Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes

Statistical methods for computing the standard errors of the branching points of an evolutionary tree are developed. These methods are for the unweighted pair-group method-determined (UPGMA) trees reconstructed from molecular data such as amino acid sequences, nucleotide sequences, restriction-sites data, and electrophoretic distances. They were applied to data for the human, chimpanzee, gorilla, orangutan, and gibbon species. Among the four different sets of data used, DNA sequences for an 895-nucleotide segment of mitochondrial DNA (Brown et al. 1982) gave the most reliable tree, whereas electrophoretic data (Bruce and Ayala 1979) gave the least reliable one. The DNA sequence data suggested that the chimpanzee is the closest and that the gorilla is the next closest to the human species. The orangutan and gibbon are more distantly related to man than is the gorilla. This topology of the tree is in agreement with that for the tree obtained from chromosomal studies and DNA-hybridization experiments. However, the difference between the branching point for the human and the chimpanzee species and that for the gorilla species and the human-chimpanzee group is not statistically significant. In addition to this analysis, various factors that affect the accuracy of an estimated tree are discussed.      

NMR studies of the backbone protons and secondary structure of pentapeptide and heptapeptide substrates bound to bovine heart protein kinase

The conformations of enzyme-bound pentapeptide (Arg-Arg-Ala-Ser-Leu) and heptapeptide (Leu-Arg-Arg-Ala-Ser-Leu-Gly) substrates of protein kinase have been studied by NMR in quaternary complexes of the type (Formula: see text). Paramagnetic effects of Mn2+ bound at the inhibitory site of the catalytic subunit on the longitudinal relaxation rates of backbone Ca protons, as well as on side-chain protons of the bound pentapeptide and heptapeptide substrates, have been used to determine Mn2+ to proton distances which range from 8.2 to 12.4 A. A combination of the paramagnetic probe-T1 method with the Redfield 2-1-4-1-2 pulse sequence for suppression of the water signal has been used to measure distances from Mn2+ to all of the backbone amide (NH) protons of the bound pentapeptide and heptapeptide substrates, which range from 6.8 to 11.1 A. Paramagnetic effects on the transverse relaxation rates yield rate constants for peptide exchange, indicating that the complexes studied by NMR dissociate rapidly enough to participate in catalysis. Model-building studies based on the Mn2+-proton distances, as well as on previously determined distances from Cr3+-AMPPCP to side-chain protons [Granot, J., Mildvan, A.S., Bramson, H. N., & Kaiser, E. T. (1981) Biochemistry 20, 602], rule out alpha-helical, beta-sheet, beta-bulge, and all possible beta-turn conformations within the bound pentapeptide and heptapeptide substrates. The distances are fit only by extended coil conformations for the bound peptide substrates with a minor difference between the pentapeptides and heptapeptides in the phi torsional angle at Arg3C alpha and in psi at Arg2C alpha. An extended coil conformation, which minimizes the number of interactions within the substrate, would facilitate enzyme-substrate interaction and could thereby contribute to the specificity of protein kinase.     

Electron paramagnetic resonance studies of heme c and its nitrosyl derivative in Vibrio (Achromobacter) fischeri nitrite reductase

Interactions of Vibrio (formerly Achromobacter) fischeri nitrite reductase were studied by electron paramagnetic resonance spectroscopy. The spectrum of the oxidized enzyme showed a number of features which were attributed to two low-spin ferric hemes. These comprised an unusual derivative peak at g = 3.7 and a spectrum at g = 2.88, 2.26, and 1.51. Neither heme was reactive in the oxidized state with the substrate nitrite and with cyanide and azide. When frozen under turnover conditions (i.e., reduction in the presence of excess nitrite), the enzyme showed the spectrum of a nitrosyl heme derivative. The g = 2.88, 2.26, and 1.51 signals reappeared partially on reoxidation by nitrite, indicating that the nitrosyl species which remained arose from the g = 3.7 heme. The nitrosyl derivative showed a 14N nuclear hyperfine splitting, Az = 1.65 mT. The nitrosyl derivative was produced by treatment of the oxidized nitrite reductase with nitric oxide or hydroxylamine. Exchange of nitric oxide between the nitrosyl derivative and NO gas in solution was observed by using the [15N]nitrosyl compound. A possible reaction cycle for the enzyme is discussed, which involves reduction of the enzyme followed by binding of nitrite to one heme and formation of the nitrosyl intermediate.     

