Abstract
Quantitative reconstructions of past environmental conditions (e.g., pH) are an important part of palaeolimnology. Such reconstructions involve three steps: (1) the development of a representative modern organism-environment training-set, (2) the development and application of appropriate numerical techniques to model the relationship between modern occurrences and abundances of the organisms in the training-set and their contemporary environment, and (3) the application of this model to stratigraphical palaeolimnological data to infer past environmental conditions, and model selection, testing, and evaluation and assessment of the final reconstruction. These three stages are discussed. Problems of spatial autocorrelation are outlined. The general approach is illustrated by a case-study. The assumptions and limitations of the calibration-function approach are presented, and violations of these assumptions are discussed in relation to different environmental reconstructions. Appropriate computer software is outlined, and future research areas are presented. The chapter challenges palaeolimnologists to be more critical of their environmental-inference models and to be alert to the problems and dangers of confounding variables, and of violating the main assumptions of the approach.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Adler S (2010) Paltran: Please provide the accessed date of references, “Adler (2010), Correa‐Metrio et~al. (2011), Juggins (2009), Oksanen et~al. (2011), R Development Core Team (2010), Simpson and Oksanen (2009), and Telford (2011)”. WA, WA-PLS, MW for paleolimnology. R package version 1.3-0. http://CRAN.R-project.org/package=paltran
Adler S, Hübener T, Dressler M, Lotter AF, Anderson NJ (2010) A comparison of relative abundance versus class data in diatom-based quantitative reconstructions. J Environ Manage 91:1380–1388
Allott TEH, Harriman R, Battarbee RW (1992) Reversibility of lake acidification at The Round Loch of Glenhead, Galloway, Scotland. Environ Pollut 77:219–225
Anderson NJ (2000) Diatoms, temperature and climate change. Eur J Phycol 35:307–314
Aykroyd RG, Lucy D, Pollard AM, Carter AHC, Robertson I (2001) Temporal variability in the strength of proxy-climate correlations. Geophys Res Lett 28:1559–1562
Barrows TT, Juggins S (2005) Sea-surface temperatures around the Australian margin and Indian ocean during the Last Glacial Maximum. Quat Sci Rev 24:1017–1047
Bartlein PJ, Whitlock C (1993) Paleoclimatic interpretation of the Elk Lake pollen record. In: Bradbury JP, Dean WE (eds) Elk Lake, Minnesota: evidence for rapid climatic change in the North-Central United States. Geological Society of America, Boulder, pp 275–293
Basheer JA, Hajmeer M (2000) Artificial neural networks: fundamentals, computing, design, and application. J Microbiol Methods 43:3–31
Battarbee RW (2000) Palaeolimnological approaches to climate change, with special regard to the biological record. Quat Sci Rev 19:107–124
Battarbee RW, Bennion H (2011) Palaeolimnology and its developing role in assessing the history and extent of human impact on lake ecosystems. J Paleolimnol 45:399–404
Battarbee RW, Juggins S, Gasse F, Anderson NJ, Bennion H, Cameron N (2000) European Diatom Database (EDDI): an information system for palaeoenvironmental reconstruction. In: European climate science conference, Vienna, 19–23 Oct 1998
Battarbee RW, Grytnes J-A, Thompson R, Appleby PG, Catalan J, Korhola A, Birks HJB, Heegaard E, Lami A (2002) Comparing palaeolimnological and instrumental evidence of climate change for remote mountain lakes over the last 2000 years. J Paleolimnol 28:161–179
Battarbee RW, Anderson NJ, Jeppesen E, Leavitt PR (2005a) Combining palaeolimnological and limnological approaches in assessing lake ecosystem response to nutrient reduction. Freshw Biol 50:1772–1780
Battarbee RW, Monteith DT, Juggins S, Evans CD, Jenkins A, Simpson GL (2005b) Reconstructing pre-acidification pH for an acidified Scottish loch: a comparison of palaeolimnological and modelling approaches. Environ Pollut 137:135–149
Battarbee RW, Monteith DT, Juggins S, Simpson GL, Shilland EW, Flower RJ, Kreiser AM (2008) Assessing the accuracy of diatom-based transfer functions in defining reference conditions for acidified lakes in the United Kingdom. The Holocene 18:57–67
Battarbee RW, Charles D, Bigler C, Cumming BF, Renberg I (2010) Diatoms as indicators of surface water acidity. In: Smol JP, Stoermer EF (eds) The diatoms: applications for the environmental and earth sciences, 2nd edn. Cambridge University Press, Cambridge, pp 98–121
Battarbee RW, Simpson GL, Bennin H, Curtis C (2011) A reference typology of low alkalinity lakes in the UK based on pre-acidification diatom assemblages from lake sediment cores. J Paleolimnol 45:489–505
Beerling DJ, Birks HH, Woodward FI (1995) Rapid late-glacial atmospheric CO2 changes reconstructed from the stomatal density record of fossil leaves. J Quat Sci 10:379–384
Bennett KD, Humphry RW (1995) Analysis of late-glacial and Holocene rates of vegetational change at two sites in the British Isles. Rev Palaeobot Palynol 85:263–287
Bennion H (1994) A diatom-phosphorus transfer function for shallow, eutrophic ponds in southeast England. Hydrobiologia 275(276):391–410
Bennion H, Simpson GL (2011) The use of diatom records to establish reference conditions for UK lakes subject to eutrophication. J Paleolimnol 45:469–488
Bennion H, Juggins S, Anderson NJ (1996) Predicting epilimnetic phosphorus concentrations using an improved diatom-based transfer function and its application to lake eutrophication management. Environ Sci Technol 30:2004–2007
