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Holmes BJ, Pope LC, Williams SM, Tibbetts IR, Bennett MB, Ovenden JR. Lack of multiple paternity in the oceanodromous tiger shark ( Galeocerdo cuvier). R Soc Open Sci 2018; 5:171385. [PMID: 29410842 PMCID: PMC5792919 DOI: 10.1098/rsos.171385] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 12/01/2017] [Indexed: 06/08/2023]
Abstract
Multiple paternity has been documented as a reproductive strategy in both viviparous and ovoviviparous elasmobranchs, leading to the assumption that multiple mating may be ubiquitous in these fishes. However, with the majority of studies conducted on coastal and nearshore elasmobranchs that often form mating aggregations, parallel studies on pelagic, semi-solitary species are lacking. The tiger shark (Galeocerdo cuvier) is a large pelagic shark that has an aplacental viviparous reproductive mode which is unique among the carcharhinids. A total of 112 pups from four pregnant sharks were genotyped at nine microsatellite loci to assess the possibility of multiple paternity or polyandrous behaviour by female tiger sharks. Only a single pup provided evidence of possible multiple paternity, but with only seven of the nine loci amplifying for this individual, results were inconclusive. In summary, it appears that the tiger sharks sampled in this study were genetically monogamous. These findings may have implications for the genetic diversity and future sustainability of this population.
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Affiliation(s)
- Bonnie J. Holmes
- School of Biomedical Sciencesy, The University of Queensland, St Lucia, Queensland 4072, Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia
- Department of Agriculture and Fisheries, Brisbane, Queensland 4001, Australia
| | - Lisa C. Pope
- Institute for Social Science Research, The University of Queensland, Long Pocket Precinct, Queensland 4072, Australia
| | - Samuel M. Williams
- School of Biomedical Sciencesy, The University of Queensland, St Lucia, Queensland 4072, Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia
- Department of Agriculture and Fisheries, Brisbane, Queensland 4001, Australia
| | - Ian R. Tibbetts
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mike B. Bennett
- School of Biomedical Sciencesy, The University of Queensland, St Lucia, Queensland 4072, Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Jennifer R. Ovenden
- School of Biomedical Sciencesy, The University of Queensland, St Lucia, Queensland 4072, Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia
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Cooper SJB, Ottewell K, MacDonald AJ, Adams M, Byrne M, Carthew SM, Eldridge MDB, Li Y, Pope LC, Saint KM, Westerman M. Phylogeography of southern brown and golden bandicoots: implications for the taxonomy and distribution of endangered subspecies and species. AUST J ZOOL 2018. [DOI: 10.1071/zo19052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Southern brown (Isoodon obesulus) and golden (Isoodon auratus) bandicoots are iconic Australian marsupials that have experienced dramatic declines since European settlement. Conservation management programs seek to protect the remaining populations; however, these programs are impeded by major taxonomic uncertainties. We investigated the history of population connectivity to inform subspecies and species boundaries through a broad-scale phylogeographic and population genetic analysis of Isoodon taxa. Our analyses reveal a major east–west phylogeographic split within I. obesulus/I. auratus, supported by both mtDNA and nuclear gene analyses, which is not coincident with the current species or subspecies taxonomy. In the eastern lineage, all Tasmanian samples formed a distinct monophyletic haplotype group to the exclusion of all mainland samples, indicative of long-term isolation of this population from mainland Australia and providing support for retention of the subspecific status of the Tasmanian population (I. o. affinis). Analyses further suggest that I. o. obesulus is limited to south-eastern mainland Australia, representing a significant reduction in known range. However, the analyses provide no clear consensus on the taxonomic status of bandicoot populations within the western lineage, with further analyses required, ideally incorporating data from historical museum specimens to fill distributional gaps.
