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

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

Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites-2

<p><b>Copyright information:</b></p><p>Taken from "Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites"</p><p>http://www.biomedcentral.com/1471-2148/7/204</p><p>BMC Evolutionary Biology 2007;7():204-204.</p><p>Published online 29 Oct 2007</p><p>PMCID:PMC2176064.</p><p></p>titution sites, dark gray; enzyme active sites, yellow. Full molecular models are shown on the left, and two cross sections are shown center and right. The inferred charge-changing sites localize to the surface of the PGI molecule (73 charge-changing sites/234 total surface sites, 3 charge-changing sites/316 total interior sites; = 0.0000, two-tailed Fisher's exact test), in contrast to the inferred charge-neutral sites (106 charge-neutral sites/234 total surface sites, 183 charge-neutral sites/316 total interior sites; = 0.1040, two-tailed Fisher's exact test) (B) Histograms of the inferred number of charge-changing and charge-neutral substitutions after the duplication. The solid green line denotes the proportion of charge-changing substitutions per total substitutions within the site classes based on solvent accessibility (horizontal axis): this proportion significantly increases with solvent-accessible surface area (= 0.0000, Cochran – Armitage trend test, = 584)

Phylogenetic tree and gene structures of the spiggin multi-gene family and its homologs

<p><b>Copyright information:</b></p><p>Taken from "Extensive lineage-specific gene duplication and evolution of the spiggin multi-gene family in stickleback"</p><p>http://www.biomedcentral.com/1471-2148/7/209</p><p>BMC Evolutionary Biology 2007;7():209-209.</p><p>Published online 4 Nov 2007</p><p>PMCID:PMC2180178.</p><p></p> Threespine and ninespine stickleback spiggin genes from the genome sequence (Gaac_spg1, 3, 4, 5, and 7; boxed), published spiggin cDNA sequences (spg1-spg4, Pungitius_spgα-γ; DDBJ/EMBL/NCBI accession numbers: AB221477, AB221481-83, DQ018713-8), and spiggin homologs in four other fish species (Tetraodon, spotted green pufferfish; Takifugu, torafugu; Oryzias, medaka; Danio, zebrafish) were subjected to phylogenetic analyses, and the resulting ML tree is shown. Numbers at nodes in internal branches indicate % bootstrap values (500 replicates). Putative corresponding relationships between genome and cDNA sequences are indicated by circles. The exon-intron structures of the corresponding genes are shown on the right. Brackets indicate the region used for phylogenetic studies (exons 7–16). The gene structure of spiggin cDNA sequences is shown in gray. Shaded boxes in the cDNA sequences indicate that the ORF could not be estimated from the genome data. Unpublished sequence gaps from ninespine stickleback genes and an undetermined region in the medaka genome are indicated by dotted lines. Asterisks in the zebrafish gene structure indicate the parts incongruent for the determination of ORFs because of indels

Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites-1

<p><b>Copyright information:</b></p><p>Taken from "Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites"</p><p>http://www.biomedcentral.com/1471-2148/7/204</p><p>BMC Evolutionary Biology 2007;7():204-204.</p><p>Published online 29 Oct 2007</p><p>PMCID:PMC2176064.</p><p></p>stimated pI. Arrow denotes a gene duplication event. (B) Amino acid sites that differ by the presence or absence of hydrophilic charged residues between current PGI-1 and PGI-2. Positively charged residues are blue; negatively charged residues, red; other residues, light gray. The numbers above refer to the amino acid positions of PGI [33]. The stars below indicate sites located on the molecular surface. (C) Inferred charge-changing substitution events mapped over the PGI phylogeny. Orange and brown bars denote upward and downward charge changes, respectively

Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites-3

<p><b>Copyright information:</b></p><p>Taken from "Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites"</p><p>http://www.biomedcentral.com/1471-2148/7/204</p><p>BMC Evolutionary Biology 2007;7():204-204.</p><p>Published online 29 Oct 2007</p><p>PMCID:PMC2176064.</p><p></p>eft) and bootstrap support values by the maximum likelihood method (right). Arrow denotes a gene duplication event. In cDNA clones, only one was identified from non-teleosts, whereas two genes were identified from teleosts. The two genes differed by about 20% in amino acid sequence, and were grouped into separate clades (and ). In both clades, the gene relationships were consistent with the evolutionary relationships of teleost species [18, 19, 21]. (B) Partial-length gel images of the RT-PCR expression analysis of genes and positive control () genes in ray-finned fishes. The tree in the left panel shows the relationships among the genes inferred in this study. The black circle on the tree denotes the timing of the gene duplication event. Letters indicate tissues: M, muscle; L, liver; H, heart; Gi, gill; B, brain; K, kidney. Full-length gels, including negative controls and size markers, are presented in Additional file : Fig. S5

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

Evolution of feeding specialization in Tanganyikan scale-eating cichlids: a molecular phylogenetic approach-4

<p><b>Copyright information:</b></p><p>Taken from "Evolution of feeding specialization in Tanganyikan scale-eating cichlids: a molecular phylogenetic approach"</p><p>http://www.biomedcentral.com/1471-2148/7/195</p><p>BMC Evolutionary Biology 2007;7():195-195.</p><p>Published online 18 Oct 2007</p><p>PMCID:PMC2212659.</p><p></p> from the upper jaws whereas black bars indicate those from the lower jaws in respective species. The mean standard length ± standard deviation (mm) and the number of specimens examined for each species are given in parentheses

Evolution of feeding specialization in Tanganyikan scale-eating cichlids: a molecular phylogenetic approach-3

<p><b>Copyright information:</b></p><p>Taken from "Evolution of feeding specialization in Tanganyikan scale-eating cichlids: a molecular phylogenetic approach"</p><p>http://www.biomedcentral.com/1471-2148/7/195</p><p>BMC Evolutionary Biology 2007;7():195-195.</p><p>Published online 18 Oct 2007</p><p>PMCID:PMC2212659.</p><p></p>ee. The coloured portion in each pie diagram corresponds to the calculated probability of the reconstruction of the respective feeding habit using the maximum likelihood method. The tree used for ancestral state estimation was inferred from AFLP data. Branch lengths are not to scale in this diagram. B) The habitat depth and oral tooth shape of each species are shown to the right. The teeth were photographed with a scanning electron microscope for species, and a Keyence digital microscope for species. Bars in the photographs indicate 0.1 mm