Congruence between patterns of localized, hierarchical variation in cranial shape and topological, molecular phylogenetic structure was investigated in a monophyletic lineage of Neotropical spiny rats of the genus Trinomys. Levels of organizational complexity in shape were assessed from two-dimensional coordinates of anatomical landmarks for dorsal, ventral and lateral views of the cranium, and the scale of variation in cranial shape was decomposed hierarchically using the statistical formalism of geometric morphometrics. The patterns of variation in cranial shape were evaluated for the five taxa of Trinomys in terms of ordinations in the reduced space of relative warps, with the scores of partial warps weighted to emphasize the hierarchical localization of shape differences in different geometric scales. The fit of the morphological shape data to the molecular phylogeny and analysis of the correlation between measures of the differences in shape and molecular phylogenetic distances demonstrated that only variation in small, localized scales in cranial shape in the lateral view of the cranium was congruent with molecular phylogenetic structure. The significance and perspectives of the application of geometric descriptors of shape and the identification of scales of variation for the study of morphological and molecular evolution are discussed. © 2003 The Linnean Society of London.803385396Ab'Saber, A.N., O domínio morfo-climático semi-árido das caatingas brasileiras (1974) Geomorfologia, 43, pp. 1-39Adams, D.C., Funk, D.J., Morphometric inferences on sibling species and sexual dimorphism in Neochlamisus bebbianae leaf beetles: Multivariate applications of the thin-plate spline (1997) Systematic Biology, 46, pp. 180-194Adams, D.C., Rohlf, F.J., Ecological character displacement in Plethodon: Biomechanical differences found from a geometric morphometric study (2000) Proceedings of the National Academy of Sciences, USA, 97, pp. 4106-4111Atchley, W.R., Cowley, D.E., Vogl, C., Mclellan, T., Evolutionary divergence, shape change, and genetic correlation structure in the rodent mandible (1992) Systematic Biology, 41, pp. 196-221Barrier, M., Robichaux, R.H., Purugganan, M.D., Accelerated regulatory gene evolution in adaptive radiation (2001) Proceedings of the National Academy of Sciences, USA, 98, pp. 10208-10213Bar-Yam, Y., (1997) Dynamics of Complex Systems, , Reading: Perseus BooksBergallo, H.G., Magnusson, W.E., Effects of climate and food availability on four rodent species in southeastern Brazil (1999) Journal of Mammalogy, 80, pp. 472-486Blelloch, R., Kimble, J., Control of organ shape by a secreted metalloprotease in the nematode Caenorhabditis elegans (1999) Nature, 399, pp. 586-590Bookstein, F.L., Principal warps: Thin-plate splines and the decomposition of deformations (1989) Transactions on Pattern Analysis and Machine Intelligence, 11, pp. 567-585Bookstein, F.L., (1991) Morphometric Tools for Landmark Data, , New York: Cambridge University PressBookstein, F.L., Biometrics, biomathematics and the morphometric synthesis (1996) Bulletin of Mathematical Biology, 58, pp. 313-365Bookstein, F.L., Creases as local features of deformation grids (2000) Medical Image Analysis, 4, pp. 93-100Bronner-Fraser, M., Sternberg, P.W., Pattern formation and developmental mechanisms - The cell biological basis of inductive signaling (2000) Current Opinion in Genetics and Development, 10, pp. 347-349Carleton, M.D., Systematics and evolution (1988) Advances in the Study of Peromyscus (Rodentia), pp. 7-140. , Kirkland GL Jr, Layne