Science Fiction Series by Linda Rigsbee
Spaceship Lyra is Planet Purlieu's Research & Rescue ship - A secondary training ship.
Donte is Supreme Commander of the Purlieu Spaceships. 
Missions on the Lyra may be anything but boring.
The Amelioration Expedition - Book 1, Spaceship Lyra Logs

  Marlin Delaney wanted to be involved in the colonization of a planet ever since she can remember. She has been accepted and she isn’t going to let anything rob her of the opportunity – not rape, pregnancy or the addition of the man she hates to their team.
  Donte’s mate has left him and he has resigned as the Ruler of Bergen on the planet Purlieu, so when he is invited to join the expedition to planet Opus, he accepts.
  Marlin blames Donte for killing her grandfather and causing the separation of her parents. Everything is falling apart in her life and he is a handy target. Marlin doesn’t want the baby or the association with Donte but she will have to compromise for the good of the expedition and the colonization of Opus. 
  When they fall into a cavern and everyone thinks they drowned, they must work together or perish.
The Genesis Project - Book 2, Spaceship Lyra Logs

 When Donte discovers that a distress signal has been received from Arcane, his first thought is that Fontalo lied about the planet being uninhabitable - the way they lied about Purlieu. He is supreme commander of the Lyra, a research and rescue spaceship that has spent the last three years assisting the colonization of Opus. Someone needs help, so he feels compelled to respond.

The death of Hayley's grandfather makes her the sole survivor of the Fontalo scientific team on Arcane. She and her grandfather were taken to a hidden canyon ten years ago to escape the Sentinels. With his death, her actions will no longer put anyone else at risk, so she sends a distress signal.

What Donte and his crew discover on Arcane sets off a chain of historic events. It is, by far, his most challenging mission - and the most tragic.