This first comprehensive checklist of the diatoms from fresh and weakly brackish water inThe Netherlands comprises 948 taxa, belonging to 776 species in 56 genera. The genera Navicula, which has a very wide ecological amplitude, and Nitzschia, which has many pollution tolerant species, are most numerous. Each taxon is identified with a unique eight-letter code, to facilitate computer processing of data. Ecological indicator values for pH, salinity, nitrogen uptake metabolism, oxygen, saprobity, trophic state and moisture are presented.

During a survey of some springs in the French Central Massif, a new Navicula species (Bacillariophyceae) was found: Navicula sanctamargaritae Beauger sp. nov. A second new Navicula species was observed during a routine biomonitoring project in Flanders: Navicula flandriae Van de Vijver & A.Mertens sp. nov.. The new species are formally described using light and scanning electron microscopy. Both species present a unique set of morphological characters including the structure of the central raphe endings, the striation pattern, the valve dimensions and outline, which allows their separation from similar Navicula taxa such as N. korzeniewskii, N. recens or N. cincta. The ecological preferences of each species are briefly discussed.

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In contrast to surveys based on a few genes that often provide limited taxonomic resolution, transcriptomes provide a wealth of genomic loci that can resolve relationships among taxonomically challenging lineages. Diatoms are a diverse group of aquatic microalgae that includes important bioindicator species and many such lineages. One example is Nitzschia palea , a widespread species complex with several morphologically defined taxonomic varieties, some of which are critical pollution indicators. Morphological differences among the varieties are subtle and phylogenetic studies based on a few genes fail to resolve their evolutionary relationships. We conducted morphometric and transcriptome analyses of 10 Nitzschia palea strains to resolve the relationships among strains and taxonomic varieties. Nitzschia palea was resolved into three clades, one of which corresponds to a group of strains with narrow linear‐lanceolate valves. The other morphological group recovered in the shape outline analysis was not monophyletic and consisted of two clades. Gene‐tree concordance analyses and phylogenetic network estimations revealed patterns of incomplete lineage sorting and gene flow between intraspecific lineages. We detected reticulated evolutionary patterns among lineages with different morphologies, resulting in a putative recent hybrid. Our study shows that phylogenomic analyses of unlinked nuclear loci, complemented with morphometrics, can resolve complex evolutionary histories of recently diverged species complexes.