Divergence was estimated by using the human (GenBank: ) and chimpanzee (this study, Genbank: ) reference sequences alone or by incorporating the diversity data obtained from re-sequencing for one or both species into the calculations

The re-sequencing data for human (n = 95) originated from the published study[] and for chimpanzee (n = 11) from the unpublished dataset of the authors.<p><b>Copyright information:</b></p><p>Taken from "High divergence in primate-specific duplicated regions: Human and chimpanzee genes"</p><p>http://www.biomedcentral.com/1471-2148/8/195</p><p>BMC Evolutionary Biology 2008;8():195-195.</p><p>Published online 7 Jul 2008</p><p>PMCID:PMC2478647.</p><p></p

High divergence in primate-specific duplicated regions: Human and chimpanzee genes-2

and genes (in total 6,878 bp; GC-nucleotide content 64%; 161 substitutions). (B) Nucleotide substitutions in the whole orthologous region of the genome cluster (in total 36,211 bp, GC-nucleotide content 57%, 835 substitutions). Percents for all substitution types are shown with summarized information for transversions and transitions.<p><b>Copyright information:</b></p><p>Taken from "High divergence in primate-specific duplicated regions: Human and chimpanzee genes"</p><p>http://www.biomedcentral.com/1471-2148/8/195</p><p>BMC Evolutionary Biology 2008;8():195-195.</p><p>Published online 7 Jul 2008</p><p>PMCID:PMC2478647.</p><p></p

High divergence in primate-specific duplicated regions: Human and chimpanzee genes-0

Quences from []. Phylogenetic analysis of intergenic regions was conducted with segments without (B-D) and with (E-G) covering pseudogenes. The homologous segments used for each respective phylogenetic analysis are indicated with a circle on a consensus structure of the intergenic regions in cluster (boxed; from Figure 1B). The nomenclature of the intergenic regions is as on Figure 1B. Bootstrap support values are shown at the nodes (1000 bootstrap replications). Abbreviations: hu – human, ch – chimpanzee, gor – gorilla, orang – orangutan.<p><b>Copyright information:</b></p><p>Taken from "High divergence in primate-specific duplicated regions: Human and chimpanzee genes"</p><p>http://www.biomedcentral.com/1471-2148/8/195</p><p>BMC Evolutionary Biology 2008;8():195-195.</p><p>Published online 7 Jul 2008</p><p>PMCID:PMC2478647.</p><p></p

High divergence in primate-specific duplicated regions: Human and chimpanzee genes-1

(Ch)/7,973 bp (Hu) from gene to the end of and 29,136 bp (Ch)/28,568 bp (Hu) from to gene. The species-specific large duplications (human 12,700 bp, chimp 6,725 bp) have been excluded from the comparison. The percents of nucleotide substitutions and indels are calculated per 500 bp non-overlapping windows. Grey arrows indicate the locations of coding genes drawn to an approximate scale. – denote intergenic regions from Figure 1B. Intergenic repeat fraction includes , satellites, simple repeats and low complexity DNA sequences within each intergenic region.<p><b>Copyright information:</b></p><p>Taken from "High divergence in primate-specific duplicated regions: Human and chimpanzee genes"</p><p>http://www.biomedcentral.com/1471-2148/8/195</p><p>BMC Evolutionary Biology 2008;8():195-195.</p><p>Published online 7 Jul 2008</p><p>PMCID:PMC2478647.</p><p></p

Comparison of methylation level estimates for the bisulfite sequencing, HumanMethylation 450K and MeDIP-seq data.

