GMYC

I encourage you to try both GMYC and PTP model on your data. They are based on quite different models, but if they give you similar delimitations, you can be more confident on the results.


Please check your results of the multiple threshold carefully. It may not improve the accuracy.

Tomochika


Result of GMYC species delimitation

method:	single
	likelihood of null model:	199.2683
	maximum likelihood of GMYC model:	202.0255
	likelihood ratio:	5.514433
	result of LR test:	0.06346818n.s.

	number of ML clusters:	7
	confidence interval:	5-7

	number of ML entities:	26
	confidence interval:	24-29

	threshold time:	-0.001406113
	
method:	multiple
	likelihood of null model:	199.2683
	maximum likelihood of GMYC model:	202.1168
	likelihood ratio:	5.696963
	result of LR test:	0.05793224n.s.

	number of ML clusters:	10
	confidence interval:	3-10

	number of ML entities:	21
	confidence interval:	6-24

	threshold time:	 -0.03297807 -0.008179366 -0.003152912 -0.0002821189

############################################################################################
PTP

# Max likilhood partition 
Species 1 (support = 0.852)
     Centrolene_charapita_AJC2732,Centrolene_charapita_MHNC_13933

Species 2 (support = 1.000)
     Centrolene_daidaleum

Species 3 (support = 1.000)
     Centrolene_savagei_MHUA_4094

Species 4 (support = 1.000)
     Centrolene_aff_savagei_MAR_1152

Species 5 (support = 1.000)
     Centrolene_geckoideum

Species 6 (support = 1.000)
     Centrolene_condor_Q_44896

Species 7 (support = 1.000)
     Centrolene_heloderma_Q_40200

Species 8 (support = 0.999)
     Centrolene_bacatum

Species 9 (support = 0.993)
     Centrolene_hesperium_MHNSM_25802

Species 10 (support = 0.993)
     Centrolene_muelleri_PV

Species 11 (support = 0.993)
     Centrolene_lynchi

Species 12 (support = 0.994)
     Centrolene_hybrida_MAR_347

Species 13 (support = 0.994)
     Centrolene_pipilatum_KU_178154

Species 14 (support = 0.588)
     Centrolene_sabini,Centrolene_sabini_MUSM_28018

Species 15 (support = 0.613)
     Centrolene_sp_MRy_547,Centrolene_sp_MRy_548

Species 16 (support = 0.987)
     Centrolene_antioquiense_NRPS_014

Species 17 (support = 0.987)
     Centrolene_peristictum

Species 18 (support = 0.511)
     Centrolene_sp_Yanayacu_Q_25744,Centrolene_sp_Yanayacu_Q_25746,Centrolene_sp_Yanayacu_Q_25745

Species 19 (support = 0.997)
     Centrolene_huilense_Q_37230

Species 20 (support = 0.997)
     Centrolene_muelleri

Species 21 (support = 0.951)
     Centrolene_buckleyi_KU_178031,Centrolene_buckleyi_MZUTI_763

Species 22 (support = 0.987)
     Centrolene_ballux

Species 23 (support = 0.466)
     Centrolene_aff_buckleyi_MAR_371

Species 24 (support = 0.452)
     Centrolene_venezuelense,Centrolene_venezuelense_EBRG_5244

Species 25 (support = 0.782)
     Centrolene_altitudinale,Centrolene_altitudinale_MHNLS_17194

Species 26 (support = 0.807)
     Centrolene_notostictum_MAR_510


# Most supported partition found by simple heuristic search
Species 1 (support = 0.852)
     Centrolene_charapita_AJC2732,Centrolene_charapita_MHNC_13933

Species 2 (support = 1.000)
     Centrolene_daidaleum

Species 3 (support = 1.000)
     Centrolene_savagei_MHUA_4094

Species 4 (support = 1.000)
     Centrolene_aff_savagei_MAR_1152

Species 5 (support = 1.000)
     Centrolene_geckoideum

Species 6 (support = 1.000)
     Centrolene_condor_Q_44896

Species 7 (support = 1.000)
     Centrolene_heloderma_Q_40200

Species 8 (support = 0.999)
     Centrolene_bacatum

Species 9 (support = 0.997)
     Centrolene_huilense_Q_37230

Species 10 (support = 0.997)
     Centrolene_muelleri

Species 11 (support = 0.993)
     Centrolene_hesperium_MHNSM_25802

Species 12 (support = 0.994)
     Centrolene_hybrida_MAR_347

Species 13 (support = 0.994)
     Centrolene_pipilatum_KU_178154

Species 14 (support = 0.993)
     Centrolene_muelleri_PV

Species 15 (support = 0.993)
     Centrolene_lynchi

Species 16 (support = 0.987)
     Centrolene_antioquiense_NRPS_014

Species 17 (support = 0.987)
     Centrolene_peristictum

Species 18 (support = 0.951)
     Centrolene_buckleyi_KU_178031,Centrolene_buckleyi_MZUTI_763

Species 19 (support = 0.987)
     Centrolene_ballux

Species 20 (support = 0.511)
     Centrolene_sp_Yanayacu_Q_25744,Centrolene_sp_Yanayacu_Q_25746,Centrolene_sp_Yanayacu_Q_25745

Species 21 (support = 0.588)
     Centrolene_sabini,Centrolene_sabini_MUSM_28018

Species 22 (support = 0.613)
     Centrolene_sp_MRy_547,Centrolene_sp_MRy_548

Species 23 (support = 0.466)
     Centrolene_aff_buckleyi_MAR_371

Species 24 (support = 0.452)
     Centrolene_venezuelense,Centrolene_venezuelense_EBRG_5244

Species 25 (support = 0.782)
     Centrolene_altitudinale,Centrolene_altitudinale_MHNLS_17194

Species 26 (support = 0.807)
     Centrolene_notostictum_MAR_510


Accptance rate: 0.15359500000000001 
Merge: 100040 
Split: 99960 
Estimated number of species is between 16 and 29 
Mean: 24.79