All organisms originated from the same organism but through evolution have ended up with significant amounts of variation.
Phylogenetic groups are how recently two species have been related (how recently they evolved apart into different species).
Sometimes organisms are organised due to observable physical characteristics which do not necessarily mean they are closely genetically related.
Classification is not yet perfected due to the sheer number and the complexity of life on earth.
The most common system is:
The definition of a species is a group of organisms which can breed to create fertile offspring.