Bayou Results

ECV ~ Body Mass

OU Un-weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	238.1995802	122.4300308	0.1730555	1.2243573	9999.06838	220.7339537	257.0483448
prior	-79.4250054	9.4717222	0.0133883	0.4989513	360.36414	-97.5722573	-62.7195212
alpha	4.4671710	7.3078805	0.0103297	0.8032901	82.76335	0.0600634	18.1867214
sigma^2	0.0225446	0.0407490	0.0000576	0.0044556	83.64089	0.0005501	0.0840875
shift number	12.5040909	2.0410771	0.0028851	0.0924041	487.90626	9.0000000	16.0000000
N theta	13.5040909	2.0410771	0.0028851	0.0924041	487.90626	10.0000000	17.0000000
root theta	-0.8949691	0.2577805	0.0003644	0.0170615	228.27908	-1.2466628	-0.5250178
root beta	0.6871632	0.1181884	0.0001671	0.0066677	314.19731	0.5758711	0.8439854
all theta	-0.9918978	0.5895005	NA	NA	NA	NA	NA
all beta	0.7673352	0.2330846	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	238.1166512	15.9358457	0.0225254	0.8746991	331.91957	224.3365057	253.4166558
prior	-79.6167181	8.7921682	0.0124278	0.4375569	403.75960	-97.4821998	-64.9896912
alpha	3.5321504	4.4306651	0.0062628	0.7400471	35.84422	0.3916937	10.9270386
sigma^2	0.0191945	0.0298866	0.0000422	0.0046974	40.48041	0.0022675	0.0530316
shift number	12.6600546	2.1089068	0.0029810	0.1036098	414.29824	10.0000000	17.0000000
N theta	13.6600546	2.1089068	0.0029810	0.1036098	414.29824	11.0000000	18.0000000
root theta	-0.7689019	0.2105803	0.0002977	0.0131899	254.89019	-0.9939623	-0.4361902
root beta	0.6729566	0.0976750	0.0001381	0.0044102	490.50384	0.5837124	0.7352264
all theta	-1.0875801	0.6176098	NA	NA	NA	NA	NA
all beta	0.7952158	0.2251197	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	239.4526688	6.4815984	0.0077431	0.2247830	831.45240	225.6856029	251.7243879
prior	-78.4965090	7.6618899	0.0091531	0.2985010	658.84054	-95.1556779	-66.0802773
alpha	3.1987946	4.6981872	0.0056126	0.4964562	89.55685	0.0651811	10.9043902
sigma^2	0.0156321	0.0223119	0.0000267	0.0026725	69.70143	0.0006273	0.0512932
shift number	12.4179982	1.7824208	0.0021293	0.0665229	717.92321	10.0000000	16.0000000
N theta	13.4179982	1.7824208	0.0021293	0.0665229	717.92321	11.0000000	17.0000000
root theta	-0.7758925	0.2306230	0.0002755	0.0123306	349.81145	-0.9966859	-0.4650088
root beta	0.6621634	0.0898212	0.0001073	0.0038586	541.86806	0.5804227	0.7233932
all theta	-1.0311697	0.5883117	NA	NA	NA	NA	NA
all beta	0.7759491	0.2254518	NA	NA	NA	NA	NA

Shifts

A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.

OU parameters

	chain1	chain2	combined chains
alpha	4.4671710	3.5321504	3.1987946
sigma squared	0.0225446	0.0191945	0.0156321
stationary variance	0.0025234	0.0027171	0.0024434
phylogenetic halflife	0.1551647	0.1962394	0.2166901
phylogenetic half life in units of tree height	0.0021255	0.0026881	0.0029682

OU Weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	237.9218364	19.7416313	0.0279049	0.6617010	890.107694	221.8920862	256.0552664
prior	-80.3339274	8.9460986	0.0126454	0.4374058	418.309945	-98.3921206	-64.9055705
alpha	5.0679840	5.1304656	0.0072519	0.7196491	50.824373	0.1436803	15.4605445
sigma^2	0.0255562	0.0251606	0.0000356	0.0079802	9.940587	0.0010899	0.0777228
shift number	12.7274411	2.0543322	0.0029038	0.0914053	505.124724	9.0000000	16.0000000
N theta	13.7274411	2.0543322	0.0029038	0.0914053	505.124724	10.0000000	17.0000000
root theta	-0.8862630	0.2704600	0.0003823	0.0232761	135.016424	-1.2755803	-0.5218193
root beta	0.6788669	0.1086343	0.0001536	0.0079276	187.780011	0.5763822	0.8559412
all theta	-1.0569796	0.5850637	NA	NA	NA	NA	NA
all beta	0.7812911	0.2295259	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	223.2348819	20.1483948	0.0284799	1.2015290	281.19810	192.7599191	252.6241780
prior	-107.7001588	17.4343657	0.0246436	0.6687513	679.64634	-143.4763521	-74.9549714
alpha	0.0541054	0.0487127	0.0000689	0.0070444	47.81810	0.0109892	0.1592881
sigma^2	0.0006807	0.0012414	0.0000018	0.0000449	763.39316	0.0003380	0.0010336
shift number	18.6463564	3.8560876	0.0054506	0.1349536	816.44099	11.0000000	26.0000000
N theta	19.6463564	3.8560876	0.0054506	0.1349536	816.44099	12.0000000	27.0000000
root theta	-0.8922021	0.1337559	0.0001891	0.0112901	140.35559	-1.1360875	-0.6469820
root beta	0.6920913	0.0547437	0.0000774	0.0056320	94.47927	0.6027534	0.7966366
all theta	-1.1677733	0.8743207	NA	NA	NA	NA	NA
all beta	0.8300406	0.4082974	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	228.4745348	14.6627923	0.0175166	1.0690629	188.11647	196.7826223	252.0807142
prior	-95.2882451	21.0600772	0.0251590	1.0741921	384.37578	-134.2203000	-62.2455525
alpha	1.5826884	2.9676490	0.0035452	0.4610920	41.42380	0.0089454	8.4162423
sigma^2	0.0081899	0.0144365	0.0000172	0.0057199	6.37012	0.0002748	0.0441031
shift number	15.9444473	4.5471523	0.0054322	0.2061424	486.56884	8.0000000	24.0000000
N theta	16.9444473	4.5471523	0.0054322	0.2061424	486.56884	9.0000000	25.0000000
root theta	-0.8391474	0.1453729	0.0001737	0.0108936	178.08515	-1.0759083	-0.5340917
root beta	0.6618703	0.0521507	0.0000623	0.0041416	158.55613	0.5731643	0.7628291
all theta	-1.1224389	0.7885545	NA	NA	NA	NA	NA
all beta	0.8170445	0.3651531	NA	NA	NA	NA	NA

Shifts

A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.

OU parameters

	chain1	chain2	combined chains
alpha	5.0679840	0.0541054	1.5826884
sigma squared	0.0255562	0.0006807	0.0081899
stationary variance	0.0025213	0.0062907	0.0025873
phylogenetic halflife	0.1367698	12.8110419	0.4379556
phylogenetic half life in units of tree height	0.0018735	0.1754862	0.0059991

BM

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	162.8501112	6.8640609	0.0097024	0.1626607	1780.7250	160.4734105	164.5401197
prior	0.2700209	0.1429087	0.0002020	0.0042257	1143.7290	-0.0015802	0.5213542
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0009615	0.0108924	0.0000154	0.0001380	6226.1991	0.0006387	0.0010156
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	-0.5479505	0.1441275	0.0002037	0.0047487	921.1743	-0.8325343	-0.2674380
root beta	0.5903931	0.0344444	0.0000487	0.0007467	2127.6723	0.5248260	0.6564211
all theta	-0.5479505	0.1441275	NA	NA	NA	NA	NA
all beta	0.5903931	0.0344444	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	162.8178485	7.1347227	0.0100850	0.1754235	1654.1646	160.4389891	164.5406391
prior	0.2719569	0.1444983	0.0002042	0.0043446	1106.2020	0.0017662	0.5256841
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0009771	0.0117742	0.0000166	0.0001598	5427.6002	0.0006428	0.0010208
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	-0.5512008	0.1472396	0.0002081	0.0050064	864.9767	-0.8293682	-0.2657456
root beta	0.5904883	0.0349657	0.0000494	0.0007775	2022.5881	0.5236656	0.6566052
all theta	-0.5512008	0.1472396	NA	NA	NA	NA	NA
all beta	0.5904883	0.0349657	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	162.9886803	1.2564426	0.0015010	0.0129584	9401.136	160.5252452	164.5397193
prior	0.2705965	0.1359536	0.0001624	0.0038109	1272.723	-0.0012333	0.5194633
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.000	0.0000010	0.0000010
sigma^2	0.0008240	0.0000970	0.0000001	0.0000005	33103.019	0.0006410	0.0010168
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.000	1.0000000	1.0000000
root theta	-0.5480353	0.1429355	0.0001708	0.0039851	1286.453	-0.8246761	-0.2654532
root beta	0.5899000	0.0333908	0.0000399	0.0005885	3219.464	0.5248356	0.6557577
all theta	-0.5480353	0.1429355	NA	NA	NA	NA	NA
all beta	0.5899000	0.0333908	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	1.000000e-06	1.000000e-06	1.000000e-06
sigma squared	9.615000e-04	9.771000e-04	8.240000e-04
stationary variance	4.807501e+02	4.885398e+02	4.119915e+02
phylogenetic halflife	6.931472e+05	6.931472e+05	6.931472e+05
phylogenetic half life in units of tree height	9.494761e+03	9.494761e+03	9.494761e+03

Model Selection

Bayes Factors

	OU un-weighted predictor	OU weighted predictor	BM
OU un-weighted predictor	0.00000	14.65512	37.51062
OU weighted predictor	-14.65512	0.00000	22.85550
BM	-37.51062	-22.85550	0.00000

ECV ~ Body Mass (alternate hominin phylogeny)

OU Un-weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	241.0540198	20.0391281	0.0283254	0.6023059	1106.93834	227.3495954	256.1030043
prior	-82.1802895	8.1332266	0.0114964	0.3561428	521.52784	-97.6786430	-69.0064584
alpha	10.2791710	11.6108181	0.0164120	1.4006483	68.71752	0.3844910	30.9124409
sigma^2	0.0504784	0.0559363	0.0000791	0.0109034	26.31837	0.0024549	0.1512941
shift number	12.7584520	1.9637988	0.0027758	0.0848774	535.31579	10.0000000	16.0000000
N theta	13.7584520	1.9637988	0.0027758	0.0848774	535.31579	11.0000000	17.0000000
root theta	-0.8688541	0.2190940	0.0003097	0.0140792	242.15982	-1.2569312	-0.5352781
root beta	0.6947123	0.0990825	0.0001401	0.0051270	373.48405	0.5764297	0.8562659
all theta	-0.9728190	0.5859950	NA	NA	NA	NA	NA
all beta	0.7697762	0.2195265	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	666.4546797	932.9969059	1.3187963	509.361964	3.355115	194.7579414	3186.2540644
prior	-102.3526238	38.0175721	0.0537381	3.632901	109.511957	-192.2762596	-67.8976336
alpha	64.0992601	93.8180351	0.1326123	60.019601	2.443354	3.4180938	243.4524576
sigma^2	0.0561179	0.0525918	0.0000743	0.024788	4.501452	0.0000000	0.1594299
shift number	16.3551182	7.7078573	0.0108951	0.651271	140.069597	9.0000000	34.0000000
N theta	17.3551182	7.7078573	0.0108951	0.651271	140.069597	10.0000000	35.0000000
root theta	-0.9353539	0.3505115	0.0004954	0.023291	226.478610	-1.6639440	-0.3997513
root beta	0.7202371	0.1426225	0.0002016	0.006797	440.287942	0.5534514	1.0253371
all theta	-1.1417433	0.8053504	NA	NA	NA	NA	NA
all beta	0.8048163	0.3516405	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	545.7824104	811.1537182	0.9690270	384.6283192	4.44758	214.3624018	2823.6849728
prior	-96.5382603	33.6101817	0.0401517	2.7978053	144.31343	-183.1634318	-66.3568036
alpha	49.5266984	82.9385960	0.0990808	40.9536624	4.10136	1.2302728	242.7536655
sigma^2	0.0581702	0.0577500	0.0000690	0.0133303	18.76836	0.0000000	0.1640829
shift number	15.2770870	6.8007837	0.0081244	0.4965903	187.55191	8.0000000	32.0000000
N theta	16.2770870	6.8007837	0.0081244	0.4965903	187.55191	9.0000000	33.0000000
root theta	-0.8795743	0.3046272	0.0003639	0.0165234	339.89058	-1.6642355	-0.4587519
root beta	0.6956257	0.1332446	0.0001592	0.0052147	652.89661	0.5450482	0.9923559
all theta	-1.0893371	0.7624987	NA	NA	NA	NA	NA
all beta	0.7957006	0.3246703	NA	NA	NA	NA	NA

Shifts

A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.

