Electronic supplementary material Phylogenies used in Quaternary climate change was not an engine of diversification in New World bats (Chiroptera) by Brian R. Barber and Garrett Jensen. Journal of Mammalian Evolution Corresponding author: BRB, brbarber76@gmail.com For each taxonomic group we show the results of the BEAST 1.6.1 analysis used to infer relationships. Results of jModeltest for each data set are provided. Posterior probabilities are shown for clades that received > 0.50 support. Star indicates the focal clade used in the LASER, sister-taxon analyses and to generate the lineage-thru-time plots. This focal clade is shown in greater detail in the second phylogeny. Outgroup taxa and multiple exemplars of species or phylogroups are removed. Shaded box indicates the Quaternary period. Node labels are dates of nodes in millions of years before the present. X-axis for all phylogenies is in millions of years before the present

Artibeus Redondo et al. (2008)

jModeltTest MODEL = GTR+I+G partition = 012345 -lnL = 21018.1994 K = 377 freqA = 0.3265 freqC = 0.3542 freqG = 0.0581 freqT = 0.2613 R(a) [AC] = 0.8127 R(b) [AG] = 28.9346 R(c) [AT] = 0.9479 R(d) [CG] = 1.7384 R(e) [CT] = 25.8536 R(f) [GT] = 1.0000 p-inv = 0.5250 gamma shape = 0.5540. Phylogeny –ln 17821.15. All collapsed clades have 1.00 posterior probability support.

Laser Results MODEL pureBirth = Parameters: r1 LH -3.12769, AIC 8.25538, r1 0.2404143. MODEL bd = Parameters: r1, a, LH -3.12769, AIC 10.25538, r1 0.2404143, a 0. MODEL DDL = Parameters: r1, k LH 10.14341, AIC -16.28682, r1 1.356561, k 21.44398. MODEL DDX = Parameters: r1, X, LH 2.371964, AIC -0.743928, r1 2.848721, x 0.9683882. MODEL yule2rate = Parameters: r1, r2, ts, LH 8.47358, AIC -10.94716, r1 0.6834744, r2 0.06691211, st 2.859916. MODEL rvbd = Parameters: r1, r2, a, ts, LH 8.698956, AIC -9.397912, r1 0.4405583, r2 0.0293879, a 0.5710853, st 2.859916. Best Constant Rate Model = pureBirth AIC 8.25538, Best Rate Variable Model = DDL AIC -16.28682, delta AICrc = 24.54220. Test Results = dAICrc calculated: 24.54, Summary: Test for rate constancy: dAICrc crit (2-tailed, alpha = 0.05): 3.954427 prob (x|rate constant): = 0.001.

Glossophaga Hoffmann and Baker (2001)

jModeltTest MODEL = GTR+I, partition = 012345, -lnL = 7846.7682, K = 133, freqA = 0.3093, freqC = 0.2948, freqG = 0.1143, freqT = 0.2816, R(a) [AC] = 0.9602, R(b) [AG] = 7.9809, R(c) [AT] = 0.7599, R(d) [CG] = 0.0831, R(e) [CT] = 10.9893, R(f) [GT] = 1.0000, p-inv = 0.5920. Phylogeny –ln 7923.89.

Laser Results MODEL pureBirth = Parameters: r1 LH -8.513312, AIC 19.02662, r1 0.0977638. MODEL bd = Parameters: r1, a, LH -8.513312, AIC 21.02662, r1 0.0977638, a 0. MODEL DDL = Parameters: r1, k, LH 16457.82, AIC -32911.65, r1 63545.27, k 5.000908. MODEL DDX = Parameters: r1, X, LH -7.317941, AIC 18.63588, r1 0.8999797, x 1.604996. MODEL yule2rate = Parameters: r1, r2, ts, LH -7.834725, AIC 21.66945, r1 0.2108803, r2 0.06363168, st 5.459904. MODEL rvbd = Parameters: r1, r2, a, ts, LH -7.558747, AIC 23.11749, r1 2.599296e-07, r2 2.81617e-08, a 0.9999996, st 5.459904. Best Constant Rate Model = pureBirth AIC 19.02662, Best Rate Variable Model = DDL AIC -32911.65, delta AICrc = 32930.68. Test Results = dAICrc calculated: 32930.68, Summary: [1] 0.0318. Test for rate constancy: dAICrc crit (2-tailed, alpha = 0.05): 13.48247, prob (x | rate constant): < 0.0318.

