Lejsek černohlavý (Ficedula hypoleuca) Bence main_photo svartkraake11_1129806335_1175933268 Iris-brevicaulis-14 iris_fulva_red varie2 MODULARIZACE VÝUKY EVOLUČNÍ A EKOLOGICKÉ BIOLOGIE CZ.1.07/2.2.00/15.0204 PF_72_100_grey_tr ubz_cz_black_transparent tok genů: Fst, Dxy test Patterson´s D = ABBA/BABA ghost introgression: Zhang19 (mám PDF) greenish warbler (Philloscopus trochiloides) ring species: Ensatina_ring Ensatina eschscholtzii - klauberi Secondary contact Chorthippus parallelus postglacial expansion Larus argenteus/L. fuscus Hybridization: 25% species of vascular plants 10% species of animals probably underestimation (only conspicuous species: ducks, birds of paradise, butterflies) often result of environmental disturbance: eg. „Darwin’s finches“ Geospiza fuliginosa, G. fortis and G. scandens after El Niño event Geospiza fortis.jpg small-ground-finch-(geospiza-fuliginosa).jpg Cactus-Finch-Galapagos-2-655-cr-300x240.jpg Geospiza fuliginosa G. fortis G. scandens new habitat hybrid swarm hybrid zone Possible outcomes of hybridization hybrid taxon Program NewHybrids: Výsledek obrázku pro structure k=2 Výsledek obrázku pro structure k=2 STRUCTURE ADMIXTURE primary secondary tension, mosaic, staggered, „mottled“ ... extrinsic selection (external environment) intrinsic selection (prezygotic or postzygotic barriers) Hybrid zones may be classified as: Hybrid zone (Barton a Hewitt 1985) = area, where genetically different populations meet, mate and give rise at least some hybrid offspring Mosaic hybrid zone: influence of environment in fact a set of several hybrid zones eg.: Gryllus firmus x G. pennsylvanicus (NE USA) sandy x clayish soils Iris fulva x I. brevicaulis: I. fulva is limited to more forested sites Hybridization_Fig.2.jpg Iris-brevicaulis-14 fire-bellied toad B. bombina: lowlands mostly in water larger water surfaces thiner skin territorial 530 Hz longer development yellow-bellied toad B. variegata: hills, highlands terrestrial mating in puddles thick skin nonterritorial 580 Hz shorter development Bombina: IMG_1756_2 mosaic HZ in Croatia, not in Poland Most hybrid zones are tension zones. Nick Barton ... i.e., they are maintained by balance between dispersal and selection (Barton & Hewitt, 1985) minnie jerry Tension zone is when… minnie jerry dispersal Þ zone widening Tension zone is when… minnie jerry selection against hybrids! ♀ ´ Tension zone is maintained by dynamic equilibrium between dispersal and selection Tension zone is when… Þ zone narrowing Hybridization_Fig.3.jpg tension zone moves along the gradient of population density Tension zone is independent of external conditions (intrinsic selection) Þ its movement ends at a geographical barrier or in the area of the lowest population density („population/density trough“) Hybridization_Fig.3.jpg „population trough“ Hybridization_Fig.3.jpg tension zone moves along population gradient Hybridization_Fig.3.jpg secondary contact: coincident and concordant clines Theory of cline: Cline = gradient of trait(s) (eg. allele frequency or mean of quantitative trait) across spatially continuous habitat According to theory, secondary contact will produce a set of parallel coincident and concordant clines CLICK  it means that these clines have the same position and the same shape or at least the width. CLICK  coincidence = same positions of zone centres concordance = same cline shapes (in practice usually same widths) clines Geographic scale secondary contact cline neutral vs. selected loci neutral locus selection against hybrids Theory of cline: But as the time is passing, clines for neutral loci get wider in comparison with loci under selection CLICK  so concordance diminishes; conversely, selection against hybrids tends to maintain the clines at the same place. CLICK  Geographic scale diffusion of neutral marker Geographic scale diffusion of neutral marker Geographic scale diffusion of neutral marker Geographic scale diffusion of neutral marker ... but (in tension zone) selection pushes clines for individual loci to each other Þ maintains coincidence with time, concordance is disappearing ... neutral vs. selected loci locus 1 locus 2 But as the time is passing, clines for neutral loci get wider in comparison with loci under selection CLICK  so concordance diminishes; conversely, selection against hybrids tends to maintain the clines at the same place. CLICK  sometimes ... ... but clines still parallel locus 1 locus 2 Sometimes we can see one or more clines which are not coincident so we have to find some explanation for the pattern CLICK  but still it holds that the clines are parallel CLICK  cline models (diffusion approximation