1
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Haines E, Bailey E, Nelson J, Fenlon LR, Suárez R. Clade-specific forebrain cytoarchitectures of the extinct Tasmanian tiger. Proc Natl Acad Sci U S A 2023; 120:e2306516120. [PMID: 37523567 PMCID: PMC10410726 DOI: 10.1073/pnas.2306516120] [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: 04/21/2023] [Accepted: 05/23/2023] [Indexed: 08/02/2023] Open
Abstract
The thylacine, or Tasmanian tiger, is the largest of modern-day carnivorous marsupials and was hunted to extinction by European settlers in Australia. Its physical resemblance to eutherian wolves is a striking example of evolutionary convergence to similar ecological niches. However, whether the neuroanatomical organization of the thylacine brain resembles that of canids and how it compares with other mammals remain unknown due to the scarcity of available samples. Here, we gained access to a century-old hematoxylin-stained histological series of a thylacine brain, digitalized it at high resolution, and compared its forebrain cellular architecture with 34 extant species of monotremes, marsupials, and eutherians. Phylogenetically informed comparisons of cortical folding, regional volumes, and cell sizes and densities across cortical areas and layers provide evidence against brain convergences with canids, instead demonstrating features typical of marsupials, and more specifically Dasyuridae, along with traits that scale similarly with brain size across mammals. Enlarged olfactory, limbic, and neocortical areas suggest a small-prey predator and/or scavenging lifestyle, similar to extant quolls and Tasmanian devils. These findings are consistent with a nonuniformity of trait convergences, with brain traits clustering more with phylogeny and head/body traits with lifestyle. By making this resource publicly available as rapid web-accessible, hierarchically organized, multiresolution images for perpetuity, we anticipate that additional comparative insights might arise from detailed studies of the thylacine brain and encourage researchers and curators to share, annotate, and preserve understudied material of outstanding biological relevance.
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Affiliation(s)
- Elizabeth Haines
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, QLD4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, QLD4072, Australia
| | - Evan Bailey
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, QLD4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, QLD4072, Australia
| | - John Nelson
- School of Biological Sciences, Monash University, Melbourne, Victoria, VIC3800, Australia
| | - Laura R. Fenlon
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, QLD4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, QLD4072, Australia
| | - Rodrigo Suárez
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, QLD4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, QLD4072, Australia
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2
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Dalal V, Pasupuleti N, Chaubey G, Rai N, Shinde V. Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide. Genes (Basel) 2023; 14:479. [PMID: 36833406 PMCID: PMC9956214 DOI: 10.3390/genes14020479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.
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Affiliation(s)
- Vasundhra Dalal
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | | | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Niraj Rai
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, Lucknow 226007, Uttar Pradesh, India
| | - Vasant Shinde
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
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3
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Beck RM, Voss RS, Jansa SA. Craniodental Morphology and Phylogeny of Marsupials. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.1206/0003-0090.457.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Robin M.D. Beck
- School of Science, Engineering and Environment University of Salford, U.K. School of Biological, Earth & Environmental Sciences University of New South Wales, Australia Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Sharon A. Jansa
- Bell Museum and Department of Ecology, Evolution, and Behavior University of Minnesota
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4
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Palandačić A, Kruckenhauser L, Ahnelt H, Mikschi E. European minnows through time: museum collections aid genetic assessment of species introductions in freshwater fishes (Cyprinidae: Phoxinus species complex). Heredity (Edinb) 2020; 124:410-422. [PMID: 31896822 DOI: 10.1038/s41437-019-0292-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 11/09/2022] Open
Abstract
Massive fish introductions have taken place throughout much of the world, mostly over the last 70 years, and present a major threat to the genetic diversity of native fishes. Introductions have been reported for European Phoxinus, a ubiquitous small cyprinid that populates a wide variety of habitats. Species delineation in European Phoxinus has proven difficult with one reason being ranges of distribution that often traverse drainage boundaries. The present study combines recent samples with museum samples to better understand the current distribution of Phoxinus species and their distributions prior to the massive introductions of fishes in Europe, and to evaluate the use of museum specimens for species distribution studies. For these purposes, genetic lineages from sites collected prior to 1900 (n = 14), and between 1900 and 1950 (n = 8), were analysed using two mitochondrial and nuclear markers. Although possible fish introductions were detected, our results show that the distribution of genetic lineages of museum samples is comparable to that of the extant lineages of European Phoxinus present in those areas. These observations suggest that in the studied ranges the distribution of Phoxinus lineages has been driven by natural processes.
