Sorry, I couldn't get this to open.
It's just a direct link to an article in Nature about the genetic differences and similarities between land animals and their aquatic brethren. The link works, so I'm not sure why you can't open it. I made sure to link to a full and free article.
This is classic....
These first whales, such as Pakicetus, were typical land animals. They had long skulls and large
carnivorous teeth. From the outside,
they don't look much like whales at all. However, their skulls — particularly in the ear region, which is surrounded by a bony wall —
strongly resemble those of living whales and are unlike those of any other mammal. Often, seemingly minor features provide critical evidence to link animals that are highly specialized for their lifestyles (such as whales) with their less extreme-looking relatives.
You should try reading what's written, and not what you highlight in your mind. These paragraphs answer the questions that you're asking in this response, and they will also answer questions that you'll have in the future. But you're reading them for what you want and not for what they are.
In your following quotes, I'll show you what I mean.
This illustration is presented as a fact, yet it is only a suggestion.
The physical and genetic connection between these ancestral species of whale are factual. The sentences that you fail to highlight because they don't make your point for you tell you as much.
Of course these artist renditions are just best guesses - Everyone should know this, if they don't already. The skeletal frames of these creatures have been discovered in their entirety. So the shape is right. The structure of the animal is known. There are only so many ways that mammals can make themselves move. Things like coloration and hair density are little more than educated guesses - but those things don't matter at all. If you stripped all humans of skin color, hair coverage, fat placement, etc, you'd still have a very good idea of how the human body moved and operated, don't you think? Paleontologists do that with ancient bones. There's really no difference.
The important part of the discussions are the facts. These were amphibious creatures, that have only ever been found around the rim of an ancient shallow sea, indicating their reliance on a wet environment. The skeletal features that they share with whales, namely the inner ear bones, are shared with no other organism. Why do you think that is? What little genetic information has been gleaned indicates a clear relation to whales, just as it does to hippos, shrews, squirrels, and all other mammals. (See the first link from Nature that I provided.) The reason for this genetic and physical connection is common descent. If that's not the answer the HOW those things got there, I'd like to know what you think the answer is...
Look at these two skeletons and tell me if you see anything even remotely resembling a whale in the lower illustration (Pakicetus). Pictured like this....
I see a clearly delineated land animal. I do not even see even a remote connection to the Ambuloceteus,
Dear, these aren't whales... You don't see whales in these pictures, or in these bones, because they're a different creature entirely. What you're looking at is the first known foray of mammalian life going through a transformational period (meaning it took a very long time and many subsequent generations) from being almost wholly land-based to a wholly water-based population. The connection is in the ancestral lineage, not in the current iteration of that species. They're long gone - extinct - a bygone remnant of a time that no longer is. You have to look under the skin to see why.
A picture of your great grandmother doesn't look like you. She no longer exists. But she's a part of you, isn't she? Part of your hair color, or maybe your eyes, or a silly way you smile sometimes came from your great grandmother, but you're two different human specimens entirely. The same is true of modern whales and their ancestors. They look nothing like Pakicetus - but their inner ear structure, the vestigial leg bones in their rear flippers, the cranial structure which allows breathing through a "snout" on top of the head, all point to the Pakicetus as being the first species to delineate and transition into the water. The ancestral lineage of all animals is found in their genetics, expressed both internally and physically externally. It didn't happen over night - there were many transitions along the way, populations that adapted to different circumstances in their environment and that solved different problems different ways became different things. But Pakicetus, because of it's vast similarities, is considered to be the first of what would become modern cetaceans.
Again I'll ask you, where do you think these organisms came from, if not from common descent? How can there be clear physical traits shared between species that never breathed the same air? Why do whales have inner ear bones that are only shared with an extinct four-legged species that lived near an ancient shallow sea? Why do those same whales share a large portion of their DNA with Hippos? Why do Manatees? Why aren't Ambulocetus fossils discovered chronologically earlier in the fossil record than Pakicetus?
Can you answer those questions? If you can, do you have anything to support your answers?
Ignoring artists renditions, do you truly see no similarities at all in these two skeletons?
"Compared to other early whales, like Indohyus and Pakicetus, Ambulocetus looks like it lived a more aquatic lifestyle. Its legs are shorter, and its hands and feet are enlarged like paddles. Its tail is longer and more muscular, too."
Think of the question that this segment is asking - Was Ambulocetus more aquatic than Pakicetus? Look at the above skeletons again and tell me what conclusions you can draw from the features of Ambulocetus, compared to Pakicetus. There's a connection that we already know of, but you're free to ignore that. Using your personal observation alone, what do you see?
Why are its front legs shorter? Why are its hands/feet enlarged? Why does it have a more muscular tail? Why is the rib cage fatter? What conclusions would you personally make about those observations of an Ambulocetus skeleton?
Do you not see the suggestions masquerading as facts here?
What most people fail to recognize in these introductory passages about most things biological is that they're reading an easier-to-digest, condensed version of the facts. These are not suggestions. The physiological connections between the organisms are known. There is no other explanation for them, given the data that has been (and is being) collected. If you would like to read more detailed (and honestly more bland) data sets, I can let you borrow a few of my journal subscriptions. The science in those is above the head of most people, and the writing style is not at all intended for the general public. But it's the data that matters, not the style.
How are these creatures even in the same ball park as a whale, let alone related?
As has been discussed, through genotypical and phenotypical expressions. The geological placement of their remains shows a chronology of their existence. Where those remains have been discovered show their environment. Their physical features and their genetic information show relatedness. General biologic knowledge tells us how offspring are conceived and how sexual organisms reproduce. That same information tells us how gene flow occurs and how environment plays a role in shaping the "preferred" traits in a population. There's all kinds of things, really. And it's all part of a comprehensive understanding of biology indicating common descent, not just of whales but of all currently living things.