what is 以及与? is it "and + and", if so why use such a thing?
他们惊讶地发现，虽然属于不同的时代，但那些动植物相互之间，以及与现代生物之间都有许多相似之处.


'以及' means "and also"; 

"与"  means "and". 

Let's break the sentence apart and see what's missing:


那些动植物相互之间 (between those animals and plants themselves)
以及 (and also)
between (subject omitted) 与 (and) 现代生物之间 (modern living things)
都有许多相似之处. (all have many similarities)


The author wanted to say:

Those (ancient) animals and plants had many similarities between themselves; and also have many similarities between them and modern living things

It would be more clear if he didn't omit the repeated subject

[那些动植物相互之间]，[以及] [(那些动植物)与现代生物之间] [都有许多相似之处]

[between those animals and plants themselves]，[and also] [between (those animals and plants) and modern living things] [all have many similarities ]

the repeated subject (那些动植物) was omitted