1
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The tails of two invasive species: genetic responses to acute and chronic bottlenecks. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02844-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractGenetic diversity can affect population viability and can be reduced by both acute and chronic mechanisms. Using the history of the establishment and management of two invasive rat species on Tetiaroa atoll, French Polynesia, we investigated the intensity and longevity of contrasting population bottleneck mechanisms on genetic diversity and bottleneck signal. Using microsatellite loci we show how both a chronic reduction over approximately 50 years of a Rattus exulans population caused by the arrival of its competitor R. rattus, and an acute reduction in a R. rattus population caused by a failed eradication approximately 10 years ago, caused similar magnitudes of genetic diversity loss. Furthermore, these strong bottleneck signals were in addition to the lasting signal from initial colonisation by each species many decades to centuries earlier, characterising a genetic paradox of biological invasion. These findings have implications for the study of population genetics of invasive species, and underscore how important historical context of population dynamics is when interpreting snapshots of genetic diversity.
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2
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Setzke C, Wong C, Russello MA. Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon. Sci Rep 2021; 11:22798. [PMID: 34815428 PMCID: PMC8611073 DOI: 10.1038/s41598-021-01958-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
Historical DNA analysis of archival samples has added new dimensions to population genetic studies, enabling spatiotemporal approaches for reconstructing population history and informing conservation management. Here we tested the efficacy of Genotyping-in-Thousands by sequencing (GT-seq) for collecting targeted single nucleotide polymorphism genotypic data from archival scale samples, and applied this approach to a study of kokanee salmon (Oncorhynchus nerka) in Kluane National Park and Reserve (KNPR; Yukon, Canada) that underwent a severe 12-year population decline followed by a rapid rebound. We genotyped archival scales sampled pre-crash and contemporary fin clips collected post-crash, revealing high coverage (> 90% average genotyping across all individuals) and low genotyping error (< 0.01% within-libraries, 0.60% among-libraries) despite the relatively poor quality of recovered DNA. We observed slight decreases in expected heterozygosity, allelic diversity, and effective population size post-crash, but none were significant, suggesting genetic diversity was retained despite the severe demographic contraction. Genotypic data also revealed the genetic distinctiveness of a now extirpated population just outside of KNPR, revealing biodiversity loss at the northern edge of the species distribution. More broadly, we demonstrated GT-seq as a valuable tool for collecting genome-wide data from archival samples to address basic questions in ecology and evolution, and inform applied research in wildlife conservation and fisheries management.
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Affiliation(s)
- Christopher Setzke
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, V1V 1V7, Canada
| | - Carmen Wong
- Parks Canada Yukon Field Unit, Suite 205 - 300 Main St, Whitehorse, YT, Y1A 2B5, Canada
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, V1V 1V7, Canada.
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3
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Rovinsky DS, Evans AR, Adams JW. Functional ecological convergence between the thylacine and small prey-focused canids. BMC Ecol Evol 2021; 21:58. [PMID: 33882837 PMCID: PMC8059158 DOI: 10.1186/s12862-021-01788-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 04/08/2021] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Morphological convergence is a fundamental aspect of evolution, allowing for inference of the biology and ecology of extinct species by comparison with the form and function of living species as analogues. The thylacine (Thylacinus cynocephalus), the iconic recently extinct marsupial, is considered a classic example of convergent evolution with the distantly related placental wolf or dog, though almost nothing is actually known regarding its ecology. This lack of data leads to questions regarding the degree of convergence with, and the similarity of, the functional ecology of the thylacine and the wolf/dog. Here, we examined the cranium of the thylacine using 3D geometric morphometrics and two quantitative tests of convergence to more precisely determine convergent analogues, within a phylogenetically informed dataset of 56 comparative species across 12 families of marsupial and placental faunivorous mammals. Using this dataset, we investigated patterns of correlation between cranial shape and diet, phylogeny, and relative prey size across these terrestrial faunivores. RESULTS We find a correlation between cranial, facial, and neurocranial shape and the ratio of prey-to-predator body mass, though neurocranial shape may not correlate with prey size within marsupials. The thylacine was found to group with predators that routinely take prey smaller than 45% of their own body mass, not with predators that take subequal-sized or larger prey. Both convergence tests find significant levels of convergence between the thylacine and the African jackals and South American 'foxes', with lesser support for the coyote and red fox. We find little support for convergence between the thylacine and the wolf or dog. CONCLUSIONS Our study finds little support for a wolf/dog-like functional ecology in the thylacine, with it instead being most similar to mid-sized canids such as African jackals and South American 'foxes' that mainly take prey less than half their size. This work suggests that concepts of convergence should extend beyond superficial similarity, and broader comparisons can lead to false interpretations of functional ecology. The thylacine was a predator of small to mid-sized prey, not a big-game specialist like the placental wolf.
