Graphical representation of the temporal patterns of trait ...

1

Ronco et al. | Drivers and dynamics of a massive adaptive radiation in cichlid fishes

Graphical representation of the temporal patterns of trait evolution in Lake Tanganyika cichlids based on alternative time-calibrated species trees (Fig. D1-D3), based on samples from the posterior tree distribution for each alternative species tree (Fig. D4-D6), and based on PC1-scores of the morphological traits (Fig. D7). Inferred rates of trait evolution per tribe are shown in Fig. D8.

2


Fig. D1 | Temporal dynamics of diversification in body shape (first row), upper oral jaw morphology (second row), lower pharyngeal jaw shape (third row), and pigmentation patterns (fourth row). a, Time-calibrated species tree (maximum likelihood tree topology inferred from genome-wide SNPs, as shown in Fig. 1 of the manuscript), with branches coloured according to the mean relative rates of trait evolution for each trait. b, Morphospace densities (number of lineages) through time for each trait. c, Comparison of slopes (blue) of morphospace expansion over time between the observed data and the BM null model of trait evolution. The shaded areas show 95% quantiles of the 500 BM simulations. Lineage accumulation through time derived from the species tree is shown in dark grey. d, Mean relative rates of trait evolution over time with standard deviation (blue). Lineage accumulation through time is shown in dark grey.

10 8 7 6 5 4 3 2 1 0

-0.05

0.00

0.05

0.10

1 17 0

20

40

60

80

100

10 8 7 6 5 4 3 2 1 0

-20

-10

0

10

20

30

Diff

eren

ce in

slo

pe

0

20

40

60

80

100

10 8 7 6 5 4 3 2 1 0

0

2

4

6

8

Rel

ativ

e ra

te o

f evo

lutio

n

10 8 7 6 5 4 3 2 1 0-0.08

-0.06

-0.04

-0.02

0.00

1 15 0

20

40

60

80

100

10 8 7 6 5 4 3 2 1 0

-20

-10

0

10

Diff

eren

ce in

slo

pe

0

20

40

60

80

100

10 8 7 6 5 4 3 2 1 0

0

1

2

3

4

5

Rel

ativ

e ra

te o

f evo

lutio

n

10 8 7 6 5 4 3 2 1 0-0.15

-0.10

-0.05

0.00

0.05

0.10

0.15

1 14 0

20

40

60

80

100

10 8 7 6 5 4 3 2 1 0

-10

0

10

20

Diff

eren

ce in

slo

pe

0

20

40

60

80

100

10 8 7 6 5 4 3 2 1 0

0

1

2

3

4

Rel

ativ

e ra

te o

f evo

lutio

n

Time (Ma)

0

20

40

60

80

100

10 8 7 6 5 4 3 2 1 0

-10

0

10

20

30

40

Time (Ma)

Diff

eren

ce in

slo

pe

0

20

40

60

80

100

10 8 7 6 5 4 3 2 1 0Time (Ma)

