The Dinosauria Eugene S. Gaffney Eugene S. Gaffney Department of Vertebrate Paleontology, American Museum of Natural HistoryNew York, New York 10024-5192, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Systematic Biology, Volume 40, Issue 3, September 1991, Pages 378–379, https://doi.org/10.1093/sysbio/40.3.378 Published: 01 September 1991
Computer-generated phylogenies were used to examine the relationship between the temporal position and completeness of additional taxa in a phylogenetic analysis and the rate of evolution or, equivalently, the temporal scope of the phylogenetic problem. In the simulations, four fossil taxa of varying temporal position and completeness were added to an analysis that included four living taxa. Additional taxa varied in completeness (25%, 50%, 75%, and 100% completeness) and in temporal position (0%, 33%, 66%, and 100% of the distance from the ancestor to the living time plane). Fifty trees were generated each for low, low intermediate, high intermediate, and high rates of evolution or temporal scope. Because additional taxa that are 100% complete and 100% of the distance to the living time plane are equivalent to the addition of living taxa, this study directly compares the effects of addition of living versus fossil taxa in phylogenetic analysis. The importance of fossil taxa varied depending on their completeness and temporal position and on the rate of evolution under which the phylogeny was generated. In general, high completeness and temporal position near the ancestor of a clade improved phylogenetic resolution as measured by the percentage of the tree-length distribution that contains the real tree. Furthermore, the conditions of completeness and temporal position under which fossil taxa improved phylogenetic resolution over living taxa became less restrictive as the rate of evolution or the temporal scope of the tree increased. A simple analytical model is proposed to explain these results.
An implementation is explored for standard assumptions (zero and one) for historical biogeographic analysis based on three-area statements specified by widespread taxa and nodes of taxon cladograms. Analysis of simple examples suggests that three-area statements permit a better measure of fit between an area cladogram and data on area relationship than do existing implementations of assumption zero, such as Brooks parsimony analysis, or existing implementations of assumption one, such as that of Nelson and Platnick (1981, Systematics and biogeography: Cladistics and vicariance, Columbia Univ. Press, New York, London), which proves defective in its oversensitivity to information specified by widespread taxa. Aspects of assumptions one and zero are adapted for evaluation of alternative assumption-two cladograms, first with data for nodes and then with data for widespread taxa.
The set of most-parsimonious trees for a data matrix may include several distinct classes (islands) of trees. An island is defined as a collection of trees, all less than a specified length, each tree connected to every other tree in the island through a series of trees, and each one differing from the next by a single rearrangement of branches. One advantage of this method of defining classes of trees is that islands are easily found by tree-searching programs. Multiple islands can be discovered by conducting many searches using a tree-searching program, each search beginning with a different tree. Among 37 data matrices examined, all 8 data matrices with two or more islands have retention indices less than 0.67. Trees are generally more similar within islands than among islands, as judged by analysis of partition metric distances between trees. As a consequence, trees in different islands may have different implications for character evolution, and for this reason should be sought.
We present a phylogenetic methodology to test hypotheses of adaptation and to discriminate adaptation from alternative causal explanations of character evolution. To constitute an adaptation, a character must be shown to provide current utility to the organism and to have been generated historically through the action of natural selection for its current biological role. The criterion of current utility is applied by comparing the performance of a derived trait to that of its phylogenetically antecedent state. If the performance of a trait exceeds that of its antecedent state, it constitutes an "aptation" for its observed biological role. Alternatively, if the performance of a trait equals or falls below that of its antecedent state, it constitutes a "nonaptation" or "disaptation," respectively. The criterion of historical genesis is applied using the concept of "selective regime," the aggregation of organismal and environmental factors that combine to determine the expected action of natural selection on actual and potential character variation. An aptation that arose on a lineage having the same selective regime as the focal taxon constitutes an "adaptation," whereas one that arose on a lineage having a different selective regime constitutes an "exaptation." For nonaptations and disaptations, the criterion of historical genesis serves to determine whether the nonaptive or disaptive status arose coincident with the trait itself or secondarily through a change of selective regime. We suggest that this phylogenetic approach will help to overcome general criticisms of adaptationist studies and will serve to bridge the gap between microevolutionary and macroevolutionary studies of adaptation.
