jpg Geographic scale cline Diffusion of neutral alleles due to gene flow between demes Deme 1 Deme 2 Deme 1 Deme 2 after first contact „stepped“ cline Bez názvu - 2.jpg Geographic scale Bez názvu - 4.jpg Geographic scale Bez názvu - 6.jpg Geographic scale Bez názvu - 8.jpg Geographic scale File:Sewall Wright.jpg Sewall Wright - F-statistics: I S T FIS (= inbreeding coefficient) ® reduction of HZ in a subpopulation due to inbreeding FIS = (HS ‒ HI)/HS -1 £ FIS £ +1 FST (= fixation index) ® reduction of HZ due to population substructuring FST = (HT ‒ HS)/HT 0 £ FST £ +1 FIT ® reduction of HZ both due to population substructuring and inbreeding FIT = (HT ‒ HI)/HT (1 ‒ FIS) (1 ‒ FST) = 1 ‒ FIT File:Sewall Wright.jpg