Determining evolutionary origin and phylogenetic relationships of mallard-like ducks of Oceania, greater Indonesia, and the Philippines with ddRAD-seq data

• Published in: Molecular phylogenetics and evolution 2024-08, Vol.197, p.108085, Article 108085
• Main Authors: Kaminski, Marissa, Brown, Joshua I., Seibert, Sara R., Hernández, Flor, Duya, Melizar V., Fontanilla, Ian Kendrich C., Roshier, David, Miles, Adam, Joseph, Leo, Peters, Jeffrey L., Lavretsky, Philip
• Format: Article
• Language: English
• Subjects: Anas; Animals; Biological Evolution; Conservation; DNA, Mitochondrial - genetics; Ducks - classification; Ducks - genetics; Evolution; Genetic Variation; Genetics, Population; Indonesia; Oceania; Philippines; Phylogenetics; Phylogeny; Phylogeography; Population genetics; Sequence Analysis, DNA
• ISSN: 1055-7903; 1095-9513; 1095-9513
• DOI: 10.1016/j.ympev.2024.108085

•Philippine and Pacific black ducks represent unique genetic lineages that diverged from the mallard 1–2 million years ago.•We found no support for the Philippine duck representing a hybrid species.•Finer population structure was only observed among Pacific black ducks, especially those from New Zealand and Australia, but also among samples within Australia.•Pacific black ducks from the Island of Aunu’u, American Samoa were genetically more similar to A. s. rogersi.•We found limited evidence of interspecific gene flow at deeper evolutionary time scales, and mallard introgression among contemporary samples. We aim to determine the evolutionary origins and population genetics of mallard-like ducks of Oceania, greater Indonesia, and the Philippines. Oceania, greater Indonesia, and the Philippines. Mallard (Anas platyrhynchos), Pacific black duck (A. superciliosa spp.), and Philippine duck (A. luzonica) Thousands of nuclear ddRAD-seq loci and the mitochondrial DNA control region were assayed across individuals representative of each species’ range. We assessed population structure and phylogenetic relationships, as well as estimated demographic histories to reconstruct the biogeographical history of each species. Philippine and Pacific black ducks represent unique genetic lineages that diverged from the mallard 1–2 million years ago. We find no support for the Philippine duck representing a hybrid species as once posited; however, their low levels of genetic diversity requires further attention. We find a lack of substructure among Philippine ducks. However, we found pronounced differentiation between subspecies of Pacific black ducks, especially between A. s. superciliosa from New Zealand and A. s. rogersi from Australia, Papua New Guinea, and Timor-Leste, Indonesia. Anas superciliosa pelewensis gave mixed results; individuals from the Solomon Islands were differentiated from the other subspecies, but those from the island of Aunu’u, American Samoa, were genetically more similar to A. s. rogersi than A. s. pelewensis samples from the Solomon Islands. Finally, we find limited evidence of interspecific gene flow at evolutionary scales, and mallard introgression among contemporary samples. Mallard-like ducks radiated across Oceania, greater Indonesia, and the Philippines within the last 2 million years. Only the Pacific black duck showed unique sub-structuring that largely followed known sub-species ranges, except for A. s. pelewensis. We posit that the high int