Syst. Biol. 49(1) 2000



Abstract.--Understanding how development varies both inter- and intraspecifically can be important for systematic and evolutionary studies. This review will explore three different ways such understanding can be applied to evolutionary analyses. First, developmental data can be useful for homology determination. Interspecific variation in development has been thought to make developmental data poor candidates for homology determination. However, an updated developmental criterion that is more broadly comparative and mechanistic augments the available criteria used in the determination of homology. Second, modern cell and molecular biology are providing a better understanding of the many developmental processes involved in a structure's formation and will augment the number of characters available for phylogenetic analyses. Recent work has revealed that what had been thought to be a highly conserved developmental stage, the pharyngula, the phylotypic and zootypic stage of craniates, is highly variable. This variation can be seen in the development of such tissues as neural crest and placodes. These tissues are particularly interesting from a phylogenetic standpoint because they and the structures they form contribute to key synapomorphies of craniates. Finally, understanding developmental processes and how they form the variety of morphologies seen in nature will help in constructing the transformations that occurred during evolution. One such example involves descriptions of how lateral line development is affected in different mutant lines of zebrafish. There is great variation across the many species of teleost fishes in the patterns of their lateral lines and this is often an important systematic character. Understanding the genetic basis of lateral line development would help in not only hypothesizing possible transformational series but also in determining how many genes may have been required for these transformations.


Abstract - Issues concerning transformational and taxic comparisons are central to understanding the impact of the recent proliferation of molecular developmental data on evolutionary biology. More importantly, an understanding of taxism and transformationalism in comparative biology is critical to assessing the impact of the recent developmental data on systematic theory and practice. We examine the philosophical and practical aspects of the transformational approach and the relevance of this approach to recent molecular based developmental data. We also examine the theoretical basis of the taxic approach to molecular developmental data and suggest that developmental data are perfectly amenable to the taxic approach. Two recent examples from the molecular developmental biology literature - the evolution of insect wings and the evolution of dorsal ventral inversion in vertebrates and invertebrates - are used to compare the taxic and transformational approaches. We conclude that the transformational approach is entirely appropriate for ontogenetic studies and furthermore can serve as an excellent source of hypotheses about the evolution of characters. However, the taxic approach is the ultimate arbiter of these hypotheses. [development, evolution, taxism, co-option.]


Abstract. -- Modified interactions among developmental regulatory genes and changes in their expression domains are likely to be an important part of the developmental basis for evolutionary changes in morphology. Although developmental regulatory genes are now being studied in an increasing number of taxa, there has been little attempt to analyze the resulting data within an explicit phylogenetic context. Here we present comparative analyses of expression data from regulatory genes in the phylum Echinodermata, considering the implications for understanding both echinoderm evolution as well as the evolution of regulatory genes in general. Reconstructing the independent evolutionary histories of regulatory genes, their expression domains, their developmental roles, and the structures in which they are expressed reveals a number of distinct evolutionary patterns. A few of these patterns correspond to interpretations common in the literature, while others have received little prior mention. Together, the analyses indicate that the evolution of echinoderms involved: (1) the appearance of many apomorphic developmental roles and expression domains, some of which have plesiomorphic bilateral symmetry and others of which have apomorphic radial symmetry or left-right asymmetry; (2) the loss of some developmental roles and expression domains thought to be plesiomorphic for Bilateria; and (3) the retention of some developmental roles thought to be plesiomorphic for Bilateria, although with modification in expression domains. Some of modifications within the Echinodermata concern adult structures and others transient larval structures. Some changes apparently appeared early in echinoderm evolution (> 450 Ma) while others probably happened more recently (< 50 Ma). Cases of likely convergence in expression domains suggest caution when using developmental regulatory genes to make inferences about homology among morphological structures of distantly related taxa.

[evolution of development, regulatory gene, homeobox gene, homology, Echinodermata, Metazoa.]


Abstract. - Understanding the phylogenetic relationships of the three major urochordate groups within the deuterostomes is central to understanding the evolution of the chordates. We have prepared a detailed phylogenetic analysis of urochordates based on comparisons of 10 new urochordate 18S ribosomal DNA sequences with other urochordate sequences in GenBank. Maximum parsimony, Neighbor-Joining, Minimum Evolution and Maximum Likelihood analyses of this large urochordate dataset are consistent with a topology in which the urochordates are monophyletic within the deuterostomes and there are four separate clades of urochordates. These four distinct clades - styelid + pyurid ascidians, molgulid ascidians, phlebobranch ascidians + thaliaceans, and larvaceans - are mostly consistent with traditional morphological hypotheses and classifications. However, we find that the ascidians may not be a monophyletic group, as they have been considered traditionally, but instead appear polyphyletic. Another disparity with traditional classification is that the thaliaceans do not form a separate urochordate clade, rather they cluster with the phlebobranch ascidians. Larvaceans have long branch lengths, which can be problematic for molecular phylogenetic methods, and their position within the urochordates cannot be unequivocally determined with 18S rDNA. This is important because the tadpole morphology of larvacean and ascidian larvae is the key trait of interest that distinguishes urochordates as chordates. Nevertheless, the present data set resolves at least three clades of urochordates and suggests strongly that urochordates form a monophyletic clade within the deuterostomes. [Urochordate Phylogeny, Ascidians, Larvaceans, Thaliaceans, Chordate Evolution, Urochordate Evolution, Deuterostome Evolution]


