Genomic data show little geographical structure across the naturally fragmented range of the purple-gaped honeyeater
Leo Joseph A C , Catriona D. Campbell A , Lynn Pedler B and Alex Drew AA Australian National Wildlife Collection, CSIRO National Research Collections Australia, GPO Box 1700, Canberra, ACT 2601, Australia.
B PO Box 58, Koolunga, SA 5464, Australia.
C Corresponding author. Email: leo.joseph@csiro.au
Australian Journal of Zoology 67(4) 226-230 https://doi.org/10.1071/ZO20074
Submitted: 13 August 2020 Accepted: 11 December 2020 Published: 23 December 2020
Journal compilation © CSIRO 2019 Open Access CC BY-NC-ND
Abstract
Using single nucleotide polymorphisms and mitochondrial DNA sequences we find some evidence of genetic structure within a widespread and naturally fragmented species, the purple-gaped honeyeater (Lichenostomus cratitius), of southern Australian mallee shrublands. The very earliest stages of differentiation either side of the Nullarbor Barrier may already have been arrested by gene flow, some of which may have been anthropogenically induced.
Keywords: purple-gaped honeyeater, honeyeater, phylogeography, Nullarbor Barrier, Eyrean Barrier, southern Australia, Lichenostomus.
References
Alpers, D. L., Walker, F. M., Taylor, A. C., Sunnucks, P., Bellman, S., Hansen, B. D., and Sherwin, W. B. (2016). Evidence of subdivisions on evolutionary timescales in a large, declining marsupial distributed across a phylogeographic barrier. PLoS One 11, e0162789.| Evidence of subdivisions on evolutionary timescales in a large, declining marsupial distributed across a phylogeographic barrier.Crossref | GoogleScholarGoogle Scholar | 27732594PubMed |
Ansari, M. H., Cooper, S. J. B., Schwarz, M. P., Ebrahimie, M., Dolman, G., Reinberger, L., Saint, K. M., Donnellan, S. C., Bull, C. M., and Gardner, M. G. (2019). Plio-Pleistocene diversification and biogeographic barriers in southern Australia reflected in the phylogeography of a widespread and common lizard species. Molecular Phylogenetics and Evolution 133, 107–119.
| Plio-Pleistocene diversification and biogeographic barriers in southern Australia reflected in the phylogeography of a widespread and common lizard species.Crossref | GoogleScholarGoogle Scholar | 30553880PubMed |
Cooper, S. J. B., Adams, M., and Labrinidis, A. (2000). Phylogeography of the Australian dunnart Sminthopsis crassicaudata (Marsupialia: Dasyuridae). Australian Journal of Zoology 48, 461–473.
| Phylogeography of the Australian dunnart Sminthopsis crassicaudata (Marsupialia: Dasyuridae).Crossref | GoogleScholarGoogle Scholar |
Cooper, S. J. B., Ottewell, K., MacDonald, A. J., Adams, M., Byrne, M., Carthew, S. M., Eldridge, M. D. B., Li, Y., Pope, L. C., Saint, K. M., and Westerman, M. (2018). Phylogeography of southern brown and golden bandicoots: implications for the taxonomy and distribution of endangered subspecies and species. Australian Journal of Zoology 66, 379–393.
| Phylogeography of southern brown and golden bandicoots: implications for the taxonomy and distribution of endangered subspecies and species.Crossref | GoogleScholarGoogle Scholar |
Courtois, B., Audebert, A., Dardou, A., Roques, S., Ghneim-Herrera, T, Droc, G, Frouin, J, Rouan, L, Gozé, E, Kilian, A, Ahmadi, N, and Dingkuhn, M (2013). Genome-wide association mapping of root traits in a japonica rice panel. PLoS One 8, e78037.
| Genome-wide association mapping of root traits in a japonica rice panel.Crossref | GoogleScholarGoogle Scholar | 24223758PubMed |
Crisp, M. D., and Cook, L. G. (2007). A congruent molecular signature of vicariance across multiple plant lineages. Molecular Phylogenetics and Evolution 43, 1106–1117.
| A congruent molecular signature of vicariance across multiple plant lineages.Crossref | GoogleScholarGoogle Scholar | 17434758PubMed |
Cruz, V. M. V., Kilian, A., and Dierig, D. A. (2013). Development of DArT marker platforms and genetic diversity assessment of the US collection of the new oilseed crop lesquerella and related species. PLoS One 8, e64062.
| Development of DArT marker platforms and genetic diversity assessment of the US collection of the new oilseed crop lesquerella and related species.Crossref | GoogleScholarGoogle Scholar |
Dolman, G., and Joseph, L. (2012). A species assemblage approach to comparative phylogeography of birds in southern Australia. Ecology and Evolution 2, 354–369.
