The phylogenetic trunk: maximal inclusion of taxa with missing data in an analysis of the lepospondyli (Vertebrata, Tetrapoda).

The importance of fossils to phylogenetic reconstruction is well established. However, analyses of fossil data sets are confounded by problems related to the less complete nature of the specimens. Taxa that are incompletely known are problematic because of the uncertainty of their placement within a tree, leading to a proliferation of most-parsimonious solutions and "wild card" behavior. Problematic taxa are commonly deleted based on a priori criteria of completeness. Paradoxically, a taxon's problematic behavior is tree dependent, and levels of completeness are not directly associated with problematic behavior. Exclusion of taxa on the basis of completeness eliminates real character conflict and, by not allowing incomplete taxa to determine tree topology, diminishes the phylogenetic hypothesis. Here, the phylogenetic trunk approach is proposed to allow optimization of taxonomic inclusion and tree stability. The use of this method in an analysis of the Paleozoic Lepospondyli finds a single most-parsimonious tree, or trunk, after the removal of one taxon identified as being problematic. Moreover, the 38 trees found at one additional step from this primary trunk were reduced to 2 by removal of one additional taxon. These trunks are compared with the trees that were found by excluding taxa with various degrees of completeness, and the effects of incomplete taxa are explored with regard to use of the trunk. Correlated characters associated with limblessness are discussed regarding the assumption of character independence; however, inclusion of intermediate taxa is found to be the single best method for breaking down long branches.

[1]  S. J. Godfrey.  The postcranial skeletal anatomy of the carboniferous tetrapod Greererpeton burkemorani Romer, 1969 , 1989 .

[2]  R. Holmes,et al.  The Carboniferous Amphibian Proterogyrinus scheelei Romer, and the Early Evolution of Tetrapods , 1984 .

[3]  A. Romer.  A New Anthracosaurian Labyrinthodont, Proterogyrinus scheelei, from the Lower Carboniferous , 1970 .

[4]  J. Bolt.  Dissorophoid relationships and ontogeny, and the origin of the Lissamphibia , 1977 .

[5]  L. Grande,et al.  A comprehensive phylogenetic study of amiid fishes (Amiidae) based on comparative skeletal anatomy : an empirical search for interconnected patterns of natural history , 1998 .

[6]  P. Currie,et al.  Microsaurs as possible apodan ancestors , 1975 .

[7]  R. Lande.  EVOLUTIONARY MECHANISMS OF LIMB LOSS IN TETRAPODS , 1978, Evolution; international journal of organic evolution.

[8]  M. Novacek.  Fossils, Topologies, Missing Data, and the Higher Level Phylogeny of Eutherian Mammals , 1992 .

[9]  M. Donoghue,et al.  The Importance of Fossils in Phylogeny Reconstruction , 1989 .

[10]  E. C. Olson,et al.  THE TERRESTRIAL ENVIRONMENT AND THE ORIGIN OF LAND VERTEBRATES , 1981 .

[11]  A. Kluge.  A Concern for Evidence and a Phylogenetic Hypothesis of Relationships among Epicrates (Boidae, Serpentes) , 1989 .

[12]  D. Baird.  The aïstopod amphibians surveyed , 1964 .

[13]  Kevin de Queiroz,et al.  Phylogeny as a Central Principle in Taxonomy: Phylogenetic Definitions of Taxon Names , 1990 .

[14]  J. Hanken.  Miniaturization and its effects on cranial morphology in plethodontid salamanders, genus Thorius (Amphibia: Plethodontidae). I. Osteological variation , 1984 .

[15]  Jerrold I. Davis,et al.  POLYMORPHIC TAXA, MISSING VALUES AND CLADISTIC ANALYSIS , 1991, Cladistics : the international journal of the Willi Hennig Society.

[16]  R. Carroll,et al.  The Order Microsauria , 1978 .

[17]  A. Romer.  A Temnospondylous Labyrinthodont from the Lower Carboniferous , 1969 .

[18]  Robert L. Carroll,et al.  Vertebrate Paleontology and Evolution , 1988 .

[19]  O. A. Lebedev,et al.  The postcranial skeleton of the Devonian tetrapod Tulerpeton curtum Lebedev , 1995 .

