Contrasting population genetic structures of freshwater eels ( Anguilla marmorata, A. bicolor, A. mossambica ) from Madagascar

Abstract Freshwater eels (genus Anguilla ) are of major biological and commercial interest due to their complex catadromous life cycle and as a high‐value fishery resource, but the biology of tropical species is still poorly understood. This study investigates the genetic integrity, diversity and population structure of three species of tropical eels ( Anguilla marmorata, A. bicolor and A. mossambica ) in the western Indian Ocean, based on partial nucleotide sequences of the mtDNA control region ( n = 107 samples) and the nuclear GTH2b gene ( n = 91 samples) for individuals collected from two freshwater systems in northern Madagascar. No first‐generation hybrids between the studied species were found, despite frequent heterozygosities at the nuclear locus. For the mtDNA control region, all species were characterized by high haplotype diversity (ranging between 0.992 and 0.996) and nucleotide diversity (ranging between 0.035 and 0.059), patterns that are consistent with a historical population expansion during the late Pleistocene as inferred from demographic modelling. In line with previous studies, we confirmed distinct mtDNA haplogroups in A. marmorata and A. bicolor which can be attributed to the partial and/or past separation of populations across the Indian Ocean, whereas the western Indian Ocean endemic A. mossambica revealed no structure. Our findings align with existing evidence for spawning areas in the western Indian Ocean for all three species, with A. marmorata partially separated from eastern Indian Ocean populations and A. bicolor showing higher connectivity. Our findings will aid in the future management of local anguillid stocks.