Prokaryotes:

ap Aeropyrum pernix

at Agrobacterium tumefaciens

aa Aquifex aeolicus

af Archaeoglobus fulgidus

bh Bacillus halodurans

bs Bacillus subtilis

bm Brucella melitensis

cj Campylobacter jejuni

cc Caulobacter crescentus (vibroides)

cte Chlorobium tepidum

ca Clostridium acetobutylicum

cpe Clostridium perfringens

cg Corynebacterium glutamicum

dr Deinococcus radiodurans

ec Escherichia coli

fn Fusobacterium nucleatum

hi Haemophilus influenzae Rd

hsp Halobacterium sp.

hp Helicobacter pylori

ll Lactococcus lactis

ml Mesorhizobium loti

mt Methanobacterium thermoautotrophicum

mj Methanococcus jannaschii

mk Methanopyrus kandleri

ma Methanosarcina acetivorans

mma Methanosarcina mazei

mle Mycobacterium leprae

mtb Mycobacterium tuberculosis

nmm Neisseria meningitidis

nmz Neisseria meningitidis

ns Nostoc sp.

pm Pasteurella multocida

psa Pseudomonas aeruginosa

pa Pyrobaculum aerophilum

pab Pyrococcus abyssi

pag Pyrobaculum aerophilum

pf Pyrococcus furiosus

ph Pyrococcus horikoshii

rs Ralstonia solanacearum

sty Salmonella typhimurium

sm Sinorhizobium meliloti

sam Staphylococcus aureus

sp Streptococcus pyogenes

sco Streptomyces coelicolor

ss Sulfolobus solfataricus

st Sulfolobus tokodaii

sy Synechocystis sp.

tt Thermoanaerobacter tengcongensis

ta Thermoplasma acidophilum

tv Thermoplasma volcanium

tm Thermotoga maritima

vc Vibrio cholerae

xa Xanthomonas axonopodis pv citri

xc Xanthomonas campestris

xf Xylella fastidiosa

yp Yersinia pestis

Eukaryotes:

ath Arabidopsis thaliana

ce Caenorhabditis elegans

dm Drosophila melanogaster

hsa Homo sapien

sc Saccharomyces cerevisiae

Data Matrix Files:

neb9_160i.nex (no eukaryotes/big. 55 taxa. Figure 1a, b & c):

aa,af,ap,at,bh,bm,bs,ca,cc,cg,cj,cpe,cte,dr,ec,fn,hi,hp,hsp,ll,ma,mj,mk,ml,mle,mma,mt,

mtb,nmm,nmz,ns,pa,pab,pf,ph,pm,psa,rs,sam,sco,sm,sp,ss,st,sty,sy,ta,tm,tt,tv,vc,xa,xc,

xf,yp

euks_160i.nex (eukaryotes, plus archaeal outgroup. 8 taxa. Figure 4):

ap,ath,ce,dm,hsa,pag,sc,ss