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Brennan IG, Lemmon AR, Moriarty Lemmon E, Hoskin CJ, Donnellan SC, Keogh JS. Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification. Syst Biol 2024; 73:1-11. [PMID: 37527840 DOI: 10.1093/sysbio/syad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 07/21/2023] [Accepted: 08/01/2023] [Indexed: 08/03/2023] Open
Abstract
The Australian continent's size and isolation make it an ideal place for studying the accumulation and evolution of biodiversity. Long separated from the ancient supercontinent Gondwana, most of Australia's plants and animals are unique and endemic, including the continent's frogs. Australian frogs comprise a remarkable ecological and morphological diversity categorized into a small number of distantly related radiations. We present a phylogenomic hypothesis based on an exon-capture dataset that spans the main clades of Australian myobatrachoid, pelodryadid hyloid, and microhylid frogs. Our time-calibrated phylogenomic-scale phylogeny identifies great disparity in the relative ages of these groups that vary from Gondwanan relics to recent immigrants from Asia and include arguably the continent's oldest living vertebrate radiation. This age stratification provides insight into the colonization of, and diversification on, the Australian continent through deep time, during periods of dramatic climatic and community changes. Contemporary Australian frog diversity highlights the adaptive capacity of anurans, particularly in response to heat and aridity, and explains why they are one of the continent's most visible faunas. [Anuran; adaptive radiation; Gondwana; phylogenetics].
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Affiliation(s)
- Ian G Brennan
- Division of Ecology & Evolution, The Australian National University, Canberra, ACT 2601, Australia
- Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32316, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Conrad J Hoskin
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Stephen C Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - J Scott Keogh
- Division of Ecology & Evolution, The Australian National University, Canberra, ACT 2601, Australia
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2
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Skeels A, Boschman LM, McFadden IR, Joyce EM, Hagen O, Jiménez Robles O, Bach W, Boussange V, Keggin T, Jetz W, Pellissier L. Paleoenvironments shaped the exchange of terrestrial vertebrates across Wallace's Line. Science 2023; 381:86-92. [PMID: 37410831 DOI: 10.1126/science.adf7122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/01/2023] [Indexed: 07/08/2023]
Abstract
Faunal turnover in Indo-Australia across Wallace's Line is one of the most recognizable patterns in biogeography and has catalyzed debate about the role of evolutionary and geoclimatic history in biotic interchanges. Here, analysis of more than 20,000 vertebrate species with a model of geoclimate and biological diversification shows that broad precipitation tolerance and dispersal ability were key for exchange across the deep-time precipitation gradient spanning the region. Sundanian (Southeast Asian) lineages evolved in a climate similar to the humid "stepping stones" of Wallacea, facilitating colonization of the Sahulian (Australian) continental shelf. By contrast, Sahulian lineages predominantly evolved in drier conditions, hampering establishment in Sunda and shaping faunal distinctiveness. We demonstrate how the history of adaptation to past environmental conditions shapes asymmetrical colonization and global biogeographic structure.