Journal Article Improving the Stability of Names: Needs and Options (Kew, 20-22 February 1991) Get access Alessandro Minelli Alessandro Minelli Department of Biology, University of PadovaVia Trieste 75,1 35121 Padova, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar Systematic Biology, Volume 40, Issue 3, September 1991, Pages 383–385, https://doi.org/10.1093/sysbio/40.3.383 Published: 01 September 1991
We sequenced 2.7 kilobase pairs of contiguous coding mitochondrial DNA from Antilocapra americana (Antilocapridae), Capra hircus (Bovidae), and Tragulus napu (Tragulidae) and compared these to previously published orthologues for other ruminant species. Phylogenetic analysis of these sequences provided no robust patterns of relationship for the four families of pecoran ruminants studied. This finding is consistent with the hypothesis that the pecoran families resulted from a rapid radiation in the Early Miocene to Late Oligocene. This hypothesis is supported by the short internal branch lengths of our most-parsimonious solutions and, more importantly, by the narrow range of interfamilial sequence divergence, suggesting that the radiation may have occurred over a period of 5 million years (about 23-28 million years ago). The importance of using large amounts of conservative sequence data for resolving relationships among members of a rapid radiation is discussed.
Studies of sexual dimorphism commonly focus on male morphology, often viewing males as divergent both evolutionarily and ontogenetically. For example, in continuously growing vertebrates such as lizards and fishes, it has been assumed that adult dimorphism arises from growth rate changes in male characters at the onset of maturity. However, there has been little explicit treatment of the ontogenetic origin of morphological sex differences. I present here a method for testing hypotheses of sex-specific allometric change, and offer an example of its application in four species of Labrisomid blennies. I develop three hierarchical models to test for allometric divergence: (1) the null model, in which adult allometries of both sexes are simply an extension of the juvenile allometries (model A); (2) a model in which either adult males or females (but not both) diverge from the juvenile trajectory (model B); and (3) a model in which adults of both sexes diverge from the juvenile allometry (model C). Growth that fits either of the two latter models results in shape dimorphism. Although size dimorphism may occur in all three cases, it is not explicitly treated here. The models were tested with size-series of four species of fish (Paraclinus, Labrisomidae). To further explore overall shape similarity among males, females, and juveniles, a multivariate analysis of shape (independent of size) was applied. Analysis of 42 mensural characters showed that divergence from juvenile allometry occurred as frequently in female traits as in male traits. Multivariate analysis showed that in all four species, female shape diverges more from juvenile shape than does male shape. In addition, similarity among adult dimorphic character states often resulted from quite different growth patterns, suggesting that resemblance of adult characters among related species is insufficient evidence to conclude character homology. Interpretations of sexual dimorphism, currently emphasizing male morphology, may be biased and may underestimate the importance of selection on the female form as a cause of sexual dimorphism.
Extremely conflicting phylogenetic conclusions for the same taxa derived from different data sets are rare. When conflicts do occur, they may result from homoplasy as well as nonindependence of characters. We present an analysis of the phylogenetic relationships of the salamander family Ambystomatidae, based on variation at 26 allozyme loci. Our results conflict strongly with those derived from Kraus's (1988, Syst. Zool. 37:106-141) morphological analysis of the same taxa. The major conflict involves five species traditionally placed in the Ambystoma subgenus "Linguaelapsus." This group, and the clades within it, are each diagnosed by many morphological synapomorphies, providing unambiguous evidence for the monophyly of the subgenus. However, our allozyme data provide equally compelling evidence that "Linguaelapsus" is polyphyletic. We jackknifed and bootstrapped our allozyme data in a likelihood and a cladistic parsimony framework, respectively; all analyses point to the same conclusions. Subdividing the allozyme data into rapidly and slowly evolving loci, and analyzing each separately by maximum likelihood, does not change our conclusions. Our results demonstrate that even apparently "well-corroborated" nodes of a cladogram may be suspect if the assumption of character independence is violated.
