Bayesian Node Dating Based on Probabilities of Fossil Sampling Supports Trans-Atlantic Dispersal of Cichlid Fishes
Total Page：16
File Type：pdf, Size：1020Kb
Supporting Information Bayesian Node Dating based on Probabilities of Fossil Sampling Supports Trans-Atlantic Dispersal of Cichlid Fishes Michael Matschiner,1,2y Zuzana Musilov´a,2,3 Julia M. I. Barth,1 Zuzana Starostov´a,3 Walter Salzburger,1,2 Mike Steel,4 and Remco Bouckaert5,6y Addresses: 1Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway 2Zoological Institute, University of Basel, Basel, Switzerland 3Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic 4Department of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand 5Department of Computer Science, University of Auckland, Auckland, New Zealand 6Computational Evolution Group, University of Auckland, Auckland, New Zealand yCorresponding author: E-mail: [email protected], [email protected] 1 Supplementary Text 1 1 Supplementary Text Supplementary Text S1: Sequencing protocols. Mitochondrial genomes of 26 cichlid species were amplified by long-range PCR followed by the 454 pyrosequencing on a GS Roche Junior platform. The primers for long-range PCR were designed specifically in the mitogenomic regions with low interspecific variability. The whole mitogenome of most species was amplified as three fragments using the following primer sets: for the region between position 2 500 bp and 7 300 bp (of mitogenome starting with tRNA-Phe), we used forward primers ZM2500F (5'-ACG ACC TCG ATG TTG GAT CAG GAC ATC C-3'), L2508KAW (Kawaguchi et al. 2001) or S-LA-16SF (Miya & Nishida 2000) and reverse primer ZM7350R (5'-TTA AGG CGT GGT CGT GGA AGT GAA GAA G-3'). The region between 7 300 bp and 12 300 bp was amplified using primers ZM7300F (5'-GCA CAT CCC TCC CAA CTA GGW TTT CAA GAT GC-3') and ZM12300R (5'-TTG CAC CAA GAG TTT TTG GTT CCT AAG ACC-3'). The region between position 12 200 bp and 2 100 bp (spanning the end and beginning of the mitogenome) was ampli- fied using forward primer ZM12200F (5'-CTA AAG ACA GAG GTT AAA ACC CCC TTA TYC ACC-3') and reverse primers ZM2100R (5'-GAC AAG TGA TTG CGC TAC CTT TGC ACG GTC-3') and Muj16SH (TGC ACC AWT AGG ATG TCC TGA TCC AAC ATC). Alternatively, in five species, two longer fragments were amplified instead using the combination of aforementioned primers (ZM7300F + ZM2100R or Muj16SH, and L2508KAW or ZM2500F + ZM7350R). Amplifi- cation of the whole mitogenome with a single primer set was successfully performed in three species using the primers ZM2500F and ZM2100R. We used the LA (long & accurate) polymerase Master Mix (TopBio) and the LA PCR Kit (TaKaRa). The amplification protocol consisted of 30 cycles of denaturation step (95 ◦C / 1 min), annealing step (60 ◦C / 1 min) and the extension step of 68 ◦C (15 min). PCR products were subsequently extracted from electrophoresis gel, purified, and pooled equimolarly. The pooled PCR products were individually barcoded by species during the library preparation (GS Rapid Library Preparation Kit, Roche). Emulsion PCR and sequencing were performed with GS Junior Titanium emPCR Kit, Lib-L (Roche) and GS Junior Titanium PicoTiterPlate (Roche) and GS Junior Titanium Sequencing Buffers Kit (Roche) following the manufacturer's protocol. To complete the circular molecule of the mitogenome, we have addition- ally sequenced the missing region of the 16S gene by conventional Sanger sequencing using mtD-32 and