1
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Feigin CY, Moreno JA, Ramos R, Mereby SA, Alivisatos A, Wang W, van Amerongen R, Camacho J, Rasweiler JJ, Behringer RR, Ostrow B, Plikus MV, Mallarino R. Convergent deployment of ancestral functions during the evolution of mammalian flight membranes. SCIENCE ADVANCES 2023; 9:eade7511. [PMID: 36961889 PMCID: PMC10038344 DOI: 10.1126/sciadv.ade7511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/21/2023] [Indexed: 05/20/2023]
Abstract
Lateral flight membranes, or patagia, have evolved repeatedly in diverse mammalian lineages. While little is known about patagium development, its recurrent evolution may suggest a shared molecular basis. By combining transcriptomics, developmental experiments, and mouse transgenics, we demonstrate that lateral Wnt5a expression in the marsupial sugar glider (Petaurus breviceps) promotes the differentiation of its patagium primordium. We further show that this function of Wnt5a reprises ancestral roles in skin morphogenesis predating mammalian flight and has been convergently used during patagium evolution in eutherian bats. Moreover, we find that many genes involved in limb development have been redeployed during patagium outgrowth in both the sugar glider and bat. Together, our findings reveal that deeply conserved genetic toolkits contribute to the evolutionary transition to flight in mammals.
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Affiliation(s)
- Charles Y. Feigin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jorge A. Moreno
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Raul Ramos
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697, USA
| | - Sarah A. Mereby
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ares Alivisatos
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Wei Wang
- Lewis Sigler Institute, Princeton University, Princeton, NJ 08544, USA
| | - Renée van Amerongen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Jasmin Camacho
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - John J. Rasweiler
- Department of Obstetrics and Gynecology, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Richard R. Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bruce Ostrow
- Department of Biology, Grand Valley State University, Allendale, MI 49401, USA
| | - Maksim V. Plikus
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697, USA
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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2
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Roycroft E, Fabre PH, MacDonald AJ, Moritz C, Moussalli A, Rowe KC. New Guinea uplift opens ecological opportunity across a continent. Curr Biol 2022; 32:4215-4224.e3. [PMID: 36057260 DOI: 10.1016/j.cub.2022.08.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 12/14/2022]
Abstract
Sahul unites the world's largest and highest tropical island and the oldest and most arid continent on the backdrop of dynamic environmental conditions. Massive geological uplift in New Guinea is predicted to have acted as a species pump from the late Miocene onward, but the impact of this process on biogeography and diversification remains untested across Sahul as a whole. To address this, we reconstruct the assembly of a recent and diverse radiation of rodents (Murinae: Hydromyini) spanning New Guinea, Australia, and oceanic islands. Using phylogenomic data from 270 specimens, including many recently extinct and highly elusive species, we find that the orogeny and expansion of New Guinea opened ecological opportunity and triggered diversification across a continent. After a single over-water colonization from Asia ca. 8.5 Ma, ancestral Hydromyini were restricted to the tropical rainforest of proto-New Guinea for 3.5 million years. Following a shift in diversification coincident with the orogeny of New Guinea ca. 5 Ma and subsequent colonization of Australia, transitions between geographic regions (n = 24) and biomes (n = 34) become frequent. Recurrent over-water colonization between mainland and islands demonstrate how islands can play a substantial role in the assembly of continental fauna. Our results are consistent with a model of increased ecological opportunity across Sahul following major geological uplift in New Guinea ca. 5 Ma, with sustained diversification facilitated by over-water colonization from the Pleistocene to present. We show how geological processes, biome transitions, and over-water colonization collectively drove the diversification of an expansive continental radiation.
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Affiliation(s)
- Emily Roycroft
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia; Sciences Department, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia; Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia.
| | - Pierre-Henri Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS-IRD-UM), Université de Montpellier, Place E. Bataillon, CC 064, 34095 Montpellier Cedex 5, France; Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Anna J MacDonald
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia; The John Curtin School of Medical Research, The Australian National University, Acton, ACT 2601, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Adnan Moussalli
- Sciences Department, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
| | - Kevin C Rowe
- Sciences Department, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
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3
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Beck RM, Voss RS, Jansa SA. Craniodental Morphology and Phylogeny of Marsupials. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.1206/0003-0090.457.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Robin M.D. Beck
- School of Science, Engineering and Environment University of Salford, U.K. School of Biological, Earth & Environmental Sciences University of New South Wales, Australia Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Sharon A. Jansa
- Bell Museum and Department of Ecology, Evolution, and Behavior University of Minnesota
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4
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Genome-wide SNPs detect fine-scale genetic structure in threatened populations of squirrel glider Petaurus norfolcensis. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01435-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractAustralian arboreal mammals are experiencing significant population declines, particularly due to land clearing and resulting habitat fragmentation. The squirrel glider, Petaurus norfolcensis, is a threatened species in New South Wales, with a stronghold population in the Lake Macquarie Local Government Area (LGA) where fragmentation due to urbanization is an ongoing problem for the species conservation. Here we report on the use of squirrel glider mitochondrial (385 bp cytochrome b gene, 70 individuals) and nuclear DNA (6,834 SNPs, 87 individuals) markers to assess their population genetic structure and connectivity across 14 locations sampled in the Lake Macquarie LGA. The mitochondrial DNA sequences detected evidence of a historical genetic bottleneck, while the genome-wide SNPs detected significant population structure in the Lake Macquarie squirrel glider populations at scales as fine as one kilometer. There was no evidence of inbreeding within patches, however there were clear effects of habitat fragmentation and biogeographical barriers on gene flow. A least cost path analysis identified thin linear corridors that have high priority for conservation. These areas should be protected to avoid further isolation of squirrel glider populations and the loss of genetic diversity through genetic drift.
