Ancient Migratory Threads Woven into the Y Chromosomes of Shanghai’s Han Men

Every man’s Y chromosome is a time capsule passed almost intact from father to son, and a massive new study of nearly 1,540 Han Chinese men in Shanghai has just decoded its message in extraordinary detail. By analyzing 38 Y-chromosome short tandem repeats (Y-STRs) and 250 Y-chromosome single nucleotide polymorphisms (Y-SNPs) across four districts—Qingpu, Songjiang, Jinshan, and Fengxian—researchers have constructed one of the finest-resolution portraits to date of the paternal genetic landscape of southwestern Shanghai. The findings, published in the International Journal of Legal Medicine, blend forensic science with deep history, tracing the paternal ancestry of these communities back to population dispersals from the neighboring Zhejiang region.

The study, led by Haolin Sun and Yanan Liu as co-first authors with senior authorship from Shilin Li, recruited unrelated Han Chinese males whose paternal ancestors had lived continuously in the sampling area for three generations. Peripheral blood samples were collected under ethics approval from the Shanghai Ethics Committee for Clinical Research and in accordance with the Declaration of Helsinki. From 396 men in Qingpu, 386 in Songjiang, 384 in Jinshan, and 372 in Fengxian, the team genotyped a panel of 38 Y-STR loci using the Yfiler Platinum system and interrogated 250 Y-SNPs through targeted next-generation sequencing on an Illumina NovaSeq 6000 platform. Haplogroups were assigned with the Yleaf software based on the binary SNP dataset, giving the researchers both a high-resolution recent-paternity lens and a deep phylogenetic framework.

Why the Y chromosome? The nonrecombining region of this chromosome carries two complementary classes of markers. Y-STRs mutate relatively rapidly—rates between roughly 3.78 × 10⁻⁴ and 7.44 × 10⁻² mutations per generation—making them exceptionally powerful for distinguishing even closely related paternal lineages. Y-SNPs, by contrast, mutate so rarely that their haplogroups remain stable over thousands of years, anchoring lineages to a well-established phylogenetic tree with strong geographic signatures. Combining the two allows scientists to discriminate individual males in a forensic context while simultaneously reconstructing ancient migration routes—a dual utility that this study exploits fully.

The forensic results are striking. Across the 1,538 men sampled, 1,518 unique Y-STR haplotypes were detected; only one haplotype appeared three times and eighteen appeared twice. The Yfiler Platinum genotyping system produced haplotype diversity values approaching unity in all four districts—0.99995 in Qingpu, 0.99996 in Songjiang, 0.99988 in Jinshan, and 0.99993 in Fengxian—while unique haplotypes accounted for between 96.09 and 98.45 percent of the observed profiles. Compared head-to-head against three other commercial marker panels, the 38-locus Yfiler Platinum system delivered the strongest discriminatory capacity, with values ranging from 0.97917 in Jinshan to 0.99223 in Songjiang. The team also cataloged a wealth of allelic variation, including null alleles, intermediate microvariants, and multi-allelic patterns at multi-copy loci such as DYS385a/b, DYF387S1a/b, and DYS527a/b, all of which enrich the local forensic reference database.

Not every marker contributes equally, and the comparative analysis made that clear. Box plots of gene diversity values across 27 shared Y-STR loci in 19 populations showed a clear hierarchy: rapidly mutating, highly polymorphic loci such as DYS518 and DYS449 maintained high and stable diversity values above 0.75 across all groups, while loci like DYS391 and DYS438 clustered at low values below 0.45. This pattern identifies core loci with universal discriminatory strength and pinpoints which markers are most valuable for distinguishing closely related paternal individuals, analyzing mixed stains, and screening patrilineal relatives in casework. The authors infer that the expanded Yfiler Platinum panel, which adds nine loci beyond the Yfiler Plus system, primarily enhances familial discrimination rather than individual identification per se.

Beyond individual identification, the study asked where these men’s paternal ancestors came from. Principal co-ordinates analysis and classical multidimensional scaling of pairwise Rst genetic distances, combined with permutational multivariate analysis of variance using 999 permutations and strict Bonferroni correction across 120 population pairs, showed that the four Shanghai district populations cluster tightly together and align most closely with southern Han Chinese populations. They are genetically close to neighboring Anhui and Jiangsu Han groups, more differentiated from Fujian and Guangdong references, and clearly demarcated from western plateau populations such as Tibetans and the Yi of the Tibetan-Yi Corridor, whose smaller effective population sizes and cultural isolation have amplified genetic drift. The researchers also noted that Jinshan and Fengxian sit particularly close together, consistent with their shared location in southern Shanghai and the historical Wu dialect cultural sphere of the lower Yangtze region.