etc.), linkage disequilibrium, evolutionary parameters ?? problem, how to analyse So even in this case we can use cline models – either based on diffusion approximation – or any other model, and to estimate cline parameters. CLICK  But what to do when the clines are not parallel? CLICK  Clearly, in this case one of the basic assumptions of cline theory is violated and it is not obvious what should we do in such a case CLICK  Hybrid zone study 1.Sampling along linear or 2D transect, geographic coordinates of localities 2.Genetic (morphological, behavioural etc.) analysis … problem of sample independence (FST, FIS … effective No. alleles) 3.Geographic clines 4.Estimation of dispersal, selection, and other parametres 5.Alternative approaches: monotonic clines 2D analysis genomic clines concordance analysis Case study: house mouse hybrid zone Map Europe.JPG Titul_mysi musculus domesticus musculus domesticus Neolithic Cucchi et al. (2005) Mouse colonization of Europe Bronze and Iron Age Cucchi et al. (2005) Mouse colonization of Europe Late Neolitnic mid 4th millenium BC Cucchi et al. (2011) Mouse colonization of Europe Vikings Prager et al. (1993); Searle et al. (2009) Mouse colonization of Europe Hybrid zone in Europe time of origin unknown… musculus domesticus domesticus musculus … than NW part … but SE part older … Co tuto zónu ovlivňuje? Hybrid zone in Europe Europe climate.gif continental climate oceanic climate Europe climate.gif climatic factors don’t determine continental climate oceanic climate Nick Barton Most hybrid zones are „tension zones“ also the mouse hybrid zone? Hybrid zone in Europe ObrA hybrid zone course may be complex.... ... moreover, usually we don’t know a priori, or we extrapolate from global direction Real local cline Cline interpolated from widescale survey ClineFit2DRGB 2D ® 1D clines 0.0 0.2 0.4 0.6 0.8 1.0 Distance along transect c Dp Multiple genes: „stepped“ model (symetrical, asymmetrical) linkage disequilibrium resulting from influx of parental allele combinations Þ synergistic effect: strenghtening of selection in zone centre Þ central step ´ introgression tails reflect selection at individual loci We can estimate some other key evolutionary parametres from LD and cline parametres: dispersal: effective selection: selection on marker loci: selection on selected loci: number of loci under selection: fitness of hybrids: nový-1 model comparison: LRT (they are nested); d.f. = difference in number of parametres likelihood profiles: Cline1 position on chromosome selected areas Cline2 centromere molecular markers hybrid zone Y1 Btk >20 km Problems – Y chromosome Monotonic clines – consensus orientation Y Monotonic clines for all the markers along the consensus direction CLICK  all the autosomal and the X clines are pretty coincident CLICK  the Y, when the cline estimated for the consensus orientation, is wider and shifted to the west CLICK  Y Interestingly, trapping sex ratio was female biased in both areas without the Y introgression (so that the proportion of males was significantly different from parity) while in the D area with the musculus Y introgression the sex ratio was close to parity and significantly different from the former two. CLICK  Btkcons YY Ycons Here is the Y cline estimated along its own direction CLICK  you can notice that the change is very abrupt and similar to the change of the X chromosome along the consensus. CLICK  for comparison, we included also the Y monotonic cline for the consensus direction we saw on the previous slide. CLICK  Y Y3 D=44%** DYM=51% M=45%*** salient/invagination » 330 km2 Interestingly, trapping sex ratio was female biased in both areas without the Y introgression (so that the proportion of males was significantly different from parity) while in the D area with the musculus Y introgression the sex ratio was close to parity and significantly different from the former two. CLICK  1. musculus Y more successful than domesticus Y on its own genetic background 2. higer proportion of males relative to other areas Either coincidence, or ... Weird behaviour of the Y in the hybrid zone – summary: kill_bill … or genetic conflict between X and Y and probably some autosomal genes as well X Y Aa A a 50% 50% Gregor Mendel segregation law Intragenomic conflict results in higher proportion of a genomic element in the next generation Aa A a 95% 5% vychýlení segregačího (transmisního) poměru = segregation distortion (SD) = transmission ratio distortion (TRD) Gregor Mendel ?! „drive“ Fig4.JPG X chromosome Fig3a.JPG Chr. X - 2D analysis Geneland ‘Genomic clines’ Z. Gompert & A. Buerkle Fig5.JPG Fig6A.jpg Concordance analysis: S.J.E. Baird