Solitude takes on many forms in Marquez's novel. The Buendia family retreats into solitude for various reasons. Jose Arcadio Buendia becomes obsessed with science and isolates himself from his family, an obsession that eventually leads to his being tied to a tree. His son the Colonel becomes isolated by his power. He draws a circle around him that he allows no one to enter. His other son Jose Arcadio marries Rebecca, and Ursula forces him to live apart from the rest of the family because she considers his marriage incestuous.
But these are only a few examples. Each Buendia in his or her own way eventually becomes isolated or alienated either from choice or from circumstances beyond his or her control. Ursula is example of the latter. Her old age causes her to shrivel up and eventually become a plaything for her great children. Throughout the novel, Marquez explores various ideas of expansion and isolation, or solitude. He shows the need to connect with others, but he also shows the compelling urge to withdraw. Each Buendia exhibits various motivations for withdrawing from others--disillusionment (Jose Arcadio Segundo), sickness (Jose Areliano Segundo), trauma (Meme), purity and extraordinary beauty (Remedios the Beauty), pretensions (Fernando), incest and lust (Amaranta Ursula), depravity (Jose Arcadio II). And this compulsion to withdraw eventually has devastating effects on the individual.
Incest is one of the key ways Marquez shows this tendency. Even though incest is not actually committed except in the first generation of Buendias and in the last, it becomes a metaphor throughout the novel for the family's withdrawal from connecting with the outside world--their solitude. Colonel Aureliano falls in love with a girl who could be his daughter. His brother marries a girl whom his mother and father raised. Amaranta's nephew wants to marry her. We see the family begin to reject outsiders and retreat into themselves. When incest does occur at the end of the book between Aureliano and Amaranta Ursula, the family line ends and the baby who is born with a pig's tail dies and Macondo is destroyed.
So, in the novel, solitude means withdrawal, alienation, retreat, and isolation.