In a 3-1/2- or 4-quart slow cooker combine onion, garlic, tomatoes, beer, chipotle pepper, cumin seeds, sugar, and salt. Stir in beans and squash.
Cover and cook on low-heat setting for 9 to 10 hours or on high-heat setting for 4-1/2 to 5 hours. Meanwhile, in a small bowl combine sour cream, lime juice, and chives; cover and chill until ready to serve.
To serve, ladle chili into bowls. Top with sour cream mixture. If desired, garnish with lime wedges.