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Pope LC, Riginos C, Ovenden J, Keyse J, Blomberg SP. Population Genetic Diversity in the Australian 'Seascape': A Bioregion Approach. PLoS One 2015; 10:e0136275. [PMID: 26375711 PMCID: PMC4574161 DOI: 10.1371/journal.pone.0136275] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 08/02/2015] [Indexed: 11/18/2022] Open
Abstract
Genetic diversity within species may promote resilience to environmental change, yet little is known about how such variation is distributed at broad geographic scales. Here we develop a novel Bayesian methodology to analyse multi-species genetic diversity data in order to identify regions of high or low genetic diversity. We apply this method to co-distributed taxa from Australian marine waters. We extracted published summary statistics of population genetic diversity from 118 studies of 101 species and > 1000 populations from the Australian marine economic zone. We analysed these data using two approaches: a linear mixed model for standardised data, and a mixed beta-regression for unstandardised data, within a Bayesian framework. Our beta-regression approach performed better than models using standardised data, based on posterior predictive tests. The best model included region (Integrated Marine and Coastal Regionalisation of Australia (IMCRA) bioregions), latitude and latitude squared. Removing region as an explanatory variable greatly reduced model performance (delta DIC 23.4). Several bioregions were identified as possessing notably high genetic diversity. Genetic diversity increased towards the equator with a 'hump' in diversity across the range studied (-9.4 to -43.7°S). Our results suggest that factors correlated with both region and latitude play a role in shaping intra-specific genetic diversity, and that bioregion can be a useful management unit for intra-specific as well as species biodiversity. Our novel statistical model should prove useful for future analyses of within species genetic diversity at broad taxonomic and geographic scales.
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Affiliation(s)
- Lisa C. Pope
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Jennifer Ovenden
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Jude Keyse
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Simon P. Blomberg
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
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4
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Pope LC, Liggins L, Keyse J, Carvalho SB, Riginos C. Not the time or the place: the missing spatio-temporal link in publicly available genetic data. Mol Ecol 2015; 24:3802-9. [DOI: 10.1111/mec.13254] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 05/07/2015] [Accepted: 05/22/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Lisa C. Pope
- School of Biological Sciences; The University of Queensland; Brisbane Qld 4072 Australia
| | - Libby Liggins
- Allan Wilson Centre for Molecular Ecology and Evolution; New Zealand Institute for Advanced Study; Institute of Natural and Mathematical Sciences; Massey University; Auckland 0745 New Zealand
- Auckland War Memorial Museum; Tāmaki Paenga Hira; Auckland 1142 New Zealand
| | - Jude Keyse
- School of Biological Sciences; The University of Queensland; Brisbane Qld 4072 Australia
| | - Silvia B Carvalho
- CIBIO/InBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - Cynthia Riginos
- School of Biological Sciences; The University of Queensland; Brisbane Qld 4072 Australia
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5
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Frantz AC, McDevitt AD, Pope LC, Kochan J, Davison J, Clements CF, Elmeros M, Molina-Vacas G, Ruiz-Gonzalez A, Balestrieri A, Van Den Berge K, Breyne P, Do Linh San E, Ågren EO, Suchentrunk F, Schley L, Kowalczyk R, Kostka BI, Ćirović D, Šprem N, Colyn M, Ghirardi M, Racheva V, Braun C, Oliveira R, Lanszki J, Stubbe A, Stubbe M, Stier N, Burke T. Revisiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations. Heredity (Edinb) 2014; 113:443-53. [PMID: 24781805 PMCID: PMC4220720 DOI: 10.1038/hdy.2014.45] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 02/04/2014] [Accepted: 02/14/2014] [Indexed: 11/09/2022] Open
Abstract
Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples from western Europe, making it difficult to draw robust conclusions about the location of refugia, patterns of postglacial expansion and recent demography. In the present study, continent-wide sampling and analyses with multiple markers provided evidence for two glacial refugia (Iberia and southeast Europe) that contributed to the genetic variation observed in badgers in Europe today. Approximate Bayesian computation provided support for a colonisation of Scandinavia from both Iberian and southeastern refugia. In the whole of Europe, we observed a decline in genetic diversity with increasing latitude, suggesting that the reduced diversity in the peripheral populations resulted from a postglacial expansion processes. Although MSVAR v.1.3 also provided evidence for recent genetic bottlenecks in some of these peripheral populations, the simulations performed to estimate the method's power to correctly infer the past demography of our empirical populations suggested that the timing and severity of bottlenecks could not be established with certainty. We urge caution against trying to relate demographic declines inferred using MSVAR with particular historic or climatological events.
