#NEXUS

Begin taxa;
	dimensions ntax=5;
	taxlabels Btho Gvar Ggal Gson Glaf;
End;

[!
						############
						## README ##
						############

This file includes four sets of phylogenomic trees for the genus Gallus:
	I.   RAxML optimal trees
	II.  RAxML bootstrap trees
	III. ASTRAL trees based on estimated gene trees
	IV.  ASTRAL trees based on perfect transversions
(details below)
	
In all cases the full taxon names are: 
	Btho = Bambusicola thoracicus (Chinese bamboo partridge)
	Gvar = Gallus varius (Green junglefowl) ** outgroup **
	Ggal = Gallus gallus (Red junglefowl)
	Gson = Gallus sonneratii (Grey junglefowl)
	Glaf = Gallus lafayetii (Sri Lankan junglefowl)

Data types are:
	CNEE	= Conservered non-exon elements (2160 DNA segments)
	EXON	= Coding exons (27227 DNA segments)
	INTRON	= Introns (19186 DNA segments)
	UCE		= Ultraconserved elements plus flanking regions (3660)
	
You may wish to rename this file with the extension .nex or .tre

This NEXUS treefile will execute in PAUP* and it can be displayed
using FigTree. If you have difficulties displaying the treefile use
one of those programs, which can be downloaded from the following
websites: 

FigTree -- https://github.com/rambaut/figtree/releases
PAUP*   -- https://paup.phylosolutions.com/

---

I.   Optimal trees generated using RAxML with concatenated data
	CNEE	= 1,089,711 sites
	EXON	= 8,563,560 sites
	INTRON	= 16,769,794 sites
	UCE		= 7,331,812 sites
	ALL		= 33,754,877 sites

II.  ML bootstrap trees generated using RAxML with concatenated data

	Generated using the same data matrices as treeset I. Trees are rooted between Btho
	and Gallus species. Branch lengths are identical to treeset I, although the root
	has been placed along the Btho branch (which has been bisected). Bootstrap support
	is presented as labels for each branch. 

III. Trees generated by ASTRAL using gene trees as input

	EXON	= ML gene trees from the 102 exons with at least 10 PI sites
	INTRON	= ML gene trees from the 2549 introns with at least 10 PI sites
	UCE		= ML gene trees from the 784 UCE alignments with at least 10 PI sites
	ALL		= ML gene trees from all UCEs with at least 10 PI sites, and for each gene 
			  with an exon or intron with at least 10 PI sites, the ML tree from the 
			  region with the most sites (3406 total trees)
			  
	Note: PI sites = parsimony informative sites
	
	Branch lengths are in coalescent units and support values are local posteriors.

IV.  Trees generated by ASTRAL using individual "perfect" transversions as input
	
	The concatenated alignments for each data types were reduced to informative sites
	with no missing data and a maximum of two character states. Then the sites were 
	coded as partially resolved gene trees:
	
		00111 = (Btho,Gvar,(Ggal,Gson,Glaf));
		01011 = (Btho,Ggal,(Gvar,Gson,Glaf));
		01101 = (Btho,Gson,(Gvar,Ggal,Glaf));
		01110 = (Btho,Glaf,(Gvar,Ggal,Gson));
		00011 = (Btho,Gvar,Ggal,(Gson,Glaf));
		00110 = (Btho,Gvar,Glaf,(Ggal,Gson));
		01100 = (Btho,Gson,Glaf,(Gvar,Ggal));
		01010 = (Btho,Ggal,Glaf,(Gvar,Gson));
		01001 = (Btho,Ggal,Gson,(Gvar,Glaf));
		00101 = (Btho,Gvar,Gson,(Ggal,Glaf));
		
	Where the first 0 in the bipartition string represents the state in Btho (either R
	or Y) and subsequent 0/1 indicators provide information regarding the state in the
	junglefowl. The taxon order in all binary strings is Btho Gvar Ggal Gson Glaf
	
	Data types are indicated and the perfect transversions were extracted. The number of
	perfect transversions for each data type is:
	
	ALL     = perfect transversions extracted from all data types below
	CNEE	= 103 perfect transversions
	EXON	= 2,284 perfect transversions
	INTRON	= 28,238 perfect transversions
	UCE		= 5,295 perfect transversions

	All numbers of sites listed above assume all five taxa are included, excluding taxa
	will reduce the number parsimony informative transversions
	
	Branch lengths are in coalescent units and support values are local posteriors.
]

