If all living things are related then where did all their differences come from?

Hox Gene

Explanation:

First, you're question is very vital, there are many ways in classifying along with identifying all living organisms that includes; morphological analysis, molecular systematics (studying the similarities and differences of the genetic data such in the sequences of DNA, RNA, and rRNA), homology, cladistics, etc. based on phylogenetic tree, which the study of the evolutionary among various species.

But through it said that all living organisms shared one common ancestor. However, what makes them different from one to another is the homeotic genes that called Hox Genes; which specify the fate of a particular segment or region of the body, meaning the number and arrangements of the Hox genes varies considerably among different types of animals.

For instance, Sponges have at least one homologous to Hox genes, also insects have nine or more Hox genes resulting in multiple Hox genes occur in a cluster in which the genes are close to each other along a chromosome. Therefore, increases in the number of Hox genes have been instrumental in the evolution of many animals species with greater complexity in body structure.

Overall, more Hox genes, more complexity in body structure resulting in the differences of their morphological structure.

Hope that answered your question!