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Affiliation(s)
- A C Frantz
- NERC Biomolecular Analysis Facility,
Department of Animal and Plant Sciences, University of Sheffield,
Sheffield, UK
- Musée National d'Histoire
Naturelle, Luxembourg, Luxembourg
| | - A D McDevitt
- School of Biology and Environmental
Science, University College Dublin, Dublin,
Ireland
| | - L C Pope
- School of Biological Science, University
of Queensland, St Lucia, Queensland,
Australia
| | - J Kochan
- Department of Genetics and Animal
Breeding, Wrocław University of Environmental and Life Sciences,
Wrocław, Poland
| | - J Davison
- Institute of Ecology and Earth Sciences,
University of Tartu, Tartu, Estonia
| | - C F Clements
- NERC Biomolecular Analysis Facility,
Department of Animal and Plant Sciences, University of Sheffield,
Sheffield, UK
| | - M Elmeros
- Department of Bioscience, Aarhus
University, Rønde, Denmark
| | - G Molina-Vacas
- Animal Biology Department, University of
Barcelona, Barcelona, Spain
| | - A Ruiz-Gonzalez
- Department of Zoology, Biogeography and
Population Dynamics Research Group, University of the Basque Country,
UPV/EHU, Vitoria-Gasteiz, Spain
| | - A Balestrieri
- Department of Biosciences, University
of Milan, Milan, Italy
| | - K Van Den Berge
- Research Institute for Nature and
Forest, Geraardsbergen, Belgium
| | - P Breyne
- Research Institute for Nature and
Forest, Geraardsbergen, Belgium
| | - E Do Linh San
- Department of Zoology and Entomology,
University of Fort Hare, Alice, South Africa
| | - E O Ågren
- National Veterinary Institute,
Department of Pathology and Wildlife Diseases, Uppsala,
Sweden
| | - F Suchentrunk
- Research Institute of Wildlife Ecology,
University of Veterinary Medicine Vienna, Vienna,
Austria
| | - L Schley
- Administration de la nature et des
forêts, Luxembourg, Luxembourg
| | - R Kowalczyk
- Mammal Research Institute,
Bialowieza, Poland
| | - B I Kostka
- Queen's University Belfast,
Northern Ireland, UK
| | - D Ćirović
- Faculty of Biology, University of
Belgrade, Belgrade, Serbia
| | - N Šprem
- Department of Fisheries, Beekeeping,
Game Management and Special Zoology, University of Zagreb,
Zagreb, Croatia
| | - M Colyn
- CNRS, UMR 6553, ECOBIO,
Université de Rennes 1, Rennes, France
| | - M Ghirardi
- Università degli Studi di
Torino, Torino, Italy
| | - V Racheva
- Balkani Wildlife Society,
Sofia, Bulgaria
| | - C Braun
- 9 chemin du Kilbs,
Bischoffsheim, France
| | - R Oliveira
- Departamento de Zoologia e
Antropologia, Faculdade de Ciências da Universidade do Porto,
Porto, Portugal
| | - J Lanszki
- Department of Nature Conservation,
University of Kaposvár, Kaposvár,
Hungary
| | - A Stubbe
- Domplatz 4,
Halle/Saale, Germany
| | - M Stubbe
- Domplatz 4,
Halle/Saale, Germany
| | - N Stier
- Institute of Forest Botany and Forest
Zoology, Dresden University of Technology, Tharandt,
Germany
| | - T Burke
- NERC Biomolecular Analysis Facility,
Department of Animal and Plant Sciences, University of Sheffield,
Sheffield, UK
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Bielby J, Donnelly CA, Pope LC, Burke T, Woodroffe R. Badger responses to small-scale culling may compromise targeted control of bovine tuberculosis. Proc Natl Acad Sci U S A 2014; 111:9193-8. [PMID: 24927589 PMCID: PMC4078854 DOI: 10.1073/pnas.1401503111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Where wildlife disease requires management, culling is frequently considered but not always effective. In the British Isles, control of cattle tuberculosis (TB) is hindered by infection in wild badger (Meles meles) populations. Large-scale badger culling can reduce the incidence of confirmed cattle TB, but these benefits are undermined by culling-induced changes in badger behavior (termed perturbation), which can increase transmission among badgers and from badgers to cattle. Test-vaccinate/remove (TVR) is a novel approach that entails testing individual badgers for infection, vaccinating test-negative animals, and killing test-positive animals. Imperfect capture success, diagnostic sensitivity, and vaccine effectiveness mean that TVR would be expected to leave some infected and some susceptible badgers in the population. Existing simulation models predict that TVR could reduce cattle TB if such small-scale culling causes no perturbation, but could increase cattle TB if considerable perturbation occurs. Using data from a long-term study, we show that past small-scale culling was significantly associated with four metrics of perturbation in badgers: expanded ranging, more frequent immigration, lower genetic relatedness, and elevated prevalence of Mycobacterium bovis, the causative agent of TB. Though we could not reject the hypothesis that culling up to three badgers per social group might avoid perturbation, we also could not reject the hypothesis that killing a single badger prompted detectable perturbation. When considered alongside existing model predictions, our findings suggest that implementation of TVR, scheduled for 2014, risks exacerbating the TB problem rather than controlling it. Ongoing illegal badger culling is likewise expected to increase cattle TB risks.