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Affiliation(s)
- Douglass S Rovinsky
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Alistair R Evans
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.,Geosciences, Museums Victoria, Melbourne, VIC, Australia
| | - Justin W Adams
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Geosciences, Museums Victoria, Melbourne, VIC, Australia
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4
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Patzold F, Zilli A, Hundsdoerfer AK. Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens. PLoS One 2020; 15:e0235222. [PMID: 32639972 PMCID: PMC7343169 DOI: 10.1371/journal.pone.0235222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/10/2020] [Indexed: 11/19/2022] Open
Abstract
Here we present and justify an approach for minimal-destructive DNA extraction from historic insect specimens for next generation sequencing applications. An increasing number of studies use insects from museum collections for biodiversity research. However, the availability of specimens for molecular analyses has been limited by the degraded nature of the DNA gained from century-old museum material and the consumptive nature of most DNA extraction procedures. The method described in this manuscript enabled us to successfully extract DNA from specimens as old as 241 years using a minimal-destructive approach. The direct comparison of the DNeasy extraction Kit and the Monarch® PCR & DNA Clean-up Kit showed a significant increase of 17.3-fold higher DNA yield extracted with the Monarch Oligo protocol on average. By using an extraction protocol originally designed for oligonucleotide clean-up, we were able to combine overcoming the restrictions by target fragment size and strand state, with minimising time consumption and labour-intensity. The type specimens used for the minimal-destructive DNA extraction exhibited no significant external change or post-extraction damage, while sufficient DNA was retrieved for analyses.
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Affiliation(s)
- Franziska Patzold
- Museum of Zoology (Museum für Tierkunde), Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Alberto Zilli
- Division Insects, Department Life Sciences, Natural History Museum, London, United Kingdom
| | - Anna K. Hundsdoerfer
- Museum of Zoology (Museum für Tierkunde), Senckenberg Natural History Collections Dresden, Dresden, Germany
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5
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Pacioni C, Atkinson A, Wayne AF, Maxwell MA, Ward CG, Spencer PBS. Spatially sensitive harvest design can minimize genetic relatedness and enhance genetic outcomes in translocation programmes. J Zool (1987) 2020. [DOI: 10.1111/jzo.12791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. Pacioni
- Environmental and Conservation Sciences Murdoch University Murdoch WA Australia
- Department of Environment, Land, Water and Planning Arthur Rylah Institute Heidelberg Vic Australia
| | - A. Atkinson
- Environmental and Conservation Sciences Murdoch University Murdoch WA Australia
| | - A. F. Wayne
- Department of Biodiversity, Conservation and Attractions Biodiveristy and Conservation Science Manjimup WA Australia
| | - M. A. Maxwell
- Department of Biodiversity, Conservation and Attractions Biodiveristy and Conservation Science Manjimup WA Australia
| | - C. G. Ward
- Department of Biodiversity, Conservation and Attractions Biodiveristy and Conservation Science Manjimup WA Australia
| | - P. B. S. Spencer
- Environmental and Conservation Sciences Murdoch University Murdoch WA Australia
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6
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Rovinsky DS, Evans AR, Adams JW. The pre-Pleistocene fossil thylacinids (Dasyuromorphia: Thylacinidae) and the evolutionary context of the modern thylacine. PeerJ 2019; 7:e7457. [PMID: 31534836 PMCID: PMC6727838 DOI: 10.7717/peerj.7457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/10/2019] [Indexed: 11/20/2022] Open
Abstract