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Affiliation(s)
- Anja Palandačić
- First Zoological Department, Vienna Museum of Natural History, Burgring 7, 1010, Vienna, Austria.
| | - Luise Kruckenhauser
- Laboratory of Molecular Systematics, Vienna Museum of Natural History, Burgring 7, 1010, Vienna, Austria
| | - Harald Ahnelt
- First Zoological Department, Vienna Museum of Natural History, Burgring 7, 1010, Vienna, Austria.,Department of Theoretical Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Ernst Mikschi
- First Zoological Department, Vienna Museum of Natural History, Burgring 7, 1010, Vienna, Austria
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5
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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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6
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Bösl E. [aDNA Research From a Historical Perspective]. NTM 2017; 25:99-142. [PMID: 28389681 DOI: 10.1007/s00048-017-0168-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
aDNA studies are a cooperative field of research with a broad range of applications including evolutionary biology, genetics, anthropology and archaeology. Scientists are using ancient molecules as source material for historical questions. Colleagues from the humanities are observing this with both interest and concern because aDNA research is affecting academic identities and both concepts of history and historiography. aDNA research developed in a way that can be described as a Hype Cycle (Chackie Fenn). Technological triggers such as Sanger Sequencing and the Polymerase Chain Reaction kicked off a multitude of experiments with ancient DNA during the 1980s and 1990s. Geneticists, microbiologists, anthropologists and many more euphorically joined a "molecule hunt". aDNA was promoted as a time machine. Media attention was enormous. As experiments and implementations began to fail and contamination was discovered to be a tremendous problem, media interest waned and many labs lost their interest. Some turned their disillusionment into systematic research into methodology and painstakingly established lab routines. The authenticity problem was first addressed by control oriented measures but later approached from a more cognitive theoretical perspective as the pitfalls and limits of aDNA became clearer. By the end of the 2000s the field reached its current plateau of productivity. Cross-disciplinary debates, conflicts and collaborations are increasing critical reflection among all participants. Historians should consider joining the field in a kind of critical friendship to both make the most of its possibilities and give an input from a constructivist perspective.
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Affiliation(s)
- Elsbeth Bösl
- Professur für Wirtschafts-, Sozial- und Technikgeschichte, Historisches Seminar, Universität der Bundeswehr München, Werner-Heisenberg-Weg 39, 85577, Neubiberg, Deutschland.
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7
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Druzhkova AS, Vorobieva NV, Trifonov VA, Graphodatsky AS. Ancient DNA: Results and prospects (The 30th anniversary). RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415060046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Flores DA, Abdala F, Martin GM, Giannini NP, Martinez JM. Post-Weaning Cranial Growth in Shrew Opossums (Caenolestidae): A Comparison with Bandicoots (Peramelidae) and Carnivorous Marsupials. J MAMM EVOL 2014. [DOI: 10.1007/s10914-014-9279-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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9
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Yates AM. New craniodental remains of Thylacinus potens (Dasyuromorphia: Thylacinidae), a carnivorous marsupial from the late Miocene Alcoota Local Fauna of central Australia. PeerJ 2014; 2:e547. [PMID: 25237601 PMCID: PMC4157238 DOI: 10.7717/peerj.547] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 08/07/2014] [Indexed: 12/02/2022] Open
Abstract
New craniodental specimens that are referrable to the thylacinid marsupial, Thylacinus potens, are described from the late Miocene Alcoota Local Fauna of the Northern Territory, Australia. The remains include a largely complete maxilla and dentary, showing for the first time the anterior dentition of the dentary. The new remains indicate that Th. potens was a more variable species than previously recognised. The dentary, in particular, is more gracile, than other specimens referred to this species. A revised apomorphy-based diagnosis of Th. potens that takes this variability into account is presented. A cladistic analysis supports previous analyses that placed Th. potens in a derived position within Thylacinidae, close to the modern Th. cynocephalus. New estimations of body size are made using published regressions of dental measurements of dasyuromorphians as well as by assuming geometric similitude with Th. cynocephalus. All methods produce body mass estimates in excess of 35 kg.
