A new non-minimal algorithm for dating phylogenies of fossil taxa

Graeme T. Lloyd, Matt Friedman and Mark A. Bell

Molecular phylogeny

(dos Reis et al. 2012)

Palaeontological phylogeny

(Motani 1999)

But what about extinct clades?

Branch lengths in palaeontology

“Ghost” diversity

(Weishampel et Jianu 2000)

Raw

Raw + “ghosts”

Raw

Raw + “ghosts”

(Brusatte et al. 2011)

Extinction survival

Aphylogenetic survival:

1/3 = 33%

Phylogenetic survival:

4/6 = 67%

(Modesto et al. 2001)

Evolutionary rates

(Lloyd et al. 2012)

Phylogenetic covariance matrix

15 1 0 0 0 0

1 15 0 0 0 0

0 0 15 14 7 7

0 0 14 15 7 7

0 0 7 7 15 9

0 0 7 7 9 15

(Slide pilfered from Chris Organ)

A

B

D

A B D

E

F

G

E F G

Evolutionary models

(Slides pilfered from Graham Slater)

Brownian Motion

Ornstein-Uhlenbeck

Early Burst

Late Burst

Trend

A brief history of fossil-onlytree dating

Traditional approach

τ7

τ8

τ6

τ5

τ4

τ2

τ1

τ3

= max( , ) = max(τ8,τ7)

(Smith 1994)

Traditional approach

τ7

τ8

τ6

τ5

τ4

τ2

τ1

τ3

Implied phylogeny

(Smith 1994)

Add k solution

τ7

τ8

τ6

τ5

τ4

τ2

τ1

τ3

= max( , ) + k

k

(Derstler 1982; Forey 1988)

Branch sharing solution

τ7

τ8

τ6

τ5

(Ruta et al. 2006; Brusatte et al. 2008)

root age

τ7

τ6

τ5

Traditional approach first Share time with preceding(non-zero length) branch

A novel approach

Hedman approach

τ7

τ8

τ6

τ5

τ4

τ2

τ1

τ3

= ƒ( )

(Hedman 2010)

Hedman approach

Age (Ma)Minimumt0

Maximum

Freq

uenc

y

Hedman approach

τ7

τ8

τ6

τ5

τ4

τ2

τ1

τ3

= ƒ( )

(Hedman 2010)

= ƒ( )

Hedman approach

(Lloyd et al. 2008)

Only 135 ‘unique’ nodes(one third of 416 total)

Hedman approach

(Lloyd et al. 2008)

Only 135 ‘unique’ nodes(one third of 416 total)

What about the other two thirds?

Modified Hedman approach

Modified Hedman approach

Modified Hedman approach

12

3

Modified Hedman approach

12

3

Min Max

Modified Hedman approach

1 2 3

12

3

Min Max

Modified Hedman approach

12

3

Molecular versus fossil-only dating in placental mammals

Placental mammals

• Informal supertree• 48 source trees• 452 OTUs (cladistically

placed)• Computation time: 6m 57s

Fossil vs. Molecular dates

PaleogeneCretaceous

Pale

ogen

eCr

etac

eous

Fossi

l age > Molecu

lar age

Molecular a

ge > Fo

ssil age

Traditional vs. Molecular

Trad

ition

al a

ppro

ach

Meredith et al. 2011

1:1 RSS31269.3

PaleogeneCretaceous

Pale

ogen

eCr

etac

eous

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

Approach comparison

Meredithet al.2011

dos Reiset al.2012

Traditionalapproach

ModifiedHedmanapproach

Approach comparison

Meredithet al.2011

Traditionalapproach

ModifiedHedmanapproach

1:1 RSS2210.1

1:1 RSS10433.7

1:1 RSS5496.0

dos Reiset al.2012

Approach comparison

Meredithet al.2011

Traditionalapproach

ModifiedHedmanapproach

1:1 RSS1837.6

1:1 RSS1514.9

1:1 RSS

4311.1

dos Reiset al.2012

Conclusions

• Novel fossil-only tree dating approach

Conclusions

• Novel fossil-only tree dating approach• Mimics molecular approach (distribution)

Conclusions

• Novel fossil-only tree dating approach• Mimics molecular approach (distribution)• Helps close molecule-fossil gap

Conclusions

• Novel fossil-only tree dating approach• Mimics molecular approach (distribution)• 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