Table S1A. Taxon sampling for the circular tree and molecular dating analyses with GenBank accession numbers for each gene. Acheilognathus typus is the only outgroup used for the molecular dating analyses.
Taxa / COI / Cyt b / ND4 / ND5 / 16SOrder Cypriniformes
Family Catostomidae
Catostomus commersonii / AB127394 / AB127394 / AB127394 / AB127394 / AB127394
Family Gyrinocheilidae
Gyrinocheilus aymonieri / AB242164 / AB242164 / AB242164 / AB242164 / AB242164
Family Cobitidae
Cobitis striata / AB054125 / AB054125 / AB054125 / AB054125 / AB054125
Family Balitoridae
Homaloptera leonardi / AB242165 / AB242165 / AB242165 / AB242165 / AB242165
Family Cyprinidae
Subfamily Leptobarbinae
Leptobarbus hoevenii / AP011286 / AP011286 / AP011286 / AP011286 / AP011286
Subfamily Acheilognathinae
Acheilognathus typus / AB239602 / AB239602 / AB239602 / AB239602 / AB239602
Rhodeus ocellatus kurumeus / AB070205 / AB070205 / AB070205 / AB070205 / AB070205
Subfamily Oxygastrinae
Ctenopharyngodon idella / EU391390 / EU391390 / EU391390 / EU391390 / EU391390
Hemigrammocypris rasborella / AP011422 / AP011422 / AP011422 / AP011422 / AP011422
Ischikauia steenackeri / AB239601 / AB239601 / AB239601 / AB239601 / AB239601
Macrochirichthys macrochirus / AP011234 / AP011234 / AP011234 / AP011234 / AP011234
Nipponocypris sieboldii / AB218898 / AB218898 / AB218898 / AB218898 / AB218898
Opsariichthys uncirostris / AB218897 / AB218897 / AB218897 / AB218897 / AB218897
Paralaubuca typus / AP011211 / AP011211 / AP011211 / AP011211 / AP011211
Xenocypris macrolepis / AP009059 / AP009059 / AP009059 / AP009059 / AP009059
Subfamily Gobioninae
Coreoleuciscus splendidus / DQ347951 / DQ347951 / DQ347951 / DQ347951 / DQ347951
Gobio gobio / AB239596 / AB239596 / AB239596 / AB239596 / AB239596
Hemibarbus barbus / AB070241 / AB070241 / AB070241 / AB070241 / AB070241
Tanichthys
Tanichthys albonubes / AP011397 / AP011397 / AP011397 / AP011397 / AP011397
Subfamily Leuciscinae
Alburnus alburnus / AB239593 / AB239593 / AB239593 / AB239593 / AB239593
Chondrostoma lemmingii / DQ536427 / DQ536427 / DQ536427 / DQ536427 / DQ536427
Mylocheilus caurinus / AP010779 / AP010779 / AP010779 / AP010779 / AP010779
Notemigonus crysoleucas / AB127393 / AB127393 / AB127393 / AB127393 / AB127393
Notropis stramineus / DQ536429 / DQ536429 / DQ536429 / DQ536429 / DQ536429
Rhynchocypris percnurus / AP009061 / AP009061 / AP009061 / AP009061 / AP009061
Subfamily Danioninae
Aspidoparia morar / AP011335 / AP011335 / AP011335 / AP011335 / AP011335
Danio rerio / AC024175 / AC024175 / AC024175 / AC024175 / AC024175
Esomus metallicus / AB239594 / AB239594 / AB239594 / AB239594 / AB239594
Subfamily Psilorhynchinae
Psilorhynchus sucatio / AP011288 / AP011288 / AP011288 / AP011288 / AP011288
Subfamily Cyprininae
Probarbus Clade
Probarbus jullieni / HM536909 / HM536810 / HM536729 / HM536848 / HM536767
Catlocarpio siamensis / HM536911 / HM536812 / HM536731 / HM536878 / HM536769
Tribe Labeonini
