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Fenker J, Melville J, Moritz C. Dragons in the tropics - Phylogeography and speciation in Diporiphora lizards and common geographic breaks in co-distributed taxa. Mol Phylogenet Evol 2024; 197:108090. [PMID: 38723791 DOI: 10.1016/j.ympev.2024.108090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 12/20/2023] [Accepted: 05/04/2024] [Indexed: 05/25/2024]
Abstract
Co-distributed taxa can respond both similarly or differently to the same climatic and geological events, resulting in a range of phylogeographic patterns across the region. Using a nested approach on a taxonomically diverse yet morphologically conservative group of agamid lizards, we first aimed to evaluate more precisely the extent of phylogeographic structuring within the genus. Then, focusing on four lineages within the more widespread species, we assessed the impact of biogeographic barriers on phylogeographic structuring and demographic history of species, comparing to patterns previously observed in co-distributed taxa. These species occur in the Australian Monsoonal Tropics, a vast tropical savanna system with high richness and endemism associated with environmental heterogeneity and past climate fluctuations. The employment of genomic data helped to determine the relationships between specific taxa that were previously difficult to place. We found a local influence of biogeographic and climatic breaks on population dynamics, analogous to other species. We detected high levels of population structure in the West Kimberley and Arnhem Plateau, which are already known for high endemism. However, we also highlighted unique lineages in areas that have been overlooked until recently, in the South Kimberley and West Top End. Climatic and geographical features in the Arnhem Plateau act as a soft barrier between populations in the east and west regions of the Top End. These observations reflect patterns observed for other vertebrates across this rich biome, indicating how climatic variation, species' ecology, and landscape features interact to shape regional diversity and endemism.
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Affiliation(s)
- Jessica Fenker
- Division of Ecology & Evolution, Research School of Biology, Australian National University, 46 Sullivans Creek Road, Acton 2601, Canberra, ACT, Australia; Department of Sciences, Museums Victoria, Melbourne Museum, 11 Nicholson StreetCarlton 3053, Melbourne, VIC, Australia.
| | - Jane Melville
- Department of Sciences, Museums Victoria, Melbourne Museum, 11 Nicholson StreetCarlton 3053, Melbourne, VIC, Australia
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, Australian National University, 46 Sullivans Creek Road, Acton 2601, Canberra, ACT, Australia
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2
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Sopniewski J, Catullo RA. Estimates of heterozygosity from single nucleotide polymorphism markers are context-dependent and often wrong. Mol Ecol Resour 2024; 24:e13947. [PMID: 38433491 DOI: 10.1111/1755-0998.13947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/18/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
Abstract
Genetic diversity is frequently described using heterozygosity, particularly in a conservation context. Often, it is estimated using single nucleotide polymorphisms (SNPs); however, it has been shown that heterozygosity values calculated from SNPs can be biased by both study design and filtering parameters. Though solutions have been proposed to address these issues, our own work has found them to be inadequate in some circumstances. Here, we aimed to improve the reliability and comparability of heterozygosity estimates, specifically by investigating how sample size and missing data thresholds influenced the calculation of autosomal heterozygosity (heterozygosity calculated from across the genome, i.e. fixed and variable sites). We also explored how the standard practice of tri- and tetra-allelic site exclusion could bias heterozygosity estimates and influence eventual conclusions relating to genetic diversity. Across three distinct taxa (a frog, Litoria rubella; a tree, Eucalyptus microcarpa; and a grasshopper, Keyacris scurra), we found heterozygosity estimates to be meaningfully affected by sample size and missing data thresholds, partly due to the exclusion of tri- and tetra-allelic sites. These biases were inconsistent both between species and populations, with more diverse populations tending to have their estimates more severely affected, thus having potential to dramatically alter interpretations of genetic diversity. We propose a modified framework for calculating heterozygosity that reduces bias and improves the utility of heterozygosity as a measure of genetic diversity, whilst also highlighting the need for existing population genetic pipelines to be adjusted such that tri- and tetra-allelic sites be included in calculations.
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Affiliation(s)
- Jarrod Sopniewski
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Renee A Catullo
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
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3
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Shelley JJ, Delaval A, Feuvre MCLE. A revision of the gudgeon genus Hypseleotris (Gobiiformes: Gobioidei: Eleotridae) of northwest Australia, describing three new species and synonymizing the genus Kimberleyeleotris. Zootaxa 2023; 5311:340-374. [PMID: 37518639 DOI: 10.11646/zootaxa.5311.3.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 08/01/2023]
Abstract
Species within the northwest Australian clade of Hypseleotris (six species) and the genus Kimberleyeleotris (two species) are reviewed following the recording of new populations in the region and a molecular study of the group that identified three undescribed candidate species. Based on the analysis of extensive morphological and nuclear and mitochondrial molecular datasets, Kimberleyeleotris is here formally synonymised with Hypseleotris. Furthermore, three species from the Kimberley region, Western Australia, are described to science: Hypseleotris maranda sp. nov., Hypseleotris wunduwala sp. nov., and Hypseleotris garawudjirri sp. nov. The presence of, or number of scales across the head and body, the pattern of sensory papillae on the head, fin ray counts, dorsal and anal fin colouration (particularly in breeding males), and body depth, can be used to distinguish the members of the northwest Australia lineage. Furthermore, the newly described species were genetically separated from all northwest Australian congeners by K2P distances ranging from 7.8-11.3% based on the CO1 gene, and 7.7-16.3 % based on the entire mitochondrial genome. Two of the new species, H. maranda sp. nov. and H. wunduwala sp. nov., have extremely narrow ranges being found in single sub-catchments of the Roe and King Edward Rivers respectively. On the other hand, H. garawudjirri sp. nov. is moderately widespread, being found across the Charnley, Calder, and Sale rivers. While the conservation risk to H. maranda sp. nov. and H. wunduwala sp. nov. is inherently high due to their small range, there are currently no obvious local threatening processes to either of these species given their remote locations that are little impacted by human activities.