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Affiliation(s)
- A Skeels
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
- Research School of Biology, Australian National University, Canberra 0200, Australia
| | - L M Boschman
- Department of Earth Sciences, Utrecht University, 3584 CB Utrecht, Netherlands
| | - I R McFadden
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, Netherlands
| | - E M Joyce
- Systematics, Biodiversity and Evolution of Plants, Ludwig Maximilian University of Munich, 80331 Munich, Germany
| | - O Hagen
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - O Jiménez Robles
- Research School of Biology, Australian National University, Canberra 0200, Australia
- Institute of Biology, École Normale Supérieure, 75005 Paris, France
| | - W Bach
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - V Boussange
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - T Keggin
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - W Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, CT 06520, USA
| | - L Pellissier
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
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3
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Torkkola JJ, Wilmer JW, Hutchinson MN, Couper PJ, Oliver PM. Die on this hill? A new monotypic, microendemic and montane vertebrate genus from the Australian Wet Tropics. ZOOL SCR 2022. [DOI: 10.1111/zsc.12550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Janne J. Torkkola
- Snake Out Brisbane Kenmore Queensland Australia
- Biodiversity and Geosciences Program Queensland Museum South Brisbane Queensland Australia
| | | | - Mark N. Hutchinson
- South Australian Museum, North Terrace Adelaide South Australia Australia
| | - Patrick J. Couper
- Biodiversity and Geosciences Program Queensland Museum South Brisbane Queensland Australia
| | - Paul M. Oliver
- Biodiversity and Geosciences Program Queensland Museum South Brisbane Queensland Australia
- Centre for Planetary Health and Food Security Griffith University Brisbane Queensland Australia
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Slavenko A, Tamar K, Tallowin OJS, Kraus F, Allison A, Carranza S, Meiri S. Revision of the montane New Guinean skink genus Lobulia (Squamata: Scincidae), with the description of four new genera and nine new species. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The skink genus Lobulia is endemic to New Guinea, the largest and highest tropical island in the world. Lobulia and its related genera represent an important component of the montane herpetofauna of New Guinea, but it remains understudied and poorly known. We here provide the first, large-scale, systematic revision of Lobulia, using molecular phylogenetic and morphological comparisons to assess the monophyly of the genus and the diversity of species within it. We find that Lobulia, as currently defined, is polyphyletic. The eight species currently assigned to it form three clades. Furthermore, many specimens from New Guinea of unknown specific affinity are genetically and morphologically distinct from each other. Based on these data, we re-diagnose Lobulia and two of its closely related genera, Prasinohaema and Papuascincus. We erect four new genera (Alpinoscincus gen. nov., Nubeoscincus gen. nov., Ornithuroscincus gen. nov. and Palaia gen. nov.) to address the problem of polyphyly and describe nine new species Lobulia fortis sp. nov., Lobulia huonensis sp. nov., Loublia marmorata sp. nov., Lobulia vogelkopensis sp. nov., Ornithuroscincus bengaun sp. nov., Ornithuroscincus inornatus sp. nov., Ornithuroscincus pterophilus sp. nov., Ornithuroscincus shearmani sp. nov. and Ornithuroscincus viridis sp. nov. We supplement this taxonomic revision by investigating the biogeographic history of Lobulia s.l. and find evidence for a large radiation in the accreted terranes of New Guinea, with multiple independent colonizations of montane habitats and subsequent recolonization of lowland habitats. Our study reinforces the uniqueness and richness of the montane herpetofauna of New Guinea and the importance of mountains to biodiversity in the Tropics.
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Affiliation(s)
- Alex Slavenko
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Karin Tamar
- The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Oliver J S Tallowin
- UN Environment Programme World Conservation Monitoring Centre, Cambridge, UK
| | - Fred Kraus
- Department of Ecology and Evolutionary Biology, University of Michigan, Michigan, USA
| | | | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Shai Meiri
- The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
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Mitchell KJ, Hugall AF, Heiniger H, Joseph L, Oliver PM. Disparate origins for endemic bird taxa from the ‘Gondwana Rainforests’ of Central Eastern Australia. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Subtropical and temperate rainforests of Central Eastern Australia are some of the largest remaining fragments of their kind globally. The biota of these rainforests appears to comprise two broad biogeographical elements: a more ancient (Miocene or older) and typically upland temperate (‘Gondwanan’) element and a younger (Plio-Pleistocene) lowland tropical element. We present the first phylogenetic synthesis of the spatiotemporal origins for the eight bird taxa endemic to Central Eastern Australian Rainforests. At least five of these eight focal taxa show Plio-Pleistocene divergences from their respective northern sister taxa, consistent with origins driven by recent expansion and contraction of lowland rainforest. In contrast, two more strictly upland species, the rufous scrub-bird (Atrichornis rufescens) and the logrunner (Orthonyx temminckii), diverged from their nearest living relatives during the Miocene, suggesting potentially longer histories of persistence and more temperate origins. Finally, we did not recover reciprocal monophyly in mitogenomes from the two extant lyrebirds, Albert’s lyrebird (Menura alberti) and the superb lyrebird (Menura novaehollandiae). The disparate divergence ages recovered among all eight taxa are consistent with the biota of the Central Eastern Australian Rainforests comprising isolates either of younger age and tropical lowland origins or of older age and temperate upland origins.