JN, eds. Lubbock: Texas Tech University PressCorti, M., Aguilera, M., Capanna, E., Size and shape changes in the skull accompanying speciation of South American spiny rats (Rodentia: Proechimys spp) (2001) Journal of Zoology, London, 253, pp. 537-547Corti, M., Fadda, C., Systematics of Arvicanthis (Rodentia, Muridae) from the horn of Africa: A geometric morphometrics evaluation (1996) Italian Journal of Zoology, 63, pp. 185-192Corti, M., Rohlf, F.J., Chromosomal speciation and phenotypic evolution in the house mouse (2001) Biological Journal of the Linnean Society, 73, pp. 99-112Dryden, I.L., Mardia, K.V., (1998) Statistical Shape Analysis, , New York: John Wiley & SonsDuarte, L.C., Monteiro, L.R., Von Zuben, F.J., Reis, S.F., Variation in mandible shape in Thrichomys apereoides (Mammalia: Rodentia): Geometric analysis of a complex morphological structure (2000) Systematic Biology, 49, pp. 563-578Goodall, C.R., Procrustes methods in the statistical analysis of shape (1991) Journal of the Royal Statistical Society B, 53, pp. 285-339Gurdon, J.B., Bourillot, P.-Y., Morphogen gradient interpretation (2001) Nature, 413, pp. 797-801Haas, A., Non-feeding and feeding tadpoles in hemiphractine frogs: Larval head morphology, heterochrony, and systematics of Flectonotus goeldii (Amphibia: Anura: Hylidae) (1996) Journal of Zoological Systematics and Evolutionary Research, 34, pp. 163-171Hanken, J., Thorogood, P., Evolution and development of the vertebrate skull - The role of pattern formation (1993) Trends in Ecology and Evolution, 8, pp. 9-15Herring, S., Epigenetic and functional influences in skull growth (1993) The Skull, pp. 153-206. , Hanken J, Hall BK, eds. Chicago: The University of Chicago PressKendall, D.G., Shape-manifolds, Procrustean metrics and complex projective spaces (1984) Bulletin of the London Mathematical Society, 16, pp. 81-121Kimura, M., A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences (1980) Journal of Molecular Evolution, 16, pp. 111-120Lara, M.C., Patton, J.L., Evolutionary diversification of spiny rats (Genus Trinomys, Rodentia: Echimyidae) in the Atlantic forest of Brazil (2000) Zoological Journal of the Linnean Society, 130, pp. 661-686Lessa, E.P., Cook, J.A., The molecular phylogenetics of tuco-tucos (genus Ctenomys, Rodentia: Octodontidae) suggests an early burst of speciation (1998) Molecular Phylogenetics and Evolution, 9, pp. 88-99Levin, S.A., The problem of scale in ecology (1992) Ecology, 73, pp. 1943-1967Levin, S.A., Complex adaptive systems: Exploring the known, the unknown and the unknowable (2003) Bulletin of the American Mathematical Society, 40, pp. 3-19Levin, S.A., Pacala, S.W., Theories of simplification and scaling of spatially distributed processes (1997) Space Ecology: The Role of Space in Population Dynamics and Interspecific Interactions, pp. 271-295. , Tilman D, Kareiva P, eds. Princeton: Princeton University PressLewontin, R.C., The problems of population genetics (2000) Evolutionary Genetics: From Molecules to Morphology, pp. 5-23. , Singh RS, Krimbas CR, eds. Cambridge: Cambridge University PressLosos, J.B., Ecological character displacement and the study of adaptation (2000) Proceedings of the National Academy of Sciences, USA, 97, pp. 5693-5695Manaf, P., Oliveira, E.S., Behavioral repertoire of the spiny rat Proechimys (Trinomys) yonenagae (Rodentia: Echimyidae) in captivity (2000) Revista de Etologia, 2, pp. 3-16Manly, B.F.J., (1997) Randomization, Bootstrap and Monte Carlo Methods in Biology. 