Diversity and Potential Endemism of New Zealand Freshwater Rotifers Revealed Using Mitochondrial DNA Barcodes

Rotifers perform key functions in aquatic food webs and respond to environmental changes, thus providing sensitive indicators of water quality. However, rotifers are small, highly diverse, and difficult to identify for those lacking expertise. Monogononta are the largest taxonomic class of rotifers with over 1500 species described globally, and around 355 known from New Zealand; only four of these are currently recognised as endemics. Here, we morphologically identified 239 specimens (41 species) of New Zealand monogonont rotifers and obtained cytochrome c oxidase subunit 1 (COI) sequences to assess species‐level diversity. We found up to 20% sequence divergence and multiple genetic lineages within species. Using Barcode Index Numbers (BINs) and generalised mixed Yule coalescence (GMYC), we estimated 71–81 distinct genetic lineages, respectively, among the 41 species we sequenced. Only five lineages matched existing Barcode of Life Datasystems (BOLD) records, and 94% of BINs are thus far known only from New Zealand. Pending a more comprehensive global database, we conclude that many New Zealand lineages are likely to be endemic. Our curated sequences contribute to global repositories and provide a reference for future research and monitoring, particularly environmental DNA (eDNA) approaches.