Taxonomy Phylogeny

Taxonomies group organisms according to phenotype, while phylogenetic systems groups organisms according to shared evolutionary heritage.

Bacteria

Taxonomy of the bacteria was historically based on phenotypical physical and chemical characteristics – phenetic taxonomy. According to "Bergey's Manual of Systematic Bacteriology", all bacteria can be classified into four divisions, or phyla according to the constituents of their cell walls.

Each division was further subdivided into sections according to :
1. Reaction of the cell wall to the Gram stain due to thick layer of peptidoglycan (Gram +ve) or thin layer of peptidoglycan (Gram -ve). The cell walls of Archaeobacteria contain no peptidoglycan.
2. Shape (left) – cocci (1), pleomorphic (2), bacillus (3), helical (4)
3. Arrangement of cells
4. Oxygen requirement – aerobic, anaerobic, or facultative anaerobe
5. Motility – flagellated, non-motile
6. Specific nutritional requirements
7. Metabolic properties – autotrophic (chemical or photosynthetic), heterotrophic


The advent of genomics and examination of 16s ribosomal RNA has led to modifications in the classification of the prokaryotes, with the older nomenclatures revised into new classifications of Phyla. (diagram at bottom) Woese and Fox proposed the Three Domain system: Eubacteria, Archaea, and Eukaryotes. When Woese and Fox proposed the 3 Domain system, the term 'Urkaryotes' was proposed for ancestors of eukaryotes prior to their endosymbiotic acquisition of mitochondria and chloroplasts from prokaryotes.

"Misunderstanding the Bacteriological Code"

The Three Domain system is increasingly accepted. Free Full Text Article : Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Woese CR, Fox GE. Proc Natl Acad Sci U S A. 1977 Nov;74(11):5088-90.


Left - click to enlarge image: Horizontal gene transfer - gene swapping - has blurred the evolutionary relationships (image) of prokaryotes, and continues to provide a mechanism for the sharing of antibiotic resistance between bacteria. See: Trees, vines and nets: Microbial evolution changes its face.

Phylogenetic separation into evolutionary relationships (clades), based on comparison of genomes is likely to supplant phenotypical (phenetic) taxonomies of the prokaryotes.(nomenclature)


Right - click to enlarge image: Based on Woese's proposed scheme based on the 16s subunit of ribosomal RNA, which appears to better illustrate evolutionary relationships within the 3 domains.

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Blogger qtr said...

Allopatric speciation occurs when a geographical barrier sub-divides a parent species, resulting in geographic and reproductive isolation such that the descendent species can no longer interbreed upon removal of the barrier.


Anagenesis differs from cladogenesis in that one species progressively transforms into a replacement species when sufficient gene mutations fix in the descendant population. At this point, the ancestral species has become extinct. This mechanism is distinct from the increase in numbers of species generated by cladogenetic branching events.

Cladogenesis is the mechanism of speciation in which one or more lineages (clades) arise from an ancestral line. Such speciation events increase the variety of plants or animals through branching of the phylogenetic tree. Cladogenesis is differentiated from anagenesis, which is the in toto replacement of one species by an anatomically distinct species.

Monophyletic taxon or clade: an accurate grouping of only (opp. polyphyletic) and all (opp. paraphyletic) descendents of a shared common ancestor. A monopyletic group is genetically homogeneous and reflects evolutionary relationships.

Paraphyletic taxon or clade: a monophyletic group that excludes one or more discrete groups descended from the most recent common ancestral species of the entire group. Other descendent species of the most recent common ancestor have been excluded from the paraphyletic taxon, usually because of morphologic distinctiveness.

Phenetic system: groupings of organisms based on mutual similarity of phenotypic (physical and chemical) characteristics. Phenetic groupings may or may not correlate with evolutionary relationships.


Phylogenetic system: groups organisms based on shared evolutionary heritage. DNA and RNA sequencing techniques are considered to give the most meaningful phylogenies.

Phylogenetic separation into evolutionary relationships (clades), based on comparison of genomes is likely to supplant phenotypical (phenetic) taxonomies of the prokaryotes.

Peripatry (paripatry) is a subset of allopatry in which an isolated group has a smaller population than the parent group. Ernst Mayr introduced the term. Peripatric speciation occurs when the smaller sub-group of a species enters a novel niche within the range of the parent species, becoming geographically and reproductively isolated. Peripatric speciation (paripatric) is distinguished from allopatric speciation by the smaller size of the isolate group, and from sympatric speciation, which involves no barrier to breeding.

Polyphyletic taxon: opposite to monophyletic taxon: A polyphyletic group is mistakenly or improperly erected on the basis of homoplasy.—characteristics that have arisen despite not sharing a common ancestor. Homoplasy arises because of convergent evolution, parallelism, evolutionary reversals, horizontal gene transfer, or gene duplications. Polyphyletic taxa are genetically heterogeneous because members do not share a common ancestor.

Neontology is a branch of biology that emphasizes the study of modern biota (living or recent organisms) rather than fossilized organisms (paleontology).

Numerical Taxonomies are a common approach to phenetic taxonomy that employ a number of phenotypic characteristics to generate similarity coefficients that may be mapped in dendrograms. Groupings based on numerical taxonomy may or may not correlate with evolutionary relationships.

Taxonomies aim to group organisms according to shared characteristics against the background of biological diversity.

Sympatry involves no geographical separation of sub-populations of individuals. Sympatric speciation events occur most often in plants by the mechanism of polyploidy in which the number of chromosomes is doubled or tripled. John Maynard Smith proposed a model called disruptive speciation, in which homozygotes might have greater fitness than heterozygotes under some environmental conditions.

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