1
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Moreno JA, Dudchenko O, Feigin CY, Mereby SA, Chen Z, Ramos R, Almet AA, Sen H, Brack BJ, Johnson MR, Li S, Wang W, Gaska JM, Ploss A, Weisz D, Omer AD, Yao W, Colaric Z, Kaur P, Leger JS, Nie Q, Mena A, Flanagan JP, Keller G, Sanger T, Ostrow B, Plikus MV, Kvon EZ, Aiden EL, Mallarino R. Emx2 underlies the development and evolution of marsupial gliding membranes. Nature 2024; 629:127-135. [PMID: 38658750 PMCID: PMC11062917 DOI: 10.1038/s41586-024-07305-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024]
Abstract
Phenotypic variation among species is a product of evolutionary changes to developmental programs1,2. However, how these changes generate novel morphological traits remains largely unclear. Here we studied the genomic and developmental basis of the mammalian gliding membrane, or patagium-an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of 15 marsupial genomes, both from gliding and non-gliding species, we find that the Emx2 locus experienced lineage-specific patterns of accelerated cis-regulatory evolution in gliding species. By combining epigenomics, transcriptomics and in-pouch marsupial transgenics, we show that Emx2 is a critical upstream regulator of patagium development. Moreover, we identify different cis-regulatory elements that may be responsible for driving increased Emx2 expression levels in gliding species. Lastly, using mouse functional experiments, we find evidence that Emx2 expression patterns in gliders may have been modified from a pre-existing program found in all mammals. Together, our results suggest that patagia repeatedly originated through a process of convergent genomic evolution, whereby regulation of Emx2 was altered by distinct cis-regulatory elements in independently evolved species. Thus, different regulatory elements targeting the same key developmental gene may constitute an effective strategy by which natural selection has harnessed regulatory evolution in marsupial genomes to generate phenotypic novelty.
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Affiliation(s)
- Jorge A Moreno
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Charles Y Feigin
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Environment and Genetics, La Trobe University, Bundoora, Victoria, Australia
| | - Sarah A Mereby
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Zhuoxin Chen
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Raul Ramos
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Harsha Sen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Benjamin J Brack
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Matthew R Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sha Li
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Wei Wang
- Lewis Sigler Center for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Jenna M Gaska
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weijie Yao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Parwinder Kaur
- The University of Western Australia, Crawley, Western Australia, Australia
| | - Judy St Leger
- Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Qing Nie
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | | | | | - Greta Keller
- Department of Biology, Loyola University, Chicago, IL, USA
| | - Thomas Sanger
- Department of Biology, Loyola University, Chicago, IL, USA
| | - Bruce Ostrow
- Department of Biology, Grand Valley State University, Allendale, MI, USA
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Evgeny Z Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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2
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Carver S, Stannard GL, Martin AM. The Distinctive Biology and Characteristics of the Bare-Nosed Wombat ( Vombatus ursinus). Annu Rev Anim Biosci 2024; 12:135-160. [PMID: 37738454 DOI: 10.1146/annurev-animal-021022-042133] [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] [Indexed: 09/24/2023]
Abstract
The bare-nosed wombat is an iconic Australian fauna with remarkable biological characteristics and mythology. This solitary, muscular, fossorial, herbivorous marsupial from southeast Australia has continent and continental island subspeciation. Vombatiformes also contains hairy-nosed wombats (Lasiorhinus spp.); koala (Phascolarctos cinereus); and extinct megafauna, Phascolonus gigas (giant wombat), Diprotodon, and Thylacoleo (marsupial lion). Culturally important to Aboriginal people, bare-nosed wombats engineer ecosystems through digging, grazing, and defecation. Olfaction and cubic fecal aggregations appear critical for communication, including identity, courtship, and mating. Though among the largest fossorial herbivores, they have a nutrient-poor diet, a home range up to an order of magnitude smaller than expected, and a metabolism among the lowest extreme for mammals >10 kg. Metabolic depression may confer advantages over resource competitors and fossorial lifestyle protection from predators, fires, and climatic extremes. Bare-nosed wombats are loved and persecuted by European colonists. Recent population increases may reflect softening attitudes toward, and greater protections of, bare-nosed wombats.
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Affiliation(s)
- Scott Carver
- Department of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia;
- Odum School of Ecology, University of Georgia, Athens, Georgia, USA;
| | - Georgia L Stannard
- Department of Archaeology and History, La Trobe University, Bundoora, Victoria, Australia;
| | - Alynn M Martin
- Caesar Kleberg Wildlife Research Institute, Texas A&M University-Kingsville, Kingsville, Texas, USA;
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3
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Alfieri F, Botton-Divet L, Wölfer J, Nyakatura JA, Amson E. A macroevolutionary common-garden experiment reveals differentially evolvable bone organization levels in slow arboreal mammals. Commun Biol 2023; 6:995. [PMID: 37770611 PMCID: PMC10539518 DOI: 10.1038/s42003-023-05371-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023] Open
Abstract
Eco-morphological convergence, i.e., similar phenotypes evolved in ecologically convergent taxa, naturally reproduces a common-garden experiment since it allows researchers to keep ecological factors constant, studying intrinsic evolutionary drivers. The latter may result in differential evolvability that, among individual anatomical parts, causes mosaic evolution. Reconstructing the evolutionary morphology of the humerus and femur of slow arboreal mammals, we addressed mosaicism at different bone anatomical spatial scales. We compared convergence strength, using it as indicator of evolvability, between bone external shape and inner structure, with the former expected to be less evolvable and less involved in convergent evolution, due to anatomical constraints. We identify several convergent inner structural traits, while external shape only loosely follows this trend, and we find confirmation for our assumption in measures of convergence magnitude. We suggest that future macroevolutionary reconstructions based on bone morphology should include structural traits to better detect ecological effects on vertebrate diversification.
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Affiliation(s)
- Fabio Alfieri
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany.
- Museum Für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstraße 43, 10115, Berlin, Germany.
| | - Léo Botton-Divet
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany
| | - Jan Wölfer
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany
| | - John A Nyakatura
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany
| | - Eli Amson
- Paleontology Department, Staatliches Museum für Naturkunde, Rosenstein 1-3, 70191, Stuttgart, Germany
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4
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Crichton AI, Beck RMD, Couzens AMC, Worthy TH, Camens AB, Prideaux GJ. A probable koala from the Oligocene of central Australia provides insights into early diprotodontian evolution. Sci Rep 2023; 13:14521. [PMID: 37666885 PMCID: PMC10477348 DOI: 10.1038/s41598-023-41471-0] [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: 06/11/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023] Open
Abstract
Diprotodontians are the morphologically and ecologically most diverse order of marsupials. However, an approximately 30-million-year gap in the Australian terrestrial vertebrate fossil record means that the first half of diprotodontian evolution is unknown. Fossil taxa from immediately either side of this gap are therefore critical for reconstructing the early evolution of the order. Here we report the likely oldest-known koala relatives (Phascolarctidae), from the late Oligocene Pwerte Marnte Marnte Local Fauna (central Australia). These include coeval species of Madakoala and Nimiokoala, as well as a new probable koala (?Phascolarctidae). The new taxon, Lumakoala blackae gen. et sp. nov., was comparable in size to the smallest-known phascolarctids, with body-mass estimates of 2.2-2.6 kg. Its bunoselenodont upper molars retain the primitive metatherian condition of a continuous centrocrista, and distinct stylar cusps B and D which lacked occlusion with the hypoconid. This structural arrangement: (1) suggests a morphocline within Phascolarctidae from bunoselenodonty to selenodonty; and (2) better clarifies the evolutionary transitions between molar morphologies within Vombatomorphia. We hypothesize that the molar form of Lumakoala blackae approximates the ancestral condition of the suborder Vombatiformes. Furthermore, it provides a plausible link between diprotodontians and the putative polydolopimorphians Chulpasia jimthorselli and Thylacotinga bartholomaii from the early Eocene Tingamarra Local Fauna (eastern Australia), which we infer as having molar morphologies consistent with stem diprotodontians.
