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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”).