Insights from DNA barcoding endangered endemic Caridina shrimps (Decapoda: Atyidae) in Lindu Lake, Indonesia

Introduction: Humanity faces a multidimensional crisis with severe threats to often poorly known freshwater biodiversity. Molecular tools, like DNA barcoding, can aid in biodiversity exploration, monitoring, and conservation. Sulawesian Caridina shrimps are both ecologically significant and endangered yet remain understudied. Objective: To contribute well-documented DNA barcode (COX1 mtDNA) sequences for three Caridina species endemic to Lindu Lake. Methods: We collected 224 Caridina shrimps from three sites around Lindu Lake in August (n = 73), and October 2023 (n = 117), and July 2024 (n = 34). We measured and analyzed morphological traits as dimensionless ratios of total length. We extracted DNA from six specimens (two per species) and COX1 mtDNA barcodes obtained through PCR (primers jgLCO and jgHCO) and Sanger sequencing. We obtained homologous sequences from GenBank (BLAST routine) and BOLD repositories for phylogenetic analyses. All molecular analyses were performed in MEGA 11. Results: One species was identified at each site. Morphological traits differ between species. Three haplotypes with low divergence: one in Caridina kaili, one in Caridina linduensis, and one in both Caridina dali and C. linduensis. Homologous sequences in GenBank and BOLD included very few Sulawesi endemic species; these formed the closest sister clades to Lindu Lake Caridina. Conclusions: We submitted to the GenBank repository the first reference DNA barcodes for each of the Lindu Lake Caridina species. The poor resolution of COX1 mtDNA for Lindu Lake Caridina may be due to recent evolutionary processes. Our study highlights the ongoing need for barcoding freshwater invertebrates, particularly atyid shrimps from Sulawesi, in the Wallacea bioregion.