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Affiliation(s)
- James J Shelley
- School of BioSciences; University of Melbourne; Victoria 3010; Australia.
| | - Aurélien Delaval
- School of BioSciences; University of Melbourne; Victoria 3010; Australia; Ichthyology; Sciences Department; Museums Victoria; Victoria 3001; Australia; Institute of Marine Research; Bergen 5817; Norway.
| | - Matthew C LE Feuvre
- School of BioSciences; University of Melbourne; Victoria 3010; Australia; Ichthyology; Sciences Department; Museums Victoria; Victoria 3001; Australia.
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4
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Oliver PM, Donnellan SC, Gunn BF. Plio–Pleistocene vicariance across arid Australia in the ‘Spiny Knob-tailed Geckos’ (. AUST J ZOOL 2022. [DOI: 10.1071/zo22008] [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
Across Australia’s monsoon tropics and vast arid zone isolated regions or ‘islands’ of upland or rocky habitat are home to disjunct populations of many taxa of plants and animals. Comparative analyses of lineages that occur across these habitat islands provide opportunities to understand when and how environmental change drove isolation and diversification across arid Australia. Here we present an analysis of mitochondrial genetic diversity across disjunct populations of geckos in the Nephrurus asper group. Dating analyses suggest that disjunct and genetically divergent populations spanning the northern half of Australia diverged through the Plio–Pleistocene. Based on the timing of divergence and current habitat associations we hypothesise that species in this lineage were isolated by the expansion of unsuitable arid-zone habitats from the late Pliocene onwards. Across most areas, these barriers appear to be sandy or stony deserts. However, in eastern Australia genetically divergent populations are separated by grassland on flat vertisol-dominated soils (‘blacksoils’), suggesting that these habitats also expanded during the late Pliocene aridification. Finally, we show that western Queensland populations formerly referred to N. asper are genetically divergent and diagnosable on the basis of colour pattern and, herein, recognise these populations as a distinct species. https://zoobank.org/urn:lsid:zoobank.org:pub:9508CAAA-D014-452D-A3DA-325851615FA7
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5
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Pavón-Vázquez CJ, Esquerré D, Fitch AJ, Maryan B, Doughty P, Donnellan SC, Scott Keogh J. Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex). Mol Phylogenet Evol 2022; 173:107516. [DOI: 10.1016/j.ympev.2022.107516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/25/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022]
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6
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Cairns NA, Cicchino AS, Stewart KA, Austin JD, Lougheed SC. Cytonuclear discordance, reticulation and cryptic diversity in one of North America's most common frogs. Mol Phylogenet Evol 2020; 156:107042. [PMID: 33338660 DOI: 10.1016/j.ympev.2020.107042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 10/28/2020] [Accepted: 12/11/2020] [Indexed: 10/22/2022]
Abstract
Complicated phylogenetic histories benefit from diverse sources of inference. Pseudacris crucifer (spring peeper) spans most of eastern North America and comprises six mtDNA lineages that form multiple contact zones. The putative Miocene or early Pliocene origins of the oldest lineages within Pseudacris crucifer imply sufficient time for species-level divergence. To understand why this species appears unified while congeners have radiated, we analyze and compare male advertisement calls, mitochondrial, and nuclear markers and speak to the complex processes that have potentially influenced its contemporary patterns. We find extensive geographic and topological mitonuclear discordance, with three nuclear lineages containing 6 more-structured mtDNA lineages, and nuclear introgression at some contact zones. Male advertisement call differentiation is incongruent with the genetic structure as only one lineage appears differentiated. Occupying the Interior Highlands of the central United States, this Western lineage also has the most concordant mitochondrial and nuclear geographic patterns. Based on our findings we suggest that the antiquity of common ancestors was not as important as the maintenance of allopatry in the divergence in P. crucifer genetic lineages. We use multiple lines of evidence to generate hypotheses of isolation, reticulation, and discordance within this species and to expand our understanding of the early stages of speciation.
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Affiliation(s)
- N A Cairns
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - A S Cicchino
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, United States.
| | - K A Stewart
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 904 Science Park, 1098XH Amsterdam, North Holland, Netherlands
| | - J D Austin
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611, United States.
| | - S C Lougheed
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.
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7
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Multi-Species Phylogeography of Arid-Zone Sminthopsinae (Marsupialia: Dasyuridae) Reveals Evidence of Refugia and Population Expansion in Response to Quaternary Change. Genes (Basel) 2020; 11:genes11090963. [PMID: 32825338 PMCID: PMC7563968 DOI: 10.3390/genes11090963] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 11/17/2022] Open
Abstract
Historical population contraction and expansion events associated with Pleistocene climate change are important drivers of intraspecific population structure in Australian arid-zone species. We compared phylogeographic patterns among arid-adapted Dasyuridae (Sminthopsis and Planigale) with close phylogenetic relationships and similar ecological roles to investigate the drivers of phylogeographic structuring and the importance of historical refugia. We generated haplotype networks for two mitochondrial (control region and cytochrome b) and one nuclear (omega-globin) gene from samples distributed across each species range. We used ΦST to test for a genetic population structure associated with the four Pilbara subregions, and we used expansion statistics and Bayesian coalescent skyline analysis to test for signals of historical population expansion and the timing of such events. Significant population structure associated with the Pilbara and subregions was detected in the mitochondrial data for most species, but not with the nuclear data. Evidence of population expansion was detected for all species, and it likely began during the mid-late Pleistocene. The timing of population expansion suggests that these species responded favorably to the increased availability of arid habitats during the mid-late Pleistocene, which is when previously patchy habitats became more widespread. We interpret our results to indicate that the Pilbara region could have acted as a refugium for small dasyurids.