Bennion H, Battarbee RW, Sayer CD, Simpson GL, Davidson TA (2011a) Defining reference conditions and restoration targets for lake ecosystems using palaeolimnology: a synthesis. J Paleolimnol 45:533–544
Bennion H, Simpson GL, Anderson NJ, Clarke G, Dong X, Hobæk A, Guilizzoni P, Marchetto A, Sayer CD, Thies H, Tolotti M (2011b) Defining ecological and chemical reference conditions and restoration targets for nine European lakes. J Paleolimnol 45:415–431
Bigler C, Hall RI (2003) Diatoms as quantitative indicators of July temperature: a validation attempt at century-scale with meteorological data from northern Sweden. Palaeogeogr Palaeoclim Palaeoecol 189:147–160
Bigler C, Larocque I, Peglar SM, Birks HJB, Hall RI (2002) Quantitative multiproxy assessment of long-term patterns of Holocene environmental change from a small lake near Abisko, northern Sweden. The Holocene 12:481–496
Bindler R, Korsman T, Renberg I, Hogberg P (2002) Pre-industrial atmospheric pollution: was it important for the pH of acid-sensitive Swedish lakes? Ambio 31:460–465
Birks HJB (1994) The importance of pollen and diatom taxonomic precision in quantitative palaeoenvironmental reconstructions. Rev Palaeobot Palynol 83:107–117
Birks HJB (1995) Quantitative palaeoenvironmental reconstructions. In: Maddy D, Brew J (eds) Statistical modelling of Quaternary science data. Technical guide 5. Quaternary Research Association, Cambridge, pp 161–254
Birks HJB (1998) Numerical tools in palaeolimnology - progress, potentialities, and problems. J Paleolimnol 20:307–322
Birks HJB (2001) Maximum likelihood environmental calibration and the computer program WACALIB - a correction. J Paleolimnol 25:111–115
Birks HJB (2003) Quantitative palaeoenvironmental reconstructions from Holocene biological data. In: Mackay A, Battarbee RW, Birks HJB, Oldfield F (eds) Global change in the Holocene. Arnold, London, pp 107–123
Birks HJB (2010) Numerical methods for the analysis of diatom assemblage data. In: Smol JP, Stoermer EF (eds) The diatoms – applications for the environmental and earth sciences. Cambridge University Press, Cambridge, pp 23–54
Birks HJBB (2012) Chapter 2: Please provide page range for the references “Birks (2012), Birks and Jones (2012), Cumming et~al. (2012), Juggins and Telford (2012), Legendre and Birks (2012), Legendre and Birks (2012), Lotter and Anderson (2012), Maher et~al. (2012), Simpson (2012), Simpson and Birks (2012), and Simpson and Hall (2012)”. Overview of numerical methods in palaeolimnology. In: Birks HJB, Lotter AF, Juggins S, Smol JP (eds) Tracking environmental change using lake sediments, vol 5: data handling and numerical techniques. Springer, Dordrecht
Birks HH, Ammann B (2000) Two terrestrial records of rapid climatic change during the glacial-Holocene transition (14,000-9,000 calendar years BP) from Europe. Proc Natl Acad Sci USA 97:139–1394
Birks HH, Birks HJB (2006) Multi-proxy studies in palaeolimnology. Veg Hist Archaeobot 15:235–251
Birks HJB, Jones VJ (2012) Chapter 3: Data-sets. In: Birks HJB, Lotter AF, Juggins S, Smol JP (eds) Tracking environmental change using lake sediments, vol 5: data handling and numerical techniques. Springer, Dordrecht
Birks HJB, Seppä H (2004) Pollen-based reconstructions of late-Quaternary climate in Europe – progress, problems, and pitfalls. Acta Palaeobot 44:317–334
Birks HJB, Line JM, Juggins S, Stevenson AC, ter Braak CJF (1990a) Diatoms and pH reconstruction. Phil Trans R Soc Lond B 327:263–278
Birks HJB, Juggins S, Line JM (1990b) Lake surface-water chemistry reconstructions from palaeolimnological data. In: Mason BJ (ed) The surface waters acidification programme. Cambridge University Press, Cambridge, pp 301–313
Birks HH, Battarbee RW, Birks HJB (2000) The development of the aquatic ecosystem at Krakenes Lake, western Norway, during the late glacial and early Holocene - a synthesis. J Paleolimnol 23:91–114
Birks HJB, Heiri O, Seppä H, Bjune AE (2010) Strengths and weaknesses of quantitative climate reconstructions based on late-Quaternary biological proxies. Open Ecol J 3:68–110
Birks HH, Jones VJ, Brooks SJ, Please update the details of references, “Birks (2011), Velle (2011b)”. Peglar SM, Telford RJ, Juggins S, Birks HJB (2011) From cold to cool in northernmost Norway: late-glacial multiproxy environmental reconstructions from Jansvatnet, Hammerfest. Quat Sci Rev (submitted)
Borcard D, Legendre P, Drapeau P (1992) Partialling out the spatial component of ecological variation. Ecology 73:1045–1055
Borcard D, Gillet F, Legendre P (2011) Numerical ecology with R. Springer, New York
Braak CJF, Šmilauer P (2002) CANOCO reference manual and CanoDraw user’s guide – software for canonical community ordination (version 4.5). Microcomputer Power, Ithaca
Bradshaw EG, Anderson NJ (2001) Validation of a diatom-phosphorus calibration set for Sweden. Freshw Biol 46:1035–1048
Bradshaw EG, Rasmussen P, Nielsen H, Anderson NJ (2005) Mid- to late-Holocene land-use change and lake development at Dallund So, Denmark: trends in lake primary production as reflected by algal and macrophyte remains. The Holocene 15:1130–1142
Brenner M, Whitmore TJ, Flannery MS, Binford MW (1993) Paleolimnological methods for defining target conditions in lake restoration: Florida case studies. Lake Reserv Manage 7: 209–217
Brewer S, Guiot J, Barboni D (2007) Use of pollen as climate proxies. In: Elias SA (ed) Encyclopedia of quaternary science. Elsevier, Oxford, pp 2497–2508
