1. Population size does not influence mitochondrial genetic diversity in animals E. Bazin, S. Glémin, N. Galtier CNRS UMR 5171 – Génome, Populations, Interactions, Adaptation Université Montpellier 2 Montpellier, France galtier@univ-montp2.fr DAWG meeting 2006

2. Evolutionary forces influencing the genetic diversity  ~ Ne.  selection demography structure mating systems On average, abundant species should be more polymorphic than scarce ones.

3. Allozyme meta-analyses - Hamrick & Godt 1996 : outcrossers > selfers (plants) - Nevo et al 1984: invertebrates > vertebrates (animals) - Frankham 1997: mainland > island (animals and plants) - Spielman et al 2004: healthy > endangered (animals and plants) What about DNA markers, especially mtDNA?

4. The Polymorphix data base GenBank/EMBL species 1 BLAST similarity CLEAN bibliography flanking ALIGN Polymorphix families ADD OUTGROUPS http://pbil.univ-lyon1.fr/~polymorphix

5. Measuring DNA polymorphism in animals - remove genome projects - remove transposons, LINE, SINE, MHC, immunoglobulin, rRNA … - manually check highly polymorphic families - start from Polymorphix 1.2 - Metazoa - focus on coding sequences - for each family, calculate the synonymous diversity  s - average over loci within species - average over species within 8 taxa:Mammals, Sauropsids, Amphibians, Fish Insects, Crustaceans, Molluscs, Echinoderms - compare to allozyme data (Nevo et al 1984)

6. Mammals Sauropsids Amphibians Fish Insects Crustaceans Molluscs Echinoderms 311 348 80 248 26 451 58 107 25 18 4 11 22 69 2 11 184 116 61 183 15 122 46 mtDNA nuclear DNAallozymes 1629162849 Data set: number of species

7. Taxonomy does not predict mtDNA sequence polymorphism ss Allozyme heterozygosity nuclear DNA Verterbates Inverterbates

8. Taxonomy does not predict mtDNA sequence polymorphism ss Allozyme heterozygosity nuclear DNA mtDNA Verterbates Inverterbates

9. Ecology does not predict mtDNA sequence polymorphism Crustaceans Branch.Dec. Branch.Dec. 0.10 ss 0.30 H AllozymesmtDNA **

10. Ecology does not predict mtDNA sequence polymorphism Crustaceans Branch.Dec. Branch.Dec. 0.10 ss 0.30 H AllozymesmtDNA Allozymes 0.40 0.08 ss H continentmarinecontinentmarine Molluscs ** *

11. Ecology does not predict mtDNA sequence polymorphism Crustaceans Branch.Dec. Branch.Dec. 0.10 ss 0.30 H AllozymesmtDNA Allozymes 0.40 0.08 ss H continentmarinecontinentmarine Molluscs mtDNAAllozymes Fish H ss 0.08 freshmarinefreshmarine ** * *

12. Ecology does not predict mtDNA sequence polymorphism Crustaceans Branch.Dec. Branch.Dec. 0.10 ss 0.30 H AllozymesmtDNA Allozymes 0.40 0.08 ss H continentmarinecontinentmarine Molluscs mtDNAAllozymes Fish H ss 0.08 freshmarinefreshmarine ** * *

13. mtDNA diversity mass (log scale) taxonomy residual Ecology does not predict mtDNA sequence polymorphism Mammals r 2 : 3% p-val : 0.04 r 2 : 0.1% p-val : 0.6

14. Why is not mtDNA sequence polymorphism correlated to Ne? - mutation: would imply a general, unplausible inverse relationship between Ne and  - demography, structure: should affect the nuclear genome as well - natural selection:. negative selection = background selection: still predicts a positive relationship between  and Ne (Charlesworth et al 1995). positive selection = genetic draft predicts an essentially flat relationship between  and Ne (Gillespie 2001)

15. Selective sweep, hitch-hiking and genetic draft SELECTIVE SWEEP sampled neutral locus linked selected locus A selective sweep, the rapid fixation of an advantageous mutation leads to sudden drop of variability at linked loci through hitch-hiking. Advantageous mutations are more frequent in large populations: the increased genetic draft compensates for the decreased genetic drift.

16. Selective sweep, hitch-hiking and genetic draft A selective sweep, the rapid fixation of an advantageous mutation leads to sudden drop of variability at linked loci through hitch-hiking. Advantageous mutations are more frequent in large populations: the increased genetic draft compensates for the decreased genetic drift. Ne  drift draft

17. Synonymous / non-synonymous evolutionary process - Neutrality Index: NI = (  N /  S ) / (d N / d S ) Vert.Invert. Vert.Invert. mtDNAnuclear DNA 0 1 5 10 NI (log scale) ** adaptative purifying neutral

18. Synonymous / non-synonymous evolutionary process - Neutrality Index: NI = (  N /  S ) / (d N / d S ) Vert.Invert. Vert.Invert. mtDNAnuclear DNA 0 1 5 10 NI (log scale) ** adaptative purifying neutral

19. Synonymous / non-synonymous evolutionary process - Neutrality index: NI = (  N /  S ) / (d N / d S ) Vert.Invert. Vert.Invert. mtDNAnuclear DNA 0 1 5 10 NI (log scale) adaptive purifying neutral

20. Synonymous / non-synonymous evolutionary process - complete mitochondrial genome: data setsaverage d N /d S Vertebrates Invertebrates 880.086 24 0.151**

21. Conclusions - population size influences nuclear, but not mitochondrial DNA diversity - recurrent adaptive evolution explains the homogeneous mtDNA pattern Implications - low-diversity mtDNA lineages might be well adapted, not endangered - mtDNA might be the worst marker of species abundance Questions - what is mtDNA adapting to ? - mtDNA might be a good marker for barcoding