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8
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Graham MR, Myers EA, Kaiser RC, Fet V. Cryptic species and co‐diversification in sand scorpions from the Karakum and Kyzylkum deserts of Central Asia. ZOOL SCR 2019. [DOI: 10.1111/zsc.12381] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Matthew R. Graham
- Department of Biology Eastern Connecticut State University Willimantic CT USA
| | - Edward A. Myers
- Department of Vertebrate Zoology National Museum of Natural History, Smithsonian Institution Washington DC USA
| | - Ronald C. Kaiser
- Department of Biology Eastern Connecticut State University Willimantic CT USA
| | - Victor Fet
- Department of Biological Sciences Marshall University Huntington WV USA
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9
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Anderson BM, Thiele KR, Grierson PF, Krauss SL, Nevill PG, Small ID, Zhong X, Barrett MD. Recent range expansion in Australian hummock grasses ( Triodia) inferred using genotyping-by-sequencing. AOB PLANTS 2019; 11:plz017. [PMID: 31037212 PMCID: PMC6481909 DOI: 10.1093/aobpla/plz017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 03/20/2019] [Indexed: 05/30/2023]
Abstract
The Australian arid zone (AAZ) has undergone aridification and the formation of vast sandy deserts since the mid-Miocene. Studies on AAZ organisms, particularly animals, have shown patterns of mesic ancestry, persistence in rocky refugia and range expansions in arid lineages. There has been limited molecular investigation of plants in the AAZ, particularly of taxa that arrived in Australia after the onset of aridification. Here we investigate populations of the widespread AAZ grass Triodia basedowii to determine whether there is evidence for a recent range expansion, and if so, its source and direction. We also undertake a dating analysis for the species complex to which T. basedowii belongs, in order to place its diversification in relation to changes in AAZ climate and landscapes. We analyse a genomic single nucleotide polymorphism data set from 17 populations of T. basedowii in a recently developed approach for detecting the signal and likely origin of a range expansion. We also use alignments from existing and newly sequenced plastomes from across Poaceae for analysis in BEAST to construct fossil-calibrated phylogenies. Across a range of sampling parameters and outgroups, we detected a consistent signal of westward expansion for T. basedowii, originating in central or eastern Australia. Divergence time estimation indicates that Triodia began to diversify in the late Miocene (crown 7.0-8.8 million years (Ma)), and the T. basedowii complex began to radiate during the Pleistocene (crown 1.4-2.0 Ma). This evidence for range expansion in an arid-adapted plant is consistent with similar patterns in AAZ animals and likely reflects a general response to the opening of new habitat during aridification. Radiation of the T. basedowii complex through the Pleistocene has been associated with preferences for different substrates, providing an explanation why only one lineage is widespread across sandy deserts.
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Affiliation(s)
- Benjamin M Anderson
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
| | - Kevin R Thiele
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Pauline F Grierson
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Siegfried L Krauss
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
| | - Paul G Nevill
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
- Australian Research Council Centre for Mine Site Restoration, Curtin University, Bentley, Western Australia, Australia
| | - Ian D Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Xiao Zhong
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Matthew D Barrett
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
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10
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Oliver PM, Ashman LG, Bank S, Laver RJ, Pratt RC, Tedeschi LG, Moritz CC. On and off the rocks: persistence and ecological diversification in a tropical Australian lizard radiation. BMC Evol Biol 2019; 19:81. [PMID: 30894117 PMCID: PMC6427882 DOI: 10.1186/s12862-019-1408-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 03/04/2019] [Indexed: 12/17/2022] Open
Abstract
Background Congruent patterns in the distribution of biodiversity between regions or habitats suggest that key factors such as climatic and topographic variation may predictably shape evolutionary processes. In a number of tropical and arid biomes, genetic analyses are revealing deeper and more localised lineage diversity in rocky ranges than surrounding habitats. Two potential drivers of localised endemism in rocky areas are refugial persistence through climatic change, or ecological diversification and specialisation. Here we examine how patterns of lineage and phenotypic diversity differ across two broad habitat types (rocky ranges and open woodlands) in a small radiation of gecko lizards in the genus Gehyra (the australis group) from the Australian Monsoonal Tropics biome. Results Using a suite of approaches for delineating evolutionarily independent lineages, we find between 26 and 41 putative evolutionary units in the australis group (versus eight species currently recognised). Rocky ranges are home to a greater number of lineages that are also relatively more restricted in distribution, while lineages in open woodland habitats are fewer, more widely distributed, and, in one case, show evidence of range expansion. We infer at least two shifts out of rocky ranges and into surrounding woodlands. Phenotypic divergence between rocky ranges specialist and more generalist taxa is detected, but no convergent evolutionary regimes linked to ecology are inferred. Conclusions In climatically unstable biomes such as savannahs, rocky ranges have functioned as zones of persistence, generators of diversity and a source of colonists for surrounding areas. Phenotypic divergence can also be linked to the use of differing habitat types, however, the extent to which ecological specialisation is a primary driver or secondary outcome of localised diversification remains uncertain. Electronic supplementary material The online version of this article (10.1186/s12862-019-1408-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul M Oliver
- Environmental Futures Research Institute, Griffith University, 170 Kessels Rd, Nathan, Queensland, 4111, Australia. .,Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, Queensland, 4101, Australia. .,Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia.