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Affiliation(s)
- Adam M Yates
- Museums and Art Galleries of the Northern Territory , Museum of Central Australia, Alice Springs, Northern Territory , Australia
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10
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Attard MRG, Parr WCH, Wilson LAB, Archer M, Hand SJ, Rogers TL, Wroe S. Virtual reconstruction and prey size preference in the mid Cenozoic thylacinid, Nimbacinus dicksoni (Thylacinidae, Marsupialia). PLoS One 2014; 9:e93088. [PMID: 24718109 PMCID: PMC3981708 DOI: 10.1371/journal.pone.0093088] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 03/01/2014] [Indexed: 11/18/2022] Open
Abstract
Thylacinidae is an extinct family of Australian and New Guinean marsupial carnivores, comprizing 12 known species, the oldest of which are late Oligocene (∼24 Ma) in age. Except for the recently extinct thylacine (Thylacinus cynocephalus), most are known from fragmentary craniodental material only, limiting the scope of biomechanical and ecological studies. However, a particularly well-preserved skull of the fossil species Nimbacinus dicksoni, has been recovered from middle Miocene (∼16-11.6 Ma) deposits in the Riversleigh World Heritage Area, northwestern Queensland. Here, we ask whether N. dicksoni was more similar to its recently extinct relative or to several large living marsupials in a key aspect of feeding ecology, i.e., was N. dicksoni a relatively small or large prey specialist. To address this question we have digitally reconstructed its skull and applied three-dimensional Finite Element Analysis to compare its mechanical performance with that of three extant marsupial carnivores and T. cynocephalus. Under loadings adjusted for differences in size that simulated forces generated by both jaw closing musculature and struggling prey, we found that stress distributions and magnitudes in the skull of N. dicksoni were more similar to those of the living spotted-tailed quoll (Dasyurus maculatus) than to its recently extinct relative. Considering the Finite Element Analysis results and dental morphology, we predict that N. dicksoni likely occupied a broadly similar ecological niche to that of D. maculatus, and was likely capable of hunting vertebrate prey that may have exceeded its own body mass.
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Affiliation(s)
- Marie R. G. Attard
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Function, Evolution and Anatomy Research laboratory, Zoology, School of Environmental and Rural Sciences, University of New England, New South Wales, Australia
- * E-mail:
| | - William C. H. Parr
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Laura A. B. Wilson
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael Archer
- Evolution of Earth and Life Sciences Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Suzanne J. Hand
- Evolution of Earth and Life Sciences Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Tracey L. Rogers
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Stephen Wroe
- Function, Evolution and Anatomy Research laboratory, Zoology, School of Environmental and Rural Sciences, University of New England, New South Wales, Australia
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11
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Flores DA, Abdala F, Giannini NP. Post-weaning cranial ontogeny in two bandicoots (Mammalia, Peramelomorphia, Peramelidae) and comparison with carnivorous marsupials. ZOOLOGY 2013; 116:372-84. [DOI: 10.1016/j.zool.2013.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 06/26/2013] [Accepted: 07/28/2013] [Indexed: 12/15/2022]
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12
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Paijmans JL, Gilbert MTP, Hofreiter M. Mitogenomic analyses from ancient DNA. Mol Phylogenet Evol 2013; 69:404-16. [DOI: 10.1016/j.ympev.2012.06.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 05/27/2012] [Accepted: 06/04/2012] [Indexed: 10/28/2022]
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13
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Zemann A, Churakov G, Donnellan S, Grützner F, Zhao F, Brosius J, Schmitz J. Ancestry of the Australian termitivorous numbat. Mol Biol Evol 2013; 30:1041-5. [PMID: 23429857 DOI: 10.1093/molbev/mst032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Australian numbat, Myrmecobius fasciatus, is the only marsupial that feeds almost exclusively on termites and that has a life following the diurnally restricted and dynamic geographical distribution of termites. The millions of years of this adaptation led to unique morphological and anatomical features, especially basicranial and dental characteristics, that make it difficult to identify a clear phylogenetic affiliation to other marsupials. From DNA sequence analyses, the family Myrmecobiidae is placed within the dasyuromorph marsupials, but the exact position varies from study to study, and support values are mostly rather modest. Here, we report the recovery and analysis of approximately 110,000 quasifossilized traces of mobile element insertions into the genome of a dasyurid marsupial (Tasmanian devil), 25 of which are phylogenetically informative for early dasyuromorphial evolution. Fourteen of these ancient retroposon insertions are shared by the 16 Dasyuromorphia species analyzed, including the numbat, but are absent in the outgroups. An additional 11 other insertions are present in all Dasyuridae but are absent in the numbat. These findings place numbats as the sister group to all living Dasyuridae and show that the investigated Dasyuromorphia, including the Myrmecobiidae, constitutes a monophyletic group that is separated from Peramelemorphia, Notoryctemorphia, and other marsupials.
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Affiliation(s)
- Anja Zemann
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
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14
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Rizzi E, Lari M, Gigli E, De Bellis G, Caramelli D. Ancient DNA studies: new perspectives on old samples. Genet Sel Evol 2012; 44:21. [PMID: 22697611 PMCID: PMC3390907 DOI: 10.1186/1297-9686-44-21] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 06/14/2012] [Indexed: 11/24/2022] Open
Abstract
In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.
