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Software tools for species risk assessment, conservation planning, and population management

References on the use of Vortex 
 

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  • 88952634      88952634 URL: http://88952634


  • 88952634      88952634 URL: http://88952634


  • Ballou, J.D., K. Traylor-Holzer, A. Turner, A.F. Malo, D. Powell, J. Maldonado, and L. Eggert. 2008. Simulation model for contraceptive management of the Assateague Island feral horse population using individual-based data. Wildlife Research 35: 502-512.      An individual-based Vortex model was developed to examine the effects of different management strategies to control population size in feral horses on Assateague Island. Model results guided the National Park Service in management to achieve and maintain the target size of this culturally significant population to minimize negative impacts on native species and ecological processes without significant compromised viability.


  • Brook, B.W., Burgman, M.A., Frankham, R. 2000. Differences and Congruencies between PVA Packages: the Importance of Sex Ratio for Predictions of Extinction Risk. Conservation Ecology. 4.1. Online: http://www.consecol.org/vol4/iss1/art6/index.html       URL: http://www.consecol.org/vol4/iss1/art6/index.html


  • Brook, B.W., J.R. Cannon, R.C. Lacy, C. Mirande, and R. Frankham. 1999. Comparison of the population viability analysis packages GAPPS, INMAT, RAMAS and VORTEX for the whooping crane (Grus americana). Animal Conservation 2:23–31      


  • Carroll, C., R.J. Frederickson, and R.C. Lacy. 2014. Developing metapopulation connectivity criteria from genetic and habitat data to recover the endangered Mexican wolf. Conservation Biology 28:76-86.      


  • Desbiez, A., K. Traylor-Holzer, R. Lacy, et al. 2012. Population Viability Analysis of jaguar populations in Brazil. In: Jaguar in Brazil. CATnews (Special Issue) 7:35-37      


  • Ebenhard, T. (2000). Population viability analyses in endangered species management: the wolf, otter and peregrine falcon in Sweden. Ecological Bulletins, 143-163.       URL: http://www.jstor.org/stable/20113254?seq=1#page_scan_tab_contents


  • Hart, R. A., J. W. Grier, and A. C. Miller. 2004. Simulation models of harvested and zebra mussel colonized threeridge mussel populations in Lake Pepin, Upper Mississippi River. The American Midland Naturalist 151:301-317.       URL: http://www.galvestonlab.sefsc.noaa.gov/publications/pdf/852.pdf


  • Heinsohn, R., R. C. Lacy, D. B. Lindenmayer, H. Marsh, D. Kwan, and I.R. Lawler. 2004. Unsustainable harvest of dugongs in Torres Strait and Cape York (Australia) waters: two case studies using population viability analysis. Animal Conservation 7:417-425.      


  • Hosack, D.A., P.S. Miller, J.J. Hervert, and R.C. Lacy. 2002. A population viability analysis for the endangered Sonoran pronghorn, Antilocapra americana sonoriensis. Mammalia 66:207-229.      


  • Jaric, I., Ebenhard, T. and Lenhardt, M. (2010). Population Viability Analysis of the Danube sturgeon populations in a VORTEX simulation model. Reviews in Fish Biology and Fisheries 20 (2), 219-237.       URL: http://link.springer.com/article/10.1007/s11160-009-9151-0


  • Jaric, I., Knezevic-Jaric, J., Cvijanovic, G. and Lenhardt, M. (2011). Population viability analysis of the European sturgeon (Acipenser sturio L.) from the Gironde Estuary system. In: P. Williot et al. (eds.), Biology and conservation of the European sturgeon Acipenser sturio L. 1758. Springer-Verlag Berlin Heidelberg, 603-619.       URL: http://link.springer.com/chapter/10.1007/978-3-642-20611-5_46


  • King, T., C. Chamberlan, and A. Courage. 2013. Assessing reintroduction success in long-lived primates through population viability analysis: western lowland gorillas Gorilla gorilla gorilla in Central Africa. Oryx (electronic pre-publication) doi:10.1017/S0030605312001391       URL: http://journals.cambridge.org/orx/long-lived-primates


  • Lacy, R.C. 2000. Structure of the VORTEX simulation model for population viability analysis. Ecological Bulletins 48:191-203.      This is the core paper that describes the basic algorithms in Vortex.


