Cladogenesis and anagenesis: a confusion of synapomorphies

Much cladistic theory is flawed because it confuses two temporal sequences: 1. cladogenetic (branching) chronology; 2. anagenetic (primitive-advanced) polarity. The first is largely inherent and exposed by a straigram; the second requires an independent polarisation of the changes subsequent to cladogenetic branchings. Failure to consistently distinguish between these always causes confusion, but destroys cladistic theory, because plesiomorphy and apomorphy refer to anagenesis, and autapomorphy and synapomorphy refer to cladogenetis. They cannot, however, be identified wholly independently, because cladogenetic chronology establishes anagenetic polarity by out-grouping, under limited conditions; and anagenetic polarity establishes cladogenetic chronology in multiple cladistic events. The principle ‘common characters are primitive’ is more accurately expressed as ‘characters of greater s read are cladogenetically earlier', and establishes cladogenetic relationships, never anagenetic polarity as usually thought. The full temporal analysis of biological patterns, therefore, involves eight stages: 1. Homologue identification; 2. Homolostrata delimitation and definition; 3. Stratigram formation; 4. Cladogenetic sequencing; 5. Anagenetic polarity determination (chronogramy); 6. Cladogenetic and anagenetic co-analysis; 7. Cladogram construction; 8. Phylogenetic interpretation.     

Homologies of the toothcomb.

A recently described juvenile specimen of Avahi was supposed to show that indriines have an unreplaced deciduous canine and that the indriine toothcomb was composed only of incisors. To the contrary, this specimen demonstrates quite dramatically a growth phenomenon earlier discussed: in indriines, the anteriormost of the four deciduous lower teeth posterior to the toothcomb migrates mesially toward the toothcomb (Schwartz, '74). In this particular Avahi, this tooth has even become associated with the toothcomb. The alignment of this tooth with the toothcomb is a strictly impermanent situation and cannot be taken into consideration when determining homologies of the teeth of the toothcomb. Morphologically and developmentally the lateral teeth of both indriine and lemur and loris toothcombs are similar to each other and distinct from the central set of teeth. Thus, if the lateral teeth of the lemur/loris toothcomb are canines, then the lateral teeth of the indriine toothcomb are canines as well.     

Perception of timbral analogies.

Recent studies have investigated the structure of perceptual relations among musical instrument timbres by multidimensional scaling (MDS) techniques. These studies have employed both acoustically produced tones and digitally synthesized imitations and hybrids of acoustic instrument tones. The analyses of dissimilarity ratings for all pairs of a set of tones are usually represented as geometrical structures in a two- or three-dimensional Euclidean space in which the shared 'perceptual' axes are shown to have a qualitative correspondence to acoustic properties such as spectral energy distribution, onset characteristics and degree of change in spectral distribution over the duration of the tone. The present study took as a point of departure a MDS analysis for complex, synthetic tones with the aim of testing whether musician and non-musician listeners used the relations defined by the perceptual space to perform an analogies task of the sort: timbre A is to timbre B as timbre C is to which of two possible timbres, D or D'? A parallelogram model was used to select the D timbres: if the relation between A and B is represented as a vector with both magnitude and direction components, then the appropriate D should form a vector with C having similar magnitude and direction in the timbre space. Aside from conceptual difficulties with the task for both non-musicians and composers, choices for both groups provide support for the parallelogram model indicating a capacity in listeners to perceive abstract relations among the timbres of complex sounds without specific training in such a task.     

Homologies between X and Y chromosomes detected by DNA probes: localisation and evolution.

We have isolated and characterized DNA probes that detect homologies between the X and Y chromosomes. Clone St25 is derived from the q13-q22 region of the X chromosome and recognizes a 98% homologous sequence on the Y chromosome. Y specific fragments were present in DNAs from 5 Yq-individuals and from 4 out of 7 XX males analysed. An X linked TaqI RFLP is detected with the St25 probe (33% heterozygosity) which should allow one to establish a linkage map including other polymorphic X-Y homologous sequences in this region and to compare it to a Y chromosome deletion map. Probe DXS31 located in Xp223-pter detects a 80% homologous sequence in the Y chromosome. The latter can be assigned to Yq11-qter outside the region which contains the Y specific satellite sequences. ACT1 and ACT2, the actin sequences present on the X and Y chromosomes respectively, have been cloned. No homology was detected between the X and Y derived fragments outside from the actin sequence. ACT2 and the Y specific sequence corresponding to DXS31 segregate together in a panel of Y chromosomes aberrations, and might be useful markers for the region important for spermatogenesis in Yq. Various primate species were analysed for the presence of sequences homologous to the three probes. Sequences detected by St25 and DXS31 are found only on the X chromosome in cercopithecoidae. The sequences which flank ACT2 detect in the same species autosomal fragments but no male specific fragments. It is suggested that the Y chromosome acquired genetic material from the X chromosome and from autosomes at various times during primate evolution.     

Homologies between enzymes involved in steroid and xenobiotic carbonyl reduction in vertebrates, invertebrates and procaryonts.