mtD-34 primers (Marescalchi 2005) and 48 ◦C of annealing temperature. The raw reads were filtered on quality and de-novo assembled in the Geneious 7 software (http://www.geneious.com, Kearse et al. 2012) to obtain the complete sequence of the mitochondrial genome. Contigs were manually corrected and merged by remapping of the raw reads. In addition to mitochondrial genomes of 26 species, markers 16S, mt-co1, mt-cyb, mt-nd2, mt- nd4, myh6, ptchd4, enc1, and tbr1b were sequenced for up to 50 species (a total of 305 sequences), following Sanger sequencing protocols given in (Matschiner et al. 2011). Of the nine markers, 16S, mt-co1, and mt-nd2 were not included in the study of Matschiner et al. (2011). Marker 16S was PCR-amplified using Amplitaq DNA polymerase (Applied Biosystems), primer pair 16Sar/16Sbr (Palumbi 1996), and the following cycling conditions: 94 ◦C for 2 min, 36 cycles of 94 ◦C for 30 sec, 48 ◦C for 30 sec, and 72 ◦C for 1 min, and finally an elongation time of 7 min at 72 ◦C. New primer pairs were designed for the two markers mt-co1 and mt-nd2: COIFc (5'-TCT CRA CYA ATC ACA 1 Supplementary Text 2 AAG ACA TCG G), COIR (5'-ATR GGG TCT CCY CCT CCK GC-3'), METc (GTT AAA CCC CTT CCT TTA CTA ATG-3'), and TRPc (G5'-AG ATT TTC ACT CCC GCT TAG-3'). Both markers were amplified with the respective primer pair and the Quiagen Multiplex Kit (Quiagen), following the manufacturer's instructions. Annealing temperatures were 58 ◦C for mt-co1 and 52 ◦C for mt-nd2, and 39 PCR cycles were used for both markers. 1 Supplementary Text 3 Supplementary Text S2: Teleost clades used in phylogenetic analyses. Classification follows Wiley & Johnson (2010) and Betancur-R et al. (2013), and diversity informa- tion is taken from Nelson (2006) unless otherwise noted. Clade IDs refer to branch labels in the RAxML phylogeny (Supplementary Figure S5) and to IDs specified in Supplementary Table S2. Dagger symbols are used to indicate extinct taxa. The timescale follows Gradstein & Ogg (2009). With the exception of clades listed in Supplementary Table S9, the sum of all 362 mutually exclusive clades listed here represents the entire extant diversity of the teleost supercohort Clupeocephala, combining the two cohorts Otomorpha and Euteleosteomorpha (Betancur-R et al. 2013). Abbreviations: myr, million years; Ma, million years ago; BS, Bootstrap support; BPP, Bayesian Posterior Probability; JRV, Jackknife resampling value. Clade 1: Otomorpha Taxonomy: One out of two cohorts of Clupeocephala. Following Betancur-R et al. (2013), we here include Alepocephaliformes in Otomorpha. Thus, Otomorpha are composed of three subcohorts, Clupei, Alepocephali, and Ostariophysi. Support: The molecular phylogenies of Betancur-R et al. (2013), Li et al. (2010b), and Lavou´e et al. (2005) strongly support inclusion of Alepocephaliformes in Otomorpha (BS 100). Our RAxML phylogeny supports the monophyly of Otomorpha with BS 100. First occurrence: yTischlingerichthys viohli Arratia, 1997, from the upper Solnhofen Limestone Formation, Bayern, Germany. The Tithonian yTischlingerichthys viohli is considered the oldest representative of Otomorpha (=Ostarioclupeomorpha) by Davis & Fielitz (2010), and the earliest ostariophysean by Benton et al. (2015). Based on ammonite zonation, the upper Solnhofen Lime- stone Formation is dated as early Tithonian, 150.8-149.9 Ma (Benton & Donoghue 2007; Benton et al. 2009). This is older than the earliest