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Affiliation(s)
- Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, Via F.lli Cervi 93, Segrate, Milan 20090, Italy
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15
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Menzies BR, Renfree MB, Heider T, Mayer F, Hildebrandt TB, Pask AJ. Limited genetic diversity preceded extinction of the Tasmanian tiger. PLoS One 2012; 7:e35433. [PMID: 22530022 PMCID: PMC3329426 DOI: 10.1371/journal.pone.0035433] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 03/16/2012] [Indexed: 11/22/2022] Open
Abstract
The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived specimens collected between 102 and 159 years ago. We examined a portion of the mitochondrial DNA hyper-variable control region and determined that all sequences were on average 99.5% identical at the nucleotide level. As a measure of accuracy we also sequenced mitochondrial DNA from a mother and two offspring. As expected, these samples were found to be 100% identical, validating our methods. We also used 454 sequencing to reconstruct 2.1 kilobases of the mitochondrial genome, which shared 99.91% identity with the two complete thylacine mitochondrial genomes published previously. Our thylacine genomic data also contained three highly divergent putative nuclear mitochondrial sequences, which grouped phylogenetically with the published thylacine mitochondrial homologs but contained 100-fold more polymorphisms than the conserved fragments. Together, our data suggest that the thylacine population in Tasmania had limited genetic diversity prior to its extinction, possibly as a result of their geographic isolation from mainland Australia approximately 10,000 years ago.
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16
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Abstract
Natural history museums around the world hold millions of animal and plant specimens that are potentially amenable to genetic analyses. With more and more populations and species becoming extinct, the importance of these specimens for phylogenetic and phylogeographic analyses is rapidly increasing. However, as most DNA extraction methods damage the specimens, nondestructive extraction methods are useful to balance the demands of molecular biologists, morphologists, and museum curators. Here, I describe a method for nondestructive DNA extraction from bony specimens (i.e., bones and teeth). In this method, the specimens are soaked in extraction buffer, and DNA is then purified from the soaking solution using adsorption to silica. The method reliably yields mitochondrial and often also nuclear DNA. The method has been adapted to DNA extraction from other types of specimens such as arthropods.
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Affiliation(s)
- Michael Hofreiter
- Department of Biology, The University of York, Wentworth Way, Heslington, York, YO10 5DD, UK.
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17
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Berglund EC, Kiialainen A, Syvänen AC. Next-generation sequencing technologies and applications for human genetic history and forensics. INVESTIGATIVE GENETICS 2011; 2:23. [PMID: 22115430 PMCID: PMC3267688 DOI: 10.1186/2041-2223-2-23] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 11/24/2011] [Indexed: 12/24/2022]
Abstract
Rapid advances in the development of sequencing technologies in recent years have enabled an increasing number of applications in biology and medicine. Here, we review key technical aspects of the preparation of DNA templates for sequencing, the biochemical reaction principles and assay formats underlying next-generation sequencing systems, methods for imaging and base calling, quality control, and bioinformatic approaches for sequence alignment, variant calling and assembly. We also discuss some of the most important advances that the new sequencing technologies have brought to the fields of human population genetics, human genetic history and forensic genetics.
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Affiliation(s)
- Eva C Berglund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Anna Kiialainen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
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18
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Spencer PBS, Schmidt D, Hummel S. Identification of historical specimens and wildlife seizures originating from highly degraded sources of kangaroos and other macropods. Forensic Sci Med Pathol 2010; 6:225-32. [PMID: 19890738 PMCID: PMC3128748 DOI: 10.1007/s12024-009-9119-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2009] [Indexed: 11/22/2022]
Abstract
Forensic investigations are an important area in the regulation of food mis-description, wildlife seizures and the international trade in wildlife and its products. An early, but important stage in dealing with many biological materials that are submitted for forensic scrutiny is species identification. We describe a method and new primers to amplify three small DNA fragments of the cytochrome b region of the mitochondrial DNA that are suitable for marsupial species identification from degraded sources, such as wildlife seizures. They were designed as consensus sequences from a comparison of 21 marsupial species. The primers also contained sequences intended specifically not to amplify human DNA, thereby reducing the likelihood of amplifying contaminants. Examples of the utility of these primers are given using a range of conditions that may be applied using such an approach, including (1) field-collected sub-fossil bones, (2) an example of museum mis-identification from a specimen collected in 1930 and (3) a skull collected from Bernier Island, in the harsh mid-west of Western Australia.
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Affiliation(s)
- P B S Spencer
- School of Biological Sciences and Biotechnology, Wildlife Forensic Laboratory, Murdoch University, Perth, Western Australia, Australia.
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19
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Computational challenges in the analysis of ancient DNA. Genome Biol 2010; 11:R47. [PMID: 20441577 PMCID: PMC2898072 DOI: 10.1186/gb-2010-11-5-r47] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 01/05/2010] [Accepted: 05/06/2010] [Indexed: 11/28/2022] Open
Abstract
A new method of next-generation sequencing analysis is presented which takes into account the biases characteristic of ancient, including Neandertal, DNA samples. High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering.