Abstract not yet available


Abstract.--The horseshoe crabs, known as living fossils, have maintained their morphology almost unchanged for the past 150 million years. The little morphological differentiation among horseshoe crab lineages has resulted in substantial controversy concerning the phylogenetic relationship among the extant species of horseshoe crabs, especially among the three species in the Indo-Pacific region. Previous studies suggest that the three species constitute a phylogenetically unresolvable trichotomy resulting from a cladogenetic process leading to the formation of all three Indo-Pacific species in a short geological time. Data from two mitochondrial genes (16S rRNA and COI) and one nuclear gene (coagulogen) in the four species of horseshoe crabs and outgroup species were used in a phylogenetic analysis with various substitution models. All three genes yield the same tree topology, with T. gigas and C. rotundicauda grouped together as a monophyletic taxon. This topology is significantly better than all the alternatives when evaluated with the RELL (resampling estimated log-likelihood) method. [Molecular phylogenetics, substitution model, RELL, Limulus polyphemus, Tachypleus gigas, T. tridentatus, Carcinoscorpius rotundicauda.]


Abstract.--Functional constraints are often assumed to influence the performance of nucleotide characters in phylogenetic analysis; first and second codon positions and sites of structural importance are considered to show less homoplasy. We investigate the performance of rbcL characters with differential functional constraints in a cladistic analysis of the plant family Apocynaceae s.l. (). Performance is measured as rescaled consistency indices, rc. We show that there is no significant difference in performance between parsimony informative sites constrained by function in the enzyme, and sites that are not. Furthermore, the substitutions in third codon position performed significantly better than those in first and second. The variation of rc within the different classes was high, however. Consequently, there is no support for routinely applied a priori differential weighting, neither of codon positions, nor of different functional classes from the present analysis of rbcL data in the Apocynaceae s.l. [Functional constraints; protein structure; codon constraints; character weighting; character performance; rescaled consistency index; Apocynaceae s.l.]


Abstract.--Antarctic waters represent a unique marine environment delimited by an oceanographic barrier, the Polar Front Zone, and characterized by constant subzero temperatures and presence of sea ice. A group of teleost fish, the Notothenioidei, have adapted to these challenging environmental conditions, undergoing a remarkable diversification. In the present study a total of 798 base pairs, generated from partial sequencing of 16S and 12S mitochondrial ribosomal RNA genes, were examined in 33 notothenioid species representative of all families included in the suborder Notothenioidei. Phylogenetic trees, reconstructed on the basis of sequence data using different methods, indicate that traditional hypotheses on notothenioid systematics and biogeography might be in need of reexamination. Molecular evidence suggests that vicariant speciation could be invoked to explain the early divergence of Eleginops maclovinus, a species previously included in the family Nototheniidae, which is now proposed as the closest sister group to all the rest of notothenioids apart from bovichtids. On the other hand, repeated, independent dispersal through the Polar Front is proposed for the divergence of other subantarctic notothenioid species. Likewise, multiple, independent transitions from benthic to pelagic habit are inferred from molecular data, at variance with the more conservative hypothesis based on cladograms reconstructed from morphological data. [Antarctic fish, mtDNA, ribosomal RNA, phylogeny, evolution, biogeography]



Abstract.--The phylogeny of the Bilateria and especially the early steps in the evolution of the bilaterian bauplan are still a controversial topic. In this context the relationships of the platyhelminths and the nematodes play a crucial role. Previous molecular studies of the relationships of these groups, which were based on 18S ribosomal DNA sequences, yielded conflicting results. In the present study a new framework is developed for the phylogenetic analysis of bilaterian relationships using concatenated amino acid sequences of several nuclear genes. In this analysis, the rhabditophoran platyhelminths are probably the sister group of all other analyzed Bilateria, the Eubilateria, which are characterized by a one-way intestine with an anus. The Eubilateria are split into the nematode lineage and the coelomates. The phylogenetic results of the present study indicate that genetic features found in the model organisms Caenorhabditis and Drosophila might be found in all Eubilateria. Estimations of the divergence times show that the major bilaterian phyla did not originate in an explosive radiation during the Cambrian but rather that the Bilateria have a several hundred million years long Precambrian history. [Bilateria, Platyhelminthes, Nematoda, Coelomata, molecular phylogeny, molecular clock.]



Abstract.--Recent studies have found strongly conflicting phylogenies for the genera of iguanid lizards based on different types of data (i.e., morphology, molecules), but have been unable to explain the basis for this incongruence. We reanalyze published data from morphology and from the mitochondrial ND4, cytochrome b, 12S, and 16S genes to explore the sources of incongruence and resolve these conflicts. Much of the incongruence centers on the genus Cyclura, which is the sister taxon of Iguana based on parsimony analyses of the morphology and the ribosomal genes but is the sister taxon of all other Iguanini according to the protein-coding genes. Maximum likelihood analyses show that there has been an increase in the rate of nucleotide substitution in Cyclura in the two protein coding genes (ND4 and cytochrome b), although this increase is not as clear when parsimony is used to estimate branch lengths. Parametric simulations suggest that Cyclura may be misplaced by the protein-coding genes due to long-branch attraction; even when Cyclura and Iguana are sister taxa in a simulated phylogeny, Cyclura is still placed as the basal member of the Iguanini by parsimony analysis in 55% of the replicates. A similar long-branch attraction problem may also exist in the morphological data involving the placement of Sauromalus with the Galápagos iguanas (Amblyrhynchus and Conolophus). The results have many implications for the analysis of diverse data sets, the impact of long branches on parsimony and likelihood methods, and the use of certain protein-coding genes in phylogeny reconstruction. [Data set incongruence; Iguanidae; likelihood, long-branch attraction, parsimony.]