Brooks SJ (2003) Chironomid analysis to interpret and quantify Holocene climate change. In: Mackay A, Battarbee RW, Birks HJB, Oldfield F (eds) Global change in the Holocene. Arnold, London, pp 328–341
Brooks SJ, Birks HJB (2001) Chironomid-inferred air temperatures from Lateglacial and Holocene sites in north-west Europe: progress and problems. Quat Sci Rev 20:1723–1741
Cameron NG, Birks HJB, Jones VJ, Berge F, Catalan J, Flower RJ, Garcia J, Kawecka B, Koinig KA, Marchetto A, Sanchez-Castillo P, Schmidt R, Sisko M, Solovieva N, Stefkova E, Toro M (1999) Surface-sediment and epilithic diatom pH calibration sets for remote European mountain lakes (AL: PE Project) and their comparison with the Surface Waters Acidification Programme (SWAP) calibration set. J Paleolimnol 22:291–317
Charles DF (1985) Relationships between surface sediment diatom assemblages and lakewater characteristics in Adirondack lakes. Ecology 66:994–1011
Clarke A (2001) A diatom-based transfer function to infer historical changes in total nitrogen from coastal sediments: a case study from Roskilde Fjord, Denmark. Unpublished PhD thesis, University of Newcastle, Newcastle upon Tyne, UK
Clarke A, Juggins S, Conley D (2003) A 150-year reconstruction of the history of coastal eutrophication in Roskilde Fjord, Denmark. Mar Pollut Bull 46:1615–1629
Cook DR, Weisberg S (1982) Residuals and influence in regression. Monographs on statistics and applied probability. Chapman & Hall, London
Correa-Metrio A, Urrego DH, Cabrera KR, Bush MB (2011) PaleoMAS: paleoecological analysis. R package version 2.0. http://CRAN.R-project.org/package=paleoMAS
Coudun C, Gégout J-C (2006) The derivation of species response curves with Gaussian logistic regression is sensitive to sampling intensity and curve characteristics. Ecol Model 199: 164–175
Crawley M (2005) Statistics. An introduction using R. Wiley, Chichester
Cumming BF, Smol JP (1993) Development of diatom-based salinity models for paleoclimatic research from lakes in British Columbia (Canada). Hydrobiologia 269(270):179–196
Cumming BF, Smol JP, Birks HJB (1992) Scaled chrysophytes (Chrysophyceae and Synurophyceae) from Adirondack Drainage Lakes and their relationship to environmental variables. J Phycol 28:162–178
Cumming BF, Laird KR, Fritz SC, Verschuren D (2012) Chapter 20: Tracking Holocene climatic change with aquatic biota from lake sediments: case studies of commonly used numerical techniques. In: Birks HJB, Lotter AF, Juggins S, Smol JP (eds) Tracking environmental change using lake sediments, vol 5: data handling and numerical techniques. Springer, Dordrecht
Curtis CJ, Juggins S, Clarke G, Battarbee RW, Kernan M, Catalan J, Thompson R, Posch M (2009) Regional influence of acid deposition and climate change in European lakes assessed using diatom transfer functions. Freshw Biol 54:2555–2572
Dabakk E, Nilsson M, Geladi P, Wold S, Renberg I (1999) Sampling reproducibility and error estimation in near infrared calibration of lake sediments for water quality monitoring. J NIR Spectrosc 7:241–250
Davies JJL, Jenkins A, Monteith DT, Evans CD, Cooper DM (2005) Trends in surface water chemistry of acidified UK freshwaters, 1988–2002. Environ Pollut 137:27–39
Davis B, Brewer S, Stevenson A, Guiot J (2003) The temperature of Europe during the Holocene reconstructed from pollen data. Quat Sci Rev 22:1701–1716
Dixit SS, Smol JP, Charles DF, Hughes RM, Paulsen SG, Collins GB (1999) Assessing water quality changes in the lakes of the northeastern United States using sediment diatoms. Can J Fish Aquat Sci 56:131–152
Dixit SS, Dixit AS, Smol JP (2002) Diatom and chrysophyte functions and inferences of post-industrial acidification and recent recovery trends in Killarney lakes (Ontario, Canada). J Paleolimnol 27:79–96
Draper NR, Smith H (1981) Applied regression analysis. Wiley, New York
Engstrom DR, Fritz SC, Almendinger JE, Juggins S (2000) Chemical and biological trends during lake evolution in recently deglaciated terrain. Nature 408:161–166
Faith DP, Minchin PR, Belbin L (1987) Compositional dissimilarity as a robust measure of ecological distance. Vegetatio 69:57–68
Finsinger W, Wagner-Cremer F (2009) Stomatal-based inference models for reconstruction of atmospheric CO2 concentration: a method assessment using a calibration and validation approach. The Holocene 19:757–764
Flower RJ (1986) The relationship between surface sediment diatom assemblages and pH in 33 Galloway lakes: some regression models for reconstructing pH and their application to sediment cores. Hydrobiologia 143:93–103
Flower R, Battarbee R (1983) Diatom evidence for recent acidification of two Scottish Lochs. Nature 305:130–133
Fritz SC (1990) Twentieth-century salinity and water-level fluctuations in Devils Lake, North Dakota: test of a diatom-based transfer function. Limnol Oceanogr 35:1171–1781
Fritz SC, Juggins S, Battarbee RW, Engstrom DR (1991) Reconstruction of past changes in salinity and climate using a diatom-based transfer function. Nature 352:706–708
Fritz SC, Kingston JC, Engstrom DR (1993) Quantitative trophic reconstruction from sedimentary diatom assemblages: a cautionary tale. Freshw Biol 30:1–23
Fritz SC, Engstrom DR, Juggins S (2004) Patterns of early lake evolution in boreal landscapes: a comparison of stratigraphic inferences with a modern chronosequence in Glacier Bay, Alaska. The Holocene 14:828–840
Gasse F, Juggins S, Ben Khelifa L (1995) Diatom-based transfer functions for inferring past hydrochemical characteristics of African lakes. Palaeogeogr Palaeoclim Palaeoecol 117:3–54
Gasse F, Barker P, Gell PA, Fritz SC, Chalie F (1997) Diatom-inferred salinity in palaeolakes: an indirect tracer of climate change. Quat Sci Rev 16:547–563