alepocephaloid record, the Oligocene yCarpathichthys polonicus Jerzmaska, 1979. Thus, the first occurrence of Otomorpha dates to 150.8-149.9 Ma. See clades 3 (Alepocephali) and 4 (Ostariophysi). Diversity: 9055 extant species. Sampled species: All sampled species of clades 2, 3, and 4. Clade 2: Clupei Taxonomy: One out of three subcohorts of Otomorpha. Clupei include several fossil lineages and the extant order Clupeiformes. Support: Synapomorphies are given in Wiley & Johnson (2010). The monophyly of extant Clupei is further supported by the molecular phylogeny of Betancur-R et al. (2013) (BS 87). Our RAxML phylogeny supports the monophyly of Clupei with BS 100. First occurrence: yEllimmichthys longicaudatus Cope, 1886, from the Marfim Formation, Rec^on- cavo Basin, Bahia, Brazil. Clupeomorph fishes appear in the fossil record in the Early Creta- ceous, with the genera yDiplomystus Cope, 1877, yEllimma Jordan, 1910, yEllimmichthys Jordan, 1919, ySpratticeps Patterson, 1970, yErichalcis Forey, 1975, yEoknightia Taverne, 1976, yHistiurus Costa, 1850, yNolfia Taverne, 1976, yParaclupea Du, 1950, ySantanaclupea Maisey, 1993, and yPseudoellimma De Figueiredo, 2009. Of these, the oldest specimens may be yDiplomystus koku- 1 Supplementary Text 4 raensis Uyeno, 1979 and yDiplomystus primotinus Uyeno, 1979 from the Wakino Formation, Kan- mon group, Kyushu Island, Japan, or yEllimmichthys longicaudatus Cope, 1886 from Bahia, north- eastern Brazil. The two specimens of yDiplomystus have been discovered in the upper layer (fourth layer) of the Wakino subgroup (Uyeno & Yabumoto 1980), which was claimed to be Neocomian (Berriasian-Hauterivian) by the original authors, but is more likely Barremian (Matsumoto et al. 1982) or Hauterivian-Barremian (Kimura et al. 1992). yEllimmichthys longicaudatus has been re- ported from the Marfim Formation, Rec^oncavo Basin, Bahia, Brazil, which is of Late Hauterivian- Early Barremian age (Maisey 2000). Thus, the first occurrence of Clupei dates to 133.9-130.0 Ma. Diversity: 364 extant species. Sampled species: Chirocentrus dorab, Clupea harengus, and Pellona flavipinnis. Clade 3: Alepocephali Taxonomy: One out of three subcohorts of Otomorpha. Alepocephali include the single order Alepocephaliformes with three families, Argentinidae, Opisthoproctidae, and Microstomatidae. Support: Synapomorphies of Alepocephali are given in Johnson and Patterson (1996). The molec- ular phylogenies of Betancur-R et al. (2013), Li et al. (2010b), and Nakatani et al. (2011) strongly support the monophyly of Alepocephali (BS 100). Our RAxML phylogeny supports the monophyly of Alepocephali with BS 100. First occurrence: yCarpathichthys polonicus Jerzmaska, 1979, from the Menilite Beds of the Carpathian flysch, Poland. yCarpathichthys polonicus is considered the earliest record of Alepo- cephaloidei, and of family Alepocephalidae (Jerzmanska 1979; Patterson 1993b), and thus of order Alepocephaliformes and subcohort Alepocephali. yCarpathichthys polonicus occurs in zones IPM 5-6 of the Menilite Beds (Jerzmanska 1979), which range between between 28.0-24.0 Ma (Tyler et al. 1993). Thus, the first occurrence of Alepocephali dates to 28.0-24.0 Ma. Diversity: 131 extant species. Sampled species: Alepocephalus bicolor, Bathylaco nigricans, and Platytroctes apus. Clade 4: Ostariophysi Taxonomy: One out of three subcohorts of Otomorpha. Ostariophysi include two sections, An- otophysa and Otophysa.