Our Vedic pundits understood genetics in depth and they made rituals that increases the 'gene pool' of the population and hence increase the survival rate of the population.

Small populations are generally at a greater risk of extinction than large populations. They are subject to rapid declines in numbers for three main reasons:

1) loss of genetic variability and related problems of inbreeding and genetic drift
2) demographic fluctuations due to random variations in birth and death rate
3) environmental fluctuations due to variation in predation, competition, disease and food supply; and natural catastrophes that occur at irregular intervals, such as fires, floods, volcanic eruptions, storms and droughts. (Source: http://faculty.plattsburgh.edu/thomas.wolosz/smallpopulations.htm)

Marrying a girl from same gotra means it will not help in increasing the genetic variability. A population with small gene pool is always at higher risk of extinction because an epidemic can hit anytime. So, it's better to increase the gene pool by marrying from different gotra. Different gotra means different genetic makeup.