Horizon annealing: A collection-based approach to automated sequencing of the fossil record

Lethaia

Volumn 45, Issue 4, 2012, Pages 532-547

  Sheets, H David ^a   Mitchell, Charles E ^b   Izard, Zachary T ^a   Willis, John M ^a   Melchin, Michael J ^c   Holmden, Christopher ^d  

^a CANISIUS COLLEGE   (United States)

^b UNIVERSITY AT BUFFALO   (United States)

^c ST FRANCIS XAVIER UNIVERSITY   (Canada)

^d UNIVERSITY OF SASKATCHEWAN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHRONOLOGY; CHRONOSTRATIGRAPHY; FOSSIL RECORD; GRAPTOLITE; OPTIMIZATION; QUANTITATIVE ANALYSIS; SIMULATED ANNEALING; TIMESCALE;

EID: 84866486857     PISSN: 00241164     EISSN: 15023931     Source Type: Journal    
DOI: 10.1111/j.1502-3931.2012.00312.x     Document Type: Article

References (54)

1. Agterberg, F.P. 1990: Automated Stratigraphic Correlation: Developments in Palaeontology and Stratigraphy 13, 424 pp. Elsevier, Amsterdam.
2. Agterberg, F.P. & Gradstein, F.M. 1996: RASC and CASC: Biostratigraphic Zonation and Correlation Software, Version 15, Canada.
3. Alroy, J. 1994: Appearance event ordination: a new biochronologic method. Paleobiology 20, 191-207.
4. Alroy, J. 2000: New methods for quantifying macroevolutionary patterns and processes. Paleobiology 26, 707-733.
5. Alroy, J. 2006: A revised quantitative time scale for North American Cretaceous and Cenozoic vertebrates. Journal of Vertebrate Paleontology 26, 36A.
6. Alroy, J. 2010: Fair sampling of taxonomic richness and unbiased estimation of origination and extinction rates. In Alroy, J. & Hunt, G. (eds): Quantitative Methods in Paleobiology. The Paleontology Society Papers 16, 55-80.
7. Bertsimas, D. & Nohadani, O. 2010: Robust optimization with simulated annealing. Journal of Global Optimization 48, 323-334.
8. Blackham, M. 1998: The unitary association method of relative dating and its application to archaeological data. Journal of Archaeology, Method & Theory 5, 165-207.
9. Chen, Xu., Melchin, M.J., Sheets, H.D., Mitchell, C.E. & Junxuan, F. 2005: Patterns and processes of latest Ordovician graptolite extinction and recovery based on data from south China. Journal of Palaeontology 79, 842-861.
10. Cisne, J.L. & Chandlee, G.O. 1982: Taconic foreland basin graptolites: age zonation, depth zonation, and use in ecostratigraphic correlation. Lethaia 15, 343-363.
11. Cisne, J.L. & Rabe, B.D. 1978: Coenocorrelation: gradient analysis of fossil communities and its applications in stratigraphy. Lethaia 11, 341-364.
12. Cisne, J.L., Karig, D.E., Rabe, B.D. & Hay, B.J. 1982: Topography and tectonics of the Taconic outer trench slope as revealed through gradient analysis of fossil assemblages. Lethaia 15, 229-246.
13. Cody, R.D., Levy, R.H., Harwood, D.M. & Sadler, P.M. 2008: Thinking outside the zone: high-resolution quantitative diatom biochronology for the Antarctic Neogene. Palaeogeography, Palaeoclimatology, Palaeoecology 260, 92-121.
14. Connolly, S.R. & Miller, A.I. 2001: Joint estimation of sampling and turnover rates from fossil databases: capture-mark-recapture methods revisited. Paleobiology 27, 751-767.
15. Cooper, R.A., Crampton, J.S., Raine, J.I., Gradstein, F.M., Morgans, H.E.G., Sadler, P.M., Strong, C.P., Waghorn, D. & Wilson, G.J. 2001: Quantitative biostratigraphy of the Taranaki Basin, New Zealand: a deterministic probabilistic approach. AAPG Bulletin 85, 1469-1498.