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5
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Shee ZQ, Frodin DG, Cámara-Leret R, Pokorny L. Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics. FRONTIERS IN PLANT SCIENCE 2020; 11:258. [PMID: 32265950 PMCID: PMC7099051 DOI: 10.3389/fpls.2020.00258] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/19/2020] [Indexed: 05/19/2023]
Abstract
With its large proportion of endemic taxa, complex geological past, and location at the confluence of the highly diverse Malesian and Australian floristic regions, Papuasia - the floristic region comprising the Bismarck Archipelago, New Guinea, and the Solomon Islands - represents an ideal natural experiment in plant biogeography. However, scattered knowledge of its flora and limited representation in herbaria have hindered our understanding of the drivers of its diversity. Focusing on the woody angiosperm genus Schefflera (Araliaceae), we ask whether its morphologically defined infrageneric groupings are monophyletic, when these lineages diverged, and where (within Papuasia or elsewhere) they diversified. To address these questions, we use a high-throughput sequencing approach (Hyb-Seq) which combines target capture (with an angiosperm-wide bait kit targeting 353 single-copy nuclear loci) and genome shotgun sequencing (which allows retrieval of regions in high-copy number, e.g., organellar DNA) of historical herbarium collections. To reconstruct the evolutionary history of the genus we reconstruct molecular phylogenies with Bayesian inference, maximum likelihood, and pseudo-coalescent approaches, and co-estimate divergence times and ancestral areas in a Bayesian framework. We find strong support for most infrageneric morphological groupings, as currently circumscribed, and we show the efficacy of the Angiosperms-353 probe kit in resolving both deep and shallow phylogenetic relationships. We infer a sequence of colonization to explain the present-day distribution of Schefflera in Papuasia: from the Sunda Shelf, Schefflera arrived to the Woodlark plate (present-day eastern New Guinea) in the late Oligocene (when most of New Guinea was submerged) and, subsequently (throughout the Miocene), it migrated westwards (to the Maoke and Bird's Head Plates and thereon) and further diversified, in agreement with previous reconstructions.
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Affiliation(s)
- Zhi Qiang Shee
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Singapore Botanic Gardens, Singapore, Singapore
| | | | - Rodrigo Cámara-Leret
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Bren School of Environmental Science and Management, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Madrid, Spain
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
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6
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Cooper CE, Withers PC, Turner JM. Physiological implications of climate change for a critically endangered Australian marsupial. AUST J ZOOL 2020. [DOI: 10.1071/zo20067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Extreme weather events (e.g. heatwaves and droughts) can expose animals to environmental conditions outside of their zones of physiological tolerance, and even resistance, and impact long-term viability of populations and species. We examined the thermal and hygric physiology of the critically endangered western ringtail possum (Pseudocheirus occidentalis), a member of a family of marsupial folivores (Pseudocheiridae) that appear particularly vulnerable to environmental extremes. Basal metabolic rate and other standard physiological variables measured at an ambient temperature of 30°C conformed to values for other marsupials. At lower temperatures, body temperature decreased slightly, and metabolic rate increased significantly at 5°C. At higher temperatures, possums experienced mild hyperthermia and increased evaporative heat loss by licking rather than panting. Their point of relative water economy (–8.7°C) was more favourable than other pseudocheirid possums and the koala (Phascolarctos cinereus). We predict that western ringtail possums should tolerate low ambient temperatures well and be more physiologically tolerant of hot and dry conditions than common (Pseudocheirus peregrinus) and particularly green (Pseudochirops archeri) ringtail possums, and koalas. Our physiological data can be incorporated into mechanistic species distribution models to test our hypothesis that western ringtail possums should physiologically tolerate the climate of habitat further inland than their current distribution, and withstand moderate impacts of climate change in the south-west of Western Australia.
