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Cladistics

There are three domains, each consisting of several kingdoms.

Bacteria and archaea are both prokaryotes, while eukarya are eukaryotes. Although bacteria and archaea are both prokaryotes, they are extremely different metabolically. It is believed that they separated into different lineages very early in the evolution of life.

Archaea
  • hyperthermophiles
  • extreme halophiles
  • methanogens
Bacteria
  • hyperthermophiles
  • chloroplast
  • cyanobacteria
  • gram-positive bacteria
  • mitochondrion
  • proteobacteria
Eukarya
  • plantae
  • fungi
  • Animalia
  • protista (mostly single-celled organisms)
    • giardia
    • flagellates
    • slime molds
Evolutionary trees (aka phylogenetic trees) began when Carolus Linnaeus began classifying more than 10,000 plants and animals over 200 years ago. Scientists are still classifying the 1.7 million identified species and organisms.

A newly discovered insect by Tennessee scientists was named Cosberalla lamaralexanderi after the Tennessee senator Lamar Alexander. Systematics, the scientific study of the diversity of organisms, reveals the evolutionary relationships between organisms. Systematists reconstruct phylogenetic trees by analyzing evolutionary changes in the traits of organisms. Information about evolutionary relationships can be of great value, as in the control of the disease schistosomiasis. Taxonomy (a subdivision of systematics) is the theory and practice of classifying organisms.

A phylogeny is a hypothesis proposed by a systematist that describes the history of descent of a group of organisms from their common ancestor. A phylogenetic tree represents that history.

In other words, phylogenetic trees display the pattern of evolution of life on Earth. A lineage is represented as a branching tree, each split or node represents a speciation event. How is phylogeny in biology similar or different from human genealogical research? The latter used to be based on written documentation or account, now could be traced by biological markers as well (DNA). Phylogeny reveals evolutionary relationship while genealogy reveals family history or lineage.

TermOverview
Phylogenyis the construction/study of phylogenetic tree or a family tree that includes all clads.
CladA group of organisms made up of an ancestor and all of its descendants.
TaxonAn evolutionary unit, such as a species, genus, ... kingdom.
TaxonomyThe discipline of grouping species into taxons.
SystematicsDeals with diversity of organisms that reveals evolutionary relationship BETWEEN organisms. It differs from phylogeny and overlaps with genealogy because it involves a closely related family vs. different families and their relatedness.

When one or more related DNA, RNA or protein sequences are compared, the consensus sequence consists of the most common base or amino acid at each position. When two different yet related sequences have segments that are very similar or identical, they represent evolutionarily conserved functional domains. A strong consensus sequence (ie, one closely matching the sources) connotes evolutionary closeness. On the other hand, a signature sequence is found in one taxonomic group but not another; this can be used to define a branch in the evolutionary tree.

For example, a signature sequence might be found in all plants but no animals; and another signature sequence may occur in all flowers but no trees; and a third in all roses but no other flowers. This would allow one to reconstruct an albeit rudimentary evolutionary tree. By studying different gene families, protein families and signature sequences, various trees of life may be formed. A consensus tree of life is based on all these analyses.

TermOverview
AncestralA trait is ancestral if it is inherited from an ancestor. Ancestral traits are highly conserved and originated in the more distant past. Very ancient.
DerivedA trait that differs from its ancestral form, appearing later in evolution and thus relatively recent.
ConservedAn ancestral trait shared between most or all of the ancestor's descendants.

Distinguishing derived traits from ancestral traits may be difficult because traits often become very dissimilar. An outgroup is a lineage that is closely related to an ingroup (the lineage of interest) but has branched off from the ingroup below its base on the evolutionary tree. Ancestral traits should be found not only in the ingroup, but also in outgroups. Derived traits would be found only in the ingroup.

The distinction between ancestral and derived traits is very important in reconstructing phylogenies. A particular trait may be ancestral or derived, depending on the group of interest. In a phylogeny of rodents, continuously growing incisors are an ancestral trait because all rodents have them. In a phylogeny of mammals, continuously growing incisors are a derived trait unique to the rodents.

TermOverview
HomologsAny two or more similar traits (nucleic acid, behavior or morphology) descended from a common ancestor. For example, an ancestral trait shared by two species is homologous between the two. Similarities in sequence and function suggest that a group of genes are part of the same family, and they are homologs to one another. (This same concept is applied to proteins, which would be called homologous proteins). These are identified by powerful computer programs that directly compare two or more sequences.
ParalogHomologs present in the same species are paralogs. An example would be human hemoglobin and myoglobin, which are considered part of the same family and are present within the same species.
OrthologHomologs present in different species are orthologs. An example would be human hemoglobin and porcine hemoglobin, which have similar sequences and the same functions yet are not within the same species.
Convergent EvolutionWhen independently evolved features subjected to similar selective pressures become superficially similar. An example is the wings of birds and insects.
Evolutionary ReversalWhen a character reverts from a derived state back to an ancestral state.
HomoplasyAlso known as homoplastic traits, they are traits similar for some reason other than inheritance from a common ancestor. For example, the wings of birds and insects are homoplasies.
AnalogousA homoplastic trait that has arisen due to convergent evolution or evolutionary reversal. For example, the wings of birds and insects are analogous traits.
VestigeA vestige (aka a vestigial structure or vestigial trait) is no longer of adaptive value and therefore not maintained by selection. For example, the forearms of Tyrannosaurus rex.