OU parameters

	chain1	chain2	combined chains
alpha	10.2791710	64.0992601	49.5266984
sigma squared	0.0504784	0.0561179	0.0581702
stationary variance	0.0024554	0.0004377	0.0005873
phylogenetic halflife	0.0674322	0.0108137	0.0139954
phylogenetic half life in units of tree height	0.0009221	0.0001479	0.0001914

OU Weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	205.9727727	3109.8776608	4.3958294	24.2784040	16407.64844	200.1220614	255.3505572
prior	-93.7790313	16.0963880	0.0227523	0.7439134	468.17920	-124.7413254	-65.6647883
alpha	0.1793578	0.3604229	0.0005095	0.0092843	1507.05208	0.0120895	0.6594773
sigma^2	0.0011933	0.0016560	0.0000023	0.0000879	355.17360	0.0003434	0.0033960
shift number	15.8801701	3.5821213	0.0050633	0.1412347	643.27646	9.0000000	22.0000000
N theta	16.8801701	3.5821213	0.0050633	0.1412347	643.27646	10.0000000	23.0000000
root theta	-0.9365646	0.1171756	0.0001656	0.0085537	187.65772	-1.1516056	-0.7076672
root beta	0.7117140	0.0495784	0.0000701	0.0052052	90.72048	0.6167695	0.8004940
all theta	-1.1249988	0.8252109	NA	NA	NA	NA	NA
all beta	0.8155196	0.3259149	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	237.9578950	216.6191804	0.3061924	2.2183967	9534.883311	223.4885566	257.9912425
prior	-82.3162170	9.9562004	0.0140731	0.4995316	397.247712	-101.0524954	-63.8737574
alpha	3.7915154	4.1301477	0.0058380	0.5583518	54.716133	0.1117776	12.4305982
sigma^2	0.0187940	0.0201610	0.0000285	0.0076801	6.891108	0.0006779	0.0625128
shift number	13.0956042	2.2711927	0.0032103	0.1045702	471.728476	9.0000000	17.0000000
N theta	14.0956042	2.2711927	0.0032103	0.1045702	471.728476	10.0000000	18.0000000
root theta	-0.9874591	0.2634702	0.0003724	0.0169862	240.586182	-1.3015174	-0.5409743
root beta	0.7294942	0.0918124	0.0001298	0.0060437	230.775367	0.5766925	0.8602008
all theta	-1.0165693	0.6576055	NA	NA	NA	NA	NA
all beta	0.7712305	0.2541231	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	238.1775393	9.5775587	0.0114416	0.4823353	394.28623	219.6433164	257.2940222
prior	-85.1495045	12.9606547	0.0154832	0.5806385	498.24416	-111.9806970	-62.1644231
alpha	1.0746598	1.8739581	0.0022387	0.2582479	52.65578	0.0187830	5.8819767
sigma^2	0.0053300	0.0087385	0.0000104	0.0024885	12.33084	0.0003362	0.0285592
shift number	14.0672495	3.0108756	0.0035969	0.1262370	568.86927	9.0000000	20.0000000
N theta	15.0672495	3.0108756	0.0035969	0.1262370	568.86927	10.0000000	21.0000000
root theta	-0.9511648	0.2148681	0.0002567	0.0116788	338.48919	-1.2453660	-0.5577720
root beta	0.7183411	0.0708559	0.0000846	0.0043567	264.50556	0.5958968	0.8487927
all theta	-1.0263472	0.6909202	NA	NA	NA	NA	NA
all beta	0.7907559	0.2768146	NA	NA	NA	NA	NA

Shifts

A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.

OU parameters

	chain1	chain2	combined chains
alpha	0.1793578	3.7915154	1.0746598
sigma squared	0.0011933	0.0187940	0.0053300
stationary variance	0.0033265	0.0024784	0.0024798
phylogenetic halflife	3.8646054	0.1828153	0.6449922
phylogenetic half life in units of tree height	0.0528462	0.0024999	0.0088199

BM

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	163.1894353	12.0707883	0.0170621	0.5242884	530.0670	161.1020518	165.1376862
prior	0.2803633	0.1566279	0.0002214	0.0050543	960.3272	0.0165250	0.5243048
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0013045	0.0240732	0.0000340	0.0004710	2612.4653	0.0006245	0.0009925
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	-0.5586863	0.1427652	0.0002018	0.0047490	903.7194	-0.8350485	-0.2824194
root beta	0.5938608	0.0336408	0.0000476	0.0007124	2229.9361	0.5289287	0.6570275
all theta	-0.5586863	0.1427652	NA	NA	NA	NA	NA
all beta	0.5938608	0.0336408	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	163.2535340	11.1414943	0.0157486	0.4335143	660.5109	161.1728961	165.1364740
prior	0.2831262	0.1539420	0.0002176	0.0046095	1115.3272	0.0191449	0.5178852
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0012573	0.0240250	0.0000340	0.0004579	2753.1532	0.0006219	0.0009859
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	-0.5610413	0.1417960	0.0002004	0.0046804	917.8314	-0.8330775	-0.2849565
root beta	0.5942846	0.0330173	0.0000467	0.0006966	2246.6902	0.5304492	0.6581839
all theta	-0.5610413	0.1417960	NA	NA	NA	NA	NA
all beta	0.5942846	0.0330173	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	163.5992852	1.2498141	0.0014931	0.0144825	7447.335	161.1426428	165.1362301
prior	0.2854568	0.1303117	0.0001557	0.0036554	1270.833	0.0173953	0.5205409
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.000	0.0000010	0.0000010
sigma^2	0.0007979	0.0000938	0.0000001	0.0000009	10645.040	0.0006221	0.0009855
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.000	1.0000000	1.0000000
root theta	-0.5610922	0.1401196	0.0001674	0.0038897	1297.652	-0.8331344	-0.2837343
root beta	0.5943018	0.0326535	0.0000390	0.0005712	3268.229	0.5300882	0.6579688
all theta	-0.5610922	0.1401196	NA	NA	NA	NA	NA
all beta	0.5943018	0.0326535	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	1.000000e-06	1.000000e-06	1.000000e-06
sigma squared	1.304500e-03	1.257300e-03	7.979000e-04
stationary variance	6.522382e+02	6.286470e+02	3.989616e+02
phylogenetic halflife	6.931472e+05	6.931472e+05	6.931472e+05
phylogenetic half life in units of tree height	9.478386e+03	9.478386e+03	9.478386e+03

Model Selection

Bayes Factors

	OU un-weighted predictor	OU weighted predictor	BM
OU un-weighted predictor	0.00000	-65.92240	-42.24757
OU weighted predictor	65.92240	0.00000	23.67484
BM	42.24757	-23.67484	0.00000

ECV

OU Un-weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	174.6214372	21.7986946	0.0308126	1.9473736	125.303279	139.1266144	211.3312720
prior	-147.8590327	14.9149016	0.0210823	0.5350832	776.959223	-176.3518343	-117.9163615
alpha	3.6219062	6.6094932	0.0093426	1.3015221	25.788922	0.0389104	18.8488394
sigma^2	0.0353459	0.0631765	0.0000893	0.0256385	6.071904	0.0009980	0.1702755
shift number	28.4165966	3.5212424	0.0049773	0.1223056	828.894222	22.0000000	35.0000000
N theta	29.4165966	3.5212424	0.0049773	0.1223056	828.894222	23.0000000	36.0000000
root theta	1.3480445	0.5757473	0.0008138	0.0405189	201.905978	0.4447422	1.9137552
root beta	-0.0311308	0.2131406	0.0003013	0.0129118	272.495534	-0.5124734	0.4104057
all theta	1.4944570	0.8417976	NA	NA	NA	NA	NA
all beta	-0.0102943	0.3882724	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	181.4026098	27.7985558	0.0392934	3.4180908	66.141993	129.0944327	221.7753231
prior	-150.1209745	15.3975558	0.0217645	0.6050480	647.625366	-181.0985482	-118.7383513
alpha	4.0728791	5.4190179	0.0076598	0.8457653	41.052670	0.0297459	16.1351651
sigma^2	0.0365275	0.0463503	0.0000655	0.0218552	4.497754	0.0012069	0.1355008
shift number	28.8274669	3.6433570	0.0051499	0.1407473	670.074766	20.0000000	35.0000000
N theta	29.8274669	3.6433570	0.0051499	0.1407473	670.074766	21.0000000	36.0000000
root theta	1.4650016	0.6003564	0.0008486	0.0394836	231.198679	0.3937086	2.5150004
root beta	0.0050696	0.2380053	0.0003364	0.0149054	254.966903	-0.5038056	0.4760795
all theta	1.4828809	0.8080249	NA	NA	NA	NA	NA
all beta	0.0274549	0.4055927	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	171.7258943	22.1196797	0.0264248	2.3800482	86.374621	131.5196106	212.2920745
prior	-147.5622771	16.2029266	0.0193565	0.4724873	1175.997978	-179.1930662	-115.6217879
alpha	0.7101747	1.1182121	0.0013358	0.1828494	37.399117	0.0335257	3.1631011
sigma^2	0.0070453	0.0090573	0.0000108	0.0034185	7.019986	0.0009930	0.0279767
shift number	28.2572627	3.7563094	0.0044874	0.1055087	1267.495319	21.0000000	35.0000000
N theta	29.2572627	3.7563094	0.0044874	0.1055087	1267.495319	22.0000000	36.0000000
root theta	1.3838629	0.5783772	0.0006909	0.0354791	265.753051	0.4353998	1.9268027
root beta	-0.0019358	0.1962923	0.0002345	0.0096032	417.805872	-0.4458041	0.3438042
all theta	1.4923729	0.8636315	NA	NA	NA	NA	NA
all beta	0.0121347	0.4083712	NA	NA	NA	NA	NA

Shifts

A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.

OU parameters

	chain1	chain2	combined chains
alpha	3.6219062	4.0728791	0.7101747
sigma squared	0.0353459	0.0365275	0.0070453
stationary variance	0.0048795	0.0044842	0.0049602
phylogenetic halflife	0.1913763	0.1701860	0.9760235
phylogenetic half life in units of tree height	0.0026215	0.0023312	0.0133696

BM

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	77.3453046	5.0946299	0.0072013	0.0977274	2717.64263	75.4206236	78.4466005
prior	0.1350335	0.6554343	0.0009265	0.0799092	67.27672	-1.2538328	0.7055855
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.00000	0.0000010	0.0000010
sigma^2	0.0027076	0.0127084	0.0000180	0.0001405	8184.67285	0.0019890	0.0031682
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.00000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.00000	1.0000000	1.0000000
root theta	1.2268522	0.1783562	0.0002521	0.0073183	593.96650	0.8796723	1.5778747
root beta	-0.1690987	0.4411284	0.0006235	0.0857306	26.47637	-1.0153639	0.6921253
all theta	1.2268522	0.1783562	NA	NA	NA	NA	NA
all beta	-0.1690987	0.4411284	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	77.2992166	4.6730409	0.0066054	0.1053644	1967.03292	75.2779899	78.4465954
prior	-0.0150455	0.7236895	0.0010229	0.0919432	61.95338	-1.5896430	0.7046351
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.00000	0.0000010	0.0000010
sigma^2	0.0026485	0.0083585	0.0000118	0.0000870	9237.90501	0.0020093	0.0031712
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.00000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.00000	1.0000000	1.0000000
root theta	1.2185557	0.1894400	0.0002678	0.0082231	530.73390	0.8534836	1.5921821
root beta	0.0142040	0.5432906	0.0007679	0.1292278	17.67472	-1.0551329	1.0040725
all theta	1.2185557	0.1894400	NA	NA	NA	NA	NA
all beta	0.0142040	0.5432906	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	77.4049901	1.0332654	0.0012344	0.0148397	4848.11431	75.3612431	78.4466005
prior	0.0474492	0.6836918	0.0008168	0.0753117	82.41295	-1.4653720	0.7055366
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.00000	0.0000010	0.0000010
sigma^2	0.0025608	0.0003037	0.0000004	0.0000013	57498.47407	0.0019968	0.0031664
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.00000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.00000	1.0000000	1.0000000
root theta	1.2293587	0.1841855	0.0002200	0.0065921	780.65078	0.8748883	1.5921417
root beta	-0.0617955	0.5133787	0.0006133	0.0966758	28.19940	-1.0810888	0.9005571
all theta	1.2293587	0.1841855	NA	NA	NA	NA	NA
all beta	-0.0617955	0.5133787	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	1.000000e-06	1.000000e-06	1.000000e-06
sigma squared	2.707600e-03	2.648500e-03	2.560800e-03
stationary variance	1.353775e+03	1.324266e+03	1.280384e+03
phylogenetic halflife	6.931472e+05	6.931472e+05	6.931472e+05
phylogenetic half life in units of tree height	9.494761e+03	9.494761e+03	9.494761e+03

