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Protocols in ecological and environmental plant physiology

 

Article << Previous     |     Next >>   Contents Vol 59(8)

Patterns of plant abundances in natural systems: is there value in modelling both species abundance and distribution?

Thomas J. Duff A C, Tina L. Bell B and Alan York A

A Forest and Fire Ecology Group, Department of Forest and Ecosystem Science, The University of Melbourne, Creswick, Vic. 3363, Australia.
B Faculty of Agriculture, Food and Natural Resources, University of Sydney, Redfern, NSW 2015, Australia.
C Corresponding author. Email: tjduff@unimelb.edu.au

Australian Journal of Botany 59(8) 719-733 http://dx.doi.org/10.1071/BT11017
Submitted: 14 January 2011  Accepted: 9 October 2011   Published: 28 November 2011


 
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Abstract

In plant ecology it is common to use biophysical models to predict species distribution; however, spatial quantitative models of plant species remain rare. In practice, occupancy models are often assumed to indicate habitant quality and are used as surrogate abundance models. This study assessed the potential value of quantitative models of plants for ecosystem management applications by assessing patterns of occupancy and abundance within two closely related understorey plant species, Xanthorrhoea australis and X. caespitosa. Vegetation quadrats were surveyed in Eucalyptus woodland and cover-abundances were assessed using a metric pin intersection technique. A zero inflated generalised additive modelling process was used to assess the relationship of species occupancies and cover-abundances to environmental properties. The models were applied to mapped environmental data to create spatial predictions of occupancy and cover-abundance. Both species shared several predictor variables, but differing responses to these variables resulted in mutually exclusive distributions. No significant correlation was observed between occupancy and cover-abundance for X. australis, but strong correlation was evident for X. caespitosa. The strength of the occupancy and abundance relationship was found to differ greatly between the two species and is therefore likely to be species specific. Occupancy models have been used successfully as proxies for habitat quality models of plant species; however where occupancy and abundance of plants are driven by different influences occupancy will be a poor surrogate for abundance. Outcomes may be improved if occupancy models are validated for abundance or quantitative models are developed and tested for individual species.



References

Accad A, Neil DT (2006) Modelling pre-clearing vegetation distribution using GIS-integrated statistical, ecological and data models: a case study from the wet tropics of northeastern Australia. Ecological Modelling 198, 85–100.
CrossRef |

Anjos RM, Macario K, Veiga R, Carvalho C, Mosquera B (2007) Radiometric analyses of beach sands from the southeast of Brazil. AIP Conference Proceedings 884, 249–253.
CrossRef | CAS |

Baeza M, Raventós J, Escarré A, Vallejo V (2006) Fire risk and vegetation structural dynamics in Mediterranean shrubland. Plant Ecology 187, 189–201.
CrossRef |

Barry SC, Welsh AH (2002) Generalized additive modelling and zero inflated count data. Ecological Modelling 157, 179–188.
CrossRef |

Batlla D, Grundy A, Dent KC, Clay HA, Finch-Savage WE (2009) A quantitative analysis of temperature-dependent dormancy changes in Polygonum aviculare seeds. Weed Research 49, 428–438.
CrossRef |

Betts MG, Diamond AW, Forbes GJ, Villard MA, Gunn JS (2006) The importance of spatial autocorrelation, extent and resolution in predicting forest bird occurrence. Ecological Modelling 191, 197–224.
CrossRef |

Bonham CD (1989) ‘Measurements for terrestrial vegetation.’ (John Wiley and Sons: New York)

Brown JH (1984) On the relationship between abundance and distribution of species. American Naturalist 124, 255–279.
CrossRef |

Brown JH, Mehlman DW, Stevens GC (1995) Spatial variation in abundance. Ecology 76, 2028–2043.
CrossRef |

Brzeziecki B, Kienast F, Wildi O (1993) A simulated map of the potential natural forest vegetation of Switzerland. Journal of Vegetation Science 4, 499–508.
CrossRef |

Brzeziecki B, Kienast F, Wildi O (1995) Modelling potential impacts of climate change on the spatial distribution of zonal forest communities in Switzerland. Journal of Vegetation Science 6, 257–268.
CrossRef |

