Syst. Biol. 44(2):125--151, 1995
A Molecular Phylogenetic Perspective on the Evolutionary Radiation of the Salamander Family Salamandridae
Tom A. Titus1 and Allan Larson
Department of Biology, Washington University,
St. Louis, Missouri 63130-4899, USA
1 Present address: Department of Biology, University of Oregon,
Eugene, Oregon 97403, USA. E-mail: firstname.lastname@example.org.
Abstract.---Phylogenetic relationships were examined within the salamander family Salamandridae using 18 species representing 14 salamandrid genera and six outgroup taxa from the families Ambystomatidae, Dicamptodontidae, Plethodontidae, and Proteidae. Mitochondrial DNA sequences encoding the 12S and 16S ribosomal RNA and the intervening valine transfer RNA provided 431 phylogenetically informative nucleotide sequence positions from a multiple alignment of approximately 1,000 bases per species. This variation was analyzed in conjunction with 44 previously reported morphological characters representing primarily hyobranchial myology and osteology, cranial osteology, and reproductive biology. The molecular and morphological character sets were highly congruent, with only 2.8% of the total character incongruence attributable to conflict between them. Parsimony analysis of the combined molecular and morphological data produced a single most-parsimonious tree whose topology was identical to that of the most-parsimonious tree derived from the molecular data alone. This tree suggests that the "true" salamanders (Chioglossa, Mertensiella, and Salamandra) form a monophyletic sister group to the newts (all remaining salamandrid genera). Within the newts, the first phylogenetic split separates Salamandrina from the remaining genera, within which Pleurodeles and Tylototriton form a monophyletic sister group to the remaining taxa. The genus Triturus appears not to be monophyletic. Using a phylogenetic reconstruction of character changes, we tested hypotheses of adaptation in the evolution of aquatic suction feeding and terrestrial feeding featuring tongue protrusion. Phylogenetic trends in the evolution of salamandrid courtship behavior were also examined. [Salamandridae; molecular phylogenetics; mitochondrial DNA; congruence; feeding morphology; courtship.]
Syst. Biol. 44(2):152--178, 1995
Continuous Track Analysis:
A New Phylogenetic and Biogeographic Method
Committee on Evolutionary Biology, University of Chicago,
5734 South Ellis Avenue, Chicago, Illinois 60637, USA
1 E-mail: email@example.com.
Abstract.---Continuous track analysis (CTA) can depict reticulate evolutionary patterns in phylogenetics and biogeography. A reticulate connection implies convergence, hybridization, or introgression in an evolutionary graph of taxa and implies dispersal in an evolutionary graph of biogeographic areas. CTA finds graphs that (1) have a minimal number of connections and (2) imply that most character states or taxa have distributions or tracks across taxa or areas (objects) that are continuous, i.e., can be traced across the connections among the objects including that state without traveling through any other objects. Continuous tracks imply either that character states in phylogenies have unique evolutionary origins or that taxa in biogeographic analyses are monophyletic. Relatively simple graphs usually cannot imply completely continuous tracks. Therefore, CTA graphs seek to minimize the number of track fragments, which are locally continuous parts of a track; tracks with more than one fragment are discontinuous. Minimizing fragments is the same as minimizing character-state transitions only if there are no reticulations. Because hypothetical ancestors do little to reduce the number of fragments, CTA tends to place known taxa or areas at internal nodes. A heuristic algorithm analogous to tree bisection-reconnection is used to find highly parsimonious CTA graphs. In phylogenetic analyses, CTA employs a special complementary binary coding convention that serendipitously solves the missing characters/missing data problem. Although the problem of ancestors "inheriting" states from hybrid descendants is irrelevant if reticulations merely represent convergence patterns, CTA includes an optional algorithm that avoids such instances by explicitly identifying ancestors and descendants. CTA was compared with standard parsimony analysis using a data set of 17 Neogene species of North American fossil hipparionine horses. CTA separates the three major clades and illustrates their convergent features with reticulations, whereas standard parsimony analysis groups the three in an unresolved polytomy. CTA also minimizes the number of hypothetical, unsampled ancestors and lineages. [Ancestors; biogeographic methods; dispersal; homology; Hipparionini; hybridization; phylogenetic methods; reticulation.]
Syst. Biol. 44(2):179--189, 1995
Morphometrics, Homology, and Phylogenetics:
Miriam Leah Zelditch,1,3 William L. Fink,2,4 and Donald L. Swiderski1,5
Quantified Characters as Synapomorphies
1Museum of Paleontology, University of Michigan,
Ann Arbor, Michigan 48109, USA
2Department of Biology and Museum of Zoology,
University of Michigan, Ann Arbor, Michigan 48109, USA
3 E-mail: firstname.lastname@example.org.
4 E-mail: email@example.com.
5 E-mail: firstname.lastname@example.org.
Abstract.---It has been claimed that quantified features are inappropriate for phylogenetic analysis. We consider that claim to be true under most conditions for characters discovered by commonly used morphometric methods, including outline-based and conventional multivariate methods. The most important reason these characters are unsuitable is that one of the tests of homology, the test of similarity, may be difficult to apply to them. This test is not even possible if the methods for comparing forms, such as outline-based techniques, do not ensure that the characters are located in the same part of the anatomy. Conventional methods, including principal components analysis, have no explicit basis for localizing characters. In addition, unless the transformation between forms is homogeneous, conventional methods cannot dissect transformations region by region to discover characters. However, one morphometric method, the thin-plate spline decomposed by its partial warps (TPS), finds characters that can be subjected to the same tests of homology (conjunction, similarity, and congruence) that we would apply to all other characters. Among available methods, TPS is unique in being able to locate the center and spatial extent of regional differences in shape and ensures that the same regions are compared among forms. We provide an example using the teleost fishes piranhas, in which tests of homology are applied to a synapomorphy found by the method. [Morphometrics; homology; synapomorphy; thin-plate spline; character analysis; piranha; Pygocentrus; Pygopristis; Serrasalmus.]
