Phylogeny of the Neotropical killifish family Rivulidae (Cyprinodontiformes, Aplocheiloidei) inferred from mitochondrial DNA sequences.

Phylogenetic relationships of 70 taxa representing 68 species of the Neotropical killifish family Rivulidae were derived from analysis of 1516 nucleotides sampled from four different segments of the mitochondrial genome: 12S rRNA, 16S rRNA, cytochrome oxidase I, and cytochrome b. The basal bifurcation of Cynolebiatinae and Rivulinae (Costa, 1990a,b) is supported; however, Terranatos, Maratecoara, and Plesiolebias are rivulins, not cynolebiatins. These three genera, along with the other recognized annual rivulin genera, form a monophyletic clade. Austrofundulus, Rachovia, Renova, Terranatos, and 3 species of the genus Pterolebias, all from northeastern South America, form a monophyletic clade excluding other species of Pterolebias. Pterolebias as presently understood is clearly polyphyletic. Trigonectes and Moema are supported as sister groups but do not form a monophyletic group with the genera Neofundulus and Renova as previously proposed. The suite of adaptations necessary for an annual life history has clearly been lost several times in the course of rivulid evolution. Also revealed is a considerable increase in substitution rate in most annual lineages relative to the nonannual Rivulus species. The widespread and speciose genus Rivulus is paraphyletic, representing both basal and terminal clades within the Rivulidae. Previous hypotheses regarding the vicariant origin of Greater Antillean Rivulus species are supported. Most rivulid clades show considerable endemism; thus, detailed analysis of rivulid phylogeny and distribution will contribute robust hypotheses to the clarification of Neotropical biogeography.

Mitochondrial DNA phylogeny of West African aplocheiloid killifishes (Cyprinodontiformes, Aplocheilidae).

African killifishes (Cyprinodontiformes, Aplocheilidae) historically associated with the genus Aphyosemion occur in two geographically distinct regions. One assemblage from far West Africa has been previously shown to be monophyletic and not closely related to the remaining eastern species of Aphyosemion (W. J. Murphy and G. E. Collier, 1997, Mol. Biol. Evol. 14, 790-799). This is supported by further analysis of mitochondrial DNA sequences from 19 species from 21 different localities, representing 19 of the putative 22 species of this western group. Phylogenetic analyses of these data corroborate the monophyly and sister-group relationship of two distinct groups of taxa: Callopanchax and Scriptaphyosemion. Many of the relationships within Scriptaphyosemion suggest that these taxa may have radiated within a short period of time relative to the rate of substitutions within these sequences. A third, and possibly paraphyletic group of species, Archiaphyosemion, is suggested to be the sister taxon to the first two groups. These three groups are elevated to generic rank and together represent the sister group to the genus Epiplatys. Biogeographic inference suggests that the ancestors of this group diversified westward through upland habitat and have only relatively recently entered the lowland habitats in which Scriptaphyosemion and Callopanchax have diversified, with the latter genus reacquiring a suite of traits collectively referred to as annualism.

Phylogenetic relationships of African killifishes in the genera Aphyosemion and Fundulopanchax inferred from mitochondrial DNA sequences.

We have analyzed the phylogenetic relationships of 52 species representing all defined species groups (J. J. Scheel, 1990, Atlas of Killifishes of the Old World, 448 pp.) of the African aplocheiloid fish genera Aphyosemion and Fundulopanchax in order to examine their interrelationships and to reveal trends of karyotypic evolution. The data set comprised 785 total nucleotides from the mitochondrial 12S rRNA and cytochrome b genes. The molecular-based topologies analyzed by both maximum parsimony and neighbor-joining support the monophyly of most previously defined species groups within these two killifish genera. The genus Aphyosemion is monophyletic except for the nested position of Fundulopanchax kunzi (batesi group; subgenus Raddaella) within this clade, suggesting that this taxon was improperly assigned to Fundulopanchax. The remaining Fundulopanchax species sampled were supported as being monophyletic in most analyses. Relationships among the species groups in both genera were not as strongly supported, suggesting that further data will be required to resolve these relationships. Additional sampling from the 16S rRNA gene allowed further resolution of relationships within Fundulopanchax, more specifically identifying the nonannual scheeli group as the basal lineage of this otherwise annual genus. Chromosomal evolution within Aphyosemion has been episodic, with the evolution of a reduced n = 9-10 metacentric complement having occurred in multiple, independent lineages. Polarity of chromosomal reductions within the elegans species group appears to support previous hypotheses concerning mechanisms of karyotypic change within the genus Aphyosemion.