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Affiliation(s)
- Jon Bielby
- Institute of Zoology, Regent's Park, London NW1 4RY, United Kingdom
| | - Christl A Donnelly
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom; and
| | - Lisa C Pope
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Rosie Woodroffe
- Institute of Zoology, Regent's Park, London NW1 4RY, United Kingdom;
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7
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Frantz AC, Pope LC, Etherington TR, Wilson GJ, Burke T. Using isolation-by-distance-based approaches to assess the barrier effect of linear landscape elements on badger (Meles meles) dispersal. Mol Ecol 2010; 19:1663-74. [PMID: 20345687 DOI: 10.1111/j.1365-294x.2010.04605.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As the European badger (Meles meles) can be of conservation or management concern, it is important to have a good understanding of the species' dispersal ability. In particular, knowledge of landscape elements that affect dispersal can contribute to devising effective management strategies. However, the standard approach of using Bayesian clustering methods to correlate genetic discontinuities with landscape elements cannot easily be applied to this problem, as badger populations are often characterized by a strong confounding isolation-by-distance (IBD) pattern. We therefore developed a two-step method that compares the location of pairs of related badgers relative to a putative barrier and utilizes the expected spatial genetic structure characterized by IBD as a null model to test for the presence of a barrier. If a linear feature disrupts dispersal, the IBD pattern characterising pairs of individuals located on different sides of a putative barrier should differ significantly from the pattern obtained with pairs of individuals located on the same side. We used our new approach to assess the impact of rivers and roads of different sizes on badger dispersal in western England. We show that a large, wide river represented a barrier to badger dispersal and found evidence that a motorway may also restrict badger movement. Conversely, we did not find any evidence for small rivers and roads interfering with badger movement. One of the advantages of our approach is that potentially it can detect features that disrupt gene flow locally, without necessarily creating distinct identifiable genetic units.
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Affiliation(s)
- A C Frantz
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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8
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Dugdale HL, Nouvellet P, Pope LC, Burke T, Macdonald DW. Fitness measures in selection analyses: sensitivity to the overall number of offspring produced in a lifetime. J Evol Biol 2009; 23:282-92. [PMID: 20002246 DOI: 10.1111/j.1420-9101.2009.01896.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Age at first (alpha) and last (omega) breeding are important life-history traits; however, the direction and strength of selection detected on traits may vary depending on the fitness measure used. We provide the first estimates of lifetime breeding success (LBS) and lambda(ind) (the population growth rate of an individual) of European badgers Meles meles, by genotyping 915 individuals, sampled over 18 years, for 22 microsatellites. Males are slightly larger than females, and the opportunity for selection was slightly greater for males, as predicted. lambda(ind) and LBS both performed well in predicting the number of grand-offspring, and both detected selection for a late omega, until the age of eight. Differential selection (S'(alpha)) for an early alpha, however, was only detected using LBS, not with lambda(ind). In declining populations (lambda(ind) < 1) selection favours reproduction later in life, whereas early reproduction is selected in increasing populations (lambda(ind) > 1). As 41% of badgers were assigned only one offspring (lambda(ind) < 1), whereas 40% were assigned more than two (lambda(ind) > 1), this cancelled out S'(alpha) measured by lambda(ind).
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Affiliation(s)
- H L Dugdale
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Tubney, Abingdon, Oxfordshire OX13 5QL, UK.