Platyrrhinus Velazco and Patterson (2008)

jModeltTest MODEL = TIM2+I+G, partition = 010232, -lnL = 7146.8789, K = 138, freqA = 0.2972, freqC = 0.3631, freqG = 0.1235, freqT = 0.2163, R(a) [AC] = 4.1492, R(b) [AG] = 30.8078, R(c) [AT] = 4.1492, R(d) [CG] = 1.0000, R(e) [CT] = 89.8502, R(f) [GT] = 1.0000, p-inv = 0.6080, gamma shape = 1.8000. Phylogeny –ln 7220.47

Laser Results MODEL pureBirth = Parameters: r1, LH -9.159142, AIC 20.31828, r1 0.1934746. MODEL bd = Parameters: r1, a, LH -9.159142, AIC 22.31828, r1 0.1934746, a 0. MODEL DDL = Parameters: r1, k, LH -4.083481, AIC 12.16696, r1 0.838297, k 13.67141. MODEL DDX = Parameters: r1, X, LH -7.075461, AIC 18.15092, r1 1.233536, x 0.8933178. MODEL yule2rate = Parameters: r1, r2, ts, LH -4.796196, AIC 15.59239 r1 0.3841126, r2 0.05557161, st 2.685174. MODEL rvbd = Parameters: r1, r2, a, ts, LH -4.626912, AIC 17.25382, r1 0.2177364, r2 0.02147142, a 0.6224061, st 2.685174. Best Constant Rate Model = pureBirth AIC 20.31828, Best Rate Variable Model = DDL AIC 12.16696, delta AICrc = 8.15132. Test Results = dAICrc calculated: 8.15, Summary: [1] 0.0078, Test for rate constancy: dAICrc crit (2-tailed, alpha = 0.05): 3.825682, prob (x | rate constant): < 0.0078.

Vampyressa Porter and Baker (2004)

jModeltTest MODEL = GTR+I+G, partition = 012345, -lnL = 6274.0883, K = 64, freqA = 0.3184, freqC = 0.3066, freqG = 0.1186, freqT = 0.2563, R(a) [AC] = 1.5697, R(b) [AG] = 4.9747, R(c) [AT] = 1.6125, R(d) [CG] = 0.0001, R(e) [CT] = 18.2804, R(f) [GT] = 1.0000, p-inv = 0.5130, gamma shape = 1.5860. Phylogeny –ln 7567.12.

Laser Results MODEL pureBirth = Parameters: r1, LH -17.06924, AIC 36.13849, r1 0.07616519. MODEL bd = Parameters: r1, a LH -17.06924, AIC 38.13849 r1 0.07616519 a 0. MODEL DDL = Parameters: r1, k, LH -7.023146, AIC 18.04629, r1 0.8755313, k 10.13029. MODEL DDX = Parameters: r1, X, LH -12.43117, AIC 28.86234, r1 2.600203, x 1.796554. MODEL yule2rate = Parameters: r1, r2, ts LH -12.37112, AIC 30.74224, r1 0.2081154, r2 0.02366051, t 7.983236. MODEL rvbd = Parameters: r1, r2, a, ts LH -12.37112, AIC 32.74224, r1 0.2081154, r2 0.02366051, a 0 st 7.983236. Best Constant Rate Model = pureBirth AIC 36.13849, Best Rate Variable Model = DDL AIC 18.04629, delta AICrc = 18.09220, dAICrc calculated: 18.09 Summary: Test for rate constancy: dAICrc crit (2-tailed, alpha = 0.05): 4.141511 prob (x | rate constant): < 4e-04.

Mycronycteris Porter et al. (2007)

jModeltTest MODEL = TVMef+G, partition = 012314, -lnL = 10310.9317, K = 135, R(a) [AC] = 24.7901, R(b) [AG] = 91.9845, R(c) [AT] = 12.2907, R(d) [CG] = 0.5198, R(e) [CT] = 91.9845, R(f) [GT] = 1.0000, gamma shape = 0.2600. Phylogeny –ln 9750.55.