The Y-SNP data told an equally coherent story. Haplogroup O dominated all four districts at frequencies between 81.82 and 87.10 percent, with O2 most prevalent at 52.59 to 54.43 percent, followed by O1a at 20.71 to 26.61 percent, then O1b, C2, and N each under 10 percent. This composition mirrors the typical paternal gene pool of southern East Asian Han populations and closely matches figures from Pudong and southern Jiangsu, reinforcing the genetic homogeneity of Han males across the Yangtze River Delta. Rarer lineages added fascinating texture: a single Songjiang man carried haplogroup T, which is exceedingly rare in East Asia and usually signals West Eurasian ancestry, prompting the authors to speculate about historical Persian, Arab, and Central Asian merchant communities—documented in Tang, Song, and Yuan dynasty records—that settled in the lower Yangtze region.

The study’s centerpiece is a median-joining network analysis of the O1a-M119 haplogroup, built from 13 single-copy Y-STR loci and spanning the Shanghai districts plus Pudong, Zhejiang, and Jiangsu reference populations. The network revealed three major clusters: an upper clade composed almost exclusively of Zhejiang-specific haplotypes branching directly from the ancestral node; a large central cluster in which Zhejiang, Jiangsu, and Shanghai haplotypes intermix in a star-like topology indicative of rapid demographic expansion; and a lower, deeply branched Shanghai cluster enriched with local district-specific haplotypes, suggesting local drift and prolonged isolation after initial divergence. The Zhejiang samples sit closest to the ancestral node of the Shanghai branches, leading the authors to conclude that the paternal origin of O1a in the four districts likely stems from population dispersal from the Zhejiang region—plausibly facilitated by maritime routes across Hangzhou Bay, given that Jinshan and Fengxian face Zhejiang across the water.

O1a-M119 itself is a signature lineage of China’s southeastern coast, dominant among coastal populations in Zhejiang, Fujian, and Guangdong, among indigenous Taiwanese peoples, and among Tai-Kadai-speaking groups. Its elevated frequency of roughly 20 to 27 percent in these Shanghai districts—higher than in many northern Han populations—ties the local gene pool to ancient southeastern coastal populations. Combined with the star-like expansion signal in the network, the data sketch a picture of sustained south-to-north paternal gene flow into the Shanghai region, layered atop a shared demographic history of migration and intermixing across the Yangtze River Delta.

For forensic practitioners, the implications are practical and immediate. Y-STR haplotypes can separate male lineages even among paternally related suspects, while Y-SNP haplogroups can narrow the geographic or ethnic origin of an unknown sample donor, providing investigative leads in familial searching. The district-level reference database constructed here—including the observed null alleles, microvariants, and multi-allelic patterns that complicate interpretation—offers a validated resource for such combined analyses in Shanghai and comparable southern Chinese populations. In an era when a single DNA swab can resurrect centuries of hidden ancestry, this study shows how two classes of markers on one small chromosome can simultaneously solve crimes and rewrite local history.

Subject of Research: Paternal genetic origin and forensic analysis of Han populations in four Shanghai districts using Y-chromosome STR and SNP markers

Article Title: Genetic origin and forensic analysis of han populations from four districts in Shanghai, China, based on Y-chromosome STR and SNP markers

Article References: Sun, H., Liu, Y., Liu, T., Tang, Z., Lei, L., Chang, S., & Li, S. (2026). Genetic origin and forensic analysis of han populations from four districts in Shanghai, China, based on Y-chromosome STR and SNP markers. International Journal of Legal Medicine. https://doi.org/10.1007/s00414-026-04019-1

Image Credits: AI Generated

DOI: 10.1007/s00414-026-04019-1

Keywords: Y chromosome, Y-STR, Y-SNP, forensic genetics, haplotype diversity, Shanghai Han population, haplogroup O1a, Zhejiang, median-joining network, population genetics, familial searching, Yfiler Platinum