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Domestication of the dog from the wolf was promoted by enhanced excitatory synaptic plasticity: a hypothesis.

Li Y, Wang GD, Wang MS, Irwin DM, Wu DD, Zhang YP - Genome Biol Evol (2014)

Bottom Line: Here, we demonstrate that genes involved in glutamate metabolism, which account partially for fear response, indeed show the greatest population differentiation by whole-genome comparison of dogs and wolves.However, the changing direction of their expression supports a role in increasing excitatory synaptic plasticity in dogs rather than reducing fear response.Because synaptic plasticity are widely believed to be cellular correlates of learning and memory, this change may alter the learning and memory abilities of ancient scavenging wolves, weaken the fear reaction toward humans, and prompt the initial interspecific contact.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China wudongdong@mail.kiz.ac.cn zhangyp@mail.kiz.ac.cn.

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Analysis of selection in the dog genome. (A) Comparisons of the nucleotide diversity (left) and Tajima’s D values (right) between genes containing large numbers of fixed SNP differences and other genes ± S.D. were presented. (B) Comparisons of the difference in expression levels between wolves and dogs between genes containing large numbers of fixed SNP differences and other genes. The expression value for each gene was log2 transformed. Left: Expression difference of each gene between the wolf and the dog was calculated by the transformed value in the dog minus the transformed value in wolf. Right: Difference of each gene between the wolf and the dog was calculated by the transformed value in the dog divided by the transformed value in the wolf. (C) Left: Negative correlation between FST values and recombination rates of genome wide SNPs. Right: Positive correlation between FST values and recombination rates of SNPs at genes in GO categories: GO: 0001640 and GO: 0007216, both of which contain only one gene: GRIK3 in the Ensembl 72 dog annotation.
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evu245-F1: Analysis of selection in the dog genome. (A) Comparisons of the nucleotide diversity (left) and Tajima’s D values (right) between genes containing large numbers of fixed SNP differences and other genes ± S.D. were presented. (B) Comparisons of the difference in expression levels between wolves and dogs between genes containing large numbers of fixed SNP differences and other genes. The expression value for each gene was log2 transformed. Left: Expression difference of each gene between the wolf and the dog was calculated by the transformed value in the dog minus the transformed value in wolf. Right: Difference of each gene between the wolf and the dog was calculated by the transformed value in the dog divided by the transformed value in the wolf. (C) Left: Negative correlation between FST values and recombination rates of genome wide SNPs. Right: Positive correlation between FST values and recombination rates of SNPs at genes in GO categories: GO: 0001640 and GO: 0007216, both of which contain only one gene: GRIK3 in the Ensembl 72 dog annotation.

Mentions: We firstly compared published resequenced genomes of three wolves and ten dogs (including five ancient dogs and five modern dogs, supplementary material, Supplementary Material online) to identify the most significant genetic legacy in the dogs deviating from their progenitors. To avoid inaccurate estimation of population differentiation due to small sample size, we only count the single nucleotide polymorphisms (SNPs) that differentiate extremely between the wolves and the dogs (allele frequency is 1 in wolves but 0 in dogs, or vice versa), which were defined as fixed SNPs. We identified 204 genes that have at least six fixed SNPs (within the 95% percentile rank). These genes showed an extremely significant lower level of nucleotide diversity and Tajima’s D values (P = 5.22E-05 and 1.23E-30, respectively, Mann–Whitney U test) compared with other genes in the genome (fig. 1A), suggesting a potential selection effects on the divergence observed here. Because only a very small number of fixed SNPs (totally 26) were nonsynonymous substitutions, this may indicate that the positive selection operated mainly on expressional regulation. Actually, the 204 genes showed appreciable changes in expression patterns between dogs and wolves than others for two different measurements: Absolute expression change and fold change (P = 0.022 and P = 0.005, respectively) (fig. 1B), based on the transcriptome data for the frontal cortex (Albert et al. 2012). These results suggest that expressional variation rather than structural variation in protein sequence is the major contributor to the currently observed differentiation between dogs and wolves.Fig. 1.—


Domestication of the dog from the wolf was promoted by enhanced excitatory synaptic plasticity: a hypothesis.

