All newts are salamanders, but not all salamanders are newts (source). What does this have to do with anything? It's not like there are any salamanders in Lonesome Dove. But we do have Newt, with a capital N, the orphan boy exploring the American West.
So, nothing, really, but it's a fact you should know, folks.
Anyway, Newt's parentage is one of the biggest questions in the book… but it's only a question to Newt. Everyone else is certain that Captain Call is Newt's father. But Newt's mother, Maggie, was friends with both Jake Spoon and Captain Call. Newt thinks Jake might be his father, but he becomes more disillusioned with Jake as the book goes on, as Jake makes worse and worse decisions right in front of him.
Sadly, Newt's other idol, Captain Call, lets him down. It doesn't start off that way: when Lorena is kidnapped on Jake's watch, Call defends Newt. "It ain't the boy's fault" (48.124), Call says to a livid Jake Spoon. Later, Newt attacks a man named Dixon who attacks Dish Boggett. Call almost beats Dixon to death for whipping Newt, and "Newt felt he might get sick just seeing the way the Captain punished the man" (85.64).
Eventually, Newt begins to suspect why Call was so angry. His suspicions are confirmed when Gus tells him that Call is his father. But Call himself never admits it.
Part of growing up is realizing your heroes aren't who you thought they would be. And this betrayal by silence from Call breaks the last bit of Newt's youthful spirit. He's growing up. He's taking charge and earning responsibility. And he's no longer searching for a father figure to guide him.
"I ain't kin to nobody in this world. […] I don't want to be. I won't be." (100.94)
In fact, we almost wonder if Newt'll end up isolated just like Captain Call, another lonesome dove. Do none of these guys have real father figures?
Newt's sadness over his father is extra poignant for us readers because, unless you're a cowboy, Newt is the most relatable character in the book. He has a sense for adventure, which you also have share in order to tackle a book that's almost 1,000 pages long. On top of that, everything is new to Newt, just as everything in this book is pretty new to us, too. We hope you haven't been almost lost in a storm of locusts, anyway.
In the first chapter, Newt "hadn't been anywhere, so it was all romance to him" (1.81). He dreams of adventure, and while there's foreshadowing that Newt will "be boss of us all" (9.141), that kind of ambition is the furthest thing from Newt's mind.
Newt's shocked when he's invited on the cattle drive, and every terrible thing that happens to the cowboys along the way features Newt as the POV character of that chapter. He's blinded by a sandstorm, he's bitten by mosquitoes until he's covered in blood, he mourns Sean O'Brien's shocking death. We see all this stuff through Newt's eyes. By the time we're done with Lonesome Dove, we, like Newt, think we've seen it all. It might be the closest any of us come to this kind of adventure.