phylogeography of the cosmopolitan genus myotis (chiroptera) using model-based reconstructions
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The fabulous odyssey of Myotis
Phylogeography of the cosmopolitan genusMyotis (Chiroptera) using model-based
Phylogeography of the cosmopolitan genusMyotis (Chiroptera) using model-based
Presented by: Yann Gager
Supervised by: Emmanuel Douzery (University of Montpellier 2 - France)
Manuel Ruedi (Museum of Geneva - Switzerland)
using model-basedreconstructions
using model-basedreconstructions
1 - The genus Myotis
The fabulous odyssey of Myotis
1 - The genus Myotis
• Global distribution (except Antarctica)
1 - The genus Myotis
• Global distribution (except Antarctica)
• More than 100 species described:
2nd most diversified genus of Mammals
1 - The genus Myotis
• Global distribution (except Antarctica)
• More than 100 species described:
2nd most diversified genus of Mammals
• Difficulty differentiating species
on the basis of morphological criteria
1 - The genus Myotis
M. brandtii M. alcathoe M. mystacinus
© Dietz & von Helversen
1 - The genus Myotis
• Phylogeny of Myotis from America
and Africa already known
1 - The genus Myotis
• Phylogeny of Myotis from America
and Africa already known
• Poor knowledge of relationships
of Eurasian Myotisof Eurasian Myotis
1 - The genus Myotis
• Phylogeny of Myotis from America
and Africa already known
• Poor knowledge of relationships
of Eurasian Myotisof Eurasian Myotis
• Incomplete picture of the genus evolution
at a worldwide scale
2 - Aims of the study
The fabulous odyssey of Myotis
2 - Aims of the study
• Important sampling of species
and molecular data
2 - Aims of the study
• Important sampling of species
and molecular data
• Phylogenetic trees of taxa
at a worldwide scaleat a worldwide scale
2 - Aims of the study
• Important sampling of species
and molecular data
• Phylogenetic trees of taxa
at a worldwide scaleat a worldwide scale
• Preliminary to the study
of biogeographic and temporal origins
3 - Samplings
The fabulous odyssey of Myotis
3 - Samplings
• 85 recognised species,
5 new species and 5 outgroups
West Palaearctic
13 species
EastPalaearctic
8
Oriental
Nearctic
17
Ethiopian
6
Oceania
1
Oriental
21
Neotropics
13
West Palaearctic
13 species
EastPalaearctic
8
Oriental
Nearctic
17
Eurasia
Ethiopian
6
Oceania
1
Oriental
21
Neotropics
13
West Palaearctic
13 species
EastPalaearctic
8
Oriental
Nearctic
17
Eurasia
Ethiopian
6
Oceania
1
Oriental
21
Neotropics
13
Africa
West Palaearctic
13 species
EastPalaearctic
8
Oriental
Nearctic
17
Eurasia America
Ethiopian
6
Oceania
1
Oriental
21
Neotropics
13
Africa
3 - Samplings
• 85 recognised species,
5 new species and 5 outgroups
• Compilation & concatenation of 2 genes:
Cyt b (mitochondrial) & Rag 2 (nuclear)Cyt b (mitochondrial) & Rag 2 (nuclear)
3 - Samplings
• 85 recognised species,
5 new species and 5 outgroups
• Compilation & concatenation of 2 genes:
Cyt b (mitochondrial) & Rag 2 (nuclear)Cyt b (mitochondrial) & Rag 2 (nuclear)
• Alignement of 136 Cyt b & 116 Rag 2,
with 164 seq. of GenBank & 88 new seq.
4 -Phylogenetic inferences
The fabulous odyssey of Myotis
4 - Phylogenetic inferences
• Search of phylogram:
Probabilistic approach
- Maximum Likelihood (PAUP*)
- Bayesian Inference (PhyloBayes)- Bayesian Inference (PhyloBayes)
Assesment methods (Nodal support)
« latirostrislineage»
AmericanClade
EthiopianClade
VIVII
EurasianClade
VIIVIII
IX
New speciesNew species
New speciesNew species
New speciesNew species
4 - Phylogenetic inferences
• A new genus for the
« latirostris lineage » ?
Drawing: Ravel et al. 2011
Nyctalodoncy
MyotodoncyMyotis latirostris
5 - Molecular dating
The fabulous odyssey of Myotis
5 - Molecular dating
• Search of chronograms (BEAST) :
- 4 chains of 5.106 generations
- Molecular clock called relaxed
- 18000 trees sampled
Fossil calibrations
Diversification American
Clade: 10.9 ±2.7
My
Colonization Oceania :
4.2 ±1.5 My
5 - Molecular dating
• Search of biogeographic origins:
- Estimate of ancestral character states
with a probabilistic model (Lagrange)
on the final chronogram
Species 1
Species 2
?