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20
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Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, Packard M, Zhang Y, McClellan LR, Qi J, Zhao F, Gilbert MTP, Dalén L, Arsuaga JL, Ericson PGP, Huson DH, Helgen KM, Murphy WJ, Götherström A, Schuster SC. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Res 2009; 19:213-20. [PMID: 19139089 DOI: 10.1101/gr.082628.108] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%-15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples' heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes.
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Affiliation(s)
- Webb Miller
- Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania 16802, USA.
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KRAJEWSKI CAREY, WROE STEPHEN, WESTERMAN MICHAEL. Molecular evidence for the pattern and timing of cladogenesis in dasyurid marsupials. Zool J Linn Soc 2008. [DOI: 10.1111/j.1096-3642.2000.tb01635.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Krajewski C, Torunsky R, Sipiorski JT, Westerman M. Phylogenetic Relationships of the Dasyurid Marsupial Genus Murexia. J Mammal 2007. [DOI: 10.1644/06-mamm-a-310r.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Abstract
Twenty years after the advent of ancient DNA studies, this discipline seems to have reached the maturity formerly lacking to the fulfilment of its objectives. In its early development paleogenetics, as it is now acknowledged, had to cope with very limited data due to the technical limitations of molecular biology. It led to phylogenetic assumptions often limited in their scope and sometimes non-focused or even spurious results that cast the reluctance of the scientific community. This time seems now over and huge amounts of sequences have become available which overcome the former limitations and bridge the gap between paleogenetics, genomics and population biology. The recent studies over the charismatic woolly mammoth (independent sequencing of the whole mitochondrial genome and of millions of base pairs of the nuclear genome) exemplify the growing accuracy of ancient DNA studies thanks to new molecular approaches. From the earliest publications up to now, the number of mammoth nucleotides was multiplied by 100,000. Likewise, populational approaches of ice-age taxa provide new historical scenarios about the diversification and extinction of the Pleistocene megafauna on the one hand, and about the processes of domestication of animal and vegetal species by Man on the other. They also shed light on the differential structure of molecular diversity between short-term populational research (below 2 My) and long-term (over 2 My) phylogenetic approaches. All those results confirm the growing importance of paleogenetics among the evolutionary biology disciplines.
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Affiliation(s)
- Régis Debruyne
- Muséum National d'Histoire Naturelle, Département Histoire de la Terre, UMR 5143 CNRS, Paléobiodiversité, 57, rue Cuvier, 75231 Paris Cedex 05, France
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Phillips MJ, McLenachan PA, Down C, Gibb GC, Penny D. Combined Mitochondrial and Nuclear DNA Sequences Resolve the Interrelations of the Major Australasian Marsupial Radiations. Syst Biol 2006; 55:122-37. [PMID: 16507529 DOI: 10.1080/10635150500481614] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Australasian marsupials include three major radiations, the insectivorous/carnivorous Dasyuromorphia, the omnivorous bandicoots (Peramelemorphia), and the largely herbivorous diprotodontians. Morphologists have generally considered the bandicoots and diprotodontians to be closely related, most prominently because they are both syndactylous (with the 2nd and 3rd pedal digits being fused). Molecular studies have been unable to confirm or reject this Syndactyla hypothesis. Here we present new mitochondrial (mt) genomes from a spiny bandicoot (Echymipera rufescens) and two dasyurids, a fat-tailed dunnart (Sminthopsis crassicaudata) and a northern quoll (Dasyurus hallucatus). By comparing trees derived from pairwise base-frequency differences between taxa with standard (absolute, uncorrected) distance trees, we infer that composition bias among mt protein-coding and RNA sequences is sufficient to mislead tree reconstruction. This can explain incongruence between trees obtained from mt and nuclear data sets. However, after excluding major sources of compositional heterogeneity, both the "reduced-bias" mt and nuclear data sets clearly favor a bandicoot plus dasyuromorphian association, as well as a grouping of kangaroos and possums (Phalangeriformes) among diprotodontians. Notably, alternatives to these groupings could only be confidently rejected by combining the mt and nuclear data. Elsewhere on the tree, Dromiciops appears to be sister to the monophyletic Australasian marsupials, whereas the placement of the marsupial mole (Notoryctes) remains problematic. More generally, we contend that it is desirable to combine mt genome and nuclear sequences for inferring vertebrate phylogeny, but as separately modeled process partitions. This strategy depends on detecting and excluding (or accounting for) major sources of non-historical signal, such as from compositional non-stationarity. [Base composition; combined data; marsupial; mitochondrial genome; phylogeny.].