[20]  M. P. Cummings,et al.  PAUP* Phylogenetic analysis using parsimony (*and other methods) Version 4 , 2000 .

[21]  R. Carroll.  Homology among divergent Paleozoic tetrapod clades. , 1999, Novartis Foundation symposium.

[22]  H. Mcginnis.  The osteology of Phlegethontia, a carboniferous and permian Aïstopod amphibian , 1967 .

[23]  J. Clack.  The neurocranium of Acanthostega gunnari Jarvik and the evolution of the otic region in tetrapods , 1998 .

[24]  E. Jarvik,et al.  The Devonian tetrapod Ichthyostega , 1996, Fossils and Strata.

[25]  R. Reisz,et al.  The first articulated skeleton of Dendrerpeton acadianum (Temnospondyli, Dendrerpetontidae) from the Lower Pennsylvanian locality of Joggins, Nova Scotia, and a review of its relationships , 1998 .

[26]  S. Sumida,et al.  A new species of Limnoscelis (Amphibia, Diadectomorpha) from the Late Pennsylvanian Sangre de Cristo Formation of central Colorado , 1990, Annals of the Carnegie Museum.

[27]  Arnold G. Kluge,et al.  AMNIOTE PHYLOGENY AND THE IMPORTANCE OF FOSSILS , 1988, Cladistics : the international journal of the Willi Hennig Society.

[28]  J. Bolt.  Amphibamus grandiceps AS A JUVENILE DISSOROPHID: EVIDENCE AND IMPLICATIONS , 1979 .

[29]  Carl Cans,et al.  LOCOMOTION OF LIMBLESS VERTEBRATES: PATTERN AND EVOLUTION , 1986 .

[30]  J. Clack,et al.  Lower jaws, lower tetrapods–a review based on the Devonian genus Acanthostega , 1998, Transactions of the Royal Society of Edinburgh: Earth Sciences.

[31]  C. Wellstead.  Taxonomic revision of the Lysorophia, Permo-Carboniferous lepospondyl amphibians. Bulletin of the AMNH ; no. 209 , 1991 .

[32]  R. Carroll.  Problems of the phylogenetic analysis of paleozoic choanates , 1995 .

[33]  K. Halanych.  Lagomorphs misplaced by more characters and fewer taxa. , 1998, Systematic biology.

[34]  K. J. Carlson.  Crossotelos, an Early Permian nectridian amphibian , 1999 .

[35]  S. Williston.  A new family of reptiles from the Permian of New Mexico , 1911 .

[36]  R. Carroll.  Batropetes from the Lower Permian of Europe—a microsaur, not a reptile , 1991 .

[37]  S. Hedges,et al.  Molecular evidence for the early history of living amphibians. , 1998, Molecular phylogenetics and evolution.

[38]  T. Smithson,et al.  CHARACTER DIAGNOSIS, FOSSILS AND THE ORIGIN OF TETRAPODS , 1987 .

[39]  R. Carroll,et al.  The Carboniferous Amphibian Tuditanus [ Eosauravus ] and the Distinction Between Microsaurs and Reptiles BY , 2022 .

[40]  John P. Huelsenbeck,et al.  WHEN ARE FOSSILS BETTER THAN EXTANT TAXA IN PHYLOGENETIC ANALYSIS , 1991 .

[41]  R. Carroll,et al.  The Order Adelospondyli: Carboniferous lepospondyl amphibians , 1991, Transactions of the Royal Society of Edinburgh: Earth Sciences.

[42]  Timothy B. Rowe,et al.  Definition, diagnosis, and origin of Mammalia , 1988 .

[43]  D. Maddison,et al.  MacClade 4: analysis of phy-logeny and character evolution , 2003 .

[44]  M. Benton.  Origins of the higher groups of tetrapods: controversy and consensus , 1991 .

[45]  J. Bolt,et al.  A microsaur from the Mississippian of illinois and a standard format for morphological characters , 1999, Journal of Paleontology.

[46]  W. Maddison.  Missing Data versus Missing Characters in Phylogenetic Analysis , 1993 .

[47]  Wayne P. Maddison,et al.  Macclade: Analysis of Phylogeny and Character Evolution/Version 3 , 1992 .