Gavin DG, Oswald WW, Wahl ER, Williams JW (2003) A statistical approach to evaluating distance metrics and analog assignments for pollen records. Quat Res 60:356–367
Geladi P, Kowalski BR (1986) Partial least squares regression: a tutorial. Anal Chim Acta 185:1–17
Gersonde R, Crosta X, Abelmann A, Armand L (2005) Sea-surface temperature and sea ice distribution of the Southern Ocean at the EPILOG Last Glacial Maximum - a circum-Antarctic view based on siliceous microfossil records. Quat Sci Rev 24:869–896
Ginn BK, Cumming BF, Smol JP (2007) Diatom-based environmental inferences and model comparisons from 494 northwestern North American lakes. J Phycol 43:647–661
Gonzales LM, Williams JW, Grimm EC (2009) Expanded response-surfaces: a new method to reconstruct paleoclimates from fossil pollen assemblages that lack modern analogues. Quat Sci Rev 28:3315–3332
Guiot J, de Vernal A (2007) Transfer functions: methods for quantitative paleoceanography based on microfossils. In: Hillaire-Marcel C, de Vernal A (eds) Proxies in late Cenozoic Paleoceanography. Elsevier, Amsterdam, pp 523–563
Hall RI, Smol JP (2010) Diatoms as indicators of lake eutrophication. In: Smol JP, Stoermer EF (eds) The diatoms – applications for the environmental and earth sciences. Cambridge University Press, Cambridge, pp 122–151
Hallgren E, Palmer M, Milberg P (1999) Data diving with cross-validation: an investigation of broad-scale gradients in Swedish weed communities. Ecology 87:1037–1051
Haslett J, Whiley M, Bhattacharya S, Salter-Townsend M, Wilson S, Allen J, Huntley B, Mitchell F (2006) Bayesian palaeoclimate reconstruction. J R Stat Soc A 169:395–438
Hausmann S, Larocque-Tobler I, Richard PJH, Pienitz R, St-Onge G, Fye F (2011) Diatom-inferred wind activity at Lac du Sommet, southern Québec, Canada: a multiproxy paleoclimate reconstruction based on diatoms, chironomids and pollen for the past 9500 years. The Holocene. doi:10.1177/0959683611
Heiri O, Lotter AF (2005) Holocene and Lateglacial summer temperature reconstruction in the Swiss Alps based on fossil assemblages of aquatic organisms: a review. Boreas 34:506–516
Heiri O, Birks HJB, Brooks SJ, Velle G, Willassen E (2003) Effects of within-lake variability of fossil assemblages on quantitative chironomid-inferred temperature reconstruction. Palaeogeogr Palaeoclim Palaeoecol 199:95–106
Hill MO (1973) Diversity and evenness: a unifying notation and its consequences. Ecology 54: 427–432
Holden P, Mackay A, Simpson GL (2008) A Bayesian palaeoenvironmental transfer function model for acidified lakes. J Paleolimnol 39:551–566
Hübener T, Dressler M, Schwarz A, Langner K, Adler S (2008) Dynamic adjustment of training-sets (‘moving-window’ reconstruction) by using transfer functions in paleolimnology – a new approach. J Paleolimnol 40:79–95
Huber K, Weckström K, Drescher-Schneider R, Knoll J, Schmidt J, Schmidt R (2010) Climate changes during the last glacial termination inferred from diatom-based temperatures and pollen in a sediment core from Längsee (Austria). J Paleolimnol 43:131–147
Imbrie J, Kipp NG (1971) A new micropaleontological method for quantitative paleoclimatology: application to a Late Pleistocene Caribbean core. In: Turekian KK (ed) The Late Cenozoic glacial ages. Yale University Press, New Haven, pp 77–181
Imbrie J, Webb T (1981) Transfer functions: calibrating micropaleontological data in climatic terms. In: Berger A (ed) Climatic variations and variability: facts and theories. Reidel, Dordrecht, pp 125–134
Jackson ST, Williams JW (2004) Modern analogs in Quaternary paleoecology: here today, gone yesterday, gone tomorrow? Annu Rev Earth Planet Sci 32:495–537
Jenkins A, Whitehead PG, Cosby BJ, Birks HJB (1990) Modelling long-term acidification: a comparison with diatom reconstructions and the implications for reversibility. Phil Trans R Soc Lond B 327:435–440
Johnson JB, Omland KS (2004) Model selection in ecology and evolution. Trends Ecol Evol 19:101–108
Jones VJ, Juggins S (1995) The construction of a diatom-based chlorophyll a transfer function and its application at three lakes on Signy Island (maritime Antarctic) subject to differing degrees of nutrient enrichment. Freshw Biol 34:433–445
Jones VJ, Stevenson AC, Battarbee RW (1986) Lake acidification and the land use hypothesis: a mid-postglacial analogue. Nature 322:157–158
Juggins S (1992) Diatoms in the Thames Estuary, England: ecology, palaeoecology, and salinity transfer function. Bibliotheca Diatomologica 25:1–216
Juggins S (2007) C2 Version 1.5 User Guide. Software for ecological and palaeoecological data analysis and visualisation. University of Newcastle, Newcastle-upon-Tyne
Juggins S (2009) Rioja: analysis of Quaternary science data, R package version 0.5-6. http://cran.r-project.org/package=rioja
Juggins S, Telford RJ (2012) Chapter 5: Exploratory data analysis and data display. In: Birks HJB, Lotter AF, Juggins S, Smol JP (eds) Tracking environmental change using lake sediments, vol 5: data handling and numerical techniques. Springer, Dordrecht
Juggins S, Battarbee RW, Fritz SC (1994) Diatom/salinity transfer functions and climate change: an assessment of methods and application to two Holocene sequences from the northern Great Plains. In: Funnell BM, Kay RLF (eds) Palaeoclimate of the last glacial/interglacial cycle. NERC Earth Sciences Directorate, Swindon, pp 37–41
Kamenik C, Schmidt R (2005) Chrysophyte resting stages: a tool for reconstructing winter/spring climate from Alpine lake sediments. Boreas 34:477–489
