Figure 1
Map of Australia showing plumages (including upper surface of tails in males), taxonomy and distributions of Golden Whistler Pachycephala pectoralis on mainland Australia and Tasmania and Western Whistler P. occidentalis at commencement of this study. Modified from Schodde and Mason (1999) whose proposed areas of intergradation are shown with hatching and whose core and non-breeding ranges of P. pectoralis youngi are also shown. The inset shows localities mentioned in the text. The map highlights that populations having cinnamon-bellied females and immatures at the study's commencement were assigned to two species, P. occidentalis and P. pectoralis fuliginosa.
Source publication
The Western Whistler Pachycephala occidentalis Ramsay, 1878, endemic to south-western Western Australia, is almost phenotypically identical with P. pectoralis fuliginosa, the westernmost of six subspecies of Golden Whistler P. pectoralis on Australia and its islands. New mitochondrial DNA (mtDNA) sequence data affirm multiple prior studies in align...
Contexts in source publication
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... literature mostly recognised one species in Australia, the Golden Whistler P. pectoralis. We first briefly review why a second species, the Western Whistler P. occidentalis, was split from it in ; Figure 1). To avoid confusion we depart from the convention of abbreviating species epithets: P. p. pectoralis is cited as P. pectoralis pectoralis, for example. ...
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... and Mason (1999) provided the most detailed analysis of plumage diversity within Australian populations. Variation in adult male tail colour and plumages of adult female and immature birds show the most taxonomically relevant and discrete populationlevel variation (Figure 1). Two groups of populations are easily recognised by adult female and immature plumages. ...
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... a possibility first raised by Horton et al. (2013) was then explored and enacted by Joseph et al. (2014): western populations of P. pectoralis fuliginosa were elevated to the taxonomic rank of species as P. occidentalis Ramsay, 1878. All eastern populations of P. pectoralis fuliginosa remained as P. pectoralis fuliginosa Vigors & Horsfield, 1827 (Figure 1). ...
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... gap of ~1000 kilometres separated specimens identified by molecular data as P. occidentalis and P. pectoralis fuliginosa. This gap spanned an area from near Esperance, Western Australia to Maralinga, South Australia, respectively ( Figure 1; the specimens are MV B23978 and ANWC B52176; see Table 1 for abbreviations and details). A secondary aim of this paper is to obtain and assess molecular data from populations within this gap. ...
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... 1 lists specimens examined in this study. Eight were collected during field work in 2017 in southeastern Western Australia between Kalgoorlie and Eucla ( Figure 1). They allow the Esperance-Maralinga gap to be sampled for molecular data (see Introduction; Figure 1). ...
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... were collected during field work in 2017 in southeastern Western Australia between Kalgoorlie and Eucla ( Figure 1). They allow the Esperance-Maralinga gap to be sampled for molecular data (see Introduction; Figure 1). Tentatively first identified as P. occidentalis, all eight are analysed here for single nucleotide polymorphisms (SNP) and mtDNA. ...
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... close the gap between specimens sampled for molecular data and assignable to P. occidentalis or P. pectoralis fuliginosa to ~400 kilometres. Most of that gap is unsuitable habitat, e.g., the treeless Nullarbor Plain (Figure 1). ...
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... was extracted from cryofrozen tissue samples of 20 specimens (Table 1): five from mainland eastern Australian populations (P. pectoralis pectoralis (n = 2), P. pectoralis youngi (2) and P. pectoralis glaucura), four P. pectoralis fuliginosa chosen to span most of that form's range, and 11 P. occidentalis comprising eight individuals that were newly collected in 2017 and three in the Australian National Wildlife Collection (ANWC) from the south-western corner of the continent (Figure 1). Because of residual uncertainty about the relationship of all of these taxa to the Mangrove Golden Whistler P. melanura (see Introduction), we included four specimens of that species (ANWC B33207, B33754, B51359, B52425; Table 1). ...
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... monomorphic loci and no duplicate loci per sequence tag were identified. A phylogenetic analysis is reported in Online Supplementary Material including Supplementary Figure S1. ...
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... data from the four South Australian specimens of P. pectoralis fuliginosa (Table 1) reinforce that they are either breeding adult male or immature P. pectoralis fuliginosa. Notably, the locality of the immature bird is from the westernmost specimenbased location, Maralinga, of P. pectoralis fuliginosa that is accompanied by molecular data (Figure 1). The P. melanura cluster was well separated on PCo1 from the three focal populations. ...
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... PCo2, there was little separation between P. melanura and the two clusters of P. occidentalis and P. pectoralis fuliginosa. Phylogenetic analysis (Supplementary Figure S1) reinforced these findings: samples of P. occidentalis and P. pectoralis fuliginosa formed a robustly supported clade, which was reciprocally monophyletic with respect to the other P. pectoralis samples. ...