16. Crampton, J.S., Foote, M., Beau, A.G., Maxwell, P.A., Cooper, R.A., Matcham, L., Marshall, B.A. & Jones, C.M. 2006: The ark was full! Constant to declining Cenozoic shallow marine biodiversity on an isolated mid latitude continent. Paleobiology 32, 509-532.
17. Edwards, L.E. 1982a: Numerical and semi-objective biostratigraphy: review and predictions. Proceedings of the Third North American Paleontological Convention 1, 147-152.
18. Edwards, L.E. 1982b: Quantitative biostratigraphy: the methods should suit the data. In Cubitt, J.M. & Reyment, R.A. (eds): Quantitative Stratigraphic Correlation, 45-60. John Wiley, New York.
19. Fan, Junxuan. & Chen, Xu. 2007: Preliminary report on the Late Ordovician graptolite extinction in the Yangtze region. Palaeogeography, Palaeoclimatology, Palaeoecology 245, 82-94.
20. Junxuan, F., Chen, X. & Yuandong, Z. 2002: Quantitative biostratigraphic study of Yangtze Platform - with the designing of SinoCor 2.0, a software program for graphic correlation. Memoirs of the Association of Australasian Palaeontologists, 27, 53-58.
21. Foote, M. 2000: Origination and extinction components of taxonomic diversity: general problems. In Erwin, D.H. & Wing, S.L. (eds): Deep Time: Paleobiology's Perspective, 74-102, The Paleontological Society, Lawrence, Kansas.
22. Foote, M. 2001: Inferring temporal patterns of preservation, origination, and extinction from taxonomic survivorship analysis. Paleobiology 27, 602-630.
23. Foote, M. 2003: Origination and extinction through the Phanerozoic: a new approach. Journal of Geology 111, 125-148.
24. Galster, F., Guex, J. & Hammer, Ø. 2010: Neogene biochronology of Antarctic diatoms: a comparison between two quantitative approaches, CONOP and UAgraph. Palaeogeography, Palaeoclimatology, Palaeoecology 285, 237-247.
25. Goldman, D., Mitchell, C.E., Bergström, S.M., Delano, J.W. & Tice, S.T. 1994: K-bentonites and graptolite stratigraphy in the Middle Ordovician of New York State and Quebec: a new chronostratigraphic model. Palaios 9, 124-143.
26. Gradstein, F.M. & Agterberg, F.P. 1999: RASC and CASC, Tools for the Biostratigraphic Workstation - Users Guide. Authors Edition 17, 68 pp. Ottawa.
27. Gradstein, F.M., Ogg, J. & Smith, A. (eds.). 2004: A Geologic Time Scale, 589 pp. Cambridge University Press, Cambridge.
28. Guex, J. 1991: Biochronological Correlations, 252 pp. Springer Verlag, Berlin.
29. Guex, J. 2011: Some recent 'refinements' of the Unitary Association Method: a short discussion. Lethaia 44, 247-249.
30. Hay, W.W. 1972: Probabilistic stratigraphy. Eclogae Geologica Helvitica 65, 255-266.
31. Ingber, L. 1989: Very fast simulated re-annealing. Mathematical and Computer Modelling 12, 967-973.
32. Ingber, L. 1993: Simulated annealing: practice versus theory. Mathematical and Computer Modelling 18, 29-57.
33. Kemple, W.G., Sadler, P.M. & Strauss, D.J. 1989: A prototype constrained optimization solution to the time correlation problem. In Agterberg, F.P. & Bonham-Carter, G.F. (eds.): Statistical Applications in the Earth Sciences. Geological Survey of Canada Paper 89-9, 417-425.
34. Kemple, W.G., Sadler, P.M. & Strauss, D.J. 1995: Extending graphic correlation to many dimensions: stratigraphic correlation as constrained optimization. In Mann, K.O., Lane, H.R., Scholle, P.A. (eds): Graphic Correlation. SEPM Special Publication 53, 65-82.
