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Perktaş U. Range shift and loss of genetic diversity under climate change in the red-backed fairywren ( Malurus melanocephalus), an Australian endemic bird species. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Climatic variability is the most important force influencing the distribution dynamics of common and widespread species, with significant effects on their current biogeographical patterns. In this study, phylogeography was integrated with ecological niche modelling to understand the range dynamics of an Australian bird species, the red-backed fairywren (Malurus melanocephalus), under various climate change scenarios. Specifically, an ecological niche modelling approach with Bayesian-based phylogeographical analysis was used to develop robust inferences regarding the demographic history of the species. The predictions of the model were mostly consistent with the present distribution of the species. However, under the Last Interglacial bioclimatic conditions, the model predicted a significantly narrower distribution than today, indicating the existence of allopatric refugia. Predictions for the Last Glacial Maximum indicated that the species had a wider distribution, extending northwards. Additionally, predictions for the future (2050 and 2070) indicated that the species will probably have a narrower distribution than at present, which will be shifted eastwards. The extended Bayesian skyline plot analysis, which provides a robust analysis of fluctuations in the effective population size throughout the evolutionary history of a species, produced results highly consistent with the ecological niche modelling predictions for the red-backed fairywren. This is the first study to investigate the Late Quaternary history of an endemic avian taxon from Australia using ecological niche modelling and Bayesian-based demographic analysis.
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Affiliation(s)
- Utku Perktaş
- Department of Biology (Biogeography Research Laboratory), Faculty of Science, Hacettepe University , 06800 Beytepe, Ankara , Turkey
- Department of Ornithology, American Museum of Natural History , Central Park West at 79th Street, New York, NY 10024 , USA
- Biodiversity Institute, University of Kansas , Lawrence, KS 66045 , USA
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Ewart KM, Lo N, Ogden R, Joseph L, Ho SYW, Frankham GJ, Eldridge MDB, Schodde R, Johnson RN. Phylogeography of the iconic Australian red-tailed black-cockatoo (Calyptorhynchus banksii) and implications for its conservation. Heredity (Edinb) 2020; 125:85-100. [PMID: 32398870 PMCID: PMC7426920 DOI: 10.1038/s41437-020-0315-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 04/08/2020] [Accepted: 04/08/2020] [Indexed: 01/31/2023] Open
Abstract
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.
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Affiliation(s)
- Kyle M Ewart
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia.
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO, Canberra, ACT, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Greta J Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Mark D B Eldridge
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Richard Schodde
- Australian National Wildlife Collection, CSIRO, Canberra, ACT, Australia
| | - Rebecca N Johnson
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
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Andersen AN, Hoffmann BD, Oberprieler S. Diversity and biogeography of a species-rich ant fauna of the Australian seasonal tropics. INSECT SCIENCE 2018; 25:519-526. [PMID: 27629082 DOI: 10.1111/1744-7917.12402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/21/2016] [Accepted: 07/18/2016] [Indexed: 06/06/2023]
Abstract
Although ants are an ecologically dominant and extensively studied faunal group throughout the tropics, there is a poor understanding of tropical ant diversity and distribution at large spatial scales. Here we use a collection developed from 3 decades of ant surveys to present the first analysis of ant diversity and biogeography of a large tropical region. Our objective was to document the species richness, composition, and biogeographic distributions of the ant fauna of the 400 000 km2 "Top End" of Australia's Northern Territory. The known Top End ant fauna comprises 901 native species from 59 genera. The richest genera are Pheidole (90 species), Melophorus (83), Monomorium (83), Camponotus (71), Meranoplus (63), Polyrhachis (57), Rhytidoponera (50), Tetramorium (43), Cerapachys (32), and Iridomyrmex (31). The fauna is the center of diverse radiations within species-groups of genera such as Meranoplus, Rhytidoponera, and Leptogenys. It also includes IndoMalayan species that have likely bypassed the normal dispersal route into Australia through Cape York Peninsula in North Queensland. Faunistic similarity with other regions of far northern Australia is associated more with rainfall than with geographic proximity. Most (60%) of Top End ant species have not been recorded elsewhere, and, despite uncertainties relating to species delimitation and sampling intensity, this appears to be a credible estimate of the level of endemism. Such exceptionally high endemism can be attributed to the Top End's geographic isolation from other regions of northern Australia with comparably high rainfall.