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7
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Murray CM, Russo P, Zorrilla A, McMahan CD. Divergent Morphology among Populations of the New Guinea Crocodile, Crocodylus novaeguineae (Schmidt, 1928): Diagnosis of an Independent Lineage and Description of a New Species. COPEIA 2019. [DOI: 10.1643/cg-19-240] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Christopher M. Murray
- Department of Biology, Tennessee Technological University, 1100 N. Dixie Ave, Cookeville, Tennessee 38505
| | - Peter Russo
- Louisiana State University Health Sciences Center, School of Allied Health, New Orleans, Louisiana 70112;
| | - Alexander Zorrilla
- Louisiana State University Health Sciences Center, School of Medicine, New Orleans, Louisiana 70112;
| | - Caleb D. McMahan
- Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, Illinois 60605;
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8
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Eldridge MDB, Beck RMD, Croft DA, Travouillon KJ, Fox BJ. An emerging consensus in the evolution, phylogeny, and systematics of marsupials and their fossil relatives (Metatheria). J Mammal 2019. [DOI: 10.1093/jmammal/gyz018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Robin M D Beck
- School of Environment and Life Sciences, University of Salford, Manchester, United Kingdom
| | - Darin A Croft
- School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | | | - Barry J Fox
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
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9
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Celik M, Cascini M, Haouchar D, Van Der Burg C, Dodt W, Evans AR, Prentis P, Bunce M, Fruciano C, Phillips MJ. A molecular and morphometric assessment of the systematics of the Macropus complex clarifies the tempo and mode of kangaroo evolution. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mélina Celik
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Manuela Cascini
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Dalal Haouchar
- Trace and Environmental DNA (TrEnD) Laboratory, Curtin University, Perth, WA, Australia
| | - Chloe Van Der Burg
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - William Dodt
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Alistair R Evans
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Peter Prentis
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, Curtin University, Perth, WA, Australia
| | - Carmelo Fruciano
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
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10
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Cascini M, Mitchell KJ, Cooper A, Phillips MJ. Reconstructing the Evolution of Giant Extinct Kangaroos: Comparing the Utility of DNA, Morphology, and Total Evidence. Syst Biol 2018; 68:520-537. [DOI: 10.1093/sysbio/syy080] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Manuela Cascini
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, 2, George Street, Brisbane, QLD 4000, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, 2, George Street, Brisbane, QLD 4000, Australia
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11
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Tallowin OJ, Tamar K, Meiri S, Allison A, Kraus F, Richards SJ, Oliver PM. Early insularity and subsequent mountain uplift were complementary drivers of diversification in a Melanesian lizard radiation (Gekkonidae: Cyrtodactylus). Mol Phylogenet Evol 2018; 125:29-39. [DOI: 10.1016/j.ympev.2018.03.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 02/20/2018] [Accepted: 03/14/2018] [Indexed: 11/30/2022]
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12
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Eldridge MDB, Potter S, Helgen KM, Sinaga MH, Aplin KP, Flannery TF, Johnson RN. Phylogenetic analysis of the tree-kangaroos (Dendrolagus) reveals multiple divergent lineages within New Guinea. Mol Phylogenet Evol 2018; 127:589-599. [PMID: 29807156 DOI: 10.1016/j.ympev.2018.05.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 11/25/2022]
Abstract
Amongst the Australasian kangaroos and wallabies (Macropodidae) one anomalous genus, the tree-kangaroos, Dendrolagus, has secondarily returned to arboreality. Modern tree-kangaroos are confined to the wet tropical forests of north Queensland, Australia (2 species) and New Guinea (8 species). Due to their behavior, distribution and habitat most species are poorly known and our understanding of the evolutionary history and systematics of the genus is limited and controversial. We obtained tissue samples from 36 individual Dendrolagus including representatives from 14 of the 17 currently recognised or proposed subspecies and generated DNA sequence data from three mitochondrial (3116 bp) and five nuclear (4097 bp) loci. Phylogenetic analysis of these multi-locus data resolved long-standing questions regarding inter-relationships within Dendrolagus. The presence of a paraphyletic ancestral long-footed and derived monophyletic short-footed group was confirmed. Six major lineages were identified: one in Australia (D. lumholtzi, D. bennettianus) and five in New Guinea (D. inustus, D. ursinus, a Goodfellow's group, D. mbaiso and a Doria's group). Two major episodes of diversification within Dendrolagus were identified: the first during the late Miocene/early Pliocene associated with orogenic processes in New Guinea and the second mostly during the early Pleistocene associated with the intensification of climatic cycling. All sampled subspecies showed high levels of genetic divergence and currently recognized species within both the Doria's and Goodfellow's groups were paraphyletic indicating that adjustments to current taxonomy are warranted.