2nd Edn., , London: Chapman & HallMantel, N., The detection of disease clustering and a generalized regression approach (1967) Cancer Research, 27, pp. 209-220Mardia, K.V., Bookstein, F.L., Moreton, I.J., Statistical assessment of bilateral symmetry of shapes (2000) Biometrika, 87, pp. 285-300Mares, M.A., Convergent evolution among desert rodents: A global perspective (1980) Bulletin Carnegie Museum, 16, pp. 1-51Monteiro, L.R., Abe, A.S., Functional and historical determinants of shape in the scapula of xenarthran mammals: Evolution of a complex morphological structure (1999) Journal of Morphology, 241, pp. 251-263Monteiro, L.R., Bordin, B., Reis, S.F., Shape distances, shape spaces and the comparison of morphometric methods (2000) Trends in Ecology and Evolution, 15, pp. 217-220Monteiro, L.R., Diniz-Filho, J.A.F., Reis, S.F., Araújo, E.D., Geometric estimates of heritability in biological shape (2002) Evolution, 56, pp. 563-572Moojen, J., Speciation in the Brazilian spiny rats (Genus Proechimys, Family Echimyidae) (1948) University of Kansas Publications of the Museum of Natural History, 1, pp. 301-406Mora, M., Olivares, A.I., Vassallo, A.I., Size, shape and structural versatility of the skull of the subterranean rodent Ctenomys (Rodentia, Caviomorpha): Functional and morphological analysis (2003) Biological Journal of the Linnean Society, 78, pp. 85-96Murray, J.D., (1990) Mathematical Biology, , New York: Springer VerlagMurray, J.D., Pattern formation in integrative biology - A marriage of theory and experiment (2000) Comptes Rendeus de L'Academie des Sciences, Serie III - Sciences de la Vie - Life Sciences, 323, pp. 5-14Penin, X., Berge, C., Baylac, M., Ontogenetic study of the skull in modern humans and the common chimpanzees: Neotenic hypothesis reconsidered with a tridimensional procrustes analysis (2002) American Journal of Physical Anthropology, 118, pp. 50-62Pessôa, L.M., Reis, S.F., The contribution of indeterminate cranial growth to nongeographic variation in adult Proechimys albispinus (Rodentia: Echimyidae) (1991) Zeitschrift für Säugetierkunde, 56, pp. 220-224Pessôa, L.M., Von Zuben, F.J., Reis, S.F., Morphological affinities of Proechimys yonenagae Rocha, 1995 (Rodentia: Echimyidae): Evidence from bacular and cranial characters (1998) Bonner Zoologischer Beiträge, 48, pp. 167-177Ponce De León, M.S., Zollikoffer, C.P.E., Neanderthal cranial ontogeny and its implications for late hominid diversity (2001) Nature, 412, pp. 534-538Pretorius, E., Scholtz, C.H., Geometric morphometrics and the analysis of higher taxa: A case study based on the metendosternite of the Scarabaeoidea (Coleoptera) (2001) Biological Journal of the Linnean Society, 74, pp. 35-50Reis, S.F., Duarte, L.C., Monteiro, L.R., Von Zuben, J.F., Geographic variation in cranial morphology in Thrichomys apereoides. I. Geometric descriptors and patterns of variation in shape (2002) Journal of Mammalogy, 83, pp. 333-344Reis, S.F., Duarte, L.C., Monteiro, L.R., Von Zuben, J.F., Geographic variation in cranial morphology in Thrichomys apereoides. II. Geographic units, morphological discontinuities, and sampling gaps (2002) Journal of Mammalogy, 83, pp. 345-353Reiss, J.O., The phylogeny of amphibian metamorphosis (2002) Zoology, 105, p. 2002Rocha, P.L.B., Proechimys yonenagae, a new species of spiny rat (Rodentia: Echimyidae) from fossil sand dunes in the Brazilian Caatinga (1995) Mammalia, 59, pp. 537-549Rohlf, F.J., Relative-warp analysis and an example of its application to mosquito wings (1993) Contributions of Morphometrics, pp. 131-159. , Marcus LF, Bello E, Garcia-Valdecasas A, eds. Madrid: Museo Nacional