The Meri Duality
If you follow the progression of his work between 1476 and 1513, you find a series of studies of the Madonna and child culminating in the Mona Lisa. The symbols of the mountain summit as heaven and water as gateway to the underworld are ancient symbols repeated many times in ancient mythology, perhaps first in the Vedic Mount Meru allegory where the heavenly summit was filled with gold and the base was surrounded by seven seas, under which would be found the dusty underworld.
The lightness-darkness or birth-death duality of the feminine goddess (Venus / Moon) was repeated many times prior to Christianity, which employed them as two Marys - one who is Jesus' birth mother and the other who attends his death. Da Vinci's drawings indicates that he had access to Greek translations and probably Qabala materials which were being collected at the time by Pope Cosimo d'Medici. This would have informed him about pre-Christian goddess figures and their connection to the Mary duality.
Mary is the short for Meriam, meaning of the sea as in the French la Mer. Mount Meru was believed to extend out of the depths of the sea like a bridge or ladder into space toward the sun (or son). So, the name Mary identifies the sacred feminine as a bridge or portal between the supernal realm of God/ heaven and Man/ earth. I think this duality of Mary or Meru that Da Vinci was secretly expressing in the Mona Lisa.
Parallel to this is the Father-Son or Man-God duality. If you look at Michelangelo's ceiling in the Sistine chapel in the center, there is the famous painting of God leaning down to touch Adam's finger. But when you look closer, you find that the background of God is a cross section of the human brain and that God is actually Jupiter (Zeus) with his arm around Botticelli's Venus (Aphrodite) and their love child Cupid (Eros). Like the Greeks, Michelangelo is telling us that God is located inside the mind, which the Greeks considered the Underworld, and that every thing is half mortal and half immortal divinity. Here's a link to a great 3D view of the Sistine chapel where you can check it out yourself: Sistine Chapel 3D.
This feminine duality idea is repeated with the inner divinity concept in these two paintings by 19th century painter William Adolph Bourguereau. The first one is his Birth of Venus while the second is Diana, the goddess of the Moon (or huntress of death). Notice that they are both posed similarly, representing the sacred feminine duality between Venus and the Moon, lightness and darkness, birth and death. Notice also that Diana's garment is shaped like the cross section of a human brain, mimicking Michelangelo's Sistine Chapel representation of God in the human brain - thus, representing the Underworld of consciousness inside the mind and beyond the physical.