[Paper Review] The dichotomy structure of Y chromosome Haplogroup N

Hu Kang, 康龙丽+17 more|arXiv (Cornell University)|Apr 24, 2015

Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities35 references8 citations

TL;DR

This study refines the Y chromosome haplogroup N phylogeny using high-throughput sequencing, identifying 33 SNPs and 16 subclades. It reveals a dichotomous structure with N1-F1206 (common in Altaic, Uralic, and Russian populations) and N2-F2930 (prevalent in Tibeto-Burman and Chinese groups), suggesting Haplogroup N originated in China during the late Paleolithic Era.

ABSTRACT

Haplogroup N-M231 of human Y chromosome is a common clade from Eastern Asia to Northern Europe, being one of the most frequent haplogroups in Altaic and Uralic-speaking populations. Using newly discovered bi-allelic markers from high-throughput DNA sequencing, we largely improved the phylogeny of Haplogroup N, in which 16 subclades could be identified by 33 SNPs. More than 400 males belonging to Haplogroup N in 34 populations in China were successfully genotyped, and populations in Northern Asia and Eastern Europe were also compared together. We found that all the N samples were typed as inside either clade N1-F1206 (including former N1a-M128, N1b-P43 and N1c-M46 clades), most of which were found in Altaic, Uralic, Russian and Chinese-speaking populations, or N2-F2930, common in Tibeto-Burman and Chinese-speaking populations. Our detailed results suggest that Haplogroup N developed in the region of China since the final stage of late Paleolithic Era.

Motivation & Objective

• To improve the phylogenetic resolution of Y chromosome Haplogroup N using newly discovered bi-allelic markers.
• To clarify the population distribution and evolutionary history of Haplogroup N across Eastern Asia and Northern Europe.
• To determine the geographic origin and timing of Haplogroup N's diversification.
• To resolve conflicting classifications of subclades previously grouped under N1a-M128, N1b-P43, and N1c-M46.

Proposed method

• High-throughput DNA sequencing to discover novel bi-allelic markers (SNPs) in Haplogroup N.
• Genotyping of 400+ male samples from 34 Chinese populations for phylogenetic assignment.
• Comparative analysis with populations from Northern Asia and Eastern Europe to assess clade distribution.
• Phylogenetic reconstruction using 33 SNPs to define 16 subclades within Haplogroup N.
• Statistical and spatial analysis to infer the geographic origin of Haplogroup N based on clade distribution patterns.
• Use of established Y-chromosome SNP nomenclature to reclassify previously ambiguous subclades.

Experimental results

Research questions

• RQ1 Where did Haplogroup N originate, and when did it begin diversifying?
• RQ2 What is the phylogenetic structure of Haplogroup N, and how do its subclades relate to one another?
• RQ3 How are the subclades N1-F1206 and N2-F2930 distributed across populations in Eastern Asia and Northern Europe?
• RQ4 Why do Altaic, Uralic, and Chinese-speaking populations show distinct subclade frequencies within Haplogroup N?
• RQ5 How does the refined phylogeny resolve prior ambiguities in the classification of N1a-M128, N1b-P43, and N1c-M46?

Key findings

• Haplogroup N diversified into two major branches: N1-F1206 and N2-F2930, forming a dichotomous phylogenetic structure.
• N1-F1206 includes the former subclades N1a-M128, N1b-P43, and N1c-M46, and is prevalent in Altaic, Uralic, Russian, and Chinese-speaking populations.
• N2-F2930 is predominantly found in Tibeto-Burman and Chinese-speaking populations, indicating a distinct lineage within Haplogroup N.
• The study identified 33 SNPs that define 16 subclades, significantly improving the resolution of Haplogroup N's phylogeny.
• All 400+ genotyped Chinese males from 34 populations were assigned to either N1-F1206 or N2-F2930, supporting a dual lineage structure.
• The data support a late Paleolithic origin of Haplogroup N in China, with subsequent dispersal across Northern Eurasia.