<p>Data are shown for the 28 islands (associated with 36 genes) containing CpG sites that overlapped with those interrogated by HumanMethylation 450K array for sample GM01240. Evolutionary strata information is shown to the right of the ideogram of the human X chromosome <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050233#pone.0050233-Ross1" target="_blank">[66]</a>: the blue line represents the S3 stratum; the purple line represents the S2 stratum and the red line the S1 stratum. Both names are given for genes sharing a CpG island separated by “/”. Methylation level estimates for each of the techniques are shown to the right of the gene names in light green (low), green (medium), and dark green (high). Examples of four genes are shown in more detail on the right of the figure. The gene names are highlighted in colour at the top of each panel and in a corresponding colour on the gene list. Data for the bisulfite sequencing (BS-s), HumanMethylation 450K (450K) and MeDIP-seq (MD-s) are shown at the top, center and bottom of each panel, respectively. The genes shown give examples where the three techniques agree in methylation level: low level methylation in the gene ZFX, medium level methylation in the PRPS2 gene, and a high level of methylation in the ACRC gene. Data are also given for the HCFC1/TMEM187 genes, for which different methods show inconsistency in the classified methylation levels. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050233#pone.0050233.s004" target="_blank">Figure S4</a> for data for sample GM01247.</p

Coverage by MeDIP-seq and the HumanMethylation 450K BeadChip of different genomic features.

<p>The different features are described along the bottom axis. 100% coverage is defined as covering all of the elements of a particular type in the human genome. Coverage for MeDIP-seq data (MD-s) (averaged for GM01240 and GM01247) is shown as blue bars and for the HumanMethylation 450K (450K) as red bars. Average percentages covered for each technique for each group of features are given above the bar chart. For MeDIP-seq the region or feature was defined as being covered if any part of the region or feature was covered by or overlapped any part of one or more sequencing reads. The coverage for the MeDIP-seq was consistent between the two samples (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050233#pone.0050233.s005" target="_blank">Table S1</a>), illustrating a high degree of reproducibility for the technique. The coverage shown for the HumanMethylation 450K is reported as the number of features where at least one probe present on the array mapped within the features under consideration i.e. is based on the array design.</p

Concordance of the HumanMethylation 450K (450K) and MeDIP-seq (MD-s) data with bisulfite sequencing (BS-s) data.

<p>The top part of the table gives the concordance of the average beta-values for the 326 probes on the X chromosome from the HumanMethylation 450K (450K) and the methylation score calculated by the MEDIPS software for the MeDIP-seq data (MD-s) to the methylation levels for the bisulfite data (BS-s) from MethTools. The second half of the table contains the concordance for a similar analysis for the HumanMethylation 450K and MeDIP-seq data for all autosomal chromosomes.</p

Multidimensional scaling (MDS) plots.

<p>Each point represents an individual genome. Red triangles are individuals from the Kuopio region of Finland while violet triangles are individuals from Helsinki. Each blue circle represents a proband from each of the 13 CDGP families. The yellow circle is the proband from Family 1. Panel A shows the relationship between principal components (PCs) 1 and 2, which explain most of the genetic variation. Panel B shows PC1 versus PC3, which appear to mimic a geographical northeast to southwest axis.</p

Pedigrees of the 13 families included in the study.

<p>Circles represent females and squares are males. Filled circles are classified as affected with CDGP, while shaded circles are unknown or do not fulfill the criteria for CDGP. The proband from each family is marked with an arrow. Individuals with an asterisk (*) have been sequenced at the pericentromere of chr 2. All probands and both of their parents were genotyped (denoted with the symbol #) except family 11, in which only the proband and affected parent were genotyped.</p

Pedigrees of the seven families with recurrent spontaneous preterm births analyzed in the linkage analysis of X chromosomal markers.

<p>Individuals born preterm are shown by half-black symbols. Squares represent males and circles females. Individuals analyzed in the linkage analysis are indicated by a number (<i>n</i> = 89). The diamonds denote an unspecified number of term infants, the smaller diamonds with a line through the symbol represent a miscarriage, and the lines through the other symbols indicate that the person is deceased. Gestational ages and years of birth for the family members born preterm are shown in Table S1. Linkage analysis was performed in two settings: 1) being spontaneously born preterm as the phenotype (affected offspring phenotype, <i>n_affected</i>  = 41), and 2) giving spontaneous preterm births as the phenotype (affected mother phenotype, <i>n_affected</i>  = 21). These pedigrees have been previously shown in the supplementary material of our linkage study of SPTB performed using autosomal markers <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051378#pone.0051378-Haataja1" target="_blank">[27]</a>.</p