The thylacine is popularly used as a classic example of convergent evolution between placental and marsupial mammals. Despite having a fossil history spanning over 20 million years and known since the 1960s, the thylacine is often presented in both scientific literature and popular culture as an evolutionary singleton unique in its morphological and ecological adaptations within the Australian ecosystem. Here, we synthesise and critically evaluate the current state of published knowledge regarding the known fossil record of Thylacinidae prior to the appearance of the modern species. We also present phylogenetic analyses and body mass estimates of the thylacinids to reveal trends in the evolution of hypercarnivory and ecological shifts within the family. We find support that Mutpuracinus archibaldi occupies an uncertain position outside of Thylacinidae, and consider Nimbacinus richi to likely be synonymous with N. dicksoni. The Thylacinidae were small-bodied (< ~8 kg) unspecialised faunivores until after the ~15-14 Ma middle Miocene climatic transition (MMCT). After the MMCT they dramatically increase in size and develop adaptations to a hypercarnivorous diet, potentially in response to the aridification of the Australian environment and the concomitant radiation of dasyurids. This fossil history of the thylacinids provides a foundation for understanding the ecology of the modern thylacine. It provides a framework for future studies of the evolution of hypercarnivory, cursoriality, morphological and ecological disparity, and convergence within mammalian carnivores.
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Affiliation(s)
- Douglass S. Rovinsky
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Alistair R. Evans
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Geosciences, Museums Victoria, Melbourne, VIC, Australia
| | - Justin W. Adams
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
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7
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Dufresnes C, Miquel C, Remollino N, Biollaz F, Salamin N, Taberlet P, Fumagalli L. Howling from the past: historical phylogeography and diversity losses in European grey wolves. Proc Biol Sci 2018; 285:rspb.2018.1148. [PMID: 30068681 DOI: 10.1098/rspb.2018.1148] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/06/2018] [Indexed: 12/18/2022] Open
Abstract
Genetic bottlenecks resulting from human-induced population declines make alarming symbols for the irreversible loss of our natural legacy worldwide. The grey wolf (Canis lupus) is an iconic example of extreme declines driven by anthropogenic factors. Here, we assessed the genetic signatures of 150 years of wolf persecution throughout the Western Palaearctic by high-throughput mitochondrial DNA sequencing of historical specimens in an unprecedented spatio-temporal framework. Despite Late Pleistocene bottlenecks, we show that historical genetic variation had remained high throughout Europe until the last several hundred years. In Western Europe, where wolves nearly got fully exterminated, diversity dramatically collapsed at the turn of the twentieth century and recolonization from few homogeneous relict populations induced drastic shifts of genetic composition. By contrast, little genetic displacement and steady levels of diversity were maintained in Eastern European regions, where human persecution had lesser effects on wolf demography. By comparing prehistoric, historic and modern patterns of genetic diversity, our study hence traces the timeframe and the active human role in the decline of the grey wolf, an emblematic yet controversial animal which symbolizes the complex relationship between human societies and nature conservation.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Christian Miquel
- Laboratoire d'Écologie Alpine (LECA), UMR5553, BP53, 38041 Grenoble, Cedex 9, France
| | - Nadège Remollino
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - François Biollaz
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Route Pra de Louetse 32, 1968 Mase, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Department of Computational Biology University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Pierre Taberlet
- Laboratoire d'Écologie Alpine (LECA), UMR5553, BP53, 38041 Grenoble, Cedex 9, France
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
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8
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Dincă V, Bálint Z, Vodă R, Dapporto L, Hebert PDN, Vila R. Use of genetic, climatic, and microbiological data to inform reintroduction of a regionally extinct butterfly. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2018; 32:828-837. [PMID: 29569277 DOI: 10.1111/cobi.13111] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 01/24/2018] [Accepted: 01/29/2018] [Indexed: 06/08/2023]
Abstract