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Affiliation(s)
- Arthur I Crichton
- College of Science and Engineering, Flinders University, Bedford Park, 5042, Australia.
| | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Salford, England
| | - Aidan M C Couzens
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Trevor H Worthy
- College of Science and Engineering, Flinders University, Bedford Park, 5042, Australia
| | - Aaron B Camens
- College of Science and Engineering, Flinders University, Bedford Park, 5042, Australia
| | - Gavin J Prideaux
- College of Science and Engineering, Flinders University, Bedford Park, 5042, Australia
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5
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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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6
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Carmelet‐Rescan D, Morgan‐Richards M, Pattabiraman N, Trewick SA. Time-calibrated phylogeny and ecological niche models indicate Pliocene aridification drove intraspecific diversification of brushtail possums in Australia. Ecol Evol 2022; 12:e9633. [PMID: 36540081 PMCID: PMC9755819 DOI: 10.1002/ece3.9633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Major aridification events in Australia during the Pliocene may have had significant impact on the distribution and structure of widespread species. To explore the potential impact of Pliocene and Pleistocene climate oscillations, we estimated the timing of population fragmentation and past connectivity of the currently isolated but morphologically similar subspecies of the widespread brushtail possum (Trichosurus vulpecula). We use ecological niche modeling (ENM) with the current fragmented distribution of brushtail possums to estimate the environmental envelope of this marsupial. We projected the ENM on models of past climatic conditions in Australia to infer the potential distribution of brushtail possums over 6 million years. D-loop haplotypes were used to describe population structure. From shotgun sequencing, we assembled whole mitochondrial DNA genomes and estimated the timing of intraspecific divergence. Our projections of ENMs suggest current possum populations were unlikely to have been in contact during the Pleistocene. Although lowered sea level during glacial periods enabled connection with habitat in Tasmania, climate fluctuation during this time would not have facilitated gene flow over much of Australia. The most recent common ancestor of sampled intraspecific diversity dates to the early Pliocene when continental aridification caused significant changes to Australian ecology and Trichosurus vulpecula distribution was likely fragmented. Phylogenetic analysis revealed that the subspecies T. v. hypoleucus (koomal; southwest), T. v. arnhemensis (langkurr; north), and T. v. vulpecula (bilda; southeast) correspond to distinct mitochondrial lineages. Despite little phenotypic differentiation, Trichosurus vulpecula populations probably experienced little gene flow with one another since the Pliocene, supporting the recognition of several subspecies and explaining their adaptations to the regional plant assemblages on which they feed.
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Affiliation(s)
- David Carmelet‐Rescan
- Wildlife and Ecology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Mary Morgan‐Richards
- Wildlife and Ecology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Nimeshika Pattabiraman
- Wildlife and Ecology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Steven A. Trewick
- Wildlife and Ecology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
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7
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Villacís Núñez CN, Ray AP, Cooper KL, Moore TY. Metatarsal fusion resisted bending as jerboas (Dipodidae) transitioned from quadrupedal to bipedal. Proc Biol Sci 2022; 289:20221322. [PMID: 36196542 PMCID: PMC9532996 DOI: 10.1098/rspb.2022.1322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Hind limbs undergo dramatic changes in loading conditions during the transition from quadrupedal to bipedal locomotion. For example, the most early diverging bipedal jerboas (Rodentia: Dipodidae) are some of the smallest mammals in the world, with body masses that range between 2–4 g. The larger jerboa species exhibit developmental and evolutionary fusion of the central three metatarsals into a single cannon bone. We hypothesize that small body size and metatarsal fusion are mechanisms to maintain the safety factor of the hind limb bones despite the higher ground reaction forces associated with bipedal locomotion. Using finite-element analysis to model collisions between the substrate and the metatarsals, we found that body size reduction was insufficient to reduce bone stress on unfused metatarsals, based on the scaled dynamics of larger jerboas, and that fused bones developed lower stresses than unfused bones when all metatarsals are scaled to the same size and loading conditions. Based on these results, we conclude that fusion reinforces larger jerboa metatarsals against high ground reaction forces. Because smaller jerboas with unfused metatarsals develop higher peak stresses in response to loading conditions scaled from larger jerboas, we hypothesize that smaller jerboas use alternative dynamics of bipedal locomotion to reduce the impact of collisions between the foot and substrate.
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Affiliation(s)
| | - Andrew P. Ray
- Materials Science Engineering Department, University of Michigan, Ann Arbor 48109, MI, USA
| | - Kimberly L. Cooper
- Department of Cell and Developmental Biology, University of California, San Diego 92093, CA, USA
| | - Talia Y. Moore
- Mechanical Engineering Department, University of Michigan, Ann Arbor 48109, MI, USA
- Robotics Department, Ecology and Evolutionary Biology Department, Museum of Zoology, University of Michigan, Ann Arbor 48109, MI, USA
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8
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Doronina L, Feigin CY, Schmitz J. Reunion of Australasian Possums by Shared SINE Insertions. Syst Biol 2022; 71:1045-1053. [PMID: 35289914 PMCID: PMC9366447 DOI: 10.1093/sysbio/syac025] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 11/29/2022] Open
Abstract
Although first posited to be of a single origin, the two superfamilies of phalangeriform marsupial possums (Phalangeroidea: brushtail possums and cuscuses and Petauroidea: possums and gliders) have long been considered, based on multiple sequencing studies, to have evolved from two separate origins. However, previous data from these sequence analyses suggested a variety of conflicting trees. Therefore, we reinvestigated these relationships by screening $\sim$200,000 orthologous short interspersed element (SINE) loci across the newly available whole-genome sequences of phalangeriform species and their relatives. Compared to sequence data, SINE presence/absence patterns are evolutionarily almost neutral molecular markers of the phylogenetic history of species. Their random and highly complex genomic insertion ensures their virtually homoplasy-free nature and enables one to compare hundreds of shared unique orthologous events to determine the true species tree. Here, we identify 106 highly reliable phylogenetic SINE markers whose presence/absence patterns within multiple Australasian possum genomes unexpectedly provide the first significant evidence for the reunification of Australasian possums into one monophyletic group. Together, our findings indicate that nucleotide homoplasy and ancestral incomplete lineage sorting have most likely driven the conflicting signal distributions seen in previous sequence-based studies. [Ancestral incomplete lineage sorting; possum genomes; possum monophyly; retrophylogenomics; SINE presence/absence.].
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Affiliation(s)
- Liliya Doronina
- Institute of Experimental Pathology (ZMBE), University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
| | - Charles Y Feigin
- Department of Molecular Biology, Princeton University, 119 Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544-1014, USA
- School of BioSciences, The University of Melbourne, BioSciences 4, Royal Pde, Parkville, VIC 3010, Australia
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
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9
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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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10
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Nasrullah Q, Renfree M, Evans AR. From Embryo to Adult: The Complete Development and Unusual Replacement of the Dentition of the Tammar Wallaby (Macropus eugenii). J MAMM EVOL 2022. [DOI: 10.1007/s10914-021-09597-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Melstrom KM, Angielczyk KD, Ritterbush KA, Irmis RB. The limits of convergence: the roles of phylogeny and dietary ecology in shaping non-avian amniote crania. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202145. [PMID: 34540239 PMCID: PMC8441121 DOI: 10.1098/rsos.202145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 08/17/2021] [Indexed: 05/28/2023]
Abstract
Cranial morphology is remarkably varied in living amniotes and the diversity of shapes is thought to correspond with feeding ecology, a relationship repeatedly demonstrated at smaller phylogenetic scales, but one that remains untested across amniote phylogeny. Using a combination of morphometric methods, we investigate the links between phylogenetic relationships, diet and skull shape in an expansive dataset of extant toothed amniotes: mammals, lepidosaurs and crocodylians. We find that both phylogeny and dietary ecology have statistically significant effects on cranial shape. The three major clades largely partition morphospace with limited overlap. Dietary generalists often occupy clade-specific central regions of morphospace. Some parallel changes in cranial shape occur in clades with distinct evolutionary histories but similar diets. However, members of a given clade often present distinct cranial shape solutions for a given diet, and the vast majority of species retain the unique aspects of their ancestral skull plan, underscoring the limits of morphological convergence due to ecology in amniotes. These data demonstrate that certain cranial shapes may provide functional advantages suited to particular dietary ecologies, but accounting for both phylogenetic history and ecology can provide a more nuanced approach to inferring the ecology and functional morphology of cryptic or extinct amniotes.