Bangana ariza / JX074154 / JX074236 / JX074313 / JX074389 / JX074079
Cirrhinus microlepis / HM536924 / HM536825 / HM536743 / HM536859 / HM536782
Crossocheilus reticulatus / HM536925 / HM536826 / HM536744 / HM536860 / HM536783
Discogobio tetrazona / JX074169 / AY953022 / JX074328 / JX074404 / DQ845888
Epalzeorhynchos bicolor / HM536917 / HM536818 / HM536706 / HM536874 / HM536775
Garra orientalis / AP011202 / AP011202 / AP011202 / AP011202 / AP011202
Labeo angra / AP011329 / AP011329 / AP011329 / AP011329 / AP011329
Labeo batesii / AB238967 / AB238967 / AB238967 / AB238967 / AB238967
Labeo parvus / JX074208 / JX074285 / JX074362 / JX074439 / JX074126
Labeo pierrei / AP011200 / AP011200 / AP011200 / AP011200 / AP011200
Labeo rohita / AP011201 / AP011201 / AP011201 / AP011201 / AP011201
Labeo senegalensis / AB238968 / AB238968 / AB238968 / AB238968 / AB238968
Labiobarbus lineatus / HM536885 / HM536789 / HM536708 / HM536865 / DQ845914
Lobocheilos melanotaenia / HM536901 / HM536803 / HM536723 / HM536845 / HM536759
Mekongina erythrospila / JX074187 / JX097081 / JX097090 / JX097090 / JX074111
Osteochilus salsburyi / HM536883 / HM536787 / HM536701 / HM536830 / DQ845892
TorClade
Barbus carnaticus / HM010713 / HM010725 / HM010737 / HM010737 / HM010701
Neolissochilus stracheyi / HM536922 / HM536823 / HM536741 / HM536857 / HM536780
Tor sinensis / HM536900 / HM536802 / HM536722 / HM536844 / DQ845876
Tor tambroides / HM536923 / HM536824 / HM536742 / HM536858 / HM536781
Puntius Clade
Barbus fasciolatus / HM536910 / HM536811 / HM536730 / HM536877 / HM536768
Barbus trimaculatus / AB239600 / AB239600 / AB239600 / AB239600 / AB239600
Eirmotus octozona / HM536918 / HM536819 / HM536737 / HM536855 / HM536776
Hampala macrolepidota / HM536886 / HM536790 / HM536709 / HM536832 / DQ845863
Oreichthys cosuatis / HM536921 / HM536822 / HM536740 / HM536856 / HM536779
Puntius brevis / HM536914 / HM536815 / HM536734 / HM536871 / HM536772
Puntius nigrofasciatus / HM536920 / HM536821 / HM536739 / HM536849 / HM536778
Puntius oligolepis / HM536919 / HM536820 / HM536738 / HM536881 / HM536777
Puntius masyai / HM536916 / HM536817 / HM536736 / HM536873 / HM536774
Puntius tetrazona / EU287909 / EU287909 / EU287909 / EU287909 / EU287909
Puntius ticto / AB238969 / AB238969 / AB238969 / AB238969 / AB238969
Puntius titteya / HM536908 / HM536809 / HM536728 / HM536876 / HM536766
Tribe Poropuntiini
Barbonymus gonionotus / AB238966 / AB238966 / AB238966 / AB238966 / AB238966
Barbonymus schwanenfeldii / HM536894 / HM536796 / HM536716 / HM536875 / HM536757
Cyclocheilichthys armatus / HM536926 / HM536827 / HM536745 / HM536861 / HM536784
Cyclocheilichthys janthochir / HM536907 / HM536808 / HM536727 / HM536870 / HM536765
Hypsibarbus malcolmi / HM536915 / HM536816 / HM536735 / HM536872 / HM536773
Hypsibarbus vernayi / HM536892 / HM536794 / HM536714 / HM536838 / DQ845870
Mystacoleucus marginatus / HM536913 / HM536814 / HM536733 / HM536880 / HM536771
Poropuntius opisthoptera / HM536891 / HM536793 / HM536713 / HM536837 / HM536755
