DataSheet1_Population structure and evolutionary history of the greater cane rat (Thryonomys swinderianus) from the Guinean Forests of West Africa.xlsx

Grasscutter (Thryonomys swinderianus) is a large-body old world rodent found in sub-Saharan Africa. The body size and the unique taste of the meat of this major crop pest have made it a target of intense hunting and a potential consideration as a micro-livestock. However, there is insufficient knowledge on the genetic diversity of its populations across African Guinean forests. Herein, we investigated the genetic diversity, population structures and evolutionary history of seven Nigerian wild grasscutter populations together with individuals from Cameroon, Republic of Benin, and Ghana, using five mitochondrial fragments, including D-loop and cytochrome b (CYTB). D-loop haplotype diversity ranged from 0.571 (± 0.149) in Republic of Benin to 0.921 (± 0.013) in Ghana. Within Nigeria, the haplotype diversity ranged from 0.659 (± 0.059) in Cross River to 0.837 (± 0.075) in Ondo subpopulation. The fixation index (FST), haplotype frequency distribution and analysis of molecular variance revealed varying levels of population structures across populations. No significant signature of population contraction was detected in the grasscutter populations. Evolutionary analyses of CYTB suggests that South African population might have diverged from other populations about 6.1 (2.6–10.18, 95% CI) MYA. Taken together, this study reveals the population status and evolutionary history of grasscutter populations in the region.

非洲蔗鼠（Grasscutter，*Thryonomys swinderianus*）是一种栖息于撒哈拉以南非洲的大型旧世界啮齿动物。作为主要农业害虫，该物种的体型与独特的肉质风味使其成为高强度猎捕的目标，同时也具备成为微型家畜的潜力。然而，目前学界对非洲几内亚林区内该物种种群的遗传多样性认知仍较为匮乏。本研究利用包含D环（D-loop）与细胞色素b（cytochrome b，CYTB）在内的5个线粒体基因片段，对7个尼日利亚野生蔗鼠种群，以及喀麦隆、贝宁共和国和加纳的蔗鼠个体的遗传多样性、种群结构与演化历史展开了探究。结果显示，D环的单倍型多样性在贝宁共和国种群中为0.571（±0.149），在加纳种群中可达0.921（±0.013）；在尼日利亚国内，克罗斯河种群的单倍型多样性为0.659（±0.059），而翁多亚种群的单倍型多样性为0.837（±0.075）。固定指数（FST）、单倍型频率分布以及分子方差分析结果表明，各蔗鼠种群间存在不同程度的种群结构分化。未在检测的蔗鼠种群中发现显著的种群收缩信号。细胞色素b基因的演化分析显示，南非种群可能于约610万年前（95%置信区间：2.6–10.18）与其他种群发生分化。综上，本研究阐明了该区域蔗鼠种群的现状及其演化历史。