de Ciencias NaturalesRohlf, F.J., Morphometric spaces, shape components and the effect of linear transformation (1996) Advances in Morphometrics, pp. 117-129. , Marcus LF, Corti M, Loy A, Naylor G, Slice DE, eds. New York: Plenum PressRohlf, F.J., (1997) TPSRELW, Version 1.25, , Stony Brook, NY: Department of Ecology and Evolution, State University of New York at Stony Brook, Stony BrookRohlf, F.J., (1999) 'Tpsdig', Version 1.18, , Stony Brook, NY: Department of Ecology and Evolution, State University of New York at Stony Brook, Stony BrookRohlf, F.J., Shape statistics: Procrustes superimpositions and tangent spaces (1999) Journal of Classification, 16, pp. 197-223Rohlf, F.J., On the use of shape spaces to compare morphometric methods (2000) Hystrix International Journal of Mammalogy, 11, pp. 8-24Rohlf, F.J., Statistical power comparisons among alternative morphometric methods (2000) American Journal of Physical Anthropology, 111, pp. 463-478Rohlf, F.J., Geometric morphometrics in phylogeny (2002) Morphology, Shape and Phylogenetics, pp. 175-193. , Forey P, Macleod N, eds. London: Francis & TaylorRohlf, F.J., Loy, A., Corti, M., Morphometric analysis of Old World Talpidae (Mammalia, Insectivora) using partial warp scores (1996) Systematic Biology, 45, pp. 344-362Rohlf, F.J., Slice, D., Extensions of the Procrustes method for the optimal superimposition of landmarks (1990) Systematic Zoology, 39, pp. 40-59Rosenberg, M.S., Fiddler crab shape variation: A geometric morphometric analysis across the genus Uca (Crustacea: Brachyura: Ocypodidae) (2002) Biological Journal of the Linnean Society, 75, pp. 147-162Ruelle, D., A departure from equilibrium (2001) Nature, 414, pp. 263-264Schoch, R.R., The early formation of the skull in extant and Paleozoic amphibians (2002) Paleobiology, 28, pp. 278-296Singh, R.S., Krimbas, C.B., (2000) Evolutionary Genetics: From Molecules to Morphology, , Cambridge: Cambridge University PressSmith, K.K., Comparative patterns of craniofacial development in eutherian and metatherian mammals (1997) Evolution, 51, pp. 1663-1678Smith, K.K., Heterochrony revisited: The evolution of developmental sequences (2001) Biological Journal of the Linnean Society, 73, pp. 169-186Sober, E., (1988) Reconstructing the Past. Parsimony, Evolution, and Inference, , Cambridge: The MIT PressStraney, D.O., Patton, J.L., Phylogenetic and environmental determinants of geographic variation in the pocket mouse Perognathus goldmani Osgood (1980) Evolution, 34, pp. 888-903Streicher, J., Donat, M.A., Strauss, B., Spörle, R., Schughart, K., Computer-based three-dimensional visualization of developmental gene expression (2000) Nature Genetics, 25, pp. 147-162Thomas, M.G., Hagelberg, E., Jones, H.B., Yang, Z., Lister, A.M., Molecular and morphologic evidence on the phylogeny of the Elephantidae (2000) Proceedings of the Royal Society London B, 267, pp. 2493-2500Tucker, A.S., Sharpe, P.T., Molecular genetics of tooth morphogenesis and patterning: The right shape in the right place (1999) Journal of Dental Research, 78, pp. 826-834Vaughan, T.A., Ryan, J.M., Czaplewski, N.J., (2000) Mammalogy, , London: HarcourtVoss, R.S., Marcus, L.F., Escalante, P., Morphological evolution in muroid rodents I. Conservative patterns of craniometric covariance and their ontogenetic basis in the neotropical genus Zygodontomys (1990) Evolution, 44, pp. 1568-1587Walker, J.A., Ecological morphology of lacustrine threespine stickleback Gasterosteus aculeatus L. (Gasterosteidae) body shape (1997) Biological Journal of the Linnean Society, 61, pp. 3-50