Testing and Quantifying Phylogenetic Signals and Homoplasy in Morphometric Data
Tóm tắt
Từ khóa
Tài liệu tham khảo
Ackerly, 1998, Leaf size, sapling allometry, and Corner's rules: phylogeny and correlated evolution in maples (Acer), Am. Nat, 152, 767, 10.1086/286208
Adams, 1995, 1998. Partial warps, phylogeny, and ontogeny: a comment on Fink and Zelditch, Syst. Biol., 47, 168, 10.1080/106351598261111
Archie, 1989, Homoplasy excess ratios: new indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index, Syst. Zool, 38, 253, 10.2307/2992286
Arhontaki, 2002, Functional constraints of the Cu, Zn superoxide dismutase in species of the Drosophila melanogaster subgroup and phylogenetic analysis, J. Mol. Evol., 55, 745, 10.1007/s00239-002-2370-9
Astúa, 2009, Evolution of scapular size and shape in didelphid marsupials (Didelphimorphia: Didelphidae), Evolution, 63, 2438, 10.1111/j.1558-5646.2009.00720.x
Blomberg, 2003, Testing for phylogenetic signal in comparative data: behavioral traits are more labile, Evolution, 57, 717, 10.1111/j.0014-3820.2003.tb00285.x
Bookstein, 1994, Can biometrical shape be a homologous character?, Homology: the hierarchical basis of comparative biology, 197, 10.1016/B978-0-08-057430-1.50011-1
Bookstein, 1996, Biometrics, biomathematics and the morphometric synthesis, Bull. Math. Biol., 58, 313, 10.1007/BF02458311
Bookstein, 2002, Creases as morphometric characters, Morphology, shape, and phylogeny, 139, 10.1201/9780203165171.ch8
Brooks, 1991, Phylogeny, ecology, and behavior: a research program in comparative biology
Cannon, 2001, Combining and comparing morphometric shape descriptors with a molecular phylogeny: the case of fruit type evolution in Bornean Lithocarpus (Fagaceae), Syst. Biol., 50, 860, 10.1080/106351501753462849
Cardini, 2003, The geometry of the marmot (Rodentia: Sciuridae) mandible: phylogeny and patterns of morphological evolution, Syst. Biol., 52, 186, 10.1080/10635150390192807
Cardini, 2008, Does the skull carry a phylogenetic signal? Evolution and modularity in the guenons, Biol. J. Linn. Soc., 93, 813, 10.1111/j.1095-8312.2008.01011.x
Cardini, 2007, A geometric morphometric approach to the study of ecogeographical and clinal variation in vervet monkeys, J. Biogeogr, 34, 1663, 10.1111/j.1365-2699.2007.01731.x
Cardini, 2004, Patterns of morphological evolution in Marmota (Rodentia, Sciuridae): geometric morphometrics of the cranium in the context of marmot phylogeny, ecology and conservation, Biol. J. Linn. Soc., 82, 385, 10.1111/j.1095-8312.2004.00367.x
Cariou, 2001, Divergence between Drosophila santomea and allopatric or sympatric populations of D. yakuba using paralogous amylase genes and migration scenarios along the Cameroon volcanic line, Mol. Ecol, 10, 649, 10.1046/j.1365-294x.2001.01225.x
Caumul, 2005, Phylogenetic and environmental components of morphological variation: skull, mandible, and molar shape in marmots (Marmota, Rodentia), Evolution, 59, 2460, 10.1111/j.0014-3820.2005.tb00955.x
Cavalli-Sforza, 1967, Phylogenetic analysis: models and estimation procedures, Evolution, 21, 550, 10.1111/j.1558-5646.1967.tb03411.x
Claude, 2004, Ecological correlates and evolutionary divergence in the skull of turtles: a geometric morphometric assessment, Syst. Biol., 53, 933, 10.1080/10635150490889498
Cole, 2002, A parametric bootstrap approach to the detection of phylogenetic signals in landmark data, Morphology, shape and phylogeny, 194, 10.1201/9780203165171.ch10
Collard, 2000, How reliable are human phylogenetic hypotheses?, Proc. Natl. Acad. Sci. USA, 97, 5003, 10.1073/pnas.97.9.5003
Corti, 1998, Phylogeny and size and shape changes in the skull of the South American rodent Proechimys, Acta Zool. Acad. Sci. Hung, 44, 139
Couette, 2005, Constructing, bootstrapping, and comparing morphometric and phylogenetic trees: a case study of New World monkeys (Platyrrhini, Primates), J. Mammal, 86, 773, 10.1644/1545-1542(2005)086[0773:CBACMA]2.0.CO;2
Courant, 1997, Quantification of cranial convergences in arvicolids (Rodentia), Biol. J. Linn. Soc., 62, 505, 10.1111/j.1095-8312.1997.tb00318.x
David, 1996, Morphometrics and cladistics: measuring phylogeny in the sea urchin Echinocardium, Evolution, 50, 348, 10.1111/j.1558-5646.1996.tb04498.x
Drosophila 12 Genomes Consortium, 2007, Evolution of genes and genomes on the Drosophila phylogeny, Nature, 450, 203, 10.1038/nature06341
Dryden, 1998, Statistical shape analysis.
