Probabilities of neighbor-joining gene topologies, inferred from the eight terminal tip data set, given two alternative species trees with differing internal:terminal branch length ratios (1:1, 1:2, and 1:10)

LocusaNJ treebSpecies topologyb1:11:21:10
AETC(Pcy1, (((Pam1, Pcy2), Pam2), ((Ccy, Pro), (Pca1, Pca2))))((((Pcy, Pam), Pca), Pro), Ccy)2.365E-094.78789E-071.8218E-05
((((Pam, Pca), Pcy), Pro), Ccy)1.62E-104.6316E-081.82953E-06
βact3(Pcy1, (((Pam1, Pcy2), Ccy), ((Pro, (Pca1, Pca2)), Pam2)))((((Pcy, Pam), Pca), Pro), Ccy)5.05E-102.77914E-072.1178E-05
((((Pam, Pca), Pcy), Pro), Ccy)3.99E-101.07017E-072.62828E-06
GADPH(Pcy1, (((Pam1, Pam2), (Pro, (Pca1, Pca2))), (Ccy, Pcy2)))((((Pcy, Pam), Pca), Pro), Ccy)3.143E-091.8008E-060.00018838
((((Pam, Pca), Pcy), Pro), Ccy)2.7306E-082.72713E-063.75984E-05
MC1R(Pcy1, ((((Pam1, Pam2), (Pca1, Pca2)), (Ccy, Pro)), Pcy2))((((Pcy, Pam), Pca), Pro), Ccy)2.124E-091.30936E-060.000149501
((((Pam, Pca), Pcy), Pro), Ccy)1.02979E-075.10169E-063.50167E-05
MPLPR(Pcy1, ((((Pam1, Pam2), Pcy2), Ccy), ((Pro, Pca1), Pca2)))((((Pcy, Pam), Pca), Pro), Ccy)5.136E-099.52899E-072.77842E-05
((((Pam, Pca), Pcy), Pro), Ccy)3.98E-105.10169E-061.74861E-05
Myo2(Pcy1, ((((Pam1, Pam2), Pcy2), Ccy), (Pro, (Pca1, Pca2))))((((Pcy, Pam), Pca), Pro), Ccy)1.53135E-066.8394E-050.000690821
((((Pam, Pca), Pcy), Pro), Ccy)1.28294E-062.86844E-059.5464E-05
ODC(Pcy1, ((((Pam1, Pcy2), (Ccy, Pro)), (Pca1, Pca2)), Pam2))((((Pcy, Pam), Pca), Pro), Ccy)<1.0E-121.393E-092.7787E-06
((((Pam, Pca), Pcy), Pro), Ccy)<1.0E-125.27E-103.8284E-07
Rho1(Pcy1, ((((Pam1, Pam2), (Pca1, Pca2)), (Ccy, Pro)), Pcy1))((((Pcy, Pam), Pca), Pro), Ccy)2.124E-091.30936E-060.000149501
((((Pam, Pca), Pcy), Pro), Ccy)1.02979E-075.10169E-063.50167E-05
TGFβ2(Pcy1, ((Pam1, (Ccy, (Pcy2, Pam2))), (Pro, (Pca1, Pca2))))((((Pcy, Pam), Pca), Pro), Ccy)1.4E-113.7386E-081.2647E-05
((((Pam, Pca), Pcy), Pro), Ccy)1.1E-116.71486E-071.4255E-08
  • Underlining indicates probabilities that are greater with a P. amoena/P. cyanea species topology than with a P. amoena/P. caerulea species topology. Italic numbers indicate the opposite pattern. All probabilities calculated using COAL (Degnan and Salter 2005).

  • a NJ gene tree search based on Tropo6 sequence data produced an unresolved topology and was dropped from COAL analyses.

  • b Species names abbreviations: Pam, P. amoena; Pcy, P. cyanea; Pca, P. caerulea; Pro, P. rositae; Ccy, C. cyanoides. Numbers following species abbreviations in NJ topologies refer to the different individuals sampled. All species were constrained to be monophyletic in the species topologies.