Fig S4 Tess - PLOS

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0.0. 0.1. 0.2. 0.3. 0.4 net-diversification rates million years ago rate. 80. 60. 40. 20. 0. 0.0. 0.5. 1.0. 1.5. 2.0. 2.5 relative-extinction rates million years ago rate. 80.
0

0

0.8 0.6 0.4 0.2

40

20

20

1

0.8

0.4

60

40

20

20

0

0.4

0.2

40

20

60

40

20

20

1.0 0.8 0.6

posterior probability

0.2

0.4

5 4 3

0.0 10

1.0 0.8 0.6 0.2

0.4

posterior probability

4 3

rate

0.0 10 5 -5

0

Bayes factors

0.8 0.6 0.4

-10 1.0 0.8 0.6

posterior probability

0.2

0.4

3 2

0.0 Bayes factors

10 5 0 -5 -10 1.0 0.8 0.6

posterior probability

0.4

2

0.0

0

0.2

80 60 40

rate

20

-5 0.4

0.2

0

0.8

0.6

0.4

0.2

0

1

0.8

0.6

0.4

0.2

0

0.6

0.4

0.2

10 5

1.0 0.8

10 6

0

2

-5

Bayes factors

0.8 0.6 0.4 0.2

6 -10

posterior probability

10

2

0.0 1

0

1

0.8

million years ago

0.6

0.4

0.2

0

1

0.8

million years ago

0.6

0.4

0.2

0

million years ago

0.6

0.4

0.2

0.6

0.4

0.2

0

0.2

0

0.8 0.6 0.4

0

0

0.6

0.4

0.2

0.4

0.2

0.8

0.2

0

0.4

0.2

0

extinction shift times 1.0

extinction rates

40 0.4

0.6

million years ago

0.8

10

0.6

2

0.6

10 0

100

6

0.8

0

Bayes factors

-5 -10

2 0.6

80

10

0

2

6

0.8

-5 0.8

6

million years ago

10

6

2

0.0

2

10

0.4

0.2

posterior probability

0.4

speciation Bayes factors

1.0 0.4

0.6

million years ago

0.8

posterior probability 0.6

0.2

0.2

0.8

6

10

0.0

0.0 0

0.0 0.8

0.4

5

1.0 rate

0.5

1.0

1.5

posterior probability

2.0

35 25 20

rate

15

0.2

0.6

100 40

0

0.4

speciation shift times

80 20

0.6

speciation rates

60 40

0.6

mass extinction Bayes factors

million years ago

rate 60

0.8

mass extinction times

million years ago

0

2

0

relative-extinction rates

0.8

20

6

0.2

net-diversification rates

10 0

10

0.6

0

0.2

0.4

million years ago

0.4

extinction shift times

0.4

0.6

million years ago

5 million years ago

0.6

posterior probability 0.8

million years ago

0 0.8

2

0.0

0 0.8

0.2

80

0

6

million years ago

30

10 0

2

60

rate

40 20

0.8

6

1.0

100 120

10 0 -5 2

10

0.8

0

2

0.6

0.2

extinction shift times

0.4

0.4

6

0.2

0.6

Bayes factors

0.8

6

extinction rates

10

10

0.6

posterior probability

1.0

speciation Bayes factors

5

speciation shift times

10

0

1.0 40

0.6

0.2

20

0.0 60

0.8

million years ago

-10 40

0.8

0

-10 0.0

1

-5

Bayes factors

5 0 -10

60

0.0

-10

0

2 1 1.0

0

extinction Bayes factors

0.2 60

1

0.8

0.6

0.4

0.2

0

0.8

0.6

0.4

0.2

0

60

40

20

million years ago

0

40

20

million years ago

0

20

0

60

40

20

million years ago

0

40

20

million years ago

0

0.8

0.6

0.4

0.2

million years ago

0

0.6

0.4

0.2

million years ago

0

0.8

0.6

0.4

0.2

million years ago

0

10

6

0

2

-5

Bayes factors

0.6

0.8

10

2 0.8

0.6

0.4

0.2

million years ago

0

-10

6

0.0

0.0 0.8

0.4

posterior probability

0.5

5 60

0

-10

-10

2

10

0.2

2.0 1.5 rate

1.0

25 20 15

rate

2

-5

0 -5

Bayes factors

0.6 0.2

40

million years ago

6

6

0.0 60

2

10

10

6

0

10

0.8 60

10

0.4

posterior probability

1.5 1.0 0.5

0.0

0.0

0.1

-5

0.2

rate

rate

2 0

2.0

0.5 0.4

6

0.3

10

5

million years ago