Farris, 1989, The retention index and the rescaled consistency index, Cladistics, 5, 417, 10.1111/j.1096-0031.1989.tb00573.x
Felsenstein, 1973, Maximum-likelihood estimation of evolutionary trees from continuous characters, Am. J. Hum. Genet., 25, 471
Felsenstein, 1988, Phylogenies and quantitative characters, Annu. Rev. Ecol. Syst, 19, 455, 10.1146/annurev.es.19.110188.002305
Felsenstein, 2002, Quantitative characters, phylogenies, and morphometrics, Morphology, shape and phylogeny., 27, 10.1201/9780203165171.ch3
Felsenstein, 2004, Inferring phylogenies
Fink, 1995, Phylogenetic analysis of ontogenetic shape transformations: a reassessment of the piranha genus Pygocentrus (Teleostei), Syst. Biol., 44, 343, 10.1093/sysbio/44.3.343
Frédérich, 2008, Comparative trophic morphology in eight species of damselfishes (Pomacentridae), J. Morphol, 269, 175, 10.1002/jmor.10586
Gidaszewski, 2009, Evolution of sexual dimorphism of wing shape in the Drosophila melanogaster subgroup, BMC Evol. Biol., 9, 110, 10.1186/1471-2148-9-110
Gilchrist, 2000, Adaptation and constraint in the evolution of Drosophila melanogaster wing shape, Evol. Dev., 2, 114, 10.1046/j.1525-142x.2000.00041.x
González-José, 2008, Cladistic analysis of continuous modularized traits provides phylogenetic signals in Homo evolution, Nature, 453, 775, 10.1038/nature06891
Good, 2000, Permutation tests: a practical guide to resampling methods for testing hypotheses, 2nd ed., 10.1007/978-1-4757-3235-1
Guill, 2003, The effect of phylogeny on interspecific body shape variation in darters (Pisces: Percidae), Syst. Biol., 52, 488, 10.1080/10635150390197019
Hansen, 2004, Evolvability, stabilizing selection, and the problem of stasis, Phenotypic integration: studying the ecology and evolution of complex phenotypes, 130, 10.1093/oso/9780195160437.003.0006
Harmon, 2005, Convergence and the multidimensional niche, Evolution, 59, 409, 10.1111/j.0014-3820.2005.tb00999.x
Harr, 2004, Patterns of microsatellite variability in the Drosophila melanogaster complex, Genetica, 120, 71, 10.1023/B:GENE.0000017631.00820.49
Harr, 1998, A microsatellite-based multilocus phylogeny of the Drosophila melanogaster species complex, Curr. Biol., 8, 1183, 10.1016/S0960-9822(07)00490-3
Houle, 2003, Automated measurement of Drosophila wings, BMC Evol. Biol., 3, 25, 10.1186/1471-2148-3-25
Huey, 1987, Phylogenetic studies of coadaptation: preferred temperatures versus optimal performance temperatures of lizards, Evolution, 41, 1098, 10.1111/j.1558-5646.1987.tb05879.x
Jolliffe, 2002, Principal component analysis, 2nd ed.
Kastanis, 2003, Macroevolutionary relationships of species of Drosophila melanogaster group based on mtDNA sequences, Mol. Phylogenet. Evol., 28, 518, 10.1016/S1055-7903(03)00070-8
Kitching, 1998, Cladistics: the theory and practice of parsimony analysis, 2nd ed.
