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