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References on the use of Vortex 
 

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  • 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.      


  • Dayananda, B., S. Gray, D. Pike, and J. K. Webb. 2016. Communal nesting under climate change: fitness consequences of higher nest temperatures for a nocturnal lizard Global Change Biology 22:2405–2414.       URL: http://onlinelibrary.wiley.com/doi/10.1111/gcb.13231/abstract


  • 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


  • Frankham, R., J.D. Ballou, K. Ralls, M.D.B. Eldridge, M.R. Dudash, C.B. Fenster, R.C. Lacy, and P. Sunnucks. 2017. Genetic Management of Fragmented Animal and Plant Populations. Oxford University Press, Oxford UK.      A highly useful textbook that provides a lot of the background for how and when to use Vortex, PMx, and other tools for guiding the management of populations.


  • Hamilton, S. and Moller, H. 1995. Can PVA models using computer packages offer useful conservation advice? Sooty Shearwaters Puffinus griseus in New Zealand as a case study. Biological Conservation 72: 107-117      


  • 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      


  • Licht, D. S. 2014. Bison (Bison bison) restoration and management options on the South Unit and adjacent range units of Badlands National Park in South Dakota: a technical evaluation. Report NPS/BADL/NRR—2014/881. National Park Service, Fort Collins, CO.       URL: http://https://irma.nps.gov/DataStore/Reference/Profile/2217346


  • Licht, D. S. 2014. Restoration of bison (Bison bison) to Agate Fossil Beds National Monument: a feasibility study. Report NPS/AGFO/NRR—2014/883. National Park Service, Fort Collins, CO.       URL: http://https://irma.nps.gov/DataStore/Reference/Profile/2217352


  • Licht, D. S. 2016. The need for reliable funding for bison management. The George Wright Forum 33:18-28.      


  • Licht, D. S. 2017. Bison conservation in Northern Great Plains national parks: no need to panic. Great Plains Research 27:83-92.      ABSTRACT— Bison (Bison bison) are a keystone species in the North American Great Plains. They are also a species of conservation concern in part because they suffered a severe population bottleneck at the end of the 19th century and now exist in mostly small and isolated populations. Wind Cave National Park introduced 20 bison in 1913– 16; Theodore Roosevelt National Park introduced 29 animals to a South Unit in 1956 and subsequently transferred 20 bison from that herd to the park’s North Unit in 1962; and Badlands National Park introduced 53 animals in 1963– 64 and another 20 in 1984. The four herds are confined within fences, and no known introduction of new bison into the gene pools has occurred. The four herds are routinely culled down to approximately 425, 350, 200, and 700 animals, respectively. I found no evidence of inbreeding depression as measured by annual population growth and reproductive rates. A population viability analysis also failed to find persuasive evidence of inbreeding depression. Under current management scenarios, gene diversity in 100 years should remain above levels currently known to cause inbreeding depression in bison. I found no compelling reason to introduce new bison into the herds or transfer bison between herds in the foreseeable future.


  • Licht, D. S., R. A. Moen, and M. Romanski. 2017. Modeling viability of a potential Canada lynx reintroduction to Isle Royale National Park. Natural Areas Journal 37:170-177.      ABSTRACT: Canada lynx (Lynx canadensis) were extirpated from Isle Royale in the 1930s. We conducted a population viability analysis (PVA) of a potential lynx reintroduction to better understand viability, uncertainty, and management options. We estimated that the 544-km2 island can support 30 lynx. The probability of 100-year population persistence was 0.36 for a model that simulated a decadal lynx-hare population cycle. A noncyclic model predicted a 0.73 probability of 100-year persistence. Inbreeding depression had a substantial negative effect on modeled persistence. Historically, periodic immigration of mainland lynx via an ice bridge probably reduced or prevented inbreeding depression on the island. The introduction of one male and one female lynx every 10 years increased the probability of 100-year persistence to 0.98 in the cyclic model. Occasional anthropogenic transfers of lynx to the island might be necessary because the frequency of ice bridge formation has decreased. However, our baseline models might underestimate viability because they used demographic rates from mainland studies where lynx were exposed to anthropogenic mortality. When we removed assumed anthropogenic mortality—which should be negligible on Isle Royale—the probability of 100-year persistence was 0.99 for the cyclic model, even without supplementation. Reintroducing lynx to Isle Royale appears feasible, assuming appropriate monitoring and management. Reintroducing lynx would restore a missing native species to Isle Royale and would increase our understanding of lynx ecology.