Kliman, 2000, The population genetics of the origin and divergence of the Drosophila simulans complex species, Genetics, 156, 1913, 10.1093/genetics/156.4.1913
Klingenberg, 2008, MorphoJ, Faculty of Life Sciences
Klingenberg, 2008, Morphological integration and developmental modularity, Annu. Rev. Ecol. Evol. Syst, 39, 115, 10.1146/annurev.ecolsys.37.091305.110054
Klingenberg, 2008, Novelty and “homology-free” morphometrics: what's in a name?, Evol. Biol., 35, 186, 10.1007/s11692-008-9029-4
Klingenberg, 2009, Morphometric integration and modularity in configurations of landmarks: tools for evaluating a-priori hypotheses, Evol. Dev., 11, 405, 10.1111/j.1525-142X.2009.00347.x
Klingenberg, 2001, Inferring developmental modularity from morphological integration: analysis of individual variation and asymmetry in bumblebee wings, Am. Nat, 157, 11, 10.1086/317002
Klingenberg, 1996, A combined morphometric and phylogenetic analysis of an ecomorphological trend: pelagization in Antarctic fishes (Perciformes: Nototheniidae), Biol. J. Linn. Soc., 59, 143, 10.1111/j.1095-8312.1996.tb01459.x
Klingenberg, 2003, Developmental integration in a complex morphological structure: how distinct are the modules in the mouse mandible?, Evol. Dev., 5, 522, 10.1046/j.1525-142X.2003.03057.x
Klingenberg, 2005, Distances and directions in multidimensional shape spaces: implications for morphometric applications, Syst. Biol., 54, 678, 10.1080/10635150590947258
Kluge, 1969, Quantitative phyletics and the evolution of anurans, Syst. Zool, 18, 1, 10.2307/2412407
Lachaise, 2003, Nine relatives from one African ancestor: population biology and evolution of the Drosophila melanogaster subgroup species, The evolution of population biology., 315
Lachaise, 1988, Historical biogeography of the Drosophila melanogaster species subgroup, Evol. Biol., 22, 159, 10.1007/978-1-4613-0931-4_4
Lachaise, 2000, Evolutionary novelties in islands: Drosophila santomea, a new melanogaster sister species, Proc. R. Soc. Lond. B Biol. Sci., 267, 1487, 10.1098/rspb.2000.1169
Laffont, 2009, Morphological modularity and assessment of developmental processes within the vole dental row (Microtus arvalis, Arvicolinae, Rodentia), Evol. Dev., 11, 302, 10.1111/j.1525-142X.2009.00332.x
Langerhans, 2004, Shared and unique features of evolutionary diversification, Am. Nat, 164, 335, 10.1086/422857
Larson, 2005, Ontogeny, phylogeny, and morphology in anuran larvae: morphometric analysis of cranial development and evolution in Rana tadpoles (Anura: Ranidae), J. Morphol, 264, 34, 10.1002/jmor.10313
Laurin, 2004, The evolution of body size, Cope's rule and the origin of amniotes, Syst. Biol., 53, 594, 10.1080/10635150490445706
Leinonen, 2006, Contrasting patterns of body shape and neutral genetic divergence in marine and lake populations of threespine sticklebacks, J. Evol. Biol., 19, 1803, 10.1111/j.1420-9101.2006.01182.x
Lemeunier, 1984, Relationships within the melanogaster species subgroup of the genus Drosophila (Sophophora). IV. The chromosomes of two new species, Chromosoma, 89, 343, 10.1007/BF00331251
Lewis, 2005, The phylogeny of the subgroups within the melanogaster species group: likelihood tests on COI and COII sequences and a Bayesian estimate of phylogeny, Mol. Phylogenet. Evol., 37, 15, 10.1016/j.ympev.2005.02.018
Li, 1999, Paleo-demography of the Drosophila melanogaster subgroup: application of the maximum likelihood method, Genes Genet. Syst, 74, 117, 10.1266/ggs.74.117
Linde, 2004, Differential correlates of diet and phylogeny on the shape of the premaxilla and anterior tooth in sparid fishes (Perciformes: Sparidae), J. Evol. Biol., 17, 941, 10.1111/j.1420-9101.2004.00763.x
Llopart, 2002, Genetics of a difference in pigmentation between Drosophila yakuba and Drosophila santomea, Evolution, 56, 2262, 10.1111/j.0014-3820.2002.tb00150.x
Lockwood, 2004, Morphometrics and hominoid phylogeny: support for a chimpanzee—human clade and differentiation among great ape subspecies, Proc. Natl. Acad. Sci. USA, 101, 4356, 10.1073/pnas.0306235101
