Organellar Genomes and Genetic Markers

1. Organellar Genomes and Genetic Markers Level 3 Molecular Evolution and Bioinformatics Jim Provan

2. Nucleus Chloroplast Mitochondrion Ploidy Recombination Inheritance Diploid Haploid Haploid    Biparental Uniparental: Angiosperms (M) Gymnosperms (P) Maternal Organellar variation

3. Nuclear (diploid) 4Nµ (4Nµ + 1) Organellar (haploid) 2Nµ (2Nµ + 1) 1.0 0.8 0.6 0.4 0.2 0.0 0.0001 0.001 0.01 0.1 1 10 100 1000 Nµ Diploid Haploid Variation at drift/mutation equilibrium

4. 3 3 3 3 A A A A B 1      1 A C 2   Selective sweeps

5. Plant organelle genomes - implications for markers • Generally lower diversity due to: • Haploid genome • Lower mutation rates • Lack of recombination - selective sweeps • Lack of intraspecific variation  species specific markers • Detection of intraspecific variation  variable regions • Non-coding regions • Tandemly-duplicated genes • Mononucleotide microsatellites • Very little mitochondrial variation

6. Genetic change during fragmentation • In fragmented populations, differentiaton due to drift will be more marked in haploid organellar genomes • Maternally inherited markers travel via seed  organellar gene flow less substantial • Maternal markers useful for recording historical events

7. Dispersal Pollen:Seed Ratio Species Pollen Seed Quercus Argania Pinus Ratios of pollen:seed flow • Combined analysis of nuclear and organellar markers can give information on relative importance of seed and pollen flow • Important for: • Dynamics of natural populations • Transgene movement Wind Bird 196 Insect Ruminant 2.5 Wind Wind 18

8. Animal mitochondrial DNA in population genetics • Maternal inheritance and relatively rapid rate of evolution have led to widespread use in studies of matrilineal gene flow • Sensitive indicator of: • Female-mediated gene flow (maternal inheritance) • Founder events (haploid genome) • Comparisons of spatial distribution of nuclear and mitochondrial markers provides information on sexual bias in dispersal

9. Geographical structuring with sedentary females • Offspring from each mother will have maternal mtDNA genotype and half paternal nuclear genotype • If mothers have different mtDNA genotypes, groups of offspring will be: • Completely different for mitochondrial markers • At least 50% similar for nuclear markers

10. The “Mitochondrial Eve” hypothesis • Studies suggested that between 140,000 and 360,000 years ago, a single mtDNA haplotype existed! • Theoretical studies dispute this: • Rate of extinction of maternal lineages is high • Even if several thousand mtDNAs were present, high probability that only one would have survived

11. Chloroplast DNA phylogeography of Alnus glutinosa (L.) Gaertn. R. Andrew King and Colin Ferris Molecular Ecology (1998) 7: 1151-1161

12. Introduction • Until recently, fossil pollen mapping was the only way to study history of plant populations • Studies in various trees have shown that after the last (Würrm) glaciation, Europe was recolonised from at least three separate refugia: • Southern Spain • Southern Italy • Balkan peninsula • Use of chloroplast-specific markers should give new insights into post-glacial histories of plant species

13. Chloroplast haplotype distribution in alder (Alnus)

14. Post-glacial history of Alnus • Obvious high levels of genetic variation below the southern limit of the ice during the last glaciation • Two dominant haplotypes found throughout northern Europe • Majority of Europe colonised from single refugium in the Balkans

15. Patterns of variation at a mitochondrial sequence-tagged-site locus provides new insights into the postglacial history of European Pinus sylvestris populations Nicole Soranzo, Ricardo Alia, Jim Provan and Wayne Powell Molecular Ecology (2000) 9: 1205-1211

16. Maternal markers in conifers • In virtually all embryophytes (seed plants), the mitochondrial genome is inherited maternally i.e. via the seed • Chloroplast genome inherited in a different manner in angiosperms and gymnosperms: • In angiosperms, chloroplast genome is also mostly inherited maternally • In gymnosperms, chloroplast genome is inherited paternally i.e. via both pollen and seed • In conifers, mitochondrial markers will be good indicators of historical events

17. Mitochondrial variation in Scots pine in Spain • Two haplotypes found in mitochondrial nadI region • General NE / SW split in haplotype distribution • Only one (dark) haplotype found in rest of Europe

18. Within populations (40%) Between populations (60%) Distribution of variation in Spanish Pinus sylvestris

19. Mitochondrial variation in European P. sylvestris • Levels of population differentiation revealed using mitochondrial markers were 10- to 30-fold higher than in previous studies using nuclear and chloroplast markers • Low degree of variation in non-Spanish populations probably due to post-glacial recolonisation from a common refugium • Spanish populations below southern limit of glaciation: • Not subjected to glaciation - represent ancient gene pools • Physical isolation of populations on different mountain ranges accounts for high levels of between-population differentiation

20. rbcL sequences reveal multiple cryptic introductions of the Japanese red alga Polysiphonia harveyii Lynne McIvor, Christine Maggs, Jim Provan and Michael Stanhope Molecular Ecology (2001) 10: 911-919

21. Introductions of Polysiphonia harveyii from Japan • Aim: to test whether global populations of P. harveyii had arisen from a single or multiple introductions • Methodology: • Sequence rbcL gene • Align sequences • Construct phylogenetic tree showing relationships between observed genotypes • Compare with geographic distribution

22. E Choshi HONSHU D C Shimoda Oshoro X Y Z HOKKAIDO North Carolina New Zealand Monterey F Europe Nova Scotia A B Akkeshi Minimum-spanning phylogenetic network

23. Multiple introductions of P. harveyii • Multiple hypothetical ancestral genotypes present which were not observed: • Consistent with Japan being the centre of diversity of P. harveyii • Most likely not observed due to limited sampling, rather than extinction • Non-Japanese populations of P. harveyii represented by two divergent genotypes: • One possibly linked to Honshu genotypes • One possibly linked to Hokkaido genotypes • Most likely represent at least two separate introductions from original centre of diversity in Japan

24. Nuclear Mitochondrial Nuclear and mitochondrial variation in Scots pine in Sweden • Scots pine believed to have recolonised Sweden from both North and South after glaciation • Nuclear (monoterpene) markers suggest clinal variation but not definite • Mitochondrial markers show definite boundary at 60°N, even after ~50 generations of contact