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Affiliation(s)
- Kieren J Mitchell
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, North Terrace Campus, Adelaide, SA, Australia
| | - Andrew F Hugall
- Department of Sciences, Museums Victoria, Melbourne, VIC, Australia
| | - Holly Heiniger
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, North Terrace Campus, Adelaide, SA, Australia
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, ACT, Australia
| | - Paul M Oliver
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
- Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, QLD, Australia
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Toussaint EFA, White LT, Shaverdo H, Lam A, Surbakti S, Panjaitan R, Sumoked B, von Rintelen T, Sagata K, Balke M. New Guinean orogenic dynamics and biota evolution revealed using a custom geospatial analysis pipeline. BMC Ecol Evol 2021; 21:51. [PMID: 33823805 PMCID: PMC8022562 DOI: 10.1186/s12862-021-01764-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The New Guinean archipelago has been shaped by millions of years of plate tectonic activity combined with long-term fluctuations in climate and sea level. These processes combined with New Guinea's location at the tectonic junction between the Australian and Pacific plates are inherently linked to the evolution of its rich endemic biota. With the advent of molecular phylogenetics and an increasing amount of geological data, the field of New Guinean biogeography begins to be reinvigorated. RESULTS We inferred a comprehensive dated molecular phylogeny of endemic diving beetles to test historical hypotheses pertaining to the evolution of the New Guinean biota. We used geospatial analysis techniques to compare our phylogenetic results with a newly developed geological terrane map of New Guinea as well as the altitudinal and geographic range of species ( https://arcg.is/189zmz ). Our divergence time estimations indicate a crown age (early diversification) for New Guinea Exocelina beetles in the mid-Miocene ca. 17 Ma, when the New Guinean orogeny was at an early stage. Geographic and geological ancestral state reconstructions suggest an origin of Exocelina ancestors on the eastern part of the New Guinean central range on basement rocks (with a shared affinity with the Australian Plate). Our results do not support the hypothesis of ancestors migrating to the northern margin of the Australian Plate from Pacific terranes that incrementally accreted to New Guinea over time. However, our analyses support to some extent a scenario in which Exocelina ancestors would have been able to colonize back and forth between the amalgamated Australian and Pacific terranes from the Miocene onwards. Our reconstructions also do not support an origin on ultramafic or ophiolite rocks that have been colonized much later in the evolution of the radiation. Macroevolutionary analyses do not support the hypothesis of heterogeneous diversification rates throughout the evolution of this radiation, suggesting instead a continuous slowdown in speciation. CONCLUSIONS Overall, our geospatial analysis approach to investigate the links between the location and evolution of New Guinea's biota with the underlying geology sheds a new light on the patterns and processes of lineage diversification in this exceedingly diverse region of the planet.
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Affiliation(s)
| | - Lloyd T White
- GeoQuEST Research Centre, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Helena Shaverdo
- Naturhistorisches Museum Wien, Burgring 7, 1010, Vienna, Austria
| | - Athena Lam
- SNSB-Zoologische Staatssammlung München, Munich, Germany
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA
| | - Suriani Surbakti
- Department of Biology, Universitas Cenderawasih (UNCEN), Waena, Papua, Indonesia
| | - Rawati Panjaitan
- Department of Biology, Faculty of Sciences and Mathematics, State University of Papua (UNIPA), Jalan Gunung Salju Amban, Manokwari, 98314, West Papua, Indonesia
| | - Bob Sumoked
- Walian 2, Tomohon Selatan, 95439, N Sulawesi, Indonesia
| | - Thomas von Rintelen
- Museum Für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115, Berlin, Germany
| | - Katayo Sagata
- University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Michael Balke
- SNSB-Zoologische Staatssammlung München, Munich, Germany.
