Aligned DNA sequence matrix of five nuclear genes

Aligned DNA sequence matrix of five nuclear genes (95 taxa, 4518 positions):Rag1 (positions 1 to 1452), Rhodopsin (positions 1453 to 2202), EGR1 (positions 2203 to 2928), EGR2 (positions 2929 to 3753), EGR3 (positions 3754 to 4518

pleuroProtGenes.123

Nexus alignment file with character sets and export block. Includes sequences generate for this study and those retrieved from GenBank

Additional file 1: Table S1. of First record of the coloured righteye flounder, Poecilopsetta colorata (Teleostei: Poecilopsettidae) from the Sakalaves seamounts in the Mozambique Channel

List of the samples collected during the cruise (campaign: PAMELA-MOZ01) and examined in this study. CP: Beam trawl. DN: NIWA sledge. DW: WarĂŠn dredge. (DOCX 27 kb

Mitogenomic Evidence for an Indo-West Pacific Origin of the Clupeoidei (Teleostei: Clupeiformes)

<div><p>The clupeoid fishes are distributed worldwide, with marine, freshwater and euryhaline species living in either tropical or temperate environments. Regional endemism is important at the species and genus levels, and the highest species diversity is found in the tropical marine Indo-West Pacific region. The clupeoid distribution follows two general pattern of species richness, the longitudinal and latitudinal gradients. To test historical hypotheses explaining the formation of these two gradients, we have examined the early biogeography of the Clupeoidei in reconstructing the evolution of their habitat preferences along with their ancestral range distributions on a time-calibrated mitogenomic phylogeny. The phylogenetic results support the distinction of nine main lineages within the Clupeoidei, five of them new. We infer several independent transitions from a marine to freshwater environment and from a tropical to temperate environment that occurred after the initial diversification period of the Clupeoidei. These results combined with our ancestral range reconstruction hypothesis suggest that the probable region of origin and diversification of the Clupeoidei during the Cretaceous period was the tropical marine precursor to the present Indo-West Pacific region. Thus, our study favors the hypotheses of “Region of origin” and “Tropical conservatism” to explain the origins of the longitudinal and latitudinal gradients of clupeoid species richness, respectively. Additional geological and paleontological evidence further define the tropical marine paleo-region of origin as the eastern Tethys Sea region. The Cretaceous fossil record of the Clupeoidei is partially incongruent with the results here as it contains taxa found outside this region. We discuss three possible causes of conflict between our biogeographical hypothesis and the distributions of the Cretaceous clupeoid fossils: regional extinction, incomplete taxonomic sampling and incorrect timescale estimation.</p> </div

Most likely ancestral ranges reconstruction of the Clupeoidei during the Cretaceous and early Cenozoic period using the dispersal–extinction–cladogenesis (DEC) model [116], [117] onto a simplified Bayesian phylogenetic chronogram.

