BPs of the three trees for the datasets constructed by successively removing the 50 most rapidly evolving genes

The horizontal axis shows the number of genes removed from the whole dataset of 2,789 genes. The dataset was analyzed using the concatenate model; the separate model, in which a category contains 50 genes grouped according to their total branch length; and the separate model, in which different parameters were provided to each gene. Each analysis was performed using nucleotide (GTR + Γ; the left-most column of panels), codon (+ Γ; the middle column of panels), and amino acid (JTT + Γ; the right-most column of panels) substitution models.<p><b>Copyright information:</b></p><p>Taken from "Rooting the eutherian tree: the power and pitfalls of phylogenomics"</p><p>http://genomebiology.com/2007/8/9/R199</p><p>Genome Biology 2007;8(9):R199-R199.</p><p>Published online 21 Sep 2007</p><p>PMCID:PMC2375037.</p><p></p

Additional file 3: Figure S3. of Distinct functions of two olfactory marker protein genes derived from teleost-specific whole genome duplication

Expression patterns of OMP1 and GÎąolf2. (PDF 4.99 mb

Additional file 5: Figure S5. of Distinct functions of two olfactory marker protein genes derived from teleost-specific whole genome duplication

Schematics of OMP duplication and subdivision of gene expressions during evolution. (PDF 4.99 mb

Additional file 2: Figure S2. of Distinct functions of two olfactory marker protein genes derived from teleost-specific whole genome duplication

Expression patterns of GÎąolf2 and GÎąo2. (PDF 4.99 mb

Additional file 1: Figure S1. of Distinct functions of two olfactory marker protein genes derived from teleost-specific whole genome duplication

Expression patterns of OMP1 and TRPC2. (PDF 4.99 mb

Functional Analysis of Kir7.1 Mutations

<div><p>(A) Positions of amino acid substitutions in the three alleles of <i>jaguar/obelix</i> with respect to wild-type. <i>obe^tc271d</i> (L130F) and <i>jag^b230</i> (T128M) have amino acid substitutions in the highly conserved P-domain (orange box), and <i>obe^td15</i> (F168L) has mutations in the transmembrane region (green box).</p><p>(B) Positions of the mutated amino acids in the 3D structure of zebrafish Kir7.1. The three-dimensional structure of Kir7.1 (residues 40 to 178) was deduced from the published X-ray crystal structure of KirBac1.1. Mutated residues (T128, L130, and F168) are highlighted as Corey-Pouling-Keltun (CPK) space-filling structures.</p><p>(C–F) The electrophysiological properties of mutant zebrafish Kir7.1 expressed exogenously on HEK293 cell membranes. The voltage-clamp protocol and typical elicited currents on HEK293 cell membranes exogenously expressing zebrafish wild-type (WT) Kir7.1 are shown in (C). Elicited currents on HEK293 cell membranes for the mutant <i>obe^tc271d</i> are shown in (D). Current inhibition in the presence of 1 mM Ba²⁺ is shown in (C) and (D), lower panel, indicating that the detected current is from potassium ions. Horizontal scale bar, 200 ms; vertical scale bar, 500 pA; arrowheads, zero-current levels.</p><p>(E) Current (I)–voltage (V) relationship; wild-type (WT) (closed circles) and <i>obe^tc271d</i> (open circles) (±SEM, <i>n</i> = 7, respectively).</p><p>(F) Current (I)–voltage (V) relationship; <i>obe^tc271d</i> (circles, ±SEM, <i>n</i> = 7), <i>obe^td15</i> (squares, ±SEM, <i>n</i> = 7), and <i>jag^b230</i> (triangles, ±SEM, <i>n</i> = 6). All mutant Kir7.1 show no functional current.</p></div

Melanophore Aggregation-Dispersion Response to the Change of Background Color

<p>Melanosome aggregation-dispersion in response to a rapid succession of background color change was measured. The upper panels show the responses of melanophores in the trunk of wild-type (WT) fish, and the lower panels show that of mutant fish <i>(obe^tc271d)</i>. The left panels depict the usual state (black background), the middle panels depict melanophores after being sustained for 3 min in a white (light) background, and the right panels depict melanophores after 3 min in a black (dark) background. The wild-type melanophores responded normally to the change of background color (<i>n</i> = 6), whereas mutant fish <i>(jag^b230</i> and <i>obe^tc271d)</i> melanophores strongly responded to the change of background color from black to white but did not respond to the change from white to black (<i>n</i> = 9 for all).</p