Rel

ativ

e ra

te o

f evo

lutio

n

10 8 7 6 5 4 3 2 1 09

9

9

9 9 9

9 9

9 9

99

Bod

y sh

ape

Upp

er o

ral j

aw m

orph

olog

yLo

wer

pha

ryng

eal j

aw s

hape

Pigm

enta

tion

patte

rns

PLS-

scor

esPL

S-sc

ores

PLS-

scor

esPC

A-sc

ores

Percentage of lineagesPercentage of lineages


PP: >90 >75 >50

0.9 15.6

1 35.9

0.6 27.5

0.3 25.6

Relative rates

Relative rates

Relative rates

Relative rates

a b c d

-5

0

5

10

0

1

2

3

4

5

6

1 17

50

3


0.9 16.7

10 9 8 7 6 5 4 3 2 1 0-0.05

0.00

0.05

0.10

1 16

Diff

eren

ce in

slo

pe

Rel

ativ

e ra

te o

f evo

lutio

n

1.1 33.1

10 9 8 7 6 5 4 3 2 1 0-0.08

-0.06

-0.04

-0.02

0.00

1 16

Diff

eren

ce in

slo

pe

Rel

ativ

e ra

te o

f evo

lutio

n

0.5 29.5

10 9 8 7 6 5 4 3 2 1 0-0.15

-0.10

-0.05

0.00

0.05

0.10

0.15

1 15

Diff

eren

ce in

slo

pe

Rel

ativ

e ra

te o

f evo

lutio

n

Pigm

enta

tion

patte

rn

0.2 17.8

10 9 8 7 6 5 4 3 2 1 0

-5

0

5

10

Time (Ma)

1 16

Time (Ma)

Diff

eren

ce in

slo

pe

Time (Ma)

Rel

ativ

e ra

te o

f evo

lutio

n



Bod

y sh

ape

Ora

l jaw

mor

phol

ogy

Low

er p

hary

ngea

l jaw

sha

pe

PC1-

scor

esPL

S-sc

ores

PLS-

scor

esPL

S-sc

ores

Relative rates

Relative rates

Relative rates

Relative rates

0

20

40

60

80

100

-30

-20

-10

0

10

20

30

0

20

40

60

80

100

0

2

4

6

8

10

0

20

40

60

80

100

-20

-10

0

10

0

20

40

60

80

100

0

1

2

3

4

5

6

0

20

40

60

80

100

-10

0

10

20

0

20

40

60

80

100

0

1

2

3

4

0

20

40

60

80

100

-10

0

10

20

30

40

0

20

40

60

80

100

0

1

2

3

4

10 9 8 7 6 5 4 3 2 1 0 10 9 8 7 6 5 4 3 2 1 0

10 9 8 7 6 5 4 3 2 1 0 10 9 8 7 6 5 4 3 2 1 0

10 9 8 7 6 5 4 3 2 1 0 10 9 8 7 6 5 4 3 2 1 0

10 9 8 7 6 5 4 3 2 1 0 10 9 8 7 6 5 4 3 2 1 0

a c db

Fig. D2 | Temporal dynamics of diversification in body shape (first row), upper oral jaw morphology (second row), lower pharyngeal jaw shape (third row), and pigmentation patterns (fourth row) based on an alternative time-calibrated species tree. a, Species tree based on the tree topology inferred with ASTRAL from selected genomic regions under the multi-species coalescent model, time-calibrated using the relaxed molecular-clock model. Branches are coloured according to the mean relative rates of trait evolution for each trait. b, Morphospace densities (number of lineages) through time for each trait. c, Comparison of slopes (blue) of morphospace expansion over time between the observed data and the BM null model of trait evolution. The shaded areas show 95% quantiles of the 500 BM simulations. Lineage accumulation through time derived from the species tree is shown in dark grey. d, Mean relative rates of trait evolution over time with standard deviation (blue). Lineage accumulation through time is shown in dark grey.

4


0.9 17.4

Diff

eren

ce in

slo

pe

Rel

ativ

e ra

te o

f evo

lutio

n

1.1 30.8

Diff

eren

ce in

slo

pe

Rel

ativ

e ra

te o

f evo

lutio

n

0.7 27

Diff

eren

ce in

slo

pe

Rel

ativ

e ra

te o

f evo

lutio

n

Pigm

enta

tion

patte

rn

0.3 24.2

Time (Ma) Time (Ma)

Diff

eren

ce in

slo

pe

Time (Ma)