Burgman MA, Lamont BB (1992) A stochastic model for the viability of Banksia cuneata populations: environmental demographic and genetic effects. Journal of Applied Ecology 29, 719–727.
CrossRef |

Burgman MA, Lindenmayer DB, Elith J (2005) Managing landscapes for conservation under uncertainty. Ecology 86, 2007–2017.
CrossRef |

Burnham KP (2004) Multimodel inference – understanding AIC and BIC in model selection. Sociological Methods & Research 33, 261–304.
CrossRef |

Cawsey EM, Austin MP, Baker BL (2002) Regional vegetation mapping in Australia: a case study in the practical use of statistical modelling. Biodiversity and Conservation 11, 2239–2274.
CrossRef |

Cawson J, Muir A (2008) ‘Fire and biodiversity monitoring. protocols for flora: users guide.’ (Department of Sustainability and Environment: Melbourne)

Cheal DC (1994) Fire succession in heathlands and implications for vegetation management. In ‘Biodiversity and fire: the effects and effectiveness of fire management’. Footscray, Melbourne.) (Department of the Environment, Sport and Territories)

Chiarucci A, Wilson JB, Barbara JA, Dominicis V (1999) Cover versus biomass as an estimate of species abundance: does it make a difference to the conclusions? Journal of Vegetation Science 10, 35–42.
CrossRef |

Coops NC, Catling PC (1997) Utilising airborne multispectral videography to predict habitat complexity in Eucalypt forests for wildlife management Wildlife Research 24, 691–702.
CrossRef |

Coops NC, Catling PC (2002) Prediction of the spatial distribution and relative abundance of ground-dwelling mammals using remote sensing imagery and simulation models. Landscape Ecology 17, 173–188.
CrossRef |

Cunningham RB, Lindenmayer DB (2005) Modeling count data of rare species: some statistical issues. Ecology 86, 1135–1142.
CrossRef |

Damgaard C (2008) Modelling pin-point plant cover data along an environmental gradient. Ecological Modelling 214, 404–410.
CrossRef |

Damgaard C (2009) On the distribution of plant abundance data. Ecological Informatics 4, 76–82.
CrossRef |

Department of Sustainability and Environment (2004a) ‘Glenelg Plains bioregion; EVC 48: heathy woodland.’ (Department of Sustainability and Environment, Victoria, Australia: Melbourne)

Department of Sustainability and Environment (2004b) ‘Portland fire protection plan.’ (Department of Sustainability and Environment, Victoria, Australia: Melbourne)

Department of Sustainability and Environment (2005a) ‘Advisory list of rare or threatened plants in Victoria – 2005.’ (Department of Sustainability and Environment: East Melbourne)

Department of Sustainability and Environment (2005b) ‘Portland Horsham forests – proposed forest management plan.’ (Department of Sustainability and Environment, Victoria, Australia: Melbourne)

Dodson JR (2001) Holocene vegetation change in the mediterranean-type climate regions of Australia. The Holocene 11, 673–680.
CrossRef |

Domenikiotis C, Dalezios NR, Loukas A, Karteris M (2002) Agreement assessment of NOAA/AVHRR NDVI with Landsat TM NDVI for mapping burned forested areas. International Journal of Remote Sensing 23, 4235–4246.
CrossRef |

Drechsler M, Lamont BB, Burgman MA, Resit Akcakaya H, Witkowski ETF, Supriyadi Y (1999) Modelling the persistence of an apparently immortal Banksia species after fire and land clearing. Biological Conservation 88, 249–259.
CrossRef |

Duncan M, Keane P (1996) Vegetation changes associated with Phytopthora cinnamomi and its decline under Xanthorrhoea australis in Kinglake National Park, Victoria. Australian Journal of Botany 44, 355–369.
CrossRef |

Elith J, Leathwick J, Hastie T (2008) A working guide to boosted regression trees. Journal of Animal Ecology 77, 802–813.
CrossRef | CAS |