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... used single nucleotide polymorphisms (SNPs) and mtDNA sequences to clarify the status of southern Australian populations of the golden whistler complex assigned to P. pectoralis fuliginosa (Figure 1). This taxon is phenotypically almost indistinguishable from the recently recognised Western Whistler P. occidentalis of south-western Australia. ...
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... from specimens of P. pectoralis pectoralis, P. pectoralis youngi, and P. pectoralis glaucura, Andersen et al. (2014) examined eight specimens now identified as Western Australian samples of P. occidentalis and one specimen of P. pectoralis fuliginosa, a specimen from Kangaroo Island, South Australia (ANWC B42504; Figure 1). They based their conclusions on concatenated analyses of mtDNA and eight nuclear loci from their samples. ...
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... other treats three species P. occidentalis, P. fuliginosa and P. pectoralis. To decide among these alternatives, we stress several points: (1) the clear correlation, given our sampling, between nuclear DNA diversity and the eastern and western phenotypes of adult females and immature birds and adult mail tail colour (Figures 1 and 2; Schodde and Mason 1999), and (2) the scant prior evidence of phenotypic intergradation and the current lack of evidence for intergradation in nuclear DNA among the two phenotypic groups, though further study is needed. Accordingly, we recommend recognising two species, P. fuliginosa and P. pectoralis, as just outlined. ...
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... the introgression is still in progress and its westwards movement has not yet reached P. fuliginosa occidentalis. A more likely alternative is that P. fuliginosa fuliginosa and P. fuliginosa occidentalis are isolated by a substantial amount of unsuitable habitat centred on the Nullarbor Plain (Figure 1). Atlas of Living Australia (ALA) records highlight this in a small but discrete gap of ~200 kilometres between the inferred ranges of the two subspecies along the southern edge of the Nullarbor Plain (accessed 13 August 2020; https://biocache.ala. ...
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... are extending the breeding range of the Western Whistler some 1500 kilometres eastwards by way of its eastern subspecies P. fuliginosa fuliginosa. Its range thus spans all of drier southern South Australia (including the Gulfs region; Figure 1) and western parts of Victoria and potentially far western New South Wales ( Schodde and Mason 1999;Supplementary Table S1). Individuals are likely to wander still further east when not breeding (see, for example, a record from near Heathcote, south-east of Bendigo, 31 March 2019: https://ebird.org/checklist/ ...
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Citations
... Phuong et al., 2017), generating conflicting patterns across the genome and making it difficult to identify causative links between pattern and process. Most cases confidently associating mitonuclear discordance with an underlying evolutionary process involve dramatic discordance caused by mitochondrial capture Joseph et al., 2021;Kearns et al., 2014;McElroy et al., 2020;Mikkelsen & Weir, 2022), directional introgression across a hybrid zone (Del-Rio et al., 2022) or recent hybridization resulting in mismatched mitochondrial and nuclear genomes in a single individual (Joseph et al., 2019;Joseph & Moritz, 1993). In contrast, few studies have identified mitonuclear discordance resulting mainly from ILS (except see Firneno et al., 2020;Wang et al., 2018). ...
Many organisms possess multiple discrete genomes (i.e. nuclear and organellar), which are inherited separately and may have unique and even conflicting evolutionary histories. Phylogenetic reconstructions from these discrete genomes can yield different patterns of relatedness, a phenomenon known as cytonuclear discordance. In many animals, mitonuclear discordance (i.e. discordant evolutionary histories between the nuclear and mitochondrial genomes) has been widely documented, but its causes are often considered idiosyncratic and inscrutable. We show that a case of mitonuclear discordance in Todiramphus kingfishers can be explained by extensive genome-wide incomplete lineage sorting (ILS), likely a result of the explosive diversification history of this genus. For these kingfishers, quartet frequencies reveal that the nuclear genome is dominated by discordant topologies, with none of the internal branches in our consensus nuclear tree recovered in >50% of genome-wide gene trees. Meanwhile, a lack of inter-species shared ancestry, non-significant pairwise tests for gene flow, and little evidence for meaningful migration edges between species, leads to the conclusion that gene flow cannot explain the mitonuclear discordance we observe. This lack of evidence for gene flow combined with evidence for extensive genome-wide gene tree discordance, a hallmark of ILS, leads us to conclude that the mitonuclear discordance we observe likely results from ILS, specifically deep coalescence of the mitochondrial genome. Based on this case study, we hypothesize that similar demographic histories in other 'great speciator' taxa across the Indo-Pacific likely predispose these groups to high levels of ILS and high likelihoods of mitonuclear discordance.
