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Population size does not influence mitochondrial genetic diversity in animals

DAWG meeting 2006. 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. mating systems. demography.

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Population size does not influence mitochondrial genetic diversity in animals

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  1. DAWG meeting 2006 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

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

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

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

  5. Measuring DNA polymorphism in animals - start from Polymorphix 1.2 - Metazoa - remove genome projects - remove transposons, LINE, SINE, MHC, immunoglobulin, rRNA … - manually check highly polymorphic families - 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. Data set: number of species mtDNA nuclear DNA allozymes Mammals 311 25 184 Sauropsids 348 18 116 Amphibians 80 4 61 Fish 248 11 183 Echinoderms 26 22 15 Insects 451 69 122 Crustaceans 58 2 122 Molluscs 107 11 46 1629 162 849

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

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

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

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

  11. Branch. Dec. Branch. Dec. continent marine continent marine 0.40 0.30 0.08 0.10 s H s H Allozymes mtDNA Allozymes mtDNA Crustaceans Molluscs fresh marine fresh marine 0.08 0.08 s H Allozymes mtDNA Fish Ecology does not predict mtDNA sequence polymorphism * ** *

  12. Branch. Dec. Branch. Dec. continent marine continent marine 0.40 0.30 0.08 0.10 s H s H Allozymes mtDNA Allozymes mtDNA Crustaceans Molluscs fresh marine fresh marine 0.08 0.08 s H Allozymes mtDNA Fish Ecology does not predict mtDNA sequence polymorphism * ** *

  13. Ecology does not predict mtDNA sequence polymorphism Mammals mtDNA diversity taxonomy residual mass (log scale) mass (log scale) r2 : 3% p-val : 0.04 r2 : 0.1% p-val : 0.6

  14. - 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) 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

  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 draft drift  Ne 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.

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

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

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

  20. Synonymous / non-synonymous evolutionary process - complete mitochondrial genome: data sets average dN/dS Vertebrates 88 0.086 Invertebrates 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 - mtDNA might be a good marker for barcoding Questions - what is mtDNA adapting to ?

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