Species reintroductions are increasingly used as means of mitigating biodiversity loss. Besides habitat quality at the site targeted for reintroduction, the choice of source population can be critical for success. The butterfly Melanargia russiae (Esper´s marbled white) was extirpated from Hungary over 100 years ago, and a reintroduction program has recently been approved. We used museum specimens of this butterfly, mitochondrial DNA data (mtDNA), endosymbiont screening, and climatic-similarity analyses to determine which extant populations should be used for its reintroduction. The species displayed 2 main mtDNA lineages across its range: 1 restricted to Iberia and southern France (Iberian lineage) and another found throughout the rest of its range (Eurasian lineage). These 2 lineages possessed highly divergent wsp alleles of the bacterial endosymbiont Wolbachia. The century-old Hungarian specimens represented an endemic haplotype belonging to the Eurasian lineage, differing by one mutation from the Balkan and eastern European populations. The Hungarian populations of M. russiae occurred in areas with a colder and drier climate relative to most sites with extant known populations. Our results suggest the populations used for reintroduction to Hungary should belong to the Eurasian lineage, preferably from eastern Ukraine (genetically close and living in areas with the highest climatic similarity). Materials stored in museum collections can provide unique opportunities to document historical genetic diversity and help direct conservation.
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Affiliation(s)
- Vlad Dincă
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, Barcelona, 08003, Spain
- Department of Ecology and Genetics, University of Oulu, P.O. Box 3000, 90014, Finland
| | - Zsolt Bálint
- Department of Zoology, Hungarian Natural History Museum, Baross utca 13, 1088, Budapest, Hungary
| | - Raluca Vodă
- DBIOS Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Via Accademia Albertina 13, 10123, Turin, Italy
| | - Leonardo Dapporto
- Dipartimento di Biologia, Università degli Studi di Firenze, Via Madonna del Piano 6, 50109, Sesto Fiorentino, Florence, Italy
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, N1G 2W1, Ontario, Canada
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, Barcelona, 08003, Spain
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9
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McDonough MM, Parker LD, Rotzel McInerney N, Campana MG, Maldonado JE. Performance of commonly requested destructive museum samples for mammalian genomic studies. J Mammal 2018. [DOI: 10.1093/jmammal/gyy080] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Molly M McDonough
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoo, Washington, DC, USA
| | - Lillian D Parker
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoo, Washington, DC, USA
- Environmental Science and Policy Department, George Mason University, Fairfax, VA, USA
| | - Nancy Rotzel McInerney
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoo, Washington, DC, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoo, Washington, DC, USA
- Environmental Science and Policy Department, George Mason University, Fairfax, VA, USA
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoo, Washington, DC, USA
- Environmental Science and Policy Department, George Mason University, Fairfax, VA, USA
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10
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Feigin CY, Newton AH, Doronina L, Schmitz J, Hipsley CA, Mitchell KJ, Gower G, Llamas B, Soubrier J, Heider TN, Menzies BR, Cooper A, O'Neill RJ, Pask AJ. Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore. Nat Ecol Evol 2017; 2:182-192. [PMID: 29230027 DOI: 10.1038/s41559-017-0417-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 11/16/2017] [Indexed: 12/30/2022]
Abstract
The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was the largest carnivorous Australian marsupial to survive into the modern era. Despite last sharing a common ancestor with the eutherian canids ~160 million years ago, their phenotypic resemblance is considered the most striking example of convergent evolution in mammals. The last known thylacine died in captivity in 1936 and many aspects of the evolutionary history of this unique marsupial apex predator remain unknown. Here we have sequenced the genome of a preserved thylacine pouch young specimen to clarify the phylogenetic position of the thylacine within the carnivorous marsupials, reconstruct its historical demography and examine the genetic basis of its convergence with canids. Retroposon insertion patterns placed the thylacine as the basal lineage in Dasyuromorphia and suggest incomplete lineage sorting in early dasyuromorphs. Demographic analysis indicated a long-term decline in genetic diversity starting well before the arrival of humans in Australia. In spite of their extraordinary phenotypic convergence, comparative genomic analyses demonstrated that amino acid homoplasies between the thylacine and canids are largely consistent with neutral evolution. Furthermore, the genes and pathways targeted by positive selection differ markedly between these species. Together, these findings support models of adaptive convergence driven primarily by cis-regulatory evolution.