... Our protocols for the extraction of DNA, library preparation and generation of single nucleotide polymorphism (SNP) data essentially followed the Diversity Arrays Technology (DArT) pipeline as described elsewhere (Joseph et al. 2019a(Joseph et al. , 2019b(Joseph et al. , 2021. Details are in Supplementary Material but some details follow. ...
The Forest Kingfisher Todiramphus macleayii inhabits eucalypt savannas, rainforests and mangroves across its distribution in Australasia. Two Australian subspecies are consistently recognised but the taxonomic status of resident New Guinean populations is unsettled. Genomic data from populations sampled across the species’ Australian and New Guinean ranges support the recognition of resident New Guinean populations at the subspecies level as T. m. elisabeth. Further work is required to examine island populations that remain unsampled genetically and to place the species in a broader phylogenetic analysis of Todiramphus kingfishers. We also report genetically based detection of a migrant individual in New Guinea either from eastern Australia or the Trans-Fly region of southern New Guinea. Our study provides a first insight into how genetic diversity is structured within this species across its range. It highlights remaining areas for study and illustrates the potential of DNA sequence data in tracking migratory movements of the species.
... Seven outgroup and 11 ingroup taxa were previously sequenced (Moyle et al., 2016;Oliveros et al., 2019; Table 1) and those data were downloaded from GenBank and added to our dataset. We sampled two individuals from widely separated populations of the recently recognized Western Whistler in Australia (P. f. fuliginosa and P. f. occidentalis; Joseph et al., 2014aJoseph et al., , 2021. ...
The utility of islands as natural laboratories of evolution is exemplified in the patterns of differentiation in widespread, phenotypically variable lineages. The whistlers (Aves: Pachycephalidae) are one of the most complex avian radiations, with a combination of widespread and locally endemic taxa spanning the vast archipelagos of the Indo-Pacific, making them an ideal group to study patterns and processes of diversification on islands. Here, we present a robust, species-level phylogeny of all five genera and 85% of species within Pachycephalidae, based on thousands of ultraconserved elements (UCEs) generated with a target-capture approach and high-throughput sequencing. We clarify phylogenetic relationships within Pachycephala and report on divergence timing and ancestral range estimation. We explored multiple biogeographic coding schemes that incorporated geological uncertainty in this complex region. The biogeographic origin of this group was difficult to discern, likely owing to aspects of dynamic Earth history in the Indo-Pacific. The Australo-Papuan region was the likely origin of crown-group whistlers, but the specific ancestral area could not be identified more precisely than Australia or New Guinea, and Wallacea may have played a larger role than previously realized in the evolutionary history of whistlers. Multiple independent colonizations of island archipelagos across Melanesia, Wallacea, and the Philippines contributed to the relatively high species richness of extant whistlers. This work refines our understanding of one of the regions’ most celebrated bird lineages and adds to our growing knowledge about the patterns and processes of diversification in the Indo-Pacific.
... Excoffier 2009 andLi andKokko 2019 andreferences in both). Multilocus datasets from a few nuclear loci such as introns may be entirely inappropriate and equally misleading in such cases because of their low and often incompletely sorted diversity (example reviewed in Joseph et al. 2020). Species limits will best be understood from genetic data when genomic methods for obtaining nDNA data from thousands of loci have been used. ...
Four main challenges that can underpin ongoing, intransigent debates about species limits in birds are reviewed: allopatry (population subdivision vs. speciation), geographically widespread introgression of mitochondrial DNA (mtDNA), recent speciation, and selection. Examples from birds of the Australian region show how these challenges, their interplay, and the molecular-phenotypic discordance they generate can clarify or mislead species limits. Examples of how phylogenetic frameworks help reject or retain hypotheses of species limits under these challenges are given. Although mtDNA’s strengths and limitations are well known, an underappreciated limitation of mtDNA is geographically widespread introgression that homogenizes mtDNA diversity across species, subspecies, or population boundaries and across hundreds of kilometers. The resulting discordance between mtDNA and phenotype can be profound. If undetected, the setting of species limits and evolutionarily significant units are misled. An example shows how recent genomic analyses can detect and solve the problem. Other examples concern legacy mtDNA-only datasets. These are often essentially unfinished studies leaving residual uncertainty in species limits. Examples illustrate when the possibility of large-scale introgression across species boundaries needs to be considered, and how genomic scale data offer solutions. Researchers must carefully parse 3 questions: has there been introgression of mtDNA and, if so, which population genetics-based driver has caused introgression, and do species limits need altering? Understanding of allopatry, mtDNA introgression, recent speciation, and selection must be properly integrated if species limits are to be robustly understood and applied with maximum benefit in downstream applications such as conservation and management.