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Affiliation(s)
- Alan N Andersen
- CSIRO Land & Water, Tropical Ecosystems Research Centre, Darwin, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Australia
| | | | - Stefanie Oberprieler
- CSIRO Land & Water, Tropical Ecosystems Research Centre, Darwin, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Australia
- Research School of Biology, Australian National University, Canberra, Australia
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Pepper M, Hamilton DG, Merkling T, Svedin N, Cser B, Catullo RA, Pryke SR, Keogh JS. Phylogeographic structure across one of the largest intact tropical savannahs: Molecular and morphological analysis of Australia’s iconic frilled lizard Chlamydosaurus kingii. Mol Phylogenet Evol 2017; 106:217-227. [DOI: 10.1016/j.ympev.2016.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 11/24/2022]
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Wadley JJ, Fordham DA, Thomson VA, Ritchie EG, Austin JJ. Phylogeography of the antilopine wallaroo ( Macropus antilopinus) across tropical northern Australia. Ecol Evol 2016; 6:8050-8061. [PMID: 27878077 PMCID: PMC5108257 DOI: 10.1002/ece3.2381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 07/13/2016] [Accepted: 07/18/2016] [Indexed: 12/03/2022] Open
Abstract
The distribution of antilopine wallaroo, Macropus antilopinus, is marked by a break in the species’ range between Queensland and the Northern Territory, coinciding with the Carpentarian barrier. Previous work on M. antilopinus revealed limited genetic differentiation between the Northern Territory and Queensland M. antilopinus populations across this barrier. The study also identified a number of divergent lineages in the Northern Territory, but was unable to elucidate any geographic structure. Here, we re‐examine these results to (1) determine phylogeographic patterns across the range of M. antilopinus and (2) infer the biogeographic barriers associated with these patterns. The tropical savannahs of northern Australia: from the Cape York Peninsula in the east, to the Kimberley in the west. We examined phylogeographic patterns in M. antilopinus using a larger number of samples and three mtDNA genes: NADH dehydrogenase subunit 2, cytochrome b, and the control region. Two datasets were generated and analyzed: (1) a subset of samples with all three mtDNA regions concatenated together and (2) all samples for just control region sequences that included samples from the previous study. Analysis included generating phylogenetic trees based on Bayesian analysis and intraspecific median‐joining networks. The contemporary spatial structure of M. antilopinus mtDNA lineages revealed five shallow clades and a sixth, divergent lineage. The genetic differences that we found between Queensland and Northern Territory M. antilopinus samples confirmed the split in the geographic distribution of the species. We also found weak genetic differentiation between Northern Territory samples and those from the Kimberley region of Western Australia, possibly due to the Kimberley Plateau–Arnhem Land barrier. Within the Northern Territory, two clades appear to be parapatric in the west, while another two clades are broadly sympatric across the Northern Territory. MtDNA diversity of M. antilopinus revealed an unexpectedly complex evolutionary history involving multiple sympatric and parapatric mtDNA clades across northern Australia. These phylogeographic patterns highlight the importance of investigating genetic variation across distributions of species and integrating this information into biodiversity conservation.
