The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves
Abstract 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 tra...
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crwiley:10.1111/mec.13480 2024-09-15T18:01:21+00:00 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. National Science Foundation National Human Genome Research Institute National Institutes of Health National Science Foundation Yellowstone National Park Yellowstone Park Foundation National Human Genome Research Institute AKC OAK National Institutes of Health 2016 http://dx.doi.org/10.1111/mec.13480 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.13480 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.13480 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/mec.13480 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor http://doi.wiley.com/10.1002/tdm_license_1.1 Molecular Ecology volume 25, issue 8, page 1838-1855 ISSN 0962-1083 1365-294X journal-article 2016 crwiley https://doi.org/10.1111/mec.13480 2024-08-01T04:23:54Z Abstract 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 >24 000 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 ( DMS s) 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, DMS s 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 Wiley Online Library Molecular Ecology 25 8 1838 1855 |
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Open Polar |
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Wiley Online Library |
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crwiley |
language |
English |
description |
Abstract 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 >24 000 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 ( DMS s) 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, DMS s 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. |
author2 |
National Science Foundation National Human Genome Research Institute National Institutes of Health National Science Foundation Yellowstone National Park Yellowstone Park Foundation National Human Genome Research Institute AKC OAK National Institutes of Health |
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. |
spellingShingle |
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 |
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 |
Wiley |
publishDate |
2016 |
url |
http://dx.doi.org/10.1111/mec.13480 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.13480 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.13480 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/mec.13480 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
Molecular Ecology volume 25, issue 8, page 1838-1855 ISSN 0962-1083 1365-294X |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor http://doi.wiley.com/10.1002/tdm_license_1.1 |
op_doi |
https://doi.org/10.1111/mec.13480 |
container_title |
Molecular Ecology |
container_volume |
25 |
container_issue |
8 |
container_start_page |
1838 |
op_container_end_page |
1855 |
_version_ |
1810438508383305728 |