README

This directory contains input files for analyses executed in 

Species tree analysis: SNAPP_input.xml
Population assignment: STRUCTURE_input.txt
Maximum likelihood UCEs: S_File_2_UCE_incomplete_matrix_alignment_labeled.phylip
Maximum likelihood mtDNA: S_File_3_mtDNA_prot_cod_reg_alignment_labeled.phylip
Maximum likelihood mtDNA partitions: S_File_4_mtDNA_partitions_for_RAxML.txt
Mapping files used in ABBA/BABA analyses: bams_for_abba_baba.zip

SNP calling final files:

vcf recoded to 012
snps_call_for_STRUCTURE_SNAPP.012
snps_call_for_STRUCTURE_SNAPP.012.indv
snps_call_for_STRUCTURE_SNAPP.012.pos

Nexus Matrix 
snps_call_for_STRUCTURE_SNAPP.nex

SNP called as vcf
snps_call_for_STRUCTURE_SNAPP.vcf
snps_call_for_STRUCTURE_SNAPP.vcf.idx

BAm files use short IDs for individuals. The table below shows the corresponding name used in the other analyses


ult_ult_hui_01	FMNH	A_ultramarina	ultramarina	393674
ult_ult_hui_02	FMNH	A_ultramarina	ultramarina	393675
utl_col_say_01	FMNH	A_ultramarina	colimae	343585
utl_col_say_02	FMNH	A_ultramarina	colimae	343586
wol_ari_ca	FMNH	A_wollweberi	arizonae	343516
wol_ari_pb_01	FMNH	A_wollweberi	arizonae	334259
wol_ari_pb_02	FMNH	A_wollweberi	arizonae	334261
wol_ari_pb_03	FMNH	A_wollweberi	arizonae	334264
wol_cou_cb	CTR	A_wollweberi	couchii	05J0230
wol_cou_dp_01	FMNH	A_wollweberi	couchii	343534
wol_cou_dp_02	FMNH	A_wollweberi	couchii	393651
wol_cou_vc	CTR	A_wollweberi	couchii	04J0128
wol_gra_vg	FMNH	A_wollweberi	gracilis	343520
wol_pot_bl_01	FMNH	A_wollweberi	potosina	343552
wol_pot_bl_02	FMNH	A_wollweberi	potosina	393663
wol_pot_ja_01	FMNH	A_wollweberi	potosina	393655
wol_pot_ja_02	FMNH	A_wollweberi	potosina	393662
wol_wol_ej_01	FMNH	A_wollweberi	wollweberi	343570
wol_wol_ej_02	FMNH	A_wollweberi	wollweberi	393742
wol_wol_ga_01	UNAM	A_wollweberi	wollweberi	Conacyt340
wol_wol_ga_02	UNAM	A_wollweberi	wollweberi	Conacyt360
wol_wol_sa_01	CTR	A_wollweberi	wollweberi	02N9800
wol_wol_sa_02	CTR	A_wollweberi	wollweberi	02N9802
wol_wol_va	FMNH	A_wollweberi	wollweberi	343575
nevadae	FMNH	Aphelocoma californica	nevadae	334087


For questions contact eugenia.zarza@gmail.com