Elzinga CL, Salzer DW, Willoughby JW (2007) ‘Measuring and monitoring plant populations.’ (Bureau of Land Management, Denver, Colorado, United States)

Enright NJ, Miller BP, Crawford A (1994) Environmental correlates of vegetation patterns and species richness in the northern Grampians, Victoria. Australian Journal of Ecology 19, 159–168.
CrossRef |

Falster DS, Murray BR, Lepschi BJ (2001) Linking abundance, occupancy and spatial structure: an empirical test of a neutral model in an open-forest woody plant community in eastern Australia. Journal of Biogeography 28, 317–323.
CrossRef |

Fernandes PM (2009) Combining forest structure data and fuel modelling to classify fire hazard in Portugal. Annals of Forest Science 66, 415
CrossRef |

Ferrier S (2002) Mapping spatial pattern in biodiversity for regional conservation planning: where to from here? Systematic Biology 51, 331–363.
CrossRef |

Ferrier S, Drielsma M, Manion G, Watson G (2002) Extended statistical approaches to modelling spatial pattern in biodiversity in northeast New South Wales. II. community-level modelling. Biodiversity and Conservation 11, 2309–2338.
CrossRef |

Floyd D, Anderson JE (1987) A comparison of three methods for estimating plant cover. Journal of Ecology 75, 221–228.

Franklin J (1998) Predicting the distribution of shrub species in Southern California from climate and terrain-derived variables. Journal of Vegetation Science 9, 733–748.
CrossRef |

Franklin J (2002) Enhancing a regional vegetation map with predictive models of dominant plant species in chaparral. Applied Vegetation Science 5, 135–146.
CrossRef |

Franklin JF (1993) Preserving biodiversity: species, ecosystems, or landscapes? Ecological Applications 3, 202–205.
CrossRef |

Frazer DS, Petit S (2007) Use of Xanthorrhoea semiplana (grass-trees) for refuge by Rattus fuscipes (southern bush rat). Wildlife Research 34, 379–386.
CrossRef |

Gallant JC, Dowling TI (2003) A multiresolution index of valley bottom flatness for mapping depositional areas. Water Resources Research 39, 1347–1353.
CrossRef |

Gary GJ, Morrison DA (1995) Effects of fire frequency on plant species composition of sandstone communities in the Sydney region: combinations of inter-fire intervals. Australian Journal of Ecology 20, 418–426.
CrossRef |

Gaston KJ (1996) The multiple forms of the interspecific abundance-distribution relationship. Oikos 76, 211–220.
CrossRef |

Gaston KJ, Blackburn TM, Greenwood JJD, Gregory RD, Quinn RM, Lawton JH (2000) Abundance-occupancy relationships. Journal of Applied Ecology 37, 39–59.
CrossRef |

Gibbons FR, Downes RG (1964) ‘A study of the land in South Western Victoria.’ (Soil Conservation Authority, Victoria: Melbourne)

Gibson M, Milne R, Cahill DM, Wilson BA, Baker BL (2002) ‘Preliminary review of the actual and potential distribution of Phytopthora cinnamomi dieback in parks and reserves across Victoria.’ (Centre for Environmental Management, University of Ballarat: Ballarat)

Guisan A, Zimmermann NE (2000) Predictive habitat distribution models in ecology. Ecological Modelling 135, 147–186.
CrossRef |

Guisan A, Theurillat JP, Kienast F (1998) Predicting the potential distribution of plant species in an alpine environment. Journal of Vegetation Science 9, 65–74.
CrossRef |

Guisan A, Weiss SB, Weiss AD (1999) GLM versus CCA spatial modeling of plant species distribution. Plant Ecology 143, 107–122.
CrossRef |

Hardin G (1960) The competitive exclusion principle. Science 131, 1292–1297.
CrossRef | CAS |

Hastie T, Tibshirani R (1987) Generalized additive models – some applications. Journal of the American Statistical Association 82, 371–386.
CrossRef |

He F, Gaston KJ (2000) Estimating species abundance from occurrence. American Naturalist 156, 553–559.
CrossRef |