Rel

ativ

e ra

te o

f evo

lutio

n



Bod

y sh

ape

Ora

l jaw

mor

phol

ogy

Low

er p

hary

ngea

l jaw

sha

pe

PC1-

scor

esPL

S-sc

ores

PLS-

scor

esPL

S-sc

ores

Relative rates

Relative rates

Relative rates

Relative rates

−0.05

0.00

0.05

0.10

1 18 0

20

40

60

80

100

−30

−20

−10

0

10

20

30

40

0

20

40

60

80

100

0

2

4

6

8

10

−0.08

−0.06

−0.04

−0.02

0.00

1 15 0

20

40

60

80

100

−30

−20

−10

0

10

0

20

40

60

80

100

0

1

2

3

4

5

6

−0.15

−0.10

−0.05

0.00

0.05

0.10

0.15

1 15 0

20

40

60

80

100

−10

0

10

20

0

20

40

60

80

100

0

1

2

3

4

10 8 7 6 5 4 3 2 1 0

−5

0

5

10

1 17 0

20

40

60

80

100

−10

0

10

20

30

40

0

20

40

60

80

100

0

1

2

3

4

5

9 10 8 7 6 5 4 3 2 1 09 10 8 7 6 5 4 3 2 1 09

10 8 7 6 5 4 3 2 1 09 10 8 7 6 5 4 3 2 1 09 10 8 7 6 5 4 3 2 1 09

10 8 7 6 5 4 3 2 1 09 10 8 7 6 5 4 3 2 1 09 10 8 7 6 5 4 3 2 1 09

10 8 7 6 5 4 3 2 1 09 10 8 7 6 5 4 3 2 1 09 10 8 7 6 5 4 3 2 1 09

a c db

Fig. D3 | Temporal dynamics of diversification in body shape (first row), upper oral jaw morphology (second row), lower pharyngeal jaw shape (third row), and pigmentation patterns (fourth row) based on an alternative time-calibrated species tree. a, Species tree based on the tree topology inferred with SNAPP from genome wide SNP data under the multi-species coalescent model, time-calibrated using the relaxed molecular-clock model. Branches are coloured according to the mean relative rates of trait evolution for each trait. b, Morphospace densities (number of lineages) through time for each trait. c, Comparison of slopes (blue) of morphospace expansion over time between the observed data and the BM null model of trait evolution. The shaded areas show 95% quantiles of the 500 BM simulations. Lineage accumulation through time derived from the species tree is shown in dark grey. d, Mean relative rates of trait evolution over time with standard deviation (blue). Lineage accumulation through time is shown in dark grey.

5


−10

10

30

0

2

4

6

−10

10

20

0

2

4

−10

10

20

0

2

3

0

2

4

6

−10

10

30

Time (Ma)

Diff

eren

ce in

slo

pe

0

40

20

Pigm

enta

tion

patte

rns

10 8 6 4 2 0

1

3

5

Time (Ma)10 8 6 4 2 0

10 8 6 4 2 0 10 8 6 4 2 0

10 8 6 4 2 0 10 8 6 4 2 0

10 8 6 4 2 0 10 8 6 4 2 0

Rel

ativ

e ra

te o

f evo

lutio

n

1

Rel

ativ

e ra

te o

f evo

lutio

n

0

Diff

eren

ce in

slo

peD

iffer

ence

in s

lope

Diff

eren

ce in

slo

pe

Bod

y sh

ape

Ora

l jaw

mor

phol

ogy

Phar

ynge

al ja

w s

hape

3

1

Rel

ativ

e ra

te o

f evo

lutio

n

0

3

1

5

20

0

40

Rel

ativ

e ra

te o

f evo

lutio

n

a b

Fig. D4 | Temporal dynamics of diversification in body shape (first row), upper oral jaw morphology (second row), lower pharyngeal jaw shape (third row), and pigmentation patterns (fourth row) based on the posterior distribution of the time-calibration. Results from 100 trees sampled from the posterior distribution of the time-calibration for the maximum likelihood tree topology inferred from genome-wide SNPs. Each line represents the mean of the results based on a one posterior tree, plotted on a relative timescale of 10-0 Ma for better visualization (true root ages of the 100 trees range from 8.79-10.41 Myr) a, Comparison of slopes of morphospace expansion over time between the observed data and the BM null model of trait evolution. b, Mean relative rates of trait evolution over time.

