Rethinking Alpha Diversity in Marker-Gene Microbiome Studies: Dominance Matters More Than Richness

In the era of widespread marker-gene sequencing, alpha diversity metrics are increasingly used to infer ecological responses and biodiversity patterns in microbial communities. We highlight key conceptual and methodological limitations underlying these metrics, particularly the open-ended nature of microbial richness and the uneven detectability of taxa. We argue that, in marker-gene-based studies, alpha diversity often reflects shifts in dominance rather than true richness. We discuss why common assumptions fail, outline the risks of misinterpretation and propose a dominance-centred perspective to improve ecological inference in microbiome research.