Phylogeography of the iconic Australian pink cockatoo, Lophochroa leadbeateri

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.

Osteofibrous Dysplasia in a Cockatiel (Nymphicus hollandicus)

Osteofibrous dysplasia is a rare and benign nonneoplastic condition of unknown etiology in humans and mammals. An adult female cockatiel (Nymphicus hollandicus) was presented with the following problems: a soft tissue mass on the left frontal area of the head that extended over the left eye, anorexia, lethargy, and emaciation. Computed tomographic imaging and ultrasonography revealed a soft tissue opacity in the left cranial area of the head with multifocal heterogeneous opacities and foci of mineralization. Cytological, histopathological, and immunohistochemistry examinations were performed on biopsy samples from tissue collected from the mass. Following surgical removal of the cranial mass the patient was treated with a nonsteroidal anti-inflammatory drug and antibiotic medication. The surgical site healed with no complications and through follow-up examinations there were no signs of reoccurrence of the abnormal tissue for 2 months. Through cytological and histopathological examination and immunohistochemistry testing of the submitted tissue, a diagnosis of osteofibrous dysplasia was determined.

Phylogeography of the iconic Australian red-tailed black-cockatoo (Calyptorhynchus banksii) and implications for its conservation

Advances in sequencing technologies have revolutionized wildlife conservation genetics. Analysis of genomic data sets can provide high-resolution estimates of genetic structure, genetic diversity, gene flow, and evolutionary history. These data can be used to characterize conservation units and to effectively manage the genetic health of species in a broad evolutionary context. Here we utilize thousands of genome-wide single-nucleotide polymorphisms (SNPs) and mitochondrial DNA to provide the first genetic assessment of the Australian red-tailed black-cockatoo (Calyptorhynchus banksii), a widespread bird species comprising populations of varying conservation concern. We identified five evolutionarily significant units, which are estimated to have diverged during the Pleistocene. These units are only partially congruent with the existing morphology-based subspecies taxonomy. Genetic clusters inferred from mitochondrial DNA differed from those based on SNPs and were less resolved. Our study has a range of conservation and taxonomic implications for this species. In particular, we provide advice on the potential genetic rescue of the Endangered and restricted-range subspecies C. b. graptogyne, and propose that the western C. b. samueli population is diagnosable as a separate subspecies. The results of our study highlight the utility of considering the phylogeographic relationships inferred from genome-wide SNPs when characterizing conservation units and management priorities, which is particularly relevant as genomic data sets become increasingly accessible.

Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species

Natural history museums harbour a plethora of biological specimens which are of potential use in population and conservation genetic studies. Although technical advancements in museum genomics have enabled genome-wide markers to be generated from aged museum specimens, the suitability of these data for robust biological inference is not well characterized. The aim of this study was to test the utility of museum specimens in population and conservation genomics by assessing the biological and technical validity of single nucleotide polymorphism (SNP) data derived from such samples. To achieve this, we generated thousands of SNPs from 47 red-tailed black cockatoo (Calyptorhychus banksii) traditional museum samples (i.e. samples that were not collected with the primary intent of DNA analysis) and 113 fresh tissue samples (cryopreserved liver/muscle) using a restriction site-associated DNA marker approach (DArTseq^™ ). Thousands of SNPs were successfully generated from most of the traditional museum samples (with a mean age of 44 years, ranging from 5 to 123 years), although 38% did not provide useful data. These SNPs exhibited higher error rates and contained significantly more missing data compared with SNPs from fresh tissue samples, likely due to considerable DNA fragmentation. However, based on simulation results, the level of genotyping error had a negligible effect on inference of population structure in this species. We did identify a bias towards low diversity SNPs in older samples that appears to compromise temporal inferences of genetic diversity. This study demonstrates the utility of a RADseq-based method to produce reliable genome-wide SNP data from traditional museum specimens.

The evolutionary history of cockatoos (Aves: Psittaciformes: Cacatuidae)

Cockatoos are the distinctive family Cacatuidae, a major lineage of the order of parrots (Psittaciformes) and distributed throughout the Australasian region of the world. However, the evolutionary history of cockatoos is not well understood. We investigated the phylogeny of cockatoos based on three mitochondrial and three nuclear DNA genes obtained from 16 of 21 species of Cacatuidae. In addition, five novel mitochondrial genomes were used to estimate time of divergence and our estimates indicate Cacatuidae diverged from Psittacidae approximately 40.7 million years ago (95% CI 51.6-30.3 Ma) during the Eocene. Our data shows Cacatuidae began to diversify approximately 27.9 Ma (95% CI 38.1-18.3 Ma) during the Oligocene. The early to middle Miocene (20-10 Ma) was a significant period in the evolution of modern Australian environments and vegetation, in which a transformation from mainly mesic to xeric habitats (e.g., fire-adapted sclerophyll vegetation and grasslands) occurred. We hypothesize that this environmental transformation was a driving force behind the diversification of cockatoos. A detailed multi-locus molecular phylogeny enabled us to resolve the phylogenetic placements of the Palm Cockatoo (Probosciger aterrimus), Galah (Eolophus roseicapillus), Gang-gang Cockatoo (Callocephalon fimbriatum) and Cockatiel (Nymphicus hollandicus), which have historically been difficult to place within Cacatuidae. When the molecular evidence is analysed in concert with morphology, it is clear that many of the cockatoo species' diagnostic phenotypic traits such as plumage colour, body size, wing shape and bill morphology have evolved in parallel or convergently across lineages.

