Except for an exotic community, Malayali Jews, there are hardly any population genetics studies on Malayali population in general. Even though many tribes in South India have been studied extensively, non-tribes are yet to be considered. Recently there was a study on Indian Muslim population which takes into account Malayali Muslim community, Mappila.
If you read the introduction to Mappila by the authors of the study then you feel the Tamil propaganda in full flow. Therefore, it is necessary to revisit my model of Dravidian civilization and the formation of various communities in South India.
In my opinion, Dravidian languages survived in South India mainly because leadership was still Dravidian. As the Dravidian tribes in Central India made transition to sedentary life, the communities were still controlled by the Dravidian chieftains. Of course, not all. The exception you can find in the only lapsed Dravidian region, Maharashtra. In that region the Dravidian tribes were controlled by the Indo-Aryan chieftains.
Generally, ruling classes change the linguistic identity of the population they control. The examples could be found in South India too.
In Karnataka and Andhra Pradesh, the ruling classes of Muslims were non-Dravidian Muslims for a long period. As a result all Dravidian converts had turned into Indo-Aryans. Even in Tamil Nadu, a short span of non-Dravidian Muslim rule was enough to shift nearly half of the Muslim population to Indo-Aryan identity. However, in Kerala, Muslims were always under either Dravidian non-Muslims or Dravidian Muslim rulers. And they have retained their linguistic identity.
That's about linguistic identity retention of Dravidians in general and Dravidian Muslims in particular. I have previously discussed about Dravidian civilization and have argued that it's a synthesis of Dravidians and Prakrits from the beginning. Malayali Muslim community is not an exception to this rule.
The earliest Prakrit entrants to the Dravidian region were herders and merchant-artisans. This is the basis for my another argument for some of the Dravidian tribes in food abundant regions to make transition to matrilineal sedentary society(Tuluvas and Malayalis). The important factor is artisan-merchants and also priests may impart cultural motifs but they would not be influential enough to change the linguistic identity of the native population. Maybe a language can get the prestigious position in a society if it's part of the power circles. Nevertheless, synthesis could be seen in the emergence of the caste system in the native Dravidian region and in the Dravidization of the assimilated Prakrit speaking brahmins and merchant-artisans.
The earliest Prakrit migrants would be from northern and eastern Indian (present day UP and Bihar) region, the centre of the Indian civilization. One would expect a high percentage of haplogroup R1a1 among these population. This is indeed the case with Mappilas.
Many Malayali communities were formed around the artisan-merchant guilds. The guilds which were initially formed in Prakrit speaking regions continued the motifs \of the earliest guilds of North India in South India. The guilds in South India of mixed Prakrit and Dravidian speakers exhibited native linguistic identity as the time passed. The castes of guilds in Andhra spoke Telugu, in Karnataka spoke Kannada, in Tamil Nadu spoke Tamil, in Tulu Nadu spoke Tulu and of course in Kerala spoke Malayalam. The migration to coastal Tulu and Malayali regions can be from either from west coastal route (Karnataka) or from Tamil Nadu. Couple of merchant guilds, Anju Varnam and Manigramam were native to Kerala region. Whereas, Valanjiar was probably a pan-Indian guild and a proof of the Prakrit migrations. Kannada term Banajiga, Telugu term Balanja (Balija), Tamil/Malayalam term Valanji are cognates with Indo-Aryan term 'Baniya'. These Prakrit or Prakrit derived terms are cognate with Sanskrit term Vanijya(trade).
As I have discussed previously many Muslim and Christian communities were formed around these merchant guilds. Since linguistic identity of these guilds were already Malayali, the immigrant Jewish, Christian and Arab merchants who assimilated with locals did not change the linguistic identity but profoundly changed the cultural identity.
Of course, the cultural identity overwrites all other identities, therefore, the popular identity of Mappilas was Arab. We can gauge the extent of Arab influence if we check the Y-haplogroup frequencies of Mappila from that study:
H1a: 22.5% - Dravidian
H2: 5% - Dravidian
J2: 10% (Dravidian if J2b)
J*(J1): 10% - Arab
L: 10% - Dravidian
K: 5% - Dravidian
R1a1: 32.5% - Indo-Aryan
R2: 5% - Dravidian
As you can see, the Arab ancestry accounts for 10% of the population. The rest are Indian. By my estimation, 40% of them descendants of Prakrit speaking merchant-artisans and the rest 50% are native Dravidian tribes.
Traces of sub-Saharan and Middle Eastern lineages in Indian Muslim populations -Muthukrishnan Eaaswarkhanth et al. 2009
European Journal of Human Genetics (2010) 18, 354–363; doi:10.1038/ejhg.2009.168; published online 7 October 2009