node support efficacy in congreve & lamsdell matrices0.2 trees1–10 0 0 0 385 385 385 770 770...

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Node support efficacy in Congreve & Lamsdell matrices

Martin R. Smith martin.smith@durham.ac.uk

2020-01-20

Contents0.1 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20.2 Trees 1–10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30.3 Trees 11–20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80.4 Trees 21–30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130.5 Trees 31–40 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180.6 Trees 41–50 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230.7 Trees 51–60 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280.8 Trees 61–70 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330.9 Trees 71–80 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380.10 Trees 81–90 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 430.11 Trees 91–100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

This page depicts the analytical results of all 100 matrices generated by Congreve & Lamsdell [1] using aternary plotting approach [2], with quartets and partitions used as distance metrics.

The most highly resolved tree is progressively reduced by collapsing nodes with a support value below anincreasing threshold.

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0.1 Summary

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MarkovBremerBootFreqBoot GCJack FreqJack GC

Though the Bootstrap GC metric systematically produces the lowest normalized tree distances (SD/MaxI), itis not significantly better than other methods. The following table reports P values that fail to reject the nullhypothesis that the specified node support metric is equally good at ascribing incorrect nodes the lowestsupport values.

eq k1 k2 k3 k5 kX kCBootstrap GC 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000Bootstrap Freq 0.9840650 0.9915189 0.9934145 0.9760370 0.9485781 0.9615921 0.9720185Jackknife GC 0.9888177 0.9995312 0.9331647 0.9599348 0.9637166 0.9268107 0.9743023Jackknife Freq 0.9942934 0.9554285 0.9509308 0.9839102 0.8639063 0.9408796 0.9723566Bremer 0.4347916 0.3324499 0.5075762 0.4474386 0.3405988 0.2397081 0.8365157

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0.2 Trees 1–10

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Dataset 1: CI=0.28. Equal weights 0

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PartitionsIncreasing R

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Dataset 7: CI=0.27. Equal weights 0

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2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

sQuartets

Decreasing resolution Increasing divergence

Dataset 9: CI=0.24. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

55

5

66

6

77

78

8

89

9

910

10

1011

11

1112

12

1213

13

1314

14

14 15

15

1516

16

1617

17

1718

18

1819

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0385

385

385

770

770

770

1155

11551155

1540

1540

1540

19251925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 10: CI=0.29. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

7

Page 8

0.3 Trees 11–20

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 11: CI=0.25. Equal weights 0

0

0

1

1

1

22

2

33

3

44

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

PartitionsIncreasing R

F distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

11551155

1155

1540

1540

1540

1925

1925

19252310

2310

23102695

2695

26953080

3080

30803465

3465

34653850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 12: CI=0.29. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

nsPartitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

8

Page 9

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

sQuartets

Decreasing resolution Increasing divergence

Dataset 13: CI=0.25. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

55

5

66

6

77

78

8

89

9

910

10

1011

11

1112

12

1213

13

1314

14

14 15

15

1516

16

1617

17

1718

18

1819

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0385

385

385

770

770

770

1155

11551155

1540

1540

1540

19251925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 14: CI=0.25. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

9

Page 10

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

sQuartets

Decreasing resolution Increasing divergence

Dataset 15: CI=0.25. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

55

5

66

6

77

78

8

89

9

910

10

1011

11

1112

12

1213

13

1314

14

14 15

15

1516

16

1617

17

1718

18

1819

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0385

385

385

770

770

770

1155

11551155

1540

1540

1540

19251925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 16: CI=0.25. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

10

Page 11

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

sQuartets

Decreasing resolution Increasing divergence

Dataset 17: CI=0.27. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

55

5

66

6

77

78

8

89

9

910

10

1011

11

1112

12

1213

13

1314

14

14 15

15

1516

16

1617

17

1718

18

1819

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0385

385

385

770

770

770

1155

11551155

1540

1540

1540

19251925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 18: CI=0.28. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

11

Page 12

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

sQuartets

Decreasing resolution Increasing divergence

Dataset 19: CI=0.3. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

55

5

66

6

77

78

8

89

9

910

10

1011

11

1112

12

1213

13

1314

14

14 15

15

1516

16

1617

17

1718

18

1819

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0385

385

385

770

770

770

1155

11551155

1540

1540

1540

19251925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 20: CI=0.25. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

