Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs
Abstract Background Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochondrial analyses have revealed important insights into the evolutionary hi...
Main Authors: | , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2018-05-01
|
Series: | BMC Genomics |
Subjects: | |
Online Access: | http://link.springer.com/article/10.1186/s12864-018-4749-z |
id |
doaj-eed8fa23fb3f40af8c12c68fbfc4f735 |
---|---|
record_format |
Article |
spelling |
doaj-eed8fa23fb3f40af8c12c68fbfc4f7352020-11-25T00:42:44ZengBMCBMC Genomics1471-21642018-05-011911910.1186/s12864-018-4749-zAnalysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogsMatthew T. Oetjens0Axel Martin1Krishna R. Veeramah2Jeffrey M. Kidd3Department of Human Genetics, University of Michigan Medical SchoolDepartment of Human Genetics, University of Michigan Medical SchoolDepartment of Ecology and Evolution, Stony Brook UniversityDepartment of Human Genetics, University of Michigan Medical SchoolAbstract Background Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochondrial analyses have revealed important insights into the evolutionary history of canids. Utilizing a recently published dog Y-chromosome reference, we analyzed Y-chromosome sequence across a diverse collection of canids and determined the Y haplogroup of three ancient European dogs. Results We identified 1121 biallelic Y-chromosome SNVs using whole-genome sequences from 118 canids and defined variants diagnostic to distinct dog Y haplogroups. Similar to that of the mitochondria and previous more limited studies of Y diversity, we observe several deep splits in the Y-chromosome tree which may be the result of retained Y-chromosome diversity which predates dog domestication or post-domestication admixture with wolves. We find that Y-chromosomes from three ancient European dogs (4700–7000 years old) belong to distinct clades. Conclusions We estimate that the time to the most recent comment ancestor of dog Y haplogroups is 68–151 thousand years ago. Analysis of three Y-chromosomes from the Neolithic confirms long stranding population structure among European dogs.http://link.springer.com/article/10.1186/s12864-018-4749-zCanidY-chromosome haplogroupsAncient dog |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Matthew T. Oetjens Axel Martin Krishna R. Veeramah Jeffrey M. Kidd |
spellingShingle |
Matthew T. Oetjens Axel Martin Krishna R. Veeramah Jeffrey M. Kidd Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs BMC Genomics Canid Y-chromosome haplogroups Ancient dog |
author_facet |
Matthew T. Oetjens Axel Martin Krishna R. Veeramah Jeffrey M. Kidd |
author_sort |
Matthew T. Oetjens |
title |
Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs |
title_short |
Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs |
title_full |
Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs |
title_fullStr |
Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs |
title_full_unstemmed |
Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs |
title_sort |
analysis of the canid y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among neolithic european dogs |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2018-05-01 |
description |
Abstract Background Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochondrial analyses have revealed important insights into the evolutionary history of canids. Utilizing a recently published dog Y-chromosome reference, we analyzed Y-chromosome sequence across a diverse collection of canids and determined the Y haplogroup of three ancient European dogs. Results We identified 1121 biallelic Y-chromosome SNVs using whole-genome sequences from 118 canids and defined variants diagnostic to distinct dog Y haplogroups. Similar to that of the mitochondria and previous more limited studies of Y diversity, we observe several deep splits in the Y-chromosome tree which may be the result of retained Y-chromosome diversity which predates dog domestication or post-domestication admixture with wolves. We find that Y-chromosomes from three ancient European dogs (4700–7000 years old) belong to distinct clades. Conclusions We estimate that the time to the most recent comment ancestor of dog Y haplogroups is 68–151 thousand years ago. Analysis of three Y-chromosomes from the Neolithic confirms long stranding population structure among European dogs. |
topic |
Canid Y-chromosome haplogroups Ancient dog |
url |
http://link.springer.com/article/10.1186/s12864-018-4749-z |
work_keys_str_mv |
AT matthewtoetjens analysisofthecanidychromosomephylogenyusingshortreadsequencingdatarevealsthepresenceofdistincthaplogroupsamongneolithiceuropeandogs AT axelmartin analysisofthecanidychromosomephylogenyusingshortreadsequencingdatarevealsthepresenceofdistincthaplogroupsamongneolithiceuropeandogs AT krishnarveeramah analysisofthecanidychromosomephylogenyusingshortreadsequencingdatarevealsthepresenceofdistincthaplogroupsamongneolithiceuropeandogs AT jeffreymkidd analysisofthecanidychromosomephylogenyusingshortreadsequencingdatarevealsthepresenceofdistincthaplogroupsamongneolithiceuropeandogs |
_version_ |
1725280676937203712 |