He F, Gaston KJ (2003) Occupancy, spatial variance, and the abundance of species. American Naturalist 162, 366–375.
CrossRef |

He HS, Shang BZ, Crow TR, Gustafson EJ, Shifley SR (2004) Simulating forest fuel and fire risk dynamics across landscapes – LANDIS fuel module design. Ecological Modelling 180, 135–151.
CrossRef |

Holt RD, Pacala SW, Smith TW, Liu J (1995) Linking contemporary vegetation models with spatially explicit animal population models. Ecological Applications 5, 20–27.
CrossRef |

Huntley B, Bartlein PJ, Prentice IC (1989) Climatic control of the distribution and abundance of beech (Fagus L.) in Europe and North America. Journal of Biogeography 16, 551–560.
CrossRef |

Iverson LR, Prasad AM (1998) Predicting abundance of 80 tree species following climate change in the eastern United States. Ecological Monographs 68, 465–485.
CrossRef |

Jacobson CR (2010) Use of linguistic estimates and vegetation indices to assess post-fire vegetation regrowth in woodland areas. International Journal of Wildland Fire 19, 94–103.
CrossRef |

Jones R (1968) Estimating productivity and apparent photosynthesis from difference in consecutive measurements of total living plant parts of an Australian heathland. Australian Journal of Botany 16, 589–602.
CrossRef |

Keane RE, Burgan R, van Wagtendonk J (2001) Mapping wildland fuels for fire management across multiple scales: integrating remote sensing, GIS and biophysical modelling. International Journal of Wildland Fire 10, 301–319.
CrossRef |

Keith DA, Bedward M (1999) Native vegetation of the South East Forests region, Eden, New South Wales. Cunninghamia 6, 1–60.

Kirkpatrick JB, Brown MJ (1994) A comparison of direct and environmental domain approaches to planning reservation of forest higher plant communities and species in Tasmania. Conservation Biology 8, 217–224.
CrossRef |

Lamont BB, Wittkuhn R, Korczynskyj D (2004) TURNER REVIEW No. 8. Ecology and ecophysiology of grasstrees. Australian Journal of Botany 52, 561–582.
CrossRef |

Land Conservation Council (1972) ‘Report on the South Western Study Area (district 1).’ (Land Conservation Council, Victoria, Australia: Melbourne)

Leps J, Hadincova V (1992) How reliable are our vegetation analyses? Journal of Vegetation Science 3, 119–124.
CrossRef |

Londo G (1976) The decimal scale for releves of permanent quadrats. Plant Ecology 33, 61–64.
CrossRef |

Mackey BG (1994) Predicting the potential distribution of rain-forest structural characteristics. Journal of Vegetation Science 5, 43–54.
CrossRef |

Martin TG, Wintle BA, Rhodes JR, Kuhnert PM, Field SA, Low-Choy SJ, Tyre AJ, Possingham HP, Anderson M (2005) Zero tolerance ecology: improving ecological inference by modelling the source of zero observations. Ecology Letters 8, 1235–1246.
CrossRef |

McCarthy GJ, Tolhurst KG, Chatto K (1999) ‘Overall fuel hazard guide.’ (Department of Natural Resources and Environment), East Melbourne, Victoria, Australia

McCaw WL, Neal JE, Smith RH (2002) Stand characteristics and fuel accumulation in a sequence of even-aged Karri (Eucalyptus diversicolor) stands in south-west Western Australia. Forest Ecology and Management 158, 263–271.
CrossRef |

McKenzie NL, Belbin L, Margules CR, Keighery GJ (1989) Selecting representative reserve systems in remote areas: a case study in the Nullarbor region, Australia. Biological Conservation 50, 239–261.
CrossRef |

Melillo JM, McGuire D, Kicklighter DW, Moore B, Vorosmarty CJ, Schloss AL (1993) Global climate change and terrestrial net primary production. Nature 363, 234–240.
CrossRef | CAS |

Menges ES, Ascencio PFQ, Weekley CW, Gaoue OG (2006) Population viability analysis and fire return intervals for an endemic Florida scrub mint. Biological Conservation 127, 115–127.
CrossRef |

Miller JM (2007) Comparing Poisson, Hurdle and ZIP model fit under varying degrees of skew and zero-inflation. PhD Thesis, University of Florida, Gainesville, Florida, United States.

