Systematics are classifications of life. Carl Linneaus came up with the binominal nomenclature for organisms and Darwin proposed that all organisms could be linked through a complex tree of life (or a phylogenetic tree)

Phylogenetic trees depict the relationships between organisms. You are always searching for homologous characteristics which are characteristics which developed in a common ancestor. Before molecular analysis scientists used morphological characteristics to construct these but now things like DNA, RNA and proteins are used to construct these

Cladograms are phylogenics which indicate the order of divergence

Morphological similarity does not always indicate the evolutionary relationship between two organisms. Closely related organisms are not always similar in appearance since small changes can lead to big morphological changes and similar morphological characteristics can evolve multiple times.

Convergent evolution is the independent origin of the same traits which are expressed in what would normally be considered largely unsimilar species. The resulting traits are called homoplasies

1. The origins and relationships among species. 2. The timing of their origins (using molecular clocks). 3. The evolution of morphological characters (including convergent evolution of traits)

Differences in amino acids between organisms can be used to help determine differences between the organisms in question. Gaps in the alignments are indicated by dashes and amino acids that stayed the same are indicated by a dot

Segregated mutations are mutations which develop in one individual and can be passed down to progeny which creates a sort of schism within the species: those individuals who have the mutation and those who don't. If, by selection or other means, a mutation becomes either widely spread or occurs in every gene we say that it has become fixed and is now the new wildtype

Over time the ratio of amino acid sequences will change gradually. These time signatures can be used to construct a time-sensitive phylogenic tree which can be used to show common ancestors and the like

No, not all regions of DNA the same rates of change. The untranslated region has the lowest amount of changes overall (there are two sides each flanking the coding region but both of these areas are very stable from a molecular point of view) while the exon and the pseudogene have much higher rates of molecular change

Homologs are evolutionarily related gene sequences; they can be within one species or between two species

Orthologs are genes in different species derived from a commmon ancestral gene. Orthologous genes retain similar functions in the two species

Paralogs are genes produced by duplication within a genome. Paralogous genes usually have new functions even if these are related to the original one

Mitochondrial DNA sequences can be used to trace human evolution. The reason why they prove so useful for this is because the mitochondrial genome acccumulates mutations about once per every 3,800 years

Whatever sort of progeny the mother is all of her children will have the same phenotype if there should be any sort of target difference with the mitochondrial DNA

Mitochondrial Eve is the most recent matrilineal common ancestor of all living humans. All of our mitochondria are somehow or another descended from hers. The represented Y chromosomes in this system would be the person who represents the "Adam" of all living humans

We can conclude that the most recent common ancestor of all living homo sapiens lived in Africa (about 170,000 years ago +/- 50,000 years ago)

Molecular analysis indicates that there was no interbreeding between human ancestors and Neanderthals