Admixture analysis of salmon representing fish collected from the local Norwegian farm, prey captured in cod stomachs, and the nearest wild Atlantic salmon population.

<p>Results of admixture analysis are presented when the number of genetic clusters (i.e., <i>k</i>) is set to 4. Each genetic cluster is represented by a colour, and each individual's genetic assignment is represented by a vertical bar. Individuals may be admixed (i.e., mixtures of genetic clusters).</p

Genetic assignment of the prey to the samples collected from a local Norwegian farm and to the nearest wild Atlantic salmon population.

<p>A =  direct assignment of prey to the genetically most similar sample, B =  exclusion of prey from each sample in turn at α 0.01 threshold, C =  exclusion of prey from each sample in turn at α 0.001 threshold. Note that individual prey can in theory be excluded from all or none of the samples, thus, exclusion does not sum to the exact number of prey in contrast to direct assignment which adds up to 37.</p

Examples of prey sampled from Atlantic cod stomachs.

<p>Most of the 36 prey were more severely digested than the specimens presented here and morphologically impossible to identify. However, not all prey were photographed.</p

Genetic relationships among the sets of samples as measured by pair-wise F_ST (data in upper right diagonal), with associated P-values (data in lower left diagonal).

<p>Genetic relationships among the sets of samples as measured by pair-wise F_ST (data in upper right diagonal), with associated P-values (data in lower left diagonal).</p

Paraffin sections from gill tissues.

<p>The sections of gill tissue from <i>Clarias gariepinus</i> have been processed for <i>in situ</i> hybridization or stained with HES. A) Primary filament showing dark-blue stained <i>Candidatus</i> Actinochlamydia clariae inclusions, stained with antisense DIG-labelled RNA-probe against <i>Ca.</i> A. clariae 16S rRNA. Cells with inclusions are particularly frequent at the filament tip. Bar = 100.0 µm. B) Same primary filament stained with a sense probe, demonstrating absence of staining in the inclusions (examples indicated by arrows). Bar = 100.0 µm. C) HES stained section of the same filament tip. Bar = 100.0 µm. D) Magnification of an IHC stained inclusion, where the actiniae are discernible (arrowhead). Bar 10.0 = µm.</p

Section through inclusion with IBs.

<p>Sections through inclusions containing mainly IBs. The IBs have condensed nucleoids, but the rest of the content of the bacteria is not condensed. A) Bar = 5.0 µm. B) Bar = 0.5 µm. C) Bar = 0.5 µm.</p

Semi-thin sections of infected primary lamellas from African sharptooth catfish.

<p>Pictures of semi-thin sections of the primary gill lamellas from African sharptooth catfish infected with <i>Candidatus</i> Actinochlamydia clariae. Arrows point to cysts of variable sizes. The majority of the cysts are located towards the apical part of the primary lamellas. A) Bar = 60.0 µm. B) Bar = 30.0 µm.</p

Phylogenetic tree.

<p>The phylogenetic tree shows the relationship between <i>Candidatus</i> Actinochlamydia clariae from African sharptooth catfish and selected members of other families within the order Chlamydiales. The best-fitting nucleotide substitution model was used during maximum likelihood analysis and the tree was bootstrapped (50 000 quartet puzzling steps) in TREE_PUZZLE. The scale bar shows the number of nucleotide substitutions as a proportion of branch lengths.</p

Nucleotide similarity of <i>Ca</i>. Actinochlamydia clariae (Accession nos: JQ480299, JQ480300, JQ480301) compared to other members of the order Chlamydiales.

<p>Nucleotide similarity of <i>Ca</i>. Actinochlamydia clariae (Accession nos: JQ480299, JQ480300, JQ480301) compared to other members of the order Chlamydiales.</p

Section through inclusion with EBs.

<p>Section through a large inclusion from the gills of <i>Clarias gariepinus</i> containing mainly EBs. A) The cyst is beginning to open to the gill surface (arrow), and the host cell cytosol shows signs of degeneration. A neighbouring cell contains an inclusion with RBs only (asterisk). Bar = 5.0 µm. B) Section through EB showing the cap area with associated protein structures (arrow). Tangential section through the cap area (ring) showing the hexagonal arrangement of the proteins. Bar = 0.2 µm. C) Section through free EBs showing the smooth cap areas (arrows) with proteins, an electron dense core (nucleoid), and condensed cytoplasm consisting mainly of ribosomes. Bar = 0.2 µm.</p