Flight muscle hypertrophy and ecophysiological variation of Yellow wagtail Motacilla flava races at Lake Chad

During the few days before emigration to the Palaearctic, the weight of Yellow wagtails wintering in Africa doubles. Most of the increase is due to the deposition of fat, as is well known, but a part of it is shown to result from hypertrophy of the pectoral muscles. The same applies to other Palaearctic birds, four warblers and a hirundine, that winter in Africa.
Eleven subspecies of M. flava occur at Lake Chad in spring. The four black-headed ones have more restricted habitat requirements than some of the others; however, no differences in diet have been found. There is no evidence of hyperphagia and little of diet change when fattening. Broadly, the races that have farthest to migrate leave earliest, and their sexual recrudescence and fattening are early.
Yellow wagtails wintering at or passing through Lake Chad breed mainly in eastern Europe (from the Adriatic to the Gulf of Finland, between about 12° and 30°E). They probably migrate on a great circle route, and during the flight lose one gram of weight, mainly fat, per 200 km.     

THE EVOLUTION AND SYSTEMATICS OF BEE-EATERS (MEROPIDAE)

Behavioural and ecological characters are used in addition to structural ones in considering the systematics of the Meropidae. The two species of Nyctyornis are the most primitive extant forms. Meropogon is retained as a monotypic genus for forsteni, and all other bee-eaters are placed in the single genus Merops, being ecologically and morphologically rather uniform except in details of wing and tail structure, which should be considered only of specific importance. M. breweri and M. oreobates are thought to be secondarily rather than primarily forest species. With the submergence of Aerops and Melittophagus, and the monotypic genera Bombylonax and Dicrocercus, which are considered to be closely related to the pusillus species-group, Merops is enlarged to 21 species which are uniform except in tail-shape, wing formula and throat feather structure. These characters are of specific importance only, and have a mosaic distribution within the genus. Their use in the definition of the formerly recognized genera results in an artificial classification. The proposed delimitation of species-groups within Merops differs somewhat from previous arrangements, and affinities argued in the text are summarized in Fig. 15, which shows superspecies and species-groups. The species recognized are formally tabulated below. The Meropidae probably originated in southeast Asian forest and spread through former forest to Africa. Only in Africa was the open-country environment invaded, and speciation in the savanna was in two main directions, producing small sedentary and large migratory species. Representatives of both types returned to Asia in open country. From the present distribution of species it is inferred that speciation has proceeded under the main influences of (1) isolation of a population and its habitat in Pleistocene Africa and (2) isolation of migrants away from their breeding range. The distributions of species with wide or rather limited ranges are discussed in terms of physiological adaptation and ecological competition. Opinion has not been expressed on the validity of subspecies, which have been discussed only in delimiting controversial species. In the following summary, the only subspecies named are those affected by changes from Peters' scheme (cf. Table 1). Superspecies are bracketed. Nyctyornis amicta N. athertoni Meropogon forsteni Merops guloris M. mülleri M. bulocki M. bullockoides M. pusillus M. variegatus (?loringi, oariegatus, lafresnayii, bangweoloensis) M. oreobates M. hirundineus M. breweri M. revoilii M. albicollis M. orientalis M. boehmi M. viridis M. superciliosus (persicus, chrysocercus, superciliosus) M. philippinus (philippinus, salvadorii) M. ornatus M. apiaster M. leschenaulti M. malimbicus M. nubicus (nubicus, nubicoides)     

The influence of self-MHC and non-MHC antigens on the selection of an antigen-specific T cell receptor repertoire

We have examined the influence of self-Ag on TCR expression and specificity in the immune response to the Ag pigeon cytochrome c. Previous work has shown that most Ek-restricted cytochrome c-specific T cells from B10 background mice express TCR alpha beta-heterodimers encoded by V beta 3 and V alpha 11 genes, but that T cells expressing V beta 3 proteins are eliminated due to self-tolerance in Mls-2a mouse strains. Thus, EK-restricted cytochrome c-specific T cells from Mls-2a mice fail to express any V beta 3. In the current study the influence of self-MHC and non-MHC Ag on TCR usage in the immune response to cytochrome c was further examined. First, it was demonstrated that the absence of V beta 3 expression in Mls-2a mice does not alter Ir gene function. Specifically, Mls-2a/Eb haplotype V beta 3- [C3H.SW x B10.A(5R)]F1 mice were high responders to cytochrome c despite the fact that previous structure function analyses have shown a very close correlation between Eb-restricted cytochrome c recognition and V beta 3 expression. This demonstration of the plasticity of TCR expression suggests that relatively few Ir gene defects result from tolerance induced by self-Ag. We also examined differences in V alpha 11 expression among cytochrome c-specific T cells from various H-2k haplotype mouse strains. In particular, the low level of expression of V alpha 11 in cytochrome c-specific T cells from C57BR (H-2k) mice was shown not to be due to self-tolerance. Rather, evidence for limited strain polymorphism of V alpha 11 genes, plus the fact that cytochrome c-specific T cells from F1 hybrids between H-2k, Mls-2b identical C57BR and B10.BR mice express high levels of V alpha 11, suggested the possibility that the variable V alpha 11 usage in the cytochrome c-specific responses of these two strains reflected differences in positive selection during ontogeny by non-MHC non-Mls self-Ag.