Evolution, population structure and morphology of the African Black Duck Anas sparsa and Yellow-billed Duck A. undulata

Abstract

Biological conservation requires a fundamental understanding of evolutionary history and established contemporary population genetics. Here, we sequenced mitochondrial DNA (mtDNA) and thousands of nuclear loci across individuals of the African Black Duck Anas sparsa and Yellow-billed Duck A. undulata to understand the evolutionary histories and to establish their current population structure. In addition to testing for possible hybridisation between these two African species, we compared the genetic ancestries with known wild and domestic Mallards A. platyrhynchos to understand whether the presence of that species in Africa is resulting in elevated interspecific hybridisation. Finally, we assessed morphological variation within the two African species; although the sample sizes limited inferences for the African Black Duck, we were able to demarcate trait cut-offs for field identification of the sexes of the Yellow-billed Duck. We recovered strong population structure between the two species and the Mallard for both mtDNA and nuclear loci. Whereas we recovered high levels of co-ancestry and low levels of nucleotide diversity among the African Black Duck samples, our demographic analysis estimated a contemporary effective population size of ∼2.5 million, which was equivalent to the estimate for the Yellow-billed Duck. We found that the increase in effective population size of both African species coincides with the onset of the last glacial cycle, with numbers peaking during the last glacial maximum. We recovered two genetic hybrids from the samples: a single hybrid between Yellow-billed Duck and wild Mallard, and the first genetically vetted Yellow-billed Duck × African Black Duck hybrid. Our study not only sheds light on the current population structures and standing genetic variation, but outlines methodologies to build morphological cut-offs for species and sex identification, which could be applied in future conservation efforts for Yellow-billed Ducks and African Black Ducks.