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Affiliation(s)
- Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, New South Wales 2010, Australia.
| | - Sally Potter
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, New South Wales 2010, Australia; Research School of Biology, Australian National University, Acton, ACT 0200, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, New South Wales 2010, Australia; School of Biological Sciences, Environment Institute, Centre for Applied Conservation Science, and ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
| | - Martua H Sinaga
- Indonesian Institute of Sciences (LIPI) & Museum Bogoriense, Cibinong, West Java, Indonesia
| | - Ken P Aplin
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, New South Wales 2010, Australia; Wildlife Conservation Society, Goroka, Papua New Guinea
| | - Tim F Flannery
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, New South Wales 2010, Australia; Melbourne Sustainable Society Institute, Melbourne University, Parkville, Vic. 3010, Australia
| | - Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, New South Wales 2010, Australia
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13
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Shiffman ME, Soo RM, Dennis PG, Morrison M, Tyson GW, Hugenholtz P. Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion. PeerJ 2017; 5:e4075. [PMID: 29177117 PMCID: PMC5697889 DOI: 10.7717/peerj.4075] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/31/2017] [Indexed: 01/09/2023] Open
Abstract
The koala has evolved to become a specialist Eucalyptus herbivore since diverging from its closest relative, the wombat, a generalist herbivore. This niche adaptation involves, in part, changes in the gut microbiota. The goal of this study was to compare koala and wombat fecal microbiomes using metagenomics to identify potential differences attributable to dietary specialization. Several populations discriminated between the koala and wombat fecal communities, most notably S24-7 and Synergistaceae in the koala, and Christensenellaceae and RF39 in the wombat. As expected for herbivores, both communities contained the genes necessary for lignocellulose degradation and urea recycling partitioned and redundantly encoded across multiple populations. Secondary metabolism was overrepresented in the koala fecal samples, consistent with the need to process Eucalyptus secondary metabolites. The Synergistaceae population encodes multiple pathways potentially relevant to Eucalyptus compound metabolism, and is predicted to be a key player in detoxification of the koala's diet. Notably, characterized microbial isolates from the koala gut appear to be minor constituents of this habitat, and the metagenomes provide the opportunity for genome-directed isolation of more representative populations. Metagenomic analysis of other obligate and facultative Eucalyptus folivores will reveal whether putatively detoxifying bacteria identified in the koala are shared across these marsupials.
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Affiliation(s)
- Miriam E. Shiffman
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Rochelle M. Soo
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Paul G. Dennis
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, Australia
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
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14
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Gaudry MJ, Jastroch M, Treberg JR, Hofreiter M, Paijmans JLA, Starrett J, Wales N, Signore AV, Springer MS, Campbell KL. Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades. SCIENCE ADVANCES 2017; 3:e1602878. [PMID: 28706989 PMCID: PMC5507634 DOI: 10.1126/sciadv.1602878] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 06/21/2017] [Indexed: 05/08/2023]
Abstract
Mitochondrial uncoupling protein 1 (UCP1) is essential for nonshivering thermogenesis in brown adipose tissue and is widely accepted to have played a key thermoregulatory role in small-bodied and neonatal placental mammals that enabled the exploitation of cold environments. We map ucp1 sequences from 133 mammals onto a species tree constructed from a ~51-kb sequence alignment and show that inactivating mutations have occurred in at least 8 of the 18 traditional placental orders, thereby challenging the physiological importance of UCP1 across Placentalia. Selection and timetree analyses further reveal that ucp1 inactivations temporally correspond with strong secondary reductions in metabolic intensity in xenarthrans and pangolins, or in six other lineages coincided with a ~30 million-year episode of global cooling in the Paleogene that promoted sharp increases in body mass and cladogenesis evident in the fossil record. Our findings also demonstrate that members of various lineages (for example, cetaceans, horses, woolly mammoths, Steller's sea cows) evolved extreme cold hardiness in the absence of UCP1-mediated thermogenesis. Finally, we identify ucp1 inactivation as a historical contingency that is linked to the current low species diversity of clades lacking functional UCP1, thus providing the first evidence for species selection related to the presence or absence of a single gene product.
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Affiliation(s)
- Michael J. Gaudry
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Martin Jastroch
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Parkring 13, 85748 Garching, Germany
- Department of Animal Physiology, Faculty of Biology, Philipps University of Marburg, D-35032 Marburg, Germany
| | - Jason R. Treberg
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Michael Hofreiter
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | | | - James Starrett
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Anthony V. Signore
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Mark S. Springer
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Kevin L. Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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15
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Oliver PM, Iannella A, Richards SJ, Lee MS. Mountain colonisation, miniaturisation and ecological evolution in a radiation of direct-developing New Guinea Frogs ( Choerophryne, Microhylidae). PeerJ 2017; 5:e3077. [PMID: 28382230 PMCID: PMC5376113 DOI: 10.7717/peerj.3077] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 02/08/2017] [Indexed: 11/20/2022] Open
Abstract
AIMS Mountain ranges in the tropics are characterised by high levels of localised endemism, often-aberrant evolutionary trajectories, and some of the world's most diverse regional biotas. Here we investigate the evolution of montane endemism, ecology and body size in a clade of direct-developing frogs (Choerophryne, Microhylidae) from New Guinea. METHODS Phylogenetic relationships were estimated from a mitochondrial molecular dataset using Bayesian and maximum likelihood approaches. Ancestral state reconstruction was used to infer the evolution of elevational distribution, ecology (indexed by male calling height), and body size, and phylogenetically corrected regression was employed to examine the relationships between these three traits. RESULTS We obtained strong support for a monophyletic lineage comprising the majority of taxa sampled. Within this clade we identified one subclade that appears to have diversified primarily in montane habitats of the Central Cordillera (>1,000 m a.s.l.), with subsequent dispersal to isolated North Papuan Mountains. A second subclade (characterised by moderately to very elongated snouts) appears to have diversified primarily in hill forests (<1,000 m a.s.l.), with inferred independent upwards colonisations of isolated montane habitats, especially in isolated North Papuan Mountains. We found no clear relationship between extremely small body size (adult SVL less than 15 mm) and elevation, but a stronger relationship with ecology-smaller species tend to be more terrestrial. CONCLUSIONS Orogeny and climatic oscillations have interacted to generate high montane biodiversity in New Guinea via both localised diversification within montane habitats (centric endemism) and periodic dispersal across lowland regions (eccentric endemism). The correlation between extreme miniaturisation and terrestrial habits reflects a general trend in frogs, suggesting that ecological or physiological constraints limit niche usage by miniaturised frogs, even in extremely wet environments such as tropical mountains.