Syst. Biol. 44(2):190--208, 1995
A Combined Morphological and Molecular Approach
B. Lafay,1,3 A. B. Smith,2 and R. Christen1
to the Phylogeny of Asteroids (Asteroidea: Echinodermata)
1Observatoire Oceanologique, CNRS and Universite Paris VI,
Station Zoologique, Villefranche sur Mer, 06230 France
2Department of Palaeontology, The Natural History Museum,
Cromwell Road, London SW7 5BD, England
3 Present address: CSIRO Division of Plant Industry,
Institute of Plant Production and Processing, GPO Box 1600,
Canberra ACT 2601, Australia.
Abstract.---Two recent analyses of asteroid phylogeny have come to surprisingly different conclusions concerning both the tree topology and rooting. We reanalyzed the problem for nine asteroids, with representatives from five of the major higher taxa: Paxillosida, Forcipulatida, Valvatida, Spinulosida, and Velatida. We combined the two previously published morphological data sets to generate a well-supported, though unrooted, phylogenetic tree. We also derived a molecular phylogeny from the analysis of the first 400 bases of the 28S ribosomal RNA sequences for the same nine taxa. This tree provides less resolution but does not contradict the morphological tree. The combined morphological and molecular data were used to derive the most well-supported unrooted topology. To avoid assumptions as to what represents derived versus primitive morphological character states among asteroids, we used only molecular data from other echinoderm classes to identify the root position. Although this approach does not resolve the rooting point unambiguously, evidence favors the Astropectenidae as the sister group to the rest of the asteroids. We then polarized the morphological characters of crown group asteroids and estimated relative rates of molecular evolution, which show a five-fold difference. Molecular data give no support to the recent suggestion that Forcipulatida diverged significantly earlier than did other asteroids. [RNA; rates of evolution; rooting; cladistics; fossil record.]
Syst. Biol. 44(2):209--220, 1995
A Phylogeny of Indo-West Pacific Megachiroptera Based on Ribosomal DNA
D. J. Colgan1 and T. F. Flannery
The Australian Museum, Sydney 2000, Australia 1
Abstract.---There have been no major advances in understanding the evolution of the Old World fruit bats (Megachiroptera: Pteropodidae) since the work of Andersen (1912, Catalogue of the Chiroptera in the collection of the British Museum, 2nd edition, Volume 1, Megachiroptera, British Museum of Natural History, London), nor have there been any rigorous cladistic analyses of megachiropteran interrelationships. Here we report a phylogenetic investigation of restriction endonuclease site variation in the ribosomal RNA cistrons of 25 species in 14 genera of Indo-West Pacific Megachiroptera. Twenty-three of the 82 mapped sites were phylogenetically informative. Analyses of these informative sites suggest three considerable modifications to the morphological understanding of megachiropteran relationships: (1) the most-parsimonious explanation of site-state distribution is that the Macroglossinae (as previously defined) is paraphyletic with respect to other groups; (2) the cynopterine and rousettine sections are not shown as monophyletic sister groups in any of the most-parsimonious trees; and (3) Pteropus and Acerodon are not closely related to any other rousettine genera. [Fruit bats; Megachiroptera; ribosomal DNA; phylogeny, restriciton fragment length polymorphisms.]
Syst. Biol. 44(2):221--236, 1995
Molecules, Morphology, And Area Cladograms: A Cladistic and Biogeographic Analysis of Gambusia (Teleostei: Poeciliidae)
Charles Lydeard,1,4 Michael C. Wooten,2 and Axel Meyer3
1Aquatic Biology Program, Department of Biological Sciences,
University of Alabama, Box 870344, Tuscaloosa, Alabama 35487, USA
2Department of Zoology and Wildlife Science, Auburn University,
Auburn, Alabama 36849-5414, USA
3Department of Ecology and Evolution, State University of New York,
Stony Brook, New York 11794-5245, USA
4 E-mail: email@example.com.
Abstract.---Researchers investigating historical biogeography rely on taxon cladograms to infer the relationships of different areas of endemism. Unfortunately, systematists are often faced with many equally parsimonious taxon cladograms from a single data set or conflicting phylogenetic hypotheses from independent data sets. We present an analysis of congruence between two conflicting phylogenetic hypotheses of the poeciliid fish genus Gambusia, one based on mitochondrial DNA sequences and the other based on morphological characters. We explore how different phylogenetic hypotheses alter interpretations of area relationships and propose a set of area relationships for the genus. Furthermore, we compared the area relationships depicted for Gambusia with that of two Middle American fish genera (Xiphophorus and Heterandria) with similar distributional limits. Our analysis revealed areas of congruence among taxa from nuclear Central America but areas of incongruence among taxa from the Panuco basin and North American components. We discuss the implications of our findings in light of conventional hypotheses regarding Caribbean biogeography. This study illustrates the importance of considering alternative phylogenetic hypotheses fully before attempting to interpret the biogeographic history of a taxon or region. [Historical biogeography; Caribbean biogeography; phylogeny; Gambusia; Poeciliidae; congruence; area cladograms.]