  • Licht, D. S., R. A. Moen, D. P. Brown, and M. Romanski. 2016. Canada lynx restoration at Isle Royale National Park: a feasibility study. Report NPS/ISRO/NRR—2016/1251. National Park Service, Fort Collins, CO.       URL: http://https://irma.nps.gov/DataStore/Reference/Profile/2230736


  • Licht, D. S., R. A. Moen, D. P. Brown, M. C. Romanski, and R. A. Gitzen. 2015. The Canada lynx of Isle Royale: over-harvest and climate change and the extirpation of an island population. Canadian Field-Naturalist 129:139-151.      In the 1930s, the Canada Lynx (Lynx canadensis) was extirpated from Isle Royale, a 535-km2 island located in western Lake Superior, 22 km from the Ontario and Minnesota shorelines. The first half of the 20th century was a time of change on Isle Royale as Caribou (Rangifer tarandus) disappeared, Coyotes (Canis latrans) briefly appeared, Moose (Alces americanus), Grey wolves (Canis lupus), and Red Foxes (Vulpes vulpes) became established, and the habitat was altered by fire, logging, and over-browsing. Although these changes may have contributed to the demise of the Canada Lynx, our results suggest that over-harvest was a primary cause. assuming a peak carrying capacity of 75 Canada Lynx and harvest rates comparable to those reported from 1890–1935, a population viability analysis indicated that the island population had a 0% chance of surviving 50 years. The analysis also indicated that, even in the absence of harvest, the population had only a 14% chance of persistence for 250 years. however, when 10 Canada Lynx were added to the modeled population every 10th year, the probability of persistence increased to 100%. Our analyses suggest that the island’s Canada Lynx population maintained itself by periodic immigration across an ice bridge; therefore, natural recolonization should be possible. however, the probability of ice-bridge formation has declined from 0.8 in the winter of 1958–59 to 0.1 in 2012–13, likely as a result of climate change. The Isle Royale situation exemplifies another impact of climate change and the possible need to augment populations to mitigate the loss of connectivity.


  • 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/


  • Olsen MT, Andersen LW, Dietz R, Teilmann J, Härkönen T, Siegismund HR. Integrating genetic data and population viability analyses for the identification of harbour seal (Phoca vitulina) populations and management units. Mol Ecol. 2014;23(4):815-31.       URL: http://onlinelibrary.wiley.com/doi/10.1111/mec.12644/full


  • Pacioni, C. and Mayer, F. (2017) vortexR: an R package for post Vortex simulation analysis. Methods in Ecology and Evolution, In press.      vortexR is an R package to automate the analysis and visualisation of outputs from the population viability modelling software Vortex. vortexR facilitates collating Vortex output files, data visualisation and basic analyses (e.g. pairwise comparisons of scenarios), as well as providing more advanced statistics, such as searching for the best regression model(s) from a list of predictors to investigate the main effect and the interaction effects of the variables of interest. This package speeds up and greatly facilitates the reproducibility and portability of post-simulation analysis results. URL: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12786/abstract


  • Pacioni, C., Williams, M., Lacy, R.C., Spencer, P.B.S. and Wayne, A.F. (2017) Predators and genetic fitness: key threatening factors for the conservation of bettong species. Pacific Concervation Biology 23, 200-212.      Globally, many wildlife species are declining and an increasing number are threatened by extinction or are extinct. Active management is generally required to mitigate these trends and population viability analysis (PVA) enables different scenarios to be evaluated and informs management decisions. Based on population parameters obtained from a threatened bettong, the woylie (Bettongia penicillata ogilbyi), we developed and validated a PVA model. We identified the demographic and genetic responses to different threatening factors and developed a general framework that would facilitate similar work in other bettong species. The two main threatening processes are predation by introduced animals and its interaction with reduced fitness (e.g. due to inbreeding depression or a disease). Although predation alone can drive a decline in certain circumstances (e.g. when predation success is independent from prey population density), synergistically, predation and reduced fitness can be particularly relevant, especially for small populations. The minimum viable population size was estimated at 1000–2000 individuals. In addition, the models identified that research into age-specific mortality rates and predation rates by introduced animals should be the focus of future work. The PVA model created here provides a basis to investigate threatening processes and management strategies in woylie populations and other extant bettong species, given the ecological and physiological similarities among these threatened species. URL: http://www.publish.csiro.au/PC/PC17002


  • 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.      


  • Rivera, C.J. (2014) Facing the 2013 Gold Rush: A Population Viability Analysis for the Endangered White-Lipped Peccary (Tayassu pecari) in Corcovado National Park, Costa Rica. Natural Resources, 5, 1007-1019. doi: 10.4236/nr.2014.516085      


  • 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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