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Table 2 Summary of Bayesian analyses

From: The rise of army ants and their relatives: diversification of specialized predatory doryline ants

Bayesian analytical treatment

Run

Taxa

Position 3

Gens

Burn-in

PBI gens

TracerHM (boots) (best run)

Error

ln Bayes Factor

All taxa, Pos3 = ACTG

1

83

ACTG

100M

50M

50M

−101022.705

0.473

1.601

 

2

83

ACTG

100M

50M

50M

−101024.305

0.231

−1.601

All taxa, Pos3 = allRY

1

83

allRY

100M

10M

90M

−55074.421

0.192

8.591

 

2

83

allRY

100M

10M

90M

−55083.012

0.198

−8.591

All taxa, Pos3 = someRY

1

83

someRY

100M

50M

50M

−83626.678

0.203

−0.646

 

2

83

someRY

100M

50M

50M

−83626.032

0.429

0.646

All taxa, Pos3s excluded

1

83

excluded

50M

5M

45M

−40654.165

0.157

0.031

 

2

83

excluded

50M

5M

45M

−40654.196

0.148

−0.031

4 wildcards excluded, Pos3 = ACTG

1

79

ACTG

100M

20M

80M

−95642.257

0.871

8.897

 

2

79

ACTG

100M

80M

20M

−95651.154

1.21

−8.897

4 wildcards excluded, Pos3 = allRY

1

79

RY

100M

60M

40M

−52539.793

0.294

5.542

 

2

79

RY

100M

60M

40M

−52545.335

0.323

−5.542

4 wildcards excluded, Pos3 = someRY

1

79

someRY

100M

50M

50M

−78967.945

0.387

0.748

 

2

79

someRY

100M

50M

50M

−78968.693

0.337

−0.748

4 wildcards excluded, Pos3s excluded

1

79

excluded

50M

5M

45M

−38944.878

0.173

−0.214

 

2

79

excluded

50M

5M

45M

−38944.664

0.181

0.214

Ingroup only, Pos3 = ACTG

1

73

ACTG

50M

20M

30M

−82585.121

0.32

4.042

 

2

73

ACTG

50M

20M

30M

−82589.162

0.41

−4.042

Ingroup only, Pos3 = allRY

1

73

RY

50M

20M

30M

−45906.942

0.289

−7.406

 

2

73

RY

50M

20M

30M

−45899.536

0.218

7.406

Ingroup only, 4 wildcards excluded, Pos3 = ACTG

1

69

ACTG

100M

80M

20M

−77128.707

0.526

−5.712

 

2

69

ACTG

100M

80M

20M

−77122.994

0.51

5.712

Ingroup only, 4 wildcards excluded, Pos3 = allRY

1

69

RY

100M

25M

75M

−43366.928

0.28

−6.19

 

2

69

RY

100M

25M

75M

−43360.738

0.366

6.19

68 taxa (army ants excluded)

1

68

ACTG

50M

30M

20M

−83784.123

0.301

8.811

 

2

68

ACTG

50M

30M

20M

−83792.934

0.283

−8.811

  1. For each treatment (column 1), the two runs of highest harmonic-mean marginal likelihood are reported and compared using Bayes Factors as calculated using 1000 bootstrap pseudoreplicates in Tracer v.1.5, which employs a weighted likelihood bootstrap estimator. Treatments include (i) modifying third positions of protein-coding genes; (ii) excluding four “wildcard” taxa (Cerapachys splendens, Sphinctomyrmex stali, Tanipone zona, and Vicinopone conciliatrix); (iii) excluding outgroups; (iv) excluding army ants; and (v) selected combinations of the foregoing. Third-position sites of protein-coding genes were modified in order to explore the effects of base frequency heterogeneity across taxa, and consisted of (i) no modifications, i.e., retaining the base identities at third positions (“ACTG”); (ii) coding all third positions as either R (purines, A or G) or Y (pyrimidines, C or T) (“allRY”); (iii) coding as RY the third positions of only a subset of taxa, differing for each gene and depending on the degree of departure of base frequencies from the average, and preserving the base identities of the remainder (“some RY”); and (iv) excluding all third positions (“excluded”).