  • Lacy, R.C. and D.B. Lindenmayer. 1995. A simulation study of the impacts of population subdivision on the mountain brushtail possum, Trichosurus caninus Ogilby (Phalangeridae: Marsupialia), in south eastern Australia. II. Loss of genetic variation within and between subpopulations. Biological Conservation 73:131-142      


  • Lacy, R.C. and T.W. Clark. 1990. Population viability assessment of the eastern barred bandicoot in Victoria. Pages 131-146 in T.W. Clark and J.H. Seebeck (eds.), The Management and Conservation of Small Populations. Chicago Zoological Society      


  • Lindenmayer, D.B. and R.C. Lacy. 1995. A simulation study of the impacts of population subdivision on the mountain brushtail possum, Trichosurus caninus Ogilby (Phalangeridae: Marsupialia), in south eastern Australia. I. Demographic stability and population persistence. Biological Conservation 73:119-129.      


  • Lindenmayer, D.B. and R.C. Lacy. 1995. Metapopulation viability of arboreal marsupials in fragmented old-growth forests: comparison among species. Ecological Applications 5:183-199.      


  • Lindenmayer, D.B. and R.C. Lacy. 1995. Metapopulation viability of Leadbeater's Possum, Gymnobelideus leadbeateri, in fragmented old-growth forests. Ecological Applications 5:164-182.      


  • Lindenmayer, D.B., and R.C. Lacy. 2002. Small mammals, habitat patches and PVA models: a field test of model predictive ability. Biological Conservation 103:247-265      


  • Lindenmayer, D.B., Burgman, M.A., Akcakaya, H.R., Lacy, R.C., Possingham, H.P. 1995. A Review of the generic computer programs ALEX, RAMAS/space and VORTEX for modelling the viability of wildlife metapopulations. Ecological Modelling 82: 161-172.      


  • Lindenmayer, D.B., R.C. Lacy, and M.L. Pope. 2000. Testing a simulation model for Population Viability Analysis. Ecological Applications 10:580-597      


  • Lindenmayer, D.B., R.C. Lacy, V.C. Thomas, and T.W. Clark. 1993. Predictions of the impacts of changes in population size and environmental variability on Leadbeater's Possum, Gymnobelideus leadbeateri McCoy (Marsupialia: Petauridae) using Population Viability Analysis: an application of the computer program VORTEX. Wildlife Research 20:67-86.      


  • Maehr, D.S., R.C. Lacy, E.D. Land, O.L. Bass, and T.S. Hoctor. 2002. Evolution of Population Viability Assessments for the Florida panther: A multiperspective approach. Pages 284-311 in S.R. Beissinger and D.R. McCullough (eds.), Population Viability Analysis. University of Chicago Press, Chicago.      


  • Maguire, L.A., R.C. Lacy, R.J. Begg, and T.W. Clark. 1990. An analysis of alternative strategies for recovering the eastern barred bandicoot in Victoria. Pages 147-164 in T.W. Clark and J.H. Seebeck (eds.), The Management and Conservation of Small Populations. Chicago Zoological Society, Brookfield, Illinois.      


  • Manlik, O., J.A. McDonald, J. Mann, H.C. Raudino, L. Bejder, M. Krützen, R.C. Connor, M.R. Heithaus, R.C. Lacy, and W.B. Sherwin. 2016. The relative importance of reproduction and survival for the conservation of two dolphin populations. Ecology & Evolution (on-line version)      It has been proposed that in slow-growing vertebrate populations survival generally has a greater influence on population growth than reproduction. Despite many studies cautioning against such generalizations for conservation, wildlife management for slow-growing populations still often focuses on perturbing survival without careful evaluation as to whether those changes are likely or feasible. Here, we evaluate the relative importance of reproduction and survival for the conservation of two bottlenose dolphin (Tursiops cf aduncus) populations: a large, apparently stable population and a smaller one that is forecast to decline. We also assessed the feasibility and effectiveness of wildlife management objectives aimed at boosting either reproduction or survival. Consistent with other analytically based elasticity studies, survival had the greatest effect on population trajectories when altering vital rates by equal proportions. However, the findings of our alternative analytical approaches are in stark contrast to commonly used proportional sensitivity analyses and suggest that reproduction is considerably more important. We show that 1 in the stable population reproductive output is higher, and adult survival is lower; 2 the difference in viability between the two populations is due to the difference in reproduction; 3 reproductive rates are variable, whereas survival rates are relatively constant over time; 4 perturbations on the basis of observed, temporal variation indicate that population dynamics are much more influenced by reproduction than by adult survival; 5 for the apparently declining population, raising reproductive rates would be an effective and feasible tool to reverse the forecast population decline; increasing survival would be ineffective. Our findings highlight the importance of reproduction – even in slow-growing populations – and the need to assess the effect of natural variation in vital rates on population viability. We echo others in cautioning against generalizations based on life-history traits and recommend that population modeling for conservation should also take into account the magnitude of vital rate changes that could be attained under alternative management scenarios. URL: http://onlinelibrary.wiley.com/doi/10.1002/ece3.2130/full


  • Marshall, A.J., R. Lacy, M. Ancrenaz, O. Byers, S.J. Husson, M. Leighton, E. Meijaard, N. Rosen, I. Singleton, S. Stephens, K. Traylor-Holzer, S.S.U. Atmoko, C.P. van Schaik, and S.A. Wich. 2009. Orangutan population biology, life history, and conservation. Pages 311-326 in: S.A. Wich, S.S.I. Atmoko, T.M. Setia, and C.P. van Schaik, eds. Orangutans. Oxford University Press, Oxford, UK.      