Puntioplites falcifer / HM536904 / HM536805 / HM536726 / HM536868 / HM536762
Puntioplites proctozystron / HM536912 / HM536813 / HM536732 / HM536879 / HM536770
Puntioplites waandersi / HM536928 / HM536829 / HM536747 / HM536863 / HM536786
Scaphognathops bandanensis / HM536927 / HM536828 / HM536746 / HM536862 / HM536785
Scaphognathops stejnegeri / HM536906 / HM536807 / HM536705 / HM536847 / HM536764
Sikukia stejnegeri / HM536898 / HM536800 / HM536720 / HM536842 / DQ845872
Barbus Clade
Acrossocheilus monticola / HM536893 / HM536795 / HM536715 / HM536839 / HM536756
Barbus barbus / AB238965 / AB238965 / AB238965 / AB238965 / AB238965
Capoeta capoeta / HM536852 / HM536882 / HM536707 / HM536850 / HM536751
Chuanchia labiosa / HM536897 / HM536799 / HM536719 / HM536841 / HM536758
Gymnocypris przewalskii / AB239595 / AB239595 / AB239595 / AB239595 / AB239595
Onychostoma simum / HM536899 / HM536801 / HM536721 / HM536843 / DQ845861
Oxygymnocypris stewartii / HM536853 / DQ491114 / HM536749 / HM536864 / DQ845918
Platypharodon extremus / HM536854 / AY463498 / HM536750 / HM536851 / DQ845855
Schizothorax oconnori / HM536902 / AY463519 / HM536724 / HM536846 / HM536760
Schizothorax waltoni / HM536903 / HM536804 / HM536725 / HM536867 / HM536761
Spinibarbus hollandi / HM536890 / AY195629 / HM536712 / HM536836 / DQ845865
Spinibarbus sinensis / HM536895 / HM536797 / HM536717 / HM536840 / DQ845864
Tribe Cyprinini
Carassioides acuminatus / AP011178 / AP011178 / AP011178 / AP011178 / AP011178
Carassius auratus / AB111951 / AB111951 / AB111951 / AB111951 / AB111951
Carassius carassius / AY714387 / AY714387 / AY714387 / AY714387 / AY714387
Carassius cuvieri / AB045144 / AB045144 / AB045144 / AB045144 / AB045144
Carassius gibelio / AB379922 / AB379922 / HM536748 / AB378300 / AB379922
Carassius langsdorfi / AB006953 / AB006953 / AB006953 / AB006953 / AB006953
Cyprinus carpio / X61010 / X61010 / X61010 / X61010 / X61010
Cyprinus multitaeniatus / HM536896 / HM536798 / HM536718 / HM536866 / DQ845845
Procypris rabaudi / EU082030 / EU082030 / EU082030 / EU082030 / EU082030
Sinocyclocheilus altishoulderus / FJ984568 / FJ984568 / FJ984568 / FJ984568 / FJ984568
Sinocyclocheilus grahami / GQ148557 / GQ148557 / GQ148557 / GQ148557 / GQ148557
Sinocyclocheilus macrophthalmus / HM536889 / HM536792 / HM536711 / HM536835 / HM536754
Sinocyclocheilus microphthalmus / HM536888 / AY854690 / HM536703 / HM536834 / HM536753
Sinocyclocheilus xunlensis / HM536887 / HM536791 / HM536710 / HM536833 / HM536752
Table S1B. Taxon sampling for phylogenetic analyses on the Poropuntiini and the Labeonini with GenBank accession numbers for each gene. For species that were investigated through microtomography for pharyngeal dentition (Labeonini and Poropuntiini), reference number is given for specimens that are from collections of the National Museum of Natural History in Paris. For specimens found in petshops, they were kept in our own facilities and are available upon request.
