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… 
View on Wiley
ncbi.nlm.nih.gov
140 Citations
Highly Influential Citations
7
Background Citations
18
Methods Citations
15
Results Citations
1

140 Citations

In silico detection of phylogenetic informative Y‐chromosomal single nucleotide polymorphisms from whole genome sequencing data
TLDR
The PENNY software presented here detects potentially phylogenetic interesting Y‐SNPs in silico based on SNP calling data files and classifies them into different types according to their position in the currently used Y‐chromosomal tree and it is proved that these newly added Y‐ SNPs indeed increased the resolution of the phylogenetic Y‐ chromosomal analysis substantially.
The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades
TLDR
The sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51× yields 13,261 high-confidence SNPs, 65.9% of which are previously unreported, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation.
Defining Y-SNP variation among the Flemish population (Western Europe) by full genome sequencing.
Simultaneous Analysis of Hundreds of Y‐Chromosomal SNPs for High‐Resolution Paternal Lineage Classification using Targeted Semiconductor Sequencing
TLDR
A high‐resolution multiplex tool for parallel genotyping‐by‐sequencing of 530 Y‐SNPs using the Ion Torrent PGM platform, which allows classification of 432 worldwide Y haplogroups and a software tool for automated data quality control and haplogroup classification is provided.
Refining the Y chromosome phylogeny with southern African sequences
TLDR
Over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan- and Bantu-speaking populations are analyzed, identifying 232 new sequences from basal haplogroups A and B and identifying new clades in the phylogeny.
Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses
TLDR
A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes.
New native South American Y chromosome lineages
TLDR
This new Y chromosome haplogroup Q phylogeny offers an informative paternal genealogy to investigate the pre-Columbian history of South America and validated the usefulness of several published SNPs among indigenous South Americans.
Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences
TLDR
High-coverage sequencing of the whole Y chromosome in a data set of 19 male Khoe-San individuals in comparison with existing whole Y-chromosome sequence data is described and the positioning of tentatively placed new branches of the ISOGG Y- Chromosome phylogeny is improved.
Towards a consensus Y-chromosomal phylogeny and Y-SNP set in forensics in the next-generation sequencing era.
The Parallel Lives of Human Y Chromosome Lineages Across the Strait of Gibraltar
TLDR
Either in Iberia or the Maghreb, most men share a common ancestor that lived just a few hundred generations ago, in line with ancient DNA discoveries and pointing to the population upheaval of the Bronze Age as a plausible agent in its origin and dispersion.
...
...

References

SHOWING 1-10 OF 56 REFERENCES
A revised root for the human Y chromosomal phylogenetic tree: the origin of patrilineal diversity in Africa.
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.
...
...