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Affiliation(s)
- Keegan M. Melstrom
- Dinosaur Institute, Natural History Museum of Los Angeles County, 900 W Exposition Boulevard, Los Angeles, CA 90007, USA
- Department of Geology and Geophysics, University of Utah, 115 S 1460 E, Salt Lake City, UT 84112-0102, USA
- Natural History Museum of Utah, University of Utah, 301 Wakara Way, Salt Lake City, UT 84108-1214, USA
| | - Kenneth D. Angielczyk
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, USA
| | - Kathleen A. Ritterbush
- Department of Geology and Geophysics, University of Utah, 115 S 1460 E, Salt Lake City, UT 84112-0102, USA
| | - Randall B. Irmis
- Department of Geology and Geophysics, University of Utah, 115 S 1460 E, Salt Lake City, UT 84112-0102, USA
- Natural History Museum of Utah, University of Utah, 301 Wakara Way, Salt Lake City, UT 84108-1214, USA
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12
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Beck RMD, Louys J, Brewer P, Archer M, Black KH, Tedford RH. A new family of diprotodontian marsupials from the latest Oligocene of Australia and the evolution of wombats, koalas, and their relatives (Vombatiformes). Sci Rep 2020; 10:9741. [PMID: 32587406 PMCID: PMC7316786 DOI: 10.1038/s41598-020-66425-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 03/30/2020] [Indexed: 01/07/2023] Open
Abstract
We describe the partial cranium and skeleton of a new diprotodontian marsupial from the late Oligocene (~26–25 Ma) Namba Formation of South Australia. This is one of the oldest Australian marsupial fossils known from an associated skeleton and it reveals previously unsuspected morphological diversity within Vombatiformes, the clade that includes wombats (Vombatidae), koalas (Phascolarctidae) and several extinct families. Several aspects of the skull and teeth of the new taxon, which we refer to a new family, are intermediate between members of the fossil family Wynyardiidae and wombats. Its postcranial skeleton exhibits features associated with scratch-digging, but it is unlikely to have been a true burrower. Body mass estimates based on postcranial dimensions range between 143 and 171 kg, suggesting that it was ~5 times larger than living wombats. Phylogenetic analysis based on 79 craniodental and 20 postcranial characters places the new taxon as sister to vombatids, with which it forms the superfamily Vombatoidea as defined here. It suggests that the highly derived vombatids evolved from wynyardiid-like ancestors, and that scratch-digging adaptations evolved in vombatoids prior to the appearance of the ever-growing (hypselodont) molars that are a characteristic feature of all post-Miocene vombatids. Ancestral state reconstructions on our preferred phylogeny suggest that bunolophodont molars are plesiomorphic for vombatiforms, with full lophodonty (characteristic of diprotodontoids) evolving from a selenodont morphology that was retained by phascolarctids and ilariids, and wynyardiids and vombatoids retaining an intermediate selenolophodont condition. There appear to have been at least six independent acquisitions of very large (>100 kg) body size within Vombatiformes, several having already occurred by the late Oligocene.
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Affiliation(s)
- Robin M D Beck
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK. .,PANGEA Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
| | - Julien Louys
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Queensland, Australia
| | - Philippa Brewer
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Michael Archer
- PANGEA Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Karen H Black
- PANGEA Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Richard H Tedford
- Division of Paleontology, American Museum of Natural History, New York, USA
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Kealy S, Donnellan SC, Mitchell KJ, Herrera M, Aplin K, O'Connor S, Louys J. Phylogenetic relationships of the cuscuses (Diprotodontia : Phalangeridae) of island Southeast Asia and Melanesia based on the mitochondrial ND2 gene. AUSTRALIAN MAMMALOGY 2020. [DOI: 10.1071/am18050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The species-level systematics of the marsupial family Phalangeridae, particularly Phalanger, are poorly understood, due partly to the family’s wide distribution across Australia, New Guinea, eastern Indonesia, and surrounding islands. In order to refine the species-level systematics of Phalangeridae, and improve our understanding of their evolution, we generated 36 mitochondrial ND2 DNA sequences from multiple species and sample localities. We combined our new data with available sequences and produced the most comprehensive molecular phylogeny for Phalangeridae to date. Our analyses (1) strongly support the monophyly of the three phalangerid subfamilies (Trichosurinae, Ailuropinae, Phalangerinae); (2) reveal the need to re-examine all specimens currently identified as ‘Phalanger orientalis’; and (3) suggest the elevation of the Solomon Island P. orientalis subspecies to species level (P. breviceps Thomas, 1888). In addition, samples of P. orientalis from Timor formed a clade, consistent with an introduction by humans from a single source population. However, further research on east Indonesian P. orientalis populations will be required to test this hypothesis, resolve inconsistencies in divergence time estimates, and locate the source population and taxonomic status of the Timor P. orientalis.
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Abstract
Marsupial genomes, which are packaged into large chromosomes, provide a powerful resource for studying the mechanisms of genome evolution. The extensive and valuable body of work on marsupial cytogenetics, combined more recently with genome sequence data, has enabled prediction of the 2n = 14 karyotype ancestral to all marsupial families. The application of both chromosome biology and genome sequencing, or chromosomics, has been a necessary approach for various aspects of mammalian genome evolution, such as understanding sex chromosome evolution and the origin and evolution of transmissible tumors in Tasmanian devils. The next phase of marsupial genome evolution research will employ chromosomics approaches to begin addressing fundamental questions in marsupial genome evolution and chromosome evolution more generally. The answers to these complex questions will impact our understanding across a broad range of fields, including the genetics of speciation, genome adaptation to environmental stressors, and species management.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2617, Australia;
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA;
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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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16
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Koala and Wombat Gammaherpesviruses Encode the First Known Viral NTPDase Homologs and Are Phylogenetically Divergent from All Known Gammaherpesviruses. J Virol 2019; 93:JVI.01404-18. [PMID: 30567986 DOI: 10.1128/jvi.01404-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/12/2018] [Indexed: 11/20/2022] Open
Abstract
There is a large taxonomic gap in our understanding of mammalian herpesvirus genetics and evolution corresponding to those herpesviruses that infect marsupials, which diverged from eutherian mammals approximately 150 million years ago (mya). We compare the genomes of two marsupial gammaherpesviruses, Phascolarctid gammaherpesvirus 1 (PhaHV1) and Vombatid gammaherpesvirus 1 (VoHV1), which infect koalas (Phascolarc tos cinereus) and wombats (Vombatus ursinus), respectively. The core viral genomes were approximately 117 kbp and 110 kbp in length, respectively, sharing 69% pairwise nucleotide sequence identity. Phylogenetic analyses showed that PhaHV1 and VoHV1 formed a separate branch, which may indicate a new gammaherpesvirus genus. The genomes contained 60 predicted open reading frames (ORFs) homologous to those in eutherian herpesviruses and 20 ORFs not yet found in any other herpesvirus. Seven of these ORFs were shared by the two viruses, indicating that they were probably acquired prespeciation, approximately 30 to 40 mya. One of these shared genes encodes a putative nucleoside triphosphate diphosphohydrolase (NTPDase). NTPDases are usually found in mammals and higher-order eukaryotes, with a very small number being found in bacteria. This is the first time that an NTPDase has been identified in any viral genome. Interrogation of public transcriptomic data sets from two koalas identified PhaHV1-specific transcripts in multiple host tissues, including transcripts for the novel NTPDase. PhaHV1 ATPase activity was also demonstrated in vitro, suggesting that the encoded NTPDase is functional during viral infection. In mammals, NTPDases are important in downregulation of the inflammatory and immune responses, but the role of the PhaHV1 NTPDase during viral infection remains to be determined.IMPORTANCE The genome sequences of the koala and wombat gammaherpesviruses show that the viruses form a distinct branch, indicative of a novel genus within the Gammaherpesvirinae Their genomes contain several new ORFs, including ORFs encoding a β-galactoside α-2,6-sialyltransferase that is phylogenetically closest to poxvirus and insect homologs and the first reported viral NTPDase. NTPDases are ubiquitously expressed in mammals and are also present in several parasitic, fungal, and bacterial pathogens. In mammals, these cell surface-localized NTPDases play essential roles in thromboregulation, inflammation, and immune suppression. In this study, we demonstrate that the virus-encoded NTPDase is enzymatically active and is transcribed during natural infection of the host. Understanding how these enzymes benefit viruses can help to inform how they may cause disease or evade host immune defenses.
