Low support values and lack of reproducibility of molecular phylogenetic analysis of Copepoda orders

2021·0.61 MB·

by  K V Mikhailov

Supplementary information

Low support values and lack of reproducibility of molecular phylogenetic analysis of
Copepoda orders

Kirill V. Mikhailov1,2, Viatcheslav N. Ivanenko3

1 Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University,
Russian Federation
2 Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences,
Russian Federation
3 Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University,
Russian Federation

Corresponding author: Viatcheslav Ivanenko
E-mails: [email protected] , [email protected]
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60 100 100 Astericola clSauVtesalilhiicinoiluas s spp..
Sabelliphilus elongatus
64 9561 57 100 S1c0a0mbicornusP 1ss0pe0.udantheLsesrinues nst1Mpo0.me0cao ams6ee4rlilnCinxha oh8ne7dterraoAcXcanCeanDcnrrthoiihtftirriomuoaidmst oisi comlpgol.gieldaural suae cgs sciplpii.is.
43 Anthessius sp. 92 91 ClausidiumH sepm.icyclops thalassius
Catiniidae sp.
93 90 100100 TMryotcilhicicoolala i netnetsetirnicauliss 110000 HIorloo9db9eosm soaloucrihduiCsla svpis.Toadeanliisa caabnbtrheuvsia ztuesugopteri
36 91 Cyclopinella sp. 100 95 9P27se9SuEiPdnrgSeeeSarcirnggistneeaailenrsusgriosilglauu paassshsni lipiumlcluuashsasr o paj ooruosarrnilntlyuduacrustoiulalsptuuss
47 77 76 Macrocyclops albid1u0s0 Ect1o0c60y52c6lopEEsu EupcEcuyouycclycclyosylcoppclposlionsp dpo smuss s umaspsceoerrnurraturiotluaidstuess
99 83 100 100 ApoHcyaclilcoypcslo rCposyy cislpo.ps sp. Acanthocyclops viridis
Euryte sp.
87 37 31 100 100 PStemriinrnoopPvstiyeplrilPnuinistdoe aspripesn.y o2slplpus.s2y lslups.1 sp.3
96 100 SmirnoviCpiyncidloapein sopd.1es sp.
Speleoithona bermudensis
81 66 82 83100 NotodelphyAsr pchrainsointOoaditehlopnhiydsa esp s.p.Paracyclopina nana
17 Cyc8lo3picina sp.9 n7ov. CMyectlaocpyinclao psipn.a sp.
100 Cyclopicina loSnugpifeurrocrantaatiremidae sp.
71 92 8658 Styrac1o0t0hoZroasxIi dmPgylaeaar dansibtpBahr.trioaadrddayyeaa s dspip.la.tata
Tisbe sp.
41 100 Volkmannia attenuata 73 69 Cerviniopsis s1p0.0 110000CCllooaannnngguuiieppeleellladda ii paape essrrpppp.lleexxaa 12
22 6241 42 NeoAcee5gr3ivsitnhiau ss psp..Aeg6is1thidae sp. A9e4gisthid5a4e gen. nov.CervinieASllaetr gasitpsio.thpiodnateo tseps. snpo.v..
90 100 PoPnotnotsotrsatrtaiottioetse fso snpta.ni Cerviniopsis longicaudata
22 15 99 100 100 100 ParTHaPinagsarrpainoamnpcomutpiscius Pufs usss l seevspnuup.tsd.irootpascihsi1d0iu0s bipartitus Aegisthidae sp.1
34 93 96 SeDwiaerltlhiar otrdoepsic sapX.ylora bathyalis
Thalestridae sp.
3040 2735223039 98 MesocCharSant teshpno.ocLcaeamSprtiptesoLt nuspaospooc .nspatthriaaoop pnshstpyoi.sldin esupss .sp.Parastenocaridae sp.
36 87 100 Cleto9d9idaLea sopp.hAosnetlilnoPaps sseipsu .dhoisnpyidchaocamptus spinifer
5 118 12 59 Thompso1n0u90l9a hyaMeniraaeciidaeN soprA.mmapnheiTPlalieesdgclataoiedsi distueepmss. sasppto.pus
7 96999875 19080100MPaisroapmheriiorSoMptpseaAsinsliarso gsc csepSoops.pap.MtsriidisyneMaalaslmeuiose soc es slppsieprph.at.o.r isdape s.sp s.p.
Misophriopsis okinawensis
99 98 110000100 MorMmBooeBrnnemitnlhloatMoon mpmiilshliaoisas poomshpmpirhnhiaeroriilarala p csaoplrl.niautata
Mormonilla sp.
48 87 978E0cbAapRCthhhoeyoturoigtophonoob nepiutcriosue lsticex omsicn aastrpuma.dcmatuilslatus
Pontoeciella abyssicola
