Map showing sampling locations.

<p>Blue diamond = <i>C</i>. <i>corax</i>, Holarctic lineage; red triangle = <i>C</i>. <i>corax</i>, California lineage; green circle = <i>C</i>. <i>cryptoleucus</i>; yellow square = <i>C</i>. <i>ruficollis</i>.</p

Sample information.

<p>Clade assignment of common ravens from North America to either California or Holarctic lineages are given for mitogenomes presented in this study and either mtDNA control region or COI sequenced in previous studies ([<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187316#pone.0187316.ref017" target="_blank">17</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187316#pone.0187316.ref018" target="_blank">18</a>]; authors’ unpubl. data).</p

Genetic distances (uncorrected p-distances) among Holarctic (HOL) and Californian (CAL) lineages of the common raven and the Chihuahuan (CHI) raven, for different partitions, the whole alignment and protein coding genes concatenated.

<p>Genetic distances (uncorrected p-distances) among Holarctic (HOL) and Californian (CAL) lineages of the common raven and the Chihuahuan (CHI) raven, for different partitions, the whole alignment and protein coding genes concatenated.</p

Graphical overview of the <i>Corvus corax</i> mitogenome.

<p>The figure contains the following information, from the outermost to the innermost layer: (1) Gene products for annotated genes. (2) Genome position, minor ticks for every kb. Red bars illustrate GC-content in 20 bp windows. (3) Forward and (4) reverse genes. Blue colours show tRNAs, red colours show rRNAs and grey colours illustrate protein coding genes. (5) Coverage plot with log transformed coverage. (6) Position for amplicon 1 and (7) position for amplicon 2. The figure was created from GenBank accession KX245135 in the software Circleator [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187316#pone.0187316.ref042" target="_blank">42</a>].</p

Beta diversity according to the ancestral HLA haplotype AH8.1 status.

<p>A principal coordinate plot of the beta diversity measure unweighted unifrac shows all samples colored according to the HLA genotype groups. There were no significant differences between the groups. <i>Yellow</i>: AH8.1 homozygous, i.e. homozygosity for both HLA-B*08 and HLA-DRB1*03. <i>Violet</i>: AH8.1 heterozygotes, i.e. at least 1 copy of HLA-B*08 and HLA-DRB1*03. <i>Turquoise</i>: Non AH8.1 heterozygotes, i.e. HLA-B*08 and HLA-DRB1*03 both not present. <i>Grey</i>: HLA-DRB1 homozygous but non AH8.1.</p

Phylogenetic diversity according to the ancestral HLA haplotype AH8.1 status.

<p>Phylogenetic diversity, an alpha diversity measure of bacterial richness, is shown according to carrier status of the AH8.1 haplotype (left), as well as the pre-defined HLA genotype groups (right, AH8.1 homozygotes, i.e. homozygosity for both HLA-B*08 and HLA-DRB1*03; AH8.1 heterozygotes, i.e. at least 1 copy of HLA-B*08 and HLA-DRB1*03; Non AH8.1 heterozygotes, i.e. HLA-B*08 and HLA-DRB1*03 both not present. Non AH8.1 homozygotes, i.e. HLA-DRB1 homozygous but non AH8.1). There were no significant differences between the groups.</p

Genus level taxonomic distribution in 117 Norwegian stool samples according to ancestral HLA haplotype AH8.1 status.

<p>(A) The genus abundances sorted according to the relative abundance of <i>Bacteroides</i>, of n = 72 AH8.1 carriers (left) are shown compared with the n = 45 non-AH8.1 samples (right). In (B) the genus abundances are shown according to all four pre-defined genotype groups; Left: AH8.1 homozygotes, i.e. homozygosity for both HLA-B*08 and HLA-DRB1*03; Middle left: AH8.1 heterozygotes, i.e. at least 1 copy of HLA-B*08 and HLA-DRB1*03; Middle right: Non AH8.1 heterozygotes, i.e. HLA-B*08 and HLA-DRB1*03 both not present; Right: <i>HLA-DRB1</i> homozygous but non AH8.1.</p

Characteristics of the study population according to HLA genotype^a.

<p>^aFour different groups were included to represent homozygosity and heterozygosity for the AH8.1 haplotype (as defined by the presence of HLA-B*0801 and DRB1*0301), absence of this haplotype as well as homozygosity for other DRB1 haplotypes. There were no significant differences (all p>0.23) for any of the parameters when applying Kruskal-Wallis test for continuous and 2x4 chi square test for categorical parameters.</p><p>^bTransport time as defined by time from sampling to the freezer.</p><p>Characteristics of the study population according to HLA genotype<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133804#t002fn001" target="_blank">^a</a>.</p

The Influence of the Autoimmunity-Associated Ancestral HLA Haplotype AH8.1 on the Human Gut Microbiota: A Cross-Sectional Study

<div><p>Multiple immune-related genes are encoded in the HLA complex on chromosome 6p21. The 8.1 ancestral haplotype (AH8.1) include the classical HLA alleles HLA-B*08:01 and HLA-DRB1*03:01, and has been associated with a large number of autoimmune diseases, but the underlying mechanisms for this association are largely unknown. Given the recently established links between the gut microbiota and inflammatory diseases, we hypothesized that the AH8.1 influences the host gut microbial community composition. To study this further, healthy individuals were selected from the Norwegian Bone Marrow Donor Registry and categorized as either I. AH8.1 homozygote (n=34), II. AH8.1 heterozygote (n=38), III. Non AH8.1 heterozygote or IV. HLA-DRB1 homozygote but non AH8.1 (n=15). Bacterial DNA from stool samples were subjected to sequencing of the V3–V5 region of the 16S rRNA gene on the 454 Life Sciences platform and data analyzed using Mothur and QIIME. The results showed that the abundances of different taxa were highly variable within all pre-defined AH8.1 genotype groups. Using univariate non-parametric statistics, there were no differences regarding alpha or beta diversity between AH8.1 carriers (categories I and II) and non-carriers (categories III and IV), however four different taxa (<i>Prevotellaceae</i>, <i>Clostridium XVIII</i>, <i>Coprococcus</i>, <i>Enterorhabdus</i>) had nominally significant lower abundances in AH8.1 carriers than non-carriers. After including possible confounders in a multivariate linear regression, only the two latter genera remained significantly associated. In conclusion, the overall contribution of the AH8.1 haplotype to the variation in gut microbiota profile of stool in the present study was small.</p></div

Pre-defined HLA genotype groups.

<p>AH8.1: Ancestral haplotype 8.1</p><p>Pre-defined HLA genotype groups.</p