A molecular phylogeny for aplocheiloid fishes (Atherinomorpha, Cyprinodontiformes): the role of vicariance and the origins of annualism.

Annual aplocheiloid killifish embryos possess a rare ability among vertebrates to enter stages of developmental arrest (diapause) when subjected to adverse environmental conditions. Previous morphological analyses have presented disparate hypotheses regarding the evolution of the intriguing life history associated with this phenomenon. We present a novel hypothesis of aplocheiloid relationships based on 1,009 bp of sequence data from three mitochondrial genes (cytochrome b, 12S rRNA, and 16S rRNA). Phylogenetic analysis using maximum parsimony, neighbor-joining, and maximum likelihood produce strongly congruent topologies. Our data confirm the monophyly of the Neotropical family Rivulidae, while demonstrating a paraphyletic Old World assemblage. The basal sister group position of Indo-Malaysian and Madagascaran taxa relative to a monophyletic South American/African dichotomy strongly indicates the role of vicariance in the diversification of these fishes in spite of their definition as secondary freshwater fish. The distribution of annualism onto this topology implies a single early origin for this suite of characters, prior to the divergence of South American and African taxa. If so, then annualism has since been lost several times during the evolution of genera now residing in permanent aquatic habitats. Paleoclimatic knowledge complements this scenario based on molecular characters.

Phylogenetic relationships within the aplocheiloid fish genus Rivulus (Cyprinodontiformes, Rivulidae): implications for Caribbean and Central American biogeography.

We examined the phylogenetic relationships of 16 northern species of the aplocheiloid genus Rivulus inhabiting the Caribbean, Central America, and South America. A total of 714 base pairs per taxon were sequenced from two segments of the mitochondrial genome, 12S rRNA and cytochrome b. Both parsimony and neighbor-joining analyses suggest an ancient vicariant origin of the Greater Antillean taxa, in addition to a quite recent dispersal of species into the Lesser Antilles from the South American mainland. Combined analyses support the monophyly of the northern South American assemblage as the sister group of a Central American/Columbian biota. However, the monophyly of the Central American biota remains uncertain. Divergence estimates for the Central American taxa are calibrated from the Last Cretaceous separation of the proto-Antilles from the Americas. These data suggest that the extant Central American taxa represent the descendants of at least two separate invasions during the Cenozoic, prior to the closing of the Panamanian isthmus. Times are consistent with the extensive evidence for reptilian and mammalian exchange throughout the Cenozoic.

Early gene interaction during prepupal expression of Drosophila arginine kinase.

Arginine kinase displays a distinctive rise and fall in specific activity and specific protein levels during the prepupal stage of Drosophila development with maximal activity occurring at morphological stage P3. This developmentally regulated peak is under the influence of ecdysone. Altered doses of the major ecdysone-inducible "early" genes at cytological regions 75B and 2B5 alter this pattern of expression while altered doses of another major "early" gene at 74EF have no effect. We hypothesize that a product of the 2B5 locus and a product of the 75B locus interact to effect this developmental pattern of expression of Drosophila arginine kinase.

Evolution of arginine kinase within the genus Drosophila.

The rate of evolution and extant levels of polymorphism for arginine kinase were examined in species of the genus Drosophila. Surveys of 11 species for electrophoretic variation revealed an average heterozygosity of 0.003. Using antisera prepared against arginine kinase purified from a representative of each of three major subdivisions of the genus, immunological distances were measured by microcomplement fixation (MC'F) assay for 20 species of Drosophila. These data are consistent with the broad outline of the phylogenetic relationships within the genus suggested by other kinds of data. The unit evolutionary period for Drosophila arginine kinase was estimated to be 59 million years (MY). This contrasts with an estimate of 30 MY as the unit evolutionary period for vertebrate creatine kinase. It is suggested that this difference in evolutionary rate arises because a single gene encodes Drosophila arginine kinase, whereas at least three different genes encode the various forms of vertebrate creatine kinase.

Cytoplasmic and mitochondrial arginine kinases in Drosophila: evidence for a single gene.

