#NEXUS

[Supplementary Software 1 | PAUP*-formatted version of our presence/absence matrix.]

[The coding of character states is “1” (presence), “0” (absence), and “?” (unspecific deletion or missing data). Presence/absence information for Alcedo + Picus, Tachybaptus/Podiceps + Phoenicopterus, and Apus + Chrysolampis was each added up and each coded as one chimaeric taxon (AnP, TnP, AnC). The order of the markers (char1 to char51) corresponds to Supplementary Table S1 and the alligator was used as outgroup for the six bird monophyly markers (char1 to char6). Taxon labels are Tgu (Taeniopygia), Ach (Acanthisitta), Nno (Nestor), Fsp (Falco), Ccr (Cariama), Aot (Asio), AnP (Alcedo + Picus), Tvi (Trogon), Bla (Buteo), Cau (Cathartes), Uma (Urocolius), Cci (Ciconia), Lri (Larus), Bpa (Balearica), Cre (Carpococcyx/Cuculus), Cpa (Columba), TnP (Tachybaptus/Podiceps + Phoenicopterus), Oho (Opisthocomus), AnC (Apus + Chrysolampis), Gga (Gallus), Ala (Alectura), Acr (Anas), Dvi (Dendrocygna), Dno (Dromaius), Eel (Eudromia), Ppe (Pterocnemia), Sca (Struthio), Ami (Alligator).]
BEGIN DATA;
DIMENSIONS NTAX=28 NCHAR=51;
FORMAT TRANSPOSE;
TAXLABELS Tgu Ach Nno Fsp Ccr Aot AnP Tvi Bla Cau Uma Cci Lri Bpa Cre Cpa TnP Oho AnC Gga Ala Acr Dvi Dno Eel Ppe Sca Ami;
MATRIX
char1  1????????1?????1???1???1???0
char2  1??????????????????1???1???0
char3  1????????1?1???1???????1???0
char4  1??????????????????????1??10
char5  1??????????????????1???1???0
char6  1????????1?1???????1???1???0
char7  1??1?????1?11??11??1?11?0?0?
char8  1??????????????1???1?1??0?0?
char9  1??????????1???????1?1????0?
char10 1??????????1???????1??1?0?0?
char11 1??????????1???????1???0????
char12 0??????????????????0???1111?
char13 0??????????????????0???1111?
char14 0??????????0???????0???1??1?
char15 0??????????0???????0???1111?
char16 1????111111111111110?00?????
char17 1????11111?1111?11100?0???0?
char18 1????111111111111110?0??????
char19 1????111111111111110?0??????
char20 1??1?1??111111111110????????
char21 1??1?11111?111111110??0?0?0?
char22 0??????????????0???1?1??0?0?
char23 0??????????0???????1?1100???
char24 0??????????0???0??0111100???
char25 0??????????0???????111??????
char26 11111111111000010000????????
char27 1?1101?0000010000100???00???
char28 1?111000000100000000????????
char29 1?1111?1000101010100???0????
char30 1?11111111100?0?0000????????
char31 1?111111111000000000?0?0????
char32 1?111111110000000000????????
char33 1?111111110000000000????????
char34 11111000000000000000????????
char35 11111000000000000000????????
char36 11110000000000000000????????
char37 1111000000000000000?????????
char38 11110000000000000000????????
char39 11110000000000000000????????
char40 11110000000000000000????????
char41 1111000?000000000000????????
char42 11110000000000000000????????
char43 11100000000000000000????????
char44 1110000000?000000000????????
char45 11100000000000000000????????
char46 1100??0??0?0??0????0????????
char47 1100??0??0?0??0????0????????
char48 1100??0?00?0??00???0????????
char49 1100??0??0?0??0????0????????
char50 1100??0??0?0??0????0????????
char51 1100??0??0?0??0????0????????
;
END;
BEGIN ASSUMPTIONS;
OPTIONS DEFTYPE=irrev.up;
END;
BEGIN PAUP;
OUTGROUP Ami;
SET CRIT=PARSIMONY;
SET INCREASE=AUTO;
END;