Vivek,
AFAIK, marrying mother's sister's daughter is forbidden amongst all hindus. However, kindly note all marriage rules have changed over time. Example: no sane people practice the rakshasa vivaha anymore.
Marrying mother's sister's daughetr it is permitted amongst muslims i think.
Marrying mother's sister's daughter has nothing to do with gothras and gothras in present time have nothing to do with genes
In my view (and as i have come across), two people of the same gothra can belong to different haplogroups.
And i suspect gotras never had anything to do with genes in the past either as sagothra marriages were preferred in the past unlike the present....And gothra in the vedic period meant just cowpens that were shared by a set of clans / were common to a tribe..if interested, do read this:
http://www.tamilbrahmins.com/sociology/4455-brother-sister-marriages-our-puranas-3.html#post50397 -- and also note inpputs that follow that post by Shri Sangom.
AFAIK, southern indians permit
a) marrying father's sister's daughter
b) marrying mother's brother's daughter
Some examples:
a) Krishna married Rukmani, his first cousin (father's sister's daughter);
b) Arjun also married his first cousin, Subhadra (his mother's brother's daughter).
Do note that in both cases, the brides were their 'murai penn' (as they are called).
However, marrying first cousins is not permitted amongst north-indians in any form.
Regards.
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