Mitochondrial and cytoplasmic isozymes of arginine kinase have been identified in Drosophila melanogaster. On the basis of their immunological similarity, parallel dosage responses, and cosegregation of electrophoretic mobility differences, it is concluded that both isozymes are the product of a single gene. The consequences of this in relation to the regulation and evolution of this unusual gene-enzyme system are discussed. It is inferred that the origin of the phosphagen shuttle must predate the divergence of invertebrates and vertebrates.

Genetic and biochemical characterization of phosphofructokinase from Drosophila melanogaster.

Phosphofructokinase (PFK;EC 2.7.1.11) activity in Drosophila melanogaster is controlled by a single dosage-sensitive region of the genome between 45F and 47E of chromosome IIR. Only a single form of PFK was detected electrophoretically in both adults and larvae. Nearly 90% of the PFK activity in adults is localized to the thorax. Purification of the enzyme was hampered by the extreme lability of Drosophila PFK; however, a 36-fold partial purification was achieved.

Localization of a dosage sensitive region for pyruvate kinase in Drosophila melanogaster.

A small segment of chromosome 1, 12AB-12C, in Drosophila melanogaster is dosage-sensitive for the glycolytic enzyme pyruvate kinase (EC 2.7.1.40). We suggest that the enzyme is coded by a gene, Pyk+, located within this region. The activity of the enzyme over developmental time also was measured.

Affinity labeling of succinyl-CoA synthetase from Escherichia coli by the 2',3'-dialdehyde derivative of adenosine 5'-diphosphate.

The 2'3'-dialdehyde of adenosine 5'-diphosphate, oADP, exhibited the properties of an affinity label with Escherichia coli succinyl-CoA synthetase. Inactivation of this synthetase by oADP followed pseudo-first-order kinetics and was competitively blocked by ADP. The stoichiometry of labeling of the synthetase was 1 mol/mol alpha beta or, extrapolated, 2 mol/mol inactive alpha 2 beta 2 molecule. oADP also exhibited the properties of a substrate, bringing about rapid dephosphorylation of the enzyme. Further specificity of oADP was demonstrated in partially inactivated succinyl-CoA synthetase by selective inhibition of the succinate in equilibrium succinyl-CoA exchange reaction, in comparison to the CoA in equilibrium succinyl-CoA exchange reaction. Modification of the synthetase by oADP resulted in cross-linking of the enzyme, casting uncertainty over the subunit binding site for ADP. Modification of the synthetase by ADP-2'-semialdehyde occurred at a faster rate than that by oADP but exhibited biphasic inhibitor concentration dependence and did not exhibit saturability.

Coenzyme A thiosulfonate (coenzyme A disulfide-S,S-dioxide), an affinity analog of coenzyme A.

The structure of the CoA affinity analog-oxidized CoA disulfide (o-CoAS2) (Collier, G. E., and Nishimura, J. S. (1978) J. Biol. Chem. 253, 4938-4939) has been deduced to be that of the thiosulfonate of CoA, i.e. coenzyme A disulfide-S,S-dioxide. This deduction is based on several considerations among which are: the cleavage of o-CoAS2 by dithiothreitol under anaerobic conditions to equimolar amounts of CoASH and CoASO2H; the alkali-catalyzed dismutation of 3 mol of o-CoAS2 to 4 mol of CoASO2H and 1 mol of CoA disulfide; and comparison of the 13C-NMR spectra of CoA disulfide and o-CoAS2. The results of studies with Clostridial phosphotransacetylase (EC 2.3.1.8) and pigeon muscle carnitine acetyltransferase (EC 2.3.1.7) were consistent with the action of o-CoAS2 as a CoA affinity analog on these enzymes. Inactivation was characterized by what appeared to be disulfide bonding between CoA and important sulfhydryl groups of the proteins.

Evidence for a second histidine at the active site of succinyl-CoA synthetase from Escherichia coli.

Ethoxyformic anhydride was used to demonstrate the existence of a second important histidine in succinyl-CoA synthetase from Escherichia coli. Differential labeling of the enzyme by [3H]ethoxyformic anhydride gave a stoichiometry of one important histidine per alpha beta catalytic unit. Data are presented suggesting that this residue and an important thiol group on the beta subunit (Collier, G., and Nishimura, J.S. (1978) J. Biol. Chem. 253, 4938-4943) interact with each other during catalysis. A mechanism of action involving these 2 residues is proposed for one of the partial reactions catalyzed by succinyl-CoA synthetase.