Kingston JC, Cumming BF, Uutala AJ, Smol JP, Camburn KE, Charles DF, Dixit SS, Kreis RG Jr (1992) Biological quality control and quality assurance: a case study in paleolimnologal biomonitoring. In: McKenzie DH, Hyatt DE, McDonald VJ (eds) Ecological indicators, vol 1. Elsevier Science Publishers, London, pp 1542–1543
Korhola A, Vasko K, Toivonen HTT, Olander H (2002) Holocene temperature changes in northern Fennoscandia reconstructed from chironomids using Bayesian modelling. Quat Sci Rev 21:1841–1860
Köster D, Racca JMJ, Pienitz R (2004) Diatom-based inference models and reconstructions revisited: methods and transformations. J Paleolimnol 32:233–245
Kucera M, Weinelt M, Kiefer T, Pflaumann U, Hayes A, Chen MT, Mix AC, Barrows TT, Cortijo E, Duprat J, Juggins S, Waelbroeck C (2005) Reconstruction of sea-surface temperatures from assemblages of planktonic foraminifera: multi-technique approach based on geographically constrained calibration data sets and its application to glacial Atlantic and Pacific Oceans. Quat Sci Rev 24:951–998
Kumke T, Schölzel C, Hense A (2004) Transfer functions for paleoclimate reconstructions - theory and methods. In: Fischer H, Kumke T, Lohmann G, Flöser G, Miller H, von Storch H, Negendank JFW (eds) The climate in historical times: towards a synthesis of Holocene proxy data and climate models. Springer, Berlin, pp 229–244
Larocque I, Bigler C (2004) Similarities and discrepancies between chironomid- and diatom-inferred temperature reconstructions through the Holocene at Lake 850, northern Sweden. Quat Int 122:109–121
Larocque I, Hall RI (2003) Chironomids as quantitative indicators of mean July air temperature: validation by comparison with century-long meteorological records from northern Sweden. J Paleolimnol 29:475–493
Larocque-Tobler I, Grosjean M, Kamenik C (2011) Calibration-in-time versus calibration-in-space (transfer function) to quantitatively infer July air temperature using biological indicators (chironomids) preserved in lake sediments. Palaeogeogr Palaeoclim Palaeoecol 299:281–288
Legendre P, Birks HJB (2012a) Chapter 7: Clustering and partitioning. In: Birks HJB, Lotter AF, Juggins S, Smol JP (eds) Tracking environmental change using lake sediments, vol 5: data handling and numerical techniques. Springer, Dordrecht
Legendre P, Birks HJB (2012b) Chapter 8: From classical to canonical ordination. In: Birks HJB, Lotter AF, Juggins S, Smol JP (eds) Tracking environmental change using lake sediments, vol 5: data handling and numerical techniques. Springer, Dordrecht
Li B, Nychka DW, Amman CM (2010) The value of multiproxy reconstruction of past climate. J Am Stat Assoc 105:883–895
Limpert E, Stahel WA, Abbt M (2001) Log-normal distributions across the sciences: keys and clues. Bioscience 51:341–352
Line JM, ter Braak CJF, Birks HJB (1994) WACALIB version 3.3 - a computer program to reconstruct environmental variables from fossil assemblages by weighted averaging and to derive sample- specific errors of prediction. J Paleolimnol 10:147–152
Lotter AF (2003) Multi-proxy climate reconstructions. In: Mackay A, Battarbee RW, Birks HJB, Oldfield F (eds) Global change in the Holocene. Arnold, London, pp 373–383
Lotter AF, Anderson NJ (2012) Chapter 18: Limnological responses to environmental changes at inter-annual to decadal time-sclaes. In: Birks HJB, Lotter AF, Juggins S, Smol JP (eds) Tracking environmental change using lake sediments, vol 5: data handling and numerical techniques. Springer, Dordrecht
Lotter AF, Birks HJB, Hofmann W, Marchetto A (1997) Modern diatom, cladocera, chironomid, and chrysophytes cyst assemblages as quantitative indicators for the reconstruction of past environmental conditions in the Alps. I. Climate. J Paleolimnol 18:395–420
Lotter AF, Walker IR, Brooks SJ, Hofmann W (1999) An intercontinental comparison of chironomid palaeotemperature inference models: Europe vs North America. Quat Sci Rev 18:717–735
Luoto T (2010) Hydrological change in lakes inferred from midge assemblages through the use of an intralake calibration set. Ecol Monogr 80:303–329
Mackay AW, Ryves DB, Battarbee RW, Flower RJ, Jewson D, Rioual P, Sturm M (2005) 1000 years of climate variability in central Asia: assessing the evidence using Lake Baikal (Russia) diatom assemblages and the application of a diatom-inferred model of snow cover on the lake. Global Planet Change 46:281–297
Maher LJ, Heiri O, Lotter AF (2012) Chapter 6: Assessment of uncertainties associated with palaeolimnological laboratory methods and microfossil analysis. In: Birks HJB, Lotter AF, Juggins S, Smol JP (eds) Tracking environmental change using lake sediments, vol 5: data handling and numerical techniques. Springer, Dordrecht
Malmgren BA, Kucera M, Nyberg J, Waelbroeck C (2001) Comparison of statistical and neural network techniques for estimating past sea-surface temperatures from planktonic foraminifer census data. Paleoceanography 16:520–530
Manly BFJ (1997) Randomization, bootstrap and Monte Carlo methods in biology, 2nd edn. Chapman & Hall, London
Martens H, Næs T (1989) Multivariate calibration. Wiley, Chichester
McCune B (1997) Influence of noisy environmental data on canonical correspondence analysis. Ecology 78:2617–2623
Meyer DG, Butler DG (1993) Statistical validation. Ecol Model 68:21–32
Mohler CL (1983) Effect of sampling pattern on estimation of species distributions along gradients. Vegetatio 54:97–102
Montgomery DC, Peck EA (1982) Introduction to linear regression analysis. Cambridge University Press, Cambridge
Mooney CZ, Duval RD (1993) Bootstrapping: a non-parametric approach to statistical inference. Sage, Newbury Park
