population size does not influence mitochondrial genetic diversity in animals e. bazin, s. glémin,...
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Population size does not influence mitochondrial genetic diversity in animals
E. Bazin, S. Glémin, N. Galtier
CNRS UMR 5171 – Génome, Populations, Interactions, AdaptationUniversité Montpellier 2
Montpellier, France
DAWG meeting 2006
Evolutionary forces influencing the genetic diversity
~ Ne .
selection
demography
structure
mating systems
On average, abundant species should be more polymorphic than scarce ones.
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?
The Polymorphix data base
GenBank/EMBL
species 1
BLAST
similarity
CLEAN
bibliographyflanking
ALIGN
Polymorphix families
ADDOUTGROUPS
http://pbil.univ-lyon1.fr/~polymorphix
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)
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
122
46
mtDNA nuclear DNA allozymes
1629 162 849
Data set: number of species
Taxonomy does not predict mtDNA sequence polymorphism
s
Allozyme heterozygosity
nuclear DNA
Verterbates Inverterbates
Taxonomy does not predict mtDNA sequence polymorphism
s
Allozyme heterozygosity
nuclear DNA
mtDNA
Verterbates Inverterbates
Ecology does not predict mtDNA sequence polymorphism
Crustaceans
Branch. Dec. Branch. Dec.
0.10
s
0.30
H
Allozymes mtDNA
**
Ecology does not predict mtDNA sequence polymorphism
Crustaceans
Branch. Dec. Branch. Dec.
0.10
s
0.30
H
Allozymes mtDNA mtDNAAllozymes
0.400.08
sH
continent marine continent marine
Molluscs
** *
Ecology does not predict mtDNA sequence polymorphism
Crustaceans
Branch. Dec. Branch. Dec.
0.10
s
0.30
H
Allozymes mtDNA mtDNAAllozymes
0.400.08
sH
continent marine continent marine
Molluscs
mtDNAAllozymes
Fish
H s
0.08 0.08
fresh marine fresh marine
** *
*
Ecology does not predict mtDNA sequence polymorphism
Crustaceans
Branch. Dec. Branch. Dec.
0.10
s
0.30
H
Allozymes mtDNA mtDNAAllozymes
0.400.08
sH
continent marine continent marine
Molluscs
mtDNAAllozymes
Fish
H s
0.08 0.08
fresh marine fresh marine
** *
*
mtDNAdiversity
mass (log scale) mass (log scale)
taxonomyresidual
Ecology does not predict mtDNA sequence polymorphism
Mammals
r2 : 3%p-val : 0.04
r2 : 0.1%p-val : 0.6
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)
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.
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
Synonymous / non-synonymous evolutionary process
- Neutrality Index: NI = (N / S) / (dN / dS)
Vert. Invert. Vert. Invert.
mtDNA nuclear DNA
0
1
5
10
NI (log scale)
**adaptative
purifying
neutral
Synonymous / non-synonymous evolutionary process
- Neutrality Index: NI = (N / S) / (dN / dS)
Vert. Invert. Vert. Invert.
mtDNA nuclear DNA
0
1
5
10
NI (log scale)
**adaptative
purifying
neutral
Synonymous / non-synonymous evolutionary process
- Neutrality index: NI = (N / S) / (dN / dS)
Vert. Invert. Vert. Invert.
mtDNA nuclear DNA
0
1
5
10
NI (log scale)
adaptive
purifying
neutral
Synonymous / non-synonymous evolutionary process
- complete mitochondrial genome:
data sets average dN/dS
Vertebrates
Invertebrates
88 0.086
24 0.151**
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