Model Selection

Bayes Factors

	OU un-weighted predictor	BM
OU un-weighted predictor	0.00000	10.33027
BM	-10.33027	0.00000

ECV (alternate hominin phylogeny)

OU Un-weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	176.9476542	21.3921933	0.0302380	1.7686473	146.29455	142.0030639	218.2957649
prior	-152.6639443	16.3640578	0.0231307	0.6161128	705.44247	-184.2026613	-119.7086741
alpha	1.1211028	3.3728059	0.0047675	0.6561153	26.42545	0.0389917	8.6316867
sigma^2	0.0137244	0.0452582	0.0000640	0.0079137	32.70622	0.0008221	0.0981914
shift number	29.4152879	3.9301172	0.0055552	0.1375691	816.14807	22.0000000	37.0000000
N theta	30.4152879	3.9301172	0.0055552	0.1375691	816.14807	23.0000000	38.0000000
root theta	1.2581681	0.5319136	0.0007519	0.0336661	249.62932	0.5023069	1.9053142
root beta	-0.0267969	0.1915037	0.0002707	0.0106305	324.52133	-0.4016019	0.3530201
all theta	1.5048462	0.8945219	NA	NA	NA	NA	NA
all beta	0.0029253	0.3997772	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	172.4067062	25.8575056	0.0365497	2.8417075	82.79698	122.7756336	215.0405743
prior	-151.7218012	16.1925867	0.0228883	0.5479957	873.12840	-185.5566625	-121.5529627
alpha	0.5826597	1.7719813	0.0025047	0.3713733	22.76653	0.0240476	3.7040336
sigma^2	0.0061988	0.0160970	0.0000228	0.0035815	20.20068	0.0008460	0.0394493
shift number	28.9683098	3.8842489	0.0054904	0.1307877	882.02319	21.0000000	36.0000000
N theta	29.9683098	3.8842489	0.0054904	0.1307877	882.02319	22.0000000	37.0000000
root theta	1.3741725	0.5605885	0.0007924	0.0371864	227.25788	0.4623881	1.9165479
root beta	0.0014975	0.1977468	0.0002795	0.0103962	361.80022	-0.3735185	0.3913545
all theta	1.4749374	0.9179613	NA	NA	NA	NA	NA
all beta	-0.0059581	0.4061569	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	170.0996299	20.3578485	0.0243201	1.9309192	111.1567	123.5051358	206.8698422
prior	-152.4099065	16.7462273	0.0200055	0.4719433	1259.0829	-185.8307039	-119.0731173
alpha	0.0920603	0.0271479	0.0000324	0.0026513	104.8449	0.0391477	0.1455830
sigma^2	0.0016867	0.0003742	0.0000004	0.0000246	231.7616	0.0010345	0.0024136
shift number	29.0411871	3.9977269	0.0047758	0.1117011	1280.8895	22.0000000	37.0000000
N theta	30.0411871	3.9977269	0.0047758	0.1117011	1280.8895	23.0000000	38.0000000
root theta	1.2980816	0.5285026	0.0006314	0.0313604	284.0089	0.5057147	1.9101070
root beta	-0.0061110	0.1884236	0.0002251	0.0086320	476.4789	-0.3761089	0.3411697
all theta	1.4905268	0.9460229	NA	NA	NA	NA	NA
all beta	0.0042702	0.4064725	NA	NA	NA	NA	NA

Shifts

A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.

OU parameters

	chain1	chain2	combined chains
alpha	1.1211028	0.5826597	0.0920603
sigma squared	0.0137244	0.0061988	0.0016867
stationary variance	0.0061209	0.0053194	0.0091606
phylogenetic halflife	0.6182726	1.1896261	7.5292716
phylogenetic half life in units of tree height	0.0084545	0.0162674	0.1029584

BM

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	74.9738061	7.0976421	0.0100326	0.2167094	1072.68574	73.1575497	76.1321140
prior	0.0456658	0.7074042	0.0009999	0.0905378	61.04861	-1.5649174	0.7042503
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.00000	0.0000010	0.0000010
sigma^2	0.0028452	0.0156300	0.0000221	0.0002838	3033.50841	0.0020177	0.0031884
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.00000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.00000	1.0000000	1.0000000
root theta	1.2287395	0.1766699	0.0002497	0.0071445	611.47415	0.8791971	1.5736220
root beta	-0.0537153	0.5149835	0.0007279	0.1173667	19.25293	-1.0102430	1.0547852
all theta	1.2287395	0.1766699	NA	NA	NA	NA	NA
all beta	-0.0537153	0.5149835	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	74.9768890	6.2645802	0.0088550	0.1565561	1601.19357	73.1190336	76.1321137
prior	0.2572294	0.5091031	0.0007196	0.0522164	95.06006	-0.6035923	0.7054618
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.00000	0.0000010	0.0000010
sigma^2	0.0027943	0.0157252	0.0000222	0.0001990	6244.80830	0.0020047	0.0031792
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.00000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.00000	1.0000000	1.0000000
root theta	1.2240672	0.1831020	0.0002588	0.0076392	574.50031	0.8654063	1.5774800
root beta	-0.0304771	0.3998772	0.0005652	0.0716526	31.14504	-0.8069548	0.7253226
all theta	1.2240672	0.1831020	NA	NA	NA	NA	NA
all beta	-0.0304771	0.3998772	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	75.1102665	1.0059315	0.0012017	0.0139145	5226.40511	73.0838470	76.1321140
prior	0.1393694	0.6454463	0.0007711	0.0750993	73.86674	-1.3272661	0.7056844
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.00000	0.0000010	0.0000010
sigma^2	0.0025748	0.0003028	0.0000004	0.0000021	21084.01496	0.0020125	0.0031804
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.00000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.00000	1.0000000	1.0000000
root theta	1.2290797	0.1833525	0.0002190	0.0064793	800.79983	0.8665186	1.5871384
root beta	-0.0806832	0.4635894	0.0005538	0.0800483	33.53993	-1.1368225	0.7192357
all theta	1.2290797	0.1833525	NA	NA	NA	NA	NA
all beta	-0.0806832	0.4635894	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	1.000000e-06	1.000000e-06	1.000000e-06
sigma squared	2.845200e-03	2.794300e-03	2.574800e-03
stationary variance	1.422615e+03	1.397139e+03	1.287402e+03
phylogenetic halflife	6.931472e+05	6.931472e+05	6.931472e+05
phylogenetic half life in units of tree height	9.478386e+03	9.478386e+03	9.478386e+03

Model Selection

Bayes Factors

	OU un-weighted predictor	BM
OU un-weighted predictor	0.00000	15.13087
BM	-15.13087	0.00000

Rest of Brain ~ Body Mass

OU Un-weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	35.0937340	6.0299857	0.0085234	0.0649782	8611.8647	30.1929017	40.6405504
prior	-17.7202080	4.9446584	0.0069893	0.0982557	2532.5455	-26.7869443	-10.1532887
alpha	3.0112156	4.1903372	0.0059231	0.3104779	182.1531	0.0443452	8.4652205
sigma^2	0.0948241	0.1305784	0.0001846	0.0117059	124.4320	0.0021275	0.2638584
shift number	1.3026228	1.1294804	0.0015965	0.0192860	3429.8312	0.0000000	3.0000000
N theta	2.3026228	1.1294804	0.0015965	0.0192860	3429.8312	1.0000000	4.0000000
root theta	1.7827258	0.0872482	0.0001233	0.0029554	871.5519	1.6181396	1.9561358
root beta	0.6365952	0.0266114	0.0000376	0.0009060	862.7057	0.5853532	0.6872355
all theta	1.8511293	0.6545371	NA	NA	NA	NA	NA
all beta	0.6227724	0.1992435	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	35.0392824	4.5948791	0.0064949	0.0761639	3639.5693	30.1469878	40.5747266
prior	-17.1633009	4.9348755	0.0069755	0.0988879	2490.3829	-25.9686790	-10.1514070
alpha	2.4245096	2.8645725	0.0040491	0.1765854	263.1541	0.0521792	7.4081067
sigma^2	0.0767684	0.0908343	0.0001284	0.0062350	212.2385	0.0019014	0.2338630
shift number	1.2701074	1.1438839	0.0016169	0.0194881	3445.2968	0.0000000	3.0000000
N theta	2.2701074	1.1438839	0.0016169	0.0194881	3445.2968	1.0000000	4.0000000
root theta	1.7751165	0.0885335	0.0001251	0.0030382	849.1326	1.6009166	1.9523789
root beta	0.6391139	0.0271911	0.0000384	0.0009071	898.5340	0.5869471	0.6924215
all theta	1.8313309	0.6389266	NA	NA	NA	NA	NA
all beta	0.6276917	0.1910389	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	35.1136970	2.5579851	0.0030558	0.0475565	2893.1841	30.1153025	40.5792956
prior	-17.3707357	4.8374886	0.0057790	0.0797489	3679.5183	-26.2353334	-10.1527919
alpha	2.4883053	2.6221166	0.0031325	0.1341058	382.3042	0.0584858	7.1128795
sigma^2	0.0783042	0.0805598	0.0000962	0.0051205	247.5177	0.0019579	0.2218412
shift number	1.2927113	1.1249445	0.0013439	0.0167169	4528.4773	0.0000000	3.0000000
N theta	2.2927113	1.1249445	0.0013439	0.0167169	4528.4773	1.0000000	4.0000000
root theta	1.7789407	0.0883499	0.0001055	0.0025610	1190.0935	1.6084118	1.9534330
root beta	0.6378374	0.0265910	0.0000318	0.0007850	1147.5760	0.5850746	0.6888699
all theta	1.8429826	0.6467617	NA	NA	NA	NA	NA
all beta	0.6250019	0.1963772	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	3.0112156	2.4245096	2.4883053
sigma squared	0.0948241	0.0767684	0.0783042
stationary variance	0.0157451	0.0158317	0.0157344
phylogenetic halflife	0.2301885	0.2858917	0.2785619
phylogenetic half life in units of tree height	0.0031531	0.0039162	0.0038158

OU Weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	34.9817404	34.0805196	0.0481730	0.2102461	26275.83766	30.1645086	40.9718681
prior	-17.4475603	5.0030986	0.0070719	0.0952160	2760.94615	-26.3314566	-10.1604904
alpha	2.4104040	2.5347325	0.0035829	0.2158898	137.84791	0.0996141	6.7482358
sigma^2	0.0759462	0.0787575	0.0001113	0.0145134	29.44729	0.0039144	0.2100656
shift number	1.3282651	1.1795765	0.0016673	0.0206004	3278.68844	0.0000000	3.0000000
N theta	2.3282651	1.1795765	0.0016673	0.0206004	3278.68844	1.0000000	4.0000000
root theta	1.7829262	0.0887056	0.0001254	0.0029828	884.42628	1.6125958	1.9623709
root beta	0.6363281	0.0304438	0.0000430	0.0009794	966.27086	0.5826177	0.6876583
all theta	1.8603783	0.6456922	NA	NA	NA	NA	NA
all beta	0.6196096	0.1963656	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	35.2581918	3.1166710	0.0044054	0.0677628	2115.43009	30.1449338	41.0102256
prior	-17.7353482	4.9462905	0.0069916	0.0997299	2459.84792	-26.8515410	-10.1709847
alpha	2.6838008	2.4766979	0.0035008	0.1901318	169.68223	0.1388916	7.6123205
sigma^2	0.0840199	0.0759003	0.0001073	0.0122242	38.55211	0.0053879	0.2318710
shift number	1.3425088	1.1561857	0.0016343	0.0210889	3005.70931	0.0000000	3.0000000
N theta	2.3425088	1.1561857	0.0016343	0.0210889	3005.70931	1.0000000	4.0000000
root theta	1.7836321	0.0882633	0.0001248	0.0030532	835.67737	1.6115112	1.9562768
root beta	0.6361178	0.0270232	0.0000382	0.0009401	826.24225	0.5840623	0.6882896
all theta	1.8569272	0.6439409	NA	NA	NA	NA	NA
all beta	0.6208193	0.1904165	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	35.2812900	2.6589546	0.0031765	0.0515555	2659.94061	30.1616298	40.9963255
prior	-17.5213760	4.9272709	0.0058863	0.0834153	3489.16662	-26.6309811	-10.1597370
alpha	2.4490592	2.6466302	0.0031617	0.1927261	188.58433	0.1026100	7.4990343
sigma^2	0.0766546	0.0816180	0.0000975	0.0123166	43.91285	0.0039715	0.2328824
shift number	1.3489990	1.1444863	0.0013672	0.0168757	4599.37818	0.0000000	3.0000000
N theta	2.3489990	1.1444863	0.0013672	0.0168757	4599.37818	1.0000000	4.0000000
root theta	1.7846413	0.0868189	0.0001037	0.0025226	1184.53069	1.6147808	1.9586763
root beta	0.6359932	0.0262720	0.0000314	0.0007701	1163.99060	0.5840369	0.6876032
all theta	1.8581881	0.6461108	NA	NA	NA	NA	NA
all beta	0.6201451	0.1929334	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	2.4104040	2.6838008	2.4490592
sigma squared	0.0759462	0.0840199	0.0766546
stationary variance	0.0157538	0.0156532	0.0156498
phylogenetic halflife	0.2875647	0.2582707	0.2830259
phylogenetic half life in units of tree height	0.0039391	0.0035378	0.0038769