mass extinction Bayes factors

1.0

million years ago

mass extinction times

10

million years ago

relative-extinction rates

5

million years ago

net-diversification rates

Bayes factors

million years ago

extinction Bayes factors

10

million years ago

mass extinction Bayes factors

5

million years ago

mass extinction times 1.0

million years ago

relative-extinction rates

10

million years ago

net-diversification rates

5

million years ago

extinction Bayes factors

-10

Bayes factors

40

0

2.5 rate

2.0

0.6

6

-5

Bayes factors

0.6 0.4

0

0.2 0.0

0.0

60

CSiii

2

Bayes factors

0.8 0.6 0.4

posterior probability

0.2 0

0.8

5

10

1.0 2

0.2

10

0.8 6

0.4

million years ago

0.8

2

extinction rates

-5

Bayes factors

0.8 0.6 0.4

posterior probability

10

10

6

2 20

0.6

6

mass extinction Bayes factors

0

6

40

0.8

-10

20

mass extinction Bayes factors

million years ago

speciation Bayes factors

1

10

million years ago

80 40

million years ago

10

60

10

1.5 1.0 0.5

0

5

speciation shift times

rate

20

million years ago

1.0

speciation rates

40

0

extinction shift times

mass extinction times

40 2

0.4

million years ago

0.4

million years ago

1.0 0.6

6

60

mass extinction times

posterior probability 60

0.8

million years ago

relative-extinction rates

speciation rates 10

0.4

0

posterior probability

0

1

million years ago

million years ago

1.5

20

0.2

1.5

0

0.8 20

1.0

million years ago

40

0

net-diversification rates

2

-5 80

posterior probability 40

0.2

rate 60

0.4

extinction shift times

rate

0

0.8

million years ago

million years ago

0.5

20

0

40

0.4

6

-10

0

0.0

0.5 0.4 0.1 0.0

-10

60

0.6

5 20

million years ago

relative-extinction rates

0.2

0

rate

2

0.3

10 5

6

-5

Bayes factors

net-diversification rates

10

6

extinction Bayes factors

1

0.2 60

0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5

extinction Bayes factors

0.8

0.5

10 5 0

1

10

-5

Bayes factors

0

2

10

0

0.2

0

2

2 1

extinction rates

6

5

20

0.4

million years ago

CS3

0.4

10

million years ago

10

0

40

million years ago

0.6

0

-10

60

40

0.0

rate

0

Bayes factors

0

2

0.8

Bayes factors

20

6

extinction rates

2

million years ago

0.8

6

0

-10

40

60

0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4

6

80 1

10

million years ago

10

40

0

2

0.0

20

6

0.4

80

-5 60

0.4

speciation Bayes factors

0.2

0

10

1.0 0.6 0.4

0

0.8

10

0.0

20

10

2

2 1

10

million years ago

25

40

-10

1.0 0.8 40

speciation Bayes factors

0.8 20

0.6 0.2

60

0.2 40

million years ago

2

million years ago

6

rate 1

6

0.0 80

0.0 60

10

0.4

posterior probability

2.5 0

speciation shift times

posterior probability

2.0 0.5 0.0 20

5

40

speciation rates 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4

1.0

rate

0.2 0.1

rate

1.5

0.3

0.4

10 0 -10

0.0

60

million years ago

1

0

20

60

million years ago

80

rate

20 0 80

mass extinction Bayes factors

0

0.2 4

rate

0.10 0.00 0.4

15

0

rate

20

million years ago

20

6

0

1.0 0.30

4

0.8

10

40

mass extinction times

40

0.4

mass extinction Bayes factors

10

60

million years ago

60

0.8

mass extinction times

