第768回千葉医学会例会・第3回磯野外科例会 68.

Aligned nucleotide sequences of the 12S rRNA gene in the mt genomes of 249 fishes. (PDF 537 kb

第809回千葉医学会例会・第一外科教室談話会 8.

Aligned nucleotide sequences of the origin of L-strand replication (blue and magenta letters) in the mt genomes of 250 fishes. (PDF 38 kb

Additional file 6: Figure S1-a. of Structure and variation of the mitochondrial genome of fishes

Aligned amino acid sequences of the ATP8 gene in mt genomes of 250 fishes. Figure S1-b. Aligned amino acid sequences of the ATP6 gene in mt genomes of 250 fishes. Figure S1-c. Aligned amino acid sequences of the COI gene in mt genomes of 250 fishes. Figure S1-d. Aligned amino acid sequences of the COII gene in mt genomes of 250 fishes. Figure S1-e. Aligned amino acid sequences of the COIII gene in mt genomes of 250 fishes. Figure S1-f. Aligned amino acid sequences of the Cyt b gene in mt genomes of 250 fishes. Figure S1-g. Aligned amino acid sequences of the ND1 gene in mt genomes of 249 fishes. Figure S1-h. Aligned amino acid sequences of the ND2 gene in mt genomes of 250 fishes. Figure S1-i. Aligned amino acid sequences of the ND3 gene in mt genomes of 250 fishes. Figure S1-j. Aligned amino acid sequences of the ND4L gene in mt genomes of 250 fishes. Figure S1-k. Aligned amino acid sequences of the ND4 gene in mt genomes of 250 fishes. Figure S1-l. Aligned amino acid sequences of the ND5 gene in mt genomes of 250 fishes. Figure S1-m. Aligned amino acid sequences of the ND6 gene in mt genomes of 249 fishes. (ZIP 3250 kb

Additional file 4: Table S4. of Structure and variation of the mitochondrial genome of fishes

Length variation in 13 protein-coding genes in the mt genomes of 250 fishes. (XLSX 53 kb

Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences-2

Ainst molecularly estimated divergence times (mean values for the divergence times shown in Fig. 2). Closed triangles show plots of the timing of continental breakups against the molecular time estimates of cichlid divergences between the corresponding continents (data taken from Fig. 2). The timings used for complete continental breakups are 112 MYA for (Africa + South America) vs. (Madagascar + Indo/Sri Lanka), 100 MYA for Africa vs. South America, and 85 MYA for Madagascar vs. Indo/Sri Lanka [-]. The solid line indicates a 1:1 relationship between paleontological and molecular time estimates.<p><b>Copyright information:</b></p><p>Taken from "Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences"</p><p>http://www.biomedcentral.com/1471-2148/8/215</p><p>BMC Evolutionary Biology 2008;8():215-215.</p><p>Published online 23 Jul 2008</p><p>PMCID:PMC2496912.</p><p></p

Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences-1

Mitogenomic DNA sequences (10,034 sites). Two sharks (and ) were used as an outgroup (not shown). The multidistribute program [] was used to estimate divergence times assuming the tree topology shown in Fig. 1. Letters indicate nodes at which maximum and/or minimum time constraints were set (see Table 2 for details of the individual constraints). Paleogeographical maps at 148 MYA, 120 MYA, 95 MYA, and 85 MYA [] are shown. Dark-gray areas on the maps represent those being fragmented within Gondwanaland at those times.<p><b>Copyright information:</b></p><p>Taken from "Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences"</p><p>http://www.biomedcentral.com/1471-2148/8/215</p><p>BMC Evolutionary Biology 2008;8():215-215.</p><p>Published online 23 Jul 2008</p><p>PMCID:PMC2496912.</p><p></p

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

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

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

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