Genomic population structure aligns with vocal dialects in Palm Cockatoos (Probosciger aterrimus); evidence for refugial late-Quaternary distribution?

ABSTRACT

Species persistence and maintenance of genetic diversity are strongly affected by dispersal and historical distribution, especially when species depend on habitat that is non-uniform or fluctuates dramatically with changing climate. Australo-Papuan rainforest has fluctuated dramatically since the last glacial maximum (around 20 kya). To understand how prehistoric climate fluctuation affected population connectivity and genetic diversity in a rainforest edge species, we screened 27 Palm Cockatoo samples from Cape York Peninsula (Australia) and southern Papua New Guinea (PNG) in 1132 single nucleotide polymorphisms in 342 nuclear loci and the mitochondrial ND2 gene. We also modelled the birds’ distribution at present, mid-Holocene (~6 kya) and the last glacial maximum (~21 kya). Population differentiation in nuclear genomic data among Australian populations aligns with distribution contraction to mountainous refugia at the mid-Holocene (~6 kya). Lack of nuclear divergence between PNG and Australia may reflect late-Holocene recolonisation, but different ND2 haplotypes suggest early stages of divergence. Although admixed individuals suggest some gene flow, recent movement restriction to/from Australian refugia is suggested by a unique ND2 haplotype, genomic divergence and a vocal dialect boundary shown previously. Our results show how prehistoric climate fluctuation affects present-day and future species conservation in dynamic rainforest edge ecosystems.

KEYWORDS:

• Australia
• conservation biogeography
• distribution model
• Iron Range
• New Guinea
• parrot
• Palm Cockatoo
• Probosciger

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Acknowledgements

We would like to thank Sam Banks, Leo Joseph and Kerensa McElroy for advice and direction, George Olah and Todd Cross for advice on feather examples, Sonal Singhal for advice on using the Rainbow assembler and Matteo Fumagalli for assistance with ngsTools. For valuable assistance and companionship in the field we thank Chris Sanderson, Maddie Castles, Zoe Reynolds, Claudia Benham, Richie Southerton and Andrew Neilen. We thank Dejan Stojanovic for assistance with grant applications, Xenia Weber and two anonymous reviewers for feedback on the manuscript, and Julie Brokenbrow, Eridani Mulder and Kristy Philliskirk for providing feathers.

Author contributions

The idea for this study was conceived by R.H. who, with N.E.L., contributed substantial resources, funding and edits of the manuscript. The molecular and modelling methods were developed, conducted and written by J.V.P., together with the results. The remaining manuscript was written with genetic samples collected and collated by M.V.K. S.A.M. extracted additional DNA from blood and tissue and commented on the manuscript.

Ethical note

This research was conducted under an Australian National University ethics protocol (No. A2012/36).

Supplemental material

Supplemental data for this article can be accessed here.

Additional information

Funding

This research is supported by an Australian Government Research Training Program Scholarship. We would like to thank the Hermon Slade Foundation and the National Geographic Society for funding fieldwork, and BirdLife Australia for funding lab costs through the Stuart Leslie Bird Research Award.