<p>Outgroups (i.e., non-clupeoids) were deleted and biogeographically redundant clupeoid taxa were merged with their respective sister group (see material and methods for details). Ancestral ranges at nodes within each major lineage not reconstructed. Horizontal timescale in million of years ago (Mya) (Paleogene epoch abbreviations: Paleo, Paleocene; Eo, Eocene; and Oligo, Oligocene). Most likely ancestral ranges reconstruction at nodes indicated by code-color boxes (see Fig. 1B for correspondence between regions and two or three-letter codes and colors). Black arrows indicate the three dispersal events predating or likely predating the K-Pg boundary and black arrowheads indicate subsequent allopatric cladogenesis. Temperate lineage branches are underlined in blue and white arrowheads indicate marine to freshwater transitions. “*” after a species name indicates that closely related species to this species have been pruned (see material and methods for details); “**” after a species name indicates that this species is a representative of a supra-specific group having a larger geographical distribution. “<i>NC</i>” at nodes indicate that the ancestral ranges were not estimated at these nodes. On the left side, the spatio-temporal context is illustrated with four schematic paleoreconstructions (at 90, 65 and 50 Mya) on which are indicated the temporally corresponding clupeoid fossil localities by white (marine/brackish) and grey (freshwater) stars. Emerged lands are displayed in black and marine environments in blue with the shallow parts in lighter blue. One additional reconstruction (D) shows the current geographical context with the biogeographical units. The clupeoid fossil localities are: 1- the Cenomanian locality “Loma la Mula” in Coahuila, northeastern Mexico (taxon:†<i>Scombroclupea occidentalis</i> currently considered as a clupeid <i>incertae sedis</i>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Giersch1" target="_blank">[88]</a>; 2- the marine shale yielded in the Taquari Member (Albian) of Riachuelo Formation (state of Sergipe, Northeastern Brazil) (taxon:†<i>Nolfia riachuelensis</i> currently considered as a clupeid <i>ad interim</i>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-DeFigueiredo1" target="_blank">[81]</a>; 3- the marine deposit from the Cenomanian of Kipala, Democratic Republic of Congo (taxon:†<i>Nolfia kwangoensis</i> currently considered as a clupeid <i>incertae sedis</i>) and the marine Santonian of Vonso, Democratic Republic of Congo (taxon:†<i>Audenaerdia casieri</i> currently considered as a clupeid <i>incertae sedis</i>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Taverne6" target="_blank">[85]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Taverne7" target="_blank">[89]</a>; 4- the Cenomanian (Upper Cretaceous) Komen (Slovenia) fossil lagerstätte (taxon: †<i>Scombroclupea macrophthalma</i> currently considered as a clupeoid <i>incertae sedis</i>); <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Forey1" target="_blank">[83]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Jurkovsek1" target="_blank">[138]</a>; 5- the Cenomanian fossil fish localities of Lebanon (e.g., Namoura, Hakel and Hajula) (taxa: †<i>Scombroclupea</i> spp. currently considered as clupeoids <i>incertae sedis</i>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Forey1" target="_blank">[83]</a>; 6- the Upper Cretaceous (Maastrichtian) of Cayara, El Molino Formation, Bolivia (taxon:†<i>Gastroclupea branisai</i> currently considered as a pristigasterid <i>incertae sedis</i>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Grande3" target="_blank">[39]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-DeFigueiredo1" target="_blank">[81]</a>; 7- the Upper Cretaceous (Campano-Maastrichtian limit, 74.0 Mya) marine sediments of Nardò, Italy (taxa: †<i>Portoselvaggioclupea whiteheadi</i> and †<i>Nardoclupea grandei</i> [Dussumieriinae], †<i>Pugliaclupea nolardi</i> [Clupeinae], †<i>Lecceclupea ehiravaensis</i> [Pellonulinae], and †<i>Italoclupea nolfi</i> [Alosinae]) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Taverne1" target="_blank">[51]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Taverne4" target="_blank">[54]</a>; 8- The Middle Paleocene Tongue River Formation (lacustrine limestone), near Bay Horse, Montana, USA (taxon: †<i>Knightia vetusta</i> currently considered as a clupeoid <i>incertae sedis</i>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Grande4" target="_blank">[40]</a>; 9- the Middle Eocene Laney Member of the Green River Formation, southwestern Wyoming, USA (lacustrine deposits)(taxon: †<i>Gosiutichthys parvus</i> currently considered as a clupeoid <i>incertae sedis</i>) and the Lower Eocene lacustrine sediments of Wyoming, Colorado and Utah, USA (taxa: †<i>Knightia alta</i> and †<i>Knightia eocaena</i> currently considered as clupeoids <i>incertae sedis</i>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Grande4" target="_blank">[40]</a>; 10- the Lower Eocene (52.0 Mya) marine sediments of Monte Bolca, Italy (taxa: several species of Clupeidae including at least one species of Dussumieriinae <i>sensu</i> Grande <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Grande1" target="_blank">[18]</a>); 11- the Upper Paleocene freshwater lacustrine deposits of Bamanbor and Ninania of Saurashtra, India (taxon: †<i>Horaclupea intertrappea</i> currently considered as a clupeid <i>incertae sedis</i>) and the Eocene Saline Series of the Salt range of Pakistan (taxon: the clupeid †<i>Horaclupea geei</i>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Grande1" target="_blank">[18]</a>; 12- the Late Paleocene fish fauna of the Danata Formation in Turkmenistan (taxon: †<i>Primisardinella genetrix</i> currently considered as a clupeid <i>incertae sedis</i>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Grande1" target="_blank">[18]</a> and 13- the Eocene (probably freshwater) deposits of Hupei, China (taxon: †<i>Knightia yuyanga</i> currently considered as a clupeid <i>incertae sedis</i>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Grande1" target="_blank">[18]</a>.</p

Phylogenetic chronogram of the Clupeoidei based on a Bayesian relaxed clock analysis (using BEAST v1.7.4 [103]) of the mitogenomic dataset, calibrated with seven fossil-based constraints (see text for details).

<p><i>Coregonus lavaretus</i> and <i>Esox lucius</i> are together used to root the tree. Horizontal timescale is in million years before present (Mya) (Paleogene Epoch abbreviations: Paleo, Paleocene; Eo, Eocene; and Oligo, Oligocene). Black horizontal bars (indicating calibration constraints on the corresponding nodes) and light grey gradient horizontal bars at nodes are 95% age credibility intervals. Numbers given at nodes are the Bayesian posterior probabilities when <1. Black arrowheads indicate the crown group origins of lineages of Clupeoidei as discussed in the text.</p

Maximum likelihood tree of the Clupeoidei from analysis of the mitogenomic dataset (using RAxML [99]).