  • Matamoros, Y., H. Vargas, R. C. Lacy, O. Byers, E. Travis, G. Montoya. (Editores). 2006. Taller para Anàlisisde Viabilidad de Poblaciòn y Hàbitat para el Pingüino de Galápagos. Informe Final. Parque Nacional Galápagos, Puerto Ayora, Santa Cruz, Galápagos, Ecuador. 8-11 de febrero, 2005      


  • Naveda-Rodríguez A, Vargas FH, Kohn S, Zapata-Ríos G (2016) Andean Condor (Vultur gryphus) in Ecuador: Geographic Distribution, Population Size and Extinction Risk. PLoS ONE 11(3): e0151827. doi:10.1371/journal.pone.0151827       URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0151827


  • Nilsson, T. 2013. Population viability analyses of the Scandinavian populations of bear (Ursus arctos), lynx (Lynx lynx) and wolverine (Gulo gulo). Swedish Environmental Protection Agency, Stockholm.       URL: http://www.naturvardsverket.se/Om-Naturvardsverket/Publikationer/ISBN/6500/978-91-620-6549-2/


  • Penn, A.M., W.B. Sherwin, G. Gordon, D. Lunney, A. Melzer, and R.C. Lacy. 2000. Demographic forecasting in koala conservation. Conservation Biology 14:629-638      


  • Pergams, O.R.W., R.C. Lacy, and M.V. Ashley. 2000. Conservation and management of Anacapa Island Deer Mice. Conservation Biology 14:819-832.      


  • Prowse, T.A.A., C.N. Johnson, R.C. Lacy, C.J.A. Bradshaw, J.P. Pollak, M.J. Watts, and B.W. Brook. 2013. No need for disease: testing extinction hypotheses for the thylacine using multi-species metamodels. Journal of Animal Ecology 82:355-364.      


  • Serrano E, Colom-Cadena A, Gilot-Fromont E, Garel M, Cabezón O, Velarde R, Fernández-Sirera L, Fernández-Aguilar X, Rosell R, Lavín S and Marco I (2015) Border Disease Virus: An Exceptional Driver of Chamois Populations Among Other Threats. Front. Microbiol. 6:1307. doi: 10.3389/fmicb.2015.01307      Though it is accepted that emerging infectious diseases are a threat to planet biodiversity, little information exists about their role as drivers of species extinction. Populations are also affected by natural catastrophes and other pathogens, making it difficult to estimate the particular impact of emerging infectious diseases. Border disease virus genogroup 4 (BDV-4) caused a previously unreported decrease in populations of Pyrenean chamois (Rupicapra pyrenaica pyrenaica) in Spain. Using a population viability analysis, we compared probabilities of extinction of a virtual chamois population affected by winter conditions, density dependence, keratoconjunctivitis, sarcoptic mange, and BD outbreaks. BD-affected populations showed double risk of becoming extinct in 50 years, confirming the exceptional ability of this virus to drive chamois populations. URL: http://journal.frontiersin.org/article/10.3389/fmicb.2015.01307/abstract


  • Vargas, F.H., R.C. Lacy, P.J. Johnson, A. Steinfurth, R.J.M. Crawford, P.D. Boersma, and D.W. MacDonald. 2007. Modelling the effect of El Niño on the persistence of small populations: The Galápagos penguin as a case study. Biological Conservation 137:138-148      


  • Wells, K., B.W. Brook, R.C. Lacy, G.J. Mutze, D.E. Peacock, R.G. Sinclair, N. Schwensow, P. Cassey, R.B. O’Hara, and D.A. Fordham. 2015. Timing and severity of immunizing diseases in rabbits is controlled by seasonal matching of host and pathogen dynamics. Journal of the Royal Society Interface 12:2014184      This paper uses MetaModel Manager to link Outbreak models of disease with a Vortex demographic model in order to examine the role of the relative timing of reproduction and disease introduction on the effectiveness of disease in controlling invasive populations of rabbits. URL: http://dx.doi.org/10.1098/rsif.2014.1184

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