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Woodroffe R, Donnelly CA, Wei G, Cox DR, Bourne FJ, Burke T, Butlin RK, Cheeseman CL, Gettinby G, Gilks P, Hedges S, Jenkins HE, Johnston WT, McInerney JP, Morrison WI, Pope LC. Social group size affects Mycobacterium bovis infection in European badgers (Meles meles). J Anim Ecol 2009; 78:818-27. [PMID: 19486382 DOI: 10.1111/j.1365-2656.2009.01545.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
1. In most social animals, the prevalence of directly transmitted pathogens increases in larger groups and at higher population densities. Such patterns are predicted by models of Mycobacterium bovis infection in European badgers (Meles meles). 2. We investigated the relationship between badger abundance and M. bovis prevalence, using data on 2696 adult badgers in 10 populations sampled at the start of the Randomized Badger Culling Trial. 3. M. bovis prevalence was consistently higher at low badger densities and in small social groups. M. bovis prevalence was also higher among badgers whose genetic profiles suggested that they had immigrated into their assigned social groups. 4. The association between high M. bovis prevalence and small badger group size appeared not to have been caused by previous small-scale culling in study areas, which had been suspended, on average, 5 years before the start of the current study. 5. The observed pattern of prevalence might occur through badgers in smaller groups interacting more frequently with members of neighbouring groups; detailed behavioural data are needed to test this hypothesis. Likewise, longitudinal data are needed to determine whether the size of infected groups might be suppressed by disease-related mortality. 6. Although M. bovis prevalence was lower at high population densities, the absolute number of infected badgers was higher. However, this does not necessarily mean that the risk of M. bovis transmission to cattle is highest at high badger densities, since transmission risk depends on badger behaviour as well as on badger density.
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10
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Pope LC, Butlin RK, Wilson GJ, Woodroffe R, Erven K, Conyers CM, Franklin T, Delahay RJ, Cheeseman CL, Burke T. Genetic evidence that culling increases badger movement: implications for the spread of bovine tuberculosis. Mol Ecol 2007; 16:4919-29. [PMID: 17944854 DOI: 10.1111/j.1365-294x.2007.03553.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Eurasian badger (Meles meles) has been implicated in the transmission of bovine tuberculosis (TB, caused by Mycobacterium bovis) to cattle. However, evidence suggests that attempts to reduce the spread of TB among cattle in Britain by culling badgers have mixed effects. A large-scale field experiment (the randomized badger culling trial, RBCT) showed that widespread proactive badger culling reduced the incidence of TB in cattle within culled areas but that TB incidence increased in adjoining areas. Additionally, localized reactive badger culling increased the incidence of TB in cattle. It has been suggested that culling-induced perturbation of badger social structure may increase individual movements and elevate the risk of disease transmission between badgers and cattle. Field studies support this hypothesis, by demonstrating increases in badger group ranges and the prevalence of TB infection in badgers following culling. However, more evidence on the effect of culling on badger movements is needed in order to predict the epidemiological consequences of this control strategy. Here, analysis of the genetic signatures of badger populations in the RBCT revealed increased dispersal following culling. While standard tests provided evidence for greater dispersal after culling, a novel method indicated that this was due to medium- and long-distance dispersal, in addition to previously reported increases in home-range size. Our results also indicated that, on average, badgers infected with M. bovis moved significantly farther than did uninfected badgers. A disease control strategy that included culling would need to take account of the potentially negative epidemiological consequences of increased badger dispersal.
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Affiliation(s)
- Lisa C Pope
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
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11
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Dawnay N, Ogden R, Thorpe RS, Pope LC, Dawson DA, McEwing R. A forensic STR profiling system for the Eurasian badger: a framework for developing profiling systems for wildlife species. Forensic Sci Int Genet 2007; 2:47-53. [PMID: 19083789 DOI: 10.1016/j.fsigen.2007.08.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Revised: 07/19/2007] [Accepted: 08/13/2007] [Indexed: 10/22/2022]
Abstract
Developing short tandem repeat (STR) profiling systems for forensic identification is complicated in animal species. Obtaining a representative number of individuals from populations, limited access to family groups and a lack of developed STR markers can make adhering to human forensic guidelines difficult. Furthermore, a lack of animal specific guidelines may explain why many wildlife forensic STR profiling systems developed to date have not appropriately addressed areas such as marker validation or the publication and analysis of population data necessary for the application of these tools to forensic science. Here we present a methodology used to develop an STR profiling system for a legally protected wildlife species, the Eurasian badger Meles meles. Ten previously isolated STR loci were selected based on their level of polymorphism, adherence to Hardy-Weinberg expectations and their fragment size. Each locus was individually validated with respect to its reproducibility, inheritance, species specificity, DNA template concentration and thermocycling parameters. The effects of chemical, substrate and environmental exposure were also investigated. All ten STR loci provided reliable and reproducible results, and optimal amplification conditions were defined. Allele frequencies from 20 representative populations in England and Wales are presented and used to calculate the level of population substructure (theta) and inbreeding (f). Accounting for these estimates, the average probability of identity (PI(ave)) was 2.18 x 10(-7). This case study can act as a framework for others attempting to develop wildlife forensic profiling systems.