S.J.E. Baird very steep cline strong introgression in both directions S.J.E. Baird introgression to the left Concordance analysis: S.J.E. Baird introgression to the right Concordance analysis: Fig7.jpg Proximal marker on the X centre of the Y introgression consensus barrier blocks around proximal marker musculus domesticus non-introgressed localities Recombination reduces size of introgressed block far of the zone centre Using cline model for analysis of reinforcement – odour preference in the mouse hybrid zone MaleABP.jpg reinforcement Using cline model for analysis of gene expression in the mouse hybrid zone – asymmetric model Svante.png Blocks of Neanderthal DNA found in modern humans can act like a biological clock, because they are fragmented more and more with each generation since interbreeding happened. The blocks of Neanderthal DNA in the Siberian man were on average three times longer than those seen in people alive today. Working backwards, the scientists calculate that Neanderthals contributed to the man’s genetic ancestry somewhere between 7,000 and 13,000 years before he lived. The findings, published in the journal Nature, suggest that humans and Neanderthals had reproductive sex around 50,000 to 60,000 years ago… The Guardian Wednesday 22 October 2014 Even worse – for these calculation I have assumed a generation time of one year. For longer lived organisms the situation is even worse…. X P F1 F2 F3 Hybridization makes a cascade of blocks advancing introgression into ‘blue’ genome junctions.jpg haplotype A haplotype B recombinant R. A. Fisher Recombination brings together DNA of different origin and makes junctions (breakpoints) they divide genome into blocks (chunks, tracts, segments) N SNP 3 junctions 4 markers N markers chromosome 12 of Neanderthal Romania, ~40 kya, mating before 200–100 years Siberia, ~45 kya, mating before 8000–5000 contemporary China, 54–49 kya Chromosome 17 MHC! >600 000 SNPs Chromozom X Why hybrid zones? Reproductive barriers and speciation! Dobzhansky-Muller model W. Bateson T. Dobzhansky H. Muller armsraces1.jpg „Arms races“ and secondary contact arms race in ancestral population subpop. 1 subpop. 2 secondary contact incompatible! genetic conflict: “classical” scenario continuing arms race http://www.independent.co.uk/incoming/article9097117.ece/binary/original/neanderthalAP.jpg http://www.11tharmoreddivision.com/member_photos/toal_files/14.jpg http://www.chlive.org/ljacobs/medievaltimes/5TournamentsandJoust/joust%201.jpg http://www.greendragonsociety.com/images/Mongol_Archer%2083.jpg MAD = mutually assured destruction Interlaced fingers, braid, fingerloop braiding, twist together arms race in ancestral population subpop. 1 subpop. 2 secondary contact genetic conflict: alternative scenario continuing arms race the winner thrives on “naive” genetic background “antispeciation genes” http://upload.wikimedia.org/wikipedia/commons/7/70/Testing_bulletproof_vest_1923.jpg http://sportbilly.co.za/wp-content/uploads/2011/12/Gun-Vs-Knife-2-BW.jpg http://www.aceros-de-hispania.com/image/rapier-sword/fencing-rapier-sword.jpg Never bring a knife to a gunfight! http://www.independent.co.uk/incoming/article9097117.ece/binary/original/neanderthalAP.jpg Interlaced fingers, braid, fingerloop braiding, twist together incompatibility loci arms victors hitchhikers neutral loci Ticking time-bomb... Why we don’t see this more often? Interlaced fingers, braid, fingerloop braiding, twist together nuclear genotype: mtDNA: AA Aa aa total M u1 v1 w1 x m u2 v2 w2 y total u v w 1 Cytonuclear disequilibria • = non/random associations of nuclear and cytoplasmic (mitochondrial) alleles • 3 ´ 2 table nuclear genotype: mtDNA: AA Aa aa M +++ 0 0 m 0 0 +++ nuclear genotype: mtDNA: AA Aa aa M ++ obs=exp 0 m 0 obs=exp ++ No hybridization Random mating, hybrid swarm nuclear genotype: mtDNA: AA Aa aa M obs=exp obs=exp obs=exp m obs=exp obs=exp obs=exp Hybridization without apparent introgression, crossing independent of sex nuclear genotype: mtDNA: AA Aa aa M ++ ++ 0 m 0 -- ++ Hybridization without apparent introgression, crossing depends on sex nuclear genotype: mtDNA: AA Aa aa M obs=exp ++ -- m obs=exp -- ++ nuclear genotype: mtDNA: AA Aa aa M ++ ++ -- m 0 0 ++ Hybrids mate more often with less discriminating species Symmetrical introgression nuclear genotype: mtDNA: AA Aa aa M ++ obs=exp -- m -- obs=exp ++ Potential introgression, crossing dependent on sex portraitTL Programs for hybrid zone analysis: Analyse: Stuart J.E. Baird, Nick H. Barton (Mac) ClineFit: Adam Porter (PC) CFit: Thomas Lenormand (PC) (Geneland) P8023328 aporter S.J.E. Baird N.H. Barton A. Porter T. Lenormand