Evidence is reported for the existence of a structurally and functionally related and probably evolutionarily conserved class of membrane-bound liver carbonyl reductases/hydroxysteroid dehydrogenases involved in steroid and xenobiotic carbonyl metabolism. Carbonyl reduction was investigated in liver microsomes of 8 vertebrate species, as well as in insect larvae total homogenate and in purified 3 alpha-hydroxysteroid dehydrogenase preparations of the procaryont Pseudomonas testosteroni, using the ketone compound 2-methyl-1,2 di-(3-pyridyl)-1-propanone (metyrapone) as substrate. The enzyme activities involved in the metyrapone metabolism were screened for their sensitivity to several steroids as inhibitors. In all fractions tested, steroids of the adrostane or pregnane class strongly inhibited xenobiotic carbonyl reduction, whereas only in the insect and procaryotic species could ecdysteroids inhibit this reaction. Immunoblot analysis with antibodies against the respective microsomal mouse liver metyrapone reductase revealed strong crossrections in all fractions tested, even in those of the insect and the procaryont. A similar crossreaction pattern was achieved when the same fractions were incubated with antibodies against 3 alpha-hydroxysteroid dehydrogenase from Pseudomonas testosteroni. The mutual immunoreactivity of the antibody species against proteins from vertebrate liver microsomes, insects and procaryonts suggests the existence of structural homologies within these carbonyl reducing enzymes. This is further confirmed by limited proteolysis of purified microsomal mouse liver carbonyl reductase and subsequent analysis of the peptide fragments with antibodies specifically purified by immunoreactivity against this respective crossreactive antigen. These immunoblot experiments revealed a 22 kDa peptide fragment which was commonly recognized by all antibodies and which might represent a conserved domain of the enzyme.     

The involucrin gene of Old-World monkeys and other higher primates: synapomorphies and parallelisms resulting from the same gene-altering mechanism.

The involucrin gene of platyrrhines and hominoids contains a segment of 10-codon repeats which were added vectorially at the same site in the coding region. We have now cloned and sequenced the involucrin gene of four cercopithecoid monkeys--two macaques (mulatta and fascicularis) and two Cercopithecus monkeys (aethiops and hamlyni). Each gene contains a similar segment of short repeats; some of these were added in a common anthropoid lineage, others were added in a common catarrhine lineage, and still others were added in a common macaque or Cercopithecus lineage. Repeats added before a lineage diverges become synapomorphies in the sister taxa resulting from the divergence. Repeats added independently in different diverged lineages become parallelisms. The synapomorphies are the result of the action of a targeted duplication mechanism acting in a common ancestral lineage, but the parallelisms are the result of the same duplication mechanism transmitted to successively divergent sublineages and acting independently in each.     

Aldehyde-fuchsin: historical and chemical considerations.

The staining mechanisms of Gomori's aldehyde-fuchsin are not yet fully understood. It seemed therefore timely to review the history of this dye class in context with current dye and aldehyde chemistry. In 1861 Lauth treated basic fuchsin with acetaldehyde. This dye became known as Aldehyde Blue, but consisted of violet and blue dyes. Schiff (1866) studied several aldehyde-fuchsins; these compounds contained two molecules of dye and three molecules of aldehyde. Acetaldehyde-fuchsin prepared according to Schiff's directions showed staining properties similar to those of Gomori's aldehyde-fuchsin. This dye class was soon superseded by new dyes more suitable for textile dyeing, and chemical investigations of aldehyde-fuchsins ceased around the turn of the century. Gomori's aldehyde-fuchsin has been regarded as a Schiff base. However, according to chemical data, low molecular aliphatic aldehydes and aromatic amines tend to form condensation products. Correlations of chemical and histochemical observations suggest such processes during aging of dye solutions. Models of dimers and polymers of aldehyde-fuchsin could be built without steric hindrance. The nature of the bonds formed by various components of aldehyde-fuchsin solutions is not clear. However, cystine in proteins, e.g. in basement membranes, apparently does not play a role in the binding of aldehyde-fuchsin by unoxidized Carnoy- or methacarn-fixed sections.     

Quantitative Aspects of Deoxyribonucleic Acid Renaturation: Base Composition, State of Chromosome Replication, and Polynucleotide Homologies

The base composition of a deoxyribonucleic acid (DNA) sample affects its intrinsic rate of renaturation. In agreement with the information of Wetmur and Davidson, it was established that high guanosine plus cytosine (GC) DNA renatures faster than expected from analytical measurement of its molecular weight. A calculated correction factor of 1.8% of the observed C(0)t(.5) is required for every mole per cent GC difference from 51% GC. The correction factor is now established in the range of 32 to 65% GC. Renaturation of DNA mixtures prepared from pairs of organisms has been studied. When no similarity existed between the two organisms, the observed C(0)t(.5) of the mixture was the sum of the independently determined C(0)t(.5) values. Lack of additivity was correlated with similarities in polynucleotide sequence of the reassociating DNA molecules. A quantitative relationship was formulated to relate C(0)t(.5) values of renatured DNA mixtures to per cent binding ("homology"). Finally, it was demonstrated that DNA prepared from log-phase cells renatures faster than stationary-phase DNA and also departs from theoretical second-order kinetics.