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Affiliation(s)
- Charles Y Feigin
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Axel H Newton
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia.,Museums Victoria, Melbourne, Victoria, Australia
| | - Liliya Doronina
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
| | - Christy A Hipsley
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia.,Museums Victoria, Melbourne, Victoria, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
| | - Graham Gower
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
| | - Julien Soubrier
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
| | - Thomas N Heider
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Brandon R Menzies
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
| | - Rachel J O'Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Andrew J Pask
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia. .,Museums Victoria, Melbourne, Victoria, Australia.
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11
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Old JM. Immunological Insights into the Life and Times of the Extinct Tasmanian Tiger (Thylacinus cynocephalus). PLoS One 2015; 10:e0144091. [PMID: 26655868 PMCID: PMC4684372 DOI: 10.1371/journal.pone.0144091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 11/12/2015] [Indexed: 11/19/2022] Open
Abstract
The thylacine (Thylacinus cynocephalus) was Australia’s largest marsupial carnivore until its extinction within the last century. There remains considerable interest and debate regarding the biology of this species. Studies of thylacine biology are now limited to preserved specimens, and parts thereof, as well as written historical accounts of its biology. This study describes the development of the immune tissues of a pouch young thylacine, one of only eleven in existence, and the only specimen to be histologically sectioned. The appearance of the immune tissue of the developing pouch young thylacine is compared to the immune tissues of extant marsupials, providing insights into the immunity, biology and ecology of the extinct thylacine.
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Affiliation(s)
- Julie M. Old
- Water and Wildlife Ecology, School of Science and Health, Hawkesbury, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
- * E-mail:
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12
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Burrell AS, Disotell TR, Bergey CM. The use of museum specimens with high-throughput DNA sequencers. J Hum Evol 2015; 79:35-44. [PMID: 25532801 PMCID: PMC4312722 DOI: 10.1016/j.jhevol.2014.10.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/08/2014] [Accepted: 10/31/2014] [Indexed: 12/30/2022]
Abstract
Natural history collections have long been used by morphologists, anatomists, and taxonomists to probe the evolutionary process and describe biological diversity. These biological archives also offer great opportunities for genetic research in taxonomy, conservation, systematics, and population biology. They allow assays of past populations, including those of extinct species, giving context to present patterns of genetic variation and direct measures of evolutionary processes. Despite this potential, museum specimens are difficult to work with because natural postmortem processes and preservation methods fragment and damage DNA. These problems have restricted geneticists' ability to use natural history collections primarily by limiting how much of the genome can be surveyed. Recent advances in DNA sequencing technology, however, have radically changed this, making truly genomic studies from museum specimens possible. We review the opportunities and drawbacks of the use of museum specimens, and suggest how to best execute projects when incorporating such samples. Several high-throughput (HT) sequencing methodologies, including whole genome shotgun sequencing, sequence capture, and restriction digests (demonstrated here), can be used with archived biomaterials.
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Affiliation(s)
- Andrew S Burrell
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA.