6


−10

10

30

0

2

4

6

−10

10

20

0

2

4

−10

10

20

0

2

3

0

2

4

−10

10

30

Time (Ma)

Diff

eren

ce in

slo

pe

0

40

20

Pigm

enta

tion

patte

rns

10 8 6 4 2 0

1

3

5

Time (Ma)10 8 6 4 2 0

10 8 6 4 2 0 10 8 6 4 2 0

10 8 6 4 2 0 10 8 6 4 2 0

10 8 6 4 2 0 10 8 6 4 2 0

Rel

ativ

e ra

te o

f evo

lutio

n

1

Rel

ativ

e ra

te o

f evo

lutio

n

0

Diff

eren

ce in

slo

peD

iffer

ence

in s

lope

Diff

eren

ce in

slo

pe

Bod

y sh

ape

Ora

l jaw

mor

phol

ogy

Phar

ynge

al ja

w s

hape

3

1

Rel

ativ

e ra

te o

f evo

lutio

n

0

3

1

5

20

0

40

Rel

ativ

e ra

te o

f evo

lutio

n

a b

Fig. D5 | Temporal dynamics of diversification in body shape (first row), upper oral jaw morphology (second row), lower pharyngeal jaw shape (third row), and pigmentation patterns (fourth row) based on the posterior distribution of the time-calibration. Results from 100 trees sampled from the posterior distribution of the time-calibration for the tree topology based on selected genomic regions inferred under the multi-species coalescent model with ASTRAL. Each line represents the mean of the results based on a one posterior tree, plotted on a relative timescale of 10-0 Ma for better visualization (true root ages of the 100 trees range from 9.41-10.86 Myr) a, Comparison of slopes of morphospace expansion over time between the observed data and the BM null model of trait evolution. b, Mean relative rates of trait evolution over time.

7


−10

10

30

0

2

4

6

−10

10

20

0

2

4

−10

10

20

0

2

3

0

2

4

−10

10

30

Time (Ma)

Diff

eren

ce in

slo

pe

0

40

20

Pigm

enta

tion

patte

rns

10 8 6 4 2 0

1

3

5

Time (Ma)10 8 6 4 2 0

10 8 6 4 2 0 10 8 6 4 2 0

10 8 6 4 2 0 10 8 6 4 2 0

10 8 6 4 2 0 10 8 6 4 2 0

Rel

ativ

e ra

te o

f evo

lutio

n

1

Rel

ativ

e ra

te o

f evo

lutio

n

0

Diff

eren

ce in

slo

peD

iffer

ence

in s

lope

Diff

eren

ce in

slo

pe

Bod

y sh

ape

Ora

l jaw

mor

phol

ogy

Phar

ynge

al ja

w s

hape

3

1

Rel

ativ

e ra

te o

f evo

lutio

n

0

3

1

5

20

0

40

Rel

ativ

e ra

te o

f evo

lutio

n

a b

Fig. D6 | Temporal dynamics of diversification in body shape (first row), upper oral jaw morphology (second row), lower pharyngeal jaw shape (third row), and pigmentation patterns (fourth row) based on the posterior distribution of the time-calibration. Results from 100 trees sampled from the posterior distribution of the time-calibration for the tree topology based on genome-wide SNPs inferred under the multi-species coalescent model with SNAPP. Each line represents the mean of the results based on a one posterior tree, plotted on a relative timescale of 10-0 Ma for better visualization (true root ages of the 100 trees range from 9.05-10.46 Myr) a, Comparison of slopes of morphospace expansion over time between the observed data and the BM null model of trait evolution. b, Mean relative rates of trait evolution over time.

