Book: Gen-manipulated intelligent squids explore space/planet

I’m looking for the author and title of a book. I believe it’s (supposed to be) the first in a trilogy, all using the same characters, but taking place in different universes – with only humans, with one type of aliens and with many aliens.

In it a gen-manipulated and very intelligent squid has been trained to fly a space-ship, and start exploring a planet and build a habitat. She (the squid) has managed to get pregnant, so by the time she dies, there are a whole colony of intelligent squids living in the habitat they’ve expanded.

Eventually there is a rift among the squids, and a group of them escapes in a space-ship they’ve built – just before the habitat is destroyed by the humans, because the squids threaten the mission.

I should point-out that most of the book was about the human characters, it’s just that the squids were so special it stuck in my mind.

I may be mixing together with another book (but I don’t think so), so here are few other things that (I think) happened:

• Some sort of spreading cataclysmic event, that would swallow first the solar-system and eventually the whole galaxy/universe, setting a distinct time limit (very long time).
• Some sort of portal that allowed travel into the very distant future – so distant actually, that one could observe the creation and destructions of several new universes, after first observing our own end. (I believe one of the squids was the first one through.)