| | - Todd R Disotell
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA; New York Consortium in Evolutionary Primatology, USA
| | - Christina M Bergey
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA; New York Consortium in Evolutionary Primatology, USA
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13
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Affiliation(s)
- Jennifer A. Marshall Graves
- La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne 3186, Australia
- Research School of Biology, Australian National University, Canberra 2060, Australia;
- Department of Zoology, University of Melbourne, Melbourne 3010, Australia
| | - Marilyn B. Renfree
- Department of Zoology, University of Melbourne, Melbourne 3010, Australia
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14
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Mondol S, Bruford MW, Ramakrishnan U. Demographic loss, genetic structure and the conservation implications for Indian tigers. Proc Biol Sci 2013; 280:20130496. [PMID: 23677341 PMCID: PMC3673047 DOI: 10.1098/rspb.2013.0496] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/23/2013] [Indexed: 11/12/2022] Open
Abstract
India is home to approximately 60 per cent of the world's remaining wild tigers, a species that has declined in the last few centuries to occupy less than 7 per cent of its former geographical range. While Indian tiger numbers have somewhat stabilized in recent years, they remain low and populations are highly fragmented. Therefore, the application of evidence-based demographic and genetic management to enhance the remaining populations is a priority. In this context, and using genetic data from historical and modern tigers, we investigated anthropogenic impacts on genetic variation in Indian tigers using mitochondrial and nuclear genetic markers. We found a very high number of historical mitochondrial DNA variants, 93 per cent of which are not detected in modern populations. Population differentiation was higher in modern tigers. Simulations incorporating historical data support population decline, and suggest high population structure in extant populations. Decreased connectivity and habitat loss as a result of ongoing fragmentation in the Indian subcontinent has therefore resulted in a loss of genetic variants and increased genetic differentiation among tiger populations. These results highlight that anthropogenic fragmentation and species-specific demographic processes can interact to alter the partitioning of genetic variation over very short time scales. We conclude that ongoing strategies to maximize the size of some tiger populations, at the expense of losing others, is an inadequate conservation strategy, as it could result in a loss of genetic diversity that may be of adaptive significance for this emblematic species.
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Affiliation(s)
- Samrat Mondol
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| | | | - Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
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15
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Morris K, Austin JJ, Belov K. Low major histocompatibility complex diversity in the Tasmanian devil predates European settlement and may explain susceptibility to disease epidemics. Biol Lett 2012; 9:20120900. [PMID: 23221872 DOI: 10.1098/rsbl.2012.0900] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The Tasmanian devil (Sarcophilus harrisii) is at risk of extinction owing to the emergence of a contagious cancer known as devil facial tumour disease (DFTD). The emergence and spread of DFTD has been linked to low genetic diversity in the major histocompatibility complex (MHC). We examined MHC diversity in historical and ancient devils to determine whether loss of diversity is recent or predates European settlement in Australia. Our results reveal no additional diversity in historical Tasmanian samples. Mainland devils had common modern variants plus six new variants that are highly similar to existing alleles. We conclude that low MHC diversity has been a feature of devil populations since at least the Mid-Holocene and could explain their tumultuous history of population crashes.
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Affiliation(s)
- Katrina Morris
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia
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Tsangaras K, Ávila-Arcos MC, Ishida Y, Helgen KM, Roca AL, Greenwood AD. Historically low mitochondrial DNA diversity in koalas (Phascolarctos cinereus). BMC Genet 2012; 13:92. [PMID: 23095716 PMCID: PMC3518249 DOI: 10.1186/1471-2156-13-92] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 09/27/2012] [Indexed: 02/04/2023] Open
Abstract
Background The koala (Phascolarctos cinereus) is an arboreal marsupial that was historically widespread across eastern Australia until the end of the 19th century when it suffered a steep population decline. Hunting for the fur trade, habitat conversion, and disease contributed to a precipitous reduction in koala population size during the late 1800s and early 1900s. To examine the effects of these reductions in population size on koala genetic diversity, we sequenced part of the hypervariable region of mitochondrial DNA (mtDNA) in koala museum specimens collected in the 19th and 20th centuries, hypothesizing that the historical samples would exhibit greater genetic diversity. Results The mtDNA haplotypes present in historical museum samples were identical to haplotypes found in modern koala populations, and no novel haplotypes were detected. Rarefaction analyses suggested that the mtDNA genetic diversity present in the museum samples was similar to that of modern koalas. Conclusions Low mtDNA diversity may have been present in koala populations prior to recent population declines. When considering management strategies, low genetic diversity of the mtDNA hypervariable region may not indicate recent inbreeding or founder events but may reflect an older historical pattern for koalas.
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