35. Kendall, C.G., Moore, P.D., Strobel, J., Cannon, R., Perlmutter, M., Bezdek, J. & Biswas, G. 1991: Simulation of the sedimentary fill of basins. In Franseen, E.K., Watney, W.L., Kendall, C.G. & Ross, W. (eds): Sedimentary Modeling: Computer Simulation and Methods for Improved Parameter Definition. Kansas Geological Survey, Bulletin 233, 9-30.
36. Kruskal, J.B. 1964: Nonmetric multidimensional scaling: a numerical method. Psychometrika 29, 115-129.
37. Liow, L.H. & Nichols, J.D. 2010: Estimating rates of origination and extinction using taxonomic occurrence data: capture-mark-recapture (CMR) approaches. In Alroy, J. & Hunt, G. (eds): Quantitative Methods in Paleobiology. The Paleontology Society Papers 16, 81-94.
38. Monnet, C., Klug, C., Goudemand, N., De Baets, K. & Bucher, H. 2011: Quantitative biochronology of Devonian ammonites from Morocco and proposals for a refined unitary association method. Lethaia 44, 469-489.
39. Palmer, A.R. 1954: The faunas of the Riley Formation in Central Texas. Journal of Paleontology 28, 709-786.
40. Paul, C.R.C. & Lamolda, M.A. 2009: Testing the precision of bioevents. Geological Magazine 146, 625-637.
41. Press, W.H., Flannery, B.P., Teukolsky, S.A. & Vetterling, W.T. 1988: Numerical Recipes in C., 768 pp. Cambridge University Press, Cambridge.
42. Puolamäki, K., Fortelius, M. & Mannila, H. 2006: Seriation in paleontological data using Markov chain Monte Carlo methods. PLoS Computational Biology 2, e6.
43. Sadler, P.M. 1999: Constrained Optimisation Approaches to the Stratigraphic Correlation and Seriation Problems: A User's Guide and Reference Manual to the CONOP Program Family, 126 pp. Riverside, California.
44. Sadler, P.M. 2003: Quantitative biostratigraphy-achieving finer resolution in global correlation. Annual Reviews of Earth and Planetary Science 32, 187-213.
45. Sadler, P.M. 2010: Brute-force Biochronology: Sequencing Paleobiologic First- and Last-Appearances. In Alroy, J., Hunt, G. (eds): Quantitative Methods in Paleobiology. The Paleontology Society Papers 16, 271-290.
46. Sadler, P.M. & Kemple, W.G. 1995: Using rapid, multidimensional, graphic correlation to evaluate chronostratigraphic models for the Mid-Ordovician of the Mohawk Valley, New York. In Cooper, J.D., Droser, M.L., Finney, S.C. (eds): Ordovician Odyssey: Short Papers for the Seventh International Symposium on the Ordovician System. SEPM Pacific Section, Book 77, 257-260.
47. Sadler, P.M., Cooper, R.A. & Melchin, M. 2009: High-resolution, early Paleozoic (Ordovician-Silurian) time scales. Geological Society of America Bulletin 121, 887-906.
48. Shaw, A.B. 1964: Time in Stratigraphy, 365 pp. McGraw Hill, New York.
49. Simpson, G.G. 1944: Tempo and Mode in Evolution, 237 pp. Columbia University Press, New York.
50. Strobel, J., Cannon, R., Kendall, C.G.S., Biswas, G. & Bezdek, J. 1989: Interactive (SEDPAK) simulation of clastic and carbonate sediments in shelf to basin settings. Computers and Geoscience 15, 1279-1290.
51. Tipper, J.C. 1988: Techniques for quantitative stratigraphic correlations: a review and annotated bibliography. Geological Magazine 125, 475-494.
52. Zhang, T. & Plotnick, R.E. 2001: Determining the line of correlation using genetic algorithms. Geological Society of America Abstracts with Programs 33, 141.
53. Zhang, T. & Plotnick, R.E. 2006: Graphic biostratigraphic correlation using genetic algorithms. Mathematical Geology 38, 781-800.
54. Zhao, X. 2010: Simulated annealing algorithm with adaptive neighborhood. Applied Soft Computing 11, 1827-1836.