Mitogenomic recognition of incognito lineages in the mud spiny lobster Panulirus polyphagus (Herbst, 1793): A tale of unique genetic structuring and diversification.

This study provides the first documentation of three deep conspecific lineages within Panulirus polyphagus in the Indian Ocean, bridging the gap in genetic research. Comparative mitogenomics between lineages (L) at both species and family levels, evolutionary relationships and heterogeneity of sequence divergence within Decapoda, and divergence time estimation were performed. The characterized mitogenomes ranged from 15,685–15,705 bp in size and exhibited a typical pancrustacean pattern. Among the three lineages, L1 predominated the Bay of Bengal, L2 the Arabian Sea, and L2.a, a less common lineage genetically closer to L2, was restricted to the latter region. A minor lineage L1.a, was observed in the Coral Triangle area. All PCGs displayed evidence of purifying selection across species and family levels. The largest genetic distance (K2P) between lineages was 9 %, notably between L1.a and L2.a. The phylogenetic tree subdivided the Achelates into Palinuridae and Scyllaridae, and the topology demonstrated a distinct pattern of lineage diversification within P. polyphagus. AliGROOVE analysis revealed no discernible divergence in Decapoda. The diversification of P. polyphagus appears to have occurred during Miocene, with further diversification in Pliocene. Furthermore, genetic stocks and population connectivity recognized here will provide valuable insight for spatial management planning of this dwindling resource. • The first mitogenomic study demonstrating the presence of cryptic, deep conspecific lineages in Panulirus polyphagus , distributed in the Indo-West Pacific. • The mitogenome-based K2P divergence between the major lineages is ~8.0 %, dating their initial divergence back to the late Miocene. • The genetic structure and population connectivity of this heavily exploited species have been revealed, indicating a unique pattern considering the extended pelagic larval duration of spiny lobsters. • Hypotheses regarding the diversification of lineages in this species have been listed. • The lineages from the Central Indo-Pacific and the Arabian Sea can be broadly categorized as two distinct genetic stocks that require separate management. [ABSTRACT FROM AUTHOR]