| A species assemblage approach to comparative phylogeography of birds in southern Australia.Crossref | GoogleScholarGoogle Scholar | 22423329PubMed |
Dolman, G., and Joseph, L. (2015). Evolutionary history of birds across southern Australia: structure, history and taxonomic implications of mitochondrial DNA diversity in an ecologically diverse suite of species. Emu 115, 35–48.
| Evolutionary history of birds across southern Australia: structure, history and taxonomic implications of mitochondrial DNA diversity in an ecologically diverse suite of species.Crossref | GoogleScholarGoogle Scholar |
Donnellan, S. C., Armstrong, J., Pickett, M., Milne, T., Baulderstone, J., Holfelder, T., and Bertozzi, T. (2009). Systematic and conservation implications of mitochondrial DNA diversity in emu-wrens, Stipiturus (Aves: Maluridae). Emu 109, 143–152.
| Systematic and conservation implications of mitochondrial DNA diversity in emu-wrens, Stipiturus (Aves: Maluridae).Crossref | GoogleScholarGoogle Scholar |
Donnellan, S. C., Foster, R., Junge, C., Huveneers, C., Rogers, P., Kilian, A., and Bertozzi, T. (2015). Fiddling with the proof: the magpie fiddler ray is a colour pattern variant of the common southern fiddler ray (Rhinobatidae: Trygonorrhina). Zootaxa 3981, 367–384.
| Fiddling with the proof: the magpie fiddler ray is a colour pattern variant of the common southern fiddler ray (Rhinobatidae: Trygonorrhina).Crossref | GoogleScholarGoogle Scholar | 26250000PubMed |
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32, 1792–1797.
| MUSCLE: multiple sequence alignment with high accuracy and high throughput.Crossref | GoogleScholarGoogle Scholar | 15034147PubMed |
Edwards, D. L., Melville, J., Joseph, L., and Keogh, J. S. (2015). Ecological divergence, adaptive radiation and the evolution of sexual signaling traits in a complex of Australian agamid lizards. American Naturalist 186, E144–E161.
| Ecological divergence, adaptive radiation and the evolution of sexual signaling traits in a complex of Australian agamid lizards.Crossref | GoogleScholarGoogle Scholar |
Gruber, B., Unmack, P. J., Berry, O. F., and Georges, A. (2018). dartR: an R package to facilitate analysis of SNP data generated from reduced representation genome sequencing. Molecular Ecology Resources 18, 691–699.
| dartR: an R package to facilitate analysis of SNP data generated from reduced representation genome sequencing.Crossref | GoogleScholarGoogle Scholar | 29266847PubMed |
Joseph, L., and Wilke, T. (2006). Molecular resolution of population history, systematics and historical biogeography of the Australian ringneck parrots Barnardius: are we there yet? Emu 106, 49–62.
| Molecular resolution of population history, systematics and historical biogeography of the Australian ringneck parrots Barnardius: are we there yet?Crossref | GoogleScholarGoogle Scholar |
Joseph, L., Toon, A., Nyári, Á. S., Longmore, N. W., Rowe, K. M. C., Haryoko, T., Trueman, J., and Gardner, J. (2014). A new synthesis of the molecular systematics and biogeography of honeyeaters (Passeriformes: Meliphagidae) highlights biogeographical complexity of a spectacular avian radiation. Zoologica Scripta 43, 235–248.
| A new synthesis of the molecular systematics and biogeography of honeyeaters (Passeriformes: Meliphagidae) highlights biogeographical complexity of a spectacular avian radiation.Crossref | GoogleScholarGoogle Scholar |
Kilian, A., Wenzl, P., Huttner, E., Carling, J., Xia, L., Blois, H., Caig, V., Heller-Uszynska, K., Jaccoud, D., Hopper, C., Aschenbrenner-Kilian, M., Evers, M., Peng, K., Cayla, C., Hok, P., and Uszynski, G. (2012). Diversity arrays technology: a generic genome profiling technology on open platforms. Methods in Molecular Biology 888, 67–89.
| Diversity arrays technology: a generic genome profiling technology on open platforms.Crossref | GoogleScholarGoogle Scholar | 22665276PubMed |
Kumar, S., Stecher, G., Li, M., Knyaz, C., and Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35, 1547–1549.
| MEGA X: Molecular evolutionary genetics analysis across computing platforms.Crossref | GoogleScholarGoogle Scholar | 29722887PubMed |
Marki, P. Z., Jønsson, K. A., Irestedt, M., Nguyen, J., Rahbek, C., and Fjeldså, J. (2017). Supermatrix phylogeny and biogeography of the Australasian Meliphagides radiation (Aves: Passeriformes). Molecular Phylogenetics and Evolution 107, 516–529.
| Supermatrix phylogeny and biogeography of the Australasian Meliphagides radiation (Aves: Passeriformes).Crossref | GoogleScholarGoogle Scholar | 28017855PubMed |
McElroy, K., Dolman, G., Horton, P., Black, A., Pedler, L., Drew, A., and Joseph, L. (2020). Robbery in progress: historical museum collections bring to light a mitochondrial capture within a bird species widespread across southern Australia, the copperback quail-thrush Cinclosoma clarum. Ecology and Evolution 10, 6785–6793.
| Robbery in progress: historical museum collections bring to light a mitochondrial capture within a bird species widespread across southern Australia, the copperback quail-thrush Cinclosoma clarum.Crossref | GoogleScholarGoogle Scholar | 32724551PubMed |
Menkhorst, P., Rogers, D., Clarke, R., Davies, J., Marsack, P., and Franklin, K. (2017). ‘The Australian Bird Guide.’ (CSIRO Publishing: Melbourne.)