Loy, 1993, Landmark data: size and shape analysis in systematics. A case study on Old World Talpidae (Mammalia, Insectivora), Contributions to morphometrics, 215
Lycett, 2005, Do homoiologies impede phylogenetic analyses of the fossil hominids? An assessment based on extant papionin craniodental morphology, J. Hum. Evol., 49, 618, 10.1016/j.jhevol.2005.07.004
Lynch, 1989, Phylogenetic hypotheses under the assumption of neutral quantitative-genetic variation, Evolution, 43, 1
Macholán, 2006, A geometric morphometric analysis of the shape of the first upper molar in mice of the genus Mus (Muridae, Rodentia), J. Zool. (Lond.), 270, 672, 10.1111/j.1469-7998.2006.00156.x
MacLeod, 2002, Phylogenetic signals in morphometric data, Morphology, shape and phylogeny., 100, 10.1201/9780203165171.ch7
Maddison, 1991, Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree, Syst. Zool, 40, 304, 10.2307/2992324
Marcus, 2000, Application of landmark morphometrics to skulls representing the orders of living mammals, Hystrix, 11, 27
Martins, 1997, Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data, Am. Nat, 149, 646, 10.1086/286013
Matsuo, 2000, Molecular evolution if the histone 3 multigene family in the Drosophila melanogaster species subgroup, Mol. Phylogenet. Evol., 16, 339, 10.1006/mpev.2000.0810
McArdle, 1994, Estimating the ancestral states of a continuous-valued character using squared-change parsimony: an analytical solution, Syst. Biol., 43, 573, 10.1093/sysbio/43.4.573
McDermott, 2008, Estimation of isolation times of the island species in the Drosophila simulans complex from multilocus DNA sequence data, PLoS ONE, 10.1371/journal.pone.0002442
McPeek, 2009, The correlated evolution of three-dimensional reproductive structures between male and female damselflies, Evolution, 63, 73, 10.1111/j.1558-5646.2008.00527.x
McPeek, 2008, The tempo and mode of three-dimensional morphological evolution in male reproductive structure, Am. Nat, 171, E158, 10.1086/587076
Miller, 2003, Floral morphometrics and the evolution of sexual dimorphism in Lycium (Solanaceae), Evolution, 57, 74, 10.1111/j.0014-3820.2003.tb00217.x
Milne, 2002, Inter-specific variation in Macropus crania: form, function and phylogeny, J. Zool, 256, 523, 10.1017/S0952836902000572
Monteiro, 2000, Why morphometrics is special: the problem with using partial warps as characters for phylogenetic inference, Syst. Biol., 49, 796, 10.1080/106351500750049833
Monteiro, 2005, Morphological evolution in the mandible of spiny rats, genus Trinomys (Rodentia: Echimyidae), J. Zool. Syst. Evol. Res., 43, 332, 10.1111/j.1439-0469.2005.00323.x
Moraes, 2004, Divergence in wing morphology among sibling species of the Drosophila buzzatii cluster, J. Zool. Syst. Evol. Res., 42, 154, 10.1111/j.1439-0469.2004.00256.x
Naylor, 1996, Can partial warp scores be used as cladistic characters?, Advances in morphometrics, 519, 10.1007/978-1-4757-9083-2_45
Neustupa, 2007, Geometric morphometrics and qualitative patterns in the morphological variation of five species of Micrasterias (Zygnemophyceae, Viridiplantae), Preslia, 79, 401
Nicola, 2003, Congruence of hierarchical, localized variation in cranial shape and molecular phylogenetic structure in spiny rats, genus Trinomys (Rodentia: Echimyidae), Biol. J. Linn. Soc., 80, 385, 10.1046/j.1095-8312.2003.00245.x
Panchetti, 2008, Shape and size variations in the cranium of elephant-shrews: a morphometric contribution to a phylogenetic debate, Zoomorphology, 127, 69, 10.1007/s00435-007-0053-1
Parsch, 2003, Selective constraints on intron evolution in Drosophila, Genetics, 165, 1843, 10.1093/genetics/165.4.1843
Polly, 2001, On morphological clocks and paleophylogeography: towards a timescale for Sorex hybrid zones, Genetica, 112–113, 339, 10.1023/A:1013395907225