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Vďačný P. Evolutionary Associations of Endosymbiotic Ciliates Shed Light on the Timing of the Marsupial-Placental Split. Mol Biol Evol 2018; 35:1757-1769. [PMID: 29659942 PMCID: PMC5995207 DOI: 10.1093/molbev/msy071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Trichostome ciliates are among the most conspicuous protists in the gastrointestinal tract of a large variety of vertebrates. However, little is still known about phylogeny of the trichostome/vertebrate symbiotic systems, evolutionary correlations between trichostome extrinsic traits, and character-dependent diversification of trichostomes. These issues were investigated here, using the relaxed molecular clock technique along with stochastic mapping of character evolution, and binary-state speciation and extinction models. Clock analyses revealed that trichostomes colonized the vertebrate gastrointestinal tract ∼135 Ma, that is, near the paleontological minimum for the split of therian mammals into marsupials and placentals. According to stochastic mapping, the last common ancestor of trichostomes most likely invaded the hindgut of a mammal. Although multiple shifts to fish/amphibian or avian hosts and to the foregut compartments took place during the trichostome phylogeny, only transition to the foregut was recognized as a key innovation responsible for the explosive radiation of ophryoscolecid trichostomes after the Cretaceous/Tertiary boundary, when ungulates began their diversification. Since crown radiations of main trichostome lineages follow those of their mammalian hosts and are in agreement with their historic dispersal routes, the present time-calibrated phylogeny might help to elucidate controversies in the geological and molecular timing of the split between marsupials and placental mammals.
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Affiliation(s)
- Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
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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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Alvarez-Ponce D, Torres-Sánchez M, Feyertag F, Kulkarni A, Nappi T. Molecular evolution of DNMT1 in vertebrates: Duplications in marsupials followed by positive selection. PLoS One 2018; 13:e0195162. [PMID: 29621315 PMCID: PMC5886458 DOI: 10.1371/journal.pone.0195162] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/16/2018] [Indexed: 01/01/2023] Open
Abstract
DNA methylation is mediated by a conserved family of DNA methyltransferases (Dnmts). The human genome encodes three active Dnmts (Dnmt1, Dnmt3a and Dnmt3b), the tRNA methyltransferase Dnmt2, and the regulatory protein Dnmt3L. Despite their high degree of conservation among different species, genes encoding Dnmts have been duplicated and/or lost in multiple lineages throughout evolution, indicating that the DNA methylation machinery has some potential to undergo evolutionary change. However, little is known about the extent to which this machinery, or the methylome, varies among vertebrates. Here, we study the molecular evolution of Dnmt1, the enzyme responsible for maintenance of DNA methylation patterns after replication, in 79 vertebrate species. Our analyses show that all studied species exhibit a single copy of the DNMT1 gene, with the exception of tilapia and marsupials (tammar wallaby, koala, Tasmanian devil and opossum), each of which displays two apparently functional DNMT1 copies. Our phylogenetic analyses indicate that DNMT1 duplicated before the radiation of major marsupial groups (i.e., at least ~75 million years ago), thus giving rise to two DNMT1 copies in marsupials (copy 1 and copy 2). In the opossum lineage, copy 2 was lost, and copy 1 recently duplicated again, generating three DNMT1 copies: two putatively functional genes (copy 1a and 1b) and one pseudogene (copy 1ψ). Both marsupial copies (DNMT1 copies 1 and 2) are under purifying selection, and copy 2 exhibits elevated rates of evolution and signatures of positive selection, suggesting a scenario of neofunctionalization. This gene duplication might have resulted in modifications in marsupial methylomes and their dynamics.
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Affiliation(s)
- David Alvarez-Ponce
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
- * E-mail:
| | - María Torres-Sánchez
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain
| | - Felix Feyertag
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
| | - Asmita Kulkarni
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
| | - Taylen Nappi
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
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Laird MK, McShea H, Murphy CR, McAllan BM, Shaw G, Renfree MB, Thompson MB. Non‐invasive placentation in the marsupials
Macropus eugenii
(Macropodidae) and
Trichosurus vulpecula
(Phalangeridae) involves redistribution of uterine Desmoglein‐2. Mol Reprod Dev 2018; 85:72-82. [DOI: 10.1002/mrd.22940] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 11/10/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Melanie K. Laird
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Hanon McShea
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMassachusetts
| | - Christopher R. Murphy
- School of Medical Sciences and Bosch InstituteUniversity of SydneySydneyNew South WalesAustralia
| | - Bronwyn M. McAllan
- School of Medical Sciences and Bosch InstituteUniversity of SydneySydneyNew South WalesAustralia
| | - Geoff Shaw
- School of BioSciencesUniversity of MelbourneVictoriaAustralia
| | | | - Michael B. Thompson
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
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Kealy S, Beck R. Total evidence phylogeny and evolutionary timescale for Australian faunivorous marsupials (Dasyuromorphia). BMC Evol Biol 2017; 17:240. [PMID: 29202687 PMCID: PMC5715987 DOI: 10.1186/s12862-017-1090-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/22/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The order Dasyuromorphia is a diverse radiation of faunivorous marsupials, comprising >80 modern species in Australia and New Guinea. It includes dasyurids, the numbat (the myrmecobiid Myrmecobius fasciatus) and the recently extinct thylacine (the thylacinid Thylacinus cyncocephalus). There is also a diverse fossil record of dasyuromorphians and "dasyuromorphian-like" taxa known from Australia. We present the first total evidence phylogenetic analyses of the order, based on combined morphological and molecular data (including a novel set of 115 postcranial characters), to resolve relationships and calculate divergence dates. We use this information to analyse the diversification dynamics of modern dasyuromorphians. RESULTS Our morphology-only analyses are poorly resolved, but our molecular and total evidence analyses confidently resolve most relationships within the order, and are strongly congruent with recent molecular studies. Thylacinidae is the first family to diverge within the order, and there is strong support for four tribes within Dasyuridae (Dasyurini, Phascogalini, Planigalini and Sminthopsini). Among fossil taxa, Ankotarinja and Keeuna do not appear to be members of Dasyuromorphia, whilst Barinya and Mutpuracinus are of uncertain relationships within the order. Divergence dates calculated using total evidence tip-and-node dating are younger than both molecular node-dating and total evidence tip-dating, but appear more congruent with the fossil record and are relatively insensitive to calibration strategy. The tip-and-node divergence dates indicate that Dasyurini, Phascogalini and Sminthopsini began to radiate almost simultaneously during the middle-to-late Miocene (11.5-13.1 MYA; composite 95% HPD: 9.5-15.9 MYA); the median estimates for these divergences are shortly after a drop in global temperatures (the middle Miocene Climatic Transition), and coincide with a faunal turnover event in the mammalian fossil record of Australia. Planigalini radiated much later, during the latest Miocene to earliest Pliocene (6.5 MYA; composite 95% HPD: 4.4-8.9 MYA); the median estimates for these divergences coincide with an increase in grass pollen in the Australian palynological record that suggests the development of more open habitats, which are preferred by modern planigale species. CONCLUSIONS Our results provide a phylogenetic and temporal framework for interpreting the evolution of modern and fossil dasyuromorphians, but future progress will require a much improved fossil record.