Neaves, L. E., Zenger, K. R., Prince, R. I. T., and Eldridge, M. D. B. (2012). Impact of Pleistocene aridity oscillations on the population history of a widespread, vagile Australian mammal, Macropus fuliginosus. Journal of Biogeography 39, 1545–1563.
| Impact of Pleistocene aridity oscillations on the population history of a widespread, vagile Australian mammal, Macropus fuliginosus.Crossref | GoogleScholarGoogle Scholar |
Norman, J. A., Blackmore, C. J., Rourke, M., and Christidis, L. (2014). Effects of mitochondrial DNA rate variation on reconstruction of Pleistocene demographic history in a social avian species, Pomatostomus superciliosus. PLoS One 9, e106267.
| Effects of mitochondrial DNA rate variation on reconstruction of Pleistocene demographic history in a social avian species, Pomatostomus superciliosus.Crossref | GoogleScholarGoogle Scholar | 25181547PubMed |
Nyári, A., and Joseph, L. (2011). Systematic dismantlement of Lichenostomus improves the basis for understanding relationships within the honeyeaters (Meliphagidae) and historical development of Australo-Papuan bird communities. Emu 111, 202–211.
| Systematic dismantlement of Lichenostomus improves the basis for understanding relationships within the honeyeaters (Meliphagidae) and historical development of Australo-Papuan bird communities.Crossref | GoogleScholarGoogle Scholar |
Pembleton, L. W., Cogan, N. O. I., and Forster, J. W. (2013). StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations. Molecular Ecology Resources 13, 946–952.
| StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations.Crossref | GoogleScholarGoogle Scholar | 23738873PubMed |
Pestell, A. J. L., Cooper, S. J. B., Saint, K., and Petit, S. (2008). Genetic structure of the western pygmy possum, Cercartetus concinnus Gould (Marsupialia: Burramyidae) based on mitochondrial DNA. Australian Mammalogy 29, 191–200.
| Genetic structure of the western pygmy possum, Cercartetus concinnus Gould (Marsupialia: Burramyidae) based on mitochondrial DNA.Crossref | GoogleScholarGoogle Scholar |
Pons, J., Barraclough, T. G., Gomez-Zurita, J., Cardoso, A., Duran, D. P., Hazell, S., Kamoun, S., Sumlin, W. D., and Vogl, A. P. (2006). Sequence-based species delimitation for the DNA taxonomy of undescribed insects Systematic Biology 55, 595–609.
| Sequence-based species delimitation for the DNA taxonomy of undescribed insectsCrossref | GoogleScholarGoogle Scholar | 16967577PubMed |
Rix, M. G., Cooper, S. J. B., Meusemann, K., Klopfstein, S., Harrison, S. E., Harvey, M. S., and Austin, A. D. (2017). Post-Eocene climate change across continental Australia and the diversification of Australasian spiny trapdoor spiders (Idiopidae: Arbanitinae). Molecular Phylogenetics and Evolution 109, 302–320.
| Post-Eocene climate change across continental Australia and the diversification of Australasian spiny trapdoor spiders (Idiopidae: Arbanitinae).Crossref | GoogleScholarGoogle Scholar | 28126515PubMed |
Rozas, J, Ferrer-Mata, A, Sanchez-Del Barrio, J. C., Guirao-Rico, S, Librado, P, Ramos-Onsins, S. E., and Sánchez-Gracia, A (2017). DnaSP v6: DNA sequence polymorphism analysis of large datasets. Molecular Biology and Evolution 34, 3299–3302.
| DnaSP v6: DNA sequence polymorphism analysis of large datasets.Crossref | GoogleScholarGoogle Scholar | 29029172PubMed |
Schodde, R., and Mason, I. J. (1999). ‘The Directory of Australian Birds: Passerines.’ (CSIRO Publishing: Melbourne.)
Sukumaran, J., and Holder, M. T. (2015). SumTrees: phylogenetic tree summarization. 4.0.0. Available at: https://github.com/jeetsukumaran/DendroPy [accessed 14 December 2020].
Tamura, K., and Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10, 512–526.
| Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.Crossref | GoogleScholarGoogle Scholar | 8336541PubMed |
Zwickl, D. J. (2006). Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion, Ph.D. Dissertation, University of Texas.