Theoretical considerations of the sensitivity of quantitative subunit hybridization.

The theoretical basis of the quantitative subunit hybridization technique and its ability to measure evolutionary amino acid substitutions is examined. Homospecific:heterospecific enzyme ratios found after subunit reassociation depend upon K1.2, the equilibrium constant for the dissociation of the heterospecific enzyme. It is shown that if this constant is near the geometric mean of the two homospecific enzyme dissociation constants, as it should be in enzymes whose subunits pair isologously, the quantitative subunit hybridization method will not detect most changes in the subunit contact regions of homologous proteins.

Quantitative subunit hybridization of drosophila alpha-glycerophosphate dehydrogenase.

The dimeric enzyme, alpha-Glycerophosphate dehydrogenase, was purified from eight Drosophila species by the method of Collier et al. (1976). The enzymes were inactivated at high pH and the conditions sufficient for reactivation were established. Electrophoretic patterns of reactivated alpha-glycerophosphate dehydrogenases which were mixed following inactivation of two species' enzymes, demonstrate that high pH dissociates the enzyme into its constituent subunits and reactivation involves subunit reassociation. Twenty interspecific combinations of dissociated enzymes were allowed to reassociate, and the amounts of both heterospecific and homospecific enzyme activity and protein were determined by densitometry. In all 20 tests there were no differences between observed and expected heterospecific:homospecific enzyme ratios. These results are consistent with the very slow rate of evolution of this enzyme in the family Drosophilidae (Collier and MacIntyre, 1977).

Affinity labeling of succinyl-CoA synthetase from porcine heart and Escherichia coli with oxidized coenzyme A disulfide.

Incubation of oxidized coenzyme A disulfide (produced by oxidation of reduced CoA with 1 eq of sodium periodiate or of CoA disulfide with 1 eq of peracetic acid) with succinyl-CoA disulfide with 1 eq of peracetic acid) with succinyl-CoA synthetase from either porcine heart or Escherichia coli led to the formation of inactive enzyme containing 1 mol of CoA per alphabeta dimer. The bound CoA was attached through a disulfide bond to a sulfhydryl group of the beta subunit. Release of CoA and restoration of activity was achieved by incubation of the modified enzyme with thiols, such as dithiothreitol. Interaction of oxidized CoA disulfide with enzyme was inhibited competitively by desulfo-CoA, which is a competitive inhibitor of the enzyme with respect to CoA. These data are evidence that oxidized CoA disulfide is an affinity label for the CoA binding site of succinyl-CoA synthetase and are the first positive results implicating the beta subunit in the catalytic mechanism of the enzyme.

Microcomplement fixation studies on the evolution of alpha-glycerophosphate dehydrogenase within the genus Drosophila.

Antisera were prepared against purified alpha-glycerophosphate dehydrogenase (EC 1.1.1.8) (alphaGPDH) from Drosophila melanogaster, D. virilis, and D. busckii. The immunological distances between the enzymes from the 3 species and those from 31 additional drosophilid species agree in general with the accepted phylogeny of the genus. These data permit an estimate that the subgenus Sophophora diverged 52 million years ago from the line leading to the subgenus Drosophila. The antiserum against melanogaster alphaGPDH was capable of distinguishing allelic variants of alphaGPDH. On the basis of presumed single amino acid substitutions, no drosophilid alphaGPDH tested differed from the melanogaster enzyme by more than eight or nine substitutions. The study was extended to include representatives of six other dipteran families. The immunological distances between alphaGPDH from Drosophila and alphaGPDH from these dipterans were reasonably consistent with a phylogeny of the order Diptera established by more conventional means. The unit evolutionary period of this enzyme was estimated to be 18 million years.

Purification of alpha-glycerophosphate dehydrogenase from Drosophila melanogaster.

A simple procedure has been devised for the purification of alpha-glycerophosphate dehydrogenase (EC 1.1.1.8) FROM Drosophila melanogaster. The method involves substrate elution of the enzyme from a carboxymethyl cellulose column, followed by salt elution from agarose-hexane-AMP and DEAE columns. The procedure requires only 3 days to complete, results in high yield, and preparations that appear homogeneous by several criteria. A subunit molecular weight of 31 700 was obtained by sodium dodecyl sulphate electrophoresis in 10% acrylamide gels. This value is half that published for the native enzyme, confirming the homodimeric structure of this enzyme suggested by genetic evidence.