Seeing the Wood for the Trees: A Minimal Reference Phylogeny for the Human Y Chromosome

@article{Oven2014SeeingTW,
  title={Seeing the Wood for the Trees: A Minimal Reference Phylogeny for the Human Y Chromosome},
  author={Mannis van Oven and Anneleen Van Geystelen and Manfred Kayser and Ronny Decorte and Maarten H. D. Larmuseau},
  journal={Human Mutation},
  year={2014},
  volume={35}
}
During the last few decades, a wealth of studies dedicated to the human Y chromosome and its DNA variation, in particular Y‐chromosome single‐nucleotide polymorphisms (Y‐SNPs), has led to the construction of a well‐established Y‐chromosome phylogeny. Since the recent advent of new sequencing technologies, the discovery of additional Y‐SNPs is exploding and their continuous incorporation in the phylogenetic tree is leading to an ever higher resolution. However, the large and increasing amount of… 
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References

SHOWING 1-10 OF 56 REFERENCES
AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications
TLDR
AMY-tree is a useful tool to determine the Y lineage of a sample based on SNP calling, to identify Y-SNPs with yet unknown phylogenetic position and to optimize the Y chromosomal phylogenetic tree in the future.
New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree.
TLDR
Major changes in the topology of the parsimony tree are described and names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002 are provided.
Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs.
A nomenclature system for the tree of human Y-chromosomal binary haplogroups.
TLDR
A simple set of rules was developed to unambiguously label the different clades nested within a single most parsimonious phylogeny, which supersedes and unifies past nomenclatures and allows the inclusion of additional mutations and haplogroups yet to be discovered.
A calibrated human Y-chromosomal phylogeny based on resequencing.
TLDR
A nearly 10-fold increase in the number of Y markers with phylogenetic information, and novel historical insights derived from placing them on a calibrated phylogenetic tree are provided.
An efficient multiplex genotyping approach for detecting the major worldwide human Y-chromosome haplogroups
TLDR
These Y-SNP assays form a valuable tool for researchers in the fields of forensic genetics and genetic anthropology to infer a man's patrilineal bio-geographic ancestry from DNA.
Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny
TLDR
A putative age for coalescence of ~180,000 to 200,000 years ago is calculated, which is consistent with previous mitochondrial DNA–based estimates and indicates the presumptive timing of coalescence with other human populations.
Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree
TLDR
The authors' data provide a highly resolved branching in the African-specific portion of the Y tree and support the hypothesis of an origin in the north-western quadrant of the African continent for the human MSY diversity.
Increased Resolution of Y Chromosome Haplogroup T Defines Relationships among Populations of the Near East, Europe, and Africa
TLDR
Estimates of the timing of the branching events within haplogroups T, along with a comprehensive geographic survey of the major T subclades, suggest that this haplogroup began to diversify in the Near East ∼25 kya and points to a complex history of dispersal of this rare and informative Haplogroup T.
...
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