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Affiliation(s)
- Nick Dawnay
- School of Biological Sciences, University of Wales, Bangor LL57 2UW, United Kingdom.
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12
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Abstract
Eurasian badgers, Meles meles, have been shown to possess limited genetic population structure within Europe; however, field studies have detected high levels of philopatry, which are expected to increase population structure. Population structure will be a consequence of both contemporary dispersal and historical processes, each of which is expected to be evident at a different scale. Therefore, to gain a greater understanding of gene flow in the badger, we examined microsatellite diversity both among and within badger populations, focusing on populations from the British Isles and western Europe. We found that while populations differed in their allelic diversity, the British Isles displayed a similar degree of diversity to the rest of western Europe. The lower genetic diversity occurring in Ireland, Norway and Scotland was more likely to have resulted from founder effects rather than contemporary population density. While there was significant population structure (F ST = 0.19), divergence among populations was generally well explained by geographic distance (P < 0.0001) across the entire range studied of more than 3000 km. Transient effects from the Pleistocene appear to have been replaced by a strong pattern of genetic isolation by distance across western Europe, suggestive of colonization from a single refugium. Analysis of individuals within British populations through Mantel tests and spatial autocorrelation demonstrated that there was significant local population structure across 3-30 km, confirming that dispersal is indeed restricted. The isolation by distance observed among badger populations across western Europe is likely to be a consequence of this restricted local dispersal.
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Affiliation(s)
- L C Pope
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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13
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Carpenter PJ, Pope LC, Greig C, Dawson DA, Rogers LM, Erven K, Wilson GJ, Delahay RJ, Cheeseman CL, Burke T. Mating system of the Eurasian badger, Meles meles, in a high density population. Mol Ecol 2005; 14:273-84. [PMID: 15643970 DOI: 10.1111/j.1365-294x.2004.02401.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Badgers are facultatively social, forming large groups at high density. Group-living appears to have high reproductive costs for females, and may lead to increased levels of inbreeding. The extent of female competition for reproduction has been estimated from field data, but knowledge of male reproductive success and the extent of extra-group paternity remains limited. Combining field data with genetic data (16 microsatellite loci), we studied the mating system of 10 badger social groups across 14 years in a high-density population. From 923 badgers, including 425 cubs, we were able to assign maternity to 307 cubs, with both parents assigned to 199 cubs (47%) with 80% confidence, and 14% with 95% confidence. Age had a significant effect on the probability of reproduction, seemingly as a result of a deficit of individuals aged two years and greater than eight years attaining parentage. We estimate that approximately 30% of the female population successfully reproduced in any given year, with a similar proportion of the male population gaining paternity across the same area. While it was known there was a cost to female reproduction in high density populations, it appears that males suffer similar, but not greater, costs. Roughly half of assigned paternity was attributed to extra-group males, the majority of which were from neighbouring social groups. Few successful matings occurred between individuals born in the same social group (22%). The high rate of extra-group mating, previously unquantified, may help reduce inbreeding, potentially making philopatry a less costly strategy.