<p>Branch lengths are proportional to the number of substitutions per nucleotide position (scale bar = 0.05 substitutions). Numbers at nodes are Bootstrap proportions (in percentage). The tree is rooted with <i>Coregonus lavaretus</i> and <i>Esox lucius</i>. Abbreviation: <i>C.</i>, <i>Chirocentrus</i>.</p

Geographical pattern of distribution of the Clupeoidei.

<p>A) Distribution and species diversity of Clupeoidei. Number of species per grid cell (4 by 4 degree latitude-longitude resolution) is represented by cool (low diversity) to warm (high diversity) colors. Individual species distribution compiled from Whitehead <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Whitehead1" target="_blank">[16]</a> and Whitehead et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Whitehead2" target="_blank">[17]</a>, Wongratana <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Wongratana1" target="_blank">[125]</a>, Gourène and Teugels <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Gourne2" target="_blank">[126]</a>, Peng and Zhao <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Peng1" target="_blank">[127]</a>, Castro-Aguirre and Viverro <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-CastroAguirre1" target="_blank">[128]</a>, Randall <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Randall1" target="_blank">[129]</a>, Nelson and McCarthy <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Nelson6" target="_blank">[130]</a>, Siebert <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Siebert1" target="_blank">[34]</a>, Britz and Kottelat <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Britz1" target="_blank">[131]</a>, Menezes and De Pinna <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Menezes1" target="_blank">[132]</a>, Stiassny <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Stiassny1" target="_blank">[97]</a>, Castro-Aguirre et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-CastroAguirre2" target="_blank">[133]</a>, Roberts <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Roberts3" target="_blank">[134]</a>, Borsa et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Borsa1" target="_blank">[135]</a>, Kimura et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Kimura1" target="_blank">[136]</a>, Loeb <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Loeb1" target="_blank">[13]</a>, DiBattista et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-DiBattista1" target="_blank">[14]</a> and Randall and DiBattista <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056485#pone.0056485-Randall2" target="_blank">[137]</a>. B) The 12 biogeographical units used in the ancestral ranges reconstruction analysis; each unit was delimited by landmasses, vast expanses of open ocean and water temperature. Within each region, total number of clupeoid species (in regular) and number of endemics (in bold) are indicated in parentheses.</p

Summarized phylogenetic tree of the IWP sciaenids inferred by partitioned maximum-likelihood method with GTR+<i>Γ</i>+<i>I</i> nucleotide substitution model based on the <i>COI</i> gene dataset and results from species delimitation analyses and other considerations by four additional criteria (see materials and methods).

<p>Branch lengths are proportional to the inferred nucleotide substitutions. Numbers at nodes represent bootstrap values in percentage. Values below 70% are not shown; * indicates 100%. Taxa name in bold indicates problematic or probable misidentification samples. Numbers within the parentheses shown after the taxon names indicate number of sequences being contained within each collapsed clade or lineage. The tree is rooted with <i>Aplodinotus grunniens</i> according to Lo et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0176623#pone.0176623.ref024" target="_blank">24</a>]. Summary of the determined OTUs (vertical bars) is presented on the right side of the phylogenetic tree. Black bar indicates congruent OTUs as suggested by both species delimitation methods (i.e. robust results). White bar with a cross inside indicates the presence of multiple OTUs determined by GMYC in the particular genetic lineage that is incongruent to ABGD result. Missing data are marked by black crosses. Abbreviations for geographic distribution of the taxa: IO, Indian Ocean; ECS, East China Sea; SCS, South China Sea; CT, Coral Triangle region; SAS, Sahul Shelf and Australia.</p

Phylogenetic tree of the IWP sciaenids inferred by partitioned maximum-likelihood method with GTR+<i>Γ</i>+<i>I</i> nucleotide substitution model based on the combined dataset.

<p>Branch lengths are proportional to the inferred nucleotide substitutions. Numbers at nodes represent bootstrap values in percentage. Values below 70% are not shown; * indicates 100%. Different colors in genus <i>Johnius</i> show that the taxa are either from the pre-recognized subgenus, <i>Johnius</i> (in blue) or subgenus <i>Johnieops</i> (in red). The tree is rooted with <i>Aplodinotus grunniens</i> according the result shown in Lo et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0176623#pone.0176623.ref024" target="_blank">24</a>]. Abbreviations for geographic distribution of the taxa: IO, Indian Ocean; ECS, East China Sea; SCS, South China Sea; CT, Coral Triangle region; SAS, Sahul Shelf and Australia.</p