5 6419 86 67 100 9A6sEtenrOtoorcmehcoetlureirdpuPaisdae aes seopp n.s. pe.lo9n3gatus PSaiprahbornaocshtioemllaa mtoeidralu scpci.i2 Calvella adunca
52 10S0tenopontius sp. 100SSiipphhoonnoossttoommaattooiiddaa sspp..31
5341 82100 NEeumdeascitsyA lliannmtohdnoeasso mniag ecrrHaastssucmhekia pagrosomi
18 63 89 41 62 LepeophtlheerniraueGse lsonaiiPoclmuapsrooa tnseleipssbr awiotatnat seeolonnigatus
100 100 Caligus Cealolingguast ueslo 2ngatus 1
97 100 100 GCeaCllGyiageelulillgsyou eicdslula ocr itsuduprast. u 2s2sp .11
18 46 100 ArchimSispoeplehoripah driiasTc ebotirvvaeegrxyoilinlaicTeeptrsaidgaoen iscpe.p1sidae sp.2
2784 NullosetPigaerraau aguacpttiisluesta buchani
23 Haloptilus longicornis
79 93 98 56 LPu9inc8ikceurPttioaanr failuahsve Mitaceomerrotbrnriidihgsiauabu edsRfufushs icnaocmalapnauctsu csornutus
100 50 100 P11s00e00udocycl6o13p5s sp4.2 49Eudiaptomus vulgariSsulcaPnounstC ecleolinnnTtfaerlio mcpptlouuarsmgae adsti asvcioaluadcaetuas PseCudaonddTiaaocprittaao nmsuimuss pg lirenaxocpiliinsus
96 5149 100 B8Ca8athlayncaulsa nh9ue8slg porlainnPcdesicpeususdocycPlosepus dxoipcShyoctylpoghpooscr yuscsclhompiian ksepi.
51 Paracalanus parvus
Subeucalanus pileatus
92 733337 EuchaCelatau smoTecedamilaaonruosp iaar cmSuapicyinouormncibasalaennussis abyssalis
100 89 Aetideus armatuTsharybis groendlandicus
7844 98 Scolecitrichopsis spD.ia1i0x0is hibePrnhSiacceaonlencait hspriixn ibferaradyi Monstrilla helgolandica
92 Monstrilla clavata
100 Monstrilla sp
95 100 Platycopia perplexaMonstrilla sp.100 CymbasMoomnas tsripll.opsis sp.
100 Nanocopia minuta
0.1
Figure S1. Maximum likelihood reconstruction with the concatenated alignment of the four genes (18S and 28S rRNA,
COI mtDNA and H3 histone) from the study by Khodami et al., 2017. The tree was reconstructed with RAxML using the
GTRGAMMAI model optimized separately for the four gene partitions; tree node support values are bootstrap
percentages evaluated with 10,000 replicates.
100 100 OCnocryaceaae sups. speciosus
99 Ditrichocorycaeus anglicus
98 99 100Lichomolgu6s0 canui SappPhaircinhao sd aprCuwnoicnptiiailitau mmirabilis
93 100 100 AstericolaV cSalatheuinlsliiciuiosl as ps.p.
Sabelliphilus elongatus
100 1S0c0ambicornus sp. 10060 97 XCAaDrrnoiiftcrioahidm imsicopool.gllagu isad gasiepli .ssp.
3979 72 98 Anthess1iu0s0 sp. Pseu1d0a0ntheMsseiLcuoesmr nseper.nintoxm hae taesroecllienCnahtroontidracanthus merluccii
97 100 MTryotcilhiciocolala in etenstetirnicauliss
Pectenophilus ornatus
78 99 100 9999 9P9s9e89uES1drinegSeraSgrisngianileasuerisslrguig laausas nsspi climaulhursaosa jrp souaoirlntuluydrsciuolalptuCusslausidiuHme mspic.yclops thalassius
Catiniidae sp.
78 75 HIorolodbeosm soaluorcidhius sp.
77 99 100 Ect1o0c6y062c8lopEsEu upEcEcyouyculcyclcyoslyocppclpsiolnos pdo psmuss ums asspcoeernrurrtaruiotluaidstuess 100 100 ClavisToadeanliisa caabnbtrheuvsia zteuusgopteri
99 Macrocyclops albidus
78 99 95 100Euryte sp. 100 ApocHycalloicpysc lroCopyysic lsopp.s sp. Acanthocyclops viridis
Cyclopinella sp.
77 37 100 SmirSnomviirpnionvidipaien isdpa.e1 sp.2
100 100 100 PterinoPptesrPyilntleuorspi nssoyppl.l2ussy llsups. 1sp.3
98 100 85 37CyclopinSopdeeleso sitph.onNao btoedrmelupdhAeysnrc sphisriansoitnoadelphys sp.
99 96 MCyectalocpyicnlao psipn.a sp.
24 100CCycylcoloppiciicnina9a 5s plo.n ngoifvuS9.ru9cpaetarornatiremidae sp. Oithonidae sp.Paracyclopina nana
54 54 Cerviniopsis sp1.00 110000CCllooaannnngguuiippeeeelllladda ii aapp eessrrpppp.lleexxaa 12
