Segregating sites in nine western lowland gorillas.

<p>A. Density of segregating sites in 1 Mbp bins. Sites passing quality and depth filtering thresholds in all nine gorillas BiKira, EB(JC), Fubu, Guy, Kamilah, Kesho, Matadi, Murphy and Ruby were binned in 1 Mb bins and the density of segregating sites calculated. Resulting densities are plotted on an ideogram, with the scale expressed as number of sites per kbp. B. Profile of mean segregating site density as a function of chromosomal position on both long and short arms, averaged over all chromosomes. Position is normalised by chromosome length, with the centromere at 0.0 and the telomere at 1.0 on both arms. An increase in genetic diversity is evident towards the centromere and telomere on both arms.</p

A Genome-Wide Survey of Genetic Variation in Gorillas Using Reduced Representation Sequencing

<div><p>All non-human great apes are endangered in the wild, and it is therefore important to gain an understanding of their demography and genetic diversity. Whole genome assembly projects have provided an invaluable foundation for understanding genetics in all four genera, but to date genetic studies of multiple individuals within great ape species have largely been confined to mitochondrial DNA and a small number of other loci. Here, we present a genome-wide survey of genetic variation in gorillas using a reduced representation sequencing approach, focusing on the two lowland subspecies. We identify 3,006,670 polymorphic sites in 14 individuals: 12 western lowland gorillas (<i>Gorilla gorilla gorilla</i>) and 2 eastern lowland gorillas (<i>Gorilla beringei graueri</i>). We find that the two species are genetically distinct, based on levels of heterozygosity and patterns of allele sharing. Focusing on the western lowland population, we observe evidence for population substructure, and a deficit of rare genetic variants suggesting a recent episode of population contraction. In western lowland gorillas, there is an elevation of variation towards telomeres and centromeres on the chromosomal scale. On a finer scale, we find substantial variation in genetic diversity, including a marked reduction close to the major histocompatibility locus, perhaps indicative of recent strong selection there. These findings suggest that despite their maintaining an overall level of genetic diversity equal to or greater than that of humans, population decline, perhaps associated with disease, has been a significant factor in recent and long-term pressures on wild gorilla populations.</p></div

Rates and ratios of heterozygous and homozygous variants in each of the gorillas sampled.

<p>Rates of heterozygous (light blue) and homozygous (dark blue) variants were called from sequence alignments against the gorilla reference genome and expressed as percentage rates. Note Kamilah’s low rate of homozygous variants, due to her providing the DNA from which the reference genome was assembled. The corresponding hom/het ratios (ratios of homozygous to heterozygous variant rates) show that eastern lowland gorillas (black) have higher ratios than western lowland gorillas (red). Additional data for Mukisi and EB(JC) (Mukisi_PvuII and EB_JC_PvuII) were taken from a previously published study <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065066#pone.0065066-Scally1" target="_blank">[3]</a>.</p

Principal components analysis (PCA).

<p>A. PCA based on 123,591 polymorphic sites in 12 western lowland gorillas and two eastern lowland gorillas. Here, PC1 separates western gorillas from eastern gorillas. B. PCA based on 110,971 polymorphic sites in the 12 western lowland gorillas only.</p

Allele frequency spectra.

<p>Conditional allele frequency spectra are shown for eight western lowland gorillas (red) and eight samples from each of three human populations: African (black), European (blue) and Asian (green). Spectra are conditioned on sites ascertained in one individual (and, for gorilla, averaged over all samples). The dashed line is the theoretical expectation for a constant population size. Error bars for the gorilla samples represent standard deviations.</p

Zooming on the region on chromosome 11 that showed the strongest signals in the Northeastern Siberian populations.

<p>The |iHS|, XP-EHH and PBS scores that showed strong signals (amongst top 10 ranking windows) in the Northeastern Siberian populations are shown in the upper panels for the different Siberian populations. The pink highlights mark the windows present in the top 10 ranking windows in the Northeastern Siberian populations. The rankings are marked on the respective windows in the respective test panels. Protein-coding genes present in the 4 Mb region are shown under the test plots with the genes present in our predefined cold adaptation list marked in bold font (<i>CPT1A</i> and <i>LRP5</i>). The position on the chromosome is given in Mb. The paintings of the phased chromosomes for the region in the Northeastern and Central Siberian individuals are shown underneath the <i>Position</i> legend. The aggregated ancestral probabilities from ChromoPainter for the Northeastern Siberian individuals are displayed below the paintings. The dotted red line shows the threshold for the upper 5% tail (0.75) and the black dotted line shows the mean of the genome-wide probabilities distribution of the Northeastern Siberian ancestor (red).</p

Population structure analyses in Siberian populations.

<p>(A) Averaged sampling locations of the Siberian populations genotyped in this study. (B) Principal component analysis of Siberian populations and reference populations from West Asia (European) and Southeast Asia (Vietnamese). Each dot in the plot represents an individual. The PC axes were rotated 180 degrees anti-clockwise to emphasize the similarity to the geographic map of Eurasia. (C) ADMIXTURE analysis at <i>K</i> = 4. (D) Coancestry heatmap for the Siberian individuals and reference populations (Europe, Vietnamese) output by ChromoPainter/fineSTRUCTURE. The heatmap shows the number of shared genetic chunks between the individuals. The raw data is shown on the bottom left and the aggregated data is shown on the upper right of the heatmap. Adjacent to the heatmap is also the ADMIXTURE plot of the respective individuals. To the left is the maximum a posteriori (MAP) tree generated by fineSTRUCTURE which shows the groupings of the different populations. The following abbreviations are used in the Figure: ALT, Altai-Kizhi; BUR, Buryats; CEU, European; CHB, Han Chinese; CHK, Chukchi; E/SE Asia, East/Southeast Asia; ESK, Eskimo; EVN, Evens; EVK, Evenks; KRK, Koryaks; SHR, Shors; TEL, Teleuts; VTN, Vietnamese; X1, Northeastern Siberian admixed individuals; X2, Southern and Central Siberian admixed individuals; YKT, Yakuts. Reference populations are labelled in italics. Outliers removed in downstream analysis are blacked out in the tree.</p