I think Sunil's post above did logically bust that argument, did it not? Same gotra marriage with no known direct relation would not necessarily lead to any dilution of the gene pool or risk to the next generation. If anything, there are are far bigger factors like access to health and medical services that will create a bigger role in determining the state of the next generation.
Here is something I found via a quick search.
Please bear in mind I do not support cousin marriages. But the point I am trying to make via the item above is that if cousin marriages in which the marrying individuals share a 1/8 common gene (as they have one common grandfather) have only a 2.2% higher mortality rate than normal, then imagine the case for same gotra marriage in which probably 1/32 gene is same (if grandfather's grandfather were related). Wouldnt that significantly lower the health risks? And in our case where we most often know the ancestors for generations, the chances of a common ancestor would be further back into time and hence the health risk would be negligible.
And with regards to shrinking of the gene pool, Jats are anyways endogamous by nature, so even if you are avoiding marrying within your gotra, you are already diluting the gene pool. So the best way to make the gene pool better is to marry outside, which of course our elders wont suggest as they do not know a lot about genetics.
I understand the fundamentals behind avoiding same gotra marriage. It made sense centuries ago when population was small and each gotra had a maximum of a few hundred families. So it made sense to avoid marrying within the gotra as medical and health services were already poor and you didnt want to increase the risk of an unhealthy generation by marrying a close relation. But now after so many centuries, the same relation's family which you avoided has now grown multiple folds enriched by genes outside of the gotra. So it shouldnt be a concern if you marry into a family with which your ancestors were related 2 centuries back.
So as a thumb rule, I'd say if no common ancestor is know, its safe to marry within gotra.
On a lighter note, we know Muslims are the most well known community practicing cousin-marriages, yet for some reason, their population keeps on increasing. In fact they are the fastest growing community wherever they go!
