Phylogeography of the iconic Australian pink cockatoo,Lophochroa leadbeateri

Abstract

The pink cockatoo (Lophochroa leadbeateri; or Major Mitchell’s cockatoo) is one of Australia’s most iconic bird species. Two subspecies based on morphology are separated by a biogeographical divide, the Eyrean Barrier. Testing the genetic basis for this subspecies delineation, clarifying barriers to gene flow and identifying any cryptic genetic diversity will likely have important implications for conservation and management. Here, we used genome-wide single nucleotide polymorphisms (SNPs) and mitochondrial DNA data to conduct the first range-wide genetic assessment of the species. The aims were to investigate the phylogeography of the pink cockatoo, to characterize conservation units and to reassess subspecies boundaries. We found consistent but weak genetic structure between the two subspecies based on nuclear SNPs. However, phylogenetic analysis of nuclear SNPs and mitochondrial DNA sequence data did not recover reciprocally monophyletic groups, indicating incomplete evolutionary separation between the subspecies. Consequently, we have proposed that the two currently recognized subspecies be treated as separate management units rather than evolutionarily significant units. Given that poaching is suspected to be a threat to this species, we assessed the utility of our data for wildlife forensic applications. We demonstrated that a subspecies identification test could be designed using as few as 20 SNPs.

Future‐proofing the koala: Synergising genomic and environmental data for effective species management

“…The single historic skin specimen, and the single contemporary sample sequenced in duplicate on the NextSeq500 platform had SNP error rates of 1.951% and 1.183%, respectively (Table .1). These SNP error rates are comparable to those documented by previous studies, indicating that the use of multiple sequencing platforms did not exert a major influence on SNP‐calling or downstream analysis (Ewart et al, 2021; Mastretta‐Yanes et al, 2014).…”

Phylogeography of the white-crowned parrot (Pionus senilis)

“…Although the Northern and the Southern groups each presented a unique haplotype, three unique haplotypes were found in the Central populations, indicating high haplotype diversity (Hd) in total (h = 0.706). These data are similar to those reported by other studies on Psittacidae, such as Cyanoliseus patagonus with a haplotype diversity of 0.943, Eolophus roseicapilla with Hd: 0.817, Anodorhynchus hyacinthinus with Hd: 0.604, Eclectus roratus with Hd: 0.500 and Lophochroa leadbeateri with Hd: 0.602 (Masello et al 2011;Engelhard et al 2015;Presti et al 2015;Astuti 2020;Ewart et al 2021). Low nucleotide diversity values (π < 0.0025) and a small number of haplotypes are characteristic of the effects of population demographic expansion over a relatively recent period (Hamilton 2009).…”

Advancing Genetic Methods in the Study of Parrot Biology and Conservation

“…A comprehensive genetic analysis (using genome-wide SNPs and mitochondrial data) of the Red-tailed Black-Cockatoo Calyptorhynchus banksii identified five ESUs over their large distribution, and advised taxonomic reassessments including recognition of a new subspecies [125]. Distinctions between ESUs and MUs were made during a genetic assessment of Major Mitchell's Cockatoo Lophochroa leadbeateri [126]. An analysis employing mtDNA and microsatellite data failed to detect genetic evidence for the two subspecies of Kākā in New Zealand, instead it is hypothesised that phenotypic diversity was due to an adaptive latitudinal size cline consistent with Bergmann's rule [127], an important consideration for possible translocation attempts.…”

“…Poachers were also arrested in Brazil intending to fly to Europe, one in 2003 with avian eggs later identified by molecular genetic techniques as of parrots and owls [170], and another in 2018 with eggs identified as of Short-tailed Parrot Graydidascalus brachyurus [171]. Ewart et al [126] developed a forensic test with 20 nuclear SNPs for the Major Mitchell's Cockatoo and demonstrated its application for subspecies identification. A similar toolkit combining various forensic techniques was developed earlier for the Glossy Black-Cockatoo Calyptorhynchus lathami [172].…”

“…Using historical DNA (hDNA) of birds can be challenging but nevertheless offers important insights into their evolution, ecology, and conservation [211]. Museum samples have been used to study the subspecies- [212] and population-level structures [138] of the Palm Cockatoo in New Guinea and Australia, of the Pezoporus ground parrots [111], and of Red-tailed Black-Cockatoos and Major Mitchell's Cockatoos in Australia [125,126,213]. Jackson et al [108] extracted mtDNA from toepad samples of three extinct Psittacula parrots (P. exsul, P. eques, P. wardi).…”