confidence intervals on node age estimates in vertebrate phylogeny
DESCRIPTION
TRANSCRIPT
![Page 1: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/1.jpg)
Confidence intervals on node age estimates in vertebrate phylogeny
Graeme T. Lloyd, Matt Friedman and Mark A. Bell
![Page 2: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/2.jpg)
Molecular dating methods
(Reis et al. 2012)
![Page 3: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/3.jpg)
But what about extinct clades?
![Page 4: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/4.jpg)
Branch lengths in palaeontology
![Page 5: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/5.jpg)
“Ghost” diversity
(Weishampel et Jianu 2000)
Raw
Raw + “ghosts”
Raw
Raw + “ghosts”
(Brusatte et al. 2011)
![Page 6: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/6.jpg)
Extinction survival
Aphylogenetic survival:
1/3 = 33%
Phylogenetic survival:
4/6 = 67%
(Modesto et al. 2001)
![Page 7: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/7.jpg)
Evolutionary rates
(Lloyd et al. 2012)
![Page 8: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/8.jpg)
Phylogenetic distance matrices
A
B C A
B
C
A B C0 3 5
3 0 4
5 4 0
10
9
8
7
Tim
e (M
a)
![Page 9: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/9.jpg)
A brief history of fossil-only tree dating
![Page 10: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/10.jpg)
Traditional approach
τ7
τ8
τ6
τ5
τ4
τ2
τ1
τ3
= max( , ) = max(τ8,τ7)
(Smith 1994)
![Page 11: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/11.jpg)
Traditional approach
τ7
τ8
τ6
τ5
τ4
τ2
τ1
τ3
Implied phylogeny
(Smith 1994)
![Page 12: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/12.jpg)
Add k solution
τ7
τ8
τ6
τ5
τ4
τ2
τ1
τ3
= max( , ) + k
k
(Derstler 1982; Forey 1988)
![Page 13: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/13.jpg)
Branch sharing solution
τ7
τ8
τ6
τ5
(Ruta et al. 2006)
root age
τ7
τ6
τ5
Traditional approach first Share time with preceding(non-zero length) branch
![Page 14: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/14.jpg)
A novel approach
![Page 15: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/15.jpg)
Hedman approach
τ7
τ8
τ6
τ5
τ4
τ2
τ1
τ3
= ƒ( )
(Hedman 2010)
![Page 16: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/16.jpg)
Hedman approach
Age (Ma)Minimumt0
Maximum
Freq
uenc
y
![Page 17: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/17.jpg)
Hedman approach
τ7
τ8
τ6
τ5
τ4
τ2
τ1
τ3
= ƒ( )
(Hedman 2010)
= ƒ( )
![Page 18: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/18.jpg)
Hedman approach
(Lloyd et al. 2008)
Only 135 ‘unique’ nodes(one third of 416 total)
![Page 19: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/19.jpg)
Hedman approach
(Lloyd et al. 2008)
Only 135 ‘unique’ nodes(one third of 416 total)
What about the other two thirds?
![Page 20: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/20.jpg)
Modified Hedman approach
![Page 21: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/21.jpg)
Modified Hedman approach
![Page 22: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/22.jpg)
Modified Hedman approach
12
3
![Page 23: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/23.jpg)
Modified Hedman approach
12
3
Min Max
![Page 24: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/24.jpg)
Modified Hedman approach
1 2 3
12
3
Min Max
![Page 25: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/25.jpg)
Modified Hedman approach
12
3
![Page 26: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/26.jpg)
Molecular versus fossil-only dating in placental mammals
![Page 27: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/27.jpg)
Placental mammals
• Informal supertree• 48 source trees• 452 OTUs (cladistically
placed)• Computation time: 6m 57s
![Page 28: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/28.jpg)
Fossil vs. Molecular dates
PaleogeneCretaceous
Pale
ogen
eCr
etac
eous
Fossi
l age > Molecu
lar age
Molecular a
ge > Fo
ssil age
![Page 29: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/29.jpg)
Traditional vs. Molecular
Trad
ition
al a
ppro
ach
Meredith et al. 2011
1:1 RSS31269.3
PaleogeneCretaceous
Pale
ogen
eCr
etac
eous
![Page 30: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/30.jpg)
PaleogeneCretaceous
Pale
ogen
eCr
etac
eous
New approach vs. Molecular
Mod
ified
Hed
man
app
roac
h
Meredith et al. 2011
1:1 RSS12340.4
1:1 RSS31269.3
![Page 31: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/31.jpg)
Approach comparison
Meredithet al.2011
Reiset al.2012
Traditionalapproach
ModifiedHedmanapproach
![Page 32: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/32.jpg)
Approach comparison
Meredithet al.2011
Reiset al.2012
Traditionalapproach
ModifiedHedmanapproach
1:1 RSS2210.1
1:1 RSS10433.7
1:1 RSS5496.0
![Page 33: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/33.jpg)
Approach comparison
Meredithet al.2011
Reiset al.2012
Traditionalapproach
ModifiedHedmanapproach
1:1 RSS1837.6
1:1 RSS1514.9
1:1 RSS
4311.1
![Page 34: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/34.jpg)
Conclusions
• Novel fossil-only tree dating approach
![Page 35: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/35.jpg)
Conclusions
• Novel fossil-only tree dating approach• Mimics molecular approach
![Page 36: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/36.jpg)
Conclusions
• Novel fossil-only tree dating approach• Mimics molecular approach• Helps close molecule-fossil gap
![Page 37: Confidence intervals on node age estimates in vertebrate phylogeny](https://reader038.vdocuments.net/reader038/viewer/2022110113/53ff8e668d7f724c088b4666/html5/thumbnails/37.jpg)
Conclusions
• Novel fossil-only tree dating approach• Mimics molecular approach• Helps close molecule-fossil gap• Implications for a wide range of topics, e.g.:• Phylogenetic diversity estimates• Extinction/Survival %s• Rates of evolution• Trait models• Better calibration distributions