### INPUT SUMMARY ###

Integer Code	Taxon Name
1:	Scincella_lateralis_LMZ99209
2:	Prasinohaema_virens_CCA02661
3:	Prasinohaema_semoni_CCA00900
4:	Fojia_bumui_CCA15922
5:	Prasinohaema_sp_nov_CCA01623
6:	Lipinia_longiceps_CCA15866
7:	Lipinia_pulchra_CCA03201
8:	Lipinia_albodorsale_CCA03500
9:	Lipinia_noctua_CCA16819
10:	Papuascincus_stanleyanus_cf_sp2_CCA02483
11:	Papuascincus_sp_nov_CCA05980
12:	Prasinohaema_prehensicauda_CCA17222
13:	Lobulia_elegans_CCA17485
14:	Lobulia_brongersmai_CCA03482
15:	Prasinohaema_flavipes_CCA17083
16:	Prasinohaema_sp_nov_CCA01005

The original species tree (smoothed, in coalescent units) is:
 (((4:7.33258,((((8:6.15616,((10:4.95866,((19:4.11805,(26:3.15309,27:3.15309)1:0.964956)1:0.682207,((28:2.74163,29:2.74163)1:1.7487,20:4.49033)1:0.309928)1:0.15841)1:1.00512,(11:4.16198,12:4.16198)1:1.80181)1:0.192372)1:0.183322,(((13:4.3182,(15:2.89732,16:2.89732)1:1.42089)1:1.29828,(((((((39:3.00753,(42:2.11104,43:2.11104)1:0.896488)1:0.903868,(40:2.81178,41:2.81178)1:1.09961)1:0.478843,(35:3.75158,36:3.75158)1:0.638659)1:0.0439519,30:4.43419)1:0.201504,((34:2.98152,(37:2.21902,38:2.21902)1:0.762497)1:0.980829,31:3.96235)1:0.673345)1:0.305846,((32:4.27606,33:4.27606)1:0.379797,21:4.65586)1:0.285684)1:0.263966,(17:5.19551,18:5.19551)1:0.01)1:0.41098)1:0.379797,(9:5.87242,(14:5.8316,((22:0.348878,23:0.348878)1:5.116,(24:5.03101,25:5.03101)1:0.433865)1:0.366725)1:0.040822)1:0.123864)1:0.343195)1:0.341083,5:6.68056)1:0.146183,(6:6.62156,7:6.62156)1:0.205181)1:0.505838)1:0.976837,3:8.30942)1:3.79424,1:12.1037,2:12.1037);

The pruned species tree (smoothed, in coalescent units) is:
 (((((((12:1.65677,(15:0.760283,16:0.760283)1:0.896488)1:0.903868,(13:1.46103,14:1.46103)1:1.09961)1:0.478843,(8:2.40082,9:2.40082)1:0.638659)1:0.0439519,3:3.08343)1:0.201504,((7:1.63076,(10:0.868267,11:0.868267)1:0.762497)1:0.980829,4:2.61159)1:0.673345)1:0.305846,((5:2.9253,6:2.9253)1:0.379797,2:3.3051)1:0.285684)1:0.263966,1:3.85475);

Regression intercept: 0.30377050367407216
Regression slope: 157.03679941027934
X (newick internals): 0.0012815673,0.0012959372,0.00317694,0.0009191566,0.0005512292,0.0033454018,0.006213709,0.0008194166,0.0010506679,0.0044981643,0.0067480232,0.001177928,0.0016731052,0.0018396006,0.0010984448,0.001227387,0.0001867431,0.0003797236,0.0015157275,0.0023765815,0.0019695856,0.00089597,0.0014684489,0.0011949237,0.0008826657,0.0004222465,0.0018758717,0.0021606072,0.0105833069,0.0017497148,0.0016005032,0.0006072962,0.0008366136,0.0022098351,0.0023517881,0.0015025786,0.0010217403,0.0047967637,0.0127776757,0.0269538886
Y (coalescent internals): 0.9649559038554361,0.6822072405216106,1.748699979767608,0.30992768139910065,0.1584097367476418,1.0051219455807703,1.8018098050815567,0.19237189264745602,0.18332205712753824,1.4208858058895102,1.298283483797177,0.8964881045779753,0.9038682118755978,1.0996127890016933,0.47884257791294005,0.6386589952758757,0.04395188752918294,0.2015043762107287,0.7624972586947387,0.9808292530117262,0.6733445532637656,0.30584604307945207,0.37979736135958664,0.2856840697891079,0.26396554583446485,0.01,0.41098028879627446,0.37979736135958664,5.1159958097540805,0.43386458262986227,0.3667252797922337,0.04082199452025509,0.12386398722238601,0.3431947823820397,0.3410828491788962,0.14618251017808126,0.20518085094003735,0.5058380822549515,0.9768372317421892,3.7942399697717617
                    ____________ 12*
            _______|
           |       |       _____ 15*
           |       |______|
        ___|              |_____ 16*
       |   |
       |   |         ____________ 13
       |   |________|
       |            |____________ 14
       |
      _|      __________________ 8
     | |_____|
     | |     |__________________ 9
     | |
    _| |________________________ 3*
   | |
   | |              ____________ 7
   | |      _______|
   | |     |       |      ______ 10
   | |_____|       |_____|
  _|       |             |______ 11
 | |       |
 | |       |____________________ 4
 | |
 | |     _______________________ 5*
_| |  __|
 | |_|  |_______________________ 6
 |   |
 |   |__________________________ 2*
 |
 |______________________________ 1

6 taxa have the derived state: 12, 15, 16, 3, 5, 2

With homoplasy only, 4 mutations are required to explain this trait pattern (Fitch parsimony)


1.00e+08 simulations performed


### RESULTS ###
2042 loci matched the species character states

"True" hemiplasy (1 mutation) occurs 726 time(s)

Combinations of hemiplasy and homoplasy (1 < # mutations < ____) occur 1316 time(s)

"True" homoplasy (>= ______ mutations) occurs 0 time(s)

2042 loci have a discordant gene tree

0 loci are concordant with the species tree

0 loci originate from an introgressed history

2042 loci originate from the species history

Distribution of mutation counts:

# Mutations	# Trees
On all trees:
1		726
2		1316

On concordant trees:

On discordant trees:
1		726
2		1316


Origins of mutations leading to observed character states for hemiplasy + homoplasy cases:

	Tip mutation	Internal branch mutation	Tip reversal
Taxa 2	0	1316	0
Taxa 3	0	1316	0
Taxa 5	0	1316	0
Taxa 12	0	1316	0
Taxa 15	0	1316	0
Taxa 16	0	1316	0