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Affiliation(s)
- Shimona Kealy
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT Australia
| | - Robin Beck
- School of Environment and Life Sciences, University of Salford, Salford, M5 4WT UK
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23
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Locomotion and basicranial anatomy in primates and marsupials. J Hum Evol 2017; 111:163-178. [DOI: 10.1016/j.jhevol.2017.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 06/27/2017] [Accepted: 07/07/2017] [Indexed: 01/19/2023]
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Duchêne DA, Bragg JG, Duchêne S, Neaves LE, Potter S, Moritz C, Johnson RN, Ho SYW, Eldridge MDB. Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families. Syst Biol 2017; 67:400-412. [DOI: 10.1093/sysbio/syx076] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 09/08/2017] [Indexed: 02/02/2023] Open
Affiliation(s)
- David A Duchêne
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Jason G Bragg
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust, Sydney, NSW 2000, Australia
| | - Sebastián Duchêne
- Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Linda E Neaves
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2000, Australia
| | - Sally Potter
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2000, Australia
| | - Craig Moritz
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2000, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2000, Australia
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Pfaff C, Czerny S, Nagel D, Kriwet J. Functional morphological adaptations of the bony labyrinth in marsupials (Mammalia, Theria). J Morphol 2017; 278:742-749. [PMID: 28345247 DOI: 10.1002/jmor.20669] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/23/2017] [Accepted: 02/19/2017] [Indexed: 11/06/2022]
Abstract
Diprotodontia represents the largest and ecologically most distinct order of marsupials occurring in Australasian being highly divers in size, locomotion, habitat preferences, feeding, and activity pattern. The spatial orientation in the habitat and therefore the three-dimensional space is detected by the vestibular system of the inner ear, more precisely by the three semicircular canals. In this study, we investigated the bony labyrinth of diprotodontian and selected non-diprotodontian marsupial mammals of almost all genera with noninvasive micro-CT scanning and 3D-reconstructions. In principal component analyses, the subterranean taxon can be separated from gliding and saltatorial taxa, whereas arboreal species can be separated from saltatorial specimens. The highest PCA loadings of this functional distinction are clearly found in the diameter of the semicircular canals, whereas the overall shape (height, width, length) of the semicircular canals is less important. Additionally, the investigated arboreal and fossorial species of South America are nested in the morphospace of the Australasian taxa. Even if a phylogenetic signal in the anatomy of the bony labyrinth cannot be excluded entirely, the main functional morphological signal of the vestibular system is found in the diameter of the semicircular canals. With the large dataset of extant marsupial mammals analysed here, the locomotion mode of extinct taxa can be inferred in future studies independent of any evidence of postcranial material.
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Affiliation(s)
- Cathrin Pfaff
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Stefan Czerny
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Doris Nagel
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Jürgen Kriwet
- Department of Palaeontology, University of Vienna, Vienna, Austria
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26
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Sánchez-Villagra MR, Forasiepi AM. On the development of the chondrocranium and the histological anatomy of the head in perinatal stages of marsupial mammals. ZOOLOGICAL LETTERS 2017; 3:1. [PMID: 28203388 PMCID: PMC5303607 DOI: 10.1186/s40851-017-0062-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 02/07/2017] [Indexed: 05/06/2023]
Abstract
An overview of the literature on the chondrocranium of marsupial mammals reveals a relative conservatism in shape and structures. We document the histological cranial anatomy of individuals representing Monodelphis domestica, Dromiciops gliroides, Perameles sp. and Macropus eugenii. The marsupial chondrocranium is generally characterized by the great breadth of the lamina basalis, absence of pila metoptica and large otic capsules. Its most anterior portion (cupula nasi anterior) is robust, and anterior to it there are well-developed tactile sensory structures, functionally important in the neonate. Investigations of ossification centers at and around the nasal septum are needed to trace the presence of certain bones (e.g., mesethmoid, parasphenoid) across marsupial taxa. In many adult marsupials, the tympanic floor is formed by at least three bones: alisphenoid (alisphenoid tympanic process), ectotympanic and petrosal (rostral and caudal tympanic processes); the squamosal also contributes in some diprotodontians. The presence of an entotympanic in marsupials has not been convincingly demonstrated. The tubal element surrounding the auditory tube in most marsupials is fibrous connective tissue rather than cartilage; the latter is the case in most placentals recorded to date. However, we detected fibrocartilage in a late juvenile of Dromiciops, and a similar tissue has been reported for Tarsipes. Contradictory reports on the presence of the tegmen tympani can be found in the literature. We describe a small tegmen tympani in Macropus. Several heterochronic shifts in the timing of development of the chondocranium and associated structures (e.g., nerves, muscles) and in the ossification sequence have been interpreted as largely being influenced by functional requirements related to the altriciality of the newborn marsupial during early postnatal life. Comparative studies of chondocranial development of mammals can benefit from a solid phylogenetic framework, research on non-classical model organisms, and integration with imaging and sectional data derived from computer-tomography.
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Affiliation(s)
- Marcelo R. Sánchez-Villagra
- Paläontologisches Institut und Museum der Universität Zürich, Karl Schmid Strasse 4, Zürich, 8006 Switzerland
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Beck RMD. The Skull of Epidolops ameghinoi from the Early Eocene Itaboraí Fauna, Southeastern Brazil, and the Affinities of the Extinct Marsupialiform Order Polydolopimorphia. J MAMM EVOL 2016; 24:373-414. [PMID: 29187780 PMCID: PMC5684316 DOI: 10.1007/s10914-016-9357-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The skull of the polydolopimorphian marsupialiform Epidolops ameghinoi is described in detail for the first time, based on a single well-preserved cranium and associated left and right dentaries plus additional craniodental fragments, all from the early Eocene (53–50 million year old) Itaboraí fauna in southeastern Brazil. Notable craniodental features of E. ameghinoi include absence of a masseteric process, very small maxillopalatine fenestrae, a prominent pterygoid fossa enclosed laterally by a prominent ectopterygoid crest, an absent or tiny transverse canal foramen, a simple, planar glenoid fossa, and a postglenoid foramen that is immediately posterior to the postglenoid process. Most strikingly, the floor of the hypotympanic sinus was apparently unossified, a feature found in several stem marsupials but absent in all known crown marsupials. “Type II” marsupialiform petrosals previously described from Itaboraí plausibly belong to E. ameghinoi; in published phylogenetic analyses, these petrosals fell outside (crown-clade) Marsupialia. “IMG VII” tarsals previously referred to E. ameghinoi do not share obvious synapomorphies with any crown marsupial clade, nor do they resemble those of the only other putative polydolopimorphians represented by tarsal remains, namely the argyrolagids. Most studies have placed Polydolopimorphia within Marsupialia, related to either Paucituberculata, or to Microbiotheria and Diprotodontia. However, diprotodonty almost certainly evolved independently in polydolopimorphians, paucituberculatans and diprotodontians, and Epidolops does not share obvious synapomorphies with any marsupial order. Epidolops is dentally specialized, but several morphological features appear to be more plesiomorphic than any crown marsupial. It seems likely Epidolops that falls outside Marsupialia, as do morphologically similar forms such as Bonapartherium and polydolopids. Argyrolagids differ markedly in their known morphology from Epidolops but share some potential apomorphies with paucituberculatans. It is proposed that Polydolopimorphia as currently recognised is polyphyletic, and that argyrolagids (and possibly other taxa currently included in Argyrolagoidea, such as groeberiids and patagoniids) are members of Paucituberculata. This hypothesis is supported by Bayesian non-clock phylogenetic analyses of a total evidence matrix comprising DNA sequence data from five nuclear protein-coding genes, indels, retroposon insertions, and morphological characters: Epidolops falls outside Marsupialia, whereas argyrolagids form a clade with the paucituberculatans Caenolestes and Palaeothentes, regardless of whether the Type II petrosals and IMG VII tarsals are used to score characters for Epidolops or not. There is no clear evidence for the presence of crown marsupials at Itaboraí, and it is possible that the origin and early evolution of Marsupialia was restricted to the “Austral Kingdom” (southern South America, Antarctica, and Australia).
