# Genetic Diversity and Population Structure of Sika Deer (Cervus nippon) Inferred by mtDNA and Y-Chromosomal Genes

## TL;DR

This study examines the genetic diversity and structure of sika deer populations using mtDNA and Y-chromosomal genes to aid in their conservation and management.

## Contribution

The study identifies nine maternal and three paternal lineages in sika deer and discovers a unique 26 bp tandem repeat motif in southern Japanese populations.

## Key findings

- Sika deer have high maternal genetic diversity but low paternal diversity.
- Japanese populations show higher diversity in tandem repeat units in the mitochondrial control region.
- A unique 26 bp tandem repeat motif was identified in southern Japanese sika deer populations.

## Abstract

A systematic investigation of the genetic diversity and structure of different sika deer populations is conducive to their population management, protection, and reproduction. Using mitochondria and genes on the Y chromosome, we found that the sika deer population consists of nine maternal lineages and three paternal lineages. The overall maternal genetic diversity of sika deer is relatively high, while that of the paternal line is low. In addition, the tandem repeat units in the control region in Japanese populations exhibit significantly higher diversity in both type and copy number. Notably, we identified a 26 bp tandem repeat motif unique to southern Japanese populations.

Sika deer (Cervus nippon), a species mainly distributed in the northeast of Asia, hold significant economic value in China due to their contributions to traditional Chinese medicine. A systematic investigation of their genetic structure is needed for population management. In this study, mitochondrial genome and AMELY, DBY, USP9Y, and SRY gene fragments on Y chromosome were used to elucidate the genetic structure of 303 individuals across 8 distinct populations. The mitosome analysis identified 72 haplotypes, with a haplotype diversity (Hd) of 0.917 and nucleotide diversity (π) of 0.0143, respectively. Meanwhile, 13 haplotypes were defined by Y chromosome genes with a Hd of 0.791. Analysis of the mitochondrial control region (CR) revealed subspecies-specific patterns of tandem repeat unit organization between continental and Japanese groups. Y chromosome analyses demonstrated a homogeneous paternal lineage across Japanese populations.