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Affiliation(s)
- Matthew J Phillips
- Henry Wellcome Ancient Biomolecules Center, Department of Zoology, Oxford University, South Parks Road, Oxford OX1 3PS, United Kingdom.
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25
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Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M. Genetic Analyses from Ancient DNA. Annu Rev Genet 2004; 38:645-79. [PMID: 15568989 DOI: 10.1146/annurev.genet.37.110801.143214] [Citation(s) in RCA: 654] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
About 20 years ago, DNA sequences were separately described from the quagga (a type of zebra) and an ancient Egyptian individual. What made these DNA sequences exceptional was that they were derived from 140- and 2400-year-old specimens. However, ancient DNA research, defined broadly as the retrieval of DNA sequences from museum specimens, archaeological finds, fossil remains, and other unusual sources of DNA, only really became feasible with the advent of techniques for the enzymatic amplification of specific DNA sequences. Today, reports of analyses of specimens hundreds, thousands, and even millions of years old are almost commonplace. But can all these results be believed? In this paper, we critically assess the state of ancient DNA research. In particular, we discuss the precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences. We also highlight some significant results and areas of promising future research.
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Affiliation(s)
- Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, D-04013 Leipzig, Germany.
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26
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Amrine-Madsen H, Scally M, Westerman M, Stanhope MJ, Krajewski C, Springer MS. Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials. Mol Phylogenet Evol 2003; 28:186-96. [PMID: 12878458 DOI: 10.1016/s1055-7903(03)00122-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Relationships among the seven extant orders of marsupials remain poorly understood. Most classifications recognize a fundamental split between Ameridelphia, which contains the American orders Didelphimorphia and Paucituberculata, and Australidelphia, which contains four Australasian orders (Dasyuromorphia, Diprotodontia, Notoryctemorphia, and Peramelina) and the South American order Microbiotheria, represented by Dromiciops gliroides. Ameridelphia and Australidelphia are each supported by key morphological characters with dichotomous character states. To date, molecular studies indexing all marsupial orders have reported inconclusive results. However, several studies have suggested that Dromiciops is nested within Australidelphia. This result has important implications for understanding the biogeographic history of living marsupials. To address questions in higher-level marsupial systematics, we sequenced portions of five nuclear genes (Apolipoprotein B gene; Breast and Ovarian cancer susceptibility gene 1; Recombination activating gene 1; Interphotoreceptor retinoid binding protein gene; and von Willebrand factor gene) for representatives of all orders of marsupials, as well as placental outgroups. The resulting 6.4kb concatenation was analyzed using maximum parsimony, distance methods, maximum likelihood, and Bayesian methods. tests were used to examine a priori hypotheses. All analyses provided robust support for the monophyly of Australidelphia (bootstrap support=99-100%; posterior probability=1.00). Ameridelphia received much lower support, although this clade was not rejected in statistical tests. Within Diprotodontia, both Vombatiformes and Phalangeriformes were supported at the 100% bootstrap level and with posterior probabilities of 1.00.
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Van Den Bussche RA, Reeder SA, Hansen EW, Hoofer SR. Utility of the dentin matrix protein 1 (DMP1) gene for resolving mammalian intraordinal phylogenetic relationships. Mol Phylogenet Evol 2003; 26:89-101. [PMID: 12470941 DOI: 10.1016/s1055-7903(02)00297-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We sequenced exon 6 of the nuclear dentin matrix protein 1 (DMP1) gene from 19 species of bats (order Chiroptera) to assess the utility of this gene for higher-level phylogenetic studies. Bayesian analysis revealed high support (posterior probabilities >/=0.95) for monophyly of Noctilionoidea (Phyllostomidae, Noctilionidae, and Mormoopidae), all genera and most families examined. Comparison of the phylogenetic information present in DMP1 with mitochondrial rDNA and nuclear RAG2 genes indicated no significant heterogeneity. Thus, we concatenated these three data sets into a single "total evidence" phylogenetic analysis. Combined analysis was congruent with study of RAG2 and combined RAG2 and mtrDNA sequences, but improved support (Bayesian posterior probabilities) for many nodes. Our results indicate that exon 6 of DMP1 is rapidly evolving, able to tolerate non-frame shifting insertion and deletion events, is more variable than RAG2, and provides phylogenetic resolution from the interfamilial to infraclass levels in mammals.
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Affiliation(s)
- Ronald A Van Den Bussche
- Department of Zoology and Collection of Vertebrates, 430 Life Sciences West, Oklahoma State University, Stillwater, OK 74078, USA.