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Affiliation(s)
- Robin M. D. Beck
- School of Environment & Life Sciences, University of Salford, M5 4WT, Manchester, UK
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052 Australia
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Convergent Traits in Mammals Associated with Divergent Behaviors: the Case of the Continuous Dental Replacement in Rock-Wallabies and African Mole-Rats. J MAMM EVOL 2016. [DOI: 10.1007/s10914-016-9348-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Smith RH, Hallwirth CV, Westerman M, Hetherington NA, Tseng YS, Cecchini S, Virag T, Ziegler ML, Rogozin IB, Koonin EV, Agbandje-McKenna M, Kotin RM, Alexander IE. Germline viral "fossils" guide in silico reconstruction of a mid-Cenozoic era marsupial adeno-associated virus. Sci Rep 2016; 6:28965. [PMID: 27377618 PMCID: PMC4932596 DOI: 10.1038/srep28965] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/07/2016] [Indexed: 12/21/2022] Open
Abstract
Germline endogenous viral elements (EVEs) genetically preserve viral nucleotide sequences useful to the study of viral evolution, gene mutation, and the phylogenetic relationships among host organisms. Here, we describe a lineage-specific, adeno-associated virus (AAV)-derived endogenous viral element (mAAV-EVE1) found within the germline of numerous closely related marsupial species. Molecular screening of a marsupial DNA panel indicated that mAAV-EVE1 occurs specifically within the marsupial suborder Macropodiformes (present-day kangaroos, wallabies, and related macropodoids), to the exclusion of other Diprotodontian lineages. Orthologous mAAV-EVE1 locus sequences from sixteen macropodoid species, representing a speciation history spanning an estimated 30 million years, facilitated compilation of an inferred ancestral sequence that recapitulates the genome of an ancient marsupial AAV that circulated among Australian metatherian fauna sometime during the late Eocene to early Oligocene. In silico gene reconstruction and molecular modelling indicate remarkable conservation of viral structure over a geologic timescale. Characterisation of AAV-EVE loci among disparate species affords insight into AAV evolution and, in the case of macropodoid species, may offer an additional genetic basis for assignment of phylogenetic relationships among the Macropodoidea. From an applied perspective, the identified AAV “fossils” provide novel capsid sequences for use in translational research and clinical applications.
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Affiliation(s)
- Richard H Smith
- Laboratory of Molecular Virology and Gene Therapy, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Michael Westerman
- Department of Biochemistry and Genetics, La Trobe University, Bundoora, Victoria, Australia
| | - Nicola A Hetherington
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Yu-Shan Tseng
- The McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Sylvain Cecchini
- Laboratory of Molecular Virology and Gene Therapy, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Tamas Virag
- Laboratory of Molecular Virology and Gene Therapy, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Mona-Larissa Ziegler
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Igor B Rogozin
- Evolutionary Genomics Research Group, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eugene V Koonin
- Evolutionary Genomics Research Group, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mavis Agbandje-McKenna
- The McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Robert M Kotin
- Laboratory of Molecular Virology and Gene Therapy, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,The University of Sydney, Discipline of Paediatrics and Child Health, Westmead, New South Wales, Australia
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30
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Cui P, Löber U, Alquezar-Planas DE, Ishida Y, Courtiol A, Timms P, Johnson RN, Lenz D, Helgen KM, Roca AL, Hartman S, Greenwood AD. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome. PeerJ 2016; 4:e1847. [PMID: 27069793 PMCID: PMC4824918 DOI: 10.7717/peerj.1847] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/04/2016] [Indexed: 11/20/2022] Open
Abstract
Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.
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Affiliation(s)
- Pin Cui
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Ulrike Löber
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute of Biochemistry & Biology, University of Potsdam, Potsdam, Germany
| | - David E Alquezar-Planas
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Alexandre Courtiol
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Peter Timms
- University of the Sunshine Coast, Sippy Downs Queensland, Australia
| | - Rebecca N Johnson
- Australian Centre for Wildlife Genomics, Australian Museum, Sydney, Australia
| | - Dorina Lenz
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Kristofer M Helgen
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Stefanie Hartman
- Institute of Biochemistry & Biology, University of Potsdam, Potsdam, Germany
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
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31
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Tourmente M, Delbarco Trillo J, Roldan ERS. No evidence of trade-offs in the evolution of sperm numbers and sperm size in mammals. J Evol Biol 2015; 28:1816-27. [DOI: 10.1111/jeb.12698] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 07/06/2015] [Accepted: 07/11/2015] [Indexed: 11/30/2022]
Affiliation(s)
- M. Tourmente
- Reproductive Ecology and Biology Group; Museo Nacional de Ciencias Naturales (CSIC); Madrid Spain
| | - J. Delbarco Trillo
- Reproductive Ecology and Biology Group; Museo Nacional de Ciencias Naturales (CSIC); Madrid Spain
| | - E. R. S. Roldan
- Reproductive Ecology and Biology Group; Museo Nacional de Ciencias Naturales (CSIC); Madrid Spain
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32
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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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33
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Llamas B, Brotherton P, Mitchell KJ, Templeton JEL, Thomson VA, Metcalf JL, Armstrong KN, Kasper M, Richards SM, Camens AB, Lee MSY, Cooper A. Late pleistocene Australian marsupial DNA clarifies the affinities of extinct megafaunal kangaroos and wallabies. Mol Biol Evol 2014; 32:574-84. [PMID: 25526902 DOI: 10.1093/molbev/msu338] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Understanding the evolution of Australia's extinct marsupial megafauna has been hindered by a relatively incomplete fossil record and convergent or highly specialized morphology, which confound phylogenetic analyses. Further, the harsh Australian climate and early date of most megafaunal extinctions (39-52 ka) means that the vast majority of fossil remains are unsuitable for ancient DNA analyses. Here, we apply cross-species DNA capture to fossils from relatively high latitude, high altitude caves in Tasmania. Using low-stringency hybridization and high-throughput sequencing, we were able to retrieve mitochondrial sequences from two extinct megafaunal macropodid species. The two specimens, Simosthenurus occidentalis (giant short-faced kangaroo) and Protemnodon anak (giant wallaby), have been radiocarbon dated to 46-50 and 40-45 ka, respectively. This is significantly older than any Australian fossil that has previously yielded DNA sequence information. Processing the raw sequence data from these samples posed a bioinformatic challenge due to the poor preservation of DNA. We explored several approaches in order to maximize the signal-to-noise ratio in retained sequencing reads. Our findings demonstrate the critical importance of adopting stringent processing criteria when distant outgroups are used as references for mapping highly fragmented DNA. Based on the most stringent nucleotide data sets (879 bp for S. occidentalis and 2,383 bp for P. anak), total-evidence phylogenetic analyses confirm that macropodids consist of three primary lineages: Sthenurines such as Simosthenurus (extinct short-faced kangaroos), the macropodines (all other wallabies and kangaroos), and the enigmatic living banded hare-wallaby Lagostrophus fasciatus (Lagostrophinae). Protemnodon emerges as a close relative of Macropus (large living kangaroos), a position not supported by recent morphological phylogenetic analyses.