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Affiliation(s)
- Paul M. Oliver
- Division of Ecology and Evolution, Research School of Biology & Centre for Biodiversity Analysis, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Amy Iannella
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | | | - Michael S.Y. Lee
- South Australian Museum, Adelaide, South Australia, Australia
- School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
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16
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Westerman M, Blacket MJ, Hintz A, Armstrong K, Woolley PA, Krajewski C. A plethora of planigales: genetic variability and cryptic species in a genus of dasyurid marsupials from northern Australia. AUST J ZOOL 2016. [DOI: 10.1071/zo16052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Multiple mitochondrial and nuclear gene sequences reveal substantial genetic variation within the dasyurid marsupial genus Planigale, suggesting greater taxonomic diversity than is currently recognised. To further investigate planigale relationships 116 new mitochondrial and nuclear gene sequences, including 16 new specimens, were added to our database. We confirm the presence of an unrecognised species (Planigale ‘species 1’) limited to the Pilbara region of Western Australia and suggest that the ‘Mt Tom Price’ animals may be closely related to Planigale ingrami subtilissima. We also confirm that at least four distinct genetic lineages make up what is currently recognised as P. maculata. This complex of closely related taxa represents a radiation of sibling species rather than a single, genetically diverse one. Three of these lineages (M1 + M2, M3 and M4) are distributed sympatrically across the Top End of Australia and one (M5 = P. maculata sensu stricto) is localised to the eastern coast of Australia. Within the Planigale ingrami complex, Planigale ‘Mt Tom Price’ (lineage Ing. 1) occurs in the Pilbara in sympatry with Planigale ‘species 1’ and lineage Ing. 2 is found in the Northern Territory in sympatry with species of the P. maculata complex. There is thus a plethora of northern Australian planigales, many of which are formally undescribed and whose geographic ranges require careful re-evaluation.
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17
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Irestedt M, Batalha-Filho H, Roselaar CS, Christidis L, Ericson PGP. Contrasting phylogeographic signatures in two Australo-Papuan bowerbird species complexes (Aves: Ailuroedus). ZOOL SCR 2015. [DOI: 10.1111/zsc.12163] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martin Irestedt
- Department of Bioinformatics and Genetics; Swedish Museum of Natural History; PO Box 50007 Stockholm 10405 Sweden
| | | | - Cees S. Roselaar
- Naturalis Biodiversity Center; Darwinweg 2 PO Box 9517 RA Leiden 2300 The Netherlands
| | - Les Christidis
- National Marine Science Centre; Southern Cross University; Coffs Harbour NSW 2450 Australia
| | - Per G. P. Ericson
- Department of Zoology; Swedish Museum of Natural History; PO Box 50007 Stockholm 10405 Sweden
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18
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Westerman M, Krajewski C, Kear BP, Meehan L, Meredith RW, Emerling CA, Springer MS. Phylogenetic relationships of dasyuromorphian marsupials revisited. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12323] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Michael Westerman
- Genetics Department; LaTrobe University; Melbourne Vic. 3086 Australia
| | - Carey Krajewski
- Zoology Department; Southern Illinois University; Carbondale IL 62901 USA
| | - Benjamin P. Kear
- Paleobiology Programme; Department of Earth Sciences; Uppsala University; Villavagen 16 SE-752 36 Uppsala Sweden
| | - Lucy Meehan
- Genetics Department; LaTrobe University; Melbourne Vic. 3086 Australia
| | | | | | - Mark S. Springer
- Department of Biology; University of California; Riverside CA 92521 USA
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19
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Springer MS, Signore AV, Paijmans JLA, Vélez-Juarbe J, Domning DP, Bauer CE, He K, Crerar L, Campos PF, Murphy WJ, Meredith RW, Gatesy J, Willerslev E, MacPhee RDE, Hofreiter M, Campbell KL. Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia. Mol Phylogenet Evol 2015; 91:178-93. [PMID: 26050523 DOI: 10.1016/j.ympev.2015.05.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 05/22/2015] [Accepted: 05/28/2015] [Indexed: 01/02/2023]
Abstract
The recently extinct (ca. 1768) Steller's sea cow (Hydrodamalis gigas) was a large, edentulous North Pacific sirenian. The phylogenetic affinities of this taxon to other members of this clade, living and extinct, are uncertain based on previous morphological and molecular studies. We employed hybridization capture methods and second generation sequencing technology to obtain >30kb of exon sequences from 26 nuclear genes for both H. gigas and Dugong dugon. We also obtained complete coding sequences for the tooth-related enamelin (ENAM) gene. Hybridization probes designed using dugong and manatee sequences were both highly effective in retrieving sequences from H. gigas (mean=98.8% coverage), as were more divergent probes for regions of ENAM (99.0% coverage) that were designed exclusively from a proboscidean (African elephant) and a hyracoid (Cape hyrax). New sequences were combined with available sequences for representatives of all other afrotherian orders. We also expanded a