| | - Lauren G Ashman
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia
| | - Sarah Bank
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia.,Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Rebecca J Laver
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia
| | - Renae C Pratt
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia
| | - Leonardo G Tedeschi
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia
| | - Craig C Moritz
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia
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11
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Cryptic biodiversity in the freshwater fishes of the Kimberley endemism hotspot, northwestern Australia. Mol Phylogenet Evol 2018; 127:843-858. [DOI: 10.1016/j.ympev.2018.06.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 06/09/2018] [Accepted: 06/19/2018] [Indexed: 11/19/2022]
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12
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Ants in Australia’s Monsoonal Tropics: CO1 Barcoding Reveals Extensive Unrecognised Diversity. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10020036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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13
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Laver RJ, Nielsen SV, Rosauer DF, Oliver PM. Trans-biome diversity in Australian grass-specialist lizards (Diplodactylidae: Strophurus). Mol Phylogenet Evol 2017; 115:62-70. [DOI: 10.1016/j.ympev.2017.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 05/30/2017] [Accepted: 07/13/2017] [Indexed: 11/27/2022]
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14
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Owen CL, Marshall DC, Hill KBR, Simon C. How the Aridification of Australia Structured the Biogeography and Influenced the Diversification of a Large Lineage of Australian Cicadas. Syst Biol 2017; 66:569-589. [PMID: 28123112 DOI: 10.1093/sysbio/syw078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/24/2016] [Indexed: 11/14/2022] Open
Abstract
Over the last 30 million years, Australia's landscape has undergone dramatic cooling and drying due to the establishment of the Antarctic Circumpolar Current and change in global CO$_{2}$ levels. Studies have shown that many Australian organisms went extinct during these major cooling events, while others experienced adaptive radiations and increases in diversification rates as a result of exploiting new niches in the arid zone. Despite the many studies on diversification and biogeography in Australia, few have been continent-wide and none have focused on a group of organisms adapted to feeding on plants. We studied 162 species of cicadas in the Australian Pauropsalta complex, a large generic lineage within the tribe Cicadettini. We asked whether there were changes in the diversification rate of Pauropsalta over time and if so: 1) which clades were associated with the rate change? 2) did timing of rate shifts correspond to known periods of dramatic historical climate change, 3) did increases in diversification rate along select lineages correspond to adaptive radiations with movement into the arid zone? To address these questions, we estimated a molecular phylogeny of the Pauropsalta complex using ${\sim}$5300 bp of nucleotide sequence data distributed among five loci (one mtDNA locus and four nDNA loci). We found that this large group of cicadas did not diversify at a constant rate as they spread through Australia; instead the signature of decreasing diversification rate changed roughly around the time of the expansion of the east Antarctic ice sheets ${\sim}$16 Ma and the glaciation of the northern hemisphere ${\sim}$3 Ma. Unlike other Australian taxa, the Pauropsalta complex did not explosively radiate in response to an early invasion of the arid zone. Instead multiple groups invaded the arid zone and experienced rates of diversification similar to mesic-distributed taxa. We found evidence for relictual groups, located in pre-Mesozoic habitat, that have not diversified and continue to reside on mesic hosts in isolated "habitat islands". Future work should focus on groups of similar ages with similar distribution patterns to determine whether this tempo and pattern of diversification and biogeography is consistent with evidence from other phytophagous insects.
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Affiliation(s)
- Christopher L Owen
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA.,Computational Biology Institute, George Washington University, Innovation Hall, Suite 305, 45085 University Drive, Ashburn, VA 20147-2766, USA
| | - David C Marshall
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA
| | - Kathy B R Hill
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA
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15
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Richmond JQ, Wood DA, Westphal MF, Vandergast AG, Leaché AD, Saslaw LR, Butterfield HS, Fisher RN. Persistence of historical population structure in an endangered species despite near‐complete biome conversion in California's San Joaquin Desert. Mol Ecol 2017; 26:3618-3635. [DOI: 10.1111/mec.14125] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 01/24/2017] [Accepted: 03/13/2017] [Indexed: 01/06/2023]
Affiliation(s)
| | | | | | | | - Adam D. Leaché
- Department of Biology & Burke Museum of Natural History and Culture University of Washington Seattle WA USA
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16
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Vertucci S, Pepper M, Edwards DL, Roberts JD, Mitchell N, Keogh JS. Evolutionary and natural history of the turtle frog, Myobatrachus gouldii, a bizarre myobatrachid frog in the southwestern Australian biodiversity hotspot. PLoS One 2017; 12:e0173348. [PMID: 28296914 PMCID: PMC5351994 DOI: 10.1371/journal.pone.0173348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 02/20/2017] [Indexed: 11/19/2022] Open
Abstract
Southwest Australia (SWA) is a global biodiversity hotspot and a centre of diversity and endemism for the Australo-Papuan myobatrachid frogs. Myobatrachus gouldii (the turtle frog) has a highly derived morphology associated with its forward burrowing behaviour, largely subterranean habit, and unusual mode of reproduction. Its sister genera Metacrinia and Arenophryne have restricted distributions in Western Australia with significant phylogeographic structure, leading to the recent description of a new species in the latter. In contrast, Myobatrachus is distributed widely throughout SWA over multiple climatic zones, but little is known of its population structure, geographic variation in morphology, or reproduction. We generated molecular and morphological data to test for genetic and morphological variation, and to assess whether substrate specialisation in this species may have led to phylogeographic structuring similar to that of other plant and animal taxa in SWA. We assembled sequence data for one mitochondrial and four nuclear DNA loci (3628 base pairs) for 42 turtle frogs sampled throughout their range. Likelihood phylogenetic analyses revealed shallow phylogeographic structure in the mtDNA locus (up to 3.3% genetic distance) and little variation in three of the four nDNA loci. The mtDNA haplotype network suggests five geographically allopatric groups, with no shared haplotypes between regions. These geographic patterns are congruent with several other SWA species, with genetic groups restricted to major hydrological divisions, the Swan Coastal Plain, and the Darling Scarp. The geographically structured genetic groups showed no evidence of significant morphological differentiation (242 individuals), and there was little sexual size dimorphism, but subtle differences in reproductive traits suggest more opportunistic breeding in lower rainfall zones. Call data were compared to sister genera Metacrinia and Arenophryne and found to be highly conservative across the three genera. Like many taxa in SWA, topographic variation and Plio-Pleistocene arid fluctuations likely were historic drivers of diversification in M. gouldii.