BM

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	18.2775948	7.4803682	0.0105735	0.5631936	176.4130	15.7843822	20.4164477
prior	0.6164713	0.2044164	0.0002889	0.0112881	327.9374	0.4440760	0.7061801
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0032838	0.0505091	0.0000714	0.0020181	626.3865	0.0008291	0.0019532
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	2.0113992	0.2309762	0.0003265	0.0119320	374.7224	1.5601547	2.4697285
root beta	0.5573060	0.0603019	0.0000852	0.0020121	898.1489	0.4406410	0.6764485
all theta	2.0113992	0.2309762	NA	NA	NA	NA	NA
all beta	0.5573060	0.0603019	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	18.3064079	7.3184538	0.0103447	0.5598556	170.8782	16.0688213	20.4153472
prior	0.6237749	0.1850790	0.0002616	0.0096982	364.1915	0.4663646	0.7061923
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0029100	0.0376909	0.0000533	0.0013298	803.3977	0.0008499	0.0019774
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	2.0012299	0.2160071	0.0003053	0.0104336	428.6126	1.5771577	2.4281743
root beta	0.5607403	0.0609605	0.0000862	0.0020502	884.0677	0.4467587	0.6751603
all theta	2.0012299	0.2160071	NA	NA	NA	NA	NA
all beta	0.5607403	0.0609605	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	18.7783360	1.3500690	0.0016128	0.0278327	2352.8896	16.1364436	20.4158315
prior	0.6284968	0.0834715	0.0000997	0.0032951	641.6917	0.4629641	0.7061923
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0013603	0.0002890	0.0000003	0.0000090	1035.1674	0.0008578	0.0019345
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	2.0101932	0.2202032	0.0002631	0.0091532	578.7599	1.5771642	2.4407832
root beta	0.5584174	0.0584850	0.0000699	0.0015991	1337.5705	0.4467370	0.6754541
all theta	2.0101932	0.2202032	NA	NA	NA	NA	NA
all beta	0.5584174	0.0584850	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	1.000000e-06	1.000000e-06	1.000000e-06
sigma squared	3.283800e-03	2.910000e-03	1.360300e-03
stationary variance	1.641894e+03	1.455002e+03	6.801678e+02
phylogenetic halflife	6.931472e+05	6.931472e+05	6.931472e+05
phylogenetic half life in units of tree height	9.494774e+03	9.494774e+03	9.494774e+03

Model Selection

Bayes Factors

	OU un-weighted predictor	OU weighted predictor	BM
OU un-weighted predictor	0.0000000	0.2036888	-13.20949
OU weighted predictor	-0.2036888	0.0000000	-13.41318
BM	13.2094895	13.4131783	0.00000

Neocortex ~ Body Mass

OU Un-weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	32.8168851	325.3523158	0.4598873	2.4571315	17532.7883	23.2103516	45.1411171
prior	-24.4030877	6.2068539	0.0087734	0.1341944	2139.3137	-35.5309484	-13.6087716
alpha	0.1716046	0.8369939	0.0011831	0.0578385	209.4166	0.0000044	0.8436107
sigma^2	0.0084372	0.0391459	0.0000553	0.0028598	187.3763	0.0003062	0.0400217
shift number	3.5202887	1.5232459	0.0021531	0.0325417	2191.0895	1.0000000	6.0000000
N theta	4.5202887	1.5232459	0.0021531	0.0325417	2191.0895	2.0000000	7.0000000
root theta	1.6313836	0.1631586	0.0002306	0.0074549	479.0057	1.3181201	1.9548490
root beta	0.7629408	0.0503600	0.0000712	0.0024286	429.9871	0.6575935	0.8571897
all theta	1.3251069	0.8957646	NA	NA	NA	NA	NA
all beta	0.7960448	0.1136990	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	34.7617046	7.5023820	0.0106047	0.1727186	1886.7743	22.2552417	45.0002571
prior	-24.5015083	6.3791129	0.0090169	0.1516194	1770.1548	-36.1846758	-13.6001526
alpha	0.3187654	1.1402167	0.0016117	0.0651448	306.3484	0.0000040	1.9669025
sigma^2	0.0129646	0.0430854	0.0000609	0.0026391	266.5399	0.0002867	0.0779887
shift number	3.5402487	1.5478234	0.0021879	0.0354216	1909.4418	1.0000000	6.0000000
N theta	4.5402487	1.5478234	0.0021879	0.0354216	1909.4418	2.0000000	7.0000000
root theta	1.6256985	0.1594735	0.0002254	0.0070665	509.2962	1.3082366	1.9456518
root beta	0.7663215	0.0528718	0.0000747	0.0028236	350.6163	0.6648005	0.8696241
all theta	1.4345007	0.8570816	NA	NA	NA	NA	NA
all beta	0.7966503	0.1280298	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	35.9948247	4.7117431	0.0056288	0.1297377	1318.9570	27.2722514	45.8533264
prior	-24.5317310	6.1340891	0.0073280	0.1147180	2859.1482	-35.6316553	-13.6113687
alpha	0.0098306	0.0164825	0.0000197	0.0007413	494.4096	0.0000044	0.0264806
sigma^2	0.0009273	0.0006842	0.0000008	0.0000256	715.2035	0.0003999	0.0015633
shift number	3.5703093	1.5090296	0.0018027	0.0277791	2950.9401	1.0000000	6.0000000
N theta	4.5703093	1.5090296	0.0018027	0.0277791	2950.9401	2.0000000	7.0000000
root theta	1.6290920	0.1649816	0.0001971	0.0065984	625.1631	1.3070906	1.9535991
root beta	0.7646730	0.0490338	0.0000586	0.0025157	379.8992	0.6680403	0.8593100
all theta	1.3535442	0.9228891	NA	NA	NA	NA	NA
all beta	0.7934831	0.1016272	NA	NA	NA	NA	NA

Shifts

A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.

OU parameters

	chain1	chain2	combined chains
alpha	0.1716046	0.3187654	0.0098306
sigma squared	0.0084372	0.0129646	0.0009273
stationary variance	0.0245834	0.0203356	0.0471645
phylogenetic halflife	4.0392108	2.1744741	70.5089047
phylogenetic half life in units of tree height	0.0553294	0.0297861	0.9658355

OU Weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	27.7299483	7.2727090	0.0102800	0.3319691	479.95107	18.1191079	45.5480671
prior	-25.5238969	7.2465200	0.0102430	0.2043728	1257.22388	-39.1606209	-13.7117725
alpha	1.9745880	1.2575676	0.0017776	0.0639144	387.13761	0.1682837	4.1813244
sigma^2	0.0791454	0.0386295	0.0000546	0.0095792	16.26233	0.0101921	0.1471391
shift number	3.5076134	1.7655332	0.0024956	0.0484508	1327.85008	1.0000000	7.0000000
N theta	4.5076134	1.7655332	0.0024956	0.0484508	1327.85008	2.0000000	8.0000000
root theta	1.5983688	0.1599716	0.0002261	0.0058570	746.00240	1.3091754	1.9102546
root beta	0.7810255	0.0784384	0.0001109	0.0027180	832.83177	0.6404256	0.9096880
all theta	1.5037504	0.6343943	NA	NA	NA	NA	NA
all beta	0.8314348	0.2018003	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	26.8093017	25.7970518	0.0364643	0.2287368	12719.44549	17.4827060	42.9254696
prior	-25.0632333	6.9830689	0.0098706	0.1805274	1496.25721	-38.4131284	-14.0243474
alpha	1.9492654	1.3485050	0.0019061	0.0738196	333.70466	0.4129059	4.8562957
sigma^2	0.0813729	0.0533122	0.0000754	0.0167145	10.17336	0.0241168	0.2133917
shift number	3.3965606	1.7061457	0.0024116	0.0427553	1592.40296	1.0000000	7.0000000
N theta	4.3965606	1.7061457	0.0024116	0.0427553	1592.40296	2.0000000	8.0000000
root theta	1.5829906	0.1601966	0.0002264	0.0063977	626.99035	1.2700234	1.8832959
root beta	0.7873342	0.0779077	0.0001101	0.0028171	764.81433	0.6397492	0.9140903
all theta	1.4860431	0.6366793	NA	NA	NA	NA	NA
all beta	0.8357730	0.2032378	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	27.4931909	6.7523610	0.0080666	0.2651818	648.37136	17.8932531	44.5848315
prior	-25.1563465	7.0231426	0.0083900	0.1587772	1956.53108	-38.3626798	-13.7289268
alpha	1.7700885	1.1364938	0.0013577	0.0498612	519.52864	0.1944426	3.9083460
sigma^2	0.0722819	0.0407478	0.0000487	0.0092439	19.43098	0.0101921	0.1513429
shift number	3.4719725	1.7267705	0.0020628	0.0385442	2007.01300	1.0000000	7.0000000
N theta	4.4719725	1.7267705	0.0020628	0.0385442	2007.01300	2.0000000	8.0000000
root theta	1.5883577	0.1578281	0.0001885	0.0051290	946.88858	1.2879207	1.8932525
root beta	0.7856376	0.0772600	0.0000923	0.0023906	1044.49521	0.6438340	0.9126602
all theta	1.4912459	0.6334104	NA	NA	NA	NA	NA
all beta	0.8340280	0.2015946	NA	NA	NA	NA	NA

Shifts

A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.

OU parameters

	chain1	chain2	combined chains
alpha	1.9745880	1.9492654	1.7700885
sigma squared	0.0791454	0.0813729	0.0722819
stationary variance	0.0200410	0.0208727	0.0204176
phylogenetic halflife	0.3510338	0.3555941	0.3915890
phylogenetic half life in units of tree height	0.0048085	0.0048709	0.0053640

BM

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	20.8715295	5.8345207	0.0082471	0.3297257	313.1157	18.3840937	22.8589064
prior	0.5385952	0.1854439	0.0002621	0.0086007	464.8978	0.2897727	0.7061340
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0023161	0.0334421	0.0000473	0.0009781	1169.0522	0.0007949	0.0017988
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	1.7390091	0.2242857	0.0003170	0.0117307	365.5590	1.3267016	2.1903187
root beta	0.7418696	0.0601616	0.0000850	0.0020899	828.6437	0.6237639	0.8507326
all theta	1.7390091	0.2242857	NA	NA	NA	NA	NA
all beta	0.7418696	0.0601616	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	21.0961872	5.8271612	0.0082367	0.3416098	290.9734	18.9708934	22.8607812
prior	0.5374127	0.1708326	0.0002415	0.0076535	498.2259	0.3308981	0.7057571
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0021657	0.0289035	0.0000409	0.0009220	982.7194	0.0007761	0.0017194
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	1.7551085	0.1884625	0.0002664	0.0083070	514.7030	1.3846736	2.1215177
root beta	0.7354261	0.0512223	0.0000724	0.0015023	1162.4672	0.6354001	0.8339267
all theta	1.7551085	0.1884625	NA	NA	NA	NA	NA
all beta	0.7354261	0.0512223	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	21.2581897	1.3037861	0.0015575	0.0242721	2885.3370	18.6966750	22.8616275
prior	0.5448964	0.1197458	0.0001431	0.0049407	587.4213	0.3132632	0.7061011
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0012331	0.0002535	0.0000003	0.0000060	1807.7957	0.0007878	0.0017434
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	1.7437475	0.2079345	0.0002484	0.0086983	571.4539	1.3434474	2.1630782
root beta	0.7393104	0.0548553	0.0000655	0.0014734	1386.1299	0.6306284	0.8450501
all theta	1.7437475	0.2079345	NA	NA	NA	NA	NA
all beta	0.7393104	0.0548553	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	1.000000e-06	1.000000e-06	1.000000e-06
sigma squared	2.316100e-03	2.165700e-03	1.233100e-03
stationary variance	1.158037e+03	1.082865e+03	6.165456e+02
phylogenetic halflife	6.931472e+05	6.931472e+05	6.931472e+05
phylogenetic half life in units of tree height	9.494774e+03	9.494774e+03	9.494774e+03