Moran PA (1950) Notes on continuous stochastic phenomena. Biometrika 37, 17–23.
| CAS |

Morrison DA, Lebrocque AF, Clarke PJ (1995) An assessment of some improved techniques for estimating the abundance (frequency) of sedentary organisms. Vegetatio 120, 131–145.
CrossRef |

Nielsen SE, Johnson CJ, Heard DC, Boyce MS (2005) Can models of presence-absence be used to scale abundance? Two case studies considering extremes in life history. Ecography 28, 197–208.
CrossRef |

Northcote KH (1979) ‘A factual key for the recognition of Australian soils.’ (Rellim Technical Publications: Adelaide)

Park SJ, Hwang CS, Vlek PLG (2005) Comparison of adaptive techniques to predict crop yield response under varying soil and land management conditions. Agricultural Systems 85, 59–81.
CrossRef |

Pearce J, Ferrier S (2001) The practical value of modelling relative abundance of species for regional conservation planning: a case study. Biological Conservation 98, 33–43.
CrossRef |

Pearce JL, Boyce MS (2006) Modelling distribution and abundance with presence-only data. Journal of Applied Ecology 43, 405–412.
CrossRef |

Petit S, Dickson CR (2005) Grass-tree (Xanthorrhoea semiplana, Liliaceae) facilitation of the endangered pink-lipped spider orchid (Caladenia syn. Arachnorchis behrii, Orchidaceae) varies in South Australia. Australian Journal of Botany 53, 455–464.
CrossRef |

Podani J (2005) Multivariate exploratory analysis of ordinal data in ecology: pitfalls, problems and solutions. Journal of Vegetation Science 16, 497–510.
CrossRef |

Podani J (2006) Braun-Blanquet’s legacy and data analysis in vegetation science. Journal of Vegetation Science 17, 113–117.
CrossRef |

Poore MED (1955) The use of phytosociological methods in ecological investigation: I. the Braun-Blanquet system. Journal of Ecology 43, 226–244.
CrossRef |

Potts JM, Elith J (2006) Comparing species abundance models. Ecological Modelling 199, 153–163.
CrossRef |

R Development Core Team (2009) ‘R: A language and environment for statistical computing’. (R Foundation for Statistical Computing: Vienna, Austria)

Radford JQ, Bennet AF, Cheers GJ (2005) Landscape level thresholds of habitat cover for woodland dependent birds. Biological Conservation 124, 317–337.
CrossRef |

Rathbun S, Fei S (2006) A spatial zero-inflated Poisson regression model for oak regeneration. Environmental and Ecological Statistics 13, 409–426.
CrossRef |

Rawlins BG, Lark RM, Webster R (2007) Understanding airborne radiometric survey signals across part of eastern England. Earth Surface Processes and Landforms 32, 1503–1515.
CrossRef |

Regan HM, Auld TD, Keith DA, Burgman MA (2003) The effects of fire and predators on the long-term persistence of an endangered shrub, Grevillea caleyi. Biological Conservation 109, 73–83.
CrossRef |

Ricotta C, Avena G (2006) On the evaluation of ordinal data with conventional multivariate procedures. Journal of Vegetation Science 17, 839–842.
CrossRef |

Ross JH, Walsh NG (2003) ‘A census of the vascular plants of Victoria.’ (Royal Botanic Gardens: South Yarra)

Sagarin RD, Gaines SD (2002) The ‘abundant centre’ distribution: to what extent is it a biogeographical rule? Ecology Letters 5, 137–147.
CrossRef |

Sagarin RD, Gaines SD, Gaylord B (2006) Moving beyond assumptions to understand abundance distributions across the ranges of species. Trends in Ecology & Evolution 21, 524–530.
CrossRef |

Shorrocks B, Albon S, Hartley S (1998) A positive relationship between local abundance and regional occupancy is almost inevitable (but not all positive relationships are the same). Journal of Animal Ecology 67, 992–994.
CrossRef |