Munro MAR, Kreiser AM, Battarbee RW, Juggins S, Stevenson AC, Anderson DS, Anderson NJ, Berge F, Birks HJB, Davis RB, Flower RJ, Fritz SC, Haworth EY, Jones VJ, Kingston JC, Renberg I (1990) Diatom quality control and data handling. Phil Trans R Soc Lond B 327: 257–261
Næs T, Isaksson T (1992) Locally weighted regression in diffuse near-infrared transmittance spectroscopy. Appl Spectrosc 46:34–43
Næs T, Kvaal K, Isaksson T, Miller C (1993) Artificial neural networks in multivariate calibration. J Near IR Spectrosc 1:1–11
Næs T, Isaksson T, Fearn T, Davies T (2002) A user-friendly guide to multivariate calibration and classification. NIR Publications, Chichester
Nilsson MB, Dabakk E, Korsman T, Renberg I (1996) Quantifying relationships between near-infrared reflectance spectra of lake sediments and water chemistry. Environ Sci Technol 30:2586–2590
Oksanen J, Blanchet FG, Kindt R, Legendre P, O’Hara RB, Simpson GL, Solymos P, Stevens MHM, Wagner H (2011) Vegan: community ecology package. R package version 1.17-8. http://CRAN.R-project.org/package=vegan
Olden JD, Jackson DA (2002) Illuminating the “black box”: a randomization approach for understanding variable contributions in artificial neural networks. Ecol Model 154:135–150
Olden JD, Joy MK, Death RG (2004) An accurate comparison of methods for quantifying variable importance in artificial neural networks using simulated data. Ecol Model 178:389–397
Ott WR (1990) A physical explanation of the lognormality of pollutant concentrations. J Air Waste Manag Assoc 40:1378–1383
Overpeck JT, Webb T, Prentice IC (1985) Quantitative interpretation of fossil pollen spectra: dissimilarity coefficients and the method of modern analogs. Quat Res 23:87–108
Paterson AM, Cumming BF, Dixit SS, Smol JP (2002a) The importance of model choice on pH inferences from scaled chrysophyte assemblages in North America. J Paleolimnol 27:379–391
Paterson AM, Morimoto DS, Cumming BF, Smol JP, Szeicz JM (2002b) A paleolimnological investigation of the effects of forest fire on lake water quality in northwestern Ontario over the past ca. 150 years. Can J Bot 80:1329–1336
Peyron O, Begeot C, Brewer S, Heiri O, Magny M, Millet L, Ruffaldi P, van Campo E, Yu G (2005) Late-Glacial climatic changes in Eastern France (Lake Lautrey) from pollen, lake-levels, and chironomids. Quat Res 64:197–211
Philibert A, Prairie YT (2002a) Diatom-based transfer functions for western Quebec lakes (Abitibi and Haute Mauricie): the possible role of epilimnetic CO2 concentration in influencing diatom assemblages. J Paleolimnol 27:465–480
Philibert A, Prairie YT (2002b) Is the introduction of benthic species necessary for open-water chemical reconstruction in diatom-based transfer functions? Can J Fish Aquat Sci 59:938–951
Pienitz R, Smol JP, Birks HJB (1995) Assessment of fresh-water diatoms as quantitative indicators of past climatic change in the Yukon and Northwest-Territories, Canada. J Paleolimnol 13: 21–49
Piñeiro G, Perelman S, Guerschman JP, Paruelo JM (2008) How to evaluate models: observed vs. predicted or predicted vs. observed? Ecol Model 216:316–332
Power M (1993) The predictive validation of ecological and environmental models. Ecol Model 68:33–50
Prell WL (1985) The stability of low-latitude sea-surface temperatures: an evaluation of the CLIMAP reconstruction with emphasis on the positive SST anomalies. Special Publication TRO 25, US. Department of Energy, Washington, DC
Prentice IC (1980) Multidimensional scaling as a research tool in Quaternary palynology - a review of theory and methods. Rev Palaeobot Palynol 31:71–104
Quinlan R, Smol JP (2001) Setting minimum head capsule abundance and taxa deletion criteria in chironomid-based inference models. J Paleolimnol 26:327–342
R Development Core Team (2010) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/
Racca JMJ, Prairie Y (2004) Apparent and real bias in numerical transfer functions in palaeolimnology. J Paleolimnol 31:117–124
Racca JMJ, Philibert A, Racca R, Prairie YT (2001) A comparison between diatom-based pH inference models using artificial neural networks (ANN), weighted averaging (WA) and weighted averaging partial least squares (WA-PLS) regressions. J Paleolimnol 26:411–422
Racca JMJ, Wild M, Birks HJB, Prairie YT (2003) Separating wheat from chaff: diatom taxon selection using an artificial neural network pruning algorithm. J Paleolimnol 29:123–133
Racca JMJ, Gregory-Eaves I, Pienitz R, Prairie YT (2004) Tailoring palaeolimnological diatom-based transfer functions. Can J Fish Aquat Sci 61:2440–2454
Racca JMJ, Racca R, Pienitz R, Prairie YT (2007) PaleoNet: new software for building, evaluating and applying neural network based transfer functions in paleoecology. J Paleolimnol 38: 467–472
Reavie ED, Neill KE, Little JL, Smol JP (2006) Cultural eutrophication trends in three southeastern Ontario lakes: a paleolimnological perspective. Lake Reserv Manage 22:44–58
Reid M (2005) Diatom-based models for reconstructing past water quality and productivity in New Zealand lakes. J Paleolimnol 33:13–38
Renberg I, Hellberg T (1982) The pH history of lakes in Southwestern Sweden, as calculated from the subfossil flora of the sediments. Ambio 11:30–33
Renberg I, Korsman T, Anderson NJ (1993) A temporal perspective of lake acidification in Sweden. Ambio 22:264–271
Robertson I, Lucy D, Baxter L, Pollard AM, Aykroyd RG, Barker AC, Carter AHC, Switsur VR, Waterhouse JS (1999) A kernel-based Bayesian approach to climatic reconstruction. The Holocene 9:495–500