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Affiliation(s)
- Petra J Carpenter
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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Frantz AC, Pope LC, Carpenter PJ, Roper TJ, Wilson GJ, Delahay RJ, Burke T. Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA. Mol Ecol 2003; 12:1649-61. [PMID: 12755892 DOI: 10.1046/j.1365-294x.2003.01848.x] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The potential link between badgers and bovine tuberculosis has made it vital to develop accurate techniques to census badgers. Here we investigate the potential of using genetic profiles obtained from faecal DNA as a basis for population size estimation. After trialling several methods we obtained a high amplification success rate (89%) by storing faeces in 70% ethanol and using the guanidine thiocyanate/silica method for extraction. Using 70% ethanol as a storage agent had the advantage of it being an antiseptic. In order to obtain reliable genotypes with fewer amplification reactions than the standard multiple-tubes approach, we devised a comparative approach in which genetic profiles were compared and replication directed at similar, but not identical, genotypes. This modified method achieved a reduction in polymerase chain reactions comparable with the maximum-likelihood model when just using reliability criteria, and was slightly better when using reliability criteria with the additional proviso that alleles must be observed twice to be considered reliable. Our comparative approach would be best suited for studies that include multiple faeces from each individual. We utilized our approach in a well-studied population of badgers from which individuals had been sampled and reliable genotypes obtained. In a study of 53 faeces sampled from three social groups over 10 days, we found that direct enumeration could not be used to estimate population size, but that the application of mark-recapture models has the potential to provide more accurate results.
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Affiliation(s)
- A C Frantz
- School of Biological Sciences, University of Sussex, Brighton, UK.
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Vernes K, Pope LC. Fecundity, pouch young survivorship and breeding season of the northern bettong (Bettongia tropica) in the wild. Aust Mammalogy 2001. [DOI: 10.1071/am01095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Reproduction in a wild population of northern bettongs (Bettongia tropica) was studied
at Davies Creek in northeastern Queensland between November 1994 and February 1997. Using
mark-recapture, we recorded 88 individual pouch young (PY) during the study (34 male, 45
female, 9 unknown sex). Using captive-derived growth equations we estimated that 90 % of PY
survived to permanent emergence from the pouch (PEP). Birth of a new PY coincided with PEP
of the previous young 78 % of the time; 12 % of births occurred within 2 - 8 weeks of PEP
while the remaining 10 % probably died before PEP. 96 % of adult females carried PY at the
time of capture. B. tropica bred continuously, with no significant differences in numbers of
births recorded in different months. Few young that were marked in the pouch were captured as
sub-adults, and none were captured as adults. Limited data on longevity indicated that B. tropica
can live to at least 5 years. Our data suggest that B. tropica has a high reproductive potential;
however, the fate of PY after PEP remains poorly known; and this may represent the period of
greatest bettong mortality.
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Abstract
The northern bettong, Bettongia tropica, is an endangered species of Potoroidae with a restricted distribution in the wet tropics of north Queensland, Australia. The species is only found within a thin strip of sclerophyll forest along the western margin of rainforest. This tight association with rainforest boundaries is predicted to have resulted in population isolation as rainforest contracted during the Pleistocene, though some have proposed that the northern bettong was not present in the wet tropics until the late Pleistocene. The dispersal ability of the species, and of the family, is not known. This study examined gene flow among populations within areas of continuous habitat complemented by a broader analysis of phylogeography. Individuals trapped at each of the four known regions (one region was subsampled at three different sites), were sequenced for 547 base pairs of the mitochondrial DNA (mtDNA) control region and typed for seven microsatellite loci. The mtDNA phylogeny showed congruence with a biogeographical hypothesis, a relatively deep split suggesting historical isolation in separate northern and southern refugia. The two divergent clades were both present within the Lamb Range, indicating an expansion from these refuges and subsequent admixture at one site. mtDNA allele frequencies indicated relatively limited gene flow within the Lamb Range over distances as short as nine km. Tests of population divergence using microsatellites (FST and assignment tests) strongly supported this result. A molecular signal indicative of a recent bottleneck was unexpectedly detected in one of the Lamb Range subpopulations. This lead us to examine the behaviour of the statistics used in this bottleneck test under a linear stepping-stone model with varying migration rates. We found that it may be more difficult to detect molecular signatures for recent bottlenecks under conditions of very low migration rates than for isolated populations and, conversely, that 'false' bottleneck signatures may be observed at higher migration rates. The Lamb Range FST estimate clearly fell within the category of potentially 'false' bottleneck signals. Despite relatively limited gene flow, evidence for asymmetric dispersal suggests more complicated population dynamics than a simple linear stepping-stone model.