Polly, 2008, Developmental dynamics and G-matrices: can morphometric spaces be used to model phenotypic evolution?, Evol. Biol., 35, 83, 10.1007/s11692-008-9020-0
Pretorius, 2001, Geometric morphometrics and the analysis of higher taxa: a case study based on the metendosternite of the Scarabaeoidea (Coleoptera), Biol. J. Linn. Soc., 74, 35, 10.1111/j.1095-8312.2001.tb01375.x
Prömel, 2002, The Steiner tree problem: a tour through graphs, algorithms, and complexity
Rohlf, 1998, On applications of geometric morphometrics to studies of ontogeny and phylogeny, Syst. Biol., 47, 147, 10.1080/106351598261094
Rohlf, 2001, Comparative methods for the analysis of continuous variables: geometric interpretations, Evolution, 55, 2143, 10.1111/j.0014-3820.2001.tb00731.x
Rohlf, 2002, Geometric morphometrics and phylogeny, Morphology, shape, and phylogeny, 175, 10.1201/9780203165171.ch9
Rohlf, 1996, Morphometric analysis of Old World Talpidae (Mammalia, Insectivora) using partial-warp scores, Syst. Biol., 45, 344, 10.1093/sysbio/45.3.344
Russo, 1995, Molecular phylogeny and divergence times of drosophilid species, Mol. Biol. Evol., 12, 391
Rzhetsky, 1992, A simple method for estimating and testing minimum-evolution trees, Mol. Biol. Evol., 9, 945
Schlick-Steiner, 2006, A multidisciplinary approach reveals cryptic diversity in Western Palearctic Tetramorium ants (Hymenoptera: Formicidae), Mol. Phylogenet. Evol., 40, 259, 10.1016/j.ympev.2006.03.005
Schluter, 2004, Parallel evolution and inheritance of quantitative traits, Am. Nat, 163, 809, 10.1086/383621
Scholtz, 2008, Termite soldier defence strategies: a reassessment of Prestwich's classification and an examination of the evolution of defence morphology using extended eigenshape analyses of head morphology, Zool. J. Linn. Soc., 153, 631, 10.1111/j.1096-3642.2008.00396.x
Sidlauskas, 2008, Continuous and arrested morphological diversification in sister clades of characiform fishes: a phylomorphospace approach, Evolution, 62, 3135, 10.1111/j.1558-5646.2008.00519.x
Smith, 1992, How to find Steiner minimal trees in Euclidean d-space, Algorithmica, 7, 137, 10.1007/BF01758756
Sneath, 1973, Numerical taxonomy: the principles and practice of numerical classification
Stayton, 2005, Morphological evolution of the lizard skull: a geometric morphometrics survey, J. Morphol, 263, 47, 10.1002/jmor.10288
Stayton, 2006, Geometric morphometrics of the skull roof of stereospondyls (Amphibia: Temnospondyli), Palaeontology, 49, 307, 10.1111/j.1475-4983.2006.00523.x
Swofford, 1996, Phylogenetic inference, Molecular systematics, 407
Tamura, 2004, Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks, Mol. Biol. Evol., 21, 36, 10.1093/molbev/msg236
Thompson, 1973, The method of minimum evolution, Ann. Hum. Genet., 36, 333, 10.1111/j.1469-1809.1973.tb00595.x
Ting, 2000, The phylogeny of closely related species as revealed by the genealogy of a speciation gene, Odysseus, Proc. Natl. Acad. Sci. USA, 97, 5313, 10.1073/pnas.090541597
Weber, 1990, Selection on wing allometry in Drosophila melanogaster, Genetics, 126, 975, 10.1093/genetics/126.4.975
Weber, 1992, How small are the smallest selectable domains of form?, Genetics, 130, 345, 10.1093/genetics/130.2.345
Wroe, 2007, Convergence and remarkably consistent constraint in the evolution of carnivore skull shape, Evolution, 61, 1251, 10.1111/j.1558-5646.2007.00101.x
Young, 2008, A comparison of the ontogeny of shape variation in the anthropoid scapula: functional and phylogenetic signal, Am. J. Phys. Anthropol, 136, 247, 10.1002/ajpa.20799
Young, 2005, Serial homology and the evolution of mammalian limb covariation structure, Evolution, 59, 2691, 10.1111/j.0014-3820.2005.tb00980.x
Zelditch, 1995, Morphometrics, homology and phylogenetics: quantified characters as synapomorphies, Syst. Biol., 44, 179, 10.1093/sysbio/44.2.179
Zelditch, 2000, Discovery of phylogenetic characters in morphometric data, Phylogenetic analysis of morphological data, 37
Zelditch, 2004, Geometric morphometrics for biologists: a primer