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Affiliation(s)
- Bastien Llamas
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Paul Brotherton
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Jennifer E L Templeton
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia School of Biological Sciences, Flinders University, SA, Australia
| | - Vicki A Thomson
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Jessica L Metcalf
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Kyle N Armstrong
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Marta Kasper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Stephen M Richards
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Aaron B Camens
- School of Biological Sciences, Flinders University, SA, Australia School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Michael S Y Lee
- School of Earth and Environmental Sciences, University of Adelaide, SA, Australia Earth Sciences Section, The South Australian Museum, SA, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
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Hobbs M, Pavasovic A, King AG, Prentis PJ, Eldridge MDB, Chen Z, Colgan DJ, Polkinghorne A, Wilkins MR, Flanagan C, Gillett A, Hanger J, Johnson RN, Timms P. A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity. BMC Genomics 2014; 15:786. [PMID: 25214207 PMCID: PMC4247155 DOI: 10.1186/1471-2164-15-786] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/03/2014] [Indexed: 11/10/2022] Open
Abstract
Background The koala, Phascolarctos cinereus, is a biologically unique and evolutionarily distinct Australian arboreal marsupial. The goal of this study was to sequence the transcriptome from several tissues of two geographically separate koalas, and to create the first comprehensive catalog of annotated transcripts for this species, enabling detailed analysis of the unique attributes of this threatened native marsupial, including infection by the koala retrovirus. Results RNA-Seq data was generated from a range of tissues from one male and one female koala and assembled de novo into transcripts using Velvet-Oases. Transcript abundance in each tissue was estimated. Transcripts were searched for likely protein-coding regions and a non-redundant set of 117,563 putative protein sequences was produced. In similarity searches there were 84,907 (72%) sequences that aligned to at least one sequence in the NCBI nr protein database. The best alignments were to sequences from other marsupials. After applying a reciprocal best hit requirement of koala sequences to those from tammar wallaby, Tasmanian devil and the gray short-tailed opossum, we estimate that our transcriptome dataset represents approximately 15,000 koala genes. The marsupial alignment information was used to look for potential gene duplications and we report evidence for copy number expansion of the alpha amylase gene, and of an aldehyde reductase gene. Koala retrovirus (KoRV) transcripts were detected in the transcriptomes. These were analysed in detail and the structure of the spliced envelope gene transcript was determined. There was appreciable sequence diversity within KoRV, with 233 sites in the KoRV genome showing small insertions/deletions or single nucleotide polymorphisms. Both koalas had sequences from the KoRV-A subtype, but the male koala transcriptome has, in addition, sequences more closely related to the KoRV-B subtype. This is the first report of a KoRV-B-like sequence in a wild population. Conclusions This transcriptomic dataset is a useful resource for molecular genetic studies of the koala, for evolutionary genetic studies of marsupials, for validation and annotation of the koala genome sequence, and for investigation of koala retrovirus. Annotated transcripts can be browsed and queried at http://koalagenome.org. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-786) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, 6 College Street, Sydney, NSW 2010, Australia.
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35
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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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Pridmore PA, Hoffmann PH. The aerodynamic performance of the feathertail glider, Acrobates pygmaeus (Marsupialia: Acrobatidae). AUST J ZOOL 2014. [DOI: 10.1071/zo13071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Photographic and videographic investigations of the aerodynamic performance of four captive adult Acrobates pygmeus are described. During short (1–4 m) glides, steep angles of descent (>45°) and large angles of attack (up to 50°) were used mid-flight, and the possums failed to achieve steady velocities. During longer (>10 m) glides steady velocities of 5.3–7.5 m s–1 were achieved, and glide angles of 21–42° and angles of attack between 36° and 45° were used. The best (lowest) glide angles used at steady velocity were similar to those documented in sugar gliders, but involved lower air speeds. During steady gliding the forelimbs of Acrobates assumed an ‘elbows-out’ disposition similar to that of Petauroides volans, and unlike that of petaurid gliders. A glide polar for Acrobates shows that it uses lower air speeds and higher sinking speeds than other gliding animals for which polars are available (several birds and one bat). Few data on the radius of turn and sinking speed were obtained; nevertheless, in accord with theory, sinking speeds were higher during tighter turns. During flight the feather-like tail was used to generate pitching movements and adjust the angle of attack and hence glide angle. However, the control of turns seems to be achieved primarily through limb adjustments.
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37
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Deakin JE, Delbridge ML, Koina E, Harley N, Alsop AE, Wang C, Patel VS, Graves JAM. Reconstruction of the ancestral marsupial karyotype from comparative gene maps. BMC Evol Biol 2013; 13:258. [PMID: 24261750 PMCID: PMC4222502 DOI: 10.1186/1471-2148-13-258] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 11/19/2013] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n = 14 and 2n = 22 ancestral marsupial karyotype. RESULTS We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n = 14) and therian mammal (2n = 19) karyotypes to be reconstructed. CONCLUSIONS Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n = 14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome.
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Affiliation(s)
- Janine E Deakin
- ARC Centre of Excellence for Kangaroo Genomics, Canberra, Australia.
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38
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Beck RMD, Travouillon KJ, Aplin KP, Godthelp H, Archer M. The Osteology and Systematics of the Enigmatic Australian Oligo-Miocene Metatherian Yalkaparidon (Yalkaparidontidae; Yalkaparidontia; ?Australidelphia; Marsupialia). J MAMM EVOL 2013. [DOI: 10.1007/s10914-013-9236-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Frynta D, Šimková O, Lišková S, Landová E. Mammalian collection on Noah's Ark: the effects of beauty, brain and body size. PLoS One 2013; 8:e63110. [PMID: 23690985 PMCID: PMC3654911 DOI: 10.1371/journal.pone.0063110] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 03/28/2013] [Indexed: 11/19/2022] Open
Abstract
The importance of today's zoological gardens as the so-called "Noah's Ark" grows as the natural habitat of many species quickly diminishes. Their potential to shelter a large amount of individuals from many species gives us the opportunity to reintroduce a species that disappeared in nature. However, the selection of animals to be kept in zoos worldwide is highly selective and depends on human decisions driven by both ecological criteria such as population size or vulnerability and audience-driven criteria such as aesthetic preferences. Thus we focused our study on the most commonly kept and bred animal class, the mammals, and we asked which factors affect various aspects of the mammalian collection of zoos. We analyzed the presence/absence, population size, and frequency per species of each of the 123 mammalian families kept in the worldwide zoo collection. Our aim was to explain these data using the human-perceived attractiveness of mammalian families, their body weight, relative brain size and species richness of the family. In agreement with various previous studies, we found that the body size and the attractiveness of mammals significantly affect all studied components of the mammalian collection of zoos. There is a higher probability of the large and attractive families to be kept. Once kept, these animals are presented in larger numbers in more zoos. On the contrary, the relative mean brain size only affects the primary selection whether to keep the family or not. It does not affect the zoo population size or the number of zoos that keep the family.
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Affiliation(s)
- Daniel Frynta
- Department of Zoology, Faculty of Sciences, Charles University in Prague, Prague, Czech Republic.