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Affiliation(s)
- L C Pope
- Department of Zoology and Entomology, University of Queensland, St. Lucia, 4072. Queensland, Australia.
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Abstract
Burkholderia gladioli colonizes the respiratory tracts of patients with cystic fibrosis and chronic granulomatous disease. However, due to the high degree of phenotypic similarity between this species and closely related species in the Burkholderia cepacia complex, accurate identification is difficult. Incorrect identification of these species may have serious repercussions for the management of patients with cystic fibrosis. To develop an accurate procedure for the identification of B. gladioli, a molecular method to discriminate between this species and other species commonly isolated from the sputa of patients with cystic fibrosis was investigated. The 23S ribosomal DNA was cloned from several clinical isolates of B. gladioli, and the nucleotide sequence was determined. Computer-assisted sequence comparisons indicated four regions of the 23S rRNA specific for this species; these regions were used to design three primer pairs for species-specific PCR. Two of the primer pairs showed 100% sensitivity and specificity for B. gladioli when tested against a panel of 47 isolates comprising 19 B. gladioli isolates and 28 isolates of 16 other bacterial species. One of the primer pairs was further assessed for species specificity by using a panel of 102 isolates obtained from the Burkholderia cepacia Research Laboratory and Repository. The species-specific PCR was positive for 70 of 74 isolates of B. gladioli and was negative for all other bacterial species examined. Overall, this primer pair displayed a sensitivity and specificity of 96% (89 of 93) and 100%, respectively. These data demonstrate the potential of species-specific PCR for the identification of B. gladioli.
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Affiliation(s)
- P W Whitby
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
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C. Pope L, Sharp A, Moritz C. The genetic diversity and distinctiveness of the Yellow-footed Rock-wallaby Petrogale xanthopus (Gray, 1854) in New South Wales. ACTA ACUST UNITED AC 1998. [DOI: 10.1071/pc980164] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Yellow-footed Rock-wallabies (YFRW) Petrogale xanthopus have declined in numbers since European settlement from past hunting for skins, habitat disturbance and predation and competition with feral animals (Gordon et al. 1978, 1993; Copley 1983; Henzell 1990). This has led to the species being classed as potentially vulnerable to extinction in Australia (Kennedy 1992), and endangered in New South Wales (Schedule 1, Threatened Species Conservation Act, 1995).
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Affiliation(s)
- L Fumagalli
- Department of Zoology, University of Queensland, Brisbane, Australia.
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Pope LC, Sharp A, Moritz C. Population structure of the yellow-footed rock-wallaby Petrogale xanthopus (Gray, 1854) inferred from mtDNA sequences and microsatellite loci. Mol Ecol 1996; 5:629-40. [PMID: 8873466 DOI: 10.1111/j.1365-294x.1996.tb00358.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The yellow-footed rock-wallaby Petrogale xanthopus is considered to be potentially vulnerable to extinction. This wallaby inhabits naturally disjunct rocky outcrops which could restrict dispersal between populations, but the extent to which that occurs is unknown. Genetic differences between populations were assessed using mitochondrial DNA (control region) sequencing and analysis of variation at four microsatellite loci among three geographically close sites in south-west Queensland (P. x. celeris) and, for mtDNA only, samples from South Australia (P. x. xanthopus) as well. Populations from South Australia and Queensland had phylogenetically distinct mtDNA, supporting the present classification of these two groups as evolutionarily distinct entities. Within Queensland, populations separated by 70 km of unsuitable habitat differed significantly for mtDNA and at microsatellite loci. Populations separated by 10 km of apparently suitable habitat had statistically homogeneous mtDNA, but a significant difference in allele frequency at one microsatellite locus. Tests for Hardy-Weinberg equilibrium and microgeographical variation at microsatellite loci did not detect any substructuring between two wallaby aggregations within a colony encircling a single rock outcrop. Although the present study was limited by small sample sizes at two of the three Queensland locations examined, the genetic results suggest that dispersal between colonies is limited, consistent with an ecological study of dispersal at one of the sites. Considering both the genetic and ecological data, we suggest that management of yellow-footed rock-wallabies should treat each colony as an independent unit and that conservation of the Queensland and South Australian populations as separate entities is warranted.
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Affiliation(s)
- L C Pope
- Centre for Conservation Biology, University of Queensland, St Lucia, Brisbane, Australia
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