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[Display omitted] • Heterogeneity index(H) is a structural parameter describing the distribution of species associations. • H is proposed to unveil the species turnover in community in this paper. • Eight lakes exhibit a eutrophication trend with different degrees from the 1950s. • H , species richness, evenness and Jaccard index respond differently to eutrophication. • H can serve as a complementary biodiversity metric to quantify functional diversity. Anthropogenic eutrophication in aquatic ecosystems has had significant negative effects on biodiversity and human wellbeing. Improving our understanding of the ways in which biological communities respond to eutrophication underlies biodiversity conservation, and diversity metrics like species richness and evenness are often used to assess environmental impacts on biodiversity. However, such studies mainly consider overall gain and loss, ignoring species replacement in community succession. This paper combines paleolimnology and network science to propose a heterogeneity index (H) to measure community successions by linking long-term changes in community structure with environmental stress. Eight lakes of different types in the middle and lower reaches of the Yangtze River Basin (MLYB) were selected, and we focused on diatom communities to reconstruct their ecological trajectories after significant anthropogenic impact. The combined results suggested that human impacts have caused eutrophication in each lake since the 1950s, but led to different degrees of impact on the diatom communities. In hypereutrophic lakes, diatom assemblages shifted to high-nutrient tolerance and the proportions of epiphytic-benthic species decreased, while in mildly eutrophic lakes, a switch to mild-nutrient tolerant assemblages occurred in planktonic and epiphytic-benthic species with no change in epiphytic-benthic proportions. The H of diatom communities declined in hypereutrophic lakes, but changed little in mildly eutrophic lakes after the 1950s. Meanwhile, no regular changes in diversity indicators such as richness, evenness and the Jaccard-index occurred with lake eutrophication. The ordered species turnover in nutrient-enriched diatom communities may account for the discrepancies in H and the above indices, such as ordered epiphytic-benthic species being replaced by higher nutrient-tolerant and planktonic species with no necessarily attendant reduction in species richness. By quantifying the alteration of species associations without being influenced by species diversity, the H index effectively reveals the succession of diatom communities, and can therefore serve as a complementary indicator of biodiversity. [ABSTRACT FROM AUTHOR]