Model Selection

Bayes Factors

	OU un-weighted predictor	OU weighted predictor	BM
OU un-weighted predictor	0.000000	-3.995941	18.21388
OU weighted predictor	3.995941	0.000000	22.20983
BM	-18.213884	-22.209825	0.00000

Neocortex ~ Rest of Brain

OU Un-weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	41.8484663	968.1801624	1.3685281	2.5734017	141545.86190	35.7727162	51.5812024
prior	-23.2532256	4.5627496	0.0064495	0.1013316	2027.51208	-31.5383428	-13.8553269
alpha	2.1636622	1.7379749	0.0024566	0.1382129	158.12120	0.0062162	5.6566696
sigma^2	0.0472127	0.0363335	0.0000514	0.0098932	13.48773	0.0010836	0.1276905
shift number	2.9008673	1.0744340	0.0015187	0.0220908	2365.57596	1.0000000	5.0000000
N theta	3.9008673	1.0744340	0.0015187	0.0220908	2365.57596	2.0000000	6.0000000
root theta	-0.6339715	0.2108443	0.0002980	0.0083834	632.53131	-1.0156088	-0.2434912
root beta	1.2418326	0.0814384	0.0001151	0.0025560	1015.15219	1.1179615	1.3615942
all theta	-0.7405324	0.6921804	NA	NA	NA	NA	NA
all beta	1.2713242	0.1649926	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	43.8279981	6.5804940	0.0093016	0.1134002	3367.35852	35.5612005	51.2919730
prior	-23.7055845	4.5388822	0.0064157	0.0925822	2403.49505	-32.5613466	-15.0578766
alpha	3.3374555	1.8237175	0.0025778	0.1051125	301.02788	0.4217073	6.7914446
sigma^2	0.0754616	0.0370812	0.0000524	0.0065471	32.07837	0.0096908	0.1453442
shift number	2.7738666	1.0584480	0.0014961	0.0201765	2752.00582	1.0000000	5.0000000
N theta	3.7738666	1.0584480	0.0014961	0.0201765	2752.00582	2.0000000	6.0000000
root theta	-0.6552091	0.1876256	0.0002652	0.0159671	138.08124	-1.0318872	-0.2518178
root beta	1.2564397	0.0626718	0.0000886	0.0062666	100.01786	1.1307464	1.3691711
all theta	-0.8135768	0.6943325	NA	NA	NA	NA	NA
all beta	1.2883986	0.1660847	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	44.2063127	3.9656266	0.0047374	0.1018626	1515.63351	35.8230725	51.3585512
prior	-23.5228093	4.4778750	0.0053494	0.0810203	3054.61546	-32.4301834	-14.9626555
alpha	2.8489993	1.6936491	0.0020233	0.0919749	339.08457	0.2918139	6.1444828
sigma^2	0.0633741	0.0349860	0.0000418	0.0061284	32.59057	0.0079628	0.1317232
shift number	2.8171182	1.0398971	0.0012423	0.0172423	3637.38195	1.0000000	5.0000000
N theta	3.8171182	1.0398971	0.0012423	0.0172423	3637.38195	2.0000000	6.0000000
root theta	-0.6374330	0.1974473	0.0002359	0.0085295	535.86534	-1.0119052	-0.2304020
root beta	1.2526926	0.0729528	0.0000872	0.0026681	747.60055	1.1146628	1.3610931
all theta	-0.7952536	0.7046166	NA	NA	NA	NA	NA
all beta	1.2832230	0.1673607	NA	NA	NA	NA	NA

Shifts

A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.

OU parameters

	chain1	chain2	combined chains
alpha	2.1636622	3.3374555	2.8489993
sigma squared	0.0472127	0.0754616	0.0633741
stationary variance	0.0109104	0.0113053	0.0111222
phylogenetic halflife	0.3203583	0.2076873	0.2432950
phylogenetic half life in units of tree height	0.0043883	0.0028449	0.0033327

OU Weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	43.8979990	4.4951105	0.0063539	0.1397838	1034.11020	35.4665226	51.2292886
prior	-23.8578417	4.8785533	0.0068959	0.1162950	1759.78704	-32.6891924	-13.9740455
alpha	3.5254850	3.3528039	0.0047392	0.2360772	201.70103	0.2385005	9.6435901
sigma^2	0.0797647	0.0732062	0.0001035	0.0096366	57.70999	0.0058361	0.2125637
shift number	2.8162541	1.0660587	0.0015069	0.0216442	2425.93778	1.0000000	5.0000000
N theta	3.8162541	1.0660587	0.0015069	0.0216442	2425.93778	2.0000000	6.0000000
root theta	-0.6657844	0.2274737	0.0003215	0.0088728	657.26922	-1.0893730	-0.1897840
root beta	1.2472358	0.0712471	0.0001007	0.0028328	632.57222	1.0979957	1.3728979
all theta	-0.7906672	0.7157514	NA	NA	NA	NA	NA
all beta	1.2814128	0.1727140	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	39.8941116	1060.6268466	1.4992020	4.2083819	63517.72602	35.5189152	51.6070603
prior	-23.5907037	4.7007118	0.0066445	0.0999258	2212.95041	-32.0702708	-14.0855715
alpha	3.0880861	2.9184596	0.0041253	0.2036243	205.42261	0.1653919	8.6588482
sigma^2	0.0698243	0.0635938	0.0000899	0.0083592	57.87616	0.0037153	0.1950417
shift number	2.8634029	1.0683404	0.0015101	0.0201095	2822.37812	1.0000000	5.0000000
N theta	3.8634029	1.0683404	0.0015101	0.0201095	2822.37812	2.0000000	6.0000000
root theta	-0.6804767	0.2052922	0.0002902	0.0178454	132.33971	-1.0563787	-0.2436789
root beta	1.2460685	0.0660245	0.0000933	0.0058992	125.26233	1.1226679	1.3698521
all theta	-0.8217033	0.6744663	NA	NA	NA	NA	NA
all beta	1.2899395	0.1654361	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	44.1407053	4.0499875	0.0048382	0.1062974	1451.6504	35.7025606	51.4354126
prior	-23.7346579	4.7996548	0.0057338	0.0949231	2556.6780	-32.4161028	-13.9690050
alpha	3.3856772	3.4595838	0.0041329	0.2157652	257.0898	0.1605903	9.9835032
sigma^2	0.0761431	0.0742844	0.0000887	0.0086867	73.1277	0.0037153	0.2226821
shift number	2.8347433	1.0601508	0.0012665	0.0179683	3481.1499	1.0000000	5.0000000
N theta	3.8347433	1.0601508	0.0012665	0.0179683	3481.1499	2.0000000	6.0000000
root theta	-0.6680813	0.2048490	0.0002447	0.0091215	504.3520	-1.0502625	-0.2483801
root beta	1.2471524	0.0672071	0.0000803	0.0031225	463.2499	1.1173492	1.3699408
all theta	-0.7952818	0.7000289	NA	NA	NA	NA	NA
all beta	1.2827302	0.1707245	NA	NA	NA	NA	NA

Shifts

A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.

OU parameters

	chain1	chain2	combined chains
alpha	3.5254850	3.0880861	3.3856772
sigma squared	0.0797647	0.0698243	0.0761431
stationary variance	0.0113126	0.0113054	0.0112449
phylogenetic halflife	0.1966104	0.2244585	0.2047293
phylogenetic half life in units of tree height	0.0026932	0.0030746	0.0028044

BM

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	17.5150011	3.6378668	0.0051421	0.1257875	836.4088	15.0151934	19.2080224
prior	0.0165669	0.3883399	0.0005489	0.0257268	227.8525	-0.7030907	0.6884311
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0018120	0.0205364	0.0000290	0.0004406	2172.3401	0.0009041	0.0020257
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	-0.0609930	0.3097906	0.0004379	0.0224731	190.0242	-0.6826560	0.5377753
root beta	1.0859743	0.0786945	0.0001112	0.0037377	443.2905	0.9333284	1.2395857
all theta	-0.0609930	0.3097906	NA	NA	NA	NA	NA
all beta	1.0859743	0.0786945	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	17.3634726	3.4730740	0.0049092	0.1065983	1061.5174	14.3767024	19.2089078
prior	0.0313275	0.4147713	0.0005863	0.0287710	207.8292	-0.7075689	0.7059280
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0018395	0.0240165	0.0000339	0.0004343	3058.6033	0.0008981	0.0020419
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	-0.0887087	0.3567984	0.0005043	0.0288710	152.7290	-0.8569471	0.5581567
root beta	1.0925840	0.0892841	0.0001262	0.0048934	332.9064	0.9224502	1.2750628
all theta	-0.0887087	0.3567984	NA	NA	NA	NA	NA
all beta	1.0925840	0.0892841	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	17.6151197	1.3390684	0.0015997	0.0202266	4382.8985	14.9845493	19.2093645
prior	0.0204465	0.3772335	0.0004507	0.0232925	262.2946	-0.6797911	0.7018271
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0014139	0.0002979	0.0000004	0.0000032	8523.5930	0.0008871	0.0020107
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	-0.0620764	0.3078858	0.0003678	0.0187659	269.1786	-0.6691354	0.5533120
root beta	1.0860732	0.0779255	0.0000931	0.0031770	601.6116	0.9318730	1.2387710
all theta	-0.0620764	0.3078858	NA	NA	NA	NA	NA
all beta	1.0860732	0.0779255	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	1.000000e-06	1.000000e-06	1.000000e-06
sigma squared	1.812000e-03	1.839500e-03	1.413900e-03
stationary variance	9.059836e+02	9.197657e+02	7.069329e+02
phylogenetic halflife	6.931472e+05	6.931472e+05	6.931472e+05
phylogenetic half life in units of tree height	9.494774e+03	9.494774e+03	9.494774e+03

Model Selection

Bayes Factors

	OU un-weighted predictor	OU weighted predictor	BM
OU un-weighted predictor	0.000000	9.287355	-5.080023
OU weighted predictor	-9.287355	0.000000	-14.367379
BM	5.080023	14.367379	0.000000

Cerebellum ~ Body Mass

OU Un-weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	36.4566292	5.2871738	0.0074734	0.1968457	721.43166	26.6512833	44.8588394
prior	-22.6710409	5.6442399	0.0079782	0.1343198	1765.75752	-35.4633553	-13.5989196
alpha	3.3967852	5.9438755	0.0084017	0.5952794	99.70060	0.0038035	9.9937069
sigma^2	0.1050424	0.2063346	0.0002917	0.0338398	37.17824	0.0010685	0.2946486
shift number	2.6200347	1.2740112	0.0018008	0.0261663	2370.62251	0.0000000	5.0000000
N theta	3.6200347	1.2740112	0.0018008	0.0261663	2370.62251	1.0000000	6.0000000
root theta	1.0382549	0.1167466	0.0001650	0.0061941	355.25057	0.8001524	1.2559433
root beta	0.7520156	0.0388820	0.0000550	0.0022372	302.06664	0.6811840	0.8329248
all theta	0.9931324	0.6417818	NA	NA	NA	NA	NA
all beta	0.7950026	0.2009048	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	36.4622926	5.0899284	0.0071946	0.1642591	960.20555	27.1691024	44.0587734
prior	-22.9663043	5.6445773	0.0079786	0.1368128	1702.19561	-35.4640343	-13.5986330
alpha	3.9902225	5.2405207	0.0074075	0.5069369	106.86637	0.0019369	13.5508251
sigma^2	0.1188536	0.1542000	0.0002180	0.0398436	14.97788	0.0008494	0.3952444
shift number	2.5623925	1.2276378	0.0017353	0.0245591	2498.71025	1.0000000	5.0000000
N theta	3.5623925	1.2276378	0.0017353	0.0245591	2498.71025	2.0000000	6.0000000
root theta	1.0432452	0.1097785	0.0001552	0.0056271	380.59146	0.8192346	1.2560838
root beta	0.7507707	0.0363652	0.0000514	0.0019621	343.51663	0.6822760	0.8259890
all theta	1.0150288	0.6476237	NA	NA	NA	NA	NA
all beta	0.7856301	0.2000887	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	36.6716941	4.8719617	0.0058202	0.1620806	903.53652	27.0331859	44.7378321
prior	-22.4925545	5.6129220	0.0067054	0.1150156	2381.57458	-35.6923940	-13.5974380
alpha	3.0593154	4.3930424	0.0052481	0.3765281	136.12444	0.0033618	8.4583884
sigma^2	0.0899002	0.1297257	0.0001550	0.0294812	19.36251	0.0008476	0.2364548
shift number	2.6073349	1.2534005	0.0014973	0.0219005	3275.45712	0.0000000	5.0000000
N theta	3.6073349	1.2534005	0.0014973	0.0219005	3275.45712	1.0000000	6.0000000
root theta	1.0458358	0.1124104	0.0001343	0.0049341	519.04028	0.8172568	1.2596879
root beta	0.7494989	0.0372117	0.0000445	0.0017705	441.74762	0.6808556	0.8273908
all theta	1.0080017	0.6410605	NA	NA	NA	NA	NA
all beta	0.7891335	0.1974405	NA	NA	NA	NA	NA

Shifts

A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.