previously published morphological matrix for living and fossil Sirenia by adding both new taxa and nine new postcranial characters. Maximum likelihood and parsimony analyses of the molecular data provide robust support for an association of H. gigas and D. dugon to the exclusion of living trichechids (manatees). Parsimony analyses of the morphological data also support the inclusion of H. gigas in Dugongidae with D. dugon and fossil dugongids. Timetree analyses based on calibration density approaches with hard- and soft-bounded constraints suggest that H. gigas and D. dugon diverged in the Oligocene and that crown sirenians last shared a common ancestor in the Eocene. The coding sequence for the ENAM gene in H. gigas does not contain frameshift mutations or stop codons, but there is a transversion mutation (AG to CG) in the acceptor splice site of intron 2. This disruption in the edentulous Steller's sea cow is consistent with previous studies that have documented inactivating mutations in tooth-specific loci of a variety of edentulous and enamelless vertebrates including birds, turtles, aardvarks, pangolins, xenarthrans, and baleen whales. Further, branch-site dN/dS analyses provide evidence for positive selection in ENAM on the stem dugongid branch where extensive tooth reduction occurred, followed by neutral evolution on the Hydrodamalis branch. Finally, we present a synthetic evolutionary tree for living and fossil sirenians showing several key innovations in the history of this clade including character state changes that parallel those that occurred in the evolutionary history of cetaceans.
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Affiliation(s)
- Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA.
| | - Anthony V Signore
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Johanna L A Paijmans
- Department of Biology, The University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Jorge Vélez-Juarbe
- Department of Mammalogy, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | - Daryl P Domning
- Laboratory of Evolutionary Biology, Department of Anatomy, Howard University, Washington, DC 20059, USA; Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Cameron E Bauer
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Kai He
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Lorelei Crerar
- Department of Biology, George Mason University, Fairfax, VA 22030, USA
| | - Paula F Campos
- Center for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Robert W Meredith
- Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA
| | - John Gatesy
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Eske Willerslev
- Center for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY 10024, USA
| | - Michael Hofreiter
- Department of Biology, The University of York, Wentworth Way, Heslington, York YO10 5DD, UK; Adaptive and Evolutionary Genomics, Institute for Biochemistry and Biology, Faculty of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Strasse 24-24, 14476 Potsdam, Germany
| | - Kevin L Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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May-Collado LJ, Kilpatrick CW, Agnarsson I. Mammals from 'down under': a multi-gene species-level phylogeny of marsupial mammals (Mammalia, Metatheria). PeerJ 2015; 3:e805. [PMID: 25755933 PMCID: PMC4349131 DOI: 10.7717/peerj.805] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 02/09/2015] [Indexed: 11/23/2022] Open
Abstract
Marsupials or metatherians are a group of mammals that are distinct in giving birth to young at early stages of development and in having a prolonged investment in lactation. The group consists of nearly 350 extant species, including kangaroos, koala, possums, and their relatives. Marsupials are an old lineage thought to have diverged from early therian mammals some 160 million years ago in the Jurassic, and have a remarkable evolutionary and biogeographical history, with extant species restricted to the Americas, mostly South America, and to Australasia. Although the group has been the subject of decades of phylogenetic research, the marsupial tree of life remains controversial, with most studies focusing on only a fraction of the species diversity within the infraclass. Here we present the first Methaterian species-level phylogeny to include 80% of the extant marsupial species and five nuclear and five mitochondrial markers obtained from Genbank and a recently published retroposon matrix. Our primary goal is to provide a summary phylogeny that will serve as a tool for comparative research. We evaluate the extent to which the phylogeny recovers current phylogenetic knowledge based on the recovery of “benchmark clades” from prior studies—unambiguously supported key clades and undisputed traditional taxonomic groups. The Bayesian phylogenetic analyses recovered nearly all benchmark clades but failed to find support for the suborder Phalagiformes. The most significant difference with previous published topologies is the support for Australidelphia as a group containing Microbiotheriidae, nested within American marsupials. However, a likelihood ratio test shows that alternative topologies with monophyletic Australidelphia and Ameridelphia are not significantly different than the preferred tree. Although further data are needed to solidify understanding of Methateria phylogeny, the new phylogenetic hypothesis provided here offers a well resolved and detailed tool for comparative analyses, covering the majority of the known species richness of the group.
