Why was Charles Darwin's theory of evolution by natural selection not accepted at the time?

There are three main reasons for this, firstly, the 1800s when Charles Darwin lived was a deeply religious time and the idea of evolution challenged the idea of God creating life on Earth. Secondly, not much evidence had been discovered at the time (e.g. fossils and differences/similarities in geology) to convince many other scientists of the theory's validity. Lastly, technology was limited in comparison to today, the idea and proof of genes, variation and inheritance was not known until several decades after Darwin's theory was published. 

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