Environmental and Spatial Processes Drive the Phylogenetic Diversity and Structure of Planktonic Microeukaryotes Revealed by 18S rDNA Metabarcoding in a Tropical Floodplain

Understanding phylogenetic diversity and community patterns is fundamental to elucidating the processes that shape biodiversity. For this, integrating community phylogenetic approaches with advanced molecular techniques is essential for providing more consistent estimates of community diversity and structure. Here, we investigate the phylogenetic diversity and structure of photosynthetic planktonic microeukaryote communities in tropical floodplain lakes using metabarcoding and tested the combined influence of environmental and spatial factors at broad geographical scales, including river network connectivity, on these metrics. We collected water samples from 140 lakes the middle Araguaia River floodplain. After filtering, DNA was extracted and amplified using primers for the 18S rRNA V4 region. To assess diversity and phylogenetic structure, we calculated Faith's PD and Net Relatedness Index (NRI) and used variance partitioning to determine the relative influence of environmental and spatial factors (directional and nondirectional). Our results showed that PD varied significantly among lakes and was positively correlated with richness. However, the observed PD was lower than expected by chance, and NRI values indicated a predominant pattern of phylogenetic clustering, suggesting that environmental filtering and dispersal limitations are important processes in community structuring. Variance partitioning revealed that both environmental and spatial predictors were important. Directional spatial predictors did not increase total explained variation compared to nondirectional filters, but increased the shared environmental–spatial fraction, indicating spatially structured environmental gradients. The community structure of planktonic microeukaryotes in the floodplain lakes of the Tocantins‐Araguaia River basin is influenced by a combination of environmental filters and spatial processes, highlighting the importance of conserving less degraded areas to preserve the evolutionary diversity of these ecosystems.