Comparison of morphometric techniques for shapes with few homologous landmarks based on machine-learning approaches to biological discrimination

Paleobiology

Volumn 36, Issue 3, 2010, Pages 497-515

  Van Bocxlaer, Bert ^a   Schultheib, Roland ^b  

^a GHENT UNIVERSITY   (Belgium)

^b JUSTUS LIEBIG UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79955419118     PISSN: 00948373     EISSN: 19385331     Source Type: Journal    
DOI: 10.1666/08068.1     Document Type: Article

References (58)

1. Adams, D. C., F. J. Rohlf, And D. E. Slice. 2004. Geometric morphometrics: ten years of progress following the ‘revolu-tion.’ Italian Journal of Zoology 71:5-16.
2. Anderson, L. C., And P. D. Roopnarine. 2003. Evolution and phylogenetic relationships of Neogene Corbulidae (Bivalvia; Myoidea) of trnpical America. Journal of Paleontology 77:1086-1102.
3. Bookstein, F. L. 1991. Morphometric tools for landmark data: geometry and biology. Cambridge University Press, Cambridge.
4. Bookstein, F. L. 1996. Applying landmark methods to biological outline data. Pp. 59–70 in K. V. Mardia, C. A. Gill, and I. L. Dryden, eds. Image fusion and shape variability. University of Leeds, Leeds, U.K.
5. Bookstein, F. L. 1997. Landmark methods for forms without landmarks: morphometrics of group differences in outline shape. Medical Image Analysis 1:225-243.
6. Bookstein, F. L. 1998. A hundred years of morphometrics. Acta Zoologica 44:7-59.
7. Bookstein, F. L., R. E. Strauss, J. M. Humphries, B. Chemoff R. L. Elder, And G. R. Smith. 1982. A comment upon the uses of Fourier methods in systematics. Systematic Zoology 31:85-92.
8. Brehm, G., And K. Fiedler. 2004. Ordinating tropical moth ensembles from an elevational gradient: a comparison of common methods. Journal of Tropical Ecology 20:165-172.
9. Brown, D. S. 1994. Freshwater snails of Africa and their medical importance. Taylor and Francis, London.
10. Brown, M. P. S., W. N. Grundy, D. Lin, N. Cristianini, C. W. Sugnet, T. S. Furey, M. Ares, And D. Haussler. 2000. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proceedings of the National Academy of Sciences USA 97:262-267.
11. Burges, C. 1998. A tutorial on support vector machines for pattern recognition. Data Mining and Knowledge Discovery 2:121-167.
12. Carvajal-Rodriguez, A., P. Conde-Padin, And E. Rolan-Alvarez. 2005. Decomposing shell form into size and shape by geometric morphometric methods in two sympatric ecotypes of Littorina saxatilis. Journal of Molluscan Studies 71:313-318.
13. Cheetham, A. H., J. Sanner, And J. B. C. Jackson. 2007. Metrarabdotos and related genera (Bryozoa: Cheilostomata) in the Late Paleogene and Neogene of tropical America. Paleontological Society Memoir 67. Journal of Paleontology 81(Suppl. to No. 1).
14. Chessel, D., A.-B. Dufour, And J. Thioulouse. 2004. The ade4 package - I: one-table methods. R News 4:5-10.
15. Clabaut, C., P. M. Bunje, W. Salzburger, And A. Meyer. 2007. Geometric morphometric analyses provide evidence for the adaptive character of the Tanganyikan cichlid fish radiations. Evolution 61:560-578.
16. Clarke, K. R. 1993. Non-parametric multivariate analyses of changes in community structure. Austral Ecology 18:117-143.
17. Conde-Padin, P., A. Carvajal-Rodriguez, M. Carballo, A. Caballero, And E. Rolan-Alvarez. 2007. Genetic variation for shell traits in a direct-developing marine snail involved in a putative sympatric ecological speciation process. Evolutionary Ecology 21:635-650.
18. Conde-Padin, P., J. W. Grahame, And E. Rolan-Alvarez. 2007. Detecting shape differences in species of the Littorina saxatilis complex by morphometric analysis. Journal of Molluscan Studies 73:147-154.
19. Conde-Padin, P., A. Caballero, And E. Rolan-Alvarez. 2009. Relative role of genetic determination and plastic response during ontogeny for shell-shape traits subjected to diversifying selection. Evolution 63:1356-1363.
20. Cortes, C., And V. N. Vapnik. 1995. Support vector networks. Machine Learning 20:273-297.
21. Cox, T. F., And M. A. A. Cox. 2000. Multidimensional scaling. Chapman and Hall, New York.
22. Crowley, T. E., T. Pain, And F. R. Woodward. 1964. A monographic review of the Mollusca of Lake Nyasa. Anna du Musee Royal de l'Afrique Centrale, Sciences Zoologiques 131:1-58.
23. Decoste, D., And B. Scholkopf. 2002. Training invariant support vector machines. Machine Learning 46:161-190.
24. Dietz, E. J. 1983. Permutation tests for association between two distance matrices. Systematic Zoology 32:21-26.
25. Dryden, I. L., And K. V. Mardia. 1998. Statistical shape analysis. Wiley, New York.
26. Ehrlich, R., R. B. Pharr, and N. Healy-Williams. 1983. Comments on the validity of Fourier descriptors in systematics: a reply to Bookstein et al. Systematic Biology 32:202-206.
27. Genner, M. J., J. A. Todd, E. Michel, D. Erpenbeck, A. Jimoh, D. A. Joyce, A. Piechocki, And J.-P. Pointier. 2007. Amassing diversity in an ancient lake: evolution of a morphologically diverse parthenogenetic gastropod assemblage in Lake Malawi. Molecular Ecology 16:517-530.