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Van Den Bussche RA, Hoofer SR, Hansen EW. Characterization and phylogenetic utility of the mammalian protamine p1 gene. Mol Phylogenet Evol 2002; 22:333-41. [PMID: 11884158 DOI: 10.1006/mpev.2001.1051] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We sequenced the protamine P1 gene (ca. 450 bp) from 20 bats (order Chiroptera) and the flying lemur (order Dermoptera). We compared these sequences with published sequences from 19 other mammals representing seven orders (Artiodactyla, Carnivora, Cetacea, Perissodactyla, Primates, Proboscidea, and Rodentia) to assess structure, base compositional bias, and phylogenetic utility. Approximately 80% of second codon positions were guanine, resulting in protamine proteins containing a high frequency of arginine residues. Our data indicate that codon usage for arginine differs among higher mammalian taxa. Parsimony analysis of 40 species representing nine orders produced a well-resolved tree in which most nodes were supported strongly, except at the lowest taxonomic levels (e.g., within Artiodactyla and Vespertilionidae). These data support monophyly of several taxa proposed by morphologic and molecular studies (all nine orders: Laurasiatheria, Cetartiodactytla, Yangochiroptera, Noctilionoidea, Rhinolophoidea, Vespertilionoidea, Phyllostomidae, Natalidae, and Vespertilionidae) and, in agreement with recent molecular studies, reject monophyly of Archonta, Volitantia, and Microchiroptera. Bats were sister to a clade containing Perissodactyla, Carnivora, and Cetartiodactyla, and, although not unequivocally, rhinolophoid bats (traditional microchiropterans) were sister to megachiropterans. Sequences of the protamine P1 gene are useful for resolving relationships at and above the familial level in bats, and generally within and among mammalian orders, but with some drawbacks. The coding and intervening sequences are small, producing few phylogenetically informative characters, and aligning the intron is difficult, even among closely related families. Given these caveats, the protamine P1 gene may be important to future systematic studies because its functional and evolutionary constraints differ from other genes currently used in systematic studies.
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Affiliation(s)
- Ronald A Van Den Bussche
- Department of Zoology and Collection of Vertebrates, 430 LSW, Oklahoma State University, Stillwater, Oklahoma 74078, USA.
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Abstract
DNA that has been recovered from archaeological and palaeontological remains makes it possible to go back in time and study the genetic relationships of extinct organisms to their contemporary relatives. This provides a new perspective on the evolution of organisms and DNA sequences. However, the field is fraught with technical pitfalls and needs stringent criteria to ensure the reliability of results, particularly when human remains are studied.
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Affiliation(s)
- M Hofreiter
- Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103 Leipzig, Germany
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Wroe S, Ebach M, Ahyong S, Muizon CD, Muirhead J. CLADISTIC ANALYSIS OF DASYUROMORPHIAN (MARSUPIALIA) PHYLOGENY USING CRANIAL AND DENTAL CHARACTERS. J Mammal 2000. [DOI: 10.1644/1545-1542(2000)081<1008:caodmp>2.0.co;2] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Colgan DJ. Phylogenetic studies of marsupials based on phosphoglycerate kinase DNA sequences. Mol Phylogenet Evol 1999; 11:13-26. [PMID: 10082607 DOI: 10.1006/mpev.1998.0553] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phosphoglycerate kinase sequences were obtained for 313 aligned bases of 41 individuals from 39 marsupial species. In contrast to previous molecular analyses, the relationships suggested by these data show a high level of congruence with morphologically defined orders and families. Four main monophyletic lineages are recognizable. These are the monogeneric orders Microbiotheria (Dromiciops australis) and Notoryctemorphia (Notoryctes typhlops), a grouping of the American orders Didelphimorphia and Paucituberculata, and the Australasian species other than N. typhlops. Within the Australasian lineage, there are again four main monophyletic groups; the Dasyuridae, two peramelemorph (bandicoot) lineages (one comprised of pseudogene sequences) and the Diprotodontia. This topology is not greatly affected by the exclusion of pseudogenes except that a clade of syndactylous species (Peramelemorphia plus Diprotodontia) is recovered. Two other peramelemorph pseudogenes have inserts of about 1 kb with high levels of similarity to LINE 1 elements. The Diprotodontia is notable for its relative lack of intersequence variation in comparison to the Dasyuromorphia.
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Affiliation(s)
- D J Colgan
- Ken and Yasuko Myer Molecular Evolutionary Biology Unit, Australian Museum, 6 College Street, Sydney, 2000, Australia.