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Affiliation(s)
| | | | - Ingi Agnarsson
- Department of Biology, University of Vermont , Burlington, VT , USA
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21
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Molecular Phylogeny, Biogeography, and Habitat Preference Evolution of Marsupials. Mol Biol Evol 2014; 31:2322-30. [DOI: 10.1093/molbev/msu176] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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The towering orogeny of New Guinea as a trigger for arthropod megadiversity. Nat Commun 2014; 5:4001. [DOI: 10.1038/ncomms5001] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 04/29/2014] [Indexed: 11/08/2022] Open
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23
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Springer MS, Meredith RW, Gatesy J, Emerling CA, Park J, Rabosky DL, Stadler T, Steiner C, Ryder OA, Janečka JE, Fisher CA, Murphy WJ. Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS One 2012; 7:e49521. [PMID: 23166696 PMCID: PMC3500307 DOI: 10.1371/journal.pone.0049521] [Citation(s) in RCA: 270] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 10/09/2012] [Indexed: 01/24/2023] Open
Abstract
Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71-63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event ("Grande Coupure") at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.
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Affiliation(s)
- Mark S. Springer
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Robert W. Meredith
- Department of Biology, University of California Riverside, Riverside, California, United States of America
- Department of Biology and Molecular Biology, Montclair State University, Montclair, New Jersey, United States of America
| | - John Gatesy
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Christopher A. Emerling
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Jong Park
- Department of Biology, University of California Riverside, Riverside, California, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Daniel L. Rabosky
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tanja Stadler
- Institut für Integrative Biologie, Eidgenössiche Technische Hochschule Zurich, Zurich, Switzerland
| | - Cynthia Steiner
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, San Diego, California, United States of America
| | - Oliver A. Ryder
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, San Diego, California, United States of America
| | - Jan E. Janečka
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Colleen A. Fisher
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
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Small mammal investigation in spotted fever focus with DNA-barcoding and taxonomic implications on rodents species from Hainan of China. PLoS One 2012. [PMID: 22952689 DOI: 10.1371/journal.pone.0043479.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although mammals are a well-studied group of animals, making accurate field identification of small mammals is still complex because of morphological variation across developmental stages, color variation of pelages, and often damaged osteological and dental characteristics. In 2008, small mammals were collected for an epidemiological study of a spotted fever outbreak in Hainan, China. Ten species of small mammals were identified by morphological characters in the field, most using pelage color characters only. The study is extended here, in order to assess whether DNA barcoding would be suitable as an identification tool in these small mammals. Barcode clusters showed some incongruence with morphospecies, especially for some species of Rattus and Niviventer, so molecular delineation was carried out with an expanded dataset of combined cytochrome b (Cyt-b) and cytochrome c oxidase subunit I (COI) sequences. COI sequences were successfully amplified from 83% of collected mammals, but failed in all specimens of Suncus murinus, which were thus excluded in DNA barcoding analysis. Of note, ten molecular taxonomic units were found from samples of nine morphologically identified species. Accordingly, 11 species of small mammals were present in the investigated areas, including four Rattus species, three Niviventer species, Callosciurus erythraeus, Neohylomys hainanensis, Tupaia belangeri, and Suncus murinus. Based on the results of the phylogenetic and molecular delineation analyses, the systematic status of some rodent species should be redefined. R. rattus hainanicus and R. rattus sladeni are synonyms of R. andamanensis. R. losea from China and Southeast Asia comprises two independent species: R. losea and R. sakeratensis. Finally, the taxonomic status of three putative species of Niviventer should be further confirmed according to morphological, molecular and ecological characters.