Cytochrome-b sequence variation among parrots

The nucleotide sequence of a 307 bp fragment of the mitochondrial cytochrome-b gene was determined for 12 species of parrot, using the polymerase chain reaction and direct sequencing. Sequence divergence ranged from 26-54 differences in pairwise comparisons, with the majority of base substitutions occurring at third positions of codons. The transition:transversion ratio was determined to be higher (approximately 24.3:1) in recently divergent parrot lineages than has generally been observed in other groups. Strongly biased base composition, particularly at the third position of codons, is evident among the sequences. Phylogenetic relationships among more divergent taxa were estimated, using only transversion substitutions, while all the substitutions were useful for closely related taxa. The African genera Psittacus and Poicephalus are closely related, in contrast to the Australian genera Nymphicus, Purpureicephalus and Melopsittacus, which represent more divergent lineages. The cockatoos appear to represent an ancient lineage within the parrots.

Phylogenetic relationships within parrots (Psittacidae) inferred from mitochondrial cytochrome-b gene sequences

Blood and tissue samples of 40 individuals including 27 parrot species (15 genera; 3 subfamilies) were collected in Indonesia. Their phylogenetic relationships were inferred from 907 bp of the mitochondrial cytochrome-b gene, using the maximum-parsimony method, the maximum-likelihood method and the neighbor-joining method with Kimura two-parameter distance. The phylogenetic analysis revealed that (1) cockatoos (subfamily Cacatuinae) form a monophyletic sister group to other parrot groups; (2) within the genus Cacatua, C. goffini and C. sanguinea form a sister group to a clade containing other congeners; (3) subfamily Psittacinae emerged as paraphyletic, consisting of three clades, with a clade of Psittaculirostris grouping with subfamily Loriinae rather than with other Psittacinae; (4) lories and lorikeets (subfamily Loriinae) emerged as monophyletic, with Charmosyna placentis a basal sister group to other Loriinae, which comprised the subclades Lorius; Trichoglossus+Eos; and Chalcopsitta+ Pseudeos.

The evolution of the spindlin gene in birds: sequence analysis of an intron of the spindlin W and Z gene reveals four major divisions of the Psittaciformes

The Psittaciformes (parrots, parakeets) are among the most widely held captive birds. Yet, their evolution and their phylogenetic relationships have been relatively little studied. This paper describes the phylogenetic relationships between a number of Psittaciformes as derived from the sequences of the third intron of the Z-chromosomal and W-chromosomal spindlin genes. The Z-chromosomal sequences of the kakapo (Strigops habroptilus), the kea (Nestor notabilis), and the kaka (Nestor meridionalis) from New Zealand form a cluster which is the sister group to all other Psittaciformes. The results show further that the Z-chromosomal sequences of the other species can be divided into two groups based on the occurrence of a sequence element ACCCT. The group with the insert (A) is mainly from species with an Australasian geographical distribution and includes such species as the Lories (Lorius, etc.), the budgerigar (Melospittacus undulatus), and the rosellas (Platycercus). It also includes the African lovebirds (Agapornidae), which are the only representative of group A outside Australasia. Group B, without the insert, includes the neotropical parrots and parakeets such as the amazons (Amazona, etc.), the macaws (Ara, etc.), and the conures (Aratinga, etc.), the Australian Cacatuini and the African species such as the African grey parrot (Psittacus erithacus) as well as Coracopsis vasa from Madagascar and Psittrichas fulgidus from New Guinea. The W-chromosomal sequence data show that another division of the Psittacidae is found in the replacement of a pyrimidine-rich segment occurring in many non-psittacines as well as the kakapo (S. habroptilus), the kea (N. notabilis), the kaka (N. meridionalis), and the Cacatuini by a microsatellite consisting of a variable number of TATTA monomers in the other Psittaciformes. The results support a Gondwanan origin of the Psittaciformes and the suggestion that paleogeographic events were a major force in psittacine divergence.

Highly repeated DNA sequences in birds: the structure and evolution of an abundant, tandemly repeated 190-bp DNA fragment in parrots

Up to 6.8% of the parrot (Psittaciformes) genome consists of a tandemly repeated, 190-bp sequence (P1) located in the centromere of many if not all chromosomes. Monomer repeats from 10 different psittacine species representing four subfamilies were isolated and cloned. The intraspecific sequence variation ranged from 1.5 to 7%. The interspecific sequence variation ranged from less than 3% between two species of cockatoos to approximately 45% between cockatoos and other parrots. The monomer sequences of all 10 parrot species contained several conserved (> 90%) sequence elements at identical locations within the repeat. A comparison with tandemly repeated DNA sequences in other avian species showed that several of these conserved elements were also present at similar locations within the 184-bp repeat of the Chilean flamingo (Phoenicopterus chilensis), suggesting a great antiquity of the repeat. One of the elements was also found in the tandemly repeated sequences of the crane (Gruidae) and falcon (Falconidae) families. The data were used for the construction of a partial most parsimonious relationship that supports a regional subdivision of the Psittaciformes.