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Springer MS, Westerman M, Kavanagh JR, Burk A, Woodburne MO, Kao DJ, Krajewski C. The origin of the Australasian marsupial fauna and the phylogenetic affinities of the enigmatic monito del monte and marsupial mole. Proc Biol Sci 1998; 265:2381-6. [PMID: 9921677 PMCID: PMC1689543 DOI: 10.1098/rspb.1998.0587] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Alternative hypotheses in higher-level marsupial systematics have different implications for marsupial origins, character evolution, and biogeography. Resolving the position of the South American monito del monte (Order Microbiotheria) is of particular importance in that alternate hypotheses posit sister-group relationships between microbiotheres and taxa with disparate temporal and geographic distributions: pediomyids; didelphids; dasyuromorphians; diprotodontians; all other australidelphians; and all other marsupials. Among Australasian marsupials, the placement of bandicoots is critical; competing views associate bandicoots with particular Australasian taxa (diprotodontians, dasyuromorphians) or outside of a clade that includes all other Australasian forms and microbiotheres. Affinities of the marsupial mole are also unclear. The mole is placed in its own order (Notoryctemorphia) and sister-group relationships have been postulated between it and each of the other Australasian orders. We investigated relationships among marsupial orders by using a data set that included mitochondrial and nuclear genes. Phylogenetic analyses provide support for the association of microbiotheres with Australasian marsupials and an association of the marsupial mole with dasyuromorphs. Statistical tests reject the association of diprotodontians and bandicoots together as well as the monophyly of Australasian marsupials. The origin of the paraphyletic Australasian marsupial fauna may be accounted for by (i) multiple entries of australidelphians into Australia or (ii) bidirectional dispersal of australidelphians between Antarctica and Australia.
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Affiliation(s)
- M S Springer
- Department of Biology, University of California, Riverside 92521, USA.
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Springer MS, Burk A, Kavanagh JR, Waddell VG, Stanhope MJ. The interphotoreceptor retinoid binding protein gene in therian mammals: implications for higher level relationships and evidence for loss of function in the marsupial mole. Proc Natl Acad Sci U S A 1997; 94:13754-9. [PMID: 9391099 PMCID: PMC28379 DOI: 10.1073/pnas.94.25.13754] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/1997] [Indexed: 02/05/2023] Open
Abstract
The subclass Theria of Mammalia includes marsupials (infraclass Metatheria) and placentals (infraclass Eutheria). Within each group, interordinal relationships remain unclear. One limitation of many studies is incomplete ordinal representation. Here, we analyze DNA sequences for part of exon 1 of the interphotoreceptor retinoid binding protein gene, including 10 that are newly reported, for representatives of all therian orders. Among placentals, the most robust clades are Cetartiodactyla, Paenungulata, and an expanded African clade that includes paenungulates, tubulidentates, and macroscelideans. Anagalida, Archonta, Altungulata, Hyracoidea + Perissodactyla, Ungulata, and the "flying primate" hypothesis are rejected by statistical tests. Among marsupials, the most robust clade includes all orders except Didelphimorphia. The phylogenetic placement of the monito del monte and the marsupial mole remains unclear. However, the marsupial mole sequence contains three frameshift indels and numerous stop codons in all three reading frames. Given that the interphotoreceptor retinoid binding protein gene is a single-copy gene that functions in the visual cycle and that the marsupial mole is blind with degenerate eyes, this finding suggests that phenotypic degeneration of the eyes is accompanied by parallel changes at the molecular level as a result of relaxed selective constraints.
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Affiliation(s)
- M S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA
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Krajewski C, Blacket M, Buckley L, Westerman M. A multigene assessment of phylogenetic relationships within the dasyurid marsupial subfamily Sminthopsinae. Mol Phylogenet Evol 1997; 8:236-48. [PMID: 9299228 DOI: 10.1006/mpev.1997.0421] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We report sequences of the mitochondrial cytochrome b (1146 bp) and 12S rRNA (961 bp) genes, as well as the nuclear protamine P1 (608 bp) gene, from 13 species representing all four genera of the dasyurid marsupial subfamily Sminthopsinae. Mitochondrial sequences are partitioned into five categories (three codon positions in cytochrome b, and stems and loops in 12S rRNA) with distinct substitution rates, transition biases, and base compositions. We extract estimates of these biases from the sequences and employ them to calculate two overall distances based on the DNAML model. Phylogenetic analyses using distance and parsimony methods yield trees with different topologies for mtDNA and protamine. These trees are compatible with respect to highly resolved nodes, but incompatible with respect to length differences in a parsimony framework. The tree from combined-data analysis is dominated by the larger data set (mtDNA). The balance of evidence favors a basal separation of Planigale from other sminthopsines. Within Planigale, Pl. maculata is sister to the remaining species. Although the precise intergeneric affinities of Antechinomys are unresolved, A. laniger does not appear to be part of the genus Sminthopsis as suggested by morphological data. The 12S rRNA resolves Ningaui ridei and N. yvonnae as sister species.
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Affiliation(s)
- C Krajewski
- Department of Zoology, Southern Illinois University, Carbondale, Illinois, 62901-6501, USA.
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