The correct answer is :

Option A : Over-exploitation, habitat loss and fragmentation.

Each of the factors listed in this option can contribute to biodiversity loss:

1. Over-exploitation : When species are over-hunted, over-fished, or harvested at rates faster than their natural ability to recover, it can lead to population declines and even extinction.
2. Habitat loss : This occurs when natural environments are destroyed or significantly altered. It's often due to human activities such as deforestation, urban development, agriculture, and mining. Habitat loss can result in local or even global extinction of species.
3. Fragmentation : This happens when a large, continuous area of habitat is divided into smaller, isolated patches, often as a result of human activities like road construction or clear-cutting for agriculture. Fragmentation can isolate populations of species, preventing gene flow and causing a decline in biodiversity.

While climate change (Option B) can also contribute to biodiversity loss, it is not the only cause, and likewise for over-exploitation (Option C) and habitat loss and fragmentation (Option D) alone. So, while these can all contribute to the problem, the option that includes all three (Option A) provides the most comprehensive answer to the question.