Cleavage site variation of 18 restriction endonucleases in the transcribed portion of the ribosomal DNA gene complex was mapped from 42 genera of New World leaf-nosed bats (family Phyllostomidae). These data were used to test the higher taxonomic relationships of a traditionally recognized phylogeny against a recently revise phylogeny and classification for the family. Major conclusions from this study are that (1) support is provided for the theory that early phyllostomid radiation proceeded by the diversification of three or four lineages; (2) New World leaf-nosed bats, including vampire bats, compose a monophyletic group; and (3) the newly proposed classification and topology are supported. This study demonstrates that additional resolution can be obtained by testing new data for congruence with existing phylogenies.
Invertebrates Get access Rich Mooi Rich Mooi Department of Invertebrate Zoology and Geology, California Academy of Sciences, Golden Gate ParkSan Francisco, California 94118, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Systematic Biology, Volume 40, Issue 2, June 1991, Pages 245–247, https://doi.org/10.1093/sysbio/40.2.245 Published: 01 June 1991
Journal Article Biogeography of the West Indies. Past, Present and Future. Get access Charles A. Woods (ed.). 1989. Sandhill Crane Press, Gainesville, Florida, xvii + 878 pp. $90.50. Jay M. Savage Jay M. Savage Department of Biology, University of Miami,P.O. Box 249118, Coral Gables, Florida 33124, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Systematic Biology, Volume 40, Issue 1, March 1991, Pages 110–111, https://doi.org/10.1093/sysbio/40.1.110 Published: 01 March 1991
Journal Article On the Monophyly of Bats Get access Robert J. Baker, Robert J. Baker 1Department of Biological Sciences and The MuseumP.O. Box 4499, Texas Tech UniversityLubbock, Texas 79409, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Michael J. Novacek, Michael J. Novacek 2Department of Vertebrate Paleontology, American Museum of Natural HistoryCentral Park West at 79th Street, New York, New York 10024, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nancy B. Simmons Nancy B. Simmons 3Department of Mammalogy, American Museum of Natural HistoryCentral Park West at 79th Street, New York, New York 10024, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Systematic Biology, Volume 40, Issue 2, June 1991, Pages 216–231, https://doi.org/10.1093/sysbio/40.2.216 Published: 01 June 1991 Article history Received: 16 August 1990 Accepted: 26 September 1990 Published: 01 June 1991
The comparative analysis of DNA molecules is a useful means for phylogenetic reconstruction, because different types of genetic elements yield resolution at different levels of taxonomic divergence. A single individual is usually characterized for each operational taxonomic unit (OTU), based on the premise that within-OTU variation can be safely ignored. Whereas that premise is expedient, it may not be generally valid. Sometimes variation within OTUs can affect the analysis. We develop a formal analytic treatment of variation in phylogenetic output as a consequence of intraspecific variation. Using restriction site data from the mitochondria of three species of cyprinid fishes to illustrate, we show that genetic variation within taxa impacts on tree topology. Genetic variation among populations is most important; that within populations is small. Genetic variation should be expected within any taxon, and it is generally useful to sample (replicate) one taxonomic level below that of interest.
Journal Article Phylogeny and the Classification of Fossil and Recent Organisms Get access David C. Cannatella David C. Cannatella Texas Memorial Museum, University of TexasAustin, Texas 78705, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Systematic Biology, Volume 40, Issue 3, September 1991, Pages 376–378, https://doi.org/10.1093/sysbio/40.3.376 Published: 01 September 1991