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Affiliation(s)
- Samantha Vertucci
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australia
| | - Mitzy Pepper
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australia
| | - Danielle L. Edwards
- School of Natural Sciences, University of California, Merced, CA, United States of America
| | - J. Dale Roberts
- Centre of Excellence in Natural Resource Management, The University of Western Australia, Albany, Western Australia
| | - Nicola Mitchell
- School of Animal Biology, The University of Western Australia, Crawley, Australia
| | - J. Scott Keogh
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australia
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17
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Luna-Ramirez K, Miller AD, Rašić G. Genetic and morphological analyses indicate that the Australian endemic scorpion Urodacus yaschenkoi (Scorpiones: Urodacidae) is a species complex. PeerJ 2017; 5:e2759. [PMID: 28123903 PMCID: PMC5244882 DOI: 10.7717/peerj.2759] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/05/2016] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Australian scorpions have received far less attention from researchers than their overseas counterparts. Here we provide the first insight into the molecular variation and evolutionary history of the endemic Australian scorpion Urodacus yaschenkoi. Also known as the inland robust scorpion, it is widely distributed throughout arid zones of the continent and is emerging as a model organism in biomedical research due to the chemical nature of its venom. METHODS We employed Bayesian Inference (BI) methods for the phylogenetic reconstructions and divergence dating among lineages, using unique haplotype sequences from two mitochondrial loci (COXI, 16S) and one nuclear locus (28S). We also implemented two DNA taxonomy approaches (GMYC and PTP/dPTP) to evaluate the presence of cryptic species. Linear Discriminant Analysis was used to test whether the linear combination of 21 variables (ratios of morphological measurements) can predict individual's membership to a putative species. RESULTS Genetic and morphological data suggest that U. yaschenkoi is a species complex. High statistical support for the monophyly of several divergent lineages was found both at the mitochondrial loci and at a nuclear locus. The extent of mitochondrial divergence between these lineages exceeds estimates of interspecific divergence reported for other scorpion groups. The GMYC model and the PTP/bPTP approach identified major lineages and several sub-lineages as putative species. Ratios of several traits that approximate body shape had a strong predictive power (83-100%) in discriminating two major molecular lineages. A time-calibrated phylogeny dates the early divergence at the onset of continental-wide aridification in late Miocene and Pliocene, with finer-scale phylogeographic patterns emerging during the Pleistocene. This structuring dynamics is congruent with the diversification history of other fauna of the Australian arid zones. DISCUSSION Our results indicate that the taxonomic status of U. yaschenkoi requires revision, and we provide recommendations for such future efforts. A complex evolutionary history and extensive diversity highlights the importance of conserving U. yaschenkoi populations from different Australian arid zones in order to preserve patterns of endemism and evolutionary potential.
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Affiliation(s)
| | - Adam D. Miller
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Victoria, Australia
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18
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Noble C, Laver RJ, Rosauer DF, Ferrier S, Moritz C. Phylogeographic evidence for evolutionary refugia in the Gulf sandstone ranges of northern Australia. AUST J ZOOL 2017. [DOI: 10.1071/zo17079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Locating and protecting climate change refugia is important to conserving biodiversity with accelerating climate change. Comparative phylogeographic analysis provides an effective tool for locating such refugia, as long-term retention of one or more populations within a refugial landscape will generate unique genetic lineages. The ranges of the western Gulf region of northern Australia are thought to represent a significant arid-zone refugium, in which case low-dispersal organisms should have strong phylogeographic structure across the region. To test for this, we conducted extensive sampling of three species of Gehyra geckos and analysed diversity for mitochondrial DNA and eight nuclear loci. These analyses revealed congruent and high phylogeographic diversity, especially, but not exclusively, in rock-restricted species. This finding, and other recent phylogeographic evidence, demonstrates that these topographically variable landforms have enabled persistence of ecologically diverse vertebrate species through the climate changes of the late Pleistocene. Identification of this relatively under-protected region as a significant climate change refugium points to the need to expand protected areas in this region and to invest in ecological management across existing National Parks and Indigenous Protected Areas.