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Affiliation(s)
- Jessica J Wadley
- Australian Centre for Ancient DNAUniversity of AdelaideNorth TerraceAdelaideSouth Australia5005Australia; Environment Institute and School of Biological SciencesUniversity of AdelaideNorth TerraceAdelaideSouth Australia5005Australia
| | - Damien A Fordham
- Environment Institute and School of Biological Sciences University of Adelaide North Terrace Adelaide South Australia 5005 Australia
| | - Vicki A Thomson
- Australian Centre for Ancient DNAUniversity of AdelaideNorth TerraceAdelaideSouth Australia5005Australia; Environment Institute and School of Biological SciencesUniversity of AdelaideNorth TerraceAdelaideSouth Australia5005Australia
| | - Euan G Ritchie
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Burwood Victoria 3125 Australia
| | - Jeremy J Austin
- Australian Centre for Ancient DNAUniversity of AdelaideNorth TerraceAdelaideSouth Australia5005Australia; Environment Institute and School of Biological SciencesUniversity of AdelaideNorth TerraceAdelaideSouth Australia5005Australia; Sciences DepartmentMuseum VictoriaCarlton GardensMelbourneVictoria3001Australia
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Marin J, Donnellan SC, Hedges SB, Puillandre N, Aplin KP, Doughty P, Hutchinson MN, Couloux A, Vidal N. Hidden species diversity of Australian burrowing snakes (Ramphotyphlops). Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12132] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julie Marin
- Departement Systematique et Evolution; UMR 7138; CP 26; Museum National d'Histoire Naturelle; 57 rue Cuvier; F-75231; Paris, Cedex 05; France
| | | | - S. Blair Hedges
- Department of Biology; 208 Mueller Lab; Pennsylvania State University; University Park; PA; 16802-5301; USA
| | - Nicolas Puillandre
- Departement Systematique et Evolution; UMR 7138; CP 26; Museum National d'Histoire Naturelle; 57 rue Cuvier; F-75231; Paris, Cedex 05; France
| | - Ken P. Aplin
- Australian National Wildlife Collection CSIRO Ecosystem Sciences; GPO Box 1700; Canberra; 2601; Australia
| | - Paul Doughty
- Western Australian Museum; 49 Kew Street; Welshpool; WA; 6106; Australia
| | | | - Arnaud Couloux
- Centre National de Séquençage; Genoscope; 2 rue Gaston-Crémieux; CP5706; 91057; Evry, Cedex; France
| | - Nicolas Vidal
- Departement Systematique et Evolution; UMR 7138; CP 26; Museum National d'Histoire Naturelle; 57 rue Cuvier; F-75231; Paris, Cedex 05; France
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Eldridge MDB, Potter S, Cooper SJB. Biogeographic barriers in north-western Australia: an overview and standardisation of nomenclature. AUST J ZOOL 2011. [DOI: 10.1071/zo12012] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Fujita MK, McGuire JA, Donnellan SC, Moritz C. Diversification and persistence at the arid-monsoonal interface: australia-wide biogeography of the Bynoe's gecko (Heteronotia binoei; Gekkonidae). Evolution 2010; 64:2293-314. [PMID: 20298463 DOI: 10.1111/j.1558-5646.2010.00993.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Late Neogene aridification in the Southern Hemisphere caused contractions of mesic biota to refugia, similar to the patterns established by glaciation in the Northern Hemisphere, but these episodes also opened up new adaptive zones that spurred range expansion and diversification in arid-adapted lineages. To understand these dynamics, we present a multilocus (nine nuclear introns, one mitochondrial gene) phylogeographic analysis of the Bynoe's gecko (Heteronotia binoei), a widely distributed complex spanning the tropical monsoon, coastal woodland, and arid zone biomes in Australia. Bayesian phylogenetic analyses, estimates of divergence times, and demographic inferences revealed episodes of diversification in the Pliocene, especially in the tropical monsoon biome, and range expansions in the Pleistocene. Ancestral habitat reconstructions strongly support recent and independent invasions into the arid zone. Our study demonstrates the varied responses to aridification in Australia, including localized persistence of lineages in the tropical monsoonal biome, and repeated invasion of and expansion through newly available arid-zone habitats. These patterns are consistent with those found in other arid environments in the Southern Hemisphere, including the South African succulent karoo and the Chilean lowlands, and highlight the diverse modes of diversification and persistence of Earth's biota during the glacial cycles of the Pliocene and Pleistocene.
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Affiliation(s)
- Matthew K Fujita
- Department of Integrative Biology, University of California, Berkeley, California 94720, USA.
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Lee JY, Edwards SV. DIVERGENCE ACROSS AUSTRALIA'S CARPENTARIAN BARRIER: STATISTICAL PHYLOGEOGRAPHY OF THE RED-BACKED FAIRY WREN (MALURUS MELANOCEPHALUS). Evolution 2008; 62:3117-34. [DOI: 10.1111/j.1558-5646.2008.00543.x] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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