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40
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The Bony Labyrinth in Diprotodontian Marsupial Mammals: Diversity in Extant and Extinct Forms and Relationships with Size and Phylogeny. J MAMM EVOL 2013. [DOI: 10.1007/s10914-013-9228-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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41
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Carlson KJ, Jashashvili T, Houghton K, Westaway MC, Patel BA. Joint loads in marsupial ankles reflect habitual bipedalism versus quadrupedalism. PLoS One 2013; 8:e58811. [PMID: 23554931 PMCID: PMC3595237 DOI: 10.1371/journal.pone.0058811] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 02/07/2013] [Indexed: 11/23/2022] Open
Abstract
Joint surfaces of limb bones are loaded in compression by reaction forces generated from body weight and musculotendon complexes bridging them. In general, joints of eutherian mammals have regions of high radiodensity subchondral bone that are better at resisting compressive forces than low radiodensity subchondral bone. Identifying similar form-function relationships between subchondral radiodensity distribution and joint load distribution within the marsupial postcranium, in addition to providing a richer understanding of marsupial functional morphology, can serve as a phylogenetic control in evaluating analogous relationships within eutherian mammals. Where commonalities are established across phylogenetic borders, unifying principles in mammalian physiology, morphology, and behavior can be identified. Here, we assess subchondral radiodensity patterns in distal tibiae of several marsupial taxa characterized by different habitual activities (e.g., locomotion). Computed tomography scanning, maximum intensity projection maps, and pixel counting were used to quantify radiodensity in 41 distal tibiae of bipedal (5 species), arboreal quadrupedal (4 species), and terrestrial quadrupedal (5 species) marsupials. Bipeds (Macropus and Wallabia) exhibit more expansive areas of high radiodensity in the distal tibia than arboreal (Dendrolagus, Phascolarctos, and Trichosurus) or terrestrial quadrupeds (Sarcophilus, Thylacinus, Lasiorhinus, and Vombatus), which may reflect the former carrying body weight only through the hind limbs. Arboreal quadrupeds exhibit smallest areas of high radiodensity, though they differ non-significantly from terrestrial quadrupeds. This could indicate slightly more compliant gaits by arboreal quadrupeds compared to terrestrial quadrupeds. The observed radiodensity patterns in marsupial tibiae, though their statistical differences disappear when controlling for phylogeny, corroborate previously documented patterns in primates and xenarthrans, potentially reflecting inferred limb use during habitual activities such as locomotion. Despite the complex nature of factors contributing to joint loads, broad observance of these patterns across joints and across a variety of taxa suggests that subchondral radiodensity can be used as a unifying form-function principle within Mammalia.
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Affiliation(s)
- Kristian J Carlson
- Institute for Human Evolution, University of the Witwatersrand, Johannesburg, South Africa.
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Gilbert C, Waters P, Feschotte C, Schaack S. Horizontal transfer of OC1 transposons in the Tasmanian devil. BMC Genomics 2013; 14:134. [PMID: 23445260 PMCID: PMC3621081 DOI: 10.1186/1471-2164-14-134] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 01/18/2013] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND There is growing recognition that horizontal DNA transfer, a process known to be common in prokaryotes, is also a significant source of genomic variation in eukaryotes. Horizontal transfer of transposable elements (HTT) may be especially prevalent in eukaryotes given the inherent mobility, widespread occurrence, and prolific abundance of these elements in many eukaryotic genomes. RESULTS Here, we provide evidence for a new case of HTT of the transposon family OposCharlie1 (OC1) in the Tasmanian devil, Sarcophilus harrisii. Bioinformatic analyses of OC1 sequences in the Tasmanian devil genome suggest that this transposon infiltrated the common ancestor of the Dasyuridae family ~17 million years ago. This estimate is corroborated by a PCR-based screen for the presence/absence of this family in Tasmanian devils and closely-related species. CONCLUSIONS This case of HTT is the first to be reported in dasyurids. It brings the number of animal lineages independently invaded by OC1 to 12, and adds a fourth continent to the pandemic-like pattern of invasion of this transposon. In the context of these data, we discuss the evolutionary history of this transposon family and its potential impact on the diversification of marsupials.
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Affiliation(s)
- Clement Gilbert
- Université de Poitiers, UMR CNRS 7267, Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France
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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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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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Beck RMD. An ‘ameridelphian’ marsupial from the early Eocene of Australia supports a complex model of Southern Hemisphere marsupial biogeography. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2012; 99:715-29. [DOI: 10.1007/s00114-012-0953-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/17/2012] [Accepted: 07/19/2012] [Indexed: 11/29/2022]
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Nilsson MA, Janke A, Murchison EP, Ning Z, Hallström BM. Expansion of CORE-SINEs in the genome of the Tasmanian devil. BMC Genomics 2012; 13:172. [PMID: 22559330 PMCID: PMC3403934 DOI: 10.1186/1471-2164-13-172] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 05/06/2012] [Indexed: 11/22/2022] Open
Abstract
Background The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species’ survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed element (SINE) retroposons. Results The temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b) that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus) around 14 million years ago. Conclusions The radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome.
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Affiliation(s)
- Maria A Nilsson
- LOEWE-Biodiversity and Climate Research Center, BiK-F, Senckenberganlage 25, Frankfurt am Main D-60325, Germany.
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Frankham GJ, Temple-Smith PD. Absence of mammary development in maleDromiciops gliroides: another link to the Australian marsupial fauna. J Mammal 2012. [DOI: 10.1644/11-mamm-a-282.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Yu W, Xu J, Wu Y, Yang G. A comparative study of mammalian diversification pattern. Int J Biol Sci 2012; 8:486-97. [PMID: 22457604 PMCID: PMC3314190 DOI: 10.7150/ijbs.3982] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 03/11/2012] [Indexed: 11/06/2022] Open
Abstract
Although mammals have long been regarded as a successful radiation, the diversification pattern among the clades is still poorly known. Higher-level phylogenies are conflicting and comprehensive comparative analyses are still lacking. Using a recently published supermatrix encompassing nearly all extant mammalian families and a novel comparative likelihood approach (MEDUSA), the diversification pattern of mammalian groups was examined. Both order- and family-level phylogenetic analyses revealed the rapid radiation of Boreoeutheria and Euaustralidelphia in the early mammalian history. The observation of a diversification burst within Boreoeutheria at approximately 100 My supports the Long Fuse model in elucidating placental diversification progress, and the rapid radiation of Euaustralidelphia suggests an important role of biogeographic dispersal events in triggering early Australian marsupial rapid radiation. Diversification analyses based on family-level diversity tree revealed seven additional clades with exceptional diversification rate shifts, six of which represent accelerations in net diversification rate as compared to the background pattern. The shifts gave origin to the clades Muridae+Cricetidae, Bovidae+Moschidae+Cervidae, Simiiformes, Echimyidae, Odontoceti (excluding Physeteridae+Kogiidae+Platanistidae), Macropodidae, and Vespertilionidae. Moderate to high extinction rates from background and boreoeutherian diversification patterns indicate the important role of turnovers in shaping the heterogeneous taxonomic richness observed among extant mammalian groups. Furthermore, the present results emphasize the key role of extinction on erasing unusual diversification signals, and suggest that further studies are needed to clarify the historical radiation of some mammalian groups for which MEDUSA did not detect exceptional diversification rates.
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Affiliation(s)
- Wenhua Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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Potter S, Cooper SJ, Metcalfe CJ, Taggart DA, Eldridge MD. Phylogenetic relationships of rock-wallabies, Petrogale (Marsupialia: Macropodidae) and their biogeographic history within Australia. Mol Phylogenet Evol 2012; 62:640-52. [DOI: 10.1016/j.ympev.2011.11.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Revised: 10/20/2011] [Accepted: 11/08/2011] [Indexed: 11/24/2022]
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Wilson-Wilde L, Norman J, Robertson J, Sarre S, Georges A. Australian marsupial species identification. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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