Taxa / Specimen reference / COI / Cyt b / RAG1 / RHOOutgroup
Acheilognathus typus / AB239602 / AB239602 / EU292688 / FJ197042
Gobio gobio / AB239596 / AB239596 / EU292689 / FJ197056
Opsariichthys uncirostris / AB218897 / AB218897 / FJ197126 / FJ197068
Rhynchocypris percnurus / AP009061 / AP009061 / EU409627 / EU409655
Poropuntiini
Albulichthys albuloides / 1987-0100 / JX066750 / JX066768 / KC690010 / KC690011
Amblyrhynchichthys truncatus / 2013-0108 / KC631183 / KC631275 / KC631208 / KC631234
Anematichthys apogon / 2012-0074 / JQ346161 / JQ346138 / JQ346113 / KC631241
Anematichthys armatus / 2012-0081 / JQ346167 / JQ346147 / JQ346126 / KC631242
Anematichthys repasson / 2012-0011 / JQ346165 / JQ346145 / JQ346124 / KC631243
Balantiocheilos melanopterus / 0000-1847 / KC631184 / KC631276 / KC631209 / KC631235
Barbonymus altus / 2012-0070 / JQ346154 / JQ346133 / JQ346117 / KC631244
Barbonymus gonionotus / 2012-0073 / JQ346157 / JQ346136 / JQ346120 / KC631245
Barbonymus schwanenfeldii / 2012-0084 / JQ346171 / JQ346151 / JQ346130 / KC631246
Cosmochilus harmandi / 2012-0075 / JQ346163 / JQ346140 / JQ346115 / KC631247
Cyclocheilichthys enoplos / 2012-0014 / JQ346162 / JQ346139 / JQ346114 / KC631248
Discherodontus ashmeadi / 2013-0110 / KC631185 / KC631277 / KC631210 / KC631236
Hypsibarbus malcolmi / 2012-0008 / JQ346169 / JQ346149 / JQ346128 / KC631249
Hypsibarbus wetmorei / 2012-0006 / JQ346158 / JQ346137 / JQ346121 / KC631250
Mystacoleucus marginatus / 2012-0079 / JQ346160 / JQ346144 / JQ346123 / KC631251
Poropuntius carinatus / 2013-0101 / KC631186 / KC631278 / KC631211 / KC631237
Poropuntius laoensis / 2013-0102 / KC631187 / KC631279 / KC631212 / KC631238
Puntioplites falcifer / 2012-0069 / JQ346153 / JQ346132 / JQ346112 / KC631252
Sawbwa resplendens / petshop / KC631188 / KC631280 / KC631213 / KC631239
Scaphognathops bandanensis / 2012-0071 / JQ346155 / JQ346134 / JQ346118 / KC631253
Scaphognathops stejnegeri / 2013-0099 / KC631189 / KC631281 / KC631214 / KC631240
Sikukia gudgeri / 2012-0085 / JQ346172 / JQ346152 / JQ346131 / KC631254
Labeonini
Cirrhinus cirrhosus / 2013-0082 / KC631190 / KC631282 / KC631215 / KC631255
Cirrhinus microlepis / 2013-0080 / KC631191 / KC631283 / KC631216 / KC631256
Cirrhinus molitorella / 2013-0088 / KC631192 / KC631284 / KC631217 / KC631257
Epalzeorhynchos frenatus / 2013-0114 / KC631193 / KC631285 / KC631218 / KC631258
Garra sp. / 2013-0117 / KC631194 / KC631286 / KC631219 / KC631259
Henicorhynchus sp. / 2013-0116 / KC631195 / KC631287 / KC631220 / KC631260
Incisilabeo behri / 2013-0076 / KC631196 / KC631288 / KC631221 / GQ913502
Labeo barbatulus / 2013-0096 / KC631197 / KC631289 / KC631222 / KC631261
Labeo chrysophekadion / 2013-0107 / KC631198 / KC631290 / KC631223 / KC631262
Labeo pierrei / 2013-0078 / KC631199 / KC631291 / KC631224 / KC631263
Labeo rohita / 2012-0072 / JQ346156 / JQ346135 / JQ346119 / KC631268
Labiobarbus lineatus / 2013-0115 / KC631200 / KC631292 / KC631225 / KC631264
Mekongina erythrospila / 2013-0090 / KC631201 / KC631293 / KC631226 / KC631265
Osteochilus melanopleurus / 2013-0118 / KC631202 / KC631294 / KC631227 / KC631266
Osteochilus vittatus / 2012-0082 / JQ346168 / JQ346148 / JQ346127 / KC631269
Osteochilus waandersii / 2013-0103 / KC631203 / KC631295 / KC631228 / KC631267
Thynnichthys thynnoides / 2013-0109 / KC631204 / KC631295 / KC631229 / JX074598
Other Cyprininae
Acrossocheilus monticola / HM536893 / HM536795 / GQ913438 / GQ913490
