Bill adaptation in parrots: finding loci involved in surface area increases by integrating morphometrics with Next Gen Sequencing

Honours project: Keira Beattie

Understanding the effects of global warming on wildlife populations is a priority for conservation science.

Recent research shows that the average bill size of two Australian parrot species, the mulga (Psephotus varius) and the red-rumped parrot (Psephotus haematonotus), has significantly increased over the past century. As bills have been shown to be important for thermoregulation, this phenotypic change has been attributed as a response to climate warming.

This research aimed to discover if this change was genetic by creating DNA sequence libraries using the museum specimens of the two species from previous research exhibiting this trend in bill size, as well as a third that did not exhibit this trend as a control. Alignment was completed using the budgerigar (Melopsittacus undulates) as the reference genome. First, these libraries were used to test for geographical bias in sampling by reconstructing mitochondrial genomes.

The genomes were then used to generate a phylogeographical analysis which showed a significant geographical bias in the P. varius specimens. Here, there were two genetically distinct clades on either side of the Eyrean barrier, with sufficient differentiation to recognise two previously suggested subspecies, Psephotus varius varius and Psephotus varius rosinae.

Nuclear genomes were also constructed, and SNPs were compared between large – billed more recent specimens, and small - billed older specimens within and then across species, to determine the basis of the phenotypic changes in bill size. This analysis showed two SNPs of interest – one on a gene of unknown function, and one in a sequence resembling a mitochondrial control region. While neither of these SNPs conclusively showed a genetic basis for the phenotypic change, the methods used in this study provide a firm foundation for further research. 

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