Online Resource 1. List of all sequences involved in the phylogenetic analyses, including the GenBank accession numbers for the rbcL, coxIII and trnGucc genes. Strain number abbreviations: ACOI - Coimbra Collection of Algae, Portugal; ACKU - Algal Culture Collection of Kyonggi University, Kyonggi, Korea; CCAP - Culture Collection of Algae and Protozoa, Oban, Scotland, UK; JH - John Hall private collection; M - Culture Collection Melkonian, University of Cologne, Germany (strains available from CCAC); NIES - National Institute for Environmental Studies, Japan; SAG - Sammlung von Algenkulturen der UniversitätGöttingen, Germany; SVCK - Sammlung von Conjugaten-Kulturen, Germany; UTEX - Culture Collection of Algae at University of Texas, USA.

GenBank accession numbers
Taxon name / Strain number / rbcL / coxIII / trnG
Actinotaenium cruciferum(De Bary) Teiling / M2025 / AM911235 / - / -
Actinotaenium cucurbita (Brébisson) Teiling / JH0383 / - / EF371066 / -
Actinotaenium curcurbitinum (Bisset) Teiling / ACOI 901 / EF371279 / EF371065 / -
Actinotaenium curtum(Brebisson ex Ralfs) Teiling / SVCK163 / FN432046 / - / -
Actinotaenium diplosporum(P.Lundell) Teiling / M3028 / FN432047 / - / -
Actinotaenium phymatosporum(Nordstedt) Coesel et Kouwets / M1368 / AM911233 / - / -
Actinotaenium silvae-nigrae (Rabanus) Kouwets et Coesel / SVCK 295 / EF371323 / EF371116 / -
Arthrodesmus validus(West &West) Sott et Grönblad / SVCK 457 / AM911343 / - / -
Bambusina borreri (Ralfs) Cleve / JH0199 / EF371283 / EF371070 / -
Cosmarium amoenumBrébisson ex Ralfs / SVCK 14 / FN432054 / - / -
Cosmarium bioculatumBrébisson ex Ralfs / M3032 / FN432056 / - / -
Cosmarium bioculatumBrébisson ex Ralfs / M3048 / FN432058 / - / -
Cosmarium biretumBrébisson ex Ralfs / M2123 / AM911267 / - / -
Cosmarium botrytis (Meneghini) Ralfs / UTEX 301 / EF371288 / EF371075 / -
Cosmarium broomeiThwaites ex Ralfs / M2075 / AM911269 / - / -
Cosmarium difficileLütkemüller / ACOI403 / AM911326 / - / -
Cosmarium granatumBrébisson / M3102 / FN432063 / - / -
Cosmarium hammeriReinsch / ACOI349 / AM911302 / - / -
Cosmarium isthmiumWest / SVCK229 / AY964169 / - / -
Cosmarium laeveRabenhorst / SVCK35 / AM911280 / - / -
Cosmarium melanosporum W. Archer / JH0011 / EF371289 / EF371076 / -
Cosmarium obsoletum (Hantzsch) Reinsch / ACKU1183 / AY964177 / AY553583 / -
Cosmarium ocellatumB.Eichler et Gutwinski / M3059 / FN432068 / - / -
oCosmarium pseudoconnatumNordstedt / JH0264 / EF371280 / EF371067 / -
Cosmarium pseudoholmiiBorge / SAG 15.87 / FN432072 / - / -
Cosmarium punctulatumBrébisson / SVCK 570 / AM911289 / - / -
Cosmarium quadrumP.Lundell / M3045 / FN432079 / - / -
Cosmarium regnelliiWille / SVCK 465 / FN432081 / - / -
Cosmarium sp. / JH0041 / EF371290 / EF371077 / -
Cosmarium sphagnicolumWest et G.S.West / M3035 / FN432084 / - / -
Cosmarium subtumidumNordstedt / M3067 / FN432088 / - / -
Cosmarium tessellatum(Delponte) Nordstedt / SVCK 381 / AM911320 / - / -