Sørensen R, Zinko U, Seibert J (2006) On the calculation of the topographic wetness index: evaluation of different methods based on field observations. Hydrology and Earth System Sciences 10, 101–112.
CrossRef |

Sun D, Hnatiuk RJ, Neldner VJ (1997) Review of vegetation classification and mapping systems undertaken by major forested land management agencies in Australia. Australian Journal of Botany 45, 929–948.
CrossRef |

Swinburn ML, Fleming PA, Craig MD, Grigg AH, Garkaklis MJ, Hobbs RJ, Hardy GES (2007) The importance of grasstrees (Xanthorrhoea preissii) as habitat for mardo (Antechinus flavipes leucogaster) during post-fire recovery. Wildlife Research 34, 640–651.
CrossRef |

Trivedi MR, Morecroft MD, Berry PM, Dawson TP (2008) Potential effects of climate change on plant communities in three montane nature reserves in Scotland, UK. Biological Conservation 141, 1665–1675.
CrossRef |

Turnbull LA, Coomes DA, Purves DW, Rees M (2007) How spatial structure alters population and community dynamics in a natural plant community. Journal of Ecology 95, 79–89.
CrossRef |

van der Maarel E (1979) Transformation of cover-abundance in phytosociology and its effects on community similarity. Vegetatio 39, 97
CrossRef |

van der Maarel E (2007) Transformation of cover-abundance values for appropriate numerical treatment: alternatives to the proposals by Podani. Journal of Vegetation Science 18, 767–770.
CrossRef |

VanDerWal J, Shoo LP, Johnson CN, Williams SE (2009) Abundance and the environmental niche: environmental suitability estimated from niche models predicts the upper limit of local abundance. American Naturalist 174, 282–291.
CrossRef |

Walsh NG, Entwisle TJ (1994) ‘Flora of Victoria. Volume 2: ferns and allied plants, conifers and monocotyledons.’ (Inkata Press: Melbourne)

Wan L, Zhang B, Kemp P, Li X (2009) Modelling the abundance of three key plant species in New Zealand hill-pasture using a decision tree approach. Ecological Modelling 220, 1819–1825.
CrossRef | CAS |

Ward DJ, Lamont BB, Burrows CL (2001) Grasstrees reveal contrasting fire regimes in eucalypt forest before and after European settlement of southwestern Australia. Forest Ecology and Management 150, 323–329.
CrossRef |

Watson M, Mullen R (2007) Understanding soil tests for plant-available phosphorus factsheet. Ohio State University, Columbus, Ohio.

Welsh AH, Cunningham RB, Donnelly CF, Lindenmayer DB (1996) Modelling the abundance of rare species: statistical models for counts with extra zeros. Ecological Modelling 88, 297–308.
CrossRef |

Weste G (2001) Interaction between Phytopthora cinnamomi and Victorian native plant species growing in the wild. Australasian Mycologist 20, 64–72.

Wikum DA, Shanholtzer GF (1978) Application of the Braun-Blanquet cover-abundance scale for vegetation analysis in land development studies. Environmental Management 2, 323–329.
CrossRef |

Wintle BA, Elith J, Potts JM (2005) Fauna habitat modelling and mapping: a review and case study in the lower Hunter Central Coast Region of NSW. Austral Ecology 30, 719–738.
CrossRef |

Wood SN (2008) Fast stable direct fitting and smoothness selection for generalized additive models. Journal of the Royal Statistical Society. Series B, Statistical Methodology 70, 495–518.
CrossRef |

Wood SN (2011) Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models. Journal of the Royal Statistical Society. Series B, Statistical Methodology 73, 3–36.
CrossRef |

Wright DH (1991) Correlations between incidence and abundance are expected by chance. Journal of Biogeography 18, 463–466.
CrossRef |

Zhang B, Valentine I, Kemp PD (2005) A decision tree approach modelling functional group abundance in a pasture ecosystem. Agriculture Ecosystems & Environment 110, 279–288.
CrossRef |


   
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