Question

if the same base pairs are used to code for all organisms, why is there so much variation among organisms

Answer 1

The order of the codons differs between organisms. 
The different order of codons lead to different protein molecules being formed by the organisms which when expressed lead to different organisms trait.

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Answer 2

Answer:

The correct answer is due to the change in the sequence of codons of genes as a result of recombination.

Explanation:

Four types of nucleotide base pairs namely adenine, cytosine, guanine and thymine are present in the DNA sequence which controls the trait of an organism as they encode "proteins."

These base pairs are read by the ribosome during translation in the form of triplet known as codons. It is the sequence of these codons which directly controls the morphological and physiological trait of an organism.

These codons are present in the genes - a coding segment of DNA on chromosomes which during meiosis I undergo recombination via crossing over between homologous chromosomes which results in the change in the order of these codons thus changing the amino acid sequence and hence proteins. This is the basis of genetic diversity.

Thus, due to the change in the sequence of codons of genes as a result of recombination is the correct answer.