28. Gould, S. J. 1991. The disparity of the Burgess Shale arthropod fauna and the limits of cladistic analysis: why we must strive to quantify morphospace. Paleobiology 17:411-423.
29. Green, W. D. K. 1996. The thin-plate spline and images with curving features. Pp. 79–87 in K. V. Mardia, C. A. Gill, and I. L. Dryden, eds. Image fusion and shape variability. University of Leeds, Leeds, U.K.
30. Haines, A. J., And J. S. Crampton. 2000. Improvements to the method of Fourier shape analysis as applied in morphometric studies. Palaeontology 43:765-783.
31. Hammer, O., And D. A. T. Harper. 2006. Paleontological data analysis. Blackwell, Oxford.
32. Hammer, O., D. A. T. Harper, And P. D. Ryan. 2001. PAST: paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4:1-9.
33. Hastie, T., And R. Tibshirani. 1998. Classification by pairwise coupling. Annals of Statistics 26(1):451—471.
34. Hotelling, H. 1933. Analysis of a complex of statistical variables into principal components. Journal of Educational Psychology 24:417-441.
35. Iwata, H., And Y. Ukai. 2002. SHAPE: a computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors. Journal of Heredity 93:384-385.
36. Jablonski, D. 1999. The future of the fossil record. Science 284:2114-2116.
37. Jackson, J. B. C., And A. H. Cheetham. 1990. Evolutionary significance of morphospecies: a test with cheilostome Bryozoa. Science 248:579-582.
38. Keerthi, S. S., S. K. Shevade, C. Bhattacharyya, And K. R. K. Murthy. 2001. Improvements to Platt's SMO algorithm for SVM classifier design. Neural Computation 13:637-649.
39. Kruskal, J. 1964. Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis. Psychometrika 29:1-27.
40. Kuhl, F. P., And C. R. Giardina. 1982. Elliptical Fourier features of a closed contour. Computer Graphics and Image Processing 18:236-258.
41. Lestrel, P. E. 1989. Method for analyzing complex two-dimen-sional forms: elliptical Fourier functions. American Journal of Human Biology 1:149-164.
42. Lestrel, P. E. 1997. Fourier descriptors and their applications in biology. Cambridge University Press, Cambridge.
43. Louda, S. M., And K. R. Mckaye. 1982. Diurnal movements in populations of the prosobranch Lanistes nyassanus at Cape Maclear, Lake Malawi, Africa. Malacologia 23:13-21.
44. Louda, S. M., W. N. Gray, K. R. Mckaye, And O. J. Mhone. 1983. Distribution of gastropod genera over a vertical depth gradient at Cape Maclear, Lake Malawi. Veliger 25:387-392.
45. Louda, S. M., K. R. Mckaye, T. D. Kocher, And C. J. Stackhouse. 1984. Activity, dispersion, and size of Lanistes nyassanus and Lanistes solidus (Gastropoda, Ampullariidae) over the depth gradient at Cape Maclear, Lake Malawi, Africa. Veliger 26:145-152.
46. Loy, A., S. Busilacchi, C. Costa, L. Ferlin, And S. Cataudella. 2000. Comparing geometric morphometrics and outline fitting methods to monitor fish shape variability of Diplodus puntazzo (Teleostea: Sparidae). Aquacultural Engineering 21:271-283.
47. Macleod, N. 1999. Generalizing and extending the eigenshape method of shape space visualization and analysis. Paleobiology 25:107-138.
48. Rohlf, F. J., and J. W. Archie. 1984. A comparison of Fourier methods for the description of wing shape in mosquitoes (Diptera: Culicidae). Systematic Zoology 33:302-317.
49. Rohlf, F. J., And L. F. Marcus. 1993. A revolution in morphometries. Trends in Ecology and Evolution 8:129-132.
50. Scholkopf, B., And A. J. Smola. 2001. Learning with kernels: support vector machines, regularization, optimization, and beyond. MIT Press, Cambridge.
51. Schopf, T. J. M. 1982. A critical assessment of punctuated equilibria. 1. Duration of taxa. Evolution 36:1144-1157.
52. Schopf, T. J. M., D. M. Raup, S. J. Gould, And D. S. Simberloff. 1975. Genomic versus morphologic rates of evolution: influence of morphologic complexity. Paleobiology 1:63-70.
53. Schultheie R., B. Van Bocxlaer, T. Wilke, And C. Albrecht. 2009. Old fossils-young species: evolutionary history of an endemic gastropod assemblage in Lake Malawi. Proceedings of the Royal Society of London B 276:2837-2846.
54. Sheets, F. D. 2008. IMP: integrated morphometries package. Department of Physics, Canisius College, Buffalo, N.Y.
55. Sheets, H. D., K. Keonho, And C. E. Mitchell. 2004. A combined landmark and outline-based approach to ontogenetic shape change in the Ordovician Trilobite Triarthrus becki. Pp. 67–81 in A. Elewa, ed. Applications of morphometries in paleontology and biology. Springer, New York.
56. Sheets, Fi. D. K. M. Corvino, J. M. Panasiewicz, And S. R. Morris. 2006. Comparison of geometric morphometric outline methods in the discrimination of age-related differences in feather shape. Frontiers in Zoology 3:15.
57. Sidlauskas, B. 2008. Continuous and arrested morphological diversification in sister clades of characiform fishes: a phylo-morphospace approach. Evolution 62:3135-3156.
58. Thompson, D. A. W. 1942. On growth and form. A new edition. University Press and Macmillan, Cambridge, U.K.