Adult Pigment Patterns in <i>jaguar/obelix</i> Mutant Zebrafish

<p>Pigment patterns of whole body (top), trunk (middle), and anal fin (bottom) in wild-type (WT), heterozygous (<i>obe^td15</i>/+), and homozygous <i>(obe^td15</i>/<i>obe^td15)</i> fish. Pigment patterns in all alleles of <i>jaguar/obelix (jag^b230, obe^tc271d,</i> and <i>obe^td15)</i> mutants are almost identical (unpublished data).</p

Rescue of the <i>jaguar/obelix</i> Phenotype by BAC Injection and Expression of <i>Kir7.1</i> mRNA

<div><p>(A) Line diagram depicting the genomic locations of the putative <i>Kir7.1</i> gene and BAC clones used for the rescue experiments. We used two BAC clones (98K22′ and 126F9, represented by gray lines) for microinjection. Numbers below the thick black line indicate the positions of the BACs and <i>Kir7.1</i> on LG15. Open boxes with vertical lines represent the positions and intron-exon structures of putative genes predicted from the ENSEMBL transcript.</p><p>(B) BAC rescue of pigment pattern in zebrafish mutants. Fertilized eggs from homozygous mutant fish <i>(jag^b230</i> and <i>obe^td15)</i> were used in the phenotype rescue experiment. For the injected fish that survived to adulthood, representative pigment patterns of whole body (top), trunk (middle), and anal fin (bottom) are shown. The left panels depict patterns resulting from phenotype rescue using BAC clone 98K22′. The middle panels depict patterns resulting from phenotype rescue using BAC clone 126F9. The right panels depict patterns of noninjected fish. All mutant fish <i>(jag^b230</i> and <i>obe^td15)</i> rescued by BAC injection had a partial stripe patterns.</p><p>(C) PCR analysis to confirm BAC integration in the rescued fin. Agarose gel analysis of PCR products derived from a BAC-specific sequence in nonrescued fins (lanes 2 and 3) and rescued fins (lanes 4 and 5). DNA fragments derived from the BAC clones were detected in all rescued fish (<i>n</i> = 6), but no PCR fragment was obtained from DNA of nonrescued fish (<i>n</i> = 6). Molecular mass markers are indicated (m).</p><p>(D) Expression of <i>Kir7.1</i> mRNA as detected by single-cell RT-PCR. Agarose gel analysis of RT-PCR products derived from individual melanophore (M), xanthophore (X), or fin dermal cells (F). Molecular mass markers are indicated (m).</p></div

Melanophore Response to an α₂-Adrenoceptor Agonist or Antagonist

<div><p>(A) Melanophore response to the agonist epinephrine. Fish were placed in black backgrounds for the duration of the experiment to block the endogenous aggregation signal from sympathetic nerves. The upper panels show the responses of melanophores in the trunk of wild-type fish (WT), and the lower panels show that of mutant fish <i>(obe^tc271d).</i> Melanophores of wild-type (<i>n</i> = 6) and mutant fish <i>(jag^b230</i> and <i>obe^tc271d)</i> (<i>n</i> = 12, for all) showed melanosome aggregation when epinephrine was added in the breading water, although the extent of aggregation in the mutant melanophores appeared to be more pronounced than in the wild-type.</p><p>(B) Melanophore response to the antagonist yohimbine. All fish were kept in an environment with a white background for several minutes (approximately 10 min) prior to addition of antagonist (left panels) and for the duration of the experiment to block endogenous dispersion. The upper panels show the responses of melanophores in the trunk of wild-type (WT) fish, and the lower panels show that of mutant fish <i>(obe^tc271d)</i>. Melanosomes of wild-type fish dispersed after adding the antagonist, because the antagonist blocks the endogenous aggregation signal (middle and right panels) (<i>n</i> = 7). However, in mutant fish <i>(jag^b230</i> and <i>obe ^tc271d),</i> many of the melanophores remained aggregated for a long time (longer than 60 min) (<i>n</i> = 12 for all) (unpublished data).</p></div