- Department of Entomology, SNSB-Zoologische Staatssammlung München, Münchhausenstrasse 21, 81247, Munich, Germany.
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7
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Natusch DJD, Esquerré D, Lyons JA, Hamidy A, Lemmon AR, Lemmon EM, Riyanto A, Keogh JS, Donnellan S. Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade. Mol Phylogenet Evol 2020; 158:106960. [PMID: 32950680 DOI: 10.1016/j.ympev.2020.106960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 11/29/2022]
Abstract
The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined analysis of 421 nuclear loci and complete mitochondrial genomes with morphological data to construct a detailed phylogeny of this group, understand their biogeographic patterns and establish the systematic diversity of this genus. Our molecular genetic data support two major clades, corresponding to L. albertisii and L. fredparkeri, but offer no support for the other four species. Our morphological data also only support two species. We therefore recognize L. albertisii and L. fredparkeri as valid species and place L. biakensis, L. meridionalis, L. huonensis and L. montanus into synonymy. We found that L. albertisii and L. fredparkeri are sympatric in western New Guinea; an atypical pattern compared to other Papuan species complexes in which the distributions of sister taxa are partitioned to the north and south of the island's central mountain range. For the purpose of conservation management, overestimation of species diversity within Leiopython has resulted in the unnecessary allocation of resources that could have been expended elsewhere. We strongly caution against revising the taxonomy of geographically widespread species groups when little or no molecular genetic data and only small morphological samples are available.
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Affiliation(s)
- Daniel J D Natusch
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia; EPIC Biodiversity, Frogs Hollow, NSW 2550, Australia
| | - Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra 0200, Australia
| | | | - Amir Hamidy
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Gd. Widyasatwaloka, Jl. Raya Jakarta-Bogor km 46 Cibinong, Bogor, West Java, Indonesia
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL 32306-4120, USA
| | - Emily Moriarty Lemmon
- Department of Biology, Florida State University, 319 Stadium Drive, P.O. Box 3064295, 17, Tallahassee, FL 32306-4295, USA
| | - Awal Riyanto
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Gd. Widyasatwaloka, Jl. Raya Jakarta-Bogor km 46 Cibinong, Bogor, West Java, Indonesia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra 0200, Australia
| | - Stephen Donnellan
- South Australian Museum, North Terrace, Adelaide 5000, Australia; School of Biological Sciences, University of Adelaide, North Terrace, Adelaide 5005, Australia
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Oliver PM, Rittmeyer EN, Torkkola J, Donnellan SC, Dahl C, Richards SJ. Multiple trans-Torres Strait colonisations by tree frogs in the Litoria caerulea group, with the description of a new species from New Guinea. AUST J ZOOL 2020. [DOI: 10.1071/zo20071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Australia and New Guinea (together referred to as Sahul) were linked by land for much of the late Tertiary and share many biotic elements. However, New Guinea is dominated by rainforest, and northern Australia by savannah. Resolving patterns of biotic interchange between these two regions is critical to understanding the expansion and contraction of both habitat types. The green tree frog (Litoria caerulea) has a vast range across northern and eastern Australia and New Guinea. An assessment of mitochondrial and morphological diversity in this nominal taxon in New Guinea reveals two taxa. True Litoria caerulea occurs in disjunct savannahs of the Trans-Fly, Central Province and across northern Australia, with very low genetic divergence, implying late Pleistocene connectivity. A previously unrecognised taxon is endemic to New Guinea and widespread in lowland swampy rainforest. Date estimates for the divergence of the new species suggest Pliocene connectivity across lowland tropical habitats of northern Australia and New Guinea. In contrast, the new species shows shallow phylogeographic structuring across the central mountains of New Guinea, implying recent dispersal between the northern and southern lowlands. These results emphasise that the extent and connectivity of lowland rainforest and savannah environments across northern Australia and southern New Guinea have undergone profound shifts since the late Pliocene.
http://zoobank.org/urn:lsid:zoobank.org:pub:A577A415-0B71-4663-B4C1-7271B97298CD
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