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19
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Levy E, Byrne M, Coates DJ, Macdonald BM, McArthur S, van Leeuwen S. Contrasting Influences of Geographic Range and Distribution of Populations on Patterns of Genetic Diversity in Two Sympatric Pilbara Acacias. PLoS One 2016; 11:e0163995. [PMID: 27768703 PMCID: PMC5074490 DOI: 10.1371/journal.pone.0163995] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/19/2016] [Indexed: 12/03/2022] Open
Abstract
The influence of geographic range on species persistence has long been of interest and there is a need for a better understanding of the genetic consequences for species with restricted distributions, particularly with the increasing rate of global species extinctions. However, the genetic effects of restricted range are often confounded by the impacts of population distribution. We compared chloroplast and nuclear genetic diversity and differentiation in two acacias, the restricted, patchily distributed Acacia atkinsiana and the widespread, semi-continuously distributed A. ancistrocarpa. Lower intra-population diversity and higher differentiation between populations were seen in A. atkinsiana compared to its widespread congener, A. ancistrocarpa. There was little evidence of geographical influences on population genetic structure in A. ancistrocarpa whereas A. atkinsiana exhibited nuclear genetic structure with isolation by distance, differentiation of near-coastal populations from those in the ranges, and differentiation of peripheral populations from those in the centre of the distribution. These results are consistent with expectations of the effect of geographic range and population distribution on genetic diversity, but indicate that distribution of populations rather than geographic range has influenced the observed genetic structure. The contrasting patterns observed here demonstrate that conservation approaches for species management and ecological restoration need to consider the distribution of populations in geographically restricted species.
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Affiliation(s)
- E. Levy
- Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia, Australia
| | - M. Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia, Australia
| | - D. J. Coates
- Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia, Australia
| | - B. M. Macdonald
- Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia, Australia
| | - S. McArthur
- Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia, Australia
| | - S. van Leeuwen
- Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia, Australia
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20
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Oliver PM, McDonald PJ. Young relicts and old relicts: a novel palaeoendemic vertebrate from the Australian Central Uplands. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160018. [PMID: 27853534 PMCID: PMC5098959 DOI: 10.1098/rsos.160018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 09/06/2016] [Indexed: 06/06/2023]
Abstract
Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus Oedura from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected Oedura cincta has close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the early Pliocene. A new taxon (described herein) diverged from all extant Oedura much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including Oedura cincta), gene flow with other parts of Australia probably occurred until at least the very late Miocene or Pliocene. There are, however, a small number of palaeoendemic taxa-often ecologically specialized forms-that show evidence of having persisted since earlier intensification of aridity in the late Miocene.
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Affiliation(s)
- Paul M. Oliver
- Division of Evolution, Ecology and Genetics, Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Building 116, Daley Road, Acton, Australian Capital Territory 2601, Australia
| | - Peter J. McDonald
- Flora and Fauna Division, Department of Land Resource Management, Alice Springs, Northern Territory 0870, Australia
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21
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Ellis RJ. A New Species of Blindsnake (Scolecophidia: Typhlopidae:Anilios) from the Kimberley Region of Western Australia. HERPETOLOGICA 2016. [DOI: 10.1655/herpetologica-d-16-00007.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Untangling a species complex of arid zone grasses (Triodia) reveals patterns congruent with co-occurring animals. Mol Phylogenet Evol 2016; 101:142-162. [DOI: 10.1016/j.ympev.2016.05.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 05/10/2016] [Accepted: 05/10/2016] [Indexed: 11/24/2022]
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23
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Nielsen SV, Oliver PM, Laver RJ, Bauer AM, Noonan BP. Stripes, jewels and spines: further investigations into the evolution of defensive strategies in a chemically defended gecko radiation (
Strophurus
, Diplodactylidae). ZOOL SCR 2016. [DOI: 10.1111/zsc.12181] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Stuart V. Nielsen
- Department of Biology University of Mississippi 214 Shoemaker Hall University MS 38677 USA
| | - Paul M. Oliver
- Division of Evolution, Ecology & Genetics Research School of Biology The Australian National University 46 Sullivans Creek Road Acton ACT 2601 Australia
| | - Rebecca J. Laver
- School of BioSciences University of Melbourne Royal Parade Parkville Vic. 3052 Australia
| | - Aaron M. Bauer
- Department of Sciences Museum Victoria Melbourne Vic. Australia
- Department of Biology Villanova University Villanova PA 19085 USA
| | - Brice P. Noonan
- Department of Biology University of Mississippi 214 Shoemaker Hall University MS 38677 USA
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24
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Vidal-García M, Keogh JS. Convergent evolution across the Australian continent: ecotype diversification drives morphological convergence in two distantly related clades of Australian frogs. J Evol Biol 2015; 28:2136-51. [DOI: 10.1111/jeb.12746] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/27/2015] [Accepted: 08/29/2015] [Indexed: 11/29/2022]
Affiliation(s)
- M. Vidal-García
- Evolution, Ecology & Genetics, Research School of Biology; The Australian National University; Canberra ACT Australia
| | - J. S. Keogh
- Evolution, Ecology & Genetics, Research School of Biology; The Australian National University; Canberra ACT Australia
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25
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Criscione F, Köhler F. Snails in the desert: Assessing the mitochondrial and morphological diversity and the influence of aestivation behavior on lineage differentiation in the Australian endemic Granulomelon Iredale, 1933 (Stylommatophora: Camaenidae). Mol Phylogenet Evol 2015; 94:101-12. [PMID: 26335041 DOI: 10.1016/j.ympev.2015.08.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/27/2015] [Accepted: 08/21/2015] [Indexed: 10/23/2022]
Abstract
Progressive aridification since the mid-Miocene has had a significant influence on the evolution of the biota in the arid zone of central Australia. Especially moisture sensitive groups, such as snails, are often restricted to topographically complex areas, which have acted as refugia in an otherwise inhospitable environment. This historical fragmentation is deemed to be a potent agent of allopatric lineage diversification. Camaenid land snails are amongst only a few terrestrial gastropods that have managed to survive in the arid zone probably due to their ability to escape desiccation through aestivation. Here, we present the first study of the mitochondrial lineage differentiation in an endemic land snail genus from the Australian 'Red Centre', Granulomelon Iredale, 1933. Exposing significant incongruence between mtDNA phylogeny and morphology-based taxonomy, we completely revise the species and genus level taxonomy of this camaenid group. We demonstrate that this genus contains three species, G. grandituberculatum, G. adcockianum and G. squamulosum, which have so far been assigned to different genera: Granulomelon Iredale, 1933 (junior synonym: Baccalena Iredale, 1937), Basedowena Iredale, 1937 and Pleuroxia Ancey, 1887. Two of these species are widespread comprising multiple divergent mitochondrial lineages. Based on a molecular clock estimate, these lineages diverged approximately during the mid-Pleistocene, a period of particularly severe aridification. The phylogeographic patterns are consistent with an isolation-by-distance model in one species but not the other. We suggest that these differences can be attributed to their distinctive aestivation behavior.