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25
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Lu L, Chesters D, Zhang W, Li G, Ma Y, Ma H, Song X, Wu H, Meng F, Zhu C, Liu Q. Small mammal investigation in spotted fever focus with DNA-barcoding and taxonomic implications on rodents species from Hainan of China. PLoS One 2012; 7:e43479. [PMID: 22952689 PMCID: PMC3430698 DOI: 10.1371/journal.pone.0043479] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 07/20/2012] [Indexed: 11/21/2022] Open
Abstract
Although mammals are a well-studied group of animals, making accurate field identification of small mammals is still complex because of morphological variation across developmental stages, color variation of pelages, and often damaged osteological and dental characteristics. In 2008, small mammals were collected for an epidemiological study of a spotted fever outbreak in Hainan, China. Ten species of small mammals were identified by morphological characters in the field, most using pelage color characters only. The study is extended here, in order to assess whether DNA barcoding would be suitable as an identification tool in these small mammals. Barcode clusters showed some incongruence with morphospecies, especially for some species of Rattus and Niviventer, so molecular delineation was carried out with an expanded dataset of combined cytochrome b (Cyt-b) and cytochrome c oxidase subunit I (COI) sequences. COI sequences were successfully amplified from 83% of collected mammals, but failed in all specimens of Suncus murinus, which were thus excluded in DNA barcoding analysis. Of note, ten molecular taxonomic units were found from samples of nine morphologically identified species. Accordingly, 11 species of small mammals were present in the investigated areas, including four Rattus species, three Niviventer species, Callosciurus erythraeus, Neohylomys hainanensis, Tupaia belangeri, and Suncus murinus. Based on the results of the phylogenetic and molecular delineation analyses, the systematic status of some rodent species should be redefined. R. rattus hainanicus and R. rattus sladeni are synonyms of R. andamanensis. R. losea from China and Southeast Asia comprises two independent species: R. losea and R. sakeratensis. Finally, the taxonomic status of three putative species of Niviventer should be further confirmed according to morphological, molecular and ecological characters.
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Affiliation(s)
- Liang Lu
- Department of Vector Biology and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Infectious Diseases Prevention and Control, Beijing, China
| | - Douglas Chesters
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wen Zhang
- Department of Bioinformatics, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Infectious Diseases Prevention and Control, Beijing, China
| | - Guichang Li
- Department of Vector Biology and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Infectious Diseases Prevention and Control, Beijing, China
| | - Ying Ma
- Department of Vector Biology and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Infectious Diseases Prevention and Control, Beijing, China
- QingHai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Huailei Ma
- Department of Vector Biology and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Infectious Diseases Prevention and Control, Beijing, China
| | - Xiuping Song
- Department of Vector Biology and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Infectious Diseases Prevention and Control, Beijing, China
| | - Haixia Wu
- Department of Vector Biology and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Infectious Diseases Prevention and Control, Beijing, China
| | - Fengxia Meng
- Department of Vector Biology and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Infectious Diseases Prevention and Control, Beijing, China
| | - Chaodong Zhu
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qiyong Liu
- Department of Vector Biology and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Infectious Diseases Prevention and Control, Beijing, China
- * E-mail:
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Oliver PM, Richards SJ, Sistrom M. Phylogeny and systematics of Melanesia’s most diverse gecko lineage (Cyrtodactylus, Gekkonidae, Squamata). ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2012.00545.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Westerman M, Kear B, Aplin K, Meredith R, Emerling C, Springer M. Phylogenetic relationships of living and recently extinct bandicoots based on nuclear and mitochondrial DNA sequences. Mol Phylogenet Evol 2012; 62:97-108. [DOI: 10.1016/j.ympev.2011.09.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 09/06/2011] [Accepted: 09/12/2011] [Indexed: 10/15/2022]
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28
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Su Y, Liao W, Wang T, Sun Y, Wei Q, Chang H. Phylogeny and evolutionary divergence times in Apterosperma and Euryodendron: Evidence of a Tertiary origin in south China. BIOCHEM SYST ECOL 2011. [DOI: 10.1016/j.bse.2011.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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29
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Westerman M, Meredith RW, Springer MS. Cytogenetics meets phylogenetics: a review of karyotype evolution in diprotodontian marsupials. ACTA ACUST UNITED AC 2010; 101:690-702. [PMID: 20581108 DOI: 10.1093/jhered/esq076] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have used a combined approach of phylogenetics and cytogenetics to describe karyotype evolution in Diprotodontia. Molecular relationships of diprotodontian marsupials have been clarified using a concatenation of 5 nuclear gene sequences from multiple exemplars of all extant genera. Our well-resolved phylogenetic tree has been used as a basis for understanding chromosome evolution both within this Order, as well as in marsupials in general. It is clear that the ancestral marsupial karyotype comprised 14 relatively large chromosomes of the form retained relatively unchanged in caenolestids, microbiotherians, peramelemorphians, vombatids, and pygmy possums. Four pericentric inversions occurred in the ancestral dasyuromorphian (chromosomes 1, 2, 4, and 6) and a different 4 in the ancestral didelphimorphian (chromosomes 1, 3, 5 and 6). Within Diprotodontia, although the ancestral marsupial karyotype has been retained in some families such as the extant wombats and pygmy possums, there have been major karytoypic repatternings early in the evolution of others. Chromosome rearrangements in diprotodontia include centric fissions and fusions, translocations, and centromere shifts. Karyotypic changes are discussed in the context of current hypotheses concerning centromeres, chromosomal fragile sites, and mobile elements in marsupials and the probable repeated involvement of these elements in karyotypic restructuring.
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Affiliation(s)
- Michael Westerman
- Genetics Department, La Trobe University, Bundoora, Victoria 3086, Australia
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