Rosén P (2005) Total organic carbon (TOC) of lake water during the Holocene inferred from lake sediments and near-infrared spectroscopy (NIRS) in eight lakes from northern Sweden. Biogeochemistry 76:503–516
Rosén P, Segerstrom U, Eriksson L, Renberg I, Birks HJB (2001) Holocene climatic change reconstructed from diatoms, chironomids, pollen and near-infrared spectroscopy at an alpine lake (Sjuodjljaure) in northern Sweden. The Holocene 11:551–562
Rosén P, Segerstrom U, Eriksson L, Renberg I (2003) Do diatom, chironomid, and pollen records consistently infer Holocene July air temperature? A comparison using sediment cores from four alpine lakes in northern Sweden. Arct Antarct Alp Res 35:279–290
Roux M (1979) Estimation des paleoclimats d’apres l’ecologie des foraminiferes. Les Cahiers de l’Analyse des donnees IV:61–79
Rühland KM, Smol JP (2002) Freshwater diatoms from the Canadian arctic treeline and development of paleolimnological inference models. J Phycol 38:249–264
Rymer N (1978) The use of uniformitarianism and analog in palaeoecology, particularly pollen analysis. In: Walker D, Guppy JC (eds) Biology and Quaternary environments. Australian Academy of Sciences, Canberra, pp 245–257
Sayer CD (2001) Problems with the application of diatom-total phosphorus transfer functions: examples from a shallow English lake. Freshw Biol 46:743–757
Schmidt R, Kamenik C, Kaiblinger C, Hetzel M (2004) Tracking Holocene environmental changes in an alpine lake sediment core: application of regional diatom calibration, geochemistry, and pollen. J Paleolimnol 32:177–196
Seppä H, Birks HJB, Odland A, Poska A, Veski S (2004) A modern pollen-climate calibration set from northern Europe: developing and testing a tool for palaeoclimatological reconstructions. J Biogeogr 31:251–267
Shurin JB, Cottenie K, Hillebrand H (2009) Spatial autocorrelation and dispersal limitation in freshwater organisms. Oecologia 159:151–159
Sieger R, Gersonde R, Zielinski U (1999) A new extended software package for quantitative paleoenvironmental reconstructions. EOS, Transactions, American Geophysical Union Electronic Supplement, 11 May 1999
Simpson GL (2007) Analogue methods in palaeoecology: using the analogue package. J Stat Softw 22:1–29
Simpson GL (2012) Chapter 15: Modern analogue techniques. In: Birks HJB, Lotter AF, Juggins S, Smol JP (eds) Tracking environmental change using lake sediments, vol 5: data handling and numerical techniques. Springer, Dordrecht
Simpson GL, Birks HJB (2012) Chapter 9: Statistical learning in palaeolimnology. In: Birks HJB, Lotter AF, Juggins S, Smol JP (eds) Tracking environmental change using lake sediments, vol 5: data handling and numerical techniques. Springer, Dordrecht
Simpson GL, Hall RI (2012) Chapter 19: Human impacts – applications of numerical methods to evaluate surface-water acidification and eutrophication. In: Birks HJB, Lotter AF, Juggins S, Smol JP (eds) Tracking environmental change using lake sediments, vol 5: data handling and numerical techniques. Springer, Dordrecht
Simpson GL, Oksanen J (2009) Analogue: analgoue and weighted averaging methods for palaeoecology. R package version 0.6-8. http://cran.r-project.org/package=analogue
Simpson GL, Shilland EM, Winterbottom JM, Keay J (2005) Defining reference conditions for acidified waters using a modern analogue approach. Environ Pollut 137:119–133
Siver PA (1999) Development of paleolimnological inference models for pH, total nitrogen and specific conductivity based on planktonic diatoms. J Paleolimnol 21:45–59
Siver PA, Hamer JS (1992) Seasonal periodicity of Chrysophyceae and Synurophyceae in a small New-England lake - implications for paleolimnological research. J Phycol 28:186–198
Smol JP (2008) Pollution of lakes and rivers: a paleoenvironmental perspective, 2nd edn. Blackwell, Oxford
Sokal RR, Rohlf FJ (1981) Biometry, 2nd edn. Freeman, San Francisco
Stauffer RE (1988) Sampling strategies and associated errors in estimating epilimnetic chlorophyll in eutrophic lakes. Water Resourc Res 24:1459–1469
Stevenson AC, Birks HJB, Flower RJ, Battarbee RW (1989) Diatom-based pH reconstruction of lake acidification using canonical correspondence analysis. Ambio 18:228–233
Stevenson AC, Juggins S, Birks HJB, Anderson DS, Anderson NJ, Battarbee RW, Berge F, Davis RB, Flower RJ, Haworth EY, Jones VJ, Kingston JC, Kreiser AM, Line JM, Munro MAR, Renberg I (1991) The surface waters acidification project palaeolimnology programme: modern diatom/lake-water chemistry data-set. ENSIS, London
Stine R (1990) An introduction to bootstrap methods: examples and ideas. In: Fox J, Long JS (eds) Modern methods of data analysis. Sage, Newbury Park, pp 325–373
Telford RJ (2011) PalaeoSig: significance tests for palaeoenvironmental reconstructions. R package version 1.0. http://cran.r-project.org/package/palaeoSig/index.html
Telford RJ, Birks HJB (2005) The secret assumption of transfer functions: problems with spatial autocorrelation in evaluating model performance. Quat Sci Rev 24:2173–2179
Telford RJ, Birks HJB (2009) Design and evaluation of transfer functions in spatially structured environments. Quat Sci Rev 28:1309–1316
Telford RJ, Birks HJB (2011a) Effect of unequal sampling along the environmental gradient on transfer functions. J Paleolimnol 46:99–106
Telford RJ, Birks HJB (2011b) A novel method for assessing the statistical significance of quantitative reconstructions inferred from biotic assemblages. Quat Sci Rev 30:1271–1278
Telford RJ, Andersson C, Birks HJB, Juggins S (2004) Biases in the estimation of transfer function prediction errors. Paleoceanography 19:PA4014