Laser Results MODEL pureBirth = Parameters: r1, LH -12.34361, AIC 26.68723, r1 0.1024565. MODEL bd = Parameters: r1, a, LH -12.34361, AIC 28.68723, r1 0.1024565, a 0. MODEL DDL = Parameters: r1, k, LH -11.34267, AIC 26.68533, r1 0.2783927, k 9.572424. MODEL DDX = Parameters: r1, X, LH -12.06261, AIC 28.12522, r1 0.229859, x 0.5068745. MODEL yule2rate = Parameters: r1, r2, ts, LH -11.84811, AIC 29.69621, r1 0.1380292, r2 0.06231023, st 3.664035. MODEL rvbd = Parameters: r1, r2, a, ts, LH -11.10267, AIC 30.20534, r1 3.534908e-07, r2 5.863715e-08, a 0.999999, st 3.664035. Best Constant Rate Model = pureBirth AIC 26.68723. Best Rate Variable Model = DDL AIC 26.68533, delta AICrc = 0.001898279. Test Results = dAICrc calculated: 0.002, Summary: [1] 0.288, Test for rate constancy: dAICrc crit (2-tailed, alpha = 0.05): 4.669866, prob (x | rate constant): < 0.288.

Mormoops + Pteronotus Lewis-Oritt (2001)

jModeltTest MODEL = TrN+I+G, partition = 010020, -lnL = 7585.8674, K = 73, freqA = 0.3542, freqC = 0.3785, freqG = 0.0816, freqT = 0.1857, R(a) [AC] = 1.0000, R(b) [AG] = 18.7411, R(c) [AT] = 1.0000, R(d) [CG] = 1.0000, R(e) [CT] = 24.4521, R(f) [GT] = 1.0000, p-inv = 0.5390, gamma shape = 1.0780. Phylogeny –ln 7627.68.

Laser Results MODEL pureBirth = Parameters: r1, LH -22.60022, AIC 47.20043, r1 0.03254096. MODEL bd = Parameters: r1, a, LH -22.60022, AIC 49.20043, r1 0.03254096, a 0. MODEL DDL = Parameters: r1, k, LH -21.8555, AIC 47.711, r1 0.0736634, k 11.60303. MODEL DDX = Parameters: r1, X, LH -22.46072, AIC 48.92143, r1 0.05309192, x 0.2950185. MODEL yule2rate = Parameters: r1, r2, ts, LH -21.81016, AIC 49.62032, r1 0.04567207, r2 0.01747142, st 12.64142. MODEL rvbd = Parameters: r1, r2, a, ts, LH -20.69978, AIC 49.39956, r1 2.882384e-08, r2 4.495361e-09, a 0.9999998, st 16.48559. Best Constant Rate Model = pureBirth AIC 47.20043, Best Rate Variable Model = DDL AIC 47.711, delta AICrc = -0.5105673. Test Results = dAICrc calculated: 0.511. Summary: [1] 0.2284, Test for rate constancy: dAICrc crit (2-tailed, alpha = 0.05): 4.335584, prob (x | rate constant): < 0.2284.

Natalus Dávalos (2005)

jModeltTest MODEL = TIM2+I+G, partition = 010232, -lnL = 7146.8789, K = 138, freqA = 0.2972, freqC = 0.3631, freqG = 0.1235, freqT = 0.2163, R(a) [AC] = 4.1492, R(b) [AG] = 30.8078, R(c) [AT] = 4.1492, R(d) [CG] = 1.0000, R(e) [CT] = 89.8502, R(f) [GT] = 1.0000, p-inv = 0.6080, gamma shape = 1.8000. Phylogeny –ln 6309.77.

