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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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Rates and ratios of heterozygous and homozygous variants in each of the gorillas sampled.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 [3].
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pone-0065066-g001: Rates and ratios of heterozygous and homozygous variants in each of the gorillas sampled.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 [3].

Mentions: Genotypes were called from the alignments of sequence data to the gorilla reference for each of the 14 individuals, with sites filtered on the basis of mapping quality and depth (Methods). Figure 1 shows the resulting rates of heterozygous and homozygous variant sites (with one or both alleles differing from the reference respectively) in each individual. With the exception of Kamilah, we observed higher levels of heterozygosity in all western gorillas compared to the two eastern gorillas, consistent with previous studies [3], [4], [18] and indicating that western lowland gorillas are more genetically diverse and have higher effective population size than their eastern relatives. Kamilah’s low rate of homozygous variants is due to the fact that her DNA provided the source for the gorilla reference genome assembly [3], so that such sites called from her sequence data are essentially due to errors either in alignment, variant calling or in the reference itself. Since the reference individual is a western lowland gorilla, the fact that we observe higher rates of homozygous variant sites in eastern gorillas is consistent with the two species being demographically distinct.


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)

Rates and ratios of heterozygous and homozygous variants in each of the gorillas sampled.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 [3].
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3672199&req=5

pone-0065066-g001: Rates and ratios of heterozygous and homozygous variants in each of the gorillas sampled.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 [3].
Mentions: Genotypes were called from the alignments of sequence data to the gorilla reference for each of the 14 individuals, with sites filtered on the basis of mapping quality and depth (Methods). Figure 1 shows the resulting rates of heterozygous and homozygous variant sites (with one or both alleles differing from the reference respectively) in each individual. With the exception of Kamilah, we observed higher levels of heterozygosity in all western gorillas compared to the two eastern gorillas, consistent with previous studies [3], [4], [18] and indicating that western lowland gorillas are more genetically diverse and have higher effective population size than their eastern relatives. Kamilah’s low rate of homozygous variants is due to the fact that her DNA provided the source for the gorilla reference genome assembly [3], so that such sites called from her sequence data are essentially due to errors either in alignment, variant calling or in the reference itself. Since the reference individual is a western lowland gorilla, the fact that we observe higher rates of homozygous variant sites in eastern gorillas is consistent with the two species being demographically distinct.

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