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A genome-wide survey of genetic variation in gorillas using reduced representation sequencing.

Scally A, Yngvadottir B, Xue Y, Ayub Q, Durbin R, Tyler-Smith C - PLoS ONE (2013)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

ABSTRACT
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 (Gorilla gorilla gorilla) and 2 eastern lowland gorillas (Gorilla beringei graueri). 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.

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Allele frequency spectra.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.
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pone-0065066-g003: Allele frequency spectra.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.

Mentions: The allele frequency spectrum (AFS) within a population provides insight into demographic and evolutionary processes. We obtained conditional allele frequency spectra by identifying heterozygous sites within one individual (taking each individual in turn) and estimating the non-reference allele frequency across all samples at each of those sites (Methods). Figure 3 shows the resulting mean conditional AFS for eight western lowland gorillas (excluding Kamilah and the three lowest-coverage samples), and comparable samples from three human populations whose ancestry derives from Africa, Asia and Europe (see Methods). In a population whose effective size has remained constant, the theoretical expectation for such a conditional AFS is a straight line of constant negative slope [22], shown by the dashed line in Figure 3. Compared to this, western lowland gorillas show a deficit of rare alleles, consistent with their having undergone genetic drift due to a bottleneck or other reduction in effective population size during their demographic history. The similar signal in non-African human populations has been attributed to population contraction associated with the out-of-Africa event [23]. By contrast to the gorillas and the non-African humans, the African population in Figure 3 shows an excess of rare alleles, consistent with population expansion and again similar to the signal seen in other human data [23].


A genome-wide survey of genetic variation in gorillas using reduced representation sequencing.

Scally A, Yngvadottir B, Xue Y, Ayub Q, Durbin R, Tyler-Smith C - PLoS ONE (2013)

Allele frequency spectra.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.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3672199&req=5

pone-0065066-g003: Allele frequency spectra.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.
Mentions: The allele frequency spectrum (AFS) within a population provides insight into demographic and evolutionary processes. We obtained conditional allele frequency spectra by identifying heterozygous sites within one individual (taking each individual in turn) and estimating the non-reference allele frequency across all samples at each of those sites (Methods). Figure 3 shows the resulting mean conditional AFS for eight western lowland gorillas (excluding Kamilah and the three lowest-coverage samples), and comparable samples from three human populations whose ancestry derives from Africa, Asia and Europe (see Methods). In a population whose effective size has remained constant, the theoretical expectation for such a conditional AFS is a straight line of constant negative slope [22], shown by the dashed line in Figure 3. Compared to this, western lowland gorillas show a deficit of rare alleles, consistent with their having undergone genetic drift due to a bottleneck or other reduction in effective population size during their demographic history. The similar signal in non-African human populations has been attributed to population contraction associated with the out-of-Africa event [23]. By contrast to the gorillas and the non-African humans, the African population in Figure 3 shows an excess of rare alleles, consistent with population expansion and again similar to the signal seen in other human data [23].

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

ABSTRACT
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 (Gorilla gorilla gorilla) and 2 eastern lowland gorillas (Gorilla beringei graueri). 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.

Show MeSH
Related in: MedlinePlus