OU parameters

	chain1	chain2	combined chains
alpha	3.3967852	3.9902225	3.0593154
sigma squared	0.1050424	0.1188536	0.0899002
stationary variance	0.0154620	0.0148931	0.0146929
phylogenetic halflife	0.2040598	0.1737114	0.2265694
phylogenetic half life in units of tree height	0.0027952	0.0023795	0.0031036

OU Weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	34.0371561	16.9841906	0.0240072	0.1725718	9686.12060	23.4572121	45.0021240
prior	-43.0414028	17.3366744	0.0245055	0.5320266	1061.85433	-74.6248220	-13.6006896
alpha	0.0862955	0.4436760	0.0006271	0.0475792	86.95550	0.0000168	0.1818922
sigma^2	0.0031725	0.0132612	0.0000187	0.0030428	18.99399	0.0003987	0.0053736
shift number	7.7708516	4.0149894	0.0056752	0.1203739	1112.51084	1.0000000	15.0000000
N theta	8.7708516	4.0149894	0.0056752	0.1203739	1112.51084	2.0000000	16.0000000
root theta	1.0471759	0.1539052	0.0002175	0.0043775	1236.10923	0.7245957	1.3450879
root beta	0.7434921	0.0493741	0.0000698	0.0012742	1501.54666	0.6455499	0.8458869
all theta	0.9581601	0.8701998	NA	NA	NA	NA	NA
all beta	0.8192586	0.4168436	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	36.2193168	5.3442745	0.0075542	0.2045992	682.29093	26.1425057	45.0325194
prior	-27.3900948	11.1956702	0.0158251	0.4123270	737.25312	-51.1514961	-10.1458263
alpha	4.2963449	6.6751439	0.0094354	0.5421482	151.59515	0.0003357	17.6570872
sigma^2	0.1248236	0.1804488	0.0002551	0.0381314	22.39451	0.0004158	0.5436612
shift number	3.6037271	2.7171061	0.0038406	0.1007678	727.05938	0.0000000	10.0000000
N theta	4.6037271	2.7171061	0.0038406	0.1007678	727.05938	1.0000000	11.0000000
root theta	1.0294418	0.1260774	0.0001782	0.0050066	634.13821	0.7858762	1.2785029
root beta	0.7534692	0.0426523	0.0000603	0.0017945	564.94620	0.6713536	0.8382244
all theta	0.9896406	0.7275289	NA	NA	NA	NA	NA
all beta	0.8054296	0.2992028	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	35.3269162	5.7027183	0.0068126	0.2043558	778.73515	24.5540173	45.3901024
prior	-36.6378793	16.7264913	0.0199819	0.5212416	1029.74934	-71.0768777	-13.5984721
alpha	2.1458487	5.8823090	0.0070272	0.4698360	156.74839	0.0000168	13.8846515
sigma^2	0.0621376	0.1604863	0.0001917	0.0324137	24.51429	0.0003820	0.4285442
shift number	6.0538573	4.0295435	0.0048138	0.1279281	992.15559	1.0000000	14.0000000
N theta	7.0538573	4.0295435	0.0048138	0.1279281	992.15559	2.0000000	15.0000000
root theta	1.0395540	0.1418021	0.0001694	0.0037238	1450.07772	0.7542402	1.3213660
root beta	0.7471385	0.0462549	0.0000553	0.0011885	1514.76778	0.6541054	0.8395345
all theta	0.9645586	0.8295112	NA	NA	NA	NA	NA
all beta	0.8174347	0.3907971	NA	NA	NA	NA	NA

Shifts

A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.

OU parameters

	chain1	chain2	combined chains
alpha	0.0862955	4.2963449	2.1458487
sigma squared	0.0031725	0.1248236	0.0621376
stationary variance	0.0183817	0.0145267	0.0144786
phylogenetic halflife	8.0322527	0.1613342	0.3230177
phylogenetic half life in units of tree height	0.1100263	0.0022100	0.0044247

BM

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	26.5485381	5.0509005	0.0071395	0.2360795	457.7421	24.1094743	28.3620457
prior	0.6108970	0.1417179	0.0002003	0.0051922	744.9891	0.4426606	0.7061943
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0017322	0.0289745	0.0000410	0.0006944	1741.0983	0.0006316	0.0014304
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	1.2015515	0.1875839	0.0002652	0.0084088	497.6499	0.8415834	1.5800614
root beta	0.6993194	0.0499740	0.0000706	0.0015356	1059.1323	0.6016079	0.8002787
all theta	1.2015515	0.1875839	NA	NA	NA	NA	NA
all beta	0.6993194	0.0499740	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	26.5629428	5.4926810	0.0077639	0.2882235	363.1700	24.2528337	28.3631810
prior	0.6183126	0.1445437	0.0002043	0.0057300	636.3396	0.4722565	0.7062234
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0018346	0.0293708	0.0000415	0.0007758	1433.3601	0.0006274	0.0014132
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	1.1845039	0.1806239	0.0002553	0.0076412	558.7645	0.8240929	1.5464148
root beta	0.7028933	0.0484279	0.0000685	0.0014403	1130.4657	0.6066532	0.7999328
all theta	1.1845039	0.1806239	NA	NA	NA	NA	NA
all beta	0.7028933	0.0484279	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	26.7706289	1.2912353	0.0015425	0.0201380	4111.2956	24.2360618	28.3620457
prior	0.6170407	0.0808391	0.0000966	0.0031029	678.7535	0.4545461	0.7062101
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0009983	0.0002071	0.0000002	0.0000036	3376.4739	0.0006390	0.0014160
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	1.1954987	0.1863705	0.0002226	0.0068648	737.0504	0.8428894	1.5792490
root beta	0.7006512	0.0495059	0.0000591	0.0012905	1471.7183	0.6033083	0.8003800
all theta	1.1954987	0.1863705	NA	NA	NA	NA	NA
all beta	0.7006512	0.0495059	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	1.000000e-06	1.000000e-06	1.000000e-06
sigma squared	1.732200e-03	1.834600e-03	9.983000e-04
stationary variance	8.661245e+02	9.172910e+02	4.991699e+02
phylogenetic halflife	6.931472e+05	6.931472e+05	6.931472e+05
phylogenetic half life in units of tree height	9.494774e+03	9.494774e+03	9.494774e+03

Model Selection

Bayes Factors

	OU un-weighted predictor	OU weighted predictor	BM
OU un-weighted predictor	0.00000	10.83171	22.78693
OU weighted predictor	-10.83171	0.00000	11.95522
BM	-22.78693	-11.95522	0.00000

Cerebellum ~ Rest of Brain

OU Un-weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	49.3269425	3.9357571	0.0055632	0.1012674	1510.4870	44.7023903	54.3961533
prior	-20.9461595	4.7152885	0.0066651	0.1177747	1602.9213	-29.6111772	-13.8759109
alpha	6.8740976	11.0784825	0.0156595	0.9947652	124.0279	0.2779672	25.3686391
sigma^2	0.1275789	0.2041039	0.0002885	0.0335094	37.0996	0.0070807	0.4817957
shift number	1.8596786	0.9390306	0.0013273	0.0162547	3337.3617	1.0000000	4.0000000
N theta	2.8596786	0.9390306	0.0013273	0.0162547	3337.3617	2.0000000	5.0000000
root theta	-0.8119928	0.1345697	0.0001902	0.0081744	271.0109	-1.0893914	-0.5548172
root beta	1.1142681	0.0367249	0.0000519	0.0017818	424.8286	1.0456704	1.1869901
all theta	-0.8537486	0.5772799	NA	NA	NA	NA	NA
all beta	1.1533021	0.1446264	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	49.2069385	24.8321423	0.0351004	0.2001908	15386.51547	44.7336228	54.3495102
prior	-20.6981186	4.5007928	0.0063619	0.0991912	2058.88521	-28.9382894	-14.0955850
alpha	5.7780187	9.4741714	0.0133918	0.8217482	132.92448	0.4593220	14.1225901
sigma^2	0.1065654	0.1706065	0.0002412	0.0373301	20.88682	0.0107418	0.2464464
shift number	1.8447236	0.9458469	0.0013370	0.0161186	3443.38114	1.0000000	4.0000000
N theta	2.8447236	0.9458469	0.0013370	0.0161186	3443.38114	2.0000000	5.0000000
root theta	-0.8175726	0.1336386	0.0001889	0.0084307	251.26502	-1.0821132	-0.5492164
root beta	1.1157420	0.0354847	0.0000502	0.0021581	270.34832	1.0438563	1.1854522
all theta	-0.8297152	0.5830575	NA	NA	NA	NA	NA
all beta	1.1484814	0.1445109	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	49.4082883	2.3190157	0.0027704	0.0330285	4929.79499	44.8529090	54.3869963
prior	-20.2735808	4.0849296	0.0048800	0.0728433	3144.77495	-27.9431388	-13.9333419
alpha	4.3403781	4.0391746	0.0048253	0.2440361	273.95365	0.3622365	11.2181190
sigma^2	0.0795458	0.0712826	0.0000852	0.0107704	43.80264	0.0077395	0.1954588
shift number	1.8437600	0.9015113	0.0010770	0.0128477	4923.73617	1.0000000	4.0000000
N theta	2.8437600	0.9015113	0.0010770	0.0128477	4923.73617	2.0000000	5.0000000
root theta	-0.8121158	0.1336923	0.0001597	0.0071305	351.53857	-1.0924216	-0.5548172
root beta	1.1143510	0.0354722	0.0000424	0.0018812	355.53859	1.0457706	1.1888983
all theta	-0.8479819	0.5802528	NA	NA	NA	NA	NA
all beta	1.1524684	0.1437857	NA	NA	NA	NA	NA

Shifts

A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.