speciation shift times

60

0.8 0.6 0.4

posterior probability

0.2 0.0 80

relative-extinction rates

million years ago

1

relative-extinction rates

1.0

1.0

0

million years ago

2

0

net-diversification rates

5

20

net-diversification rates

6

10

million years ago

million years ago

2

million years ago

10

extinction shift times

million years ago

1

0

40

6

Bayes factors

60

10

0

million years ago

million years ago

0

speciation rates

1.2 0.8 rate

0.6 0.0

80

0.4

0.8 0.6 0.4 0.2

extinction shift times

0.4

0 -10

0

1

million years ago

million years ago

100 120

20

0.8

2

0

0 1

0

0

60

40

0.8 0.6 0.4 0.2

0.2 40

rate

60

6

0

2

-5 60

6

extinction rates 10

-5 0.4

2

million years ago

0.2 80

1

2

3

6

0.8

10

million years ago

0.8 0.4

extinction Bayes factors 10

2

0

speciation Bayes factors

2 1

20

0

0.8 0.6 0.4 0.2

6

0

-10 100 80

1.0

10

2

0.2 0.0 20

-5

Bayes factors

6

0

6

million years ago

0.6

posterior probability 0.4

10

0.0 1

0.2 0.8

rate

0 -10

0

extinction Bayes factors

80

rate

10

-5

Bayes factors

0.8 0.6 0.4

posterior probability

0.2 0.0

40

5

CS2

60

posterior probability

0.4 rate

0.2 0.1 0.0 0

10

million years ago

6

extinction rates

5

1.0 1.2 1.0 0.8 0.6 0.4

rate

80

0.8 0.6 0.4 0.2

MCMCTree

10

2

1

0.5 4 3 rate

1 0

0.8 0.6 0.4 0.2

0.0 1

10

million years ago

speciation Bayes factors

6

2

0

mass extinction Bayes factors

1

Bayes factors

3

0

2

2 60

0.8 0.6 0.4 0.2

mass extinction times

6

100 80

million years ago

speciation shift times

1

relative-extinction rates

PL speciation rates

0

net-diversification rates

1.0 20

-5

0

10 4

40

10

1.0 0.2 20

0.8 0.6 0.4 0.2

6

million years ago

speciation shift times

0

2 60

0.8 0.6

10

0.0

million years ago

40

1

10

million years ago

speciation rates

2

rate 6

100 80

0.4

posterior probability

0.3 0.2

rate

0.1 0.0

million years ago

60

0

million years ago

10

0

mass extinction Bayes factors

100 80

extinction shift times

million years ago

1

5

20

mass extinction times

0

0

0

40

0

million years ago

million years ago

1

0.2 60

relative-extinction rates

20

0.8 0.6 0.4 0.2

1.0

10

0.0 100 80

0

2

2

Bayes factors

-5 -10 1

net-diversification rates

40

5

10 5

0

million years ago

60

0

Bayes factors

0

20

million years ago

100 80

2

-10

40

million years ago

0.02

0

60

0.8

0.04 rate

0.01 0

6

extinction shift times

0.00 20

2

60

20

40

6

rate

40

60

10

6

1

10

million years ago

million years ago

0.00

-5 -10

60

0

Bayes factors

100 80

0.01

0

rate

2

100 80

2

0

0.04

6

100 80

posterior probability

0.05

6

0.03

10 5

extinction Bayes factors

20

0

5

million years ago

40

20

extinction rates

10

-10

2 60

40

million years ago

6

100 80

60

0.4

5 0.8 0.6 0.4 0.2

extinction Bayes factors

-5 100 80

-5

0.4

0

10

0.6

0

0.03

1.0 0.6

posterior probability 20

6

Bayes factors

20

speciation Bayes factors

10

0.2 40

10

0.6

40

0.8

million years ago

-5

0.4

10

Bayes factors

0.6

posterior probability 1

0.4

60

million years ago

1

0

0

2

2

0.0 100 80

0

extinction rates

10

1.0 20

0.8 0

0.0 60

0.4 0.2

20

0.8

0.05 0.04 0.03 0.02 0.01

