DNA Barcoding Reveals Frequent Conflicts between Molecular and Morphological Identifications in Wild-Caught Shrimp from Coastal East Kalimantan, Indonesia

Abstract

Unreliable species identification can hinder management of key fisheries, including shrimp, in Coastal East Kalimantan. This study integrated preliminary morphological identification with COI DNA barcoding to validate species assignments of wild-caught shrimp landed at three coastal sites in East Kalimantan. Wild-caught shrimp from coastal East Kalimantan, were first identified using morphological characters. These identifications were then verified using COI DNA barcoding. Sequences were identified via database percentage similarity in NCBI and BOLD databases, and barcoding gap based on Kimura 2-parameter (K2P) was calculated to assess reliability of molecular species identification. A total of 25 shrimp specimens were morphologically assigned to Penaeidae and Solenoceridae, identifying 16 morphospecies (15 at species level and one assigned only to genus level). DNA barcoding identified three families (Palaemonidae, Penaeidae and Solenoceridae) and 15 species, with sequence similarities ranging from 98.17% to 100% (~99% query cover). In contrast, the BOLD database identified 12 specimens to species level and 12 to genus level with top match similarities ranged from 93.74% to 100%. Morphological and genetic identifications conflicted in 15 specimens and agreed in nine specimens. Genetic distances (K2P) ranged 0.000–0.238 with mean interspecific distance (0.197) exceeded mean intraspecific distance (0.00205). One species (Metapenaeus ensis) showed a negative barcoding gap, suggesting cryptic diversity or misidentification. The partial sequence of COI DNA barcoding supplements morphological shrimp identification, but conflicting results and incomplete databases remain challenges. Building well curated reference sequences is required to close these gaps and enhance the accuracy of species identification.