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Affiliation(s)
| | - Frank Köhler
- Australian Museum, 1 William Street, Sydney, NSW 2010, Australia
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26
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Schwentner M, Just F, Richter S. Evolutionary systematics of the Australian Cyzicidae (Crustacea, Branchiopoda, Spinicaudata) with the description of a new genus. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martin Schwentner
- Institut für Biowissenschaften; Allgemeine und Spezielle Zoologie; Universität Rostock; Rostock Germany
| | - Franziska Just
- Institut für Biowissenschaften; Allgemeine und Spezielle Zoologie; Universität Rostock; Rostock Germany
| | - Stefan Richter
- Institut für Biowissenschaften; Allgemeine und Spezielle Zoologie; Universität Rostock; Rostock Germany
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27
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Autumn K, Niewiarowski PH, Puthoff JB. Gecko Adhesion as a Model System for Integrative Biology, Interdisciplinary Science, and Bioinspired Engineering. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-120213-091839] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kellar Autumn
- Department of Biology, Lewis & Clark College, Portland, Oregon 97219; ,
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28
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Agarwal I, Bauer AM, Jackman TR, Karanth KP. Insights into Himalayan biogeography from geckos: A molecular phylogeny of Cyrtodactylus (Squamata: Gekkonidae). Mol Phylogenet Evol 2014; 80:145-55. [DOI: 10.1016/j.ympev.2014.07.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 07/08/2014] [Accepted: 07/24/2014] [Indexed: 11/15/2022]
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29
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Aridification drove repeated episodes of diversification between Australian biomes: Evidence from a multi-locus phylogeny of Australian toadlets (Uperoleia: Myobatrachidae). Mol Phylogenet Evol 2014; 79:106-17. [DOI: 10.1016/j.ympev.2014.06.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 06/11/2014] [Accepted: 06/13/2014] [Indexed: 02/06/2023]
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30
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Rabosky DL, Hutchinson MN, Donnellan SC, Talaba AL, Lovette IJ. Phylogenetic disassembly of species boundaries in a widespread group of Australian skinks (Scincidae: Ctenotus). Mol Phylogenet Evol 2014; 77:71-82. [DOI: 10.1016/j.ympev.2014.03.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 10/25/2022]
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31
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Agarwal I, Bauer AM, Jackman TR, Karanth P. Cryptic species and Miocene diversification of Palaearctic naked-toed geckos (Squamata: Gekkonidae) in the Indian dry zone. ZOOL SCR 2014. [DOI: 10.1111/zsc.12062] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ishan Agarwal
- Centre for Ecological Sciences; Indian Institute of Science; Bangalore 560012 India
| | - Aaron M. Bauer
- Department of Biology; Villanova University; 800 Lancaster Avenue Villanova PA 19085 USA
| | - Todd R. Jackman
- Department of Biology; Villanova University; 800 Lancaster Avenue Villanova PA 19085 USA
| | - Praveen Karanth
- Centre for Ecological Sciences; Indian Institute of Science; Bangalore 560012 India
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32
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Arribas P, Andújar C, Abellán P, Velasco J, Millán A, Ribera I. Tempo and mode of the multiple origins of salinity tolerance in a water beetle lineage. Mol Ecol 2013; 23:360-73. [DOI: 10.1111/mec.12605] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 11/14/2013] [Accepted: 11/22/2013] [Indexed: 01/10/2023]
Affiliation(s)
- Paula Arribas
- Departamento de Ecología e Hidrología; Universidad de Murcia; Murcia 30100 Spain
| | - Carmelo Andújar
- Departamento de Zoología y Antropología Física; Universidad de Murcia; Murcia 30100 Spain
| | - Pedro Abellán
- Departamento de Ecología e Hidrología; Universidad de Murcia; Murcia 30100 Spain
| | - Josefa Velasco
- Departamento de Ecología e Hidrología; Universidad de Murcia; Murcia 30100 Spain
| | - Andrés Millán
- Departamento de Ecología e Hidrología; Universidad de Murcia; Murcia 30100 Spain
| | - Ignacio Ribera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra); Barcelona 08003 Spain
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33
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Migliore J, Baumel A, Juin M, Fady B, Roig A, Duong N, Médail F. Surviving in mountain climate refugia: new insights from the genetic diversity and structure of the relict shrub Myrtus nivellei (Myrtaceae) in the Sahara Desert. PLoS One 2013; 8:e73795. [PMID: 24058489 PMCID: PMC3776782 DOI: 10.1371/journal.pone.0073795] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 07/23/2013] [Indexed: 11/27/2022] Open
Abstract
The identification of past glacial refugia has become a key topic for conservation under environmental change, since they contribute importantly to shaping current patterns of biodiversity. However, little attention has been paid so far to interglacial refugia despite their key role for the survival of relict species currently occurring in climate refugia. Here, we focus on the genetic consequences of range contraction on the relict populations of the evergreen shrub Myrtus nivellei, endemic in the Saharan mountains since at least the end of the last Green Sahara period, around 5.5 ka B.P. Multilocus genotypes (nuclear microsatellites and AFLP) were obtained from 215 individuals collected from 23 wadis (temporary rivers) in the three main mountain ranges in southern Algeria (the Hoggar, Tassili n'Ajjer and Tassili n'Immidir ranges). Identical genotypes were found in several plants growing far apart within the same wadis, a pattern taken as evidence of clonality. Multivariate analyses and Bayesian clustering revealed that genetic diversity was mainly structured among the mountain ranges, while low isolation by distance was observed within each mountain range. The range contraction induced by the last episode of aridification has likely increased the genetic isolation of the populations of M. nivellei, without greatly affecting the genetic diversity of the species as a whole. The pattern of genetic diversity observed here suggests that high connectivity may have prevailed during humid periods, which is consistent with recent paleoenvironmental reconstructions.
