0.2 
0.2 0.2 
1 4 500 
254 36 98 11 
0.2 154 262 0.2 0.2 
0.2 0.2 183 862 0.2 262 
200 0.2 121 12 81 3 44 
0.2 41 180 0.2 12 314 15 0.2 
26 2 21 7 63 11 7 3 0.2 
4 2 13 1 79 16 2 1 6 515 
0.2 209 467 2 0.2 349 106 0.2 0.2 3 4 
121 5 79 0.2 312 67 0.2 56 0.2 515 885 106 
13 5 20 0.2 184 0.2 0.2 1 14 118 263 11 322 
49 0.2 17 0.2 0.2 39 8 0.2 1 0.2 12 17 5 15 
673 3 398 44 664 52 31 226 11 7 8 144 112 36 87 
244 0.2 166 0.2 183 44 43 0.2 19 204 48 70 289 14 47 660 
0.2 0.2 8 0.2 22 7 11 2 0.2 0.2 21 16 71 54 0.2 2 0.2 
1 4 251 0.2 72 87 8 9 191 12 20 117 71 792 18 30 46 38 
340 0.2 23 0.2 350 0.2 14 3 0.2 1855 85 26 281 52 32 61 544 0.2 2 

0.054116 0.018227 0.039903 0.020160 0.009709 0.018781 0.024289 0.068183 0.024518 0.092638 
0.148658 0.021718 0.061453 0.088668 0.041826 0.091030 0.049194 0.029786 0.039443 0.057700 



// this is the end of the file. The rest are notes. 

Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 

This model has been derived from 36 artropoda mitochondrial genomes. 

Each gene of the given species was aligned individually. Then, alignments of the whole set 
of 13 genes where concatenated and passed through GBlocks (Castresana, 2000, in JME) with 
parameters and output: 

Minimum Number Of Sequences For A Conserved Position: 20 
Minimum Number Of Sequences For A Flanking Position: 32 
Maximum Number Of Contiguous Nonconserved Positions: 8 
Minimum Length Of A Block: 10 
Allowed Gap Positions: With Half 
Use Similarity Matrices: Yes 

Flank positions of the 40 selected block(s) 
Flanks: [6 22] [26 44] [61 70] [77 143] [145 185] [208 236] [309 640] 
[644 802] [831 941] [956 966] [973 1062] [1085 1339] [1343 1702] 
[1754 1831] [1840 1911] [1916 1987] [2011 2038] [2097 2118] [2125 2143] 
[2179 2215] [2243 2268] [2277 2288] [2333 2347] [2476 2518] [2539 2558] 
[2600 2613] [2637 2672] [2738 2759] [2784 2839] [2882 2924] [2948 3097] 
[3113 3123] [3210 3235] [3239 3322] [3348 3392] [3406 3526] [3588 3617] 
[3660 3692] [3803 3830] [3909 3928] 

New number of positions in MtArt-strict.phy.fasta-gb: <b> 2664 </b> (67% of the original 3933 positions) 

The species included in the analysis were: 
Harpiosquilla harpax [NCBI_TaxID 287944] 
Ixodes uriae [NCBI_TaxID 59655] 
Heptathela hangzhouensis [NCBI_TaxID 216259] 
Triops longicaudatus [NCBI_TaxID 58777] 
Gryllotalpa orientalis [NCBI_TaxID 213494] 
lepidopsocid RS-2001 [NCBI_TaxID 159971] 
Locusta migratoria [NCBI_TaxID 7004] 
Drosophila yakuba [NCBI_TaxID 7245] 
Ostrinia furnacalis [NCBI_TaxID 93504] 
Megabalanus volcano [NCBI_TaxID 266495] 
Periplaneta fuliginosa [NCBI_TaxID 36977] 
Thermobia domestica [NCBI_TaxID 89055] 
Aleurochiton aceris [NCBI_TaxID 266942] 
Schizaphis graminum [NCBI_TaxID 13262] 
Pteronarcys princeps [NCBI_TaxID 285953] 
Aleurodicus dugesii [NCBI_TaxID 30099] 
Pollicipes polymerus [NCBI_TaxID 36137] 
Gomphiocephalus hodgsoni [NCBI_TaxID 221270] 
Habronattus oregonensis [NCBI_TaxID 130930] 
Speleonectes tulumensis [NCBI_TaxID 84346] 
Hutchinsoniella macracantha [NCBI_TaxID 84335] 
Haemaphysalis flava [NCBI_TaxID 181088] 
Scutigera coleoptrata [NCBI_TaxID 29022] 
Vargula hilgendorfii [NCBI_TaxID 6674] 
Tricholepidion gertschi [NCBI_TaxID 89825] 
Varroa destructor [NCBI_TaxID 109461] 
Bombyx mandarina [NCBI_TaxID 7092] 
Thyropygus sp. [NCBI_TaxID 174155] 
Tribolium castaneum [NCBI_TaxID 7070] 
Pagurus longicarpus [NCBI_TaxID 111067] 
Limulus polyphemus [NCBI_TaxID 6850] 
Tetrodontophora bielanensis [NCBI_TaxID 48717] 
Penaeus monodon [NCBI_TaxID 6687] 
Daphnia pulex [NCBI_TaxID 6669] 
Apis mellifera [NCBI_TaxID 7469] 
Anopheles gambiae [NCBI_TaxID 7165] 

The topology used for inferring the model was: 

(((Daph_pulex,Trio_longi),((((((Aleu_aceri,Aleu_duges),Schi_grami),lepi_RS_20), 
((((Ostr_furna,Bomb_manda),(Dros_yakub,Anop_gambi)),Apis_melli),Trib_casta)), 
((Gryl_orien,Locu_migra),(Pter_princ,Peri_fulig))),(Tric_gerts,Ther_domes)), 
(Scut_coleo,Thyr_sp),Varg_hilge,Hutc_macra,((((Ixod_uriae,Haem_flava),Varr_destr), 
(Habr_orego,Hept_hangz)),Limu_polyp),(Poll_polym,Mega_volca),(Gomp_hodgs,Tetr_biela), 
((Pagu_longi,Pena_monod),Harp_harpa),Spel_tulum)); 

Note this is not the ML topology but the consensus one (based on morphological data, 
phylogenetic reconstruction using nuclear genes, etc). Where relationships are 
not clear, a polytomy was introduced (it contains quite a lot of polytomies!). 

The model was estimated using Ziheng Yang's Paml software package. 
A four-categorized gamma distribution was used to account for heterogeneity (alpha 
was estimated to be 0.47821). Sites with ambiguity data were taken into account.


Reference

Abascal, F., D. Posada, and R. Zardoya. 2007. MtArt: A new Model of
amino acid replacement for Arthropoda. Mol. Biol. Evol. 24:1-5.