How would lack of sunlight affect a human population?
Other than photosynthesis being an issue, if the Earth's surface became inhospitable and humans were forced to live underground, what biological changes would they be expected to go through to adapt to the new environment?
For example, let's say the makeup of the atmosphere changes and the environment aboveground becomes too harsh to exist on, forcing the population to live underground. How would generations of no sunlight effect skin colour? Or the ability to absorb needed vitamins? Would eyes develop to adjust for less light or would new senses replace the less useful ones?
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You've touched on the major points already: vitamins and skin colour. They are linked to an extent.
Vitamin D is the major vitamin we get from sunlight. It's partly a "happy vitamin" in that it provokes serotonin neurotic responses, which makes you happier (have a look over at Biology.SE for more details on this response). So, one big problem you'd have is higher depression rates (and at risk of being a bit more morbid, higher suicide rates). You would, however, find that light-skinned people suffer less: they are capable of producing vitamin D through UV-B exposure faster. On that note, bring the tanning beds underground with you.
Melanin is a pigment found in hair and skin. It is the chemical that determines your skin colour. It appears to be an adaptation to sunlight. This is why, generally, people who live by the equator have darker skin. When underground, this chemical would be needed far far less, so you would find that over time and several tens of cycles of macroevolution, most people are fair-skinned.
Depending on the conditions underground, you may also find people's senses altering. Moles, for example, live their entire life underground and have almost no sense of vision, despite having binocular eyes. If the underground homes that humans now live in are dark, you will find that through both adaptation and evolution, they de-evolve having such good vision. You can find better definitions for micro and macro evolution on Biology.SE, but in general terms:
Adaptation is small changes that can take place over an individual's lifetime. For example, you might find that the colour-sensitive cones in a human retina degrade in favour of the light-sensitive rods.
Evolution is the Darwinian theory: individuals with characteristics that make them more likely to survive are more likely to reproduce and pass these characteristics on (natural selection). This means over time, cones may be eliminated completely.
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