Cosmocladium saxonicum Hilse / ACOI 95 / EF371292 / EF371079 / -
Desmidium baileyi (Ralfs) Nordstedt / JH0228 / EF371299 / EF371086 / -
Docidium baculumBrébisson ex Ralfs / C6 / HE613541 / HE613522 / -
Docidium baculumBrébisson ex Ralfs / I1 / HE613505 / HE613523 / -
Docidium undulatumJ.W.Bailey / NIES285 / FN432109 / - / -
Euastrum bidentatumNägeli / ACOI282 / FN432103 / - / -
Euastrum binaleEhrenberg ex Ralfs / ACOI488 / AM911245 / - / -
Euastrum crassum var. michiganense Prescott / JH0018 / EF371300 / EF371087 / -
Euastrum gayanumDe Toni / M3050 / FN432105 / - / -
Euastrum pectinatumRalfs / M3033 / FN432075 / - / -
Euastrum prowseiA.M.Scott et G.W.Prescott / SVCK353 / FN432107 / - / -
Euastrum verrucosum Ehrenberg ex Ralfs / JH0068 / EF371301 / EF371088 / -
Haplotaenium minutum (Ralfs) Bando / SVCK 302 / EF371326 / EF371120 / -
Heimansia pusillum (Hilse) Coesel / SVCK 428 / EF371291 / EF371078 / -
Hyalotheca dissiliens Brébisson ex Ralfs / SAG 384-2 / AF203499 / EF371095 / -
Hyalotheca mucosaRalfs / JH0063 / EF371306 / EF371097 / -
Micrasterias furcataC. Agardh ex Ralfs / JH0064 / EF371313 / EF371104 / -
Onychonema filiforme(Ehrenberg ex Ralfs) Roy et Bisset / JH0420 / EF463094 / - / -
Penium cf. didymocarpum Lundell / JH0212 / EF371316 / EF371109 / -
Peniumcylindrus (Ehrenberg) Brébisson ex Ralfs / ACOI 780 / EF371320 / EF371113 / -
Penium margaritaceum (Ehrenberg) Brébisson ex Ralfs / UTEX 600 / EF371321 / EF371114 / -
Penium spirostriolatum J. Barker / SVCK 205 / EF371324 / EF371117 / -
Phymatodocis nordstedtianaWolle / JH0164 / EF371325 / EF371119 / -
Pleurotaenium archeriDelponte / H50 / HE613542 / HE613543 / HE613544
Pleurotaenium archeriDelponte / H51 / - / - / HE613545
Pleurotaenium baculoides (J. Roy et J. P. Bisset) Playfair / JH0008 / EF371327 / EF371121 / -
Pleurotaenium constrictum (Bailey) H. C. Wood / JH0135 / EF371328 / EF371122 / -
Pleurotaenium crenulatum (Ehrenberg ex Ralfs) Rabenhorst / 592 / HE613513 / HE613531 / HE613555
Pleurotaenium ehrenbergii(Brébisson ex Ralfs) Delponte / 737 / HE613506 / HE613524 / HE613546
Pleurotaenium ehrenbergii(Brébisson ex Ralfs) Delponte / Q15 / HE613507 / HE613525 / HE613547
Pleurotaenium ehrenbergii(Brébisson ex Ralfs) Delponte / Q19 / - / - / HE613548
Pleurotaenium ehrenbergii(Brébisson ex Ralfs) Delponte / H13 / - / - / HE613549
Pleurotaenium ehrenbergii(Brébisson ex Ralfs) Delponte / H55 / HE613508 / HE613526 / HE613550
Pleurotaenium ehrenbergii(Brébisson ex Ralfs) Delponte / H1 / HE613509 / HE613527 / HE613551
Pleurotaenium ehrenbergii(Brébisson ex Ralfs) Delponte / 579 / HE613511 / HE613529 / HE613553
Pleurotaenium ehrenbergii(Brébisson ex Ralfs) Delponte / Q12 / HE613512 / HE613530 / HE613554
Pleurotaenium ehrenbergii f. columellare Irénée-Marie / JH0331 / EF371329 / EF371123 / -
Pleurotaenium nodosum(F.M.Bailey) P.Lundell / I8 / HE613514 / HE613532 / HE613556
Pleurotaenium nodosum(F.M.Bailey) P.Lundell / I3 / HE613515 / HE613533 / HE613557
