The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves
The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits obser...
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ftcdlib:oai:escholarship.org:ark:/13030/qt06p8k9fh 2024-01-07T09:42:36+01:00 The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves Janowitz Koch, Ilana Clark, Michelle M Thompson, Michael J Deere-Machemer, Kerry A Wang, Jun Duarte, Lionel Gnanadesikan, Gitanjali E McCoy, Eskender L Rubbi, Liudmilla Stahler, Daniel R Pellegrini, Matteo Ostrander, Elaine A Wayne, Robert K Sinsheimer, Janet S vonHoldt, Bridgett M 1838 - 1855 2016-04-01 application/pdf https://escholarship.org/uc/item/06p8k9fh unknown eScholarship, University of California qt06p8k9fh https://escholarship.org/uc/item/06p8k9fh public Molecular Ecology, vol 25, iss 8 Biological Sciences Genetics Human Genome Biotechnology Animals DNA Methylation DNA Transposable Elements Dogs Domestication Evolution Molecular Inheritance Patterns Pedigree Polymorphism Genetic Sequence Analysis DNA Species Specificity Wolves canid genome regulation methylation Evolutionary Biology article 2016 ftcdlib 2023-12-11T19:06:54Z The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified two primary groups, domestic vs. wild canids. A scan for significantly differentially methylated sites (DMSs) revealed species-specific patterns at 68 sites after correcting for cell heterogeneity, with weak yet significant hypermethylation typical of purebred dogs when compared to wolves (59% and 58%, P<0.05, respectively). Additionally, methylation patterns at eight genes significantly deviated from neutrality, with similar trends of hypermethylation in purebred dogs. The majority (>66%) of differentially methylated regions contained or were associated with repetitive elements, indicative of a genotype-mediated trend. However, DMSs were also often linked to functionally relevant genes (e.g. neurotransmitters). Finally, we utilized known genealogical relationships among Yellowstone wolves to survey transmission stability of methylation marks, from which we found a substantial fraction that demonstrated high heritability (both H(2) and h(2) >0.99). These analyses provide a unique epigenetic insight into the molecular consequences of recent selection and radiation of our most ancient domesticated companion, the dog. These findings suggest selection has acted on methylation patterns, providing a new genomic perspective on phenotypic diversification in domesticated species. Article in Journal/Newspaper Canis lupus University of California: eScholarship |
institution |
Open Polar |
collection |
University of California: eScholarship |
op_collection_id |
ftcdlib |
language |
unknown |
topic |
Biological Sciences Genetics Human Genome Biotechnology Animals DNA Methylation DNA Transposable Elements Dogs Domestication Evolution Molecular Inheritance Patterns Pedigree Polymorphism Genetic Sequence Analysis DNA Species Specificity Wolves canid genome regulation methylation Evolutionary Biology |
spellingShingle |
Biological Sciences Genetics Human Genome Biotechnology Animals DNA Methylation DNA Transposable Elements Dogs Domestication Evolution Molecular Inheritance Patterns Pedigree Polymorphism Genetic Sequence Analysis DNA Species Specificity Wolves canid genome regulation methylation Evolutionary Biology Janowitz Koch, Ilana Clark, Michelle M Thompson, Michael J Deere-Machemer, Kerry A Wang, Jun Duarte, Lionel Gnanadesikan, Gitanjali E McCoy, Eskender L Rubbi, Liudmilla Stahler, Daniel R Pellegrini, Matteo Ostrander, Elaine A Wayne, Robert K Sinsheimer, Janet S vonHoldt, Bridgett M The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves |
topic_facet |
Biological Sciences Genetics Human Genome Biotechnology Animals DNA Methylation DNA Transposable Elements Dogs Domestication Evolution Molecular Inheritance Patterns Pedigree Polymorphism Genetic Sequence Analysis DNA Species Specificity Wolves canid genome regulation methylation Evolutionary Biology |
description |
The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified two primary groups, domestic vs. wild canids. A scan for significantly differentially methylated sites (DMSs) revealed species-specific patterns at 68 sites after correcting for cell heterogeneity, with weak yet significant hypermethylation typical of purebred dogs when compared to wolves (59% and 58%, P<0.05, respectively). Additionally, methylation patterns at eight genes significantly deviated from neutrality, with similar trends of hypermethylation in purebred dogs. The majority (>66%) of differentially methylated regions contained or were associated with repetitive elements, indicative of a genotype-mediated trend. However, DMSs were also often linked to functionally relevant genes (e.g. neurotransmitters). Finally, we utilized known genealogical relationships among Yellowstone wolves to survey transmission stability of methylation marks, from which we found a substantial fraction that demonstrated high heritability (both H(2) and h(2) >0.99). These analyses provide a unique epigenetic insight into the molecular consequences of recent selection and radiation of our most ancient domesticated companion, the dog. These findings suggest selection has acted on methylation patterns, providing a new genomic perspective on phenotypic diversification in domesticated species. |
format |
Article in Journal/Newspaper |
author |
Janowitz Koch, Ilana Clark, Michelle M Thompson, Michael J Deere-Machemer, Kerry A Wang, Jun Duarte, Lionel Gnanadesikan, Gitanjali E McCoy, Eskender L Rubbi, Liudmilla Stahler, Daniel R Pellegrini, Matteo Ostrander, Elaine A Wayne, Robert K Sinsheimer, Janet S vonHoldt, Bridgett M |
author_facet |
Janowitz Koch, Ilana Clark, Michelle M Thompson, Michael J Deere-Machemer, Kerry A Wang, Jun Duarte, Lionel Gnanadesikan, Gitanjali E McCoy, Eskender L Rubbi, Liudmilla Stahler, Daniel R Pellegrini, Matteo Ostrander, Elaine A Wayne, Robert K Sinsheimer, Janet S vonHoldt, Bridgett M |
author_sort |
Janowitz Koch, Ilana |
title |
The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves |
title_short |
The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves |
title_full |
The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves |
title_fullStr |
The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves |
title_full_unstemmed |
The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves |
title_sort |
concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves |
publisher |
eScholarship, University of California |
publishDate |
2016 |
url |
https://escholarship.org/uc/item/06p8k9fh |
op_coverage |
1838 - 1855 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
Molecular Ecology, vol 25, iss 8 |
op_relation |
qt06p8k9fh https://escholarship.org/uc/item/06p8k9fh |
op_rights |
public |
_version_ |
1787423637134901248 |