ena-STUDY-Uppsala  University-23-08-2018-13:00:30:451-158
Sequences mapping to the wolf Y chromosome
Analyses of Y chromosome haplotypes uniquely provide a paternal portray of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA. However, for a number of technical reasons many genome assemblies do not include the Y chromosome, which has hampered the use of Y chromosome haplotype analyses in studies of natural populations. Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf Y chromosome, likely representing most of the male-specific, non-ampliconic sequence from the euchromatic part of the chromosome. We characterized this sequenced and then identified ˜1,500 Y-linked SNPs in a sample of 145 re-sequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in dogs and other canids. We found 54 Y chromosome haplotypes, of which 27 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated by that individual haplotypes were never shared between geographically distant areas, and that genetically similarly haplotypes were only found within the same geographical region. The deepest split between haplogroups was estimated to have occurred 121,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, starting 28,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as recent immigrant haplotypes were present in the neighbouring Finnish population, but not in wolves from elsewhere in the world, or in dogs. This study serves as a roadmap to the inclusion of Y chromosome analyses in molecular ecological research.
Analyses of Y chromosome haplotypes uniquely provide a paternal portray of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA. However, for a number of technical reasons many genome assemblies do not include the Y chromosome, which has hampered the use of Y chromosome haplotype analyses in studies of natural populations. Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf Y chromosome, likely representing most of the male-specific, non-ampliconic sequence from the euchromatic part of the chromosome. We characterized this sequenced and then identified ˜1,500 Y-linked SNPs in a sample of 145 re-sequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in dogs and other canids. We found 54 Y chromosome haplotypes, of which 27 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated by that individual haplotypes were never shared between geographically distant areas, and that genetically similarly haplotypes were only found within the same geographical region. The deepest split between haplogroups was estimated to have occurred 121,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, starting 28,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as recent immigrant haplotypes were present in the neighbouring Finnish population, but not in wolves from elsewhere in the world, or in dogs. This study serves as a roadmap to the inclusion of Y chromosome analyses in molecular ecological research.