12

Page 13

0.4 Trees 21–30

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 21: CI=0.26. Equal weights 0

0

0

1

1

1

22

2

33

3

44

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

PartitionsIncreasing R

F distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

11551155

1155

1540

1540

1540

1925

1925

19252310

2310

23102695

2695

26953080

3080

30803465

3465

34653850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 22: CI=0.26. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

nsPartitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

13

Page 14

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

sQuartets

Decreasing resolution Increasing divergence

Dataset 23: CI=0.25. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

55

5

66

6

77

78

8

89

9

910

10

1011

11

1112

12

1213

13

1314

14

14 15

15

1516

16

1617

17

1718

18

1819

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0385

385

385

770

770

770

1155

11551155

1540

1540

1540

19251925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 24: CI=0.23. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

14

Page 15

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

sQuartets

Decreasing resolution Increasing divergence

Dataset 25: CI=0.28. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

55

5

66

6

77

78

8

89

9

910

10

1011

11

1112

12

1213

13

1314

14

14 15

15

1516

16

1617

17

1718

18

1819

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0385

385

385

770

770

770

1155

11551155

1540

1540

1540

19251925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 26: CI=0.27. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

15

Page 16

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

sQuartets

Decreasing resolution Increasing divergence

Dataset 27: CI=0.26. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

55

5

66

6

77

78

8

89

9

910

10

1011

11

1112

12

1213

13

1314

14

14 15

15

1516

16

1617

17

1718

18

1819

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0385

385

385

770

770

770

1155

11551155

1540

1540

1540

19251925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 28: CI=0.27. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

16

Page 17

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

sQuartets

Decreasing resolution Increasing divergence

Dataset 29: CI=0.29. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

55

5

66

6

77

78

8

89

9

910

10

1011

11

1112

12

1213

13

1314

14

14 15

15

1516

16

1617

17

1718

18

1819

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0385

385

385

770

770

770

1155

11551155

1540

1540

1540

19251925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 30: CI=0.25. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

17

Page 18

0.5 Trees 31–40

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 31: CI=0.26. Equal weights 0

0

0

1

1

1

22

2

33

3

44

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

PartitionsIncreasing R

F distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

11551155

1155

1540

1540

1540

1925

1925

19252310

2310

23102695

2695

26953080

3080

30803465

3465

34653850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 32: CI=0.25. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

nsPartitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

18

Page 19

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

sQuartets

Decreasing resolution Increasing divergence

Dataset 33: CI=0.27. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

55

5

66

6

77

78

8

89

9

910

10

1011

11

1112

12

1213

13

1314

14

14 15

15

1516

16

1617

17

1718

18

1819

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0385

385

385

770

770

770

1155

11551155

1540

1540

1540

19251925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 34: CI=0.29. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

19

Page 20

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

sQuartets

Decreasing resolution Increasing divergence

Dataset 35: CI=0.25. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

55

5

66

6

77

78

8

89

9

910

10

1011

11

1112

12

1213

13

1314

14

14 15

15

1516

16

1617

17

1718

18

1819

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0385

385

385

770

770

770

1155

11551155

1540

1540

1540

19251925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 36: CI=0.24. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

20

Page 21

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

sQuartets

Decreasing resolution Increasing divergence

Dataset 37: CI=0.26. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

55

5

66

6

77

78

8

89

9

910

10

1011

11

1112

12

1213

13

1314

14

14 15

15

1516

16

1617

17

1718

18

1819

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0385

385

385

770

770

770

1155

11551155

1540

1540

1540

19251925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Dataset 38: CI=0.29. Equal weights 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

0

0

0

385

385

385

770

770

770

1155

11551155

1540

1540

1540

1925

1925

1925

2310

2310

2310

2695

2695

2695

3080

3080

3080

3465

3465

3465

3850

3850

3850 unresolved quartets

different quarte

ts

iden

tical

qua

rtet

s

Quartets

Decreasing resolution Increasing divergence

Implied weights (k = 3) 0

0

0

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

66

7

77

8

8

8

9

9

9

10

10

10

11

11

11

12

12

12

13

13

13

14

14

14 15

15

15

16

16

16

17

17

17

18

18

18

19

19

19 unresolved partitions

different partiti

onsiden

tical

par

titio

ns

Partitions

Increasing RF

distance

MarkovBremerBootFreqBoot GCJack FreqJack GC

21