Pleurotaenium nodulosum(Brébisson ex Ralfs) Rabenhorst / H37 / HE613516 / HE613534 / HE613558
Pleurotaenium ovatum(Nordstedt) Nordstedt / J2 / - / HE613535 / -
Pleurotaenium sp. / Q18 / - / - / HE613559
Pleurotaenium sp. / H14 / - / - / HE613560
Pleurotaenium sp. / H41 / HE613517 / HE613536 / HE613561
Pleurotaenium sp. / H39 / - / - / HE613562
Pleurotaenium sp. / J-E9 / - / - / HE613563
Pleurotaenium sp. / H38 / - / - / HE613564
Pleurotaenium trabecula(Ehrenberg) Nägeli / 655 / HE613518 / HE613537 / HE613565
Pleurotaenium trabecula(Ehrenberg) Nägeli / 634 / HE613519 / HE613538 / HE613566
Pleurotaenium trabecula (Ehrenberg) Nägeli / 748 / HE613510 / HE613528 / HE613552
Pleurotaenium trabecula(Ehrenberg) Nägeli / H40 / HE613520 / HE613539 / HE613567
Pleurotaenium trabecula(Ehrenberg) Nägeli / M1369 / FN432113 / - / -
Pleurotaenium trabecula(Ehrenberg) Nägeli / UTEX 489 / AF203503 / - / -
Spondylosium luetkemuelleriGrondblad / - / FN432115 / - / -
Spondylosium panduriforme(Heimerl) Teiling / SAG 52.88 / AJ553969 / - / -
Spondylosium pulchellum Archer / SVCK 365 / AF203505 / EF371137 / -
Spondylosium pulchrum (Bailey ex Ralfs) Archer / JH0269 / EF371341 / EF371138 / -
Spondylosium tetragonumWest et G.S.West / SVCK 440 / EF371336 / EF371094 / -
Staurastrum arctiscon (Ehrenberg) Lundell / JH0014 / EF371343 / EF371140 / -
Staurastrum orbiculareMeneghini ex Ralfs / M2217 / AM911331 / - / -
Staurastrum pingueTeiling / UTEX 1606 / AF203506 / - / -
Staurastrum polytrichum f. biseriatum Kaiser / JH0015 / EF371344 / EF371141 / -
Staurastrum pseudosuecicum Prescott et A. M. Scott / JH0010 / EF371342 / EF371139 / -
Staurodesmus brevispinus Brébisson ex Ralfs / JH0180 / EF371349 / - / -
Staurodesmus bulnheimii(Raciborski) Round & Brook / SVCK84 / FN432118 / - / -
Staurodesmus convergens (Ehrenb.) Teiling / UTEX 2508 / EF371281 / EF371068 / -
Staurodesmus dejectus(Brébisson) Teiling / CCAP681/1 / FN432122 / - / -
Staurodesmus extensus (Anders.) Teiling / JH0386 / EF371317 / EF371110 / -
Staurodesmus isthmosus(Heimerl) Croasdale / SVCK466 / FN432125 / - / -
Staurodesmus mamillatus (Nordstedt) Teiling / JH0090 / EF371348 / EF371145 / -
Staurodesmus mucronatus(Ralfs ex Ralfs) Croasdale / M1394 / AM911342 / - / -

Teilingia granulata(J.Roy et Bisset) Bourrelly

/ SAG 25.88 / EF371350 / EF371147 / -
Teilingia granulata(J.Roy et Bisset) Bourrelly / JH0140 / EF371351 / EF371148 / -
Tetmemorus laevis (Kützing) Ralfs / SVCK 227 / EF371353 / EF371150 / -
Triplastrum simplex(P.Allorge) Iyengar et Ramanathan / Q13 / HE613521 / HE613540 / -
Triploceras gracile Bailey / SAG 24.82 / EF371354 / EF371151 / -
Xanthidium antilopaeum (Brébisson ex Meneghini) Kützing / JH0261 / EF371355 / EF371153 / -
Xanthidium armatumBrébisson ex Ralfs / ASW07059 / DQ026262 / - / -
Xanthidium brebissoniiRalfs / SVCK379 / DQ026261 / - / -
Xanthidium hastiferum W. B. Turner / JH0054 / EF378638 / EF371152 / -