[48]  A. Milner,et al.  The temnospondyl amphibians from the Viséan of East Kirkton, West Lothian, Scotland , 1993, Earth and Environmental Science Transactions of the Royal Society of Edinburgh.

[49]  D. Baird.  PALEOZOIC LEPOSPONDYL AMPHIBIANS , 1965 .

[50]  A. Romer.  A Carboniferous Labyrinthodont Amphibian with Complete Dermal Armor , 1972 .

[51]  A. Milner.  THE PALEOZOIC RELATIVES OF LISSAMPHIBIANS , 1993 .

[52]  J. Bolt.  Lissamphibian Origins: Possible Protolissamphibian from the Lower Permian of Oklahoma , 1969, Science.

[53]  A. Graybeal,et al.  Is it better to add taxa or characters to a difficult phylogenetic problem? , 1998, Systematic biology.

[54]  A. Greer.  Limb reduction in squamates : identification of the lineages and discussion of the trends , 1991 .

[55]  Carl Gans,et al.  Tetrapod Limblessness: Evolution and Functional Corollaries , 1975 .

[56]  Michel Laurin,et al.  A reevaluation of early amniote phylogeny , 1995 .

[57]  David P. Mindell,et al.  MacClade: Analysis of Phylogeny and Character Evolution. Version 3.0 Wayne P. Maddison David R. Maddison , 1994 .

[58]  M. Laurin.  The importance of global parsimony and historical bias in understanding tetrapod evolution. Part I. Systematics, middle ear evolution and jaw suspension , 1998 .

[59]  A. Romer.  The primitive reptile Limnoscelis restudied , 1946 .

[60]  R. Reisz,et al.  CHAPTER 2 – A NEW PERSPECTIVE ON TETRAPOD PHYLOGENY , 1997 .

[61]  O. Bininda-Emonds,et al.  Supraspecific taxa as terminals in cladistic analysis: implicit assumptions of monophyly and a comparison of methods , 1998 .

[62]  Zerina Johanson,et al.  Osteolepiforms and the ancestry of tetrapods , 1998, Nature.

[63]  J. O. J. W. Iens.  Testing Phylogenetic Methods with Tree Congruence: Phylogenetic Analysis of Polymorphic Morphological Characters in Phrynosomatid Lizards , 2003 .

[64]  T. Smithson.  The cranial morphology of Greererpeton burkemorani Romer (Amphibia: Temnospondyli) , 1982 .

[65]  R. Carroll,et al.  The skull and jaw musculature as guides to the ancestry of salamanders , 1980 .

[66]  Mark Wilkinson,et al.  Coping with Abundant Missing Entries in Phylogenetic Inference Using Parsimony , 1995 .

[67]  J. Beerbower.  Morphologyc paleoecologyc and phylogeny of the Permo-Pennsylvania amphibian Diploceraspis , 1963 .

[68]  D. Watson.  Vertebrate Paleontology , 1946, Nature.

[69]  R. Carroll,et al.  Vertebral Development in the Oldest Microsaur and the Problem of “Lepospondyl” Relationships , 1995 .

[70]  Michael I. Coates,et al.  The Devonian tetrapod Acanthostega gunnari Jarvik: postcranial anatomy, basal tetrapod interrelationships and patterns of skeletal evolution , 1996, Transactions of the Royal Society of Edinburgh: Earth Sciences.

[71]  R. Reisz,et al.  Archerpeton anthracos from the Joggins Formation of Nova Scotia: a microsaur, not a reptile , 1996 .

[72]  T. Smithson.  The morphology and relationships of the Carboniferous amphibian Eoherpeton watsoni Panchen , 1985 .

[73]  R. Reisz,et al.  Seymouria sanjuanensis (Amphibia, Batrachosauria) from the Lower Permian Cutler Formation of north-central New Mexico and the occurrence of sexual dimorphism in that genus questioned , 1987 .

[74]  R. Carroll.  Developmental aspects of lepospondyl vertebrae in Paleozoic tetrapods , 1989 .

[75]  D. Walsh,et al.  An Early Jurassic caecilian with limbs , 1993, Nature.