Laser Results MODEL pureBirth = Parameters: r1, LH -11.88806, AIC 25.77612, r1 0.09051827. MODELbd = Parameters: r1, a, LH -11.88131, AIC 27.76262, r1 0.07816502, a 0.2021423. MODELDDL = Parameters: r1, k, LH -11.67046, AIC 27.34092, r1 0.1623593, k 11.20421. MODELDDX = Parameters: r1, X, LH -11.75021, AIC 27.50041, r1 0.1838403, x 0.4824824. MODELyule2rate = Parameters: r1, r2, ts, LH -11.77876, AIC 29.55751, r1 0.1216036, r2 0.08025991, st 9.283501. MODELrvbd = Parameters: r1, r2, a, ts, LH -11.27435, AIC 30.5487, r1 1.481674e-07, r2 3.567179e-08, a 0.9999997, st 9.283501. Best Constant Rate Model = pureBirth AIC 25.77612, Best Rate Variable Model = DDL AIC 27.34092, delta AICrc = -1.564802. Test Results = dAICrc calculated: 1.56, Summary: [1] 0.1576, Test for rate constancy: dAICrc crit (2-tailed, alpha = 0.05): 5.417032, prob (x | rate constant): < 0.1576.

Myotis Stadelmann et al. (2007)

jModeltest MODEL = TPM1uf+I+G partition = 012210, -lnL = 9894.0989, K = 127, freqA = 0.3325, freqC = 0.2887, freqG = 0.0971, freqT = 0.2818, R(a) [AC] = 1.0000, R(b) [AG] = 27.5315, R(c) [AT] = 0.6519, R(d) [CG] = 0.6519, R(e) [CT] = 27.5315, R(f) [GT] = 1.0000, p-inv = 0.5560, gamma shape = ß1.6220. Phylogeny –ln 9965.68.

Laser Results MODEL pureBirth = Parameters: r1, LH -9.337601, AIC 20.67520, r1 0.1448416. MODEL bd = Parameters: r1, a, LH -9.337601, AIC 22.67520, r1 0.1448416, a 0. MODEL DDL = Parameters: r1, k, LH -7.845699, AIC 19.69140, r1 0.2456054, k 48.16684. MODEL DDX = Parameters: r1, X, LH -8.161695, AIC 20.32339, r1 0.4015907, x 0.3732035. MODEL yule2rate = Parameters: r1, r2, ts, LH -6.925914, AIC 19.85183, r1 0.2182974,r2 0.09880621, st 5.310303. MODEL rvbd = Parameters: r1, r2, a, ts, LH -6.58561, AIC 21.17122,r1 0.1452243, r2 0.04364962, a 0.6207978, st 5.310303. Best Constant Rate Model = pureBirth AIC 0.67520, Best Rate Variable Model = DDL AIC 19.69140, delta AICrc = 0.9838046. Test Results = dAICrc calculated: 0.98, Summary: [1] 0.2126, Test for rate constancy: dAICrc crit (2-tailed, alpha = 0.05): 4.125653, prob (x | rate constant): < 0.2126.

Rhogeesa Baird et al. (2008)

jModeltTest MODEL = TPM2uf+G, partition = 010212, -lnL = 8432.6525, K = 194, freqA = 0.3509, freqC = 0.2955, freqG = 0.0884, freqT = 0.2652, R(a) [AC] = 1.3648, R(b) [AG] = 42.4171, R(c) [AT] = 1.3648, R(d) [CG] = 1.0000, R(e) [CT] = 42.4171, R(f) [GT] = 1.0000, gamma shape = 0.1630. Phylogeny –ln 7359.33.

Laser Results MODEL pureBirth = Parameters: r1, LH -7.892736, AIC 17.78547, r1 0.1935001. MODEL bd = Parameters: r1, a LH -7.892736 AIC 19.78547 r1 0.1935001, a 0. MODEL DDL = Parameters: r1, k, LH 1.450371, AIC 1.099258, r1 3.221393, k 8.082752. MODEL DDX = Parameters: r1, X, LH -5.302652, AIC 14.60530, r1 2.710613, x 1.498169. MODEL yule2rate = Parameters: r1, r2, ts, LH -4.717532 AIC 15.43506, r1 0.5347571, r2 0.07455552, st 3.037918. MODEL rvbd = Parameters: r1, r2, a, ts LH -4.54412, AIC 17.08824, r1 0.03749765, r2 0.002480865, a 0.9671426, st 3.037918. Best Constant Rate Model = pureBirth AIC 17.78547, Best Rate Variable Model = DDL AIC 1.099258, delta AICrc = 16.68622. Test Results = dAICrc calculated: 16.69, Summary: [1] 0.003. Test for rate constancy: dAICrc crit (2-tailed, alpha = 0.05): 4.856896, prob (x | rate constant): < 0.003.

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