24 55 23 1710012PoPnNotonestAoo1tcAers7aegtertrigiavsoititstniheotiuhastesi dfss osaAp nspe.ept. agg.niesinth. idnaoev. sp.100 93 CervAiengieiSslltatrh asidtpiao.ep osnpt.o nteosv .s.p.
22 10035 TisbeV soplk.mannia attenuata100 Cerviniopsis lAoenggiisctahuiddaaeta sp.1
8099 52 StyracothZoorsIadixmy agenl asthdpii.daatoer sp.
10 84 100 100 ParBarbarTHdaiyadgaryrpi aosa ppdcu.itlisac tufaustl avsups.
89 100 100ParananPnsoapmusm Psissp e.suednotitraocphsiidsius bipartitus
24 3428 2866 100 10T0hoTmhaplseSosentDrwuiidaelMaarll teiihhar ayrs otacprdoie.iedpnsaiac eeXsa psy.plo.ra bathyalis
43 52 93 110000 NormaAnmePpllTehidelitaagidseaic ussomtpied. ses pss pa.topus Tetragonicepsidae sp.1
37 100 10079 100100 6S7MtMeAanelrSaogsccaeooorscspptlaeisidimtynaolaeledue iesrs ass ps p.ssp.pp... Tetragonicepsidae sp.2
Parameiropsis sp.
Cletodidae sp.
19 2589 100 Mes1o0c0hra sp.98 LaopPhsoAensuteidnlolaon psyspci.hs ohcisapmidpatus spinifer
7954 CanthocaLmeppttuosp ostnatpiah syplin.us
97 99 LaophontoPdeasra sspte.nocaridae sp.
100 88 100100 BenthoBmeinstoSoptmehSnirsiotaoec pnpahoarirclsilaai asr tcopaop.rsnisu tsap.
Misophriella sp.
97 97 11000M086isopMhMrisioooprpmshiosrin ooiplklasini spa hMwsapeos.Mnrmmsisiaosonpilhlari as ps.p.
Mormonilla minor
100 100 CymbMasoonmstari lslopp.sis sp.
99 Monstrilla sp.
50 100 95 MonstrMilloan csltarvillaat asp Monstrilla helgolandica
Pontoeciella abyssicola
51 50 79 99 1009E7cbAaCtpRhheyhouroittooghnpoo obepnicruoetsiulti excssio cm nsatpaur.madcamtuilslatus
28 97 100 AsteOr1or0ce0hceturriduase s psp.P.aeon elo1n0g0atus Parabrachiella merluccii Calvella adunca
42 100 Entomolepidae sp.
Siphonostomatoida sp.2
98 100 N1E0eu0mdeascitsy llianmodneas niger 100SSiipphhoonnoossttoommaattooiiddaa sspp..31
9949 99 94 Ste1n0o0ponAtinutsh ospso.ma Hcraatssscuhmekia pagrosomi73 92 LepeophltehreniaGruelseo niPsoiaacpluromastelo essnbp iwisroaanttt saeoelonnigatus
100 100CaliguCs aelliognugs aetluosn g2atus 1
Archimisophria discoveryi 100 100 CaCliagluigsu csu cruturtsu 2s 1
72 62 9S0p1e0le0ophria bivexillaNullosetPigaerarau gaaupcttiilsuest abuchan1i00 GeGlyeelylleolildoaid sap s.2p.1
34 Haloptilus longicornis
59 59 59 Lu5ci9cuPtiaar aflhaevMitceeorotrrnridhisiaabR edhfufiunssc caaolamnpuasc ctuosrnutus
Pinkertonius ambiguus
67 99 Sulcanus conflictus Tortanus gracilis
99 Pontellina plumata
100 100 100 72 CentrToepmagoeras dviisoclaacueduasta Candacia simplex
Eudiaptomus vulgaris
59 100 100100100 PseudocyPcsleoupds oxcipyhcSlootpyphgsoo srcucyhscmloipnikae sip. Pseudodiaptomus inopinus
Pseudocyclops sp.
34 589070 BatChayclaanlaunsu hse plgroinlacenpdsicus Paracalanus parvus
Subeucalanus pileatus
59 59 STpienmocoarolapniau sm aabyyusmsablaisensis
10098 100 ECuAcleahtuiadseeotuacs am laaernmduiaast uasrcuicornis
9310073 100 ScolecitrichoTphsairsy 1sbD0pisi0a. gixriosPe hShniabcdoeelalnrennncdiaciitca hsurpisxin bifreardayi Platycopia perplexa
100 Nanocopia minuta
0.2
Figure S2. Bayesian inference with the concatenated alignment of the four genes (18S and 28S rRNA, COI mtDNA
and H3 histone) from the study by Khodami et al., 2017. The tree was reconstructed by MrBayes using the GTR
model for the rDNA partitions and the codon models in conjunction with GTR for the protein coding gene partitions;
tree node support values are posterior probabilities given as percentage values.