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 in eukaryotic 5.8S ribosomal RNA.

The primary nucleotide sequence of Novikoff hepatoma ascites cell 5.8S rRNA (also known as 5.5 or 7S RNA) has been determined to be:

This sequence is 75% homologous with the primary nucleotide sequence of yeast 5.8S rRNA and 100% homologous with oligonucleotide marker fragments from HeLa cell RNA. In constrast, only limited homology is evident with oligonucleotides from 5.8S RNA of several flowering plants and many of the characteristic fragments differ.     

Pollen and seed analogies

Abstract

The dispersal units of plants are seeds but pollen is also dispersed and there are many similarities to be found between these two types of diaspores, especially in their environmental interactions. The economy of natural processes suggests that Nature would not “re-invent the wheel” and indeed there are many similarities, if not identical types of mechanisms, in the metabolic activities of seed and pollen responses to environmental conditions. The main differences regard scale and the responses/mechanisms available to bi-or tri-cellular systems compared to those operating at cytological or organ level. Intriguing parallels are highlighted in this paper without implying homologies.     

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.