Begin trees;
	tree ALL_RAxML_bestTree    = [&U] (((Glaf:0.00369989197499028585,Gson:0.00363094145484307200):0.00166146404234831873,Ggal:0.00527018741968782699):0.00141315010531245424,Btho:0.03782516256917587555,Gvar:0.00575280483515928573):0.0;
	tree CNEE_RAxML_bestTree   = [&U] (Btho:0.00774437052311374111,((Glaf:0.00076606899120314860,Gson:0.00081319354563118133):0.00013030949365307754,Ggal:0.00106886477459915532):0.00013738956283216441,Gvar:0.00127793272738475905):0.0;
	tree EXON_RAxML_bestTree   = [&U] (((Glaf:0.00207176375836249467,Gson:0.00198155511172665340):0.00081004143659164538,Ggal:0.00276182508601778088):0.00077733230306853873,Btho:0.01969710049897555049,Gvar:0.00305827156234978869):0.0;
	tree INTRON_RAxML_bestTree = [&U] (Btho:0.05253730469114323981,((Glaf:0.00495433270315775044,Gson:0.00478552928148973274):0.00239944663546075689,Ggal:0.00719938623007498630):0.00185650074247134859,Gvar:0.00783229622529998254):0.0;
	tree UCE_RAxML_bestTree    = [&U] (((Gson:0.00283141155057237571,Glaf:0.00270105751629770487):0.00094319662258316968,Ggal:0.00366828308049879735):0.00095295549391772520,Btho:0.02830105320389648613,Gvar:0.00422695790313780146):0.0;

	tree ALL_MLbootstrap    = [&U] (Btho:0.0189126,(((Glaf:0.00369989197499028585,Gson:0.00363094145484307200)100:0.00166146404234831873,Ggal:0.00527018741968782699)100:0.00141315010531245424,Gvar:0.00575280483515928573)100:0.0189126)100;
	tree CNEE_MLbootstrap   = [&U] (Btho:0.00387219,(((Glaf:0.00076606899120314860,Gson:0.00081319354563118133)91:0.00013030949365307754,Ggal:0.00106886477459915532)99:0.00013738956283216441,Gvar:0.00127793272738475905)100:0.00387219)100;
	tree EXON_MLbootstrap   = [&U] (Btho:0.00984855,(((Glaf:0.00207176375836249467,Gson:0.00198155511172665340)89:0.00081004143659164538,Ggal:0.00276182508601778088)62:0.00077733230306853873,Gvar:0.00305827156234978869)100:0.00984855)100;
	tree INTRON_MLbootstrap = [&U] (Btho:0.0262687,(((Glaf:0.00495433270315775044,Gson:0.00478552928148973274)100:0.00239944663546075689,Ggal:0.00719938623007498630)98:0.00185650074247134859,Gvar:0.00783229622529998254)100:0.0262687)100;
	tree UCE_MLbootstrap    = [&U] (Btho:0.0141505,(((Gson:0.00283141155057237571,Glaf:0.00270105751629770487)100:0.00094319662258316968,Ggal:0.00366828308049879735)100:0.00095295549391772520,Gvar:0.00422695790313780146)100:0.0141505)100;

	tree ALL_ASTRALgt    = [&U] (Gson,((Ggal,(Gvar,Btho)1:0.5070172113703065)1:0.6680752202284066,Glaf):0.0); 
	tree EXON_ASTRALgt   = [&U] (Gvar,(Btho,(Ggal,(Gson,Glaf)1:0.2876820724517809)1:0.618345967477247):0.0); 
	tree INTRON_ASTRALgt = [&U] (Ggal,((Gvar,Btho)1:0.49285088672814054,(Gson,Glaf)1:0.7266431349881274):0.0); 
	tree UCE_ASTRALgt    = [&U] (Gson,((Ggal,(Gvar,Btho)1:0.5382688310625939)1:0.533370862087047,Glaf):0.0); 

	tree ALL_ASTRALtv    = [&U] (Btho,(Gvar,((Gson,Glaf)1:0.4618446105738479,Ggal)1:0.4254448156830442):0.0); 
	tree CNEE_ASTRALtv   = [&U] (Btho,(Gvar,((Gson,Glaf)1:0.4874782597689995,Ggal)1:0.838329190404443):0.0); 
	tree EXON_ASTRALtv   = [&U] (Btho,(Gvar,(Ggal,(Glaf,Gson)1:0.3788585646634521)1:0.5111859192121511):0.0); 
	tree INTRON_ASTRALtv = [&U] (Btho,(Gvar,((Gson,Glaf)1:0.48211288400998425,Ggal)1:0.39974365760567765):0.0);
	tree UCE_ASTRALtv    = [&U] (Btho,((Ggal,(Gson,Glaf)1:0.39156220293917304)1:0.5258894579643181,Gvar):0.0); 
End;