ter Braak CJF (1995) Non-linear methods for multivariate statistical calibration and their use in palaeoecology: a comparison of inverse (k-nearest neighbours, partial least squares and weighted averaging partial least squares) and classical approaches. Chemom Intell Lab Syst 28:165–180
ter Braak CJF, Barendregt LG (1986) Weighted averaging of species indicator values: its efficiency in environmental calibration. Math Biosci 78:57–72
ter Braak CJF, Juggins S (1993) Weighted averaging partial least squares regression (WA-PLS): an improved method for reconstructing environmental variables from species assemblages. Hydrobiologia 269:485–502
ter Braak CJF, Looman CWN (1986) Weighted averaging, logistic regression and the Gaussian response model. Vegetatio 65:3–11
ter Braak CJF, Prentice IC (1988) A theory of gradient analysis. Adv Ecol Res 18:271–317
ter Braak CJF, van Dam H (1989) Inferring pH from diatoms: a comparison of old and new calibration methods. Hydrobiologia 178:209–223
ter Braak CJF, Verdonschot PFM (1995) Canonical correspondence analysis and related multivariate methods in aquatic ecology. Aquat Sci 57:255–289
ter Braak CJF, Juggins S, Birks HJB, van der Voet H (1993) Weighted averaging partial least squares regression (WA-PLS): definition and comparison with other methods for species-environment calibration. In: Patil GP, Rao CR (eds) Multivariate environmental statistics. Elsevier Science Publishers, Amsterdam, pp 525–560
Thompson R, Price D, Cameron N, Jones VJ, Bigler C, Rosen P, Hall RI, Catalan J, Garcia J, Weckstrom J, Korhola A (2005) Quantitative calibration of remote mountain-lake sediments as climatic recorders of air temperature and ice-cover duration. Arct Antarct Alp Res 37:626–635
Toivonen H, Manilla H, Korhola A, Olander H (2001) Applying Bayesian statistics to organism-based environmental reconstruction. Ecol App 11:618–630
van der Voet H (1994) Comparing the predictive accuracy of models using a simple randomization test. Chemom Intell Lab Syst 25:313–323
Varmuza K, Filzmoser P (2009) Introduction to multivariate statistical analysis in chemometrics. CRC Press, Boca Raton
Vasko K, Toivonen H, Korhola A (2000) A Bayesian multinomial Gaussian response model for organism-based environmental reconstruction. J Paleolimnol 24:243–250
Velle G, Brodersen KP, Birks HJB, Willassen E (2010) Midges as quantitative temperature indicator species: lessons for palaeoecology. The Holocene 20:989–1002
Velle G, Kongshavn K, Birks HJB (2011a) Minimizing the edge-effect in environmental reconstructions by trimming the calibration-set: chironomid-inferred temperatures from Spitsbergen. The Holocene 21:417–430
Velle G, Telford RJ, Birks HJB (2011b) Validity of intra-site transfer functions. J Paleolimnol (submitted)
Verschuren D (2003) Lake-based climate reconstruction in Africa: progress and challenges. Hydrobiologia 500:315–330
Verschuren D, Cumming BF, Laird KR (2004) Quantitative reconstruction of past salinity variations in African lakes: assessment of chironomid-based inference models (Insecta: Diptera) in space and time. Can J Fish Aquat Sci 61:986–998
Walker IR, Levesque AJ, Cwynar LC, Lotter AF (1997) An expanded surface-water palaeotemperature inference model for use with fossil midges from eastern Canada. J Paleolimnol 18:165–178
Wallach D, Goffinet B (1989) Mean squared error of prediction as a criterion for evaluating and comparing system models. Ecol Model 44:299–306
Webb A (2002) Statistical pattern recognition, 2nd edn. Arnold, London
Weckström K, Juggins S, Korhola A (2004) Quantifying background nutrient concentrations in coastal waters: a case study from an urban embayment of the Baltic Sea. Ambio 33:324–327
Wehrens R (2011) Chemometrics with R. Springer, New York
Werner P, Smol JP (2005) Diatom-environmental relationships and nutrient transfer functions from contrasting shallow and deep limestone lakes in Ontario, Canada. Hydrobiologia 533:145–173
Wilson SE, Cumming BF, Smol JP (1996) Assessing the reliability of salinity inference models from diatom assemblages: an examination of a 219-lake data set from western North America. Can J Fish Aquat Sci 53:1580–1594
Xu Q, Li Y, Bunting MJ, Tian F, Liu J (2010) The effects of training set selection on the relationship between pollen assemblages and climate parameters: implications for reconstructing past climate. Palaeogeogr Palaeoclim Palaeoecol 1289:123–133
Yang XD, Kamenik C, Schmidt R, Wang SM (2003) Diatom-based conductivity and water-level inference models from eastern Tibetan (Qinghai-Xizang) Plateau lakes. J Paleolimnol 30:1–19
Yuan LL (2007) Maximum likelihood method for predicting environmental conditions from assemblage composition: the R package bio.infer. J Stat Softw 22:1–20
Acknowledgements
We thank Richard J. Telford, Cajo ter Braak, John Smol, and Hilary Birks for helpful discussions and/or reading an early draft of the Chapter and Cathy Jenks for invaluable editorial help. This is publication A360 from the Bjerknes Centre for Climate Research.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media B.V.
About this chapter
Cite this chapter
Juggins, S., Birks, H.J.B. (2012). Quantitative Environmental Reconstructions from Biological Data. In: Birks, H., Lotter, A., Juggins, S., Smol, J. (eds) Tracking Environmental Change Using Lake Sediments. Developments in Paleoenvironmental Research, vol 5. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-2745-8_14
Download citation
DOI: https://doi.org/10.1007/978-94-007-2745-8_14
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-007-2744-1
Online ISBN: 978-94-007-2745-8
eBook Packages: Earth and Environmental ScienceEarth and Environmental Science (R0)