Species 3
?
Palaearctic
Oriental region
5 - Molecular dating
• Search of biogeographic origins:
- Estimate of ancestral character states
with a probabilistic model (Lagrange)
on the final chronogram
Species 1
Species 2
Species 3
Palaearctic
Oriental region
5 - Molecular dating
• Search of biogeographic origins:
- Consideration of branch lengths
5 - Molecular dating
• Search of biogeographic origins:
- Consideration of branch lengths
- Area-adjacency matrix
A B
C
DOceanian
E
F
G
A B C D E F G
A 1 1 1 0 1 0 0
B 1 1 1 0 1 1 0
C 1 1 1 1 1 0 0
D 0 0 1 1 0 0 0
E 1 1 1 0 1 0 0
F 0 1 0 0 0 1 1
G 0 0 0 0 0 1 1
5 - Molecular dating
• Search of biogeographic origins:
- Consideration of branch lengths
- Area-adjacency matrix
- Area-dispersal matrix
A B
C
DOceanian
E
F
G
A B C D E F G
A 1 1 1 0 1 0 0
B 1 1 1 0 1 1 0
C 1 1 1 1 1 0 0
D 0 0 1 1 0 0 0
E 1 1 1 0 1 0 0
F 0 1 0 0 0 1 1
G 0 0 0 0 0 1 1
« latirostrislineage»
AmericanClade
EthiopianClade
EurasianClade
C
EurasianClade:
Oriental
C
C
Ethiopian Clade:
Oriental
C
C
Old World Clade:
Oriental
C
Oriental
C
C
C
BAmerican Clade:E. Pal.
C
C
C
B
BC
E. Pal. + Oriental
17.7 ±3.9
My
Oriental
Cradle ofMyotis
17.7 ±3.9
My
Cradle ofMyotis
15.1 ±3.4
My
Cradle ofMyotis
15.1 ±3.4
My
11.1 ±2.7
My
Cradle ofMyotis
15.1 ±3.4
My
10.9 ±2.7
My
?
11.1 ±2.7
My
Cradle ofMyotis
15.1 ±3.4
My
10.9 ±2.7
My
?
5.2 ±1.4
11.1 ±2.7
My
8.3 ±2.1
My
5.2 ±1.4
My
Cradle ofMyotis
15.1 ±3.4
My
10.9 ±2.7
My
?
5.2 ±1.4
11.1 ±2.7
My
8.3 ±2.1
My
5.2 ±1.4
My
4.2 ±1.5
My
6 - Perspectives
The fabulous odyssey of Myotis
6 - Perspectives
• Phylogenies: working basis
for many research !
BiogeographySystematics
ConservationLife-history
traits
Thank you !
QuickTime™ et undécompresseur
sont requis pour visionner cette image.
Merci !© M. König
Order Chiroptera
Jones and Teeling, 2006
Chiroptera
Phylogeography
• Study of the historical processes that may be
responsible for the contemporary geographic
distribution of individuals.
• This is accomplished by considering the• This is accomplished by considering the
geographic distribution of individuals in light
of the patterns associated with a gene
genealogy.
Biogeographic reconstructions
• H0 = without constraints : lnL = 146.8
• H1 = with constraints : lnL = 139.5
Better likelihood with the area-adjacency matrix
and the area-dispersal matrix !and the area-dispersal matrix !
Biogeographic reconstructions
• Relative probabilities for each node
e.g. Node of the Myotis sensu lato:
• E.g. At node X:
• split lnL Rel.Prob
• [BC|C] -141.2 0.7381 • [BC|C] -141.2 0.7381
• [C|C] -143.6 0.06645
• [B|C] -144 0.04323
• [A|C] -144.5 0.02802
• [AB|A] -144.5 0.02596
• [AB|B] -144.6 0.02476
• [AC|C] -145 0.01643
• [BC|B] -145.5 0.009844
Phylogenetic analyses
• Maximum likelihood (GTR + Γ + INV)
P ,MP ,M
• Nucleotidic model of evolution:
- General Time Reversible (GTR)
- Gamma distribution of the variation rate (ΓΓΓΓ)
- Proportion of invariant sites (INV)
GTR + Γ + INV
• Base frequencies ∏, substitution rates (from
a to f) and branch lengths
A C G T
A - a∏C b∏G c∏T
C a∏A - d∏G e∏T
G b∏A d∏C - f∏T
T c∏A e∏C f∏G -