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Affiliation(s)
- Jérémy Migliore
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE), Aix-Marseille Université, UMR CNRS 7263/IRD 237/Avignon Université, Campus Aix - Technopôle de l’Environnement Arbois-Méditerranée, Aix-en-Provence, France
| | - Alex Baumel
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE), Aix-Marseille Université, UMR CNRS 7263/IRD 237/Avignon Université, Campus Aix - Technopôle de l’Environnement Arbois-Méditerranée, Aix-en-Provence, France
| | - Marianick Juin
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE), Aix-Marseille Université, UMR CNRS 7263/IRD 237/Avignon Université, Campus Aix - Technopôle de l’Environnement Arbois-Méditerranée, Aix-en-Provence, France
| | - Bruno Fady
- INRA, UR 629, Ecologie des Forêts Méditerranéennes (URFM), Site Agroparc - Domaine Saint Paul, Avignon, France
| | - Anne Roig
- INRA, UR 629, Ecologie des Forêts Méditerranéennes (URFM), Site Agroparc - Domaine Saint Paul, Avignon, France
| | - Nathalie Duong
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE), Aix-Marseille Université, UMR CNRS 7263/IRD 237/Avignon Université, Campus Aix - Technopôle de l’Environnement Arbois-Méditerranée, Aix-en-Provence, France
| | - Frédéric Médail
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE), Aix-Marseille Université, UMR CNRS 7263/IRD 237/Avignon Université, Campus Aix - Technopôle de l’Environnement Arbois-Méditerranée, Aix-en-Provence, France
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34
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Huang Y, Guo X, Ho SYW, Shi H, Li J, Li J, Cai B, Wang Y. Diversification and Demography of the Oriental Garden Lizard (Calotes versicolor) on Hainan Island and the Adjacent Mainland. PLoS One 2013; 8:e64754. [PMID: 23840304 PMCID: PMC3694074 DOI: 10.1371/journal.pone.0064754] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 04/17/2013] [Indexed: 01/16/2023] Open
Abstract
The Oriental garden lizard (Calotes versicolor) is one of the few non-gekkonid lizards that are geographically widespread in the tropics. We investigated its population dynamics on Hainan Island and the adjacent mainland of China and Vietnam, focusing on the impact of cyclic upheaval and submergence of land bridges during the Pleistocene. Our Bayesian phylogenetic analysis reveals two mitochondrial lineages, A and B, which are estimated to have coalesced about 0.26 million years ago (95% credibility interval: 0.05–0.61 million years ago). Lineage A contains individuals mainly from central and southern Wuzhi Mountain on Hainan Island, whereas lineage B mainly comprises individuals from other sites on the island plus the adjacent mainland. The estimated coalescence times within lineages A (0.05 million years ago) and B (0.13 million years ago) fall within a period of cyclical land-bridge formation and disappearance in the Pleistocene. A spatial analysis of molecular variance identified two distinct population groupings: I, primarily containing lineage A, and II, mainly consisting of lineage B. However, haplotypes from lineages A and B occur sympatrically, suggesting that gene flow is ongoing. Neither Wuzhi Mountain nor Qiongzhou Strait and Gulf of Tonkin act as barriers to gene flow among C. versicolor populations. Analyses of the data using mismatch distributions and extended Bayesian skyline plots provide evidence of a relatively stable population size through time for Group I, and moderate population expansions and contractions during the end of the Pleistocene for Group II. We conclude that the phylogeographical patterns of C. versicolor are the combined product of Pleistocene sea-level oscillations and nonphysical barriers to gene flow.
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Affiliation(s)
- Yong Huang
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu Sichuan, P.R. China
- Guangxi Botanical Garden of Medicinal Plants, Nanning Guangxi, P.R. China
| | - Xianguang Guo
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu Sichuan, P.R. China
| | - Simon Y. W. Ho
- School of Biological Sciences, University of Sydney, New South Wales, Australia
| | - Haitao Shi
- College of Life Sciences, Hainan Normal University, Haikou Hainan, P.R. China
| | - Jiatang Li
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu Sichuan, P.R. China
| | - Jun Li
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu Sichuan, P.R. China
| | - Bo Cai
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu Sichuan, P.R. China
| | - Yuezhao Wang
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu Sichuan, P.R. China
- * E-mail:
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Pepper M, Doughty P, Hutchinson MN, Scott Keogh J. Ancient drainages divide cryptic species in Australia’s arid zone: Morphological and multi-gene evidence for four new species of Beaked Geckos (Rhynchoedura). Mol Phylogenet Evol 2011; 61:810-22. [DOI: 10.1016/j.ympev.2011.08.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 07/22/2011] [Accepted: 08/04/2011] [Indexed: 10/17/2022]
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