8


Fig. D7 | Temporal dynamics of diversification in body shape (first row), upper oral jaw morphology (second row), and lower pharyngeal jaw shape (third row) using PC1-scores. a, Time-calibrated species tree (maximum likelihood tree topology inferred from genome-wide SNPs, as shown in Fig. 1 of the manuscript), with branches coloured according to the mean relative rates of trait evolution for each trait. b, Morphospace densities (number of lineages) through time for each trait. c, Comparison of slopes (blue) of morphospace expansion over time between the observed data and the BM null model of trait evolution. The shaded areas show 95% quantiles of the 500 BM simulations. Lineage accumulation through time derived from the species tree is shown in dark grey. d, Mean relative rates of trait evolution over time with standard deviation (blue). Lineage accumulation through time is shown in dark grey.

Bod

y sh

ape

1.1 16.7

Diff

eren

ce in

slo

pe

Rel

ativ

e ra

te o

f evo

lutio

n

Ora

l jaw

mor

phol

ogy

1 40.5

Diff

eren

ce in

slo

pe

Rel

ativ

e ra

te o

f evo

lutio

n

Low

er p

hary

ngea

l jaw

sha

pe

1 25.6

Time (Ma)

Diff

eren

ce in

slo

pe

Rel

ativ

e ra

te o

f evo

lutio

n

Time (Ma) Time (Ma)


Percentage of lineages

Relative rates

Relative rates

Relative rates

PC1-

scor

esPC

1-sc

ores

PC1-

scor

es

-0.10

-0.05

0.00

0.05

1 12 0

20

40

60

80

100

-20

-10

0

10

20

30

0

20

40

60

80

100

0

2

4

6

8

-0.04

-0.02

0.00

0.02

0.04

1 17 0

20

40

60

80

100

-20

-10

0

10

20

0

20

40

60

80

100

0

1

2

3

4

5

6

10 8 7 6 5 4 3 2 1 0-0.20

-0.15

-0.10

-0.05

0.00

0.05

0.10

0.15

1 18 0

20

40

60

80

100

-20

-10

0

10

0

20

40

60

80

100

0

1

2

3

4

5

6

9 10 8 7 6 5 4 3 2 1 09 10 8 7 6 5 4 3 2 1 09

10 8 7 6 5 4 3 2 1 09 10 8 7 6 5 4 3 2 1 09 10 8 7 6 5 4 3 2 1 09

10 8 7 6 5 4 3 2 1 09 10 8 7 6 5 4 3 2 1 09 10 8 7 6 5 4 3 2 1 09

a c db

9


Fig. D8 | Cumulative rate-transformed branch length per tribe and trait. Boxplot per tribe of the cumulative rate-transformed branch length derived from the variable rates model using the time-calibrated species tree (maximum likelihood tree topology). Thus, species values represent time-weighted estimates over the inferred evolutionary rates.

Body shape Upper oral jaw morphology

Lower pharyngeal jaw shape Pigmentation pattern

Boul

enge

roch

rom

ini

Bent

hoch

rom

ini

Cyp

hotil

apiin

iEr

etm

odin

iBa

thyb

atin

iPe

risso

dini

Trem

atoc

arin

iLi

mno

chro

min

iC

ypric

hrom

ini

Trop

hein

iEc

todi

niLa

mpr

olog

ini

10

20

30

40

20

40

60

80

10

20

30

40

50

60

70

80

10

20

30

40

50

60

Cum

ulat

ive

bran

ch le

ngth

(rate

tran

sfor

med

)C

umul

ativ

e br

anch

leng

th(ra

te tr

ansf

orm

ed)

Boul

enge

roch

rom

ini

Bent

hoch

rom

ini

Cyp

hotil

apiin

iEr

etm

odin

iBa

thyb

atin

iPe

risso

dini

Trem

atoc

arin

iLi

mno

chro

min

iC

ypric

hrom

ini

Trop

hein

iEc

todi

niLa

mpr

olog

ini

Graphical representation of the temporal patterns of trait ...

Documents

Transcript of Graphical representation of the temporal patterns of trait ...