OU parameters

	chain1	chain2	combined chains
alpha	6.8740976	5.7780187	4.3403781
sigma squared	0.1275789	0.1065654	0.0795458
stationary variance	0.0092797	0.0092216	0.0091635
phylogenetic halflife	0.1008346	0.1199628	0.1596974
phylogenetic half life in units of tree height	0.0013812	0.0016433	0.0021875

OU Weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	49.3481274	2.7736407	0.0039206	0.0517473	2872.9267	44.9024246	54.2997755
prior	-19.6678169	4.1849779	0.0059155	0.0888331	2219.4042	-27.4896496	-13.7336059
alpha	3.7221887	5.8580373	0.0082804	0.4490953	170.1482	0.0861110	11.8009314
sigma^2	0.0686369	0.1055998	0.0001493	0.0102375	106.4000	0.0016914	0.2156493
shift number	1.8430573	0.9128674	0.0012903	0.0152115	3601.4190	1.0000000	4.0000000
N theta	2.8430573	0.9128674	0.0012903	0.0152115	3601.4190	2.0000000	5.0000000
root theta	-0.8220552	0.1245090	0.0001760	0.0076035	268.1453	-1.0632893	-0.5772153
root beta	1.1169222	0.0329857	0.0000466	0.0019887	275.1177	1.0503486	1.1789120
all theta	-0.8348596	0.5893023	NA	NA	NA	NA	NA
all beta	1.1494329	0.1432998	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	49.2633328	11.9856559	0.0169418	0.1048105	13077.1885	44.4475506	54.6753513
prior	-19.5913878	4.1938216	0.0059280	0.0836046	2516.2815	-27.3412844	-13.6981301
alpha	3.0033150	3.1793302	0.0044940	0.1988068	255.7459	0.1220655	8.8839884
sigma^2	0.0554521	0.0580222	0.0000820	0.0047153	151.4141	0.0022603	0.1624690
shift number	1.8739583	0.9437113	0.0013339	0.0160975	3436.8470	1.0000000	4.0000000
N theta	2.8739583	0.9437113	0.0013339	0.0160975	3436.8470	2.0000000	5.0000000
root theta	-0.8433433	0.1415927	0.0002001	0.0095398	220.2925	-1.1111085	-0.5703628
root beta	1.1226095	0.0395323	0.0000559	0.0018656	449.0013	1.0502957	1.1927854
all theta	-0.8553063	0.6042763	NA	NA	NA	NA	NA
all beta	1.1545158	0.1485375	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	49.3834736	2.3793226	0.0028424	0.0377764	3967.0407	44.7301931	54.5654094
prior	-19.5954467	4.1241172	0.0049268	0.0724996	3235.8677	-27.3738546	-13.7444268
alpha	3.2850853	4.4575868	0.0053252	0.2784352	256.3016	0.0949506	9.8046308
sigma^2	0.0607616	0.0831734	0.0000994	0.0066471	156.5705	0.0017156	0.1805526
shift number	1.8560947	0.9205252	0.0010997	0.0132498	4826.7162	1.0000000	4.0000000
N theta	2.8560947	0.9205252	0.0010997	0.0132498	4826.7162	2.0000000	5.0000000
root theta	-0.8378266	0.1351284	0.0001614	0.0074360	330.2258	-1.0776892	-0.5727548
root beta	1.1210664	0.0361976	0.0000432	0.0020173	321.9858	1.0518719	1.1855103
all theta	-0.8414627	0.5941776	NA	NA	NA	NA	NA
all beta	1.1507620	0.1444982	NA	NA	NA	NA	NA

Shifts

A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.

OU parameters

	chain1	chain2	combined chains
alpha	3.7221887	3.0033150	3.2850853
sigma squared	0.0686369	0.0554521	0.0607616
stationary variance	0.0092200	0.0092318	0.0092481
phylogenetic halflife	0.1862203	0.2307940	0.2109982
phylogenetic half life in units of tree height	0.0025509	0.0031614	0.0028903

BM

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	27.7751952	2.4020119	0.0033953	0.0459851	2728.4557	25.2802762	29.4104014
prior	0.3937618	0.2363242	0.0003340	0.0136611	299.2596	-0.0585239	0.7062204
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0010826	0.0120831	0.0000171	0.0001197	10198.0175	0.0006101	0.0013692
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	-0.5335550	0.2761243	0.0003903	0.0183661	226.0361	-1.0676802	0.0195057
root beta	1.0371505	0.0694229	0.0000981	0.0031915	473.1717	0.9005716	1.1748000
all theta	-0.5335550	0.2761243	NA	NA	NA	NA	NA
all beta	1.0371505	0.0694229	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	27.7948634	2.2579275	0.0031916	0.0416064	2945.1048	25.2930660	29.4091996
prior	0.4024882	0.2212113	0.0003127	0.0125847	308.9778	-0.0115160	0.7062136
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0010673	0.0121688	0.0000172	0.0000996	14925.6437	0.0006119	0.0013760
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	-0.5423194	0.2701564	0.0003819	0.0170906	249.8696	-1.0794213	-0.0185238
root beta	1.0386770	0.0680850	0.0000962	0.0030871	486.4145	0.9043142	1.1715899
all theta	-0.5423194	0.2701564	NA	NA	NA	NA	NA
all beta	1.0386770	0.0680850	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	27.8347888	1.2748328	0.0015230	0.0145494	7677.4573	25.3257300	29.4090188
prior	0.4060624	0.2165916	0.0002587	0.0117126	341.9621	-0.0058340	0.7061951
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0009620	0.0002027	0.0000002	0.0000010	37254.5836	0.0006154	0.0013760
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	-0.5446117	0.2660055	0.0003178	0.0144844	337.2734	-1.0719802	-0.0308299
root beta	1.0392547	0.0673263	0.0000804	0.0025535	695.1869	0.9079109	1.1714135
all theta	-0.5446117	0.2660055	NA	NA	NA	NA	NA
all beta	1.0392547	0.0673263	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	1.000000e-06	1.000000e-06	1.000000e-06
sigma squared	1.082600e-03	1.067300e-03	9.620000e-04
stationary variance	5.412753e+02	5.336342e+02	4.809976e+02
phylogenetic halflife	6.931472e+05	6.931472e+05	6.931472e+05
phylogenetic half life in units of tree height	9.494774e+03	9.494774e+03	9.494774e+03

Model Selection

Bayes Factors

	OU un-weighted predictor	OU weighted predictor	BM
OU un-weighted predictor	0.0000000	-0.1973664	-10.65050
OU weighted predictor	0.1973664	0.0000000	-10.45313
BM	10.6504986	10.4531321	0.00000

Medulla ~ Body Mass

OU Un-weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	41.5090395	3.8289470	0.0054122	0.1171954	1067.4259	35.8256584	49.7403512
prior	-13.2359031	4.2147195	0.0059575	0.0975562	1866.4989	-21.1753098	-7.5672757
alpha	3.3050082	3.6660083	0.0051819	0.2550397	206.6196	0.1363300	10.3375381
sigma^2	0.0480708	0.0487685	0.0000689	0.0043616	125.0206	0.0026400	0.1485004
shift number	0.9079163	0.9474716	0.0013393	0.0188478	2527.0234	0.0000000	3.0000000
N theta	1.9079163	0.9474716	0.0013393	0.0188478	2527.0234	1.0000000	4.0000000
root theta	1.0677990	0.0784913	0.0001109	0.0023994	1070.1740	0.9133303	1.2251224
root beta	0.5870589	0.0223279	0.0000316	0.0006535	1167.5238	0.5429637	0.6312144
all theta	1.0574266	0.4913659	NA	NA	NA	NA	NA
all beta	0.5829843	0.1672830	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	41.3631024	266.9873493	0.3773881	0.7808967	116894.5314	36.3959447	51.5809923
prior	-14.2426511	4.7314415	0.0066879	0.1238551	1459.3499	-22.8511111	-7.5456825
alpha	4.6785248	6.8827947	0.0097289	0.5139241	179.3625	0.0000963	15.8941958
sigma^2	0.0683668	0.1023175	0.0001446	0.0100184	104.3035	0.0002943	0.2297625
shift number	1.0391208	1.0308954	0.0014572	0.0225655	2087.0883	0.0000000	3.0000000
N theta	2.0391208	1.0308954	0.0014572	0.0225655	2087.0883	1.0000000	4.0000000
root theta	1.0785224	0.0819400	0.0001158	0.0026366	965.8252	0.9241345	1.2383921
root beta	0.5848160	0.0231503	0.0000327	0.0007174	1041.1920	0.5402858	0.6285270
all theta	1.0486085	0.5214857	NA	NA	NA	NA	NA
all beta	0.5846585	0.1845006	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	41.9231253	3.8363852	0.0045831	0.1238482	959.5443	36.1171349	51.0201071
prior	-13.6856649	4.4820591	0.0053544	0.0951877	2217.1404	-22.0645257	-7.5456825
alpha	3.7860633	5.5320481	0.0066087	0.3588624	237.6381	0.0000963	12.1936336
sigma^2	0.0551960	0.0811289	0.0000969	0.0067506	144.4347	0.0002899	0.1765419
shift number	0.9848495	0.9948119	0.0011884	0.0179993	3054.7043	0.0000000	3.0000000
N theta	1.9848495	0.9948119	0.0011884	0.0179993	3054.7043	1.0000000	4.0000000
root theta	1.0745056	0.0792044	0.0000946	0.0020732	1459.4939	0.9194360	1.2309349
root beta	0.5855490	0.0225094	0.0000269	0.0005687	1566.8394	0.5411605	0.6294026
all theta	1.0552870	0.5152106	NA	NA	NA	NA	NA
all beta	0.5832427	0.1810461	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	3.3050082	4.6785248	3.7860633
sigma squared	0.0480708	0.0683668	0.0551960
stationary variance	0.0072724	0.0073064	0.0072894
phylogenetic halflife	0.2097263	0.1481551	0.1830786
phylogenetic half life in units of tree height	0.0028728	0.0020294	0.0025078

OU Weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	41.2835153	13.7754579	0.0194717	0.0830299	27525.98063	35.7122525	49.9597488
prior	-13.6388157	4.3165686	0.0061015	0.0992767	1890.52593	-21.5471531	-7.5688246
alpha	4.2604272	4.4098640	0.0062334	0.3547219	154.55194	0.1307626	13.0623479
sigma^2	0.0632336	0.0605777	0.0000856	0.0117015	26.80038	0.0029137	0.1846570
shift number	0.8863359	0.9398395	0.0013285	0.0173897	2920.92708	0.0000000	3.0000000
N theta	1.8863359	0.9398395	0.0013285	0.0173897	2920.92708	1.0000000	4.0000000
root theta	1.0628151	0.0790345	0.0001117	0.0024745	1020.15246	0.9071124	1.2185394
root beta	0.5884737	0.0227734	0.0000322	0.0006632	1179.28354	0.5447026	0.6336061
all theta	1.0306371	0.4868995	NA	NA	NA	NA	NA
all beta	0.5931910	0.1673254	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	41.5112926	15.1526428	0.0214183	0.1079103	19717.46412	35.9587216	50.9632229
prior	-14.8072017	4.5998722	0.0065019	0.1174755	1533.19221	-23.2159396	-7.6044929
alpha	6.5957192	7.4787290	0.0105712	0.6444929	134.65402	0.1690026	21.1131089
sigma^2	0.0982441	0.1050929	0.0001485	0.0224355	21.94206	0.0035006	0.3049199
shift number	0.9375865	0.9927251	0.0014032	0.0205929	2323.92104	0.0000000	3.0000000
N theta	1.9375865	0.9927251	0.0014032	0.0205929	2323.92104	1.0000000	4.0000000
root theta	1.0684390	0.0821825	0.0001162	0.0025050	1076.35167	0.9122302	1.2245628
root beta	0.5873688	0.0235899	0.0000333	0.0006783	1209.47255	0.5432975	0.6302896
all theta	1.0416593	0.4914309	NA	NA	NA	NA	NA
all beta	0.5890748	0.1662890	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	41.4593996	3.6096713	0.0043122	0.1089838	1097.01189	35.8481951	50.5724231
prior	-14.1893126	4.5347975	0.0054174	0.0990316	2096.85432	-22.5942861	-7.5687857
alpha	5.5380599	6.3335626	0.0075663	0.4609355	188.80603	0.1310891	17.7483074
sigma^2	0.0818695	0.0862560	0.0001030	0.0148852	33.57929	0.0029077	0.2550722
shift number	0.9019543	0.9517985	0.0011370	0.0160179	3530.83604	0.0000000	3.0000000
N theta	1.9019543	0.9517985	0.0011370	0.0160179	3530.83604	1.0000000	4.0000000
root theta	1.0661482	0.0799066	0.0000955	0.0021172	1424.37666	0.9119163	1.2294966
root beta	0.5878956	0.0222287	0.0000266	0.0005490	1639.57971	0.5433200	0.6319634
all theta	1.0401616	0.4894724	NA	NA	NA	NA	NA
all beta	0.5901547	0.1660488	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	4.2604272	6.5957192	5.5380599
sigma squared	0.0632336	0.0982441	0.0818695
stationary variance	0.0074210	0.0074476	0.0073915
phylogenetic halflife	0.1626943	0.1050905	0.1251607
phylogenetic half life in units of tree height	0.0022286	0.0014395	0.0017145