Hampala dispar / KC618392 / KC631297 / KC631230 / KC631270
Hampala macrolepidota / HM536886 / JQ346142 / JQ346122 / KC631271
Onychostoma ovale / JX074164 / JX074246 / GQ913440 / GQ913492
Oreichthys parvus / KC631207 / KC631299 / KC631233 / KC631274
Puntius brevis / KC631206 / - / KC631232 / KC631273
Puntius tetrazona / KC631205 / KC631298 / KC631231 / KC631272
Scaphiodonichthys acanthopterus / KC690006 / KC690007 / KC690008 / KC690009
Text S10: Molecular dating analyses
The entire dataset was partitioned into five partitions (one partition each for the three codon positions of protein-coding genes and the stem region and loop region of the 16s rRNA). Substitution and clock models were unlinked and the underlying trees were linked among partitions. Based on results from jModelTest 2.1.1 (48), the model HKY + I + G was used for protein-coding genes and the 16S loop region and the model GTR + I + G was used for the 16S stem region.An uncorrelated lognormal relaxed clock model was employed. Yule speciation process was used for the tree prior. The starting tree was generated by BEAST using a strict molecular clock and without specifying any a priori age information. A lognormal prior distribution was adopted. Three nodes, each with a hard minimum bound and a soft maximum bound, were used for calibration. The first calibration prior was placed on the crown node of the monophyletic African Labeo clade (L. parvus, L. senegalensis, and L. batesii). The hard minimum bound was set as 17.0 Ma based on the age of the oldest African Labeo-like fossil (41)and the soft maximum bound was set as 48.6 Ma based on the age of the oldest cyprind fossil known (Parabarbus, (52)). Parameters related to prior distribution of this calibration prior were set as follows: Mean=1.8082, Stdev=1.0, and Offset=17.0. The second calibration prior was placed on the stem node of Cyprinus. The hard minimum bound was set as 33.9 Ma based on the age of the oldest Cyprinus-like fossil(42) and the soft maximum bound was set as the same as that of the first calibration prior (48.6 Ma). For the second calibration prior, related parameters were set as below: Mean=0.53, Stdev=1.0, and Offset=28.4. The third calibration prior was placed on the crown node of all Puntius. The fossil stratigraphic occurrence(43) was translated into age constraints using the upper and lower age of the stratigraphic interval as hard minimum bound (28.4 Ma) and soft maximum bound (37.2 Ma), respectively(44). For this calibration prior, related parameters were set as follows: Mean=0.53, Stdev=1.0, and Offset=28.4. All other parameters in BEAUti were left at default. Markov Chain Monte Carlo (MCMC) analyses were run for 25,000,000 generations (sampled frequency = 2000) and four independent runs were performed. Tracer 1.5 (45)was used to summarize BEAST output (burn-in = 5,000,000). Effective sample size (ESS) scores were used to assess convergence and stationarity of multiple runs. Results from the four runs (burn-in = 5,000,000 for each run) were combined using LogCombiner 1.7.2 with a resampling frequency of 4000 generations. One maximum clade credibility (MCC) tree was created using TreeAnnotator 1.7.2 (45)and the posterior probability limit was set as 0.5. The 95% Highest Posterior Density (HPD) limits of the node heights were summarized.
Patterson C. 1993 The fossil record 2, pp. 622–656. London, UK: Chapman and Hall.