rate

40

speciation shift times

0.00 100 80

Bayes factors

60

million years ago

0.4

mass extinction Bayes factors

0.02

100 80

speciation rates

CSiii

posterior probability

0.10

0

rate

speciation Bayes factors

0.8 40

6

10

20

2

speciation shift times

0.8

million years ago

5 60

million years ago

10

5

40

0.00

0.00 60

million years ago

0 1.0

speciation rates

2 100 80

1.0

0.30 0.20 rate

0.03 rate

0.02 0.01

0 -10 100 80

0.0

0.0

million years ago

6

0

mass extinction times

0.04

10 5

2

-5

Bayes factors

6

2 1

million years ago

2

6

0

million years ago

4

10

million years ago

relative-extinction rates

0.4

5

extinction shift times

20

6

0.8

40

0.8

0.6

60

10

million years ago

0.8 100 80

1

0.4

0

million years ago

net-diversification rates

10

0 0.3

3 2

rate

1 0

-10 20

million years ago

extinction Bayes factors

Bayes factors

0.4

4

10 5 0 -5

0 -5 -10

40

0

posterior probability

20

60

0.4

0.0

40

Bayes factors

10 Bayes factors

0.6

100

0.8

10

20

million years ago

60

mass extinction Bayes factors

0

100 80

mass extinction times

0.2

-10

0

relative-extinction rates

-10

20

net-diversification rates

0.0

40

million years ago

1

2

-5

million years ago

60

0

1.0 rate

2

million years ago

0

1

5

6

0

Bayes factors

0.6 0.4

2 100 80

20

extinction rates

6

0

40

10

10

1.0 20

60

million years ago

0.8 posterior probability

10

0.2 40

100

speciation Bayes factors

0.0 60

0.4

0

0.4

3

20

rate

40

0.8

0

60

million years ago

speciation shift times

0.00 0.01 0.02 0.03 0.04 0.05 100 80

5

posterior probability 100

million years ago

speciation rates

rate

0.2

0

0.6

20

1

0.4

40

2

posterior probability

60

6

0

million years ago

2

6

0.0

rate 100

million years ago

CS3

0.2 0.1 0.0

0.02

0

2

0.2

20

6

0.0

40

10

0.00 0.01 0.02 0.03 0.04 0.05

60

0.01

-10 100

0.00

0

rate

2

10

0.4

million years ago

10

0.8

0.4 0.3

0.03

5

6

-5

Bayes factors

0.04

10

10

1.0

extinction Bayes factors

0.8

0

million years ago

mass extinction Bayes factors

2 1

Bayes factors

million years ago

mass extinction times

6

0

-5

million years ago

relative-extinction rates

0.4

-10

million years ago

net-diversification rates

0.8

0.8

million years ago

10

5

million years ago

extinction Bayes factors

-10

0.0

0

0

1

0.6

20

0

0.4

40

0.4

posterior probability

60

0.8

0.2

100

1

0.2

-5

0.4

3

0

rate

20

1

0.2

40

0

0.1

60

0.6

posterior probability

4 100

rate 2 1

0.2 0.0

0

0.4

0.3

20

0.8

10

40

2 1

5

60

extinction shift times

6

0

0

100

0.8

1.0 0.8

0.03 rate

0.02 0.01 0.00

-10

0

0.4

Bayes factors

20

0.8

-10

40

1

0.20

60

2

2

10

100

6

5

0

6

10

0

20

10

extinction rates 10

1.0

40

0 -5

0.4 0.2

2

0.6

0.04

2

0.4

6

6

0.0 60

Bayes factors

0.6

posterior probability

10

speciation Bayes factors 10

speciation shift times

5

speciation rates

extinction shift times

posterior probability

10 5

1.0

10

0.8

0.04 0.03 rate

0.02 0.00 100

CS2

B

extinction rates

1.0

speciation Bayes factors

5

speciation shift times

0.01

A

MCMCTree

PL speciation rates

0.8

0.6

0.4

0.2

million years ago

0

0