Li Y, Wang GD, Wang MS, Irwin DM, Wu DD, Zhang YP - Genome Biol Evol (2014)

Analysis of selection in the dog genome. (A) Comparisons of the nucleotide diversity (left) and Tajima’s D values (right) between genes containing large numbers of fixed SNP differences and other genes ± S.D. were presented. (B) Comparisons of the difference in expression levels between wolves and dogs between genes containing large numbers of fixed SNP differences and other genes. The expression value for each gene was log2 transformed. Left: Expression difference of each gene between the wolf and the dog was calculated by the transformed value in the dog minus the transformed value in wolf. Right: Difference of each gene between the wolf and the dog was calculated by the transformed value in the dog divided by the transformed value in the wolf. (C) Left: Negative correlation between FST values and recombination rates of genome wide SNPs. Right: Positive correlation between FST values and recombination rates of SNPs at genes in GO categories: GO: 0001640 and GO: 0007216, both of which contain only one gene: GRIK3 in the Ensembl 72 dog annotation.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4255776&req=5

evu245-F1: Analysis of selection in the dog genome. (A) Comparisons of the nucleotide diversity (left) and Tajima’s D values (right) between genes containing large numbers of fixed SNP differences and other genes ± S.D. were presented. (B) Comparisons of the difference in expression levels between wolves and dogs between genes containing large numbers of fixed SNP differences and other genes. The expression value for each gene was log2 transformed. Left: Expression difference of each gene between the wolf and the dog was calculated by the transformed value in the dog minus the transformed value in wolf. Right: Difference of each gene between the wolf and the dog was calculated by the transformed value in the dog divided by the transformed value in the wolf. (C) Left: Negative correlation between FST values and recombination rates of genome wide SNPs. Right: Positive correlation between FST values and recombination rates of SNPs at genes in GO categories: GO: 0001640 and GO: 0007216, both of which contain only one gene: GRIK3 in the Ensembl 72 dog annotation.
Mentions: We firstly compared published resequenced genomes of three wolves and ten dogs (including five ancient dogs and five modern dogs, supplementary material, Supplementary Material online) to identify the most significant genetic legacy in the dogs deviating from their progenitors. To avoid inaccurate estimation of population differentiation due to small sample size, we only count the single nucleotide polymorphisms (SNPs) that differentiate extremely between the wolves and the dogs (allele frequency is 1 in wolves but 0 in dogs, or vice versa), which were defined as fixed SNPs. We identified 204 genes that have at least six fixed SNPs (within the 95% percentile rank). These genes showed an extremely significant lower level of nucleotide diversity and Tajima’s D values (P = 5.22E-05 and 1.23E-30, respectively, Mann–Whitney U test) compared with other genes in the genome (fig. 1A), suggesting a potential selection effects on the divergence observed here. Because only a very small number of fixed SNPs (totally 26) were nonsynonymous substitutions, this may indicate that the positive selection operated mainly on expressional regulation. Actually, the 204 genes showed appreciable changes in expression patterns between dogs and wolves than others for two different measurements: Absolute expression change and fold change (P = 0.022 and P = 0.005, respectively) (fig. 1B), based on the transcriptome data for the frontal cortex (Albert et al. 2012). These results suggest that expressional variation rather than structural variation in protein sequence is the major contributor to the currently observed differentiation between dogs and wolves.Fig. 1.—

Bottom Line: Here, we demonstrate that genes involved in glutamate metabolism, which account partially for fear response, indeed show the greatest population differentiation by whole-genome comparison of dogs and wolves.However, the changing direction of their expression supports a role in increasing excitatory synaptic plasticity in dogs rather than reducing fear response.Because synaptic plasticity are widely believed to be cellular correlates of learning and memory, this change may alter the learning and memory abilities of ancient scavenging wolves, weaken the fear reaction toward humans, and prompt the initial interspecific contact.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China wudongdong@mail.kiz.ac.cn zhangyp@mail.kiz.ac.cn.

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Related in: MedlinePlus