BM

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	39.2152166	5.3639924	0.0075820	0.3038042	311.7373	36.7448552	41.1466455
prior	0.6788686	0.1204073	0.0001702	0.0043025	783.1856	0.6330636	0.7062662
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0011216	0.0287079	0.0000406	0.0007992	1290.1996	0.0001907	0.0004964
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	1.1952786	0.1189474	0.0001681	0.0033782	1239.7808	0.9562364	1.4226816
root beta	0.5441943	0.0294542	0.0000416	0.0006725	1918.4505	0.4873376	0.6020805
all theta	1.1952786	0.1189474	NA	NA	NA	NA	NA
all beta	0.5441943	0.0294542	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	39.2401535	5.2602146	0.0074353	0.2921217	324.2496	36.7917790	41.1481149
prior	0.6801823	0.1247115	0.0001763	0.0046029	734.0918	0.6372407	0.7062661
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.0000	0.0000010	0.0000010
sigma^2	0.0011499	0.0297980	0.0000421	0.0008503	1227.9455	0.0001909	0.0005005
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.0000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.0000	1.0000000	1.0000000
root theta	1.1881919	0.1198608	0.0001694	0.0034659	1195.9835	0.9607080	1.4220706
root beta	0.5460381	0.0290105	0.0000410	0.0006493	1996.5603	0.4887957	0.6019384
all theta	1.1881919	0.1198608	NA	NA	NA	NA	NA
all beta	0.5460381	0.0290105	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	39.5398235	1.3237531	0.0015814	0.0206836	4096.012	36.9633492	41.1481359
prior	0.6843679	0.0222519	0.0000266	0.0004679	2261.199	0.6398485	0.7062674
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.000	0.0000010	0.0000010
sigma^2	0.0003298	0.0000817	0.0000001	0.0000019	1931.510	0.0001955	0.0004949
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.000	1.0000000	1.0000000
root theta	1.1910668	0.1129721	0.0001350	0.0025704	1931.692	0.9652457	1.4101063
root beta	0.5454135	0.0279189	0.0000334	0.0005067	3036.491	0.4910910	0.6011421
all theta	1.1910668	0.1129721	NA	NA	NA	NA	NA
all beta	0.5454135	0.0279189	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	1.000000e-06	1.000000e-06	1.000000e-06
sigma squared	1.121600e-03	1.149900e-03	3.298000e-04
stationary variance	5.608190e+02	5.749726e+02	1.648884e+02
phylogenetic halflife	6.931472e+05	6.931472e+05	6.931472e+05
phylogenetic half life in units of tree height	9.494774e+03	9.494774e+03	9.494774e+03

Model Selection

Bayes Factors

	OU un-weighted predictor	OU weighted predictor	BM
OU un-weighted predictor	0.000000	2.781395	10.203771
OU weighted predictor	-2.781395	0.000000	7.422375
BM	-10.203771	-7.422375	0.000000

Medulla ~ Brain - Medulla

OU Un-weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	1.7522090	3.7995359	0.0053707	0.0776254	2395.81636	-4.5470349	10.0104748
prior	-22.4496164	7.5935414	0.0107335	0.1237780	3763.58437	-35.9808618	-7.5510880
alpha	1.8312202	5.4169974	0.0076570	0.3958960	187.22117	0.0018216	5.2534384
sigma^2	0.1965629	0.5648455	0.0007984	0.0604427	87.33156	0.0016171	0.5731199
shift number	3.2620115	1.8079498	0.0025555	0.0278850	4203.70457	0.0000000	6.0000000
N theta	4.2620115	1.8079498	0.0025555	0.0278850	4203.70457	1.0000000	7.0000000
root theta	0.0386984	0.1469366	0.0002077	0.0049100	895.55421	-0.2463257	0.3293682
root beta	2.0211784	0.0989513	0.0001399	0.0033985	847.73257	1.8246235	2.2197310
all theta	-0.0000263	0.5695715	NA	NA	NA	NA	NA
all beta	2.0143173	0.3559705	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	1.6152515	4.0382400	0.0057081	0.0762111	2807.6801	-4.7612341	9.9148239
prior	-22.3536421	7.3950545	0.0104530	0.1184226	3899.5440	-35.5151023	-7.5568869
alpha	1.6134493	2.4163646	0.0034155	0.1557324	240.7505	0.0077718	4.9349811
sigma^2	0.1748316	0.2657741	0.0003757	0.0228881	134.8354	0.0027762	0.5349240
shift number	3.1977419	1.7763906	0.0025109	0.0261610	4610.7304	0.0000000	6.0000000
N theta	4.1977419	1.7763906	0.0025109	0.0261610	4610.7304	1.0000000	7.0000000
root theta	0.0328168	0.1477508	0.0002088	0.0050882	843.2126	-0.2506327	0.3332717
root beta	2.0255728	0.0978225	0.0001383	0.0034046	825.5666	1.8298877	2.2177652
all theta	-0.0096880	0.5575420	NA	NA	NA	NA	NA
all beta	2.0231221	0.3577688	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	1.7491591	3.8474998	0.0045963	0.0681550	3186.8492	-4.7366259	10.1403367
prior	-22.3965279	7.5550059	0.0090254	0.1058632	5093.0693	-35.8767328	-7.5518260
alpha	1.8112893	4.8132570	0.0057501	0.3052256	248.6772	0.0016737	5.1942068
sigma^2	0.1947053	0.5049689	0.0006033	0.0434987	134.7647	0.0015708	0.5593491
shift number	3.2251050	1.8005597	0.0021510	0.0236563	5793.2264	0.0000000	6.0000000
N theta	4.2251050	1.8005597	0.0021510	0.0236563	5793.2264	1.0000000	7.0000000
root theta	0.0379746	0.1478402	0.0001766	0.0043464	1156.9536	-0.2504921	0.3326066
root beta	2.0219536	0.0985401	0.0001177	0.0029649	1104.5665	1.8254760	2.2181488
all theta	-0.0018032	0.5640189	NA	NA	NA	NA	NA
all beta	2.0164429	0.3569081	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	1.8312202	1.6134493	1.8112893
sigma squared	0.1965629	0.1748316	0.1947053
stationary variance	0.0536699	0.0541795	0.0537477
phylogenetic halflife	0.3785166	0.4296058	0.3826816
phylogenetic half life in units of tree height	0.0051849	0.0058848	0.0052420

OU Weighted Predictor

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	1.6870223	6.4239754	0.0090803	0.0806102	6350.79032	-4.5209183	9.7571172
prior	-22.8214888	8.0430091	0.0113688	0.1381083	3391.54429	-37.1071472	-7.5475393
alpha	0.8953529	0.7386092	0.0010440	0.0476398	240.37498	0.0050705	2.2895193
sigma^2	0.0937568	0.0717741	0.0001015	0.0233151	9.47674	0.0024696	0.2249473
shift number	3.4919511	1.9689116	0.0027831	0.0335574	3442.50539	0.0000000	7.0000000
N theta	4.4919511	1.9689116	0.0027831	0.0335574	3442.50539	1.0000000	8.0000000
root theta	0.0248345	0.1556828	0.0002201	0.0053766	838.43474	-0.2825694	0.3339287
root beta	2.0288008	0.1038741	0.0001468	0.0036624	804.42878	1.8130806	2.2263659
all theta	-0.0130095	0.5930876	NA	NA	NA	NA	NA
all beta	2.0217922	0.3737887	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	1.8445543	15.6968246	0.0221875	0.1206296	16932.28259	-4.6937270	10.1958533
prior	-22.7489227	8.3598458	0.0118167	0.1454702	3302.54166	-37.8490750	-7.5504050
alpha	0.2823932	0.2564308	0.0003625	0.0173332	218.86754	0.0029359	0.7942673
sigma^2	0.0289217	0.0233267	0.0000330	0.0080629	8.36999	0.0024580	0.0803564
shift number	3.7266799	2.0425844	0.0028872	0.0349737	3410.96417	0.0000000	7.0000000
N theta	4.7266799	2.0425844	0.0028872	0.0349737	3410.96417	1.0000000	8.0000000
root theta	0.0323440	0.1572310	0.0002222	0.0053410	866.63044	-0.2792059	0.3391053
root beta	2.0226985	0.1046363	0.0001479	0.0036066	841.73636	1.8171688	2.2287718
all theta	-0.0123135	0.6117893	NA	NA	NA	NA	NA
all beta	2.0166927	0.3750270	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	1.8177312	3.7712204	0.0045052	0.0766203	2422.56664	-4.6856370	10.0190088
prior	-22.6661914	8.0869967	0.0096610	0.1176754	4722.84043	-37.1673859	-7.5519056
alpha	0.6444566	0.6271871	0.0007493	0.0382279	269.17373	0.0031093	1.9495866
sigma^2	0.0673232	0.0619972	0.0000741	0.0187136	10.97568	0.0024284	0.2001058
shift number	3.5607389	1.9872417	0.0023740	0.0286543	4809.74818	0.0000000	7.0000000
N theta	4.5607389	1.9872417	0.0023740	0.0286543	4809.74818	1.0000000	8.0000000
root theta	0.0266911	0.1558989	0.0001862	0.0045077	1196.11490	-0.2792444	0.3398225
root beta	2.0273719	0.1044117	0.0001247	0.0031082	1128.44610	1.8109234	2.2274215
all theta	-0.0158730	0.5957897	NA	NA	NA	NA	NA
all beta	2.0223107	0.3721234	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	0.8953529	0.2823932	0.6444566
sigma squared	0.0937568	0.0289217	0.0673232
stationary variance	0.0523574	0.0512082	0.0522326
phylogenetic halflife	0.7741609	2.4545467	1.0755530
phylogenetic half life in units of tree height	0.0106045	0.0336225	0.0147330

BM

Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.

Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.

Summary Statistics

chain1

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	-3.1043191	4.9844194	0.0070455	0.3717504	179.77376	-5.6082686	-0.7790303
prior	0.0007215	0.5969700	0.0008438	0.0597636	99.77721	-1.0837300	0.7060184
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.00000	0.0000010	0.0000010
sigma^2	0.0046895	0.0451218	0.0000638	0.0021074	458.45575	0.0016114	0.0040762
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.00000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.00000	1.0000000	1.0000000
root theta	0.5914128	0.3553966	0.0005024	0.0282264	158.53195	-0.1616797	1.2283366
root beta	1.6128707	0.2279454	0.0003222	0.0230127	98.11330	1.2001830	2.0837462
all theta	0.5914128	0.3553966	NA	NA	NA	NA	NA
all beta	1.6128707	0.2279454	NA	NA	NA	NA	NA

chain2

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	-3.2260003	5.0025544	0.0070711	0.3792135	174.02681	-6.1554430	-0.7650817
prior	-0.1125735	0.7441400	0.0010518	0.0877217	71.96071	-1.6193891	0.7055136
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.00000	0.0000010	0.0000010
sigma^2	0.0044840	0.0399889	0.0000565	0.0015834	637.79695	0.0015618	0.0042720
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.00000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.00000	1.0000000	1.0000000
root theta	0.6250258	0.4270128	0.0006036	0.0403877	111.78477	-0.2627850	1.4495799
root beta	1.5974439	0.2674953	0.0003781	0.0315393	71.93302	1.0813234	2.1265179
all theta	0.6250258	0.4270128	NA	NA	NA	NA	NA
all beta	1.5974439	0.2674953	NA	NA	NA	NA	NA

combined chains

	Mean	SD	Naive SE	Time-series SE	Effective Size	HPD95Lower	HPD95Upper
lnL	-2.8217676	1.4453849	0.0017267	0.0513652	791.82508	-5.6473066	-0.7748568
prior	-0.0812564	0.6907863	0.0008252	0.0710773	94.45503	-1.4578125	0.7059570
alpha	0.0000010	0.0000000	0.0000000	0.0000000	0.00000	0.0000010	0.0000010
sigma^2	0.0027455	0.0006764	0.0000008	0.0000286	559.47729	0.0015901	0.0040769
shift number	0.0000000	0.0000000	0.0000000	0.0000000	0.00000	0.0000000	0.0000000
N theta	1.0000000	0.0000000	0.0000000	0.0000000	0.00000	1.0000000	1.0000000
root theta	0.6301677	0.3939463	0.0004706	0.0292737	181.10074	-0.2056259	1.3646437
root beta	1.5939555	0.2496945	0.0002983	0.0232804	115.03656	1.1096241	2.1067321
all theta	0.6301677	0.3939463	NA	NA	NA	NA	NA
all beta	1.5939555	0.2496945	NA	NA	NA	NA	NA

Shifts

No shifts were detected with a posterior probability above the cutoff.

OU parameters

	chain1	chain2	combined chains
alpha	1.000000e-06	1.000000e-06	1.000000e-06
sigma squared	4.689500e-03	4.484000e-03	2.745500e-03
stationary variance	2.344731e+03	2.241980e+03	1.372757e+03
phylogenetic halflife	6.931472e+05	6.931472e+05	6.931472e+05
phylogenetic half life in units of tree height	9.494774e+03	9.494774e+03	9.494774e+03

Model Selection

Bayes Factors

	OU un-weighted predictor	OU weighted predictor	BM
OU un-weighted predictor	0.000000	-38.11658	3.868261
OU weighted predictor	38.116580	0.00000	41.984840
BM	-3.868261	-41.98484	0.000000