The mitochondrial D-loop is a robust maternal-species identifier in gibbons (Hylobatidae)

Some gibbon species are difficult to distinguish phenotypically. This issue is compounded by recent changes in the gibbon taxonomy, which have sometimes occurred long after individuals were taken from the wild for captive breeding programmes. Furthermore, gibbon species within the Hylobates and Nomascus genera have been documented to hybridize to produce viable, fertile offspring, both in captivity and in the wild. This raises the possibility of cryptic hybrids within captive populations, threatening the genetic integrity of these genera. Phylogenetic methods using the mitochondrial D-loop and cox1 gene were compared to genetically identify gibbon species. Both loci identified lineages with cryptic hybrid ancestry. However, the D-loop outperformed the cox1 gene, providing higher resolution, particularly for Nomascus spp ., which for some species were not monophyletic when using the cox1 gene. The D-loop also revealed a significantly higher number of unique sequences, making it more suitable for investigations into relatedness, such as female dispersal patterns.